Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 130 of 153
Found at i:41008563 original size:69 final size:70
Alignment explanation
Indices: 41008431--41008570 Score: 201
Period size: 69 Copynumber: 2.0 Consensus size: 70
41008421 CCTAATGGCC
* * * *
41008431 GATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 GATGTGATGAATGTGAAAG-GTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGA
41008496 AAGTGT
65 AAGTGT
* * *
41008502 GATGTGATGAATGTGAAA-GTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 GATGTGATGAATGTGAAAGGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAA
41008566 AGTGT
66 AGTGT
41008571 ATAAATGTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 44 0.71
71 18 0.29
ACGTcount: A:0.30, C:0.07, G:0.34, T:0.29
Consensus pattern (70 bp):
GATGTGATGAATGTGAAAGGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAA
AGTGT
Found at i:41016785 original size:43 final size:41
Alignment explanation
Indices: 41016720--41016838 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 41
41016710 AGCTCGTACA
* *
41016720 ATGCCATCGTCCCAGACGAGGTCTTACATGTAATCAAATATA-G
1 ATGCCAT-GTCCCAGACAAGGTCTTACACGTAATC--ATATACG
41016763 ATGCCACTGTCCCAGACAAGGTCTTACACGTAAATCATATACG
1 ATGCCA-TGTCCCAGACAAGGTCTTACACGT-AATCATATACG
* *
41016806 ATGCCAATGTCCTAGACATGGTCTTACACGTAA
1 ATGCC-ATGTCCCAGACAAGGTCTTACACGTAA
41016839 ATCTCAAATC
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
42 7 0.10
43 55 0.81
44 6 0.09
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
ATGCCATGTCCCAGACAAGGTCTTACACGTAATCATATACG
Found at i:41016872 original size:44 final size:43
Alignment explanation
Indices: 41016739--41016873 Score: 157
Period size: 43 Copynumber: 3.1 Consensus size: 43
41016729 TCCCAGACGA
* * * * *
41016739 GGTCTTACATGT-AATCAAATATAGATGCCACTGTCCCAGACAA
1 GGTCTTACACGTAAATCAAATA-CGATGCCAATGTCCTAGACAT
*
41016782 GGTCTTACACGTAAATCATATACGATGCCAATGTCCTAGACAT
1 GGTCTTACACGTAAATCAAATACGATGCCAATGTCCTAGACAT
* *
41016825 GGTCTTACACGTAAATCTCAAAT-CGTTGCCAATGTCCTAGACTT
1 GGTCTTACACGTAAA--TCAAATACGATGCCAATGTCCTAGACAT
41016869 GGTCT
1 GGTCT
41016874 CTTACACAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
43 43 0.54
44 32 0.40
45 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAAATACGATGCCAATGTCCTAGACAT
Found at i:41024771 original size:43 final size:44
Alignment explanation
Indices: 41024724--41024869 Score: 178
Period size: 43 Copynumber: 3.4 Consensus size: 44
41024714 TCCCAGACGA
* * *
41024724 GGTCTTACATGT-AATCAAATATAGATGCCACTGTCCCACACAG
1 GGTCTTACACGTAAATCAAATATAGATGCCAATGTCCCACACAT
*
41024767 GGTCTTACACGTAAATC--ATATACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAAATCAAATATA-GATGCCAATGTCCCACACAT
*
41024810 GGTCTTACACGTAAATCTCAAAT-T-GATGCCAATGTCCCATACAT
1 GGTCTTACACGTAAA--TCAAATATAGATGCCAATGTCCCACACAT
41024854 GGTCTTACACG-AAATC
1 GGTCTTACACGTAAATC
41024870 GTATATCGGA
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
43 46 0.50
44 34 0.37
45 2 0.02
46 1 0.01
47 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (44 bp):
GGTCTTACACGTAAATCAAATATAGATGCCAATGTCCCACACAT
Found at i:41024869 original size:86 final size:86
Alignment explanation
Indices: 41024705--41024874 Score: 215
Period size: 86 Copynumber: 2.0 Consensus size: 86
41024695 AGCTTGTACA
* *
41024705 ATGCCATCGTCCCAGACGAGGTCTTACATGTAATCAAATATAGATGCCACTGTCCCACACAGGGT
1 ATGCCATCGTCCCAGACGAGGTCTTACACGTAATCAAATATAGATGCCAATGTCCCACACAGGGT
41024770 CTTACACGTAAATCATATACG
66 CTTACACGTAAATCATATACG
*
41024791 ATGCCAAT-GTCCCAGAC-ATGGTCTTACACGTAAATCTCAAAT-T-GATGCCAATGTCCCATAC
1 ATGCC-ATCGTCCCAGACGA-GGTCTTACACGT-AA--TCAAATATAGATGCCAATGTCCCACAC
* *
41024852 ATGGTCTTACACG-AAATCGTATA
61 AGGGTCTTACACGTAAATCATATA
41024875 TCGGAATTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
85 1 0.01
86 34 0.46
87 32 0.43
88 1 0.01
89 6 0.08
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (86 bp):
ATGCCATCGTCCCAGACGAGGTCTTACACGTAATCAAATATAGATGCCAATGTCCCACACAGGGT
CTTACACGTAAATCATATACG
Found at i:41035557 original size:35 final size:35
Alignment explanation
Indices: 41035434--41035560 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
41035424 GTACATCGTC
* * * * *
41035434 AGTCAAACCAAAACACACCAGATGCTCACACGGGCC
1 AGTCCAACCAAAACACACCA-ATGCTCATAAGAGCT
* ** *
41035470 AATCCCTCCAAAACACAACAATGCTCATAAGAGCT
1 AGTCCAACCAAAACACACCAATGCTCATAAGAGCT
*
41035505 AGTCCAATCAAAACACACCAATGCTCATAAGAGCT
1 AGTCCAACCAAAACACACCAATGCTCATAAGAGCT
*
41035540 AGTCCAACCGAAACACACCAA
1 AGTCCAACCAAAACACACCAA
41035561 AAAGATAGTA
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 60 0.80
36 15 0.20
ACGTcount: A:0.43, C:0.33, G:0.12, T:0.13
Consensus pattern (35 bp):
AGTCCAACCAAAACACACCAATGCTCATAAGAGCT
Found at i:41039468 original size:2 final size:2
Alignment explanation
Indices: 41039461--41039491 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41039451 AAATTTTTAA
41039461 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41039492 ACGCTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41045949 original size:15 final size:16
Alignment explanation
Indices: 41045929--41045958 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41045919 AAATCCTTAC
41045929 TCTTTTT-TTTTTTCT
1 TCTTTTTCTTTTTTCT
41045944 TCTTTTTCTTTTTTC
1 TCTTTTTCTTTTTTC
41045959 ACATCTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TCTTTTTCTTTTTTCT
Found at i:41046225 original size:19 final size:19
Alignment explanation
Indices: 41046176--41046227 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
41046166 TATAAATCAT
* *
41046176 AAAAGATATAAAAATTGTA
1 AAAAGAAATTAAAATTGTA
** *
41046195 AAAATTATTTAAAATTGTA
1 AAAAGAAATTAAAATTGTA
41046214 AAAAGAAATTAAAA
1 AAAAGAAATTAAAA
41046228 AATATATAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (19 bp):
AAAAGAAATTAAAATTGTA
Found at i:41046245 original size:19 final size:18
Alignment explanation
Indices: 41046219--41046314 Score: 61
Period size: 19 Copynumber: 5.2 Consensus size: 18
41046209 TTGTAAAAAG
41046219 AAAT-TAAAAAATATATA
1 AAATATAAAAAATATATA
*
41046236 AAATAATAAATAATGATA-A
1 AAAT-ATAAAAAAT-ATATA
** *
41046255 AAATGATAAAACGTACAATA
1 AAAT-ATAAAAAATA-TATA
* * *
41046275 AAACATATAAAAATCTAGA
1 AAATATA-AAAAATATATA
*
41046294 AAATATAAAATATATATA
1 AAATATAAAAAATATATA
41046312 AAA
1 AAA
41046315 ATGTTTTTTC
Statistics
Matches: 57, Mismatches: 16, Indels: 11
0.68 0.19 0.13
Matches are distributed among these distances:
17 4 0.07
18 12 0.21
19 30 0.53
20 11 0.19
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (18 bp):
AAATATAAAAAATATATA
Found at i:41046315 original size:19 final size:19
Alignment explanation
Indices: 41046219--41046316 Score: 57
Period size: 17 Copynumber: 5.2 Consensus size: 19
41046209 TTGTAAAAAG
*
41046219 AAAT-TAAAAAATATAT-A
1 AAATATAAAATATATATAA
41046236 AAATA-ATAAATA-ATGATAA
1 AAATATA-AAATATAT-ATAA
*
41046255 AAATGATAAAACGTACA-ATAA
1 AAAT-ATAAAA--TATATATAA
* *
41046276 AACATATAAAA-ATCTA-GA
1 AA-ATATAAAATATATATAA
41046294 AAATATAAAATATATATAA
1 AAATATAAAATATATATAA
41046313 AAAT
1 AAAT
41046317 GTTTTTTCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
17 15 0.24
18 14 0.23
19 11 0.18
20 4 0.06
21 13 0.21
22 4 0.06
23 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
AAATATAAAATATATATAA
Found at i:41047802 original size:15 final size:15
Alignment explanation
Indices: 41047779--41047808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41047769 AGCGCCGCAA
*
41047779 AAAAGGTCGCTAACG
1 AAAACGTCGCTAACG
41047794 AAAACGTCGCTAACG
1 AAAACGTCGCTAACG
41047809 TTTGCAACGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.13
Consensus pattern (15 bp):
AAAACGTCGCTAACG
Found at i:41047947 original size:42 final size:42
Alignment explanation
Indices: 41047822--41047948 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 42
41047812 GCAACGTTTA
*
41047822 CAAAAATAAACGCAGCTAAAGATCATGTTCTTTAGCGGCACTT
1 CAAAAA-AAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * *
41047865 GAAAAAAAACGCTGCTAAAGGTCATGTTCTTTAGCGGCGCTT
1 CAAAAAAAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * *
41047907 CAAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCAGCGCTT
1 CAAAAAAAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTT
41047949 TATTCACAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 70 0.93
43 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (42 bp):
CAAAAAAAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:41048380 original size:21 final size:21
Alignment explanation
Indices: 41048312--41048382 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
41048302 TTTTGCTCTG
* * *
41048312 CTCTGCTTCTCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTACAGC
*
41048333 CTCTGCTTCCCTCGTTACAGC
1 CTCTGCTTCCCTCGCTACAGC
* *
41048354 CGCTGCTTCCCTCGCTACTGC
1 CTCTGCTTCCCTCGCTACAGC
*
41048375 TTCTGCTT
1 CTCTGCTT
41048383 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.07, C:0.42, G:0.15, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTACAGC
Found at i:41050000 original size:115 final size:115
Alignment explanation
Indices: 41049647--41049992 Score: 613
Period size: 115 Copynumber: 3.0 Consensus size: 115
41049637 AAATATTTGT
* *
41049647 GGTGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
1 GGTGTTTTTCAAATTCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
41049712 GAAATTTGCGGTGTTTCTTCGTAAAACGCCGCTAATGTATCACCTTTAGC
66 GAAATTTGCGGTGTTTCTTCGTAAAACGCCGCTAATGTATCACCTTTAGC
41049762 GGTGTTTTTCAAATTCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
1 GGTGTTTTTCAAATTCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
41049827 GAAATTTGCGGTGTTTCTTCGTAAAACGCCGCTAATGTATCACCTTTAGC
66 GAAATTTGCGGTGTTTCTTCGTAAAACGCCGCTAATGTATCACCTTTAGC
41049877 GGTGTTTTTCAAATTCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
1 GGTGTTTTTCAAATTCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
* ** * *
41049942 GAAATTTGCGGCGTTTCTTCACAAAATGCCAG-TAATATATCACCTTTAGC
66 GAAATTTGCGGTGTTTCTTCGTAAAACGCC-GCTAATGTATCACCTTTAGC
41049992 G
1 G
41049993 ACGTTTTTTC
Statistics
Matches: 223, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
115 222 1.00
116 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (115 bp):
GGTGTTTTTCAAATTCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTACAGTTAAAG
GAAATTTGCGGTGTTTCTTCGTAAAACGCCGCTAATGTATCACCTTTAGC
Found at i:41050502 original size:14 final size:14
Alignment explanation
Indices: 41050478--41050529 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
41050468 ACTAAACCCC
41050478 AAACCTAAAACTC-T
1 AAACCT-AAACTCGT
41050492 AAACTCTAAAC-CGT
1 AAAC-CTAAACTCGT
41050506 AAACCCTAAA-TCGT
1 AAA-CCTAAACTCGT
41050520 AAACCTAAAC
1 AAACCTAAAC
41050530 CATATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.21
14 23 0.70
15 3 0.09
ACGTcount: A:0.48, C:0.29, G:0.04, T:0.19
Consensus pattern (14 bp):
AAACCTAAACTCGT
Found at i:41050502 original size:21 final size:21
Alignment explanation
Indices: 41050469--41050528 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
41050459 ATCCTAAATA
* * *
41050469 CTAAACCCCAAACCTAAAACT
1 CTAAACTCTAAACCTAAAACC
41050490 CTAAACTCTAAACCGT-AAACC
1 CTAAACTCTAAACC-TAAAACC
41050511 CTAAA-TCGTAAACCTAAA
1 CTAAACTC-TAAACCTAAA
41050529 CCATATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 29 0.88
22 1 0.03
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (21 bp):
CTAAACTCTAAACCTAAAACC
Found at i:41050617 original size:19 final size:19
Alignment explanation
Indices: 41050595--41050632 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41050585 ATATTATTAT
41050595 ATTATATATATAATATGGC
1 ATTATATATATAATATGGC
41050614 ATTATATATATAATATGGC
1 ATTATATATATAATATGGC
41050633 TGTAGTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
ATTATATATATAATATGGC
Found at i:41050722 original size:20 final size:20
Alignment explanation
Indices: 41050684--41050740 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
41050674 TCTTCAATTT
41050684 CCAAACT-AAACCCTAAAACC
1 CCAAACTCAAA-CCTAAAACC
* *
41050704 CTAAACTCAAACCTTAAACC
1 CCAAACTCAAACCTAAAACC
41050724 CCAAACTCAAACTCTAA
1 CCAAACTCAAAC-CTAA
41050741 CACATAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (20 bp):
CCAAACTCAAACCTAAAACC
Found at i:41054337 original size:91 final size:91
Alignment explanation
Indices: 41054182--41054424 Score: 344
Period size: 91 Copynumber: 2.7 Consensus size: 91
41054172 ACACCGGGTT
* * * ***
41054182 GTGGATGAACCATCAAATGTTGTAGGTTAATACGTTACTAGACAATTGTGAATACACAACATAAT
1 GTGGATGAACCACCAAATGTTGTAGGTTAATATGCTACTAGATGGTTGTGAATACACAACATAAT
* *
41054247 TGTAGATAAAAGCTGCCAGATAATGG
66 TGAAGATAAAAACTGCCAGATAATGG
* *
41054273 GTGGATGAGCCACCAAATGTTGCAGGTTAATATGCTACTAGATGGTTGTGAATACACAACATAAT
1 GTGGATGAACCACCAAATGTTGTAGGTTAATATGCTACTAGATGGTTGTGAATACACAACATAAT
*
41054338 TGAAGATAAAAACTGCTAGATAATGG
66 TGAAGATAAAAACTGCCAGATAATGG
** * *
41054364 GTGGGCGAACCACC-AAGGTTGTAGGTTAATATGCTACCAGATGGTTGTGAATACACAACAT
1 GTGGATGAACCACCAAATGTTGTAGGTTAATATGCTACTAGATGGTTGTGAATACACAACAT
41054425 GCAGATAAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 44 0.33
91 91 0.67
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (91 bp):
GTGGATGAACCACCAAATGTTGTAGGTTAATATGCTACTAGATGGTTGTGAATACACAACATAAT
TGAAGATAAAAACTGCCAGATAATGG
Found at i:41055885 original size:14 final size:15
Alignment explanation
Indices: 41055866--41055894 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41055856 CCTAATTGCT
