Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1109096 original size:3 final size:3
Alignment explanation
Indices: 1109088--1109119 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1109078 GTCGAAAAAA
1109088 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1109120 ACAAAAATAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1114184 original size:25 final size:26
Alignment explanation
Indices: 1114130--1114184 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
1114120 AGATTAGAAC
**
1114130 AAAATAAACAAAAGATAAAGAAATTG
1 AAAATAAACAAAAGATAAAGAAATAA
*
1114156 AAAATAAA-ATAAGATAAA-ATAATAA
1 AAAATAAACAAAAGATAAAGA-AATAA
1114181 AAAA
1 AAAA
1114185 ATCAAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 1 0.04
25 16 0.64
26 8 0.32
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (26 bp):
AAAATAAACAAAAGATAAAGAAATAA
Found at i:1115523 original size:19 final size:21
Alignment explanation
Indices: 1115482--1115524 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1115472 GGAAAAGATA
1115482 GAGAGAAACATAACGAAATAT
1 GAGAGAAACATAACGAAATAT
*
1115503 GAGAGAAA-ATAAGGAAA-AT
1 GAGAGAAACATAACGAAATAT
1115522 GAG
1 GAG
1115525 GTTACCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.58, C:0.05, G:0.26, T:0.12
Consensus pattern (21 bp):
GAGAGAAACATAACGAAATAT
Found at i:1116504 original size:30 final size:30
Alignment explanation
Indices: 1116442--1116504 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1116432 ATAATTATTG
* ** **
1116442 TTTAGTCCTTCAAATTTTTGTTTTTGTTAT
1 TTTAGTCCTTCAAAATTTTGTTAGTGCCAT
*
1116472 TTTAGTCCTTTAAAATTTTGTTAGTGCCAT
1 TTTAGTCCTTCAAAATTTTGTTAGTGCCAT
1116502 TTT
1 TTT
1116505 GGAGCCTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTAGTCCTTCAAAATTTTGTTAGTGCCAT
Found at i:1116691 original size:19 final size:19
Alignment explanation
Indices: 1116667--1116723 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 19
1116657 ATGTATGTTG
*
1116667 TTATTTTTTATTTATTTTA
1 TTATTTTTTATTTATTTCA
1116686 TTATTTAATATTATTTATTTCA
1 TTATTT--T-TTATTTATTTCA
*
1116708 TGT-TTTTTTATCTATT
1 T-TATTTTTTATTTATT
1116724 GTATGGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 14 0.44
20 1 0.03
21 1 0.03
22 15 0.47
23 1 0.03
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTTTTTATTTATTTCA
Found at i:1119474 original size:147 final size:147
Alignment explanation
Indices: 1119207--1119502 Score: 583
Period size: 147 Copynumber: 2.0 Consensus size: 147
1119197 CAGTTTATAT
*
1119207 GATAAATGACAGTAGATGAATGAATAAAGGAAAAATTAGTAGAATAACTAAAGGAATGAAAGAGT
1 GATAAATGACAATAGATGAATGAATAAAGGAAAAATTAGTAGAATAACTAAAGGAATGAAAGAGT
1119272 AAGTAAAAGAGACAACATAAGAACATTAGGAGATGTGTATCAATGTGTGCAATGAAAATTCGAGG
66 AAGTAAAAGAGACAACATAAGAACATTAGGAGATGTGTATCAATGTGTGCAATGAAAATTCGAGG
1119337 ACGAATTTTCTTAAAAG
131 ACGAATTTTCTTAAAAG
1119354 GATAAATGACAATAGATGAATGAATAAAGGAAAAATTAGTAGAATAACTAAAGGAATGAAAGAGT
1 GATAAATGACAATAGATGAATGAATAAAGGAAAAATTAGTAGAATAACTAAAGGAATGAAAGAGT
1119419 AAGTAAAAGAGACAACATAAGAACATTAGGAGATGTGTATCAATGTGTGCAATGAAAATTCGAGG
66 AAGTAAAAGAGACAACATAAGAACATTAGGAGATGTGTATCAATGTGTGCAATGAAAATTCGAGG
1119484 ACGAATTTTCTTAAAAG
131 ACGAATTTTCTTAAAAG
1119501 GA
1 GA
1119503 GGGGAGATTT
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 148 1.00
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (147 bp):
GATAAATGACAATAGATGAATGAATAAAGGAAAAATTAGTAGAATAACTAAAGGAATGAAAGAGT
AAGTAAAAGAGACAACATAAGAACATTAGGAGATGTGTATCAATGTGTGCAATGAAAATTCGAGG
ACGAATTTTCTTAAAAG
Found at i:1121534 original size:63 final size:62
Alignment explanation
Indices: 1121435--1121655 Score: 259
Period size: 63 Copynumber: 3.5 Consensus size: 62
1121425 AGAGTCGAGG
* ** *
1121435 AATTACCTATGTCTCTCAAGACATATGGACAGTATACCTATGTTCTATGGACCATATGGACAT
1 AATTACCTATGT-TTTCGGGACATATGGACAGTATACCTATGTTCTATGGAACATATGGACAT
* *
1121498 AATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCT-TCGGAACATATGGATAG
1 AATTACCTATGT-TTTCGGGACATATGGACAGTATACCTATGTTCTAT-GGAACATATGGACAT
* * * *
1121561 AATTACATATGTTTCTCGGGACTTATGGACAGTATAACTATGTTCTAAGGAACATATGGACAGT
1 AATTACCTATGTTT-TCGGGACATATGGACAGTATACCTATGTTCTATGGAACATATGGACA-T
* *
1121625 --TTACCTAGGTTCTTCGGGACCTATGGACAGT
1 AATTACCTATGTT-TTCGGGACATATGGACAGT
1121656 TGCCGAGGTT
Statistics
Matches: 138, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
62 29 0.21
63 109 0.79
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (62 bp):
AATTACCTATGTTTTCGGGACATATGGACAGTATACCTATGTTCTATGGAACATATGGACAT
Found at i:1121656 original size:31 final size:31
Alignment explanation
Indices: 1121437--1121656 Score: 182
Period size: 31 Copynumber: 7.0 Consensus size: 31
1121427 AGTCGAGGAA
**
1121437 TTACCTATG-TCTCTCAAGACATATGGACAGT
1 TTACCTATGTTCT-TCGGGACATATGGACAGT
*
1121468 ATACCTATGTTCTAT--GGACCATATGGACA-T
1 TTACCTATGTTCT-TCGGGA-CATATGGACAGT
1121498 AATTACCTATG-TCTTTCGGGACATATGGACAGT
1 --TTACCTATGTTC-TTCGGGACATATGGACAGT
* * * *
1121531 ATACCTATGTTCTTCGGAACATATGGATAGAA
1 TTACCTATGTTCTTCGGGACATATGGACAG-T
* *
1121563 TTACATATGTT-TCTCGGGACTTATGGACAGT
1 TTACCTATGTTCT-TCGGGACATATGGACAGT
* * ** *
1121594 ATAACTATGTTCTAAGGAACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* *
1121625 TTACCTAGGTTCTTCGGGACCTATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
1121656 T
1 T
1121657 GCCGAGGTTC
Statistics
Matches: 149, Mismatches: 28, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
30 3 0.02
31 93 0.62
32 49 0.33
33 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:1123081 original size:2 final size:2
Alignment explanation
Indices: 1123063--1123105 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1123053 TTACTTGACC
* *
1123063 AT AT AT TT A- AT AA 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 AT AT
1123104 AT
1 AT
1123106 CATTCTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1124410 original size:449 final size:449
Alignment explanation
Indices: 1123572--1124414 Score: 1481
Period size: 449 Copynumber: 1.9 Consensus size: 449
1123562 CCATGCATAA
* *
1123572 TGTTGGGTTATGGGGCCCATCGATCACCCTTAGAGATTCTATCGTGTATGAGCGCGATATCGATA
1 TGTTGGGTTATGGGGCCAATCGATCACCCTTAGAGATTCTATCGTGTATGAGCACGATATCGATA
1123637 CGTGACTGTCCAACCTGCCGAGGCCCACGTGTGCCTTATAAAGCCCCTAGGCCCGCCCGCAGTAC
66 CGTGACTGTCCAACCTGCCGAGGCCCACGTGTGCCTTATAAAGCCCCTAGGCCCGCCCGCAGTAC
*
1123702 GCTATAGATGCGGGGCTTTGCAATGCCGTGGTGAACTGTGGCGGGTGCCCCAAAAGAATCTACCT
131 GCTATAGATGCGGGGCTTTGCAATGCCGTGGTGAACTGTGGCGGGTGCCCCAAAAGAATCCACCT
*
1123767 TGGCTTGGGGGAACCCAGTGATCACCCACTACAAAGATATAAGGTTAAAATGGCCCACCTACTTA
196 TGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATAAGGTTAAAATGGCCCACCTACTTA
*
1123832 TCACCAATTGGTTTTAAGAAGGAATGGTGATCATTCGCTTCAGAACTCTATAGTTAAGCGTGCTT
261 TCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATAGTTAAGCGTGCTT
* * *
1123897 TGACAAGGGAAATACAGGGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCGATCC
326 GGACAAGGGAAATACAGGGATGGGTAACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGATCC
1123962 TACAATTGCTATTAGAGCAGGTTGTAGGTTCGAATCCCCCAGGTGTCGTTGGGGGTGAT
391 TACAATTGCTATTAGAGCAGGTTGTAGGTTCGAATCCCCCAGGTGTCGTTGGGGGTGAT
* * * * * *
1124021 TGTTGGGTTATAGGGTCCAAT-GATCACCCTTAGGGATTCTATTGTGTATGGGCATGATATCGGT
1 TGTTGGGTTAT-GGGGCCAATCGATCACCCTTAGAGATTCTATCGTGTATGAGCACGATATCGAT
*
1124085 ACGTGACTGTCCAACCTGTCGAGGCCCACGTGTGCCTTATAAAGCCCCTAGGCCCGCCCGCAGTA
65 ACGTGACTGTCCAACCTGCCGAGGCCCACGTGTGCCTTATAAAGCCCCTAGGCCCGCCCGCAGTA
* *
1124150 CGCTATAGATGCGGGGCTTTGCAATGCCGTGGTGAACTGTGTCGGGTGCCCTAAAAGAATCCACC
130 CGCTATAGATGCGGGGCTTTGCAATGCCGTGGTGAACTGTGGCGGGTGCCCCAAAAGAATCCACC
1124215 TTGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATAAGGTTAAAATGGCCCACCTACTT
195 TTGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATAAGGTTAAAATGGCCCACCTACTT
*
1124280 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTGTAGTTAAGCGTGCT
260 ATCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATAGTTAAGCGTGCT
* * *
1124345 TGGACAAGGGCAATCCAGGGATGGGTAACCCACTAGGAAGTTGTTTAGAAATGAATGACTCGATC
325 TGGACAAGGGAAATACAGGGATGGGTAACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGATC
1124410 CTACA
390 CTACA
1124415 GAAGGCGTCA
Statistics
Matches: 372, Mismatches: 21, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
449 365 0.98
450 7 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (449 bp):
TGTTGGGTTATGGGGCCAATCGATCACCCTTAGAGATTCTATCGTGTATGAGCACGATATCGATA
CGTGACTGTCCAACCTGCCGAGGCCCACGTGTGCCTTATAAAGCCCCTAGGCCCGCCCGCAGTAC
GCTATAGATGCGGGGCTTTGCAATGCCGTGGTGAACTGTGGCGGGTGCCCCAAAAGAATCCACCT
TGGCTTGGGGGAACCCAATGATCACCCACTACAAAGATATAAGGTTAAAATGGCCCACCTACTTA
TCACCAATTGGTTTTAAGAAGGAATGGTGACCATTCGCTTCAGAACTCTATAGTTAAGCGTGCTT
GGACAAGGGAAATACAGGGATGGGTAACCCACTAGGAAGTTGTTCAGAAATGAATGACTCGATCC
TACAATTGCTATTAGAGCAGGTTGTAGGTTCGAATCCCCCAGGTGTCGTTGGGGGTGAT
Found at i:1126216 original size:159 final size:159
Alignment explanation
Indices: 1125939--1126237 Score: 528
Period size: 159 Copynumber: 1.9 Consensus size: 159
1125929 ATACTAAGGC
1125939 ATGCTAAAAGCCCATATCATCCTTCAGAAAGATCATTGATTTGAACAAATATTTACAATGATACA
1 ATGCTAAAAGCCCATATCATCCTTCAGAAAGATCATTGATTTGAACAAATATTTACAATGATACA
* * *
1126004 GAAAGGTATGAAGAATGAAAATGGTGAAATAGTGACAATGGAGATGACTATATATGATCATTTTT
66 GAAAGGAATGAAGAATGAAAATGGTGAAATAGTGACAATGGAGATGACCATATATGATCATTTTG
1126069 TTCATCATACGGTTAGCAAACACTGGGGT
131 TTCATCATACGGTTAGCAAACACTGGGGT
*
1126098 ATGCTAAAAGCCCATATTATCCTTCAGAAAGATCATTGATTTGAACAAATATTT-CTAATGATAC
1 ATGCTAAAAGCCCATATCATCCTTCAGAAAGATCATTGATTTGAACAAATATTTAC-AATGATAC
* *
1126162 AGAAAGGAATGAAGAATGGAAATGGTGAAATAGTGACAATGGAGATTACCATATATGATCATTTT
65 AGAAAGGAATGAAGAATGAAAATGGTGAAATAGTGACAATGGAGATGACCATATATGATCATTTT
1126227 GTTCATCATAC
130 GTTCATCATAC
1126238 TGTTGCATTA
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
158 1 0.01
159 132 0.99
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (159 bp):
ATGCTAAAAGCCCATATCATCCTTCAGAAAGATCATTGATTTGAACAAATATTTACAATGATACA
GAAAGGAATGAAGAATGAAAATGGTGAAATAGTGACAATGGAGATGACCATATATGATCATTTTG
TTCATCATACGGTTAGCAAACACTGGGGT
Found at i:1127843 original size:23 final size:23
Alignment explanation
Indices: 1127809--1127877 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1127799 CACCACAGCT
*
