Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold439
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: 246264
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.31
Warning! 21786 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5034 original size:38 final size:38
Alignment explanation
Indices: 4939--5040 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 38
4929 ATTGAATAAA
* * *
4939 TCAACACTAGCAGTAATCATGCTTAACATGCATTCAGT
1 TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
** * * * *
4977 TCATTACTAGCAATTAACATGATTTACGTGTATTCAGT
1 TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
* *
5015 TCAACACAAGCAGTAAACATGTTTTA
1 TCAACACTAGCAGTAAACATGATTTA
5041 ACAAGTATTC
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (38 bp):
TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
Found at i:9963 original size:38 final size:38
Alignment explanation
Indices: 9868--9969 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 38
9858 ATTGAATAAA
* * *
9868 TCAACACTAGCAGTAATCATGCTTAACATGCATTCAGT
1 TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
** * * * *
9906 TCATTACTAGCAATTAACATGATTTACGTGTATTCAGT
1 TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
* *
9944 TCAACACAAGCAGTAAACATGTTTTA
1 TCAACACTAGCAGTAAACATGATTTA
9970 ACAAGTATTC
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (38 bp):
TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
Found at i:10965 original size:559 final size:559
Alignment explanation
Indices: 9908--11024 Score: 2020
Period size: 559 Copynumber: 2.0 Consensus size: 559
9898 CATTCAGTTC
*
9908 ATTACTAGCAATTAACATGATTTACGTGTATTCAGTTCAACACAAGCAGTAAACATGTTTTAACA
1 ATTACTAGCAATTAACATGATTTACGTGTATTCAGTTCAACACAAGCAGTAAACATGATTTAACA
* *
9973 AGTATTCAATAGGGTGGTGACAATATTAACACTAACAGTTTATCAGTTTTTCACAATGACAGTAG
66 AGTATTCAATAGGGTGGTGACAATATTAACACTAACAGTTTATCAATTTTTCACAATGACAATAG
10038 CATGTACTATACACTTCACATACGATATAGACTTAACACTTCAATCATTAAATCACAAATGCCAG
131 CATGTACTATACACTTCACATACGATATAGACTTAACACTTCAATCATTAAATCACAAATGCCAG
*
10103 AAAAATACAATATCAGTGACTTAATTGAACAAATAAAAACTCTAAAAATAATTCAGAACATACAT
196 AAAAACACAATATCAGTGACTTAATTGAACAAATAAAAACTCTAAAAATAATTCAGAACATACAT
10168 AGGGACTAAACTGAACATAATGTAAATTTTTGGGCAAAACTATAAAATAGGGGTCACATGGCCGT
261 AGGGACTAAACTGAACATAATGTAAATTTTTGGGCAAAACTATAAAATAGGGGTCACATGGCCGT
* ** * *
10233 TGGAGATGTTATATGCCGTGTGGAAGGGTTACATAGCTGTGTTGCTGGGCCTTGTAACAGGCTGT
326 TGGAGATGTTATATGCCGTGTGGAAGGGTTACACAGCCATGTTGATGGGCCGTGTAACAGGCTGT
* *
10298 AGTCATGTGTCAAACGTTAAAATTACCCTATAGGAAGGATACTACCGTGTGGTTCACGAACTATA
391 AGTCATGTGTCAAACGTTAAAATTACCCTATAGGAAGGATACTACCGTGTGGTTAACGAACTACA
* **
10363 CTAGGGTTTTTAGGGTACATGGTCATAATTTTGAGAGCATTATATATGTGTTGTGTTTGTCATAG
456 CTAGGGTTTTCAGGGTACATGGTCATAATTCCGAGAGCATTATATATGTGTTGTGTTTGTCATAG
10428 CCCGAATATTACTCTTAGTGATATGAAACATTCTTGCAA
521 CCCGAATATTACTCTTAGTGATATGAAACATTCTTGCAA
*
10467 ATTACTAGCAATTAACATGCTTTACGTGTATTCAGTTCAACACAAGCAGTAAACATGATTTAACA
1 ATTACTAGCAATTAACATGATTTACGTGTATTCAGTTCAACACAAGCAGTAAACATGATTTAACA
*
10532 AGTATTCAATAGGGTGGTGACAATATTAACACTAACAGTTTTTCAATTTTTCACAATGACAATAG
66 AGTATTCAATAGGGTGGTGACAATATTAACACTAACAGTTTATCAATTTTTCACAATGACAATAG
10597 CATGTACTATACACTTCACATACGATATAGACTTAACACTTCAATCATTAAATCACAAATGCCAG
131 CATGTACTATACACTTCACATACGATATAGACTTAACACTTCAATCATTAAATCACAAATGCCAG
*
10662 AAAAACACAATATCAGTGACTTAATTGAACAAATAAAAACTCTAAAAATAATTCAGAGCATACAT
196 AAAAACACAATATCAGTGACTTAATTGAACAAATAAAAACTCTAAAAATAATTCAGAACATACAT
*
10727 AGGGACTAAACTGAACATAATGTAAATTTTTGGGCAAAACTATAAAATAGGGTTCACATGGCCG-
261 AGGGACTAAACTGAACATAATGTAAATTTTTGGGCAAAACTATAAAATAGGGGTCACATGGCCGT
* *
10791 TGTGAGATGTTATATGCCGTGTGGAAGGGTTACACGGCCATGTTGATGGGCCGTGTAATAGGCTG
326 TG-GAGATGTTATATGCCGTGTGGAAGGGTTACACAGCCATGTTGATGGGCCGTGTAACAGGCTG
*
10856 TAGTCATGTGTCAAACGTTAAAATTACCCTATAGGAAGGATACTACCGTGTGGTTAATGAACTAC
390 TAGTCATGTGTCAAACGTTAAAATTACCCTATAGGAAGGATACTACCGTGTGGTTAACGAACTAC
10921 ACTAGGGTTTTCAGGGTACATGGTCATAATTCCGAGAGCATTATATATGTGTTGTGTTTGTCATA
455 ACTAGGGTTTTCAGGGTACATGGTCATAATTCCGAGAGCATTATATATGTGTTGTGTTTGTCATA
*
10986 GCCCGAATATTACTCTTAGTGATATGACACATTCTTGCA
520 GCCCGAATATTACTCTTAGTGATATGAAACATTCTTGCA
11025 TTAGGTCTAT
Statistics
Matches: 535, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
558 2 0.00
559 533 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (559 bp):
ATTACTAGCAATTAACATGATTTACGTGTATTCAGTTCAACACAAGCAGTAAACATGATTTAACA
AGTATTCAATAGGGTGGTGACAATATTAACACTAACAGTTTATCAATTTTTCACAATGACAATAG
CATGTACTATACACTTCACATACGATATAGACTTAACACTTCAATCATTAAATCACAAATGCCAG
AAAAACACAATATCAGTGACTTAATTGAACAAATAAAAACTCTAAAAATAATTCAGAACATACAT
AGGGACTAAACTGAACATAATGTAAATTTTTGGGCAAAACTATAAAATAGGGGTCACATGGCCGT
TGGAGATGTTATATGCCGTGTGGAAGGGTTACACAGCCATGTTGATGGGCCGTGTAACAGGCTGT
AGTCATGTGTCAAACGTTAAAATTACCCTATAGGAAGGATACTACCGTGTGGTTAACGAACTACA
CTAGGGTTTTCAGGGTACATGGTCATAATTCCGAGAGCATTATATATGTGTTGTGTTTGTCATAG
CCCGAATATTACTCTTAGTGATATGAAACATTCTTGCAA
Found at i:12229 original size:5 final size:5
Alignment explanation
Indices: 12219--12253 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
12209 TAGAATATGT
* *
12219 TTTTA TTTTA TTGTA TTATA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
12254 AAACAGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:17891 original size:38 final size:38
Alignment explanation
Indices: 17796--17897 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 38
17786 ATTGAATAAA
* * *
17796 TCAACACTAGCAGTAATCATGCTTAACATGCATTCAGT
1 TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
** * * * *
17834 TCATTACTAGCAATTAACATGATTTACGTGTATTCAGT
1 TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
* *
17872 TCAACACAAGCAGTAAACATGTTTTA
1 TCAACACTAGCAGTAAACATGATTTA
17898 ACAAGTATTC
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (38 bp):
TCAACACTAGCAGTAAACATGATTTACATGCATTCAGT
Found at i:29923 original size:15 final size:16
Alignment explanation
Indices: 29895--29924 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29885 TAAATTCATA
29895 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
29911 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
29925 AATTATATGT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:29944 original size:18 final size:17
Alignment explanation
Indices: 29917--29950 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29907 TTATTAAGAA
*
29917 TTTTATTAAATTATATG
1 TTTTATTAAAATATATG
29934 TTTTAATTAAAATATAT
1 TTTT-ATTAAAATATAT
29951 TTAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTATTAAAATATATG
Found at i:30151 original size:39 final size:44
Alignment explanation
Indices: 30097--30202 Score: 123
Period size: 39 Copynumber: 2.5 Consensus size: 44
30087 TTTTCTTATG
* *
30097 CTATTACACCTCTATTCCATT-CA-A-CCAAACACAAGAA-TA-
1 CTATTACGCCTCTATTCCATTCCATAGCCAAACAAAAGAATTAC
*
30136 CTATTATGCCTCTATTCCATTCCATTCAGCCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCATTCCA-T-AGCCAAACAAAAGAATTAC
*
30182 CTATTACGCCTCTATTTCATT
1 CTATTACGCCTCTATTCCATT
30203 ACACCTCTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
39 19 0.35
40 2 0.04
43 1 0.02
44 12 0.22
45 2 0.04
46 19 0.35
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CTATTACGCCTCTATTCCATTCCATAGCCAAACAAAAGAATTAC
Found at i:30159 original size:44 final size:46
Alignment explanation
Indices: 30110--30202 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
30100 TTACACCTCT
* *
30110 ATTCCATTCAACCAAACACAAGAA-TA-CTATTATGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
* *
30154 ATTCCATTCAGCCAAACAAAAGAATTACCTATTACGCCTCTATTTC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
30200 ATT
1 ATT
30203 ACACCTCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 22 0.51
45 2 0.05
46 19 0.44
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:30209 original size:16 final size:16
Alignment explanation
Indices: 30184--30221 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30174 AGAATTACCT
* *
30184 ATTACGCCTCTATTTC
1 ATTACACCTCTATTCC
30200 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
30216 ATTACA
1 ATTACA
30222 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:37190 original size:72 final size:72
Alignment explanation
Indices: 37068--37222 Score: 222
Period size: 72 Copynumber: 2.2 Consensus size: 72
37058 AACGTGGTTC
* * *
37068 CAACATCTCACATCACTCCGAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCTGA
1 CAACACCTCACATCACTCCAAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
37133 A-GAGATG
66 AGGA-ATG
* * * * *
37140 CAACACCTCACATCCCTTCAAAGTCTTGAAATTGATGATTGCCCAGAGCTGTCGTTTCTGCCCGA
1 CAACACCTCACATCACTCCAAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
37205 AGGAATG
66 AGGAATG
37212 CAACACCTCAC
1 CAACACCTCAC
37223 TGCACTCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 72 0.97
73 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (72 bp):
CAACACCTCACATCACTCCAAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
AGGAATG
Found at i:37246 original size:72 final size:72
Alignment explanation
Indices: 37068--37246 Score: 204
Period size: 72 Copynumber: 2.5 Consensus size: 72
37058 AACGTGGTTC
* * * * *
37068 CAACATCTCACATCACTCCGAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCTGA
1 CAACACCTCACATCACTTCAAAGTATTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
37133 AGAGATG
