Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 63 of 65
Found at i:12365722 original size:22 final size:22
Alignment explanation
Indices: 12365694--12365830 Score: 110
Period size: 20 Copynumber: 6.6 Consensus size: 22
12365684 TCGAAACTGA
*
12365694 GTTGCGAATTTGTGAGATTCGT
1 GTTGCGAATTTGTGAAATTCGT
12365716 GTTGCGAATTTGTGAAATTCGT
1 GTTGCGAATTTGTGAAATTCGT
**
12365738 GTTGCG-ATTT-ACAAATTCGT
1 GTTGCGAATTTGTGAAATTCGT
** * *
12365758 GTTGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGTGAAATTCGT
* *
12365778 GTTGCGTATTTG-GAAACT-GT
1 GTTGCGAATTTGTGAAATTCGT
* * *
12365798 GTTGCGAAATTG-G-AGTTCGC
1 GTTGCGAATTTGTGAAATTCGT
12365818 GTTGCGAATTTGT
1 GTTGCGAATTTGT
12365831 TGGTCATTTT
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.02
20 56 0.58
21 11 0.11
22 27 0.28
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.39
Consensus pattern (22 bp):
GTTGCGAATTTGTGAAATTCGT
Found at i:12380339 original size:10 final size:10
Alignment explanation
Indices: 12380324--12380357 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
12380314 GGATCGGCTG
12380324 AAAACCGGAA
1 AAAACCGGAA
12380334 AAAACCGGAA
1 AAAACCGGAA
*
12380344 AAAGCCGGAA
1 AAAACCGGAA
12380354 AAAA
1 AAAA
12380358 TCGGGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.62, C:0.18, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:12380649 original size:14 final size:14
Alignment explanation
Indices: 12380630--12380657 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12380620 AAGTGAAAAA
12380630 ATAGTTATATAATT
1 ATAGTTATATAATT
12380644 ATAGTTATATAATT
1 ATAGTTATATAATT
12380658 TTATTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:12382027 original size:23 final size:23
Alignment explanation
Indices: 12382001--12382045 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12381991 GTAACGATCG
* *
12382001 TTTATGTTCGTTTATTTATGTTT
1 TTTACGTTCGTTCATTTATGTTT
*
12382024 TTTACGTTCGTTCGTTTATGTT
1 TTTACGTTCGTTCATTTATGTT
12382046 CATTCCTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.09, G:0.16, T:0.64
Consensus pattern (23 bp):
TTTACGTTCGTTCATTTATGTTT
Found at i:12382330 original size:24 final size:24
Alignment explanation
Indices: 12382303--12382353 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
12382293 AAGTTGTTTG
* * *
12382303 TTCGTTTATCTTCGATTATGTTCA
1 TTCGCTTATATTCGATTACGTTCA
*
12382327 TTCGCTTATATTCGTTTACGTTCA
1 TTCGCTTATATTCGATTACGTTCA
12382351 TTC
1 TTC
12382354 ATTTGTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.12, T:0.53
Consensus pattern (24 bp):
TTCGCTTATATTCGATTACGTTCA
Found at i:12391185 original size:10 final size:10
Alignment explanation
Indices: 12391170--12391221 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
12391160 TATAAAATAA
12391170 TTATTAAATT
1 TTATTAAATT
12391180 TTATTAAATT
1 TTATTAAATT
* * *
12391190 AATATAAAATAA
1 -TTATTAAAT-T
*
12391202 TTATTAAAAT
1 TTATTAAATT
12391212 TTATTAAATT
1 TTATTAAATT
12391222 GTTACAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 19 0.59
11 13 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTATTAAATT
Found at i:12391187 original size:22 final size:22
Alignment explanation
Indices: 12391162--12391221 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
12391152 GGAGTTACTA
12391162 TAAAATAATTATTAAATTTTAT
1 TAAAATAATTATTAAATTTTAT
* * *
12391184 TAAATTAA-TATAAAATAATTAT
1 TAAAATAATTATTAAAT-TTTAT
12391206 TAAAAT--TTATTAAATT
1 TAAAATAATTATTAAATT
12391222 GTTACAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATAATTATTAAATTTTAT
Found at i:12391196 original size:32 final size:32
Alignment explanation
Indices: 12391160--12391221 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12391150 ATGGAGTTAC
*
12391160 TATAAAATAATTATTAAATTTTATTAAATTAA
1 TATAAAATAATTATTAAAATTTATTAAATTAA
12391192 TATAAAATAATTATTAAAATTTATTAAATT
1 TATAAAATAATTATTAAAATTTATTAAATT
12391222 GTTACAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TATAAAATAATTATTAAAATTTATTAAATTAA
Found at i:12391241 original size:32 final size:32
Alignment explanation
Indices: 12391163--12391232 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
12391153 GAGTTACTAT
* *
12391163 AAAATAATTATTAAATTTTATTAAATTAATAT
1 AAAATAATTATTAAAATTTATTAAATTAATAC
**
12391195 AAAATAATTATTAAAATTTATTAAATTGTTAC
1 AAAATAATTATTAAAATTTATTAAATTAATAC
12391227 AAAATA
1 AAAATA
12391233 TTCTTTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (32 bp):
AAAATAATTATTAAAATTTATTAAATTAATAC
Found at i:12391895 original size:31 final size:32
Alignment explanation
Indices: 12391850--12391935 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 32
12391840 TAATTTTTAA
* *
12391850 AAAAATTGAAAGTTTAGGTACTAAAACGAA-T
1 AAAAACTGATAGTTTAGGTACTAAAACGAACT
12391881 AAAAACTGATAGTTTAGGTACTAAAACGAACT
1 AAAAACTGATAGTTTAGGTACTAAAACGAACT
12391913 -AAAACTGATAG-TTAGGTACTAAA
1 AAAAACTGATAGTTTAGGTACTAAA
12391936 TGTGTTAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 12 0.23
31 39 0.75
32 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (32 bp):
AAAAACTGATAGTTTAGGTACTAAAACGAACT
Found at i:12401526 original size:36 final size:36
Alignment explanation
Indices: 12401474--12401553 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
12401464 CTCCACTGCC
*
12401474 TGTTTAATCTGTAGGCTTCACCTGTATGTATATTAG
1 TGTTTAATCTGCAGGCTTCACCTGTATGTATATTAG
*
12401510 TGTTTAATCTGCAGGCTTCACCTGTATGTATGTTAG
1 TGTTTAATCTGCAGGCTTCACCTGTATGTATATTAG
12401546 TGTTTAAT
1 TGTTTAAT
12401554 AGGCTTGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (36 bp):
TGTTTAATCTGCAGGCTTCACCTGTATGTATATTAG
Found at i:12403572 original size:18 final size:17
Alignment explanation
Indices: 12403533--12403585 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
12403523 ACCGTTGACC
12403533 GAAAAATCAAATTTTAT
1 GAAAAATCAAATTTTAT
12403550 GAAAAATCAAATTTTAT
1 GAAAAATCAAATTTTAT
*
12403567 GAAAAATCATATGTTTAT
1 GAAAAATCAAAT-TTTAT
12403585 G
1 G
12403586 TTTTTCGACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 28 0.82
18 6 0.18
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
GAAAAATCAAATTTTAT
Found at i:12405066 original size:319 final size:320
Alignment explanation
Indices: 12404465--12405108 Score: 1197
Period size: 319 Copynumber: 2.0 Consensus size: 320
12404455 ACGCTTCGGC
12404465 TAGG-GTAAGACCTTATGACCCAAGGTACTCCCTTTGGTTGGCACCTACGCCCTTCGGGCTTAGG
1 TAGGCGTAAGACCTTATGACCCAAGGTACTCCCTTTGGTTGGCACCTACGCCCTTCGGGCTTAGG
12404529 GTAAGTCATTATGGATGTAGTTCTGGGGAACTACATATGGTGTTCTGTTGGAGGGTGATTCTGTA
66 GTAAGTCATTATGGATGTAGTTCTGGGGAACTACATATGGTGTTCTGTTGGAGGGTGATTCTGTA
12404594 TTTTAAGCTAAAAACACTACTGATGTTTTCAAAACTTGAAATTGAGCTGATTTTGGAAACTCTAT
131 TTTTAAGCTAAAAACACTACTGATGTTTTCAAAACTTGAAATTGAGCTGATTTTGGAAACTCTAT
12404659 CGACGTTTCATGACTTTAATGTCGAAATGATTTTGAAATATTAATTATATGTTTATTTCTGCACT
196 CGACGTTTCATGACTTTAATGTCGAAATGATTTTGAAATATTAATTATATGTTTATTTCTGCACT
12404724 GTTGGAATACACTGAGCTCCCTAGCTCACTCCCCCAAAC-TTTCC-TTTAGATACTTTTTGA
261 GTTGGAATACACTGAGCTCCCTAGCTCACTCCCCCAAACTTTTCCTTTTA-A-ACTTTTTGA
*
12404784 TAGGCGTAAGACCTTATGACCC-AGGTACTCTCTTTGGTTGGCACCTACGCCCTTCGGGCTTAGG
1 TAGGCGTAAGACCTTATGACCCAAGGTACTCCCTTTGGTTGGCACCTACGCCCTTCGGGCTTAGG
*
12404848 GTAAGTCCTTATGGATGTAGTTCTGGGGAACTACATATGGTGTTCTGTTGGAGGGTGATTCTGTA
66 GTAAGTCATTATGGATGTAGTTCTGGGGAACTACATATGGTGTTCTGTTGGAGGGTGATTCTGTA
*
12404913 TTTTAAGCTAGAAACACTACTGATGTTTTCAAAACTTGAAATTGAGCTGATTTTGGAAACTCTAT
131 TTTTAAGCTAAAAACACTACTGATGTTTTCAAAACTTGAAATTGAGCTGATTTTGGAAACTCTAT
* *
12404978 CGACGTTTCATGACTTTAATGTCGAAATGATTTTGGAATCTTAATTATATGTTTATTTCTGCACT
196 CGACGTTTCATGACTTTAATGTCGAAATGATTTTGAAATATTAATTATATGTTTATTTCTGCACT
12405043 GTTGGAATACACTGAGCTCCCTAGCTCACTCCCCCAAACTTTTCCTTTTAAACTTTTTGA
261 GTTGGAATACACTGAGCTCCCTAGCTCACTCCCCCAAACTTTTCCTTTTAAACTTTTTGA
12405103 TAGGCG
1 TAGGCG
12405109 ACCCGGATCT
Statistics
Matches: 317, Mismatches: 5, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
319 290 0.91
320 23 0.07
321 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (320 bp):
TAGGCGTAAGACCTTATGACCCAAGGTACTCCCTTTGGTTGGCACCTACGCCCTTCGGGCTTAGG
GTAAGTCATTATGGATGTAGTTCTGGGGAACTACATATGGTGTTCTGTTGGAGGGTGATTCTGTA
TTTTAAGCTAAAAACACTACTGATGTTTTCAAAACTTGAAATTGAGCTGATTTTGGAAACTCTAT
CGACGTTTCATGACTTTAATGTCGAAATGATTTTGAAATATTAATTATATGTTTATTTCTGCACT
GTTGGAATACACTGAGCTCCCTAGCTCACTCCCCCAAACTTTTCCTTTTAAACTTTTTGA
Found at i:12407743 original size:33 final size:35
Alignment explanation
Indices: 12407705--12407776 Score: 114
Period size: 33 Copynumber: 2.1 Consensus size: 35
12407695 ATTTTCGGGA
12407705 TTTTGCTA-TTTTGGCAAAATTCGAAT-AA-ACGAT
1 TTTTGCTATTTTTGGCAAAA-TCGAATAAAGACGAT
12407738 TTTTGCTATTTTTGGCAAAATCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATCGAATAAAGACGAT
12407773 TTTT
1 TTTT
12407777 TTTAGCTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
33 14 0.39
34 13 0.36
35 9 0.25
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (35 bp):
