Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold119
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: 3173904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 20
Found at i:1023659 original size:38 final size:38
Alignment explanation
Indices: 1023602--1023677 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
1023592 AGCCACTTCA
* *
1023602 ATTTTTTAATCACCTATGAAATCAACAGGTTAAAAGAT
1 ATTTTTCAATCACCTATGAAATCAAAAGGTTAAAAGAT
1023640 ATTTTTCAATCATCC-ATGAAATCAAAAGGTTAAAAGAT
1 ATTTTTCAATCA-CCTATGAAATCAAAAGGTTAAAAGAT
1023678 TGTTTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (38 bp):
ATTTTTCAATCACCTATGAAATCAAAAGGTTAAAAGAT
Found at i:1023781 original size:8 final size:8
Alignment explanation
Indices: 1023768--1023810 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1023758 ATTTCATATT
1023768 TTTTTTTC
1 TTTTTTTC
1023776 TTTTTTTC
1 TTTTTTTC
*
1023784 CTTTTTTC
1 TTTTTTTC
*
1023792 TTCATTTTC
1 TT-TTTTTC
*
1023801 TTTCTTTC
1 TTTTTTTC
1023809 TT
1 TT
1023811 ACCTTTAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1024975 original size:28 final size:28
Alignment explanation
Indices: 1024929--1025465 Score: 296
Period size: 28 Copynumber: 18.5 Consensus size: 28
1024919 CATCAACTTG
*
1024929 TGTGGGCTTTGAAAA-GATGCCATTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * * *
1024957 TGTGAGCTTTAAAACGATGTCACTTACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * *
1024985 TATGGGCTTTAAAAGGGTGCCACTGACA
1 TGTGGGCTTTAAAAGGATGCCACTGACT
*
1025013 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
1025041 TGTGGGCTTTAAAAGGGTGCTAGTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * * *
1025069 TGCGGCCTTTTGAAAGGATTGAAAGGATGTCAATAACT
1 TGTGGGC-TTT------A---AAAGGATGCCACTGACT
* * *
1025107 TGTGGGCTTTGAAAGGGTGCCACTGATT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * * *
1025135 TGGGGGCTTTTGAAAGGGTGTCACTAACT
1 TGTGGGC-TTTAAAAGGATGCCACTGACT
* * *
1025164 TGTAGGCTTTGAAAAGGGTGTCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
*
1025193 TGTGGGCTTTAAAA-AAGTGCCACTGACT
1 TGTGGGCTTTAAAAGGA-TGCCACTGACT
* * *
1025221 TGTGGGCTTTGAAAAGGTTTACCTCTGACT
1 TGTGGGCTTT-AAAAGG-ATGCCACTGACT
* *
1025251 TGTGGGCTTTGAAAAGGGTTACCACTGACT
1 TGTGGGCTTT-AAAA-GGATGCCACTGACT
** * *
1025281 TGCAGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
** *
1025309 TGTGGGCTTTGAAAA-GATTTGGTACTAACT
1 TGTGGGCTTT-AAAAGGA--TGCCACTGACT
* *
1025339 TGTGGGCTTTGAAA-GATGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACT
* * * *
1025366 TGTGGGCTTTGAGAATG-TACCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
* * *
1025394 TGTGGGCTTTGAGAATG-TGCCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACT
** * *
1025422 TGTGGATTTTAAAAAGAAGCCACAT-ACT
1 TGTGGGCTTTAAAAGGATGCCAC-TGACT
*
1025450 TATGGGCTTTGAAAAG
1 TGTGGGCTTT-AAAAG
1025466 AAGTCTATTG
Statistics
Matches: 409, Mismatches: 74, Indels: 51
0.77 0.14 0.10
Matches are distributed among these distances:
27 27 0.07
28 224 0.55
29 72 0.18
30 62 0.15
31 2 0.00
35 1 0.00
37 3 0.01
38 18 0.04
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTGACT
Found at i:1025175 original size:57 final size:56
Alignment explanation
Indices: 1025087--1025426 Score: 285
Period size: 57 Copynumber: 5.9 Consensus size: 56
1025077 TTTGAAAGGA
* * * * *
1025087 TTGAAAGGATGTCAATAACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGGGGGCTT
1 TTGAAAGGGTGTCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC-T
* * *
1025144 TTGAAAGGGTGTCACTAACTTGTAGGCTTTGAAAAGGGTGTCACTGACTTGTGGGCT
1 TTGAAAGGGTGTCACTAACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCT
* ** * * * * *
1025201 TTAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTTTACCTCTGACTTGTGGGCT
1 TTGAAAGGGTGTCACTAACTTGTGGGCTTTG-AAAGG-ATGCCACTGACTTGTGGGCT
* ** *
1025259 TTGAAAAGGGT-TACCACTGACTTGCAGGCTTTGAAAGGATGCCACTAACTTGTGGGCT
1 TTG-AAAGGGTGT--CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
** *
1025317 TTGAAAAGATTTGGT-ACTAACTTGTGGGCTTTGAAA-GATGCCACTAACTTGTGGGCT
