Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2341.1
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: 257253
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.31
Warning! 17925 characters in sequence are not A, C, G, or T
Found at i:3524 original size:53 final size:54
Alignment explanation
Indices: 3455--3661 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 54
3445 TTCCTTTTTA
* * * *
3455 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * *
3508 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * * *
3562 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
3617 AACTTACCAATGTCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
3662 AAACCTTAAT
Statistics
Matches: 123, Mismatches: 29, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 45 0.37
54 37 0.30
55 41 0.33
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:3610 original size:55 final size:53
Alignment explanation
Indices: 3467--3661 Score: 192
Period size: 55 Copynumber: 3.6 Consensus size: 53
3457 CTTACCATTT
* *
3467 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCATTG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
* * * * ** * *
3520 CCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AACTCACCAATG
* * * * *
3575 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATG
* * * *
3629 TCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGTATCCTT
3662 AAACCTTAAT
Statistics
Matches: 113, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 35 0.31
54 37 0.33
55 41 0.36
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
Found at i:8578 original size:15 final size:15
Alignment explanation
Indices: 8558--8588 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8548 GTATGCTTAT
8558 CTCATATACGCATGA
1 CTCATATACGCATGA
8573 CTCATATACGCATGA
1 CTCATATACGCATGA
8588 C
1 C
8589 ATGCTATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (15 bp):
CTCATATACGCATGA
Found at i:12123 original size:19 final size:19
Alignment explanation
Indices: 12087--12125 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12077 TATCACAATT
*
12087 ATATTATAACATAATATAA
1 ATATTATAACAAAATATAA
12106 ATATTATAA-AAAATTATAA
1 ATATTATAACAAAA-TATAA
12125 A
1 A
12126 ACATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATTATAACAAAATATAA
Found at i:13024 original size:46 final size:46
Alignment explanation
Indices: 12972--13063 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
12962 ATAATGACCC
*
12972 AAGCTCTCTTTATTTATGGAGAGTTCAGAGAGAGTTCAACTAGGAT
1 AAGCTCTCTTTATATATGGAGAGTTCAGAGAGAGTTCAACTAGGAT
13018 AAGCTCTCTTTATATATGGAGAGTTCAGAGAGAGTTCAACTAGGAT
1 AAGCTCTCTTTATATATGGAGAGTTCAGAGAGAGTTCAACTAGGAT
13064 TAGAATTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (46 bp):
AAGCTCTCTTTATATATGGAGAGTTCAGAGAGAGTTCAACTAGGAT
Found at i:13131 original size:37 final size:39
Alignment explanation
Indices: 13078--13173 Score: 97
Period size: 42 Copynumber: 2.4 Consensus size: 39
13068 ATTAAACAAA
* *
13078 TTAATATTAAATTAATA-A-AATATTATCTAGACAAATAT
1 TTAAT-TTAATTTAATACATAATAATATCTAGACAAATAT
* *
13116 TTAATTTAATTTAATATCTCATATTAATATCTAGATAAATAT
1 TTAATTTAATTTAATA---CATAATAATATCTAGACAAATAT
*
13158 TAAATTTAATTTAATA
1 TTAATTTAATTTAATA
13174 TTAAATTCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
37 10 0.21
38 5 0.10
41 1 0.02
42 32 0.67
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (39 bp):
TTAATTTAATTTAATACATAATAATATCTAGACAAATAT
Found at i:16880 original size:35 final size:35
Alignment explanation
Indices: 16841--16911 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
16831 CTTTTTGCCT
16841 AAAACTAATTCCGTTCATCTATTTATTCACCTACA
1 AAAACTAATTCCGTTCATCTATTTATTCACCTACA
16876 AAAACTAATTCCGTTCATCTATTTATTCACCTACA
1 AAAACTAATTCCGTTCATCTATTTATTCACCTACA
16911 A
1 A
16912 CTGATTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (35 bp):
AAAACTAATTCCGTTCATCTATTTATTCACCTACA
Found at i:26855 original size:7 final size:7
Alignment explanation
Indices: 26843--26867 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26833 TTATATTTGT
26843 GTTTTAC
1 GTTTTAC
26850 GTTTTAC
1 GTTTTAC
26857 GTTTTAC
1 GTTTTAC
26864 GTTT
1 GTTT
26868 CGGTTATTTC
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:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (7 bp):
GTTTTAC
Found at i:33859 original size:33 final size:33
Alignment explanation
Indices: 33821--33886 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
33811 GACTAAGTGG
* * *
33821 GAGTGTTTGGTTGTTGGACAGGAGTTGGAATGT
1 GAGTGTTTGGTTGCTGGACAAGAGCTGGAATGT
*
33854 GAGTGTTTTGTTGCTGGACAAGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAAGAGCTGGAATGT
33887 CAAGAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.06, G:0.39, T:0.35
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGACAAGAGCTGGAATGT
Found at i:46495 original size:7 final size:6
Alignment explanation
Indices: 46454--46494 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
46444 ATAATTTAAT
*
46454 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
46495 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:46495 original size:20 final size:20
Alignment explanation
Indices: 46457--46496 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46447 ATTTAATAAA
**
46457 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
46477 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
46497 ATATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:46573 original size:9 final size:9
Alignment explanation
Indices: 46514--46572 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
46504 TTTATACAAA
46514 TAATTCGGT
1 TAATTCGGT
46523 TAATTCGGT
1 TAATTCGGT
* *
46532 CAATTCGGG
1 TAATTCGGT
46541 TAATTCGGT
1 TAATTCGGT
* *
46550 CAATTCGAT
1 TAATTCGGT
*
46559 TAATTTGGT
1 TAATTCGGT
46568 TAATT
1 TAATT
46573 TTATACTTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:46936 original size:14 final size:14
Alignment explanation
Indices: 46917--46945 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46907 CGCCCATGTG
46917 ATAGAGACTTCAAT
1 ATAGAGACTTCAAT
46931 ATAGAGACTTCAAT
1 ATAGAGACTTCAAT
46945 A
1 A
46946 ATCTCAGTCA
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:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAGAGACTTCAAT
Found at i:47985 original size:17 final size:17
Alignment explanation
Indices: 47963--47997 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47953 TAGAAGAACC
*
47963 CCAAATGAATTATCTAA
1 CCAAATAAATTATCTAA
*
47980 CCAAATAAATTGTCTAA
1 CCAAATAAATTATCTAA
47997 C
1 C
47998 ATCCCAACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (17 bp):
CCAAATAAATTATCTAA
Found at i:52180 original size:17 final size:17
Alignment explanation
Indices: 52158--52190 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52148 ATTCGACAAA
52158 ACCCGATAAATGATAAT
1 ACCCGATAAATGATAAT
*
52175 ACCCGATACATGATAA
1 ACCCGATAAATGATAA
52191 ATGATAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (17 bp):
ACCCGATAAATGATAAT
Found at i:55421 original size:52 final size:52
Alignment explanation
Indices: 55350--55449 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
55340 ATCAAGTGAC
* *
55350 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTGG
*
55402 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGAGACAA
55450 AGTGATAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTGG
Found at i:55473 original size:37 final size:37
Alignment explanation
Indices: 55423--55532 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
55413 TAATAGCTTC
*
55423 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
55460 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
55497 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
55532 G
1 G
55533 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:57529 original size:51 final size:51
Alignment explanation
Indices: 57469--57571 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
57459 TTTGGAAACT
*
57469 TAGAAAAATTTCAACCATATAGGGGTCACACGCCCATGTGAACAGGCCGTG
1 TAGAAAAATTTCAACCATACAGGGGTCACACGCCCATGTGAACAGGCCGTG
*
57520 TAGAAAAATTTCAACCATACAGGGGTCACACGCCCGTGTGAACAGGCCGTG
1 TAGAAAAATTTCAACCATACAGGGGTCACACGCCCATGTGAACAGGCCGTG
57571 T
1 T
57572 GCCTTACATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (51 bp):
TAGAAAAATTTCAACCATACAGGGGTCACACGCCCATGTGAACAGGCCGTG
Found at i:58837 original size:40 final size:40
Alignment explanation
Indices: 58776--58872 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
58766 ACTCGATATC
*
58776 TCGCACACTAAGTGCCGTATATAGCCGAAGCTATCTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
* * * **
58816 TCGCATACTAAGTGCTATATATAGCCGAAGCTATGTTGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
58856 TCGCACACTAAGTGCCA
1 TCGCACACTAAGTGCCA
58873 CAAATAACCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
Found at i:60990 original size:460 final size:459
Alignment explanation
Indices: 60100--61014 Score: 1409
Period size: 460 Copynumber: 2.0 Consensus size: 459
60090 CTCAGGTTCC
* *
60100 CATGTAGCTTCTTCAACCCCGTGTCGATACCATAATACTTTCACTAATGTGATTATCTTATTTAC
1 CATGTAGCTTCTTCAACCCCGTGTCAATACCATAATACTTTCACTAATGCGATTATCTTATTTAC
* ** * *
60165 CAGTTCTTTGATCTCACAAGCTGAAATTCGAATTGGTTCTTCAGCATATGACATATCATATTGAA
66 CAGTTCTTTGATCTCACAAGCTAAAATTCGAACCGATTCTTCAGCATATGACATATCAGATTGAA
** * * *
60230 TTTCAACCTCGGTCGGGGAAATGACTTGTGATGGGTCAGATGGTATCATCGAAGCATCGACACAT
131 TTTCAACCTCGACCGGGGAAATGACATGTGAAGGGTCAGATGGGATCATCGAAGCATCGACACAT
* *
60295 GAAACACATTCTGTATTTTCTCTAACTCAGACAGTAAAGATAGTCGATATGCCACTGGCCCAACT
196 GAAACACATTATGTATTTTCTCTAACTCAGACAGTAAAGATAGTCGACATGCCACTGGCCCAACT
60360 CGCTCAGTAATCTCATACGGTCCGATGAATCGCGAACTCAATTTCCCTTTCCGACCAAACCGCAA
261 CGCTCAGTAATCTCATACGGTCCGATGAATCGCGAACTCAATTTCCCTTTCCGACCAAACCGCAA
* * *
60425 TATCTTATTCCACGGCGACACTTTTAAAAACACTTTATCCCTAATGTGGAACTCAATATCTTTCC
326 TATCTTATTCCACGGCGACACTTTTAAAAACACTTTATCCCCAATCTAGAACTCAATATCTTTCC
* * *
60490 ATTTCAAGGCTGCACACAATTTCTGTCGATTCGGAGCTGCTTTCAAACTATCGCGAATTACTTTC
391 ATTTCAAGGCTGCACACAATTTCTGTCGATCCGAAGCTGCTTTCAAACTATCACGAATTACTTTC
60555 AGTA
456 AGTA
* * * **
60559 CATGTAGCTTCTTCAACCTCGTGTCAATGCCATAATACTTTCACTAATGCGATTCTCTTATTTTT
1 CATGTAGCTTCTTCAACCCCGTGTCAATACCATAATACTTTCACTAATGCGATTATCTTATTTAC
* * * * * *
60624 TAGTTTTTTGGTCTCATAAGCTAAAATTCGAACCGATTCTTCAGCATATGACATGTTAGATTGAA
66 CAGTTCTTTGATCTCACAAGCTAAAATTCGAACCGATTCTTCAGCATATGACATATCAGATTGAA
* *
60689 TTTCAACCTCGACCGGGGAAATGCCATGTGAAGGGTC-GAATCGGGATCGTCGAAGCATCGACAC
131 TTTCAACCTCGACCGGGGAAATGACATGTGAAGGGTCAG-AT-GGGATCATCGAAGCATCGACAC
60753 ATGAAACACATTATGTATTTTCTCTAACTCAGACAGTAAAGATAGTCGACATGCCACTGGCCCAA
194 ATGAAACACATTATGTATTTTCTCTAACTCAGACAGTAAAGATAGTCGACATGCCACTGGCCCAA
* * * *
60818 CTCGCTCAGTAATTTCATACGGTCCGATGAATCGCGGACTCAATTTCCCTTTCCTACCAAACTGC
259 CTCGCTCAGTAATCTCATACGGTCCGATGAATCGCGAACTCAATTTCCCTTTCCGACCAAACCGC
*
60883 AATATCTTATTCCACGGTGACACTTTTAAAAACACTTTATCCCCAATCTAGAACTCAATATCTTT
324 AATATCTTATTCCACGGCGACACTTTTAAAAACACTTTATCCCCAATCTAGAACTCAATATCTTT
* * * * * *
60948 CTATTTCAAGTCTGCATACGATTTTTGTTGATCCGAAGCTGCTTTCAAACTATCACGAATTACTT
389 CCATTTCAAGGCTGCACACAATTTCTGTCGATCCGAAGCTGCTTTCAAACTATCACGAATTACTT
61013 TC
454 TC
61015 TCTTTTTCTT
Statistics
Matches: 410, Mismatches: 44, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
458 1 0.00
459 146 0.36
460 263 0.64
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (459 bp):
CATGTAGCTTCTTCAACCCCGTGTCAATACCATAATACTTTCACTAATGCGATTATCTTATTTAC
CAGTTCTTTGATCTCACAAGCTAAAATTCGAACCGATTCTTCAGCATATGACATATCAGATTGAA
TTTCAACCTCGACCGGGGAAATGACATGTGAAGGGTCAGATGGGATCATCGAAGCATCGACACAT
GAAACACATTATGTATTTTCTCTAACTCAGACAGTAAAGATAGTCGACATGCCACTGGCCCAACT
CGCTCAGTAATCTCATACGGTCCGATGAATCGCGAACTCAATTTCCCTTTCCGACCAAACCGCAA
TATCTTATTCCACGGCGACACTTTTAAAAACACTTTATCCCCAATCTAGAACTCAATATCTTTCC
ATTTCAAGGCTGCACACAATTTCTGTCGATCCGAAGCTGCTTTCAAACTATCACGAATTACTTTC
AGTA
Found at i:66900 original size:123 final size:123
Alignment explanation
Indices: 66681--66927 Score: 485
Period size: 123 Copynumber: 2.0 Consensus size: 123
66671 GCTAGGAGAG
*
66681 ATGACCAAATGTTAAAGCTTCACCCATGGCTATCTTAAGCTAAATTTTTGGTTGAAGATTAGCAA
1 ATGACCAAATGTTAAAGCTTCACCCATGGCTATCTTAAGCTAAATTTTTGGTTGAAGATGAGCAA
66746 AGAAAGATAGTGGTTTTGTTTTATTATTTTTATCATTAATTACCAAATTACCTTTTTA
66 AGAAAGATAGTGGTTTTGTTTTATTATTTTTATCATTAATTACCAAATTACCTTTTTA
66804 ATGACCAAATGTTAAAGCTTCACCCATGGCTATCTTAAGCTAAATTTTTGGTTGAAGATGAGCAA
1 ATGACCAAATGTTAAAGCTTCACCCATGGCTATCTTAAGCTAAATTTTTGGTTGAAGATGAGCAA