41055866 GAAAAAT-AAAAGAG
1 GAAAAATGAAAAGAG
41055880 GAAAAATGAAAAGAG
1 GAAAAATGAAAAGAG
41055895 TGGGGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (15 bp):
GAAAAATGAAAAGAG
Found at i:41057408 original size:10 final size:10
Alignment explanation
Indices: 41057395--41057419 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41057385 GATATCCTCG
41057395 TTTATCGATT
1 TTTATCGATT
41057405 TTTATCGATT
1 TTTATCGATT
41057415 TTTAT
1 TTTAT
41057420 GTATACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (10 bp):
TTTATCGATT
Found at i:41063873 original size:16 final size:16
Alignment explanation
Indices: 41063852--41063882 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41063842 TTAGTTCCAG
41063852 TTTAGTTAAATCTCAT
1 TTTAGTTAAATCTCAT
41063868 TTTAGTTAAATCTCA
1 TTTAGTTAAATCTCA
41063883 ATCTTGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTAGTTAAATCTCAT
Found at i:41064305 original size:135 final size:135
Alignment explanation
Indices: 41064063--41064311 Score: 392
Period size: 135 Copynumber: 1.8 Consensus size: 135
41064053 TGCTTCCACA
* * * * *
41064063 GTTCATATATTTTGTTCTTATTAATTTTCATTGAATTTGTTTGTTATATTAATTGAATTCTAAAC
1 GTTCATATATTTTGTTCTTATTAATTTCCATAGAATTTGTTTGCTATATTAATTAAATACTAAAC
41064128 CTTGTATTAGTGTCATTCATGTTGATTAGTTATTACTAATTTATTAATTATTATCATTCATGTTG
66 CTTGTATTAGTGTCATTCATGTTGATTAGTTATTACTAATTTATTAATTATTATCATTCATGTTG
41064193 AATTT
131 AATTT
*
41064198 GTTCATATATTTTGTTCTTATTAATTTCCATAGAATTTGTTTGCTATATTAATTAAATACTAAAT
1 GTTCATATATTTTGTTCTTATTAATTTCCATAGAATTTGTTTGCTATATTAATTAAATACTAAAC
* * * *
41064263 CTTGTATTAGTTTCATTCATGTTGGATT-GTTTTTATTGATTTATTAATT
66 CTTGTATTAGTGTCATTCATGTT-GATTAGTTATTACTAATTTATTAATT
41064312 GTTTGTTTAT
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
135 99 0.96
136 4 0.04
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.54
Consensus pattern (135 bp):
GTTCATATATTTTGTTCTTATTAATTTCCATAGAATTTGTTTGCTATATTAATTAAATACTAAAC
CTTGTATTAGTGTCATTCATGTTGATTAGTTATTACTAATTTATTAATTATTATCATTCATGTTG
AATTT
Found at i:41064561 original size:11 final size:11
Alignment explanation
Indices: 41064545--41064570 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41064535 TAGTACAGAC
41064545 TGTTGTTTGTT
1 TGTTGTTTGTT
41064556 TGTTGTTTGTT
1 TGTTGTTTGTT
41064567 TGTT
1 TGTT
41064571 TCAGTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (11 bp):
TGTTGTTTGTT
Found at i:41064793 original size:172 final size:173
Alignment explanation
Indices: 41064501--41064831 Score: 488
Period size: 172 Copynumber: 1.9 Consensus size: 173
41064491 TGATAATCAG
* * *
41064501 GATGTTCTGGACCTCATTGAAAAGGTCTGTTGGATAGTACAGACTGTTGTTTGTTTGTTGTTTGT
1 GATGTTCTAGACCTCATTGAAAAGGTCTGTTGGATAGTACAGACTGTTATTTG--TCTTGTTTGT
** * * *
41064566 TTGTTTCAGTTTAGTTAAATCCCAATCTTGTTCTTATTAATTTTCATTGAATTTGTTTGCTATAT
64 TAATTCCAATTTAGTTAAATCCCAATCTTGTTCTTATTAATTTTCATTAAATTTGTTTGCTATAT
41064631 TAACTGAGTTCT-ATATCTTGTATTAGTGTCAATCATGTTGGTCAA
129 TAACTGAGTTCTGA-ATCTTGTATTAGTGTCAATCATGTTGGTCAA
* **
41064676 GATGTTCTAGATCTCATTGAAAAGGTCTGTTGGATCTTACAGACTGTTATTTG-CTTGTTTGTTA
1 GATGTTCTAGACCTCATTGAAAAGGTCTGTTGGATAGTACAGACTGTTATTTGTCTTGTTTGTTA
*
41064740 ATTCCAATTTAGTTAAATCTCAATCTTGTTCTTATTAA-TTTCTATTAAATTTGTTTGCTATATT
66 ATTCCAATTTAGTTAAATCCCAATCTTGTTCTTATTAATTTTC-ATTAAATTTGTTTGCTATATT
*
41064804 AATTGAGTTCTGAATCTTGTATTAGTGT
130 AACTGAGTTCTGAATCTTGTATTAGTGT
41064832 AATTTATGTT
Statistics
Matches: 141, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
171 4 0.03
172 88 0.62
173 1 0.01
175 48 0.34
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (173 bp):
GATGTTCTAGACCTCATTGAAAAGGTCTGTTGGATAGTACAGACTGTTATTTGTCTTGTTTGTTA
ATTCCAATTTAGTTAAATCCCAATCTTGTTCTTATTAATTTTCATTAAATTTGTTTGCTATATTA
ACTGAGTTCTGAATCTTGTATTAGTGTCAATCATGTTGGTCAA
Found at i:41065095 original size:16 final size:15
Alignment explanation
Indices: 41065070--41065100 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
41065060 TTATTTGTTT
41065070 GTTTGTTAAATCTCA
1 GTTTGTTAAATCTCA
41065085 GTTTAGTTAAATCTCA
1 GTTT-GTTAAATCTCA
41065101 ATCTTGTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
GTTTGTTAAATCTCA
Found at i:41066449 original size:946 final size:955
Alignment explanation
Indices: 41064596--41066571 Score: 2497
Period size: 946 Copynumber: 2.1 Consensus size: 955
41064586 CCCAATCTTG
* * * *
41064596 TTCTTATTAATTTTCATTGAATTTGTTTGCTATATTAACTGAGTTCTATATCTTGTATTAGTGTC
1 TTCTTATTAATTTTCATTGAATTTGTTTGTTATATTAATTGAGTTCTAAATTTTGTATTAGTGTC
* * * **
41064661 AATCATGTTGGTCAAGATGTTCTAGATCTCATTGAAAAGGTCTGTTGGATCTTACAGACTGTTAT
66 ATTCATGTTGGTCAAGATGTTCTAGACCTCATTGAAAAGATCTGTTACATCTTACAGACTGTTAT
* *
41064726 TTGCTTGTTTGTTAATTCCAATTTAGTTAAATCTCAATCTTGTTCTTATTAATTTCTATTAAATT
131 TTGCTTGTTTGTTAATTCCAATTTAGTTAAATCTCAATATTGTTCTTATAAATTTCTATTAAATT
* * * * * *
41064791 TGTTTGCTATATTAATTGAGTTCTGAATCTTGTATTAGTGTAATTTATGTTAGATTGTTATTATT
196 TGTTTGCTATATTAACTAAGTTCTGAAACTTGTATTAGTGTAATTCAAGTTAGATTGTTATTACT
* ** * * *
41064856 GATTTATTAATTATTGTTATTCTTTTAGAATTTGCAAACTAGTTTGCTTGATATTTATGCCCCAT
261 GATTTATTAATTATTGTCATTCGGTTAGAATTTGCAAACTAGTTTGCTTGATATATATACACCAT
* * *
41064921 CCTTCCACTACTGCTTCCGCAGTTCATATATTTTGTTCTTATTAATTTCTATTGAATTTTTTTGC
326 CCTTCCACTACTGCTTCCACAGTTCATATATTTTGTTCTTATTAATTTCTATTGAATTTGTTTAC
* *
41064986 TATATTAACTGAGTTCTAAATCTTGTATCAGTGTCATTCATGCTGGATTGTACTTACTGATTTAT
391 TATATGAACTAAGTTCTAAATCTTGTATCAGTGTCATTCATGCTGGATTGTACTTACTGATTTAT
* * *
41065051 TAATTACTATTATTTGTTTGTTTGTTAAATCTCAGTTTAGTTAAATCTCAATCTTGTTCCTATTA
456 TAATTACTATTATTTGTTTATTTGTTAAATCTCAATTTAGTTAAATCTCAATCTTGTTACTATTA
* * * *
41065116 ATTTTCATTGAATTTGTTTTCTATATTAATTGAGTTCTAAATATCATATTAGTGTAATTATTGTT
521 ATTTTCATTGAATTTGTTTGCTATATTAACTCAGTTCTAAATATC--A-TA-TGTAATTAGTGTT
* * * **
41065181 GGATTATTCTTATTGATTTATTTATTCCTGATTTATTAATTATTTCATCCATGTTGAATTTTTTT
582 GCATTAATCTTA-TGATTGATTTA-T-CTGATTTATTAATTATTTCATCCATGTTGAATTTGCTT
**** * * * *
41065246 GCTCAATGTTTTGTTGTGAATTGCTGGTCATTTTGACTTTTCTTATTATTTGATGATTTAATGTT
644 GCTCAATGTTTTCCCATGAAGTGCTGGTCATTTTGACTTTTCTTATTATTCGATGATTCAATATT
* *
41065311 TTGCTCAATGTTTTTTTAGATCAAATATTATACTTTTTTAACACTACCAACAAGTTATATATAAC
709 TTGCTCAATGTTTTTTTAGATCAAATATTATACTTTTCTAAAACTACCAACAAGTTATATATAAC
* * * *
41065376 AACTTTTTTAGTTGACAATACTCGTCAATTCAATGGCCTCCAATGACATTGTCTGTCCGTCTCCT
774 AACCTTTTTAGTTGACAATACTCGTCAATTCAATGACCTCCAATGACACTGTCTGCCCGTCTCCT
* * * * * * *
41065441 ACTTCCTCTGTCAACTTCTCTGCTCCATCTTTCAGTCGTCGCCTTCGTTGTCCCACTAGTTTGCT
839 ACTTCCTCTATCAACTTCTCTGCTCCAGCCTTCAGTCATCGCCATCATCGTCCCACTAGTTTGCT
* * * *
41065506 CGGTATATATCCACTATGCTTCCCATTCTTCTTTCACAATTCATATATTTTA
904 CGGTATATATCCACCATGCTTCCCATGCTACTTCCACAATTCATATATTTTA
*
41065558 TTCTTATTAATTTTCATTGAATTTGTTTGTTATATTAATTGAGTTCTAAATTTTGTATTATTGTC
1 TTCTTATTAATTTTCATTGAATTTGTTTGTTATATTAATTGAGTTCTAAATTTTGTATTAGTGTC
* * *
41065623 ATTCATGTTGGTCACGATGTTCTGGACCTCATTGAAAAGATTTGTTACATCTTACAGACTGTTAT
66 ATTCATGTTGGTCAAGATGTTCTAGACCTCATTGAAAAGATCTGTTACATCTTACAGACTGTTAT
* * * *
41065688 TT-CTTTGTTTGTTAATTCTAGTTTAGTTAAATCTCAATATTTTTCTTATAAATTT-TCATTGAA
131 TTGC-TTGTTTGTTAATTCCAATTTAGTTAAATCTCAATATTGTTCTTATAAATTTCT-ATTAAA
* * * *
41065751 TTTTTTTGCTATATTAACTAAGTT-TTAAACTTGTATTAGTGTCATTCAAGTTTGATTGTTATTA
194 TTTGTTTGCTATATTAACTAAGTTCTGAAACTTGTATTAGTGTAATTCAAGTTAGATTGTTATTA
**** * *
41065815 CTGATTTATTAATTACTT-TCATTCAGGTTA-AATTTGTTGTCTGGTTTGCTTGGTATATATACA
259 CTGATTTATTAATTA-TTGTCATTC-GGTTAGAATTTGCAAACTAGTTTGCTTGATATATATACA
* * ** *
41065878 CCATGCTTCCATTGTTGTTTCCACAGTTCATATATTTTGTTCTTATTAATTTAC-ATTGAATTTG
322 CCATCCTTCCACTACTGCTTCCACAGTTCATATATTTTGTTCTTATTAATTT-CTATTGAATTTG
* * * * * *
41065942 TTTACTATATGAATTAAGTTCTAATTCTTTTATTATTGTCATTCATGTTGGATTGTTA-TTACTG
386 TTTACTATATGAACTAAGTTCTAAATCTTGTATCAGTGTCATTCATGCTGGATTG-TACTTACTG
***
41066006 ATTTATTAATTACTATTATTTGTTTATTTGTTTGTTC-CAATTTAGTTAAATCTCAATCTTGTTA
450 ATTTATTAATTACTATTATTTGTTTATTTGTTAAATCTCAATTTAGTTAAATCTCAATCTTGTTA
* *
41066070 TTATTAATTTTCATTTAATTTGTTTGCTATATTAACTCAGTTCT-AA-ATC-T-TGT-ATTAGTG
515 CTATTAATTTTCATTGAATTTGTTTGCTATATTAACTCAGTTCTAAATATCATATGTAATTAGTG
* * *
41066130 -T-CATTAATGTTA-GATTGATCTTA-CTGGTTTATTAATTATTGTCATTCATGTTGAATTTGCT
580 TTGCATTAATCTTATGATTGAT-TTATCTGATTTATTAATTATT-TCATCCATGTTGAATTTGCT
* * *
41066191 TGCTCAATGTTTTCCCATGCAGTGCTGGTCATTTTGACTTTTCTTTTTATTCGATGGTTCAATAT
643 TGCTCAATGTTTTCCCATGAAGTGCTGGTCATTTTGACTTTTCTTATTATTCGATGATTCAATAT
* *
41066256 TTTGCTCAATGTTTTTTTAGATTAAATATTATACTTTTCTAAAACTACTAACAAGTTATATATAA
708 TTTGCTCAATGTTTTTTTAGATCAAATATTATACTTTTCTAAAACTACCAACAAGTTATATATAA
* * *
41066321 CAACCTTTTTAGTT-ATCAGTACTCGTCAATTTC-GTGACCTTC-A-G-CACTG-CTGCCCGTCT
773 CAACCTTTTTAGTTGA-CAATACTCGTCAA-TTCAATGACCTCCAATGACACTGTCTGCCCGTC-
* * * * * *
41066380 ATCTCTCGCTTTCTTTATCAGCTTCTCTGCTCTAGCCTTCAGTCATCGCCATCATCGTCTCACTA
835 -TC-CT-ACTTCCTCTATCAACTTCTCTGCTCCAGCCTTCAGTCATCGCCATCATCGTCCCACTA
* * * *
41066445 GTTTGCTCGGTATTTATTCACCATGCTTCCCCTGCTACTTCCACAGTTCATATATTTTA
897 GTTTGCTCGGTATATATCCACCATGCTTCCCATGCTACTTCCACAATTCATATATTTTA
*
41066504 TTCTTATTAATTTCCATTGAATTTGTTTGTTATATTAATTGAGTTCT-AATTCTTGTATTAGTGT
1 TTCTTATTAATTTTCATTGAATTTGTTTGTTATATTAATTGAGTTCTAAATT-TTGTATTAGTGT
41066568 CATT
65 CATT
41066572 TATATTGGAT
Statistics
Matches: 877, Mismatches: 122, Indels: 46
0.84 0.12 0.04
Matches are distributed among these distances:
942 8 0.01
943 4 0.00
944 3 0.00
945 24 0.03
946 320 0.36
947 9 0.01
948 3 0.00
949 8 0.01
950 1 0.00
951 6 0.01
952 3 0.00
954 1 0.00
958 3 0.00
959 2 0.00
960 64 0.07
961 219 0.25
962 199 0.23
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (955 bp):
TTCTTATTAATTTTCATTGAATTTGTTTGTTATATTAATTGAGTTCTAAATTTTGTATTAGTGTC
ATTCATGTTGGTCAAGATGTTCTAGACCTCATTGAAAAGATCTGTTACATCTTACAGACTGTTAT
TTGCTTGTTTGTTAATTCCAATTTAGTTAAATCTCAATATTGTTCTTATAAATTTCTATTAAATT
TGTTTGCTATATTAACTAAGTTCTGAAACTTGTATTAGTGTAATTCAAGTTAGATTGTTATTACT
GATTTATTAATTATTGTCATTCGGTTAGAATTTGCAAACTAGTTTGCTTGATATATATACACCAT
CCTTCCACTACTGCTTCCACAGTTCATATATTTTGTTCTTATTAATTTCTATTGAATTTGTTTAC
TATATGAACTAAGTTCTAAATCTTGTATCAGTGTCATTCATGCTGGATTGTACTTACTGATTTAT
TAATTACTATTATTTGTTTATTTGTTAAATCTCAATTTAGTTAAATCTCAATCTTGTTACTATTA
ATTTTCATTGAATTTGTTTGCTATATTAACTCAGTTCTAAATATCATATGTAATTAGTGTTGCAT
TAATCTTATGATTGATTTATCTGATTTATTAATTATTTCATCCATGTTGAATTTGCTTGCTCAAT
GTTTTCCCATGAAGTGCTGGTCATTTTGACTTTTCTTATTATTCGATGATTCAATATTTTGCTCA
ATGTTTTTTTAGATCAAATATTATACTTTTCTAAAACTACCAACAAGTTATATATAACAACCTTT
TTAGTTGACAATACTCGTCAATTCAATGACCTCCAATGACACTGTCTGCCCGTCTCCTACTTCCT
CTATCAACTTCTCTGCTCCAGCCTTCAGTCATCGCCATCATCGTCCCACTAGTTTGCTCGGTATA
TATCCACCATGCTTCCCATGCTACTTCCACAATTCATATATTTTA
Found at i:41067130 original size:170 final size:169
Alignment explanation
Indices: 41066638--41067144 Score: 606
Period size: 172 Copynumber: 3.0 Consensus size: 169
41066628 GATAATCAGG
* *
41066638 TGTTCTGGACCTTATTGAAAAGGTCTGTTGGATCTTACAGATTGTTATTTGTTTGTTTGTT-G-T
1 TGTTCTGGACCTTATTGAAAAGGTTTGTTGGATCTTAC--ATAGTTATTTGTTTG-TTGTTAGTT
* *
41066701 TCTAGTTTAATTAAATCTCAATCTTGTTTTTATTAA-TTTCTATTGAATTTGTTTACTATATTAA
63 TC-AGTTTAATTAAATCTGAATCTTGTTTTTATTAATTTTC-ATTGAATTTGTTTGCTATATTAA
* * *
41066765 TTGAATTCTAAATATTGTATAAGTGTCATTAATGTTGGTAAAGA
126 TTGAATTCTAAATCTTGTATTAGTGTCATTCATGTTGGTAAAGA
* *
41066809 TGTTCTAGACCTTATTGAAAAGGTTTGTTGGATCTTACAAACTGTTATTTGTTTGTTAGTTAGTT
1 TGTTCTGGACCTTATTGAAAAGGTTTGTTGGATCTTACATA--GTTATTTGTTTGTT-GTTAGTT
* * * * ** * *
41066874 CCAGTTTAGTTAAATATGAATCTTGTTTTTATTAATTTCCATCAAATTTGATTGCTATATTAACT
63 TCAGTTTAATTAAATCTGAATCTTGTTTTTATTAATTTTCATTGAATTTGTTTGCTATATTAATT
* * * **
41066939 AAATTCTAAATCTTTTATTAGTGTCACTCATGTTGGTATGGA
128 GAATTCTAAATCTTGTATTAGTGTCATTCATGTTGGTAAAGA
* *
41066981 TGTTCTGGACCTCATTGAAGAGGTTTGTTGGATCTTACATAGTTATTTGTTTGCTTGTTAGTTTC
1 TGTTCTGGACCTTATTGAAAAGGTTTGTTGGATCTTACATAGTTATTTGTTTG-TTGTTAGTTTC
** * * * *
41067046 AGTTTAATTAAATCTGAATCTTGTGCTTATCAATTTTCATTGAATTTGTTTGTTGTATTAGTTGA
65 AGTTTAATTAAATCTGAATCTTGTTTTTATTAATTTTCATTGAATTTGTTTGCTATATTAATTGA
* * * *
41067111 GTTATTAATCTTGTATTAGTGTCATTCAAGTTGG
130 ATTCTAAATCTTGTATTAGTGTCATTCATGTTGG
41067145 ATTGTTATTA
Statistics
Matches: 282, Mismatches: 47, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
169 1 0.00
170 101 0.36
171 53 0.19
172 122 0.43
173 5 0.02
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (169 bp):
TGTTCTGGACCTTATTGAAAAGGTTTGTTGGATCTTACATAGTTATTTGTTTGTTGTTAGTTTCA
GTTTAATTAAATCTGAATCTTGTTTTTATTAATTTTCATTGAATTTGTTTGCTATATTAATTGAA
TTCTAAATCTTGTATTAGTGTCATTCATGTTGGTAAAGA
Found at i:41067369 original size:21 final size:21
Alignment explanation
Indices: 41067339--41067378 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41067329 TGGATTGTTC
41067339 TTATCAATTTATTAATTAATA
1 TTATCAATTTATTAATTAATA
* * *
41067360 TTATCTATTTGTTAGTTAA
1 TTATCAATTTATTAATTAA
41067379 ATCCTAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
TTATCAATTTATTAATTAATA
Found at i:41067509 original size:15 final size:15
Alignment explanation
Indices: 41067489--41067530 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
41067479 TTGGATTGTT
41067489 ATTACTTATTTATTA
1 ATTACTTATTTATTA
*
41067504 ATTACTGATTTATTA
1 ATTACTTATTTATTA
41067519 ATTA-TT-TTTATT
1 ATTACTTATTTATT
41067531 CATGGTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 6 0.24
14 1 0.04
15 18 0.72
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTACTTATTTATTA
Found at i:41067804 original size:135 final size:138
Alignment explanation
Indices: 41067596--41067853 Score: 342
