Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 134 of 240
Found at i:41637348 original size:28 final size:30
Alignment explanation
Indices: 41637316--41637371 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
41637306 TACTTATAAA
* *
41637316 TAACATCTAATACCTC-AA-ATTCATCATT
1 TAACACCTAAAACCTCAAAGATTCATCATT
*
41637344 TAACACCTAAAATCTCAAAGATTCATCA
1 TAACACCTAAAACCTCAAAGATTCATCA
41637372 ACGAAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 13 0.57
29 2 0.09
30 8 0.35
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (30 bp):
TAACACCTAAAACCTCAAAGATTCATCATT
Found at i:41638548 original size:37 final size:37
Alignment explanation
Indices: 41638498--41638576 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
41638488 TTATTACGAA
* * *
41638498 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACAAAGTTATCGG
41638535 GTCTTACCCGGACAAAATCCCCACACAAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACAAAGTTATCGG
41638572 GTCTT
1 GTCTT
41638577 TAGAGCTCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACAAAGTTATCGG
Found at i:41638991 original size:49 final size:47
Alignment explanation
Indices: 41638695--41639251 Score: 884
Period size: 47 Copynumber: 11.7 Consensus size: 47
41638685 CCCTTCAGGA
* * * * * *
41638695 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41638742 C-TGTCGCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41638788 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41638835 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41638882 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41638929 CTTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41638976 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41639025 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41639074 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41639123 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41639170 ATTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41639217 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
41639252 AGAATCCTAA
Statistics
Matches: 484, Mismatches: 22, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 39 0.08
47 302 0.62
49 143 0.30
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41639154 original size:25 final size:25
Alignment explanation
Indices: 41639126--41639204 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
41639116 ACTAGGCCTT
41639126 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
**** ***
41639151 ATCACAT-CGGCCA-TTAGGCATT-
1 ATCACATATATACACTTTCACATTC
41639173 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
41639198 ATCACAT
1 ATCACAT
41639205 CAGCCATTAG
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 14 0.38
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41639327 original size:241 final size:238
Alignment explanation
Indices: 41638696--41639251 Score: 723
Period size: 241 Copynumber: 2.3 Consensus size: 238
41638686 CCTTCAGGAC
* * * ** * * * *
41638696 TTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCC-TGTCGC-ATATATACAC
1 TTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACAATATATACAC
* * * *
41638759 TTTCACATTCATCACATCGGCCATTAGGCCTTATC--ACATATATACACTTTCACATTCATCACA
66 TTTCACATCCATCACATCAG-CA-TAGGCCTAATCAAATATATATACACTTTCACATTCATCACA
* * * * *
41638822 TCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT
129 TCAGCCATTAGGCCATACCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCTT
* *
41638885 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC
194 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCA
* *
41638930 TTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
1 TTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACA-ATATATACA
* * * *
41638995 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
65 CTTTCACATCCATCACATCAG-CA-TAGGCCTAATCAAATATATATACACTTTCACATTCATCAC
* * *
41639060 ATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCT
128 ATCAGCCATTAGGCCATACCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCT
41639125 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCA
193 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCA
* *
41639171 TTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCTC-ATATATGCA-
1 TTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACAATATATACAC
41639234 TGTTCACATCCATCACAT
66 T-TTCACATCCATCACAT
41639252 AGAATCCTAA
Statistics
Matches: 295, Mismatches: 19, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
234 40 0.14
235 4 0.01
237 45 0.15
238 1 0.00
239 71 0.24
241 134 0.45
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (238 bp):
TTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACAATATATACAC
TTTCACATCCATCACATCAGCATAGGCCTAATCAAATATATATACACTTTCACATTCATCACATC
AGCCATTAGGCCATACCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCTTAT
CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCA
Found at i:41642143 original size:22 final size:22
Alignment explanation
Indices: 41642109--41642163 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41642099 TATTGCCATG
*
41642109 GATTTATTATGCCAATATAATT
1 GATTGATTATGCCAATATAATT
*
41642131 GATTGATTGTGCCAATATAATT
1 GATTGATTATGCCAATATAATT
* *
41642153 GAATGTTTATG
1 GATTGATTATG
41642164 TGTTAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (22 bp):
GATTGATTATGCCAATATAATT
Found at i:41646795 original size:40 final size:40
Alignment explanation
Indices: 41646602--41646866 Score: 252
Period size: 40 Copynumber: 6.7 Consensus size: 40
41646592 GCTCCTCGTT
* * * * *
41646602 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* ** *
41646642 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* ** *
41646681 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
*
41646721 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
* *
41646761 CAAAGGCCTTCGGGGCTTAACCCGGGATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GGATTTAGTATCTCGCA
* ** * * *
41646801 CAAAAGCCTTC-GGATCTTAGTCCGGATATATTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-ATC-TCGCA
*
41646842 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41646867 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
39 41 0.21
40 139 0.70
41 18 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
Found at i:41646826 original size:120 final size:119
Alignment explanation
Indices: 41646604--41646866 Score: 282
Period size: 120 Copynumber: 2.2 Consensus size: 119
41646594 TCCTCGTTCA
* * *
41646604 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * * *
41646669 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAAGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* * * * *
41646722 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGG
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCC-GG
** * ** *
41646787 ATTT-GTATCTCGCACAAAAGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAACAACTCGCACAAAAGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
41646843 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41646867 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
119 37 0.31
120 70 0.59
121 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAACAACTCGCACAAAAGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:41646875 original size:41 final size:41
Alignment explanation
Indices: 41646798--41646875 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41646788 TTTGTATCTC
* * *
41646798 GCACAAAAGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41646839 GCAC-AAAGCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAAGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41646876 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41654022 original size:39 final size:40
Alignment explanation
Indices: 41653977--41654148 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
41653967 GCTCCTCGTT
* * *
41653977 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
41654017 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
41654056 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
41654096 CAAAGGCCTTCGGGGCTTAACCCGGGATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCC-GGATTTAGTAACTCGCA
*
41654136 CAAAAGCCTTCGG
1 CAAATGCCTTCGG
41654149 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 77 0.66
41 6 0.05
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:41654161 original size:80 final size:79
Alignment explanation
Indices: 41653977--41654201 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 79
41653967 GCTCCTCGTT
* * * * *
41653977 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGA
41654042 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * * * * *
41654056 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCC-G
** *
41654121 GATTT-GTATCTCGCA
64 GATTTAACAACTCGCA
** * * * * * * *
41654136 CAAAAGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAAGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CACAAGGCCTTCGGGACATAACCCG
41654200 GA
64 GA
41654202 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
79 41 0.35
80 67 0.57
81 9 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CAAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGA
TTTAACAACTCGCA
Found at i:41654210 original size:41 final size:41
Alignment explanation
Indices: 41654133--41654210 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41654123 TTTGTATCTC
* * *
41654133 GCACAAAAGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41654174 GCAC-AAAGCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAAGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41654211 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAAGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41668310 original size:29 final size:29
Alignment explanation
Indices: 41668277--41668337 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