1127809 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
1127832 CGTAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1127855 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1127878 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1128741 original size:21 final size:21
Alignment explanation
Indices: 1128685--1128733 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1128675 ATACCGTTGA
1128685 TGCATCGGTACACATTGAATG
1 TGCATCGGTACACATTGAATG
1128706 TGCATCGGTACACATTGAATG
1 TGCATCGGTACACATTGAATG
1128727 TGCATCG
1 TGCATCG
1128734 ATGCACATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGGTACACATTGAATG
Found at i:1130839 original size:541 final size:541
Alignment explanation
Indices: 1129817--1130896 Score: 2061
Period size: 541 Copynumber: 2.0 Consensus size: 541
1129807 CCGAGAAAAC
*
1129817 AACATTAGATCTTCTTTAAATATAATTAACATACACTTTAAAGAATCTTTTCACATCACTTTGCA
1 AACATTAGATCTTCTTTAAATATAATTAACATACACTTTAAAGAATCTTTTCACATCACCTTGCA
1129882 CACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCATATCCGAT
66 CACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCATATCCGAT
1129947 CCTTTAACTCATCCCTTTCATTTCTTTATTCCATTATTCCTATATTTATTCCTTATACCCAAATC
131 CCTTTAACTCATCCCTTTCATTTCTTTATTCCATTATTCCTATATTTATTCCTTATACCCAAATC
*
1130012 ATATCTTTCCTTTCATGTTCACATACTCTTGTCTTATCATCTATACTCATCTCTATGTATCAATC
196 ATATATTTCCTTTCATGTTCACATACTCTTGTCTTATCATCTATACTCATCTCTATGTATCAATC
*
1130077 TTCATTGCATCCTCATAACTTTGATAATCCATTTACCTATATAGAACTTCATTCTTTATCATTTC
261 TTCATTGCATCCTCATAACTTTGATAACCCATTTACCTATATAGAACTTCATTCTTTATCATTTC
1130142 TTATACTTGTATTTTTCTTCCTTAAGGTTCCATGCAAATACTTATCTCCTTTTCTACATCATAGC
326 TTATACTTGTATTTTTCTTCCTTAAGGTTCCATGCAAATACTTATCTCCTTTTCTACATCATAGC
1130207 TATCTGATCAGAATACACAACTATATTCAGATTCACTTCATAATCAATTAACTCAACTTTATCTT
391 TATCTGATCAGAATACACAACTATATTCAGATTCACTTCATAATCAATTAACTCAACTTTATCTT
1130272 TTCCTCCAATCTTATAACTCTATCACCTTTACTCTGAAAACTAGTCAATAACATCTGTTCAATCT
456 TTCCTCCAATCTTATAACTCTATCACCTTTACTCTGAAAACTAGTCAATAACATCTGTTCAATCT
1130337 AGGGCACAAGCCCTAGTCAAT
521 AGGGCACAAGCCCTAGTCAAT
1130358 AACATTAGATCTTCTTTAAATATAATTAACATACACTTTAAAGAATCTTTTCACATCACCTTGCA
1 AACATTAGATCTTCTTTAAATATAATTAACATACACTTTAAAGAATCTTTTCACATCACCTTGCA
*
1130423 CACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCATATCTGAT
66 CACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCATATCCGAT
* *
1130488 CCTTTAACTCATCCCTTTCATTTCTTTATTTCATTATTCCTATATTTATTCCTTATATCCAAATC
131 CCTTTAACTCATCCCTTTCATTTCTTTATTCCATTATTCCTATATTTATTCCTTATACCCAAATC
1130553 ATATATTTCCTTTCATGTTCACATACTCTTGTCTTATCATCTATACTCATCTCTATGTATCAATC
196 ATATATTTCCTTTCATGTTCACATACTCTTGTCTTATCATCTATACTCATCTCTATGTATCAATC
*
1130618 TTCATTGCATTCTCATAACTTTGATAACCCATTTACCTATATAGAACTTCATTCTTTATCATTTC
261 TTCATTGCATCCTCATAACTTTGATAACCCATTTACCTATATAGAACTTCATTCTTTATCATTTC
*
1130683 TTATACTTGTATTTTTGTTCCTTAAGGTTCCATGCAAATACTTATCTCCTTTTCTACATCATAGC
326 TTATACTTGTATTTTTCTTCCTTAAGGTTCCATGCAAATACTTATCTCCTTTTCTACATCATAGC
1130748 TATCTGATCAGAATACACAACTATATTCAGATTCACTTCATAATCAATTAACTCAACTTTATCTT
391 TATCTGATCAGAATACACAACTATATTCAGATTCACTTCATAATCAATTAACTCAACTTTATCTT
* * *
1130813 TTCCTTCAATCTTATAACTCTATCACCTTTACTCTGACAACTAGTCAATAACATTTGTTCAATCT
456 TTCCTCCAATCTTATAACTCTATCACCTTTACTCTGAAAACTAGTCAATAACATCTGTTCAATCT
1130878 AGGGCACAAGCCCTAGTCA
521 AGGGCACAAGCCCTAGTCA
1130897 TCCAATCATA
Statistics
Matches: 528, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
541 528 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (541 bp):
AACATTAGATCTTCTTTAAATATAATTAACATACACTTTAAAGAATCTTTTCACATCACCTTGCA
CACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCATATCCGAT
CCTTTAACTCATCCCTTTCATTTCTTTATTCCATTATTCCTATATTTATTCCTTATACCCAAATC
ATATATTTCCTTTCATGTTCACATACTCTTGTCTTATCATCTATACTCATCTCTATGTATCAATC
TTCATTGCATCCTCATAACTTTGATAACCCATTTACCTATATAGAACTTCATTCTTTATCATTTC
TTATACTTGTATTTTTCTTCCTTAAGGTTCCATGCAAATACTTATCTCCTTTTCTACATCATAGC
TATCTGATCAGAATACACAACTATATTCAGATTCACTTCATAATCAATTAACTCAACTTTATCTT
TTCCTCCAATCTTATAACTCTATCACCTTTACTCTGAAAACTAGTCAATAACATCTGTTCAATCT
AGGGCACAAGCCCTAGTCAAT
Found at i:1132672 original size:23 final size:23
Alignment explanation
Indices: 1132646--1132727 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
1132636 GCTCGTATAT
**
1132646 ATTGCACCGAAGTGCCACACAGA
1 ATTGCACCGAAGTGCCACGTAGA
1132669 ATTGCACCGAAGTGCCACGTAGA
1 ATTGCACCGAAGTGCCACGTAGA
* *
1132692 ATTGCACCGTAGTGCCGCGTAGA
1 ATTGCACCGAAGTGCCACGTAGA
*
1132715 AATGCACCGAAGT
1 ATTGCACCGAAGT
1132728 ACCATATAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (23 bp):
ATTGCACCGAAGTGCCACGTAGA
Found at i:1138853 original size:21 final size:21
Alignment explanation
Indices: 1138817--1138898 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 21
1138807 TTGGTGCAGA
*
1138817 GGGAATCGATGCCCCCTTGAAG
1 GGGAATCGAT-TCCCCTTGAAG
*
1138839 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATT-CCCC-TTGAAG
*
1138862 GGGAATCGATTCCCCCTGTAA-
1 GGGAATCGATTCCCCTTG-AAG
*
1138883 GGGAATCGATACCCCT
1 GGGAATCGATTCCCCT
1138899 CTGGGTTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
21 16 0.31
22 19 0.37
23 16 0.31
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (21 bp):
GGGAATCGATTCCCCTTGAAG
Found at i:1138859 original size:23 final size:23
Alignment explanation
Indices: 1138817--1138897 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
1138807 TTGGTGCAGA
*
1138817 GGGAATCGATGCCCCC-TTGAAG
1 GGGAATCGATTCCCCCTTTGAAG
*
1138839 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCTTTGAAG
*
1138862 GGGAATCGATTCCCCCTGT-AA-
1 GGGAATCGATTCCCCCTTTGAAG
*
1138883 GGGAATCGATACCCC
1 GGGAATCGATTCCCC
1138898 TCTGGGTTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 14 0.26
22 16 0.30
23 23 0.43
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (23 bp):
GGGAATCGATTCCCCCTTTGAAG
Found at i:1139294 original size:9 final size:10
Alignment explanation
Indices: 1139262--1139292 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1139252 AAAACATAAG
1139262 AATTTTTGAA
1 AATTTTTGAA
1139272 AATTTTTGAA
1 AATTTTTGAA
1139282 AATTTTTGAA
1 AATTTTTGAA
1139292 A
1 A
1139293 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (10 bp):
AATTTTTGAA
Found at i:1142661 original size:2 final size:2
Alignment explanation
Indices: 1142654--1142693 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1142644 ATGTCTTATC
1142654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
1142694 GGTCCATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1144889 original size:42 final size:42
Alignment explanation
Indices: 1144821--1144902 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
1144811 CACAAATTTA
* * * *
1144821 TAAATCCTTTGGGTTATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
1144863 TAAAACCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1144903 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TAAAACCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
Found at i:1145140 original size:42 final size:42
Alignment explanation
Indices: 1145070--1145151 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
1145060 CACAAATTTG
* * *
1145070 TAAATCCTTCGGGTCATTTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTTCGGGTCATCTGTTAGTCTTTCGAGCAAGATGCT
1145112 TAAAACCTTCGGGTCATCTGTCTA-TCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTGT-TAGTCTTTCGAGCAAGATG
1145152 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTGTTAGTCTTTCGAGCAAGATGCT
Found at i:1145195 original size:249 final size:249
Alignment explanation
Indices: 1144735--1145607 Score: 1523
Period size: 249 Copynumber: 3.5 Consensus size: 249
1144725 CCCAACCAAC
* * *
1144735 AAGTTTCTCATTTAATCTTTTTTAGAAAATGAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
1 AAGTTTCTCATTTAA--TGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
* * *
1144800 AAAGTATTTCCCACAAATTTATAAATCCTTTGGGTTATCTGTTAGTCTTTCGAGCATGATGCTTA
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
*
1144865 AAACCTTTGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
129 AAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
1144930 CTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
194 CTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
*
1144986 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAATAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
* *
1145051 AATATTTCCCACAAATTTGTAAATCCTTCGGGTCATTTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
1145116 ACCTTCGGGTCATCTGTCTA-TCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCC
131 ACCTTCGGGTCATCTGTC-AGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCC
*
1145180 TTTGGGTAGGATGTTCACATATGATTTTCGTATGAAAATGAGATAGCGATTTTCA
195 TTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
* *
1145235 AAGTTTCTCATTTAATGTTTTAGAAAATGAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
* *
1145300 AGTATTTCCCACAAATTAGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAACATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
* * *
1145365 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCTTTAAGGCCATCCGTAAAGCTT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
1145430 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
*
1145484 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
* *
1145549 AGTATTTCCCACAAATTTGTAAATCCTTTGGGTCATCTGTTAGTCTTTCGAGCAAGATG
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATG
1145608 ATAAGTCCTT
Statistics
Matches: 591, Mismatches: 29, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
248 1 0.00
249 574 0.97
250 1 0.00
251 15 0.03
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (249 bp):
AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
Found at i:1145846 original size:48 final size:47
Alignment explanation
Indices: 1145735--1145924 Score: 330
Period size: 47 Copynumber: 4.0 Consensus size: 47
1145725 TCCGAGTAAT
1145735 AAAA-CCTTCGGGTCATCCATAAGACCTTCAGTGCAAGG-TGTTTTCA
1 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGC-AGGATGTTTTCA
1145781 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTTCA
1 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATG-TTTTCA
1145829 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