Period size: 135 Copynumber: 1.9 Consensus size: 138
41067586 TGCTTCCATG
* * * * * * * *
41067596 GTTCATATATTATTTTTTTTATTAATTTTCATTGAGTTTTTTTTCCTATATTAACTTAATTCTAG
1 GTTCATATATTATTGTTCTTATTAATTTCCATTGAGATCTGTTTCCTATATTAACTGAATTCTAA
* **
41067661 ATCTTGTATTAGTGTTATTAATGTTGGATTATTCTTACTAATTTATTAATT-ATTGTTATTCCTG
66 ATCTTGTATTAGTGTAATTAATGTTGGATTATTAGTACTAATTTATTAATTAATTGTTATTCCTG
41067725 TTGAATTT
131 TTGAATTT
* * * *
41067733 GTTCATATATT-TTGTTCTTATTAATTTCCATTGA-ATCTGTTTGCTATATTGACTGAGTTTTAA
1 GTTCATATATTATTGTTCTTATTAATTTCCATTGAGATCTGTTTCCTATATTAACTGAATTCTAA
* *
41067796 ATCTTGTATTAGTGTAATTCATGTTGGATTGTTAGTACTAATTTATTAATTAATTGTT
66 ATCTTGTATTAGTGTAATTAATGTTGGATTATTAGTACTAATTTATTAATTAATTGTT
41067854 TGTTAGTTCT
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
135 66 0.64
136 26 0.25
137 11 0.11
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (138 bp):
GTTCATATATTATTGTTCTTATTAATTTCCATTGAGATCTGTTTCCTATATTAACTGAATTCTAA
ATCTTGTATTAGTGTAATTAATGTTGGATTATTAGTACTAATTTATTAATTAATTGTTATTCCTG
TTGAATTT
Found at i:41067829 original size:340 final size:348
Alignment explanation
Indices: 41067151--41067847 Score: 841
Period size: 340 Copynumber: 2.0 Consensus size: 348
41067141 TTGGATTGTT
* * *
41067151 ATTATTGATTTATTAATTATTGTCATTCATGTTGAATTTTGTATTGGTTTGCTCGGTATATATGC
1 ATTACTGATTTATTAATTATTGTCATTCATGGTGAATTTTGTACTGGTTTGCTCGGTATATATGC
* *
41067216 ATCATGTTTCCATTGCTGCTTCCACAGTTCATATATTTTCTTATTATTAATTTACATTGAATTTG
66 ATCATGCTTCCACTGCTGCTTCCACAGTTCATATATTTTCTTATTATTAATTTACATTGAATTTG
* * *
41067281 TTTGTTATATTAACTGAGTTCTAAATCTTGTATTAATGTTATTCATGTTGGATTGTTCTTATCAA
131 TTTGTTATATTAACTGAATTCTAAATCTTGTATTAATGTTATTAATGTTGGATTATTCTTATCAA
** * *
41067346 TTTATTAATTAATATTATCTATTTGTTAGTTAAATCCTAGTTTAGTTAAATCTCAATCTTGTTTT
196 TTTATTAATT-ATATTATCTATTTCCTAGTTAAA--C-AGTTTAGTTAAATAT-AATCTTGTTCT
* * *
41067411 TATTAATTGTCATTGAATTTGTTTGCTATATTAATTGAGTTATAAATCTTGTATTAGTGTCATTC
256 TATTAATTGTCATTGAATCTGTTTGCTATATTAACTGAGTTATAAATCTTGTATTAGTGTAATTC
* *
41067476 ATGTTGGATTGTTATTACTTATTTATTA
321 ATGTTGGATTGTTAGTACTAATTTATTA
* *
41067504 ATTACTGATTTATTAATTATTTTTATTCATGGTGAA-TTTGTTGACTGGTTTGCTCGGTATATAT
1 ATTACTGATTTATTAATTATTGTCATTCATGGTGAATTTTG-T-ACTGGTTTGCTCGGTATATAT
* ** * * * *
41067568 GCA-CTATGCTTCCACTGTTGCTTCCATGGTTCATATATTATTTTTTTTATTAATTTTCATTGAG
64 GCATC-ATGCTTCCACTGCTGCTTCCACAGTTCATATATT-TTCTTATTATTAATTTACATTGAA
* * * *
41067632 TTT-TTTTTCCTATATTAACTTAATTCTAGATCTTGTATTAGTGTTATTAATGTTGGATTATTCT
127 TTTGTTTGT--TATATTAACTGAATTCTAAATCTTGTATTAATGTTATTAATGTTGGATTATTCT
* * * *
41067696 TA-CTAATTTATTAA-T-TATTGT-TA-TTCCT-GTT-GA-A-TTT-GTT-CATAT-ATTTTGTT
190 TATC-AATTTATTAATTATATTATCTATTTCCTAGTTAAACAGTTTAGTTAAATATAATCTTGTT
* *
41067749 CTTATTAATT-TCCATTGAATCTGTTTGCTATATTGACTGAGTTTTAAATCTTGTATTAGTGTAA
254 CTTATTAATTGT-CATTGAATCTGTTTGCTATATTAACTGAGTTATAAATCTTGTATTAGTGTAA
41067813 TTCATGTTGGATTGTTAGTACTAATTTATTA
318 TTCATGTTGGATTGTTAGTACTAATTTATTA
41067844 ATTA
1 ATTA
41067848 ATTGTTTGTT
Statistics
Matches: 300, Mismatches: 36, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
339 1 0.00
340 96 0.32
342 3 0.01
343 3 0.01
344 3 0.01
345 1 0.00
349 1 0.00
350 3 0.01
351 3 0.01
352 6 0.02
353 39 0.13
354 56 0.19
355 25 0.08
356 60 0.20
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (348 bp):
ATTACTGATTTATTAATTATTGTCATTCATGGTGAATTTTGTACTGGTTTGCTCGGTATATATGC
ATCATGCTTCCACTGCTGCTTCCACAGTTCATATATTTTCTTATTATTAATTTACATTGAATTTG
TTTGTTATATTAACTGAATTCTAAATCTTGTATTAATGTTATTAATGTTGGATTATTCTTATCAA
TTTATTAATTATATTATCTATTTCCTAGTTAAACAGTTTAGTTAAATATAATCTTGTTCTTATTA
ATTGTCATTGAATCTGTTTGCTATATTAACTGAGTTATAAATCTTGTATTAGTGTAATTCATGTT
GGATTGTTAGTACTAATTTATTA
Found at i:41091481 original size:14 final size:15
Alignment explanation
Indices: 41091462--41091496 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
41091452 CATAGCAAGT
41091462 AAAAACAAAAA-AAC
1 AAAAACAAAAAGAAC
*
41091476 AAAAACAAAAAGGAC
1 AAAAACAAAAAGAAC
41091491 AAAAAC
1 AAAAAC
41091497 GGTGGCGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAGAAC
Found at i:41092850 original size:25 final size:25
Alignment explanation
Indices: 41092821--41092878 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
41092811 ACCAACTTCA
* *
41092821 TTTAATCTACTTCATACATTTTTAT
1 TTTAATATACTTCATACATATTTAT
** *
41092846 TTTAATATGTTTTATACATATTTAT
1 TTTAATATACTTCATACATATTTAT
41092871 TTTAATAT
1 TTTAATAT
41092879 GTAAAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTAATATACTTCATACATATTTAT
Found at i:41093555 original size:116 final size:114
Alignment explanation
Indices: 41093340--41093654 Score: 384
Period size: 114 Copynumber: 2.7 Consensus size: 114
41093330 TAAGCATTAG
* *
41093340 CAGCGTTTTTGCGAAAGCGCCGC-AAAATACCTAAGCCCAACGACGCCGTTTTCCT-AGCTTTCG
1 CAGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTT-CTGAGCTTTC-
* * ** *
41093403 GGGGATTTACCGGCGTTTTTAAGGAAGCGCTGCTAATGCTTAGGGATTTA-
64 GGGGATTTAGCGGCGTTTTTGAGGAAGCGCTGCTAATGCCCAAGGATTTAC
** **
41093453 GTGCGTTTTTGCGAAAGCGCCACAAAAAAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTTT
1 CAGCGTTTTTGCGAAAGCGCCAC---AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * * * *
41093518 TGGGGATTTAGCGGCATTTTTGGGGAAGCGCTGCTAATTCCCAAGGCTTTAC
63 CGGGGATTTAGCGGCGTTTTTGAGGAAGCGCTGCTAATGCCCAAGGATTTAC
* * *
41093570 CAGCGATTTTGCGAAAGTGCCACAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGG
1 CAGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGG
*
41093635 GTATTTAGCGGCGTTTTTGA
66 GGATTTAGCGGCGTTTTTGA
41093655 TAAGCGCCAC
Statistics
Matches: 169, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
113 20 0.12
114 55 0.33
116 43 0.25
117 51 0.30
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (114 bp):
CAGCGTTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGG
GGATTTAGCGGCGTTTTTGAGGAAGCGCTGCTAATGCCCAAGGATTTAC
Found at i:41093695 original size:71 final size:72
Alignment explanation
Indices: 41093588--41093723 Score: 213
Period size: 71 Copynumber: 1.9 Consensus size: 72
41093578 TTGCGAAAGT
*
41093588 GCCACAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCG-GGTATTTAGCGGCGTTTT
1 GCCACAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGAGG-ATTTAGCGGCATTTT
41093652 TGATAAGC
65 TGATAAGC
* * *
41093660 GCCAC-AAAAAACCTAATCCCAACGACGTCGTTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTT
1 GCCACAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTT
41093724 CAGAAAGCGA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
71 52 0.88
72 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (72 bp):
GCCACAAAAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTT
GATAAGC
Found at i:41093792 original size:185 final size:186
Alignment explanation
Indices: 41093480--41093848 Score: 501
Period size: 185 Copynumber: 2.0 Consensus size: 186
41093470 CGCCACAAAA
* * ** *
41093480 AAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTTTTGGGGATTTAGCGGCATTTTTGGGGAA
1 AAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTTCAGAAA
* * *
41093545 GCGCTGCTAATTCCCAAGGCTTTACCAGCGATTTTGCGAAAGTGCCACAAAAAAACCTAAGCCCA
66 GCGCTGCTAATACCCAAGGCTTTACCAGCGATTTTGCGAAAGCGCAACAAAAAAACCTAAGCCCA
* *
41093610 ACGACGCCGCTTTCTGAGCTTTCGGGTATTTAGCGGCGTTTTTGA-TAAGCGCCAC
131 ACGACGCCGCTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAATTAAGCGCCAC
* *
41093665 AAAAAACCTAATCCCAACGACG-TCGTTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTTCAGAA
1 AAAAAACCTAAGCCCAACGACGCT-ATTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTTCAGAA
* * *** * * *
41093729 AGCGAC-GCTAATACCTAGGGCTTTAGGGGTGTTTTTGCTAAAGCGCAACAAAAAAACCTAAGCC
65 AGCG-CTGCTAATACCCAAGGCTTTACCAGCGATTTTGCGAAAGCGCAACAAAAAAACCTAAGCC
* *
41093793 CAACGACGCCGTTTTCTGAGCTTTTGGGGATTTAGCGGCGTTTTTAATTAAGCGCC
129 CAACGACGCCGCTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAATTAAGCGCC
41093849 GCTAATGCTC
Statistics
Matches: 159, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
184 1 0.01
185 149 0.94
186 9 0.06
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (186 bp):
AAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTTTCGAGGATTTAGCGGCATTTTTCAGAAA
GCGCTGCTAATACCCAAGGCTTTACCAGCGATTTTGCGAAAGCGCAACAAAAAAACCTAAGCCCA
ACGACGCCGCTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAATTAAGCGCCAC
Found at i:41093914 original size:115 final size:114
Alignment explanation
Indices: 41093638--41093963 Score: 467
Period size: 115 Copynumber: 2.9 Consensus size: 114
41093628 CTTTCGGGTA
* * *
41093638 TTTAGCGGCGTTTTTGAT-AAGCGCCAC-AAAAAACCTAATCCCAACGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * * * *
41093701 TTCGAGGATTTAGCGGCATTTTTCAGAAAGCGACGCTAATACCTAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATACCAAGGGC
* * *
41093750 TTTAGGGGTGTTTTTGCTAAAGCGCAACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
41093815 TTTGGGGATTTAGCGGCGTTTTTAATTAAGCGCCGCTAATGCTCAAGGGC
66 TTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATAC-CAAGGGC
* *
41093865 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTTTGAGCT
1 TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
41093930 TTCGGGGATTTAGCGGCGTTTTTTATAAAGCGCC
66 TTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCC
41093964 ACAAAAAAAC
Statistics
Matches: 188, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
112 15 0.08
113 8 0.04
114 68 0.36
115 97 0.52
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATACCAAGGGC
Found at i:41093984 original size:73 final size:73
Alignment explanation
Indices: 41093860--41094063 Score: 354
Period size: 73 Copynumber: 2.8 Consensus size: 73
41093850 CTAATGCTCA
* ** *
41093860 AGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTTT
1 AGGGATTTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTCT
41093925 GAGCTTTC
66 GAGCTTTC
* *
41093933 GGGGATTTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
1 AGGGATTTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTCT
41093998 GAGCTTTC
66 GAGCTTTC
41094006 AGGGATTTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCC
1 AGGGATTTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCC
41094064 TCGAGCCTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 124 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (73 bp):
AGGGATTTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCATTTTCT
GAGCTTTC
Found at i:41094018 original size:302 final size:299
Alignment explanation
Indices: 41093336--41094035 Score: 913
Period size: 302 Copynumber: 2.3 Consensus size: 299
41093326 AAAATAAGCA
* ** * *
41093336 TTAGCAGCGTTTTTGCGAAAGCGCCGCAAAATACCTAAGCCCAACGACGCCGTTTTCCT-AGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTT-CTGAGCTT
* * * * *
41093400 TCGGGGGATTTACCGGCGTTTTTAAGGAAGCGCTGCTAATGCTTAGGGATTTAGTGCGTTTTTGC
65 TC--GGGATTTAGCGGCGTTTTTAAGAAAGCGCTGCTAATACCTAGGGATTTAGGGCGTTTTTGC
*
41093465 GAAAGCGCCACAAAAAAAAAACCTAAGCCCAACGACGCTATTTTCTGAGCTTTTGGGGATTTAGC
128 GAAAGCG-C-CAAAAAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTTTTGGGGATTTAGC
** * * *
41093530 GGCATTTTTGGGGAAGCGCTGCTAATTCCCAAGGCTTTACCAGCGATTTTGCGAAAGTGCCACAA
191 GGCATTTTTAAGGAAGCGCCGCTAATGCCCAAGGCTTTACCAGCGATTTTGCGAAAGCGCCACAA
* *
41093595 AAAAACCTAAGCCCAACGACGCCGCTTTCTGAGCTTTCGGGTAT
256 AAAAACCTAAGCCCAACGACGCCACTTTCTGAGCTTTCGGGGAT
* *
41093639 TTAGCGGCGTTTTTGAT-AAGCGCCACAAAAAACCTAATCCCAACGACGTCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * * *
41093703 CGAGGATTTAGCGGCATTTTTCAGAAAGCGAC-GCTAATACCTAGGGCTTTAGGGGTGTTTTTGC
66 CG-GGATTTAGCGGCGTTTTTAAGAAAGCG-CTGCTAATACCTAGGGATTTA-GGGCGTTTTTGC
* * *
41093767 TAAAGCG-CAACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTTGGGGATTTAGCGG
128 GAAAGCGCCAAAAAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTTTTGGGGATTTAGCGG
* ** * * * * *
41093831 CGTTTTTAATTAAGCGCCGCTAATGCTCAAGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAA
193 CATTTTTAAGGAAGCGCCGCTAATGCCCAA-GGCTTTACCAGCGATTTTGCGAAAGCGCCACAAA
* *
41093896 AAAACCTAAGCCCAACGACGCCATTTTTTGAGCTTTCGGGGAT
257 AAAACCTAAGCCCAACGACGCCACTTTCTGAGCTTTCGGGGAT
*
41093939 TTAGCGGCGTTTTTTATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
41094004 TCAGGGATTTAGCGGCGTTTTTTATAAAGCGC
65 TC-GGGATTTAGCGGCGTTTTTAAGAAAGCGC
41094036 CACAAAAAAA
Statistics
Matches: 346, Mismatches: 43, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
299 76 0.22
300 85 0.25
301 51 0.15
302 119 0.34
303 15 0.04
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (299 bp):
TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGATTTAGCGGCGTTTTTAAGAAAGCGCTGCTAATACCTAGGGATTTAGGGCGTTTTTGCGAA
AGCGCCAAAAAAAAAACCTAAGCCCAACGACGCCATTTTCTGAGCTTTTGGGGATTTAGCGGCAT
TTTTAAGGAAGCGCCGCTAATGCCCAAGGCTTTACCAGCGATTTTGCGAAAGCGCCACAAAAAAA
CCTAAGCCCAACGACGCCACTTTCTGAGCTTTCGGGGAT
Found at i:41094249 original size:41 final size:40
Alignment explanation
Indices: 41094064--41094265 Score: 158
Period size: 41 Copynumber: 5.0 Consensus size: 40
41094054 CAACGACGCC
* *
41094064 TCGAGCCTTTAGCGGCGTTTTTG-CGAATGCGACGCTAATGA
1 TCGAG-CTTTAGCGGCGTTTTTGTCTAA-GCGCCGCTAATGA
* *
41094105 TCGGACCTTTAGCGGCGTTTTTAGT-TAAGCGCCGCTAATGC
1 TC-GAGCTTTAGCGGCGTTTTT-GTCTAAGCGCCGCTAATGA
* * * * * * *
41094146 TCGGGCCTTTAGTGGCGTTTCTGTCTATGCGCTGCTACTGC
1 TCGAG-CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGA
* * * * *
41094187 TTGGGCTTTAGTGGCGCTTTTGTCTAAGCGCCACTAATGAA
1 TCGAGCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATG-A
* *
