Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 212 of 230
Found at i:63001130 original size:12 final size:12
Alignment explanation
Indices: 63001108--63001137 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
63001098 AAACTAGATG
63001108 TTTATTAACAATA
1 TTTA-TAACAATA
63001121 TTTATAACAATA
1 TTTATAACAATA
63001133 TTTAT
1 TTTAT
63001138 GTTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTATAACAATA
Found at i:63003362 original size:19 final size:20
Alignment explanation
Indices: 63003330--63003374 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
63003320 AAAAAATGTA
* *
63003330 AAAAAATATTTAATATTTTTT
1 AAAAAATA-TTAATAATTTGT
63003351 AAAAAATA-TAATAATTTGT
1 AAAAAATATTAATAATTTGT
63003370 AAAAA
1 AAAAA
63003375 GTTATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAAAATATTAATAATTTGT
Found at i:63005461 original size:20 final size:19
Alignment explanation
Indices: 63005438--63005485 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
63005428 ATTTAAATAA
*
63005438 TATTATTTGAATAGTTATAG
1 TATTATTTGAATAATTAT-G
**
63005458 TATTAAATGAATAATTATG
1 TATTATTTGAATAATTATG
63005477 TATTTATTT
1 TA-TTATTT
63005486 TAAAGACATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (19 bp):
TATTATTTGAATAATTATG
Found at i:63007386 original size:20 final size:20
Alignment explanation
Indices: 63007361--63007400 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
63007351 GATTACGAAG
63007361 AACAAA-AAAAGAAATTAATT
1 AACAAAGAAAAGAAA-TAATT
*
63007381 AACAAAGAAAATAAATAATT
1 AACAAAGAAAAGAAATAATT
63007401 GAAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (20 bp):
AACAAAGAAAAGAAATAATT
Found at i:63021190 original size:16 final size:16
Alignment explanation
Indices: 63021171--63021205 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
63021161 TTTTAATTTT
*
63021171 TATAATTTTTTAAAAA
1 TATAAATTTTTAAAAA
*
63021187 TATAAATTTTTATAAA
1 TATAAATTTTTAAAAA
63021203 TAT
1 TAT
63021206 CTTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAAATTTTTAAAAA
Found at i:63023012 original size:41 final size:43
Alignment explanation
Indices: 63022923--63023013 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 43
63022913 CTAGAATAAA
* * *
63022923 AAAACTAGAACCACTACAACATTTGGAGAAAATAGAATTATCT
1 AAAACTAGAACCACTACAACATTTAGAGAAAATAAAATGATCT
* * *
63022966 GAAACTAGAACCACTGC-A-ATTTAGAGGAAATAAAATGGAT-T
1 AAAACTAGAACCACTACAACATTTAGAGAAAATAAAAT-GATCT
63023007 AAAACTA
1 AAAACTA
63023014 AAAACTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 22 0.55
42 3 0.08
43 15 0.38
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (43 bp):
AAAACTAGAACCACTACAACATTTAGAGAAAATAAAATGATCT
Found at i:63025047 original size:3 final size:3
Alignment explanation
Indices: 63025041--63025067 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
63025031 TTATTAATAC
63025041 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
63025068 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:63025072 original size:3 final size:3
Alignment explanation
Indices: 63025066--63025111 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
63025056 CATCATCATC
**
63025066 ATT ATT ATT ATT ATT ATT ATT ATT ACC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
63025112 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:63045764 original size:24 final size:25
Alignment explanation
Indices: 63045737--63045783 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
63045727 GTTAAAAAGG
*
63045737 TTAAAGCCACATC-GTGAATCTTGA
1 TTAAAGCCACAACAGTGAATCTTGA
*
63045761 TTAAAGCTACAACAGTGAATCTT
1 TTAAAGCCACAACAGTGAATCTT
63045784 ACTCCCCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (25 bp):
TTAAAGCCACAACAGTGAATCTTGA
Found at i:63046233 original size:87 final size:85
Alignment explanation
Indices: 63046011--63046434 Score: 412
Period size: 87 Copynumber: 4.9 Consensus size: 85
63046001 TTGAAGCCAG
*
63046011 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAAACA-CTA-TCTTATCTCCCTGAAGT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATC----ACATCTAGTCTTATCTCCCTGAAGT
* **
63046074 TACAGTGGAGTGGATTAAAAATAA
62 TACAGTGGAGTAGACCAAAAATAA
* * * * * *
63046098 AGGATCTTATTTCTCTGA-AGTTACAGTAGAGTAGATCGCATC-AGGTCTTATCTCCCTGAGGTT
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCACATCTA-GTCTTATCTCCCTGAAGTT
* *
63046161 ATAGTGGAGTAGACCAAAGAATTTGA
63 ACAGTGGAGTAGACCAAA-AA--TAA
*
63046187 A-ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACTTCTAGTCTTATCTCCCTGAAGTTACA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTACA
* **
63046251 GTGGAGTGGATTAAAAATAA
66 GTGGAGTAGACCAAAAATAA
* * * * * *
63046271 AGGATCTTATTTCTCTGA-AGTTACAGTAGAGTAGATCGCAT-TAGGTCTTATCTCCCTGAGGTT
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCACATCTA-GTCTTATCTCCCTGAAGTT
* **
63046334 ACAGCGGAGTAGACCAAAGAATTTG
63 ACAGTGGAGTAGACCAAA-AA-TAA
* *
63046359 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACATCTAGTTTTATCTCCTTGAAGTTACA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTACA
*
63046424 GTGGAGCAGAC
66 GTGGAGTAGAC
63046435 TAAGACCACA
Statistics
Matches: 272, Mismatches: 47, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
84 6 0.02
85 4 0.01
86 95 0.35
87 129 0.47
88 35 0.13
89 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (85 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTACA
GTGGAGTAGACCAAAAATAA
Found at i:63046304 original size:173 final size:172
Alignment explanation
Indices: 63046013--63046429 Score: 701
Period size: 173 Copynumber: 2.4 Consensus size: 172
63046003 GAAGCCAGAG
* *
63046013 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAAACACTA-TCTTATCTCCCTGAAGTTAC
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATC----ACTCTAGTCTTATCTCCCTGAAGTTAC
63046077 AGTGGAGTGGATTAAAAATAAAGGATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
62 AGTGGAGTGGATTAAAAATAAAGGATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
63046142 GTCTTATCTCCCTGAGGTTATAGTGGAGTAGACCAAAGAATTTGAA
127 GTCTTATCTCCCTGAGGTTACAGCGGAGTAGACCAAAGAATTTGAA
63046188 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACTTCTAGTCTTATCTCCCTGAAGTTACAGT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAC-TCTAGTCTTATCTCCCTGAAGTTACAGT
*
63046253 GGAGTGGATTAAAAATAAAGGATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCATTAGGTC
65 GGAGTGGATTAAAAATAAAGGATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTC
*
63046318 TTATCTCCCTGAGGTTACAGCGGAGTAGACCAAAGAATTTGAG
130 TTATCTCCCTGAGGTTACAGCGGAGTAGACCAAAGAATTTGAA
* *
63046361 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACATCTAGTTTTATCTCCTTGAAGTTACAGT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAC-TCTAGTCTTATCTCCCTGAAGTTACAGT
63046426 GGAG
65 GGAG
63046430 CAGACTAAGA
Statistics
Matches: 231, Mismatches: 9, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
171 2 0.01
172 3 0.01
173 193 0.84
175 33 0.14
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (172 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATCACTCTAGTCTTATCTCCCTGAAGTTACAGTG
GAGTGGATTAAAAATAAAGGATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
TATCTCCCTGAGGTTACAGCGGAGTAGACCAAAGAATTTGAA
Found at i:63046430 original size:41 final size:41
Alignment explanation
Indices: 63046014--63046433 Score: 197
Period size: 41 Copynumber: 9.8 Consensus size: 41
63046004 AAGCCAGAGA
*
63046014 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAAACA-CTA-
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATC----ACATCTAG
** * * **
63046057 TCTTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAAATAAAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-T-CACATCTA-G
* * * * *
63046101 ATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCATC-AGG
1 -TCTTATCTCCCTGAAGTTACAGTGGAGCAGATCACATCTA-G
* * * * * * *
63046143 TCTTATCTCCCTGAGGTTATAGTGGAGTAGACCAAAGAATTTGAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATC--A-CATCT--AG
*
63046189 TCTTATCTCCCTG-AGATTACAGTGGAGCAGATCACTTCTAG
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCACATCTAG
** * * **
63046230 TCTTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAAATAAAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-T-CACATCTA-G
* * * * *
63046274 ATCTTATTTCTCTGAAGTTACAGTAGAGTAGATCGCAT-TAGG
1 -TCTTATCTCCCTGAAGTTACAGTGGAGCAGATCACATCTA-G
* * * * * *
63046316 TCTTATCTCCCTGAGGTTACAGCGGAGTAGACCAAAGAATTTGAG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATC--A-CATCT-AG
