Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 121 of 168
Found at i:35122441 original size:24 final size:23
Alignment explanation
Indices: 35122398--35122442 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
35122388 TAAAAATATA
**
35122398 TTTTTAAAAAATATTTTTAAAAT
1 TTTTTAAAAAATATAATTAAAAT
35122421 TTTTTAAAAAATAATAATTAAA
1 TTTTTAAAAAAT-ATAATTAAA
35122443 TGCTGACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTAAAAAATATAATTAAAAT
Found at i:35122443 original size:23 final size:23
Alignment explanation
Indices: 35122369--35122443 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
35122359 TGTCATCATT
**
35122369 TAATT-AATTTTTTAAAATTTAA
1 TAATTAAATTTTTTAAAAAATAA
* *
35122391 -AAATATA-TTTTTAAAAAAT-A
1 TAATTAAATTTTTTAAAAAATAA
**
35122411 TTTTTAAAATTTTTTAAAAAATAA
1 TAATT-AAATTTTTTAAAAAATAA
35122435 TAATTAAAT
1 TAATTAAAT
35122444 GCTGACATGT
Statistics
Matches: 38, Mismatches: 10, Indels: 9
0.67 0.18 0.16
Matches are distributed among these distances:
20 1 0.03
21 14 0.37
22 3 0.08
23 16 0.42
24 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTAAATTTTTTAAAAAATAA
Found at i:35124153 original size:14 final size:14
Alignment explanation
Indices: 35124129--35124164 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
35124119 CTATATAAGG
35124129 TTTTCAATTTAAAAA
1 TTTT-AATTTAAAAA
35124144 TTTTAATTTAAAAA
1 TTTTAATTTAAAAA
*
35124158 TTATAAT
1 TTTTAAT
35124165 AATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAATTTAAAAA
Found at i:35124157 original size:15 final size:15
Alignment explanation
Indices: 35124129--35124159 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35124119 CTATATAAGG
35124129 TTTTCAATTTAAAAA
1 TTTTCAATTTAAAAA
35124144 TTTT-AATTTAAAAA
1 TTTTCAATTTAAAAA
35124158 TT
1 TT
35124160 ATAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTCAATTTAAAAA
Found at i:35124170 original size:22 final size:21
Alignment explanation
Indices: 35124134--35124191 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
35124124 TAAGGTTTTC
*
35124134 AATTTAAAAATTTTAAT-TTAAA
1 AATTTAATAA-TTTAATATT-AA
35124156 AATTATAATAATTT-ATATTAA
1 AATT-TAATAATTTAATATTAA
*
35124177 AATTTATTAATTTAA
1 AATTTAATAATTTAA
35124192 CATATAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 8 0.26
21 9 0.29
22 9 0.29
23 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTAATAATTTAATATTAA
Found at i:35135625 original size:14 final size:14
Alignment explanation
Indices: 35135607--35135647 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
35135597 TAAATTTTTT
35135607 AAATTTAATTCGAA
1 AAATTTAATTCGAA
* *
35135621 CAATTTAATTCAAA
1 AAATTTAATTCGAA
*
35135635 AAATTTCATTCGA
1 AAATTTAATTCGA
35135648 TTCAACTTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (14 bp):
AAATTTAATTCGAA
Found at i:35142969 original size:23 final size:21
Alignment explanation
Indices: 35142930--35142985 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 21
35142920 AATTGCATTT
35142930 TTGTTTTTATTGCTTCTCTAC
1 TTGTTTTTATTGCTTCTCTAC
*
35142951 TTGTTTTTCGATTGTTTCTCTAC
1 TTGTTTTT--ATTGCTTCTCTAC
*
35142974 TTTTTTTTATTG
1 TTGTTTTTATTG
35142986 GTTTTTATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.39
23 19 0.61
ACGTcount: A:0.09, C:0.14, G:0.11, T:0.66
Consensus pattern (21 bp):
TTGTTTTTATTGCTTCTCTAC
Found at i:35166452 original size:19 final size:19
Alignment explanation
Indices: 35166439--35166475 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35166429 AATATGTTAT
*
35166439 AAATTACATAATATATAAA
1 AAATAACATAATATATAAA
35166458 AAATAACATAATATATAA
1 AAATAACATAATATATAA
35166476 TATTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAACATAATATATAAA
Found at i:35168582 original size:10 final size:10
Alignment explanation
Indices: 35168567--35168592 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
35168557 TTCAAATTTT
35168567 AAAATTTAAA
1 AAAATTTAAA
35168577 AAAATTTAAA
1 AAAATTTAAA
35168587 AAAATT
1 AAAATT
35168593 ATTTAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:35188385 original size:32 final size:32
Alignment explanation
Indices: 35188344--35188435 Score: 175
Period size: 32 Copynumber: 2.9 Consensus size: 32
35188334 GATATTAACA
*
35188344 AATATGTAAAACTCATATCAAGCAAGAGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
35188376 AATATGTAAAACTCACATCAAGCAAGAGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
35188408 AATATGTAAAACTCACATCAAGCAAGAG
1 AATATGTAAAACTCACATCAAGCAAGAG
35188436 GACTTTTATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (32 bp):
AATATGTAAAACTCACATCAAGCAAGAGTGTT
Found at i:35193056 original size:21 final size:21
Alignment explanation
Indices: 35193032--35193072 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35193022 TTTTTTTCTA
35193032 TTTTTGAAT-AAATTTTAAATG
1 TTTTT-AATGAAATTTTAAATG
35193053 TTTTTAATGAAATTTTAAAT
1 TTTTTAATGAAATTTTAAAT
35193073 TATTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTTAATGAAATTTTAAATG
Found at i:35197302 original size:12 final size:12
Alignment explanation
Indices: 35197277--35197317 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
35197267 TCATTTCTTG
35197277 TTTTCATTTCCA
1 TTTTCATTTCCA
* *
35197289 TTTCCATTTTCA
1 TTTTCATTTCCA
*
35197301 TTTTCATTTCTA
1 TTTTCATTTCCA
35197313 TTTTC
1 TTTTC
35197318 GTTTTCATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTCATTTCCA
Found at i:35197322 original size:18 final size:18
Alignment explanation
Indices: 35197266--35197326 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
35197256 TGTAAATGAA
*
35197266 TTCATTTCTTGTTTTCATT
1 TTCATTTC-TATTTTCATT
* *
35197285 TCCATTTCCATTTTCATT
1 TTCATTTCTATTTTCATT
*
35197303 TTCATTTCTATTTTCGTT
1 TTCATTTCTATTTTCATT
35197321 TTCATT
1 TTCATT
35197327 CAACACGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
18 29 0.81
19 7 0.19
ACGTcount: A:0.13, C:0.20, G:0.03, T:0.64
Consensus pattern (18 bp):
TTCATTTCTATTTTCATT
Found at i:35203970 original size:23 final size:23
Alignment explanation
Indices: 35203940--35203985 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35203930 GTGTGAATTG
35203940 TGTTAAGGAAAAGTAAGACAAAC
1 TGTTAAGGAAAAGTAAGACAAAC
35203963 TGTTAAGGAAAAGTAAGACAAAC
1 TGTTAAGGAAAAGTAAGACAAAC
35203986 ATAGAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.22, T:0.17
Consensus pattern (23 bp):
TGTTAAGGAAAAGTAAGACAAAC
Found at i:35203996 original size:23 final size:22
Alignment explanation
Indices: 35203947--35204000 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
35203937 TTGTGTTAAG
*
35203947 GAAAAGTAAGACAAACTGTTAAG
1 GAAAAGTAAGACAAACTG-TAAA
35203970 GAAAAGTAAGACAAACATAG-AAA
1 GAAAAGTAAGACAAAC-T-GTAAA
35203993 GAAAAGTA
1 GAAAAGTA
35204001 CCAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 26 0.93
24 1 0.04
25 1 0.04
ACGTcount: A:0.59, C:0.07, G:0.20, T:0.13
Consensus pattern (22 bp):
GAAAAGTAAGACAAACTGTAAA
Found at i:35204186 original size:21 final size:21
Alignment explanation
Indices: 35204144--35204186 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35204134 AATTAGTGAC
*
35204144 AAATATTCTATATTATGCTTA
1 AAATATTCTATATTATACTTA
35204165 AAATATT-TATATTATACATTA
1 AAATATTCTATATTATAC-TTA
35204186 A
1 A
35204187 TGCATCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATTCTATATTATACTTA
Found at i:35215683 original size:13 final size:11
Alignment explanation
Indices: 35215644--35215686 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
35215634 TCTTTCAATA
*
35215644 TTCTCTCATAT
1 TTCTCTCAAAT
35215655 TTCTCTCAAAT
1 TTCTCTCAAAT
35215666 TTCTCTCAAAT
1 TTCTCTCAAAT
*
35215677 TCCTCTCAAA
1 TTCTCTCAAA
35215687 GCTCTCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:35215692 original size:22 final size:22
Alignment explanation
Indices: 35215645--35215693 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
35215635 CTTTCAATAT
* * **
35215645 TCTCTCATATTTCTCTCAAATT
1 TCTCTCAAATTCCTCTCAAAGC
35215667 TCTCTCAAATTCCTCTCAAAGC
1 TCTCTCAAATTCCTCTCAAAGC
35215689 TCTCT
1 TCTCT
35215694 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (22 bp):
TCTCTCAAATTCCTCTCAAAGC
Found at i:35215693 original size:11 final size:10
Alignment explanation
Indices: 35215638--35215686 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
35215628 CTTCAATCTT
35215638 TCAATATTCTC
1 TCAA-ATTCTC
*
35215649 TCATATTTCTC
1 TCA-AATTCTC
35215660 TCAAATTTCTC
1 TCAAA-TTCTC
35215671 TCAAATTCCTC
1 TCAAATT-CTC
35215682 TCAAA
1 TCAAA
35215687 GCTCTCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 3 0.09
11 29 0.88
12 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:35216100 original size:17 final size:17
Alignment explanation
Indices: 35216078--35216110 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35216068 GTGCGTTGAT
35216078 AGAGAGGTGGAGACCCA
1 AGAGAGGTGGAGACCCA
35216095 AGAGAGGTGGAGACCC
1 AGAGAGGTGGAGACCC
35216111 GAGACGCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.42, T:0.06
Consensus pattern (17 bp):
AGAGAGGTGGAGACCCA
Found at i:35216114 original size:15 final size:16
Alignment explanation
Indices: 35216078--35216114 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
35216068 GTGCGTTGAT
35216078 AGAGAGGTGGAGACCC
1 AGAGAGGTGGAGACCC
35216094 AAGAGAGGTGGAGACCC
1 -AGAGAGGTGGAGACCC
35216111 -GAGA
1 AGAGA
35216115 CGCACACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
17 16 0.80
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.05
Consensus pattern (16 bp):
AGAGAGGTGGAGACCC
Found at i:35216874 original size:7 final size:7
Alignment explanation
Indices: 35216862--35216886 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35216852 TAGTCAATTC
35216862 GTATTTA
1 GTATTTA
35216869 GTATTTA
1 GTATTTA
35216876 GTATTTA
1 GTATTTA
35216883 GTAT
1 GTAT
35216887 ATAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:35217436 original size:30 final size:30
Alignment explanation
Indices: 35217377--35217459 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
35217367 GACGACAATG
*
35217377 CAGGCCCATCAACAGTGCCCACACAATCAC
1 CAGGCCCATCAACAGCGCCCACACAATCAC
** * * *
35217407 TTGGCCCATCAACAGCGCTCATACGATCAC
1 CAGGCCCATCAACAGCGCCCACACAATCAC
* *
35217437 CAGGCCCAGCAACAGCACCCACA
1 CAGGCCCATCAACAGCGCCCACA