TTTTGCTATTTTTGGCAAAATCGAATAAAGACGAT
Found at i:12412626 original size:36 final size:36
Alignment explanation
Indices: 12412585--12412660 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
12412575 ATTTTCGGGA
*
12412585 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
12412621 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
12412657 TTTT
1 TTTT
12412661 TTTAGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:12416715 original size:34 final size:34
Alignment explanation
Indices: 12416677--12416756 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
12416667 TATGATTTAA
12416677 AAAATAATAATAATTAAATAAATAAAACAGAAAT
1 AAAATAATAATAATTAAATAAATAAAACAGAAAT
* *
12416711 AAAATAATAATAATTAAATAATTAAAACATAAAT
1 AAAATAATAATAATTAAATAAATAAAACAGAAAT
12416745 AAAATAATAATA
1 AAAATAATAATA
12416757 TGTGATTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (34 bp):
AAAATAATAATAATTAAATAAATAAAACAGAAAT
Found at i:12418449 original size:29 final size:30
Alignment explanation
Indices: 12418413--12418478 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
12418403 ACCGGGTGAC
12418413 ATTTTGGGAA-TTAATTC-AAAATAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAA-AGGTGCT
*
12418442 ATTTTGGGAATTTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGGTGCT
12418472 ATTTTGG
1 ATTTTGG
12418479 TAATATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 10 0.29
30 20 0.59
31 4 0.12
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCGAAAAAGGTGCT
Found at i:12425647 original size:29 final size:28
Alignment explanation
Indices: 12425612--12425786 Score: 166
Period size: 29 Copynumber: 6.2 Consensus size: 28
12425602 ACCGGGTGAC
**
12425612 ATTTTGGGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTC-AAA-AAGTGCT
*
12425641 ATTTTGGGAATTTAAATT-AAAAATGGTGAT
1 ATTTTGGGAATTT-AATTCAAAAA--GTGCT
12425671 AGTTTT-GGAATTTAATTC-AAAAGTGCT
1 A-TTTTGGGAATTTAATTCAAAAAGTGCT
12425698 ATTTTGGGAATTTAATTCAAAAAAGTGCT
1 ATTTTGGGAATTTAATTC-AAAAAGTGCT
12425727 ATTTTGGGAA-TTAATTCAAAAAGAGTGCT
1 ATTTTGGGAATTTAATTC-AAAA-AGTGCT
* * *
12425756 ATTTTGGTAA-TT-ATTTAAAAAGTGTT
1 ATTTTGGGAATTTAATTCAAAAAGTGCT
12425782 ATTTT
1 ATTTT
12425787 TGTAAAATGG
Statistics
Matches: 129, Mismatches: 7, Indels: 23
0.81 0.04 0.14
Matches are distributed among these distances:
26 14 0.11
27 21 0.16
28 15 0.12
29 57 0.44
30 14 0.11
31 8 0.06
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (28 bp):
ATTTTGGGAATTTAATTCAAAAAGTGCT
Found at i:12425705 original size:57 final size:57
Alignment explanation
Indices: 12425607--12425767 Score: 186
Period size: 57 Copynumber: 2.8 Consensus size: 57
12425597 CGTTGACCGG
* * * *
12425607 GTGACATTTTGGGAATTAATTCGAAATGGGTGCTATTTTGGGAATTTAAATT-AAAAATG
1 GTGATATTTTGGGAATTAATTC-AAAAGAGTGCTATTTTGGGAATTT-AATTCAAAAA-A
12425666 GTGATAGTTTT-GGAATTTAATTC-AAA-AGTGCTATTTTGGGAATTTAATTCAAAAAA
1 GTGATA-TTTTGGGAA-TTAATTCAAAAGAGTGCTATTTTGGGAATTTAATTCAAAAAA
* *
12425722 GTGCTATTTTGGGAATTAATTCAAAAAGAGTGCTATTTTGGTAATT
1 GTGATATTTTGGGAATTAATTC-AAAAGAGTGCTATTTTGGGAATT
12425768 ATTTAAAAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
55 11 0.12
56 13 0.15
57 26 0.29
58 19 0.21
59 9 0.10
60 11 0.12
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (57 bp):
GTGATATTTTGGGAATTAATTCAAAAGAGTGCTATTTTGGGAATTTAATTCAAAAAA
Found at i:12430470 original size:17 final size:18
Alignment explanation
Indices: 12430445--12430481 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
12430435 TATACATCAC
*
12430445 TTATGTAAATTT-TTAAT
1 TTATATAAATTTATTAAT
12430462 TTATATAAATTTATTAAT
1 TTATATAAATTTATTAAT
12430480 TT
1 TT
12430482 TAGTGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATATAAATTTATTAAT
Found at i:12431075 original size:19 final size:19
Alignment explanation
Indices: 12431043--12431084 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12431033 GTGTTTTGAG
12431043 ATATATCAGATTTT-AGTAT
1 ATATATCAGATTTTGAG-AT
* *
12431062 ATATATCGGGTTTTGAGAT
1 ATATATCAGATTTTGAGAT
12431081 ATAT
1 ATAT
12431085 GTGATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (19 bp):
ATATATCAGATTTTGAGAT
Found at i:12434323 original size:39 final size:39
Alignment explanation
Indices: 12434278--12434381 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
12434268 TTTTAAAAAT
12434278 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
*
12434317 AATTTAGAATGTT-ATGGTGGCAAAT--TTTAAGAAATTAGG
1 AATTTAGAATGTTAAT-GT-G-AAATAATTTAAGAAATTAAG
12434356 AATTTAGAATGTTAGA-GTGAAATAAT
1 AATTTAGAATGTTA-ATGTGAAATAAT
12434382 ATGATAATTA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
37 4 0.07
38 3 0.05
39 44 0.77
40 1 0.02
41 5 0.09
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:12434409 original size:26 final size:26
Alignment explanation
Indices: 12434378--12434466 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 26
12434368 TAGAGTGAAA
12434378 TAATATGATAATTATAAATAAAAAT-T
1 TAATAT-ATAATTATAAATAAAAATAT
*
12434404 T-A-ATATAATATAAAAATAAAAATAT
1 TAATATATAAT-TATAAATAAAAATAT
* * * *
12434429 T-ATATATATTTATATATATACATAT
1 TAATATATAATTATAAATAAAAATAT
12434454 ATATATATATAAT
1 -TA-ATATATAAT
12434467 AAAACAGGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
23 5 0.10
24 14 0.28
25 15 0.30
26 8 0.16
28 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (26 bp):
TAATATATAATTATAAATAAAAATAT
Found at i:12434420 original size:24 final size:25
Alignment explanation
Indices: 12434380--12434436 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
12434370 GAGTGAAATA
*
12434380 ATATGATAATTATAAATAAAAAT-TT
1 ATAT-ATAATTAAAAATAAAAATATT
12434405 A-ATATAATATAAAAATAAAAATATT
1 ATATATAAT-TAAAAATAAAAATATT
12434430 ATATATA
1 ATATATA
12434437 TTTATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 14 0.50
25 4 0.14
26 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATATAATTAAAAATAAAAATATT
Found at i:12434436 original size:2 final size:2
Alignment explanation
Indices: 12434425--12434464 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
12434415 AAAAATAAAA
* *
12434425 AT AT -T AT AT AT AT TT AT AT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12434465 ATAAAACAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12435816 original size:21 final size:22
Alignment explanation
Indices: 12435792--12435832 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12435782 ATGATGAATG
*
12435792 CATTTT-TATGATATTGTAGGA
1 CATTTTCTATAATATTGTAGGA
*
12435813 CATTTTCTATAATTTTGTAG
1 CATTTTCTATAATATTGTAG
12435833 TATGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (22 bp):
CATTTTCTATAATATTGTAGGA
Found at i:12436409 original size:29 final size:29
Alignment explanation
Indices: 12436354--12436411 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
12436344 TCTCTATATA
12436354 AAAATAATAAATTATATTAATACATTATT
1 AAAATAATAAATTATATTAATACATTATT
*
12436383 AAAATAA-AAATATAATATT-ATATATTATT
1 AAAATAATAAAT-T-ATATTAATACATTATT
12436412 GTATGGATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 17 0.65
30 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATAATAAATTATATTAATACATTATT
Found at i:12438515 original size:24 final size:24
Alignment explanation
Indices: 12438488--12438560 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 24
12438478 CTTTCAAAAT
12438488 TAAATTTCAATCCTTACTAATGTG
1 TAAATTTCAATCCTTACTAATGTG
* * * *
12438512 TAAAATT--ATGTCTTTC-AAAGT-
1 TAAATTTCAAT-CCTTACTAATGTG
12438533 TAAATTTCAATCCTTACTAATGTG
1 TAAATTTCAATCCTTACTAATGTG
12438557 TAAA
1 TAAA
12438561 ATTATGTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 6 0.17
22 10 0.28
23 10 0.28
24 10 0.28
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (24 bp):
TAAATTTCAATCCTTACTAATGTG
Found at i:12438540 original size:45 final size:45
Alignment explanation
Indices: 12438476--12438567 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
12438466 ATTACTCCAA
12438476 GTCTTTCAAAATTAAATTTCAATCCTTACTAATGTGTAAAATTAT
1 GTCTTTCAAAATTAAATTTCAATCCTTACTAATGTGTAAAATTAT
*
12438521 GTCTTTCAAAGTTAAATTTCAATCCTTACTAATGTGTAAAATTAT
1 GTCTTTCAAAATTAAATTTCAATCCTTACTAATGTGTAAAATTAT
12438566 GT
1 GT
12438568 TTTATACTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (45 bp):
GTCTTTCAAAATTAAATTTCAATCCTTACTAATGTGTAAAATTAT
Found at i:12442638 original size:24 final size:24
Alignment explanation
Indices: 12442611--12442683 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 24
12442601 CTTTCAAAGT
12442611 TAAATTTCAATCCTTACTAATGTG
1 TAAATTTCAATCCTTACTAATGTG
* * * *
12442635 TAAAATT--ATGTCTTTC-AAAGT-
1 TAAATTTCAAT-CCTTACTAATGTG
12442656 TAAATTTCAATCCTTACTAATGTG
1 TAAATTTCAATCCTTACTAATGTG
12442680 TAAA
1 TAAA
12442684 ATTATGTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 6 0.17
22 10 0.28
23 10 0.28
24 10 0.28
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (24 bp):
TAAATTTCAATCCTTACTAATGTG