66 AGAGATG
* * * * *
37140 CAACACCTCACATCCCTTCAAAGTCTTGAAATTGATGATTGCCCAGAGCTGTCGTTTCTGCCCGA
1 CAACACCTCACATCACTTCAAAGTATTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
37205 AG-GAATG
66 AGAG-ATG
37212 CAACACCTCAC-TGCAC-TCAAAAG-ATTAAAGATTGA
1 CAACACCTCACAT-CACTTC-AAAGTATTAAA-ATTGA
37247 AGGGTGTCCA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
71 8 0.09
72 84 0.91
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (72 bp):
CAACACCTCACATCACTTCAAAGTATTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
AGAGATG
Found at i:39653 original size:22 final size:24
Alignment explanation
Indices: 39615--39663 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
39605 GTTTATATGT
*
39615 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATGTACTAAAAGTATAAA
39637 ATATGTATGTA-TAAAAAGTATAAA
1 ATATGTATGTACT-AAAAGTATAAA
39661 ATA
1 ATA
39664 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATGTATGTACTAAAAGTATAAA
Found at i:53064 original size:16 final size:15
Alignment explanation
Indices: 53035--53078 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
53025 AAATTAGAGA
53035 ATTCTATTAAATTTT
1 ATTCTATTAAATTTT
* *
53050 ATTCTTATTATATTTA
1 ATTC-TATTAAATTTT
53066 ATTTCTATTAAAT
1 A-TTCTATTAAAT
53079 CCATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 17 0.71
17 3 0.12
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTCTATTAAATTTT
Found at i:56706 original size:20 final size:20
Alignment explanation
Indices: 56677--56753 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
56667 CGTAAAATAG
*
56677 ATAAAAAAATTATAATTTAA
1 ATAAATAAATTATAATTTAA
*
56697 ATAAATAAATGTGATGTTATCTTTATA
1 ATAAATAAAT-T-A---TA-ATTTA-A
56724 GATAAA-AAATTATAATTTAA
1 -ATAAATAAATTATAATTTAA
56744 ATAAATAAAT
1 ATAAATAAAT
56754 GTGATGTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 18
0.68 0.05 0.27
Matches are distributed among these distances:
19 5 0.11
20 14 0.31
21 5 0.11
22 3 0.07
25 3 0.07
26 5 0.11
27 5 0.11
28 5 0.11
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (20 bp):
ATAAATAAATTATAATTTAA
Found at i:56738 original size:47 final size:48
Alignment explanation
Indices: 56673--56769 Score: 187
Period size: 47 Copynumber: 2.0 Consensus size: 48
56663 GTAACGTAAA
56673 ATAGATAAAAAAATTATAATTTAAATAAATAAATGTGATGTTATCTTT
1 ATAGATAAAAAAATTATAATTTAAATAAATAAATGTGATGTTATCTTT
56721 ATAGAT-AAAAAATTATAATTTAAATAAATAAATGTGATGTTATCTTT
1 ATAGATAAAAAAATTATAATTTAAATAAATAAATGTGATGTTATCTTT
56768 AT
1 AT
56770 TCCATATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 43 0.88
48 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.40
Consensus pattern (48 bp):
ATAGATAAAAAAATTATAATTTAAATAAATAAATGTGATGTTATCTTT
Found at i:70804 original size:21 final size:20
Alignment explanation
Indices: 70760--70856 Score: 133
Period size: 21 Copynumber: 4.8 Consensus size: 20
70750 ATTTTCGAGG
*
70760 ATATACAATCTTAGATAT-T
1 ATATGCAATCTTAGATATAT
70779 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATAT-AT
70800 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATAT-AT
*
70821 ATATGTAATCTTAGATATAT
1 ATATGCAATCTTAGATATAT
*
70841 GATATGCAATATTAGA
1 -ATATGCAATCTTAGA
70857 AGATATGATT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 17 0.24
20 2 0.03
21 52 0.73
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (20 bp):
ATATGCAATCTTAGATATAT
Found at i:70874 original size:44 final size:42
Alignment explanation
Indices: 70760--70879 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
70750 ATTTTCGAGG
* * **
70760 ATATACAATCTTAGATAT--TATATGCAATCTTAGATATGAT
1 ATATGCAATATTAGATATGATATATATAATCTTAGATATGAT
* *
70800 ATATGCAATCTTAGATATGATATATGTAATCTTAGATAT-AT
1 ATATGCAATATTAGATATGATATATATAATCTTAGATATGAT
*
70841 GATATGCAATATTAGAAGATATGAT-TTTATAATCTTAGA
1 -ATATGCAATATT---AGATATGATATATATAATCTTAGA
70880 GATTTAATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
40 17 0.25
41 2 0.03
42 29 0.42
44 12 0.17
45 9 0.13
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (42 bp):
ATATGCAATATTAGATATGATATATATAATCTTAGATATGAT
Found at i:71127 original size:23 final size:23
Alignment explanation
Indices: 71083--71127 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
71073 TCTTATTTTG
* *
71083 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
71106 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
71128 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:83007 original size:20 final size:19
Alignment explanation
Indices: 82959--83013 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
82949 TTCATGTTTT
* *
82959 TTTTTTAACT-TTGTTATA
1 TTTTTTAAATATTTTTATA
82977 TTTTTTAAAATATTTTTATAA
1 TTTTTT-AAATATTTTTAT-A
82998 TTTTTTAAATGATTTT
1 TTTTTTAAAT-ATTTT
83014 GTGACGTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 3 0.10
20 10 0.32
21 12 0.39
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTTTAAATATTTTTATA
Found at i:91047 original size:14 final size:15
Alignment explanation
Indices: 91030--91067 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
91020 ATTTTCTAGT
*
91030 AAATCATTTTTC-AA
1 AAATCATTTTCCGAA
91044 AAATCATTTTCCGAA
1 AAATCATTTTCCGAA
91059 AAA-CATTTT
1 AAATCATTTT
91068 ACTGTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCCGAA
Found at i:91352 original size:20 final size:20
Alignment explanation
Indices: 91327--91366 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
91317 AATATTTTCT
*
91327 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
91347 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
91367 TCATTTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:91369 original size:34 final size:35
Alignment explanation
Indices: 91315--91381 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
91305 TAAACACCAG
* *
91315 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
91350 AAAACATTTTCCAG-AAATCATTTTAGAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
91382 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:93100 original size:13 final size:13
Alignment explanation
Indices: 93082--93109 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
93072 TTGCATAAAA
93082 TTCAAAATATCTT
1 TTCAAAATATCTT
93095 TTCAAAATATCTT
1 TTCAAAATATCTT
93108 TT
1 TT
93110 GTTGTAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
TTCAAAATATCTT
Found at i:100944 original size:2 final size:2
Alignment explanation
Indices: 100937--100961 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100927 CATTGAATGC
100937 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 A
100962 CACTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101585 original size:113 final size:114
Alignment explanation
Indices: 101376--101602 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 114
101366 ATTGAATACA
101376 GAAAACTATTGGGAAATGGATTGGAACCATGTTCTCTTAACGAGCTAAATCAGTTGGAAACCAAT
1 GAAAACTATTGGGAAATGGATTGGAACCATGTTCTCTTAACGAGCTAAATCAGTTGGAAACCAAT
101441 TTGGAACGAAGCTTAAGCAGGATAAGGGAAAGAAAGGTACATTATATAT
66 TTGGAACGAAGCTTAAGCAGGATAAGGGAAAGAAAGGTACATTATATAT
101490 GAAAACTATT-GGAAATGGATTGGAACCATGTTCTCTTAACGAGCTAAATCAGTTGGAAACCAAT
1 GAAAACTATTGGGAAATGGATTGGAACCATGTTCTCTTAACGAGCTAAATCAGTTGGAAACCAAT
101554 TTGGAACGAAGCTTAAGCAGGATAAGGGAAAGAAAGGTACATTATATAT
66 TTGGAACGAAGCTTAAGCAGGATAAGGGAAAGAAAGGTACATTATATAT
101603 ATATATATAT
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 103 0.91
114 10 0.09
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (114 bp):
GAAAACTATTGGGAAATGGATTGGAACCATGTTCTCTTAACGAGCTAAATCAGTTGGAAACCAAT
TTGGAACGAAGCTTAAGCAGGATAAGGGAAAGAAAGGTACATTATATAT
Found at i:101603 original size:2 final size:2
Alignment explanation
Indices: 101596--101641 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
101586 AAAGGTACAT
*
101596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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 TA TA
101638 TA TA
1 TA TA
101642 AACACATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:101987 original size:25 final size:25
Alignment explanation
Indices: 101959--102039 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
101949 ATTTTCACAC
101959 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTTGGACTGCATTTATACAT
* *
101984 CAAAAATT-GACAGCA--TATACAT
1 CAAAATTTGGACTGCATTTATACAT
* *
102006 -ATATATTTGGACTGCATTTGTACAT
1 CA-AAATTTGGACTGCATTTATACAT
102031 CAAAATTTG
1 CAAAATTTG
102040 ACAGCATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
21 1 0.02
22 11 0.25
23 6 0.14
24 6 0.14
25 19 0.43
26 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (25 bp):
CAAAATTTGGACTGCATTTATACAT
Found at i:102003 original size:22 final size:22
Alignment explanation
Indices: 101959--102052 Score: 73
Period size: 25 Copynumber: 4.0 Consensus size: 22
101949 ATTTTCACAC
*
101959 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTT-GACAGCA--TATACAT
*
101984 CAAAAATTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
* * *
102006 -ATATATTTGGACTGCATTTGTACAT
1 CA-AAATTT-GACAGCA--TATACAT
102031 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
102053 ANNNNNNNNN
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
21 1 0.02
22 17 0.31
23 6 0.11
24 12 0.22
25 18 0.33
26 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
CAAAATTTGACAGCATATACAT
Found at i:102018 original size:47 final size:47