41668267 TGCAATTGAA
*
41668277 CTACACTACTAATGAGAAGGAACTATTGG
1 CTACACTACTAATGAAAAGGAACTATTGG
*
41668306 CTACACTACTAATGAAAATGAACTATTGG
1 CTACACTACTAATGAAAAGGAACTATTGG
41668335 CTA
1 CTA
41668338 TGGTATTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (29 bp):
CTACACTACTAATGAAAAGGAACTATTGG
Found at i:41674538 original size:21 final size:21
Alignment explanation
Indices: 41674512--41674553 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41674502 ACGGAGTTAG
41674512 TGTCAAAATGTTTGACTTGCT
1 TGTCAAAATGTTTGACTTGCT
41674533 TGTCAAAATGTTTGACTTGCT
1 TGTCAAAATGTTTGACTTGCT
41674554 AGCAAGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (21 bp):
TGTCAAAATGTTTGACTTGCT
Found at i:41678779 original size:18 final size:17
Alignment explanation
Indices: 41678746--41678784 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
41678736 TTATATAAAT
41678746 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
41678764 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
41678781 TGTG
1 TGTG
41678785 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:41679037 original size:23 final size:23
Alignment explanation
Indices: 41679011--41679108 Score: 124
Period size: 23 Copynumber: 4.3 Consensus size: 23
41679001 GTGTTATTGA
*
41679011 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
*
41679034 TCAGTGGTAGCTACGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* *
41679057 ACAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
** * *
41679080 TCAGTGGTAAATTTGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
41679103 TCAGTG
1 TCAGTG
41679109 TGGAACTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:41679358 original size:23 final size:25
Alignment explanation
Indices: 41679312--41679358 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
41679302 GAAATTGCTA
* *
41679312 AGAAATGTTTGATTAGTTATATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
41679337 AGAAATG-TTAATT-GTTAAATGA
1 AGAAATGTTTAATTAGTTAAATGA
41679359 ATATTTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTAGTTAAATGAG
Found at i:41693251 original size:20 final size:21
Alignment explanation
Indices: 41693228--41693268 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
41693218 AAAAGGGGAA
41693228 TATGTT-CTAAAAAAAAAAGG
1 TATGTTACTAAAAAAAAAAGG
*
41693248 TATGTTGACTAAAAAGAAAAG
1 TATGTT-ACTAAAAAAAAAAG
41693269 AAAGAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (21 bp):
TATGTTACTAAAAAAAAAAGG
Found at i:41694527 original size:79 final size:79
Alignment explanation
Indices: 41694396--41694554 Score: 273
Period size: 79 Copynumber: 2.0 Consensus size: 79
41694386 AAAATATGAT
*
41694396 TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTGATT
1 TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
41694461 TTCATGATCTGTTG
66 TTCATGATCTGTTG
* * **
41694475 TCTAACAAATCCAGTCATAAACTCATTTTGAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
1 TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
41694540 TTCATGATCTGTTG
66 TTCATGATCTGTTG
41694554 T
1 T
41694555 GTGTGGATAG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (79 bp):
TCTAAAAAATCCAATCATAAACTCATTTCAAAATTTGTTAAGGTGATATCCCATGGAATTTAATT
TTCATGATCTGTTG
Found at i:41694724 original size:42 final size:42
Alignment explanation
Indices: 41694652--41694867 Score: 254
Period size: 42 Copynumber: 5.1 Consensus size: 42
41694642 GGAAAGCATT
* *
41694652 CATTACATTTAG-AGACCCAGGTGTGAAGGTCCATTTACTTTG
1 CATTGCATTTAGAAG-CCCAGGTGTGGAGGTCCATTTACTTTG
* * *
41694694 CATTGCATTTAGAATCCTAGGTATGGAGGTCCATTTACTTTG
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * * * *
41694736 CATTGCATTTGGAATCCCAAGTGTGGAGGTCGATTTACTTTT
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * * *
41694778 CATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTT
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * *
41694820 CATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTAATTTTG
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTT-ACTTTG
41694863 CATTG
1 CATTG
41694868 TATATGAAAG
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 142 0.93
43 10 0.07
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (42 bp):
CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
Found at i:41694891 original size:84 final size:85
Alignment explanation
Indices: 41694650--41694867 Score: 280
Period size: 84 Copynumber: 2.6 Consensus size: 85
41694640 AAGGAAAGCA
* * * *
41694650 TTCATTACATTTAGAGACCCAGGTGTGAAGGTCCATTT-ACTTTGCATTGCATTTAGAATCCTAG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTAATTTTGCATTGCATTTAGAAGCCTAG
* *
41694714 GTATGGAGGTCCATTTACTT
66 GTGTGGAGGTCTATTTACTT
* * * * * *
41694734 TGCATTGCATTTGGA-ATCCCAAGTGTGGAGGTCGATTTACTTTT-CATTGCATTTAGAGGCCTA
1 TTCATTGCATTTAGAGA-CCCAGGTGTGGAGGTCCATTTAATTTTGCATTGCATTTAGAAGCCTA
41694797 GGTGTGGAGGTCTATTTACTT
65 GGTGTGGAGGTCTATTTACTT
* *
41694818 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTAATTTTGCATTG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTAATTTTGCATTG
41694868 TATATGAAAG
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
83 1 0.01
84 103 0.92
85 8 0.07
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (85 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTAATTTTGCATTGCATTTAGAAGCCTAG
GTGTGGAGGTCTATTTACTT
Found at i:41694891 original size:126 final size:126
Alignment explanation
Indices: 41694650--41694913 Score: 307
Period size: 126 Copynumber: 2.1 Consensus size: 126
41694640 AAGGAAAGCA
* * *
41694650 TTCATTACATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAATCCTAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
* * * * * *
41694715 TATGGAGGTCCATTTACTTTGCATTGCATTTGGAATCCCAAGTGTGGAGGTCG-ATTTACTT
66 TATGGAGGTCCATTTACTTTGCATTGCATATGAAAGCACAAGTGTGGAGGT-GTAATTACAT
* * * * * *
41694776 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
* * * * *
41694841 TGTGGAGGTCTATTTAATTTTGCATTGTATATGAAAGCACATGTGT-GAGGTGTAATTACAT
66 TATGGAGGTCCATTT-ACTTTGCATTGCATATGAAAGCACAAGTGTGGAGGTGTAATTACAT
41694902 TTCATCTGCATT
1 TTCAT-TGCATT
41694914 CTCATTTCAA
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
125 1 0.01
126 85 0.74
127 29 0.25
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (126 bp):
TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
TATGGAGGTCCATTTACTTTGCATTGCATATGAAAGCACAAGTGTGGAGGTGTAATTACAT
Found at i:41695321 original size:15 final size:15
Alignment explanation
Indices: 41695301--41695340 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
41695291 AAGGGCCCAA
*
41695301 ATCATTATTACTATT
1 ATCATTATTACTACT
*
41695316 ATCATTACTACTACT
1 ATCATTATTACTACT
*
41695331 ATTATTATTA
1 ATCATTATTA
41695341 ATAAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCATTATTACTACT
Found at i:41695847 original size:19 final size:18
Alignment explanation
Indices: 41695807--41695849 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
41695797 TAAAGCTTTG
* * *
41695807 ATTTTTAAGAAAAATAGT
1 ATTTTTAAAAAAAAGAGA
41695825 ATTTTTAAAAAAAAGAGA
1 ATTTTTAAAAAAAAGAGA
*
41695843 AATTTTA
1 ATTTTTA
41695850 GATTTTTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (18 bp):
ATTTTTAAAAAAAAGAGA
Found at i:41697897 original size:20 final size:19
Alignment explanation
Indices: 41697850--41697902 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
41697840 TTACTAGCCC
41697850 CCGTACTCTTATGTAGGCA
1 CCGTACTCTTATGTAGGCA
* * *
41697869 ACTTACTCTTATGTAGGCCT
1 CCGTACTCTTATGTAGG-CA
41697889 CCGTACTCTTATGT
1 CCGTACTCTTATGT
41697903 TAGTAAGTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (19 bp):
CCGTACTCTTATGTAGGCA
Found at i:41710757 original size:23 final size:22
Alignment explanation
Indices: 41710725--41710767 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
41710715 TAATATCTCA
*
41710725 ACATTTCATACCATTCAATAAG
1 ACATTTCATACCATGCAATAAG
*
41710747 ACATTCTCATATCATGCAATA
1 ACATT-TCATACCATGCAATA
41710768 TAATTATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
ACATTTCATACCATGCAATAAG
Found at i:41717044 original size:27 final size:27
Alignment explanation
Indices: 41716999--41717348 Score: 337
Period size: 27 Copynumber: 13.0 Consensus size: 27
41716989 CACCGAGACC
41716999 CCGAAATACCC-CATAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
41717025 CCGAAATATCCTCATAGGGTAAATTGA
1 CCGAAATACCCTCATAGGGTAAAATGA
** * *
41717052 CTAAAATACCCCCATAAGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * * *
41717079 CCAAAATACCCCCATATGGTAAAATAA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
41717106 TCGAAATACCCCCATAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * * *
41717133 CAGCAATACCCTTATAGTGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * * *
41717160 CCAAAATACCCCCATGGGGTAAAATAA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
41717187 TCGAAATACCCTCACAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
** * * *
41717214 TTGAAATACCCTTATAAGATAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
*
41717241 CCAAAATACCC-CATAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* *
41717267 CCAAAATACCCTCGTAGGGTAAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
* * *
41717294 CTGAAATA-CCTCTGTAGGGTAGAATGA
1 CCGAAATACCCTC-ATAGGGTAAAATGA
** * *
41717321 CAAAAATACCCTGATAGGGTCAAATGA
1 CCGAAATACCCTCATAGGGTAAAATGA
41717348 C
1 C
41717349 TGTTCTACCC
Statistics
Matches: 264, Mismatches: 56, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
26 37 0.14
27 224 0.85
28 3 0.01
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
CCGAAATACCCTCATAGGGTAAAATGA
Found at i:41717142 original size:81 final size:81
Alignment explanation
Indices: 41717002--41717345 Score: 390
Period size: 81 Copynumber: 4.3 Consensus size: 81
41716992 CGAGACCCCG
* * * *
41717002 AAATA-CCCCATAGGGTAAAATGACCGAAATATCCTCATAGGGTAAATTGACTA-AAATACCCCC