1 TTG-AAAG-GGT-GTCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
* ** * *
1025374 TTGAGAA-TGTACCACTAACTTGTGGGCTTTGAGAATG-TGCCACTAACTTGTGG
1 TTGA-AAGGGTGTCACTAACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGG
1025427 ATTTTAAAAA
Statistics
Matches: 237, Mismatches: 34, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
55 21 0.09
56 19 0.08
57 87 0.37
58 81 0.34
59 11 0.05
60 17 0.07
61 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (56 bp):
TTGAAAGGGTGTCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
Found at i:1025255 original size:58 final size:56
Alignment explanation
Indices: 1025102--1025463 Score: 289
Period size: 58 Copynumber: 6.3 Consensus size: 56
1025092 AGGATGTCAA
* * * * * *
1025102 TAACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGGGGGCTTTTGAAAGGGTGTCAC
1 TAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTTAAAAAGGTGCCAC
* * * *
1025159 TAACTTGTAGGCTTTGAAAAGGGTGTCACTGACTTGTGGGCTTTAAAAAAGTGCCAC
1 TAACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGTGCCAC
* * * * * *
1025216 TGACTTGTGGGCTTTGAAAAGGTTTACCTCTGACTTGTGGGCTTTGAAAAGGGTTACCAC
1 TAACTTGTGGGCTTTG-AAAGG-ATGCCACTGACTTGTGGGCTTT-AAAAAGG-TGCCAC
* ** * ** **
1025276 TGACTTGCAGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATTTGGTAC
1 TAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-AAAA-AGGTGCCAC
* * * * *
1025334 TAACTTGTGGGCTTTGAAA-GATGCCACTAACTTGTGGGCTTTGAGAATGTACCAC
1 TAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGTGCCAC
* * ** **
1025389 TAACTTGTGGGCTTTGAGAATG-TGCCACTAACTTGTGGATTTTAAAAAGAAGCCAC
1 TAACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTAAAAAGGTGCCAC
*
1025445 -ATACTTATGGGCTTTGAAA
1 TA-ACTTGTGGGCTTTGAAA
1025464 AGAAGTCTAT
Statistics
Matches: 250, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
55 25 0.10
56 44 0.18
57 71 0.28
58 81 0.32
59 10 0.04
60 19 0.08
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (56 bp):
TAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGGTGCCAC
Found at i:1025303 original size:88 final size:85
Alignment explanation
Indices: 1025111--1025405 Score: 267
Period size: 88 Copynumber: 3.4 Consensus size: 85
1025101 ATAACTTGTG
* * * * * * *
1025111 GGCTTTGAAAGGGTGCCACTGATTTGGGGGCTTTTGAAAGGGTGTCACTAACTTGTAGGCTTTGA
1 GGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAAGGTTTCTCTAACTTGTGGGCTTTGA
**
1025176 AAAGGGTGTCACTGACTTGTG
65 AAAGGGTGTCACTGACTTGCA
** *
1025197 GGCTTT-AAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTTTACCTCTGACTTGTGGGCTTT
1 GGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGGTTT--CTCTAACTTGTGGGCTTT
1025261 GAAAAGGGT-TACCACTGACTTGCA
63 GAAAAGGGTGT--CACTGACTTGCA
* * *
1025285 GGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATTTGGTACTAACTTGTGGGCTTTG
1 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTT-CT-CTAACTTGTGGGCTTTG
* * * **
1025350 -AAA-GATGCCACTAACTTGTG
64 AAAAGGGTGTCACTGACTTGCA
* * *
1025370 GGCTTTGAGAATG-TACCACTAACTTGTGGGCTTTGA
1 GGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGA
1025406 GAATGTGCCA
Statistics
Matches: 174, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
85 53 0.30
86 28 0.16
87 28 0.16
88 61 0.35
89 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (85 bp):
GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTTTCTCTAACTTGTGGGCTTTGAA
AAGGGTGTCACTGACTTGCA
Found at i:1026782 original size:10 final size:10
Alignment explanation
Indices: 1026769--1026803 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1026759 TTTGTATTAT
1026769 TTTTTTTTGG
1 TTTTTTTTGG
*
1026779 TTTTTGTT-G
1 TTTTTTTTGG
1026788 TTTTTTTTGG
1 TTTTTTTTGG
1026798 TTTTTT
1 TTTTTT
1026804 GAGAAGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (10 bp):
TTTTTTTTGG
Found at i:1026803 original size:9 final size:9
Alignment explanation
Indices: 1026770--1026803 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1026760 TTGTATTATT
1026770 TTTTTTTGG
1 TTTTTTTGG
*
1026779 TTTTTGTTGT
1 TTTTT-TTGG
1026789 TTTTTTTGG
1 TTTTTTTGG
1026798 TTTTTT
1 TTTTTT