63046361 ATCTTATCTCCCTG-AGATTACAGTGGAGCAGATCACATCTAG
1 -TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATCACATCTAG
* *
63046403 TTTTATCTCCTTGAAGTTACAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA
63046434 CTAAGACCAC
Statistics
Matches: 286, Mismatches: 64, Indels: 56
0.70 0.16 0.14
Matches are distributed among these distances:
41 109 0.38
42 14 0.05
43 37 0.13
44 12 0.04
45 58 0.20
46 55 0.19
47 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATCACATCTAG
Found at i:63048207 original size:4 final size:4
Alignment explanation
Indices: 63048198--63048232 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
63048188 CTATAATATT
63048198 TACA TACA TACA TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TAC
63048233 GTATATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:63048684 original size:110 final size:109
Alignment explanation
Indices: 63048489--63048792 Score: 416
Period size: 110 Copynumber: 2.8 Consensus size: 109
63048479 CTAAATAAAT
* * *
63048489 GCAATGTTTTGCGTTTGGAGATTCGAGAAAACGCGCCCTAAGGTGCTAGGTGTCGATTTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
** * * **
63048554 TTCAAGAAAATGGCTTAATATCCCTTTTAAAAATTTTAAAATAAG
66 TTCAACCAAATGGCTAAATATCCC-TTCAAAAATTACAAAATAAG
*
63048599 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
*
63048664 TTCAACCAAATAGCTAAATATCCCTTCAAAAATTACAAAATAAG
66 TTCAACCAAATGGCTAAATATCCCTTCAAAAATTACAAAATAAG
* * * * *
63048708 ACAATGTTTTGCGTCTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCTTG
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
* *
63048770 TTTAACCAAATGGCCAAATATCC
66 TTCAACCAAATGGCTAAATATCC
63048793 TCTCGAATTT
Statistics
Matches: 174, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
106 26 0.15
108 25 0.14
109 42 0.24
110 81 0.47
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (109 bp):
GCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
TTCAACCAAATGGCTAAATATCCCTTCAAAAATTACAAAATAAG
Found at i:63053282 original size:29 final size:29
Alignment explanation
Indices: 63053250--63053307 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
63053240 TTATCTATAT
*
63053250 GATAAATATAAAATTAAATTTAATATTAA
1 GATAAAGATAAAATTAAATTTAATATTAA
* *
63053279 GATAAGGATTAAATTAAATTTAATATTAA
1 GATAAAGATAAAATTAAATTTAATATTAA
63053308 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
GATAAAGATAAAATTAAATTTAATATTAA
Found at i:63055079 original size:16 final size:16
Alignment explanation
Indices: 63055058--63055088 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63055048 ATCATAAACG
63055058 TCACAAATGAATTAAT
1 TCACAAATGAATTAAT
*
63055074 TCACAAATGGATTAA
1 TCACAAATGAATTAA
63055089 GAATTAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (16 bp):
TCACAAATGAATTAAT
Found at i:63056126 original size:5 final size:5
Alignment explanation
Indices: 63056116--63056141 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
63056106 TGAGCATTCG
63056116 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
63056142 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:63057174 original size:9 final size:9
Alignment explanation
Indices: 63057160--63057196 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
63057150 TATAGTTTGA
63057160 TATTCGAAT
1 TATTCGAAT
63057169 TATTCGAAT
1 TATTCGAAT
*
63057178 TATTCGAGT
1 TATTCGAAT
63057187 TATTCGAAT
1 TATTCGAAT
63057196 T
1 T
63057197 CAAAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:63060873 original size:21 final size:19
Alignment explanation
Indices: 63060848--63060897 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
63060838 TATAGTTTTT
*
63060848 AAAATTATACAAAAATTCTAA
1 AAAATTATA-AAAAATTAT-A
*
63060869 AAAATTATTAAAACATTATA
1 AAAATTA-TAAAAAATTATA
63060889 AAAATTATA
1 AAAATTATA
63060898 TTGTTAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 8 0.31
21 14 0.54
22 2 0.08
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTATAAAAAATTATA
Found at i:63060881 original size:9 final size:10
Alignment explanation
Indices: 63060848--63060897 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
63060838 TATAGTTTTT
63060848 AAAATTATACA
1 AAAATTATA-A
*
63060859 AAAATTCTAA
1 AAAATTATAA
63060869 AAAATTATTAA
1 AAAATTA-TAA
*
63060880 AACATTAT-A
1 AAAATTATAA
63060889 AAAATTATA
1 AAAATTATA
63060898 TTGTTAGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 17 0.52
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:63061469 original size:19 final size:19
Alignment explanation
Indices: 63061432--63061470 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
63061422 TTTATAATGC
**
63061432 TTTTGTAATTTTTGTAATT
1 TTTTGTAATTTTTAAAATT
*
63061451 TTTTTTAATTTTTAAAATT
1 TTTTGTAATTTTTAAAATT
63061470 T
1 T
63061471 ATATCTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTGTAATTTTTAAAATT
Found at i:63070302 original size:7 final size:6
Alignment explanation
Indices: 63070282--63070311 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
63070272 CAAAAATGCA
63070282 TTTGAT TTTGAT TTCTGAT TTTGAT TTTGA
1 TTTGAT TTTGAT TT-TGAT TTTGAT TTTGA
63070312 GTAATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
TTTGAT
Found at i:63070302 original size:13 final size:13
Alignment explanation
Indices: 63070284--63070308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63070274 AAAATGCATT
63070284 TGATTTTGATTTC
1 TGATTTTGATTTC
63070297 TGATTTTGATTT
1 TGATTTTGATTT
63070309 TGAGTAATAT
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TGATTTTGATTTC
Found at i:63077943 original size:15 final size:15
Alignment explanation
Indices: 63077904--63077946 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
63077894 TGATCCCAAT
* *
63077904 GGAATGTGATTCTTT
1 GGAATGTGATTGTTG
* *
63077919 GAAATATGATTGTTG
1 GGAATGTGATTGTTG
63077934 GGAATGTGATTGT
1 GGAATGTGATTGT
63077947 CGAGAAATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.42
Consensus pattern (15 bp):
GGAATGTGATTGTTG
Found at i:63081630 original size:13 final size:13
Alignment explanation
Indices: 63081588--63081630 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
63081578 GTCACTATTT
*
63081588 TTAAATTTTTAAA
1 TTAAATTTTTATA
* *
63081601 TAAAATTTTAATA
1 TTAAATTTTTATA
*
63081614 TTAAATTTTTATT
1 TTAAATTTTTATA
63081627 TTAA
1 TTAA
63081631 TGCTTTGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATTTTTATA
Found at i:63083129 original size:3 final size:3
Alignment explanation
Indices: 63083107--63083176 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
63083097 CATATGTACA
* *
63083107 AAT AA- AAT AAT GAC AAT AAT AAT AAT AAT AAAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
63083151 ACAT AAT GAT -AT AAT -AT AAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT
63083177 TAATTAATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 8 0.14
3 42 0.75
4 6 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63083135 original size:18 final size:17
Alignment explanation
Indices: 63083107--63083176 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 17
63083097 CATATGTACA
63083107 AATAA-AATAATGACAAT
1 AATAATAATAAT-ACAAT
63083124 AATAATAATAATA-AAT
1 AATAATAATAATACAAT
63083140 AAT-ATAATAATAC-AT
1 AATAATAATAATACAAT
* *
63083155 AATGAT-ATAATATAAT
1 AATAATAATAATACAAT
63083171 AATAAT
1 AATAAT
63083177 TAATTAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
15 20 0.43
16 15 0.32
17 6 0.13
18 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AATAATAATAATACAAT
Found at i:63083180 original size:15 final size:14
Alignment explanation
Indices: 63083122--63083176 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 14
63083112 AATAATGACA
63083122 ATAATAATAATAAT
1 ATAATAATAATAAT
63083136 A-AATAAT-ATAAT
1 ATAATAATAATAAT
63083148 AATACATAATGATATAAT
1 -ATA-ATAAT-A-ATAAT
63083166 ATAATAATAAT
1 ATAATAATAAT
63083177 TAATTAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 5 0.14
13 7 0.20
14 4 0.11
15 6 0.17
16 5 0.14
17 3 0.09
18 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:63084835 original size:44 final size:44
Alignment explanation
Indices: 63084784--63084971 Score: 118
Period size: 44 Copynumber: 4.3 Consensus size: 44
63084774 CCGCTGCAAC
* * *
63084784 CTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAAATCCGCCATCTTCAATCTACTCCACTACTG
* * * ** * *
63084828 CTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTG
1 CTCAGGGAGATAAAATCCGCCATCTTCAATCTACTCCACTACTG
* * * *