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGAC-AGAAATACCCCT
41717065 ATAAGGTAAAATGACCA
65 ATAAGGTAAAATGACCA
* * * * *
41717082 AAATACCCCCATATGGTAAAATAATCGAAATACCCCCATAGGGTAAAATGACAGCAATACCCTTA
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
41717147 T-AGTGTAAAATGACCA
66 TAAG-GTAAAATGACCA
* * * ** *
41717163 AAATACCCCCATGGGGTAAAATAATCGAAATACCCTCACAGGGTAAAATGATTGAAATACCCTTA
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
*
41717228 TAAGATAAAATGACCA
66 TAAGGTAAAATGACCA
* * * * * *
41717244 AAATA-CCCCATAGGGTAAAATGACCAAAATACCCTCGTAGGGTAAAATGACTGAAATACCTCTG
1 AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
* * *
41717308 TAGGGTAGAATGACAA
66 TAAGGTAAAATGACCA
** *
41717324 AAATACCCTGATAGGGTCAAAT
1 AAATACCCCCATAGGGTAAAAT
41717346 GACTGTTCTA
Statistics
Matches: 225, Mismatches: 34, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
80 74 0.33
81 149 0.66
82 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (81 bp):
AAATACCCCCATAGGGTAAAATAACCGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCTA
TAAGGTAAAATGACCA
Found at i:41717358 original size:134 final size:135
Alignment explanation
Indices: 41717001--41717376 Score: 321
Period size: 134 Copynumber: 2.8 Consensus size: 135
41716991 CCGAGACCCC
* * * * * *
41717001 GAAATACCC-CATAGGGTAAAATGACCGAAATATCCTCATAGGGTAAATTGA-CTAAAATACCCC
1 GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATC-AAAATACCCT
* * ** * * * * * * *
41717064 CATAAGGTAAAATGACCAAAATACCCCCATATGGTAAAATAATCGAAATACCCCCATAGGGTAAA
65 CACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACCAAAATACCCCCATAGGGTAAA
41717129 ATGACA
130 ATGACA
* * * * *
41717135 GCAATACCCTTATAGTGTAAAATGACCAAAATACCCCCATGGGGTAAAATAATCGAAATACCCTC
1 GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCAAAATACCCTC
* * *
41717200 ACAGGGTAAAATGATTGAAATACCCTTATAAGATAAAATGACCAAAATA-CCCCATAGGGTAAAA
66 ACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACCAAAATACCCCCATAGGGTAAAA
41717264 TGACCA
131 TGA-CA
* ** * ** * *
41717270 -AAATACCCTCGTAGGGTAAAATGACTGAAATACCTCTGTAGGGTAGAATGA-CAAAAATACCCT
1 GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATC-AAAATACCCT
* * * *** * *
41717333 GATAGGGTCAAATGACTGTTCTACCCCTAGGAGATGAAATGACC
65 CACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACC
41717377 GTTATAGTCT
Statistics
Matches: 191, Mismatches: 47, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
133 1 0.01
134 107 0.56
135 82 0.43
136 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (135 bp):
GAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCAAAATACCCTC
ACAGGGTAAAATGACTGAAATACCCCTAGAAGATAAAATGACCAAAATACCCCCATAGGGTAAAA
TGACA
Found at i:41719712 original size:25 final size:25
Alignment explanation
Indices: 41719617--41719712 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
41719607 TACTGATTTT
* * *
41719617 AGCTCGTATGAGCTTACCGCTACTT-
1 AGCTCGAAGGAGCTTACCGTTA-TTC
* *
41719642 AGCTC-ACATGAGCTTACTGTTATTC
1 AGCTCGA-AGGAGCTTACCGTTATTC
** *
41719667 AGCTCGGTGGAGCTTATCGTTATTC
1 AGCTCGAAGGAGCTTACCGTTATTC
41719692 AGCTCGAAGGAGCTTACCGTT
1 AGCTCGAAGGAGCTTACCGTT
41719713 TACAACTCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.04
25 55 0.96
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (25 bp):
AGCTCGAAGGAGCTTACCGTTATTC
Found at i:41725184 original size:20 final size:20
Alignment explanation
Indices: 41725144--41725184 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
41725134 GGTTGAGATC
41725144 GGTTTGCTGTAATTTGAAATT
1 GGTTTGCTGT-ATTTGAAATT
41725165 GGTTTGCTGT-TTTAGAAATT
1 GGTTTGCTGTATTT-GAAATT
41725185 TAATTCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 6 0.32
21 10 0.53
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (20 bp):
GGTTTGCTGTATTTGAAATT
Found at i:41732132 original size:15 final size:16
Alignment explanation
Indices: 41732104--41732136 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
41732094 TTTGGAAAGG
41732104 TTTTTGATATAGTGAT
1 TTTTTGATATAGTGAT
*
41732120 TTTTTTATA-AGTGAT
1 TTTTTGATATAGTGAT
41732135 TT
1 TT
41732137 ATTAAGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (16 bp):
TTTTTGATATAGTGAT
Found at i:41733388 original size:25 final size:25
Alignment explanation
Indices: 41733351--41733498 Score: 126
Period size: 25 Copynumber: 6.0 Consensus size: 25
41733341 GTCATTAGGG
*
41733351 TTACCGAT-TTTAGCTCGTATGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
* * **
41733375 TTACTGTTACTTAGCTCACATGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
* * *
41733400 TTACCATTATTTAGCTTAG-AGGAGC
1 TTACCGTTATTTAGC-TCGTATGAGC
*
41733425 TTACCGTTATTTAGCTCGTAAGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
* *
41733450 TTACCGTT-TATAGCTCGTAAGAGC
1 TTACCGTTATTTAGCTCGTATGAGC
*
41733474 ATACCG--ATTTAGAGCTCGTATGAGC
1 TTACCGTTATTT--AGCTCGTATGAGC
41733499 ATACATGTAC
Statistics
Matches: 100, Mismatches: 18, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
23 2 0.02
24 28 0.28
25 69 0.69
26 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (25 bp):
TTACCGTTATTTAGCTCGTATGAGC
Found at i:41737645 original size:6 final size:6
Alignment explanation
Indices: 41737634--41737660 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41737624 TACTCACACA
41737634 GGCACG GGCACG GGCACG GGCACG GGC
1 GGCACG GGCACG GGCACG GGCACG GGC
41737661 TGGGACACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.52, T:0.00
Consensus pattern (6 bp):
GGCACG
Found at i:41738087 original size:39 final size:39
Alignment explanation
Indices: 41738031--41738108 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
41738021 TAGGTTTGCA
41738031 AAGTGTTTTGAGAATAGGATAGGTGATGGATCGGCTAAG
1 AAGTGTTTTGAGAATAGGATAGGTGATGGATCGGCTAAG
* *
41738070 AAGTGTTTT-AGGGATAGGATAGGTGATGGCTCGGCTAAG
1 AAGTGTTTTGA-GAATAGGATAGGTGATGGATCGGCTAAG
41738109 GATAAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.28, C:0.06, G:0.37, T:0.28
Consensus pattern (39 bp):
AAGTGTTTTGAGAATAGGATAGGTGATGGATCGGCTAAG
Found at i:41739785 original size:13 final size:13
Alignment explanation
Indices: 41739767--41739792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41739757 TCCCAATATA
41739767 GCTCATTACTTTC
1 GCTCATTACTTTC
41739780 GCTCATTACTTTC
1 GCTCATTACTTTC
41739793 CAGTTGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
GCTCATTACTTTC
Found at i:41742501 original size:18 final size:18
Alignment explanation
Indices: 41742478--41742572 Score: 87
Period size: 18 Copynumber: 5.6 Consensus size: 18
41742468 TCTTCACACA
41742478 TTTCTTTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
*
41742496 TCTCTTTTTC-A-CTCGT-
1 TTTCTTTTTCAAGCTC-TC
41742512 TTTC-TTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
* *
41742529 TTTCCTTTTC-A-CTCGC
1 TTTCTTTTTCAAGCTCTC
41742545 TTTC-TTTTCAAAGCTCTC
1 TTTCTTTTTC-AAGCTCTC
*
41742563 TTTCCTTTTC
1 TTTCTTTTTC
41742573 TTGCTCACAC
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.16
16 16 0.25
17 11 0.17
18 22 0.34
19 5 0.08
ACGTcount: A:0.09, C:0.31, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTCTTTTTCAAGCTCTC
Found at i:41742519 original size:16 final size:16
Alignment explanation
Indices: 41742498--41742552 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
41742488 AAGCTCTCTC
41742498 TCTTTTTCACTCGTTT
1 TCTTTTTCACTCGTTT
41742514 TC-TTTTCAAGCTC-TCTT
1 TCTTTTTC-A-CTCGT-TT
* *
41742531 TCCTTTTCACTCGCTT
1 TCTTTTTCACTCGTTT
41742547 TCTTTT
1 TCTTTT
41742553 CAAAGCTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 5 0.16
16 14 0.44
17 8 0.25
18 5 0.16
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.58
Consensus pattern (16 bp):
TCTTTTTCACTCGTTT
Found at i:41742520 original size:33 final size:33
Alignment explanation
Indices: 41742478--41742572 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
41742468 TCTTCACACA
* * *
41742478 TTTCTTTTTCAAGCTCTCTCTCTTTTTCACTCGT
1 TTTC-TTTTCAAGCTCTCTTTCCTTTTCACTCGC
41742512 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
1 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
41742545 TTTCTTTTCAAAGCTCTCTTTCCTTTTC
1 TTTCTTTTC-AAGCTCTCTTTCCTTTTC
41742573 TTGCTCACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 35 0.61
34 22 0.39
ACGTcount: A:0.09, C:0.31, G:0.05, T:0.55
Consensus pattern (33 bp):
TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
Found at i:41742521 original size:15 final size:15
Alignment explanation
Indices: 41742501--41742554 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
41742491 CTCTCTCTCT
41742501 TTTTCACTCGTTTTC
1 TTTTCACTCGTTTTC
41742516 TTTTCAAGCTC-TCTTTCC
1 TTTTC-A-CTCGT-TTT-C
*
41742534 TTTTCACTCGCTTTC
1 TTTTCACTCGTTTTC
41742549 TTTTCA
1 TTTTCA
41742555 AAGCTCTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
15 12 0.36
16 8 0.24
17 7 0.21
18 6 0.18
ACGTcount: A:0.09, C:0.30, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTTCACTCGTTTTC
Found at i:41742664 original size:33 final size:33
Alignment explanation
Indices: 41742599--41742664 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
41742589 TTGCTCTCAA
**
41742599 TCTCTTTTTCTTTTTCAATTCTTTTGTTTCATT
1 TCTCTTTTTCTTTTTCAATTCTTTTGACTCATT
*
41742632 TCTCTTTTTCTTTTT-ATTTCTTTTTGACTCATT
1 TCTCTTTTTCTTTTTCAATTC-TTTTGACTCATT
41742665 CTTTCATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (33 bp):
TCTCTTTTTCTTTTTCAATTCTTTTGACTCATT
Found at i:41750244 original size:4 final size:4
Alignment explanation
Indices: 41750237--41750266 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
41750227 AATTAATCAA
*
41750237 TCAT TCAT TCAT CCAT TCAT TCAT TCAT TC
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TC
41750267 GCTCATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (4 bp):
TCAT
Found at i:41759529 original size:9 final size:9
Alignment explanation
Indices: 41759515--41759628 Score: 86