1 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
* *
1145876 AAAAGCCTTCGGTTCATCCATAAGACCTTCAGGGCAGGATGTTTTCA
1 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
1145923 AA
1 AA
1145925 TGAGATTTTA
Statistics
Matches: 139, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
46 7 0.05
47 85 0.61
48 47 0.34
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (47 bp):
AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
Found at i:1145902 original size:95 final size:93
Alignment explanation
Indices: 1145735--1145924 Score: 328
Period size: 95 Copynumber: 2.0 Consensus size: 93
1145725 TCCGAGTAAT
1145735 AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGGTGTTTTCAAAAAGCCTTCGGGTCATCC
1 AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGGTGTTTTCAAAAAGCCTTCGGGTCATCC
*
1145800 ATAAGACCTTCAGTGCAGGATGTTTTTCA
66 ATAAGACCTTCAGGGCAGGATG-TTTTCA
*
1145829 AAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGC-AGGATGTTTTCAAAAAGCCTTCGGTTCAT
1 AAAA-CCTTCGGGTCATCCATAAGACCTTCAGTGCAAGG-TGTTTTCAAAAAGCCTTCGGGTCAT
1145893 CCATAAGACCTTCAGGGCAGGATGTTTTCA
64 CCATAAGACCTTCAGGGCAGGATGTTTTCA
1145923 AA
1 AA
1145925 TGAGATTTTA
Statistics
Matches: 92, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
94 15 0.16
95 77 0.84
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (93 bp):
AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGGTGTTTTCAAAAAGCCTTCGGGTCATCC
ATAAGACCTTCAGGGCAGGATGTTTTCA
Found at i:1146502 original size:28 final size:28
Alignment explanation
Indices: 1146470--1146544 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
1146460 TACCTTTCAT
1146470 ACCCAGCAGCCCCTCCACGTTTCAAAAA
1 ACCCAGCAGCCCCTCCACGTTTCAAAAA
* **
1146498 ACCCAGTAGCCCCTCCACGTTTCAAGTA
1 ACCCAGCAGCCCCTCCACGTTTCAAAAA
1146526 ACCCAGCAGCCCCCTCCAC
1 ACCCAGCAG-CCCCTCCAC
1146545 CACAACAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.79
29 9 0.21
ACGTcount: A:0.27, C:0.47, G:0.12, T:0.15
Consensus pattern (28 bp):
ACCCAGCAGCCCCTCCACGTTTCAAAAA
Found at i:1147246 original size:19 final size:19
Alignment explanation
Indices: 1147219--1147256 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1147209 TTTGTGCCCT
*
1147219 TTTTGTTTTATTT-ATATTA
1 TTTTATTTT-TTTAATATTA
1147238 TTTTATTTTTTTAATATTA
1 TTTTATTTTTTTAATATTA
1147257 ATACTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTATTTTTTTAATATTA
Found at i:1155802 original size:15 final size:15
Alignment explanation
Indices: 1155782--1155813 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1155772 TAATATGAAG
1155782 GACCATAACAAGGAA
1 GACCATAACAAGGAA
1155797 GACCATAACAAGGAA
1 GACCATAACAAGGAA
1155812 GA
1 GA
1155814 TCAACAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.06
Consensus pattern (15 bp):
GACCATAACAAGGAA
Found at i:1156331 original size:21 final size:21
Alignment explanation
Indices: 1156300--1156405 Score: 103
Period size: 21 Copynumber: 5.1 Consensus size: 21
1156290 CGATTTACAT
*
1156300 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* **
1156321 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAGTCCAA
*
1156342 ATT--CGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATAGTCCAA
* *
1156361 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
1156384 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
1156403 ATT
1 ATT
1156406 TGTTTCTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
19 25 0.37
21 35 0.51
23 8 0.12
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:1156355 original size:40 final size:42
Alignment explanation
Indices: 1156307--1156402 Score: 169
Period size: 40 Copynumber: 2.3 Consensus size: 42
1156297 CATATTCGCA
1156307 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1156347 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1156389 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1156403 ATTTGTTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 26 0.50
41 2 0.04
42 24 0.46
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1156996 original size:5 final size:5
Alignment explanation
Indices: 1156988--1157027 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
1156978 CCGCCGTCCG
*
1156988 TCTCG TCTCT TCTC- TCTCT TCTCT TCTCT TCTCT TCTCT T
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT T
1157028 TTCGGGTCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.00, C:0.40, G:0.03, T:0.57
Consensus pattern (5 bp):
TCTCT
Found at i:1157307 original size:40 final size:42
Alignment explanation
Indices: 1157145--1157445 Score: 497
Period size: 42 Copynumber: 7.3 Consensus size: 42
1157135 TGCGATTTTG
1157145 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1157187 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1157229 AACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1157271 GACTATCGCAACGAATTTGG-A-AAATCACAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1157311 GACTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1157353 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1157393 GACTATCGCAACGAATTTGG-A-AAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1157433 GACTATCGCAACG
1 GACTATCGCAACG
1157446 CGAACTTGGA
Statistics
Matches: 246, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
40 108 0.44
41 3 0.01
42 135 0.55
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1157470 original size:82 final size:82
Alignment explanation
Indices: 1157145--1157445 Score: 507
Period size: 82 Copynumber: 3.7 Consensus size: 82
1157135 TGCGATTTTG
1157145 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-A-
*
1157210 AAATCGCAACACGAACTTC
64 AAATCGCAACGCGAACTTC
* *
1157229 AACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
* *
1157294 ATCACAATGCGAACTTC
66 ATCGCAACGCGAACTTC
*
1157311 GACTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1157376 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
*
1157393 GACTATCGCAACGAATTTGG-A-AAATCGCAATGCGAACTTCGACTATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
1157446 CGAACTTGGA
Statistics
Matches: 205, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
80 30 0.15
81 1 0.00
82 113 0.55
83 1 0.00
84 60 0.29
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTC
Found at i:1157508 original size:21 final size:21
Alignment explanation
Indices: 1157479--1157568 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 21
1157469 AATATGTAAA
*
1157479 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1157500 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* ** *
1157521 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTCCAAGT
*
1157542 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1157561 TTGCGTTG
1 TCGCGTTG
1157569 TGAATTATCG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.25
21 41 0.75
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1157558 original size:40 final size:41
Alignment explanation
Indices: 1157479--1157561 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 41
1157469 AATATGTAAA
*
1157479 TCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAATTC-CGTTGCGATAGTCGAAGT
**
1157521 TCGCATTGCGATTTTCCAAATT-CGTTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAATTCCGTTGCGATAGTCGAAGT
1157561 T
1 T
1157562 TGCGTTGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 19 0.50
42 19 0.50
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATAGTCCAAATTCCGTTGCGATAGTCGAAGT
Found at i:1161134 original size:15 final size:16
Alignment explanation
Indices: 1161114--1161143 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1161104 AAATAAAATA
1161114 TAATTAAT-AATTTAT
1 TAATTAATCAATTTAT
1161129 TAATTAATCAATTTA
1 TAATTAATCAATTTA
1161144 GATAATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTAATCAATTTAT
Found at i:1165792 original size:86 final size:86
Alignment explanation
Indices: 1165646--1165817 Score: 310
Period size: 86 Copynumber: 2.0 Consensus size: 86
1165636 ATAGTGGTTC
* *
1165646 GACTTCTAAACAAGTCTACATCCACTACCTTAGCACCACACTAAGGATTTTATAATAAATTCACT
1 GACTTCTAAACAAGTCTACATCCACTACCTTAACACCACACTAAGGATTTTATAACAAATTCACT
1165711 AATTTGGTT-TTTCTTTTTCTA
66 AATTT-GTTCTTTCTTTTTCTA
1165732 GACTTCTAAACAAGTCTACATCCACTACCTTAACACCACACTAAGGATTTTATAACAAATTCACT
1 GACTTCTAAACAAGTCTACATCCACTACCTTAACACCACACTAAGGATTTTATAACAAATTCACT
1165797 AATTTGTTCTTTCTTTTTCTA
66 AATTTGTTCTTTCTTTTTCTA
1165818 TGCTCAAGAG
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
85 3 0.04
86 80 0.96
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (86 bp):
GACTTCTAAACAAGTCTACATCCACTACCTTAACACCACACTAAGGATTTTATAACAAATTCACT
AATTTGTTCTTTCTTTTTCTA
Found at i:1168598 original size:24 final size:22
Alignment explanation
Indices: 1168547--1168604 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
1168537 AATTTAAAAT
*
1168547 TAATTTTATTTCAAATAAATAA
1 TAATATTATTTCAAATAAATAA
1168569 TAAATATTATTTCCAAATAAATAAA
1 T-AATATTATTT-CAAATAAAT-AA
*
1168594 TAATATGATTT
1 TAATATTATTT
1168605 TAAAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 18 0.58
25 3 0.10
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATATTATTTCAAATAAATAA
Found at i:1168666 original size:23 final size:22
Alignment explanation
Indices: 1168640--1168700 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
1168630 CTATTTTCAT
* *
1168640 AATATTATAAATATACTTTTTA
1 AATATTATAAATAAACTTTATA
1168662 GAATAATT-TAATATAAACTTTATA
1 -AAT-ATTATAA-ATAAACTTTATA
1168686 AATATATATAAATAA
1 AATAT-TATAAATAA
1168701 TTATTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.44
24 16 0.50
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATTATAAATAAACTTTATA
Found at i:1173136 original size:16 final size:16
Alignment explanation
Indices: 1173115--1173146 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1173105 TGAGATAACG
1173115 TAAAGAAAATAAAACA
1 TAAAGAAAATAAAACA
1173131 TAAAGAAAATAAAACA
1 TAAAGAAAATAAAACA
1173147 CTTAAAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
TAAAGAAAATAAAACA
Found at i:1176228 original size:17 final size:17
Alignment explanation
Indices: 1176170--1176234 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 17
1176160 AAAGTACATC
*
1176170 TTTAATATTTAAATTA-
1 TTTAATTTTTAAATTAT