35217460 GCACAGCCTT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.31, C:0.42, G:0.16, T:0.11
Consensus pattern (30 bp):
CAGGCCCATCAACAGCGCCCACACAATCAC
Found at i:35217850 original size:18 final size:18
Alignment explanation
Indices: 35217827--35217911 Score: 134
Period size: 18 Copynumber: 4.7 Consensus size: 18
35217817 TTTGGTTAAA
*
35217827 AATTAACCTAATTACCCG
1 AATTAACCGAATTACCCG
35217845 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
35217863 AATTAACCGAATTACCCA
1 AATTAACCGAATTACCCG
*
35217881 AATTAACTGAATTACCCG
1 AATTAACCGAATTACCCG
*
35217899 AATTAATCGAATT
1 AATTAACCGAATT
35217912 GAATCACTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:35217909 original size:9 final size:9
Alignment explanation
Indices: 35217827--35217911 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
35217817 TTTGGTTAAA
*
35217827 AATTAACCT
1 AATTAACCG
*
35217836 AATTACCCG
1 AATTAACCG
35217845 AATTAACCG
1 AATTAACCG
*
35217854 AATTACCCG
1 AATTAACCG
35217863 AATTAACCG
1 AATTAACCG
* *
35217872 AATTACCCA
1 AATTAACCG
*
35217881 AATTAACTG
1 AATTAACCG
*
35217890 AATTACCCG
1 AATTAACCG
*
35217899 AATTAATCG
1 AATTAACCG
35217908 AATT
1 AATT
35217912 GAATCACTAC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:35218721 original size:61 final size:60
Alignment explanation
Indices: 35218651--35218842 Score: 211
Period size: 61 Copynumber: 3.2 Consensus size: 60
35218641 TTTATATTTT
*
35218651 TAATAAAATAGAAATTCTTTTAAATAATGCAATATTTTGAATATTTCTATATTATTTCATG
1 TAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTCTATATTATTT-ATG
* * * * *
35218712 TAATAAAATA-AAAGGTTGTTTTGAATAAAG-AA-ATTGT-AAT-TTACT-T-TTATATT-TT
1 TAATAAAATAGAAA--TTCTTTTAAATAAAGCAATATTTTGAATATTTCTATATTAT-TTATG
*
35218767 TAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTGAATATTTCTATATTATTTGATG
1 TAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTCTATATTATTT-ATG
*
35218828 TAATAAAATATAAAT
1 TAATAAAATAGAAAT
35218843 AATACAACAT
Statistics
Matches: 106, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
54 12 0.11
55 13 0.12
56 11 0.10
57 6 0.06
58 8 0.08
59 6 0.06
60 11 0.10
61 27 0.25
62 12 0.11
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (60 bp):
TAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTCTATATTATTTATG
Found at i:35218803 original size:116 final size:118
Alignment explanation
Indices: 35218562--35218837 Score: 448
Period size: 116 Copynumber: 2.3 Consensus size: 118
35218552 TTGTACAAAC
* * **
35218562 ATTTTGAATATTTTTATATTATTTCATGTAATGAAATGGAAGGTTGTTTTGAATAAAGTAATTGT
1 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAG-AA---T
*
35218627 AATTGTAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAATGCAAT
62 AATTGTAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
35218684 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAG-A-AATT
1 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGAATAATT
35218747 GTAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
66 GTAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
*
35218800 ATTTTGAATATTTCTATATTATTTGATGTAATAAAATA
1 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATA
35218838 TAAATAATAC
Statistics
Matches: 148, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
116 93 0.63
120 1 0.01
122 54 0.36
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (118 bp):
ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGAATAATT
GTAATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
Found at i:35218818 original size:55 final size:55
Alignment explanation
Indices: 35218643--35218819 Score: 175
Period size: 55 Copynumber: 3.1 Consensus size: 55
35218633 AATTTACTTT
*
35218643 TATATTTTTAATAAAATAGAAATTCTTTTAAATAATGCAATATTTTGAATATTTC
1 TATATTTTTAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTC
* * *
35218698 TATATTATTTCATGTAATAAAATA-AAAGGTTGTTTTGAATAAAG-AA-ATTGT-AATTTACTTT
1 --TA-TATTT--T-TAATAAAATAGAAA--TTCTTTTAAATAAAGCAATATTTTGAA--TA-TTT
35218759 -
55 C
*
35218759 TATATTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTGAATATTTC
1 TATATTTTTAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTC
35218814 TATATT
1 TATATT
35218820 ATTTGATGTA
Statistics
Matches: 98, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
54 15 0.15
55 20 0.20
56 8 0.08
57 4 0.04
58 10 0.10
59 4 0.04
60 8 0.08
61 14 0.14
62 15 0.15
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (55 bp):
TATATTTTTAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTC
Found at i:35221868 original size:126 final size:125
Alignment explanation
Indices: 35221643--35221929 Score: 484
Period size: 126 Copynumber: 2.3 Consensus size: 125
35221633 GCCAAATAGA
* * *
35221643 AACTATTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAAAGCATCT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATCT
**
35221708 TGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTCTTTCAGG
66 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATT-TTTCAGG
* * *
35221769 AACTACTGTAGCAAAAAAACGTTCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATCT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATCT
*
35221834 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTTTTCAAAATTATTTTTCAGG
66 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTCAGG
35221894 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
35221930 TTTTAAATTA
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
125 40 0.27
126 109 0.73
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (125 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATCT
TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTCAGG
Found at i:35222063 original size:104 final size:103
Alignment explanation
Indices: 35221945--35222315 Score: 436
Period size: 104 Copynumber: 3.7 Consensus size: 103
35221935 AATTAAACAA
* * * * *
35221945 TAATTTAATTAAGTAACCCTAAACCCCAAACCCTGATTTATTTAATTTTTTCCTTAAAAACCCTA
1 TAATTTACTCAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTTTTTCCTTAAAAACCCTA
*
35222010 AACACTAAACCCTAATCGAATTTTTTTAAAATTTATAAT
66 AACACTAAACCCTAATCTAA-TTTTTTAAAATTTATAAT
*
35222049 TAATGTACTCAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTTTTTCCTTAAAAACCCTA
1 TAATTTACTCAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTTTTTCCTTAAAAACCCTA
*
35222114 AACGCTAAACCCTAATCTAATTTTTTAAAATTTTATAAT
66 AACACTAAACCCTAATCTAATTTTTTAAAA-TTTATAAT
* ** *
35222153 TAATTTACACAAG-----C--AACCTTAAGCCCTAATTTATTTGATTTTTTCCTTAAAAACCATA
1 TAATTTACTCAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTTTTTCCTTAAAAACCCTA
* * ** *
35222211 AAAACGAAACCCTAATCTAATTTTAAAAAAATTATAAT
66 AACACTAAACCCTAATCTAATTTTTTAAAATTTATAAT
* * * * * * *
35222249 TAATTTAATTAAGAAACCCTAAACCCTAAGCTCTTATTTATTT-ATTTATTT-CTTTAAAACCCT
1 TAATTTACTCAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTT-TTTCCTTAAAAACCCT
35222312 AAAC
65 AAAC
35222316 TCAAAAACCC
Statistics
Matches: 230, Mismatches: 28, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
96 17 0.07
97 66 0.29
99 1 0.00
101 1 0.00
102 17 0.07
103 32 0.14
104 96 0.42
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (103 bp):
TAATTTACTCAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTTTTTCCTTAAAAACCCTA
AACACTAAACCCTAATCTAATTTTTTAAAATTTATAAT
Found at i:35226385 original size:28 final size:29
Alignment explanation
Indices: 35226353--35226412 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
35226343 GCACAGACAT
35226353 AGATAA-GTCTACTAGGACAGCAAACACA
1 AGATAACGTCTACTAGGACAGCAAACACA
* * * *
35226381 AGATAACGTCTGCTGGGACAGTAAACATA
1 AGATAACGTCTACTAGGACAGCAAACACA
35226410 AGA
1 AGA
35226413 ACTGTTCGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (29 bp):
AGATAACGTCTACTAGGACAGCAAACACA
Found at i:35231487 original size:41 final size:40
Alignment explanation
Indices: 35231359--35231526 Score: 169
Period size: 41 Copynumber: 4.1 Consensus size: 40
35231349 TAAAAACAGA
* * * * * *
35231359 TTCACCGGTATTTAGCCTGCTAGGCTTAAAGCCTGATTCAA
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATT-AT
* * * *
35231400 TACACCGGCACTT-AGCCTGCTAGACATATAGTCCGA-TAT
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATTAT
35231439 GTATCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 -T-TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-ATTAT
*
35231482 TTCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-ATTAT
35231523 TTCA
1 TTCA
35231527 ATCACTTTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.01
40 4 0.04
41 96 0.89
42 4 0.04
43 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (40 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATTAT
Found at i:35244558 original size:28 final size:27
Alignment explanation
Indices: 35244526--35244594 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
35244516 AAATAAAAAA
*
35244526 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
35244554 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
35244581 TTACCAAAATATAT
1 TTACCAAAATATAT
35244595 CAAAAAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.59
28 10 0.27
29 5 0.14
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:35244610 original size:11 final size:11
Alignment explanation
Indices: 35244605--35244634 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
35244595 CAAAAAAAAC
35244605 AAAAAAACAGA
1 AAAAAAACAGA
35244616 AAAAAAACAGA
1 AAAAAAACAGA
35244627 AAAAAAAC
1 AAAAAAAC
35244635 CTGAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAACAGA
Found at i:35244740 original size:27 final size:27
Alignment explanation
Indices: 35244659--35244741 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 27
35244649 AACTCCCTGG
35244659 GTGGAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
****
35244686 AACAAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
*
35244713 GTGGAGGGAACCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
35244740 GT
1 GT
35244742 CCTGCCAACC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.43, T:0.11
Consensus pattern (27 bp):
GTGGAGGGAAGCAGGTTGGCGGCACCA
Found at i:35244751 original size:27 final size:27
Alignment explanation
Indices: 35244670--35244764 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
35244660 TGGAGGGAAG
** * ** *
35244670 CAGGTTGGCGGCACCAAACAAGGGAAG