Period size: 9 Copynumber: 12.7 Consensus size: 9
41759505 CAAGTTTGGG
*
41759515 CATGCACTC
1 CATGCATTC
41759524 CATGCATTC
1 CATGCATTC
***
41759533 CATGCAAAA
1 CATGCATTC
*
41759542 CATGCTTTC
1 CATGCATTC
41759551 CATGCATTC
1 CATGCATTC
* ***
41759560 CACGCAAAA
1 CATGCATTC
41759569 CATGCATTC
1 CATGCATTC
41759578 CATGCATTC
1 CATGCATTC
**
41759587 CATGCAACC
1 CATGCATTC
*
41759596 CATGCATTT
1 CATGCATTC
*
41759605 CATGCGA-AC
1 CATGC-ATTC
*
41759614 CATGCATCC
1 CATGCATTC
41759623 CATGCA
1 CATGCA
41759629 ATTTGCTACA
Statistics
Matches: 78, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
8 1 0.01
9 76 0.97
10 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (9 bp):
CATGCATTC
Found at i:41759553 original size:27 final size:27
Alignment explanation
Indices: 41759515--41759609 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
41759505 CAAGTTTGGG
*
41759515 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATTCCATGCAAAA
* *
41759542 CATGCTTTCCATGCATTCCACGCAAAA
1 CATGCATTCCATGCATTCCATGCAAAA
**
41759569 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATTCCATGCAAAA
*
41759596 CATGCATTTCATGC
1 CATGCATTCCATGC
41759610 GAACCATGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.12, T:0.26
Consensus pattern (27 bp):
CATGCATTCCATGCATTCCATGCAAAA
Found at i:41759616 original size:27 final size:27
Alignment explanation
Indices: 41759515--41759628 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 27
41759505 CAAGTTTGGG
* * **
41759515 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
* * * **
41759542 CATGCTTTCCATGCATTCCACGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
*
41759569 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATACCATGCAACC
* *
41759596 CATGCATTTCATGCGA-ACCATGCATCC
1 CATGCATTCCATGC-ATACCATGCAACC
41759623 CATGCA
1 CATGCA
41759629 ATTTGCTACA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 75 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (27 bp):
CATGCATTCCATGCATACCATGCAACC
Found at i:41759791 original size:41 final size:41
Alignment explanation
Indices: 41759744--41759827 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
41759734 GTTTAGACAT
*
41759744 TTTAAATGTGTGTCTTAAATACTGCACTTTAATTATAAGTC
1 TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
* *
41759785 TTTAAATATGTGTCTTAAATATTGCACTTTAATTATATGTC
1 TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
41759826 TT
1 TT
41759828 AGTTCTTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (41 bp):
TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
Found at i:41761490 original size:37 final size:37
Alignment explanation
Indices: 41761449--41761523 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
41761439 CCCCAAAAAG
41761449 AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
1 AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
*
41761486 AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
1 AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
41761523 A
1 A
41761524 CCAAGCTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (37 bp):
AATGATGCTTGGGGTGGTGGTGTGCCCAATATAACAT
Found at i:41762976 original size:27 final size:27
Alignment explanation
Indices: 41762936--41763030 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
41762926 CGAGTTTAGG
* *
41762936 CATGCACTCTATGCATTCTATGAAAAA
1 CATGCATTCCATGCATTCTATGAAAAA
* ** *
41762963 CCTGCATTCCATGCGCTCTATGTAAAA
1 CATGCATTCCATGCATTCTATGAAAAA
* * * **
41762990 CATGCATTTCATGCATTCCATGCAACC
1 CATGCATTCCATGCATTCTATGAAAAA
*
41763017 CATGCATTTCATGC
1 CATGCATTCCATGC
41763031 GAATGCATCC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (27 bp):
CATGCATTCCATGCATTCTATGAAAAA
Found at i:41765829 original size:20 final size:19
Alignment explanation
Indices: 41765804--41765917 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 19
41765794 CATGCGGTTT
41765804 AGCTCACTTGAGCTCAAGTC
1 AGCTCA-TTGAGCTCAAGTC
*
41765824 AGCTCATTTGAGCTCAAGTA
1 AGCTCA-TTGAGCTCAAGTC
*
41765844 AGCTCATTCAAGCTCAAGTC
1 AGCTCATT-GAGCTCAAGTC
* * * *
41765864 GGCTTATTTAAGCTCAATTC
1 AGCTCA-TTGAGCTCAAGTC
* * * *
41765884 AACTTATTCGAGCTCAATTT
1 AGCTCATT-GAGCTCAAGTC
41765904 AGCTCATTGAGCTC
1 AGCTCATTGAGCTC
41765918 GTTATTAGCT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.13
20 66 0.85
21 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (19 bp):
AGCTCATTGAGCTCAAGTC
Found at i:41765848 original size:40 final size:40
Alignment explanation
Indices: 41765814--41765911 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 40
41765804 AGCTCACTTG
*
41765814 AGCTCAAGTCAGCTCATTTGAGCTCAAGTAAGCTCATTCA
1 AGCTCAAGTCAGCTCATTTAAGCTCAAGTAAGCTCATTCA
* * * * *
41765854 AGCTCAAGTCGGCTTATTTAAGCTCAATTCAA-CTTATTCG
1 AGCTCAAGTCAGCTCATTTAAGCTCAAGT-AAGCTCATTCA
* *
41765894 AGCTCAATTTAGCTCATT
1 AGCTCAAGTCAGCTCATT
41765912 GAGCTCGTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 45 0.96
41 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
AGCTCAAGTCAGCTCATTTAAGCTCAAGTAAGCTCATTCA
Found at i:41767455 original size:15 final size:16
Alignment explanation
Indices: 41767435--41767474 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
41767425 GAAGAAATTT
41767435 CAAAAAAAAAGT-GAG
1 CAAAAAAAAAGTCGAG
41767450 C-AAAAAAAA-TCGAG
1 CAAAAAAAAAGTCGAG
41767464 CAAAAAAAAAG
1 CAAAAAAAAAG
41767475 AATTGAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 9 0.41
ACGTcount: A:0.70, C:0.10, G:0.15, T:0.05
Consensus pattern (16 bp):
CAAAAAAAAAGTCGAG
Found at i:41768573 original size:18 final size:18
Alignment explanation
Indices: 41768552--41768586 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41768542 GAGTGGGGGT
41768552 GAAAA-AAAATCTGAAAAC
1 GAAAAGAAAAT-TGAAAAC
41768570 GAAAAGAAAATTGAAAA
1 GAAAAGAAAATTGAAAA
41768587 TGAGATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (18 bp):
GAAAAGAAAATTGAAAAC
Found at i:41770377 original size:10 final size:9
Alignment explanation
Indices: 41770362--41770479 Score: 67
Period size: 10 Copynumber: 12.0 Consensus size: 9
41770352 CATTTGGTTT
41770362 AGCTCACTTG
1 AGCTCA-TTG
41770372 AGCTCAAGTT-
1 AGCTC-A-TTG
41770382 AGCTCATTCG
1 AGCTCATT-G
* *
41770392 AGCTCAAGTC
1 AGCTC-ATTG
41770402 AGCTCATTCG
1 AGCTCATT-G
* *
41770412 AGCTCAAGTC
1 AGCTC-ATTG
41770422 AGCTCATTCG
1 AGCTCATT-G
* *
41770432 AGCTCAAATC
1 AGCTC-ATTG
41770442 AGCTCATTCG
1 AGCTCATT-G
*
41770452 AGCTCAATTT
1 AGCTC-ATTG
41770462 AGCTCATTG
1 AGCTCATTG
41770471 AGCTCATTG
1 AGCTCATTG
41770480 TTAGCTCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 21
0.70 0.13 0.18
Matches are distributed among these distances:
8 2 0.02
9 19 0.23
10 50 0.60
11 12 0.14
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (9 bp):
AGCTCATTG
Found at i:41770385 original size:20 final size:20
Alignment explanation
Indices: 41770360--41770486 Score: 168
Period size: 20 Copynumber: 6.3 Consensus size: 20
41770350 CTCATTTGGT
41770360 TTAGCTCACTT-GAGCTCAAG
1 TTAGCTCA-TTCGAGCTCAAG
41770380 TTAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAG
*
41770400 TCAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAG
* *
41770420 TCAGCTCATTCGAGCTCAAA
1 TTAGCTCATTCGAGCTCAAG
* *
41770440 TCAGCTCATTCGAGCTCAAT
1 TTAGCTCATTCGAGCTCAAG
*
41770460 TTAGCTCATT-GAGCTCATTG
1 TTAGCTCATTCGAGCTCA-AG
41770480 TTAGCTC
1 TTAGCTC
41770487 TTTAGTTCAT
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
19 9 0.09
20 90 0.91
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
TTAGCTCATTCGAGCTCAAG
Found at i:41781615 original size:8 final size:8
Alignment explanation
Indices: 41781599--41781632 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
41781589 CAGGTATTCC
*
41781599 AAAAGAAA
1 AAAATAAA
41781607 AAAATAAAA
1 AAAAT-AAA
41781616 AAAATAAA
1 AAAATAAA
41781624 AAAATAAA
1 AAAATAAA
41781632 A
1 A
41781633 TGTCTAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (8 bp):
AAAATAAA
Found at i:41781618 original size:9 final size:9
Alignment explanation
Indices: 41781604--41781632 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41781594 ATTCCAAAAG
41781604 AAAAAAATA
1 AAAAAAATA
41781613 AAAAAAAT-
1 AAAAAAATA
41781621 AAAAAAATA
1 AAAAAAATA
41781630 AAA
1 AAA
41781633 TGTCTAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:41781624 original size:17 final size:17
Alignment explanation
Indices: 41781599--41781632 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41781589 CAGGTATTCC
41781599 AAAAGAAAAAAATAAAA
1 AAAAGAAAAAAATAAAA
*
41781616 AAAATAAAAAAATAAAA
1 AAAAGAAAAAAATAAAA
41781633 TGTCTAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAAATAAAA
Found at i:41787690 original size:27 final size:30
Alignment explanation
Indices: 41787654--41787735 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 30
41787644 GAATATAAAG
41787654 GGGGTTGCTAAGTGCTGATTCCC-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCACTCATA
*
41787681 GGGGTTGCTAAGTGCTGATTCCCTGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCC--ACTCATA
41787713 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
41787736 ACCGTATCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 23 0.48
30 1 0.02
31 2 0.04
32 2 0.04
33 20 0.42
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCACTCATA
Found at i:41787793 original size:105 final size:105
Alignment explanation
Indices: 41787653--41787844 Score: 312
Period size: 105 Copynumber: 1.8 Consensus size: 105
41787643 TGAATATAAA
* * * * * *
41787653 GGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCATTGGTGG
1 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
*
41787718 TTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTAAAAG
66 TTGCTAAGTGCTGAATCCACCGTATCTTTGAATGTAAAAG
41787758 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
1 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
*
41787823 TTGCTAAGTTCTGAATCCACCG
66 TTGCTAAGTGCTGAATCCACCG