* *
1176186 -TT-AGTTTTAATTTAT
1 TTTAATTTTTAAATTAT
*
1176201 TTTAATATTTAAATT-T
1 TTTAATTTTTAAATTAT
1176217 TTTAAGTTTTTAAATTAT
1 TTTAA-TTTTTAAATTAT
1176235 ACATAAAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 8 0.22
17 17 0.46
18 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAATTTTTAAATTAT
Found at i:1179223 original size:22 final size:22
Alignment explanation
Indices: 1179198--1179240 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1179188 TTAATCGAAT
*
1179198 CATTCAGCTCTGAATGTTGAAG
1 CATTCAACTCTGAATGTTGAAG
*
1179220 CATTCAATTCTGAATGTTGAA
1 CATTCAACTCTGAATGTTGAA
1179241 ATCGTTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (22 bp):
CATTCAACTCTGAATGTTGAAG
Found at i:1179325 original size:22 final size:23
Alignment explanation
Indices: 1179284--1179331 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1179274 TGAATGATTC
1179284 AGTGCTGACTGATTCATCAAAAT
1 AGTGCTGACTGATTCATCAAAAT
*
1179307 AGTGTTGACTGA-TCATCAAAAT
1 AGTGCTGACTGATTCATCAAAAT
1179329 AGT
1 AGT
1179332 AATGAATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (23 bp):
AGTGCTGACTGATTCATCAAAAT
Found at i:1179341 original size:22 final size:22
Alignment explanation
Indices: 1179297--1179341 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1179287 GCTGACTGAT
** *
1179297 TCATCAAAATAGTGTTGACTGA
1 TCATCAAAATAGTAATGAATGA
1179319 TCATCAAAATAGTAATGAATGA
1 TCATCAAAATAGTAATGAATGA
1179341 T
1 T
1179342 TCAGCACAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (22 bp):
TCATCAAAATAGTAATGAATGA
Found at i:1179380 original size:28 final size:29
Alignment explanation
Indices: 1179334--1179402 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1179324 AAAATAGTAA
1179334 TGAATGATTC--AGCACAGAA-TACATTC
1 TGAATGATTCAGAGCACAGAAGTACATTC
*
1179360 TGAATGATTGAGAGCACAGAAGTACATTC
1 TGAATGATTCAGAGCACAGAAGTACATTC
1179389 TGAATGATTCAGAG
1 TGAATGATTCAGAG
1179403 TTATATCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 9 0.24
28 9 0.24
29 20 0.53
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (29 bp):
TGAATGATTCAGAGCACAGAAGTACATTC
Found at i:1181916 original size:58 final size:58
Alignment explanation
Indices: 1181827--1181952 Score: 188
Period size: 58 Copynumber: 2.2 Consensus size: 58
1181817 ATGTTTTAAA
* *
1181827 TAATTATTTTTTACTTTTAATGTTTTAGGTTTGGACC-AAACAGGCCTAATAACAAAT
1 TAATTATTTTTTACTTTTAATGTTATAGGTTTGGACCAAAACAGACCTAATAACAAAT
1181884 TAATTAATTTTTTACTTTTAATGTTATAGGTTTGGACCAAAACAGACCTAAT---AAAT
1 TAATT-ATTTTTTACTTTTAATGTTATAGGTTTGGACCAAAACAGACCTAATAACAAAT
*
1181940 TAATTATATTTTA
1 TAATTATTTTTTA
1181953 GATTTGATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
55 7 0.11
56 9 0.14
57 5 0.08
58 31 0.48
59 12 0.19
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (58 bp):
TAATTATTTTTTACTTTTAATGTTATAGGTTTGGACCAAAACAGACCTAATAACAAAT
Found at i:1186950 original size:18 final size:18
Alignment explanation
Indices: 1186929--1186980 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
1186919 AACAATAAAT
1186929 TAATTTAAATAAAATTGA
1 TAATTTAAATAAAATTGA
* * *
1186947 TAATTT-ATTAAAAATGT
1 TAATTTAAATAAAATTGA
1186964 TAGATTTATAATAAAAT
1 TA-ATTTA-AATAAAAT
1186981 AATAGAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 10 0.38
18 10 0.38
20 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (18 bp):
TAATTTAAATAAAATTGA
Found at i:1187645 original size:32 final size:32
Alignment explanation
Indices: 1187566--1187674 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
1187556 AGCTAAACCG
* *
1187566 AAAATCAACCGATCCGATATTGACTCGACCC-
1 AAAATCAACCGATTCGATATTGACCCGACCCA
* * * *
1187597 GAAATCTAAGCTATTCGATATTAACCCGACCCA
1 AAAATC-AACCGATTCGATATTGACCCGACCCA
* *
1187630 AAAATCAACCGATTCGGTATTGACCCGATCCA
1 AAAATCAACCGATTCGATATTGACCCGACCCA
1187662 AAAATCAACCGAT
1 AAAATCAACCGAT
1187675 CCAAACCGAA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
31 5 0.08
32 54 0.84
33 5 0.08
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (32 bp):
AAAATCAACCGATTCGATATTGACCCGACCCA
Found at i:1188402 original size:30 final size:31
Alignment explanation
Indices: 1188366--1188434 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1188356 CTTTTAAAAC
*
1188366 TTGCAATACAGT-CCCCAACATTTAG-CATGT
1 TTGCAATACAGTCCCCCAACATTTAGTC-CGT
*
1188396 TTGCAATACAGTCCCCCAATATTTAGTCCGT
1 TTGCAATACAGTCCCCCAACATTTAGTCCGT
1188427 TTGCAATA
1 TTGCAATA
1188435 TGGTCCCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 12 0.34
31 22 0.63
32 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACATTTAGTCCGT
Found at i:1190502 original size:31 final size:31
Alignment explanation
Indices: 1190429--1190502 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1190419 ATTTACGTCG
* * *
1190429 GGGACCATATTGTAAACGGACTAAATGTTGA
1 GGGACTATATTGCAAACGGACCAAATGTTGA
*
1190460 GGGATTATATTGCAAACGGACCAAATGTTG-
1 GGGACTATATTGCAAACGGACCAAATGTTGA
*
1190490 GGAGACTGTATTG
1 GG-GACTATATTG
1190503 TAAGTTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.27
Consensus pattern (31 bp):
GGGACTATATTGCAAACGGACCAAATGTTGA
Found at i:1198243 original size:31 final size:31
Alignment explanation
Indices: 1198205--1198270 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1198195 ACATGGGATG
1198205 ACCACATCTTAATTAAATAAAAACGAAAGTA
1 ACCACATCTTAATTAAATAAAAACGAAAGTA
* *
1198236 ACCACATCTTAATTAACTAAAAACGAAAGTG
1 ACCACATCTTAATTAAATAAAAACGAAAGTA
1198267 ACCA
1 ACCA
1198271 TAACTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.21
Consensus pattern (31 bp):
ACCACATCTTAATTAAATAAAAACGAAAGTA
Found at i:1198930 original size:4 final size:4
Alignment explanation
Indices: 1198921--1198967 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
1198911 CATACATGTA
** *
1198921 TATG TATG TATG TATG TATG TACA TATG TATG TATG TATA TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1198968 ACTGAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1199474 original size:21 final size:21
Alignment explanation
Indices: 1199448--1199490 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1199438 AGTTGTGGTT
*
1199448 AAGAAAATAAGAATTAAATAA
1 AAGAAAAAAAGAATTAAATAA
**
1199469 AAGAAAAAAATTATTAAATAA
1 AAGAAAAAAAGAATTAAATAA
1199490 A
1 A
1199491 CAAATTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AAGAAAAAAAGAATTAAATAA
Found at i:1200175 original size:19 final size:19
Alignment explanation
Indices: 1200119--1200181 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1200109 CTATTTAAAC
**
1200119 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1200139 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1200159 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1200178 TAAA
1 TAAA
1200182 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1200209 original size:64 final size:68
Alignment explanation
Indices: 1200084--1200281 Score: 208
Period size: 64 Copynumber: 2.8 Consensus size: 68
1200074 TAAAACATCT
* ** *
1200084 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC--CTA-AAAAAT-AATATAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAAT
*
1200144 ATTC
65 ATCC
1200148 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC------AAAGATAAAA-ATAAA
1200213 AATAATATCC
59 AATAATATCC
* *
1200223 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAA-ATAA
1200282 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 5 0.04
64 36 0.32
70 15 0.13
72 1 0.01
73 4 0.04
74 2 0.02
75 28 0.25
76 23 0.20
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAATA
TCC
Found at i:1200226 original size:75 final size:76
Alignment explanation
Indices: 1200139--1200303 Score: 244
Period size: 76 Copynumber: 2.2 Consensus size: 76
1200129 AAAAAATAAT
*
1200139 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1200203 AAAAT-ATAAAA
65 AAAATGATAAAA
* *
1200214 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
1200279 TAATGTTTAAA
66 AAATGATAAAA
*
1200290 ATATTATCCTAAAT
1 ATAATATCCTAAAT
1200304 TTGAGTTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:1208332 original size:21 final size:20
Alignment explanation
Indices: 1208308--1208362 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
1208298 TTCAAAATCC
1208308 TAAAAAC-AAGTTAAAACATCT
1 TAAAAACTAA-TTAAAACA-CT
**
1208329 TAAATTCTAATTAAAACACT
1 TAAAAACTAATTAAAACACT
*
1208349 T-AAAACTATTTAAA
1 TAAAAACTAATTAAA
1208363 TTAAAATACC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 13 0.46
22 2 0.07
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAACTAATTAAAACACT
Found at i:1208543 original size:76 final size:74
Alignment explanation
Indices: 1208385--1208547 Score: 211
Period size: 76 Copynumber: 2.2 Consensus size: 74
1208375 AAAAAATAAT
* * * *
1208385 ATAATATTCTAAATCCTAATTAAAATACTAAAACTATATAAATTAAAATACAAAGATAAAGATAA
1 ATAATATCCTAAAACTTAATTAAAATACTAAAACTATATAAACTAAAATACAAAGATAAAGATAA
1208450 AATATAAAA
66 AATATAAAA
*
1208459 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACTTAATTAAAATACT-AAAA-CTATATAAACTAAAATACAAAGATAAAGAT
* * *
1208523 ATAATGTTTAAA
64 AAAAT-ATAAAA
*
1208535 ATATTATCCTAAA
1 ATAATATCCTAAA
1208548 TTTGAGTTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
74 26 0.34
75 10 0.13
76 41 0.53
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (74 bp):
ATAATATCCTAAAACTTAATTAAAATACTAAAACTATATAAACTAAAATACAAAGATAAAGATAA
AATATAAAA
Found at i:1208720 original size:17 final size:17
Alignment explanation
Indices: 1208666--1208721 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1208656 AAAAATGAAT
* *
1208666 TAAAATAAATAAATAAA
1 TAAAAAAAATTAATAAA
* * *
1208683 TCACAAAAATTAATAAT
1 TAAAAAAAATTAATAAA
1208700 TAAAAAAAATTTAA-AAA
1 TAAAAAAAA-TTAATAAA
1208717 TAAAA
1 TAAAA
1208722 TATTAATTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAAAAATTAATAAA
Found at i:1212945 original size:20 final size:20
Alignment explanation
Indices: 1212893--1212965 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
1212883 ATGTGCGATG
*
1212893 GTATCGATACTGAGCCTCTTTA
1 GTATCGATACTGA-CC-CTTGA
* * *
1212915 GTATTGGTACTGACCCATGA
1 GTATCGATACTGACCCTTGA
*
1212935 GTATCGATACTCG-CCCTTGG
1 GTATCGATACT-GACCCTTGA
1212955 GTATCGATACT
1 GTATCGATACT
1212966 TACACGGTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 28 0.67