63084872 AC-CAGGGAGATAGAATTACG---GCTTCAATGTACTCCACTGTAAC--
1 -CTCAGGGAGATA-AAATCCGCCATCTTCAATCTACTCCAC--T-ACTG
* * * *
63084915 CACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
1 CTCAGGGAGATAAAATCCGCCATCTTCAATCTACTCCACTACTG
*
63084959 CTTAGGGAGATAA
1 CTCAGGGAGATAA
63084972 GATCTGTAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 22
0.67 0.19 0.14
Matches are distributed among these distances:
42 22 0.21
43 10 0.10
44 54 0.52
45 18 0.17
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (44 bp):
CTCAGGGAGATAAAATCCGCCATCTTCAATCTACTCCACTACTG
Found at i:63084921 original size:131 final size:132
Alignment explanation
Indices: 63084720--63084988 Score: 432
Period size: 131 Copynumber: 2.0 Consensus size: 132
63084710 GATCTGCTTT
* * *
63084720 TTCAATCAATTCCACTGCCGACCGGGGAGGTAGAATTACTAGATTCAATATACTCCGCTGCAACC
1 TTCAATCAATTCCACTGCCGACCAGGGAGATAGAATTACTAGATTCAATATACTCCACTGCAACC
*
63084785 TCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA
66 ACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA
63084850 TC
131 TC
* * * * * *
63084852 TTCAATCTATTCCACTGCTGACCAGGGAGATAGAATTAC-GGCTTCAATGTACTCCACTGTAACC
1 TTCAATCAATTCCACTGCCGACCAGGGAGATAGAATTACTAGATTCAATATACTCCACTGCAACC
*
63084916 ACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
66 ACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA
63084981 TC
131 TC
63084983 TTCAAT
1 TTCAAT
63084989 TTGCTCAACT
Statistics
Matches: 126, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
131 91 0.72
132 35 0.28
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (132 bp):
TTCAATCAATTCCACTGCCGACCAGGGAGATAGAATTACTAGATTCAATATACTCCACTGCAACC
ACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA
TC
Found at i:63084984 original size:44 final size:44
Alignment explanation
Indices: 63084805--63084994 Score: 113
Period size: 44 Copynumber: 4.3 Consensus size: 44
63084795 AAAATCCGCC
* * *
63084805 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTGCTCCACTACTGCTCAGGGAGATAAGATCTGTA
** * *
63084849 ATCTTCAATCTATTCCACTGCTGAC-CAGGGAGAT-AGA-AT-TA
1 ATCTTCAATCTGCTCCACTACTG-CTCAGGGAGATAAGATCTGTA
** * * * * * * **
63084890 CGGCTTCAATGTACTCCACTGTAAC--CACAGGGAGGTAAAATCCGCC
1 -ATCTTCAATCTGCTCCAC--T-ACTGCTCAGGGAGATAAGATCTGTA
* *
63084936 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAATCTGCTCCACTACTGCTCAGGGAGATAAGATCTGTA
*
63084980 ATCTTCAATTTGCTC
1 ATCTTCAATCTGCTC
63084995 AACTGCAATG
Statistics
Matches: 103, Mismatches: 32, Indels: 22
0.66 0.20 0.14
Matches are distributed among these distances:
41 1 0.01
42 18 0.17
43 12 0.12
44 57 0.55
45 15 0.15
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ATCTTCAATCTGCTCCACTACTGCTCAGGGAGATAAGATCTGTA
Found at i:63085115 original size:100 final size:99
Alignment explanation
Indices: 63085008--63085195 Score: 279
Period size: 100 Copynumber: 1.9 Consensus size: 99
63084998 TGCAATGTCG
* * *
63085008 GGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCCACCGCAC-CGTTAGAGAAGTAAGATCT
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACAC-TAAG-GAAGTAAGATCC
* *
63085072 GTCGTTGTGGCTTTAATCTTTTTAATTGCAATATTA
64 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATATTA
* *
63085108 GGGAAACCAGATCCGCCGTCGTAGCTTCAATTTGTTCCACTGCACTACTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCAC-ACTAAGGAAGTAAGATCCG
63085173 CCGTTGTGGCTTCAATCTTTTTA
65 CCGTTGTGGCTTCAATCTTTTTA
63085196 CTTTTCAACC
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
100 75 0.95
101 3 0.04
102 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (99 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACACTAAGGAAGTAAGATCCGC
CGTTGTGGCTTCAATCTTTTTAATTGCAATATTA
Found at i:63097116 original size:3 final size:3
Alignment explanation
Indices: 63097094--63097161 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
63097084 CATATGTACA
* *
63097094 AAT AA- AAT AAT GAC AAT AAT AAT AAAT AAT -AT AAT AAT ACAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT
*
63097139 GAT -AT AAT -AT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT
63097162 TAATTAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
2 8 0.15
3 36 0.68
4 9 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63097124 original size:27 final size:26
Alignment explanation
Indices: 63097094--63097179 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
63097084 CATATGTACA
63097094 AATAAAATAATGACAATAATAATAAAT
1 AATAAAATAAT-ACAATAATAATAAAT
* *
63097121 AATATAATAATAC-ATAATGAT--AT
1 AATAAAATAATACAATAATAATAAAT
*
63097144 AATATAATAATA-AATAATTAATTAAAT
1 AATAAAATAATACAATAA-TAA-TAAAT
*
63097171 AGTAAAATA
1 AATAAAATA
63097180 GTTCAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
23 18 0.37
24 2 0.04
25 8 0.16
26 2 0.04
27 19 0.39
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAAAATAATACAATAATAATAAAT
Found at i:63097127 original size:15 final size:15
Alignment explanation
Indices: 63097109--63097161 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
63097099 AATAATGACA
63097109 ATAATAATAAATAAT
1 ATAATAATAAATAAT
*
63097124 ATAATAATACATAAT
1 ATAATAATAAATAAT
63097139 GAT-ATAATATAATAAT
1 -ATAATAATA-AATAAT
63097155 A-AATAAT
1 ATAATAAT
63097162 TAATTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 26 0.79
16 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:63106457 original size:13 final size:13
Alignment explanation
Indices: 63106439--63106465 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
63106429 AATTCAATCC
63106439 ATCTCACGAGTTA
1 ATCTCACGAGTTA
63106452 ATCTCACGAGTTA
1 ATCTCACGAGTTA
63106465 A
1 A
63106466 CATCTAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (13 bp):
ATCTCACGAGTTA
Found at i:63106980 original size:24 final size:22
Alignment explanation
Indices: 63106953--63107008 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
63106943 AAGTTTCATA
63106953 ATTTTTTTATTCAT-ATTTTATGGC
1 ATTTTTTTATT-ATCATTTT-T-GC
* *
63106977 ATTTTTTCATTTTCATTTTTGC
1 ATTTTTTTATTATCATTTTTGC
63106999 ATTTTTTTAT
1 ATTTTTTTAT
63107009 ATTTTCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 11 0.39
23 2 0.07
24 15 0.54
ACGTcount: A:0.18, C:0.09, G:0.05, T:0.68
Consensus pattern (22 bp):
ATTTTTTTATTATCATTTTTGC
Found at i:63111566 original size:23 final size:23
Alignment explanation
Indices: 63111510--63111566 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
63111500 ACGGCACACG
* *
63111510 AAGTGCCTGAAATACGACACATA
1 AAGTGACTGATATACGACACATA
63111533 AAGTGACTGATATACGACACATA
1 AAGTGACTGATATACGACACATA
*
63111556 AAGTGTCTGAT
1 AAGTGACTGAT
63111567 TGACAAAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (23 bp):
AAGTGACTGATATACGACACATA
Found at i:63114293 original size:29 final size:29
Alignment explanation
Indices: 63114256--63114313 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
63114246 TTTAATATTA
* *
63114256 TAAAAAAATTATAATTAAATTA-AATATG
1 TAAAAAAATTATAATGAAAGTATAATATG
63114284 TAAAATAAATTATAATGAAAGTATAATATG
1 TAAAA-AAATTATAATGAAAGTATAATATG
63114314 GTAGAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 15 0.58
30 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAAAAAATTATAATGAAAGTATAATATG
Found at i:63115422 original size:13 final size:13
Alignment explanation
Indices: 63115404--63115428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63115394 TCAAACCCAT
63115404 AACCTTAAACTCA
1 AACCTTAAACTCA
63115417 AACCTTAAACTC
1 AACCTTAAACTC
63115429 CAAGCTTGTA
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:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (13 bp):
AACCTTAAACTCA
Found at i:63116163 original size:16 final size:17
Alignment explanation
Indices: 63116138--63116171 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
63116128 TTCTTATACG
63116138 AAAGCAAGAG-GAAAGA
1 AAAGCAAGAGAGAAAGA
*
63116154 AAAGCGAGAGAGAAAGA
1 AAAGCAAGAGAGAAAGA
63116171 A
1 A
63116172 GAGAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.62, C:0.06, G:0.32, T:0.00
Consensus pattern (17 bp):
AAAGCAAGAGAGAAAGA
Found at i:63117787 original size:21 final size:21
Alignment explanation
Indices: 63117744--63117787 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
63117734 TCTAGCTCAA
*
63117744 TTTTTACTGTTTTGTCACTAT
1 TTTTTACTGTTTTGTCACCAT
*
63117765 TTTTTATTGTTTTG-CTACCAT
1 TTTTTACTGTTTTGTC-ACCAT
63117786 TT
1 TT
63117788 CGCTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTACTGTTTTGTCACCAT
Found at i:63125898 original size:38 final size:38
