Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 8 of 172
Found at i:2430673 original size:16 final size:17
Alignment explanation
Indices: 2430652--2430687 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2430642 ATAAATTTAG
2430652 TTTTTAAT-ATTTAATT
1 TTTTTAATAATTTAATT
*
2430668 TTTTTATTAATTTAATT
1 TTTTTAATAATTTAATT
2430685 TTT
1 TTT
2430688 AATCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTAATAATTTAATT
Found at i:2430681 original size:24 final size:23
Alignment explanation
Indices: 2430654--2430710 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
2430644 AAATTTAGTT
*
2430654 TTTAATATTTAATTTTTTTATTAA
1 TTTAATATTTAATCTTTTT-TTAA
*
2430678 TTTAATTTTTAATCTTTTTTTAA
1 TTTAATATTTAATCTTTTTTTAA
*
2430701 GTTAA-ATTTA
1 TTTAATATTTA
2430711 GTCATTAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 4 0.14
23 8 0.28
24 17 0.59
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTAATATTTAATCTTTTTTTAA
Found at i:2430999 original size:30 final size:28
Alignment explanation
Indices: 2430915--2431031 Score: 103
Period size: 29 Copynumber: 4.0 Consensus size: 28
2430905 AAAATTATGT
**
2430915 TTTAACCCCTGTACATTT-TAAAATTTACA
1 TTTAACCCCTAAAC-TTTCTAAAA-TTACA
* *
2430944 TTTTGACCCC-AAATTTTCTAAAATTACA
1 -TTTAACCCCTAAACTTTCTAAAATTACA
*
2430972 TTTAAACCCTTAAACTTTCTCAAAATTACA
1 TTT-AACCCCTAAACTTTCT-AAAATTACA
* *
2431002 CTTGACCCCTAAACTTTCTAAAAATTACA
1 TTTAACCCCTAAACTTTCT-AAAATTACA
2431031 T
1 T
2431032 CTTGGCTCTA
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
27 3 0.04
28 12 0.17
29 37 0.52
30 19 0.27
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (28 bp):
TTTAACCCCTAAACTTTCTAAAATTACA
Found at i:2432174 original size:69 final size:69
Alignment explanation
Indices: 2432063--2432198 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
2432053 TATTTTAATG
* * * * * *
2432063 CATAAGGCAACGGACCGATTTAACATCTAGCCGTTGATTTCATCGTTATGTTGGGTGAATATCGA
1 CATAAGGCAACGAACCGATTTAACATCGAGCCATCGAATTCATCGCTATGTTGGGTGAATATCGA
2432128 TAAC
66 TAAC
* * *
2432132 CATAAGGCAACGAACCGATTTAGCATCGAGTCATCGAATTCATCGCTATGTTGGGTGGATATCGA
1 CATAAGGCAACGAACCGATTTAACATCGAGCCATCGAATTCATCGCTATGTTGGGTGAATATCGA
2432197 TA
66 TA
2432199 GCTCGTGTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (69 bp):
CATAAGGCAACGAACCGATTTAACATCGAGCCATCGAATTCATCGCTATGTTGGGTGAATATCGA
TAAC
Found at i:2432462 original size:30 final size:30
Alignment explanation
Indices: 2432426--2432483 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2432416 TCATGTTTCC
*
2432426 AAAATTTCCCGTGTTTCAAAAAATAATAAT
1 AAAATTTCCCGTGTTTCAAAAAAAAATAAT
*
2432456 AAAATTTCTCGTGTTTCAAAAAAAAATA
1 AAAATTTCCCGTGTTTCAAAAAAAAATA
2432484 TATTCGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAATTTCCCGTGTTTCAAAAAAAAATAAT
Found at i:2432491 original size:23 final size:24
Alignment explanation
Indices: 2432464--2432524 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
2432454 ATAAAATTTC
2432464 TCGTGTTTCAAAAAAAAAT-ATAT
1 TCGTGTTTCAAAAAAAAATAATAT
** *
2432487 TCGTGTTTTTAAAAAAAATAATTT
1 TCGTGTTTCAAAAAAAAATAATAT
2432511 TCGTGTTTTCAAAA
1 TCGTG-TTTCAAAA
2432525 TTTCTCGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 17 0.55
24 8 0.26
25 6 0.19
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (24 bp):
TCGTGTTTCAAAAAAAAATAATAT
Found at i:2432513 original size:24 final size:24
Alignment explanation
Indices: 2432458--2432524 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
2432448 ATAATAATAA
*
2432458 AATTTCTCGTGTTTCAAAAAAAAAT
1 AATTT-TCGTGTTTTAAAAAAAAAT
* *
2432483 -ATATTCGTGTTTTTAAAAAAAAT
1 AATTTTCGTGTTTTAAAAAAAAAT
*
2432506 AATTTTCGTGTTTTCAAAA
1 AATTTTCGTGTTTTAAAAA
2432525 TTTCTCGTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (24 bp):
AATTTTCGTGTTTTAAAAAAAAAT
Found at i:2432546 original size:27 final size:26
Alignment explanation
Indices: 2432516--2432570 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
2432506 AATTTTCGTG
*
2432516 TTTTCAAAATTTCTCGTGTTTTAAAAA
1 TTTTCAAAATTTCTCGT-TTTCAAAAA
* **
2432543 TTTTCGATTTTTCTCGTTTTCAAAAA
1 TTTTCAAAATTTCTCGTTTTCAAAAA
2432569 TT
1 TT
2432571 GTCGTGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (26 bp):
TTTTCAAAATTTCTCGTTTTCAAAAA
Found at i:2432554 original size:17 final size:17
Alignment explanation
Indices: 2432506--2432548 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
2432496 TAAAAAAAAT
*
2432506 AATTTTCGTGTTTTCAA
1 AATTTTCGTGTTTTAAA
2432523 AATTTCTCGTGTTTTAAA
1 AATTT-TCGTGTTTTAAA
2432541 AATTTTCG
1 AATTTTCG
2432549 ATTTTTCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (17 bp):
AATTTTCGTGTTTTAAA
Found at i:2432606 original size:15 final size:16
Alignment explanation
Indices: 2432585--2432631 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
2432575 TGTTTTAAAA
2432585 AAAAATTCGTGTTTCT
1 AAAAATTCGTGTTTCT
* *
2432601 -AAAATTCTTGTATTTT
1 AAAAATTCGTGT-TTCT
2432617 AAAAAATTCGTGTTT
1 -AAAAATTCGTGTTT
2432632 TCAAAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 10 0.40
16 3 0.12
17 2 0.08
18 10 0.40
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (16 bp):
AAAAATTCGTGTTTCT
Found at i:2432637 original size:17 final size:17
Alignment explanation
Indices: 2432558--2432639 Score: 69
Period size: 18 Copynumber: 4.7 Consensus size: 17
2432548 GATTTTTCTC
*
2432558 GTTTTCAAAAATTGTCGT
1 GTTTTCAAAAAAT-TCGT
*
2432576 GTTTTAAAAAAAAATTCGT
1 GTTTT--CAAAAAATTCGT
* *
2432595 G-TTTC-TAAAATTCTT
1 GTTTTCAAAAAATTCGT
*
2432610 GTATTTTAAAAAATTCGT
1 GT-TTTCAAAAAATTCGT
2432628 GTTTTCAAAAAA
1 GTTTTCAAAAAA
2432640 GGAAAAAGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
15 9 0.18
17 12 0.24
18 18 0.36
19 5 0.10
20 6 0.12
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (17 bp):
GTTTTCAAAAAATTCGT
Found at i:2436072 original size:148 final size:148
Alignment explanation
Indices: 2435804--2436099 Score: 592
Period size: 148 Copynumber: 2.0 Consensus size: 148
2435794 GAGAGGGGGG
2435804 ACTTCAGTTGAATTTGTGAATAATTGGTTATTTTTTTACTTTTGGCCTGTTAATGAGTGGAACTG
1 ACTTCAGTTGAATTTGTGAATAATTGGTTATTTTTTTACTTTTGGCCTGTTAATGAGTGGAACTG
2435869 GTGTATTTTTTTTAAATTGTATATTATTGGTATACAGAAAATTGGAAAAAAAAGGGAAAAAATTA
66 GTGTATTTTTTTTAAATTGTATATTATTGGTATACAGAAAATTGGAAAAAAAAGGGAAAAAATTA
2435934 TTGTAGAAAGGGGGTGCC
131 TTGTAGAAAGGGGGTGCC
2435952 ACTTCAGTTGAATTTGTGAATAATTGGTTATTTTTTTACTTTTGGCCTGTTAATGAGTGGAACTG
1 ACTTCAGTTGAATTTGTGAATAATTGGTTATTTTTTTACTTTTGGCCTGTTAATGAGTGGAACTG
2436017 GTGTATTTTTTTTAAATTGTATATTATTGGTATACAGAAAATTGGAAAAAAAAGGGAAAAAATTA
66 GTGTATTTTTTTTAAATTGTATATTATTGGTATACAGAAAATTGGAAAAAAAAGGGAAAAAATTA
2436082 TTGTAGAAAGGGGGTGCC
131 TTGTAGAAAGGGGGTGCC
2436100 GGCTAGGGGT
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 148 1.00
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.39
Consensus pattern (148 bp):
ACTTCAGTTGAATTTGTGAATAATTGGTTATTTTTTTACTTTTGGCCTGTTAATGAGTGGAACTG
GTGTATTTTTTTTAAATTGTATATTATTGGTATACAGAAAATTGGAAAAAAAAGGGAAAAAATTA
TTGTAGAAAGGGGGTGCC
Found at i:2437444 original size:30 final size:30
Alignment explanation
Indices: 2437402--2437502 Score: 157
Period size: 30 Copynumber: 3.4 Consensus size: 30
2437392 GCTTTTCTAT
*
2437402 GGCTTCTACATGGACAGTCGGCGCTTCTGC
1 GGCTTCTGCATGGACAGTCGGCGCTTCTGC
* *
2437432 GGCTTCGGCATGGACAGTCGGCACTTCTGC
1 GGCTTCTGCATGGACAGTCGGCGCTTCTGC
* *
2437462 GGCTTCTGCATGGACAGTCGACGTTTCTGC
1 GGCTTCTGCATGGACAGTCGGCGCTTCTGC
2437492 GGCTTCTGCAT
1 GGCTTCTGCAT
2437503 AGTCCGTCGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.28
Consensus pattern (30 bp):
GGCTTCTGCATGGACAGTCGGCGCTTCTGC
Found at i:2438358 original size:108 final size:103
Alignment explanation
Indices: 2438161--2438562 Score: 422
Period size: 108 Copynumber: 3.8 Consensus size: 103
2438151 TCTTTTTATT
*
2438161 TTGTATAAAGTGGGTGCC-AGCCATTGCCAGACCACCTCTAATTTTTTTTTTACTTTTTTCGTAT
1 TTGTATAAAG-GGGTGCCGA-CCATTGCCAGGCCACC-C-AATTTTTTTTTTACTTTTTTCGTAT
**
2438225 ACTGGTGCCGGCCATTGTCACACCAAAAGTAAAAAAAATATTTA
62 ACTGGTGCCGGCCATTAACA-ACCAAAAGTAAAAAAAA-ATTTA
*
2438269 TTGTATAAAGGGAGTGCCGACTATTGCCAGGCCACCCCAAATTTTTTTTTTACTTTTTTCGTATA
1 TTGTATAAAGGG-GTGCCGACCATTGCCAGGCCA-CCC-AATTTTTTTTTTACTTTTTTCGTATA
*
2438334 CTGGTGCCGGCCATTAACAGACCAAAAG-GAAAAAAAA---A
63 CTGGTGCCGGCCATTAACA-ACCAAAAGTAAAAAAAAATTTA
* * * * *
2438372 TTGTATAAATGGGGTGTCGGCCATTGCCAGGCCACCTGAA-TTTTTTTTTACATTTTTCGTATGC
1 TTGTATAAA-GGGGTGCCGACCATTGCCAGGCCACC-CAATTTTTTTTTTACTTTTTTCGTATAC
*
2438436 TGGTGCCGGCCAATTATAC-ATCAAAAGTAAAAAACAAAAATTTA
64 TGGTGCCGGCC-ATTA-ACAACCAAAAGT--AAAA-AAAAATTTA
* * * * *
2438480 TTGTAAAAAGGGGGTGTCGACCATTGCCAGGTCACTCAATTTTTTTTTTACTTTTTTCGTATTCT
1 TTGTATAAA-GGGGTGCCGACCATTGCCAGGCCACCCAATTTTTTTTTTACTTTTTTCGTATACT
* * *
2438545 GATGCTGGCCATTGACAA
65 GGTGCCGGCCATTAACAA
2438563 AACAACACCC
Statistics
Matches: 252, Mismatches: 26, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
101 40 0.16
102 8 0.03
103 30 0.12
104 6 0.02
105 5 0.02
106 3 0.01
107 15 0.06
108 142 0.56
109 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (103 bp):
TTGTATAAAGGGGTGCCGACCATTGCCAGGCCACCCAATTTTTTTTTTACTTTTTTCGTATACTG
GTGCCGGCCATTAACAACCAAAAGTAAAAAAAAATTTA
Found at i:2438579 original size:209 final size:212
Alignment explanation
Indices: 2438161--2438615 Score: 555
Period size: 209 Copynumber: 2.2 Consensus size: 212
2438151 TCTTTTTATT
* * * * *
2438161 TTGTATAAAGTGGGTGCCAGCCATTGCCAGACCACCTCTAATTTTTTTTTTACTTTTTTCGTATA
1 TTGTATAAAGCGGGTGCCGGCCATTGCCAGGCCACCTCGAATTTTTTTTTTACATTTTTCGTATA
* * * *
2438226 CTGGTGCCGGCCATTGTCACACCAAAAGTAAAAAAAATATTTATTGTATAAAGGGAGTGCCGACT
66 CTGGTGCCGGCCATTATCACACCAAAAGTAAAAAAAAAATTTATTGTAAAAAGGGAGTGCCGACC
* * *
2438291 ATTGCCAGGCCACCCCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCGGCCATTAACAGAC
131 ATTGCCAGGCCACCCCAAATTTTTTTTTTACTTTTTTCGTATACTGATGCCGGCCATTAACAAAA
**
2438356 CAAAA-GGAAAAAAAAA
196 CAAAACCAAAAAAAAAA
*
2438372 TTGTATAAATG-GGGTGTCGGCCATTGCCAGGCCACCT-GAA-TTTTTTTTTACATTTTTCGTAT
1 TTGTATAAA-GCGGGTGCCGGCCATTGCCAGGCCACCTCGAATTTTTTTTTTACATTTTTCGTAT
* * * *
2438434 GCTGGTGCCGGCCAATTAT-ACATCAAAAGTAAAAAACAAAAATTTATTGTAAAAAGGGGGTGTC
65 ACTGGTGCCGGCC-ATTATCACACCAAAAGT-AAAAA-AAAAATTTATTGTAAAAAGGGAGTGCC
* * * * *
2438498 GACCATTGCCAGGTCA-CTC-AATTTTTTTTTTACTTTTTTCGTATTCTGATGCTGGCCATTGAC
127 GACCATTGCCAGGCCACCCCAAATTTTTTTTTTACTTTTTTCGTATACTGATGCCGGCCATTAAC
* *
2438561 AAAACAACACCCAAAAAAAAA
192 AAAACAAAACCAAAAAAAAAA
* *
2438582 TTACGTATAAAGCAGGTGCCGGCCATTGACAGGC
1 TT--GTATAAAGCGGGTGCCGGCCATTGCCAGGC
2438616 TAACACCAAA
Statistics
Matches: 209, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
209 89 0.43
210 24 0.11
211 70 0.33
212 26 0.12
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (212 bp):
TTGTATAAAGCGGGTGCCGGCCATTGCCAGGCCACCTCGAATTTTTTTTTTACATTTTTCGTATA
CTGGTGCCGGCCATTATCACACCAAAAGTAAAAAAAAAATTTATTGTAAAAAGGGAGTGCCGACC
ATTGCCAGGCCACCCCAAATTTTTTTTTTACTTTTTTCGTATACTGATGCCGGCCATTAACAAAA
CAAAACCAAAAAAAAAA
Found at i:2440072 original size:50 final size:51
Alignment explanation
Indices: 2439997--2440095 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 51
2439987 TTTTCACACA
2439997 AAAAGTAAAAAAAAATTATTATATAATGTGGGTGCCTGCCATTGCCAGGTC
1 AAAAGTAAAAAAAAATTATTATATAATGTGGGTGCCTGCCATTGCCAGGTC
*
2440048 AAAAG-AAAAAAAAATTATTGTATAATGTGGGTGCCTGCCATTGCCAGG
1 AAAAGTAAAAAAAAATTATTATATAATGTGGGTGCCTGCCATTGCCAGG
2440096 CCACCCCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 42 0.89
51 5 0.11
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (51 bp):
AAAAGTAAAAAAAAATTATTATATAATGTGGGTGCCTGCCATTGCCAGGTC
Found at i:2442515 original size:30 final size:30
Alignment explanation
Indices: 2442467--2442560 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
2442457 TTTCTCAATT
* **
2442467 GTCGGCTCTTCTGTGGCTTCTGCATGGATA
1 GTCGGCACTTCTCCGGCTTCTGCATGGATA
** * *
2442497 GTCGGTGCTTTTCCGGCTTCGGCATGGATA
1 GTCGGCACTTCTCCGGCTTCTGCATGGATA
* * *
2442527 GTCGGCACTTCTGCGGCTTTTGCATGGACA
1 GTCGGCACTTCTCCGGCTTCTGCATGGATA
2442557 GTCG
1 GTCG
2442561 ACGTTTCTGC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.11, C:0.24, G:0.32, T:0.33
Consensus pattern (30 bp):
GTCGGCACTTCTCCGGCTTCTGCATGGATA
Found at i:2442599 original size:30 final size:30
Alignment explanation
Indices: 2442474--2442583 Score: 94
Period size: 30 Copynumber: 3.7 Consensus size: 30
2442464 ATTGTCGGCT
* * * **
2442474 CTTCTGTGGCTTCTGCATGGATAGTCGGTG
1 CTTCTGCGGCTTTTGCATGGACAGTCGACG
* * ** * * *
2442504 CTTTTCCGGCTTCGGCATGGATAGTCGGCA
1 CTTCTGCGGCTTTTGCATGGACAGTCGACG
2442534 CTTCTGCGGCTTTTGCATGGACAGTCGACG
1 CTTCTGCGGCTTTTGCATGGACAGTCGACG
* *
2442564 TTTCTGCGGCTTTTGTATGG
1 CTTCTGCGGCTTTTGCATGG
2442584 TCTATCGGTG
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.11, C:0.23, G:0.31, T:0.35
Consensus pattern (30 bp):
CTTCTGCGGCTTTTGCATGGACAGTCGACG
Found at i:2443668 original size:30 final size:30
Alignment explanation
Indices: 2443626--2443726 Score: 157
Period size: 30 Copynumber: 3.4 Consensus size: 30
2443616 GCTTTTCTAT
*
2443626 GGCTTCTACATGGACAGTCGGCGCTTCTGC
1 GGCTTCTGCATGGACAGTCGGCGCTTCTGC
* *
2443656 GGCTTCGGCATGGACAGTCGGCACTTCTGC
1 GGCTTCTGCATGGACAGTCGGCGCTTCTGC
* *
2443686 GGCTTCTGCATGGACAGTCGACGTTTCTGC
1 GGCTTCTGCATGGACAGTCGGCGCTTCTGC
2443716 GGCTTCTGCAT
1 GGCTTCTGCAT
2443727 AGTCCGTCGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.28
Consensus pattern (30 bp):
GGCTTCTGCATGGACAGTCGGCGCTTCTGC
Found at i:2446325 original size:19 final size:19
Alignment explanation
Indices: 2446301--2446413 Score: 181
Period size: 19 Copynumber: 5.8 Consensus size: 19
2446291 AATCATATAT
2446301 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
2446320 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
2446339 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2446358 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
*
2446379 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2446398 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2446414 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 68 0.79
21 18 0.21
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2446388 original size:40 final size:40
Alignment explanation
Indices: 2446301--2446412 Score: 201
Period size: 40 Copynumber: 2.9 Consensus size: 40
2446291 AATCATATAT
2446301 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
2446339 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
2446379 TCTAGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
2446413 CCTCAAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
38 28 0.39
40 43 0.61
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:2446394 original size:59 final size:56
Alignment explanation
Indices: 2446294--2446413 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 56
2446284 ATTACAAAAT
*
2446294 CATAT-ATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
* *
2446349 CATATCATATCTAAGATTGCATATATCATATCTAGGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCTAAGATTACATATCATATCTAAGATTG
2446408 CATATC
1 CATATC
2446414 CTCAAAAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.03
57 11 0.19
59 40 0.69
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:2446737 original size:44 final size:43
Alignment explanation
Indices: 2446675--2447180 Score: 329
Period size: 44 Copynumber: 11.7 Consensus size: 43
2446665 ACTAGATGCG
* * *
2446675 ATCTGCT-CTCTGTAACTTCAGAGAGATAAGATATAAGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAAGGTTTTA
* * * *
2446718 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-AGGTTTTA
**** *
2446762 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAAGGT-TTTA
* * *
2446807 GTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTT--GCTTACTTA
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTAAGGTT--TTA
* * * ***
2446851 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATT--TGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAAGGTTTTA
* *
2446892 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAAGGTTTTA
* * *
2446935 AT-TCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
1 ATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTA-AGGTTTTA
**** *
2446979 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAAGGT-TTTA
* * * * * *
2447024 GTTTGCCCCACTACAACTTTA-GGAGGATAAGACTT--GCTTACTTA
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTAAGGTT--TTA
* * * * ***
2447068 GTCTGCTCCACTGCAACTTCAGAGAGATAAGACT-A-GATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAAGGTTTTA
* *
2447109 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATATAAGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAAGGTTTTA
*
2447152 ATCCGCTCCACTGCAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
2447181 GGATCTACAA
Statistics
Matches: 363, Mismatches: 74, Indels: 51
0.74 0.15 0.10
Matches are distributed among these distances:
40 46 0.13
41 14 0.04
42 4 0.01
43 32 0.09
44 196 0.54
45 71 0.20
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAAGGTTTTA
Found at i:2446856 original size:89 final size:88
Alignment explanation
Indices: 2446763--2447101 Score: 290
Period size: 89 Copynumber: 3.9 Consensus size: 88
2446753 TCGGCTTTAA
2446763 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATCTTCAGTCTGCCCCACTGCAACTTCA
2446828 G-GAGGATAAGACTTGCTTACTTAG
65 GAGA-GATAAGACTTGCTTACTTAG
* * * *
2446852 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-A--TGC-GATCTG-CTCTCTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAG-TCTGCCCCACTGCAACTTCA
* * *
2446912 GAGAGATAAGATCTAAGGTT--TTAA
65 GAGAGATAAGA-CT-TGCTTACTTAG
* * ** * * *
2446936 T-TCGCTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTTTAATCTGCTCCACTGCAACTTC
1 TCT-GCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAGTCTGCCCCACTGCAACTTC
* *
2446999 AGGGAGATAAGACTTGC-CATCTTCAG
64 AGAGAGATAAGACTTGCTTA-CTT-AG
* * * * * *
2447025 TTTGCCCCACTACAACTTTA-GGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTC
1 TCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTCTGCCCCACTGCAACTTC
2447088 AGAGAGATAAGACT
64 AGAGAGATAAGACT
2447102 AGATGCGATC
Statistics
Matches: 201, Mismatches: 30, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
83 3 0.01
84 53 0.26
85 10 0.05
86 4 0.02
87 8 0.04
88 27 0.13
89 90 0.45
90 6 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (88 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAGTCTGCCCCACTGCAACTTCAG
AGAGATAAGACTTGCTTACTTAG
Found at i:2446959 original size:217 final size:217
Alignment explanation
Indices: 2446579--2447184 Score: 1041
Period size: 217 Copynumber: 2.8 Consensus size: 217
2446569 TAGGAATTAG
* * * * * * * *
2446579 TGCCTTCTTCAGTCTACCTCGCTGTAACTTCAGGAGGATAAGACTTGCTTATTTAGTATGCTTCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
* * *
2446644 CTGCAACTTCAAGGAAATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATAT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATAT
2446709 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
2446774 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
2446796 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
* * *
2446861 CTGCAACTTCAGGGAGATAAGATTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATAT
*
2446926 AAGGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
2446991 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
* * *