Alignment explanation
Indices: 101963--102053 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
101953 TCACACCAAA
101963 ATTTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
1 ATTTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
* *
102010 ATTTGGACTGCATTTGTACATCAAAATTTGACAGCATATACATA
1 ATTTGGACTGCATTTATACATCAAAAATTGACAGCATATACATA
102054 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (47 bp):
ATTTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATAT
Found at i:106473 original size:2 final size:2
Alignment explanation
Indices: 106466--106511 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
106456 AAAGGTACAT
* *
106466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106508 TA TA
1 TA TA
106512 AGAAAAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:108446 original size:28 final size:29
Alignment explanation
Indices: 108388--108446 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
108378 GATCATAACA
* * *
108388 ATTATAAATATTAAAATTGATATAAACTT
1 ATTATAAATAATAAAATTGATAAAAAATT
108417 ATTA-AAATAATAAGAATT-ATAAAAAATT
1 ATTATAAATAATAA-AATTGATAAAAAATT
108445 AT
1 AT
108447 AAAGATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (29 bp):
ATTATAAATAATAAAATTGATAAAAAATT
Found at i:109073 original size:19 final size:19
Alignment explanation
Indices: 109051--109094 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
109041 TTTTTATAGA
*
109051 AATTTAAT-ATGTTTTTATT
1 AATTTAATAAT-TTTTTAAT
*
109070 AATTTTATAATTTTTTAAT
1 AATTTAATAATTTTTTAAT
109089 AATTTA
1 AATTTA
109095 TTAGAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AATTTAATAATTTTTTAAT
Found at i:120690 original size:31 final size:31
Alignment explanation
Indices: 120651--120740 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
120641 AAAAAAACTT
120651 AATA-TTTAGTGACTTAAATAAAAACTTTTG
1 AATAGTTTAGTGACTTAAATAAAAACTTTTG
*
120681 AATAGTTTAGT-AGCTTAAATGAAAACTTTTG
1 AATAGTTTAGTGA-CTTAAATAAAAACTTTTG
* * *
120712 AATAGTTCAGTGAC-TAAATTATAACTTTT
1 AATAGTTTAGTGACTTAAATAAAAACTTTT
120741 TTTAGTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.34
31 34 0.64
32 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (31 bp):
AATAGTTTAGTGACTTAAATAAAAACTTTTG
Found at i:124404 original size:12 final size:11
Alignment explanation
Indices: 124386--124448 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
124376 CATATATACA
124386 AATTTTTATTT
1 AATTTTTATTT
*
124397 ATATTTTTCTATT
1 A-ATTTTTAT-TT
124410 AATTTTTTATTT
1 AA-TTTTTATTT
*
124422 AAATTTTATTT
1 AATTTTTATTT
*
124433 AAATTTTATTT
1 AATTTTTATTT
124444 -ATTTT
1 AATTTT
124449 CCAATTTTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
10 4 0.09
11 20 0.44
12 12 0.27
13 9 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
AATTTTTATTT
Found at i:126775 original size:21 final size:21
Alignment explanation
Indices: 126751--126790 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
126741 AACTTTTTTT
*
126751 TTATTTACCAATATATATATA
1 TTATTTACCAAAATATATATA
126772 TTATTTACCAAAATATATA
1 TTATTTACCAAAATATATA
126791 AAAAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATTTACCAAAATATATATA
Found at i:126800 original size:17 final size:17
Alignment explanation
Indices: 126780--126831 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
126770 TATTATTTAC
* *
126780 CAAAATATATAAAAAAA
1 CAAAAAATAAAAAAAAA
126797 CAAAAAATAAAAAAAAA
1 CAAAAAATAAAAAAAAA
*
126814 TAAAAACA-AAAAAAAAA
1 CAAAAA-ATAAAAAAAAA
126831 C
1 C
126832 CTGGACTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 29 0.97
18 1 0.03
ACGTcount: A:0.83, C:0.08, G:0.00, T:0.10
Consensus pattern (17 bp):
CAAAAAATAAAAAAAAA
Found at i:126806 original size:15 final size:16
Alignment explanation
Indices: 126788--126829 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
126778 ACCAAAATAT
*
126788 ATAAAAAAACA-AAAA
1 ATAAAAAAAAATAAAA
126803 ATAAAAAAAAATAAAA
1 ATAAAAAAAAATAAAA
*
126819 ACAAAAAAAAA
1 ATAAAAAAAAA
126830 ACCTGGACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (16 bp):
ATAAAAAAAAATAAAA
Found at i:126898 original size:27 final size:27
Alignment explanation
Indices: 126860--126936 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
126850 TCCTTGGTGG
*
126860 AGGGAACACTGTTGGCGGCACCAAACA
1 AGGGAACCCTGTTGGCGGCACCAAACA
126887 AGGGAACCCTGTTGGCGGCACCAAACA
1 AGGGAACCCTGTTGGCGGCACCAAACA
**
126914 AGGGTTCCCTGTTGGCGGCACCA
1 AGGGAACCCTGTTGGCGGCACCA
126937 CTCGTGTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.26, C:0.29, G:0.31, T:0.14
Consensus pattern (27 bp):
AGGGAACCCTGTTGGCGGCACCAAACA
Found at i:127037 original size:27 final size:28
Alignment explanation
Indices: 126989--127057 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
126979 AAATAAAAAA
126989 TTACCAAAATAT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
* *
127016 TTACCAAAAAATATATAATTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
127044 TTATCAAAATATAT
1 TTACCAAAATATAT
127058 CAAAAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 11 0.30
28 26 0.70
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:127080 original size:17 final size:16
Alignment explanation
Indices: 127058--127089 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
127048 CAAAATATAT
127058 CAAAAAAATTAAAAAAA
1 CAAAAAAA-TAAAAAAA
127075 CAAAAAAATAAAAAA
1 CAAAAAAATAAAAAA
127090 GAAACAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.09
Consensus pattern (16 bp):
CAAAAAAATAAAAAAA
Found at i:127784 original size:17 final size:18
Alignment explanation
Indices: 127746--127787 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
127736 TTTAGTGTGT
127746 TTTTTTTCTGTTTTTTTA
1 TTTTTTTCTGTTTTTTTA
127764 TTTTTTT-TG-TTTTTTA
1 TTTTTTTCTGTTTTTTTA
127780 CTTTTTTT
1 -TTTTTTT
127788 GATATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
17 9 0.39
18 7 0.30
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.86
Consensus pattern (18 bp):
TTTTTTTCTGTTTTTTTA
Found at i:127821 original size:28 final size:30
Alignment explanation
Indices: 127789--127859 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
127779 ACTTTTTTTG
127789 ATATATTTTGGTAAAT-AAAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAAGTTAT
127817 ATATATTTTGGTAAATAAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAAGTTAT
127847 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
127860 TTTTTTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 16 0.39
29 20 0.49
30 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (30 bp):
ATATATTTTGGTAAATAAAAAAAAAGTTAT
Found at i:127918 original size:19 final size:19
Alignment explanation
Indices: 127896--127936 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
127886 TATAAAACCC
*
127896 ATAATAAAACATTACAAAA
1 ATAATAAAACATTAAAAAA
*
127915 ATAATAAAATATTAAAAAA
1 ATAATAAAACATTAAAAAA
127934 ATA
1 ATA
127937 CCAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAATAAAACATTAAAAAA
Found at i:127942 original size:19 final size:19
Alignment explanation
Indices: 127896--127947 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
127886 TATAAAACCC
* * *
127896 ATAATAAAACATTACAAAA
1 ATAACAAAATATTAAAAAA
*
127915 ATAATAAAATATTAAAAAA
1 ATAACAAAATATTAAAAAA
*
127934 ATACCAAAATATTA
1 ATAACAAAATATTA
127948 TATATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAACAAAATATTAAAAAA
Found at i:128627 original size:27 final size:27
Alignment explanation
Indices: 128554--128630 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
128544 ATAACACGAG
**
128554 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
128581 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
128608 TGGTGCCGCCAACAGTGTTCCCT
1 TGGTGCCGCCAACAGGGTTCCCT
128631 CCACCAAGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:128665 original size:1 final size:1
Alignment explanation
Indices: 128659--128701 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
128649 ATCAGTCTAG
* * * *
128659 TTTTTTTTTTGTTTTTTATTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
128702 GATATATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.02, C:0.00, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:128675 original size:8 final size:8
Alignment explanation
Indices: 128662--128700 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
128652 AGTCTAGTTT
128662 TTTTTTTG
1 TTTTTTTG
128670 TTTTTTAT-
1 TTTTTT-TG
128678 TTTTTTTG
1 TTTTTTTG
128686 TTTTTTTG
1 TTTTTTTG
128694 TTTTTTT
1 TTTTTTT
128701 TGATATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.90
Consensus pattern (8 bp):
TTTTTTTG
Found at i:128682 original size:16 final size:17
Alignment explanation
Indices: 128661--128702 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
128651 CAGTCTAGTT
128661 TTTTTTTTG-TTTTTTA
1 TTTTTTTTGTTTTTTTA
*
128677 TTTTTTTTGTTTTTTTG
1 TTTTTTTTGTTTTTTTA
128694 TTTTTTTTG
1 TTTTTTTTG
128703 ATATATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTTA
Found at i:128682 original size:17 final size:16
Alignment explanation
Indices: 128659--128702 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
128649 ATCAGTCTAG
128659 TTTTTTTTTTGTTTTT
1 TTTTTTTTTTGTTTTT
*
128675 TATTTTTTTTGTTTTT
1 TTTTTTTTTTGTTTTT
128691 TTGTTTTTTTTG
1 TT-TTTTTTTTG
128703 ATATATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTTGTTTTT
Found at i:128711 original size:27 final size:27
Alignment explanation
Indices: 128658--128712 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
128648 AATCAGTCTA
* * *
128658 GTTTTTTTTTTGTTTTTTATTTTTTTT
1 GTTTTTTTTTTGTTTTTGATATATTTT
128685 GTTTTTTTGTTT-TTTTTGATATATTTT
1 GTTTTTTT-TTTGTTTTTGATATATTTT
128712 G
1 G
128713 GTAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.07, C:0.00, G:0.11, T:0.82
Consensus pattern (27 bp):
GTTTTTTTTTTGTTTTTGATATATTTT
Found at i:128734 original size:28 final size:29
Alignment explanation
Indices: 128703--128771 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
128693 GTTTTTTTTG
*
128703 ATATATTTTGGTAAAT-AAAAAAATTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
128731 ATATATTTTGATAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
128760 A-ACATTTTGGTA
1 ATATATTTTGGTA
128772 TTTTTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:132180 original size:33 final size:33
Alignment explanation
Indices: 132116--132181 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
132106 CAGACAATTT
* * *
132116 AACAAAGATACCAGCATCTTAGTTTCGAGTAAC
1 AACAAAGATACCAACATCTGAGTTTCCAGTAAC
132149 AACAAAGATACCAACATCCTGA-TTTCCAGTAAC
1 AACAAAGATACCAACAT-CTGAGTTTCCAGTAAC
132182 CAAGGTATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (33 bp):
AACAAAGATACCAACATCTGAGTTTCCAGTAAC
Found at i:133471 original size:29 final size:29
Alignment explanation
Indices: 133411--133475 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
133401 AAATTTTAAA
* ** * *
133411 TTAATAATGATAAAATTTTGTTTTGATTCT
1 TTAA-AATGATAAAAATTTAATTTAATCCT
133441 TTAAAATGATAAAAATTTAATTTAATCCT
1 TTAAAATGATAAAAATTTAATTTAATCCT
133470 TTAAAA
1 TTAAAA
133476 ATATTAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
TTAAAATGATAAAAATTTAATTTAATCCT
Found at i:134357 original size:27 final size:28
Alignment explanation
Indices: 134307--134375 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
134297 AAATAAAAAA
*
134307 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
134335 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
134362 TTACCAAAATATAT
1 TTACCAAAATATAT
134376 CAAAAAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 23 0.59
28 11 0.28
29 5 0.13
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:134483 original size:27 final size:27
Alignment explanation
Indices: 134445--134518 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
134435 TGGGTGGAGG
* *
134445 GAAGCAGATTGGCAGCACCAAACAAGA
1 GAAGCAGGTTGGCGGCACCAAACAAGA
** * *
134472 GAAGCAGGTTGGCGGCACCAGTCGAGG
1 GAAGCAGGTTGGCGGCACCAAACAAGA
*
134499 GAACCAGGTTGGCGGCACCA
1 GAAGCAGGTTGGCGGCACCA
134519 GTCCTGCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.35, T:0.09
Consensus pattern (27 bp):
GAAGCAGGTTGGCGGCACCAAACAAGA
Found at i:134537 original size:27 final size:27
Alignment explanation
Indices: 134480--134543 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
134470 GAGAAGCAGG
* ** *
134480 TTGGCGGCACCAGTCGAGGGAACCAGG
1 TTGGCGGCACCAGTCCAGCCAACCAGA
* *
134507 TTGGCGGCACCAGTCCTGCCAACTAGA
1 TTGGCGGCACCAGTCCAGCCAACCAGA
134534 TTGGCGGCAC
1 TTGGCGGCAC
134544 TACTCGTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.30, G:0.34, T:0.16
Consensus pattern (27 bp):
TTGGCGGCACCAGTCCAGCCAACCAGA
Found at i:137717 original size:15 final size:15
Alignment explanation
Indices: 137693--137731 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
137683 CAATAAGCAC
*
137693 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
137708 AATAATT-AAATTAG
1 AATAATTAAAACTAG
137722 AATAATTAAA
1 AATAATTAAA
137732 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:137724 original size:14 final size:14
Alignment explanation
Indices: 137705--137733 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
137695 TAACTAAAAC
137705 TAGAATAATTAAAT
1 TAGAATAATTAAAT
137719 TAGAATAATTAAAT
1 TAGAATAATTAAAT
137733 T
1 T
137734 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:138625 original size:12 final size:12
Alignment explanation
Indices: 138608--138636 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
138598 TATAATTTCT
138608 GGCGTTCGGTAC
1 GGCGTTCGGTAC
138620 GGCGTTCGGTAC
1 GGCGTTCGGTAC
138632 GGCGT
1 GGCGT
138637 CCATATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.24, G:0.45, T:0.24
Consensus pattern (12 bp):
GGCGTTCGGTAC
Found at i:140014 original size:19 final size:19
Alignment explanation
Indices: 139990--140030 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
139980 TATAAAACCC
139990 ATAATAAAACA-TTACAAAA
1 ATAATAAAACATTTA-AAAA
*
140009 ATAATAAAATATTTAAAAA
1 ATAATAAAACATTTAAAAA
140028 ATA
1 ATA
140031 CCAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAATAAAACATTTAAAAA
Found at i:140769 original size:24 final size:24
Alignment explanation
Indices: 140742--140789 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
140732 TTTTCCTTGC
*
140742 TTTTTCTTCTTCTTCTTTCATTTTT
1 TTTTTC-TCTTCTCCTTTCATTTTT
*
140767 TTTTTCTCTTCTCCTTTCCTTTT
1 TTTTTCTCTTCTCCTTTCATTTT
140790 CTTTCCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTCTCTTCTCCTTTCATTTTT
Found at i:140795 original size:10 final size:10
Alignment explanation
Indices: 140780--140880 Score: 70
Period size: 10 Copynumber: 10.5 Consensus size: 10
140770 TTCTCTTCTC
140780 CTTTCCTTTT
1 CTTTCCTTTT
*
140790 CTTTCCTAATT
1 CTTTCCT-TTT
140801 -TTT-C-TTT
1 CTTTCCTTTT
***
140808 CTTTCCTCCC
1 CTTTCCTTTT
140818 CTTTCCTTTT
1 CTTTCCTTTT
140828 CTTTCCTTCTT
1 CTTTCCTT-TT
140839 -TTT-C-TTT
1 CTTTCCTTTT
* *
140846 CTTTCCTCTC
1 CTTTCCTTTT
140856 CTTTCCTTTT
1 CTTTCCTTTT
* *
140866 CCTTCTTTTT
1 CTTTCCTTTT
140876 CTTTC
1 CTTTC
140881 TTCCTTTCTT
Statistics
Matches: 68, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
7 4 0.06
8 7 0.10
9 4 0.06
10 49 0.72
11 4 0.06
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:140808 original size:18 final size:18
Alignment explanation
Indices: 140787--140882 Score: 72
Period size: 18 Copynumber: 5.3 Consensus size: 18
140777 CTCCTTTCCT
*
140787 TTTCTTTCCTAATTTTTC
1 TTTCTTTCCTACTTTTTC
* * *
140805 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-ACTTTTTC
*
140824 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTACTTTTTC
*
140843 TTTCTTTCCT-CTCCTTTC
1 TTTCTTTCCTACT-TTTTC
* *
140861 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTACTTTTTC
140877 TTTCTT
1 TTTCTT
140883 CCTTTCTTTC
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
16 10 0.16
17 6 0.10
18 26 0.43
19 9 0.15
20 10 0.16
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCTTTCCTACTTTTTC
Found at i:140813 original size:76 final size:73
Alignment explanation
Indices: 140723--140901 Score: 170
Period size: 76 Copynumber: 2.4 Consensus size: 73
140713 AATTACCTTA
* * * *
140723 TTTTCTTTTTTTTCCTTGCTTTTTCTTCTTC-TTCTTTCATTTTT-TTT-TTCTCTTCTCCTTTC
1 TTTTC-TTTCTTTCCTTCCTTTTTCTTCTTCTTTCCTTC-TTTTTCTTTCTT-TCCTCTCCTTTC
*
140785 CTTTTCTTTCCTAAT
63 CTTTTCCTT-C---T
* * *
140800 TTTTCTTTCTTTCCTCCCCTTTCCTT-TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTT
1 TTTTCTTTCTTTCCTTCCTTTTTCTTCTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTT
140864 TTCCTTCT
66 TTCCTTCT
*
140872 TTTTCTTTC-TTCCTTTCTTTCTTCTTCTTC
1 TTTTCTTTCTTTCCTTCCTTT-TTCTTCTTC
140902 CCCTCTCCTT
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
71 8 0.09
72 14 0.16
73 3 0.04
75 9 0.11
76 44 0.52
77 7 0.08
ACGTcount: A:0.02, C:0.30, G:0.01, T:0.68
Consensus pattern (73 bp):
TTTTCTTTCTTTCCTTCCTTTTTCTTCTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTT
TTCCTTCT
Found at i:140828 original size:38 final size:38
Alignment explanation
Indices: 140779--140866 Score: 149
Period size: 38 Copynumber: 2.3 Consensus size: 38
140769 TTTCTCTTCT
140779 CCTTTCCTTTTCTTTCCTAATTTTTCTTTCTTTCCTCC
1 CCTTTCCTTTTCTTTCCTAATTTTTCTTTCTTTCCTCC
** *
140817 CCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1 CCTTTCCTTTTCTTTCCTAATTTTTCTTTCTTTCCTCC
140855 CCTTTCCTTTTC
1 CCTTTCCTTTTC
140867 CTTCTTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.62
Consensus pattern (38 bp):
CCTTTCCTTTTCTTTCCTAATTTTTCTTTCTTTCCTCC
Found at i:140841 original size:14 final size:14
Alignment explanation
Indices: 140824--140897 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
140814 TCCCCTTTCC
140824 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
140838 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
140853 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
140872 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
140884 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
140897 T
1 T
140898 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:140849 original size:28 final size:28
Alignment explanation
Indices: 140818--140897 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
140808 CTTTCCTCCC
140818 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
140846 CTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCTTT
1 CTTT-C-CT--TTT-C-TTTCCTTCTTTTTCTTT
140880 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
140898 CTTCCCCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
27 1 0.02
28 7 0.15
29 1 0.02
30 2 0.04
31 1 0.02
32 4 0.09
33 3 0.07
34 18 0.39
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTT
Found at i:140881 original size:10 final size:10
Alignment explanation
Indices: 140723--140900 Score: 58
Period size: 10 Copynumber: 16.7 Consensus size: 10
140713 AATTACCTTA
140723 TTTTCTTT-T
1 TTTTCTTTCT
*
140732 TTTTCCTTGCT
1 TTTT-CTTTCT
140743 TTTTC-TTCT
1 TTTTCTTTCT
*
140752 TCTTCTTTCATT
1 TTTTCTTTC--T
*
140764 TTTTTTTTCT
1 TTTTCTTTCT
* *
140774 CTTCTCCTTTCC
1 -TT-TTCTTTCT
140786 TTTTCTTTCCTAAT
1 TTTTCTTT-C---T
140800 TTTTCTTTC-
1 TTTTCTTTCT
* ** *
140809 TTTCCTCCCC
1 TTTTCTTTCT
*
140819 TTTCCTTT-T
1 TTTTCTTTCT
* *
140828 CTTTCCTTCT
1 TTTTCTTTCT
140838 TTTTCTTTCT
1 TTTTCTTTCT
*
140848 TTCCTCTCCTTTCC
1 TT--T-T-CTTTCT
*
140862 TTTTCCTTCT
1 TTTTCTTTCT
140872 TTTTCTTTCT
1 TTTTCTTTCT
140882 TCCTTTCTTTCT
1 T--TTTCTTTCT
*
140894 TCTTCTT
1 TTTTCTT
140901 CCCCTCTCCT
Statistics
Matches: 124, Mismatches: 26, Indels: 37
0.66 0.14 0.20
Matches are distributed among these distances:
9 22 0.18
10 49 0.40
11 11 0.09
12 25 0.20
13 2 0.02
14 15 0.12
ACGTcount: A:0.02, C:0.30, G:0.01, T:0.68
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:140881 original size:38 final size:38
Alignment explanation
Indices: 140776--140888 Score: 147
Period size: 38 Copynumber: 3.0 Consensus size: 38
140766 TTTTTTCTCT
* **
140776 TCTCCTTTCCTTTTCTTTCCTAATTTTTCTTTCTTTCC
1 TCTCCTTTCCTTTTCCTTCCTTTTTTTTCTTTCTTTCC
* * *
140814 TCCCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TCTCCTTTCCTTTTCCTTCCTTTTTTTTCTTTCTTTCC
*
140852 TCTCCTTTCCTTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 TCTCCTTTCCTTTTCCTTCCTTTTT-TTTCTTTCTTTC
140889 TTTCTTCTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 5 0.07
38 62 0.93
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (38 bp):
TCTCCTTTCCTTTTCCTTCCTTTTTTTTCTTTCTTTCC
Found at i:140893 original size:22 final size:23
Alignment explanation
Indices: 140858--140900 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
140848 TTCCTCTCCT
*
140858 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
140881 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
140901 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:140898 original size:28 final size:30
Alignment explanation
Indices: 140820--140901 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 30
140810 TTCCTCCCCT
*
140820 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
*
140852 TCTCCTTTCCTTT-TCCTTCTT-TTTCTTT-C
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
140881 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
140902 CCCTCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 4 0.09
28 13 0.30
29 2 0.05
30 7 0.16
31 6 0.14
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:140911 original size:42 final size:40
Alignment explanation
Indices: 140799--140914 Score: 105
Period size: 42 Copynumber: 2.9 Consensus size: 40
140789 TCTTTCCTAA
* *
140799 TTTTTCTTTCTTTCCTCCCCTT-TCCT-T--TTCTTTCCTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT--TTC
* * *
140837 TTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
* *
140877 TTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
140915 CCCCCCACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
38 21 0.33
39 2 0.03
40 7 0.11
41 2 0.03
42 32 0.50
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
Found at i:141070 original size:10 final size:10
Alignment explanation
Indices: 141055--141090 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
141045 ATCGGTTCAG
141055 GTTTTTTTTT
1 GTTTTTTTTT
*
141065 GTTTTTTTAT
1 GTTTTTTTTT
141075 -TTTTTTTTT
1 GTTTTTTTTT
141084 GTTTTTT
1 GTTTTTT
141091 AGTTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:141079 original size:18 final size:19
Alignment explanation
Indices: 141056--141099 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
141046 TCGGTTCAGG
141056 TTTTTTTTTGTTTTTTTA-T
1 TTTTTTTTTG-TTTTTTAGT
141075 TTTTTTTTTGTTTTTTAGT
1 TTTTTTTTTGTTTTTTAGT
141094 TTTTTT
1 TTTTTT
141100 GATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.05, C:0.00, G:0.07, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTAGT
Found at i:141080 original size:19 final size:18
Alignment explanation
Indices: 141055--141099 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
141045 ATCGGTTCAG
141055 GTTTTTTTTTGTTTTTTTA
1 GTTTTTTTTTG-TTTTTTA
*
141074 TTTTTTTTTTGTTTTTTA
1 GTTTTTTTTTGTTTTTTA
141092 GTTTTTTT
1 GTTTTTTT
141100 GATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.04, C:0.00, G:0.09, T:0.87
Consensus pattern (18 bp):
GTTTTTTTTTGTTTTTTA
Found at i:141131 original size:27 final size:29
Alignment explanation
Indices: 141101--141169 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
141091 AGTTTTTTTG
141101 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
141128 ATATACTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
141157 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
141170 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.41
28 17 0.46
29 5 0.14
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:143117 original size:20 final size:20
Alignment explanation
Indices: 143092--143162 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 20
143082 AATTACCTTA
143092 TTTTCTTTTTTTTCCTTCCT
1 TTTTCTTTTTTTTCCTTCCT
* * *
143112 TTTTCTTCTTCTT-CTTTCT
1 TTTTCTTTTTTTTCCTTCCT
*
143131 TTTTTTTTTCTCTTCTCCTTTCCT
1 TTTTCTTTT-T-TT-TCC-TTCCT
143155 TTTTCTTT
1 TTTTCTTT
143163 CCTTATTTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 12 0.32
20 12 0.32
21 1 0.03
22 1 0.03
23 1 0.03
24 11 0.29
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTTTTTTTCCTTCCT
Found at i:143137 original size:23 final size:23
Alignment explanation
Indices: 143111--143179 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
143101 TTTTCCTTCC
143111 TTTTTCTTCTTCTTCTTTCTTTT
1 TTTTTCTTCTTCTTCTTTCTTTT
*
143134 TTTTT-TCTCTTCTCCTTTCCTTTT
1 TTTTTCT-TCTTCTTCTTT-CTTTT
* *
143158 TCTTTCCTTATT-TTCTTTCTTT
1 T-TTTTCTTCTTCTTCTTTCTTT
143180 CCTCCCCTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 1 0.03
23 19 0.50
24 11 0.29
25 6 0.16
26 1 0.03
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTCTTCTTCTTCTTTCTTTT
Found at i:143138 original size:24 final size:24
Alignment explanation
Indices: 143111--143179 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
143101 TTTTCCTTCC
143111 TTTTTCTTCTTCTTCTTTCTTTTT
1 TTTTTCTTCTTCTTCTTTCTTTTT
*
143135 TTTTTC-TCTTCTCCTTTCCTTTTT
1 TTTTTCTTCTTCTTCTTT-CTTTTT
* * *
143159 CTTTCCTTATT-TTCTTTCTTT
1 TTTTTCTTCTTCTTCTTTCTTT
143180 CCTCCCCTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 14 0.37
24 21 0.55
25 3 0.08
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTTCTTCTTCTTCTTTCTTTTT
Found at i:143155 original size:43 final size:40
Alignment explanation
Indices: 143107--143238 Score: 124
Period size: 43 Copynumber: 3.2 Consensus size: 40
143097 TTTTTTTTCC
*
143107 TTCCTTTTTCTTCTTCTTCTTTCTTTTTTTTTTCTCTTCTCCT
1 TTCCTTTTTCTT-TCCTTCTTTCTTTTTTTTTTC-C-TCTCCT
* * ** *
143150 TTCCTTTTTCTTTCCTTATTTTCTTTCTTTCCTCCCCTCCCCT
1 TTCCTTTTTCTTTCCTT-CTTTCTTT-TTT-TTTTCCTCTCCT
* *
143193 TTCC-TTTTCTTTCCTTCTTT-TTCTTTCTTTCCTCTCCT
1 TTCCTTTTTCTTTCCTTCTTTCTTTTTTTTTTCCTCTCCT
143231 TTCCTTTT
1 TTCCTTTT
143239 CCTTCTTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
38 13 0.18
39 6 0.08
40 2 0.03
41 3 0.04
42 16 0.22
43 28 0.38
44 4 0.05
45 2 0.03
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (40 bp):
TTCCTTTTTCTTTCCTTCTTTCTTTTTTTTTTCCTCTCCT
Found at i:143206 original size:10 final size:10
Alignment explanation
Indices: 143191--143253 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
143181 CTCCCCTCCC
143191 CTTTCCTTTT
1 CTTTCCTTTT
143201 CTTTCCTTCTT
1 CTTTCCTT-TT
143212 -TTT-C-TTT
1 CTTTCCTTTT
* *
143219 CTTTCCTCTC
1 CTTTCCTTTT
143229 CTTTCCTTTT
1 CTTTCCTTTT
* *
143239 CCTTCTTTTT
1 CTTTCCTTTT
143249 CTTTC
1 CTTTC
143254 TTCCTTTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 2 0.05
10 32 0.76
11 2 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:143216 original size:14 final size:14
Alignment explanation
Indices: 143197--143270 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
143187 TCCCCTTTCC
143197 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
143211 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
143226 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
143245 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
143257 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
143270 T
1 T
143271 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:143239 original size:38 final size:38
Alignment explanation
Indices: 143092--143255 Score: 130
Period size: 38 Copynumber: 4.3 Consensus size: 38
143082 AATTACCTTA
* * *
143092 TTTTCTTTTTTTTCCT-TCCTTTTTCTTCTTC-TTCTTTCT
1 TTTTC-TTTCTTTCCTCTCC-TTTCCTT-TTCTTTCCTTCT
* *
143131 TTTT-TTT-TTCTCTTCTCCTTTCCTTTTTCTTTCCTT-A
1 TTTTCTTTCTT-TCCTCTCCTTTCC-TTTTCTTTCCTTCT
143168 TTTTCTTTCTTTCCTCCCCTCCCCTTTCCTTTTCTTTCCTTCT
1 TTTTCTTTCTTTCCT---CT--CCTTTCCTTTTCTTTCCTTCT
143211 TTTTCTTTCTTTCCTCTCCTTTCC---T-TTTCCTTCT
1 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCCTTCT
143245 TTTTCTTTCTT
1 TTTTCTTTCTT
143256 CCTTTCTTTC
Statistics
Matches: 107, Mismatches: 6, Indels: 29
0.75 0.04 0.20
Matches are distributed among these distances:
34 20 0.19