66869 AGAAAGATAGTGGTTTTGTTTTATTATTTTTATCATTAATTACCAAATTACCTTTTTA
66 AGAAAGATAGTGGTTTTGTTTTATTATTTTTATCATTAATTACCAAATTACCTTTTTA
66927 A
1 A
66928 CATTTTAAAA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (123 bp):
ATGACCAAATGTTAAAGCTTCACCCATGGCTATCTTAAGCTAAATTTTTGGTTGAAGATGAGCAA
AGAAAGATAGTGGTTTTGTTTTATTATTTTTATCATTAATTACCAAATTACCTTTTTA
Found at i:67332 original size:58 final size:58
Alignment explanation
Indices: 67242--67357 Score: 182
Period size: 58 Copynumber: 2.0 Consensus size: 58
67232 ACACATAAAC
* *
67242 TTTAAGATAATGCAAATAAGAGCATCTGAGGTACTTACCTTTTGGATGCTTTAGAATA
1 TTTAAGATAATGCAAATAAGAGCATCCGAGGTACTTACCTTTTGGATGCTCTAGAATA
67300 TTTAAGAT-A-GCATAAGTAAGAGCATCCGAGGTACTTACCTTTTGGATGCTCTAGAATA
1 TTTAAGATAATGCA-AA-TAAGAGCATCCGAGGTACTTACCTTTTGGATGCTCTAGAATA
67358 CAAAATCATG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 3 0.06
57 3 0.06
58 48 0.89
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (58 bp):
TTTAAGATAATGCAAATAAGAGCATCCGAGGTACTTACCTTTTGGATGCTCTAGAATA
Found at i:72904 original size:31 final size:26
Alignment explanation
Indices: 72801--72910 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
72791 CATGAAATTC
*
72801 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
72827 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
72853 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
* *
72879 TTATCATGGAACATTTACTTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
72905 TTATCA
1 TTATCA
72911 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:74900 original size:59 final size:56
Alignment explanation
Indices: 74858--74974 Score: 146
Period size: 58 Copynumber: 2.1 Consensus size: 56
74848 CCATTGCCGT
**
74858 GAATG-TAAGAAAGAAAACAAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCC
1 GAATGTTAAGAAAG-AAACAAAAAAAAAGTGTCCATCTTTCTTCACCTCTCTTGGCC
* * **
74914 GAATGTTCTAAGGAAGAAAGAAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCC
1 GAATG-T-TAAGAAAGAAACAAAAAAAAAGTGTCCATCTTTCTTCACCTCTCTTGGCC
74972 GAA
1 GAA
74975 AATTCAAAGG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
56 5 0.09
58 44 0.79
59 7 0.12
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (56 bp):
GAATGTTAAGAAAGAAACAAAAAAAAAGTGTCCATCTTTCTTCACCTCTCTTGGCC
Found at i:74985 original size:58 final size:58
Alignment explanation
Indices: 74876--74987 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
74866 GAAAGAAAAC
** *
74876 AAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCCGAATGTTCTAAGGAAGAAAG
1 AAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCCGAAAATTCAAAGGAAGAAAG
74934 AAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCCGAAAATTCAAAGGAAG
1 AAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCCGAAAATTCAAAGGAAG
74988 GAGGAAGGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (58 bp):
AAAAAAAAAGTGTCCATCTTTCTTCATTTCTCTTGGCCGAAAATTCAAAGGAAGAAAG
Found at i:76111 original size:79 final size:81
Alignment explanation
Indices: 75975--76159 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
75965 TTGAATGATG
*
75975 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
76039 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
76054 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
76116 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
76134 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
76160 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:76173 original size:40 final size:40
Alignment explanation
Indices: 75976--76159 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
75966 TGAATGATGT
* * * *
75976 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
76016 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
76056 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
76094 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
76135 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
76160 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:76181 original size:79 final size:79
Alignment explanation
Indices: 75976--76192 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
75966 TGAATGATGT
** * * * **
75976 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
76039 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
76056 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
76121 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
76135 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
76193 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:79882 original size:20 final size:21
Alignment explanation
Indices: 79857--79897 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
79847 CTTATCTTGC
79857 AATCAAAA-CCCAAAATTAAA
1 AATCAAAAGCCCAAAATTAAA
*
79877 AATCAAAAGCCCTAAATTAAA
1 AATCAAAAGCCCAAAATTAAA
79898 CCCTCTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.17
Consensus pattern (21 bp):
AATCAAAAGCCCAAAATTAAA
Found at i:80846 original size:21 final size:22
Alignment explanation
Indices: 80799--80853 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
80789 AATTATTTTA
** *
80799 TTTTTACTTTACCCCTCTAACC
1 TTTTTACTTTTTCCCTCAAACC
*
80821 CTTTTACTTTTTCCCT-AAACC
1 TTTTTACTTTTTCCCTCAAACC
*
80842 TTTTTACCTTTT
1 TTTTTACTTTTT
80854 ACTTTCCCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTACTTTTTCCCTCAAACC
Found at i:85686 original size:4 final size:4
Alignment explanation
Indices: 85677--85770 Score: 188
Period size: 4 Copynumber: 23.5 Consensus size: 4
85667 GTGGTAGCAA
85677 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
85725 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
85771 GATGACATTG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 90 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:87077 original size:49 final size:49
Alignment explanation
Indices: 86976--87070 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
86966 GGGGGCCAGT
** *
86976 GTTATACTTCAACTCGTGACTGTATAACCATCGTCAACTAGGAGCCCTA
1 GTTATACTTCAACTCGTGACCATATAACCACCGTCAACTAGGAGCCCTA
*
87025 GTTATACTTCAACTCGTGACCATATAACCACCGTGAACTAGGAGCC
1 GTTATACTTCAACTCGTGACCATATAACCACCGTCAACTAGGAGCC
87071 TAAGTTACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
GTTATACTTCAACTCGTGACCATATAACCACCGTCAACTAGGAGCCCTA
Found at i:88717 original size:46 final size:46