2447013 TGCCATCTTCAGTTTGCCCCACTACAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
*
2447078 CTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATAT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATAT
2447143 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
2447185 CTACAATCTT
Statistics
Matches: 366, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 366 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATAT
AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
GCAACTTCAGGGAGATAAGACT
Found at i:2447055 original size:173 final size:176
Alignment explanation
Indices: 2446722--2447180 Score: 469
Period size: 173 Copynumber: 2.6 Consensus size: 176
2446712 GTTTTAATCC
* * * *
2446722 GCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCTGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTA-AGGATTTAATCTGCTCCACTGCAACTTCAGGG
** ** * * * *
2446786 AGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTT
65 AGATAAGA-TTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTT
* * * *
2446850 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-ATGC-GA-TCT
128 AGTCTGCCCCACTACAACTTCAGGGAGATAAGACTTGCATACTGAGTCT
* *
2446896 GCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAAT-TCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTAAGGATTTAATCT-GCTCCACTGCAACTTCAGGG
*
2446959 AGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT-CTTC
65 AGATAAGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATACTT-
* * * *
2447023 AGTTTGCCCCACTACAACTTTA-GGAGGATAAGACTTGCTTACTTAGTCT
128 AGTCTGCCCCACTACAACTTCAGGGA-GATAAGACTTGCATACTGAGTCT
*** * *
2447072 GCTCCACTGCAACTTCAGAGAGATAAGA-CT-A-GATGCGATCTGCT-CTCTGCAACTTCAGAGA
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTAAGGATTTAATCTGCTCCACTGCAACTTCAGGGA
* * *
2447133 GATAAGA-TATAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
66 GATAAGATTAT-CGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
2447181 GGATCTACAA
Statistics
Matches: 240, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
172 47 0.20
173 145 0.60
174 14 0.06
175 3 0.01
176 8 0.03
177 23 0.10
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (176 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATCTAAGGATTTAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGT
CTGCCCCACTACAACTTCAGGGAGATAAGACTTGCATACTGAGTCT
Found at i:2448585 original size:14 final size:14
Alignment explanation
Indices: 2448562--2448608 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
2448552 TTTCTTTCAC
2448562 TTTTATTTTTTGTTT
1 TTTTA-TTTTTGTTT
2448577 TTTTATTTTTGTTT
1 TTTTATTTTTGTTT
*
2448591 TTGTT-TTTTCGTTT
1 TT-TTATTTTTGTTT
2448605 TTTT
1 TTTT
2448609 TAATCTGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 2 0.07
14 21 0.70
15 7 0.23
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTATTTTTGTTT
Found at i:2448605 original size:20 final size:20
Alignment explanation
Indices: 2448568--2448606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2448558 TCACTTTTAT
*
2448568 TTTTTGTTTTTTTATTTTTG
1 TTTTTGTTTTTTCATTTTTG
*
2448588 TTTTTGTTTTTTCGTTTTT
1 TTTTTGTTTTTTCATTTTT
2448607 TTTAATCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (20 bp):
TTTTTGTTTTTTCATTTTTG
Found at i:2454051 original size:3 final size:3
Alignment explanation
Indices: 2454043--2454082 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
2454033 ATATAGCTAA
2454043 AAT AAT AAT AATT ACAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T A-AT AAT AAT AAT AAT AAT AAT AAT AAT
2454083 TACATTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 28 0.82
4 3 0.09
5 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2454083 original size:28 final size:29
Alignment explanation
Indices: 2454026--2454087 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
2454016 GAAACAAGTA
*
2454026 TACATATATATAGCTAAAATAATAATAAT
1 TACATATATATAGATAAAATAATAATAAT
2454055 TACATATA-ATA-ATAATAATAATAATAAT
1 TACATATATATAGATAA-AATAATAATAAT
2454083 TACAT
1 TACAT
2454088 TAACAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 3 0.10
28 20 0.65
29 8 0.26
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (29 bp):
TACATATATATAGATAAAATAATAATAAT
Found at i:2454672 original size:19 final size:19
Alignment explanation
Indices: 2454648--2454739 Score: 150
Period size: 19 Copynumber: 4.8 Consensus size: 19
2454638 AAACATATAT
2454648 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
2454667 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
2454686 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2454705 TCT-AGAATTGCATATCATA
1 TCTAAG-ATTGCATATCATA
2454724 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2454740 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
18 2 0.03
19 63 0.94
20 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2456136 original size:30 final size:30
Alignment explanation
Indices: 2456102--2456245 Score: 141
Period size: 30 Copynumber: 4.8 Consensus size: 30
2456092 TTCCCCAATT
* * * *
2456102 GTCGGCTCTTTTGTGGCTTCTCCATGGACG
1 GTCGGCGCTTTTGCGGCTTCTGCATGGACA
2456132 GTCGGCGCTTTTGCGGCTT-TGGCATGGACA
1 GTCGGCGCTTTTGCGGCTTCT-GCATGGACA
** *
2456162 GTCGGAACTTCTGCGGCTT-TGCATGGACA
1 GTCGGCGCTTTTGCGGCTTCTGCATGGACA
* * *
2456191 ATCGACGTTTTTGCGGCTTCTGCATGGA-A
1 GTCGGCGCTTTTGCGGCTTCTGCATGGACA
* *
2456220 CGTCGGCGCTTCTGTGGCTTCTGCAT
1 -GTCGGCGCTTTTGCGGCTTCTGCAT
2456246 AAACCGTGGG
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
29 24 0.26
30 69 0.74
ACGTcount: A:0.11, C:0.25, G:0.31, T:0.33
Consensus pattern (30 bp):
GTCGGCGCTTTTGCGGCTTCTGCATGGACA
Found at i:2456205 original size:29 final size:29
Alignment explanation
Indices: 2456139--2456218 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
2456129 ACGGTCGGCG
*
2456139 CTTTTGCGGCTTTGGCATGGACAGTCGGAA
1 CTTTTGCGGCTTT-GCATGGACAATCGGAA
*
2456169 CTTCTGCGGCTTTGCATGGACAATC-G-A
1 CTTTTGCGGCTTTGCATGGACAATCGGAA
2456196 CGTTTTTGCGGCTTCTGCATGGA
1 C--TTTTGCGGCTT-TGCATGGA
2456219 ACGTCGGCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.05
28 1 0.02
29 21 0.48
30 20 0.45
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.33
Consensus pattern (29 bp):
CTTTTGCGGCTTTGCATGGACAATCGGAA
Found at i:2456269 original size:30 final size:30
Alignment explanation
Indices: 2456196--2456271 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2456186 GGACAATCGA
* *
2456196 CGTTTTTGCGGCTTCTGCATGGAACGTCGG
1 CGTTTTTGAGGCTTCTGCATGAAACGTCGG
* * * *
2456226 CGCTTCTGTGGCTTCTGCAT-AAACCGTGGG
1 CGTTTTTGAGGCTTCTGCATGAAA-CGTCGG
2456256 CGTTTTTGAGGCTTCT
1 CGTTTTTGAGGCTTCT
2456272 AGTTCTCCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.11, C:0.24, G:0.30, T:0.36
Consensus pattern (30 bp):
CGTTTTTGAGGCTTCTGCATGAAACGTCGG
Found at i:2457129 original size:105 final size:102
Alignment explanation
Indices: 2456944--2457217 Score: 266
Period size: 105 Copynumber: 2.6 Consensus size: 102
2456934 CTCTTTTTAT
*
2456944 TTTGTATAAAGTGGGTGCCGGCCATTGCCAGGCCACCCCTAATTTTTTTTTTACTTTTTTCTTAT
1 TTTGTATAAAG-GGGTGCC-GCCATTGCCAGGCCACCCC-AATTTTTTTTTTACTTTTTTCGTAT
**** * *
2457009 ACCGGTGTTGGCAATTGTCACACCAAAA-GTAAAAAAAAAA
63 ACCGGTGCAACCAATT-ACACAACAAAATGTAAAAAAAAAA
* *
2457049 TTTGTATAAAGGGGTTGCCTGCCATTGCCAGGCCACCCCAATTGTTTTTTTACTTTTTTCGTATG
1 TTTGTATAAAGGGG-TGCC-GCCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTTTTCGTATA
* * ***
2457114 CTGGTGCCAACCAATTACACAACAAAATTTTAAAAAAAGGT
64 CCGGTG-CAACCAATTACACAACAAAA-TGTAAAAAAAAAA
* ** *
2457155 TATTGTAGGATGGGGGTGTCGACCATTGCCAGGCCA--CCAATTTTTTTTTTACTTTTTTCGTAT
1 T-TTGTA-TAAAGGGGTGCCG-CCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTTTTCGTAT
2457218 TTTGGTGCTG
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
104 40 0.28
105 65 0.46
106 10 0.07
107 22 0.15
108 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (102 bp):
TTTGTATAAAGGGGTGCCGCCATTGCCAGGCCACCCCAATTTTTTTTTTACTTTTTTCGTATACC
GGTGCAACCAATTACACAACAAAATGTAAAAAAAAAA
Found at i:2459103 original size:30 final size:30
Alignment explanation
Indices: 2459031--2459161 Score: 120
Period size: 30 Copynumber: 4.4 Consensus size: 30
2459021 GCTCTTTTGT
*
2459031 GGCTTCTGCATGGACAGTCGGCACTTCTGC
1 GGCTTCTGCATGGACAGTCGCCACTTCTGC
2459061 GGCTT-TGGCATGGACAGTCGCCACTTCTGC
1 GGCTTCT-GCATGGACAGTCGCCACTTCTGC
* * * ** **
2459091 GGCTTCTCCATGGACAATCGACGTTTCTAT
1 GGCTTCTGCATGGACAGTCGCCACTTCTGC
* * * * *
2459121 GGCTTCTGCATGGTCCGTCGGCGCTTCTGT
1 GGCTTCTGCATGGACAGTCGCCACTTCTGC
*
2459151 GGCTTTTGCAT
1 GGCTTCTGCAT
2459162 AAACCGTGGG
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
29 1 0.01
30 81 0.98
31 1 0.01
ACGTcount: A:0.12, C:0.28, G:0.28, T:0.31
Consensus pattern (30 bp):
GGCTTCTGCATGGACAGTCGCCACTTCTGC
Found at i:2460160 original size:100 final size:100
Alignment explanation
Indices: 2459857--2460245 Score: 394
Period size: 102 Copynumber: 3.8 Consensus size: 100
2459847 TCTTTCTATT
* *
2459857 TTGTATAAAGTCGGTGCCGGCCATTGCCAGGCCACCCCTAA-CTTTTTTTACTTTTTTCGTATAC
1 TTGTATAAAG-GGGTGCCGGCCATTGCCAGGCCACCCC-AATTTTTTTTTACTTTTTTCGTATAC
**
2459921 TGGTGCCGGCAATTGTTACACCAAAAGTAAAAAAAATTTA
64 TGGTG-CGGCAATTGACACACCAAAAGTAAAAAAAA--TA
* * * ** *
2459961 TCGTATAAAGGGGGTGCCTGCTATTTTCAGGCCACCCCAAATTTTTTTTTACTTTTTTCTTATAC
1 TTGTATAAA-GGGGTGCCGGCCATTGCCAGGCCACCCC-AATTTTTTTTTACTTTTTTCGTATAC
* * *
2460026 TGGTGCTGGCCATTGACAGAGCAAAAGTAAAAAAAA-A
64 TGGTGC-GGCAATTGACACACCAAAAGTAAAAAAAATA
* *
2460063 TTGTATAAATGGGGTGCCGGCCATTGCCAGGCCACCCGAA-TTTTTTTTACTTTTTTCGTATGCT
1 TTGTATAAA-GGGGTGCCGGCCATTGCCAGGCCACCCCAATTTTTTTTTACTTTTTTCGTATACT
2460127 GGTGTCGGCTAATT-ACACACCAAAAGTAAAAAAAATTA
65 GGTG-CGGC-AATTGACACACCAAAAGTAAAAAAAA-TA