1026804 GAGAAGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:1037892 original size:13 final size:13
Alignment explanation
Indices: 1037870--1037907 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1037860 TAGTACCTAA
1037870 TGTATCGATACAT
1 TGTATCGATACAT
* *
1037883 TGTATTGATATAT
1 TGTATCGATACAT
1037896 TGTATCGATACA
1 TGTATCGATACA
1037908 AGGAATATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1044097 original size:33 final size:33
Alignment explanation
Indices: 1044053--1044119 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
1044043 GTCATAGGCT
1044053 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
1044086 ATGTATTGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
1044119 A
1 A
1044120 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1046847 original size:25 final size:25
Alignment explanation
Indices: 1046819--1046868 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1046809 CTATATGAGG
*
1046819 TTCAAGGTGACATCTAGATAGGTAT
1 TTCAAGGTGACACCTAGATAGGTAT
1046844 TTCAAGGTGACACCTAGATAGGTAT
1 TTCAAGGTGACACCTAGATAGGTAT
1046869 CCGAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (25 bp):
TTCAAGGTGACACCTAGATAGGTAT
Found at i:1049480 original size:17 final size:17
Alignment explanation
Indices: 1049445--1049482 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1049435 CTTGATAAAA
* *
1049445 AATCATAAATTCGTGCT
1 AATCATAAATTCATACT
1049462 AATCATAAATTCATACT
1 AATCATAAATTCATACT
1049479 AATC
1 AATC
1049483 CTCATTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (17 bp):
AATCATAAATTCATACT
Found at i:1051085 original size:16 final size:16
Alignment explanation
Indices: 1051066--1051106 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1051056 AGATAAATAC
1051066 TATTAATAATAAAAAA
1 TATTAATAATAAAAAA
1051082 TATTTAA-AAT-AAAAA
1 TA-TTAATAATAAAAAA
1051097 -ATTAATAATA
1 TATTAATAATA
1051107 TAATGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.18
14 4 0.18
15 5 0.23
16 5 0.23
17 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATTAATAATAAAAAA
Found at i:1051109 original size:16 final size:17
Alignment explanation
Indices: 1051066--1051109 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1051056 AGATAAATAC
1051066 TATTAATAATA-AAAAA
1 TATTAATAATATAAAAA
*
1051082 TATT--TAAAATAAAAA
1 TATTAATAATATAAAAA
1051097 -ATTAATAATATAA
1 TATTAATAATATAA
1051110 TGAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 7 0.30
15 5 0.22
16 11 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TATTAATAATATAAAAA
Found at i:1051256 original size:16 final size:16
Alignment explanation
Indices: 1051237--1051280 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1051227 CTCATTCGGG
1051237 TTCGAGCTTTTTTGGA
1 TTCGAGCTTTTTTGGA
*
1051253 TTCGAGCTTGTTTGGA
1 TTCGAGCTTTTTTGGA
* *
1051269 TTTGGGCTTTTT
1 TTCGAGCTTTTT
1051281 CGGGTTCTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.09, C:0.11, G:0.27, T:0.52
Consensus pattern (16 bp):
TTCGAGCTTTTTTGGA
Found at i:1052118 original size:18 final size:19
Alignment explanation
Indices: 1052082--1052118 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1052072 CAAAAACTTT
1052082 TAATTTATAAGTATGCTTA
1 TAATTTATAAGTATGCTTA
*
1052101 TAATTTAT-AGTATTCTTA
1 TAATTTATAAGTATGCTTA
1052119 CCTTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (19 bp):
TAATTTATAAGTATGCTTA
Found at i:1052493 original size:16 final size:15
Alignment explanation
Indices: 1052466--1052495 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1052456 ATGTTAACTT
1052466 TATATTCTATTCTAC
1 TATATTCTATTCTAC
1052481 TATATTGCTATTCTA
1 TATATT-CTATTCTA
1052496 AGTGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:1053985 original size:27 final size:27
Alignment explanation
Indices: 1053954--1054053 Score: 89
Period size: 27 Copynumber: 3.8 Consensus size: 27
1053944 CCACCATTTG
* *
1053954 TATTTGTCACAAATAGTGGTTAC-TTTA
1 TATTTGTCAAAAATAGTGGCT-CTTTTA
* *
1053981 TATTTGTCAAAAATGGTGGCTCTTTTT
1 TATTTGTCAAAAATAGTGGCTCTTTTA
* *
1054008 TATTTGTCAAAAATTGTGGCT-TGTTA