21 3 0.07
22 11 0.26
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (20 bp):
GTATCGATACTGACCCTTGA
Found at i:1214877 original size:23 final size:23
Alignment explanation
Indices: 1214847--1214896 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1214837 TGTATATAGA
1214847 ACTTCCATCTTTTAAAAGAAAAG
1 ACTTCCATCTTTTAAAAGAAAAG
*
1214870 ACTTCCATCTTTTACAAGAAAAG
1 ACTTCCATCTTTTAAAAGAAAAG
1214893 ACTT
1 ACTT
1214897 AGAAGAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (23 bp):
ACTTCCATCTTTTAAAAGAAAAG
Found at i:1219989 original size:21 final size:20
Alignment explanation
Indices: 1219960--1220000 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1219950 ATGAATCAAA
*
1219960 TGAATAGTATCAATATTGAT
1 TGAATAGTATCAATACTGAT
*
1219980 TGAAGTAGTATCGATACTGAT
1 TGAA-TAGTATCAATACTGAT
1220001 GTGGGGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (20 bp):
TGAATAGTATCAATACTGAT
Found at i:1220711 original size:15 final size:15
Alignment explanation
Indices: 1220691--1220738 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
1220681 ATGTCAATTG
1220691 GTTATACGTGAAAAT
1 GTTATACGTGAAAAT
* *
1220706 GTTATATGTGAATAT
1 GTTATACGTGAAAAT
*
1220721 GTTCTACGTGAAAAT
1 GTTATACGTGAAAAT
1220736 GTT
1 GTT
1220739 TTATATGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (15 bp):
GTTATACGTGAAAAT
Found at i:1220714 original size:30 final size:30
Alignment explanation
Indices: 1220674--1220738 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1220664 GGATTTAAAT
*
1220674 ATGTTCTATGTCAAT-TGGTTATACGTGAAA
1 ATGTTATATGTCAATAT-GTTATACGTGAAA
* *
1220704 ATGTTATATGTGAATATGTTCTACGTGAAA
1 ATGTTATATGTCAATATGTTATACGTGAAA
1220734 ATGTT
1 ATGTT
1220739 TTATATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (30 bp):
ATGTTATATGTCAATATGTTATACGTGAAA
Found at i:1220748 original size:30 final size:30
Alignment explanation
Indices: 1220695--1220751 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1220685 CAATTGGTTA
*
1220695 TACGTGAAAATGTTATATGTGAATATGTTC
1 TACGTGAAAATGTTATATATGAATATGTTC
*
1220725 TACGTGAAAATGTTTTATATGAATATG
1 TACGTGAAAATGTTATATATGAATATG
1220752 AACTATGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (30 bp):
TACGTGAAAATGTTATATATGAATATGTTC
Found at i:1220916 original size:23 final size:23
Alignment explanation
Indices: 1220882--1220956 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
1220872 GAGTCGAGGG
1220882 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * *
1220905 TTCTACGTGGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCGGGA-TAA
*
1220929 TTCTACGCGGTCCTTCAGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
*
1220952 ATCTA
1 TTCTA
1220957 TGTGGCACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 24 0.56
24 19 0.44
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGATAA
Found at i:1220953 original size:24 final size:23
Alignment explanation
Indices: 1220882--1220953 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
1220872 GAGTCGAGGG
1220882 TTCTACGCGGTCCTTCGGGAT-AA
1 TTCTACGCGGTCCTTC-GGATAAA
* *
1220905 TTCTACGTGGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCG-GATAAA
1220929 TTCTACGCGGTCCTTCAGGATAAA
1 TTCTACGCGGTCCTTC-GGATAAA
1220953 T
1 T
1220954 CTATGTGGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 17 0.40
24 23 0.55
25 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGATAAA
Found at i:1220968 original size:47 final size:47
Alignment explanation
Indices: 1220882--1220985 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 47
1220872 GAGTCGAGGG
* *
1220882 TTCTACGCGGTCCTTCGGGATAATTCTACGTGGTCCTTCGAG-ACAAA
1 TTCTACGCGGTCCTTCAGGATAAATCTACGTGGTCCTTCG-GTACAAA
* *
1220929 TTCTACGCGGTCCTTCAGGATAAATCTATGTGG-CACTTCGGTGCAAA
1 TTCTACGCGGTCCTTCAGGATAAATCTACGTGGTC-CTTCGGTACAAA
*
1220976 TTCTTCGCGG
1 TTCTACGCGG
1220986 CAGTTTCGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
46 2 0.04
47 48 0.96
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (47 bp):
TTCTACGCGGTCCTTCAGGATAAATCTACGTGGTCCTTCGGTACAAA
Found at i:1227501 original size:141 final size:141
Alignment explanation
Indices: 1227308--1227564 Score: 406
Period size: 141 Copynumber: 1.8 Consensus size: 141
1227298 CACTTTAGTC
* * *
1227308 CTTTAATTTAGGGAGTAATTTGAACTGGCTCTCGCATTAACATGCCTAAGGGACCATTTCAATTA
1 CTTTAATTTAGCGAGTAATTTGAACTGGCTCTCGCATTAACATGCCCAAGGGACCATCTCAATTA
* *
1227373 TTCGACTCAATAATTTGTTAAAATAAATTAGGATTAATATTAGAGCTTCCACTTTAGGTTTAATT
66 TTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTTAGGTTTAATT
1227438 TCATTTTAATA
131 TCATTTTAATA
** * * * *
1227449 CTTTAATTTAGCGAGTAATTTGATTTGTCTTTCGCATTAACATGCCCGAGGGACCATCTCGATTA
1 CTTTAATTTAGCGAGTAATTTGAACTGGCTCTCGCATTAACATGCCCAAGGGACCATCTCAATTA
*
1227514 TTCGACTCAATAATTGGTTAAAATAAATTAGGATTACTATTAGAGCCTCCA
66 TTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCA
1227565 TTTTCTGGTT
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
141 104 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (141 bp):
CTTTAATTTAGCGAGTAATTTGAACTGGCTCTCGCATTAACATGCCCAAGGGACCATCTCAATTA
TTCGACTCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCCTCCACTTTAGGTTTAATT
TCATTTTAATA
Found at i:1232266 original size:19 final size:19
Alignment explanation
Indices: 1232242--1232294 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1232232 ATAATGTTTA
*
1232242 AAAGTATCGATACTTATAT
1 AAAGTATCGATACTTATAC
* *
1232261 AAAGTATCGAAACTTTTAC
1 AAAGTATCGATACTTATAC
1232280 ATAAGTATCGATACT
1 A-AAGTATCGATACT
1232295 CGTGGGCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (19 bp):
AAAGTATCGATACTTATAC
Found at i:1234697 original size:27 final size:27
Alignment explanation
Indices: 1234666--1234744 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
1234656 ATCCAGGCAG
* *
1234666 ATTTCTCAGTCATGATCAGAGATTCGA
1 ATTTCTCGGTCATGATCAGAGATCCGA
1234693 ATTTCTCGGTCATGATCAGAGATCCGA
1 ATTTCTCGGTCATGATCAGAGATCCGA
*
1234720 ATTTCTCGGTTATGATCAGAGATCC
1 ATTTCTCGGTCATGATCAGAGATCC
1234745 CGTGAAAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAGAGATCCGA
Found at i:1235012 original size:20 final size:20
Alignment explanation
Indices: 1234975--1235017 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1234965 ATTCCACCTC
* *
1234975 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
1234995 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
1235015 ATG
1 ATG
1235018 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:1237574 original size:13 final size:13
Alignment explanation
Indices: 1237558--1237597 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1237548 AGGAAACTAG
1237558 AAAGTGAAAGTAA
1 AAAGTGAAAGTAA
* *
1237571 AAAGAGAAAGTGA
1 AAAGTGAAAGTAA
1237584 AAAGTGAAAAGTAA
1 AAAGTG-AAAGTAA
1237598 GTGGGGTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (13 bp):
AAAGTGAAAGTAA
Found at i:1244996 original size:27 final size:27
Alignment explanation
Indices: 1244965--1245016 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1244955 ATCTAGGCAG
1244965 ATTTCTCGGTCATGATCAAAGATCCGA
1 ATTTCTCGGTCATGATCAAAGATCCGA
*
1244992 ATTTCTCGGTCATGATCAGAGATCC
1 ATTTCTCGGTCATGATCAAAGATCC
1245017 CGTGAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAAAGATCCGA
Found at i:1245285 original size:20 final size:20
Alignment explanation
Indices: 1245248--1245290 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1245238 ATTCCACCTC
* *
1245248 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
1245268 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
1245288 ATG
1 ATG
1245291 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:1248056 original size:59 final size:59
Alignment explanation
Indices: 1247952--1248104 Score: 168
Period size: 60 Copynumber: 2.6 Consensus size: 59
1247942 ATATATGTAA
*
1247952 AATTTGGGATGAAATT-AGAATGTTCAAAAAGTTTGGAGACCAATTT-GAATGAAGGCCAT
1 AATTTGGGATGAAATTGA-AATGTTC-AAAAGTTTGGAGACCAATTTAGAATGAAAGCCAT
* * * *
1248011 AGTTTGGAGATTAAATTGAAATGTTCAAAAGTTT-GATGACTAATTTAGAATGAAAGTCAT
1 AATTTGG-GATGAAATTGAAATGTTCAAAAGTTTGGA-GACCAATTTAGAATGAAAGCCAT
* * *
1248071 AATTTAGGGATGAAACTGAAATATTTAAAAGTTT
1 AATTT-GGGATGAAATTGAAATGTTCAAAAGTTT
1248105 AAGGACAAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
58 2 0.03
59 22 0.28
60 52 0.66
61 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (59 bp):
AATTTGGGATGAAATTGAAATGTTCAAAAGTTTGGAGACCAATTTAGAATGAAAGCCAT
Found at i:1248091 original size:60 final size:57
Alignment explanation
Indices: 1247952--1248123 Score: 157
Period size: 60 Copynumber: 2.9 Consensus size: 57
1247942 ATATATGTAA
* * *
1247952 AATTTGGGATGAAATTAGAATGTTCAAAAAGTTTGGAGACCAATTT-GAATGAAGGCCAT
1 AATTTGGGATGAAATGA-AATGTTC-AAAAGTTT-GAGACAAATTTAGAATGAAAGCCAT
* * * *
1248011 AGTTTGGAGATTAAATTGAAATGTTCAAAAGTTTGATGACTAATTTAGAATGAAAGTCAT
1 AATTTGG-GATGAAA-TGAAATGTTCAAAAGTTTGA-GACAAATTTAGAATGAAAGCCAT
* * * *
1248071 AATTTAGGGATGAAACTGAAATATTTAAAAGTTTAAGGACAAATTTATAATGA
1 AATTT-GGGATGAAA-TGAAATGTTCAAAAGTTTGA-GACAAATTTAGAATGA
1248124 GGGTCATATG
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.02
59 22 0.24
60 65 0.70
61 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (57 bp):
AATTTGGGATGAAATGAAATGTTCAAAAGTTTGAGACAAATTTAGAATGAAAGCCAT
Found at i:1258629 original size:62 final size:65
Alignment explanation
Indices: 1258509--1258644 Score: 226
Period size: 62 Copynumber: 2.1 Consensus size: 65
1258499 ATTAGAATCT
1258509 AATTTAAAATTTATCTATAATACTAATAATAAATAAATAAATAATTTCACAGATCTATAGTTTAG
1 AATTTAAAATTTATCTATAATACTAATAATAAATAAATAAATAATTTCACAGATCTATAGTTTAG
*
1258574 AATTTAAAATTTATCTAT-A-A-TAATAATAAAT-AATAAAATAATTTCACATATCTATAGTTTA
1 AATTTAAAATTTATCTATAATACTAATAATAAATAAAT-AAATAATTTCACAGATCTATAGTTTA
1258635 G
65 G
1258636 AATTTAAAA
1 AATTTAAAA
1258645 CTTAAAGTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
61 3 0.04
62 46 0.67
63 1 0.01
64 1 0.01
65 18 0.26
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (65 bp):
AATTTAAAATTTATCTATAATACTAATAATAAATAAATAAATAATTTCACAGATCTATAGTTTAG
Found at i:1258654 original size:21 final size:22
Alignment explanation
Indices: 1258629--1258672 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1258619 ACATATCTAT