Found at i:12442663 original size:45 final size:45
Alignment explanation
Indices: 12442599--12442690 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
12442589 ATTACTCCAA
12442599 GTCTTTCAAAGTTAAATTTCAATCCTTACTAATGTGTAAAATTAT
1 GTCTTTCAAAGTTAAATTTCAATCCTTACTAATGTGTAAAATTAT
12442644 GTCTTTCAAAGTTAAATTTCAATCCTTACTAATGTGTAAAATTAT
1 GTCTTTCAAAGTTAAATTTCAATCCTTACTAATGTGTAAAATTAT
12442689 GT
1 GT
12442691 TTTATACTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (45 bp):
GTCTTTCAAAGTTAAATTTCAATCCTTACTAATGTGTAAAATTAT
Found at i:12449318 original size:276 final size:280
Alignment explanation
Indices: 12448819--12449374 Score: 1057
Period size: 276 Copynumber: 2.0 Consensus size: 280
12448809 ATGCCCTAAG
12448819 GAATCACATTTACTAGATGTTAAGAGACTCTTTAGATACCTTAAGGACACTCTTAATTTAGGACT
1 GAATCACATTTACTAGATGTTAAGAGACTCTTTAGATACCTTAAGGACACTCTTAATTTAGGACT
12448884 TTGGTATCCTAGAGACTCTAGCTTTAACTTGCATGCCTTTTCTGATGCGGATTATGGAGGATGCA
66 TTGGTATCCTAGAGACTCTAGCTTTAACTTGCATGCCTTTTCTGATGCGGATTATGGAGGATGCA
*
12448949 AATTAGATAGCAAAAGCACCTCCGGTACTTTCCAATTCCTTGGAAATATGTTGATTTCTTGGTTT
131 AATTAGATAGCAAAAGCACCTCCGGTACTTGCCAATTCCTTGGAAATATGTTGATTTCTTGGTTT
12449014 TCAAAGAAACAAAATTGTGTTACATTATCTACCACTG-AGCCGAATACATTTCAGCCGGTAG-TG
196 TCAAAGAAACAAAATTGTGTTACATTATCTACCACTGAAGCCGAATACATTTCAGCCGGTAGTTG
*
12449077 -TGTGCACAAG-TTTATGGA
261 TTATGCACAAGTTTTATGGA
12449095 GAATCACATTTACTAGATGTTAAGAGACTCTTTAGATACCTTAAGGACACTCTTAATTTAGGACT
1 GAATCACATTTACTAGATGTTAAGAGACTCTTTAGATACCTTAAGGACACTCTTAATTTAGGACT
12449160 TTGGTATCCTAGAGACTCTAGCTTTAACTTGCATGCCTTTTCTGATGCGGATTATGGAGGATGCA
66 TTGGTATCCTAGAGACTCTAGCTTTAACTTGCATGCCTTTTCTGATGCGGATTATGGAGGATGCA
12449225 AATTAGATAGCAAAAGCACCTCCGGTACTTGCCAATTCCTTGGAAATATGTTGATTTCTTGGTTT
131 AATTAGATAGCAAAAGCACCTCCGGTACTTGCCAATTCCTTGGAAATATGTTGATTTCTTGGTTT
*
12449290 TCAAAGAAACAAAATTGTGTTGCATTATCTACCACTGAAGCCGAATACATTTCAGCCGGTAGTTG
196 TCAAAGAAACAAAATTGTGTTACATTATCTACCACTGAAGCCGAATACATTTCAGCCGGTAGTTG
12449355 TTATGCACAAGTTTTATGGA
261 TTATGCACAAGTTTTATGGA
12449375 TGAAACAACA
Statistics
Matches: 273, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
276 230 0.84
277 24 0.09
278 2 0.01
279 9 0.03
280 8 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (280 bp):
GAATCACATTTACTAGATGTTAAGAGACTCTTTAGATACCTTAAGGACACTCTTAATTTAGGACT
TTGGTATCCTAGAGACTCTAGCTTTAACTTGCATGCCTTTTCTGATGCGGATTATGGAGGATGCA
AATTAGATAGCAAAAGCACCTCCGGTACTTGCCAATTCCTTGGAAATATGTTGATTTCTTGGTTT
TCAAAGAAACAAAATTGTGTTACATTATCTACCACTGAAGCCGAATACATTTCAGCCGGTAGTTG
TTATGCACAAGTTTTATGGA
Found at i:12449999 original size:21 final size:22
Alignment explanation
Indices: 12449920--12449999 Score: 101
Period size: 22 Copynumber: 3.6 Consensus size: 22
12449910 TAGTGCAGAA
*
12449920 GGAACCGATTCCCCCTTTGAAGG
1 GGAATCGATT-CCCCTTTGAAGG
12449943 GGAATCGATTCCCCTTTGAAGG
1 GGAATCGATTCCCCTTTGAAGG
*
12449965 GGAA-CTGATTCCCC-TTGTAGG
1 GGAATC-GATTCCCCTTTGAAGG
*
12449986 GGAATCGATACCCC
1 GGAATCGATTCCCC
12450000 CTGGGGGTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
21 18 0.35
22 25 0.48
23 9 0.17
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.24
Consensus pattern (22 bp):
GGAATCGATTCCCCTTTGAAGG
Found at i:12452270 original size:11 final size:12
Alignment explanation
Indices: 12452254--12452286 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12452244 TAAGGGTGTG
12452254 TAATTTCAAAC-
1 TAATTTCAAACT
12452265 TAATTTCAAACT
1 TAATTTCAAACT
*
12452277 TGATTTCAAA
1 TAATTTCAAA
12452287 ATCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (12 bp):
TAATTTCAAACT
Found at i:12453375 original size:48 final size:47
Alignment explanation
Indices: 12453296--12453392 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 47
12453286 TTTTAATTTG
* *
12453296 CCAATTCACCCCCTCTTGGCCAATTTCATCGATCGATTAGCTCAACA
1 CCAATTCACCCCCTCTTGACCAATTTCATCGATCGATTAACTCAACA
*
12453343 CCAATTCACCCCCCTCTTGACCGATTAT-ATCGATCGATTAACTCAACA
1 CCAATTCA-CCCCCTCTTGACCAATT-TCATCGATCGATTAACTCAACA
12453391 CC
1 CC
12453393 TTTGTATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 8 0.18
48 36 0.80
49 1 0.02
ACGTcount: A:0.27, C:0.37, G:0.09, T:0.27
Consensus pattern (47 bp):
CCAATTCACCCCCTCTTGACCAATTTCATCGATCGATTAACTCAACA
Found at i:12453546 original size:2 final size:2
Alignment explanation
Indices: 12453539--12453563 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12453529 TTTTTATTAT
12453539 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12453564 TTTTTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12453625 original size:18 final size:17
Alignment explanation
Indices: 12453602--12453636 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
12453592 TAATATTTAT
12453602 TTTTTTCAACTTTTTTTC
1 TTTTTTCAA-TTTTTTTC
12453620 TTTTTTCAATTTTTTTC
1 TTTTTTCAATTTTTTTC
12453637 AACATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTCAATTTTTTTC
Found at i:12453675 original size:17 final size:17
Alignment explanation
Indices: 12453641--12453695 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
12453631 TTTTTCAACA
*
12453641 TTTTCAAC-ATTTTCTT
1 TTTTCAACTATTTTATT
*
12453657 TTTTCAACTATTTAATT
1 TTTTCAACTATTTTATT
*
12453674 TTTT-AATCTTTTTTATT
1 TTTTCAA-CTATTTTATT
12453691 TTTTC
1 TTTTC
12453696 CTTTTTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTCAACTATTTTATT
Found at i:12453787 original size:31 final size:31
Alignment explanation
Indices: 12453724--12453787 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
12453714 ATTATTTTTC
* * * *
12453724 TAATTTTTTTTCTTTTTTTCTTTTTTTAATT
1 TAATATTTTTTATTTTTTTATTCTTTTAATT
12453755 TAATATTTTTTATTCTTTTTATTCTTTT-ATT
1 TAATATTTTTTATT-TTTTTATTCTTTTAATT
12453786 TA
1 TA
12453788 TTTCTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (31 bp):
TAATATTTTTTATTTTTTTATTCTTTTAATT
Found at i:12453835 original size:41 final size:44
Alignment explanation
Indices: 12453758--12453838 Score: 107
Period size: 42 Copynumber: 1.9 Consensus size: 44
12453748 TTTAATTTAA
*
12453758 TATTTTTTATTCTTTTTATTCTTTTATTTATTTCTTTAAAAATT
1 TATTTTTTATTCTTTTTATTCTTTTATTTATCTCTTTAAAAATT
*
12453802 TATTTTTTA-T-TTTTTCTTCATTTT-TTT-TCTCTTTAAA
1 TATTTTTTATTCTTTTTATTC-TTTTATTTATCTCTTTAAA
12453839 CTTGATTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 9 0.26
42 11 0.32
43 5 0.15
44 9 0.26
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (44 bp):
TATTTTTTATTCTTTTTATTCTTTTATTTATCTCTTTAAAAATT
Found at i:12461055 original size:18 final size:19
Alignment explanation
Indices: 12461020--12461056 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12461010 CACGGAATGT
12461020 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
12461040 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
12461057 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:12468703 original size:103 final size:104
Alignment explanation
Indices: 12468524--12468731 Score: 393
Period size: 103 Copynumber: 2.0 Consensus size: 104
12468514 TTCATTTTAG
12468524 TACCCGTCGTTAAAAACTTAACGTATTTAGTATCTAATCTATTAGTGTGGTCCGTTTTAGTACCT
1 TACCCGTCGTTAAAAACTTAACGTATTTAGTATCTAATCTATTAGTGTGGTCCGTTTTAGTACCT
12468589 AAACTTTCA-TTTTTTCTCTCAAAATTTAACGTTAAATT
66 AAACTTTCATTTTTTTCTCTCAAAATTTAACGTTAAATT
12468627 TACCCGTCGTTAAAAACTT-ACGTATTTAGTATCTAATCTATTAGTTGTGGTCCGTTTTAGTACC
1 TACCCGTCGTTAAAAACTTAACGTATTTAGTATCTAATCTATTAG-TGTGGTCCGTTTTAGTACC
12468691 TAAACTTTCATTTTTTTCTCTCAAAATTTAACGTTAAATT
65 TAAACTTTCATTTTTTTCTCTCAAAATTTAACGTTAAATT
12468731 T
1 T
12468732 TGAACGTGGT
Statistics
Matches: 103, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
102 25 0.24
103 48 0.47
104 30 0.29
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (104 bp):
TACCCGTCGTTAAAAACTTAACGTATTTAGTATCTAATCTATTAGTGTGGTCCGTTTTAGTACCT
AAACTTTCATTTTTTTCTCTCAAAATTTAACGTTAAATT
Found at i:12470296 original size:35 final size:34
Alignment explanation
Indices: 12470248--12470316 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
12470238 ACACACATAA
*
12470248 TATTATATTACAAT-TAATATAATT-ATAATTAAT
1 TATTATATTACAATGTAACA-AATTGATAATTAAT
12470281 TATTATAATTTACAATGTAACAAATTGATAATTAAT
1 TATTAT-A-TTACAATGTAACAAATTGATAATTAAT
12470317 GTATAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 6 0.19
34 1 0.03
35 11 0.35
36 13 0.42
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (34 bp):
TATTATATTACAATGTAACAAATTGATAATTAAT
Found at i:12478891 original size:15 final size:15
Alignment explanation
Indices: 12478858--12478899 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
12478848 AACAAGTATT
*
12478858 ATAAAAAA-AATGAA
1 ATAAAAAATAATTAA
12478872 ATAAAAAATAATTAA
1 ATAAAAAATAATTAA
*
12478887 GTAAAAAATAATT
1 ATAAAAAATAATT
12478900 TAAAAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAAAAAATAATTAA
Found at i:12491128 original size:16 final size:17
Alignment explanation
Indices: 12491104--12491136 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12491094 TTCATAAAAT