35 1 0.01
36 2 0.02
37 17 0.16
38 23 0.21
39 6 0.06
40 2 0.02
41 2 0.02
42 12 0.11
43 22 0.21
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.68
Consensus pattern (38 bp):
TTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCCTTCT
Found at i:143244 original size:28 final size:28
Alignment explanation
Indices: 143191--143273 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
143181 CTCCCCTCCC
* * *
143191 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTCTCCTTTCCTTCTTCTTCTTT
143219 CTTTCCTCTCCTTTCCTT-TTCCTTCTTTTT
1 CTTTCCTCTCCTTTCCTTCTT-CTTC--TTT
*
143249 CTTT-CT-TCCTTTCTTTCTTCTTCTT
1 CTTTCCTCTCCTTTCCTTCTTCTTCTT
143274 CCCCTCTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 32 0.68
29 4 0.09
30 7 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (28 bp):
CTTTCCTCTCCTTTCCTTCTTCTTCTTT
Found at i:143254 original size:10 final size:10
Alignment explanation
Indices: 143202--143273 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
143192 TTTCCTTTTC
*
143202 TTTCCTTCTT
1 TTTCTTTCTT
143212 TTTCTTTCTT
1 TTTCTTTCTT
*
143222 TCCTCTCCTTTCCT
1 T--T-T-CTTTCTT
*
143236 TTTCCTTCTT
1 TTTCTTTCTT
143246 TTTCTTTCTT
1 TTTCTTTCTT
143256 CCTTTCTTTCTT
1 --TTTCTTTCTT
*
143268 CTTCTT
1 TTTCTT
143274 CCCCTCTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 29 0.58
11 1 0.02
12 12 0.24
13 1 0.02
14 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:143266 original size:22 final size:23
Alignment explanation
Indices: 143231--143273 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
143221 TTCCTCTCCT
*
143231 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
143254 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
143274 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:143272 original size:18 final size:17
Alignment explanation
Indices: 143198--143275 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
143188 CCCCTTTCCT
143198 TTTCTTTCCTTCTTTTTC
1 TTTC-TTCCTTCTTTTTC
*
143216 TTTCTTTCC-TCTCCTTTC
1 TTTC-TTCCTTCT-TTTTC
*
143234 CTT-TTCCTTCTTTTTC
1 TTTCTTCCTTCTTTTTC
143250 TTTCTTCCTTTCTTTCTTC
1 TTTCTTCC-TTCTTT-TTC
143269 -TTCTTCC
1 TTTCTTCC
143276 CCTCTCCTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
16 10 0.20
17 10 0.20
18 28 0.55
19 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTCTTCCTTCTTTTTC
Found at i:143284 original size:42 final size:40
Alignment explanation
Indices: 143168--143287 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 40
143158 TCTTTCCTTA
* *
143168 TTTTCTTTCTTTCCTC-CCCTCCCCTTTCCTTTTCTTTCCTTCT
1 TTTTCTTTCTTTCCTCTCCTTCCCCTCTCC--TTCTTT--TTCT
* * *
143211 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCT
1 TTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTCT
* *
143251 TTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
143288 CCCCCCACCA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
40 6 0.09
41 2 0.03
42 32 0.48
43 16 0.24
44 10 0.15
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTCT
Found at i:146631 original size:23 final size:22
Alignment explanation
Indices: 146605--146647 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
146595 TTCTTCTTAA
*
146605 TTTTTAGTATTTTTAATTAAAAT
1 TTTTTA-TATTATTAATTAAAAT
146628 TTTTTATATTATTAATTAAA
1 TTTTTATATTATTAATTAAA
146648 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTATATTATTAATTAAAAT
Found at i:147411 original size:33 final size:33
Alignment explanation
Indices: 147347--147412 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
147337 CAGACAATTT
* *
147347 AACAAAGATACCAACATCTTAGTTTCGAGTAAC
1 AACAAAGATACCAACATCTGAGTTTCCAGTAAC
147380 AACAAAGATACCAACATCCTGA-TTTCCAGTAAC
1 AACAAAGATACCAACAT-CTGAGTTTCCAGTAAC
147413 CAAGGTATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (33 bp):
AACAAAGATACCAACATCTGAGTTTCCAGTAAC
Found at i:148956 original size:29 final size:29
Alignment explanation
Indices: 148914--148978 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
148904 AAATTTTAAA
* * * *
148914 TTAATAATGATAAAATTTTATTTTGATTCT
1 TTAA-AATGATAAAAATTTAATTTAATCCT
*
148944 TTAAAATTATAAAAATTTAATTTAATCCT
1 TTAAAATGATAAAAATTTAATTTAATCCT
148973 TTAAAA
1 TTAAAA
148979 ATATTAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (29 bp):
TTAAAATGATAAAAATTTAATTTAATCCT
Found at i:151777 original size:13 final size:13
Alignment explanation
Indices: 151759--151783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
151749 AAAATGAGTA
151759 AATAATAATAATC
1 AATAATAATAATC
151772 AATAATAATAAT
1 AATAATAATAAT
151784 ACAAGATTAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAATAATAATC
Found at i:151831 original size:15 final size:17
Alignment explanation
Indices: 151811--151852 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
151801 TTAAACTTAG
151811 ATAAATA-AATAA-AAT
1 ATAAATACAATAACAAT
151826 ATAAATACAATAACAAT
1 ATAAATACAATAACAAT
151843 A-ATAATACAA
1 ATA-AATACAA
151853 ACTAATAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAATACAATAACAAT
Found at i:152480 original size:30 final size:30
Alignment explanation
Indices: 152438--152498 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
152428 CGATATTTTG
152438 AAATAAACAAAAA-AATAAAAAACAAATAAA
1 AAATAAACAAAAATAATAAAAAA-AAATAAA
* *
152468 AAATATAA-AAAAATGATAAAACAAAATAAA
1 AAATA-AACAAAAATAATAAAAAAAAATAAA
152498 A
1 A
152499 CGAAAATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.13
Consensus pattern (30 bp):
AAATAAACAAAAATAATAAAAAAAAATAAA
Found at i:152499 original size:10 final size:9
Alignment explanation
Indices: 152446--152498 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 9
152436 TGAAATAAAC
152446 AAAAAAATAA
1 AAAAAAAT-A
152456 AAAACAAATA
1 AAAA-AAATA
*
152466 AAAAATATA
1 AAAAAAATA
152475 AAAAAATGATA
1 AAAAAA--ATA
152486 AAACAAAATA
1 AAA-AAAATA
152496 AAA
1 AAA
152499 CGAAAATCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 9 0.24
10 15 0.41
11 10 0.27
12 3 0.08
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Found at i:155421 original size:33 final size:33
Alignment explanation
Indices: 155360--155422 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
155350 CACATGAATG
* *
155360 AAAGATACCAACATCTTAGTTTCGAGTAACAAC
1 AAAGATACCAACATCTGAGTTTCCAGTAACAAC
*
155393 AAAGATACCAACGTCCTGA-TTTCCAGTAAC
1 AAAGATACCAACAT-CTGAGTTTCCAGTAAC
155423 CAAGGTATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (33 bp):
AAAGATACCAACATCTGAGTTTCCAGTAACAAC
Found at i:158027 original size:13 final size:13
Alignment explanation
Indices: 158006--158080 Score: 87
Period size: 13 Copynumber: 5.8 Consensus size: 13
157996 ACACTCAAAT
158006 TTTTCAAAAGTAC
1 TTTTCAAAAGTAC
* *
158019 TTCTCAAAAGCAC
1 TTTTCAAAAGTAC
*
158032 TTCTCAAAAGTAC
1 TTTTCAAAAGTAC
* * *
158045 TTTTCCACAGCAC
1 TTTTCAAAAGTAC
*
158058 TTTTCAAAAATAC
1 TTTTCAAAAGTAC
158071 TTTTCAAAAG
1 TTTTCAAAAG
158081 CAATGAAGAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:158045 original size:26 final size:26
Alignment explanation
Indices: 158009--158082 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
157999 CTCAAATTTT
*
158009 TCAAAAGTACTTCTCAAAAGCACTTC
1 TCAAAAGTACTTTTCAAAAGCACTTC
* * *
158035 TCAAAAGTACTTTTCCACAGCACTTT
1 TCAAAAGTACTTTTCAAAAGCACTTC
*
158061 TCAAAAATACTTTTCAAAAGCA
1 TCAAAAGTACTTTTCAAAAGCA
158083 ATGAAGAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (26 bp):
TCAAAAGTACTTTTCAAAAGCACTTC
Found at i:168106 original size:17 final size:17
Alignment explanation
Indices: 168067--168126 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 17
168057 GACAATAAAA
* *
168067 ATAATATAATAACAAAGT
1 ATAATTTAAAAAC-AAGT
168085 ATAATTTAAAAACAAGT
1 ATAATTTAAAAACAAGT
* *
168102 GTAATTT-AAAA-AATT
1 ATAATTTAAAAACAAGT
168117 ATAATTTAAA
1 ATAATTTAAA
168127 TATTATATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.25
16 6 0.17
17 10 0.28
18 11 0.31
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (17 bp):
ATAATTTAAAAACAAGT
Found at i:168123 original size:15 final size:16
Alignment explanation
Indices: 168067--168126 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
168057 GACAATAAAA
*
168067 ATAATATAATAACAAAGT
1 ATAATTTAA-AAC-AAGT
168085 ATAATTTAAAAACAAGT
1 ATAATTT-AAAACAAGT
* *
168102 GTAATTTAAAA-AATT
1 ATAATTTAAAACAAGT
168117 ATAATTTAAA
1 ATAATTTAAA
168127 TATTATATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 12 0.32
16 4 0.11
17 10 0.27
18 9 0.24
19 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (16 bp):
ATAATTTAAAACAAGT
Found at i:171764 original size:2 final size:2
Alignment explanation
Indices: 171757--171794 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
171747 AAGCCTGAGG
*
171757 GA GA GA GA GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
171795 AATGAGCACA
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:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:173246 original size:6 final size:6
Alignment explanation
Indices: 173235--173263 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
173225 AGGTATGCTC
173235 GTTTTT GTTTTT GTTTTT GTTTTT GTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTT
173264 ATAGCATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
GTTTTT
Found at i:174235 original size:16 final size:18
Alignment explanation
Indices: 174214--174253 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