1258629 AGTTTAGAATT-TAAAACTTAA
1 AGTTTAGAATTATAAAACTTAA
* *
1258650 AGTTTTGAATTATAAAATTTAA
1 AGTTTAGAATTATAAAACTTAA
1258672 A
1 A
1258673 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (22 bp):
AGTTTAGAATTATAAAACTTAA
Found at i:1260852 original size:26 final size:25
Alignment explanation
Indices: 1260823--1260881 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1260813 AAATCATATT
*
1260823 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1260849 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1260875 ATTATTA
1 ATTATTA
1260882 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1263774 original size:26 final size:26
Alignment explanation
Indices: 1263745--1263814 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
1263735 TTTGATGATT
1263745 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1263771 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
1263797 TAATAATGATTTAATAAT
1 TAGTAATGATTTGATAAT
1263815 GATTTAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1263868 original size:26 final size:26
Alignment explanation
Indices: 1263839--1264335 Score: 348
Period size: 26 Copynumber: 20.2 Consensus size: 26
1263829 ATGAACAAAT
1263839 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1263865 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1263891 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
* * * *
1263917 TA-AAATGATTTAATAATGAATTA-AA
1 TAGTAATGATTTGATAAT-AATCATTA
* *
1263942 TATTTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATCATTA
1263962 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1263988 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
1264014 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1264036 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
1264060 TAGTAATTATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1264086 TAGTAATGATTTGATAATAATC-TTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
1264111 TAATAATGA-TT--TAGTAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1264133 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
1264157 TAGTAATTATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1264183 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1264209 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1264235 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1264257 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1264281 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
1264307 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
1264332 TAGT
1 TAGT
1264336 TATTATTTAG
Statistics
Matches: 387, Mismatches: 42, Indels: 85
0.75 0.08 0.17
Matches are distributed among these distances:
19 13 0.03
20 20 0.05
22 15 0.04
23 25 0.06
24 29 0.07
25 58 0.15
26 201 0.52
27 26 0.07
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1263980 original size:97 final size:98
Alignment explanation
Indices: 1263771--1264329 Score: 652
Period size: 97 Copynumber: 5.8 Consensus size: 98
1263761 ATAATCATTA
* *
1263771 TAGTAATGATTTGATAATAATCATTATAATAATGA-TT--TAATAATGATT-T-A-AAT-ATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
** * * * *
1263829 ATGAACAAATTAGTAATGATTTGAT-A-ATAATCATT
66 AT-AATGAATTA--AAT-ATTTAATGATTTGATGATT
*
1263864 ATAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAA-AATGATT
1 -TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATT
1263927 TAATAATGAATTAAATATTTAATGATTTGATGATT
64 TAATAATGAATTAAATATTTAATGATTTGATGATT
1263962 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
*
1264027 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGAATTAAATATTTAATGATTTGATGATT
*
1264060 TAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATC-TTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
* *
1264124 GTAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGAATTAAATATTTAATGATTTGATGATT
*
1264157 TAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
* * * ** *
1264222 GTAAT-AA-TCATTATAAAAATGATTTAATAATGATT
66 ATAATGAATTAAATAT-TTAATGA-TT--TGATGATT
* * * *
1264257 TA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATGATT
1 TAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATT
*
1264318 TTATAAT-AATTA
64 TAATAATGAATTA
1264330 TTTAGTTATT
Statistics
Matches: 423, Mismatches: 24, Indels: 31
0.88 0.05 0.06
Matches are distributed among these distances:
94 35 0.08
95 2 0.00
96 11 0.03
97 174 0.41
98 167 0.39
99 18 0.04
100 16 0.04
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATGAATTAAATATTTAATGATTTGATGATT
Found at i:1264000 original size:123 final size:119
Alignment explanation
Indices: 1263745--1264031 Score: 459
Period size: 123 Copynumber: 2.4 Consensus size: 119
1263735 TTTGATGATT
*
1263745 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAATAATGATTTA
*
1263810 ATAATGATTTAAATATTTAATGAACAAATTAGTAATGATTTGATAATAATCATTA
65 ATAATGAATTAAATATTTAATGAACAAATTAGTAATGATTTGATAATAATCATTA
1263865 TAGTAATGATTTGATAATAATCATTATAATAATGATTTATTAATAATCATTATAA-AATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAATAATGATTTA
** *
1263929 ATAATGAATTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
65 ATAATGAATTAAATATTTAATGA----ACAAATTAGTAATGATTTGATAATAATCATTA
1263988 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAAT
1264032 GATTTAAATA
Statistics
Matches: 156, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
119 32 0.21
120 52 0.33
123 71 0.46
124 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.43
Consensus pattern (119 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAATAATGATTTAA
TAATGAATTAAATATTTAATGAACAAATTAGTAATGATTTGATAATAATCATTA
Found at i:1264112 original size:123 final size:119
Alignment explanation
Indices: 1263745--1264122 Score: 417
Period size: 123 Copynumber: 3.1 Consensus size: 119
1263735 TTTGATGATT
* * * * *
1263745 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATATTTAATAT-ATAATGA-TT-
*
1263810 ATAATGATTTA-AATATTTAATGAACAA-A-TTAGTAATGATTTGATAATAATCATTA
63 -TAATGATTTATAATATTTAATGAATAATATTTAGTAATGATTTGATAATAATCATTA
* * * * *
1263865 TAGTAATGATTTGATAATAATCATTATAATAATGATTTATTAATAATCATTATAAAATGATTTAA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATATTTAATATATAATGA-TT--
* * *
1263930 TAATGAATTA-AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
63 TAATGATTTATAATATTTAATGA-ATAAT-ATTTAGTAATGATTTGATAATAATCATTA
*
1263988 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAAT-ATTT-AATATATAATGATTT
* *
1264053 GATGATTTAGTAATTATTTGAT-AATAATCATTATAGTAATGATTTGATAATAATC-TTA
64 AATGATTTA-TAA-TATTTAATGAATAAT-ATT-TAGTAATGATTTGATAATAATCATTA
*
1264111 TAATAATGATTT
1 TAGTAATGATTT
1264123 AGTAATGATT
Statistics
Matches: 227, Mismatches: 21, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
119 32 0.14
120 51 0.22
122 9 0.04
123 90 0.40
124 29 0.13
125 16 0.07
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (119 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATATTTAATATATAATGATTTAA
TGATTTATAATATTTAATGAATAATATTTAGTAATGATTTGATAATAATCATTA
Found at i:1264229 original size:221 final size:221
Alignment explanation
Indices: 1263701--1264327 Score: 901
Period size: 221 Copynumber: 2.9 Consensus size: 221
1263691 TATCATTATA
** * * *
1263701 AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAT
1 AAAATGATTTAATAATGAAGTAAATATTTAATGATATAATCATTTAGTAATGATTTGATAATAAT
1263766 CATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAAT
66 CATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAAT
** *
1263831 GA----ACAAATTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTAT
131 GATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTAT
* * *
1263892 AATAATGATTTATTAATAATCATTAT
196 AATAATGATTTAGTAATAATAAATAT
* * * *
1263918 AAAATGATTTAATAATGAATTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAT
1 AAAATGATTTAATAATGAAGTAAATATTTAATGATATAATCATTTAGTAATGATTTGATAATAAT
1263983 CATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAAT
66 CATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAAT
*
1264048 GATTTGATGATTTAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATC-TTAT
131 GATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTAT
*
1264112 AATAATGATTTAGTAATGATTTAAATAT
196 AATAATGATTTAGTAAT-A-ATAAATAT
** * * ** * *
1264140 TTAATGATTTGATGATTTAGTAATTATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAA
1 AAAATGATTTAATAATGAAGTAAATATTTAATGATATAATCATT-TAGTAATGATTTGATAATAA
* *
1264203 TCATTATAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTA
65 TCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTA
* *
1264267 ATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAAT
129 ATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAAT
1264328 TATTTAGTTA
Statistics
Matches: 376, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
217 131 0.35
220 27 0.07
221 190 0.51
222 28 0.07
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (221 bp):
AAAATGATTTAATAATGAAGTAAATATTTAATGATATAATCATTTAGTAATGATTTGATAATAAT
CATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAAT
GATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTAT
AATAATGATTTAGTAATAATAAATAT
Found at i:1264274 original size:124 final size:123
Alignment explanation
Indices: 1264060--1264327 Score: 448
Period size: 124 Copynumber: 2.2 Consensus size: 123
1264050 TTTGATGATT
* * * *
1264060 TAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCTTATAATAATGATTTAG
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCTTATAAAAATGATTTAA
*
1264125 TAATGATTTAAATATTTAATGATTTGATGATTTAGTAATTATTTGATAATAATCATTA
66 TAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
1264183 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAATC-TTATAAAAATGATTT
1264247 AATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
64 AATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
* *
1264307 TAATAATGATTTTATAATAAT
1 TAGTAATGATTTGATAATAAT
1264328 TATTTAGTTA
Statistics
Matches: 136, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
122 1 0.01
123 44 0.32
124 91 0.67
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (123 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCTTATAAAAATGATTTAA
TAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