12491104 ACTAAAAAAATT-GTTA
1 ACTAAAAAAATTAGTTA
*
12491120 ACTAGAAAAATTAGTTA
1 ACTAAAAAAATTAGTTA
12491137 TATTGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (17 bp):
ACTAAAAAAATTAGTTA
Found at i:12497262 original size:21 final size:21
Alignment explanation
Indices: 12497220--12497262 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12497210 TTTCTGGGCT
*
12497220 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
12497241 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
12497262 A
1 A
12497263 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:12497325 original size:19 final size:20
Alignment explanation
Indices: 12497287--12497327 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12497277 CCAGAACGCT
*
12497287 AGGGGGGAATCGATACCCCC
1 AGGGGGGAACCGATACCCCC
*
12497307 AGGGGGGAACCGATTCCCCC
1 AGGGGGGAACCGATACCCCC
12497327 A
1 A
12497328 TAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (20 bp):
AGGGGGGAACCGATACCCCC
Found at i:12498137 original size:103 final size:103
Alignment explanation
Indices: 12497809--12498129 Score: 624
Period size: 103 Copynumber: 3.1 Consensus size: 103
12497799 GTAGAGGGTC
12497809 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
12497874 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
12497912 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
12497977 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
12498015 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
12498080 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
12498118 TATGTGGTCCTT
1 TATGTGGTCCTT
12498130 ATGGACATTA
Statistics
Matches: 216, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 216 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:12498179 original size:23 final size:23
Alignment explanation
Indices: 12498146--12498208 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
12498136 ATTATTATAT
12498146 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
12498169 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
12498192 GTCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
12498209 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:12499067 original size:123 final size:123
Alignment explanation
Indices: 12498938--12499215 Score: 441
Period size: 123 Copynumber: 2.3 Consensus size: 123
12498928 CAATAGAGTG
** *
12498938 GTAATTTAGCGGCGTTTAT-AGCTCAAACGCTGGAATATAGTTGTTTATAGTGGCGTTTTTATAC
1 GTAATTTAGCGGCGTTTATCA-AACAAACGCCGGAATATAGTTGTTTATAGTGGCGTTTTTATAC
* *
12499002 AAACGACATAATAGGGTTGCTTACAGTGGCATTTGTCCAACAAACGACGCTATATAGAA
65 AAACGACACAATAGGGTTGCTTACAGTGGCATTTGTCCAACAAACAACGCTATATAGAA
12499061 GTAATTTAGCGGCGTTTATCAAACAAACGCCGGAATATAGTTGTTTATAGTGGCGTTTTTATACA
1 GTAATTTAGCGGCGTTTATCAAACAAACGCCGGAATATAGTTGTTTATAGTGGCGTTTTTATACA
* * * * * *
12499126 GATGCCGCAATAGGGTTGCTTACAGTGGCATTTTTCCAACAAACAACGCTATATATAA
66 AACGACACAATAGGGTTGCTTACAGTGGCATTTGTCCAACAAACAACGCTATATAGAA
12499184 GTAATTTAGCGGCGTTTATCAAACAAACGCCG
1 GTAATTTAGCGGCGTTTATCAAACAAACGCCG
12499216 CAATCAGTAA
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
123 142 0.99
124 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (123 bp):
GTAATTTAGCGGCGTTTATCAAACAAACGCCGGAATATAGTTGTTTATAGTGGCGTTTTTATACA
AACGACACAATAGGGTTGCTTACAGTGGCATTTGTCCAACAAACAACGCTATATAGAA
Found at i:12499541 original size:11 final size:11
Alignment explanation
Indices: 12499516--12499553 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12499506 TTTTTCCGTA
*
12499516 TCTTCCCT-CT
1 TCTTCCCTAAT
12499526 TCTTCCCTAAT
1 TCTTCCCTAAT
12499537 TCTTCCCTAAT
1 TCTTCCCTAAT
12499548 TCTTCC
1 TCTTCC
12499554 TCGAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (11 bp):
TCTTCCCTAAT
Found at i:12502413 original size:14 final size:14
Alignment explanation
Indices: 12502394--12502425 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12502384 TACCATTCGG
12502394 TTACGTTGTGCACT
1 TTACGTTGTGCACT
12502408 TTACGTTGTGCACT
1 TTACGTTGTGCACT
12502422 TTAC
1 TTAC
12502426 AGTAGTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (14 bp):
TTACGTTGTGCACT
Found at i:12503208 original size:42 final size:42
Alignment explanation
Indices: 12503136--12503335 Score: 183
Period size: 42 Copynumber: 4.7 Consensus size: 42
12503126 GGCGTTTGTG
* * * * *
12503136 GCCGCTATAGATTTCACCTTTTACGACGTTTGTATCTAAAAAC
1 GCCGCTATAAATCTGACCTTTTGCGGCGTTTGT-TCTAAAAAC
* * * *
12503179 GCCGCTATAAATCTGA-CATTTACGGCGTTTGTT-TCAAAAT
1 GCCGCTATAAATCTGACCTTTTGCGGCGTTTGTTCTAAAAAC
* *
12503219 GCTGCTATAGATATC-GACCTTTTGCGGCGTTTGTTCCAAAAAC
1 GCCGCTATA-A-ATCTGACCTTTTGCGGCGTTTGTTCTAAAAAC
* *
12503262 GCCGTTATAGATCTGACCTTTTGCGGCGTTTGTTAC-AAAAAC
1 GCCGCTATAAATCTGACCTTTTGCGGCGTTTGTT-CTAAAAAC
* * *
12503304 GCCGCGATAGATCTTGACCTATTGCGGCGTTT
1 GCCGCTATAAATC-TGACCTTTTGCGGCGTTT
12503336 TTTGTTCTCA
Statistics
Matches: 131, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
40 13 0.10
41 7 0.05
42 69 0.53
43 42 0.32
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (42 bp):
GCCGCTATAAATCTGACCTTTTGCGGCGTTTGTTCTAAAAAC
Found at i:12503265 original size:83 final size:86
Alignment explanation
Indices: 12503136--12503335 Score: 237
Period size: 83 Copynumber: 2.4 Consensus size: 86
12503126 GGCGTTTGTG
* * * *
12503136 GCCGCTATAGATTTC-ACCTTTTACGACGTTTGTATCTAAAAACGCCGCTATAAATCTGA-CATT
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAAATCTGACCATT
* *
12503199 TACGGCGTTTGTTTC-AAAAT
66 TACGGCGTTTGTTACAAAAAC
* * * *
12503219 GCTGCTATAGATATCGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGTTATAGATCTGACCTTT
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAAATCTGACCATT
*
12503283 TGCGGCGTTTGTTACAAAAAC
66 TACGGCGTTTGTTACAAAAAC
* * * *
12503304 GCCGCGATAGATCTTGACCTATTGCGGCGTTT
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTT
12503336 TTTGTTCTCA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
83 35 0.36
84 32 0.33
85 31 0.32
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (86 bp):
GCCGCTATAGATATCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAAATCTGACCATT
TACGGCGTTTGTTACAAAAAC
Found at i:12513979 original size:21 final size:22
Alignment explanation
Indices: 12513943--12514066 Score: 118
Period size: 21 Copynumber: 5.8 Consensus size: 22
12513933 ATTGTGATAG
12513943 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTTAT
*
12513966 TCCAAGTT-CGTTGCGA--TAG
1 TCCAAGTTCCGTTGCGATTTAT
*
12513985 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTTAT
* *
12514008 TCCAAATT-CGTTGCGA--TAG
1 TCCAAGTTCCGTTGCGATTTAT
*
12514027 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTC-CGTTGCGATTTAT
*
12514050 TCCAAATT-CGTTGCGAT
1 TCCAAGTTCCGTTGCGAT
12514067 AGGATAGTCC
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
19 17 0.21
21 41 0.50
23 24 0.29
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (22 bp):
TCCAAGTTCCGTTGCGATTTAT
Found at i:12513992 original size:42 final size:42
Alignment explanation
Indices: 12513938--12514068 Score: 244
Period size: 42 Copynumber: 3.1 Consensus size: 42
12513928 TTCACATTGT
* *
12513938 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
1 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
12513980 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
12514022 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
12514064 GATAG
1 GATAG
12514069 GATAGTCCAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
Found at i:12514849 original size:21 final size:21
Alignment explanation
Indices: 12514823--12515038 Score: 203
Period size: 21 Copynumber: 10.4 Consensus size: 21
12514813 TGGACTATCA
12514823 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
* *
12514844 CATTGCGAT-TTACATA-TTCG
1 CATTGCGATAGTCCA-AGTTCG
**
12514864 CATTGCGATAGTTGATTA-TT-G
1 CATTGCGATAGTCCA--AGTTCG
*
12514885 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
* *
12514906 TATTACGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
** *
12514927 CATTGCGATAGTTTAAGTTTG
1 CATTGCGATAGTCCAAGTTCG
* *
12514948 CATTGCGATAGT-CGACTATCG
1 CATTGCGATAGTCCAAGT-TCG
* *
12514969 CATTGCGAT-TTACATA-TTCG
1 CATTGCGATAGTCCA-AGTTCG
12514989 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
12515010 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
12515031 CGTTGCGA
1 CATTGCGA
12515039 ATCTGGAAAC
Statistics
Matches: 162, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
19 1 0.01
20 34 0.21
21 122 0.75
22 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:12515019 original size:83 final size:86
Alignment explanation
Indices: 12514823--12515021 Score: 254
Period size: 83 Copynumber: 2.4 Consensus size: 86
12514813 TGGACTATCA
* * *
12514823 CATTGCGATAGTCCAAGTTCGCATTGCG--A-TTTACATATTCGCATTGCGATAGTTGATTATTG
1 CATTGCGATAGTCCAAGTTCGCATTGCGATAGTTTACATATTCGCATTGCGATAGTCGACTATCG
12514885 CATTGCGATAGTCGAAGTTCG