** * * * ** *
2460165 TTGTAGGAAGTGGGTGTCGACTATTGCCAAACCA--CCAATTTTTTTTTTACTTTTTTCGTATTC
1 TTGTATAAAG-GGGTGCCGGCCATTGCCAGGCCACCCCAA-TTTTTTTTTACTTTTTTCGTATAC
2460228 TGGTGCTGGCAATTGACA
64 TGGTGC-GGCAATTGACA
2460246 AATCCACATC
Statistics
Matches: 238, Mismatches: 35, Indels: 26
0.80 0.12 0.09
Matches are distributed among these distances:
100 51 0.21
101 12 0.05
102 91 0.38
104 33 0.14
105 51 0.21
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (100 bp):
TTGTATAAAGGGGTGCCGGCCATTGCCAGGCCACCCCAATTTTTTTTTACTTTTTTCGTATACTG
GTGCGGCAATTGACACACCAAAAGTAAAAAAAATA
Found at i:2460845 original size:109 final size:106
Alignment explanation
Indices: 2460760--2461056 Score: 324
Period size: 109 Copynumber: 2.7 Consensus size: 106
2460750 TTTTCGGGTG
*
2460760 TTATTCTGTCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAAATTTTGGGGGTGGCTTG
1 TTATTCTGTCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAAATTTT-GGGGTGGCCTG
*
2460825 GCAATGGCCGGCACCCCCTTTCTACAATAAAATATATGTTTTTTTACTT
65 GCAATGGCCGGCACCCCCTTTATAC----AAAT-T-T-TTTTTTTACTT
** * * * * *
2460874 TTGGTGTATCAATGGCCGGCACCAGCATACGAAAAAAATAAAAAAACAAAAATTTTTGGGTGGCC
1 TTATTCTGTCAATGGCCGGCACCAGAATACG-AAAAAAT-TAAAAA-AAAAATTTTGGGGTGGCC
* * * **
2460939 TAGCAATAGCCAGCACCCTTTTTATACAAATTTTTTTTTTACTT
63 TGGCAATGGCCGGCACCCCCTTTATACAAATTTTTTTTTTACTT
* ** * *
2460983 TTATTCTGTCAATAGCCGGCACCAGTGTACGAAAAAAGTAAAAAAAAAAATTTGGGGTGGCCTGG
1 TTATTCTGTCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAAATTTTGGGGTGGCCTGG
2461048 CAATGGCCG
66 CAATGGCCG
2461057 ACATCCTTTT
Statistics
Matches: 152, Mismatches: 28, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
106 25 0.16
107 5 0.03
108 6 0.04
109 35 0.23
110 1 0.01
111 1 0.01
112 4 0.03
114 26 0.17
115 7 0.05
116 33 0.22
117 9 0.06
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (106 bp):
TTATTCTGTCAATGGCCGGCACCAGAATACGAAAAAATTAAAAAAAAAATTTTGGGGTGGCCTGG
CAATGGCCGGCACCCCCTTTATACAAATTTTTTTTTTACTT
Found at i:2462438 original size:30 final size:30
Alignment explanation
Indices: 2462404--2462537 Score: 133
Period size: 30 Copynumber: 4.5 Consensus size: 30
2462394 ATTGTCGGCT
*
2462404 CTTCTGTGGCTTTTGCATGGACAGTCGACG
1 CTTCTGTGGCTTCTGCATGGACAGTCGACG
** * * *
2462434 CTTCTGCAGCTTCAGCATGGACAGTCGGCA
1 CTTCTGTGGCTTCTGCATGGACAGTCGACG
* *
2462464 CTTCTGTAGCTTCTGCATGGACAGTCGATG
1 CTTCTGTGGCTTCTGCATGGACAGTCGACG
* * * * * *
2462494 TTTCTGCGGCTTCTACATGGTCCGTCGGCG
1 CTTCTGTGGCTTCTGCATGGACAGTCGACG
*
2462524 CTTCTATGGCTTCT
1 CTTCTGTGGCTTCT
2462538 ACATAAACCG
Statistics
Matches: 82, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.13, C:0.27, G:0.27, T:0.33
Consensus pattern (30 bp):
CTTCTGTGGCTTCTGCATGGACAGTCGACG
Found at i:2462490 original size:60 final size:60
Alignment explanation
Indices: 2462397--2462537 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 60
2462387 TTTCTCAATT
* *
2462397 GTCGGCTCTTCTGTGGCTTTTGCATGGACAGTCGACGCTTCTGCAGCTTC-AGCATGGACA
1 GTCGGCACTTCTGTGGCTTCTGCATGGACAGTCGACGCTTCTGCAGCTTCTA-CATGGACA
* * * * * *
2462457 GTCGGCACTTCTGTAGCTTCTGCATGGACAGTCGATGTTTCTGCGGCTTCTACATGGTCC
1 GTCGGCACTTCTGTGGCTTCTGCATGGACAGTCGACGCTTCTGCAGCTTCTACATGGACA
* *
2462517 GTCGGCGCTTCTATGGCTTCT
1 GTCGGCACTTCTGTGGCTTCT
2462538 ACATAAACCG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
60 68 0.99
61 1 0.01
ACGTcount: A:0.13, C:0.27, G:0.28, T:0.33
Consensus pattern (60 bp):
GTCGGCACTTCTGTGGCTTCTGCATGGACAGTCGACGCTTCTGCAGCTTCTACATGGACA
Found at i:2471614 original size:21 final size:21
Alignment explanation
Indices: 2471563--2471614 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2471553 ACCATTGTTT
*
2471563 CTAATCTCACTGCTACAGTAT
1 CTAATCTCACTGCTACAGTAA
*
2471584 CCAATCTCACTGCTACAGTAA
1 CTAATCTCACTGCTACAGTAA
*
2471605 CTAATGTCAC
1 CTAATCTCAC
2471615 CGCCACCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (21 bp):
CTAATCTCACTGCTACAGTAA
Found at i:2473610 original size:21 final size:21
Alignment explanation
Indices: 2473559--2473610 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2473549 ACCATTGTTT
*
2473559 CTAATCTCACTGCTACAGTAT
1 CTAATCTCACTGCTACAGTAA
*
2473580 CCAATCTCACTGCTACAGTAA
1 CTAATCTCACTGCTACAGTAA
*
2473601 CTAATGTCAC
1 CTAATCTCAC
2473611 CGCCACCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (21 bp):
CTAATCTCACTGCTACAGTAA
Found at i:2482059 original size:44 final size:44
Alignment explanation
Indices: 2482004--2482093 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
2481994 ACCATTTTTA
*
2482004 GAAAGAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATGAAGTAT
1 GAAAAAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATGAAGTAT
2482048 GAAAAAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATGAAGTAT
1 GAAAAAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATGAAGTAT
2482092 GA
1 GA
2482094 CTGTTTTACC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (44 bp):
GAAAAAGCCGCTAAATCAAGTTCTCAGCTAGGTGAATGAAGTAT
Found at i:2490272 original size:31 final size:32
Alignment explanation
Indices: 2490213--2490277 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
2490203 GGCAAATTAC
2490213 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
2490245 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
2490276 AA
1 AA
2490278 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:2493412 original size:12 final size:11
Alignment explanation
Indices: 2493387--2493411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2493377 GTACCTTAAG
2493387 AAATTAAAAAA
1 AAATTAAAAAA
2493398 AAATTAAAAAA
1 AAATTAAAAAA
2493409 AAA
1 AAA
2493412 ACTCAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:2494643 original size:14 final size:14
Alignment explanation
Indices: 2494624--2494654 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2494614 AGGGATCAGG
2494624 ACCTCGTTCTATAA
1 ACCTCGTTCTATAA
2494638 ACCTCGTTCTATAA
1 ACCTCGTTCTATAA
2494652 ACC
1 ACC
2494655 GAGCCGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (14 bp):
ACCTCGTTCTATAA
Found at i:2500292 original size:17 final size:17
Alignment explanation
Indices: 2500257--2500292 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2500247 CCCGATTTAC
*
2500257 AAAATAATAAGAATAAA
1 AAAATAATAAAAATAAA
2500274 AAAATAATAAAAAATAAA
1 AAAATAAT-AAAAATAAA
2500292 A
1 A
2500293 GGGTTGCCCT
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:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAATAATAAAAATAAA
Found at i:2500705 original size:13 final size:13
Alignment explanation
Indices: 2500687--2500712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2500677 TATTTGTTCA
2500687 TTATTATTTTTTT
1 TTATTATTTTTTT
2500700 TTATTATTTTTTT
1 TTATTATTTTTTT
2500713 GAAACGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTATTATTTTTTT
Found at i:2522197 original size:9 final size:9
Alignment explanation
Indices: 2522183--2522233 Score: 77
Period size: 9 Copynumber: 5.7 Consensus size: 9
2522173 TTTGGTTAAA
2522183 AATTAACCG
1 AATTAACCG
2522192 AATTAACCG
1 AATTAACCG
*
2522201 AATTACCCG
1 AATTAACCG
2522210 AATTAACCG
1 AATTAACCG
2522219 AATT-ACCTG
1 AATTAACC-G
2522228 AATTAA
1 AATTAA
2522234 ATCACTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 3 0.08
9 34 0.89
10 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:2522937 original size:28 final size:28
Alignment explanation
Indices: 2522889--2522944 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2522879 AATTGTTATT
*
2522889 TAACTTGTTTATGATTTTGATAAAAAAA
1 TAACTTGTTTATGATTGTGATAAAAAAA
*
2522917 TAACTTGTTTATTATTGTGATAAAAAAA
1 TAACTTGTTTATGATTGTGATAAAAAAA
2522945 ACATTCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (28 bp):
TAACTTGTTTATGATTGTGATAAAAAAA
Found at i:2524829 original size:3 final size:3
Alignment explanation
Indices: 2524821--2524852 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2524811 ACTAGTTACC
2524821 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2524853 TGGGGCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2525839 original size:3 final size:3
Alignment explanation
Indices: 2525831--2525868 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2525821 AAAAGCCTCA
2525831 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2525869 AAGAACAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2527013 original size:90 final size:92
Alignment explanation
Indices: 2526895--2527148 Score: 228
Period size: 95 Copynumber: 2.7 Consensus size: 92
2526885 CTTCAAGGAG
* * *
2526895 ATAAGACTTGTAACTTCAATTTGCTCCACTGCAACTTT-A-AGTAG-A-TTTGTAACTTGTAGCT
1 ATAAGATTTGTAACTTCAATCTGCTCCACTGCAA-TTTCAGAG-AGAAGTTTATAACTTGTAGCT
* *
2526956 TTAACCTGTTCCACTACAACTTTAGGAAA
64 TTAACCTATTCCACTACAACTTCAGGAAA
* *
2526985 ATAAGATTTGTAGCTTTAATCTGCTCCACTGCAATTTCAGGGAGAGAAAGTTTATAACTTGTAGC
1 ATAAGATTTGTAACTTCAATCTGCTCCACTGCAATTTCA--GAGAG-AAGTTTATAACTTGTAGC
* *
2527050 TTTAATCTATTCCACTACAACTTCAGGGAA
63 TTTAACCTATTCCACTACAACTTCAGGAAA
* ** * * * * * * *
2527080 ATATGATTCACTATCTTCAATCTGATCCAGTGCAACTTCAGGGAGATAAGATTTGTATCTTGTAG
1 ATAAGATT-TGTAACTTCAATCTGCTCCACTGCAATTTCA--GAGAGAAG-TTTATAACTTGTAG
2527145 CTTT
62 CTTT
2527149 GTATTTTGTC
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
89 3 0.02
90 31 0.23
92 2 0.01
93 2 0.01
94 1 0.01
95 50 0.37
96 46 0.34
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (92 bp):
ATAAGATTTGTAACTTCAATCTGCTCCACTGCAATTTCAGAGAGAAGTTTATAACTTGTAGCTTT
AACCTATTCCACTACAACTTCAGGAAA
Found at i:2527146 original size:96 final size:95
Alignment explanation
Indices: 2526937--2527148 Score: 264
Period size: 95 Copynumber: 2.2 Consensus size: 95
2526927 AACTTTAAGT
* * ** *