1 TATTTGTCAAAAATAGTGGCTCTTTTA
* * *
1054034 T-TTTATCAAAATTGGTGGCT
1 TATTTGTCAAAAATAGTGGCT
1054054 AATTTTTATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 16 0.26
26 5 0.08
27 41 0.66
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATAGTGGCTCTTTTA
Found at i:1059445 original size:19 final size:18
Alignment explanation
Indices: 1059420--1059484 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
1059410 ATTTCAACAA
1059420 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1059438 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
1059454 --TGTATCGATACATATG
1 TTTGTATCGATACATAAG
1059470 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1059485 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
17 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1059459 original size:13 final size:14
Alignment explanation
Indices: 1059441--1059470 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1059431 ACATAAGTGT
1059441 TGTATCGATACA-A
1 TGTATCGATACATA
1059454 TGTATCGATACATA
1 TGTATCGATACATA
1059468 TGT
1 TGT
1059471 TTTGTATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:1059459 original size:32 final size:32
Alignment explanation
Indices: 1059422--1059492 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1059412 TTCAACAATT
1059422 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1059454 TGTATCGATACATATGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1059486 TGTATCG
1 TGTATCG
1059493 CTATAAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1059636 original size:46 final size:46
Alignment explanation
Indices: 1059565--1059658 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
1059555 TTTATATCGA
*
1059565 TACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
*
1059611 TACATACAGGCAAATTTGCCTAGATGTATCGATACACTATGAAATG
1 TACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1059657 TA
1 TA
1059659 TCGATACATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (46 bp):
TACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
Found at i:1063372 original size:27 final size:27
Alignment explanation
Indices: 1063341--1063412 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
1063331 AAAGCCACTA
1063341 TTTGTATTTGTCAAAAATAGTGGTTAC
1 TTTGTATTTGTCAAAAATAGTGGTTAC
* *
1063368 TTTGTATTTGTCAAAAATGGTGGTTCC
1 TTTGTATTTGTCAAAAATAGTGGTTAC
* *
1063395 TTTTTGTTTGTCAAAAAT
1 TTTGTATTTGTCAAAAAT
1063413 TGTGACTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.47
Consensus pattern (27 bp):
TTTGTATTTGTCAAAAATAGTGGTTAC
Found at i:1063459 original size:25 final size:24
Alignment explanation
Indices: 1063401--1063461 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1063391 TTCCTTTTTG
*
1063401 TTTGTCAAAAATTGTGACTTATTAT
1 TTTGTC-AAAATTGTGACTAATTAT
*
1063426 TTTGTCAAAATTGGTGACTAATTTT
1 TTTGTCAAAATT-GTGACTAATTAT
1063451 TATTG-CAAAAT
1 T-TTGTCAAAAT
1063462 GGGGGAGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.19
25 23 0.72
26 3 0.09
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGTGACTAATTAT
Found at i:1068547 original size:15 final size:12
Alignment explanation
Indices: 1068517--1068592 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
1068507 TTTTTTCACC
*
1068517 TTTTTTTCCTTT
1 TTTTTTTCTTTT
***
1068529 TTTTTCAATTTT
1 TTTTTTTCTTTT
1068541 CTTTTTTTCTTTT
1 -TTTTTTTCTTTT
*
1068554 TTTTTTTATTTT
1 TTTTTTTCTTTT
** *
1068566 TTTAATT-TTAT
1 TTTTTTTCTTTT
*
1068577 TTTTTTCCTTTT
1 TTTTTTTCTTTT
1068589 TTTT
1 TTTT
1068593 AAAGAAAATA
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
11 7 0.15
12 31 0.66
13 9 0.19
ACGTcount: A:0.08, C:0.09, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:1068547 original size:35 final size:34
Alignment explanation
Indices: 1068515--1068591 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 34
1068505 ATTTTTTTCA
*
1068515 CCTTTTTTTCCTT-TTTTTTCAATTTTCTTTTTT
1 CCTTTTTTTCCTTATTTTTTCAATTTTATTTTTT
* ** *
1068548 TCTTTTTTTTTTTATTTTTTTAATTTTATTTTTTT
1 CCTTTTTTTCCTTATTTTTTCAATTTTA-TTTTTT