66 CATTGCGATAGTCGAAGTTCG
* *
12514906 TATTACGATAGTCCAAGTTCGCATTGCGATAGTTTA-AGT-TT-GCATTGCGATAGTCGACTATC
1 CATTGCGATAGTCCAAGTTCGCATTGCGATAGTTTACA-TATTCGCATTGCGATAGTCGACTATC
*
12514968 GCATTGCGAT-TTAC-ATA-TTCG
65 GCATTGCGATAGT-CGA-AGTTCG
12514989 CATTGCGATAGTCCAAGTTCGCATTGCGATAGT
1 CATTGCGATAGTCCAAGTTCGCATTGCGATAGT
12515022 CCAAGTTCGC
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
83 63 0.62
84 30 0.29
85 4 0.04
86 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (86 bp):
CATTGCGATAGTCCAAGTTCGCATTGCGATAGTTTACATATTCGCATTGCGATAGTCGACTATCG
CATTGCGATAGTCGAAGTTCG
Found at i:12515491 original size:21 final size:22
Alignment explanation
Indices: 12515467--12515508 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12515457 AAACATGAGA
12515467 TTCA-TCAACTTTTTAAATAAC
1 TTCATTCAACTTTTTAAATAAC
* *
12515488 TTCATTTAATTTTTTAAATAA
1 TTCATTCAACTTTTTAAATAA
12515509 AAATCTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (22 bp):
TTCATTCAACTTTTTAAATAAC
Found at i:12522243 original size:23 final size:22
Alignment explanation
Indices: 12522210--12522274 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
12522200 ATAGGAATAA
*
12522210 TTATGTATTTGTGATACGTTTAT
1 TTATGTCTTTGTGATA-GTTTAT
12522233 TTATGTCTTTGTG-TCATGTTTAT
1 TTATGTCTTTGTGAT-A-GTTTAT
* *
12522256 CTAAGTCTTT-TGATAGTTT
1 TTATGTCTTTGTGATAGTTT
12522275 CTGAGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 28 0.78
ACGTcount: A:0.18, C:0.08, G:0.17, T:0.57
Consensus pattern (22 bp):
TTATGTCTTTGTGATAGTTTAT
Found at i:12523581 original size:23 final size:24
Alignment explanation
Indices: 12523551--12523613 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
12523541 AATAAAAATC
12523551 TTTGTTCTTGTGACACAC-TTTTA
1 TTTGTTCTTGTGACACACTTTTTA
*
12523574 TTTGTTCTTGTGGCACACTTTTTA
1 TTTGTTCTTGTGACACACTTTTTA
*
12523598 TCTGCTT-TTGTGACAC
1 TTTG-TTCTTGTGACAC
12523614 GTTCCTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.49
24 16 0.46
25 2 0.06
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.51
Consensus pattern (24 bp):
TTTGTTCTTGTGACACACTTTTTA
Found at i:12523608 original size:24 final size:23
Alignment explanation
Indices: 12523553--12523613 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
12523543 TAAAAATCTT
*
12523553 TGTTCTTGTGACACACTTTTATT
1 TGTTCTTGTGACACACTTTTATC
*
12523576 TGTTCTTGTGGCACACTTTTTATC
1 TGTTCTTGTGACACAC-TTTTATC
12523600 TGCTT-TTGTGACAC
1 TG-TTCTTGTGACAC
12523614 GTTCCTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.45
24 16 0.48
25 2 0.06
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.49
Consensus pattern (23 bp):
TGTTCTTGTGACACACTTTTATC
Found at i:12524640 original size:22 final size:22
Alignment explanation
Indices: 12524612--12524671 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
12524602 CCGTAAGCTA
*
12524612 TCAAAAGCTAGAGAAAAACGTG
1 TCAAAAGATAGAGAAAAACGTG
*
12524634 TCAAAAGATAGAGATAAACGTG
1 TCAAAAGATAGAGAAAAACGTG
* *
12524656 CCATAAAGGTAGAGAA
1 TCA-AAAGATAGAGAA
12524672 TATGTCACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (22 bp):
TCAAAAGATAGAGAAAAACGTG
Found at i:12533603 original size:43 final size:41
Alignment explanation
Indices: 12533511--12533798 Score: 183
Period size: 42 Copynumber: 6.9 Consensus size: 41
12533501 CTTGGATTTT
** * *
12533511 ATTTTTTATCTTTATAATTGAAGTACATAATTTTTTAATCTC
1 ATTTTTTATCTTTATAATTG-AGGCCCTAATTTTTTAATCCC
* *
12533553 ACTTTTTATCTTTATAATTGATGCCCTTAATTTTTTAATCCC
1 ATTTTTTATCTTTATAATTGAGGCCC-TAATTTTTTAATCCC
**** * *
12533595 ATTTTTT-TACATTTATAATTGATGATTTTAAATTTTTCAATCAC
1 ATTTTTTAT-C-TTTATAATTGA-GGCCCT-AATTTTTTAATCCC
* * * * * *
12533639 ACTTTGTACCTATATAATTGA-ACTCCT-ATTTTTTCAATCAC
1 ATTTTTTATCTTTATAATTGAGGC-CCTAATTTTTT-AATCCC
* * *
12533680 -TTTTTTACCTTTATAACTGAGGCTCCTAATTTTTTAATCTC
1 ATTTTTTATCTTTATAATTGAGGC-CCTAATTTTTTAATCCC
* ** *
12533721 ACTTTTTATCTTTATAATTGAGGGTCTAATTTTGTCCAATCCC
1 ATTTTTTATCTTTATAATTGAGGCCCTAATTTT-T-TAATCCC
*
12533764 -TTTTTTA-CTTATATAATTTAGGCCCTTAATTTTTT
1 ATTTTTTATCTT-TATAATTGAGGCCC-TAATTTTTT
12533799 TTCAATCTAA
Statistics
Matches: 191, Mismatches: 40, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
40 22 0.12
41 31 0.16
42 86 0.45
43 34 0.18
44 18 0.09
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (41 bp):
ATTTTTTATCTTTATAATTGAGGCCCTAATTTTTTAATCCC
Found at i:12533743 original size:42 final size:42
Alignment explanation
Indices: 12533513--12533753 Score: 201
Period size: 42 Copynumber: 5.8 Consensus size: 42
12533503 TGGATTTTAT
* *
12533513 TTTTTATCTTTATAATTGAAG-TACATAATTTTTTAATCTCAC
1 TTTTTATCTTTATAATTGAGGCT-CCTAATTTTTTAATCTCAC
* *
12533555 TTTTTATCTTTATAATTGATGC-CCTTAATTTTTTAATCCCA-
1 TTTTTATCTTTATAATTGAGGCTCC-TAATTTTTTAATCTCAC
* * * ** * *
12533596 TTTTTTTACATTTATAATTGATGATTTTAAATTTTTCAATCACAC
1 TTTTTAT-C-TTTATAATTGAGGCTCCT-AATTTTTTAATCTCAC
* * * *
12533641 TTTGTACCTATATAATTGA-ACTCCT-ATTTTTTCAA--TCAC
1 TTTTTATCTTTATAATTGAGGCTCCTAATTTTTT-AATCTCAC
* *
12533680 TTTTTTACCTTTATAACTGAGGCTCCTAATTTTTTAATCTCAC
1 -TTTTTATCTTTATAATTGAGGCTCCTAATTTTTTAATCTCAC
*
12533723 TTTTTATCTTTATAATTGAGGGT-CTAATTTT
1 TTTTTATCTTTATAATTGAGGCTCCTAATTTT
12533754 GTCCAATCCC
Statistics
Matches: 160, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
39 3 0.02
40 22 0.14
41 24 0.15
42 65 0.41
43 28 0.17
44 14 0.09
45 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (42 bp):
TTTTTATCTTTATAATTGAGGCTCCTAATTTTTTAATCTCAC
Found at i:12533795 original size:84 final size:80
Alignment explanation
Indices: 12533512--12533798 Score: 252
Period size: 82 Copynumber: 3.4 Consensus size: 80
12533502 TTGGATTTTA
* ** *
12533512 TTTTTTATCTTTATAATTGAAGTACATAATTTTTTAATCTCACTTTTTATCTTTATAATTGATGC
1 TTTTTTA-CTTTATAATTGAGGCCCTTAATTTTTTAATCTCACTTTTTATCTTTATAATTGA-GC
* *
12533577 CCTTAATTTTTTAATCCC
64 TC-TAATTTTTCAATCCC
* *** * * * * *
12533595 ATTTTTTTACATTTATAATTGATGATTTTAAATTTTTCAATCACACTTTGTACCTATATAATTGA
1 --TTTTTTAC-TTTATAATTGAGGCCCTT-AATTTTTTAATCTCACTTTTTATCTTTATAATTGA
* * *
12533660 ACTCCTATTTTTTCAATCAC
62 GCT-CTAATTTTTCAATCCC
*
12533680 TTTTTTACCTTTATAACTGAGGCTCC-TAATTTTTTAATCTCACTTTTTATCTTTATAATTGAGG
1 TTTTTTA-CTTTATAATTGAGGC-CCTTAATTTTTTAATCTCACTTTTTATCTTTATAATTGA-G
*
12533744 GTCTAATTTTGTCCAATCCC
63 CTCTAATTTT-T-CAATCCC
*
12533764 TTTTTTACTTATATAATTTAGGCCCTTAATTTTTT
1 TTTTTTACTT-TATAATTGAGGCCCTTAATTTTTT
12533799 TTCAATCTAA
Statistics
Matches: 161, Mismatches: 31, Indels: 21
0.76 0.15 0.10
Matches are distributed among these distances:
82 37 0.23
83 26 0.16
84 34 0.21
85 33 0.20
86 31 0.19
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (80 bp):
TTTTTTACTTTATAATTGAGGCCCTTAATTTTTTAATCTCACTTTTTATCTTTATAATTGAGCTC
TAATTTTTCAATCCC
Found at i:12534073 original size:20 final size:20
Alignment explanation
Indices: 12534050--12534116 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
12534040 ATTTTCCAAT
12534050 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
12534070 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
12534090 TCGCAACGCGAATCTGTAAT
1 TCGCAACGCGAATCTGTAAA
12534110 TCGCAAC
1 TCGCAAC
12534117 ACATAAGTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:12534134 original size:40 final size:40
Alignment explanation
Indices: 12534047--12534135 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
12534037 GCGATTTTCC
* **
12534047 AATTCGCAACGCGAATCTGTAAATCGCAACGCGAATCTGTA
1 AATTCGCAACGCGAATCTGTAAATCGCAACAC-AATAAGTA
*
12534088 AA-TCGCAACGCGAATCTGTAATTCGCAACAC-ATAAGTCA
1 AATTCGCAACGCGAATCTGTAAATCGCAACACAATAAGT-A
12534127 AATTCGCAA
1 AATTCGCAA
12534136 AGCGCGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 4 0.10
39 3 0.07
40 33 0.79
41 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
AATTCGCAACGCGAATCTGTAAATCGCAACACAATAAGTA
Found at i:12534333 original size:22 final size:22
Alignment explanation
Indices: 12534294--12534335 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12534284 GATGACATCC
*
12534294 GTCCCCATCTCTGACGAAATTT
1 GTCCCCATCTCAGACGAAATTT
12534316 GTCCCCATCTCCAG-CGAAAT
1 GTCCCCATCT-CAGACGAAAT
12534336 CCGTCTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.36, G:0.14, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCAGACGAAATTT
Found at i:12535910 original size:24 final size:24
Alignment explanation
Indices: 12535883--12535935 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
12535873 ATCTCATATT
12535883 GTTTATATACGAAATTTTTAAAGC
1 GTTTATATACGAAATTTTTAAAGC
* * *
12535907 GTTTATGTATGAATTTTTTAAAGC
1 GTTTATATACGAAATTTTTAAAGC
12535931 GTTTA
1 GTTTA
12535936 AATATAGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (24 bp):
GTTTATATACGAAATTTTTAAAGC
Found at i:12543413 original size:16 final size:16
Alignment explanation
Indices: 12543383--12543431 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
12543373 TTTATATATC
*
12543383 TTTAAAAATATTTTTA
1 TTTATAAATATTTTTA
12543399 TTTATTAAATATTTTTA
