Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold263
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: 1338270
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 9 of 10
Found at i:1128887 original size:23 final size:23
Alignment explanation
Indices: 1128840--1128902 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
1128830 TAATAAAATA
* * *
1128840 TAAATTTAAACTTAAA-TCCATT
1 TAAATCTAAACTAAAAGCCCATT
1128862 TAAATCTAAACTAAAAGCCCATT
1 TAAATCTAAACTAAAAGCCCATT
* *
1128885 TAAACCTAAATTAAAAGC
1 TAAATCTAAACTAAAAGC
1128903 TTAATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.30
Consensus pattern (23 bp):
TAAATCTAAACTAAAAGCCCATT
Found at i:1128910 original size:23 final size:23
Alignment explanation
Indices: 1128861--1128911 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1128851 TTAAATCCAT
* *
1128861 TTAAATCTAAACTAAAAGCCCAT
1 TTAAACCTAAACTAAAAGCCCAA
* **
1128884 TTAAACCTAAATTAAAAGCTTAA
1 TTAAACCTAAACTAAAAGCCCAA
1128907 TTAAA
1 TTAAA
1128912 ACAAAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (23 bp):
TTAAACCTAAACTAAAAGCCCAA
Found at i:1129562 original size:27 final size:27
Alignment explanation
Indices: 1129521--1129590 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 27
1129511 ATTTTTTATT
**
1129521 TTAATATAATTATAAAATATATAAATA
1 TTAATATAAAAATAAAATATATAAATA
* *
1129548 TTAATATAAAAAT--AATATTTTAATA
1 TTAATATAAAAATAAAATATATAAATA
*
1129573 TTATTATAAATAATAAAA
1 TTAATATAAA-AATAAAA
1129591 CAAAGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 19 0.54
26 3 0.09
27 11 0.31
28 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TTAATATAAAAATAAAATATATAAATA
Found at i:1132931 original size:23 final size:22
Alignment explanation
Indices: 1132903--1132961 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
1132893 TTTTGAATTT
1132903 ATATAATAAAAATAATATATTAA
1 ATATAATAAAAATAATA-ATTAA
*
1132926 ATATAA-AAAAAT-TTAATTAA
1 ATATAATAAAAATAATAATTAA
*
1132946 ATAATAAT-TAAATAAT
1 AT-ATAATAAAAATAAT
1132962 TTTTTATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.23
21 10 0.33
22 7 0.23
23 6 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAATAAAAATAATAATTAA
Found at i:1132955 original size:11 final size:11
Alignment explanation
Indices: 1132912--1132961 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1132902 TATATAATAA
1132912 AAATAATATATT
1 AAATAATA-ATT
**
1132924 AAAT-ATAAAA
1 AAATAATAATT
*
1132934 AAAT-TTAATT
1 AAATAATAATT
1132944 AAATAATAATT
1 AAATAATAATT
1132955 AAATAAT
1 AAATAAT
1132962 TTTTTATCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 12 0.39
11 15 0.48
12 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATAATAATT
Found at i:1132962 original size:24 final size:21
Alignment explanation
Indices: 1132905--1132963 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
1132895 TTGAATTTAT
*
1132905 ATAATAAAAATAATATATTAA
1 ATAATAAAAATAATTTATTAA
1132926 AT-ATAAAAA-AATTTAATTAA
1 ATAATAAAAATAATTT-ATTAA
1132946 ATAATAATTAAATAATTT
1 ATAATAA--AAATAATTT
1132964 TTTATCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.12
20 14 0.44
21 6 0.19
23 3 0.09
24 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATAAAAATAATTTATTAA
Found at i:1133917 original size:148 final size:146
Alignment explanation
Indices: 1133646--1133940 Score: 482
Period size: 148 Copynumber: 2.0 Consensus size: 146
1133636 GAGAAAATTT
* * *
1133646 ACTTTTATCGATATTTATTAGTAAAACAATTATAAATTTGCTTTTATTAGTATTATTTATAAGTT
1 ACTTTTATCGATATTTACTAGTAAAAAAATTATAAAATTGCTTTTATTAGTATTATTTATAAGTT
* * *
1133711 TATTTTTTGTTGATTAGTTATCGATTATACCAATGTAGGTAAAAATATTTTCATGGTTAAATTAT
66 TATTTTTTGTTGATTAGTTATCGATTATACCAATATACGTAAAAATATTTTCACGGTTAAATTAT
*
1133776 TAGTGTCAGTGAAGAA
131 TAGTGTCAGTAAAGAA
1133792 ACTTTTATCGATATTTACTAGTAAAAAAAATTATAAAATTGCTTTTATTAGTATTATTTATAAGT
1 ACTTTTATCGATATTTACTAGT-AAAAAAATTATAAAATTGCTTTTATTAGTATTATTTATAAGT
* * *
1133857 TTTTTTTATTGTTGATTAGTTATCGATTATACTAATATACGTAAAAATATTTTGACGGTTAAATT
65 TTATTTT-TTGTTGATTAGTTATCGATTATACCAATATACGTAAAAATATTTTCACGGTTAAATT
1133922 ATTAGTGTCAGTAAAGAA
129 ATTAGTGTCAGTAAAGAA
1133940 A
1 A
1133941 ATTTACTTTT
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 21 0.15
147 46 0.34
148 70 0.51
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (146 bp):
ACTTTTATCGATATTTACTAGTAAAAAAATTATAAAATTGCTTTTATTAGTATTATTTATAAGTT
TATTTTTTGTTGATTAGTTATCGATTATACCAATATACGTAAAAATATTTTCACGGTTAAATTAT
TAGTGTCAGTAAAGAA
Found at i:1134316 original size:20 final size:21
Alignment explanation
Indices: 1134293--1134341 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1134283 TACATCTTTT
1134293 TATATTTAATTT-TTCTTAA-A
1 TATATTT-ATTTATTCTTAATA
*
1134313 TATAATTTATTTATTTTTAATA
1 TAT-ATTTATTTATTCTTAATA
1134335 TATATTT
1 TATATTT
1134342 TACGTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATTTATTTATTCTTAATA
Found at i:1134343 original size:22 final size:20
Alignment explanation
Indices: 1134293--1134343 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1134283 TACATCTTTT
*
1134293 TATATTTAATTTTTCTTAAA
1 TATATTTTATTTTTCTTAAA
* *
1134313 TATAATTTATTTATTTTTAATA
1 TATATTTTATTT-TTCTTAA-A
1134335 TATATTTTA
1 TATATTTTA
1134344 CGTATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.40
21 6 0.24
22 9 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTTTATTTTTCTTAAA
Found at i:1135015 original size:23 final size:23
Alignment explanation
Indices: 1134989--1135062 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
1134979 ACTACACAGC
1134989 CTTACCGGTTCAAACAACCTCAA
1 CTTACCGGTTCAAACAACCTCAA
* ** * *
1135012 CTTACTAGG-AAAAACTA-CACAA
1 CTTAC-CGGTTCAAACAACCTCAA
*
1135034 CCTTACCGGTTCAAACCACCTCAA
1 -CTTACCGGTTCAAACAACCTCAA
1135058 CTTAC
1 CTTAC
1135063 TTTTATCGAC
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 6 0.16
23 25 0.68
24 6 0.16
ACGTcount: A:0.36, C:0.34, G:0.08, T:0.22
Consensus pattern (23 bp):
CTTACCGGTTCAAACAACCTCAA
Found at i:1135038 original size:46 final size:47
Alignment explanation
Indices: 1134960--1135063 Score: 165
Period size: 46 Copynumber: 2.2 Consensus size: 47
1134950 TTAACAACAG
* *
1134960 TCAACGTACTAGGAAAAAAACTACACAGCCTTACCGGTTCAAACAACC
1 TCAACTTACTAGG-AAAAAACTACACAACCTTACCGGTTCAAACAACC
*
1135008 TCAACTTACTAGG-AAAAACTACACAACCTTACCGGTTCAAACCACC
1 TCAACTTACTAGGAAAAAACTACACAACCTTACCGGTTCAAACAACC
1135054 TCAACTTACT
1 TCAACTTACT
1135064 TTTATCGACT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
46 41 0.77
48 12 0.23
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (47 bp):
TCAACTTACTAGGAAAAAACTACACAACCTTACCGGTTCAAACAACC
Found at i:1135342 original size:22 final size:22
Alignment explanation
Indices: 1135317--1135358 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1135307 TTAAAAATTG
1135317 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1135339 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1135359 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1136066 original size:2 final size:2
Alignment explanation
Indices: 1136059--1136089 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1136049 TCTACCCCTT
1136059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1136090 TAAAATGCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1136659 original size:8 final size:8
Alignment explanation
Indices: 1136646--1136741 Score: 51