1068583 CCTTTTTTT
1 CCTTTTTTT
1068592 TAAAGAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 10 0.28
34 12 0.33
35 14 0.39
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (34 bp):
CCTTTTTTTCCTTATTTTTTCAATTTTATTTTTT
Found at i:1068555 original size:34 final size:35
Alignment explanation
Indices: 1068505--1068592 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 35
1068495 GCTTAAATAA
*
1068505 ATTTTTTTCACCTTTTTTTCCTT-TTTTTTCAATTTT
1 ATTTTTTT--CCTTTTTTTTCTTATTTTTTCAATTTT
* * *
1068541 CTTTTTTT-CTTTTTTTTTTTATTTTTTTAATTTT
1 ATTTTTTTCCTTTTTTTTCTTATTTTTTCAATTTT
1068575 ATTTTTTTCCTTTTTTTT
1 ATTTTTTTCCTTTTTTTT
1068593 AAAGAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.22
34 19 0.42
35 9 0.20
36 7 0.16
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (35 bp):
ATTTTTTTCCTTTTTTTTCTTATTTTTTCAATTTT
Found at i:1075959 original size:21 final size:22
Alignment explanation
Indices: 1075926--1075970 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1075916 AAATTTTCAG
* *
1075926 AATGTATCGATACAT-TAAAAA
1 AATGAATCAATACATCTAAAAA
*
1075947 AATGAATCAATACATCTAGAAA
1 AATGAATCAATACATCTAAAAA
1075969 AA
1 AA
1075971 CCCAGATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (22 bp):
AATGAATCAATACATCTAAAAA
Found at i:1077978 original size:22 final size:23
Alignment explanation
Indices: 1077953--1078000 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1077943 TTAAAAATTT
* *
1077953 TTTATTTTACACTTTATATA-AA
1 TTTAATTTACAATTTATATATAA
1077975 TTTAATTTACAATTTATATATAA
1 TTTAATTTACAATTTATATATAA
1077998 TTT
1 TTT
1078001 TTTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTAATTTACAATTTATATATAA
Found at i:1078742 original size:2 final size:2
Alignment explanation
Indices: 1078731--1078766 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1078721 ATGTTATTTA
1078731 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1078767 CCCCCCCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1079908 original size:23 final size:23
Alignment explanation
Indices: 1079873--1079917 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1079863 TAAGATTTAT
* *
1079873 ATTTGATATATTATCATTAAATA
1 ATTTGATAAATTATCAATAAATA
*
1079896 ATTTTATAAATTATCAATAAAT
1 ATTTGATAAATTATCAATAAAT
1079918 CAAATAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTGATAAATTATCAATAAATA
Found at i:1082934 original size:22 final size:24
Alignment explanation
Indices: 1082908--1082952 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1082898 AAAAATTTAA
*
1082908 TTTTTATAT-TAAAAATATAATTG
1 TTTTCATATATAAAAATATAATTG
*
1082931 TTTTCATATATAAATATATAAT
1 TTTTCATATATAAAAATATAAT
1082953 AAAATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTTCATATATAAAAATATAATTG
Found at i:1082959 original size:10 final size:11
Alignment explanation
Indices: 1082936--1082970 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
1082926 AATTGTTTTC
1082936 ATAT-ATAAAT
1 ATATAATAAAT
1082946 ATATAATAAAAT
1 ATATAAT-AAAT
1082958 ATATAATAAAT
1 ATATAATAAAT
1082969 AT
1 AT
1082971 TTACTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 8 0.35
12 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAATAAAT
Found at i:1083286 original size:25 final size:24
Alignment explanation
Indices: 1083205--1083286 Score: 62
Period size: 25 Copynumber: 3.3 Consensus size: 24
1083195 TAATATTAGA
1083205 TATTATTGTTAA-AAT-ATTATTATTT
1 TATTATT-TTAATAATAATTA--ATTT
* *
1083230 TA-TATTATAATAATAAATAATTTT
1 TATTATTTTAATAATAATTAA-TTT
**
1083254 TAACATTTTAATAATACATTAATTT
1 TATTATTTTAATAATA-ATTAATTT
1083279 TATTATTT
1 TATTATTT
1083287 GAAAAATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
23 4 0.09
24 12 0.27
25 25 0.56
26 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (24 bp):
TATTATTTTAATAATAATTAATTT
Found at i:1084566 original size:4 final size:4
Alignment explanation
Indices: 1084557--1084583 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1084547 TCTTATCTAT