Alignment explanation
Indices: 88666--88758 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
88656 GATATTTTTG
88666 TTAAAAAAGATAATTTTCTTTATTTTTTAATAAATATATATCATAT
1 TTAAAAAAGATAATTTTCTTTATTTTTTAATAAATATATATCATAT
88712 TTAAAAAAGATAATTTTCTTTATTTTTTAATAAATATATATCATAT
1 TTAAAAAAGATAATTTTCTTTATTTTTTAATAAATATATATCATAT
88758 T
1 T
88759 ATTCAATAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (46 bp):
TTAAAAAAGATAATTTTCTTTATTTTTTAATAAATATATATCATAT
Found at i:88740 original size:26 final size:26
Alignment explanation
Indices: 88661--88741 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 26
88651 TAATCGATAT
88661 TTTTGTTAAAAAAGATAATTTTCTTTA
1 TTTT-TTAAAAAAGATAATTTTCTTTA
* * *
88688 TTTTTTAATAAATAT-A-TATC---A
1 TTTTTTAAAAAAGATAATTTTCTTTA
*
88709 -TATTTAAAAAAGATAATTTTCTTTA
1 TTTTTTAAAAAAGATAATTTTCTTTA
88734 TTTTTTAA
1 TTTTTTAA
88742 TAAATATATA
Statistics
Matches: 40, Mismatches: 8, Indels: 13
0.66 0.13 0.21
Matches are distributed among these distances:
20 11 0.28
21 2 0.05
22 3 0.08
24 3 0.08
25 2 0.05
26 15 0.38
27 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTTTAAAAAAGATAATTTTCTTTA
Found at i:99761 original size:63 final size:63
Alignment explanation
Indices: 99691--99816 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
99681 TTAAATGTTA
99691 GAACCTATTTGATATATCCTAATGAGGTGAATTTGGCCAAGTTTTGGTTAGCTTATTATGTGT
1 GAACCTATTTGATATATCCTAATGAGGTGAATTTGGCCAAGTTTTGGTTAGCTTATTATGTGT
99754 GAACCTATTTGATATATCCTAATGAGGTGAATTTGGCCAAGTTTTGGTTAGCTTATTATGTGT
1 GAACCTATTTGATATATCCTAATGAGGTGAATTTGGCCAAGTTTTGGTTAGCTTATTATGTGT
99817 TTAGGTAAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (63 bp):
GAACCTATTTGATATATCCTAATGAGGTGAATTTGGCCAAGTTTTGGTTAGCTTATTATGTGT
Found at i:104534 original size:42 final size:42
Alignment explanation
Indices: 104471--104553 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
104461 ATATTTGTAC
104471 ATCATAATCATAGACCCAAACTCACAAGGTCATCACCATTTT
1 ATCATAATCATAGACCCAAACTCACAAGGTCATCACCATTTT
* *
104513 ATCATAATCATAGACCTAAACTCACAAGGTCATTACCATTT
1 ATCATAATCATAGACCCAAACTCACAAGGTCATCACCATTT
104554 CATTCTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.28
Consensus pattern (42 bp):
ATCATAATCATAGACCCAAACTCACAAGGTCATCACCATTTT
Found at i:116707 original size:28 final size:26
Alignment explanation
Indices: 116676--116741 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 26
116666 AATTTTCTAG
* *
116676 AATTTTTTATTTTTATTACCTTTTTAT
1 AATTTTATATTTTTA-TAACTTTTTAT
*
116703 CAATTTTATATTTTTATAATTTTTTAT
1 -AATTTTATATTTTTATAACTTTTTAT
116730 AATTTTA-ATTTT
1 AATTTTATATTTT
116742 AATTTTCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.14
26 7 0.20
27 9 0.26
28 14 0.40
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (26 bp):
AATTTTATATTTTTATAACTTTTTAT
Found at i:116709 original size:10 final size:9
Alignment explanation
Indices: 116664--116735 Score: 53
Period size: 10 Copynumber: 7.9 Consensus size: 9
116654 TAGGTCATAG
116664 ATAATTTTCT
1 ATAATTTT-T
*
116674 AGAATTTTT
1 ATAATTTTT
116683 -T-ATTTTT
1 ATAATTTTT
*
116690 ATTACCTTTTT
1 A-TA-ATTTTT
116701 ATCAA-TTTT
1 AT-AATTTTT
116710 AT-ATTTTT
1 ATAATTTTT
116718 ATAATTTTTT
1 ATAA-TTTTT
116728 ATAATTTT
1 ATAATTTT
116736 AATTTTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
7 7 0.14
8 6 0.12
9 13 0.26
10 17 0.34
11 7 0.14
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (9 bp):
ATAATTTTT
Found at i:116711 original size:9 final size:8
Alignment explanation
Indices: 116697--116782 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 8
116687 TTTATTACCT
116697 TTTTATCAA
1 TTTTAT-AA
*
116706 TTTTATAT
1 TTTTATAA
116714 TTTTATAA
1 TTTTATAA
116722 TTTTTTATAA
1 --TTTTATAA
116732 -TTT-TAA
1 TTTTATAA
*
116738 TTTTA-AT
1 TTTTATAA
116745 TTTCTATAA
1 TTT-TATAA
116754 -TTTAT--
1 TTTTATAA
116759 TTTTAT-A
1 TTTTATAA
*
116766 TTTTTTAA
1 TTTTATAA
*
116774 TTTTCTAA
1 TTTTATAA
116782 T
1 T
116783 ATAAATTTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
6 8 0.13
7 18 0.29
8 21 0.34
9 7 0.11
10 8 0.13
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAA
Found at i:116725 original size:26 final size:28
Alignment explanation
Indices: 116667--116741 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
116657 GTCATAGATA
* * *
116667 ATTTTCTAGAATTTTTTATTTTTATTAC
1 ATTTTTTATAATTTTATATTTTTATTAC
*
116695 -CTTTTTATCAATTTTATATTTTTA-TA-
1 ATTTTTTAT-AATTTTATATTTTTATTAC
116721 ATTTTTTATAATTTTA-ATTTT
1 ATTTTTTATAATTTTATATTTT
116742 AATTTTCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 5 0.12
26 7 0.17
27 14 0.35
28 14 0.35
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (28 bp):
ATTTTTTATAATTTTATATTTTTATTAC
Found at i:116753 original size:32 final size:32
Alignment explanation
Indices: 116704--116780 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
116694 CCTTTTTATC
*
116704 AATTTTATATTTT-TATAATTT-TTTATAATTTT
1 AATTTTA-ATTTTCTATAATTTATTT-TAATATT
*
116736 AATTTTAATTTTCTATAATTTATTTTTATATT
1 AATTTTAATTTTCTATAATTTATTTTAATATT
116768 --TTTTAATTTTCTA
1 AATTTTAATTTTCTA
116781 ATATAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 13 0.32
31 5 0.12
32 20 0.49
33 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (32 bp):
AATTTTAATTTTCTATAATTTATTTTAATATT
Found at i:116754 original size:10 final size:10
Alignment explanation
Indices: 116713--116772 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 10
116703 CAATTTTATA
116713 TTTTTATAAT
1 TTTTTATAAT
116723 TTTTTATAAT
1 TTTTTATAAT
*
116733 TTTAATTTTAAT
1 TTT--TTATAAT
*
116745 TTTCTATAAT
1 TTTTTATAAT
*
116755 TTATTTTTATAT
1 TT-TTTATA-AT
116767 TTTTTA
1 TTTTTA
116773 ATTTTCTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
10 20 0.50
11 7 0.17
12 13 0.32
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:117025 original size:18 final size:19
Alignment explanation
Indices: 117004--117043 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
116994 TTTTTATGTT
*
117004 TTTTTA-ATTTGTTATTAA
1 TTTTTATATTTGTTATAAA
117022 TTTTTATATTTGTTATAAA
1 TTTTTATATTTGTTATAAA
117041 TTT
1 TTT
117044 ATAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTATATTTGTTATAAA
Found at i:122424 original size:14 final size:14
Alignment explanation