Period size: 8 Copynumber: 12.2 Consensus size: 8
1136636 ATATTAATAT
1136646 TATATAAA
1 TATATAAA
1136654 TATATAAA
1 TATATAAA
1136662 TATATTAAA
1 TATA-TAAA
* *
1136671 TTTTTATAA
1 TATATA-AA
* *
1136680 TAAAAATAA
1 TATATA-AA
*
1136689 TATATTAA
1 TATATAAA
*
1136697 -ATATAAT
1 TATATAAA
1136704 TATAATAAA
1 TAT-ATAAA
1136713 TA-A-AAA
1 TATATAAA
1136719 TATA-AAA
1 TATATAAA
1136726 -ATAT-AA
1 TATATAAA
*
1136732 TATAAAAA
1 TATATAAA
1136740 TA
1 TA
1136742 CAAATCATCT
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
6 10 0.15
7 13 0.19
8 22 0.33
9 22 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATATAAA
Found at i:1136678 original size:27 final size:27
Alignment explanation
Indices: 1136613--1136741 Score: 96
Period size: 27 Copynumber: 4.9 Consensus size: 27
1136603 TTATATTACA
1136613 TAAATA-TATAT-ATAAAAAAAATAATAT
1 TAAATATTATATAAT-AAAAAAAT-ATAT
* *
1136640 T-AATATTATATAAATATATAAATATAT
1 TAAATATTATAT-AATAAAAAAATATAT
*
1136667 TAAAT-TTTTATAATAAAAATAATATAT
1 TAAATATTATATAATAAAAA-AATATAT
*
1136694 TAAATATAATTATAATAAATAAAA-ATA-
1 TAAATATTA-TATAATAAA-AAAATATAT
*
1136721 TAAA-A--ATATAATATAAAAATA
1 TAAATATTATATAATAAAAAAATA
1136742 CAAATCATCT
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
22 4 0.05
23 9 0.11
24 1 0.01
26 11 0.13
27 32 0.38
28 13 0.15
29 13 0.15
30 2 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAATATTATATAATAAAAAAATATAT
Found at i:1136702 original size:23 final size:22
Alignment explanation
Indices: 1136675--1136741 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
1136665 ATTAAATTTT
*
1136675 TATAATAAAAATAATATATTAAA
1 TATAATAAAAATAATATA-AAAA
* *
1136698 TATAATTATAATAA-ATAAAAA
1 TATAATAAAAATAATATAAAAA
*
1136719 TATAA-AAATATAATATAAAAA
1 TATAATAAAAATAATATAAAAA
1136740 TA
1 TA
1136742 CAAATCATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 5 0.14
21 17 0.46
22 3 0.08
23 12 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TATAATAAAAATAATATAAAAA
Found at i:1136727 original size:29 final size:30
Alignment explanation
Indices: 1136644--1136746 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 30
1136634 TAATATTAAT
*
1136644 ATTAT-ATAAATATATAAATATATTAAAT-T-
1 ATTATAATAAATA-A-AAATATATAAAATATA
* * *
1136673 TTTATAATAAA-AATAATATATTAAATATA
1 ATTATAATAAATAAAAATATATAAAATATA
1136702 ATTATAATAAATAAAAATATA-AAAATATA
1 ATTATAATAAATAAAAATATATAAAATATA
*
1136731 A-TATAA-AAATACAAAT
1 ATTATAATAAATAAAAAT
1136747 CATCTAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.33
28 7 0.11
29 23 0.36
30 13 0.20
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
ATTATAATAAATAAAAATATATAAAATATA
Found at i:1137843 original size:21 final size:24
Alignment explanation
Indices: 1137801--1137844 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
1137791 ATTAATAAAA
1137801 AAATTATTTTATATTAATATTTAT
1 AAATTATTTTATATTAATATTTAT
1137825 AAATT-TTTTA-ATTAA-ATTTA
1 AAATTATTTTATATTAATATTTA
1137845 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 5 0.25
24 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATTATTTTATATTAATATTTAT
Found at i:1137849 original size:23 final size:26
Alignment explanation
Indices: 1137796--1137850 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
1137786 TTATAATTAA
*
1137796 TAAAAAAATTATTTTATATTAATATT
1 TAAATAAATTATTTTATATTAATATT
1137822 T--ATAAATT-TTTTA-ATTAA-ATT
1 TAAATAAATTATTTTATATTAATATT
1137843 TAAATAAA
1 TAAATAAA
1137851 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 10 0.38
24 6 0.23
26 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAATAAATTATTTTATATTAATATT
Found at i:1137878 original size:35 final size:35
Alignment explanation
Indices: 1137816--1137882 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1137806 ATTTTATATT
* * *
1137816 AATATTTATAAATTTTTTAATTAAATTTAAATAAA
1 AATATTTATAAATTATTAAATAAAATTTAAATAAA
1137851 AATATTTAT-AATTATTAAATAATAATTTAAAT
1 AATATTTATAAATTATTAAATAA-AATTTAAAT
1137883 CAAACTGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
AATATTTATAAATTATTAAATAAAATTTAAATAAA
Found at i:1138221 original size:20 final size:20
Alignment explanation
Indices: 1138183--1138221 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1138173 TATATTTTAT
* *
1138183 ATAAATATAAAATTTCAAAA
1 ATAAATATAAAAATACAAAA
*
1138203 ATAATTATAAAAATACAAA
1 ATAAATATAAAAATACAAA
1138222 TAAAAAATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAATATAAAAATACAAAA
Found at i:1138284 original size:2 final size:2
Alignment explanation
Indices: 1138279--1138311 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1138269 GTGTTTGCAT
1138279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1138312 CACAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1138650 original size:20 final size:19
Alignment explanation
Indices: 1138594--1138659 Score: 50
Period size: 20 Copynumber: 3.6 Consensus size: 19
1138584 TTATTTTTAC
1138594 TATTTATT-ATA-TTTAA-
1 TATTTATTAATATTTTAAT
* **
1138610 TACTTATTTAATATTAAAAT
1 TATTTA-TTAATATTTTAAT
1138630 TATTTATCTAATATTTTAAT
1 TATTTAT-TAATATTTTAAT
*
1138650 T-TTTTTTAAT
1 TATTTATTAAT
1138660 TAAATAATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 5 0.13
17 2 0.05
18 7 0.18
19 8 0.21
20 16 0.42
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTATTAATATTTTAAT
Found at i:1139663 original size:21 final size:21
Alignment explanation
Indices: 1139622--1139664 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1139612 TATATATTCG
* *
1139622 TTTTAATATAATAATATAATT
1 TTTTAATATAATAAAAAAATT
1139643 TTTTAA-ATATATAAAAAAATT
1 TTTTAATATA-ATAAAAAAATT
1139664 T
1 T
1139665 AATAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAATATAATAAAAAAATT
Found at i:1144542 original size:21 final size:21
Alignment explanation
Indices: 1144483--1144539 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
1144473 TTGAAATATA
*
1144483 AAAATTAAAAAATTATTTTTT
1 AAAATTTAAAAATTATTTTTT
*
1144504 -ATATTTAAATTAATTATTTTTAT
1 AAAATTTAAA--AATTATTTTT-T
1144527 AAAATTTAAAAAT
1 AAAATTTAAAAAT
1144540 ATTATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.24
22 13 0.45
23 1 0.03
24 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTTAAAAATTATTTTTT
Found at i:1144826 original size:25 final size:25
Alignment explanation
Indices: 1144797--1144867 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 25
1144787 TATTTAAATA
1144797 TTATTTAAATAATAAAAATT-ATTAT
1 TTATTTAAATAATAAAAATTAATT-T
1144822 TTATTTAAAATTAATATAAAATTAATTT
1 TTATTT-AAA-TAATA-AAAATTAATTT
*
1144850 TTAATTATAATAATAAAA
1 TTATTTA-AATAATAAAA
1144868 TAAAATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 6 0.15
26 6 0.15
27 11 0.28
28 14 0.35
29 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTATTTAAATAATAAAAATTAATTT
Found at i:1144868 original size:25 final size:24
Alignment explanation
Indices: 1144833--1144879 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1144823 TATTTAAAAT
* *
1144833 TAATATAAAATTAATTTTTAATTA
1 TAATATAAAATAAAATTTTAATTA
1144857 TAATAATAAAATAAAATTTTAAT
1 TAAT-ATAAAATAAAATTTTAAT
1144880 CAATCTAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATAAAATAAAATTTTAATTA
Found at i:1145173 original size:14 final size:15
Alignment explanation
Indices: 1145120--1145174 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
1145110 AACTAAAAAT
1145120 TTTAAATTTAAATTTAA
1 TTTAAATTT--ATTTAA
* *
1145137 ATTAAATTAATTTAA