2526937 AGATTTGTAACTTGTAGCTTTAACCTGTTCCACTACAACTTTAGGAAAATAAGATTTGTAGCTTT
1 AGATTTGTAACTTGTAGCTTTAACCTATTCCACTACAACTTCAGGAAAATAAGATTACTAGCTTC
* *
2527002 AATCTGCTCCACTGCAATTTCAGGGAGAGA
66 AATCTGATCCACTGCAACTTCAGGGAGAGA
* * * * *
2527032 A-AGTTTATAACTTGTAGCTTTAATCTATTCCACTACAACTTCAGGGAAATATGATTCACTATCT
1 AGA-TTTGTAACTTGTAGCTTTAACCTATTCCACTACAACTTCAGGAAAATAAGATT-ACTAGCT
* *
2527096 TCAATCTGATCCAGTGCAACTTCAGGGAGATA
64 TCAATCTGATCCACTGCAACTTCAGGGAGAGA
*
2527128 AGATTTGTATCTTGTAGCTTT
1 AGATTTGTAACTTGTAGCTTT
2527149 GTATTTTGTC
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
94 1 0.01
95 48 0.49
96 48 0.49
97 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (95 bp):
AGATTTGTAACTTGTAGCTTTAACCTATTCCACTACAACTTCAGGAAAATAAGATTACTAGCTTC
AATCTGATCCACTGCAACTTCAGGGAGAGA
Found at i:2540423 original size:27 final size:27
Alignment explanation
Indices: 2540393--2540454 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
2540383 TATAAGCGAA
2540393 TAATATTATCAATAATAACAACAA-TAG
1 TAATATTATCAATAATAACAA-AAGTAG
* * *
2540420 TAATAATATTAATAATAATAAAAGTAG
1 TAATATTATCAATAATAACAAAAGTAG
2540447 TAATATTA
1 TAATATTA
2540455 ATAGTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (27 bp):
TAATATTATCAATAATAACAAAAGTAG
Found at i:2540432 original size:24 final size:24
Alignment explanation
Indices: 2540405--2540457 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2540395 ATATTATCAA
*
2540405 TAATAACAACAATAGTAATAATAT
1 TAATAACAACAAAAGTAATAATAT
* * *
2540429 TAATAATAATAAAAGTAGTAATAT
1 TAATAACAACAAAAGTAATAATAT
2540453 TAATA
1 TAATA
2540458 GTGATAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
TAATAACAACAAAAGTAATAATAT
Found at i:2541863 original size:21 final size:21
Alignment explanation
Indices: 2541839--2541903 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2541829 AACAGAAACC
2541839 CATAAGGGTTGAATGGAAGCT
1 CATAAGGGTTGAATGGAAGCT
* * * *
2541860 CATAAGAGCTGAATGGAAACC
1 CATAAGGGTTGAATGGAAGCT
*
2541881 CATAAGGGTTAAACT-GAAGCT
1 CATAAGGGTTGAA-TGGAAGCT
2541902 CA
1 CA
2541904 AAAGAGCTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.20
Consensus pattern (21 bp):
CATAAGGGTTGAATGGAAGCT
Found at i:2541865 original size:42 final size:41
Alignment explanation
Indices: 2541813--2541936 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 41
2541803 TGATGTACAA
* * *
2541813 AAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAA-TGG
1 AAGCTCATAAGAGCTAAAC-GAAACCCATAAGGGTTAAACT-G
**
2541855 AAGCTCATAAGAGCTGAATGGAAACCCATAAGGGTTAAACTG
1 AAGCTCATAAGAGCT-AAACGAAACCCATAAGGGTTAAACTG
* *
2541897 AAGCTCAAAAGAGCTAAACGAAAACTCATTAA-GGTTAAAC
1 AAGCTCATAAGAGCTAAACG-AAACCCA-TAAGGGTTAAAC
2541937 AAAAACTCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
41 3 0.04
42 60 0.87
43 6 0.09
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (41 bp):
AAGCTCATAAGAGCTAAACGAAACCCATAAGGGTTAAACTG
Found at i:2546277 original size:41 final size:41
Alignment explanation
Indices: 2546231--2546434 Score: 236
Period size: 41 Copynumber: 5.0 Consensus size: 41
2546221 TATTGGAATG
* *
2546231 ATACACCGGC-ATGAAGCCTGCTAGGC-CTAAAGCCTGATTTG
1 ATACACCGGCAAT-AAGCCTGCTAGGCAC-AAAGCCTGAATTA
* * * * *
2546272 GTACACCGGC-ATGAAGCCTGCTAGACATAAAGTCTGAAATA
1 ATACACCGGCAAT-AAGCCTGCTAGGCACAAAGCCTGAATTA
2546313 ACT-CACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTA
1 A-TACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTA
*
2546354 ATTCACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTA
1 ATACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTA
* * * *
2546395 ATTCACCGGCAATAAGCCTACTAGGCACAAGGCTTGAATT
1 ATACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATT
2546435 TCACTGATAC
Statistics
Matches: 144, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.01
41 140 0.97
42 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (41 bp):
ATACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATTA
Found at i:2552815 original size:114 final size:112
Alignment explanation
Indices: 2552616--2552943 Score: 392
Period size: 114 Copynumber: 2.9 Consensus size: 112
2552606 TAGCGGCGTT
* * * * * *
2552616 TTTAGCGGCATTTTCAGGAAAGCGCCGC-AAAAAACCGAAGCTCAACGACATCGTTTTCTTAGTT
1 TTTAGCGGCGTTTT-AGGAAAGCGCCGCAAAAAAAACTAAGCACAACGGCGTCGTTTTCTTAGTT
* *
2552680 TTCGGGGATTTAGCGACATTTTTTAGAAAGCGCCGCTAATTCTCAGGTC
65 TTCGGGGATTTAGCG-CATTTTTTAGAAAGCGCCGCTAATGCTCAGGGC
* * *
2552729 TTTAGCGGCGTTTCTAGAAAAGCACCGCAAAAAAAACTAAGCACAACGGCGTCGTTTTCTTAGCT
1 TTTAGCGGCGTTT-TAGGAAAGCGCCGCAAAAAAAACTAAGCACAACGGCGTCGTTTTCTTAGTT
*
2552794 TTCGGGGATTTAGCAGCA-TTTTTAGGAAAGCGTCGCTAATGCTCAGGGC
65 TTCGGGGATTTAGC-GCATTTTTTA-GAAAGCGCCGCTAATGCTCAGGGC
* * * * *
2552843 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGTGCCGTTTT-TTGAGT
1 TTTAGCGGCG-TTTTAGGAAAGCGCCGCAAAAAAAACTAAGCACAACGGCGTCGTTTTCTT-AGT
* *
2552907 TTTCGGGGATTTAGTGGCGTTTTTTAGAAAGCGCCGC
64 TTTCGGGGATTTAG-CGCATTTTTTAGAAAGCGCCGC
2552944 AAAAAAAATA
Statistics
Matches: 184, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
113 31 0.17
114 143 0.78
115 10 0.05
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (112 bp):
TTTAGCGGCGTTTTAGGAAAGCGCCGCAAAAAAAACTAAGCACAACGGCGTCGTTTTCTTAGTTT
TCGGGGATTTAGCGCATTTTTTAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:2552964 original size:73 final size:73
Alignment explanation
Indices: 2552843--2553016 Score: 260
Period size: 73 Copynumber: 2.4 Consensus size: 73
2552833 TGCTCAGGGC
* ** * *
2552843 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGTGCCGTTTTTTGAGTT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAAACTAAACCCAACGGCGCCGTTTTTTGAGTT
2552908 TTCGGGGA
66 TTCGGGGA
* * *
2552916 TTTAGTGGCGTTTTTTAGAAAGCGCCGCAAAAAAAA-TAAACCCAAACGGCGCTGTTTTTTGAGT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAAACTAAACCC-AACGGCGCCGTTTTTTGAGT
2552980 TTTCGGGGA
65 TTTCGGGGA
2552989 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
2553017 TAATGCTCAG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 6 0.07
73 85 0.93
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAAACTAAACCCAACGGCGCCGTTTTTTGAGTT
TTCGGGGA
Found at i:2553315 original size:17 final size:16
Alignment explanation
Indices: 2553290--2553337 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
2553280 AGTGTTATGC
2553290 TTTAGGGGTTAGGGGAA
1 TTTAGGGGTTAGGGG-A
* *
2553307 TTTATGGGTTAGAGGA
1 TTTAGGGGTTAGGGGA
2553323 TTTAGGGGTTAGGGG
1 TTTAGGGGTTAGGGG
2553338 TTAGGGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (16 bp):
TTTAGGGGTTAGGGGA
Found at i:2553348 original size:22 final size:23
Alignment explanation
Indices: 2553312--2553358 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
2553302 GGGAATTTAT
2553312 GGGTTAGAGGATTTAGGGGTTAG
1 GGGTTAGAGGATTTAGGGGTTAG
*
2553335 GGGTTAG-GGATTTAGGGTTTAG
1 GGGTTAGAGGATTTAGGGGTTAG
2553357 GG
1 GG
2553359 TTTCAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.32
Consensus pattern (23 bp):
GGGTTAGAGGATTTAGGGGTTAG
Found at i:2553359 original size:7 final size:7
Alignment explanation
Indices: 2553323--2553361 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
2553313 GGTTAGAGGA
2553323 TTTAGGG
1 TTTAGGG
*
2553330 GTTAGGG
1 TTTAGGG
*
2553337 GTTAGGG
1 TTTAGGG
2553344 ATTTAGGG
1 -TTTAGGG
2553352 TTTAGGG
1 TTTAGGG
2553359 TTT
1 TTT
2553362 CAACAGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:2556965 original size:194 final size:193
Alignment explanation
Indices: 2556632--2557077 Score: 633
Period size: 194 Copynumber: 2.3 Consensus size: 193
2556622 GAAATATTGT
* ** * *
2556632 TGTATATTGC-TTTGAGTTTTTCAAAAATCGAAGAGAAATGTCTTTGAAAAACGGGAATACAGGT
1 TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACAT-TTTTAAGAACGGGAATACAGGT
* * * * * * *
2556696 TTTGTTTAACTGTCTGAATTGCTTCTCGACAAAACCCAGTTTACAACATTTCTGACGTTATAAAA
65 GTTGTTTAACTGTCCGAATTGCTTCTCAACAAAACCCAGTTTACAACATATCCGAAGCTATAAAA
2556761 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
130 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
* * *
2556825 TGTATATTGCTTTTGAGTTTTACAAAAGTCGAAGAGAAACATTTTTAAGAATGGGAATTCAGGTG
1 TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACATTTTTAAGAACGGGAATACAGGTG
* * ** *
2556890 TTGTTTAACTGTCCGAATTTCTTCTCAACAAAACCCCATTTTATGACATATCCGAAGCTATGAAA
66 TTGTTTAACTGTCCGAATTGCTTCTCAACAAAA-CCCAGTTTACAACATATCCGAAGCTATAAAA
2556955 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
130 TCTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
* * * * *
2557019 TATATATTGCTTTTGAGTTTTTCAAGAGTCGAAGAAAAACGACTTTTAAGAACAGGAAT
1 TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAAC-ATTTTTAAGAACGGGAAT
2557078 CTGTTTGTCG
Statistics
Matches: 223, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
193 58 0.26
194 150 0.67
195 15 0.07
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (193 bp):
TGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACATTTTTAAGAACGGGAATACAGGTG
TTGTTTAACTGTCCGAATTGCTTCTCAACAAAACCCAGTTTACAACATATCCGAAGCTATAAAAT
CTTGATTCCTTAACGATTCTGCTGAATTTGTGTTTATGATTGTCGATATATGCTGTTTGTTGC
Found at i:2558722 original size:43 final size:43
Alignment explanation
Indices: 2558579--2558707 Score: 129
Period size: 43 Copynumber: 3.1 Consensus size: 43
2558569 TATTTTTAAA
* * ** * *
2558579 AAAAGTAAT-ATTTTTAGCGGCGTTTGT-CAAAAAGCGCCGCT
1 AAAAGTCATGATTTTTAGTGGCGTTTGTGGTAGAAGCGCTGCT
* ** * *
2558620 AAAAGTCCT-ATTCATAGTGGCGTTTGTGGTAGCAGTGCTGCT
1 AAAAGTCATGATTTTTAGTGGCGTTTGTGGTAGAAGCGCTGCT
*
2558662 AAAAGTCATGATTTTTAGTGGCGTTTGTGTTAGAAGCGCTGCT
1 AAAAGTCATGATTTTTAGTGGCGTTTGTGGTAGAAGCGCTGCT
2558705 AAA
1 AAA
2558708 GGTCTTGTTC
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
41 22 0.32
42 16 0.23
43 31 0.45
