Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 9 of 19
Found at i:1553952 original size:22 final size:21
Alignment explanation
Indices: 1553913--1553956 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1553903 AAATAAAATT
*
1553913 AAATTAAATATTACATAAATAA
1 AAATTAAATAATACAT-AATAA
1553935 AAATTAAATAAATA-ATAATAA
1 AAATTAAAT-AATACATAATAA
1553956 A
1 A
1553957 TTTTATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 11 0.55
23 3 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTAAATAATACATAATAA
Found at i:1554757 original size:22 final size:22
Alignment explanation
Indices: 1554725--1554790 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1554715 AATATTAAAA
*
1554725 AAATATTTTTATATTAATATTT
1 AAATATATTTATATTAATATTT
*
1554747 ATATATATTTATAATTAA-ATTT
1 AAATATATTTAT-ATTAATATTT
* * *
1554769 AAATAAAATTATTTTAATATTT
1 AAATATATTTATATTAATATTT
1554791 GAGAAATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 4 0.11
22 27 0.75
23 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATATATTTATATTAATATTT
Found at i:1554898 original size:14 final size:14
Alignment explanation
Indices: 1554861--1554899 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
1554851 TTATAATTGT
1554861 ATAATATATATTTC
1 ATAATATATATTTC
1554875 ATAAATTATATATTTC
1 AT-AA-TATATATTTC
1554891 ATAATATAT
1 ATAATATAT
1554900 GAATAACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 12 0.52
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAATATATATTTC
Found at i:1555600 original size:4 final size:4
Alignment explanation
Indices: 1555593--1555633 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
1555583 TAAAAATATC
*
1555593 ATTA ATTA ATTA AGTA ATTA A-T- ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1555634 GTAAATACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 2 0.06
4 30 0.91
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:1555620 original size:18 final size:18
Alignment explanation
Indices: 1555597--1555632 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1555587 AATATCATTA
1555597 ATTAATTAAGTAATTAAT
1 ATTAATTAAGTAATTAAT
*
1555615 ATTAATTAATTAATTAAT
1 ATTAATTAAGTAATTAAT
1555633 TGTAAATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAATTAAGTAATTAAT
Found at i:1560681 original size:2 final size:2
Alignment explanation
Indices: 1560674--1560757 Score: 105
Period size: 2 Copynumber: 42.0 Consensus size: 2
1560664 ATTGTCTTTA
* *
1560674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1560716 AC AC AT AT AA AG AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1560758 GTTATATTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1562342 original size:2 final size:2
Alignment explanation
Indices: 1562335--1562368 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1562325 GCCATCAACA
1562335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1562369 CATAATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1562718 original size:35 final size:35
Alignment explanation
Indices: 1562651--1562718 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1562641 TTAAATCTAC
* * * * * *
1562651 TATTAGTTTGTTAAAATATAAATTATATAAAAAAT
1 TATTAATTTGATAAAATACAAATCACAAAAAAAAT
1562686 TATTAATTTGATAAAATACAAATCACAAAAAAA
1 TATTAATTTGATAAAATACAAATCACAAAAAAA
1562719 GTTACGAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (35 bp):
TATTAATTTGATAAAATACAAATCACAAAAAAAAT
Found at i:1567523 original size:215 final size:219
Alignment explanation
Indices: 1567100--1567543 Score: 725
Period size: 215 Copynumber: 2.0 Consensus size: 219
1567090 GCAAGGGATC
1567100 CCTAATAATAATGAGGATTGCAAAGGAGTACCACAGCAAAAAAAAAAAAAAAAAAAAAACCCTTC
1 CCTAATAATAATGAGGATTGCAAAGGAGTACCACAGC-----AAAAAAAAAAAAAAAAACCCTTC
*
1567165 CCTGTTTACGCAAATTGCCAAAAAAATCTATTTGTTGTTTACAGCAGGTCTTTCATCTATTACAA
61 CCTGTTTACGCAAATTGCCAAAAAAATCTATTTGTTGTTTACAGCAGG--TATCATCTATTACAA
*
1567230 TCCATGGACAGTGGTTCTAGTCCTACAGAGATCTCTTCAAAATTATAACACTACCTATATCATGC
124 TCCATGGACAGTAGTTCTAGTCCTACAGAGATCTCTTCAAAATTATAACACTACCTATATCATGC
1567295 AACTATAACTCCAAAGGTGCATCAACACATA
189 AACTATAACTCCAAAGGTGCATCAACACATA
* * ** *
1567326 CCTAGTAATAATGAGGATTGCAAAGGAGTACCACCGC-AACCAAAAAAAAAAAA-CCTTTCCTGT
1 CCTAATAATAATGAGGATTGCAAAGGAGTACCACAGCAAAAAAAAAAAAAAAAACCCTTCCCTGT
1567389 TTACGCAAATTGCCAAAAAAATCTATTTGTTGTTTACAGCA-G-ATCATCTATTACAATCCATGG
66 TTACGCAAATTGCCAAAAAAATCTATTTGTTGTTTACAGCAGGTATCATCTATTACAATCCATGG
*
1567452 ACAGTAGTTCTAGTCCTATAGAGATCTCTTCAAAATTATAACACTACCTATATCATGCAACTATA
131 ACAGTAGTTCTAGTCCTACAGAGATCTCTTCAAAATTATAACACTACCTATATCATGCAACTATA
1567517 ACTCCAAAGGTGCATCAACACATA
196 ACTCCAAAGGTGCATCAACACATA
1567541 CCT
1 CCT
1567544 TGTCACAATG
Statistics
Matches: 210, Mismatches: 8, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
215 110 0.52
218 1 0.00
219 50 0.24
220 14 0.07
226 35 0.17
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (219 bp):
CCTAATAATAATGAGGATTGCAAAGGAGTACCACAGCAAAAAAAAAAAAAAAAACCCTTCCCTGT
TTACGCAAATTGCCAAAAAAATCTATTTGTTGTTTACAGCAGGTATCATCTATTACAATCCATGG
ACAGTAGTTCTAGTCCTACAGAGATCTCTTCAAAATTATAACACTACCTATATCATGCAACTATA
ACTCCAAAGGTGCATCAACACATA
Found at i:1569165 original size:21 final size:21
Alignment explanation
Indices: 1569141--1569181 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1569131 GCAAGGTTAA
1569141 AATAAATAAATAA-ATAAATTT
1 AATAAATAAA-AATATAAATTT
*
1569162 AATAATTAAAAATATAAATT
1 AATAAATAAAAATATAAATT
1569182 ATTAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAATAAAAATATAAATTT
Found at i:1569341 original size:19 final size:19
Alignment explanation
Indices: 1569317--1569354 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1569307 AAATATAAAA
1569317 ATTTAT-ATATTTATTTTAT
1 ATTTATAAT-TTTATTTTAT
1569336 ATTTATAATTTTATTTTAT
1 ATTTATAATTTTATTTTAT
1569355 TATAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATAATTTTATTTTAT
Found at i:1569362 original size:19 final size:20
Alignment explanation
Indices: 1569323--1569368 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1569313 AAAAATTTAT
*
1569323 ATATTTATTTTATATTTATA
1 ATATTTATTTTATATTAATA
1569343 AT-TTTATTTTAT-TATAATA
1 ATATTTATTTTATAT-TAATA
1569362 ATATTTA
1 ATATTTA
1569369 AAATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTATTTTATATTAATA
Found at i:1569392 original size:27 final size:27
Alignment explanation
Indices: 1569312--1569393 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
1569302 TATATAAATA
*
1569312 TAAAA-ATTTATATATTTATTTTATATT
1 TAAAATATTT-TATATTTATATTATATT
* * * *
1569339 TATAATTTTATTTTA-TTATAATAATATT
1 TAAAATATT-TTATATTTAT-ATTATATT
1569367 TAAAATATTTTATATTTATATTATATT
1 TAAAATATTTTATATTTATATTATATT
1569394 ATGTTATTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
27 19 0.45
28 22 0.52
29 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TAAAATATTTTATATTTATATTATATT
Found at i:1570558 original size:31 final size:31
Alignment explanation
Indices: 1570523--1570586 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1570513 TATAAATATA
1570523 AATTAAAAATTTATTTAAAAATAAAATTAAT
1 AATTAAAAATTTATTTAAAAATAAAATTAAT
*