1 TTTAAATTTATTTAA
*
1145152 TTT-GATTTATTT-A
1 TTTAAATTTATTTAA
1145165 TTTAAATTTA
1 TTTAAATTTA
1145175 AATTATTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 4 0.13
14 12 0.39
15 8 0.26
17 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTAAATTTATTTAA
Found at i:1145186 original size:22 final size:21
Alignment explanation
Indices: 1145125--1145244 Score: 70
Period size: 22 Copynumber: 5.7 Consensus size: 21
1145115 AAAATTTTAA
** *
1145125 ATTTAAATTTAAATTAAATTA
1 ATTTAAATTTAAATTATTTTT
* *
1145146 ATTT-AATTT-GATT-TATTT
1 ATTTAAATTTAAATTATTTTT
1145164 ATTTAAATTTAAATTATTATTT
1 ATTTAAATTTAAATTATT-TTT
* *
1145186 ATTT-TATTAAAAAATTATTTTT
1 ATTTAAATT--TAAATTATTTTT
*
1145208 ATATTAATATTTATA-TATTTTAT
1 AT-TTAA-ATTTAAATTATTTT-T
*
1145231 AATTAAATTTAAAT
1 ATTTAAATTTAAAT
1145245 AAAAATATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
18 7 0.09
19 8 0.11
20 8 0.11
21 14 0.18
22 22 0.29
23 14 0.18
25 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
ATTTAAATTTAAATTATTTTT
Found at i:1145273 original size:19 final size:19
Alignment explanation
Indices: 1145236--1145281 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1145226 TTTATAATTA
*
1145236 AATTTAAATAAAAATATAT
1 AATTTTAATAAAAATATAT
*
1145255 ATTTTTAATATAAAA-ATAT
1 AATTTTAATA-AAAATATAT
1145274 AATTTTAA
1 AATTTTAA
1145282 GTTAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTTAATAAAAATATAT
Found at i:1145287 original size:19 final size:21
Alignment explanation
Indices: 1145238--1145279 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1145228 TATAATTAAA
1145238 TTTAA-ATAAAAATATATATT
1 TTTAATATAAAAATATATATT
1145258 TTTAATATAAAAATATA-ATT
1 TTTAATATAAAAATATATATT
1145278 TT
1 TT
1145280 AAGTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATATAAAAATATATATT
Found at i:1151884 original size:22 final size:22
Alignment explanation
Indices: 1151859--1151911 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1151849 GCTTTCTATT
1151859 TTTATGGATTTTTGG-GTTCTTC
1 TTTATGGATTTTTGGAGTT-TTC
*
1151881 TTTAATGTATTTTTGGAGTTTTC
1 TTT-ATGGATTTTTGGAGTTTTC
*
1151904 TATATGGA
1 TTTATGGA
1151912 ATTCATGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.27
23 16 0.62
24 3 0.12
ACGTcount: A:0.17, C:0.06, G:0.21, T:0.57
Consensus pattern (22 bp):
TTTATGGATTTTTGGAGTTTTC
Found at i:1152252 original size:4 final size:4
Alignment explanation
Indices: 1152243--1152277 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1152233 GCATATACAT
*
1152243 ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1152278 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1152274 original size:16 final size:16
Alignment explanation
Indices: 1152216--1152277 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
1152206 TGCACGCATG
*
1152216 CATGCATGCATAC--A
1 CATGCATACATACATA
* * *
1152230 CATGCATATACATATA
1 CATGCATACATACATA
*
1152246 CATACATACATACATA
1 CATGCATACATACATA
1152262 CATGCATACATACATA
1 CATGCATACATACATA
1152278 TATATATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
14 9 0.24
16 28 0.76
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (16 bp):
CATGCATACATACATA
Found at i:1155812 original size:2 final size:2
Alignment explanation
Indices: 1155805--1155832 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1155795 TTCTAATTAT
1155805 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
1155833 AGAAGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1155940 original size:2 final size:2
Alignment explanation
Indices: 1155927--1155968 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1155917 AAACTAACCA
*
1155927 AT AT AA 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
1155969 CCCCTGCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1159497 original size:63 final size:63
Alignment explanation
Indices: 1159418--1159543 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
1159408 CACAGTCACG
*
1159418 GATATAATAAATATTATTATGATTAAATTATAATAAATAATTATAAAATAACGATTATAAGAT
1 GATATAATAAATATTATTATAATTAAATTATAATAAATAATTATAAAATAACGATTATAAGAT
1159481 GATATAATAAATATTATTATAATTAAATTATAATAAATAATTATAAAATAACGATTATAAGAT
1 GATATAATAAATATTATTATAATTAAATTATAATAAATAATTATAAAATAACGATTATAAGAT
1159544 AACGCTGTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (63 bp):
GATATAATAAATATTATTATAATTAAATTATAATAAATAATTATAAAATAACGATTATAAGAT
Found at i:1159516 original size:14 final size:13
Alignment explanation
Indices: 1159420--1159526 Score: 71
Period size: 13 Copynumber: 8.4 Consensus size: 13
1159410 CAGTCACGGA
1159420 TATAATAAAT-AT
1 TATAATAAATAAT
* * *
1159432 TATTATGATTAAAT
1 TATAATAAAT-AAT
1159446 TATAATAAATAAT
1 TATAATAAATAAT
*
1159459 TAT-A-AAATAAC
1 TATAATAAATAAT
* * *
1159470 GATTATAAGATGA-
1 TATAATAA-ATAAT
1159483 TATAATAAAT-AT
1 TATAATAAATAAT
* *
1159495 TATTATAATTAAAT
1 TATAATAAAT-AAT
1159509 TATAATAAATAAT
1 TATAATAAATAAT
1159522 TATAA
1 TATAA
1159527 AATAACGATT
Statistics
Matches: 72, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
11 9 0.12
12 19 0.26
13 22 0.31
14 22 0.31
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (13 bp):
TATAATAAATAAT
Found at i:1160687 original size:21 final size:21
Alignment explanation
Indices: 1160661--1160704 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1160651 ATTAAAATTT
1160661 AATTATAAATTTTAAT-ATAAA
1 AATTAT-AATTTTAATAATAAA
**
1160682 AATTATTTTTTTAATAATAAA
1 AATTATAATTTTAATAATAAA
1160703 AA
1 AA
1160705 CGAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATAATTTTAATAATAAA
Found at i:1160712 original size:21 final size:20
Alignment explanation
Indices: 1160670--1160713 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1160660 TAATTATAAA
** *
1160670 TTTTAATATAAAAATTATTT
1 TTTTAATATAAAAACGAATT
1160690 TTTTAATAATAAAAACGAATT
1 TTTTAAT-ATAAAAACGAATT
1160711 TTT
1 TTT
1160714 AAATTACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTAATATAAAAACGAATT
Found at i:1161427 original size:21 final size:19
Alignment explanation
Indices: 1161403--1161450 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1161393 GTTTCTTGAA
1161403 TTTATAAATAAATATTAGATT
1 TTTATAAATAAAT-TTA-ATT
* *
1161424 TTTATGAATATATTTAATT
1 TTTATAAATAAATTTAATT
*
1161443 TTTTTAAA
1 TTTATAAA
1161451 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 3 0.13
21 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTATAAATAAATTTAATT
Found at i:1161456 original size:19 final size:19
Alignment explanation
Indices: 1161434--1161474 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1161424 TTTATGAATA
* *
1161434 TATTTAATTTTTTTAAAAT
1 TATTTAATATTTTAAAAAT
*
1161453 TATTTTATATTTTAAAAAT
1 TATTTAATATTTTAAAAAT
1161472 TAT
1 TAT
1161475 AATTTTCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTAATATTTTAAAAAT
Found at i:1161822 original size:2 final size:2
Alignment explanation
Indices: 1161809--1161841 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1161799 CATCTCTTGC
*
1161809 AT AT AT AC 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 AT A
1161842 CACCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1162505 original size:14 final size:14
Alignment explanation
Indices: 1162486--1162513 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1162476 CTTTCGAAGA
1162486 TTATATTTTTATAT
1 TTATATTTTTATAT
1162500 TTATATTTTTATAT
1 TTATATTTTTATAT