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
AAAAGTCATGATTTTTAGTGGCGTTTGTGGTAGAAGCGCTGCT
Found at i:2561111 original size:21 final size:21
Alignment explanation
Indices: 2561087--2561195 Score: 69
Period size: 21 Copynumber: 5.2 Consensus size: 21
2561077 CGGGTCGTTG
*
2561087 CAGAAACCCATAGGGGTTGAA
1 CAGAAACCCATAGGGGTTAAA
* * * * *
2561108 CAGAAGCTCATAGGAGCTGAA
1 CAGAAACCCATAGGGGTTAAA
* * *
2561129 CGGAAATCCATAAGGGTTAAA
1 CAGAAACCCATAGGGGTTAAA
* *
2561150 CGGAAACCCATTA-AGGTTAAA
1 CAGAAACCCA-TAGGGGTTAAA
* * *
2561171 CAGAAACTCATATGAGTT-AA
1 CAGAAACCCATAGGGGTTAAA
2561191 CAGAA
1 CAGAA
2561196 GTTCGTGAGA
Statistics
Matches: 68, Mismatches: 18, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
20 9 0.13
21 57 0.84
22 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
CAGAAACCCATAGGGGTTAAA
Found at i:2566450 original size:30 final size:30
Alignment explanation
Indices: 2566416--2566478 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2566406 ACTTAACAAG
*
2566416 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
2566446 CAAATACTTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
2566476 CAA
1 CAA
2566479 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:2573685 original size:6 final size:6
Alignment explanation
Indices: 2573674--2573700 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2573664 ACATTACATC
2573674 TATTTA TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TAT
2573701 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:2579721 original size:16 final size:16
Alignment explanation
Indices: 2579700--2579733 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2579690 TCAAAACATA
2579700 AACTTACTAATAATTT
1 AACTTACTAATAATTT
2579716 AACTTACTAATAATTT
1 AACTTACTAATAATTT
2579732 AA
1 AA
2579734 TAAACTCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
AACTTACTAATAATTT
Found at i:2580692 original size:58 final size:58
Alignment explanation
Indices: 2580602--2580718 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
2580592 ATGGAGAAAG
2580602 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
1 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
2580660 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
1 TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
2580718 T
1 T
2580719 TCCTCCATAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (58 bp):
TATGTCAATTATTCTTTTGAGGTCAAACAGTTCCCTCTAAAGAGCCTTCATTAGCTCT
Found at i:2585012 original size:10 final size:10
Alignment explanation
Indices: 2585010--2585068 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
2585000 CAACCAAACA
*
2585010 CAAACACAAAC
1 CAAACCCAA-C
2585021 CAAACCCAAC
1 CAAACCCAAC
*
2585031 CCAACCCAAC
1 CAAACCCAAC
*
2585041 CCAACCCAAC
1 CAAACCCAAC
*
2585051 CCAACCCAAC
1 CAAACCCAAC
*
2585061 CCAACCCA
1 CAAACCCA
2585069 GTGACGGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
10 38 0.83
11 8 0.17
ACGTcount: A:0.46, C:0.54, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAACCCAAC
Found at i:2585026 original size:5 final size:5
Alignment explanation
Indices: 2585018--2585068 Score: 93
Period size: 5 Copynumber: 10.2 Consensus size: 5
2585008 CACAAACACA
*
2585018 AACCA AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC
1 AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC AACCC
2585068 A
1 A
2585069 GTGACGGGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.43, C:0.57, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCC
Found at i:2585746 original size:19 final size:19
Alignment explanation
Indices: 2585722--2585760 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2585712 CGGATAGCTT
2585722 TAACTTTGGAGAGATTTTA
1 TAACTTTGGAGAGATTTTA
*
2585741 TAACTTTGGGGAGATTTTA
1 TAACTTTGGAGAGATTTTA
2585760 T
1 T
2585761 TACCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (19 bp):
TAACTTTGGAGAGATTTTA
Found at i:2594248 original size:24 final size:23
Alignment explanation
Indices: 2594203--2594250 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2594193 ATTTTTAATT
*
2594203 AATAAAATAATTAAATAAATAAA
1 AATAAAATAATTAAACAAATAAA
* *
2594226 AATAAAAGTAATTGAACATATAAA
1 AATAAAA-TAATTAAACAAATAAA
2594250 A
1 A
2594251 TACAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (23 bp):
AATAAAATAATTAAACAAATAAA
Found at i:2595855 original size:28 final size:28
Alignment explanation
Indices: 2595801--2595857 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2595791 TAATTTGACA
* * * *
2595801 TTCTTTTTCTAATGTGATACTTGTATTT
1 TTCTTTGTCTAATATGATACCTATATTT
*
2595829 TTCTTTGTCTAATATGGTACCTATATTT
1 TTCTTTGTCTAATATGATACCTATATTT
2595857 T
1 T
2595858 ACAAAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (28 bp):
TTCTTTGTCTAATATGATACCTATATTT
Found at i:2596055 original size:21 final size:22
Alignment explanation
Indices: 2596029--2596073 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2596019 ATTTTGTTTG
2596029 ATAAATT-A-AATGCAAAACTAA
1 ATAAATTCACAAT-CAAAACTAA
2596050 ATAAATTCACAATCAAAACTAA
1 ATAAATTCACAATCAAAACTAA
2596072 AT
1 AT
2596074 TTATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 12 0.55
23 3 0.14
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAATTCACAATCAAAACTAA
Found at i:2604222 original size:8 final size:8
Alignment explanation
Indices: 2604211--2604278 Score: 56
Period size: 8 Copynumber: 9.0 Consensus size: 8
2604201 TGGTAACTCT
2604211 TAAAATTA
1 TAAAATTA
2604219 TAAAATT-
1 TAAAATTA
2604226 T--AATT-
1 TAAAATTA
* *
2604231 TAATATTT
1 TAAAATTA
2604239 TAAAATTA
1 TAAAATTA
*
2604247 TAAAAATA
1 TAAAATTA
2604255 T-AAATTA
1 TAAAATTA
*
2604262 TTAAAATAA
1 -TAAAATTA
2604271 TAAAATTA
1 TAAAATTA
2604279 CATTTTGAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
5 5 0.10
7 9 0.19
8 29 0.60
9 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAAATTA
Found at i:2604273 original size:16 final size:15
Alignment explanation
Indices: 2604241--2604274 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2604231 TAATATTTTA
2604241 AAATTATAAAAATAT
1 AAATTATAAAAATAT
*
2604256 AAATTATTAAAATAAT
1 AAATTATAAAAAT-AT
2604272 AAA
1 AAA
2604275 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTATAAAAATAT
Found at i:2604291 original size:16 final size:16
Alignment explanation
Indices: 2604272--2604302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2604262 TTAAAATAAT
2604272 AAAATTACATTTTGAG
1 AAAATTACATTTTGAG
*
2604288 AAAATTATATTTTGA
1 AAAATTACATTTTGA
2604303 CAATATTTTA
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:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (16 bp):
AAAATTACATTTTGAG
Found at i:2609922 original size:6 final size:6
Alignment explanation
Indices: 2609870--2609921 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
2609860 AATATAATAT
* *
2609870 ATATAG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATAG
1 ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG ATATCG
2609918 ATAT
1 ATAT
2609922 ATGTTATGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATCG
Found at i:2616010 original size:18 final size:18
Alignment explanation
Indices: 2615966--2616012 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2615956 TAAAAAATTG
*
2615966 TATTTAATTATAAATATAA
1 TATTTAA-TATAAATAAAA
*
2615985 T-TAATAATATAAATAAAA
1 TAT-TTAATATAAATAAAA
2616003 TATTTAATAT
1 TATTTAATAT
2616013 CGGAAACAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTTAATATAAATAAAA
Found at i:2616226 original size:18 final size:18
Alignment explanation
Indices: 2616182--2616228 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2616172 TAAAAAATTG
*
2616182 TATTTAATTATAAATATAA
1 TATTTAA-TATAAATAAAA
*
2616201 T-TAATAATATAAATAAAA
1 TAT-TTAATATAAATAAAA
2616219 TATTTAATAT
1 TATTTAATAT
2616229 CGGAAACAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTTAATATAAATAAAA
Found at i:2616290 original size:216 final size:216
Alignment explanation
Indices: 2615916--2616347 Score: 855
Period size: 216 Copynumber: 2.0 Consensus size: 216
2615906 AAAATTTTTA
2615916 TCAAATTAACTCAATTCAATTTAAATTATTGTTCATTTAATAAAAAATTGTATTTAATTATAAAT
1 TCAAATTAACTCAATTCAATTTAAATTATTGTTCATTTAATAAAAAATTGTATTTAATTATAAAT
2615981 ATAATTAATAATATAAATAAAATATTTAATATCGGAAACAGATTTAAGAGTTAACTTGAGTCGAG
66 ATAATTAATAATATAAATAAAATATTTAATATCGGAAACAGATTTAAGAGTTAACTTGAGTCGAG
2616046 TTTAGAAAGAAAAAAAGAAGAAGCTTCTTATTGGTACTCAAGGACAAATTTAGTTGTGTGTAGAG
131 TTTAGAAAGAAAAAAAGAAGAAGCTTCTTATTGGTACTCAAGGACAAATTTAGTTGTGTGTAGAG
*
2616111 CCTACAATGGAGATGATTAAG
196 CCTACAATGAAGATGATTAAG
2616132 TCAAATTAACTCAATTCAATTTAAATTATTGTTCATTTAATAAAAAATTGTATTTAATTATAAAT
1 TCAAATTAACTCAATTCAATTTAAATTATTGTTCATTTAATAAAAAATTGTATTTAATTATAAAT
2616197 ATAATTAATAATATAAATAAAATATTTAATATCGGAAACAGATTTAAGAGTTAACTTGAGTCGAG
66 ATAATTAATAATATAAATAAAATATTTAATATCGGAAACAGATTTAAGAGTTAACTTGAGTCGAG
2616262 TTTAGAAAGAAAAAAAGAAGAAGCTTCTTATTGGTACTCAAGGACAAATTTAGTTGTGTGTAGAG
131 TTTAGAAAGAAAAAAAGAAGAAGCTTCTTATTGGTACTCAAGGACAAATTTAGTTGTGTGTAGAG
2616327 CCTACAATGAAGATGATTAAG
196 CCTACAATGAAGATGATTAAG
2616348 GAATGAAAAT
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 215 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (216 bp):
TCAAATTAACTCAATTCAATTTAAATTATTGTTCATTTAATAAAAAATTGTATTTAATTATAAAT
ATAATTAATAATATAAATAAAATATTTAATATCGGAAACAGATTTAAGAGTTAACTTGAGTCGAG
TTTAGAAAGAAAAAAAGAAGAAGCTTCTTATTGGTACTCAAGGACAAATTTAGTTGTGTGTAGAG
CCTACAATGAAGATGATTAAG
Found at i:2619854 original size:17 final size:17
Alignment explanation
Indices: 2619832--2619865 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2619822 AAAATATTAT
2619832 TTAAATTCA-TTTCTCAA
1 TTAAATT-ATTTTCTCAA
2619849 TTAAATTATTTTCTCAA