Indices: 122405--122433 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
122395 TTTTGAACAA
122405 AAGCATTGATCATT
1 AAGCATTGATCATT
122419 AAGCATTGATCATT
1 AAGCATTGATCATT
122433 A
1 A
122434 TGATGAAATG
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:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
AAGCATTGATCATT
Found at i:124028 original size:7 final size:7
Alignment explanation
Indices: 123992--124027 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
123982 ACAAACATAC
123992 AATAAAA
1 AATAAAA
123999 AATAAAA
1 AATAAAA
124006 AATAAAA
1 AATAAAA
124013 AATAAAA
1 AATAAAA
*
124020 ACTAAAA
1 AATAAAA
124027 A
1 A
124028 CAAAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:126270 original size:23 final size:22
Alignment explanation
Indices: 126243--126288 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
126233 AACAACTACA
126243 GATA-TTTATACTATTAAAATATT
1 GATATTTTATA-TA-TAAAATATT
126266 GATATTTTATATCATAAAATATT
1 GATATTTTATAT-ATAAAATATT
126289 TGTTATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
GATATTTTATATATAAAATATT
Found at i:128655 original size:32 final size:32
Alignment explanation
Indices: 128619--128679 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
128609 TATACAAGTA
*
128619 ATTTAACA-TATATTTCAATAAATAATTATAAT
1 ATTTAACATTATAATTCAA-AAATAATTATAAT
* *
128651 ATTTAATATTATAATTCTAAAATAATTAT
1 ATTTAACATTATAATTCAAAAATAATTAT
128680 TTTTTATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 17 0.68
33 8 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTTAACATTATAATTCAAAAATAATTATAAT
Found at i:130450 original size:30 final size:30
Alignment explanation
Indices: 130411--130472 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
130401 CAACTTAACA
* *
130411 AACAGATGTCTCTAGAATAATAAAAAAATT
1 AACAAATGTCTCTAAAATAATAAAAAAATT
* *
130441 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAAAAAAATT
130471 AA
1 AA
130473 TAATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.27
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAAAAAAATT
Found at i:131561 original size:20 final size:19
Alignment explanation
Indices: 131519--131561 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
131509 TGAATAATTT
* *
131519 TAAATTCATATATATCTTT
1 TAAATTCATATATATATTA
*
131538 TAAATTTATATAATATATTA
1 TAAATTCATAT-ATATATTA
131558 TAAA
1 TAAA
131562 AAAAACTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTCATATATATATTA
Found at i:132635 original size:17 final size:18
Alignment explanation
Indices: 132605--132640 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
132595 ATTTTTTAAT
132605 TTAAAAATTCAAAAATTA
1 TTAAAAATTCAAAAATTA
*
132623 TTAAAAATT-AAAATTTA
1 TTAAAAATTCAAAAATTA
132640 T
1 T
132641 AGAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAAATTCAAAAATTA
Found at i:134095 original size:26 final size:29
Alignment explanation
Indices: 134047--134100 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
134037 TACAATTTAA
* *
134047 TATGATTATATATTTTCTTAAAA-AAAAG
1 TATGATTATATATATTCTAAAAATAAAAG
134075 TATGATTATAT-TATT-TAAAAATAAAA
1 TATGATTATATATATTCTAAAAATAAAA
134101 AAATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 7 0.30
28 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (29 bp):
TATGATTATATATATTCTAAAAATAAAAG
Found at i:137369 original size:14 final size:14
Alignment explanation
Indices: 137346--137376 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
137336 CAATTTTCAC
137346 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
137360 AAAAAGAAAAAAAG
1 AAAAAAAAAAAAAG
137374 AAA
1 AAA
137377 TGGTCAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:146141 original size:316 final size:316
Alignment explanation
Indices: 145561--146192 Score: 1255
Period size: 316 Copynumber: 2.0 Consensus size: 316
145551 CTGTGACAAC
*
145561 CAGGCAGCAGTTAGCATAGCTCATAACCCTGTACACCATGACCGTACCAAGCATGTGGAAATTGA
1 CAGGCAACAGTTAGCATAGCTCATAACCCTGTACACCATGACCGTACCAAGCATGTGGAAATTGA
145626 TCGCCACTTTATTACGGAGAAAATTAACAAAGGGGAAGTTTGTGTTTCATATCTACCTACAAGAC
66 TCGCCACTTTATTACGGAGAAAATTAACAAAGGGGAAGTTTGTGTTTCATATCTACCTACAAGAC
145691 AACAAGTAGCAGACGTGTTAACCAAAAGCTTGAGCAGAAAAATGTTCGAAGAAATTATGGGCAAG
131 AACAAGTAGCAGACGTGTTAACCAAAAGCTTGAGCAGAAAAATGTTCGAAGAAATTATGGGCAAG
145756 CTGGGTTTGATTAACATCTACACTCCAGCTTGAGGGGGAGTGTTGGAATTCCTTAAATTAAGCAG
196 CTGGGTTTGATTAACATCTACACTCCAGCTTGAGGGGGAGTGTTGGAATTCCTTAAATTAAGCAG
145821 ATTTTCTACCTTAGTTCTAGGAATTTCCTTGTACTATTAGCCATAATCAAATTACT
261 ATTTTCTACCTTAGTTCTAGGAATTTCCTTGTACTATTAGCCATAATCAAATTACT
145877 CAGGCAACAGTTAGCATAGCTCATAACCCTGTACACCATGACCGTACCAAGCATGTGGAAATTGA
1 CAGGCAACAGTTAGCATAGCTCATAACCCTGTACACCATGACCGTACCAAGCATGTGGAAATTGA
145942 TCGCCACTTTATTACGGAGAAAATTAACAAAGGGGAAGTTTGTGTTTCATATCTACCTACAAGAC
66 TCGCCACTTTATTACGGAGAAAATTAACAAAGGGGAAGTTTGTGTTTCATATCTACCTACAAGAC
146007 AACAAGTAGCAGACGTGTTAACCAAAAGCTTGAGCAGAAAAATGTTCGAAGAAATTATGGGCAAG
131 AACAAGTAGCAGACGTGTTAACCAAAAGCTTGAGCAGAAAAATGTTCGAAGAAATTATGGGCAAG
146072 CTGGGTTTGATTAACATCTACACTCCAGCTTGAGGGGGAGTGTTGGAATTCCTTAAATTAAGCAG
196 CTGGGTTTGATTAACATCTACACTCCAGCTTGAGGGGGAGTGTTGGAATTCCTTAAATTAAGCAG
146137 ATTTTCTACCTTAGTTCTAGGAATTTCCTTGTACTATTAGCCATAATCAAATTACT
261 ATTTTCTACCTTAGTTCTAGGAATTTCCTTGTACTATTAGCCATAATCAAATTACT
146193 AATTTTTAGG
Statistics
Matches: 315, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
316 315 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (316 bp):
CAGGCAACAGTTAGCATAGCTCATAACCCTGTACACCATGACCGTACCAAGCATGTGGAAATTGA
TCGCCACTTTATTACGGAGAAAATTAACAAAGGGGAAGTTTGTGTTTCATATCTACCTACAAGAC
AACAAGTAGCAGACGTGTTAACCAAAAGCTTGAGCAGAAAAATGTTCGAAGAAATTATGGGCAAG
CTGGGTTTGATTAACATCTACACTCCAGCTTGAGGGGGAGTGTTGGAATTCCTTAAATTAAGCAG
ATTTTCTACCTTAGTTCTAGGAATTTCCTTGTACTATTAGCCATAATCAAATTACT
Found at i:148769 original size:17 final size:17
Alignment explanation
Indices: 148723--148772 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
148713 ATTTAAAAAA
*
148723 ACAAAATTTATAAACATT
1 ACAAAATTTAT-AATATT
** *
148741 TTAAAATATATAATATT
1 ACAAAATTTATAATATT
148758 ACAAAATTTATAATA
1 ACAAAATTTATAATA
148773 AGATTTTTCA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ACAAAATTTATAATATT
Found at i:156179 original size:6 final size:6
Alignment explanation