1084557 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1084584 GTTAAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:1088651 original size:3 final size:3
Alignment explanation
Indices: 1088643--1088686 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1088633 TACAAAATCC
1088643 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1088687 ACTCCAAACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1091376 original size:16 final size:16
Alignment explanation
Indices: 1091357--1091387 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1091347 TAAAATATAA
1091357 ATTTAAACTTAAACTT
1 ATTTAAACTTAAACTT
*
1091373 ATTTAAATTTAAACT
1 ATTTAAACTTAAACT
1091388 AAAAGTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAACTTAAACTT
Found at i:1091424 original size:23 final size:23
Alignment explanation
Indices: 1091382--1091425 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1091372 TATTTAAATT
*
1091382 TAAACTAAAAGTCCATTTAAACC
1 TAAACTAAAAGTCCAATTAAACC
1091405 TAAACTAAAAG-CTCAATTAAA
1 TAAACTAAAAGTC-CAATTAAA
1091426 ATAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (23 bp):
TAAACTAAAAGTCCAATTAAACC
Found at i:1092163 original size:2 final size:2
Alignment explanation
Indices: 1092156--1092191 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1092146 AACCTTAAGG
1092156 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
1092192 TAGCATAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1092703 original size:22 final size:22
Alignment explanation
Indices: 1092678--1092719 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1092668 ATAAAAATAT
1092678 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1092700 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1092720 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:1099590 original size:2 final size:2
Alignment explanation
Indices: 1099583--1099609 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1099573 TTTTCTTTTA
1099583 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 A
1099610 CTTTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1099910 original size:2 final size:2
Alignment explanation
Indices: 1099903--1099936 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1099893 CCCCTAACTA
*
1099903 AT AT AT AT AT AC 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
1099937 GATTCTCTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1100323 original size:14 final size:13
Alignment explanation
Indices: 1100298--1100340 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
1100288 AATTTATTTA
1100298 AAATTA-TAAAAT
1 AAATTATTAAAAT
1100310 AAATTATTTAAAAT
1 AAATTA-TTAAAAT
* *
1100324 AAAATATTACAAT
1 AAATTATTAAAAT
1100337 AAAT
1 AAAT
1100341 AATATTTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.23
13 9 0.35
14 11 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATTATTAAAAT
Found at i:1102738 original size:2 final size:2
Alignment explanation
Indices: 1102726--1102763 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1102716 TTTTTGTGCC
1102726 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1102764 ATACGAGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1103274 original size:2 final size:2
Alignment explanation
Indices: 1103269--1103300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1103259 TTAATCTCTC
1103269 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
1103301 GTAAAAGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1108535 original size:2 final size:2
Alignment explanation
Indices: 1108530--1108563 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1108520 TGACACACAC
*
1108530 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1108564 GCAAGCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1109583 original size:22 final size:21
Alignment explanation
Indices: 1109545--1109591 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1109535 GGTAATTTAT
1109545 ATTATACATACATATAAATATA
1 ATTATACATACATAT-AATATA
*
1109567 ATTATACATAC-TAATAATTTA
1 ATTATACATACAT-ATAATATA
1109588 ATTA
1 ATTA