174204 AATGTTTTTT
174214 ATTAAATTTTTA-C-TTA
1 ATTAAATTTTTATCATTA
174230 ATTAAATTTTTATCATTA
1 ATTAAATTTTTATCATTA
174248 ATTAAA
1 ATTAAA
174254 ATAATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 12 0.55
17 1 0.05
18 9 0.41
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAATTTTTATCATTA
Found at i:174434 original size:26 final size:26
Alignment explanation
Indices: 174379--174448 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
174369 ATTTTTTTCA
*
174379 TAAAAATTATTAAAAATATATATATAT
1 TAAAAA-TATTAAAAATATATAAATAT
* *
174406 TAAAAATATTAAAATTGCTATAAAT-T
1 TAAAAATATTAAAAAT-ATATAAATAT
*
174432 TAAAAGATAATAAAAAT
1 TAAAA-ATATTAAAAAT
174449 TTGAAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (26 bp):
TAAAAATATTAAAAATATATAAATAT
Found at i:174463 original size:19 final size:18
Alignment explanation
Indices: 174427--174466 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
174417 AAATTGCTAT
*
174427 AAATTTAAAAGATAATAA
1 AAATTTAAAAAATAATAA
*
174445 AAATTTGAAAAAATTATAA
1 AAATTT-AAAAAATAATAA
174464 AAA
1 AAA
174467 AATATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATTTAAAAAATAATAA
Found at i:174468 original size:22 final size:22
Alignment explanation
Indices: 174438--174482 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
174428 AATTTAAAAG
*
174438 ATAATAAAAAT-TTGAAAAAATT
1 ATAA-AAAAATATTTAAAAAATT
*
174460 ATAAAAAAATATTTAAAACATT
1 ATAAAAAAATATTTAAAAAATT
174482 A
1 A
174483 AAATTGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATATTTAAAAAATT
Found at i:175844 original size:9 final size:9
Alignment explanation
Indices: 175830--175855 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
175820 TTATTTTAAC
175830 GGTCAATGT
1 GGTCAATGT
175839 GGTCAATGT
1 GGTCAATGT
175848 GGTCAATG
1 GGTCAATG
175856 ACAGAAACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.31
Consensus pattern (9 bp):
GGTCAATGT
Found at i:176946 original size:15 final size:15
Alignment explanation
Indices: 176926--176961 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
176916 AGAAACATTG
176926 GATACTCTGTTGTTT
1 GATACTCTGTTGTTT
176941 GATACTCTGTTGTTT
1 GATACTCTGTTGTTT
*
176956 AATACT
1 GATACT
176962 GCATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (15 bp):
GATACTCTGTTGTTT
Found at i:179057 original size:2 final size:2
Alignment explanation
Indices: 179050--179078 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
179040 ATAAAATAAC
179050 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 A
179079 CTATTTAAGA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184645 original size:13 final size:13
Alignment explanation
Indices: 184627--184654 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
184617 TTAGAAAGAT
184627 TAGTATAAATACA
1 TAGTATAAATACA
184640 TAGTATAAATACA
1 TAGTATAAATACA
184653 TA
1 TA
184655 CACAAATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (13 bp):
TAGTATAAATACA
Found at i:193104 original size:515 final size:514
Alignment explanation
Indices: 192134--193159 Score: 1944
Period size: 515 Copynumber: 2.0 Consensus size: 514
192124 GTTCTATTTA
* *
192134 TTTTTAATTTTTAAATCCATAATAAGCAATACGTATCACTAATAATCCGATTTAGTGTCAAATTA
1 TTTTTAACTTTTAAATCCATAATAAGCAATACGTATCACTAATAATCCGATTTAGTGTCAAATCA
192199 TTTACTAAATTAATTAAAAACTAAAATTAAGCTAGTCAGAGTAAAAAATTATTTTTGACAAATAT
66 TTTACTAAATTAATTAAAAACTAAAATTAAGCTAGTCAGAGTAAAAAATTATTTTTGACAAATAT
192264 TAAATTATTTATATAATTTTAAAATTTATATTCTCTATTATTTTTAATGGTGTTTAGTTAATTTC
131 TAAATTATTTATATAATTTTAAAATTTATATTCTCTATTATTTTTAATGGTGTTTAGTTAATTTC
192329 TAACACTAACTTCTTAAAAATATAAACAAAAGGGGTTATGTACCGAATTAGATAATTTCAACCAT
196 TAACACTAACTTCTTAAAAATATAAACAAAAGGGGTTATGTACCGAATTAGATAATTTCAACCAT
* * *
192394 AGAGAAAACAATTAATAGATGCGGAATGTCTTTGTTTTAAAATTTGAAAGCTTTGGTTTGGAAGT
261 AGAGAAAACAATTAATAAATGCGGAATGTCTTTGTTTTAAAATCTGAAAGCTTTGGTTAGGAAGT
*
192459 TTGAGGATGAAATTGATAGAATTTATAAATGTGAAGGGTTAAATTTATTGAATTATTTAGAATTA
326 TTGAGGATCAAATTGATAGAATTTATAAATGTGAAGGGTTAAATTTATTGAATTATTTAGAATTA
192524 GGATCAATTTGATAGAATATGAAAGTATTGAGGACTAAATGTGTTATTATACCAGTTAGAAAAAG
391 GGATCAATTTGATAGAATATGAAAGTATTGAGGACTAAATGTGTTATTATACCAGTTAGAAAAAG
192589 GCTTCCATTATCAATTTAACAACAGGTGACCAAAATAGTAAAAAATTCAAATTTTAATG
456 GCTTCCATTATCAATTTAACAACAGGTGACCAAAATAGTAAAAAATTCAAATTTTAATG
*
192648 TTTTTAACTTTTAAATCCATAATAGGCAATACGTATCACTAATAATCCGATTTAGTGTCAAATCA
1 TTTTTAACTTTTAAATCCATAATAAGCAATACGTATCACTAATAATCCGATTTAGTGTCAAATCA
* *
192713 TTTACTAAATTAATTAAAAACTAAAATTATGCTAGTCAGAGTAAAAAAATTATTTTTTACAAATA
66 TTTACTAAATTAATTAAAAACTAAAATTAAGCTAGTCAGAGT-AAAAAATTATTTTTGACAAATA
192778 TTAAATTATTTATATAATTTTAAAATTTATATTCTCTATTATTTTTAATGGTGTTTAGTTAATTT
130 TTAAATTATTTATATAATTTTAAAATTTATATTCTCTATTATTTTTAATGGTGTTTAGTTAATTT
192843 CTAACACTAACTTCTTAAAAATATAAACAAAAGGGGTTATGTACCGAATTAGATAATTTCAACCA
195 CTAACACTAACTTCTTAAAAATATAAACAAAAGGGGTTATGTACCGAATTAGATAATTTCAACCA
* *
192908 TAGATAAAACAATTAATAAATGTGGAATGTCTTTGTTTTAAAATCTGAAAGCTTTGGTTAGGAAG
260 TAGAGAAAACAATTAATAAATGCGGAATGTCTTTGTTTTAAAATCTGAAAGCTTTGGTTAGGAAG
192973 TTTGAGGATCAAATTGATAGAATTTATAAATGTGAAGGGTTAAATTTATTGAATTATTTAGAATT
325 TTTGAGGATCAAATTGATAGAATTTATAAATGTGAAGGGTTAAATTTATTGAATTATTTAGAATT
193038 AGGATCAATTTGATAGAATATGAAAGTATTGAGGACTAAATGTGTTATTATACCAGTTAGAAAAA
390 AGGATCAATTTGATAGAATATGAAAGTATTGAGGACTAAATGTGTTATTATACCAGTTAGAAAAA
193103 GGCTTCCATTATCAATTTAACAACAGGTGACCAAAATAGTAAAAAATTCAAATTTTA
455 GGCTTCCATTATCAATTTAACAACAGGTGACCAAAATAGTAAAAAATTCAAATTTTA
193160 GTGCCTAAAT
Statistics
Matches: 500, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
514 103 0.21
515 397 0.79
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (514 bp):
TTTTTAACTTTTAAATCCATAATAAGCAATACGTATCACTAATAATCCGATTTAGTGTCAAATCA
TTTACTAAATTAATTAAAAACTAAAATTAAGCTAGTCAGAGTAAAAAATTATTTTTGACAAATAT
TAAATTATTTATATAATTTTAAAATTTATATTCTCTATTATTTTTAATGGTGTTTAGTTAATTTC
TAACACTAACTTCTTAAAAATATAAACAAAAGGGGTTATGTACCGAATTAGATAATTTCAACCAT
AGAGAAAACAATTAATAAATGCGGAATGTCTTTGTTTTAAAATCTGAAAGCTTTGGTTAGGAAGT
TTGAGGATCAAATTGATAGAATTTATAAATGTGAAGGGTTAAATTTATTGAATTATTTAGAATTA
GGATCAATTTGATAGAATATGAAAGTATTGAGGACTAAATGTGTTATTATACCAGTTAGAAAAAG
GCTTCCATTATCAATTTAACAACAGGTGACCAAAATAGTAAAAAATTCAAATTTTAATG
Found at i:193780 original size:32 final size:32
Alignment explanation
Indices: 193739--193803 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
193729 AAGCCCTAAG
193739 GATAATTTTCCTTTGCCACACATCGATACGTT
1 GATAATTTTCCTTTGCCACACATCGATACGTT
193771 GATAATTTTCCTTTGCCACACATCGATACGTT
1 GATAATTTTCCTTTGCCACACATCGATACGTT
193803 G
1 G
193804 GTGGATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (32 bp):
GATAATTTTCCTTTGCCACACATCGATACGTT
Found at i:195414 original size:32 final size:32
Alignment explanation
Indices: 195373--195438 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
195363 TGGTTATAGA
*
195373 TTACTTCATAAAATGGGTAGAAGCCTCTTCGT
1 TTACTTCATAAAATGGGTAGAAGCCACTTCGT
195405 TTACTTCATAAAATGGGTAGAAGCCACTTCGT
1 TTACTTCATAAAATGGGTAGAAGCCACTTCGT
195437 TT
1 TT
195439 GCCCATGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
TTACTTCATAAAATGGGTAGAAGCCACTTCGT
Found at i:196199 original size:17 final size:17
Alignment explanation
Indices: 196179--196211 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
196169 ATATTTTGCC
196179 TAAAAAAACAAAAAAAA
1 TAAAAAAACAAAAAAAA
*
196196 TAAAAAAATAAAAAAA
1 TAAAAAAACAAAAAAA
196212 TCAAGATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (17 bp):
TAAAAAAACAAAAAAAA
Found at i:196200 original size:7 final size:8
Alignment explanation
Indices: 196179--196212 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
196169 ATATTTTGCC
196179 TAAAAAAA
1 TAAAAAAA
*
196187 CAAAAAAAA
1 -TAAAAAAA
196196 TAAAAAAA
1 TAAAAAAA
196204 TAAAAAAA
1 TAAAAAAA
196212 T
1 T
196213 CAAGATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:196809 original size:20 final size:20
Alignment explanation
Indices: 196770--196813 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
196760 GGGTTACTCG
* *
196770 CAAAACTTGAGGAGAGAAGT
1 CAAAACTAGAGGAGAAAAGT
196790 ACAAAACTAGA-GAGAAAAGT
1 -CAAAACTAGAGGAGAAAAGT
196810 CAAA
1 CAAA
196814 GATTGAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (20 bp):
CAAAACTAGAGGAGAAAAGT
Found at i:197196 original size:77 final size:76
Alignment explanation
Indices: 197072--198857 Score: 1923
Period size: 77 Copynumber: 23.3 Consensus size: 76
197062 GAATTATTTG
* * * *
197072 TTTCAATTTCTTTTTTTTTCAAAAATAAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGCCAC
1 TTTCAATTTC-TGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
197137 ACGCCGAGGTAT
65 ATGCCGAGGTAT
* * *
197149 TTTCAATTTTTGTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGAGTCAC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
197214 ACGCCGAGCGT-T
65 ATGCCGAG-GTAT
* * * *
197226 ATTTCAATTTATG-TTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACAC
1 -TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
197289 ATGCCGAGGTACTT
65 ATGCCGAGGTA--T
* * * * *
197303 TTTAAAATTTCTATTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCCCGAG-CAC
1 TTT-CAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
197367 ACGCCGATGTATT
65 ATGCCGAGGTA-T
* * *
197380 TTTCAATTTCTGTTTTTTCAAAAATAAACTCATAATGTGAGAGGTGAGTTGAGCCTCGGGTCACG
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