41094228 T-GTAGCTTTAGCGGCGTTTTTGACGAAGCGCCGCTAAT
1 TCG-AGCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
41094266 AGTAACAAAA
Statistics
Matches: 129, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
40 32 0.25
41 92 0.71
42 5 0.04
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (40 bp):
TCGAGCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGA
Found at i:41094676 original size:14 final size:14
Alignment explanation
Indices: 41094651--41094690 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
41094641 ATATATTAAA
*
41094651 TAAGGTTTAGGGGT
1 TAAGGATTAGGGGT
*
41094665 TATGGATTAGGGGT
1 TAAGGATTAGGGGT
*
41094679 TAAGGGTTAGGG
1 TAAGGATTAGGG
41094691 ATTTAGGATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.33
Consensus pattern (14 bp):
TAAGGATTAGGGGT
Found at i:41095137 original size:73 final size:72
Alignment explanation
Indices: 41095045--41095218 Score: 312
Period size: 73 Copynumber: 2.4 Consensus size: 72
41095035 TACGGATCAT
*
41095045 ATAATATATATAGTTAATTAATTATTTAATTTGTATATATAGGACCAAAATATAAGAAAAAATAA
1 ATAA-ATAAATAGTTAATTAATTATTTAATTTGTATATATAGGACCAAAATATAAGAAAAAATAA
41095110 ATAAACAA
65 ATAAACAA
41095118 ATAAATAAAATAGTTAATTAATTATTTAATTTGTATATATAGGACCAAAATATAAGAAAAAATAA
1 ATAAAT-AAATAGTTAATTAATTATTTAATTTGTATATATAGGACCAAAATATAAGAAAAAATAA
41095183 ATAAACAA
65 ATAAACAA
*
41095191 ATAAATAAATAGGTAATTAATTATTTAA
1 ATAAATAAATAGTTAATTAATTATTTAA
41095219 ATTAATTTTT
Statistics
Matches: 98, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
72 23 0.23
73 75 0.77
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (72 bp):
ATAAATAAATAGTTAATTAATTATTTAATTTGTATATATAGGACCAAAATATAAGAAAAAATAAA
TAAACAA
Found at i:41095219 original size:24 final size:24
Alignment explanation
Indices: 41095192--41095272 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
41095182 AATAAACAAA
41095192 TAAATAAATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
* *
41095216 TAAATTAATTTTTAGGTAATTAATTGTT
1 TAAA-TAA---ATAGGTAATTAATTATT
*
41095244 TAAATAGATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
41095268 TAAAT
1 TAAAT
41095273 GAATGATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 24 0.50
25 3 0.06
27 2 0.04
28 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (24 bp):
TAAATAAATAGGTAATTAATTATT
Found at i:41095220 original size:28 final size:28
Alignment explanation
Indices: 41095189--41095272 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
41095179 ATAAATAAAC
41095189 AAATAAATAAATAGGTAATTAATTATTT
1 AAATAAATAAATAGGTAATTAATTATTT
* *** *
41095217 AAATTAATTTTTAGGTAATTAATT-GTT
1 AAATAAATAAATAGGTAATTAATTATTT
*
41095244 ---TAAATAGATAGGTAATTAATTATTT
1 AAATAAATAAATAGGTAATTAATTATTT
41095269 AAAT
1 AAAT
41095273 GAATGATACA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
24 17 0.40
25 2 0.05
27 2 0.05
28 21 0.50
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (28 bp):
AAATAAATAAATAGGTAATTAATTATTT
Found at i:41095992 original size:365 final size:365
Alignment explanation
Indices: 41095322--41096035 Score: 1158
Period size: 365 Copynumber: 2.0 Consensus size: 365
41095312 GATTTAGCGG
* *
41095322 CGTTTTGATAAAAAACGCCACAAAAATTTATTGTATTTACCGATACGGCGTCGTTTCGGCTTAGG
1 CGTTTTGATAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGACGTCGTTTCGGCTTAGG
* * *
41095387 GAATAAGTTTTAGTTGTGGTGTTTTTCCGAAAAGCATCGTAAATAATATTTAAACTTTACCAAAA
66 GAATAAATTTTAGTTGTGGCGTTTTTCCGAAAAGCACCGTAAATAATATTTAAACTTTACCAAAA
* *
41095452 CGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGCCGTTTTATTATAAACGCCGCAAGGATG
131 CGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGCCGTTTTATTAAAAACGCCGCAAAGATG
* * * ** *
41095517 TATAAAATTTTCTGAAAACGGCGTCGGTTCGATAATATATTAATTGTGGCATTTTTGGGAAAACG
196 TATAAAATTTACTAAAAACGACACCGGTTCGATAATATATTAATTGTGGCATGTTTGGGAAAACG
* *
41095582 CCAGAATGTTTCTTTATATTTTTATAAAATGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGG
261 CCAGAATGTTTCCTTATATTTTTATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGG
* *
41095647 CATTTTTAATTAGAACGTCGCAAAAGGTAGACATTACCGA
326 CATTTTTAATTAAAACGCCGCAAAAGGTAGACATTACCGA
*
41095687 CGTTTTGATAAAAAACGCCACAAATATTTATTGCATTTACCGATACGACGTCGTTTCGGCTTAGG
1 CGTTTTGATAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGACGTCGTTTCGGCTTAGG
* * * * *
41095752 GAATAAATTTTAGTTGTGGCGTTTTTCCTAAAAGCGCCGTAAATAATATTTGAACTTTGCGAAAA
66 GAATAAATTTTAGTTGTGGCGTTTTTCCGAAAAGCACCGTAAATAATATTTAAACTTTACCAAAA
* *
41095817 CGGCGCCGTTTCAGTTGAAGGATGGAATCTTTTAGTGGCGTTTTATTAAAAACGCCGCAAAGATG
131 CGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGCCGTTTTATTAAAAACGCCGCAAAGATG
* *
41095882 TATAAAATTTACTAAAAACGATACCGGTTCGATAATATATTAATTGTGGCGTGTTTGGGAAAACG
196 TATAAAATTTACTAAAAACGACACCGGTTCGATAATATATTAATTGTGGCATGTTTGGGAAAACG
*
41095947 CCAGAATGTTTCCTTATATTTTTATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTGGTGG
261 CCAGAATGTTTCCTTATATTTTTATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGG
**
41096012 TGTTTTTAATTAAAACGCCGCAAA
326 CATTTTTAATTAAAACGCCGCAAA
41096036 TGTCGATGCA
Statistics
Matches: 319, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
365 319 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (365 bp):
CGTTTTGATAAAAAACGCCACAAAAATTTATTGCATTTACCGATACGACGTCGTTTCGGCTTAGG
GAATAAATTTTAGTTGTGGCGTTTTTCCGAAAAGCACCGTAAATAATATTTAAACTTTACCAAAA
CGGCGCCGTTTCAGTTGAAGGATGGAATATTTTAGTGCCGTTTTATTAAAAACGCCGCAAAGATG
TATAAAATTTACTAAAAACGACACCGGTTCGATAATATATTAATTGTGGCATGTTTGGGAAAACG
CCAGAATGTTTCCTTATATTTTTATAAAACGGCGCCGTTTCTTTCTGTACTTGAAATTTTAGTGG
CATTTTTAATTAAAACGCCGCAAAAGGTAGACATTACCGA
Found at i:41096720 original size:18 final size:18
Alignment explanation
Indices: 41096697--41096734 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
41096687 TGTTTGTTAG
*
41096697 TTACTTGTAGTGTTAATA
1 TTACTTGCAGTGTTAATA
41096715 TTACTTGCAGTGTTAATA
1 TTACTTGCAGTGTTAATA
41096733 TT
1 TT
41096735 TTTGAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (18 bp):
TTACTTGCAGTGTTAATA
Found at i:41097869 original size:23 final size:23
Alignment explanation
Indices: 41097841--41097884 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41097831 CTTATATGTA
*
41097841 AACTTACATAATACATTACTTTT
1 AACTTACATAATACATAACTTTT
41097864 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
41097885 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:41098028 original size:18 final size:17
Alignment explanation
Indices: 41098005--41098989 Score: 171
Period size: 18 Copynumber: 56.4 Consensus size: 17
41097995 ACTTACATAA
41098005 TACATAGCATACATAACT
1 TACATA-CATACATAACT
*
41098023 TACATA-ATACAAAACT
1 TACATACATACATAACT
* * *
41098039 TACATAACTTAAATATCT
1 TACAT-ACATACATAACT
* * *
41098057 TACACAACTTACATAACC
1 TACA-TACATACATAACT
41098075 TACATA-ATACATTTAACT
1 TACATACATACA--TAACT
*
41098093 TACATAACTTACATAACT
1 TACAT-ACATACATAACT
41098111 TACATA-ATACATAATAACT
1 TACATACATAC---ATAACT
*
41098130 TACA-AC-TCACATAACA
1 TACATACAT-ACATAACT
* **
41098146 TACATTACTTTGATAACT
1 TACA-TACATACATAACT
*
41098164 TACATAACTTACATAA--
1 TACAT-ACATACATAACT
*
41098180 TACATA-ATAACTTACAACT
1 TACATACAT-AC--ATAACT
* *
41098199 CACATAACATACATTACT
1 TACAT-ACATACATAACT
** *
41098217 TTGATAACTTACATAACT
1 TACAT-ACATACATAACT
41098235 TACATA-ATACATAATAACT
1 TACATACATAC---ATAACT
*
41098254 TACA-AC-TCACATAACA
1 TACATACAT-ACATAACT
* **
41098270 TACATTACTTTGATAACT
1 TACA-TACATACATAACT
*
41098288 TACATAACTTACATAA--
1 TACAT-ACATACATAACT
*
41098304 TACATA-ATAACTTACAACT
1 TACATACAT-AC--ATAACT
* *
41098323 CACATAACATACATTACT
1 TACAT-ACATACATAACT
** *
41098341 TTGATAACTTACATAACT
1 TACAT-ACATACATAACT
41098359 TACATA-ATACATAATAACT
1 TACATACATAC---ATAACT
*
41098378 TACA-AC-TCACATAACA
1 TACATACAT-ACATAACT
* **
41098394 TACATTACTTTGATAACT
1 TACA-TACATACATAACT
*
41098412 TACATAACTTACATAA--
1 TACAT-ACATACATAACT
*
41098428 TACATA-ATAACTTACAACT
1 TACATACAT-AC--ATAACT
* *
41098447 CACATAACATACATTACT
1 TACAT-ACATACATAACT
** *
41098465 TTGATAACTTACATAACT
1 TACAT-ACATACATAACT
41098483 TACATA-ATACATAATAACT
1 TACATACATAC---ATAACT
*
41098502 TACA-AC-TCACATAACA
1 TACATACAT-ACATAACT
* **
41098518 TACATTACTTTGATAACT
1 TACA-TACATACATAACT
*
41098536 TACATAACTTACATAA--
1 TACAT-ACATACATAACT
*
41098552 TACATA-ATAACTTACAACT
1 TACATACAT-AC--ATAACT
* *
41098571 CACATAACATACATTACT
1 TACAT-ACATACATAACT
** *
41098589 TTGATAACTTACATAACT
1 TACAT-ACATACATAACT
41098607 TACATA-ATACATAATAACT
1 TACATACATAC---ATAACT
*
41098626 TACA-AC-TCACATAACA
1 TACATACAT-ACATAACT
* **
41098642 TACATTACTTTGATAACT
1 TACA-TACATACATAACT
*
41098660 TACATAACTTACATAA--
1 TACAT-ACATACATAACT
*
41098676 TACATA-ATAACTTACAACT
1 TACATACAT-AC--ATAACT
* *
41098695 CACATAACATACATTACT
1 TACAT-ACATACATAACT
** *
41098713 TTGATAACTTACATAACT
1 TACAT-ACATACATAACT
41098731 TACATA-ATACATAATAACT
1 TACATACATAC---ATAACT
*
41098750 TACA-AC-TCACATAACA
1 TACATACAT-ACATAACT
* **
41098766 TACATTACTTTGATAACT
1 TACA-TACATACATAACT
*
41098784 TACATAACTTACATAA--
1 TACAT-ACATACATAACT
*
41098800 TACATA-ATAACTTACAACT
1 TACATACAT-AC--ATAACT
*
41098819 CACATA-ATACATTTAACT
1 TACATACATACA--TAACT
*
41098837 TACATAACTTACATAACT
1 TACAT-ACATACATAACT
41098855 TACATA-ATACATAA--
1 TACATACATACATAACT
*
41098869 T--A-ACTTAC--AACT
1 TACATACATACATAACT
* *
41098881 CACATAACATACATTACT
1 TACAT-ACATACATAACT
** *
41098899 TTGATAACTTACATAACT
1 TACAT-ACATACATAACT
*
41098917 TACATA-ATACACAACT
1 TACATACATACATAACT
* *
41098933 TACATAGCTTACTTAA--
1 TACATA-CATACATAACT
*
41098949 TACATAACTTACATAACT
1 TACAT-ACATACATAACT
* * *
41098967 TATACACGTACATAACT
1 TACATACATACATAACT
41098984 TACATA
1 TACATA
41098990 ATTTACTTAT
Statistics
Matches: 704, Mismatches: 144, Indels: 239
0.65 0.13 0.22
Matches are distributed among these distances:
10 2 0.00
11 1 0.00
12 4 0.01
14 8 0.01
15 18 0.03
16 160 0.23
17 50 0.07
18 321 0.46
19 107 0.15
20 23 0.03
21 10 0.01
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (17 bp):
TACATACATACATAACT
Found at i:41098080 original size:36 final size:35
Alignment explanation
Indices: 41097992--41098990 Score: 226
Period size: 36 Copynumber: 31.4 Consensus size: 35
41097982 TAACAACATA
* * *
41097992 ACAACTTACATAA-TACATAGCATACATAACTTAC
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * *
41098026 ATAA--TACAAAACTTACATAACTTAAATATCTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098060 ACAACTTACATAACCTACATAA--TACATTTAACTTAC
1 ACAACTTACATAA-CTACATAACTTA-A-ATAACTTAC
* *
41098096 ATAACTTACATAACTTACATAA-TACATAATAACTT--
1 ACAACTTACATAAC-TACATAACT-TA-AATAACTTAC
* * **
41098131 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098167 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098193 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098229 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098255 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098291 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098317 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098353 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098379 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098415 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098441 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098477 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098503 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098539 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098565 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098601 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098627 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098663 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098689 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098725 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098751 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
*
41098787 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* *
41098813 ACAACTCACATAA-TACATTTAACTTACATAACTTAC
1 ACAACTTACATAACTACA--TAACTTAAATAACTTAC
*
41098849 ATAACTTACATAA-TAC---A--T-AATAACTT--
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
* * **
41098875 ACAACTCACATAACATACATTACTTTGATAACTTAC
1 ACAACTTACATAAC-TACATAACTTAAATAACTTAC
* * * *
41098911 ATAACTTACATAA-TACACAACTTACATAGCTTAC
1 ACAACTTACATAACTACATAACTTAAATAACTTAC
** *
41098945 TTAA--TACATAACTTACATAACTT--ATACACGTAC
1 ACAACTTACATAAC-TACATAACTTAAATA-ACTTAC
*
41098978 ATAACTTACATAA
1 ACAACTTACATAA
41098991 TTTACTTATC
Statistics
Matches: 722, Mismatches: 105, Indels: 275
0.66 0.10 0.25
Matches are distributed among these distances:
26 135 0.19
28 117 0.16
29 12 0.02
31 24 0.03
32 16 0.02
33 19 0.03
34 177 0.25
35 27 0.04
36 186 0.26
37 7 0.01
38 2 0.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (35 bp):
ACAACTTACATAACTACATAACTTAAATAACTTAC
Found at i:41098166 original size:62 final size:62
Alignment explanation
Indices: 41098096--41098927 Score: 1614
Period size: 62 Copynumber: 13.4 Consensus size: 62
41098086 TTTAACTTAC
41098096 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098158 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098220 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098282 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098344 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098406 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098468 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098530 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098592 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098654 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098716 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