41787845 ATAACGGACA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (105 bp):
GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
TTGCTAAGTGCTGAATCCACCGTATCTTTGAATGTAAAAG
Found at i:41793513 original size:11 final size:11
Alignment explanation
Indices: 41793492--41793527 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
41793482 TAAAACCTGC
41793492 TAAAA-CAAAT
1 TAAAAGCAAAT
41793502 TAAAAGCAAAT
1 TAAAAGCAAAT
*
41793513 TTAAAGCAAAT
1 TAAAAGCAAAT
41793524 TAAA
1 TAAA
41793528 CACACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.22
Consensus pattern (11 bp):
TAAAAGCAAAT
Found at i:41794790 original size:22 final size:21
Alignment explanation
Indices: 41794765--41794806 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
41794755 TTAAATAAAT
*
41794765 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
41794787 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
41794807 GTTAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:41796067 original size:28 final size:28
Alignment explanation
Indices: 41796025--41796087 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
41796015 CTATTCACTA
41796025 ACAGT-ACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
41796052 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
41796080 ACAGTAAC
1 ACAGTAAC
41796088 CAATACAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:41796470 original size:27 final size:27
Alignment explanation
Indices: 41796440--41796840 Score: 358
Period size: 27 Copynumber: 14.9 Consensus size: 27
41796430 GGGTATAACA
*
41796440 GTCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *** * **
41796467 GTCATTCTACCCTGCAGAGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
41796494 GCCATTTTACCCTACGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
41796521 GTCATTTTACCCTATGGTGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTG
41796548 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * ** **
41796575 GTCATTTTATCTTATAAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
41796602 ATCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
41796629 ATTATTTTACCCTATGGGGGGATTCTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
41796656 GTCATTTTACACTATGAGGGTATTGCT-
1 GTCATTTTACCCTATGGGGGTATT-TTG
*
41796683 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
41796710 ATTATTTTACCATATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * **
41796737 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
41796764 GTTAATTTATCCTATGGGGATATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
41796791 GTAATTTTATCCTAT--GGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
41796816 TTCATTTTACCCTATGGGGGTATTT
1 GTCATTTTACCCTATGGGGGTATTT
41796841 GGGCTCTCGA
Statistics
Matches: 295, Mismatches: 75, Indels: 8
0.78 0.20 0.02
Matches are distributed among these distances:
25 21 0.07
27 272 0.92
28 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:41796822 original size:25 final size:25
Alignment explanation
Indices: 41796769--41796832 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
41796759 TTTCAGTTAA
*
41796769 TTTATCCTATGGGGATATTTTGGTAAT
1 TTTATCCTAT--GGATATTTCGGTAAT
* *
41796796 TTTATCCTATGGATATTTCGTTCAT
1 TTTATCCTATGGATATTTCGGTAAT
*
41796821 TTTACCCTATGG
1 TTTATCCTATGG
41796833 GGGTATTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 23 0.70
27 10 0.30
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.48
Consensus pattern (25 bp):
TTTATCCTATGGATATTTCGGTAAT
Found at i:41804677 original size:33 final size:34
Alignment explanation
Indices: 41804626--41804700 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
41804616 AGAGTTAAAC
*
41804626 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
41804660 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
41804693 AATTTAAT
1 AAATTAAT
41804701 AAACCAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:41805847 original size:27 final size:27
Alignment explanation
Indices: 41805815--41805867 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
41805805 CTTGTCTGTT
41805815 TCTTTTTCACTCTCAATCTCTTTTTTC
1 TCTTTTTCACTCTCAATCTCTTTTTTC
* **
41805842 TCTTTTTCATTCTCTTTCTCTTTTTT
1 TCTTTTTCACTCTCAATCTCTTTTTT
41805868 GATTTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTTC
Found at i:41806715 original size:11 final size:11
Alignment explanation
Indices: 41806699--41806724 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41806689 TTAGAAAGTG
41806699 TAAAGGATGAA
1 TAAAGGATGAA
41806710 TAAAGGATGAA
1 TAAAGGATGAA
41806721 TAAA
1 TAAA
41806725 AGCAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (11 bp):
TAAAGGATGAA
Found at i:41812968 original size:20 final size:20
Alignment explanation
Indices: 41812935--41812979 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41812925 TAAATTCACA
41812935 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
41812955 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
41812975 TAATT
1 TAATT
41812980 CGGTTAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:41813932 original size:28 final size:28
Alignment explanation
Indices: 41813892--41814045 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
41813882 TAAATTGTAC
41813892 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
41813920 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
41813948 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41813976 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
41814004 AGCACTAAGTGTGCAAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41814031 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41814046 GACTTAATAT
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 23 0.19
28 99 0.81
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:41813958 original size:56 final size:56
Alignment explanation
Indices: 41813867--41814045 Score: 270
Period size: 56 Copynumber: 3.2 Consensus size: 56
41813857 GAGATTGGCG
* * * *
41813867 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41813924 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* *
41813980 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41814035 CTGAGTGTGCG
1 CTAAGTGTGCG
41814046 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 23 0.20
56 75 0.66
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:41821247 original size:28 final size:28
Alignment explanation
Indices: 41821182--41821387 Score: 299
Period size: 28 Copynumber: 7.4 Consensus size: 28
41821172 GAAATTGGCG
* * * *
41821182 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
41821211 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41821239 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41821267 C-AAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41821294 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41821322 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
41821350 CTAAGTGTGCAAG-TTGATTATATAGCT
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41821377 CTGAGTGTGCG
1 CTAAGTGTGCG
41821388 GACTTAATAT
Statistics
Matches: 166, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
27 49 0.30
28 102 0.61
29 15 0.09
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:41821278 original size:55 final size:56
Alignment explanation
Indices: 41821182--41821387 Score: 308
Period size: 55 Copynumber: 3.7 Consensus size: 56
41821172 GAAATTGGCG
* * * *
41821182 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41821239 CTAAGTGTGCGAGTTTGATTATGTAGCAC-AAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41821294 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* * *
41821350 CTAAGTGTGCAAG-TTGATTATATAGCTCTGAGTGTGCG
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCG
41821388 GACTTAATAT
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
55 77 0.56
56 46 0.33
57 15 0.11
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:41821349 original size:83 final size:83
Alignment explanation
Indices: 41821207--41821387 Score: 292
Period size: 83 Copynumber: 2.2 Consensus size: 83
41821197 TAAATTGTAC
* *
41821207 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCAC-AAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
* *
41821271 TGTGCGAGTTTGATTATGT
66 TGTGCAAG-TTGATTATAT
41821290 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
41821355 TGTGCAAGTTGATTATAT
66 TGTGCAAGTTGATTATAT
* *
41821373 AGCTCTGAGTGTGCG
1 AGCACTAAGTGTGCG
41821388 GACTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 81 0.89
84 10 0.11
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (83 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
TGTGCAAGTTGATTATAT
Found at i:41827045 original size:28 final size:28
Alignment explanation
Indices: 41826980--41827185 Score: 299
Period size: 28 Copynumber: 7.4 Consensus size: 28
41826970 GAAATTGGCG
* * * *
41826980 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
41827009 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41827037 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41827065 C-AAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41827092 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41827120 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
41827148 CTAAGTGTGCAAG-TTGATTATATAGCT
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41827175 CTGAGTGTGCG
1 CTAAGTGTGCG
41827186 GACTTAATAT
Statistics
Matches: 166, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
27 49 0.30
28 102 0.61
29 15 0.09
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:41827076 original size:55 final size:56
Alignment explanation
Indices: 41826980--41827185 Score: 308
Period size: 55 Copynumber: 3.7 Consensus size: 56
41826970 GAAATTGGCG
* * * *