1 CAGGTTGGCGGCACCAGTCCAGCCAAC
** **
35244697 CAGGTTGGCGGCACCAGTGGAGGGAAC
1 CAGGTTGGCGGCACCAGTCCAGCCAAC
*
35244724 CAGGTTGGCGGCACCAGTCCTGCCAAC
1 CAGGTTGGCGGCACCAGTCCAGCCAAC
*
35244751 CAGATTGGCGGCAC
1 CAGGTTGGCGGCAC
35244765 TACTCGTGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.24, C:0.27, G:0.37, T:0.12
Consensus pattern (27 bp):
CAGGTTGGCGGCACCAGTCCAGCCAAC
Found at i:35244759 original size:54 final size:54
Alignment explanation
Indices: 35244659--35244764 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 54
35244649 AACTCCCTGG
* ** * *
35244659 GTGGAGGGAAGCAGGTTGGCGGCACCAAACAAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAACCAGGTTGGCGGCACCAAACAAGCCAACCAGATTGGCGGCACCA
** **
35244713 GTGGAGGGAACCAGGTTGGCGGCACCAGTCCTGCCAACCAGATTGGCGGCAC
1 GTGGAGGGAACCAGGTTGGCGGCACCAAACAAGCCAACCAGATTGGCGGCAC
35244765 TACTCGTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.40, T:0.11
Consensus pattern (54 bp):
GTGGAGGGAACCAGGTTGGCGGCACCAAACAAGCCAACCAGATTGGCGGCACCA
Found at i:35245250 original size:15 final size:15
Alignment explanation
Indices: 35245226--35245264 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
35245216 CAGTAAGCAC
*
35245226 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
35245241 AATAATT-AAATTAG
1 AATAATTAAAACTAG
35245255 AATAATTAAA
1 AATAATTAAA
35245265 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:35245257 original size:14 final size:14
Alignment explanation
Indices: 35245238--35245266 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35245228 TAACTAAAAC
35245238 TAGAATAATTAAAT
1 TAGAATAATTAAAT
35245252 TAGAATAATTAAAT
1 TAGAATAATTAAAT
35245266 T
1 T
35245267 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:35247915 original size:33 final size:32
Alignment explanation
Indices: 35247876--35248009 Score: 85
Period size: 33 Copynumber: 3.9 Consensus size: 32
35247866 TTCTTCTTCT
35247876 TTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
1 TTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
*
35247908 TTATTTTTCTTCTTTCCTCCCCATTTCCCTTTTCTTTCC
1 TTTTTTTTC-TC-TT-CT--CC-TTT-CCTTTTCTTTCC
* * *
35247947 TTCTTTTTCT-TTCTTTCCTCTCC-TTCCTTTTCC
1 TTTTTTTTCTCTTC--TCCTTTCCTTTTC-TTTCC
* *
35247980 TTCTTTTTCT-TTCTTCCTTTCTTTCTTCTT
1 TTTTTTTTCTCTTC-TCCTTTCCTT-TTCTT
35248010 CTTCCCCTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 23
0.73 0.06 0.20
Matches are distributed among these distances:
32 18 0.22
33 25 0.30
34 6 0.07
35 5 0.06
36 2 0.02
37 3 0.04
38 4 0.05
39 20 0.24
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCC
Found at i:35247993 original size:10 final size:10
Alignment explanation
Indices: 35247942--35248012 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 10
35247932 TTCCCTTTTC
*
35247942 TTTCCTTCTT
1 TTTCTTTCTT
35247952 TTTCTTTCTT
1 TTTCTTTCTT
* *
35247962 TCCTCTCCTTCCT
1 T--T-TCTTTCTT
*
35247975 TTTCCTTCTT
1 TTTCTTTCTT
35247985 TTTCTTTCTT
1 TTTCTTTCTT
35247995 CCTTTCTTTCTT
1 --TTTCTTTCTT
*
35248007 CTTCTT
1 TTTCTT
35248013 CCCCTCTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
10 31 0.62
11 1 0.02
12 11 0.22
13 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:35247995 original size:23 final size:23
Alignment explanation
Indices: 35247937--35248012 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
35247927 CCCATTTCCC
*
35247937 TTTTCTTTCCTTCTTTTTCTTTC-
1 TTTTCTTT-CTTCCTTTTCTTTCT
* * *
35247960 TTTCCTCTCCTTCCTTTTCCTTCT
1 TTTTCT-TTCTTCCTTTTCTTTCT
35247984 TTTTCTTTCTTCC-TTTCTTTCT
1 TTTTCTTTCTTCCTTTTCTTTCT
*
35248006 TCTTCTT
1 TTTTCTT
35248013 CCCCTCTCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 14 0.33
23 23 0.53
24 6 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTCTTTCTTCCTTTTCTTTCT
Found at i:35248011 original size:18 final size:18
Alignment explanation
Indices: 35247938--35248014 Score: 57
Period size: 18 Copynumber: 4.0 Consensus size: 18
35247928 CCATTTCCCT
*
35247938 TTTCTTTCCTTCTT-TTTC
1 TTTCTTT-CTTCTTCTTCC
* *
35247956 TTTCTTTCCTCTCCTTCC
1 TTTCTTTCTTCTTCTTCC
*
35247974 TTTTCCTTCTTTTTCTTTCTTCC
1 -TTT-C-T-TTCTTC-TTCTTCC
35247997 TTTCTTTCTTCTTCTTCC
1 TTTCTTTCTTCTTCTTCC
35248015 CCTCTCCTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 4 0.09
18 17 0.37
19 8 0.17
20 2 0.04
21 2 0.04
22 7 0.15
23 6 0.13
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCTTTCTTCTTCTTCC
Found at i:35249098 original size:14 final size:14
Alignment explanation
Indices: 35249056--35249100 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
35249046 ATAAGGAAAT
35249056 ATAAATGAAATATA
1 ATAAATGAAATATA
* *
35249070 AT-AA--AAATTTT
1 ATAAATGAAATATA
35249081 ATAAATGAAATATA
1 ATAAATGAAATATA
35249095 ATAAAT
1 ATAAAT
35249101 ATTCTAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
11 7 0.29
12 2 0.08
13 2 0.08
14 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (14 bp):
ATAAATGAAATATA
Found at i:35256537 original size:71 final size:71
Alignment explanation
Indices: 35256398--35256530 Score: 223
Period size: 71 Copynumber: 1.9 Consensus size: 71
35256388 TCCTTTCAAA
* *
35256398 CTCAAGTTTTAAACGATCTCGGGAATTAAAAGGAGATCGTGTCCTAACTTATTGGGCATGATTCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAAAGAAGATCGTGTCCTAACTTACTGGGCATGATTCC
35256463 TTTTTT
66 TTTTTT
*
35256469 CTCAAGTTTTAAACGATCTCGGGAATTAAGAA-AAGATTGTGTCCTAACTTACTGGGCATGAT
1 CTCAAGTTTTAAACGATCTCGGGAATTAA-AAGAAGATCGTGTCCTAACTTACTGGGCATGAT
35256531 CTCTTTTCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 56 0.97
72 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (71 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAAAGAAGATCGTGTCCTAACTTACTGGGCATGATTCC
TTTTTT
Found at i:35260794 original size:18 final size:19
Alignment explanation
Indices: 35260769--35260814 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
35260759 AAAAATGCGT
*
35260769 ATATATATATATATTATAAA
1 ATATATATA-AGATTATAAA
*
35260789 ATATATGTCAAGATTATAAA
1 ATATATAT-AAGATTATAAA
35260809 ATATAT
1 ATATAT
35260815 GGATGCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (19 bp):
ATATATATAAGATTATAAA
Found at i:35262730 original size:2 final size:2
Alignment explanation
Indices: 35262717--35262761 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
35262707 TAATAAAGTA
35262717 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35262760 AT
1 AT
35262762 GAAAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35264568 original size:44 final size:44
Alignment explanation
Indices: 35264512--35264758 Score: 161
Period size: 44 Copynumber: 5.6 Consensus size: 44
35264502 GACTTGATGT
*
35264512 GATCTGCTCCACTACTGCTTAGGGAGAAAAGATCTTAAATCTTC
1 GATCTACTCCACTACTGCTTAGGGAGAAAAGATCTTAAATCTTC
* * * * *
35264556 AATCTACTCCACTACTACTCAGGGAGATAGGATTGGTGGCTTAAATC-T-
1 GATCTACTCCACTACTGCTTAGGGAGA-A--A-AGAT--CTTAAATCTTC
* * *
35264604 G--CTTCTCCACTA-T-CTT-GGGAAAATAAGAT-TTACCATCTTC
1 GATCTACTCCACTACTGCTTAGGGAGAA-AAGATCTTA-AATCTTC
* * ** *
35264644 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTT
1 GATCTACTCCACTACTGCTTAGGGAGAAAAGATCTTAAATCTTC
* * * * * *
35264688 GACCTACTCCACTACAGCTTAGGGAGATAGGATC-TACCATCTTT
1 GATCTACTCCACTACTGCTTAGGGAGAAAAGATCTTA-AATCTTC
*
35264732 GACCTACTCCACTACTGCTTAGGGAGA
1 GATCTACTCCACTACTGCTTAGGGAGA
35264759 TAGGACTGGT
Statistics
Matches: 158, Mismatches: 29, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
37 3 0.02
38 3 0.02
39 1 0.01
40 3 0.02
41 1 0.01
42 11 0.07
43 6 0.04
44 100 0.63
45 8 0.05
46 10 0.06
47 1 0.01
48 2 0.01
49 1 0.01
50 8 0.05
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
GATCTACTCCACTACTGCTTAGGGAGAAAAGATCTTAAATCTTC
Found at i:35264759 original size:44 final size:44
Alignment explanation
Indices: 35264634--35264763 Score: 197
Period size: 44 Copynumber: 3.0 Consensus size: 44
35264624 AAATAAGATT
* * * *
35264634 TACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
1 TACCATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGATC
* * *
35264678 TGCAATCTTTGACCTACTCCACTACAGCTTAGGGAGATAGGATC
1 TACCATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGATC
35264722 TACCATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGA
1 TACCATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGA
35264764 CTGGTGGTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (44 bp):
TACCATCTTTGACCTACTCCACTACTGCTTAGGGAGATAGGATC
Found at i:35264969 original size:86 final size:86
Alignment explanation
Indices: 35264784--35265356 Score: 912
Period size: 86 Copynumber: 6.6 Consensus size: 86
35264774 TGATCTACTC
** *
35264784 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTTTTTCTGCTTCGCTGTTCA
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTG-TTTTTGATCTGCTTCGCTGTTAA
35264849 CGCAGGAAGGCAAAATCTGCTT
65 CGCAGGAAGGCAAAATCTGCTT
*
35264871 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTACTTCGCTGTTAAC
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAAC
* *
35264936 GCAGGAAGACAAAATCTACTT
66 GCAGGAAGGCAAAATCTGCTT
* *
35264957 CTTTAACTAGCTCCACTGCAACCGATGGAGGCAAGGCCTTGTTTTTGATCTGCTTCGCTGTTAAC
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAAC
35265022 GCAGGAAGGCAAAATCTGCTT
66 GCAGGAAGGCAAAATCTGCTT
*
35265043 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAGGGCTTTGTTTTTGATCTGCTTCGCTGTTAAC
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAAC
*
35265108 GCAGGAAGGCAAGATCTGCTT
66 GCAGGAAGGCAAAATCTGCTT
* * * *
35265129 CTTTAACCAGCACCACTGCAACCGATGGAGGCAAGGCTTTATTTTTTTGATCTGCTTCACTGTTC
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGC-TT-TGTTTTTGATCTGCTTCGCTGTTA
35265194 ACGCAGGAAGGCAAAATCTGCTT
64 ACGCAGGAAGGCAAAATCTGCTT
* *
35265217 TTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTTTTTATCTGCTTCGCTGTT
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTG---TTTTTGATCTGCTTCGCTGTT
*
35265282 AACGCAGGAAGGCAAGATCTGCTT
63 AACGCAGGAAGGCAAAATCTGCTT
* * *
35265306 CTTTAACCAGCTCCACTGCAACTGATGGAGGCAAGGCTTCGTTTTCGATCT
1 CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCT
35265357 TCACTGGTCT
Statistics
Matches: 448, Mismatches: 33, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
86 246 0.55
87 45 0.10
88 78 0.17
89 79 0.18
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (86 bp):
CTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAAC
GCAGGAAGGCAAAATCTGCTT
Found at i:35267017 original size:6 final size:6
Alignment explanation
Indices: 35267002--35267035 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35266992 CTCTTTTTCT
* *
35267002 TTTTGT TTTTTA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
35267036 TTTCTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (6 bp):
TTTTGA
Found at i:35267044 original size:41 final size:41
Alignment explanation
Indices: 35266967--35267051 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
35266957 GCTTTTCATA
* *
35266967 TTTTTATTTTGACTTTGATTGATTTCTCTTTTTCTTTTTGT
1 TTTTTATTTTGACTTTGATTGATTTCTCTTTCTCTTTTTCT
*
35267008 TTTTTATTTTGATTTTGATTTTGATTT-T-TTTCTCTTTTTCT
1 TTTTTATTTTGACTTTGA--TTGATTTCTCTTTCTCTTTTTCT
35267049 TTT
1 TTT
35267052 CCTTTTTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
41 31 0.79
42 1 0.03
43 7 0.18
ACGTcount: A:0.09, C:0.08, G:0.08, T:0.74
Consensus pattern (41 bp):
TTTTTATTTTGACTTTGATTGATTTCTCTTTCTCTTTTTCT
Found at i:35267058 original size:47 final size:47
Alignment explanation
Indices: 35266965--35267059 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
35266955 TTGCTTTTCA
* **
35266965 TATTTTTATTTTGACTTTGATTGATTTCTCTTTTTCTTTTTGTTTTT
1 TATTTTGATTTTGACTTTGATTGATTTCTCTTTTTCTTTTCCTTTTT
* **
35267012 TATTTTGATTTTGATTTTGATTTTTTTCTCTTTTTCTTTTCCTTTTT
1 TATTTTGATTTTGACTTTGATTGATTTCTCTTTTTCTTTTCCTTTTT
35267059 T
1 T
35267060 TCGAATCGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.74
Consensus pattern (47 bp):
TATTTTGATTTTGACTTTGATTGATTTCTCTTTTTCTTTTCCTTTTT
Found at i:35272595 original size:24 final size:24
Alignment explanation
Indices: 35272568--35272613 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
35272558 ACAGAATTTT
35272568 TTAAAAATTAGTTTTTAAATTACA
1 TTAAAAATTAGTTTTTAAATTACA
*
35272592 TTAAAAATTATTTTTTAAATTA
1 TTAAAAATTAGTTTTTAAATTA
35272614 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TTAAAAATTAGTTTTTAAATTACA
Found at i:35277450 original size:2 final size:2
Alignment explanation
Indices: 35277443--35277483 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35277433 NNNNNNNNCG
35277443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35277484 TAAGTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35277534 original size:23 final size:24
Alignment explanation
Indices: 35277476--35277536 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
35277466 ATATATATAT
* *
35277476 ATATATATTAAGTTTTTACTTTCA
1 ATATATATTAAGTTTTGACTATCA
*
35277500 ATA-A-ATTAAGTTTTGA-TATGA
1 ATATATATTAAGTTTTGACTATCA
35277521 ATATATATTAAGTTTT
1 ATATATATTAAGTTTT
35277537 AATTCTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.19
22 12 0.38
23 11 0.34
24 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (24 bp):
ATATATATTAAGTTTTGACTATCA
Found at i:35279826 original size:24 final size:25
Alignment explanation
Indices: 35279794--35279854 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
35279784 ATATATATAT
35279794 ATATAATATTTGATTAAAAATAAAACA
1 ATAT-ATATTTGATTAAAAATAAAA-A
35279821 ATATATATTTGATTAAAAAT-AAAA
1 ATATATATTTGATTAAAAATAAAAA
35279845 ATATATATTT
1 ATATATATTT
35279855 AATATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.32
25 3 0.09
26 16 0.47
27 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (25 bp):
ATATATATTTGATTAAAAATAAAAA
Found at i:35282365 original size:21 final size:21
Alignment explanation
Indices: 35282341--35282380 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35282331 TCTTAAGATG
*
35282341 TGAATTGGATTGAATTGAGTA
1 TGAATTGGATTAAATTGAGTA
*
35282362 TGAATTGTATTAAATTGAG
1 TGAATTGGATTAAATTGAG
35282381 CTAAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (21 bp):
TGAATTGGATTAAATTGAGTA
Found at i:35283516 original size:13 final size:13
Alignment explanation
Indices: 35283500--35283552 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
35283490 TTTGAACCAA
35283500 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
35283513 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
35283526 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
35283539 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
35283552 A
1 A
35283553 ATGAAGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 4 0.12
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:35288501 original size:28 final size:28
Alignment explanation
Indices: 35288469--35288568 Score: 164
Period size: 28 Copynumber: 3.6 Consensus size: 28
35288459 TAATGAGATT
* * *
35288469 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGTTTGATTATTA
*
35288497 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGTTTGATTATTA
35288525 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTGATTATTA
35288553 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
35288569 ACTTATTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATTA
Found at i:35289379 original size:71 final size:71
Alignment explanation
Indices: 35289292--35289962 Score: 920
Period size: 71 Copynumber: 9.5 Consensus size: 71
35289282 TAATGCTTAA
* *
35289292 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
35289357 ATATAT
66 ATATAT
* * * **
35289363 ATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTTTGGTGTAAAAATGCTGCTCAATTTATT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
35289428 GTATTT
66 ATATAT
* *
35289434 ATGCTGCCCAAATTGTTGTATATATGCTATCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
35289498 ATATAT
66 ATATAT
* * * *
35289504 ATGCTGCCCAATTTGTTGTATATATGCTGTCTAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
35289569 GTATTT
66 ATATAT
*
35289575 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
35289639 ATATAT
66 ATATAT
* * * *
35289645 ATGCTGCCCAATTTGTTGTATATATGCTGTCTAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
35289710 GTATTT
66 ATATAT
* *
35289716 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AGTTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
35289780 ATATAT
66 ATATAT
* * * * * * * *
35289786 ATACTACCTAATTTGCTGTATATATGCTGTCCAATTTTTGGTGTAAAAATACTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
*
35289851 GTATAT
66 ATATAT
* *
35289857 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGCTG-TCTAGTTTGG
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTC-AATTTGG
*
35289921 TATATAA
65 TATATAT
* * *
35289928 ATGCTGTCCAAATTGATGTATA-AGAGCTGTCCAAA
1 ATGCTGCCCAAATTGTTGTATATA-TGCTGTCCAAA
35289963 CAGGGTAGAT
Statistics
Matches: 523, Mismatches: 72, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
70 187 0.36
71 336 0.64
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (71 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
ATATAT
Found at i:35289499 original size:141 final size:141
Alignment explanation
Indices: 35289292--35289949 Score: 1084
Period size: 141 Copynumber: 4.7 Consensus size: 141
35289282 TAATGCTTAA
* * *
35289292 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
*
35289357 ATATATATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTTTGGTGTAAAAATGCTGCTCAA
65 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
*
35289422 TTTATTGTATTT
130 TTTGTTGTATTT
*
35289434 ATGCTGCCCAAATTGTTGTATATATGCTATCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
*
35289499 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCTAATTTTTGGTGTAAAAATGCTGCTCAAT
66 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
35289564 TTGTTGTATTT
131 TTGTTGTATTT
35289575 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
*
35289640 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCTAATTTTTGGTGTAAAAATGCTGCTCAAT
66 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
35289705 TTGTTGTATTT
131 TTGTTGTATTT
*
35289716 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAGTTTTGATGTAAAAATGCTGCTCAATTTGGTA
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
* * * * *
35289781 TATATATACTACCTAATTTGCTGTATATATGCTGTCCAATTTTTGGTGTAAAAATACTGCTCAAT
66 TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
*
35289846 TTGTTGTATAT
131 TTGTTGTATTT
* * *
35289857 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGCTG-TCTAGTTTGG
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGCTGCTC-AATTTGG
* * * *
35289921 TATATAAATGCTGTCCAAATTGATGTATA
64 TATATATATGCTGCCCAATTTGTTGTATA
35289950 AGAGCTGTCC
Statistics
Matches: 487, Mismatches: 27, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
141 411 0.84
142 76 0.16
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (141 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTA
TATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAAT
TTGTTGTATTT
Found at i:35289950 original size:23 final size:23
Alignment explanation
Indices: 35289292--35289949 Score: 391
Period size: 23 Copynumber: 28.0 Consensus size: 23
35289282 TAATGCTTAA
* * * *
35289292 ATGCTGCCCAAATTGTTATATAT
1 ATGCTGTCCAATTTGGTGTATAT
* *
35289315 ATGCTGTCCAAATTTTGGTGTAAAA
1 ATGCTGTCC-AA-TTTGGTGTATAT
* *
35289340 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* *
35289363 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * *
35289386 ATGCTGCCCAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
** *
35289411 ATGCTG-CTCAATTTATTGTATTT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
35289434 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * * *
35289457 ATGCTATCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGGTGTATAT
*
35289481 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* *
35289504 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * *
35289527 ATGCTGTCTAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
* *
35289552 ATGCTG-CTCAATTTGTTGTATTT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
35289575 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * *
35289598 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGGTGTATAT
*
35289622 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* *
35289645 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * *
35289668 ATGCTGTCTAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
* *
35289693 ATGCTG-CTCAATTTGTTGTATTT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