1 TTAAATTATTTTCTCAA
2619866 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTATTTTCTCAA
Found at i:2625174 original size:9 final size:9
Alignment explanation
Indices: 2625160--2625219 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
2625150 AAAGTATTTT
*
2625160 AAAATTAAA
1 AAAATTTAA
2625169 AAAATTTAA
1 AAAATTTAA
*
2625178 AAAGTATTTTA
1 AAA--ATTTAA
*
2625189 AAAATTTTA
1 AAAATTTAA
2625198 AAAATTTAA
1 AAAATTTAA
2625207 AAAATTTAA
1 AAAATTTAA
2625216 AAAA
1 AAAA
2625220 AGTATTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
9 38 0.83
11 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTTAA
Found at i:2625192 original size:40 final size:41
Alignment explanation
Indices: 2625143--2625252 Score: 156
Period size: 40 Copynumber: 2.8 Consensus size: 41
2625133 TAAAACAAAA
*
2625143 ATTTAAAAAAGTATTTTAAAATTAAAAAAATTT-AAAAAGT
1 ATTTTAAAAAGTATTTTAAAATTAAAAAAATTTAAAAAAGT
* *
2625183 ATTTTAAAAA-T-TTTAAAAATTTAAAAAATTTAAAAAAAGT
1 ATTTTAAAAAGTATTTTAAAATTAAAAAAATTT-AAAAAAGT
2625223 ATTTT-AAAAGTATTTTAAAATTAAAAAAAT
1 ATTTTAAAAAGTATTTTAAAATTAAAAAAAT
2625253 AAAAAATAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
38 18 0.30
39 5 0.08
40 22 0.36
41 16 0.26
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (41 bp):
ATTTTAAAAAGTATTTTAAAATTAAAAAAATTTAAAAAAGT
Found at i:2625231 original size:11 final size:11
Alignment explanation
Indices: 2625217--2625242 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2625207 AAAATTTAAA
2625217 AAAAGTATTTT
1 AAAAGTATTTT
2625228 AAAAGTATTTT
1 AAAAGTATTTT
2625239 AAAA
1 AAAA
2625243 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:2626526 original size:75 final size:76
Alignment explanation
Indices: 2626436--2626588 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 76
2626426 TACATAGCAT
* *
2626436 ACCTAAGCTAGTCATTGATTTAAC-TTTTTTCCATTTTAGTTTTATGATATTTGTTATACATAAT
1 ACCTAAGCTACTCATTGATTTAACTTTTTTTCCATTTTAGTTTTATGATATTTGTTAGACATAAT
2626500 AACTCTTTTTA
66 AACTCTTTTTA
*
2626511 ACCTAAGCTACTCATTGATTTAACTTTTTTTTCCATTTTAGTTTTATGATATTTGTTAGGCATAA
1 ACCTAAGCTACTCATTGATTTAAC-TTTTTTTCCATTTTAGTTTTATGATATTTGTTAGACATAA
2626576 TAACTCTTTTTA
65 TAACTCTTTTTA
2626588 A
1 A
2626589 ATATTTAATA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
75 23 0.32
77 50 0.68
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.50
Consensus pattern (76 bp):
ACCTAAGCTACTCATTGATTTAACTTTTTTTCCATTTTAGTTTTATGATATTTGTTAGACATAAT
AACTCTTTTTA
Found at i:2628835 original size:20 final size:20
Alignment explanation
Indices: 2628810--2628847 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2628800 TTGAATCTGA
2628810 ATAACTGTG-TGTACATTTTG
1 ATAACTGTGAT-TACATTTTG
2628830 ATAACTGTGATTACATTT
1 ATAACTGTGATTACATTT
2628848 GTATTGGGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
ATAACTGTGATTACATTTTG
Found at i:2630081 original size:20 final size:20
Alignment explanation
Indices: 2630056--2630093 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2630046 TTGTACTTTT
*
2630056 TTTTTTGGTTTTAGTTGTTG
1 TTTTTTGATTTTAGTTGTTG
*
2630076 TTTTTTTATTTTAGTTGT
1 TTTTTTGATTTTAGTTGT
2630094 AAGACTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.18, T:0.74
Consensus pattern (20 bp):
TTTTTTGATTTTAGTTGTTG
Found at i:2632704 original size:17 final size:17
Alignment explanation
Indices: 2632678--2632720 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2632668 TTTTTTTTTG
2632678 TTTTTATAAAAAAATAA
1 TTTTTATAAAAAAATAA
*
2632695 TTTTTTTAAAAAAATATA
1 TTTTTATAAAAAAATA-A
*
2632713 TATTTATA
1 TTTTTATA
2632721 CGAGTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTATAAAAAAATAA
Found at i:2633031 original size:9 final size:9
Alignment explanation
Indices: 2633001--2633025 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2632991 GAAAGAAAGG
2633001 AGAAGAATA
1 AGAAGAATA
2633010 AGAAGAATA
1 AGAAGAATA
2633019 AGAAGAA
1 AGAAGAA
2633026 AGAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (9 bp):
AGAAGAATA
Found at i:2633313 original size:12 final size:12
Alignment explanation
Indices: 2633296--2633329 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2633286 ATTAATGTAA
2633296 AATTATTTTGTT
1 AATTATTTTGTT
2633308 AATTATTTTGTT
1 AATTATTTTGTT
*
2633320 -AGTATTTTGT
1 AATTATTTTGT
2633330 GTTTTGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (12 bp):
AATTATTTTGTT
Found at i:2633538 original size:101 final size:98
Alignment explanation
Indices: 2633373--2633563 Score: 319
Period size: 101 Copynumber: 1.9 Consensus size: 98
2633363 TATATATATT
*
2633373 TTTATAGTTATTTTTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTAGTTTAGGGTTTT
1 TTTATAGTTATTTTTTAGTAATTTATGATTAGTTTACAAATTGTTAGTGTTTAGTTTAGGGTTTT
2633438 GTGATTTTTTAGTAATGTAATTTTTTCAAAAAA
66 GTGATTTTTTAGTAATGTAATTTTTTCAAAAAA
*
2633471 TTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTTAGTGT
1 TTTATAGTTATTTT-TTAGTAATTTATGATTA-GTT-TACAAATTGTTAGTGTTTAGTTTAGGGT
* *
2633536 TTTGTGATTTTTTATTAATTTAATTTTT
63 TTTGTGATTTTTTAGTAATGTAATTTTT
2633564 ATTTATTTTA
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
98 14 0.16
99 17 0.20
100 3 0.03
101 52 0.60
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (98 bp):
TTTATAGTTATTTTTTAGTAATTTATGATTAGTTTACAAATTGTTAGTGTTTAGTTTAGGGTTTT
GTGATTTTTTAGTAATGTAATTTTTTCAAAAAA
Found at i:2635965 original size:75 final size:76
Alignment explanation
Indices: 2635871--2636152 Score: 387
Period size: 75 Copynumber: 3.7 Consensus size: 76
2635861 CTTTTTTGCC
* *
2635871 ATTTTAGTTTTTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAA-TCTTGTATTTATGTAAT
1 ATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACT-TTGTATTTATGTAAT
2635935 GA-TTTTTCACT
65 GACTTTTTCACT
* * * *
2635946 AATTCAGTAATTAATTTTAGGGTTTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTAGGTAAT
1 ATTTCAGTTATTAATTTTAGGG-GTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAAT
2636011 GACTTTTTCAGC-
65 GACTTTTTCA-CT
2636023 ATTTCAGTTATTAATTTTA-GGGTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAATG
1 ATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAATG
*
2636087 ACTTTTTC-GT
66 ACTTTTTCACT
* * * *
2636097 CATTTCAGTTATTAATTTTTGGGG-TTTTTTGTAATTTAAATAATAAACTTTGTATT
1 -ATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACTTTGTATT
2636153 ATTTACGTAA
Statistics
Matches: 185, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
75 114 0.62
76 45 0.24
77 25 0.14
78 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.52
Consensus pattern (76 bp):
ATTTCAGTTATTAATTTTAGGGGTTTTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAATG
ACTTTTTCACT
Found at i:2639308 original size:18 final size:18
Alignment explanation
Indices: 2639263--2639315 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
2639253 AACTAAAATA
* *
2639263 CCTTATCTT-TTTTTTTT
1 CCTTATCTTCTTTCTTCT
* *
2639280 CCTTTTTTTCTTTCTTCT
1 CCTTATCTTCTTTCTTCT
*
2639298 CCTTATCTTCTTACTTCT
1 CCTTATCTTCTTTCTTCT
2639316 GTTCTGCTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (18 bp):
CCTTATCTTCTTTCTTCT
Found at i:2645366 original size:3 final size:3
Alignment explanation
Indices: 2645346--2645408 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
2645336 ACATATATGT
*
2645346 ATA ATA ATG ATGA A-A ATA ATA ATA ATA ATA ATGA A-A ATAA ATA AT-
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA
*
2645391 ATA ATA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA
2645409 GTAAAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 6 0.12
3 38 0.76
4 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2645372 original size:21 final size:21
Alignment explanation
Indices: 2645346--2645408 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2645336 ACATATATGT
*
2645346 ATAATAATGATGAAAATAATA
1 ATAATAATAATGAAAATAATA
2645367 ATAATAATAATGAAAATAAATA
1 ATAATAATAATGAAAAT-AATA
*
2645389 AT-ATAATAATAAAAATAATA
1 ATAATAATAATGAAAATAATA
2645409 GTAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
20 4 0.10
21 29 0.74
22 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
ATAATAATAATGAAAATAATA
Found at i:2645406 original size:12 final size:12
Alignment explanation
Indices: 2645360--2645415 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
2645350 TAATGATGAA
*
2645360 AATAATAATAAT
1 AATAATAAAAAT
*
2645372 AATAATGAAAAT
1 AATAATAAAAAT
*
2645384 -A-AAT-AATAT
1 AATAATAAAAAT
2645393 AATAATAAAAAT
1 AATAATAAAAAT
*
2645405 AATAGTAAAAA
1 AATAATAAAAA
2645416 AAAGATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 4 0.11
12 24 0.67
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:2645576 original size:26 final size:26
Alignment explanation
Indices: 2645516--2645580 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
2645506 TACGAAGAAG
*
2645516 TATATATAATATAATAATAATATTAA
1 TATAAATAATATAATAATAATATTAA
*
2645542 AATACAATAAT-TAA-AAGTAATATTATA
1 TATA-AATAATATAATAA-TAATATTA-A
2645569 TATAAAT-ATATA
1 TATAAATAATATA
2645581 CAATATTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 4 0.12
26 19 0.59
27 9 0.28
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
TATAAATAATATAATAATAATATTAA
Found at i:2647135 original size:23 final size:22
Alignment explanation
Indices: 2647082--2647146 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
2647072 GTTTTAAAAT
* *
2647082 TTGGGCTCAGGTAGTTTTA-GGA
1 TTGGGCT-AGGTTGGTTTAGGGA
*
2647104 TTAGGCTAGGTTGGTTTAGGGTA
1 TTGGGCTAGGTTGGTTTAGGG-A
2647127 TTGGGCTAGGTTGGTTTAGG
1 TTGGGCTAGGTTGGTTTAGG
2647147 CTTGGTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 9 0.24
22 8 0.22
23 20 0.54
ACGTcount: A:0.15, C:0.06, G:0.40, T:0.38
Consensus pattern (22 bp):
TTGGGCTAGGTTGGTTTAGGGA