1162514 ATGTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATATTTTTATAT
Found at i:1164115 original size:41 final size:41
Alignment explanation
Indices: 1164051--1164139 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
1164041 TATATTTTAT
*
1164051 ATTAATTTGATTTAATTTAAATTAT-TATTTATATAATAAAA
1 ATTAATTTGATTTAATTTAAATTATAAATTTATAT-ATAAAA
* * *
1164092 ATTAGTTTTATTTAAATTT-AATTATAAATTTTTATATAAAA
1 ATTAATTTGATTT-AATTTAAATTATAAATTTATATATAAAA
1164133 A-TAATTT
1 ATTAATTT
1164140 AATATTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
40 5 0.12
41 24 0.59
42 12 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
ATTAATTTGATTTAATTTAAATTATAAATTTATATATAAAA
Found at i:1164373 original size:23 final size:22
Alignment explanation
Indices: 1164343--1164402 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
1164333 TTATTTAATA
*
1164343 AATA-AAAAATTATTTAAATTT
1 AATATAAAAATTATTTAAAATT
*
1164364 AATTATAAAATATT-TTAAAAAATT
1 AA-TATAAAA-ATTATT-TAAAATT
1164388 AATATAAAAA-TATTT
1 AATATAAAAATTATTT
1164403 TTTAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
21 3 0.10
22 5 0.16
23 13 0.42
24 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATAAAAATTATTTAAAATT
Found at i:1164584 original size:3 final size:3
Alignment explanation
Indices: 1164576--1164602 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1164566 AGATATGTAT
1164576 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1164603 CTATTATTAT
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):
ATA
Found at i:1170447 original size:2 final size:2
Alignment explanation
Indices: 1170440--1170465 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1170430 GTTGATGCTT
1170440 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
1170466 GTTTAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1171978 original size:25 final size:25
Alignment explanation
Indices: 1171950--1172019 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 25
1171940 TTGGCATGGT
1171950 TTATTTTGTAATTATATAATATAAA
1 TTATTTTGTAATTATATAATATAAA
*
1171975 TTATTTT-T-A-TATTTAATAT--A
1 TTATTTTGTAATTATATAATATAAA
* *
1171995 -TATTATGTAATT-TATATTATAAA
1 TTATTTTGTAATTATATAATATAAA
1172018 TT
1 TT
1172020 TAAACATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
19 5 0.14
20 2 0.06
21 7 0.20
22 10 0.29
23 2 0.06
24 2 0.06
25 7 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (25 bp):
TTATTTTGTAATTATATAATATAAA
Found at i:1176747 original size:2 final size:2
Alignment explanation
Indices: 1176740--1176768 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1176730 CTTATTTTAT
1176740 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1176769 ATAGCGTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1180236 original size:59 final size:59
Alignment explanation
Indices: 1180140--1180257 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
1180130 TCATATCTAT
* * *
1180140 AGATTCTAGACAAAAAATATGTTAGTTGAGATTTCAATGATATAAAGAGGACAAATAGG
1 AGATTCTAGACAAAAAATATGTTAGATGAGATGTCAATGACATAAAGAGGACAAATAGG
* *
1180199 AGATTCTAGACACAAAATATGTTAGATGGGATGTCAATGACATAAAGAGGACAAATAGG
1 AGATTCTAGACAAAAAATATGTTAGATGAGATGTCAATGACATAAAGAGGACAAATAGG
1180258 TACGACCTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (59 bp):
AGATTCTAGACAAAAAATATGTTAGATGAGATGTCAATGACATAAAGAGGACAAATAGG
Found at i:1181531 original size:2 final size:2
Alignment explanation
Indices: 1181526--1181556 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1181516 CGTGTATATA
1181526 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1181557 TGCCAAGATA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1183934 original size:15 final size:16
Alignment explanation
Indices: 1183906--1183935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1183896 TTCATAAGGT
1183906 ATTTACTCTCTATAAC
1 ATTTACTCTCTATAAC
1183922 ATTTACT-TCTATAA
1 ATTTACTCTCTATAA
1183936 TTTGTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTACTCTCTATAAC
Found at i:1185574 original size:22 final size:21
Alignment explanation
Indices: 1185547--1185601 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1185537 TATTATGTTA
**
1185547 TTATATTTTTACGTTTTATAAT
1 TTATATTTTTAAATTTTA-AAT
* *
1185569 TTATATTATATAAATTTTAATT
1 TTATATT-TTTAAATTTTAAAT
1185591 TTATATTTTTA
1 TTATATTTTTA
1185602 TTATGTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.11
22 16 0.59
23 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTATATTTTTAAATTTTAAAT
Found at i:1185640 original size:19 final size:21
Alignment explanation
Indices: 1185590--1185644 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
1185580 AAATTTTAAT
1185590 TTTATATTTTTATTATGTTCATA
1 TTTATATTTTTA-TA-GTTCATA
*
1185613 TTAAT-TTTTTATA-TT-ATA
1 TTTATATTTTTATAGTTCATA
1185631 TTTATATTTTTATA
1 TTTATATTTTTATA
1185645 ATTTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 7 0.24
19 10 0.34
21 2 0.07
22 6 0.21
23 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATATTTTTATAGTTCATA
Found at i:1192413 original size:18 final size:18
Alignment explanation
Indices: 1192370--1192414 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1192360 TTGTTAATAT
1192370 TTATATT-TA-TAATAAA
1 TTATATTATATTAATAAA
*
1192386 TTTTGA-TATATTAATAAA
1 TTAT-ATTATATTAATAAA
1192404 TTATATTATAT
1 TTATATTATAT
1192415 AAATTTCGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATATTATATTAATAAA
Found at i:1192431 original size:32 final size:34
Alignment explanation
Indices: 1192370--1192432 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
1192360 TTGTTAATAT
* * *
1192370 TTATATTTATAATAAATTTTGATATATTAATAAA
1 TTATATTTATAATAAATTTCGACAAATTAATAAA
1192404 TTATA-TTAT-ATAAATTTCGACAAATTAAT
1 TTATATTTATAATAAATTTCGACAAATTAAT
1192433 TTATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 17 0.65
33 4 0.15
34 5 0.19
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (34 bp):
TTATATTTATAATAAATTTCGACAAATTAATAAA
Found at i:1192446 original size:32 final size:32
Alignment explanation
Indices: 1192368--1192446 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
1192358 TTTTGTTAAT
* * * *
1192368 ATTTATATTTATA-ATAAATTTTGATATATTA
1 ATTTATATATATATATAAATTTCGACAAATTA
**
1192399 ATAAAT-TATATTATATAAATTTCGACAAATTA
1 ATTTATATATA-TATATAAATTTCGACAAATTA
1192431 ATTTATATATATATAT
1 ATTTATATATATATAT
1192447 CATATTCATA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
30 3 0.08
31 6 0.16
32 24 0.65
33 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
ATTTATATATATATATAAATTTCGACAAATTA
Found at i:1193472 original size:3 final size:3
Alignment explanation
Indices: 1193464--1193504 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1193454 CTATTATCAA
1193464 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1193505 ACAGTTCTTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1194460 original size:3 final size:3
Alignment explanation
Indices: 1194452--1194480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1194442 TTGAAATTGA
1194452 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1194481 ATAAAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1194765 original size:36 final size:34
Alignment explanation
Indices: 1194725--1194791 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
1194715 TATATAATTG
1194725 TTATATTCGT-ATTATTTTTTAATATCATATTTTATA
1 TTATATT-GTAATTATTTTTT--TATCATATTTTATA
*