35289716 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * * *
35289739 ATGCTGTCCAGTTTTGATGTAAAA
1 ATGCTGTCCA-ATTTGGTGTATAT
*
35289763 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
35289786 ATACT-ACCTAATTTGCTGTATAT
1 ATGCTGTCC-AATTTGGTGTATAT
* *
35289809 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
* *
35289834 ATACTG-CTCAATTTGTTGTATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
35289857 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
*
35289880 ATGCTGTCCAAATTTTGGTGTGA-AA
1 ATGCTGTCC-AA-TTTGGTGT-ATAT
* * * *
35289905 ATGCTGTCTAGTTTGGTATATAA
1 ATGCTGTCCAATTTGGTGTATAT
* *
35289928 ATGCTGTCCAAATTGATGTATA
1 ATGCTGTCCAATTTGGTGTATA
35289950 AGAGCTGTCC
Statistics
Matches: 491, Mismatches: 109, Indels: 70
0.73 0.16 0.10
Matches are distributed among these distances:
22 2 0.00
23 321 0.65
24 70 0.14
25 97 0.20
26 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (23 bp):
ATGCTGTCCAATTTGGTGTATAT
Found at i:35290654 original size:12 final size:12
Alignment explanation
Indices: 35290633--35290666 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35290623 CGTGTCTCGT
* *
35290633 ACACGGCCATGG
1 ACACGTCCATGC
35290645 ACACGTCCATGC
1 ACACGTCCATGC
35290657 ACACGTCCAT
1 ACACGTCCAT
35290667 ATGATGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.38, G:0.21, T:0.15
Consensus pattern (12 bp):
ACACGTCCATGC
Found at i:35292767 original size:30 final size:30
Alignment explanation
Indices: 35292731--35292813 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
35292721 GTAATCTCGA
35292731 TATAATGTCAGCTTATGTGAGCAATCCGGT
1 TATAATGTCAGCTTATGTGAGCAATCCGGT
*
35292761 TATAATGTCAACTTATGTGAGCAATCCGGT
1 TATAATGTCAGCTTATGTGAGCAATCCGGT
* *
35292791 TATAATTTCAGCTTGTGTGAGCA
1 TATAATGTCAGCTTATGTGAGCA
35292814 TTACACTCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (30 bp):
TATAATGTCAGCTTATGTGAGCAATCCGGT
Found at i:35294191 original size:7 final size:7
Alignment explanation
Indices: 35294181--35294216 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
35294171 TTAATAAGAG
35294181 ATAAATA
1 ATAAATA
35294188 ATAAATA
1 ATAAATA
35294195 ATAAATA
1 ATAAATA
35294202 ATAAATA
1 ATAAATA
35294209 ATAAATA
1 ATAAATA
35294216 A
1 A
35294217 AAGAGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAAATA
Found at i:35294197 original size:21 final size:21
Alignment explanation
Indices: 35294167--35294221 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
35294157 TCTAATTAAT
35294167 TAAATTAATAAGAGATAAATAA
1 TAAA-TAATAAGAGATAAATAA
*
35294189 TAAATAATAA-ATAATAAATAA
1 TAAATAATAAGA-GATAAATAA
35294210 TAAATAA-AAGAG
1 TAAATAATAAGAG
35294222 TTTAATTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 22 0.76
22 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAATAATAAGAGATAAATAA
Found at i:35300835 original size:17 final size:16
Alignment explanation
Indices: 35300808--35300857 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
35300798 GGTTGAATAT
35300808 TTTAAATTTTTTCGAA
1 TTTAAATTTTTTCGAA
*
35300824 TTTAAATATTTTT-AAA
1 TTTAAAT-TTTTTCGAA
*
35300840 TTCAAATTATTTTCGAA
1 TTTAAATT-TTTTCGAA
35300857 T
1 T
35300858 AATTGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 19 0.68
17 8 0.29
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (16 bp):
TTTAAATTTTTTCGAA
Found at i:35309802 original size:28 final size:28
Alignment explanation
Indices: 35309733--35309804 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
35309723 TAATGAGATT
* * *
35309733 AGCACTAAGTGTGAGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* * *
35309761 AGCATTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
35309789 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
35309805 ACTTATTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:35310658 original size:70 final size:70
Alignment explanation
Indices: 35310573--35310948 Score: 531
Period size: 70 Copynumber: 5.3 Consensus size: 70
35310563 TCGTTGTATT
*
35310573 TATGCTGCCTAAATTGTTGTATATATACTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
35310638 ATATA
66 ATATA
* * *
35310643 TACGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAGTGTTGCTCAATTTGTT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
35310708 ATATA
66 ATATA
35310713 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
35310778 ATATA
66 ATATA
* * * * *
35310783 TATGCTGCCCAATTTGTTGTATATATGCTGTTCAATTTTTGGTGTAAAAATGCTGCTCAATTTTG
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCCAA-TTTTGATGTAAAAATGTTGCTCAA-TTTG
* *
35310848 TTGTATA
64 GTATATA
* * * *
35310855 TATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGTTG-TCTAGTTTG
1 TATGCTGCCTAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGTTGCTC-AATTTG
35310919 GTATATA
64 GTATATA
* * *
35310926 AATGCTATCC-AAATTGATGTATA
1 TATGCT-GCCTAAATTGTTGTATA
35310949 AGGGCTGTCC
Statistics
Matches: 277, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
70 165 0.60
71 50 0.18
72 60 0.22
73 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.43
Consensus pattern (70 bp):
TATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATTTGGT
ATATA
Found at i:35310665 original size:23 final size:23
Alignment explanation
Indices: 35310528--35310892 Score: 153
Period size: 23 Copynumber: 15.6 Consensus size: 23
35310518 TGATGCTTAA
* *
35310528 ATGCTGCC-CAATTCGTTGTATTT
1 ATGCTGCCTAAATT-GTTGTATAT
* *
35310551 ATGCTGCC-CAATTCGTTGTATTT
1 ATGCTGCCTAAATT-GTTGTATAT
35310574 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * * *
35310597 ATACTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * *
35310621 ATGTTG-CTCAATT-TGGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
35310642 ATACGCTGCCTAAATTGTTGTATAT
1 AT--GCTGCCTAAATTGTTGTATAT
* * *
35310667 ATGCTGTCC-AATTTTGATGTA-AA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * *
35310690 AGTGTTG-CTCAATTTGTTATATAT
1 A-TGCTGCCT-AAATTGTTGTATAT
35310714 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * *
35310737 ATGCTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * * *
35310761 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGCCT-AAATTGTTGTATAT
* *
35310784 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * * *
35310807 ATGCTG-TTCAATTTTTGGTGTAAAA
1 ATGCTGCCT-AA--ATTGTTGTATAT
*
35310832 ATGCTG-CTCAATTTTGTTGTATAT
1 ATGCTGCCT-AA-ATTGTTGTATAT
*
35310856 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
35310879 ATGCTGTCC-AAATT
1 ATGCTG-CCTAAATT
35310893 TTGGTGTGAA
Statistics
Matches: 265, Mismatches: 52, Indels: 50
0.72 0.14 0.14
Matches are distributed among these distances:
21 6 0.02
22 5 0.02
23 144 0.54
24 81 0.31
25 29 0.11
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (23 bp):
ATGCTGCCTAAATTGTTGTATAT
Found at i:35322748 original size:18 final size:18
Alignment explanation
Indices: 35322711--35322749 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35322701 AAAGAGAGAG
*
35322711 TACAAAATATAATTTATA
1 TACAAAATATAATATATA
35322729 TACAAAATA-AATATATTA
1 TACAAAATATAATATA-TA
35322747 TAC
1 TAC
35322750 TATTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
TACAAAATATAATATATA
Found at i:35329797 original size:31 final size:31
Alignment explanation
Indices: 35329753--35329813 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
35329743 TTGGTCACTA
** *
35329753 AACTATTTGAAAGTTTCCATTTAAGTCATTT
1 AACTATTCAAAAGTTTCCATTTAACTCATTT
**
35329784 AACTATTCAAAAGTTTTTATTTAACTCATT
1 AACTATTCAAAAGTTTCCATTTAACTCATT
35329814 GGGCTATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (31 bp):
AACTATTCAAAAGTTTCCATTTAACTCATTT
Found at i:35333418 original size:61 final size:67
Alignment explanation
Indices: 35333349--35333493 Score: 162
Period size: 69 Copynumber: 2.2 Consensus size: 67
35333339 GTTACCTTAC
* *
35333349 CCTTTTGTATTAG-TT-T-CT-TT-C-TTTTCATAATATGTAATAG-TTTCTTGTGTTGTTGAGT
1 CCTTTTGTATTAGCTTCTACTATTGCATTTTCATAATATGTAATAGATGT-TTGTGTTGTTAAGT
35333407 TGT
65 TGT
* *
35333410 CCTTTTGTATGAGCTTCTATTATTGGGCATTTTCATAATATGTAATAGATGTTTGTGTTGTTAAG
1 CCTTTTGTATTAGCTTCTACTATT--GCATTTTCATAATATGTAATAGATGTTTGTGTTGTTAAG
35333475 TTGT
64 TTGT
*
35333479 -CTTTCGTATTAGCTT
1 CCTTTTGTATTAGCTT
35333494 TGATTTATTG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
61 12 0.17
62 2 0.03
63 1 0.01
64 1 0.01
65 2 0.03
68 14 0.20
69 35 0.51
70 2 0.03
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (67 bp):
CCTTTTGTATTAGCTTCTACTATTGCATTTTCATAATATGTAATAGATGTTTGTGTTGTTAAGTT
GT
Found at i:35337865 original size:151 final size:150
Alignment explanation
Indices: 35337630--35338053 Score: 769
Period size: 151 Copynumber: 2.8 Consensus size: 150
35337620 ATTCATATTG
* * * *
35337630 TAATATATAAAGCAAGAAAGTAA-AAATAAATTTATATTTTGCTGGCTGTGAGGTTCGAACTCAC
1 TAATATATAAAGCAAAAAAGTAATAAA-AAAATTAAAATTTGCTGGCTGTGAGGTTCGAACTCAC
35337694 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGT
65 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGT
35337759 TTCACAATTATCTTTTCATTA
130 TTCACAATTATCTTTTCATTA
35337780 TAATATATAAAGCAAAAAATGTAATAAAAAAATTAAAATTTGCTGGCTGTGAGGTTCGAACTCAC
1 TAATATATAAAGCAAAAAA-GTAATAAAAAAATTAAAATTTGCTGGCTGTGAGGTTCGAACTCAC
35337845 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGT
65 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGT
35337910 TTCACAATTATCTTTTCATTA
130 TTCACAATTATCTTTTCATTA
35337931 TAATATATAAAGCAAAAAAAGTAATAAAAAAATTAAAATTTGCTGGCTGTGAGGTTCGAACTCAC
1 TAATATATAAAGC-AAAAAAGTAATAAAAAAATTAAAATTTGCTGGCTGTGAGGTTCGAACTCAC
*
35337996 GCGCACTTTTGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGC
65 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGC
35338054 CAACTGTTCA
Statistics
Matches: 266, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
150 18 0.07
151 239 0.90
152 9 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (150 bp):
TAATATATAAAGCAAAAAAGTAATAAAAAAATTAAAATTTGCTGGCTGTGAGGTTCGAACTCACG
CGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGTT
TCACAATTATCTTTTCATTA
Found at i:35339609 original size:18 final size:17
Alignment explanation
Indices: 35339555--35339615 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
35339545 ACCTCTTCGT
35339555 CTTCATCCTCGGAATCA
1 CTTCATCCTCGGAATCA
* * *
35339572 TCTTCATCATCAGAACCA
1 -CTTCATCCTCGGAATCA