1 TTTA-TAAATATTTTTA
12543416 TTTATAAATATATTTT
1 TTTATAAATAT-TTTT
12543432 TCTTAACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATAAATATTTTTA
Found at i:12543512 original size:28 final size:28
Alignment explanation
Indices: 12543478--12543596 Score: 100
Period size: 28 Copynumber: 4.2 Consensus size: 28
12543468 ATATTTAAAA
*
12543478 ATTTTATTCTTATCTTAGCTT-AAATAT
1 ATTTTATTCTTATCTTAACTTAAAATAT
* *
12543505 ATATTTATTCTTATTTTAATTTAAAATAT
1 AT-TTTATTCTTATCTTAACTTAAAATAT
* * **
12543534 ATTTTATTTTTATTATTCATTTTAAAAATAT
1 ATTTTATTCTTA-TCTT-AACTT-AAAATAT
* *
12543565 ATTTTATT-TTATCTTAATTTATAA-AT
1 ATTTTATTCTTATCTTAACTTAAAATAT
12543591 ATTTTA
1 ATTTTA
12543597 AAAATGTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.10
27 5 0.06
28 29 0.37
29 14 0.18
30 7 0.09
31 15 0.19
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTTATTCTTATCTTAACTTAAAATAT
Found at i:12543562 original size:31 final size:28
Alignment explanation
Indices: 12543499--12543596 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 28
12543489 ATCTTAGCTT
*
12543499 AAATATATATTTATTCTTATTTTAATTTA
1 AAATATAT-TTTATTTTTATTTTAATTTA
*
12543528 AAATATATTTTATTTTTATTATTCATTTTAA
1 AAATATATTTTATTTTTATT-TT-AATTT-A
*
12543559 AAATATATTTTA-TTTTATCTTAATTTA
1 AAATATATTTTATTTTTATTTTAATTTA
*
12543586 TAA-ATATTTTA
1 AAATATATTTTA
12543597 AAAATGTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 8 0.13
27 3 0.05
28 15 0.25
29 12 0.20
30 10 0.16
31 13 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
AAATATATTTTATTTTTATTTTAATTTA
Found at i:12543573 original size:18 final size:17
Alignment explanation
Indices: 12543516--12543575 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
12543506 TATTTATTCT
*
12543516 TATTTTAATTTAAAATA
1 TATTTTATTTTAAAATA
*
12543533 TATTTTATTTT--TAT-
1 TATTTTATTTTAAAATA
*
12543547 TA-TTCATTTTAAAAATA
1 TATTTTATTTT-AAAATA
12543564 TATTTTATTTTA
1 TATTTTATTTTA
12543576 TCTTAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
13 7 0.21
14 2 0.06
15 2 0.06
16 2 0.06
17 13 0.39
18 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTATTTTAAAATA
Found at i:12543734 original size:30 final size:28
Alignment explanation
Indices: 12543685--12543842 Score: 116
Period size: 30 Copynumber: 5.6 Consensus size: 28
12543675 ACATAAAGTT
12543685 TAAAA-ATATTTTTAAATTAAGATAAAAA
1 TAAAATATATTTTTAAATTAA-ATAAAAA
*
12543713 TAAAATATATTTTTAAAATTAAAAAAAGAA
1 TAAAATATATTTTT-AAATTAAATAAA-AA
*
12543743 TAAAAAATATATTTTTAAATT-AA-AAAAT
1 T--AAAATATATTTTTAAATTAAATAAAAA
* * *
12543771 TAAAA-A-A--ATTAAGTTAAATTAATAA
1 TAAAATATATTTTTAAATTAAA-TAAAAA
* *
12543796 TAAAATGTATTTAATAAGA-TAAGATAAAAA
1 TAAAATATATTT-TTAA-ATTAA-ATAAAAA
12543826 TAAAATATATTTTTAAA
1 TAAAATATATTTTTAAA
12543843 GATATATAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
22 6 0.06
23 2 0.02
24 1 0.01
25 9 0.09
26 4 0.04
27 1 0.01
28 8 0.08
29 18 0.18
30 34 0.33
31 6 0.06
32 13 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAATATATTTTTAAATTAAATAAAAA
Found at i:12552300 original size:21 final size:21
Alignment explanation
Indices: 12552249--12552301 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
12552239 ATTATGACTA
*
12552249 TCGCAATGCGATTTTACAATT
1 TCGCAATGCGATTTCACAATT
** *
12552270 TCGCGTTGCGATTCTCCCAA-T
1 TCGCAATGCGATT-TCACAATT
12552291 TCGCAATGCGA
1 TCGCAATGCGA
12552302 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTCACAATT
Found at i:12552316 original size:20 final size:21
Alignment explanation
Indices: 12552291--12552342 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12552281 TTCTCCCAAT
*
12552291 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
12552311 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
12552332 TCGCAATGCGA
1 TCGCAATGCGA
12552343 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:12552355 original size:41 final size:41
Alignment explanation
Indices: 12552328--12552444 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 41
12552318 GCGAATTTGG
*
12552328 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
12552369 AAAATCGTAACGCGATACTGACTTTCGCAACACGATACTGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-AC
** * * *
12552411 --TTTCGCAACTCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAT
12552445 TCTGACTTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 28 0.44
41 34 0.53
42 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:12552356 original size:20 final size:20
Alignment explanation
Indices: 12552332--12552460 Score: 143
Period size: 20 Copynumber: 6.4 Consensus size: 20
12552322 ATTTGGAAAA
* *
12552332 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
12552352 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
*
12552373 TCGTAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
12552393 TCGCAACACGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
12552413 TCGCAACTCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
12552433 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
12552453 TCGCAACG
1 TCGCAACG
12552461 AGATTCTGAA
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 76 0.81
21 14 0.15
22 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:12552465 original size:20 final size:20
Alignment explanation
Indices: 12552386--12552469 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
12552376 TAACGCGATA
*
12552386 CTGACTTTCGCAAC-ACGATA
1 CTGACTTTCGCAACGA-GATT
**
12552406 CTGACTTTCGCAACTCGATT
1 CTGACTTTCGCAACGAGATT
*
12552426 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGAGATT
12552446 CTGACTTTCGCAACGAGATT
1 CTGACTTTCGCAACGAGATT
12552466 CTGA
1 CTGA
12552470 AAATCGCAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.30
Consensus pattern (20 bp):
CTGACTTTCGCAACGAGATT
Found at i:12552476 original size:20 final size:20
Alignment explanation
Indices: 12552433--12552478 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
12552423 ATTCTGACTT
* ***
12552433 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGAAAA
12552453 TCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGAAAA
12552473 TCGCAA
1 TCGCAA
12552479 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGATTCTGAAAA
Found at i:12552477 original size:40 final size:40
Alignment explanation
Indices: 12552393--12552478 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
12552383 ATACTGACTT
** ***
12552393 TCGCAACACGATACTGACTTTCGCAACTCGATTCTGACTT
1 TCGCAACACGATACTGACTTTCGCAACGAGATTCTGAAAA
* *
12552433 TCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGAAAA
1 TCGCAACACGATACTGACTTTCGCAACGAGATTCTGAAAA
12552473 TCGCAA
1 TCGCAA
12552479 TCATCTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (40 bp):
TCGCAACACGATACTGACTTTCGCAACGAGATTCTGAAAA
Found at i:12552770 original size:20 final size:20
Alignment explanation
Indices: 12552676--12552766 Score: 155
Period size: 20 Copynumber: 4.5 Consensus size: 20
12552666 ATTCATTTGA
12552676 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
12552696 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
12552716 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATGG
* *
12552736 CTATCGCAATGAGAAAATGG
1 CTATCGCAACGCGAAAATGG
12552756 CTATCGCAACG
1 CTATCGCAACG
12552767 AGAATCGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:12552806 original size:20 final size:20
Alignment explanation
Indices: 12552790--12552836 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
12552780 GATTTTCTCA
12552790 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
12552810 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
12552830 TTGCGAT
1 TTGCGAT
12552837 TCTCTCGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:12552868 original size:20 final size:20
Alignment explanation
Indices: 12552790--12552879 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
12552780 GATTTTCTCA
* *
12552790 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGTCAGTTTCGCG
* *
12552810 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGTCAGTTTCGCG
*
12552830 TTGCGAT--TC----TCTCG
1 TTGCGATAGTCAGTTTCGCG
*
12552844 TTGCGATAGTCAGTTTCGTG
1 TTGCGATAGTCAGTTTCGCG
*
12552864 TTGCGATAGTCTGTTT
1 TTGCGATAGTCAGTTT
12552880 TGCCTTCAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
14 11 0.19
16 2 0.03
18 1 0.02
20 45 0.76
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCAGTTTCGCG
Found at i:12554421 original size:42 final size:42
Alignment explanation
Indices: 12554375--12554467 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
12554365 CCTCTTCAAC
* * *
12554375 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* *
12554417 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
12554459 GATGACAGG
1 GATGACAGG
12554468 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.20, C:0.15, G:0.43, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:12554427 original size:21 final size:21