**
41098778 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACAT-A-ATACATTTAACTTAC
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACA-TT-ACTTTG
41098840 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
1 ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
41098902 ATAACTTACATAACTTACATAATACA
1 ATAACTTACATAACTTACATAATACA
41098928 CAACTTACAT
Statistics
Matches: 762, Mismatches: 4, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
60 5 0.01
61 3 0.00
62 746 0.98
63 3 0.00
64 5 0.01
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (62 bp):
ATAACTTACATAACTTACATAATACATAATAACTTACAACTCACATAACATACATTACTTTG
Found at i:41098938 original size:25 final size:25
Alignment explanation
Indices: 41097999--41098923 Score: 176
Period size: 27 Copynumber: 36.9 Consensus size: 25
41097989 ATAACAACTT
* *
41097999 ACATAATACATAGCATACATAACTT
1 ACATAATACATAACTTACATAACTT
*
41098024 ACATAATACAAAACTTACATAACTT
1 ACATAATACATAACTTACATAACTT
* * * *
41098049 AAATATCTTACACAACTTACATAACCT
1 ACATA--ATACATAACTTACATAACTT
41098076 ACATAATACATTTAACTTACATAACTT
1 ACATAATACA--TAACTTACATAACTT
*
41098103 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098131 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098156 TGATAACTTACATAACTTACATAA--T
1 ACATAA--TACATAACTTACATAACTT
*
41098181 AC---ATA-ATAACTTAC--AACTC
1 ACATAATACATAACTTACATAACTT
* **
41098200 ACATAACATACATTACTTTGATAACTT
1 ACAT-A-ATACATAACTTACATAACTT
*
41098227 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098255 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098280 TGATAACTTACATAACTTACATAA--T
1 ACATAA--TACATAACTTACATAACTT
*
41098305 AC---ATA-ATAACTTAC--AACTC
1 ACATAATACATAACTTACATAACTT
* **
41098324 ACATAACATACATTACTTTGATAACTT
1 ACAT-A-ATACATAACTTACATAACTT
*
41098351 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098379 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098404 TGATAACTTACATAACTTACATAA--T
1 ACATAA--TACATAACTTACATAACTT
*
41098429 AC---ATA-ATAACTTAC--AACTC
1 ACATAATACATAACTTACATAACTT
* **
41098448 ACATAACATACATTACTTTGATAACTT
1 ACAT-A-ATACATAACTTACATAACTT
*
41098475 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098503 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098528 TGATAACTTACATAACTTACATAA--T
1 ACATAA--TACATAACTTACATAACTT
*
41098553 AC---ATA-ATAACTTAC--AACTC
1 ACATAATACATAACTTACATAACTT
* **
41098572 ACATAACATACATTACTTTGATAACTT
1 ACAT-A-ATACATAACTTACATAACTT
*
41098599 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098627 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098652 TGATAACTTACATAACTTACATAA--T
1 ACATAA--TACATAACTTACATAACTT
*
41098677 AC---ATA-ATAACTTAC--AACTC
1 ACATAATACATAACTTACATAACTT
* **
41098696 ACATAACATACATTACTTTGATAACTT
1 ACAT-A-ATACATAACTTACATAACTT
*
41098723 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098751 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098776 TGATAACTTACATAACTTACATAA--T
1 ACATAA--TACATAACTTACATAACTT
* *
41098801 ACATAATAACTTACAACTCACATAA--T
1 ACATAAT-AC--ATAACTTACATAACTT
41098827 ACAT--T---TAACTTACATAACTT
1 ACATAATACATAACTTACATAACTT
*
41098847 ACATAACTTACATAATACATA-ATAACTT
1 ACATAA--TACAT-A-ACTTACATAACTT
* * *
41098875 ACA-ACTCACATAACATACATTACTT
1 ACATAAT-ACATAACTTACATAACTT
**
41098900 TGATAACTTACATAACTTACATAA
1 ACATAA--TACATAACTTACATAA
41098924 TACACAACTT
Statistics
Matches: 655, Mismatches: 118, Indels: 252
0.64 0.12 0.25
Matches are distributed among these distances:
17 10 0.02
18 10 0.02
19 55 0.08
20 15 0.02
22 5 0.01
23 1 0.00
24 54 0.08
25 138 0.21
26 56 0.09
27 205 0.31
28 79 0.12
29 27 0.04
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (25 bp):
ACATAATACATAACTTACATAACTT
Found at i:41098943 original size:25 final size:25
Alignment explanation
Indices: 41098832--41098995 Score: 107
Period size: 25 Copynumber: 6.3 Consensus size: 25
41098822 ATAATACATT
*
41098832 TAACTTACATAACTTACATAACTTACA
1 TAACTTACATAA--TACACAACTTACA
*
41098859 TAA--TACATAATAACTTACAACTCACA
1 TAACTTACATAAT-AC--ACAACTTACA
* * ** *
41098885 TAACATACATTACTTTGATAACTTACA
1 TAACTTACA-TA-ATACACAACTTACA
41098912 TAACTTACATAATACACAACTTACA
1 TAACTTACATAATACACAACTTACA
* * *
41098937 TAGCTTACTTAATACATAACTTACA
1 TAACTTACATAATACACAACTTACA
* * * *
41098962 TAACTTATACACGTACATAACTTACA
1 TAACTTACATA-ATACACAACTTACA
*
41098988 TAATTTAC
1 TAACTTAC
41098996 TTATCTATGA
Statistics
Matches: 107, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 46 0.43
26 32 0.30
27 19 0.18
28 4 0.04
29 2 0.02
30 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (25 bp):
TAACTTACATAATACACAACTTACA
Found at i:41100910 original size:21 final size:21
Alignment explanation
Indices: 41100858--41100950 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
41100848 CTACAACTTA
* * *
41100858 AAGCAGAGGCGGCAACGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
*
41100879 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
* *
41100900 AAGCAGAGGCTACAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* *
41100921 AAGCAGAGGCTGCAGTGTGAG
1 AAGCAGAGGCTGCAGCGAGAG
41100942 AAGCAGAGG
1 AAGCAGAGG
41100951 TTCAAAAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.34, C:0.17, G:0.43, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:41103877 original size:2 final size:2
Alignment explanation
Indices: 41103870--41103913 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
41103860 AAAGTTAGAA
41103870 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41103912 CT
1 CT
41103914 ACTATAGTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41106799 original size:30 final size:30
Alignment explanation
Indices: 41106765--41106822 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41106755 AATCATTATC
41106765 AATTAATTTGGAGTCTATTAATTATCCATT
1 AATTAATTTGGAGTCTATTAATTATCCATT
* * *
41106795 AATTAATTTGGGGTTTGTTAATTATCCA
1 AATTAATTTGGAGTCTATTAATTATCCA
41106823 ACACAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.47
Consensus pattern (30 bp):
AATTAATTTGGAGTCTATTAATTATCCATT
Found at i:41111448 original size:39 final size:38
Alignment explanation
Indices: 41111312--41111441 Score: 161
Period size: 39 Copynumber: 3.3 Consensus size: 38
41111302 CGCAGCCCGT
* *
41111312 TGATTTACGATCATGACCTTCGACTTTCTTATGATCCAC
1 TGATTTACGATCATGACCTTCGGCTTTCTTATGGTCC-C
* * *
41111351 TGATTTACGATCATTACCTTTGGTTTTCTTATGGTCCC
1 TGATTTACGATCATGACCTTCGGCTTTCTTATGGTCCC
* *
41111389 TTGATTTACAATCATGACCTTCGGCCTTCTTATGGTCCGC
1 -TGATTTACGATCATGACCTTCGGCTTTCTTATGGTCC-C
*
41111429 TGATTTATGATCA
1 TGATTTACGATCA
41111442 CAACCTTTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 75 0.97
40 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (38 bp):
TGATTTACGATCATGACCTTCGGCTTTCTTATGGTCCC
Found at i:41111486 original size:54 final size:54
Alignment explanation
Indices: 41111423--41111627 Score: 277
Period size: 54 Copynumber: 3.8 Consensus size: 54
41111413 CCTTCTTATG
* * * * *
41111423 GTCCGCTGATTTATGATCACAACCTTTTACTTACGAGATTTTACGAATCTTACA
1 GTCCACTGATTTACGATCACGACCTTTTACTTACGAGATTTTACAAATCTTGCA
* *
41111477 GTCTACTGATTTACGATCATGACCTTTTACTTACGAGATTTTACAAATCTTGCA
1 GTCCACTGATTTACGATCACGACCTTTTACTTACGAGATTTTACAAATCTTGCA
* * *
41111531 GTCCACTGATTTACGATCACGACCTTTTACTTA-TAGGATTTTACAAATCTCGCG
1 GTCCACTGATTTACGATCACGACCTTTTACTTACGA-GATTTTACAAATCTTGCA
* * *
41111585 GTCCAGTGATTTATGATCACGACCTTTTACTTATGAGATTTTA
1 GTCCACTGATTTACGATCACGACCTTTTACTTACGAGATTTTA
41111628 TGAACCTCGC
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 132 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (54 bp):
GTCCACTGATTTACGATCACGACCTTTTACTTACGAGATTTTACAAATCTTGCA
Found at i:41111709 original size:39 final size:39
Alignment explanation
Indices: 41111662--41111861 Score: 161
Period size: 39 Copynumber: 5.1 Consensus size: 39
41111652 CAATTGCGAT
* *
41111662 CTTTAGCTTTCTTACGATCCACTGATTTACGGTTATGAC
1 CTTTAGCTTTCTTACGATCCACTGATTTACGATCATGAC
* * * * *
41111701 CTTCAGCTTTCTTAGGGGTCCGCTGATTTACGATCACGAC
1 CTTTAGCTTTCTTA-CGATCCACTGATTTACGATCATGAC
*
41111741 TTTTAGCTTTCTTAC-AGTCCA-TGGATTTACGATCATGAC
1 CTTTAGCTTTCTTACGA-TCCACT-GATTTACGATCATGAC
* * * * * *
41111780 CTTTAGTTTTCTTACGGTTCGCTAATTTACGATCATGGC
1 CTTTAGCTTTCTTACGATCCACTGATTTACGATCATGAC
** * * * ** *
41111819 CTTCGGTTTTCTTATGGTCCGTTGATTTACGATCACGAC
1 CTTTAGCTTTCTTACGATCCACTGATTTACGATCATGAC
41111858 CTTT
1 CTTT
41111862 TACTTATAGG
Statistics
Matches: 127, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 94 0.74
40 32 0.25
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (39 bp):
CTTTAGCTTTCTTACGATCCACTGATTTACGATCATGAC
Found at i:41111728 original size:79 final size:79
Alignment explanation
Indices: 41111645--41111793 Score: 187
Period size: 79 Copynumber: 1.9 Consensus size: 79
41111635 CGCGATCTGT
** * *
41111645 TGATTTACAATTGCGA-TCTTTAGCTTTCTTAC-GATCCACT-GATTTACGGTTATGACCTTCAG
1 TGATTTACAATCACGACT-TTTAGCTTTCTTACAG-TCCA-TGGATTTACGATCATGACCTTCAG
41111707 CTTTCTTAGGGGTCCGC
63 CTTTCTTAGGGGTCCGC
* * *
41111724 TGATTTACGATCACGACTTTTAGCTTTCTTACAGTCCATGGATTTACGATCATGACCTTTAGTTT
1 TGATTTACAATCACGACTTTTAGCTTTCTTACAGTCCATGGATTTACGATCATGACCTTCAGCTT
41111789 TCTTA
66 TCTTA
41111794 CGGTTCGCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 1 0.02
79 57 0.95
80 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (79 bp):
TGATTTACAATCACGACTTTTAGCTTTCTTACAGTCCATGGATTTACGATCATGACCTTCAGCTT
TCTTAGGGGTCCGC
Found at i:41111901 original size:54 final size:54
Alignment explanation
Indices: 41111842--41111944 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
41111832 ATGGTCCGTT
* **
41111842 GATTTACGATCACGACCTTTTACTTATAGGATTTTATGAATCTCGCGGTCTACC
1 GATTTACGATCACGACCTTCTACTTATAGGATTTTACAAATCTCGCGGTCTACC
* * *
41111896 GATTTACGATCATGACCTTCTACTTATGGGCTTTTACAAATCTCGCGGT
1 GATTTACGATCACGACCTTCTACTTATAGGATTTTACAAATCTCGCGGT
41111945 TCGTTGATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (54 bp):
GATTTACGATCACGACCTTCTACTTATAGGATTTTACAAATCTCGCGGTCTACC
Found at i:41111954 original size:54 final size:53
Alignment explanation
Indices: 41111838--41111955 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 53
41111828 TCTTATGGTC
* **
41111838 CGTTGATTTACGATCACGACCTTTTACTTATAGGATTTTATGAATCTCGCGGT
1 CGTTGATTTACGATCACGACCTTCTACTTATAGGATTTTACAAATCTCGCGGT
* * * *
41111891 C-TACCGATTTACGATCATGACCTTCTACTTATGGGCTTTTACAAATCTCGCGGTT
1 CGT--TGATTTACGATCACGACCTTCTACTTATAGGATTTTACAAATCTCGCGG-T
41111946 CGTTGATTTA
1 CGTTGATTTA
41111956 TGATTACTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
52 1 0.02
53 1 0.02
54 48 0.91
55 2 0.04
56 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (53 bp):
CGTTGATTTACGATCACGACCTTCTACTTATAGGATTTTACAAATCTCGCGGT
Found at i:41112061 original size:24 final size:24
Alignment explanation
Indices: 41112020--41112119 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 24
41112010 TATGGATTAC
* *
41112020 AATACAGTTCGCAGTATTTCTGTA
1 AATACAGTTCGTAGTATTTCTATA
*
41112044 AATACAGTTCGTAATA-TTCTAT-
1 AATACAGTTCGTAGTATTTCTATA
* * *
41112066 GATATAGTTCGTGGTATTTCTATA
1 AATACAGTTCGTAGTATTTCTATA
* * *
41112090 AATATAGTTCGTAGCATTTCTAAA
1 AATACAGTTCGTAGTATTTCTATA
41112114 AATACA
1 AATACA
41112120 ATTCACAGCA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
22 12 0.19
23 11 0.18
24 39 0.63
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (24 bp):
AATACAGTTCGTAGTATTTCTATA
Found at i:41115459 original size:26 final size:26
Alignment explanation
Indices: 41115429--41115481 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
41115419 TTATAATTTA
41115429 ATTTCAACCAC-TTAAAAGAAATTTCT
1 ATTTCAACCACGTT-AAAGAAATTTCT
* *
41115455 ATTTCAACCCCGTTAAAGAATTTTCT
1 ATTTCAACCACGTTAAAGAAATTTCT
41115481 A
1 A
41115482 ACTTCGCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (26 bp):
ATTTCAACCACGTTAAAGAAATTTCT
Found at i:41117807 original size:7 final size:7
Alignment explanation
Indices: 41117795--41117828 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
41117785 AAAAAATATT
41117795 TATTTAA
1 TATTTAA
41117802 TATTTAA
1 TATTTAA
41117809 TATTTAA
1 TATTTAA
*
41117816 TAATTATA
1 TATTTA-A
41117824 TATTT
1 TATTT
41117829 CTTTTACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTTAA
Found at i:41118482 original size:20 final size:20
Alignment explanation
Indices: 41118457--41118497 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41118447 TCTAGCTAAG
41118457 TTTGAATCTTTTATGGATTA
1 TTTGAATCTTTTATGGATTA
*
41118477 TTTGAATCTTTTGTGGATTA
1 TTTGAATCTTTTATGGATTA
41118497 T
1 T
41118498 AGTAACATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (20 bp):
TTTGAATCTTTTATGGATTA
Found at i:41127923 original size:16 final size:16
Alignment explanation
Indices: 41127902--41127937 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41127892 AATCAAATTA
*
41127902 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
41127918 ATATAAACAAATATTT
1 ATATAAACAAATATTT
41127934 ATAT
1 ATAT
41127938 TTATGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:41127969 original size:5 final size:5
Alignment explanation
Indices: 41127959--41127985 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41127949 CACTAGATCT
41127959 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