Found at i:1264287 original size:195 final size:192
Alignment explanation
Indices: 1263771--1264329 Score: 639
Period size: 195 Copynumber: 2.9 Consensus size: 192
1263761 ATAATCATTA
* *
1263771 TAGTAATGATTTGATAATAATCATTATAATAATGA-TT--TAATAATGATT-T-A-AAT-ATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
* * * * * *
1263829 ATGAA-CAAATTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATA
66 AT-AATC-ATTTA--AAT-ATTTAATGAT-ATGATT-TAG-AATTATTTAATAATAATCATTATA
*
1263893 ATAATGATTT-ATTAATAATCATTATAA-AATGATTTAATAATGAATTAAATATTTAATGATTTG
123 GTAATGATTTGA-TAATAATCATTATAATAATGATTTAATAATGAATTAAATATTTAATGATTTG
1263956 ATGATT
187 ATGATT
1263962 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
* *
1264027 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATTATTTGATAATAATCATTATAGTAA
66 ATAATCATTTAAATATTTAATGA--T-ATGATTTAG-AATTATTTAATAATAATCATTATAGTAA
* *
1264092 TGATTTGATAATAATC-TTATAATAATGATTTAGTAATGATTTAAATATTTAATGATTTGATGAT
127 TGATTTGATAATAATCATTATAATAATGATTTAATAATGAATTAAATATTTAATGATTTGATGAT
1264156 T
192 T
*
1264157 TAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TT-
* * *
1264222 GTAATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-AA-TATTTAATGATTTGATGATT-T
64 -TAATAATCATT-T--AAAT-ATTTAATGATATGATTTAGAATTATTTAAT-A-ATAATCATTAT
*
1264282 AGTAATGATTTGATAATAATCATTATAATAATGATTTTATAAT-AATTA
122 AGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAATTA
1264330 TTTAGTTATT
Statistics
Matches: 325, Mismatches: 21, Indels: 40
0.84 0.05 0.10
Matches are distributed among these distances:
191 34 0.10
192 2 0.01
194 30 0.09
195 177 0.54
196 35 0.11
197 17 0.05
198 17 0.05
199 1 0.00
201 5 0.02
202 7 0.02
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (192 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATCATTTAAATATTTAATGATATGATTTAGAATTATTTAATAATAATCATTATAGTAATGAT
TTGATAATAATCATTATAATAATGATTTAATAATGAATTAAATATTTAATGATTTGATGATT
Found at i:1264560 original size:17 final size:17
Alignment explanation
Indices: 1264535--1264567 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1264525 ACTAAATATC
*
1264535 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1264552 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1264568 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1266987 original size:44 final size:47
Alignment explanation
Indices: 1266912--1267001 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 47
1266902 CAACAAACAA
1266912 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTC
1 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTC
* * *
1266959 ATATAAC-TAACTA-TTAAC-AATACAAACTAATTAATTATTTTTT
1 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTT
1267002 AACTATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 22 0.55
45 5 0.12
46 6 0.15
47 7 0.17
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTC
Found at i:1267231 original size:17 final size:16
Alignment explanation
Indices: 1267232--1267263 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1267222 CCCTTTCTTT
1267232 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
1267249 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1267264 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:1267233 original size:4 final size:4
Alignment explanation
Indices: 1267205--1267262 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
1267195 TTTCGAATTC
* ** **
1267205 TTCT TACT TTCCT TTCT CCCT TTCT TTCT TTCT TTCCT TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT
1267255 TTCT TTCT
1 TTCT TTCT
1267263 CGGCTGCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (4 bp):
TTCT
Found at i:1267239 original size:25 final size:25
Alignment explanation
Indices: 1267205--1267262 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
1267195 TTTCGAATTC
*
1267205 TTCTTACTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
1267230 TTCTTTCTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
1267255 TTCTTTCT
1 TTCTTTCT
1267263 CGGCTGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCTCCCTTTCT
Found at i:1267352 original size:25 final size:25
Alignment explanation
Indices: 1267324--1267375 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1267314 TTTCTTTTAT
*
1267324 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
1267349 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
1267374 AA
1 AA
1267376 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:1267543 original size:26 final size:23
Alignment explanation
Indices: 1267486--1267545 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1267476 ACACGTGAAG
1267486 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
1267509 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
*
1267532 GAATGGACGATGGG
1 GAATGGATGATGGG
1267546 AATGGCGCCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.23
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:1267593 original size:28 final size:29
Alignment explanation
Indices: 1267551--1267658 Score: 166
Period size: 29 Copynumber: 3.8 Consensus size: 29
1267541 ATGGGAATGG
1267551 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
1267580 CGCC-GGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
*
1267608 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
* *
1267637 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1267659 CTCTCCTATT
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 28 0.38
29 44 0.59
30 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTATAAGGT
Found at i:1267690 original size:19 final size:19
Alignment explanation
Indices: 1267666--1267703 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1267656 CCTCTCTCCT
1267666 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
1267685 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
1267704 TCGCATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (19 bp):
ATTCCACTGCATGGCCACC
Found at i:1267831 original size:55 final size:55
Alignment explanation
Indices: 1267766--1267876 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
1267756 GAACGACCTC
1267766 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1267821 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1267876 T
1 T
1267877 GGGGACCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:1267853 original size:139 final size:139
Alignment explanation
Indices: 1267685--1267960 Score: 552
Period size: 139 Copynumber: 2.0 Consensus size: 139
1267675 CATGGCCACC
1267685 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1267750 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
1267815 TATGCATCT
131 TATGCATCT
1267824 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1267889 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
1267954 TATGCAT
131 TATGCAT
1267961 GGGGAGAACC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.24
Consensus pattern (139 bp):
ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
TATGCATCT
Found at i:1267858 original size:27 final size:27
Alignment explanation
Indices: 1267773--1267858 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1267763 CTCTCTATTC
1267773 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
* * * * ***
1267800 CACTCGTATGG-CTCGTATGCATCTATTC-
1 CACT-GCATGGCCACCT-CGCAT-GGCTCG
1267828 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
1267855 CACT
1 CACT
1267859 CGTATGGCTC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.24
Consensus pattern (27 bp):
CACTGCATGGCCACCTCGCATGGCTCG
Found at i:1267885 original size:41 final size:41
Alignment explanation
Indices: 1267831--1267962 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
1267821 TCTATTCCAC
1267831 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
1267872 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
1267914 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1267956 TGCATGG
1 TGCATGG
1267963 GGAGAACCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:1273943 original size:60 final size:60
Alignment explanation
Indices: 1273833--1273946 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
1273823 CTACATAACA
* * **
1273833 TTACTTTGATGAGCCTCTCGACTATTAAAAGTTATAAAATGCTTCTTCGATTATAGGACG
1 TTACTTTGATGAGCCTCTCGACTATTAAAAGCTACAAAATGCCACTTCGATTATAGGACG
1273893 TTACTTT-ATTGAGTCC-CTCGACTATTAAAAGCTACAAAATGACCAC-TCGATTAT
1 TTACTTTGA-TGAG-CCTCTCGACTATTAAAAGCTACAAAATG-CCACTTCGATTAT
1273947 TCTTATATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
59 1 0.02
60 42 0.89
61 4 0.09
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (60 bp):
TTACTTTGATGAGCCTCTCGACTATTAAAAGCTACAAAATGCCACTTCGATTATAGGACG
Found at i:1278623 original size:16 final size:16
Alignment explanation
Indices: 1278604--1278638 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1278594 TTTTTTTGAA
*
1278604 TTCGAGCTTTTTCGAG
1 TTCGAGCCTTTTCGAG
1278620 TTCGAGCCTTTTCGAG
1 TTCGAGCCTTTTCGAG
1278636 TTC
1 TTC
1278639 AAGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (16 bp):
TTCGAGCCTTTTCGAG
Found at i:1278886 original size:20 final size:20
Alignment explanation
Indices: 1278863--1278905 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1278853 TTTCAGCCAA
* *
1278863 TTCACCCCGTTTTATCGATT
1 TTCACCCCGTTCTACCGATT
* *
1278883 TTCAGCCGGTTCTACCGATT
1 TTCACCCCGTTCTACCGATT
1278903 TTC
1 TTC
1278906 GGCCATTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.42
Consensus pattern (20 bp):
TTCACCCCGTTCTACCGATT
Found at i:1279301 original size:21 final size:21
Alignment explanation
Indices: 1279277--1279317 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1279267 GTTAATTGTT
*
1279277 GTTTGTTGGATTATCTTGTCA
1 GTTTGTTGAATTATCTTGTCA
* *
1279298 GTTTTTTTAATTATCTTGTC
1 GTTTGTTGAATTATCTTGTC
1279318 TATAACTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.59
Consensus pattern (21 bp):
GTTTGTTGAATTATCTTGTCA
Found at i:1280609 original size:20 final size:19
Alignment explanation
Indices: 1280567--1280608 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1280557 CTAAATTTAC
1280567 TTTATTTTATCATTTATTT
1 TTTATTTTATCATTTATTT
*
1280586 TTTATTTTTACTCTTTTATTT
1 TTTA-TTTTA-TCATTTATTT
1280607 TT