Alignment explanation
Indices: 12554403--12554463 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
12554393 AACGGTGGGG
*
12554403 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
12554424 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
12554445 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
12554464 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:12554830 original size:20 final size:20
Alignment explanation
Indices: 12554805--12554857 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12554795 GAAGAATAGT
*
12554805 TTACTTTCGCAACATGAAAC
1 TTACTTTCGCAACATGAAAA
*
12554825 TTACTTTCGCAACGTGAAAA
1 TTACTTTCGCAACATGAAAA
* *
12554845 TGACTATCGCAAC
1 TTACTTTCGCAAC
12554858 GCGATAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (20 bp):
TTACTTTCGCAACATGAAAA
Found at i:12554876 original size:21 final size:20
Alignment explanation
Indices: 12554850--12554924 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
12554840 GAAAATGACT
12554850 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
* *
12554871 ATCGCAACGCGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAA
* *
12554891 TTCGCAACGAGATAATACATA
1 ATCGCAACGCGATAATACA-A
*
12554912 ATCGCAATGCGAT
1 ATCGCAACGCGAT
12554925 TTTCAAAGCG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.31
21 25 0.60
22 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:12554897 original size:20 final size:20
Alignment explanation
Indices: 12554827--12554906 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
12554817 CATGAAACTT
* *
12554827 ACTTTCGCAACGTGAAAATG
1 ACTTTCGCAACGCGATAATG
*
12554847 ACTATCGCAACGCGATAAT-
1 ACTTTCGCAACGCGATAATG
** *
12554866 ACAAAATCGCAACGCGATACTG
1 AC--TTTCGCAACGCGATAATG
*
12554888 ACTTTCGCAACGAGATAAT
1 ACTTTCGCAACGCGATAAT
12554907 ACATAATCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.60
21 15 0.31
22 2 0.04
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
ACTTTCGCAACGCGATAATG
Found at i:12554924 original size:41 final size:41
Alignment explanation
Indices: 12554831--12554924 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
12554821 AAACTTACTT
* * * *
12554831 TCGCAACGTGAAAATGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATACTGACTATCGCAACGAGATAATACAAAA
* *
12554872 TCGCAACGCGATACTGACTTTCGCAACGAGATAATACATAA
1 TCGCAACGCGATACTGACTATCGCAACGAGATAATACAAAA
*
12554913 TCGCAATGCGAT
1 TCGCAACGCGAT
12554925 TTTCAAAGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACGCGATACTGACTATCGCAACGAGATAATACAAAA
Found at i:12555119 original size:22 final size:22
Alignment explanation
Indices: 12555091--12555134 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12555081 CACTCTCTCA
*
12555091 CCCATCTCCGATGAAATCCATC
1 CCCATCTCCGACGAAATCCATC
12555113 CCCATCTCCGACGAAATCCATC
1 CCCATCTCCGACGAAATCCATC
12555135 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.43, G:0.09, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCATC
Found at i:12555436 original size:18 final size:18
Alignment explanation
Indices: 12555413--12555460 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
12555403 CGGGTCGATC
12555413 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
12555431 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
12555449 AGGTGATGGCTC
1 AGGTGATGGCTC
12555461 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:12556838 original size:20 final size:20
Alignment explanation
Indices: 12556789--12556838 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12556779 TGAAATTGAA
*
12556789 AATCGCAACACGAAAATGAC
1 AATCGCAACGCGAAAATGAC
**
12556809 AATCGCAACGCGAATTTGAC
1 AATCGCAACGCGAAAATGAC
*
12556829 TATCGCAACG
1 AATCGCAACG
12556839 AGAGAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAAAATGAC
Found at i:12557359 original size:20 final size:20
Alignment explanation
Indices: 12557331--12557403 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
12557321 GATTATGTAT
*
12557331 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12557351 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
12557371 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
12557391 TATCGCATTGCGA
1 TATCGCGTTGCGA
12557404 TTTTCAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:12557419 original size:21 final size:21
Alignment explanation
Indices: 12557393--12557445 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12557383 ATAGTCAGTA
12557393 TCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCAAAAT
* *
12557414 TCGCATTACGATTTTCCAAAT
1 TCGCATTGCGATTTTCAAAAT
*
12557435 TCGCTTTGCGA
1 TCGCATTGCGA
12557446 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCAAAAT
Found at i:12557952 original size:2 final size:2
Alignment explanation
Indices: 12557945--12557974 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12557935 ATAAAAATAC
12557945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12557975 TTTATATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12559444 original size:21 final size:20
Alignment explanation
Indices: 12559414--12559463 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
12559404 TTATTGAAAA
* *
12559414 AATAAAGAAAATAAAGATAC
1 AATAAAGAAAAGAAAAATAC
*
12559434 AATATAAGAAAAGAAAAATAT
1 AATA-AAGAAAAGAAAAATAC
12559455 AATAAAGAA
1 AATAAAGAA
12559464 TACAGCGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (20 bp):
AATAAAGAAAAGAAAAATAC
Found at i:12563976 original size:18 final size:18
Alignment explanation
Indices: 12563933--12563978 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
12563923 CAACGGTCAA
* * *
12563933 CGGGTCGAGTCAATGGGT
1 CGGGTCGGGTAAACGGGT
12563951 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
12563969 CGGGTCGGGT
1 CGGGTCGGGT
12563979 TGTGACCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:12568425 original size:2 final size:2
Alignment explanation
Indices: 12568413--12568450 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12568403 AAAAGAAAGA
*
12568413 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12568451 CATGGTGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12571090 original size:18 final size:18
Alignment explanation
Indices: 12571069--12571167 Score: 180
Period size: 18 Copynumber: 5.5 Consensus size: 18
12571059 TTTGTCCTGT
12571069 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
12571087 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
12571105 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
12571123 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
12571141 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
12571159 AAGACCACT
1 AGGACCACT
12571168 GATAATCCCT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 78 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.16
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:12572848 original size:20 final size:20
Alignment explanation
Indices: 12572823--12572876 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
12572813 TGACAACAAA
12572823 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
12572843 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
12572863 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
12572877 GCGAATATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:12572929 original size:20 final size:20
Alignment explanation
Indices: 12572906--12572957 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
12572896 TGCGATTTTC
*
12572906 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
12572926 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
12572946 CAAATTCGCAAC
1 CAAATTCGCAAC
12572958 TGGATTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:12572971 original size:19 final size:19
Alignment explanation
Indices: 12572945--12572995 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
12572935 AACGCGAAAG
*
12572945 TCAAATTCGCAACTGGATT
1 TCAAATTCGCAACTGAATT
*
12572964 TGAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
12572983 TCAAATTCGCAAC
1 TCAAATTCGCAAC
12572996 ACAAATGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:12578174 original size:21 final size:21
Alignment explanation
Indices: 12578150--12578205 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
12578140 GGCTTCTTCG
12578150 ATGATGATATAG-GCCTCTTGA
1 ATGATGATA-AGTGCCTCTTGA
* *
12578171 ATGAT-AGGAGGTGCCTCTTGA
1 ATGATGA-TAAGTGCCTCTTGA
*
12578192 ATGATGATAGGTGC
1 ATGATGATAAGTGC
12578206 ATCGGGCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (21 bp):
ATGATGATAAGTGCCTCTTGA
Found at i:12579041 original size:30 final size:30
Alignment explanation
Indices: 12579005--12579068 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
12578995 GAAGGACCTG
* *
12579005 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
12579035 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
12579065 TCCA
1 TCCA