197445 TGCCGAGGTAT
66 TGCCGAGGTAT
* * * *
197456 TTTTAATTTCTATTTTTGTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGCCAC
1 TTTCAATTTCTGTTTTT-TCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
197521 ACGCCGAGTTATT
65 ATGCCGAGGTA-T
* *
197534 TTTCAATTTATG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
197598 TGCCGAGGTATTT
66 TGCCGAGGTA--T
* * * *
197611 TTTTAATTTTTG-TTTTTCAAGAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAT
1 TTTCAATTTCTGTTTTTTCAA-AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
** *
197675 ATGTAGAAGTAGT
65 ATGCCGAGGTA-T
* * * *
197688 TTTTAATTTATG-TTTTTCAAAAAAAT-AACTCATAATACGAGATGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTGTTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
197751 CACGCCGAGGTATT
64 CATGCCGAGGTA-T
* **
197765 TTTCAATTTTTGTTTTTTTTTTAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTG--TTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
197830 CGTGCCGAGGTAT
64 CATGCCGAGGTAT
* * * ** * *
197843 TTTCAATTTCT-ATTTTTCAAGAATCAACTCATAATGCGAGAGGTGAATTGAGCCTTTGGCCGCA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
197907 CGCCGAGGTAT
66 TGCCGAGGTAT
**** * * *
197918 TTTCAA-TTCATGTTTCAAAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
1 TTTCAATTTC-TGTTT--TTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
197982 ACACGCTGAGGTATT
63 ACATGCCGAGGTA-T
* * * *
197997 TTTTAA--T-T-TTTTTTCAGAAATCAACTCATAATGCGAGATGTGAGTTGAGCCTCGGGCCACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
***
198058 CAACGAGGTAT
66 TGCCGAGGTAT
* * *
198069 TTTTAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA---TCGGG-CAC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
198130 ATGCCAAGGTATTT
65 ATGCCGAGGTA--T
* * * **
198144 TTTTAATTTTTG-TTTTTCAAAAAATCAACTCATAATGCG-GAAGTGAGTTGAGCCTCGGGTTGC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
198207 ACGCCGAGGTAT
65 ATGCCGAGGTAT
* * *
198219 TTTCAATTTCTATTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
1 TTTCAATTTCTGTTTTTTC---AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
198284 ACATGCCGAGGTATT
63 ACATGCCGAGGTA-T
* * * * *
198299 TTTTAACTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGCCGCA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
198363 TGCCTAGGTAT
66 TGCCGAGGTAT
* * *
198374 TTTCAATTTCTGTCTTTTTGAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTGT-TTTTT-CAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
* ** *
198439 CACGTTGAGGAATT
64 CATGCCGAGGTA-T
* ** * *
198453 TTTTAATTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTATGGCCGCA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
198517 TTCCGAGGTAT
66 TGCCGAGGTAT
* * * *
198528 TTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAGCCTCGGGTCAC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
198593 ATGCCGAGTTCTT
65 ATGCCGAGGT-AT
* *
198606 TTTC-ATTTCTGTTTTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCCCGGGT-AC
1 TTTCAATTTCTG-TTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
198669 ACGCTGAGGTATT
65 ATGCCGAGGTA-T
* **
198682 TTTCAATTTTTGTTTTTTCAAAAATCAACTCATAATGTTAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
* *
198747 TACCGAAGTATT
66 TGCCGAGGTA-T
* * *
198759 TTTCAATTTCTG-TTTTTCAAAAGTCAACTCATAATGCGAGAGGTGAGTTAAGCCTCAGG-CACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
198822 TGCCGATGTAT
66 TGCCGAGGTAT
*
198833 CTTTCAATTTATGTTTTTTCAAAAA
1 -TTTCAATTTCTGTTTTTTCAAAAA
198858 AAAAAAAAGG
Statistics
Matches: 1448, Mismatches: 207, Indels: 109
0.82 0.12 0.06
Matches are distributed among these distances:
72 7 0.00
73 68 0.05
74 38 0.03
75 143 0.10
76 402 0.28
77 403 0.28
78 270 0.19
79 102 0.07
80 15 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (76 bp):
TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
TGCCGAGGTAT
Found at i:197415 original size:76 final size:77
Alignment explanation
Indices: 197072--198857 Score: 1995
Period size: 76 Copynumber: 23.3 Consensus size: 77
197062 GAATTATTTG
* * * *
197072 TTTCAATTTCTTTTTTTTTCAAAAATAAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGCCAC
1 TTTCAATTTC-TGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
197137 ACGCCGAGGTA-T
65 ATGCCGAGGTATT
* * *
197149 TTTCAATTTTTGTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGAGTCAC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
197214 ACGCCGAGCGT-TA
65 ATGCCGAG-GTATT
* * * *
197227 TTTCAATTTATG-TTTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
197290 TGCCGAGGTACTT
66 TGCCGAGGTA-TT
* * * * *
197303 TTTAAAATTTCTATTTTTTCAAAAATTAACTCATAATGCGAGAGGTGAGTTGAGCCCCGAG-CAC
1 TTT-CAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
197367 ACGCCGATGTATT
65 ATGCCGAGGTATT
* * *
197380 TTTCAATTTCTGTTTTTTCAAAAATAAACTCATAATGTGAGAGGTGAGTTGAGCCTCGGGTCACG
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
197445 TGCCGAGGTATT
66 TGCCGAGGTATT
* * *
197457 TTT-AATTTCTATTTTTGTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGCCAC
1 TTTCAATTTCTGTTTTT-TCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
197521 ACGCCGAGTTATT
65 ATGCCGAGGTATT
* *
197534 TTTCAATTTATG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCCACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
197598 TGCCGAGGTATTT
66 TGCCGAGGTA-TT
* * * *
197611 TTTTAATTTTTG-TTTTTCAAGAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAT
1 TTTCAATTTCTGTTTTTTCAA-AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
** *
197675 ATGTAGAAGTAGTT
65 ATGCCGAGGTA-TT
* * *
197689 TTT-AATTTATG-TTTTTCAAAAAAAT-AACTCATAATACGAGATGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTGTTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
197751 CACGCCGAGGTATT
64 CATGCCGAGGTATT
* **
197765 TTTCAATTTTTGTTTTTTTTTTAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTG--TTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
197830 CGTGCCGAGGTA-T
64 CATGCCGAGGTATT
* * * ** * *
197843 TTTCAATTTCT-ATTTTTCAAGAATCAACTCATAATGCGAGAGGTGAATTGAGCCTTTGGCCGCA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
197907 CGCCGAGGTA-T
66 TGCCGAGGTATT
**** * * *
197918 TTTCAA-TTCATGTTTCAAAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
1 TTTCAATTTC-TGTTT--TTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
197982 ACACGCTGAGGTATT
63 ACATGCCGAGGTATT
* * * *
197997 TTTTAA--T-T-TTTTTTCAGAAATCAACTCATAATGCGAGATGTGAGTTGAGCCTCGGGCCACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
***
198058 CAACGAGGTATT
66 TGCCGAGGTATT
* *
198070 TTT-AATTTTTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA---TCGGG-CAC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
198130 ATGCCAAGGTATTT
65 ATGCCGAGGTA-TT
* * * **
198144 TTTTAATTTTTG-TTTTTCAAAAAATCAACTCATAATGCG-GAAGTGAGTTGAGCCTCGGGTTGC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
198207 ACGCCGAGGTA-T
65 ATGCCGAGGTATT
* * *
198219 TTTCAATTTCTATTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
1 TTTCAATTTCTGTTTTTTC---AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
198284 ACATGCCGAGGTATT
63 ACATGCCGAGGTATT
* * * * *
198299 TTTTAACTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCGGGCCGCA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
198363 TGCCTAGGTA-T
66 TGCCGAGGTATT
* * *
198374 TTTCAATTTCTGTCTTTTTGAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTGT-TTTTT-CAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
* ** *
198439 CACGTTGAGGAATT
64 CATGCCGAGGTATT
* ** * *
198453 TTTTAATTTCTG-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTATGGCCGCA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
198517 TTCCGAGGTA-T
66 TGCCGAGGTATT
* * * *
198528 TTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTAAGCCTCGGGTCAC
1 TTTCAATTTCTGTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
198593 ATGCCGAGTTCTT
65 ATGCCGAGGTATT
* *
198606 TTTC-ATTTCTGTTTTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCCCGGGT-AC
1 TTTCAATTTCTG-TTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
198669 ACGCTGAGGTATT
65 ATGCCGAGGTATT
* **
198682 TTTCAATTTTTGTTTTTTCAAAAATCAACTCATAATGTTAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
* *
198747 TACCGAAGTATT
66 TGCCGAGGTATT
* * *
198759 TTTCAATTTCTG-TTTTTCAAAAGTCAACTCATAATGCGAGAGGTGAGTTAAGCCTCAGG-CACA
1 TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
* *
198822 TGCCGATGTATC
66 TGCCGAGGTATT
*
198834 TTTCAATTTATGTTTTTTCAAAAA
1 TTTCAATTTCTGTTTTTTCAAAAA
198858 AAAAAAAAGG
Statistics
Matches: 1451, Mismatches: 206, Indels: 105
0.82 0.12 0.06
Matches are distributed among these distances:
72 2 0.00
73 73 0.05
74 42 0.03
75 139 0.10
76 405 0.28
77 402 0.28
78 271 0.19
79 102 0.07
80 15 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (77 bp):
TTTCAATTTCTGTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA
TGCCGAGGTATT
Found at i:199050 original size:30 final size:30
Alignment explanation
Indices: 199016--199082 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
199006 ATAAACACAT
*
199016 TTGAAAATAGATATAACGTAAAAAAACCTA
1 TTGAAAATAGATATAACGTAAAAAAAACTA
*
199046 TTGAACATAGATATAACGTAAAAAAAACTA
1 TTGAAAATAGATATAACGTAAAAAAAACTA
199076 TTGAAAA
1 TTGAAAA
199083 AAGAATACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (30 bp):
TTGAAAATAGATATAACGTAAAAAAAACTA
Done.