Alignment explanation
Indices: 63125847--63125922 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
63125837 GTTAGTCTTT
*
63125847 TATACAACCACAACAAAGCACAATGGACCAACAACCAG
1 TATACAACCACAACAAAGCACAAAGGACCAACAACCAG
*
63125885 TATACAACCACAACCAAGCACAAAGGACCAACAACCAG
1 TATACAACCACAACAAAGCACAAAGGACCAACAACCAG
63125923 CAAATGTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.50, C:0.33, G:0.11, T:0.07
Consensus pattern (38 bp):
TATACAACCACAACAAAGCACAAAGGACCAACAACCAG
Found at i:63140263 original size:16 final size:17
Alignment explanation
Indices: 63140223--63140265 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
63140213 AATGTTAAGA
*
63140223 TTATTATATAAAAATAT
1 TTATTAAATAAAAATAT
* *
63140240 TCAATAAATAAAAA-AT
1 TTATTAAATAAAAATAT
63140256 TTATTAAATA
1 TTATTAAATA
63140266 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATTAAATAAAAATAT
Found at i:63140284 original size:21 final size:19
Alignment explanation
Indices: 63140248--63140286 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
63140238 ATTCAATAAA
*
63140248 TAAAAAATTTATTAAATAT
1 TAAAAAATTAATTAAATAT
63140267 TAAAAAATATAATATAAATA
1 TAAAAAAT-TAAT-TAAATA
63140287 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTAATTAAATAT
Found at i:63140284 original size:33 final size:32
Alignment explanation
Indices: 63140242--63140313 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
63140232 AAAAATATTC
*
63140242 AATAA-ATAAAAAATTTATTAAATATTAAAAA
1 AATAATATAAAAAATTTATTAAAAATTAAAAA
* * **
63140273 ATATAATATAAATAATTTTTTAAAAATTTTAAA
1 A-ATAATATAAAAAATTTATTAAAAATTAAAAA
63140306 AATAATAT
1 AATAATAT
63140314 GGGTGGGCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.03
32 11 0.32
33 22 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AATAATATAAAAAATTTATTAAAAATTAAAAA
Found at i:63144771 original size:3 final size:3
Alignment explanation
Indices: 63144763--63144789 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
63144753 TTGGCAAAAG
63144763 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
63144790 GACGTCGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:63148320 original size:11 final size:11
Alignment explanation
Indices: 63148290--63148347 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
63148280 CAAAAAAAAA
63148290 TCTTGTT-TTT
1 TCTTGTTGTTT
*
63148300 TTTTGTTTGTTT
1 TCTTG-TTGTTT
63148312 TCTTGTTGTTT
1 TCTTGTTGTTT
* * *
63148323 TGTTGCTATTT
1 TCTTGTTGTTT
63148334 TCTTGTTGTTT
1 TCTTGTTGTTT
63148345 TCT
1 TCT
63148348 CACTATTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
10 4 0.11
11 27 0.71
12 7 0.18
ACGTcount: A:0.02, C:0.09, G:0.16, T:0.74
Consensus pattern (11 bp):
TCTTGTTGTTT
Found at i:63148353 original size:22 final size:22
Alignment explanation
Indices: 63148309--63148356 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
63148299 TTTTTGTTTG
* **
63148309 TTTTCTTGTTGTTTTGTTGCTA
1 TTTTCTTGTTGTTTTCTCACTA
63148331 TTTTCTTGTTGTTTTCTCACTA
1 TTTTCTTGTTGTTTTCTCACTA
63148353 TTTT
1 TTTT
63148357 ACTACAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.69
Consensus pattern (22 bp):
TTTTCTTGTTGTTTTCTCACTA
Found at i:63151996 original size:20 final size:20
Alignment explanation
Indices: 63151959--63151996 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
63151949 AAAAACACAA
*
63151959 TTGAAATTATTTTTTTTTTT
1 TTGAAATTATTTTCTTTTTT
63151979 TTGAAATT-TTTTACTTTT
1 TTGAAATTATTTT-CTTTT
63151997 ATAGGCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (20 bp):
TTGAAATTATTTTCTTTTTT
Found at i:63152726 original size:14 final size:15
Alignment explanation
Indices: 63152702--63152732 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
63152692 TATTAATATT
63152702 ATTATCATTATTATA
1 ATTATCATTATTATA
63152717 ATTA-CATTATTATA
1 ATTATCATTATTATA
63152731 AT
1 AT
63152733 ATTCCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTATCATTATTATA
Found at i:63155353 original size:15 final size:15
Alignment explanation
Indices: 63155304--63155354 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
63155294 TTTAAAAATG
63155304 ATTATGTTTACTTTT
1 ATTATGTTTACTTTT
*
63155319 ATTGTAT-TATATATTTTT
1 A-T-TATGT-T-TACTTTT
63155337 ATTATGTTTACTTTT
1 ATTATGTTTACTTTT
63155352 ATT
1 ATT
63155355 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 10 0.34
16 6 0.21
17 6 0.21
18 7 0.24
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (15 bp):
ATTATGTTTACTTTT
Found at i:63160779 original size:21 final size:21
Alignment explanation
Indices: 63160754--63160793 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
63160744 TATAATCTAA
* *
63160754 ATCTTAGATGTTGTTATAAGT
1 ATCTTAGATGCTATTATAAGT
63160775 ATCTTAGATGCTATTATAA
1 ATCTTAGATGCTATTATAA
63160794 ATGTATAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (21 bp):
ATCTTAGATGCTATTATAAGT
Found at i:63170358 original size:90 final size:90
Alignment explanation
Indices: 63170201--63170382 Score: 346
Period size: 90 Copynumber: 2.0 Consensus size: 90
63170191 GAATTTGTGT
*
63170201 CAGATAAGGAAATATTCAGTTTTCTCTAAGTTTTTCTGTATATTTGAAGAATCCTTTAAGGAGCA
1 CAGATAAGGAAATATTCAGTTTTATCTAAGTTTTTCTGTATATTTGAAGAATCCTTTAAGGAGCA
63170266 TATCCCATACCGATGGCCAAACATG
66 TATCCCATACCGATGGCCAAACATG
*
63170291 CAGATAAGGAAATATTCAGTTTTATCTAAGTTTTTCTGTATATTTGAAGAATCCTTTAAGGATCA
1 CAGATAAGGAAATATTCAGTTTTATCTAAGTTTTTCTGTATATTTGAAGAATCCTTTAAGGAGCA
63170356 TATCCCATACCGATGGCCAAACATG
66 TATCCCATACCGATGGCCAAACATG
63170381 CA
1 CA
63170383 TCCACGCGGA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (90 bp):
CAGATAAGGAAATATTCAGTTTTATCTAAGTTTTTCTGTATATTTGAAGAATCCTTTAAGGAGCA
TATCCCATACCGATGGCCAAACATG
Found at i:63174843 original size:61 final size:58
Alignment explanation
Indices: 63174748--63174864 Score: 198
Period size: 61 Copynumber: 2.0 Consensus size: 58
63174738 GTATACACTC
63174748 CATTACACAACCTATTTATACTAATAATCAGATATACTAAGAAGGAAAGTCAAAGATTACA
1 CATTACACAACCTATTTATACTAATAATCAGATATAC--A-AAGGAAAGTCAAAGATTACA
*
63174809 CATTACACAACCTATTTATGCTAATAATCAGATATACAAAGGAAAGTCAAAGATTA
1 CATTACACAACCTATTTATACTAATAATCAGATATACAAAGGAAAGTCAAAGATTA
63174865 TAAATCCTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
58 18 0.33
59 1 0.02
61 36 0.65
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.26
Consensus pattern (58 bp):
CATTACACAACCTATTTATACTAATAATCAGATATACAAAGGAAAGTCAAAGATTACA
Found at i:63181081 original size:29 final size:29
Alignment explanation
Indices: 63181036--63181095 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
63181026 TAACCACCTT
*
63181036 TTTTTGCTAATCAAGAACAATAGAAATAA
1 TTTTTGCTAATCAAGAACAACAGAAATAA
* * *
63181065 TTTTTGCTACTCGAGAACAACAGCAATAA
1 TTTTTGCTAATCAAGAACAACAGAAATAA
63181094 TT
1 TT
63181096 AAGAGTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (29 bp):
TTTTTGCTAATCAAGAACAACAGAAATAA
Found at i:63182633 original size:2 final size:2
Alignment explanation
Indices: 63182626--63182681 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
63182616 TGTGCGTGCA
63182626 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
63182668 TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG
63182682 AGAGAGAGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:63187021 original size:20 final size:20
Alignment explanation
Indices: 63186996--63187035 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
63186986 AATATTTTCC
*
63186996 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
63187016 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
63187036 TTATTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:63190369 original size:22 final size:22
Alignment explanation
Indices: 63190339--63190385 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
63190329 AGTTTTAATG
*
63190339 TTTAATTTGATAT-TTGAATTTT
1 TTTAATTTGAT-TCTTAAATTTT
*
63190361 TTTAGTTTGATTCTTAAATTTT
1 TTTAATTTGATTCTTAAATTTT
63190383 TTT
1 TTT
63190386 TATTCCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (22 bp):
TTTAATTTGATTCTTAAATTTT
Found at i:63197287 original size:41 final size:40
Alignment explanation
Indices: 63197242--63197381 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
63197232 AGCGGCATTT
* *
63197242 TTAGCGG-GATTTTGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGATTTT-A-AAAAAACGCCACTAAAAATAGAGAA
* * * *
63197283 TTAGCGGCGCTTTTATAAAAACGCCGCTAAAGATAGAGAA
1 TTAGCGGCGATTTTAAAAAAACGCCACTAAAAATAGAGAA
* * *
63197323 TTAGCGGCG--CTTAACACAAAACGCCGCTAAAAAT-TAGAA