1194761 TTATATTTTAATTATTTTTTTATCATATTTT
1 TTATATTGTAATTATTTTTTTATCATATTTT
1194792 TTTCATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 11 0.38
35 1 0.03
36 17 0.59
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (34 bp):
TTATATTGTAATTATTTTTTTATCATATTTTATA
Found at i:1194766 original size:12 final size:12
Alignment explanation
Indices: 1194734--1194791 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
1194724 GTTATATTCG
*
1194734 TATTATTTTTTAA
1 TATTATATTTT-A
*
1194747 TATCATATTTTA
1 TATTATATTTTA
1194759 TATTATATTTTA
1 TATTATATTTTA
*
1194771 -ATTAT-TTTTT
1 TATTATATTTTA
*
1194781 TATCATATTTT
1 TATTATATTTT
1194792 TTTCATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
10 4 0.11
11 9 0.24
12 16 0.42
13 9 0.24
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1194791 original size:11 final size:11
Alignment explanation
Indices: 1194747--1194799 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1194737 TATTTTTTAA
1194747 TATCATATTTT
1 TATCATATTTT
*
1194758 ATATTATATTTT
1 -TATCATATTTT
* * *
1194770 AATTATTTTTT
1 TATCATATTTT
1194781 TATCATATTTT
1 TATCATATTTT
*
1194792 TTTCATAT
1 TATCATAT
1194800 AATTATGTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (11 bp):
TATCATATTTT
Found at i:1196075 original size:3 final size:3
Alignment explanation
Indices: 1196067--1196101 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1196057 CTCTTCTATC
*
1196067 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1196102 CTGCTTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1207708 original size:17 final size:17
Alignment explanation
Indices: 1207694--1207727 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1207684 TTATTTTATA
1207694 TTAAAAATAATTTTAAT
1 TTAAAAATAATTTTAAT
*
1207711 TTAAAATTAATTATTAA
1 TTAAAAATAATT-TTAA
1207728 ATATATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAATAATTTTAAT
Found at i:1207762 original size:20 final size:20
Alignment explanation
Indices: 1207711--1207755 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1207701 TAATTTTAAT
* *
1207711 TTAAAATTAATTATTAAATATA
1 TTAATATTAA-TA-TAAAAATA
1207733 TTAATATTAATATAAAAATA
1 TTAATATTAATATAAAAATA
1207753 TTA
1 TTA
1207756 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATATTAATATAAAAATA
Found at i:1208234 original size:14 final size:14
Alignment explanation
Indices: 1208211--1208262 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1208201 AAAAATATAA
*
1208211 ATATATTAAAATTT
1 ATATAATAAAATTT
1208225 ATATAATAAAAATTATTT
1 ATATAAT--AAA--ATTT
*
1208243 ACATAATAAAATTT
1 ATATAATAAAATTT
1208257 ATATAA
1 ATATAA
1208263 AAATATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 15 0.48
16 6 0.19
18 10 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:1208235 original size:32 final size:32
Alignment explanation
Indices: 1208194--1208262 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1208184 ATATTTAAAT
* *
1208194 TATAATAAAAAATATAAATATATTAAAATTTA
1 TATAATAAAAAATATAAACATAATAAAATTTA
* **
1208226 TATAATAAAAATTATTTACATAATAAAATTTA
1 TATAATAAAAAATATAAACATAATAAAATTTA
1208258 TATAA
1 TATAA
1208263 AAATATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TATAATAAAAAATATAAACATAATAAAATTTA
Found at i:1208242 original size:18 final size:18
Alignment explanation
Indices: 1208221--1208258 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1208211 ATATATTAAA
*
1208221 ATTTATATAATAAAAATT
1 ATTTACATAATAAAAATT
*
1208239 ATTTACATAATAAAATTT
1 ATTTACATAATAAAAATT
1208257 AT
1 AT
1208259 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTACATAATAAAAATT
Found at i:1208648 original size:17 final size:18
Alignment explanation
Indices: 1208626--1208663 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1208616 ATAAAAAAAA
*
1208626 TTAAAAATTT-ATTTATT
1 TTAAAAATTTAATATATT
*
1208643 TTAAAATTTTAATATATT
1 TTAAAAATTTAATATATT
1208661 TTA
1 TTA
1208664 TAATTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAAAATTTAATATATT
Found at i:1208662 original size:18 final size:17
Alignment explanation
Indices: 1208626--1208668 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1208616 ATAAAAAAAA
* *
1208626 TTAAAAATTTATTTATT
1 TTAAAATTTTATATATT
1208643 TTAAAATTTTAATATATT
1 TTAAAATTTT-ATATATT
*
1208661 TTATAATT
1 TTAAAATT
1208669 AAATGTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAAATTTTATATATT
Found at i:1221982 original size:25 final size:25
Alignment explanation
Indices: 1221954--1222031 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 25
1221944 TAAAAAAATT
* *
1221954 AAAAATTTTAAATATATTTATTTTA
1 AAAAATATTAAATATATATATTTTA
*
1221979 AAAAATATTATATATATATATTTATATA
1 AAAAATATTAAATATATATA-TT-T-TA
1222007 ATATAAATATTAAAT-T-TATATTTTA
1 A-A-AAATATTAAATATATATATTTTA
1222032 TAATTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
25 19 0.43
26 3 0.07
27 3 0.07
28 7 0.16
29 2 0.05
30 10 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAAATATTAAATATATATATTTTA
Found at i:1222049 original size:17 final size:18
Alignment explanation
Indices: 1222020--1222054 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1222010 TAAATATTAA
1222020 ATTTATATTTTATAATTT
1 ATTTATATTTTATAATTT
*
1222038 ATTTAT-TTTTATTATTT
1 ATTTATATTTTATAATTT
1222055 TTACATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATATTTTATAATTT
Found at i:1222107 original size:23 final size:24
Alignment explanation
Indices: 1222076--1222120 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1222066 TATTAATTTA
* *
1222076 AAAATTATTTATTTATTTTATTAT
1 AAAATTATTGATATATTTTATTAT
1222100 AAAA-TATTGATATATTTTATT
1 AAAATTATTGATATATTTTATT
1222121 TGCTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
AAAATTATTGATATATTTTATTAT
Found at i:1222326 original size:6 final size:6
Alignment explanation
Indices: 1222317--1222382 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
1222307 ATTTTTAATT
* * * *
1222317 TTTAAA TTTATAA ATTAAA -TTAAA TTTAAA TTT-AA TTAAAA ATAAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1222364 TTTTTAAA TTTAAA TTTAA
1 --TTTAAA TTTAAA TTTAA
1222383 TTAAATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 9 0.18
6 32 0.64
7 5 0.10
8 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:1226788 original size:19 final size:19
Alignment explanation
Indices: 1226758--1226809 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1226748 AAAGATTATG
1226758 ATATTGTATTAATAAAAATT
1 ATATT-TATTAATAAAAATT
1226778 ATATTTATTAATAAAAATT
1 ATATTTATTAATAAAAATT
*
1226797 ATATTTAATAATA
1 ATATTTATTAATA
1226810 TAATTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATTTATTAATAAAAATT
Found at i:1226806 original size:16 final size:16
Alignment explanation
Indices: 1226766--1226822 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 16
1226756 TGATATTGTA
1226766 TTAATAAAAATTATATTT
1 TTAATAAAAATTATA--T
1226784 ATTAATAAAAATTATAT
1 -TTAATAAAAATTATAT
*
1226801 TTAATAATATAATTATTT
1 TTAATAA-A-AATTATAT
1226819 TTAA
1 TTAA
1226823 AAGATAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 7 0.20
17 2 0.06
18 11 0.31
19 15 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATAAAAATTATAT
Found at i:1230532 original size:17 final size:17
Alignment explanation
Indices: 1230510--1230544 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1230500 AACATAGGTT
1230510 TTGATTAATTTTCTGCA
1 TTGATTAATTTTCTGCA