Indices: 156168--156192 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
156158 TATTTTCTCC
156168 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
156193 TTTTTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:157457 original size:6 final size:6
Alignment explanation
Indices: 157446--157484 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
157436 TTCAGAATAA
*
157446 AAAAAT AAAAAT AAAAAT AAAATTT AATAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAA-AT AA-AAAT AAAAAT A
157485 TTGAGCTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 21 0.72
7 6 0.21
8 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:169045 original size:22 final size:24
Alignment explanation
Indices: 169008--169051 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
168998 AATAATGATT
*
169008 TAAAAATTAAAAATACTTTTAAAA
1 TAAAAATTAAAAATACTATTAAAA
169032 TAAAAA-T-AAAATACTATTAA
1 TAAAAATTAAAAATACTATTAA
169052 TTTTTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 1 0.05
24 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAAATTAAAAATACTATTAAAA
Found at i:169544 original size:50 final size:50
Alignment explanation
Indices: 169487--169589 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
169477 TATAAAAAGA
169487 TATAAAAAATATTTAATATTATTTTAATTTATATGTGCAACTAACCCTTG
1 TATAAAAAATATTTAATATTATTTTAATTTATATGTGCAACTAACCCTTG
169537 TATAAAAAATATTTAATATTATTTTAATTTATATGTGCAACTAACCCTTG
1 TATAAAAAATATTTAATATTATTTTAATTTATATGTGCAACTAACCCTTG
169587 TAT
1 TAT
169590 CTCACAAGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.45
Consensus pattern (50 bp):
TATAAAAAATATTTAATATTATTTTAATTTATATGTGCAACTAACCCTTG
Found at i:171156 original size:3 final size:3
Alignment explanation
Indices: 171140--171175 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
171130 ATCTTTGTGA
* *
171140 ATT ATT ACT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
171176 TTGTATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:172882 original size:37 final size:37
Alignment explanation
Indices: 172811--172912 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 37
172801 TAAAAATTCC
* *
172811 AATAAATAGAAAATTATTA-AATTTATTTTTAAAATCTTGT
1 AATAAATA-AAAA-TATTATAATTT-TTTTAAAAAT-TTGG
172851 AA-AAATAAAAATATTATAATTTTTTTAAAAATTTGG
1 AATAAATAAAAATATTATAATTTTTTTAAAAATTTGG
* * *
172887 AATATATTAAAA-AGTATAATTTTTTT
1 AATAAATAAAAATATTATAATTTTTTT
172913 TATTATTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
36 18 0.33
37 21 0.38
38 9 0.16
39 5 0.09
40 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (37 bp):
AATAAATAAAAATATTATAATTTTTTTAAAAATTTGG
Found at i:175246 original size:123 final size:123
Alignment explanation
Indices: 175069--175315 Score: 485
Period size: 123 Copynumber: 2.0 Consensus size: 123
175059 GAATGTGAAT
175069 GAGGAAAAAATTATATTTGCTATGAATCACTCTTGCAATGAATCTACCTATTTTGATTTTTGAAA
1 GAGGAAAAAATTATATTTGCTATGAATCACTCTTGCAATGAATCTACCTATTTTGATTTTTGAAA
175134 AAGATAGAGAAAGATCGAGTTCTTAAATTATATTATGCATCGTCCTTGAATGTTTAAA
66 AAGATAGAGAAAGATCGAGTTCTTAAATTATATTATGCATCGTCCTTGAATGTTTAAA
175192 GAGGAAAAAATTATATTTGCTATGAATCACTCTTGCAATGAATCTACCTATTTTGATTTTTGAAA
1 GAGGAAAAAATTATATTTGCTATGAATCACTCTTGCAATGAATCTACCTATTTTGATTTTTGAAA
*
175257 AAGATAGAGAAAGATCGAGTTCTTAAATTTTATTATGCATCGTCCTTGAATGTTTAAA
66 AAGATAGAGAAAGATCGAGTTCTTAAATTATATTATGCATCGTCCTTGAATGTTTAAA
175315 G
1 G
175316 TTTTGATTGA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (123 bp):
GAGGAAAAAATTATATTTGCTATGAATCACTCTTGCAATGAATCTACCTATTTTGATTTTTGAAA
AAGATAGAGAAAGATCGAGTTCTTAAATTATATTATGCATCGTCCTTGAATGTTTAAA
Found at i:175494 original size:16 final size:16
Alignment explanation
Indices: 175473--175525 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
175463 TAAGAATATG
175473 ATAATTTTATGATTGA
1 ATAATTTTATGATTGA
*
175489 ATAATTTCATAGGAATATG-
1 ATAATTT--TATG-AT-TGA
175508 ATAATTTTATGATTGA
1 ATAATTTTATGATTGA
175524 AT
1 AT
175526 GCACTTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 2 0.07
16 11 0.37
17 3 0.10
18 3 0.10
19 9 0.30
20 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (16 bp):
ATAATTTTATGATTGA
Found at i:177706 original size:21 final size:21
Alignment explanation
Indices: 177664--177706 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
177654 ATTTTGATGA
* **
177664 AGGTATCAATACCTTGGGTTT
1 AGGTAACAATACCTTGCCTTT
*
177685 AGGTAACAGTACCTTGCCTTT
1 AGGTAACAATACCTTGCCTTT
177706 A
1 A
177707 AAATTAATAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (21 bp):
AGGTAACAATACCTTGCCTTT
Found at i:192605 original size:42 final size:43
Alignment explanation
Indices: 192545--192667 Score: 124
Period size: 42 Copynumber: 2.8 Consensus size: 43
192535 ACAAATTACA
* * *
192545 AATCTTATCTCCCTAAAGTTACAGTAGAGTAGATTGGAGTTAG
1 AATCTTATCTCCTTAAAGTTACAGTAGAGTAGATTAGAGATAG
** * *
192588 -ATCTTATCTCCTTAAAGTTGTAGTGGAGTAGATCAGAGATAG
1 AATCTTATCTCCTTAAAGTTACAGTAGAGTAGATTAGAGATAG
* *
192630 CAAATCTTATCT-CTCTGAAGTTACAGTAGAGAAGATTA
1 --AATCTTATCTCCT-TAAAGTTACAGTAGAGTAGATTA
192668 AAGCTATATA
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 35 0.56
44 2 0.03
45 26 0.41
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (43 bp):
AATCTTATCTCCTTAAAGTTACAGTAGAGTAGATTAGAGATAG
Found at i:192657 original size:87 final size:90
Alignment explanation
Indices: 192542--192760 Score: 255
Period size: 90 Copynumber: 2.5 Consensus size: 90
192532 GCTACAAATT
* * * *
192542 ACAAATCTTATCTCCCTAAAGTTACAGTAGAGTAGATTGGAG-T-TAGATCTTATCTCCTTAAAG
1 ACAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTATAGACCTTATCTCCCTAAAG
* * * *
192605 TTGTAGTGGAGTAGATCAGAGAT-A
66 TCGCAGTGGAGTAGATCAAAAATAA
* * * * * *
192629 GCAAATCTTATCTCTCTGAAGTTACAGTAGAGAAGATTAAAGCTATATACCTTATCTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTATAGACCTTATCTCCCTAAAG
* *
192694 TCGCAGTGGAGTAGTTTAAAAATAA
66 TCGCAGTGGAGTAGATCAAAAATAA
* *
192719 ACAAATTTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAG
1 ACAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAG
192761 ACAGGTTACA
Statistics
Matches: 107, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
87 36 0.34
88 1 0.01
89 33 0.31
90 37 0.35
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (90 bp):
ACAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTGAAGCTATAGACCTTATCTCCCTAAAG