1 TTAGCGGCGATTTTAA-A-AAAACGCCACTAAAAATAGAGAA
*
63197362 TTAGCGGCGTTTTCTAAAAA
1 TTAGCGGCGATTT-TAAAAA
63197382 TTGCCGCAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
38 3 0.04
39 14 0.17
40 47 0.57
41 10 0.12
42 8 0.10
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGATTTTAAAAAAACGCCACTAAAAATAGAGAA
Found at i:63197388 original size:39 final size:40
Alignment explanation
Indices: 63197259--63197381 Score: 144
Period size: 40 Copynumber: 3.1 Consensus size: 40
63197249 GATTTTGACA
* * * *
63197259 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTAT
1 AAAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTTCT
* **
63197299 AAAAACGCCGCTAAAGATAGAGAATTAGCGGCGCTTAAC-
1 AAAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTTCT
*
63197338 ACAAAACGCCGCTAAAAAT-TAGAATTAGCGGCG-TTTTCT
1 A-AAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTTCT
63197377 AAAAA
1 AAAAA
63197382 TTGCCGCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
38 7 0.10
39 15 0.21
40 48 0.69
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTTCT
Found at i:63197498 original size:41 final size:40
Alignment explanation
Indices: 63197430--63197669 Score: 198
Period size: 41 Copynumber: 5.9 Consensus size: 40
63197420 GAGTTTTTGG
* *
63197430 GGCCCTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCG-TTTTTGAGAAGCGCCGCTAATGCTCT
* *
63197471 GGCCTTTAGCGGCGTTTTTGAGTAAGCGCCGCTAAAAGC-CA
1 GGCCTTTAGCGGCGTTTTTGAG-AAGCGCCGCT-AATGCTCT
* * * * * *
63197512 GAG-CATTAGCGGCGCTTCTTAAAAAACGCCGCTAATTCTCT
1 G-GCCTTTAGCGGCG-TTTTTGAGAAGCGCCGCTAATGCTCT
** * *
63197553 ATCCTTTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAATGCTCT
* * **
63197594 GGCCTTTAGCGGCATTTTTGAGGAAGCGCCGCTAATACTAA
1 GGCCTTTAGCGGCGTTTTTGA-GAAGCGCCGCTAATGCTCT
** *
63197635 GATCTTTAG-GGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAAT
63197670 ATATTTTTTA
Statistics
Matches: 156, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
40 37 0.24
41 109 0.70
42 10 0.06
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (40 bp):
GGCCTTTAGCGGCGTTTTTGAGAAGCGCCGCTAATGCTCT
Found at i:63197977 original size:15 final size:16
Alignment explanation
Indices: 63197957--63197990 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
63197947 CAAATATGGT
63197957 GTTTATGGATTT-AGG
1 GTTTATGGATTTAAGG
63197972 GTTTATGGATTTAAGG
1 GTTTATGGATTTAAGG
63197988 GTT
1 GTT
63197991 AGAGGTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GTTTATGGATTTAAGG
Found at i:63198464 original size:23 final size:23
Alignment explanation
Indices: 63198434--63198479 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
63198424 TATGGTTTAA
* *
63198434 GGTTTAGGGGTTAGGAGTTAGGG
1 GGTTTAGGGGTTAAGAGCTAGGG
63198457 GGTTTAGGGGTTAAGAGCTAGGG
1 GGTTTAGGGGTTAAGAGCTAGGG
63198480 ATTTAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.50, T:0.28
Consensus pattern (23 bp):
GGTTTAGGGGTTAAGAGCTAGGG
Found at i:63202247 original size:5 final size:5
Alignment explanation
Indices: 63202237--63202267 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
63202227 CTCGAAAATT
*
63202237 TTCGA TTCGA TTTGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
63202268 CGAATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (5 bp):
TTCGA
Found at i:63202462 original size:12 final size:12
Alignment explanation
Indices: 63202447--63202480 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
63202437 TAACCTACAT
63202447 AACTTACATAGA
1 AACTTACATAGA
*
63202459 AACTTATATAGA
1 AACTTACATAGA
*
63202471 AACTTGCATA
1 AACTTACATA
63202481 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:63202539 original size:16 final size:16
Alignment explanation
Indices: 63202520--63202597 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 16
63202510 ATACATAGCG
63202520 TACATAACTTACATAA
1 TACATAACTTACATAA
**
63202536 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
63202551 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
**
63202565 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
63202580 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
63202594 TACA
1 TACA
63202598 CCACTATACC
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
13 16 0.36
14 4 0.09
15 4 0.09
16 21 0.47
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:63202565 original size:29 final size:29
Alignment explanation
Indices: 63202523--63202602 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
63202513 CATAGCGTAC
*
63202523 ATAACTTACATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
63202552 ATAACTTGCATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
63202581 ATAACTTGCATAATACACCACT
1 ATAACTTGCATAATACACCACT
63202603 ATACCTTAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAACTTGCATAATACACCACTTACATAA
Found at i:63207974 original size:66 final size:65
Alignment explanation
Indices: 63207867--63208037 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
63207857 GAGCAAATTA
* * * *
63207867 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
63207931 G
65 G
* *
63207932 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
63207997 G
65 G
* * ** *
63207998 CAGCAGCTTAAAGCAGATGCGGCAGTAAGAGAAGCGGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
63208038 CGGCAGCTAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.29, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:63208032 original size:21 final size:21
Alignment explanation
Indices: 63208008--63208080 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
63207998 CAGCAGCTTA
*
63208008 AAGCAGATGCGGCAG-TAAGAG
1 AAGCAGAGGCGGCAGCT-AGAG
*
63208029 AAGCGGAGGCGGCAGCTAGAG
1 AAGCAGAGGCGGCAGCTAGAG
* * ** *
63208050 AAGTACAGGCTACAGCGAGAG
1 AAGCAGAGGCGGCAGCTAGAG
63208071 AAGCAGAGGC
1 AAGCAGAGGC
63208081 TAAAGCGAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.40, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCTAGAG
Found at i:63208081 original size:21 final size:21
Alignment explanation
Indices: 63208025--63208099 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
63208015 TGCGGCAGTA
* ** *
63208025 AGAGAAGCGGAGGCGGCAGCT
1 AGAGAAGCAGAGGCTACAGCG
* *
63208046 AGAGAAGTACAGGCTACAGCG
1 AGAGAAGCAGAGGCTACAGCG
*
63208067 AGAGAAGCAGAGGCTAAAGCG
1 AGAGAAGCAGAGGCTACAGCG
*
63208088 AGGGAAGCAGAG
1 AGAGAAGCAGAG
63208100 CAGCTTCAGA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.37, C:0.16, G:0.41, T:0.05
Consensus pattern (21 bp):
AGAGAAGCAGAGGCTACAGCG
Found at i:63208442 original size:43 final size:42
Alignment explanation
Indices: 63208367--63208660 Score: 200
Period size: 43 Copynumber: 6.9 Consensus size: 42
63208357 ATCTGCCAAA
* ** * * * * *
63208367 TTTAGTGGCATTTTTTTTAAAAACGCCACTAAAGGTGTTGGCC
1 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGAT-ATGGTC
* *
63208410 TTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTC
1 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGAT-ATGGTC
* * * *
63208453 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGAT-ATGGTC
* **
63208496 TTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGAT-TAGGTTC
1 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGATAT-GG-TC
** * *
63208539 TTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT-
1 TTTAGTGGCGTTTT-TGGTAAAAGCGCCGCTAAAGAT-ATGGTC
* * * ** *
63208582 TTATTGCGGCGTTTTAGG-GGAAGCGCCACTAAAGAT-TAGGTTC
1 TT-TAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGATAT-GG-TC
* * *
63208625 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGAT
1 TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGAT
63208661 CAGGGTCTAT
Statistics
Matches: 198, Mismatches: 43, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
41 3 0.02
42 29 0.15
43 135 0.68
44 29 0.15
45 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (42 bp):
TTTAGTGGCGTTTTTGGTAAAAGCGCCGCTAAAGATATGGTC
Found at i:63208512 original size:86 final size:85
Alignment explanation
Indices: 63208409--63208668 Score: 306
Period size: 86 Copynumber: 3.0 Consensus size: 85
63208399 AGGTGTTGGC
* * * * *
63208409 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
1 CTTTAGCGGCGTTTTTGG-GAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGAAAA
*
63208474 AGCGCCACTAAAGATCATGGT
65 AGCGCCACTAAAGATCAGGGT
***
63208495 CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCG
1 CTTTAGCGGCGTTTTT-GGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGAAA
* *