*
1230527 TTGATTACTTTTCTGCA
1 TTGATTAATTTTCTGCA
1230544 T
1 T
1230545 CAGATCCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (17 bp):
TTGATTAATTTTCTGCA
Found at i:1234056 original size:27 final size:27
Alignment explanation
Indices: 1234026--1234105 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 27
1234016 ATTTAATTTT
1234026 TATTTTATTTATATATTTTAAAAATAA
1 TATTTTATTTATATATTTTAAAAATAA
*
1234053 TATTTTATATT-TATA-TTTAAATAT-A
1 TATTTTAT-TTATATATTTTAAAAATAA
** * *
1234078 TATTAGATATAAATATTTTAAAAA-AA
1 TATTTTATTTATATATTTTAAAAATAA
1234104 TA
1 TA
1234106 AAAAAATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
24 1 0.02
25 10 0.23
26 18 0.42
27 12 0.28
28 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TATTTTATTTATATATTTTAAAAATAA
Found at i:1234351 original size:22 final size:22
Alignment explanation
Indices: 1234326--1234403 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
1234316 AATTTTTATT
1234326 TAAATA-TAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1234348 TAAATATTAATATAAAAATA-A
1 TAAATATTAATATAAAAATATA
* *
1234369 T--ATTTTAATATAAAAATAAAA
1 TAAATATTAATATAAAAAT-ATA
*
1234390 TAAAT-TTAAAATAA
1 TAAATATTAATATAA
1234404 TTTAATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
19 15 0.31
20 1 0.02
21 4 0.08
22 24 0.49
23 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1237402 original size:16 final size:16
Alignment explanation
Indices: 1237363--1237403 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1237353 TATAAAATTA
1237363 ATTATAT-TTAAATAT
1 ATTATATATTAAATAT
*
1237378 A-TATTTATTAAATAT
1 ATTATATATTAAATAT
1237393 ATTATATATTA
1 ATTATATATTA
1237404 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTATATATTAAATAT
Found at i:1237407 original size:25 final size:25
Alignment explanation
Indices: 1237312--1237395 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 25
1237302 AAATAAAATA
*
1237312 TATTAAA-AT-TTTAAATATAAATT
1 TATTAAATATATTTAAATATATATT
* * * * *
1237335 CAATAAATATA-TTACACATATA-A
1 TATTAAATATATTTAAATATATATT
* *
1237358 AATTAATTATATTTAAATATATATT
1 TATTAAATATATTTAAATATATATT
1237383 TATTAAATATATT
1 TATTAAATATATT
1237396 ATATATTATA
Statistics
Matches: 43, Mismatches: 14, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
23 13 0.30
24 19 0.44
25 11 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTAAATATATTTAAATATATATT
Found at i:1237486 original size:3 final size:3
Alignment explanation
Indices: 1237478--1237515 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1237468 GTTTGCTTGG
1237478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1237516 ATCTCTTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1238107 original size:17 final size:17
Alignment explanation
Indices: 1238087--1238122 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1238077 TAATATTATC
*
1238087 TATTAAATATTTAAATT
1 TATTAAAAATTTAAATT
1238104 TATTAAAAATTTAAATT
1 TATTAAAAATTTAAATT
1238121 TA
1 TA
1238123 ATAAGTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAAAATTTAAATT
Found at i:1238576 original size:21 final size:21
Alignment explanation
Indices: 1238520--1238581 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
1238510 AATATTAAAT
1238520 TATTTGAATCAATCAA-TATTAA
1 TATTTGAATCAAT-AATTA-TAA
*
1238542 TATTACGAAT-AATAATTATAA
1 TATT-TGAATCAATAATTATAA
*
1238563 TATTTGAATCAATATTTAT
1 TATTTGAATCAATAATTAT
1238582 TTTGAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 4 0.12
21 17 0.50
22 9 0.26
23 4 0.12
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (21 bp):
TATTTGAATCAATAATTATAA
Found at i:1238836 original size:17 final size:15
Alignment explanation
Indices: 1238818--1238850 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1238808 ATTTATTAAA
1238818 TAATA-AAATATATT
1 TAATATAAATATATT
1238832 TAATATAAATATATT
1 TAATATAAATATATT
1238847 TAAT
1 TAAT
1238851 TTTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATAAATATATT
Found at i:1239144 original size:17 final size:18
Alignment explanation
Indices: 1239122--1239155 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1239112 TCTAATTGTA
1239122 ATTTAAATTAT-TTTAAT
1 ATTTAAATTATATTTAAT
*
1239139 ATTTAATTTATATTTAA
1 ATTTAAATTATATTTAA
1239156 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTAAATTATATTTAAT
Found at i:1239145 original size:28 final size:28
Alignment explanation
Indices: 1239100--1239187 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1239090 ATATTGAAAT
*
1239100 AATT-TTTTAA-ATTCTAATTGTAATTTA
1 AATTATTTTAATATTATAATT-TAATTTA
1239127 AATTATTTTAATATT-TAATTTATATTTA
1 AATTATTTTAATATTATAATTTA-ATTTA
*
1239155 AATAATTTT--T-TTATAATTATAATTTA
1 AATTATTTTAATATTATAATT-TAATTTA
*
1239181 GATTATT
1 AATTATT
1239188 CAAGCAAGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
25 2 0.04
26 16 0.30
27 8 0.15
28 24 0.45
29 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (28 bp):
AATTATTTTAATATTATAATTTAATTTA
Found at i:1241421 original size:141 final size:141
Alignment explanation
Indices: 1241167--1241447 Score: 544
Period size: 141 Copynumber: 2.0 Consensus size: 141
1241157 GGGAAACTGA
1241167 TTCTGGCATCAGTTAAGGACTCATTATAAAGAAGCACAAAAGAAGTACCACATAGCAGAAGTAAA
1 TTCTGGCATCAGTTAAGGACTCATTATAAAGAAGCACAAAAGAAGTACCACATAGCAGAAGTAAA
*
1241232 ATATTCAGTTTTTTCCTATGTTGTTCTGACTTTTCAGTTTTCTTGAAGTACCTATGACCGAAACT
66 ATATTCAGTTTTTTCCTATGTTGTTCCGACTTTTCAGTTTTCTTGAAGTACCTATGACCGAAACT
1241297 CGTGTCCGACT
131 CGTGTCCGACT
*
1241308 TTCTGGCATCAGTTAAGGACTCATTATAAAGAAGCACAAAATAAGTACCACATAGCAGAAGTAAA
1 TTCTGGCATCAGTTAAGGACTCATTATAAAGAAGCACAAAAGAAGTACCACATAGCAGAAGTAAA
1241373 ATATTCAGTTTTTTCCTATGTTGTTCCGACTTTTCAGTTTTCTTGAAGTACCTATGACCGAAACT
66 ATATTCAGTTTTTTCCTATGTTGTTCCGACTTTTCAGTTTTCTTGAAGTACCTATGACCGAAACT
1241438 CGTGTCCGAC
131 CGTGTCCGAC
1241448 GTATTTTTTG
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (141 bp):
TTCTGGCATCAGTTAAGGACTCATTATAAAGAAGCACAAAAGAAGTACCACATAGCAGAAGTAAA
ATATTCAGTTTTTTCCTATGTTGTTCCGACTTTTCAGTTTTCTTGAAGTACCTATGACCGAAACT
CGTGTCCGACT
Found at i:1245070 original size:22 final size:21
Alignment explanation
Indices: 1245045--1245111 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 21
1245035 TTAAAAATTG
* *
1245045 AATTAATTAATTTTATTTAAAT
1 AATTAATTAA-ATTAATTAAAT
1245067 AATTAATTAAATTAATTAAAT
1 AATTAATTAAATTAATTAAAT
* *
1245088 AA--AATT-GATTAATTAAAA
1 AATTAATTAAATTAATTAAAT
1245106 AATTAA
1 AATTAA
1245112 AATTTATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.31
19 4 0.10
20 2 0.05
21 11 0.28
22 10 0.26
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
AATTAATTAAATTAATTAAAT
Found at i:1245209 original size:25 final size:25
Alignment explanation
Indices: 1245181--1245232 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1245171 TTGTTATGTA
1245181 ATCTTAAAAT-ATATTATATAATATT
1 ATCTTAAAATAAT-TTATATAATATT
*
1245206 ATCTTAAAATAATTTATATTATATT
1 ATCTTAAAATAATTTATATAATATT
1245231 AT
1 AT
1245233 ATATCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
ATCTTAAAATAATTTATATAATATT
Found at i:1245244 original size:25 final size:25
Alignment explanation
Indices: 1245181--1245257 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
1245171 TTGTTATGTA
*
1245181 ATCTTAAAATATATTATATAATATT
1 ATCTTAAATTATATTATATAATATT
*
1245206 ATCTTAAAATA-ATTTATATTATATTATAT
1 ATCTTAAATTATA-TTATA-TA-A-TAT-T
*