35339590 CTTCCATCCTCGGAATCA
1 CTT-CATCCTCGGAATCA
35339608 CTATCATC
1 CT-TCATC
35339616 ATCATCGTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.09
18 31 0.89
19 1 0.03
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.30
Consensus pattern (17 bp):
CTTCATCCTCGGAATCA
Found at i:35344685 original size:19 final size:19
Alignment explanation
Indices: 35344662--35344728 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
35344652 TAAATACATT
35344662 TTTTTTATTTTTTA-TTTA
1 TTTTTTATTTTTTACTTTA
*
35344680 TCTTTTTATCTTTTACTTTA
1 T-TTTTTATTTTTTACTTTA
35344700 TTTCTTTATTTCCTTT-CTTT-
1 TTT-TTTATTT--TTTACTTTA
35344720 TTTTTTATT
1 TTTTTTATT
35344729 AATTCATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 1 0.02
19 20 0.48
20 14 0.33
21 4 0.10
22 3 0.07
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTTTACTTTA
Found at i:35358860 original size:2 final size:2
Alignment explanation
Indices: 35358855--35358889 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
35358845 TTTAATTATT
35358855 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35358890 ATGTAAAGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:35360748 original size:14 final size:14
Alignment explanation
Indices: 35360729--35360755 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35360719 TTTGTTTGCA
35360729 CGTAAAATATTTTT
1 CGTAAAATATTTTT
35360743 CGTAAAATATTTT
1 CGTAAAATATTTT
35360756 CATTGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (14 bp):
CGTAAAATATTTTT
Found at i:35365240 original size:18 final size:18
Alignment explanation
Indices: 35365217--35365259 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35365207 ACCCAATCTA
**
35365217 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
35365235 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
35365253 AACCCAA
1 AACCCAA
35365260 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:35365381 original size:9 final size:9
Alignment explanation
Indices: 35365367--35365425 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
35365357 GTAGTGATTC
35365367 AATTTGGTT
1 AATTTGGTT
35365376 AATTTGGTT
1 AATTTGGTT
35365385 AATTTGGTT
1 AATTTGGTT
* *
35365394 AATTCGGGT
1 AATTTGGTT
**
35365403 AATTCAGTT
1 AATTTGGTT
*
35365412 AATTCGGTT
1 AATTTGGTT
35365421 AATTT
1 AATTT
35365426 TTAACCAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (9 bp):
AATTTGGTT
Found at i:35365390 original size:18 final size:18
Alignment explanation
Indices: 35365367--35365425 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
35365357 GTAGTGATTC
*
35365367 AATTTGGTTAATTTGGTT
1 AATTTGGTTAATTCGGTT
*
35365385 AATTTGGTTAATTCGGGT
1 AATTTGGTTAATTCGGTT
**
35365403 AATTCAGTTAATTCGGTT
1 AATTTGGTTAATTCGGTT
35365421 AATTT
1 AATTT
35365426 TTAACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (18 bp):
AATTTGGTTAATTCGGTT
Found at i:35366425 original size:15 final size:14
Alignment explanation
Indices: 35366387--35366429 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
35366377 TTTTAGTTTT
35366387 TTTTATATATTATTAA
1 TTTTAT-TA-TATTAA
35366403 TTTTATTATATTAA
1 TTTTATTATATTAA
35366417 TTATTATTATATT
1 TT-TTATTATATT
35366430 GTATATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.31
15 12 0.46
16 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATTATATTAA
Found at i:35366581 original size:38 final size:37
Alignment explanation
Indices: 35366538--35366625 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 37
35366528 ATGTAGTACG
35366538 TATATATTTTAT-TATCATATCATATTATTTT-T-ATAGTT
1 TATATATTTTATGTA-CAT-TCATATT-TTTTATGATA-TT
35366576 TATATATTTTATGTACATTCATATTTTTTATGATATT
1 TATATATTTTATGTACATTCATATTTTTTATGATATT
*
35366613 TATAT-TTTCATGT
1 TATATATTTTATGT
35366626 TTTATAATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
36 11 0.24
37 15 0.33
38 18 0.39
39 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (37 bp):
TATATATTTTATGTACATTCATATTTTTTATGATATT
Found at i:35366617 original size:18 final size:18
Alignment explanation
Indices: 35366540--35366620 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
35366530 GTAGTACGTA
*
35366540 TATATTTTATTATCATA-T
1 TATATTTT-TTATGATATT
*
35366558 CATATTATTTT-T-ATAGTT
1 TATATT-TTTTATGATA-TT
* *
35366576 TATATATTTTATGTACATT
1 TATATTTTTTATG-ATATT
*
35366595 CATATTTTTTATGATATT
1 TATATTTTTTATGATATT
35366613 TATATTTT
1 TATATTTT
35366621 CATGTTTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
16 3 0.06
17 5 0.10
18 24 0.49
19 15 0.31
20 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.62
Consensus pattern (18 bp):
TATATTTTTTATGATATT
Found at i:35370138 original size:24 final size:24
Alignment explanation
Indices: 35370110--35370159 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
35370100 CCAAATGCAT
*
35370110 TTCAAGATAAAATCTTGATGACCC
1 TTCAAGATAAAATCTAGATGACCC
* *
35370134 TTCAAGATAAAGTCTAGGTGACCC
1 TTCAAGATAAAATCTAGATGACCC
35370158 TT
1 TT
35370160 AGATCGAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (24 bp):
TTCAAGATAAAATCTAGATGACCC
Found at i:35370296 original size:53 final size:53
Alignment explanation
Indices: 35370193--35370344 Score: 250
Period size: 53 Copynumber: 2.8 Consensus size: 53
35370183 AGCATCAAAG
* *
35370193 GATTTCCTTGCATTCAACAAACTTCCAAAGATTGTAGCTCAAATTTATAAATAA
1 GATTTCTTTGCATTCAACAAACTT-CAGAGATTGTAGCTCAAATTTATAAATAA
*
35370247 GATTTCTTTGCATTCAATAAACTTCAGAGATTGTAGCTCAAATTTATAAATAA
1 GATTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTTATAAATAA
* *
35370300 GATTTCTTTGCACTCAACAAACTTTAGAGATTGTAGCTCAAATTT
1 GATTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTT
35370345 CTATCATTCC
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 70 0.76
54 22 0.24
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (53 bp):
GATTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTTATAAATAA
Found at i:35375964 original size:26 final size:26
Alignment explanation
Indices: 35375935--35375990 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
35375925 AGTAGAAGGA
35375935 CGAAAATGGAAATTATCCCCTCCATG
1 CGAAAATGGAAATTATCCCCTCCATG
35375961 CGAAAATGGAAATTATCCCCTCCATG
1 CGAAAATGGAAATTATCCCCTCCATG
35375987 -GAAA
1 CGAAA
35375991 TCTTAGGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (26 bp):
CGAAAATGGAAATTATCCCCTCCATG
Found at i:35380624 original size:30 final size:30
Alignment explanation
Indices: 35380590--35380648 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
35380580 CTTATTTTAT
35380590 TGTTAATTTTGTTATTATTTTAAAGACATC
1 TGTTAATTTTGTTATTATTTTAAAGACATC
*
35380620 TGTTAATTTTGTTATTATTTTAGAGACAT
1 TGTTAATTTTGTTATTATTTTAAAGACAT
35380649 TTACTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTTAATTTTGTTATTATTTTAAAGACATC
Found at i:35380796 original size:12 final size:12
Alignment explanation
Indices: 35380775--35380808 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35380765 TATATATTTT
*
35380775 AAAATTATATAA
1 AAAATAATATAA
35380787 AAAATAATATAA
1 AAAATAATATAA
*
35380799 AAATTAATAT
1 AAAATAATAT
35380809 GGGCGGGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:35382987 original size:16 final size:16
Alignment explanation
Indices: 35382963--35382993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35382953 GCAACAAGTA
*
35382963 GCTGGACATTCATGTG
1 GCTGAACATTCATGTG
35382979 GCTGAACATTCATGT
1 GCTGAACATTCATGT
35382994 ACTTGGCCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (16 bp):
GCTGAACATTCATGTG
Found at i:35389893 original size:41 final size:41
Alignment explanation
Indices: 35389836--35389985 Score: 237
Period size: 41 Copynumber: 3.7 Consensus size: 41
35389826 TTTAACATAT
* * * *
35389836 TCACCGGCATTTAGCCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGACACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
35389877 TCACCGACACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGACACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
35389918 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGACACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
35389959 TCACCGACACTTAGCCTGCTAGACTTA
1 TCACCGACACTTAGCCTGCTAGGCTTA
35389986 AAGTCTGAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (41 bp):
TCACCGACACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:35391252 original size:13 final size:13
Alignment explanation
Indices: 35391234--35391258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35391224 CAATCAAATG
35391234 CACACAAAATAAA
1 CACACAAAATAAA
35391247 CACACAAAATAA
1 CACACAAAATAA
35391259 TATTAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:35393256 original size:50 final size:50
Alignment explanation
Indices: 35393156--35393258 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
35393146 CAGGCAAAGG
* *
35393156 ACACGAGCGTGTGTCTAGGCCGTGTAACTTACTATTTATGACTTAGAACC
1 ACACGAGCATGTGTCTAGGCCGTGTAACTTACTATTTATGACTTAAAACC
* * **
35393206 ACACGGGCATGTGTCTAGGCCGTGTAACTCT-CTGTTTATGTTTTAAAACC
1 ACACGAGCATGTGTCTAGGCCGTGTAACT-TACTATTTATGACTTAAAACC
35393256 ACA
1 ACA
35393259 TGGGTAGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 45 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
ACACGAGCATGTGTCTAGGCCGTGTAACTTACTATTTATGACTTAAAACC
Found at i:35400860 original size:29 final size:29
Alignment explanation
Indices: 35400819--35400877 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
35400809 AGTGCGAATG
35400819 TTTTTACTTGAGGTCATAACCCTCATAAT
1 TTTTTACTTGAGGTCATAACCCTCATAAT
35400848 TTTTTACTTGAGGTCATAACCCTCATAAT
1 TTTTTACTTGAGGTCATAACCCTCATAAT
35400877 T
1 T
35400878 CGACTGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTTTACTTGAGGTCATAACCCTCATAAT
Found at i:35404733 original size:20 final size:22
Alignment explanation
Indices: 35404694--35404733 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35404684 TAATTTCAAT
*
35404694 TTTCTCTCAAGTTCCTCTTTAA
1 TTTCTCTCAAGCTCCTCTTTAA
35404716 TTTCTCTCAA-CTCC-CTTT
1 TTTCTCTCAAGCTCCTCTTT
35404734 TTTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.15, C:0.33, G:0.03, T:0.50
Consensus pattern (22 bp):
TTTCTCTCAAGCTCCTCTTTAA
Found at i:35407032 original size:25 final size:25
Alignment explanation
Indices: 35407004--35407086 Score: 139
Period size: 25 Copynumber: 3.3 Consensus size: 25