1570554 AATTAATAATTTATTTAAAAATAAAATTAAT
1 AATTAAAAATTTATTTAAAAATAAAATTAAT
1570585 AA
1 AA
1570587 AATAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
AATTAAAAATTTATTTAAAAATAAAATTAAT
Found at i:1571303 original size:39 final size:39
Alignment explanation
Indices: 1571249--1571332 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
1571239 ATAACTAACG
1571249 AATCTCATCTAAGTTTTTTATTTTTTATTAGTATTGAGT
1 AATCTCATCTAAGTTTTTTATTTTTTATTAGTATTGAGT
1571288 AATCTCATCTAAGTTTTTTATTTTTTATTAGTATTGAGT
1 AATCTCATCTAAGTTTTTTATTTTTTATTAGTATTGAGT
1571327 AATCTC
1 AATCTC
1571333 CATTCGACTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (39 bp):
AATCTCATCTAAGTTTTTTATTTTTTATTAGTATTGAGT
Found at i:1573220 original size:12 final size:12
Alignment explanation
Indices: 1573203--1573227 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1573193 AATCAAGCAG
1573203 ATTTTATGATAA
1 ATTTTATGATAA
1573215 ATTTTATGATAA
1 ATTTTATGATAA
1573227 A
1 A
1573228 AGATGTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATTTTATGATAA
Found at i:1577309 original size:38 final size:39
Alignment explanation
Indices: 1577266--1577339 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
1577256 AAAGATGATT
*
1577266 AAATAATATAAAAATAATTAAAATATA-ATAAAAATAAA
1 AAATAATATAAAAATAATGAAAATATATATAAAAATAAA
* * * *
1577304 AAATAATTTGAATATAATGAAAATATATATTAAAAT
1 AAATAATATAAAAATAATGAAAATATATATAAAAAT
1577340 TATTATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 23 0.77
39 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (39 bp):
AAATAATATAAAAATAATGAAAATATATATAAAAATAAA
Found at i:1577310 original size:27 final size:28
Alignment explanation
Indices: 1577265--1577330 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
1577255 TAAAGATGAT
1577265 TAAATAATATAAAAATAATTAAAATATAA
1 TAAA-AATATAAAAATAATTAAAATATAA
**
1577294 TAAAAATA-AAAAATAATTTGAATATAA
1 TAAAAATATAAAAATAATTAAAATATAA
*
1577321 TGAAAATATA
1 TAAAAATATA
1577331 TATTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 24 0.73
28 5 0.15
29 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (28 bp):
TAAAAATATAAAAATAATTAAAATATAA
Found at i:1577945 original size:2 final size:2
Alignment explanation
Indices: 1577938--1577981 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1577928 TCCTTATCAC
1577938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1577980 AT
1 AT
1577982 TTCAAAGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1578098 original size:2 final size:2
Alignment explanation
Indices: 1578091--1578124 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1578081 ATTCATATTC
1578091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1578125 TTCAAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1578129 original size:143 final size:143
Alignment explanation
Indices: 1577948--1578259 Score: 597
Period size: 143 Copynumber: 2.2 Consensus size: 143
1577938 ATATATATAT
1577948 ATATATATATATATATATATATATATATATATATTTCAAAGCAAAGAAAGTTAATGATTTAACAT
1 ATATATATATATATATATATATATATATATATATTTCAAAGCAAAGAAAGTTAATGATTTAACAT
*
1578013 TAAAATTAACAAATTAAGCATTTCTATGTTTTTTTGGTTTATTTGTTATAGTTTACATATGTTTC
66 TAAAATTAACAAATTAAGCATTTCTATGTTTTTTTGGTTTATTTGTAATAGTTTACATATGTTTC
1578078 AAGATTCATATTC
131 AAGATTCATATTC
1578091 ATATATATATATATATATATATATATATATATATTTCAAAGCAAAGAAAGTTAATGATTTAACAT
1 ATATATATATATATATATATATATATATATATATTTCAAAGCAAAGAAAGTTAATGATTTAACAT
*
1578156 TAAAATTAACAAATTAAGCATTTCTATGTTTTTTTGGTTTATTTGTAATAGTTTACGTATGTTTC
66 TAAAATTAACAAATTAAGCATTTCTATGTTTTTTTGGTTTATTTGTAATAGTTTACATATGTTTC
1578221 AAGATTCATATTC
131 AAGATTCATATTC
*
1578234 ATATATATATATATATATATACATAT
1 ATATATATATATATATATATATATAT
1578260 GAAAATTGAT
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 166 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (143 bp):
ATATATATATATATATATATATATATATATATATTTCAAAGCAAAGAAAGTTAATGATTTAACAT
TAAAATTAACAAATTAAGCATTTCTATGTTTTTTTGGTTTATTTGTAATAGTTTACATATGTTTC
AAGATTCATATTC
Found at i:1578394 original size:13 final size:13
Alignment explanation
Indices: 1578378--1578402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1578368 AATTAATTAA
1578378 TATATTATATATT
1 TATATTATATATT
1578391 TATATTATATAT
1 TATATTATATAT
1578403 GAGAGTGATT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTATATATT
Found at i:1578734 original size:27 final size:25
Alignment explanation
Indices: 1578694--1578749 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1578684 ATTTTATAAA
*
1578694 AAAATCTTATATTTTAATTTTATTTAT-
1 AAAATCTTA-AATTT-A-TTTATTTATG
*
1578721 AAAATTTTAAATTTATTTATTTATG
1 AAAATCTTAAATTTATTTATTTATG
1578746 AAAA
1 AAAA
1578750 AGTGTAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.35
25 5 0.19
26 4 0.15
27 8 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
AAAATCTTAAATTTATTTATTTATG
Found at i:1578887 original size:5 final size:5
Alignment explanation
Indices: 1578877--1578956 Score: 53
Period size: 5 Copynumber: 16.2 Consensus size: 5
1578867 TTTAAAATGT
* * *
1578877 ATATA ATATA A-ATT ATATT ATATTA AAATTA ATATAA ATATA AT-T-
1 ATATA ATATA ATATA ATATA ATA-TA ATA-TA ATAT-A ATATA ATATA
*
1578922 ATAATA ATATA ATAAA ATAT- ATA-A ATATA ATATA A
1 AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA A
1578957 AATTTATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
3 2 0.03
4 10 0.16
5 34 0.56
6 15 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1578905 original size:16 final size:16
Alignment explanation
Indices: 1578868--1578945 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 16
1578858 AAATATATTT
1578868 TTAAAATGTATATAATA
1 TTAAAAT-TATATAATA
*
1578885 -T-AAATTATATTATA
1 TTAAAATTATATAATA
1578899 TTAAAATTAATATAA-A
1 TTAAAATT-ATATAATA
*
1578915 -TATAATTATAATAATA
1 TTAAAATTAT-ATAATA
1578931 TAATAAAA-TATATAA
1 T--TAAAATTATATAA
1578946 ATATAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 10 0.20
15 15 0.31
16 8 0.16
17 9 0.18
18 3 0.06
19 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAAAATTATATAATA
Found at i:1578912 original size:31 final size:29
Alignment explanation
Indices: 1578851--1578924 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 29
1578841 ATTATATAAA
1578851 ATAATATAAA-TATATTTTTAAAATGTAT
1 ATAATATAAATTATATTTTTAAAATGTAT
1578879 ATAATATAAATTATATTATATTAAAAT-TAAT
1 ATAATATAAATTATATT-T-TTAAAATGT-AT
1578910 ATAA-ATATAATTATA
1 ATAATATA-AATTATA
1578925 ATAATATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
28 10 0.24
29 6 0.15
30 5 0.12
31 20 0.49
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
ATAATATAAATTATATTTTTAAAATGTAT
Found at i:1578922 original size:26 final size:25
Alignment explanation
Indices: 1578837--1578942 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 25
1578827 TATTATTAAT
1578837 TATAATTATA-TAAAATAATATAAA
1 TATAATTATATTAAAATAATATAAA
*
1578861 TAT-ATT-T-TTAAAATGTATATAATA
1 TATAATTATATTAAAAT-AATATAA-A
1578885 TAAATTATATTATATTAAAATTAATATAAA
1 T--A-TA-ATTATATTAAAA-TAATATAAA
* *
1578915 TATAATTATAATAATATAATA-AAA
1 TATAATTATATTAAAATAATATAAA
1578939 TATA
1 TATA
1578943 TAAATATAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