41127986 TATTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:41128448 original size:20 final size:20
Alignment explanation
Indices: 41128423--41128471 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
41128413 CTGCATTAAT
*
41128423 AAATCAATTTGAATAAAATC
1 AAATCAAATTGAATAAAATC
* **
41128443 AAATCAAATTGATTGGAATC
1 AAATCAAATTGAATAAAATC
41128463 AAATCAAAT
1 AAATCAAAT
41128472 CAAGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGAATAAAATC
Found at i:41131527 original size:26 final size:26
Alignment explanation
Indices: 41131474--41131527 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
41131464 AGCTTGGTCT
*
41131474 AGGGAAAGACAAGCTTGGGTTGTGCA
1 AGGGAAAGACAAGCTTGGGTTGTCCA
41131500 AGGGAAAGACAAGCTTGGG-TGTTCCA
1 AGGGAAAGACAAGCTTGGGTTG-TCCA
41131526 AG
1 AG
41131528 TCTGAGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.31, C:0.13, G:0.37, T:0.19
Consensus pattern (26 bp):
AGGGAAAGACAAGCTTGGGTTGTCCA
Found at i:41134926 original size:83 final size:76
Alignment explanation
Indices: 41134815--41135035 Score: 250
Period size: 76 Copynumber: 2.8 Consensus size: 76
41134805 ACAGTAGGAT
* * *
41134815 TAAATCCCGAAACAAAATTATTTAATTAAATCTTGTTTAGCAACAAAATCGAAATCGAATAAAAT
1 TAAATTCCGAAACAGAATTATTTAATTAAATCTTGTTTAGAAACAAAATC--AA---AATAAAAT
*
41134880 CTATTAAACGGCGAGAA
61 CTATTAAA-GGCAAGAA
* * *
41134897 TAAATTCCGAAACAGAATTTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTTT
1 TAAATTCCGAAACAGAA-TTATTTAATTAAATCTTGTTTAGAAACAAAATCAAAATAAAATCTAT
*
41134962 TAAATGCAAGAA
65 TAAAGGCAAGAA
41134974 TAAA-TCCAGAAACAGAATTATTTAATTAAATCTTGTTT-GAAA-ATAAATTCAAAATCAAAATC
1 TAAATTCC-GAAACAGAATTATTTAATTAAATCTTGTTTAGAAACA-AAA-TCAAAAT-AAAATC
41135036 AAAATCAAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
74 1 0.01
75 7 0.06
76 30 0.24
77 25 0.20
78 15 0.12
81 2 0.02
82 15 0.12
83 30 0.24
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (76 bp):
TAAATTCCGAAACAGAATTATTTAATTAAATCTTGTTTAGAAACAAAATCAAAATAAAATCTATT
AAAGGCAAGAA
Found at i:41135033 original size:6 final size:6
Alignment explanation
Indices: 41135013--41135062 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
41135003 ATCTTGTTTG
*
41135013 AAAAT- AAATTC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
41135060 AAA
1 AAA
41135063 TCTATTAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:41135083 original size:184 final size:183
Alignment explanation
Indices: 41134858--41135213 Score: 488
Period size: 184 Copynumber: 1.9 Consensus size: 183
41134848 TGTTTAGCAA
* * * * * *
41134858 CAAAATCGAAATCGAATAAAATCTATTAAACGGCGAGAATAAATTCCGAAACAGAATTTATTTGA
1 CAAAATCAAAATCAAATAAAATCTATTAAACGACAAGAATAAATCCCGAAACAGAA-TTATTTAA
*
41134923 TTAAATCTT-GTTTGGAAACAAAATCAAAATAAAATCTTTTAAAT-GCAAGAATAAATC-CAGAA
65 TTAAATCTTCGTTTGGAAACAAAATC-AAATAAAATCTGTTAAATGGCAAGAATAAATCTC-GAA
* *
41134985 ACAGAATTATTTAATTAAATCTTGTTT-GAAA-ATAAATTCAAAATCAAAATCAAAAT
128 ACAAAATTATTTAATTAAATCCTGTTTAGAAACA-AAA-TCAAAATCAAAATCAAAAT
* *
41135041 CAAAATCAAAATCAAAATCAAATCTATTAAACGACAAGAATAAATCCCGAAATAGAATTATTTAA
1 CAAAATCAAAATC-AAATAAAATCTATTAAACGACAAGAATAAATCCCGAAACAGAATTATTTAA
* ***
41135106 TTAAATCTTCGTTTGGAAACAAAATCGAATAAAATCTGTTAAATGGTGGGAATAAATCTCGAAAC
65 TTAAATCTTCGTTTGGAAACAAAATCAAATAAAATCTGTTAAATGGCAAGAATAAATCTCGAAAC
41135171 AAAATTATTTAATTAAATCCTGTTTAGAAACAAAATCAAAATC
130 AAAATTATTTAATTAAATCCTGTTTAGAAACAAAATCAAAATC
41135214 GAATAAAATC
Statistics
Matches: 152, Mismatches: 15, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
183 44 0.29
184 99 0.65
185 8 0.05
186 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.28
Consensus pattern (183 bp):
CAAAATCAAAATCAAATAAAATCTATTAAACGACAAGAATAAATCCCGAAACAGAATTATTTAAT
TAAATCTTCGTTTGGAAACAAAATCAAATAAAATCTGTTAAATGGCAAGAATAAATCTCGAAACA
AAATTATTTAATTAAATCCTGTTTAGAAACAAAATCAAAATCAAAATCAAAAT
Found at i:41135240 original size:82 final size:82
Alignment explanation
Indices: 41135041--41135349 Score: 328
Period size: 82 Copynumber: 3.8 Consensus size: 82
41135031 AAATCAAAAT
* * ** *
41135041 CAAAATCAAAATCAAAATCAAATCTATTAAACGACAAGAATAAATCCCGAAATAGAATTATTTAA
1 CAAAATCAAAATC-AAATAAAATCTATTAAACGGCGGGAATAAATCCCGAAATAGAATTATTCAA
*
41135106 TTAAATCTTCGTTTG---
65 TTAAATCCTCGTTTGAAA
* * * * * * * * *
41135121 -GAAA-CAAAATCGAATAAAATCTGTTAAATGGTGGGAATAAATCTCGAAACAAAATTATTTAAT
1 CAAAATCAAAATCAAATAAAATCTATTAAACGGCGGGAATAAATCCCGAAATAGAATTATTCAAT
41135184 TAAATCCT-GTTTAGAAA
66 TAAATCCTCGTTT-GAAA
* ** *
41135201 CAAAATCAAAATCGAATAAAATCGGTTAAACGGCGGGAATAAATTCCGAAATAGAATTATTCAAT
1 CAAAATCAAAATCAAATAAAATCTATTAAACGGCGGGAATAAATCCCGAAATAGAATTATTCAAT
*
41135266 T-AATTCTCGTTTGGAAA
66 TAAATCCTCGTTT-GAAA
* * *
41135283 CAAAATCAAAAT-AAATAAAACCTATTGAACGGTGGGAATAAATCCCGAAATAGAATTATTCAAT
1 CAAAATCAAAATCAAATAAAATCTATTAAACGGCGGGAATAAATCCCGAAATAGAATTATTCAAT
41135347 TAA
66 TAA
41135350 TTCTCATTCG
Statistics
Matches: 190, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
76 4 0.02
77 49 0.26
78 7 0.04
79 3 0.02
81 54 0.28
82 73 0.38
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (82 bp):
CAAAATCAAAATCAAATAAAATCTATTAAACGGCGGGAATAAATCCCGAAATAGAATTATTCAAT
TAAATCCTCGTTTGAAA
Found at i:41135333 original size:81 final size:81
Alignment explanation
Indices: 41135078--41135374 Score: 354
Period size: 81 Copynumber: 3.7 Consensus size: 81
41135068 TAAACGACAA
*
41135078 GAATAAATCCCGAAATAGAATTATTTAATTAAATCTTCGTTTGGAAACAAAATC-----GAATAA
1 GAATAAATCCCGAAATAGAATTATTCAATTAAATC-TCGTTTGGAAACAAAATCAAAATGAATAA
*
41135138 AATCTGTTAAATGGTGG
65 AATCTGTTAAACGGTGG
* * * * *
41135155 GAATAAATCTCGAAACAAAATTATTTAATTAAATC-CTGTTTAGAAACAAAATCAAAATCGAATA
1 GAATAAATCCCGAAATAGAATTATTCAATTAAATCTC-GTTTGGAAACAAAATCAAAAT-GAATA
* *
41135219 AAATCGGTTAAACGGCGG
64 AAATCTGTTAAACGGTGG
* * *
41135237 GAATAAATTCCGAAATAGAATTATTCAATTAATTCTCGTTTGGAAACAAAATCAAAATAAATAAA
1 GAATAAATCCCGAAATAGAATTATTCAATTAAATCTCGTTTGGAAACAAAATCAAAATGAATAAA
* * *
41135302 ACCTATTGAACGGTGG
66 ATCTGTTAAACGGTGG
* * * *
41135318 GAATAAATCCCGAAATAGAATTATTCAATTAATTCTCATTCGGAAACAAAATAAAAA
1 GAATAAATCCCGAAATAGAATTATTCAATTAAATCTCGTTTGGAAACAAAATCAAAA
41135375 AAAGGAATAA
Statistics
Matches: 188, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.01
76 15 0.08
77 32 0.17
81 70 0.37
82 69 0.37
83 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (81 bp):
GAATAAATCCCGAAATAGAATTATTCAATTAAATCTCGTTTGGAAACAAAATCAAAATGAATAAA
ATCTGTTAAACGGTGG
Found at i:41136594 original size:16 final size:16
Alignment explanation
Indices: 41136573--41136618 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
41136563 ATAGGCTAAT
41136573 TATATTTAATATTAAA
1 TATATTTAATATTAAA
** *
41136589 TATATTTCTTATTAAT
1 TATATTTAATATTAAA
41136605 TAT-TTTAAT-TTAAA
1 TATATTTAATATTAAA
41136619 AATAAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 4 0.17
15 4 0.17
16 16 0.67
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTTAATATTAAA
Found at i:41138362 original size:22 final size:20
Alignment explanation
Indices: 41138314--41138354 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41138304 CATTCCAATT
*
41138314 CATTTCACATATTACATTTC
1 CATTTCACATATTAAATTTC
41138334 CATTTCACATATATAAATTTC
1 CATTTCACATAT-TAAATTTC
41138355 ATAATTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (20 bp):
CATTTCACATATTAAATTTC
Found at i:41141236 original size:144 final size:142
Alignment explanation
Indices: 41140971--41141255 Score: 462
Period size: 144 Copynumber: 2.0 Consensus size: 142
41140961 ATTTAACTTT
*
41140971 ACATTCATGAAAATTGCAAACTAAAATTCACAACAGAAAAACCCTAACGCGTAACGAAAAAAAAA
1 ACATTCATGAAAATTGCAAACTAAAACTCACAACAGAAAAACCCTAACGCGTAACGAAAAAAAAA
* * **
41141036 GGGTACTTACGAAAAACCCGACTGTAGTACCAACAATTAGAAGCACCTGAACGATTAAACAAAAT
66 GGGTACTTACCAAAAACCCGACTGTAGAACCAACAATTAGAAGCACCCAAACGATTAAACAAAAT
41141101 CGAAGACTTACA
131 CGAAGACTTACA
* *
41141113 ACATTCATGAAAATTGCAACCTAAAACTCACAACAGAAAAAACCCTAATGCGTAACGAAAAAGAA
1 ACATTCATGAAAATTGCAAACTAAAACTCACAACAG-AAAAACCCTAACGCGTAACGAAAAA-AA
*
41141178 AAGGGTACTTACCAAAAACCCGACTGTAGAACCAACAATTAGAAGCACCCAAATGATTAAACAAA
64 AAGGGTACTTACCAAAAACCCGACTGTAGAACCAACAATTAGAAGCACCCAAACGATTAAACAAA
* *
41141243 ATTGAAGGCTTAC
129 ATCGAAGACTTAC
41141256 CACCTCGCCG
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
142 34 0.26
143 24 0.18
144 73 0.56
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.17
Consensus pattern (142 bp):
ACATTCATGAAAATTGCAAACTAAAACTCACAACAGAAAAACCCTAACGCGTAACGAAAAAAAAA
GGGTACTTACCAAAAACCCGACTGTAGAACCAACAATTAGAAGCACCCAAACGATTAAACAAAAT
CGAAGACTTACA
Found at i:41147212 original size:42 final size:42
Alignment explanation
Indices: 41146985--41147278 Score: 258
Period size: 42 Copynumber: 7.0 Consensus size: 42
41146975 CGCTTACAGA
* * *
41146985 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCTCTTAGG
1 AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTAGG
* *
41147027 AAAAAAAACGCCGCT-AATGATCATGTTCTTTA--GGCGCTTAGG
1 --AAAAAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTAGG
* * * *
41147069 AAAAAACGCTGCT-AATGATCATGTTCTTTAGCGGCGCTTTGG
1 AAAAAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTAGG
* * ** *
41147111 AAAAAACGCCGCT-AAAGAACATGATCTTTAGTAGCGTTTAGG
1 AAAAAACGCCGCTAAAAGTA-ATGTTCTTTAGCGGCGCTTAGG
* *
41147153 AAAAAAACGCCACTAAAAGTAATGTTCTATAGCGGCGCTT-GG
1 -AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTAGG
* * **
41147195 TAAAAAACGCCGCTAAAAGTAATATTCTTTAGTGGCGCTTCATC
1 -AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-AGG
* * * *
41147239 TACAAACGCTGCTAAAAGTAGTGTTCTTTAGCGGCGCTTA
1 AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTA
41147279 TTTCACAAAC
Statistics
Matches: 209, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
40 29 0.14
42 88 0.42
43 62 0.30
44 30 0.14
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTAGG
Found at i:41147224 original size:85 final size:82
Alignment explanation
Indices: 41146974--41147277 Score: 269
Period size: 85 Copynumber: 3.6 Consensus size: 82
41146964 AACTTTTGTG
* * *
41146974 GCGCTTACAGAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCTCTTAGGAAAAAAAACGCC
1 GCGCTTA-GGAAAAAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTT-GG--AAAAAACGCC
* * *
41147039 GCTAATGATCATGTTCTTTAG-
62 GCTAAAG-TAATATTCTTTAGT
* *
41147060 GCGCTTAGG-AAAAAACGCTGCT-AATGATCATGTTCTTTAGCGGCGCTTTGGAAAAAACGCCGC
1 GCGCTTAGGAAAAAAACGCCGCTAAAAG-TCATGTTCTTTAGCGGCGC-TTGGAAAAAACGCCGC
*
41147123 TAAAG-AACATGATCTTTAGT
64 TAAAGTAATAT--TCTTTAGT
* * * *
41147143 AGCGTTTAGGAAAAAAACGCCACTAAAAGTAATGTTCTATAGCGGCGCTTGGTAAAAAACGCCGC
1 -GCGCTTAGGAAAAAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTGG-AAAAAACGCCGC
41147208 TAAAAGTAATATTCTTTAGT
64 T-AAAGTAATATTCTTTAGT
*** * *
41147228 GGCGCTTCA-TCTACAAACGCTGCTAAAAGT-AGTGTTCTTTAGCGGCGCTT
1 -GCGCTT-AGGAAAAAAACGCCGCTAAAAGTCA-TGTTCTTTAGCGGCGCTT
41147278 ATTTCACAAA
Statistics
Matches: 181, Mismatches: 24, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
80 2 0.01
82 23 0.13
83 3 0.02
84 45 0.25
85 89 0.49
86 15 0.08
87 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (82 bp):
GCGCTTAGGAAAAAAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGCTTGGAAAAAACGCCGCTA
AAGTAATATTCTTTAGT
Found at i:41147287 original size:43 final size:42
Alignment explanation
Indices: 41147157--41147288 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 42
41147147 TTTAGGAAAA
* * * * *
41147157 AAACGCCACTAAAAGTAATGTTCTATAGCGGCGCTTGGT-AAA
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-ATCTAC
* *
41147199 AAACGCCGCTAAAAGTAATATTCTTTAGTGGCGCTTCATCTAC
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-ATCTAC
* * *
41147242 AAACGCTGCTAAAAGTAGTGTTCTTTAGCGGCGCTTATTTCAC
1 AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTATCT-AC
41147285 AAAC
1 AAAC
41147289 ACCACTATAT
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
42 36 0.48
43 39 0.52
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTATCTAC
Found at i:41147731 original size:12 final size:12
Alignment explanation
Indices: 41147714--41147741 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41147704 TTTTGAACCT
41147714 CTGCTTCTCTCG
1 CTGCTTCTCTCG
41147726 CTGCTTCTCTCG
1 CTGCTTCTCTCG
41147738 CTGC
1 CTGC
41147742 GGCCTCTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.18, T:0.39
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:41147791 original size:21 final size:21
Alignment explanation
Indices: 41147726--41147791 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
41147716 GCTTCTCTCG
*
41147726 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
41147747 CTACTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
41147768 CTGCTTCCCTCACTGCTGCCT
1 CTGCTTCTCTCGCTGCAGCCT
41147789 CTG
1 CTG
41147792 TTTTAAGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.05, C:0.44, G:0.18, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:41152712 original size:9 final size:9
Alignment explanation
Indices: 41152698--41153057 Score: 219
Period size: 9 Copynumber: 42.2 Consensus size: 9
41152688 AAGTTATACA
41152698 TTATGTAAG
1 TTATGTAAG
41152707 TTATGTAAG
1 TTATGTAAG
41152716 TTATGTAAG
1 TTATGTAAG
*
41152725 TTGTGTAAG
1 TTATGTAAG
*
41152734 TTGTGT-A-
1 TTATGTAAG
* *
41152741 TTATGAAAC
1 TTATGTAAG
41152750 TTATGTAAG
1 TTATGTAAG
*
41152759 TTATGT--C
1 TTATGTAAG
41152766 TTATGTAAG
1 TTATGTAAG
*
41152775 TTATGTAAA
1 TTATGTAAG
41152784 TTATGT-A-
1 TTATGTAAG
*
41152791 TTATGTAAA
1 TTATGTAAG