Found at i:2658925 original size:20 final size:21
Alignment explanation
Indices: 2658892--2658942 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
2658882 CAGGTCTTTG
* *
2658892 TTTTTTTTT-GTTTTCCA-AC
1 TTTTTTTTTAATTTTCAAGAC
2658911 TTTTTTTTTAATTTTCAAGAC
1 TTTTTTTTTAATTTTCAAGAC
2658932 TCTTTTTTTTA
1 T-TTTTTTTTA
2658943 GTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 6 0.22
21 3 0.11
22 9 0.33
ACGTcount: A:0.16, C:0.12, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTTTTTAATTTTCAAGAC
Found at i:2660550 original size:12 final size:12
Alignment explanation
Indices: 2660527--2660563 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2660517 CGTGAGAAAA
*
2660527 AAATATAAATAT
1 AAATATATATAT
*
2660539 ACATATATATAT
1 AAATATATATAT
2660551 AAATATATATAT
1 AAATATATATAT
2660563 A
1 A
2660564 TAAAATGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATATAT
Found at i:2660558 original size:14 final size:14
Alignment explanation
Indices: 2660541--2660567 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2660531 ATAAATATAC
2660541 ATATATATATAAAT
1 ATATATATATAAAT
2660555 ATATATATATAAA
1 ATATATATATAAA
2660568 ATGAGTATTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:2660720 original size:3 final size:3
Alignment explanation
Indices: 2660702--2660763 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
2660692 AATGATAGTC
* * * **
2660702 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2660750 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
2660764 TGATTAAACA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2662538 original size:44 final size:44
Alignment explanation
Indices: 2662392--2662873 Score: 191
Period size: 44 Copynumber: 10.8 Consensus size: 44
2662382 ATCTGATACG
* * * **
2662392 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTAAATTTTA
** * * * ** * *
2662436 ATCCACTCCACTGAAATCTCAGGGGGATAGGATAGT--GTCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTAAAT-TTTA
*
2662479 ATCTGCTCC-GTCGTAATCTCAGGGAGATAAGATCCTAAATTTTA
1 ATCTGCTCCACT-GTAATCTCAGGGAGATAAGATCCTAAATTTTA
* * * * *
2662523 ATCCGCTCCACCGTAA-CTTCAGGGAGATAGGATTATCGGCTTCAATCTGATGTG
1 ATCTGCTCCACTGTAATC-TCAGGGAGATA--A-GATC--C-TAAAT-T--T-TA
* * * * **
2662577 ATCTACTCTACTGTAA-CTTTAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTAAATTTTA
* * * * *
2662621 ATCCGCTCCACTGTAATTTCAGGGAGATAGGAT--TACTATCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTA-AAT-TTTA
* *
2662665 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-AAATT-TT-A
* * * * ***
2662711 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCT-GA-TGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTTA
* * * *
2662752 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTTA
* * * * ** *
2662796 ATCCGCTCCACTGTAA-CTTCAGAGAGATAGGATTACT-AGCTTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-TCCTAAATTTTA
**
2662840 ATCTGCTCTGCTGTAATCTCAGGGAGATAAGATC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC
2662874 TGAAATTCTT
Statistics
Matches: 327, Mismatches: 80, Indels: 63
0.70 0.17 0.13
Matches are distributed among these distances:
41 30 0.09
42 6 0.02
43 37 0.11
44 168 0.51
45 11 0.03
46 32 0.10
47 4 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 4 0.01
52 1 0.00
53 1 0.00
54 24 0.07
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTTA
Found at i:2662867 original size:175 final size:175
Alignment explanation
Indices: 2662569--2662883 Score: 549
Period size: 175 Copynumber: 1.8 Consensus size: 175
2662559 CGGCTTCAAT
* * * **
2662569 CTGATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
* * *
2662634 TAATTTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
2662699 TGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
131 TGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
2662744 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
*
2662809 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATC
66 TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
2662874 TGAAATTCTT
131 TGAAATTCTT
2662884 TGATCTGCTT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 131 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (175 bp):
CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTG
TAACTTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
TGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGAC
Found at i:2665563 original size:12 final size:12
Alignment explanation
Indices: 2665527--2665568 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
2665517 TTAAAAAAAA
2665527 CATTATTATTAT
1 CATTATTATTAT
2665539 -ATTATATATTAT
1 CATTAT-TATTAT
*
2665551 CATTATTACTAT
1 CATTATTATTAT
2665563 CATTAT
1 CATTAT
2665569 CTCTATGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
CATTATTATTAT
Found at i:2666829 original size:31 final size:31
Alignment explanation
Indices: 2666736--2666831 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 31
2666726 GGAAAATTAC
* *
2666736 AAGACTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
2666767 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
2666799 AAGAGTAATAGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
2666830 AA
1 AA
2666832 ATTATCTAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:2670090 original size:12 final size:13
Alignment explanation
Indices: 2670068--2670093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2670058 TACAAAACAG
2670068 AAAAGTAAAAAAA
1 AAAAGTAAAAAAA
2670081 AAAAGTAAAAAAA
1 AAAAGTAAAAAAA
2670094 GGATGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAGTAAAAAAA
Found at i:2671380 original size:5 final size:5
Alignment explanation
Indices: 2671372--2671419 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
2671362 CGAACAAATA
* *
2671372 ATTCG ATTCG ATTCG ATTCG ATTTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG A-TTCG AT-TCG ATTCG ATTCG ATTCG AT
2671420 AAAACTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 29 0.78
6 6 0.16
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (5 bp):
ATTCG
Found at i:2681548 original size:3 final size:3
Alignment explanation
Indices: 2681530--2681582 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
2681520 AATGATAGTC
* * * **
2681530 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2681578 ATA AT
1 ATA AT
2681583 TGATTAAACA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2684100 original size:18 final size:17
Alignment explanation
Indices: 2684067--2684105 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2684057 TTTTATAAAT
2684067 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2684085 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2684102 TGTG
1 TGTG
2684106 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2684365 original size:23 final size:23
Alignment explanation
Indices: 2684330--2684400 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
2684320 AGTGTTATTG
*
2684330 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
2684353 TTCAATGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
2684376 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
2684399 AT
1 AT
2684401 TAGTGTGGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAATGGTAGCTTCGGCTACAT
Found at i:2696355 original size:21 final size:22
Alignment explanation
Indices: 2696316--2696356 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2696306 AAATAGGGAG
*
2696316 AAAACAACAAGAGAATAGCATT
1 AAAACAACAAGAAAATAGCATT
2696338 AAAACAACAA-AAAATAGCA
1 AAAACAACAAGAAAATAGCA
2696357 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.66, C:0.15, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAACAACAAGAAAATAGCATT
Found at i:2697505 original size:22 final size:22
Alignment explanation
Indices: 2697475--2697530 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2697465 TAGAAATTAT
* * * *
2697475 AAAAGATCATTAAAAATATTTA
1 AAAAAATCATAAAAAAAAGTTA
2697497 AAAAAATCATAAAAAAAAGTTA
1 AAAAAATCATAAAAAAAAGTTA
*
2697519 TAAAAATCATAA
1 AAAAAATCATAA
2697531 GAATTTTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAAAATCATAAAAAAAAGTTA
Found at i:2697742 original size:23 final size:21
Alignment explanation
Indices: 2697690--2697742 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
2697680 TGAAATATAT
*
2697690 ATAATATCTATTGTTTAAAAA
1 ATAATATTTATTGTTTAAAAA
2697711 AT-ATCATTTATTGTTTAACAAA
1 ATAAT-ATTTATTGTTTAA-AAA
2697733 ATTAATATTT
1 A-TAATATTT
2697743 TTGAAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 4 0.15
23 5 0.19
24 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (21 bp):
ATAATATTTATTGTTTAAAAA
Found at i:2699056 original size:34 final size:35
Alignment explanation
Indices: 2699012--2699078 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
2699002 CAGTAAAATG
2699012 TTTTCCGTAAAATGATTT-CTTG-AAAATATTTTAC
1 TTTTCCGTAAAATGATTTAC-TGAAAAATATTTTAC
*
2699046 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
2699079 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 19 0.63
35 11 0.37
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:2699137 original size:32 final size:32
Alignment explanation
Indices: 2699069--2699143 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
2699059 GATTTACTGA
* **
2699069 AAAATATTTTCTGGTGTTTGATTGAATTGTGT
1 AAAATATTTTCTGCTGTTTGACAGAATTGTGT
* *
2699101 AAAATATTTTCTGCTGTTTGACAGATTTCT-T
1 AAAATATTTTCTGCTGTTTGACAGAATTGTGT
2699132 GAAAATATTTTC
1 -AAAATATTTTC
2699144 CGGAAAAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 36 0.97
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (32 bp):
AAAATATTTTCTGCTGTTTGACAGAATTGTGT
Done.