22 7 0.10
23 9 0.13
24 12 0.18
25 5 0.07
26 11 0.16
27 3 0.04
28 1 0.01
29 3 0.04
30 3 0.04
31 12 0.18
32 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (25 bp):
TATAATTATATTAAAATAATATAAA
Found at i:1578943 original size:26 final size:27
Alignment explanation
Indices: 1578837--1578953 Score: 102
Period size: 26 Copynumber: 4.5 Consensus size: 27
1578827 TATTATTAAT
1578837 TATAATTAT-ATAAAATAATATAAATA
1 TATAATTATAATAAAATAATATAAATA
** * * *
1578863 TATTTTTAAAATGTATATAATATAAAT-
1 TATAATTATAAT-AAAATAATATAAATA
*
1578890 TAT-ATTATATTAAAATTAATAT-AA-A
1 TATAATTATAATAAAA-TAATATAAATA
*
1578915 TATAATTATAATAATATAATA-AAATA
1 TATAATTATAATAAAATAATATAAATA
*
1578941 TATAAATATAATA
1 TATAATTATAATA
1578954 TAAAATTTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
25 14 0.20
26 40 0.56
27 5 0.07
28 12 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
TATAATTATAATAAAATAATATAAATA
Found at i:1578958 original size:54 final size:52
Alignment explanation
Indices: 1578844--1578960 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 52
1578834 AATTATAATT
* * * * *
1578844 ATATAAAA-TAATATAAATATATTTTTAAAATGTATATAATATAAATTATATT
1 ATATAAAATTAATATAAATATAATTATAAAATATATAAAATATAAA-TATATA
1578896 ATATTAAAATTAATATAAATATAATTATAATAATATAATAAAATATATAA-ATATA
1 ATA-TAAAATTAATATAAATATAATTATAA-AATAT-ATAAAATATA-AATATATA
1578951 ATATAAAATT
1 ATATAAAATT
1578961 TATAAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
52 3 0.05
53 5 0.09
54 25 0.45
55 11 0.20
56 9 0.16
57 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (52 bp):
ATATAAAATTAATATAAATATAATTATAAAATATATAAAATATAAATATATA
Found at i:1578965 original size:32 final size:34
Alignment explanation
Indices: 1578877--1578970 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 34
1578867 TTTAAAATGT
*
1578877 ATATAATATAAATTATATTATATTAAAATTAATATAA
1 ATATAATATAAA--AT-TTATAATAAAATTAATATAA
1578914 ATATAATTATAATAA--TATAATAAAA-T-ATATAA
1 ATATAA-TATAA-AATTTATAATAAAATTAATATAA
*
1578946 ATATAATATAAAATTTATAAAAAAA
1 ATATAATATAAAATTTATAATAAAA
1578971 CCAAAAGAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
30 2 0.04
31 5 0.10
32 21 0.41
33 1 0.02
34 9 0.18
37 7 0.14
38 5 0.10
39 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
ATATAATATAAAATTTATAATAAAATTAATATAA
Found at i:1579203 original size:5 final size:5
Alignment explanation
Indices: 1579182--1579221 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
1579172 AACATATATT
*
1579182 TAATA -AATA TAAAA TAATA TAATA -AATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
1579222 TTAAATTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
TAATA
Found at i:1579206 original size:19 final size:19
Alignment explanation
Indices: 1579182--1579227 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1579172 AACATATATT
1579182 TAATAAATATAAAATAATA
1 TAATAAATATAAAATAATA
*
1579201 TAATAAATATAATATAATA
1 TAATAAATATAAAATAATA
*
1579220 TATTAAAT
1 TAATAAAT
1579228 TAAGATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATAAATATAAAATAATA
Found at i:1579212 original size:14 final size:13
Alignment explanation
Indices: 1579190--1579219 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1579180 TTTAATAAAT
1579190 ATAAAATAATATA
1 ATAAAATAATATA
1579203 ATAAATATAATATA
1 ATAAA-ATAATATA
1579217 ATA
1 ATA
1579220 TATTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAAATAATATA
Found at i:1579237 original size:19 final size:19
Alignment explanation
Indices: 1579182--1579233 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1579172 AACATATATT
*
1579182 TAATAAATATAAAATAATA
1 TAATAAATATAAGATAATA
*
1579201 TAATAAATATAATATAATA
1 TAATAAATATAAGATAATA
*
1579220 TATTAAAT-TAAGAT
1 TAATAAATATAAGAT
1579234 TAATGCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAATAAATATAAGATAATA
Found at i:1580099 original size:28 final size:28
Alignment explanation
Indices: 1580068--1580121 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1580058 TCGAATTGAG
*
1580068 TTATAATTTTA-AAAATATTTTAATTTTT
1 TTATAA-TTTACAAAATAATTTAATTTTT
* *
1580096 TTATTATTTACATAATAATTTAATTT
1 TTATAATTTACAAAATAATTTAATTT
1580122 AAATTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATAATTTACAAAATAATTTAATTTTT
Found at i:1581822 original size:9 final size:9
Alignment explanation
Indices: 1581805--1581838 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1581795 TATTTGATAT
1581805 AAATATTTA
1 AAATATTTA
*
1581814 AAATTTTTA
1 AAATATTTA
*
1581823 ATATATTTA
1 AAATATTTA
1581832 AAATATT
1 AAATATT
1581839 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AAATATTTA
Found at i:1581938 original size:44 final size:44
Alignment explanation
Indices: 1581888--1581982 Score: 181
Period size: 44 Copynumber: 2.1 Consensus size: 44
1581878 ATTTAAAAAT
1581888 ATTTCAAATAACCTAACTTAAAACATGTATAAAATCCAACATAA
1 ATTTCAAATAACCTAACTTAAAACATGTATAAAATCCAACATAA
1581932 ATTTCAAATAACCTAACTTAAAACATGTATAAAATCCAACATAA
1 ATTTCAAATAACCTAACTTAAAACATGTATAAAATCCAACATAA
1581976 ATATTCA
1 AT-TTCA
1581983 TTGAAAAGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 46 0.92
45 4 0.08
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.28
Consensus pattern (44 bp):
ATTTCAAATAACCTAACTTAAAACATGTATAAAATCCAACATAA
Found at i:1582236 original size:8 final size:8
Alignment explanation
Indices: 1582218--1582266 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
1582208 TTCGAATATT
1582218 TATTT-TA
1 TATTTATA
1582225 TATTTATA
1 TATTTATA
*
1582233 TATTTTAAA
1 TA-TTTATA
*
1582242 TATTTAAA
1 TATTTATA
1582250 TA-TTATA
1 TATTTATA
1582257 TATTTATA
1 TATTTATA
1582265 TA
1 TA
1582267 AATATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
7 11 0.30
8 19 0.51
9 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTATA
Found at i:1582238 original size:15 final size:15
Alignment explanation
Indices: 1582218--1582266 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1582208 TTCGAATATT
1582218 TATTTTATATTTATA
1 TATTTTATATTTATA
*
1582233 TATTTTAAATATTTAAA
1 TATTTT--ATATTTATA
*
1582250 TATTATATATTTATA
1 TATTTTATATTTATA
1582265 TA
1 TA
1582267 AATATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 16 0.55
17 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTATATTTATA
Found at i:1582716 original size:20 final size:21
Alignment explanation
Indices: 1582671--1582717 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1582661 TTAATATTTT
* *
1582671 TTTAA-AATATTTTTTAAATA
1 TTTAATAATATTTTTAAAAAA
*
1582691 TATAATAATA-TTTTAAAAAA
1 TTTAATAATATTTTTAAAAAA
1582711 TTTAATA
1 TTTAATA
1582718 TTTTTATATC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAATAATATTTTTAAAAAA
Found at i:1584710 original size:15 final size:15
Alignment explanation
Indices: 1584690--1584725 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1584680 TAAGTTTAAT
*
1584690 ATTTAAATTAATAAA
1 ATTTAAATCAATAAA
*
1584705 ATTTAAATCAATTAA
1 ATTTAAATCAATAAA
1584720 ATTTAA
1 ATTTAA
1584726 TACTCAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAAATCAATAAA
Found at i:1586348 original size:21 final size:22
Alignment explanation