12579069 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:12579833 original size:64 final size:64
Alignment explanation
Indices: 12579745--12580015 Score: 236
Period size: 64 Copynumber: 4.2 Consensus size: 64
12579735 CAATGAAGGT
* * *
12579745 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TCCTTATTAATGA
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTATCATT-TTAATGA
12579808 G
64 G
** ** * *
12579809 ATGCATCGATGCA-TACCTTATGCATCGATGCACTACTTGCATTTTATGTTCT-ATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATT-TTAATGA
12579872 G
64 G
* * * *
12579873 ATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAA-AAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATTTTAATGA-
12579936 G
64 G
* * * * *
12579937 ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTC-TTTTAAAG-
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTT-ATCATTTTAATGA
12579999 G
64 G
12580000 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
12580016 TATGAATGTG
Statistics
Matches: 171, Mismatches: 25, Indels: 22
0.78 0.11 0.10
Matches are distributed among these distances:
63 4 0.02
64 159 0.93
65 8 0.05
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTATCATTTTAATGAG
Found at i:12579979 original size:128 final size:128
Alignment explanation
Indices: 12579740--12580015 Score: 301
Period size: 128 Copynumber: 2.2 Consensus size: 128
12579730 TCTTTCAATG
* * * *
12579740 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAA
* *** **
12579805 TGAGATGCATCGATGCATACCTTATGCATCGATGCACTACTTGCATTTTATGTTCTAT-TATTA
66 AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTCGATGTTCT-TCTATTA
* * * ** * *
12579868 ATGGGATGCATCGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATT-TTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TCATTATTA
* *
12579932 AA-AGGATGCATCGATGCATTAGC-TATGCATCGATGCA-TCAAAGGCATTCGATGTTCTTCTTT
65 AAGA-GATGCATCGATGCA-TACCTTATGCATCGATGCACT-AAAGGCATTCGATGTTCTTCTAT
12579994 TA
127 TA
12579996 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
12580016 TATGAATGTG
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
127 3 0.02
128 114 0.93
129 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (128 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAA
AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTCGATGTTCTTCTATTA
Found at i:12584146 original size:64 final size:64
Alignment explanation
Indices: 12584058--12584328 Score: 218
Period size: 64 Copynumber: 4.2 Consensus size: 64
12584048 CAATGAAGGT
* * *
12584058 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TCCTTATTAATGA
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTATCATT-TTAATGA
12584121 G
64 G
** ** * *
12584122 ATGCATCGATGCA-TACCTTATGCATCGATGCACTACTTGCATTTTATGTTCT-ATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATT-TTAATGA
12584185 G
64 G
* * * *
12584186 ATGCATCGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAA-AAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATTTTAATGA-
12584249 G
64 G
* * * * * * *
12584250 ATGCATCGATGCATTAGC-TATGTATCGATGCATCAAAGGCATTTGATGTTCTTC-TTTTAAAG-
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTT-ATCATTTTAATGA
12584312 G
64 G
12584313 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
12584329 TATGAATGTG
Statistics
Matches: 169, Mismatches: 27, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
63 4 0.02
64 157 0.93
65 8 0.05
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTATCATTTTAATGAG
Found at i:12584292 original size:128 final size:128
Alignment explanation
Indices: 12584053--12584328 Score: 301
Period size: 128 Copynumber: 2.2 Consensus size: 128
12584043 TCTTTCAATG
* * * *
12584053 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAA
* *** *
12584118 TGAGATGCATCGATGCATACCTTATGCATCGATGCACTACTTGCATTTTATGTTCTAT-TATTA
66 AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTTGATGTTCT-TCTATTA
* * * ** * *
12584181 ATGGGATGCATCGATGCACTCCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATT-TTA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTT-TCATTATTA
* * *
12584245 AA-AGGATGCATCGATGCATTAGC-TATGTATCGATGCA-TCAAAGGCATTTGATGTTCTTCTTT
65 AAGA-GATGCATCGATGCA-TACCTTATGCATCGATGCACT-AAAGGCATTTGATGTTCTTCTAT
12584307 TA
127 TA
12584309 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
12584329 TATGAATGTG
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
127 3 0.02
128 114 0.93
129 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (128 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAA
AGAGATGCATCGATGCATACCTTATGCATCGATGCACTAAAGGCATTTGATGTTCTTCTATTA
Found at i:12585176 original size:12 final size:12
Alignment explanation
Indices: 12585157--12585198 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
12585147 GGGCCGCTGA
12585157 AAATAAATTAAT
1 AAATAAATTAAT
* *
12585169 ATATAAATTAGT
1 AAATAAATTAAT
*
12585181 AAATAAATAAAT
1 AAATAAATTAAT
12585193 AAATAA
1 AAATAA
12585199 TACCGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:12585452 original size:13 final size:13
Alignment explanation
Indices: 12585434--12585460 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12585424 CGTAAAGTAC
12585434 CGACCTCATGACG
1 CGACCTCATGACG
12585447 CGACCTCATGACG
1 CGACCTCATGACG
12585460 C
1 C
12585461 AAAGCACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.41, G:0.22, T:0.15
Consensus pattern (13 bp):
CGACCTCATGACG
Found at i:12587283 original size:13 final size:13
Alignment explanation
Indices: 12587265--12587290 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12587255 GGGTTTCTTC
12587265 AACAAAAAGACAA
1 AACAAAAAGACAA
12587278 AACAAAAAGACAA
1 AACAAAAAGACAA
12587291 CAAAGACAAA
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:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:12587539 original size:22 final size:22
Alignment explanation
Indices: 12587508--12587558 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
12587498 GATGGAGATA
12587508 GACGGATTTCGTCAGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
* * *
12587530 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
12587552 GACGGAT
1 GACGGAT
12587559 GTCACCGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:12587711 original size:20 final size:20
Alignment explanation
Indices: 12587686--12587770 Score: 134
Period size: 20 Copynumber: 4.2 Consensus size: 20
12587676 GCGTAAAAAC
* *
12587686 ATTTGACTTTCGCGTTGTGA
1 ATTTGACTATCGCGTTGCGA
12587706 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
12587726 ATTTGACTTTCGCGTTGAGA
1 ATTTGACTATCGCGTTGCGA
12587746 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
12587766 ATTTG
1 ATTTG
12587771 GAAAATCGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:12587731 original size:40 final size:40
Alignment explanation
Indices: 12587686--12587770 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
12587676 GCGTAAAAAC
*
12587686 ATTTGACTTTCGCGTTGTGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
12587726 ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
12587766 ATTTG
1 ATTTG
12587771 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (40 bp):
ATTTGACTTTCGCGTTGAGAATTTGACTATCGCGTTGCGA
Found at i:12589104 original size:2 final size:2
Alignment explanation
Indices: 12589097--12589121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12589087 GATCTGACTT
12589097 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12589122 CTTATGCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12590448 original size:18 final size:18
Alignment explanation
Indices: 12590378--12590440 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
12590368 GCGTAGAATT
*
12590378 TGTCCCGAATGACCACTG
1 TGTCCCGAATGACCACTA
*
12590396 TGTCCCGAATGATCACTA
1 TGTCCCGAATGACCACTA
*
12590414 TGCCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
12590432 TGTCCCGAA
1 TGTCCCGAA
12590441 AAACCACTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:12592885 original size:33 final size:33
Alignment explanation
Indices: 12592848--12592910 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
12592838 AAATGAAAAT
*
12592848 GGATTTTGAA-AATCAAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAATGAAAT-TTGAAGAA
**
12592881 GGATTTAGAACTCTCAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAATGAAATTTGAA
12592911 AGTATTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (33 bp):
GGATTTAGAACAATCAAAATGAAATTTGAAGAA
Found at i:12596832 original size:22 final size:21
Alignment explanation
Indices: 12596799--12596846 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
12596789 GGGATCGATC
12596799 CCCCCTTTA-GGGAACCAATT
1 CCCCCTTTAGGGGAACCAATT
*
12596819 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTT--AGGGGAACCAATT
12596842 CCCCC
1 CCCCC
12596847 CCACAGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
CCCCCTTTAGGGGAACCAATT
Done.