63208560 AAGCGCCGCTATAGATCAGGGT
64 AAGCGCCACTAAAGATCAGGGT
* * * * **
63208582 -TTATTGCGGCGTTTTAGGGGAAGCGCCACTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAA
1 CTT-TAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGAAAA
* *
63208646 AGCGCCGCTATAGATCAGGGT
65 AGCGCCACTAAAGATCAGGGT
63208667 CT
1 CT
63208669 ATTCCGGCTT
Statistics
Matches: 154, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
85 31 0.20
86 84 0.55
87 39 0.25
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (85 bp):
CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGAAAAA
GCGCCACTAAAGATCAGGGT
Found at i:63208606 original size:129 final size:129
Alignment explanation
Indices: 63208409--63208660 Score: 332
Period size: 129 Copynumber: 2.0 Consensus size: 129
63208399 AGGTGTTGGC
63208409 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
* *
63208474 AGCGCCACTAAAGATCATGG-TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
66 AGCGCCACTAAAGATCA-GGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATTAGGTT
* * * *
63208538 CTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT-TTATTGCGGCGTTT-TAGG-
1 CTTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATAAGGGTCTT-TAGCGGCGTTTGT-GGA
** * * * *
63208600 GGAAGCGCCACTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGAT
63 AAAAGCGCCACTAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGAT
63208661 CAGGGTCTAT
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
128 2 0.02
129 68 0.64
130 37 0.35
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (129 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAA
AGCGCCACTAAAGATCAGGTTCTTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATTAGGTT
Found at i:63209207 original size:26 final size:25
Alignment explanation
Indices: 63209160--63209222 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
63209150 AAAAAGTATT
63209160 TTAAAAATATTTTAAAATTAAAAAAA
1 TTAAAAATATTTTAAAATT-AAAAAA
63209186 TTAAAAAGTATTTTAAAA-TAAAAAA
1 TTAAAAA-TATTTTAAAATTAAAAAA
*
63209211 TAAAAAATATTT
1 TTAAAAATATTT
63209223 ATTATATTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 5 0.14
25 12 0.34
26 8 0.23
27 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TTAAAAATATTTTAAAATTAAAAAA
Found at i:63209543 original size:16 final size:16
Alignment explanation
Indices: 63209522--63209561 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
63209512 ATCTGTAATG
63209522 TTAATCGAGTTAAGAC
1 TTAATCGAGTTAAGAC
63209538 TTAATCGAGTTAAGAC
1 TTAATCGAGTTAAGAC
*
63209554 TCAATCGA
1 TTAATCGA
63209562 CTAGACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (16 bp):
TTAATCGAGTTAAGAC
Found at i:63211099 original size:17 final size:17
Alignment explanation
Indices: 63211077--63211112 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
63211067 ATTTTTCTCG
63211077 TTTGCTTGTATTGTGTT
1 TTTGCTTGTATTGTGTT
63211094 TTTGCTTGTATTGTGTT
1 TTTGCTTGTATTGTGTT
63211111 TT
1 TT
63211113 CTTTGCCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.67
Consensus pattern (17 bp):
TTTGCTTGTATTGTGTT
Found at i:63218260 original size:30 final size:30
Alignment explanation
Indices: 63218217--63218278 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
63218207 CCCTTCTCTT
* * * *
63218217 TTTCTCTCTTTCCTTTCT-TCATCCTCTGCC
1 TTTCTATCATTCCTTCCTATCATCATCT-CC
63218247 TTTCTATCATTCCTTCCTATCATCATCTCC
1 TTTCTATCATTCCTTCCTATCATCATCTCC
63218277 TT
1 TT
63218279 CATCTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.10, C:0.37, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTCTATCATTCCTTCCTATCATCATCTCC
Found at i:63220642 original size:6 final size:6
Alignment explanation
Indices: 63220633--63220673 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
63220623 ATTAGGGATT
63220633 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAA
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAA
63220674 TGATCGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:63221486 original size:17 final size:16
Alignment explanation
Indices: 63221457--63221489 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
63221447 TATTAAAAAT
63221457 AATAATAAAATATATA
1 AATAATAAAATATATA
63221473 AATAATACAAATATATA
1 AATAATA-AAATATATA
63221490 CAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAAAATATATA
Found at i:63221488 original size:19 final size:18
Alignment explanation
Indices: 63221453--63221510 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
63221443 TTTATATTAA
*
63221453 AAATAATAATAAAATATAT
1 AAATAATAA-AATATATAT
*
63221472 AAATAATACAAATATATAC
1 AAATAATA-AAATATATAT
*
63221491 AAAT-TTAAAATAT-TAT
1 AAATAATAAAATATATAT
63221507 AAAT
1 AAAT
63221511 TTATAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 2 0.06
19 19 0.56
20 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATAAAATATATAT
Found at i:63222560 original size:21 final size:21
Alignment explanation
Indices: 63222536--63222594 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
63222526 GAAAATTATT
63222536 AAAATTGTTAATAAAATATAC
1 AAAATTGTTAATAAAATATAC
* * *
63222557 AAAA-TATT-ATAAAA-AGCAT
1 AAAATTGTTAATAAAATA-TAC
63222576 AAAATTGTTAATAAAATAT
1 AAAATTGTTAATAAAATAT
63222595 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 6 0.21
21 10 0.34
22 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAATTGTTAATAAAATATAC
Found at i:63222601 original size:40 final size:39
Alignment explanation
Indices: 63222509--63222602 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 39
63222499 TAACTATGAA
* **
63222509 AAAATATTTAAAATATAGAAAATTATTAAAATTGTTAAT
1 AAAATATTTAAAATATAAAAAAGCATTAAAATTGTTAAT
**
63222548 AAAATATACAAAATATTATAAAAAGCA-TAAAATTGTTAAT
1 AAAATATTTAAAATA-TA-AAAAAGCATTAAAATTGTTAAT
63222588 AAAATATTTAAAATA
1 AAAATATTTAAAATA
63222603 ATTAAGTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 13 0.28
40 28 0.61
41 5 0.11
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (39 bp):
AAAATATTTAAAATATAAAAAAGCATTAAAATTGTTAAT
Found at i:63222607 original size:21 final size:20
Alignment explanation
Indices: 63222509--63222607 Score: 55
Period size: 21 Copynumber: 5.0 Consensus size: 20
63222499 TAACTATGAA
*
63222509 AAAATATTTAAAATA-T-AG
1 AAAATATTTAAAATATTAAT
*
63222527 AAAAT-TATTAAAATTGTTAAT
1 AAAATAT-TTAAAA-TATTAAT
**
63222548 AAAATATACAAAATATT-AT
1 AAAATATTTAAAATATTAAT
** *
63222567 AAAA-AGCATAAAATTGTTAAT
1 AAAATA-TTTAAAA-TATTAAT
63222588 AAAATATTTAAAATAATTAA
1 AAAATATTTAAAAT-ATTAA
63222608 GTTAGTATCA
Statistics
Matches: 60, Mismatches: 11, Indels: 17
0.68 0.12 0.19
Matches are distributed among these distances:
17 1 0.02
18 12 0.20
19 12 0.20
20 8 0.13
21 25 0.42
22 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAATATTTAAAATATTAAT
Found at i:63226223 original size:21 final size:22
Alignment explanation
Indices: 63226194--63226240 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
63226184 CAGAAGGAGT
*
63226194 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
63226216 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
63226237 GAGT
1 GAGT
63226241 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:63228336 original size:26 final size:26
Alignment explanation
Indices: 63228300--63228356 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
63228290 TTACCACATT
63228300 CAGCTCTTCACAAAATTGATGAACAC
1 CAGCTCTTCACAAAATTGATGAACAC
63228326 CAGCTCTTCACAAAATTGATGAACAC
1 CAGCTCTTCACAAAATTGATGAACAC
*
63228352 AAGCT
1 CAGCT
63228357 AAAGCTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (26 bp):
CAGCTCTTCACAAAATTGATGAACAC
Found at i:63233175 original size:34 final size:34
Alignment explanation
Indices: 63233132--63233200 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
63233122 CCAAAGAAAG
63233132 AAAGAGAGATAAAGGAGAAGATATAGTTCATTGC
1 AAAGAGAGATAAAGGAGAAGATATAGTTCATTGC
*
63233166 AAAGAGAGATAAATGAGAAGATATAGTTCATTGC
1 AAAGAGAGATAAAGGAGAAGATATAGTTCATTGC
63233200 A
1 A
63233201 GTCCATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.25, T:0.22
Consensus pattern (34 bp):
AAAGAGAGATAAAGGAGAAGATATAGTTCATTGC
Found at i:63236396 original size:19 final size:19
Alignment explanation
Indices: 63236374--63236418 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
63236364 ATAAAAATTG
63236374 TAAAATTAT-GAAAAATATT
1 TAAAATTATAGAAAAATA-T
* *
63236393 TAAAAATATAGAAAATTAT
1 TAAAATTATAGAAAAATAT
63236412 TAAAATT
1 TAAAATT
63236419 GTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TAAAATTATAGAAAAATAT