Indices: 1586306--1586383 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1586296 ATGTAAATTA
*
1586306 TTTATAAATTAAATTATTTATT
1 TTTATAAATTAAATTATATATT
*
1586328 TTTATAATTTAAATT-TATATT
1 TTTATAAATTAAATTATATATT
* *
1586349 TTTATCTAATAAAATGATATATATT
1 TTTAT-AAATTAAAT--TATATATT
1586374 TTTA-AAATTA
1 TTTATAAATTA
1586384 TTTTTAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 10 0.22
22 20 0.44
23 4 0.09
24 1 0.02
25 10 0.22
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (22 bp):
TTTATAAATTAAATTATATATT
Found at i:1586427 original size:37 final size:35
Alignment explanation
Indices: 1586356--1586437 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
1586346 ATTTTTATCT
1586356 AATAAAATGATATATATTTTTAAAATTATTTTTAAAA
1 AATAAAAT-ATATATATTTTTAAAATTATTTTT-AAA
*
1586393 AATAAAATATATAATAATTTTT-TAATT-TTATTTAAA
1 AATAAAATATAT-AT-ATTTTTAAAATTATT-TTTAAA
*
1586429 ATTAAAATA
1 AATAAAATA
1586438 AAATTACAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 17 0.43
37 17 0.43
38 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (35 bp):
AATAAAATATATATATTTTTAAAATTATTTTTAAA
Found at i:1593990 original size:18 final size:18
Alignment explanation
Indices: 1593964--1594005 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1593954 GCAGTTCCCA
*
1593964 ACTTACTTAATCTTAATT
1 ACTTCCTTAATCTTAATT
1593982 ACTTCCTTAATCTTAATT
1 ACTTCCTTAATCTTAATT
1594000 ACTTCC
1 ACTTCC
1594006 ATTGTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.48
Consensus pattern (18 bp):
ACTTCCTTAATCTTAATT
Found at i:1596820 original size:23 final size:25
Alignment explanation
Indices: 1596781--1596830 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
1596771 ATTCTATTTT
*
1596781 TTTTAATATTAAATATTAAATTTAG
1 TTTTAATATTAAATATTAAATATAG
1596806 TTTTAA-A-TAAATATTAAATATAG
1 TTTTAATATTAAATATTAAATATAG
1596829 TT
1 TT
1596831 AATAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 1 0.04
25 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TTTTAATATTAAATATTAAATATAG
Found at i:1596841 original size:23 final size:23
Alignment explanation
Indices: 1596783--1596841 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1596773 TCTATTTTTT
*
1596783 TTAAT-ATTAAATATTAAATTTAG
1 TTAATAATT-AATATTAAATATAG
* *
1596806 TT-TTAAATAAATATTAAATATAG
1 TTAAT-AATTAATATTAAATATAG
1596829 TTAATAATTAATA
1 TTAATAATTAATA
1596842 AAGATATGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.04
23 24 0.86
24 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
TTAATAATTAATATTAAATATAG
Found at i:1597871 original size:21 final size:21
Alignment explanation
Indices: 1597847--1597888 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1597837 ATAATATTTT
1597847 TATATAAAT-TTAATTATAAAA
1 TATATAAATATTAA-TATAAAA
1597868 TATATAAATATTAATATAAAA
1 TATATAAATATTAATATAAAA
1597889 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:1597891 original size:35 final size:34
Alignment explanation
Indices: 1597826--1597891 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
1597816 GAATCATTAT
** *
1597826 TTATAAAATACATAATATTTTTATATAAATTTAA
1 TTATAAAATACATAATATTAATATAAAAATTTAA
*
1597860 TTATAAAATATATAAATATTAATATAAAAATT
1 TTATAAAATACAT-AATATTAATATAAAAATT
1597892 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 12 0.44
35 15 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (34 bp):
TTATAAAATACATAATATTAATATAAAAATTTAA
Found at i:1598880 original size:2 final size:2
Alignment explanation
Indices: 1598873--1598908 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1598863 GATTGTCAAC
1598873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1598909 TGATAAGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1600403 original size:32 final size:33
Alignment explanation
Indices: 1600353--1600414 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1600343 TATGAACATA
* *
1600353 AAAATAATTC-GAATTTAAAATAAATTAAACTT
1 AAAATAATTCAAAATTAAAAATAAATTAAACTT
* *
1600385 AAAATAATTTAAAATTAAAAATAATTTAAA
1 AAAATAATTCAAAATTAAAAATAAATTAAA
1600415 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 9 0.36
33 16 0.64
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (33 bp):
AAAATAATTCAAAATTAAAAATAAATTAAACTT
Found at i:1600415 original size:16 final size:16
Alignment explanation
Indices: 1600351--1600415 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
1600341 AATATGAACA
**
1600351 TAAAAATAATTCGAAT
1 TAAAAATAATTTAAAT
* *
1600367 TTAAAATAAATTAAACT
1 TAAAAATAATTTAAA-T
1600384 T-AAAATAATTTAAAAT
1 TAAAAATAATTT-AAAT
1600400 TAAAAATAATTTAAAT
1 TAAAAATAATTTAAAT
1600416 ATTTAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 26 0.63
17 15 0.37
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAAAATAATTTAAAT
Found at i:1600523 original size:7 final size:7
Alignment explanation
Indices: 1600511--1600537 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1600501 AATATTTTTT
1600511 AAAAATA
1 AAAAATA
1600518 AAAAATA
1 AAAAATA
1600525 AAAAATA
1 AAAAATA
1600532 AAAAAT
1 AAAAAT
1600538 TCGAATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:1601127 original size:14 final size:15
Alignment explanation
Indices: 1601104--1601134 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1601094 TTATTCATAT
1601104 TATTATATTATATAA
1 TATTATATTATATAA
1601119 TATTA-ATTATATAA
1 TATTATATTATATAA
1601133 TA
1 TA
1601135 AGATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATATTATATAA
Found at i:1601449 original size:12 final size:12
Alignment explanation
Indices: 1601419--1601457 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1601409 TTCTTAATTG
*
1601419 AAAAAACAAAAA
1 AAAAAAGAAAAA
1601431 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1601443 AAAAAAGAAATAA
1 AAAAAAGAAA-AA
1601456 AA
1 AA
1601458 CCATTGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.90, C:0.03, G:0.05, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:1605996 original size:13 final size:14
Alignment explanation
Indices: 1605976--1606029 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
1605966 ATATATACGG
1605976 ATATATTTTATAAAA
1 ATATA-TTTATAAAA
*
1605991 ATAT-TTTTTAAAA
1 ATATATTTATAAAA
1606004 TATATATTTA-AAAA
1 -ATATATTTATAAAA
1606018 AGTATATTTATA
1 A-TATATTTATA
1606030 TATTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 9 0.27
14 16 0.48
15 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATATTTATAAAA
Found at i:1606387 original size:14 final size:14
Alignment explanation
Indices: 1606368--1606401 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1606358 TACTTTACTA
*
1606368 ATATATGTGTGTGT
1 ATATATGTGTGTAT
1606382 ATATATGTGTGTAT
1 ATATATGTGTGTAT
1606396 ATATAT
1 ATATAT
1606402 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
ATATATGTGTGTAT
Found at i:1606390 original size:12 final size:12
Alignment explanation
Indices: 1606369--1606399 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1606359 ACTTTACTAA
*
1606369 TATATGTGTGTG
1 TATATATGTGTG
1606381 TATATATGTGTG
1 TATATATGTGTG
1606393 TATATAT
1 TATATAT
1606400 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (12 bp):