41826980 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41827037 CTAAGTGTGCGAGTTTGATTATGTAGCAC-AAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41827092 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* * *
41827148 CTAAGTGTGCAAG-TTGATTATATAGCTCTGAGTGTGCG
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCG
41827186 GACTTAATAT
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
55 77 0.56
56 46 0.33
57 15 0.11
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:41827147 original size:83 final size:83
Alignment explanation
Indices: 41827005--41827185 Score: 292
Period size: 83 Copynumber: 2.2 Consensus size: 83
41826995 TAAATTGTAC
* *
41827005 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCAC-AAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
* *
41827069 TGTGCGAGTTTGATTATGT
66 TGTGCAAG-TTGATTATAT
41827088 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
41827153 TGTGCAAGTTGATTATAT
66 TGTGCAAGTTGATTATAT
* *
41827171 AGCTCTGAGTGTGCG
1 AGCACTAAGTGTGCG
41827186 GACTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 81 0.89
84 10 0.11
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (83 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
TGTGCAAGTTGATTATAT
Found at i:41832828 original size:28 final size:28
Alignment explanation
Indices: 41832785--41832989 Score: 306
Period size: 28 Copynumber: 7.4 Consensus size: 28
41832775 GAAATTGGCG
* * * *
41832785 CTAAGTGTGCGGGTTTAATTGTACAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41832813 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41832841 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41832869 C-AAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41832896 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
41832924 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
41832952 CTAAGTGTGCAAG-TTGATTATATAGCT
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
41832979 CTGAGTGTGCG
1 CTAAGTGTGCG
41832990 GACTTAATAT
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
27 49 0.30
28 117 0.70
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:41832885 original size:55 final size:56
Alignment explanation
Indices: 41832785--41832989 Score: 315
Period size: 55 Copynumber: 3.7 Consensus size: 56
41832775 GAAATTGGCG
* * * *
41832785 CTAAGTGTGCGGGTTTAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41832841 CTAAGTGTGCGAGTTTGATTATGTAGCAC-AAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
41832896 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
* * *
41832952 CTAAGTGTGCAAG-TTGATTATATAGCTCTGAGTGTGCG
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCG
41832990 GACTTAATAT
Statistics
Matches: 138, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
55 77 0.56
56 61 0.44
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:41832926 original size:83 final size:83
Alignment explanation
Indices: 41832809--41832989 Score: 292
Period size: 83 Copynumber: 2.2 Consensus size: 83
41832799 TTAATTGTAC
* *
41832809 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCAC-AAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
* *
41832873 TGTGCGAGTTTGATTATGT
66 TGTGCAAG-TTGATTATAT
41832892 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
41832957 TGTGCAAGTTGATTATAT
66 TGTGCAAGTTGATTATAT
* *
41832975 AGCTCTGAGTGTGCG
1 AGCACTAAGTGTGCG
41832990 GACTTAATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 81 0.89
84 10 0.11
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.34
Consensus pattern (83 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAG
TGTGCAAGTTGATTATAT
Found at i:41836357 original size:45 final size:45
Alignment explanation
Indices: 41836292--41836401 Score: 116
Period size: 45 Copynumber: 2.4 Consensus size: 45
41836282 TCTTCTTCCT
* ** *
41836292 TCAATTTC-TTTTTCAATTTTCTCTTTCTCACATC-CTTTTTCAATC
1 TCAATTTCTTTTTTC-TTTTTCTCAATCTCAC-TCTCATTTTCAATC
** *
41836337 TCAATTTCTTTTTTCTTTTTCTCAATCTCACTCTCATTTTCTTTT
1 TCAATTTCTTTTTTCTTTTTCTCAATCTCACTCTCATTTTCAATC
41836382 TCAATTTCTTGTTTTCTTTT
1 TCAATTTCTT-TTTTCTTTT
41836402 ATGTTCATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
44 2 0.04
45 38 0.69
46 15 0.27
ACGTcount: A:0.15, C:0.24, G:0.01, T:0.61
Consensus pattern (45 bp):
TCAATTTCTTTTTTCTTTTTCTCAATCTCACTCTCATTTTCAATC
Found at i:41836361 original size:27 final size:26
Alignment explanation
Indices: 41836327--41836383 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41836317 TCTCACATCC
* *
41836327 TTTT-TCAATCTCAATTTCTTTTTTCT
1 TTTTCTCAATCTCAATCTC-ATTTTCT
*
41836353 TTTTCTCAATCTCACTCTCATTTTCT
1 TTTTCTCAATCTCAATCTCATTTTCT
41836379 TTTTC
1 TTTTC
41836384 AATTTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTCTCAATCTCAATCTCATTTTCT
Found at i:41846230 original size:20 final size:20
Alignment explanation
Indices: 41846207--41846250 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
41846197 CGCTCCAACC
*
41846207 AGCTCATTTGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
41846227 AGCTCATTCGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
41846247 AGCT
1 AGCT
41846251 TTCCATCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAATTT
Found at i:41848344 original size:27 final size:26
Alignment explanation
Indices: 41848314--41848368 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
41848304 TTAAACCTAC
41848314 TTCTAA-AGAAAAAAACTCAAGAGAGAA
1 TTCTAAGAG-AAAAAACTCAA-AGAGAA
**
41848341 TTCTTGGAGAAAAAACTCAAAGAGAA
1 TTCTAAGAGAAAAAACTCAAAGAGAA
41848367 TT
1 TT
41848369 TTCAATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 15 0.60
28 2 0.08
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (26 bp):
TTCTAAGAGAAAAAACTCAAAGAGAA
Found at i:41856803 original size:9 final size:9
Alignment explanation
Indices: 41856789--41856822 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41856779 TTTCACAATT
41856789 TTTTTTTAG
1 TTTTTTTAG
41856798 TTTTTTTAG
1 TTTTTTTAG
*
41856807 TTTTTTT-C
1 TTTTTTTAG
41856815 TTTTTTTA
1 TTTTTTTA
41856823 CGATACCGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTAG
Found at i:41860318 original size:39 final size:39
Alignment explanation
Indices: 41860264--41860341 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41860254 CATAGGAATT
41860264 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
*
41860303 TATTCATGAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
41860342 AATTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (39 bp):
TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
Found at i:41863415 original size:43 final size:43
Alignment explanation
Indices: 41863354--41863474 Score: 181
Period size: 43 Copynumber: 2.8 Consensus size: 43
41863344 GTATCGCTAA
* *
41863354 CTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
41863397 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * *
41863440 CTTTAGCGACGC-TTTCTCCAAAAACGCCACTAAAG
1 CTTTAGCGGCGCTTTTC-CCACAAACGCCGCTAAAG
41863475 GTCACGAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 4 0.06
43 68 0.94
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:41864393 original size:23 final size:23
Alignment explanation
Indices: 41864359--41864843 Score: 333
Period size: 23 Copynumber: 21.3 Consensus size: 23
41864349 AATGGAAAGT
*
41864359 AGCACTTTAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41864382 AGCGA-TAAAACA-TCTCAATTTGC
1 AGC-ACTTAAACACT-TCAATTTAC
* **
41864405 AACAAC-TAAACACTTCAATTTGT
1 AGC-ACTTAAACACTTCAATTTAC
*
41864428 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
41864451 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
41864474 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41864496 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTAC
* *
41864519 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTAC
41864542 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* * *
41864565 AGCATTTAAACACTTAAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
41864588 AGCACTT-AACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
41864610 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41864632 AGCAATAAAACA-TCTCAATTT-C
1 AGCACTTAAACACT-TCAATTTAC
* *
41864654 TAGCAAC-TAAAAACTTCAATTTGC
1 -AGC-ACTTAAACACTTCAATTTAC
41864678 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* * * *
41864701 AACATTTAAACACTTAAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
41864724 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
41864747 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41864769 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTAC
*
41864792 AGCAAC-TAAATACTTCAATTTAC
1 AGC-ACTTAAACACTTCAATTTAC
*
41864815 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTAC
41864838 AGCACT
1 AGCACT
41864844 ATCAAATTTC
Statistics
Matches: 357, Mismatches: 74, Indels: 62
0.72 0.15 0.13
Matches are distributed among these distances:
21 1 0.00
22 70 0.20
23 279 0.78
24 7 0.02
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (23 bp):
AGCACTTAAACACTTCAATTTAC
Found at i:41864800 original size:137 final size:137
Alignment explanation
Indices: 41864396--41864841 Score: 770
Period size: 137 Copynumber: 3.3 Consensus size: 137
41864386 ATAAAACATC
* ** * *
41864396 TCAATTTGCAACAAC-TAAACACTTCAATTTGTAGCACTTAAACACTTCAATTTGCAGCACTTAA
1 TCAATTTGCAGC-ACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAA
41864460 ACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
65 ACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
41864525 TAAATACT
130 TAAATACT
41864533 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTT-AA
1 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
* *
41864597 CATATCAATTAACAACATTTATACACCTCAATTACAGCAATAAAACATCTCAATTTCTAGCAACT
66 CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
*
41864662 AAAAACT
131 AAATACT
*
41864669 TCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAA
1 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
41864734 CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
66 CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
41864799 AAATACT
131 AAATACT
* *
41864806 TCAATTTACAGCACTTAAACACTTCAATTTGCAGCA
1 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCA
41864842 CTATCAAATT
Statistics
Matches: 292, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
136 134 0.46
137 158 0.54
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (137 bp):
TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
AAATACT
Found at i:41865262 original size:41 final size:39
Alignment explanation
Indices: 41865179--41865262 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
41865169 GCACGATACA
* **
41865179 ATATAAAAAGCATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
*
41865218 ATATAAAAAGCATATATAAATATATGTATGTCACAGAAACT
1 ATATAAAAAGCATATATAAATATATGAATGT-ACAGAAA-T
41865259 ATAT
1 ATAT
41865263 TCATTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 30 0.77
40 4 0.10
41 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (39 bp):
ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
Found at i:41870100 original size:18 final size:18
Alignment explanation
Indices: 41870015--41870102 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
41870005 TTCTTTTGTT
** *
41870015 TCTTTTTCTAATTCATTT
1 TCTTTTTCTTTTTCATTC
*
41870033 TC-TCTTCTTTTTCAATT-
1 TCTTTTTCTTTTTC-ATTC
** * *
41870050 TCTTTTTCACTCTCAATC
1 TCTTTTTCTTTTTCATTC
41870068 TCTTTTTGCTCTTTTTCATTC
1 TC-TTTT--TCTTTTTCATTC
41870089 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
41870103 CTCACTTGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 12 0.23
18 22 0.42
19 4 0.08
20 4 0.08
21 10 0.19
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.65
Consensus pattern (18 bp):
TCTTTTTCTTTTTCATTC
Found at i:41873207 original size:22 final size:23
Alignment explanation
Indices: 41873164--41873210 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
41873154 CCACAATTGT
41873164 TTTTTTATAAATTGATTTATTTTTTA
1 TTTTTTATAAATTG---TATTTTTTA
41873190 TTTTTTATAAATTG-ATTTTTT
1 TTTTTTATAAATTGTATTTTTT
41873211 GTGGCGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
26 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTATAAATTGTATTTTTTA
Found at i:41873209 original size:15 final size:15
Alignment explanation
Indices: 41873158--41873210 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
41873148 AAAACGCCAC
*
41873158 AATTGTTTTTTTATA
1 AATTGATTTTTTATA
41873173 AATTGATTTATTT-T-
1 AATTGATTT-TTTATA
41873187 --TT-ATTTTTTATA
1 AATTGATTTTTTATA
41873199 AATTGATTTTTT
1 AATTGATTTTTT
41873211 GTGGCGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 3 0.10
11 5 0.16
12 2 0.06
14 2 0.06
15 16 0.52
16 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
AATTGATTTTTTATA
Found at i:41874304 original size:8 final size:8
Alignment explanation
Indices: 41874293--41874371 Score: 80
Period size: 8 Copynumber: 10.5 Consensus size: 8
41874283 CTGAATCCCT
41874293 AACCCTTA
1 AACCCTTA
41874301 AACCCTTA
1 AACCCTTA
41874309 AACCCTT-
1 AACCCTTA
41874316 AACCCTTA
1 AACCCTTA
*
41874324 AACCCCTA
1 AACCCTTA
*
41874332 AACCCCT-
1 AACCCTTA
*
41874339 AACCCCTA
1 AACCCTTA
41874347 AA-CCTTA
1 AACCCTTA
41874354 AATCCC---
1 AA-CCCTTA
41874360 AACCCTTA
1 AACCCTTA
41874368 AACC
1 AACC
41874372 ATAATCCCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
5 3 0.05
6 2 0.03
7 20 0.32
8 35 0.56
9 2 0.03
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (8 bp):
AACCCTTA
Found at i:41874305 original size:23 final size:23
Alignment explanation
Indices: 41874279--41874371 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 23
41874269 CCTTAACTCG
*
41874279 ACCCCTGAATCCCTAACCCTTAA
1 ACCCCTAAATCCCTAACCCTTAA
*
41874302 ACCCTTAAA-CCCTTAACCCTTAA
1 ACCCCTAAATCCC-TAACCCTTAA
* *
41874325 ACCCCTAAACCCCTAACCCCTAA
1 ACCCCTAAATCCCTAACCCTTAA
*
41874348 A-CCTTAAATCCC-AACCCTTAA
1 ACCCCTAAATCCCTAACCCTTAA
41874369 ACC
1 ACC
41874372 ATAATCCCTA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.15
22 13 0.22
23 35 0.58
24 3 0.05
ACGTcount: A:0.34, C:0.44, G:0.01, T:0.20
Consensus pattern (23 bp):
ACCCCTAAATCCCTAACCCTTAA
Found at i:41874388 original size:15 final size:14
Alignment explanation
Indices: 41874366--41874400 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
41874356 TCCCAACCCT
41874366 TAAACCATAATCCC
1 TAAACCATAATCCC
*
41874380 TAAATCCATACTCCC
1 TAAA-CCATAATCCC
41874395 TAAACC
1 TAAACC
41874401 TTAAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:41874592 original size:33 final size:33
Alignment explanation
Indices: 41874541--41874618 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
41874531 AATAATTAAT
* * *
41874541 CTAAACCCAAAACCCTAACCTGACCCTGAATCC
1 CTAAACCCTAAACCCTAACCTAACCCAGAATCC
* *
41874574 CTAATCCCTAAACCCTAACCTAACCCAGAATTC
1 CTAAACCCTAAACCCTAACCTAACCCAGAATCC
* *
41874607 ATAACCCCTAAA
1 CTAAACCCTAAA
41874619 TATTATTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.38, C:0.40, G:0.04, T:0.18
Consensus pattern (33 bp):
CTAAACCCTAAACCCTAACCTAACCCAGAATCC
Found at i:41874687 original size:15 final size:15
Alignment explanation
Indices: 41874667--41874695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41874657 TAAATCTAAC
41874667 CCCTAAATCCATAAA
1 CCCTAAATCCATAAA
41874682 CCCTAAATCCATAA
1 CCCTAAATCCATAA
41874696 TTGATCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCCATAAA
Found at i:41875545 original size:41 final size:41
Alignment explanation
Indices: 41875475--41875797 Score: 447
Period size: 41 Copynumber: 7.9 Consensus size: 41
41875465 TTTTATTATT
* **
41875475 ATTAGCGGCGCTTTTTTC-AAAACAACGCTAAAGGCCAGAGC
1 ATTAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* *
41875516 ATTAGCGGCGCTT-TCTCAAAAATGCCGCTAAAGATCC-GAGC
1 ATTAGCGGCGCTTCT-TCAAAAACGCCGCTAAAG-GCCAGAGC
* *
41875557 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCTAGACC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * *
41875598 ATTAGCGGCGCTACATCAAAAACGCCGCTAAAGCCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* *
41875639 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGACC-GAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG-CCAGAGC
* *
41875680 ATTAGCAGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
41875721 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
41875762 ATTAGCGGCGCTTCTTCAAAAACGACGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
41875798 CCAAAAACTC
Statistics
Matches: 251, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.00
40 7 0.03
41 238 0.95
42 5 0.02
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:41875958 original size:40 final size:38
Alignment explanation
Indices: 41875846--41875968 Score: 129
Period size: 40 Copynumber: 3.1 Consensus size: 38
41875836 TTTGCGGCAC
* * *
41875846 TTTTCAAAAAACGCCACTAATGCTTATTTTTAGCGGCG
1 TTTTTAAAAAGCGCCGCTAATGCTTATTTTTAGCGGCG
** **
41875884 TTTCCCAAAAAGCGCCGCTAATGCTCTACCTTTAGCGGCG
1 TTT-TTAAAAAGCGCCGCTAATGCT-TATTTTTAGCGGCG
* *
41875924 TTTTTATAAAAGCGCCGCTAATGCTGGATTTTTAGTGGCG
1 TTTTTA-AAAAGCGCCGCTAATGCT-TATTTTTAGCGGCG
41875964 TTTTT
1 TTTTT
41875969 TGTCCAAACG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 3 0.04
39 19 0.27
40 48 0.69
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (38 bp):
TTTTTAAAAAGCGCCGCTAATGCTTATTTTTAGCGGCG
Found at i:41877573 original size:20 final size:21
Alignment explanation
Indices: 41877519--41877574 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
41877509 AAAAGAAACA
*
41877519 AGCT-GAAAGTAAGCTAAATTG
1 AGCTCGAAA-TAAGCTGAATTG
*
41877540 AGCTCGAAA-GAGCTGAATTG
1 AGCTCGAAATAAGCTGAATTG
41877560 AGCTC-AAATAAGCTG
1 AGCTCGAAATAAGCTG
41877575 GTTGGAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.10
20 19 0.63
21 4 0.13
22 4 0.13
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (21 bp):
AGCTCGAAATAAGCTGAATTG
Found at i:41879475 original size:56 final size:56
Alignment explanation
Indices: 41879389--41879508 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
41879379 ACAAGGGATG
*
41879389 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAAAAGC
*
41879445 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAAAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAAAAGC
41879501 ATGGGCAA
1 ATGGGCAA
41879509 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAAAAGC
Found at i:41880875 original size:40 final size:40
Alignment explanation
Indices: 41880637--41880861 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
41880627 TCGAATGATG
* * * *
41880637 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
41880677 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41880717 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41880756 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41880796 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41880837 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41880862 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41880884 original size:119 final size:119
Alignment explanation
Indices: 41880637--41880868 Score: 290
Period size: 119 Copynumber: 1.9 Consensus size: 119
41880627 TCGAATGATG
* *
41880637 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
41880702 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
41880756 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
41880819 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGT
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGT
41880869 AGCTATATCT
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 3 0.03
119 68 0.71
120 25 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:41887443 original size:56 final size:56
Alignment explanation
Indices: 41887357--41887476 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41887347 ACAAGGGATG