Found at i:63236447 original size:19 final size:19
Alignment explanation
Indices: 63236411--63236446 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
63236401 TAGAAAATTA
*
63236411 TTAAAATTGTTAATAAAAT
1 TTAAAAATGTTAATAAAAT
63236430 TTAAAAATGTT-ATAAAA
1 TTAAAAATGTTAATAAAA
63236447 AAAGCATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (19 bp):
TTAAAAATGTTAATAAAAT
Found at i:63236880 original size:16 final size:17
Alignment explanation
Indices: 63236843--63236880 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
63236833 ATATTTAGAT
63236843 TTAATTCATAAATAAAG
1 TTAATTCATAAATAAAG
*
63236860 -AAATT-ATAAATAAAG
1 TTAATTCATAAATAAAG
63236875 TTAATT
1 TTAATT
63236881 TCAATATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (17 bp):
TTAATTCATAAATAAAG
Found at i:63238177 original size:18 final size:19
Alignment explanation
Indices: 63238129--63238177 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
63238119 TATTGTATCC
63238129 TTATTATTAT-ATTATTTA
1 TTATTATTATCATTATTTA
63238147 TTATT-TCTATCATTA-TTA
1 TTATTAT-TATCATTATTTA
*
63238165 TTATTATTTTCAT
1 TTATTATTATCAT
63238178 ACATGTACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 21 0.78
19 5 0.19
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATTATCATTATTTA
Found at i:63238223 original size:27 final size:25
Alignment explanation
Indices: 63238192--63238243 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
63238182 GTACACACGC
*
63238192 ATTTTTTATTATAATATATATGCATAT
1 ATTTTTTA-TA-AATACATATGCATAT
*
63238219 ATTTTTTATAAATACATGTGCATAT
1 ATTTTTTATAAATACATATGCATAT
63238244 TATATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 2 0.09
27 8 0.35
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
ATTTTTTATAAATACATATGCATAT
Found at i:63240938 original size:30 final size:30
Alignment explanation
Indices: 63240892--63240985 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
63240882 TTTTATTATG
*
63240892 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
63240923 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * * *
63240953 CTATTATTTGATACCCATATCTTTAATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
63240983 CCA
1 CCA
63240986 TAAATATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 50 0.88
31 7 0.12
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:63240947 original size:15 final size:15
Alignment explanation
Indices: 63240902--63240976 Score: 55
Period size: 15 Copynumber: 5.0 Consensus size: 15
63240892 CCAATATCTC
63240902 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
63240917 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
63240932 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
63240947 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
63240962 GATACCCATATCTTT
1 GATACCCATATCTTT
63240977 AATTTTCCAT
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
14 8 0.19
15 26 0.62
16 8 0.19
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:63245568 original size:30 final size:30
Alignment explanation
Indices: 63245522--63245645 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
63245512 TTTTATTATG
* *
63245522 CCAATATCTCGATACCCATATCTTTAACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
63245553 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
63245583 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
63245613 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
63245643 CCA
1 CCA
63245646 TAAATATGGA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 80 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:63245607 original size:15 final size:15
Alignment explanation
Indices: 63245532--63245639 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
63245522 CCAATATCTC
63245532 GATACCCATATCTTT
1 GATACCCATATCTTT
* ** *
63245547 AACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
63245562 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
63245577 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
63245592 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
63245607 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
63245622 GATACCCATATCTTT
1 GATACCCATATCTTT
63245637 GAT
1 GAT
63245640 TTTCCATAAA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
14 12 0.18
15 41 0.63
16 12 0.18
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:63248779 original size:19 final size:20
Alignment explanation
Indices: 63248739--63248779 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
63248729 CCAAAACCCT
*
63248739 CAAAACTTTTTATTTTCCCC
1 CAAAACTTTTTATCTTCCCC
63248759 CAAAA-TTTTTA-CTTCCTCC
1 CAAAACTTTTTATCTTCC-CC
63248778 CA
1 CA
63248780 CTTTTCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (20 bp):
CAAAACTTTTTATCTTCCCC
Found at i:63250729 original size:19 final size:18
Alignment explanation
Indices: 63250690--63250738 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
63250680 TACAAAAAAT
*
63250690 AAAATTTTAAAATTATGAA
1 AAAATTTTAAAAATAT-AA
63250709 AAAATATTTAAAAATATAA
1 AAAAT-TTTAAAAATATAA
63250728 AAAATTGTTAA
1 AAAATT-TTAA
63250739 TAAAATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 1 0.04
19 16 0.59
20 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAAATTTTAAAAATATAA
Found at i:63250743 original size:21 final size:21
Alignment explanation
Indices: 63250719--63250786 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
63250709 AAAATATTTA
63250719 AAAATATAAAAAATTGTTAAT
1 AAAATATAAAAAATTGTTAAT
* * *
63250740 AAAATTTACAAAA-TATT-AT
1 AAAATATAAAAAATTGTTAAT
* *
63250759 AAAA-AGCATAAAATTGTTAAT
1 AAAATA-TAAAAAATTGTTAAT
63250780 AAAATAT
1 AAAATAT
63250787 TTAAAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 11 0.31
20 6 0.17
21 17 0.49
22 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAATATAAAAAATTGTTAAT
Found at i:63257984 original size:18 final size:18
Alignment explanation
Indices: 63257961--63258071 Score: 150
Period size: 18 Copynumber: 6.2 Consensus size: 18
63257951 CCCAACTACT
*
63257961 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
63257979 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
*
63257997 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
63258015 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* **
63258033 ATATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
*
63258051 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
63258069 GTA
1 GTA
63258072 AACGGTCGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:63261674 original size:6 final size:6
Alignment explanation
Indices: 63261639--63261673 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
63261629 ATTGTTTGAA
*
63261639 TATATC TATATC TATATC TATATC TATATA TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
63261674 AATACAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:63265951 original size:6 final size:6
Alignment explanation
Indices: 63265942--63265976 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
63265932 ATTAGGGATT
63265942 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAA
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAA
63265977 TGATCGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:63266763 original size:10 final size:10
Alignment explanation
Indices: 63266735--63266765 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
63266725 AAAAATAAAT
63266735 ATATATACAA
1 ATATATACAA
63266745 ATA-ATACAA
1 ATATATACAA
63266754 ATATATACAA
1 ATATATACAA
63266764 AT
1 AT
63266766 TTAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (10 bp):
ATATATACAA
Found at i:63266783 original size:16 final size:17
Alignment explanation
Indices: 63266752--63266784 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
63266742 CAAATAATAC
*
63266752 AAATATATACAAATTTA
1 AAATATATAAAAATTTA
63266769 AAATAT-TAAAAATTTA
1 AAATATATAAAAATTTA
63266785 TAAAAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATATAAAAATTTA
Found at i:63266971 original size:19 final size:19
Alignment explanation
Indices: 63266949--63266993 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
63266939 ATAAAAATTG
63266949 TAAAATTAT-GAAAAATATT
1 TAAAATTATAGAAAAATA-T
* *
63266968 TAAAAATATAGAAAATTAT
1 TAAAATTATAGAAAAATAT
63266987 TAAAATT
1 TAAAATT
63266994 GTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TAAAATTATAGAAAAATAT
Found at i:63267005 original size:21 final size:21