35406994 TATTTTGATA
35407004 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
35407029 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
35407054 TTATTTGATATAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
*
35407079 TTTTTTGA
1 TTATTTGA
35407087 GTTATTTTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:35408344 original size:125 final size:125
Alignment explanation
Indices: 35408122--35408493 Score: 566
Period size: 125 Copynumber: 3.0 Consensus size: 125
35408112 CAAATATGCT
* * *
35408122 ACTGTAGCAAAAGCGCATCCACGTGGGTGCGATTTCACAAATTCTTCTCATAAAGCATCCTAGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
* *
35408187 GAAGCGATTTTACACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* *
35408247 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCAACTTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
* *
35408312 GAAGCAATTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACCA
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* * * *
35408372 ACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGGT
* ** *
35408436 TGAAGCGTTTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTCCAGG
65 AGAAGC-AATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGG
35408494 GCCTAAAACC
Statistics
Matches: 224, Mismatches: 21, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
124 2 0.01
125 176 0.79
126 46 0.21
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
GAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
Found at i:35408881 original size:16 final size:16
Alignment explanation
Indices: 35408860--35408892 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35408850 TGTCGAGACA
*
35408860 CCATTAATATTGTAGG
1 CCATTAATATTGCAGG
35408876 CCATTAATATTGCAGG
1 CCATTAATATTGCAGG
35408892 C
1 C
35408893 TACTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (16 bp):
CCATTAATATTGCAGG
Found at i:35411149 original size:2 final size:2
Alignment explanation
Indices: 35411142--35411179 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35411132 TGTTAGTAAG
35411142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35411180 CATTTATCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35413525 original size:28 final size:25
Alignment explanation
Indices: 35413494--35413579 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 25
35413484 AAGGCAATCC
35413494 AAAATAAATAATGTATACGAAACAATTT
1 AAAATAAATAAT-TAT-CG-AACAATTT
*
35413522 AAAATAGATAA-TATCGAACAATTT
1 AAAATAAATAATTATCGAACAATTT
** *
35413546 AATGTAAATAA-TA-C-ATATAATTT
1 AAAATAAATAATTATCGA-ACAATTT
35413569 AAAATAAATAA
1 AAAATAAATAA
35413580 AATATAAACC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
23 16 0.32
24 18 0.36
25 2 0.04
26 3 0.06
28 10 0.20
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAATAAATAATTATCGAACAATTT
Found at i:35413576 original size:23 final size:23
Alignment explanation
Indices: 35413517--35413586 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
35413507 TATACGAAAC
* *
35413517 AATTTAAAATAGATAATATCGA-AC
1 AATTTAAAATAAATAATA-C-ATAT
**
35413541 AATTTAATGTAAATAATACATAT
1 AATTTAAAATAAATAATACATAT
35413564 AATTTAAAATAAATAA-A-ATAT
1 AATTTAAAATAAATAATACATAT
35413585 AA
1 AA
35413587 ACCGTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 6 0.15
22 2 0.05
23 16 0.41
24 15 0.38
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTTAAAATAAATAATACATAT
Found at i:35417797 original size:27 final size:27
Alignment explanation
Indices: 35417765--35417995 Score: 268
Period size: 27 Copynumber: 8.6 Consensus size: 27
35417755 AGACCCTAAA
*
35417765 ATAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
35417792 ATAGGGTAAAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
35417819 ATAAGGTAAAATGACCAAAATA-CCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
35417845 ATAGGATAAAATGATCGAAATACCCTCC
1 ATAGGGTAAAATGACCGAAATACCC-CC
* * ** **
35417873 ATAGGATAAAATGATCGATTTACCCTT
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
35417900 ATAGGGTAAAATGATCGAAATA-CCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
35417926 ATAGGGTAAAATGACCAAAATACCCCTA
1 ATAGGGTAAAATGACCGAAATACCCC-C
* *
35417954 ATAGGGTAGAATAACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
35417981 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
35417996 TGTTATACGC
Statistics
Matches: 174, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
26 44 0.25
27 82 0.47
28 48 0.28
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:35417983 original size:108 final size:108
Alignment explanation
Indices: 35417765--35417994 Score: 329
Period size: 108 Copynumber: 2.1 Consensus size: 108
35417755 AGACCCTAAA
35417765 ATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAA
1 ATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAA
* *
35417830 TGACCAAAATACCCCATAGGATAAAATGATCGAAATACCCTCC
66 TGACCAAAATACCCCATAGGATAAAATAACCGAAATACCCTCC
* ** ** * *
35417873 ATAGGATAAAATGATCGATTTACCCTTATAGGGTAAAATGATCGAAATACCCT-ATAGGGTAAAA
1 ATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAA
* *
35417937 TGACCAAAATACCCCTAATAGGGTAGAATAACCGAAATACCC-CC
66 TGACCAAAATACCCC--ATAGGATAAAATAACCGAAATACCCTCC
35417981 ATAGGGTAAAATGA
1 ATAGGGTAAAATGA
35417995 CTGTTATACG
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
107 25 0.23
108 62 0.57
109 21 0.19
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (108 bp):
ATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAAA
TGACCAAAATACCCCATAGGATAAAATAACCGAAATACCCTCC
Found at i:35418522 original size:33 final size:35
Alignment explanation
Indices: 35418456--35418529 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 35
35418446 TCATTGCATG
** *
35418456 ACTGATATCTATTATTGTTATGGGCCAAGGTCCC-
1 ACTGATATCTATTATTGAAATGGGCCAAAGTCCCT
35418490 ACTGATA-CTATTATTGAAATTGGG-CAAAGTCCCT
1 ACTGATATCTATTATTGAAA-TGGGCCAAAGTCCCT
35418524 ACTGAT
1 ACTGAT
35418530 TACTGGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 18 0.51
34 17 0.49
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (35 bp):
ACTGATATCTATTATTGAAATGGGCCAAAGTCCCT
Found at i:35419190 original size:12 final size:12
Alignment explanation
Indices: 35419162--35419191 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35419152 AAATAAATAA
*
35419162 ATAAAAATAATC
1 ATAATAATAATC
35419174 ATAATAATAATC
1 ATAATAATAATC
35419186 ATAATA
1 ATAATA
35419192 GATTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATAATAATC
Found at i:35424747 original size:16 final size:16
Alignment explanation
Indices: 35424726--35424762 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
35424716 CCTAGAAGAT
35424726 TAAAAATAAAA-AACAA
1 TAAAAATAAAATAA-AA
35424742 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
35424758 TAAAA
1 TAAAA
35424763 GTGGATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:35424979 original size:2 final size:2
Alignment explanation
Indices: 35424974--35425003 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35424964 CTAAAAAACC
35424974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35425004 GAAAGAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35426846 original size:44 final size:44
Alignment explanation
Indices: 35426784--35427498 Score: 378
Period size: 44 Copynumber: 16.5 Consensus size: 44
35426774 GATCCATGCT
* * *
35426784 ACTGTAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTGCTTTAATCCGCTCC
* * * * *
35426828 ACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTAT-TGCTTTAATCCGCTCC
* * * * *
35426872 ACTGCAACCTCAGGGAGATAAGACCTGA-TGC---GATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGATCT-ATTGCTTTAATCCGCTCC
* *
35426913 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTGCTTTAATCCGCTCC
* * * *
35426957 ACTACAACTTCAGGGAGAT-AGAAT-TATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAG-ATCTAT-TGCTTTAATCCGCTCC
* * * * ** *
35427001 ATTGCAACCTCAGGGAGATAAGATTTGCTT-CTTCGATCTG-TCCC
1 ACTGCAACTTCAGGGAGATAAGATCT-ATTGCTTTAATCCGCT-CC
* * * * *
35427045 ACTACAACTTCAAGGG-GATAAGACCTGA-TGC---GATCCACTCT
1 ACTGCAACTTC-AGGGAGATAAGATCT-ATTGCTTTAATCCGCTCC
* * *
35427086 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTGCTTTAATCCGCTCC
* * * * ** *
35427130 ACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTACTTC
1 ACTGCAACTTCAGGGAGATAAGATCTAT-TGCTTTAATCCGCTCC
* ** * * * *
35427174 ACTGCAACCTCAAAGAGATAAGATTTGTT--TTCTCAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTGCTT-T-AATCCGCTCC
* * * *
35427218 ACTGCAACCTT-AGGGAGATAAGACCTGA-TG---TGATCCACTCT
1 ACTGCAA-CTTCAGGGAGATAAGATCT-ATTGCTTTAATCCGCTCC
* *
35427259 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTGCTTTAATCCGCTCC
* * * * *
35427303 ACTACAACTTCAGGGAGA-AGGAT-TATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTAT-TGCTTTAATCCGCTCC
* * * *
35427346 ACTGCAACCTT-AGGGAGATAAGACCTGA-TGC---GATCCACTCT
1 ACTGCAA-CTTCAGGGAGATAAGATCT-ATTGCTTTAATCCGCTCC
* * * *
35427387 ACTGCAACTTCAGAGAGATAAAATCTATTACTTTAACCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATCTATTGCTTTAATCCGCTCC
* * * * *
35427431 ACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAA-CCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGATCTAT-TGCTTTAATCC-GCTCC
*
35427475 ACTGCAACCTT-AGAGAGATAAGAT
1 ACTGCAA-CTTCAGGGAGATAAGAT
35427499 TTGCCATCTT
Statistics
Matches: 500, Mismatches: 125, Indels: 92
0.70 0.17 0.13
Matches are distributed among these distances:
40 13 0.03
41 110 0.22
42 7 0.01
43 47 0.09
44 304 0.61
45 16 0.03
46 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATCTATTGCTTTAATCCGCTCC
Found at i:35426868 original size:129 final size:129
Alignment explanation
Indices: 35426735--35427023 Score: 526
Period size: 129 Copynumber: 2.2 Consensus size: 129
35426725 GTTTTCTCAG
* *
35426735 TCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGCGATCCA-TGCTACTGTAACTTCAGAG
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACT-CTACTGCAACTTCAGAG
*
35426799 AGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAA
65 AGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTATCGGCTTCAA
35426864 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
35426929 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTATCGGCTTCAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTATCGGCTTCAA
*
35426993 TCTGCTCCATTGCAACCTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGA
35427024 TTTGCTTCTT
Statistics
Matches: 155, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
129 154 0.99
130 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (129 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTATCGGCTTCAA
Found at i:35427067 original size:173 final size:173
Alignment explanation
Indices: 35426818--35427368 Score: 835
Period size: 173 Copynumber: 3.2 Consensus size: 173
35426808 CTATTACTTT
* * * * ** *
35426818 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTAT-CGGCTTCAATCTGCTCCACTGCAACCT
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCTTCTTCAATCTGCTCCACTGCAACTT
35426882 CAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTT
65 CAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTT
*
35426947 AATCCGCTCCACTACAACTTCAGGGAGATAGAATTATCGGCTTC
130 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
* * *
35426991 AATCTGCTCCATTGCAACCTCAGGGAGATAAGATTTGCTTCTTCGATCTG-TCCCACTACAACTT
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCAATCTGCT-CCACTGCAACTT
35427055 CAAGGG-GATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT
65 C-AGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT
*
35427119 TAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
129 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
* * ** * *
35427164 AATCTACTTCACTGCAACCTCAAAGAGATAAGATTTG-TTTTCTCAGTCTGCTCCACTGCAACCT
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCT-TCAATCTGCTCCACTGCAA-CT
*
35427228 T-AGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT
64 TCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT
35427292 TAATCCGCTCCACTACAACTTCAGGGAGA-AGGATTATCGGCTTC
129 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
*
35427336 AATCTGCTCCACTGCAACCTTAGGGAGATAAGA
1 AATCTGCTCCACTGCAACCTCAGGGAGATAAGA
35427369 CCTGATGCGA
Statistics
Matches: 343, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
172 52 0.15
173 283 0.83
174 8 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (173 bp):
AATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCAATCTGCTCCACTGCAACTTC
AGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
Found at i:35427277 original size:41 final size:41
Alignment explanation
Indices: 35427218--35427407 Score: 113
Period size: 41 Copynumber: 4.5 Consensus size: 41
35427208 AGTCTGCTCC
35427218 ACTGCAACCTT-AGGGAGATAAGACCTGATGTGATCCACTCT
1 ACTGCAA-CTTCAGGGAGATAAGACCTGATGTGATCCACTCT
* * * * * * *
35427259 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGA-C-CTGA-TGTGATCCACTCT
* * * * *
35427303 ACTACAACTTCAGGGAGA-AGGA--TTATCG-GCTTCAATCTGCT
1 ACTGCAACTTCAGGGAGATAAGACCTGAT-GTG-ATCCA-CT-CT
*
35427344 CCACTGCAACCTT-AGGGAGATAAGACCTGATGCGATCCACTCT
1 --ACTGCAA-CTTCAGGGAGATAAGACCTGATGTGATCCACTCT
*
35427387 ACTGCAACTTCAGAGAGATAA
1 ACTGCAACTTCAGGGAGATAA
35427408 AATCTATTAC
Statistics
Matches: 111, Mismatches: 22, Indels: 32
0.67 0.13 0.19
Matches are distributed among these distances:
38 1 0.01
39 5 0.05
40 8 0.07
41 35 0.32
42 1 0.01
43 20 0.18
44 33 0.30
45 4 0.04
46 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (41 bp):
ACTGCAACTTCAGGGAGATAAGACCTGATGTGATCCACTCT
Found at i:35427354 original size:128 final size:129
Alignment explanation
Indices: 35427210--35427497 Score: 515
Period size: 128 Copynumber: 2.2 Consensus size: 129
35427200 GTTTTCTCAG
*
35427210 TCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGTGATCCACTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
* *
35427275 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGA-AGGATTATCGGCTTCAA
66 GATAAAATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAA
35427338 TCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
35427403 GATAAAATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAA
66 GATAAAATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAA
* * *
35427467 CCTGCTCTACTGCAACCTTAGAGAGATAAGA
1 TCTGCTCCACTGCAACCTTAGGGAGATAAGA
35427498 TTTGCCATCT
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
128 108 0.71
129 45 0.29
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (129 bp):
TCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGA
GATAAAATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAA
Found at i:35427693 original size:129 final size:129
Alignment explanation
Indices: 35427548--35428963 Score: 2226
Period size: 129 Copynumber: 11.0 Consensus size: 129
35427538 TAAGACCTAC
*
35427548 AATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* ** *
35427613 CACTTAAAGATAAGATTCGTAGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
*
35427677 AATTTCCCAACCTATT-CACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
*
35427741 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTAATGCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
* *
35427805 AATTTCCCAACCTATTCCACTGTTGACCAGGGATATAGGACTTGTGGCTTAAATTTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* * * * *
35427870 CTCTTGAAGATAAAAATCGCCGTCTTCGATCTGCTCCGCTATTGTTTAGGGAGATAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
* **
35427934 AATTTCCCAACCTATTCCACTGCTAACCAAAGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* *** * * * *
35427999 CACTTTAAGATAAGATTTATCGTCTTCAATCTGCTCTGTTATTGTTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
* *
35428063 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGAACTTATGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* *
35428128 CTCTTGAAGATAAGATTCGCCGTTTTCGCAT-TGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCG-ATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
* * *
35428192 AATTTTCCATCCTATTCCACTGCTAACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* * ** *
35428257 CTCTTGAAGATAAGATTCTCCGTCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
* * * * *
35428321 AATTTTCTAAACTATTCTACTGCTGACCAGGGATATAAGACTTGTGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* * *
35428386 CACTTGAAGATAAGATTCGCCGTCTTCGATCTCCTCTGCTATTTCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
*
35428450 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* * * *
35428515 CTCTTGAAGATAAGATTCGCCATCTTCGATTTGCTCCACTATTGCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
*
35428579 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATA-GACTTGTGGCTTAAATCTGTTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
* * * * * * *
35428643 CGCTTGAAGATAAGATTCACCATATTCGATCTACTCCGCTACTGTTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
* * * *
35428707 AATTTCTCTACCTATTCCACTGCTGACCAGGGATATAGAACTTGTGGCTTAAATCTACTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
*
35428772 CACTTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
35428836 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
1 AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
*
35428901 CACTTAAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTG
66 CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTG
35428964 CTATCTTCAC
Statistics
Matches: 1177, Mismatches: 106, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
128 242 0.21
129 933 0.79
130 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (129 bp):
AATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTA
CACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGT
Found at i:35430204 original size:7 final size:7
Alignment explanation
Indices: 35430185--35430234 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
35430175 TTAGCCTCTC
35430185 CATTTTT
1 CATTTTT
35430192 -ACTTTTT
1 CA-TTTTT
35430199 CATTTTT
1 CATTTTT
35430206 CATTCTTT
1 CATT-TTT
*
35430214 --GTTTT
1 CATTTTT
35430219 CATTTTT
1 CATTTTT
35430226 CATTTTT
1 CATTTTT
35430233 CA
1 CA
35430235 CATTTTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
5 3 0.08
6 2 0.06
7 27 0.75
8 4 0.11
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:35435111 original size:2 final size:2
Alignment explanation
Indices: 35435106--35435133 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35435096 CTAAAAAACC
35435106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35435134 GAAAGAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35435617 original size:12 final size:12
Alignment explanation
Indices: 35435588--35435618 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
35435578 ATGAGGTAAC
35435588 AATTAAAAATCA
1 AATTAAAAATCA
35435600 AA-TAAAAATCA
1 AATTAAAAATCA
35435611 AATTAAAA
1 AATTAAAA
35435619 TGAAAGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (12 bp):
AATTAAAAATCA
Found at i:35441014 original size:3 final size:3
Alignment explanation
Indices: 35441006--35441060 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
35440996 ATAAGTAAAT
* *
35441006 ATA ATA ATA AT- ATA ATA ATA ATA GTA ATA ATAA ATG ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
*
35441051 ATC ATA ATA A
1 ATA ATA ATA A
35441061 CATCAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35441045 original size:22 final size:22
Alignment explanation
Indices: 35440939--35441060 Score: 83
Period size: 25 Copynumber: 5.4 Consensus size: 22
35440929 ATCACAAAAG
* *
35440939 ATATAAGTAATTACATAATAATA
1 ATATAA-TAATAATATAATAATA
* *
35440962 ATAT-ATAATAAAACAA-AAT-
1 ATATAATAATAATATAATAATA
* *
35440981 ATAT-TTAA-AATTTAAATAAGTAA
1 ATATAATAATAATAT-AATAA-T-A
35441004 ATATAATAATAATATAATAATA
1 ATATAATAATAATATAATAATA
35441026 ATAGTAATAATAAATGATAATAATA
1 ATA-TAATAAT-AAT-ATAATAATA
35441051 ATCATAATAA
1 AT-ATAATAA
35441061 CATCAAATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.03
19 9 0.11
20 5 0.06
21 9 0.11
22 5 0.06
23 16 0.20
24 11 0.14
25 21 0.27
26 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (22 bp):
ATATAATAATAATATAATAATA
Found at i:35442491 original size:19 final size:19
Alignment explanation
Indices: 35442467--35442507 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
35442457 TTGCTTTATT
* *
35442467 CATTAAATTTAAGTATTTG
1 CATTAAATTCAAATATTTG
35442486 CATTAAATTCAAATATTTG
1 CATTAAATTCAAATATTTG
35442505 CAT
1 CAT
35442508 ATGCAACTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (19 bp):
CATTAAATTCAAATATTTG
Done.