41887357 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
41887413 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
41887469 ATGGGCAA
1 ATGGGCAA
41887477 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:41888831 original size:40 final size:40
Alignment explanation
Indices: 41888600--41888824 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
41888590 TCGAATGATG
* * * * *
41888600 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * * *
41888640 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
41888680 TCCGGGATAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
41888719 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41888759 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
41888800 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
41888825 AACGAGTAGC
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 33 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41890845 original size:18 final size:17
Alignment explanation
Indices: 41890810--41890905 Score: 88
Period size: 18 Copynumber: 5.5 Consensus size: 17
41890800 TTTTCTTTCG
*
41890810 TTTCTTTTTCATCATCTT
1 TTTCTTTTTCAT-TTCTT
** *
41890828 TTTCAATTTCTTTTTCTT
1 TTTCTTTTTC-ATTTCTT
* *
41890846 TTTGTTTTGCAATTTCTT
1 TTTCTTTTTC-ATTTCTT
41890864 TTTCTTTTTCACTTTCTT
1 TTTCTTTTTCA-TTTCTT
41890882 TTTCTTTTTC--TTCTT
1 TTTCTTTTTCATTTCTT
41890897 TTTCTTTTT
1 TTTCTTTTT
41890906 TATTACAACG
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
15 14 0.22
17 1 0.02
18 48 0.75
19 1 0.02
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTCTTTTTCATTTCTT
Found at i:41890868 original size:24 final size:24
Alignment explanation
Indices: 41890826--41890872 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41890816 TTTCATCATC
*
41890826 TTTTTCAATTTCTTTTTCTTTTTG
1 TTTTGCAATTTCTTTTTCTTTTTG
41890850 TTTTGCAATTTCTTTTTCTTTTT
1 TTTTGCAATTTCTTTTTCTTTTT
41890873 CACTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTGCAATTTCTTTTTCTTTTTG
Found at i:41890871 original size:5 final size:6
Alignment explanation
Indices: 41890810--41890905 Score: 72
Period size: 6 Copynumber: 16.5 Consensus size: 6
41890800 TTTTCTTTCG
* ** ** * * **
41890810 TTTCTT TTTCAT CATCTT TTTCAA TTTCTT TTTCTT TTTGTT TTGCAA
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
**
41890858 TTTCTT TTTCTT TTTCAC TTTCTT TTTCTT TTTC-- -TTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
41890903 TTT
1 TTT
41890906 TATTACAACG
Statistics
Matches: 65, Mismatches: 22, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
3 3 0.05
6 62 0.95
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTCTT
Found at i:41896340 original size:21 final size:20
Alignment explanation
Indices: 41896303--41896354 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
41896293 AAAGGAAGAC
41896303 AGAAAAAGA-AATAAAAAAAA
1 AGAAAAAGAGAAT-AAAAAAA
* *
41896323 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATAAAAAAA
41896343 AGCAAAAAGAGA
1 AG-AAAAAGAGA
41896355 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATAAAAAAA
Found at i:41898064 original size:33 final size:34
Alignment explanation
Indices: 41898027--41898098 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
41898017 GAGTTAGTTT
*
41898027 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
* *
41898060 ATTAATTTTAGTTCACCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
41898094 ATTAA
1 ATTAA
41898099 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
Found at i:41900746 original size:18 final size:17
Alignment explanation
Indices: 41900725--41900760 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
41900715 TTTTATTTGA
*
41900725 TTTTGTCTTTTTCTATTT
1 TTTTGACTTTTTCT-TTT
41900743 TTTTGACTTTTTCTTTT
1 TTTTGACTTTTTCTTTT
41900760 T
1 T
41900761 AATATTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTGACTTTTTCTTTT
Found at i:41901745 original size:10 final size:11
Alignment explanation
Indices: 41901727--41901759 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
41901717 TCGATTTCAC
41901727 GAAATTTTTTT
1 GAAATTTTTTT
41901738 GAAATTTTTTTT
1 GAAA-TTTTTTT
41901750 G-AATTTTTTT
1 GAAATTTTTTT
41901760 ATTTTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (11 bp):
GAAATTTTTTT
Found at i:41901748 original size:12 final size:12
Alignment explanation
Indices: 41901727--41901759 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
41901717 TCGATTTCAC
41901727 GAAA-TTTTTTT
1 GAAATTTTTTTT
41901738 GAAATTTTTTTT
1 GAAATTTTTTTT
41901750 G-AATTTTTTT
1 GAAATTTTTTT
41901760 ATTTTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (12 bp):
GAAATTTTTTTT
Found at i:41905360 original size:39 final size:39
Alignment explanation
Indices: 41905306--41905383 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41905296 CATAGTAAGT
41905306 TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
*
41905345 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
41905384 AATTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (39 bp):
TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
Found at i:41910373 original size:40 final size:40
Alignment explanation
Indices: 41910342--41910553 Score: 243
Period size: 40 Copynumber: 5.3 Consensus size: 40
41910332 GGACTAAGAT
41910342 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
41910382 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
41910422 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * ** * *
41910462 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCC
* * * * * *
41910502 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
41910541 CCGAAGGCATTTG
1 CCGAAGGCATTTG
41910554 AACGAGGAGC
Statistics
Matches: 154, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
39 32 0.21
40 119 0.77
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:41910426 original size:80 final size:80
Alignment explanation
Indices: 41910342--41910553 Score: 268
Period size: 80 Copynumber: 2.7 Consensus size: 80
41910332 GGACTAAGAT
*
41910342 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGAT-AC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGAC
41910405 AAATTCCGGGTTAAGCC
65 AAA-TCCGGGTTAAGCC
* * * **
41910422 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACA
* *
41910487 AATCCGGGTTATGTC
66 AATCCGGGTTAAGCC
* * * * *
41910502 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
41910554 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
79 37 0.32
80 72 0.63
81 6 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACA
AATCCGGGTTAAGCC
Found at i:41910571 original size:79 final size:80
Alignment explanation
Indices: 41910342--41910586 Score: 205
Period size: 80 Copynumber: 3.1 Consensus size: 80
41910332 GGACTAAGAT
* * * * ** *
41910342 CCGAAGG-CATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCATTTGTGCGA-GATA
1 CCGAAGGCCA-TTGTGCGAGATACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-G
*
41910404 C-AAATTCCGGGTTAAGCC
63 CTAAA-TCCGGGTTAAGTC
* * * ** ** *
41910422 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
41910487 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * * *
41910502 CCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
41910566 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
41910580 CCGAAGG
1 CCGAAGG
41910587 TACGTGATTT
Statistics
Matches: 137, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
78 14 0.10
79 49 0.36
80 67 0.49
81 7 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:41915683 original size:13 final size:13
Alignment explanation
Indices: 41915665--41915689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41915655 TGGTCATCAT
41915665 GGTGTGAACACAA
1 GGTGTGAACACAA
41915678 GGTGTGAACACA
1 GGTGTGAACACA
41915690 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:41920042 original size:32 final size:34
Alignment explanation
Indices: 41919974--41920134 Score: 155
Period size: 37 Copynumber: 4.4 Consensus size: 34
41919964 GGACTAAGAT
41919974 CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGC
1 CCGAAGGCA-TTGTGCGAGAT---AATCCGGGTTAAGC
41920012 CCGAAGGCATTGTGCGAGAT-A-CCGGGTTAAGC
1 CCGAAGGCATTGTGCGAGATAATCCGGGTTAAGC
* *
41920044 CCGAAGGCTTTGTGCGAGATACTAATCCGGGTTAAGT
1 CCGAAGGCATTGTGCGAG--A-TAATCCGGGTTAAGC
* *
41920081 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGA---GAT-AATCCGGGTTAAG-C
41920121 CCGAAGGCATTGTG
1 CCGAAGGCATTGTG
41920135 TGAGTTACTA
Statistics
Matches: 106, Mismatches: 6, Indels: 21
0.80 0.05 0.16
Matches are distributed among these distances:
32 28 0.26
33 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
37 31 0.29
38 16 0.15
39 15 0.14
40 11 0.10
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (34 bp):
CCGAAGGCATTGTGCGAGATAATCCGGGTTAAGC
Found at i:41920116 original size:39 final size:39
Alignment explanation
Indices: 41919921--41920170 Score: 209
Period size: 39 Copynumber: 6.6 Consensus size: 39
41919911 TTGAATGCTG
* * ** * * *
41919921 TCCGGGCTAAGTCCCGAAGGCTTTGTGATAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTG-CGAGTTACTAAA
** *
41919961 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
41920000 TCCGGGTTAAG-CCCGAAGGCATTGTGCGAG--A-T--A
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
41920033 -CCGGGTTAAG-CCCGAAGGCTTTGTGCGAGATACT-AA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
**
41920069 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* *
41920108 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
41920147 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41920171 TGAACGAGGA
Statistics
Matches: 176, Mismatches: 21, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
32 28 0.16
33 1 0.01
34 1 0.01
35 2 0.01
36 1 0.01
37 29 0.16
38 18 0.10
39 58 0.33
40 32 0.18
41 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Done.