1109592 CAATAGACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATACATACATATAATATA
Found at i:1109848 original size:25 final size:25
Alignment explanation
Indices: 1109801--1109848 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1109791 AATATTAAAT
* *
1109801 ATTAATAACTAATAAAGATGATATG
1 ATTAATAACTAATAAACAAGATATG
* *
1109826 ATTAATAATTTATAAACAAGATA
1 ATTAATAACTAATAAACAAGATA
1109849 AGTTTAGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (25 bp):
ATTAATAACTAATAAACAAGATATG
Found at i:1111627 original size:24 final size:22
Alignment explanation
Indices: 1111600--1111655 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 22
1111590 ACTTTTCCAC
1111600 ACTTCACTACTTAATTTTTGTTCT
1 ACTTC-CTA-TTAATTTTTGTTCT
1111624 ACTTTCCTATTAATTTTTGTTCT
1 AC-TTCCTATTAATTTTTGTTCT
1111647 ACTTTCCTA
1 AC-TTCCTA
1111656 CTCACTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 23 0.74
24 5 0.16
25 3 0.10
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (22 bp):
ACTTCCTATTAATTTTTGTTCT
Found at i:1111636 original size:23 final size:23
Alignment explanation
Indices: 1111610--1111655 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1111600 ACTTCACTAC
1111610 TTAATTTTTGTTCTACTTTCCTA
1 TTAATTTTTGTTCTACTTTCCTA
1111633 TTAATTTTTGTTCTACTTTCCTA
1 TTAATTTTTGTTCTACTTTCCTA
1111656 CTCACTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.61
Consensus pattern (23 bp):
TTAATTTTTGTTCTACTTTCCTA
Found at i:1112203 original size:2 final size:2
Alignment explanation
Indices: 1112173--1112221 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
1112163 CTGTAAAATT
* * * *
1112173 TA TA TA TT TA CA TA TA AA TA TA CA 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 TA TA TA TA TA TA
1112215 TA TA TA T
1 TA TA TA T
1112222 TTTCTAACAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1114783 original size:24 final size:22
Alignment explanation
Indices: 1114756--1114807 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
1114746 ATAATTTAAT
*
1114756 TATAAAGTAAACATATAAAACTAA
1 TATAAAATAAAC-TA-AAAACTAA
1114780 TATAAAATAAACTAAAAACT-A
1 TATAAAATAAACTAAAAACTAA
1114801 T-TAAAAT
1 TATAAAAT
1114808 TTGACTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 6 0.22
21 2 0.07
22 6 0.22
23 2 0.07
24 11 0.41
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (22 bp):
TATAAAATAAACTAAAAACTAA
Found at i:1117335 original size:16 final size:16
Alignment explanation
Indices: 1117314--1117364 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
1117304 AGAACTTTTC
1117314 ATAATAAAG-AAATAA
1 ATAATAAAGAAAATAA
*
1117329 TATAATAATGAAAATAA
1 -ATAATAAAGAAAATAA
1117346 ATAATTAAA-AAAATGAA
1 ATAA-TAAAGAAAAT-AA
1117363 AT
1 AT
1117365 GGATAAGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (16 bp):
ATAATAAAGAAAATAA
Found at i:1117483 original size:30 final size:30
Alignment explanation
Indices: 1117449--1117510 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1117439 TCCCAGGTCC
1117449 AACAATTTAATTTGAGGCCTTAAAATCCAA
1 AACAATTTAATTTGAGGCCTTAAAATCCAA
1117479 AACAATTTAATTTGAGGCCTTAAAATCCAA
1 AACAATTTAATTTGAGGCCTTAAAATCCAA
1117509 AA
1 AA
1117511 ATAGAAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (30 bp):
AACAATTTAATTTGAGGCCTTAAAATCCAA
Found at i:1122941 original size:13 final size:13
Alignment explanation
Indices: 1122923--1122948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1122913 ATATTTTTTG
1122923 TGTATCGATACAT
1 TGTATCGATACAT
1122936 TGTATCGATACAT
1 TGTATCGATACAT
1122949 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1122959 original size:32 final size:33
Alignment explanation
Indices: 1122902--1122966 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1122892 TACAAGCCAA
1122902 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1122936 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1122967 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1122960 original size:19 final size:19
Alignment explanation
Indices: 1122902--1122966 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1122892 TACAAGCCAA