TATATATGTGTG
Found at i:1606904 original size:14 final size:15
Alignment explanation
Indices: 1606883--1606923 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
1606873 TTTTAATTTC
1606883 AAATATATTTTATT-
1 AAATATATTTTATTA
*
1606897 AGATATATTTTATTA
1 AAATATATTTTATTA
1606912 AAATATATTTTA
1 AAATATATTTTA
1606924 ACTATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
AAATATATTTTATTA
Found at i:1607075 original size:27 final size:27
Alignment explanation
Indices: 1607045--1607097 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1607035 ATTTAAACTG
1607045 ATTAAATAAAATTTAATTAATTTTTTA
1 ATTAAATAAAATTTAATTAATTTTTTA
* * *
1607072 ATTAAATCAATTTTAATTGATTTTTT
1 ATTAAATAAAATTTAATTAATTTTTT
1607098 CTTCCCTACT
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:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTAAATAAAATTTAATTAATTTTTTA
Found at i:1607253 original size:19 final size:19
Alignment explanation
Indices: 1607222--1607259 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1607212 TTTTAAAATT
*
1607222 TTTATATAATTAATTAAAA
1 TTTATATAATTAAATAAAA
1607241 TTTA-ATAATTTAAATAAAA
1 TTTATATAA-TTAAATAAAA
1607260 AATTAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTATATAATTAAATAAAA
Found at i:1607350 original size:9 final size:8
Alignment explanation
Indices: 1607313--1607380 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
1607303 TAAAACTAAA
1607313 TTTATTATT
1 TTTA-TATT
1607322 TTTATATT
1 TTTATATT
*
1607330 TTTAAATT
1 TTTATATT
1607338 TTTATTATT
1 TTTA-TATT
* *
1607347 TTTAAATA
1 TTTATATT
*
1607355 TATATATT
1 TTTATATT
1607363 TTTA-ATT
1 TTTATATT
**
1607370 TAAATATT
1 TTTATATT
1607378 TTT
1 TTT
1607381 TATCAAAATT
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
7 5 0.11
8 29 0.64
9 11 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTATATT
Found at i:1607351 original size:17 final size:16
Alignment explanation
Indices: 1607319--1607380 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
1607309 TAAATTTATT
1607319 ATTTTTATATTTTTAA
1 ATTTTTATATTTTTAA
1607335 ATTTTTATTATTTTTAA
1 ATTTTTA-TATTTTTAA
* *
1607352 ATATATATATTTTT-A
1 ATTTTTATATTTTTAA
**
1607367 ATTTAAATATTTTT
1 ATTTTTATATTTTT
1607381 TATCAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
15 13 0.32
16 14 0.34
17 14 0.34
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTATATTTTTAA
Found at i:1607363 original size:25 final size:25
Alignment explanation
Indices: 1607313--1607366 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1607303 TAAAACTAAA
* * *
1607313 TTTATTATTTTTATATTTTTAAATT
1 TTTATTATTTTTAAATATATAAATT
*
1607338 TTTATTATTTTTAAATATATATATT
1 TTTATTATTTTTAAATATATAAATT
1607363 TTTA
1 TTTA
1607367 ATTTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTATTATTTTTAAATATATAAATT
Found at i:1608563 original size:22 final size:21
Alignment explanation
Indices: 1608521--1608579 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1608511 AAATATTAAA
1608521 AAATATTTTTTATTAATATTT
1 AAATATTTTTTATTAATATTT
*
1608542 ATATATTTTTATAATTAA-ATTT
1 AAATATTTTT-T-ATTAATATTT
1608564 AAATATTATTTT-TTAA
1 AAATATT-TTTTATTAA
1608580 AAGTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 9 0.27
22 12 0.36
23 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATATTTTTTATTAATATTT
Found at i:1608627 original size:3 final size:3
Alignment explanation
Indices: 1608619--1608654 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1608609 TTTTCAGTTA
*
1608619 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1608655 TACATTTCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1609181 original size:32 final size:34
Alignment explanation
Indices: 1609118--1609186 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
1609108 ATTAATTTTA
1609118 ATAAATATATTAATATATTAAAATTTATAT-AAT
1 ATAAATATATTAATATATTAAAATTTATATAAAT
* *
1609151 ATAAA-ATATTGATATA-TAAAATTTTTTATAAAT
1 ATAAATATATTAATATATTAAAA-TTTATATAAAT
1609184 ATA
1 ATA
1609187 TAAAATAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 5 0.16
32 16 0.50
33 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
ATAAATATATTAATATATTAAAATTTATATAAAT
Found at i:1609770 original size:21 final size:20
Alignment explanation
Indices: 1609733--1609774 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1609723 ATTTGATTCT
*
1609733 AATAGATTTTTAAAATTTAAA
1 AATAGA-TTTTAAAAATTAAA
1609754 AATA-ATTTTAAATAATTAAA
1 AATAGATTTTAAA-AATTAAA
1609774 A
1 A
1609775 TTATATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATAGATTTTAAAAATTAAA
Found at i:1610238 original size:18 final size:18
Alignment explanation
Indices: 1610213--1610247 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1610203 TAATATTAGT
1610213 ATAAATTAAA-TTATATG
1 ATAAATTAAATTTATATG
1610230 ATAATATTAAATTTATAT
1 ATAA-ATTAAATTTATAT
1610248 TTATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATAAATTAAATTTATATG
Found at i:1610343 original size:17 final size:17
Alignment explanation
Indices: 1610321--1610374 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1610311 TAAAAAATAT
1610321 ATTTTTATTAATTTTTA
1 ATTTTTATTAATTTTTA
**
1610338 ATTTTTTATTAA-AGTTA
1 A-TTTTTATTAATTTTTA
*
1610355 TATTTTTATTAATTTATA
1 -ATTTTTATTAATTTTTA
1610373 AT
1 AT
1610375 ATGTCTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTATTAATTTTTA
Found at i:1610629 original size:122 final size:121
Alignment explanation
Indices: 1610409--1610631 Score: 324
Period size: 122 Copynumber: 1.8 Consensus size: 121
1610399 ATAGGGTGTT
* * *
1610409 TAAATTTAAAATTAGATATTTTGGAGAGAAGATGGAGGATTTTAGATCGTAGAGAGAGAATGAAA
1 TAAATTTAAAATTAGATATTTTAGAGAGAAGATGAAGGATTTTAGATCGTAGAGAGAGAATAAAA
*
1610474 ATTTGAAAAATAAAAAATTTAAAGTATTGTAAGAGTGGGGTCGAATTTATAGATGTC
66 ATTTGAAAAATAAAAAATTTAAAG-ATTATAAGAGTGGGGTCGAATTTATAGATGTC
* * *
1610531 TAAATTTAAAATTAGATATTTTAGAGAGACGATGAAGGATTTTA-AGTTGTAGAGAGAGAGTAAA
1 TAAATTTAAAATTAGATATTTTAGAGAGAAGATGAAGGATTTTAGA-TCGTAGAGAGAGAATAAA
*
1610595 AATTTTAAAAATAAAAAATATATAAAG-TTATAAGAGT
65 AATTTGAAAAATAAAAAAT-T-TAAAGATTATAAGAGT
1610632 AAGGTAGGAT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
121 1 0.01
122 83 0.92
123 1 0.01
124 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (121 bp):
TAAATTTAAAATTAGATATTTTAGAGAGAAGATGAAGGATTTTAGATCGTAGAGAGAGAATAAAA
ATTTGAAAAATAAAAAATTTAAAGATTATAAGAGTGGGGTCGAATTTATAGATGTC
Found at i:1618463 original size:2 final size:2
Alignment explanation
Indices: 1618456--1618493 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1618446 AAAATATCAG
* *
1618456 TA TA TA TA TA TA CA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1618494 AAAATTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1618778 original size:13 final size:14
Alignment explanation
Indices: 1618754--1618782 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1618744 AATAAATTTA
1618754 TAAATATTTAAATT
1 TAAATATTTAAATT
1618768 TAAAT-TTTAAATT
1 TAAATATTTAAATT
1618781 TA
1 TA
1618783 TCAAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATATTTAAATT
Found at i:1618793 original size:16 final size:15
Alignment explanation