Alignment explanation
Indices: 63266979--63267054 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 21
63266969 AAAAATATAG
63266979 AAAATTATTAAAATTGTTAAT
1 AAAATTATTAAAATTGTTAAT
* * *
63267000 AAAATT-TAAAAAATATT-AT
1 AAAATTATTAAAATTGTTAAT
**
63267019 AAAAAGCA-TAAAATTGTTAAT
1 -AAAATTATTAAAATTGTTAAT
*
63267040 AAAAATATTTAAAAT
1 AAAATTA-TTAAAAT
63267055 GATTAAGTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
19 2 0.05
20 24 0.60
21 8 0.20
22 6 0.15
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAATTATTAAAATTGTTAAT
Found at i:63267323 original size:21 final size:21
Alignment explanation
Indices: 63267299--63267357 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
63267289 GAAAATTATT
63267299 AAAATTGTTAATAAAATATAC
1 AAAATTGTTAATAAAATATAC
* *
63267320 AAAA-TATT-ATAAAA-AGTAT
1 AAAATTGTTAATAAAATA-TAC
63267339 AAAATTGTTAATAAAATAT
1 AAAATTGTTAATAAAATAT
63267358 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 6 0.19
21 11 0.35
22 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAATTGTTAATAAAATATAC
Found at i:63267364 original size:40 final size:39
Alignment explanation
Indices: 63267272--63267365 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 39
63267262 TAACCATGAA
* *
63267272 AAAATATTTAAAATATAGAAAATTATTAAAATTGTTAAT
1 AAAATATTTAAAATATAAAAAAGTATTAAAATTGTTAAT
**
63267311 AAAATATACAAAATATTATAAAAAGTA-TAAAATTGTTAAT
1 AAAATATTTAAAATA-TA-AAAAAGTATTAAAATTGTTAAT
63267351 AAAATATTTAAAATA
1 AAAATATTTAAAATA
63267366 ATTAAGTTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 13 0.28
40 28 0.60
41 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (39 bp):
AAAATATTTAAAATATAAAAAAGTATTAAAATTGTTAAT
Found at i:63267370 original size:21 final size:20
Alignment explanation
Indices: 63267272--63267370 Score: 64
Period size: 21 Copynumber: 5.0 Consensus size: 20
63267262 TAACCATGAA
*
63267272 AAAATATTTAAAATA-T-AG
1 AAAATATTTAAAATATTAAT
*
63267290 AAAAT-TATTAAAATTGTTAAT
1 AAAATAT-TTAAAA-TATTAAT
**
63267311 AAAATATACAAAATATT-AT
1 AAAATATTTAAAATATTAAT
* *
63267330 AAAA-AGTATAAAATTGTTAAT
1 AAAATA-TTTAAAA-TATTAAT
63267351 AAAATATTTAAAATAATTAA
1 AAAATATTTAAAAT-ATTAA
63267371 GTTAGTTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
17 1 0.02
18 12 0.19
19 13 0.21
20 8 0.13
21 26 0.42
22 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAATATTTAAAATATTAAT
Found at i:63270078 original size:54 final size:54
Alignment explanation
Indices: 63269996--63270103 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
63269986 GTATCATGGC
*
63269996 ATGATGAAGACCCATCTAAAGTAATTGCCTAATTTGCAAGAAAAGAACAAAATT
1 ATGATGAAGACCCATCCAAAGTAATTGCCTAATTTGCAAGAAAAGAACAAAATT
*
63270050 ATGATGAAGACTCATCCAAAGTAATTGCCTAATTTGCAAGAAAAGAACAAAATT
1 ATGATGAAGACCCATCCAAAGTAATTGCCTAATTTGCAAGAAAAGAACAAAATT
63270104 TACTTTAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (54 bp):
ATGATGAAGACCCATCCAAAGTAATTGCCTAATTTGCAAGAAAAGAACAAAATT
Found at i:63271135 original size:6 final size:6
Alignment explanation
Indices: 63271126--63271305 Score: 171
Period size: 6 Copynumber: 30.0 Consensus size: 6
63271116 GATGAAGAAC
* * * * * *
63271126 GAGAAT GAGAGT GTGAGT GAGGGT GAGAGT GAGAGT GAGATT AAGAAT
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
* * * * *
63271174 GAGAGT GTGAGT GAGAAT GAGAGT GTGAGT GAGATT GAGAAT GAGAGT
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
* * * * *
63271222 GAGAGT GAGAGT GAGAGT GTGAGC GAGAAT GAGAAT GAGAGT GTGAGT
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
* * * * *
63271270 GTGAGT GAGAGT GTGAGC GAGAAT GAGAAT GAGAGT
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
63271306 CACGACAATT
Statistics
Matches: 141, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 141 1.00
ACGTcount: A:0.34, C:0.01, G:0.44, T:0.21
Consensus pattern (6 bp):
GAGAGT
Found at i:63271186 original size:42 final size:42
Alignment explanation
Indices: 63271121--63271305 Score: 271
Period size: 42 Copynumber: 4.4 Consensus size: 42
63271111 ATGGAGATGA
* * * *
63271121 AGAACGAGAATGAGAGTGTGAGTGAGGGTGAGAGTGAGAGTG
1 AGAATGAGAATGAGAGTGTGAGTGAGAGTGAGAGTGTGAGCG
* * * *
63271163 AGATTAAGAATGAGAGTGTGAGTGAGAATGAGAGTGTGAGTG
1 AGAATGAGAATGAGAGTGTGAGTGAGAGTGAGAGTGTGAGCG
* *
63271205 AGATTGAGAATGAGAGTGAGAGTGAGAGTGAGAGTGTGAGCG
1 AGAATGAGAATGAGAGTGTGAGTGAGAGTGAGAGTGTGAGCG
*
63271247 AGAATGAGAATGAGAGTGTGAGTGTGAGTGAGAGTGTGAGCG
1 AGAATGAGAATGAGAGTGTGAGTGAGAGTGAGAGTGTGAGCG
63271289 AGAATGAGAATGAGAGT
1 AGAATGAGAATGAGAGT
63271306 CACGACAATT
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 130 1.00
ACGTcount: A:0.35, C:0.02, G:0.44, T:0.20
Consensus pattern (42 bp):
AGAATGAGAATGAGAGTGTGAGTGAGAGTGAGAGTGTGAGCG
Found at i:63274512 original size:18 final size:17
Alignment explanation
Indices: 63274488--63274533 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
63274478 TGTCTTGCAT
63274488 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
63274505 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
63274524 TTTCAAAACA
1 TTTCAAAACA
63274534 CTTTTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 3 0.13
18 16 0.70
19 4 0.17
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:63281844 original size:5 final size:5
Alignment explanation
Indices: 63281834--63281902 Score: 129
Period size: 5 Copynumber: 13.8 Consensus size: 5
63281824 ACTAAACAAC
63281834 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
*
63281884 ATCAT ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTAT ATTA
63281903 CTAAAGAAAC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 62 1.00
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:63283247 original size:45 final size:45
Alignment explanation
Indices: 63283177--63283283 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 45
63283167 ATGTGCCGAC
*
63283177 TACTGTTACTGTTACCGATTCGATTCGACACTTTGTATGTCGAATACTAT
1 TACTGTTACTGTTACAGATTC-A---G-CACTTTGTATGTCGAATACTAT
* * * *
63283227 TA-TCGTTACTGTTACAGATTCAGCACTTTGTGTTTTGAATACTGT
1 TACT-GTTACTGTTACAGATTCAGCACTTTGTATGTCGAATACTAT
63283272 TACTGTTACTGT
1 TACTGTTACTGT
63283284 GAAAGAAACT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
45 28 0.56
46 2 0.04
49 2 0.04
50 18 0.36
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTATGTCGAATACTAT
Found at i:63286163 original size:15 final size:15
Alignment explanation
Indices: 63286143--63286173 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63286133 CAAACATCAC
63286143 TCATAGCAACTTTAT
1 TCATAGCAACTTTAT
*
63286158 TCATAGCAATTTTAT
1 TCATAGCAACTTTAT
63286173 T
1 T
63286174 GAATTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (15 bp):
TCATAGCAACTTTAT
Found at i:63286973 original size:18 final size:18
Alignment explanation
Indices: 63286950--63286991 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
63286940 GTAGCAGGCA
* * *
63286950 GCCCAATACGATCATTTG
1 GCCCAAAACCATCAATTG
63286968 GCCCAAAACCATCAATTG
1 GCCCAAAACCATCAATTG
63286986 GCCCAA
1 GCCCAA
63286992 GATTGCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.19
Consensus pattern (18 bp):
GCCCAAAACCATCAATTG
Found at i:63287247 original size:33 final size:33
Alignment explanation
Indices: 63287205--63287301 Score: 185
Period size: 33 Copynumber: 2.9 Consensus size: 33
63287195 GCACAATAAT
63287205 TTTGACCAAGTGGAAAGCTATTTTGACCATAGC
1 TTTGACCAAGTGGAAAGCTATTTTGACCATAGC
*
63287238 TTTGACCAAGTGGAAAACTATTTTGACCATAGC
1 TTTGACCAAGTGGAAAGCTATTTTGACCATAGC
63287271 TTTGACCAAGTGGAAAGCTATTTTGACCATA
1 TTTGACCAAGTGGAAAGCTATTTTGACCATA
63287302 TCTATTTTGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (33 bp):
TTTGACCAAGTGGAAAGCTATTTTGACCATAGC
Found at i:63287308 original size:15 final size:15
Alignment explanation
Indices: 63287288--63287316 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
63287278 AAGTGGAAAG
63287288 CTATTTTGACCATAT
1 CTATTTTGACCATAT
63287303 CTATTTTGACCATA
1 CTATTTTGACCATA
63287317 GCCATAATGA
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:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
CTATTTTGACCATAT
Found at i:63292449 original size:3 final size:3
Alignment explanation
Indices: 63292443--63292492 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
63292433 ATTTAAGTTA
* * * *
63292443 ATT ATT ATT ATT ATT ATT ATT AGT GTT ATC ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63292491 AT
1 AT
63292493 ACTAATATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Done.