1245235 ATCTTAAATTATAATATA-AATAT
1 ATCTTAAATTATATTATATAATAT
1245258 GTTTTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
24 1 0.02
25 19 0.43
26 3 0.07
27 2 0.05
28 3 0.07
29 15 0.34
30 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
ATCTTAAATTATATTATATAATATT
Found at i:1246022 original size:17 final size:18
Alignment explanation
Indices: 1246000--1246040 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1245990 ATAAAATATT
1246000 TTAATTATTTATAAA-AA
1 TTAATTATTTATAAATAA
* *
1246017 TTAATT-TTTTTAAATAC
1 TTAATTATTTATAAATAA
1246034 TTAATTA
1 TTAATTA
1246041 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATTATTTATAAATAA
Found at i:1246491 original size:17 final size:18
Alignment explanation
Indices: 1246469--1246519 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1246459 ATTTGATTTG
1246469 ATTTAATTTTAATTAA-T
1 ATTTAATTTTAATTAATT
* *
1246486 ATTTAATAATTAATAAAATT
1 ATTTAAT-TTTAAT-TAATT
1246506 ATTTAA-TTTAATTA
1 ATTTAATTTTAATTA
1246520 TAAAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.30
18 10 0.37
19 2 0.07
20 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAATTTTAATTAATT
Found at i:1246524 original size:21 final size:20
Alignment explanation
Indices: 1246485--1246545 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1246475 TTTTAATTAA
1246485 TATTTAATAATTAATAAAAT
1 TATTTAATAATTAATAAAAT
1246505 TATTTAATTTAATT-ATAAAAT
1 TATTTAA--TAATTAATAAAAT
*
1246526 TA-TAAAT-ATTAATATAAAT
1 TATTTAATAATTAATA-AAAT
1246545 T
1 T
1246546 TTTTGAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 5 0.14
20 10 0.28
21 9 0.25
22 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTTAATAATTAATAAAAT
Found at i:1247001 original size:25 final size:22
Alignment explanation
Indices: 1246959--1247041 Score: 60
Period size: 25 Copynumber: 3.5 Consensus size: 22
1246949 AGCTAATTAA
* *
1246959 ATTTATTTAAAAATTAAATTATTT
1 ATTTATTTAATAA-TAAACT-TTT
1246983 ATTTGATTTAATAAGTAAAACTTTT
1 ATTT-ATTTAATAA-T-AAACTTTT
*
1247008 ATTTTTATTTAATAATAAAAATTTT
1 A--TTTATTTAATAAT-AAACTTTT
1247033 -TTTATTTAA
1 ATTTATTTAA
1247042 AATTAATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
22 9 0.18
24 4 0.08
25 22 0.43
26 13 0.25
27 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTATTTAATAATAAACTTTT
Found at i:1247028 original size:26 final size:25
Alignment explanation
Indices: 1246980--1247041 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
1246970 AATTAAATTA
1246980 TTTATTTGATTTAATAAGTAAAACT
1 TTTATTTGATTTAATAAGTAAAACT
* *
1247005 TTTATTTTTATTTAATAA-TAAAAAT
1 TTTA-TTTGATTTAATAAGTAAAACT
1247030 TTT-TTT-ATTTAA
1 TTTATTTGATTTAA
1247042 AATTAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 6 0.18
23 3 0.09
25 13 0.38
26 12 0.35
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTATTTGATTTAATAAGTAAAACT
Found at i:1247215 original size:2 final size:2
Alignment explanation
Indices: 1247202--1247231 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1247192 TGTAAGAAAT
*
1247202 TA TA TA TG 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
1247232 ATTTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1248911 original size:15 final size:15
Alignment explanation
Indices: 1248891--1248937 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1248881 CACTTATTAC
1248891 TTTTTAAATATATAT
1 TTTTTAAATATATAT
* * *
1248906 TTTTTAACTTTTTATT
1 TTTTTAAATATATA-T
1248922 TTTTTAAA-ATATAT
1 TTTTTAAATATATAT
1248936 TT
1 TT
1248938 ATATATGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 3 0.12
15 14 0.56
16 8 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAAATATATAT
Found at i:1251859 original size:25 final size:26
Alignment explanation
Indices: 1251810--1251862 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
1251800 TTGAATTATT
*
1251810 ATTTAATTAATAAAAATTTTATTTAA
1 ATTTAATTAATAAAAATATTATTTAA
1251836 ATTTAATT-ATAAAAATAATT-TTTAA
1 ATTTAATTAATAAAAAT-ATTATTTAA
1251861 AT
1 AT
1251863 ATTTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAATTAATAAAAATATTATTTAA
Found at i:1252009 original size:21 final size:21
Alignment explanation
Indices: 1251982--1252025 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1251972 CTTGTGTTTG
* *
1251982 TAAAAAATTTATGT-TTTTTA
1 TAAAAAAATTATATATTTTTA
1252002 TAAAAAAATTATATATTTTTA
1 TAAAAAAATTATATATTTTTA
1252023 TAA
1 TAA
1252026 TTATCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TAAAAAAATTATATATTTTTA
Found at i:1252029 original size:16 final size:16
Alignment explanation
Indices: 1252008--1252039 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1251998 TTTATAAAAA
1252008 AATTATATATTTTTAT
1 AATTATATATTTTTAT
*
1252024 AATTATCTATTTTTAT
1 AATTATATATTTTTAT
1252040 GAATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATATATTTTTAT
Found at i:1255042 original size:27 final size:27
Alignment explanation
Indices: 1255004--1255057 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1254994 AACAAACGCA
*
1255004 ACGTTAATTATCGGTCA-GATTATCCAT
1 ACGTTAATTATCAGTCACG-TTATCCAT
1255031 ACGTTAATTATCAGTCACGTTATCCAT
1 ACGTTAATTATCAGTCACGTTATCCAT
1255058 TTGTCTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (27 bp):
ACGTTAATTATCAGTCACGTTATCCAT
Found at i:1261039 original size:15 final size:16
Alignment explanation
Indices: 1260986--1261040 Score: 69
Period size: 15 Copynumber: 3.4 Consensus size: 16
1260976 TATTTAAATA
1260986 AAAATAATTATATTATTT
1 AAAAT-ATT-TATTATTT
*
1261004 AAAAT-TTTATTTTTT
1 AAAATATTTATTATTT
1261019 AAAATATTTA-TATTT
1 AAAATATTTATTATTT
1261034 AAAATAT
1 AAAATAT
1261041 ATTTAGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 23 0.68
16 6 0.18
18 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATTTATTATTT
Found at i:1261056 original size:16 final size:16
Alignment explanation
Indices: 1261016--1261057 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
1261006 AATTTTATTT
*
1261016 TTTAAA-ATATTTATA
1 TTTAAATATATTTAGA
1261031 TTTAAAATATATTTAGA
1 TTT-AAATATATTTAGA
1261048 TTTAAATATA
1 TTTAAATATA
1261058 AGTATTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTAAATATATTTAGA
Found at i:1261249 original size:25 final size:26
Alignment explanation
Indices: 1261203--1261252 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1261193 AAATAATTTT
1261203 TATTAATTAAAATATATAAATATTAC
1 TATTAATTAAAATATATAAATATTAC
* * *
1261229 TATTAA-TATAATATTTTAATATTA
1 TATTAATTAAAATATATAAATATTA
1261253 TTTTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTAATTAAAATATATAAATATTAC
Found at i:1262411 original size:202 final size:203
Alignment explanation
Indices: 1262009--1262415 Score: 604
Period size: 202 Copynumber: 2.0 Consensus size: 203
1261999 GACATGTGTT
*
1262009 CCAGTTCAGCAGACACGATAGTGCAGACCAACATTAGATGCCTACGTAGAAAATTATGCTTATGT
1 CCAGTTCAGCAGACACGATAGTGCAGACCAACATTAGATGCCTACGTAGAAAATTATACTTATGT
* * *
1262074 TTTATGTTTTAATATATCGGACATAACTATTAAACATAAAAATATAAAAAAGTAAATAATTCAGA
66 TTTATATTTTAATATATCGAACATAAATATTAAACATAAAAATAT--AAAAG-AAATAATTCAGA
* * * *
1262139 AGAGTATTAAAATGTTAGGGGTATGAAGCAACTCATGTCATCTGTGTTTTCGTGTTGTGGTATTT
128 AGAGTATTAAAATGTTAGGGGTATGAAACAACTCATGTCATCTGTATTTTCCTGTTGTGGTATGT
1262204 TGCTTGAAATC
193 TGCTTGAAATC
* *
1262215 CCAGTTCAGGAGACACGATAGTGCAGACCAACATTAGATGCCTACTTAGAAAATTATACTTAATG
1 CCAGTTCAGCAGACACGATAGTGCAGACCAACATTAGATGCCTACGTAGAAAATTATACTT-ATG
* * * * *