Indices: 1618746--1618798 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
1618736 AAACACAAAA
1618746 TAAATTTATAAATATT
1 TAAATTTATAAATA-T
*
1618762 TAAA-TT-TAAATTT
1 TAAATTTATAAATAT
1618775 TAAATTTATCAAATAT
1 TAAATTTAT-AAATAT
*
1618791 TAACTTTA
1 TAAATTTA
1618799 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 3 0.10
16 16 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATTTATAAATAT
Found at i:1620255 original size:13 final size:13
Alignment explanation
Indices: 1620237--1620262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1620227 CTTTTTAAAT
1620237 TATTTATGTTTAA
1 TATTTATGTTTAA
1620250 TATTTATGTTTAA
1 TATTTATGTTTAA
1620263 GTATATTAAA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTATGTTTAA
Found at i:1620303 original size:17 final size:17
Alignment explanation
Indices: 1620281--1620314 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1620271 AAATATTAAC
*
1620281 ATATTTGTATTAAATAT
1 ATATTTATATTAAATAT
*
1620298 ATATTTATATTTAATAT
1 ATATTTATATTAAATAT
1620315 TCATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATTTATATTAAATAT
Found at i:1621641 original size:13 final size:13
Alignment explanation
Indices: 1621623--1621648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1621613 AATATTTATA
1621623 AAATATAAATATT
1 AAATATAAATATT
1621636 AAATATAAATATT
1 AAATATAAATATT
1621649 TTTTTAAAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:1622395 original size:22 final size:22
Alignment explanation
Indices: 1622371--1622413 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1622361 AAAATCAGAA
*
1622371 AAAAAATT-TTAATATAAAAAT
1 AAAAAATTATAAATATAAAAAT
1622392 AAAAAATTATAAATATAAAAAT
1 AAAAAATTATAAATATAAAAAT
1622414 TCGAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAATTATAAATATAAAAAT
Found at i:1622748 original size:3 final size:3
Alignment explanation
Indices: 1622742--1622782 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1622732 AACGATGATG
1622742 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1622783 CTGCGGGTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1622993 original size:17 final size:19
Alignment explanation
Indices: 1622968--1623016 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
1622958 AATTAATAAA
*
1622968 AATAAATTTATA-AATT-T
1 AATATATTTATATAATTAT
1622985 AATATATTTATATAATTAT
1 AATATATTTATATAATTAT
* *
1623004 ATTTTATTTATAT
1 AATATATTTATAT
1623017 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 11 0.41
18 4 0.15
19 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATATTTATATAATTAT
Found at i:1623016 original size:27 final size:28
Alignment explanation
Indices: 1622941--1623043 Score: 73
Period size: 29 Copynumber: 3.5 Consensus size: 28
1622931 TTATATTTTA
* * *
1622941 TATATTTTATTTATTTTAATTAATAAAAA
1 TATATTTTATTTATATTATTTAA-AAAAT
* * *
1622970 TAAATTTATAAATTTA-ATATATTTATATAAT
1 TATATTT-T--ATTTATAT-TATTTAAAAAAT
*
1623001 TATATTTTATTTATATTTTTTTAAAAAAT
1 TATATTTTATTTATA-TTATTTAAAAAAT
*
1623030 TATTTTTTATTTAT
1 TATATTTTATTTAT
1623044 GTAGTTACGT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 5 0.09
29 29 0.51
30 3 0.05
31 10 0.18
32 10 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATATTTTATTTATATTATTTAAAAAAT
Found at i:1624241 original size:23 final size:25
Alignment explanation
Indices: 1624204--1624257 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
1624194 TTTTAATATA
1624204 TTTTTATATTAATATCATA-TTTAT
1 TTTTTATATTAATATCATATTTTAT
1624228 TTTTTATATT-ATATCATATTTTAT
1 TTTTTATATTAATATCATATTTTAT
1624252 TATTTT
1 T-TTTT
1624258 TAATTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
25 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTATATTAATATCATATTTTAT
Found at i:1625699 original size:19 final size:19
Alignment explanation
Indices: 1625667--1625708 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1625657 AAGGTAAGTT
1625667 ATTTATTTAGTTAAA-TAA
1 ATTTATTTAGTTAAATTAA
*
1625685 ATTTAATTTATTTAAATTAA
1 ATTT-ATTTAGTTAAATTAA
1625705 ATTT
1 ATTT
1625709 TAGATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 10 0.48
20 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTATTTAGTTAAATTAA
Found at i:1625702 original size:15 final size:15
Alignment explanation
Indices: 1625682--1625784 Score: 54
Period size: 15 Copynumber: 6.7 Consensus size: 15
1625672 TTTAGTTAAA
1625682 TAAATTTAATTTATT
1 TAAATTTAATTTATT
* *
1625697 TAAATTAAATTTTAGAT
1 TAAATTTAA-TTTA-TT
* * *
1625714 AAAATTTTTATTAATT
1 TAAA-TTTAATTTATT
1625730 TAAA-TTAATTTAATT
1 TAAATTTAATTT-ATT
1625745 TAAA-TTAA--TATT
1 TAAATTTAATTTATT
*
1625757 TAGTAATTAAATTT-TT
1 TA--AATTTAATTTATT
1625773 TAAAATTTAATT
1 T-AAATTTAATT
1625785 ATAAATTATA
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
12 5 0.08
13 1 0.02
14 7 0.11
15 30 0.45
16 11 0.17
17 9 0.14
18 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TAAATTTAATTTATT
Found at i:1626084 original size:32 final size:31
Alignment explanation
Indices: 1625999--1626084 Score: 77
Period size: 32 Copynumber: 2.8 Consensus size: 31
1625989 GTATTTAATG
* *
1625999 TATTAT-ATATTTAAATTTATTTTGATACAT
1 TATTATCATATTTATATTCATTTTGATACAT
* ** *
1626029 TAATATTCATA-TTATATAGATTTTGATAATAT
1 TATTA-TCATATTTATATTCATTTTGAT-ACAT
*
1626061 TCTTATCATATTTATATTCATTTT
1 TATTATCATATTTATATTCATTTT
1626085 TATATCATGT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
30 4 0.09
31 19 0.44
32 20 0.47
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (31 bp):
TATTATCATATTTATATTCATTTTGATACAT
Found at i:1626124 original size:38 final size:39
Alignment explanation
Indices: 1626055--1626128 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
1626045 TAGATTTTGA
*
1626055 TAATATTCTTATCATATTTATATTCATTTTTATATCATG
1 TAATATTCTTATCACATTTATATTCATTTTTATATCATG
* * *
1626094 TAATATTTTTATTACATTT-TATTTATTTTTATATC
1 TAATATTCTTATCACATTTATATTCATTTTTATATC
1626129 GTATAATCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 15 0.48
39 16 0.52
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.61
Consensus pattern (39 bp):
TAATATTCTTATCACATTTATATTCATTTTTATATCATG
Found at i:1626452 original size:23 final size:23
Alignment explanation
Indices: 1626415--1626478 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
1626405 TATTTATATT
** *
1626415 TAATATATTAATAATATATG-AA
1 TAATATATTTTTAATAAATGAAA
*
1626437 TATATATATTTTTAATAAATTAAA
1 TA-ATATATTTTTAATAAATGAAA
*
1626461 TAATATAATTTTAATAAA
1 TAATATATTTTTAATAAA
1626479 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 2 0.06
23 29 0.83
24 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATATATTTTTAATAAATGAAA
Found at i:1626519 original size:26 final size:25
Alignment explanation
Indices: 1626481--1626542 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1626471 TTAATAAAAA
* *
1626481 TTTTAAAATAAATATAAATAATTTTAT
1 TTTTAATA-AAATA-AAATAATTTAAT
* *
1626508 TTTTAATAAAATAATATTATTTAAT
1 TTTTAATAAAATAAAATAATTTAAT
1626533 TTATTAATAA
1 TT-TTAATAA
1626543 TATGTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 11 0.37
26 12 0.40
27 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTAATAAAATAAAATAATTTAAT
Found at i:1626521 original size:20 final size:21
Alignment explanation
Indices: 1626491--1626529 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1626481 TTTTAAAATA
*
1626491 AATATAAATAATTTTATTTTT
1 AATATAAATAATATTATTTTT
1626512 AATA-AAATAATATTATTT
1 AATATAAATAATATTATTT
1626530 AATTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATATTATTTTT
Found at i:1626529 original size:25 final size:26
Alignment explanation
Indices: 1626487--1626542 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1626477 AAAATTTTAA
*
1626487 AATAAATATAAATAATTTTATTT-TT
1 AATAAATATAAATAATTTAATTTATT
*
1626512 AATAAA-ATAATATTATTTAATTTATT
1 AATAAATATAA-ATAATTTAATTTATT
1626538 AATAA
1 AATAA
1626543 TATGTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
26 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAAATATAAATAATTTAATTTATT
Found at i:1626560 original size:24 final size:21
Alignment explanation
Indices: 1626517--1626561 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
1626507 TTTTTAATAA
*
1626517 AATAATATTATTTAATTTATT
1 AATAATATTATATAATTTATT
1626538 AATAATATGTATATACATATTATT
1 AATAATAT-TATATA-AT-TTATT
1626562 TATGCATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 2 0.10
24 5 0.25
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AATAATATTATATAATTTATT
Found at i:1626808 original size:7 final size:7
Alignment explanation
Indices: 1626796--1626831 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
1626786 TGTTTGATTT
1626796 ATTTAAA
1 ATTTAAA
1626803 ATTTAAA
1 ATTTAAA
1626810 ATTTAAA
1 ATTTAAA
1626817 ATTTATAA
1 ATTTA-AA
*
1626825 AATTAAA
1 ATTTAAA
1626832 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:1626860 original size:28 final size:27
Alignment explanation
Indices: 1626807--1626862 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
1626797 TTTAAAATTT
* *
1626807 AAAATTTAAAATTTATAAAATTAAATA
1 AAAAATTAAAATTTATAAAATCAAATA
1626834 AAAAATTAAAA-TTATATAAATGCAAATA
1 AAAAATTAAAATTTATA-AAAT-CAAATA
1626862 A
1 A
1626863 GCATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 14 0.56
28 6 0.24
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAATTAAAATTTATAAAATCAAATA
Found at i:1626916 original size:12 final size:12
Alignment explanation
Indices: 1626901--1626947 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1626891 AAATAAATAA
*
1626901 ATTTATTTTTAT
1 ATTTATTTATAT
1626913 ATTTATTTATAT
1 ATTTATTTATAT
*
1626925 A-AT-TTTATAT
1 ATTTATTTATAT
1626935 ATATTATTTATAT
1 AT-TTATTTATAT
1626948 TACATACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
12 13 0.45
13 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTATTTATAT
Found at i:1626945 original size:23 final size:21
Alignment explanation
Indices: 1626905--1626947 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
1626895 AAATAAATTT
1626905 ATTTTTATATTTATTTATATA
1 ATTTTTATATTTATTTATATA
1626926 ATTTTATATATATTATTTATAT
1 ATTTT-TATAT-TTATTTATAT
1626948 TACATACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTATATTTATTTATATA
Found at i:1630662 original size:2 final size:2
Alignment explanation
Indices: 1630655--1630684 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1630645 CAATGCTTTG
1630655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1630685 ATAGTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1631066 original size:21 final size:21
Alignment explanation
Indices: 1631041--1631081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1631031 TATTTAAAAA
*
1631041 ATATTTTTAT-ATTAATATTTT
1 ATATTCTTATAATT-ATATTTT
1631062 ATATTCTTATAATTATATTT
1 ATATTCTTATAATTATATTT
1631082 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTCTTATAATTATATTTT
Found at i:1631208 original size:2 final size:2
Alignment explanation
Indices: 1631201--1631231 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1631191 TTAAGAGAAA
1631201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1631232 ATGACAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1632433 original size:3 final size:3
Alignment explanation
Indices: 1632425--1632451 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1632415 CTTTTTACAA
1632425 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1632452 TTAAATATTT
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:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1633065 original size:18 final size:18
Alignment explanation
Indices: 1633038--1633079 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1633028 TTAACATTTA
*
1633038 TAATAAAAATATAAATAT
1 TAATATAAATATAAATAT
* *
1633056 TAATATAAATATAATTTT
1 TAATATAAATATAAATAT
1633074 TAATAT
1 TAATAT
1633080 TTTAATATAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAAATATAAATAT
Found at i:1633745 original size:29 final size:28
Alignment explanation
Indices: 1633698--1633757 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1633688 GAATTTTTTT
*
1633698 AAAATTTAAATTATTATTTAATAAATAAA
1 AAAATTTAAATTATAATTTAAT-AATAAA
*
1633727 AAAATTTAAATT-TAAATTTAATTATAAA
1 AAAATTTAAATTAT-AATTTAATAATAAA
1633755 AAA
1 AAA
1633758 TATAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATTTAAATTATAATTTAATAATAAA
Found at i:1635819 original size:12 final size:12
Alignment explanation
Indices: 1635802--1635835 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1635792 GAACAATAAT
1635802 AATAAAGAAAAA
1 AATAAAGAAAAA
1635814 AATAAAGAGAAAA
1 AATAAAGA-AAAA
1635827 AA-AAAGAAA
1 AATAAAGAAA
1635836 TATAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 13 0.62
13 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (12 bp):
AATAAAGAAAAA
Found at i:1636541 original size:2 final size:2
Alignment explanation
Indices: 1636528--1636565 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1636518 CCATGGAAGG
*
1636528 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1636566 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1636650 original size:6 final size:6
Alignment explanation
Indices: 1636639--1636689 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
1636629 TTACGATATT
* * * *
1636639 TAAATA TAAATA TAAAATA TAAATA CATATA TATATA TATATA TAAATA
1 TAAATA TAAATA T-AAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1636688 TA
1 TA
1636690 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:1639297 original size:27 final size:25
Alignment explanation
Indices: 1639265--1639339 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 25
1639255 ATCATAATCA
1639265 TATTTAAAATATTATATATTTATAT
1 TATTTAAAATATTATATATTTATAT
*
1639290 TAATTTTAATATATTA-ATATTTTATAT
1 T-A-TTTAAAATATTATATA-TTTATAT
* * *
1639317 TATTTAAATTATAATAAATTTAT
1 TATTTAAAATATTATATATTTAT
1639340 TTACATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 15 0.37
26 7 0.17
27 19 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTAAAATATTATATATTTATAT
Found at i:1639300 original size:25 final size:24
Alignment explanation
Indices: 1639272--1639329 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
1639262 TCATATTTAA
1639272 AATATTATATA-TTTATATTAATTTT