TCGCAGTGGAGTAGATCAAAAATAA
Found at i:192805 original size:139 final size:133
Alignment explanation
Indices: 192401--192948 Score: 357
Period size: 138 Copynumber: 4.0 Consensus size: 133
192391 TCTAATATGG
* * * * * ** *
192401 CGAACCTTATCTCCCTAAAGTTGTAGTGGAGCATGTTGAAGTTAAACAAGTCTTATCTCCCTGAA
1 CGAACCTTATCTCCCTGAAGTCGCAGTAGAGCAGGTT-AAAAT-AACAAATCTTATCTCCCTGAA
* * * * * * * * *
192466 GTTGCAGTGGAGAAGACTGAAAACTGCAAATCTTATTTCCTTGAAGTTGCAGTGGAACAGATTAA
64 GTTACAGTGAAGCAGATTGAAGACAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA
192531 AGCTA
129 AGCTA
* * ** * * ** * * *
192536 CAAATTACAAATCTTATCTCCCTAAAGTTACAGTAGAGTAGATTGGAGT--TAGATCTTATCTCC
1 C-GA--AC----CTTATCTCCCTGAAGTCGCAGTAGAGCAGGTTAAAATAACAAATCTTATCTCC
* * ** * * * * * * * *
192599 TTAAAGTTGTAGTGGAGTAGA-TCAGAGATAGCAAATCTTATCTCTCTGAAGTTACAGTAGAGAA
59 CTGAAGTTACAGTGAAGCAGATTGA-AGACAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
192663 GATTAAAGCTA
123 GATTAAAGCTA
* * * * *
192674 -TATACCTTATCTCCCTGAAGTCGCAGTGGAGTAGTTTAAAAATAAACAAATTTTATCTCCCTGA
1 CGA-ACCTTATCTCCCTGAAGTCGCAGTAGAGCAGGTT-AAAAT-AACAAATCTTATCTCCCTGA
* * * *
192738 AGTTACAGTGGAGTAGATTGAAGACAGGTTACAAATCTTATCTCCCTGAAGTTGTAATGGAGCAG
63 AGTTACAGTGAAGCAGATTGAAGACA-G---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
*
192803 ATTAAAGCCA
124 ATTAAAGCTA
* * * * * * *
192813 CGAACCTTTTCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCTTGAAGT
1 CGAACCTTATCTCCCTGAAGTCGCAGTAGAGCAGGTTAAAATAACAAATCTTATCTCCCTGAAGT
* * * * *
192878 TGCAGTGAAGCAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAG
66 TACAGTGAAGCAGATTGAAGACAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
192943 CTA
131 CTA
192946 CGA
1 CGA
192949 GTTACAAGTC
Statistics
Matches: 319, Mismatches: 76, Indels: 38
0.74 0.18 0.09
Matches are distributed among these distances:
131 27 0.08
132 2 0.01
133 41 0.13
135 36 0.11
136 6 0.02
137 40 0.13
138 73 0.23
139 66 0.21
140 1 0.00
141 1 0.00
142 26 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (133 bp):
CGAACCTTATCTCCCTGAAGTCGCAGTAGAGCAGGTTAAAATAACAAATCTTATCTCCCTGAAGT
TACAGTGAAGCAGATTGAAGACAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
CTA
Found at i:192845 original size:44 final size:44
Alignment explanation
Indices: 192632--192948 Score: 201
Period size: 44 Copynumber: 7.0 Consensus size: 44
192622 AGAGATAGCA
* * * * * *
192632 AATCTTATCTCTCTGAAGTTACAGTAGAGAAGATTAAAGCTA-T
1 AATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACG
* * * * * ** *
192675 ATACCTTATCTCCCTGAAGTCGCAGTGGAGTAGTTTAAAAATAAACA
1 A-ATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT--ACG
* * * *
192722 AAT-TTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGACAGGTTACA
1 AATCTTT-TCTCCCTGAAGTTGCAGTGGAGCAGATT--A-A-A-GCTACG
* * * *
192771 AATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAAGCCACG
1 AATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACG
* * * * *
192815 AACCTTTTCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTAC-
1 AATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACG
* * * * *
192858 AAGTCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATAGCG
1 AA-TCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CG
*
192904 AATCTTATT-TCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACG
1 AATCTT-TTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACG
192948 A
1 A
192949 GTTACAAGTC
Statistics
Matches: 212, Mismatches: 47, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
43 3 0.01
44 104 0.49
45 36 0.17
46 31 0.15
47 2 0.01
48 1 0.00
49 31 0.15
50 3 0.01
51 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTTTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACG
Found at i:192890 original size:88 final size:89
Alignment explanation
Indices: 192765--192928 Score: 224
Period size: 88 Copynumber: 1.9 Consensus size: 89
192755 TTGAAGACAG
* * *
192765 GTTACAAATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAAGCCA-CGAACCTT-TTCTCCC
1 GTTACAAATCTTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGACAGCGAACCTTATT-TCCC
192828 TGAAGTTGCAGTAGAGCAGGTTGAA
65 TGAAGTTGCAGTAGAGCAGGTTGAA
* * * * * *
192853 GTTACAAGTCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGATAGCGAATCTTATTTCCCT
1 GTTACAAATCTTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGACAGCGAACCTTATTTCCCT
192918 GAAGTTGCAGT
66 GAAGTTGCAGT
192929 GGAACAGATT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
88 40 0.62
89 23 0.35
90 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (89 bp):
GTTACAAATCTTATCTCCCTGAAGTTGCAATGAAGCAGATTAAAGACAGCGAACCTTATTTCCCT
GAAGTTGCAGTAGAGCAGGTTGAA
Found at i:195058 original size:20 final size:20
Alignment explanation
Indices: 195033--195073 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
195023 TCTTTTATTC
195033 TTATTTATTTTAAGTTTCTT
1 TTATTTATTTTAAGTTTCTT
195053 TTATTTATTTTAAGTTTCTT
1 TTATTTATTTTAAGTTTCTT
195073 T
1 T
195074 CATATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTATTTATTTTAAGTTTCTT
Found at i:195081 original size:20 final size:20
Alignment explanation
Indices: 195038--195081 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
195028 TATTCTTATT
* *
195038 TATTTTAAGTTTCTTTTATT
1 TATTTTAAGTTTCTTTCATA
195058 TATTTTAAGTTTCTTTCATA
1 TATTTTAAGTTTCTTTCATA
195078 TATT
1 TATT
195082 ATTTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTAAGTTTCTTTCATA
Found at i:195164 original size:39 final size:39
Alignment explanation
Indices: 195126--195202 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
195116 TAAATTTTTA
* *
195126 TATATTATT--TTTT-AATTGTTTTATATGTTATTTCTTT
1 TATATTATTCATTTTAAATTGTTTTAT-TATTATTTATTT
*
195163 TATATTGTTCATTTTAAATTGTTTTATTATTATTTATTT
1 TATATTATTCATTTTAAATTGTTTTATTATTATTTATTT
195202 T
1 T
195203 GAGTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 8 0.24
39 15 0.44
40 11 0.32
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (39 bp):
TATATTATTCATTTTAAATTGTTTTATTATTATTTATTT
Found at i:195171 original size:26 final size:23
Alignment explanation
Indices: 195102--195158 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
195092 AACTGATACA
* *
195102 TATATATTATCTTTTAAAT-TTT
1 TATATATTATTTTTTAATTGTTT
195124 TATATATTATTTTTTAATTGTTT