41152800 TTATGTAAG
1 TTATGTAAG
*
41152809 TTGTGT-A-
1 TTATGTAAG
*
41152816 TTATATAAG
1 TTATGTAAG
41152825 TTATGTAAG
1 TTATGTAAG
*
41152834 TTGTGT-A-
1 TTATGTAAG
41152841 TTATGTAAG
1 TTATGTAAG
41152850 TTATGTAAG
1 TTATGTAAG
* **
41152859 TTTTTGT-TT
1 -TTATGTAAG
*
41152868 TTGTGT-A-
1 TTATGTAAG
*
41152875 TTATGTAAC
1 TTATGTAAG
* *
41152884 TTATTTAAT
1 TTATGTAAG
* *
41152893 TTAGGTAGG
1 TTATGTAAG
*
41152902 GTATGTATTA-
1 TTATGTA--AG
*
41152912 TTATGTAAC
1 TTATGTAAG
* *
41152921 TTATTTAAT
1 TTATGTAAG
*
41152930 TTATGTAGG
1 TTATGTAAG
*
41152939 GTATGTAAG
1 TTATGTAAG
41152948 TTATGTAAG
1 TTATGTAAG
*
41152957 TTGTGT-A-
1 TTATGTAAG
*
41152964 TTATTTACA-
1 TTATGTA-AG
*
41152973 -CATGTAAG
1 TTATGTAAG
* *
41152981 CTGTGT-A-
1 TTATGTAAG
41152988 TTATGTAAG
1 TTATGTAAG
*
41152997 TTATGCAAG
1 TTATGTAAG
41153006 TTATGT-A-
1 TTATGTAAG
* *
41153013 TTAAGTAGG
1 TTATGTAAG
41153022 TTATGTAAG
1 TTATGTAAG
41153031 TTATGT-A-
1 TTATGTAAG
41153038 TTATGTAAG
1 TTATGTAAG
41153047 TTATGTAAG
1 TTATGTAAG
41153056 TT
1 TT
41153058 TTTGTTTTTG
Statistics
Matches: 271, Mismatches: 54, Indels: 52
0.72 0.14 0.14
Matches are distributed among these distances:
7 50 0.18
8 25 0.09
9 185 0.68
10 11 0.04
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:41152756 original size:25 final size:25
Alignment explanation
Indices: 41152698--41152860 Score: 186
Period size: 25 Copynumber: 6.4 Consensus size: 25
41152688 AAGTTATACA
*
41152698 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGAAAG
* * *
41152725 TTGTGTAAGTTGTGTATTATGAAAC
1 TTATGTAAGTTATGTATTATGAAAG
* *
41152750 TTATGTAAGTTATGTCTTATGTAAG
1 TTATGTAAGTTATGTATTATGAAAG
*
41152775 TTATGTAAATTATGTATTATGTAAA-
1 TTATGTAAGTTATGTATTATG-AAAG
*
41152800 TTATGTAAGTTGTGTATTAT-ATAAG
1 TTATGTAAGTTATGTATTATGA-AAG
* *
41152825 TTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGAAAG
41152850 TTATGTAAGTT
1 TTATGTAAGTT
41152861 TTTGTTTTTG
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.01
24 2 0.02
25 98 0.84
26 3 0.03
27 13 0.11
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGAAAG
Found at i:41152768 original size:16 final size:17
Alignment explanation
Indices: 41152697--41153054 Score: 176
Period size: 16 Copynumber: 21.1 Consensus size: 17
41152687 TAAGTTATAC
41152697 ATTATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
*
41152714 AGTTATGTAAGTTGTGTA
1 A-TTATGTAAGTTATGTA
* *
41152732 AGTTGTGT-A-TTATGAA
1 A-TTATGTAAGTTATGTA
41152748 ACTTATGTAAGTTATGT-
1 A-TTATGTAAGTTATGTA
*
41152765 CTTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGT-A
41152783 ATTATGT-A-TTATGTAA
1 ATTATGTAAGTTATGT-A
*
41152799 ATTATGTAAGTTGTGT-
1 ATTATGTAAGTTATGTA
*
41152815 ATTATATAAGTTATGTA
1 ATTATGTAAGTTATGTA
*
41152832 AGTTGTGT-A-TTATGTA
1 A-TTATGTAAGTTATGTA
* *
41152848 AGTTATGTAAGTTTTTGTT
1 A-TTATGTAAG-TTATGTA
* *
41152867 TTTGTGT-A-TTATGTA
1 ATTATGTAAGTTATGTA
* * *
41152882 ACTTATTTAATTTAGGTA
1 A-TTATGTAAGTTATGTA
**
41152900 GGGTATGTATTA-TTATGTA
1 -ATTATGTA--AGTTATGTA
* *
41152919 ACTTATTTAATTTATGTA
1 A-TTATGTAAGTTATGTA
**
41152937 GGGTATGTAAGTTATGTA
1 -ATTATGTAAGTTATGTA
* *
41152955 AGTTGTGT-A-TTATTTA
1 A-TTATGTAAGTTATGTA
* * *
41152971 CA-CATGTAAGCTGTGT-
1 -ATTATGTAAGTTATGTA
*
41152987 ATTATGTAAGTTATGCA
1 ATTATGTAAGTTATGTA
*
41153004 AGTTATGT-A-TTAAGTA
1 A-TTATGTAAGTTATGTA
*
41153020 GGTTATGTAAGTTATGT-
1 -ATTATGTAAGTTATGTA
41153037 ATTATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
41153054 A
1 A
41153055 GTTTTTGTTT
Statistics
Matches: 255, Mismatches: 54, Indels: 64
0.68 0.14 0.17
Matches are distributed among these distances:
15 9 0.04
16 116 0.45
17 20 0.08
18 93 0.36
19 16 0.06
20 1 0.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.47
Consensus pattern (17 bp):
ATTATGTAAGTTATGTA
Found at i:41152782 original size:50 final size:49
Alignment explanation
Indices: 41152697--41153057 Score: 229
Period size: 50 Copynumber: 7.2 Consensus size: 49
41152687 TAAGTTATAC
*
41152697 ATTATGTAAGTTATGTAAGTTATGTAAGTTGTGTAAGTTGTGTATTATGAA
1 ATTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTGTGTATTATGAA
* * *
41152748 ACTTATGTAAGTTATGTCTTATGTAAGTTATGTAAATTATGTATTATGTAA
1 A-TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTATTATG-AA
* *
41152799 ATTATGTAAGTTGTGTATTATATAAGTTATGTAAGTTGTGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTATTATG-AA
* * * * *
41152849 GTTATGTAAGTTTTTGT-TTTTGTGTA-TTATGTAA---CT-TATT-T-AA
1 ATTATGTAAG-TTATGTATTATGT-AAGTTATGTAAGTTGTGTATTATGAA
* * * * * * * * *
41152892 TTTAGGTAGGGTATGTATTATTATGTAACTTATTTAATTTATGTAGGGTATGTAA
1 ATTATGTAAGTTATG---TATTATGTAAGTTATGTAAGTTGTGTA--TTATG-AA
* * * * *
41152947 GTTATGTAAGTTGTGTATTATTTACA--CATGTAAGCTGTGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGTA-AGTTATGTAAGTTGTGTATTATG-AA
* * * * *
41152996 GTTATGCAAGTTATGTATTAAGTAGGTTATGTAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTATTATG-AA
*
41153046 GTTATGTAAGTT
1 ATTATGTAAGTT
41153058 TTTGTTTTTG
Statistics
Matches: 243, Mismatches: 46, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
42 3 0.01
43 9 0.04
45 3 0.01
46 16 0.07
47 1 0.00
49 28 0.12
50 125 0.51
51 20 0.08
52 24 0.10
53 2 0.01
55 12 0.05
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (49 bp):
ATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGAA
Found at i:41152918 original size:37 final size:37
Alignment explanation
Indices: 41152873--41152945 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
41152863 TGTTTTTGTG
41152873 TATTATGTAACTTATTTAATTTAGGTAGGGTATGTAT
1 TATTATGTAACTTATTTAATTTAGGTAGGGTATGTAT
*
41152910 TATTATGTAACTTATTTAATTTATGTAGGGTATGTA
1 TATTATGTAACTTATTTAATTTAGGTAGGGTATGTA
41152946 AGTTATGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.49
Consensus pattern (37 bp):
TATTATGTAACTTATTTAATTTAGGTAGGGTATGTAT
Found at i:41153024 original size:25 final size:25
Alignment explanation
Indices: 41152910--41153194 Score: 157
Period size: 25 Copynumber: 11.5 Consensus size: 25
41152900 GGGTATGTAT
* * *
41152910 TATTATGTAACTTATTTAATTTATG
1 TATTATGTAAGTTATGTAAGTTATG
* *
41152935 TAGGGTATGTAAGTTATGTAAGTTGTG
1 TA--TTATGTAAGTTATGTAAGTTATG
* * * *
41152962 TATTATTTACA--CATGTAAGCTGTG
1 TATTATGTA-AGTTATGTAAGTTATG
*
41152986 TATTATGTAAGTTATGCAAGTTATG
1 TATTATGTAAGTTATGTAAGTTATG
* *
41153011 TATTAAGTAGGTTATGTAAGTTATG
1 TATTATGTAAGTTATGTAAGTTATG
*
41153036 TATTATGTAAGTTATGTAAGTTTTTG
1 TATTATGTAAGTTATGTAAG-TTATG
* * * *
41153062 T-TTTTGTGTA-TTATGTAACTTATT
1 TATTATGT-AAGTTATGTAAGTTATG
* *
41153086 TAGTTTATGT-AG---GGTATG-TAT-
1 TA--TTATGTAAGTTATGTAAGTTATG
* *
41153107 TATTATGTAAGTTAT-TATG-TAAG
1 TATTATGTAAGTTATGTAAGTTATG
41153130 ATATTATGTAAGATATTATGTAAGTTATG
1 -TATTATGTAAG---TTATGTAAGTTATG
*
41153159 TATTATGT-A-TTATATAAGTTATG
1 TATTATGTAAGTTATGTAAGTTATG
* *
41153182 TGTTGTGTAAGTT
1 TATTATGTAAGTT
41153195 TATATATAAA
Statistics
Matches: 200, Mismatches: 36, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.03
20 2 0.01
21 2 0.01
22 9 0.05
23 23 0.12
24 35 0.17
25 72 0.36
26 7 0.04
27 30 0.15
28 11 0.05
29 3 0.01
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (25 bp):
TATTATGTAAGTTATGTAAGTTATG
Found at i:41153123 original size:12 final size:12
Alignment explanation
Indices: 41153106--41153277 Score: 101
Period size: 12 Copynumber: 14.3 Consensus size: 12
41153096 AGGGTATGTA
41153106 TTATTATGTAAG
1 TTATTATGTAAG
41153118 TTATTATGTAAG
1 TTATTATGTAAG
*
41153130 ATATTATGTAAG
1 TTATTATGTAAG
*
41153142 ATATTATGTAAG
1 TTATTATGTAAG
*
41153154 TTATGTAT-TATG
1 TTAT-TATGTAAG
*
41153166 -TATTATATAAG
1 TTATTATGTAAG
*
41153177 TTATGTGTTGTGTAAG
1 TTA----TTATGTAAG
* *
41153193 TTTATATAT-AAAA
1 -TTAT-TATGTAAG
* *
41153206 TT-TGATTTAAG
1 TTATTATGTAAG
41153217 TTATGTATGTAAG
1 TTAT-TATGTAAG
*
41153230 TTA-TATATAAG
1 TTATTATGTAAG
*
41153241 TT-TATATATAAG
1 TTAT-TATGTAAG
41153253 ---TTATGTAAG
1 TTATTATGTAAG
41153262 TTATTATGTAAG
1 TTATTATGTAAG
41153274 TTAT
1 TTAT
41153278 GTGTTGTGTA
Statistics
Matches: 127, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
9 7 0.06
10 6 0.05
11 20 0.16
12 67 0.53
13 15 0.12
14 2 0.02
16 7 0.06
17 3 0.02
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:41153151 original size:197 final size:196
Alignment explanation
Indices: 41152787--41153164 Score: 566
Period size: 197 Copynumber: 1.9 Consensus size: 196
41152777 ATGTAAATTA
* * *
41152787 TGTATTATGTAAATTATGTAAGTTGTGTATTATATAAGTTATGTAAGTTGTGTATTATGTAAGTT
1 TGTATTATGTAAATTATGCAAGTTATGTATTATATAAGTTATGTAAGTTATGTATTATGTAAGTT
41152852 ATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTAGGTAGGGTATGTATTATTATG
66 ATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTAGGTAGGGTATGTATTATTATG
* * *
41152917 TAACTTATTTAATTTATGTAGGGTATGTAAGTTATGTAAGTTGTGTATTATTTACACATGTAAGC
131 TAACTTATTTAATGTAAGTA-GGTATGTAAGTTATGTAAGTTATGTATTATTTACACATGTAAGC
41152982 TG
195 TG
* *
41152984 TGTATTATGTAAGTTATGCAAGTTATGTATTA-AGTAGGTTATGTAAGTTATGTATTATGTAAGT
1 TGTATTATGTAAATTATGCAAGTTATGTATTATA-TAAGTTATGTAAGTTATGTATTATGTAAGT
* *
41153048 TATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAGTTTATGTAGGGTATGTATTATTAT
65 TATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTAGGTAGGGTATGTATTATTAT
* *
41153113 GTAAGTTA-TT-ATGTAAGATA-TTATGTAAGATATTATGTAAGTTATGTATTAT
130 GTAACTTATTTAATGTAAG-TAGGTATGTAAG---TTATGTAAGTTATGTATTAT
41153165 GTATTATATA
Statistics
Matches: 164, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
194 8 0.05
195 5 0.03
196 5 0.03
197 146 0.89
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (196 bp):
TGTATTATGTAAATTATGCAAGTTATGTATTATATAAGTTATGTAAGTTATGTATTATGTAAGTT
ATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTAGGTAGGGTATGTATTATTATG
TAACTTATTTAATGTAAGTAGGTATGTAAGTTATGTAAGTTATGTATTATTTACACATGTAAGCT
G
Found at i:41153245 original size:48 final size:44
Alignment explanation
Indices: 41153189--41153277 Score: 124
Period size: 48 Copynumber: 1.9 Consensus size: 44
41153179 ATGTGTTGTG
* *
41153189 TAAGTTTATATATAAAATTTGATTTAAGTTATGTATGTAAGTTATATA
1 TAAGTTTATATAT--AAGTT-ATGTAAGTTAT-TATGTAAGTTATATA
41153237 TAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTAT
1 TAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTAT
41153278 GTGTTGTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 12 0.31
45 10 0.26
46 4 0.10
48 13 0.33
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.48
Consensus pattern (44 bp):
TAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTATATA
Found at i:41153253 original size:36 final size:37
Alignment explanation
Indices: 41153106--41153259 Score: 113
Period size: 36 Copynumber: 4.2 Consensus size: 37
41153096 AGGGTATGTA
* * *
41153106 TTAT-TATGTAAGTTATTATGTAAG-ATATTATGTAAG
1 TTATGTATGTAAGTTA-TATATAAGTTTATTATATAAG
* * * *
41153142 ATAT-TATGTAAGTTATGTATTA-TGTATTATATAAG
1 TTATGTATGTAAGTTATATATAAGTTTATTATATAAG
* ** * *
41153177 TTATGTGTTGTGTAAGTTTATATATAAAATT-TGATTTAAG
1 TTA--TG-TATGTAAG-TTATATATAAGTTTATTATATAAG
41153217 TTATGTATGTAAGTTATATATAAGTTTA-TATATAAG
1 TTATGTATGTAAGTTATATATAAGTTTATTATATAAG
41153253 TTATGTA
1 TTATGTA
41153260 AGTTATTATG
Statistics
Matches: 91, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
35 16 0.18
36 39 0.43
37 8 0.09
38 2 0.02
39 7 0.08
40 18 0.20
41 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (37 bp):
TTATGTATGTAAGTTATATATAAGTTTATTATATAAG
Found at i:41153263 original size:21 final size:21
Alignment explanation
Indices: 41153187--41153279 Score: 62
Period size: 21 Copynumber: 4.1 Consensus size: 21
41153177 TTATGTGTTG
*
41153187 TGTAAGTTTATATATAAAATTTGA
1 TGTAAGTTTATATAT--AAGTT-A
* * *
41153211 TTTAAGTTATGTATGTAAGTTATA
1 TGTAAGTT-TATATATAAG-T-TA
*
41153235 TATAAGTTTATATATAAGTTA
1 TGTAAGTTTATATATAAGTTA
*
41153256 TGTAAG-TTATTATGTAAGTTA
1 TGTAAGTTTA-TATATAAGTTA
41153277 TGT
1 TGT
41153280 GTTGTGTAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.05
21 20 0.36
22 1 0.02
23 10 0.18
24 16 0.29
25 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (21 bp):
TGTAAGTTTATATATAAGTTA
Found at i:41153282 original size:97 final size:96
Alignment explanation
Indices: 41153109--41153333 Score: 278
Period size: 97 Copynumber: 2.3 Consensus size: 96
41153099 GTATGTATTA
* * * *
41153109 TTATGTAAGTTAT-TATGTAAGATATTATGTAAGATATTATGTAAGTTATGTATTATGTATTATA
1 TTATATAAGTTATGTATGTAAGTTA-TATATAAGATATTATATAAGTTATGTA-TATGTATTATA
41153173 TAAGTTATGTGTTGTGTAAGTTTATATATAAAAT
64 TAAGTTATGTGTTGTGTAAGTTTATATAT-AAAT
* *
41153207 TTGATTTAAGTTATGTATGTAAGTTATATATAAG-TTTATATATAAGTTATGTA-A-GTTATTAT
1 TT-ATATAAGTTATGTATGTAAGTTATATATAAGATAT-TATATAAGTTATGTATATG-TATTAT
*
41153269 GTAAGTTATGTGTTGTGTAAGTTTATATATAAAT
63 ATAAGTTATGTGTTGTGTAAGTTTATATATAAAT
* *
41153303 TTATATATGTTATGTATGTAAATTATGATAT
1 TTATATAAGTTATGTATGTAAGTTAT-ATAT
41153334 GATTGATAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
95 21 0.19
96 11 0.10
97 36 0.32
98 4 0.04
99 31 0.27
100 10 0.09
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (96 bp):
TTATATAAGTTATGTATGTAAGTTATATATAAGATATTATATAAGTTATGTATATGTATTATATA
AGTTATGTGTTGTGTAAGTTTATATATAAAT
Found at i:41153376 original size:19 final size:20
Alignment explanation
Indices: 41153354--41153400 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41153344 TTTTTCAAAT
* *
41153354 ATATATAAAATTTTA-ATAA
1 ATATATAAAACTGTATATAA
41153373 ATATATTAAAACTGTATATAA
1 ATATA-TAAAACTGTATATAA
41153394 ATATATA
1 ATATATA
41153401 TATCAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATATAAAACTGTATATAA
Found at i:41153376 original size:21 final size:22
Alignment explanation
Indices: 41153350--41153402 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
41153340 TAAATTTTTC
* *
41153350 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
41153371 AAATATAT-TAAAACTGTATAT
1 AAATATATATAAAACTGTATAT
41153392 AAATATATATA
1 AAATATATATA
41153403 TCAAAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:41155853 original size:12 final size:10
Alignment explanation
Indices: 41155835--41155864 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
41155825 TTAATAACTA
41155835 CATATATATC
1 CATATATATC
41155845 CATATATATC
1 CATATATATC
41155855 CATATATATC
1 CATATATATC
41155865 AAAAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (10 bp):
CATATATATC
Found at i:41158037 original size:14 final size:14
Alignment explanation
Indices: 41158018--41158085 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
41158008 ATGACCGTTG
41158018 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
41158032 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
41158047 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
41158060 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
41158073 AAACCTTAAATCT
1 AAACCCTAAATCT
41158086 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:41158041 original size:15 final size:15
Alignment explanation
Indices: 41158021--41158058 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
41158011 ACCGTTGAAA
41158021 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
41158036 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
41158051 CCCTAAAT
1 CCCTAAAT
41158059 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:41158636 original size:41 final size:40
Alignment explanation
Indices: 41158569--41158808 Score: 237
Period size: 41 Copynumber: 5.9 Consensus size: 40
41158559 TTTTGTTACT
* ** *
41158569 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTAAATGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGA-GC
* * * *
41158610 ATTAGCGGCGCTTAGATACAAGCGCCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-TAGAGC
* * * ** *
41158651 ATTAGTGGCGCTCAGATAAAAACACCGCTAAATATCCGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-AGAGC
* * *
41158692 ATTAGCGGCGCTTAGATAAAAACGCCGCTAACGGCCAGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG-TAGAGC
* * ** *
41158733 ATTAGCGGCGCTCAGATAAAAACGCCACTAAATATCTGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT-AGAGC
41158774 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGT
41158809 TTAAAAAATC
Statistics
Matches: 156, Mismatches: 39, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
41 154 0.99
42 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (40 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGTAGAGC
Found at i:41158706 original size:82 final size:82
Alignment explanation
Indices: 41158608--41158807 Score: 337
Period size: 82 Copynumber: 2.4 Consensus size: 82
41158598 AAAGGTAAAT
* * *
41158608 GCATTAGCGGCGCTTAGATACAAGCGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
*
41158673 CACCGCTAAATATCCGA
66 CACCACTAAATATCCGA
*
41158690 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAACGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
* *
41158755 CGCCACTAAATATCTGA
66 CACCACTAAATATCCGA
41158772 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
1 GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
41158808 TTTAAAAAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 110 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (82 bp):
GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGAATTAGCGGCGCTCAGATAAAAA
CACCACTAAATATCCGA
Found at i:41158791 original size:123 final size:123
Alignment explanation
Indices: 41158569--41158805 Score: 287
Period size: 123 Copynumber: 1.9 Consensus size: 123
41158559 TTTTGTTACT
* * * * * * *
41158569 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTAAATGCATTAGCGGCGCTTAGATACAAGCG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCAAATGAATTAGCGGCGCTCAGATAAAAACG
* * *
41158634 CCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACACCGCTAAATATCCGAGC
66 CCACTAAAGACCAGAGAATTAGCGGCGCTCAGATAAAAACACCGCTAAATATCCGAGC
* * *
41158692 ATTAGCGGCGCTTAGATAAAAACGCCGCTAACGGCCAGA-GAATTAGCGGCGCTCAGATAAAAAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGG-CAAATGAATTAGCGGCGCTCAGATAAAAAC
* * * * * *
41158756 GCCACTAAATATCTGAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAA
65 GCCACTAAAGACCAGAGAATTAGCGGCGCTCAGATAAAAACACCGCTAAA
41158806 GGTTTAAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
123 92 0.98
124 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (123 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGCAAATGAATTAGCGGCGCTCAGATAAAAACG
CCACTAAAGACCAGAGAATTAGCGGCGCTCAGATAAAAACACCGCTAAATATCCGAGC
Found at i:41158926 original size:40 final size:40
Alignment explanation
Indices: 41158858--41158950 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
41158848 TTATATAAAA
* **
41158858 CGCCGCTAATTCT-TATTTTTAGCGGCGCTTCTGG-GAAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTT-TGGCGAAAT
* *
41158897 CGCCGCTGATGCTCTACCTTTAGCGGCGCTTTGGCTAAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTTGGCGAAAT
*
41158937 TGCCGCTAATGCTC
1 CGCCGCTAATGCTC
41158951 GATTTTTTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 14 0.31
40 31 0.69
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (40 bp):
CGCCGCTAATGCTCTACCTTTAGCGGCGCTTTGGCGAAAT
Found at i:41171865 original size:23 final size:23
Alignment explanation
Indices: 41171828--41171876 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
41171818 GGGGTATAAA
* * *
41171828 ACACCCGCCCTTCCCTACCCACC
1 ACACCCACCCATCCCTACACACC
41171851 ACACCCACCCATCCCTACACACC
1 ACACCCACCCATCCCTACACACC
41171874 ACA
1 ACA
41171877 TAGTGTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.61, G:0.02, T:0.10
Consensus pattern (23 bp):
ACACCCACCCATCCCTACACACC
Found at i:41181374 original size:17 final size:16
Alignment explanation
Indices: 41181337--41181375 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
41181327 AATAAACAAT
41181337 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
41181352 TAAAATTAAATTAGGAAA
1 T-AAATTAAATT-GGAAA
41181370 TAAATT
1 TAAATT
41181376 TAGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:41185233 original size:58 final size:58
Alignment explanation
Indices: 41185144--41185651 Score: 998
Period size: 58 Copynumber: 8.8 Consensus size: 58
41185134 CAGAGTTTAA
* *
41185144 TTAAAGTTTTGTTGGAAAATTTTATCATTTCAATAGTTAATTAAACTATCATGTGGTA
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185202 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185260 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185318 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185376 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185434 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185492 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185550 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
41185608 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAA
1 TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAA
41185652 GTAAAAAGGA
Statistics
Matches: 448, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 448 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.45
Consensus pattern (58 bp):
TTAAAGTTTTGTTGGAAAATTTTATCGTTTCAATAGTTAATTAAACTATCATGTGGTG
Found at i:41187606 original size:15 final size:15
Alignment explanation
Indices: 41187586--41187618 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
41187576 TTTTTTTTTT
41187586 TTTATAAAATCCTAC
1 TTTATAAAATCCTAC
41187601 TTTATAAAATCCTAC
1 TTTATAAAATCCTAC
41187616 TTT
1 TTT
41187619 GTTAGGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTATAAAATCCTAC
Found at i:41192163 original size:5 final size:5
Alignment explanation
Indices: 41192153--41192186 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
41192143 TTAGCCGAAG
41192153 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
41192187 ACCAGTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41193317 original size:17 final size:17
Alignment explanation
Indices: 41193297--41193333 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
41193287 ATCATCCGTG
41193297 ACATAAATTCATTATTA
1 ACATAAATTCATTATTA
41193314 ACATAAATTCATTATTA
1 ACATAAATTCATTATTA
41193331 ACA
1 ACA
41193334 GTATTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATAAATTCATTATTA
Found at i:41196166 original size:21 final size:21
Alignment explanation
Indices: 41196132--41196180 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
41196122 CACTTTGCCT
* *
41196132 ATATTCTGGTAGCTTGACTGC
1 ATATTATGGCAGCTTGACTGC
41196153 ATATTATGGCAGCTTGACTGC
1 ATATTATGGCAGCTTGACTGC
41196174 ATATTAT
1 ATATTAT
41196181 CTGTGATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (21 bp):
ATATTATGGCAGCTTGACTGC
Found at i:41203848 original size:49 final size:50
Alignment explanation
Indices: 41203791--41203976 Score: 159
Period size: 52 Copynumber: 3.7 Consensus size: 50
41203781 AATGCATGAA
41203791 AGGAGGCTTACAGAA-GGTAATAAAGTGACCCTGCTCCTAAACGTATGGG
1 AGGAGGCTTACAGAATGGTAATAAAGTGACCCTGCTCCTAAACGTATGGG
* ** *
41203840 AGGGGGCTTATGGAATGTAGTAATAAAG-G-CCCTGCTCCTGAACGTATGGG
1 AGGAGGCTTACAGAATG--GTAATAAAGTGACCCTGCTCCTAAACGTATGGG
* * ** * * *
41203890 -GGAAGGCTTGTAGAAAATTATAATAAAGTGACCCTGCTCCTAAACGCATAGA
1 AGG-AGGC-T-TACAGAATGGTAATAAAGTGACCCTGCTCCTAAACGTATGGG
**
41203942 AGGAGGCTTAC-GAAAAGTAAT-AAGATGACCCTGCT
1 AGGAGGCTTACAGAATGGTAATAAAG-TGACCCTGCT
41203977 TCCAAATGCA
Statistics
Matches: 108, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
48 3 0.03
49 30 0.28
50 34 0.31
51 4 0.04
52 35 0.32
53 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22
Consensus pattern (50 bp):
AGGAGGCTTACAGAATGGTAATAAAGTGACCCTGCTCCTAAACGTATGGG
Found at i:41203914 original size:50 final size:52
Alignment explanation
Indices: 41203807--41203976 Score: 169
Period size: 50 Copynumber: 3.4 Consensus size: 52
41203797 CTTACAGAAG
* *
41203807 GTAATAAAGTGACCCTGCTCCTAAACGTATGGGAGGGGGCTTATGGAATGTA
1 GTAATAAAGTGACCCTGCTCCTAAACGTATGGGAGGAGGCTTATGAAATGTA
* *
41203859 GTAATAAAG-G-CCCTGCTCCTGAACGTATGGG-GGAAGGCTTGTAGAAAAT-TA
1 GTAATAAAGTGACCCTGCTCCTAAACGTATGGGAGG-AGGCTTAT-G-AAATGTA
* * * *
41203910 -TAATAAAGTGACCCTGCTCCTAAACGCATAGAAGGAGGCTTACGAAA---A
1 GTAATAAAGTGACCCTGCTCCTAAACGTATGGGAGGAGGCTTATGAAATGTA
41203958 GTAAT-AAGATGACCCTGCT
1 GTAATAAAG-TGACCCTGCT
41203977 TCCAAATGCA
Statistics
Matches: 100, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
48 4 0.04
49 16 0.16
50 37 0.37
51 6 0.06
52 35 0.35
53 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (52 bp):
GTAATAAAGTGACCCTGCTCCTAAACGTATGGGAGGAGGCTTATGAAATGTA
Found at i:41205227 original size:28 final size:28
Alignment explanation
Indices: 41205187--41205245 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
41205177 GTCAAAAATA
* *
41205187 TTTGACATATTATTCATTCTTTGAATGT
1 TTTGAAATATTATTCATGCTTTGAATGT
*
41205215 TTTGAAATATTATTCATGCTTTGAATTT
1 TTTGAAATATTATTCATGCTTTGAATGT
41205243 TTT
1 TTT
41205246 TTGTTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTGAAATATTATTCATGCTTTGAATGT
Found at i:41210554 original size:18 final size:18
Alignment explanation
Indices: 41210531--41210567 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41210521 TAAGGTAAAG
41210531 ATTCTCTTAAGGGCATAT
1 ATTCTCTTAAGGGCATAT
41210549 ATTCTCTTAAGGGCATAT
1 ATTCTCTTAAGGGCATAT
41210567 A
1 A
41210568 AATGTAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
ATTCTCTTAAGGGCATAT
Found at i:41218735 original size:27 final size:27
Alignment explanation
Indices: 41218701--41218766 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
41218691 TAAAGCATAT
*
41218701 AGTCATTTTATAACATAGGGGCATGAC
1 AGTCATTTTATAACATAGGGGCATAAC
** ** *
41218728 AGTCATTTTACCAGGTGGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
41218755 AGTCATTTTATA
1 AGTCATTTTATA
41218767 TCATTTTGGG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
AGTCATTTTATAACATAGGGGCATAAC
Found at i:41223786 original size:29 final size:31
Alignment explanation
Indices: 41223734--41223792 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
41223724 AATGTGACTA
* *
41223734 AACTATTCCATTTATTCTATTTTAGGCATTG
1 AACTATTCAATTTATTCTAGTTTAGGCATTG
*
41223765 AACTATT-AATTT-TTCTAGTTTAGTCATT
1 AACTATTCAATTTATTCTAGTTTAGGCATT
41223793 AAATTTTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.56
30 4 0.16
31 7 0.28
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (31 bp):
AACTATTCAATTTATTCTAGTTTAGGCATTG
Found at i:41224349 original size:3 final size:3
Alignment explanation
Indices: 41224341--41224381 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
41224331 AACAGGAATT
41224341 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41224382 GTGATGAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41229889 original size:19 final size:19
Alignment explanation
Indices: 41229865--41229904 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41229855 ATGTAAGAAA
41229865 ATAAAACATGT-AAAACAAC
1 ATAAAA-ATGTCAAAACAAC
*
41229884 ATAAAAATGTCAAAATAAC
1 ATAAAAATGTCAAAACAAC
41229903 AT
1 AT
41229905 CAACTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAAAATGTCAAAACAAC
Done.