1 AATATTATATATTTTATATT-A-TTT
1639297 AATA-TATTAATATTTTATATTATTT
1 AATATTA-T-ATATTTTATATTATTT
1639322 AA-ATTATA
1 AATATTATA
1639330 ATAAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
23 1 0.03
24 4 0.14
25 12 0.41
26 4 0.14
27 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AATATTATATATTTTATATTATTT
Found at i:1639304 original size:14 final size:14
Alignment explanation
Indices: 1639285--1639360 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
1639275 ATTATATATT
1639285 TATATTAATTTTAA
1 TATATTAATTTTAA
*
1639299 TATATTAATATTTTA
1 TATATTAAT-TTTAA
*
1639314 TATTATTTAAATTATAA
1 TA-TA-TT-AATTTTAA
* *
1639331 TAAATTTA-TTTACA
1 TATATTAATTTTA-A
1639345 TATATTATATTTTAA
1 TATATTA-ATTTTAA
1639360 T
1 T
1639361 TAATTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
13 3 0.06
14 16 0.34
15 11 0.23
16 7 0.15
17 7 0.15
18 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATTAATTTTAA
Found at i:1639313 original size:16 final size:15
Alignment explanation
Indices: 1639267--1639360 Score: 65
Period size: 16 Copynumber: 6.4 Consensus size: 15
1639257 CATAATCATA
*
1639267 TTTAAAATATTATAT
1 TTTAATATATTATAT
*
1639282 ATT--TATATTA-AT
1 TTTAATATATTATAT
1639294 TTTAATATATTAATAT
1 TTTAATATATT-ATAT
*
1639310 TTT-ATATTATTTAAAT
1 TTTAATA-TA-TTATAT
* *
1639326 TATAATAAATT-TA-
1 TTTAATATATTATAT
1639339 TTTACATATATTATAT
1 TTTA-ATATATTATAT
1639355 TTTAAT
1 TTTAAT
1639361 TAATTTTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
12 4 0.07
13 9 0.15
14 13 0.22
15 12 0.20
16 17 0.28
17 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATATATTATAT
Found at i:1639356 original size:19 final size:19
Alignment explanation
Indices: 1639305--1639356 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1639295 TTAATATATT
*
1639305 AATATTTTATA-TTATTTA
1 AATATATTATATTTATTTA
* *
1639323 AATTATAATAAATTTATTTA
1 AA-TATATTATATTTATTTA
*
1639343 CATATATTATATTT
1 AATATATTATATTT
1639357 TAATTAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.08
19 16 0.62
20 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATATTATATTTATTTA
Found at i:1640569 original size:22 final size:21
Alignment explanation
Indices: 1640536--1640586 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1640526 ATTTTTCATC
*
1640536 TTTAATACTTTTAAAGATGATT
1 TTTAAT-CTTTTAAAAATGATT
1640558 TTTAATCTTTTTAAAAATGATT
1 TTTAATC-TTTTAAAAATGATT
*
1640580 ATTAATC
1 TTTAATC
1640587 ATTCTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTAATCTTTTAAAAATGATT
Found at i:1641451 original size:2 final size:2
Alignment explanation
Indices: 1641444--1641478 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1641434 CTTCTTTCTT
1641444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1641479 AAACAGCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1642401 original size:17 final size:18
Alignment explanation
Indices: 1642379--1642426 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1642369 TCATATTCAT
*
1642379 ATTATATATTTTT-ATAG
1 ATTATATATTTTTAAAAG
*
1642396 ATTATAATTATTTTTAAAAT
1 ATTAT-A-TATTTTTAAAAG
1642416 ATTATATATTT
1 ATTATATATTT
1642427 AAATAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 6 0.23
19 8 0.31
20 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTATATATTTTTAAAAG
Found at i:1642945 original size:18 final size:18
Alignment explanation
Indices: 1642922--1642966 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1642912 TTAAAAAAAT
1642922 TAAATTAATATAATTTTA
1 TAAATTAATATAATTTTA
* **
1642940 TAAATTTATATTTTTTTA
1 TAAATTAATATAATTTTA
*
1642958 TAATTTAAT
1 TAAATTAAT
1642967 TTATATAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAAATTAATATAATTTTA
Found at i:1642962 original size:17 final size:17
Alignment explanation
Indices: 1642935--1642968 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1642925 ATTAATATAA
1642935 TTTTATAAATTTATATTT
1 TTTTATAAATTTA-ATTT
1642953 TTTTAT-AATTTAATTT
1 TTTTATAAATTTAATTT
1642969 ATATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATAAATTTAATTT
Found at i:1643341 original size:22 final size:21
Alignment explanation
Indices: 1643303--1643344 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1643293 ATTTTTTATT
1643303 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1643324 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
1643344 T
1 T
1643345 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1644092 original size:15 final size:15
Alignment explanation
Indices: 1644074--1644103 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1644064 ATTTAATAGG
1644074 ATACATCACTAAAAT
1 ATACATCACTAAAAT
1644089 ATACATCACTAAAAT
1 ATACATCACTAAAAT
1644104 GTAAATTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
ATACATCACTAAAAT
Found at i:1645686 original size:14 final size:14
Alignment explanation
Indices: 1645667--1645693 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1645657 ATATTCAAAT
1645667 CATATAATAAAAAC
1 CATATAATAAAAAC
1645681 CATATAATAAAAA
1 CATATAATAAAAA
1645694 AATTAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
CATATAATAAAAAC
Found at i:1646333 original size:38 final size:38
Alignment explanation
Indices: 1646281--1646362 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1646271 ACAAATTGAG
*
1646281 TTTAAACATCTTAATATTTAACTTAAAT-AATTTATAAA
1 TTTAAACATCTTAATATTTAACTTAAATAAAATT-TAAA
* * * *
1646319 TTTAAATATTTTAATTTTTATCTTAAATAAAATTTAAA
1 TTTAAACATCTTAATATTTAACTTAAATAAAATTTAAA
1646357 TTTAAA
1 TTTAAA
1646363 AATAAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 34 0.89
39 4 0.11
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (38 bp):
TTTAAACATCTTAATATTTAACTTAAATAAAATTTAAA
Found at i:1647379 original size:11 final size:11
Alignment explanation
Indices: 1647347--1647381 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1647337 TATATTTAAT
**
1647347 TTTTTAAAATT
1 TTTTTAAAAGA
1647358 TTTTTAAAAGA
1 TTTTTAAAAGA
1647369 TTTTTAAAAGA
1 TTTTTAAAAGA
1647380 TT
1 TT
1647382 ATATCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (11 bp):
TTTTTAAAAGA
Found at i:1650082 original size:22 final size:21
Alignment explanation
Indices: 1650056--1650097 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1650046 ATAATAAAAA
1650056 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1650076 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1650097 A
1 A
1650098 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1650395 original size:20 final size:20
Alignment explanation
Indices: 1650366--1650461 Score: 62
Period size: 20 Copynumber: 4.8 Consensus size: 20
1650356 TATAATTATA
*
1650366 TTTAAAATATTTATATAAAT
1 TTTAATATATTTATATAAAT
1650386 TTTAATATA-TTA-AT-AAT
1 TTTAATATATTTATATAAAT
1650403 TTATATGATATATTTATAT--A-
1 TT-TA--ATATATTTATATAAAT
*
1650423 TTTATATAATAATTATATAAACT
1 TTTA-AT-ATATTTATATAAA-T
*
1650446 TTTTATATATTT-TATA
1 TTTAATATATTTATATA
1650462 TTTTAATTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
17 5 0.08
18 6 0.10
19 14 0.23
20 19 0.31
21 10 0.16
22 4 0.07
23 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTAATATATTTATATAAAT
Done.