1262280 TTTTATATTTTAATATATCGAACTTAAATATTAAATATAAAGATAT-TAA-AAA-AATTCCGATA
65 TTTTATATTTTAATATATCGAACATAAATATTAAACATAAAAATATAAAAGAAATAATTCAGA-A
*
1262342 GAGTATTAAACTGTTAGGGGTATGAAACAACTCATGTCATCTGTATTTTCCTGTTGTGGTATGTT
129 GAGTATTAAAATGTTAGGGGTATGAAACAACTCATGTCATCTGTATTTTCCTGTTGTGGTATGTT
1262407 GCTTGAAAT
194 GCTTGAAAT
1262416 GTGGTTTTTG
Statistics
Matches: 183, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
201 7 0.04
202 73 0.40
204 2 0.01
206 58 0.32
207 43 0.23
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (203 bp):
CCAGTTCAGCAGACACGATAGTGCAGACCAACATTAGATGCCTACGTAGAAAATTATACTTATGT
TTTATATTTTAATATATCGAACATAAATATTAAACATAAAAATATAAAAGAAATAATTCAGAAGA
GTATTAAAATGTTAGGGGTATGAAACAACTCATGTCATCTGTATTTTCCTGTTGTGGTATGTTGC
TTGAAATC
Found at i:1263369 original size:6 final size:6
Alignment explanation
Indices: 1263360--1263391 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1263350 GAAAAGAAGA
1263360 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AG
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AG
1263392 GGGGAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:1266385 original size:34 final size:34
Alignment explanation
Indices: 1266347--1266437 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 34
1266337 TAGGTGAAGC
* *
1266347 ATATTAGGTGTGTTAGGTGATGTATTTGGTGAAA
1 ATATTAGGTGTGTTAGGTGATATATTTGATGAAA
1266381 ATATTAGGTGTGTTAGGTGATATATTTGATGAAA
1 ATATTAGGTGTGTTAGGTGATATATTTGATGAAA
* * *
1266415 ATGTTAAGTGTGTTAGGTAATAT
1 ATATTAGGTGTGTTAGGTGATAT
1266438 GTTAAGTGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.30, C:0.00, G:0.29, T:0.42
Consensus pattern (34 bp):
ATATTAGGTGTGTTAGGTGATATATTTGATGAAA
Found at i:1270963 original size:34 final size:34
Alignment explanation
Indices: 1270925--1271007 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
1270915 GTGAAGCATA
*
1270925 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGATGAGAATG
1270959 TTAGGTGTGTTAGGTGATGTATTTGATGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGATGAGAATG
1270993 TTAGGTGTGTTAGGT
1 TTAGGTGTGTTAGGT
1271008 AATATGTTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.42
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTGATGTATTTGATGAGAATG
Found at i:1278376 original size:40 final size:42
Alignment explanation
Indices: 1278315--1278408 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 42
1278305 TGATACTAAA
* *
1278315 AAAATA-ATA-AAAATACGATTATAAATCTA-TAAATATTT-T
1 AAAATATATATAAAATACAATTATAAATATATTAAA-ATTTAT
*
1278354 AAAATATATATAAAATA-AATTATTAATATATTAAAATTTAT
1 AAAATATATATAAAATACAATTATAAATATATTAAAATTTAT
1278395 ATAAATATAATATA
1 A-AAATAT-ATATA
1278409 CATATACGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
39 6 0.13
40 17 0.37
41 12 0.26
42 6 0.13
43 5 0.11
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (42 bp):
AAAATATATATAAAATACAATTATAAATATATTAAAATTTAT
Found at i:1278388 original size:32 final size:34
Alignment explanation
Indices: 1278334--1278404 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 34
1278324 AAAATACGAT
*
1278334 TATAAATCTATAAATATTTTAAAATATATATAAA
1 TATAAATCTATAAATATATTAAAATATATATAAA
* *
1278368 -ATAAAT-TATTAATATATTAAAATTTATATAAA
1 TATAAATCTATAAATATATTAAAATATATATAAA
1278400 TATAA
1 TATAA
1278405 TATACATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 23 0.70
33 10 0.30
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
TATAAATCTATAAATATATTAAAATATATATAAA
Found at i:1278401 original size:20 final size:20
Alignment explanation
Indices: 1278334--1278403 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1278324 AAAATACGAT
*
1278334 TATAAATCTA-TAAATATTT-
1 TATAAATATATTAAA-ATTTA
**
1278353 TA-AAATATATATAAAATAAA
1 TATAAATATAT-TAAAATTTA
*
1278373 TTATTAATATATTAAAATTTA
1 -TATAAATATATTAAAATTTA
1278394 TATAAATATA
1 TATAAATATA
1278404 ATATACATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
18 6 0.15
19 4 0.10
20 13 0.33
21 9 0.23
22 7 0.18
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
TATAAATATATTAAAATTTA
Found at i:1278565 original size:13 final size:14
Alignment explanation
Indices: 1278539--1278567 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1278529 TTTTAAAACT
1278539 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
1278553 TTTTAAAAA-AAAA
1 TTTTAAAAATAAAA
1278566 TT
1 TT
1278568 GTCAGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:1279559 original size:28 final size:28
Alignment explanation
Indices: 1279524--1279591 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
1279514 ATATCTTTTC
*
1279524 TTTT-ATTTTTA-TTATACTTAAATAACT
1 TTTTAATTTTTAGTTATA-TTAAATAAAT
*
1279551 TTTTAATTTTTAAGTTGTATTAAATAAAT
1 TTTTAATTTTT-AGTTATATTAAATAAAT
1279580 TTTTAATTTTTA
1 TTTTAATTTTTA
1279592 ATTTGTACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 4 0.11
28 7 0.19
29 21 0.58
30 4 0.11
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTAATTTTTAGTTATATTAAATAAAT
Found at i:1279561 original size:29 final size:30
Alignment explanation
Indices: 1279538--1279604 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
1279528 ATTTTTATTA
*
1279538 TACTTAAATAACTTTTTAATTTTTAAGTTG
1 TACTTAAATAAATTTTTAATTTTTAAGTTG
*
1279568 TA-TTAAATAAATTTTTAATTTTTAATTTG
1 TACTTAAATAAATTTTTAATTTTTAAGTTG
1279597 TACTTAAA
1 TACTTAAA
1279605 AGAAATTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (30 bp):
TACTTAAATAAATTTTTAATTTTTAAGTTG
Found at i:1279909 original size:17 final size:18
Alignment explanation
Indices: 1279876--1279910 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1279866 TTATTATTTG
*
1279876 TTTAAATATTTTTTGTAA
1 TTTAAATATTTTATGTAA
1279894 TTTAAA-ATTTTATGTAA
1 TTTAAATATTTTATGTAA
1279911 CTGAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTAAATATTTTATGTAA
Found at i:1281246 original size:22 final size:22
Alignment explanation
Indices: 1281208--1281291 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
1281198 TTTAATACTT
1281208 TAAATAT-ATA-AAAAATAATA
1 TAAATATGATATAAAAATAATA
1281228 TAAATATGATATAAAAATAAT-
1 TAAATATGATATAAAAATAATA
*
1281249 TAAAATATAATATAAAAATGAATA
1 T-AAATATGATATAAAAAT-AATA
* *
1281273 -CAATACGAATATAAAAATA
1 TAAATATG-ATATAAAAATA
1281292 TAAAAAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.13
21 4 0.07
22 30 0.56
23 13 0.24
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
TAAATATGATATAAAAATAATA
Found at i:1281823 original size:33 final size:33
Alignment explanation
Indices: 1281781--1281843 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1281771 AAGGTGTAGT
* *
1281781 TGGTGCCCAAGGTTCAGGAGTTGGTACTGGTTC
1 TGGTGCCCAAGGTCCAGGACTTGGTACTGGTTC
*
1281814 TGGTGCCCAAGGTCCAGGACTTGGTGCTGG
1 TGGTGCCCAAGGTCCAGGACTTGGTACTGG
1281844 GGCTGGTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.21, G:0.38, T:0.27
Consensus pattern (33 bp):
TGGTGCCCAAGGTCCAGGACTTGGTACTGGTTC
Found at i:1281850 original size:33 final size:33
Alignment explanation
Indices: 1281781--1281855 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
1281771 AAGGTGTAGT
* * **
1281781 TGGTGCCCAAGGTTCAGGAGTTGGTACTGGTTC
1 TGGTGCCCAAGGTCCAGGACTTGGTACTGGGGC
*
1281814 TGGTGCCCAAGGTCCAGGACTTGGTGCTGGGGC
1 TGGTGCCCAAGGTCCAGGACTTGGTACTGGGGC
*
1281847 TGGTTCCCA
1 TGGTGCCCA
1281856 GGGTGTTCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (33 bp):
TGGTGCCCAAGGTCCAGGACTTGGTACTGGGGC
Done.