1 TT
1280609 AAAATTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 11 0.55
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATTTTATCATTTATTT
Found at i:1292730 original size:46 final size:46
Alignment explanation
Indices: 1292662--1292755 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
1292652 GTATAGATAG
*
1292662 TGCCGTTATGGTATTTAGTCAGATGCCTCATCTAGATGTTGCTGCA
1 TGCCGTTATGGTATTTAATCAGATGCCTCATCTAGATGTTGCTGCA
*
1292708 TGCCGTTATGGTATTTAATCAGATGCCTCATCTAGATGTTGTTGCA
1 TGCCGTTATGGTATTTAATCAGATGCCTCATCTAGATGTTGCTGCA
1292754 TG
1 TG
1292756 TAATTGTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (46 bp):
TGCCGTTATGGTATTTAATCAGATGCCTCATCTAGATGTTGCTGCA
Found at i:1297295 original size:14 final size:14
Alignment explanation
Indices: 1297276--1297309 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1297266 CCATAGAAAC
1297276 TCAAATAACTCAAA
1 TCAAATAACTCAAA
* *
1297290 TCAAATAATTCAAC
1 TCAAATAACTCAAA
1297304 TCAAAT
1 TCAAAT
1297310 TTCTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (14 bp):
TCAAATAACTCAAA
Found at i:1297590 original size:21 final size:22
Alignment explanation
Indices: 1297550--1297591 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1297540 AGTTAAATAA
* *
1297550 AAGATTTCGTTGTCCTAACATG
1 AAGATTTCGTAGTACTAACATG
1297572 AAGATTTCGTAG-ACTAACAT
1 AAGATTTCGTAGTACTAACAT
1297592 TAATAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (22 bp):
AAGATTTCGTAGTACTAACATG
Found at i:1308104 original size:9 final size:9
Alignment explanation
Indices: 1308064--1308101 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1308054 ATCATCACCA
1308064 TCATCGTCG
1 TCATCGTCG
*
1308073 TCATCGTTG
1 TCATCGTCG
1308082 TCATCGTCG
1 TCATCGTCG
*
1308091 TCGTCGTCG
1 TCATCGTCG
1308100 TC
1 TC
1308102 GTCTTGCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.08, C:0.32, G:0.24, T:0.37
Consensus pattern (9 bp):
TCATCGTCG
Found at i:1310481 original size:51 final size:50
Alignment explanation
Indices: 1310377--1310503 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 50
1310367 AGATATACAG
* * * * **
1310377 GTATAGCGCGCTGCAGGGGCCGCGCTATACCTACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGTGCTATACCCACGTGGCGCCAAATCACC
* *
1310427 GTATAGCGCGGTGCAGGGGGCGTGCTATACCCCACGTGGTGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGTGCTATA-CCCACGTGGCGCCAAATCACC
* *
1310478 GTATAGCACGGTGCAGGGGGCTTGCT
1 GTATAGCGCGGTGCAGGGGGCGTGCT
1310504 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 26 0.39
51 40 0.61
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGTGCTATACCCACGTGGCGCCAAATCACC
Found at i:1314187 original size:29 final size:29
Alignment explanation
Indices: 1314155--1314402 Score: 288
Period size: 29 Copynumber: 8.6 Consensus size: 29
1314145 ACAGAATTAA
*
1314155 TTACGAAACTAACACCCTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
1314184 TTACGAAAATAACA--CTTATTAAAAATAT
1 TTACGAAAATAACACCCTT-TTAAAAATAT
* *
1314212 TTACGAAAATAACACCTTTTTTAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* *
1314241 TTACAAAAATAACACCCTTTTAGAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* *
1314270 TTACGAAAAATTACACCCTTTTAGAAATAT
1 TTACG-AAAATAACACCCTTTTAAAAATAT
** *
1314300 TTACGAAAATAACACATTTTTAACAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAT
* * *
1314329 TTACGAAACTAACA-CCTTCTTAACAGTAT
1 TTACGAAAATAACACCCTT-TTAAAAATAT
* *
1314358 TTACGGAACTAACACCCTTTCTAAAAATAT
1 TTACGAAAATAACACCCTTT-TAAAAATAT
*
1314388 TTAC-AAAATACCACC
1 TTACGAAAATAACACC
1314403 ATAACTGAAA
Statistics
Matches: 188, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
27 3 0.02
28 26 0.14
29 114 0.61
30 45 0.24
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (29 bp):
TTACGAAAATAACACCCTTTTAAAAATAT
Found at i:1314303 original size:59 final size:57
Alignment explanation
Indices: 1314155--1314402 Score: 279
Period size: 59 Copynumber: 4.3 Consensus size: 57
1314145 ACAGAATTAA
*
1314155 TTACGAAACTAACACCCTTTTAAAAATATTTACGAAAATAACA--CTTATTAAAAATAT
1 TTACGAAAATAACACCCTTTT-AAAATATTTACGAAAATAACACCCTT-TTAAAAATAT
* * *
1314212 TTACGAAAATAACACCTTTTTTAAAATATTTACAAAAATAACACCCTTTTAGAAATAT
1 TTACGAAAATAACACC-CTTTTAAAATATTTACGAAAATAACACCCTTTTAAAAATAT
* ** *
1314270 TTACGAAAAATTACACCCTTTTAGAAATATTTACGAAAATAACACATTTTTAACAATAT
1 TTACG-AAAATAACACCCTTTTA-AAATATTTACGAAAATAACACCCTTTTAAAAATAT
* * * *
1314329 TTACGAAACTAACA-CCTTCTTAACAGTATTTACGGAACTAACACCCTTTCTAAAAATAT
1 TTACGAAAATAACACCCTT-TTAA-AATATTTACGAAAATAACACCCTTT-TAAAAATAT
*
1314388 TTAC-AAAATACCACC
1 TTACGAAAATAACACC
1314403 ATAACTGAAA
Statistics
Matches: 161, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
57 40 0.25
58 60 0.37
59 61 0.38
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (57 bp):
TTACGAAAATAACACCCTTTTAAAATATTTACGAAAATAACACCCTTTTAAAAATAT
Found at i:1314328 original size:88 final size:86
Alignment explanation
Indices: 1314155--1314404 Score: 303
Period size: 88 Copynumber: 2.9 Consensus size: 86
1314145 ACAGAATTAA
*
1314155 TTACGAAACTAACACCCTTTTAAAAATATTTACGAAAA-TA-ACACTTATTAAAAATATTTACGA
1 TTACGAAACTAACACCCTTTT-AAAATATTTACGAAAATTACACCCTT-TTAAAAATATTTACGA
*
1314218 AAATAACACCTTTTTTAAAATAT
64 AAATAACACCATTTTTAAAATAT
* * *
1314241 TTACAAAAATAACACCCTTTTAGAAATATTTACGAAAAATTACACCCTTTTAGAAATATTTACGA
1 TTACGAAACTAACACCCTTTTA-AAATATTTACG-AAAATTACACCCTTTTAAAAATATTTACGA
1314306 AAATAACA-CATTTTTAACAATAT
64 AAATAACACCATTTTTAA-AATAT
* * * *
1314329 TTACGAAACTAACA-CCTTCTTAACAGTATTTACGGAACTAACACCCTTTCTAAAAATATTTAC-
1 TTACGAAACTAACACCCTT-TTAA-AATATTTACGAAAATTACACCCTTT-TAAAAATATTTACG
*
1314392 AAAATACCACCAT
63 AAAATAACACCAT
1314405 AACTGAAATT
Statistics
Matches: 142, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
85 1 0.01
86 30 0.21
87 37 0.26
88 69 0.49
89 5 0.04
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.32
Consensus pattern (86 bp):
TTACGAAACTAACACCCTTTTAAAATATTTACGAAAATTACACCCTTTTAAAAATATTTACGAAA
ATAACACCATTTTTAAAATAT
Found at i:1314421 original size:59 final size:59
Alignment explanation
Indices: 1314358--1314507 Score: 137
Period size: 59 Copynumber: 2.5 Consensus size: 59
1314348 TTAACAGTAT
1314358 TTACGGAACTA-ACACCCTTTCTAAAAATATTTAC-AAAATACCACCATAAC-TGAAATTAA
1 TTAC-GAACTAGACACCCTTT-TAAAAATATTTACAAAAATACCACCATAACAT-AAATTAA
* * * ** * *
1314417 TTACGTATTAGTCATTCTTTTAAAACTATTTACAAAAATAGCACCATAACATAAATTAA
1 TTACGAACTAGACACCCTTTTAAAAATATTTACAAAAATACCACCATAACATAAATTAA
* * * *
1314476 TTAC-ATAATAGTCACTCTTTTAAAACTATTTA
1 TTACGA-ACTAGACACCCTTTTAAAAATATTTA
1314508 TCAATAATCT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
58 16 0.21
59 60 0.78
60 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (59 bp):
TTACGAACTAGACACCCTTTTAAAAATATTTACAAAAATACCACCATAACATAAATTAA
Found at i:1314450 original size:58 final size:59
Alignment explanation
Indices: 1314374--1314507 Score: 191
Period size: 59 Copynumber: 2.3 Consensus size: 59
1314364 AACTAACACC
* * * *
1314374 CTTTCTAAAAATATTTAC-AAAATACCACCATAAC-TGAAATTAATTACGTATTAGTCATT
1 CTTT-TAAAACTATTTACAAAAATACCACCATAACAT-AAATTAATTACATAATAGTCACT
*
1314433 CTTTTAAAACTATTTACAAAAATAGCACCATAACATAAATTAATTACATAATAGTCACT
1 CTTTTAAAACTATTTACAAAAATACCACCATAACATAAATTAATTACATAATAGTCACT
1314492 CTTTTAAAACTATTTA
1 CTTTTAAAACTATTTA
1314508 TCAATAATCT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
58 12 0.18
59 55 0.81
60 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (59 bp):
CTTTTAAAACTATTTACAAAAATACCACCATAACATAAATTAATTACATAATAGTCACT
Found at i:1315056 original size:20 final size:20
Alignment explanation
Indices: 1315011--1315056 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1315001 GACCAATAAA
*
1315011 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
1315031 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
1315050 ATCGCAA
1 ATCGCAA
1315057 ATCAGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:1315121 original size:21 final size:21
Alignment explanation
Indices: 1315091--1315140 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1315081 ATTCTGACTA
1315091 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
1315112 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
1315133 TCGCAATG
1 TCGCAATG
1315141 TGAATAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:1315204 original size:20 final size:20
Alignment explanation
Indices: 1315176--1315307 Score: 131
Period size: 20 Copynumber: 6.5 Consensus size: 20
1315166 TTGGAAAATT
* *
1315176 GCAATGCGATACTGGCTATC
1 GCAACGCGATACTGACTATC
*
1315196 GCAACGCGATACTGGCTATC
1 GCAACGCGATACTGACTATC
* *
1315216 GCAACGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
*
1315237 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
** * *
1315257 GCAACGTAATACTTACTTTC
1 GCAACGCGATACTGACTATC
*
1315277 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
*
1315297 GCAACGAGATA
1 GCAACGCGATA
1315308 ATACATAATC
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 77 0.81
21 15 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:1315235 original size:61 final size:61
Alignment explanation
Indices: 1315170--1315287 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
1315160 GCGAATTTGG
* * * * *
1315170 AAAATTGCAATGCGATACTGGCTATCGCAACGCGATACTGGCTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
* * * *
1315231 AAAATCGCAACGCGATACTGACTTTCGCAACGTAATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATA
1315288 CTGACTTTCG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
Found at i:1315238 original size:41 final size:41
Alignment explanation
Indices: 1315193--1315327 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
1315183 GATACTGGCT
* *
1315193 ATCGCAACGCGATACTGGCTATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
**
1315234 ATCGCAACGCGATACTGACTTTCGCAA--CG-TAATACTTACT
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC--AAA
* * *
1315274 TTCGCAACGCGATACTGACTTTCGCAACGAGATAATACATA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
*
1315315 ATCGCAATGCGAT
1 ATCGCAACGCGAT
1315328 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
38 6 0.08
39 2 0.03
40 27 0.34
41 37 0.47
42 1 0.01
43 6 0.08
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
Done.