1 TATATATTATTTTTTAATTGTTT
*
195147 TATATGTTATTT
1 TATATATTATTT
195159 CTTTTATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
TATATATTATTTTTTAATTGTTT
Found at i:196780 original size:26 final size:26
Alignment explanation
Indices: 196740--196846 Score: 169
Period size: 26 Copynumber: 4.1 Consensus size: 26
196730 TGGTACAAAT
196740 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
196766 TGAAAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
196792 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
196818 TGATAATGGTTTAGATAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
196844 TGA
1 TGA
196847 CGGGCATTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:198528 original size:27 final size:27
Alignment explanation
Indices: 198431--198535 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
198421 AGGAAGCGTC
*
198431 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
198458 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
198485 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
198512 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
198536 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:202771 original size:28 final size:28
Alignment explanation
Indices: 202703--202856 Score: 238
Period size: 28 Copynumber: 5.5 Consensus size: 28
202693 CATGAGATTG
* * * *
202703 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
202732 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
202760 GCACTAAGTGTGCGAGTTGGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
202788 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
202816 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
202843 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
202857 GACTTAATAT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.20
28 76 0.64
29 18 0.15
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:215613 original size:26 final size:26
Alignment explanation
Indices: 215584--215691 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
215574 TGGTACAAAT
215584 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
215610 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
215636 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
215662 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
215688 TGAT
1 TGAT
215692 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:217330 original size:27 final size:27
Alignment explanation
Indices: 217290--217421 Score: 139
Period size: 27 Copynumber: 4.9 Consensus size: 27
217280 AGGAAGCGTC
* *
217290 CTGGTGCCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
217317 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
217343 CCTGGTGGCTAC-GCCTCAATTATCTGAT
1 -CTGGTGGCT-CTGCCACAATTATCTGAT
* *
217371 CTGGTGGCTCTACCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
217398 CCGGTGGCTCTGCCACAA-TATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
217422 TGTGACAGCC
Statistics
Matches: 89, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
26 12 0.13
27 72 0.81
28 5 0.06
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:217369 original size:54 final size:54
Alignment explanation
Indices: 217287--217421 Score: 195
Period size: 54 Copynumber: 2.5 Consensus size: 54
217277 TGGAGGAAGC
* * *
217287 GTCCTGGTGCCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTACGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
*
217341 GTCCTGGTGGCTACGCCTCAATTATCTGATCTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTACGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
217395 GTTCC-GGTGGCT-CTGCCACAA-TATCTG
1 G-TCCTGGTGGCTAC-GCCACAATTATCTG
217422 TGTGACAGCC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
53 7 0.09
54 64 0.86
55 3 0.04
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (54 bp):
GTCCTGGTGGCTACGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
Found at i:229238 original size:19 final size:19
Alignment explanation
Indices: 229210--229246 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
229200 ATGACTACTT
229210 TTCATATTTTCCTCCACTC
1 TTCATATTTTCCTCCACTC
* *
229229 TTCATCTTTTTCTCCACT
1 TTCATATTTTCCTCCACT
229247 TTTCTACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51
Consensus pattern (19 bp):
TTCATATTTTCCTCCACTC
Found at i:234523 original size:17 final size:16
Alignment explanation
Indices: 234501--234534 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
234491 AAATACGTCC
234501 TCTCTTTGCTCTCTTAT
1 TCTCTTTG-TCTCTTAT
*
234518 TCTCTTTGTCTTTTAT
1 TCTCTTTGTCTCTTAT
234534 T
1 T
234535 TTATAAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.06, C:0.24, G:0.06, T:0.65
Consensus pattern (16 bp):
TCTCTTTGTCTCTTAT
Found at i:237090 original size:37 final size:37
Alignment explanation
Indices: 237040--237118 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
237030 TTATTACGAA
* *
237040 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
237077 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
237114 GTCTT
1 GTCTT
237119 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:237315 original size:47 final size:47
Alignment explanation
Indices: 237237--237727 Score: 775
Period size: 47 Copynumber: 10.4 Consensus size: 47
237227 CCCTTCGGGA
* * * * ** * *
237237 CTTATCACATTTATGCACTTTCACATCCATCACGTTAGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
237284 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
237331 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
237378 CTTATCACAGATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
237425 CTTATCACAGATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
237472 CTTATCACAGATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
237519 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
237566 CTTATCACACATATACACTTTTACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
237613 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
237662 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
237709 CTTATCACATATATACACT
1 CTTATCACATATATACACT
237728 GTCTTGGCTG
Statistics
Matches: 421, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 376 0.89
49 45 0.11
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.