1122902 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1122923 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1122936 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1122955 TGTATCGATACA
1 TGTATCGATACA
1122967 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1123071 original size:20 final size:20
Alignment explanation
Indices: 1123018--1123073 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1123008 ACATCTTTTT
*
1123018 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
1123038 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
1123057 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
1123074 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:1125755 original size:32 final size:31
Alignment explanation
Indices: 1125719--1125898 Score: 146
Period size: 32 Copynumber: 5.6 Consensus size: 31
1125709 TCAGGTTTAA
*
1125719 GTTCGAGCTTGTTCGGGTTCAAGCTTTTTCAG
1 GTTCGAGCTTATTCGGGTTC-AGCTTTTTCAG
* * ** *
1125751 GTTCGGGCTTATTCGAGTTTGGGCTTTTTCGG
1 GTTCGAGCTTATTCG-GGTTCAGCTTTTTCAG
* * * *
1125783 GTTCGGGCTTATTCAGGTTTGAGCTTTTTCAA
1 GTTCGAGCTTATTC-GGGTTCAGCTTTTTCAG
* * *
1125815 GTTCGAGCTTATTTGGGTTCAGACTTATTCGG
1 GTTCGAGCTTATTCGGGTTCAG-CTTTTTCAG
* *
1125847 GTTCGGGCTTATTCGGGTTCAGATCTTTTC-G
1 GTTCGAGCTTATTCGGGTTCAGCT-TTTTCAG
* *
1125878 AGTTCGAGCTTTTTCAGGTTC
1 -GTTCGAGCTTATTCGGGTTC
1125899 GGGTTCGAGT
Statistics
Matches: 120, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
31 8 0.07
32 108 0.90
33 4 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.42
Consensus pattern (31 bp):
GTTCGAGCTTATTCGGGTTCAGCTTTTTCAG
Found at i:1125760 original size:16 final size:16
Alignment explanation
Indices: 1125741--1125901 Score: 96
Period size: 16 Copynumber: 10.1 Consensus size: 16
1125731 TCGGGTTCAA
1125741 GCTTTTTCAGGTTCGG
1 GCTTTTTCAGGTTCGG
* *
1125757 GCTTATTC-GAGTTTGG
1 GCTTTTTCAG-GTTCGG
*
1125773 GCTTTTTCGGGTTCGG
1 GCTTTTTCAGGTTCGG
* * *
1125789 GCTTATTCAGGTTTGA
1 GCTTTTTCAGGTTCGG
* *
1125805 GCTTTTTCAAGTTCGA
1 GCTTTTTCAGGTTCGG
* *
1125821 GCTTATTT-GGGTTCAG
1 GCTT-TTTCAGGTTCGG
* * *
1125837 ACTTATTCGGGTTCGG
1 GCTTTTTCAGGTTCGG
* * *
1125853 GCTTATTCGGGTTC-A
1 GCTTTTTCAGGTTCGG
* *
1125868 GATCTTTTC-GAGTTCGA
1 GCT-TTTTCAG-GTTCGG
1125885 GCTTTTTCAGGTTCGG
1 GCTTTTTCAGGTTCGG
1125901 G
1 G
1125902 TTCGAGTTCG
Statistics
Matches: 113, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
15 6 0.05
16 99 0.88
17 8 0.07
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (16 bp):
GCTTTTTCAGGTTCGG
Found at i:1125819 original size:64 final size:64
Alignment explanation
Indices: 1125740--1125888 Score: 174
Period size: 64 Copynumber: 2.3 Consensus size: 64
1125730 TTCGGGTTCA
* * ** * *
1125740 AGCTTTTTCAGGTTCGGGCTTATTCGAGTTTGGGCTTTTTCGGGTTCGGGCTTATTCAGGTTTG
1 AGCTTTTTCAAGTTCGAGCTTATTCGAGTTCAGACTTATTCGGGTTCGGGCTTATTCAGGTTTG
* * * *
1125804 AGCTTTTTCAAGTTCGAGCTTATTTGGGTTCAGACTTATTCGGGTTCGGGCTTATTC-GGGTTC
1 AGCTTTTTCAAGTTCGAGCTTATTCGAGTTCAGACTTATTCGGGTTCGGGCTTATTCAGGTTTG
* *
1125867 AGATCTTTTCGAGTTCGAGCTT
1 AGCT-TTTTCAAGTTCGAGCTT
1125889 TTTCAGGTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 7 0.10
64 65 0.90
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.42
Consensus pattern (64 bp):
AGCTTTTTCAAGTTCGAGCTTATTCGAGTTCAGACTTATTCGGGTTCGGGCTTATTCAGGTTTG
Found at i:1127058 original size:2 final size:2
Alignment explanation
Indices: 1127047--1127080 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1127037 ATTCATTTGC
*
1127047 TA TA -A TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1127081 TTAGAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1127081 original size:12 final size:12
Alignment explanation
Indices: 1127047--1127083 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1127037 ATTCATTTGC
*
1127047 TATA-ATATATA
1 TATATATATATT
1127058 TATATATATATT
1 TATATATATATT
1127070 TATATATATATT
1 TATATATATATT
1127082 TA
1 TA
1127084 GAATTTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATATATATT
Found at i:1129211 original size:21 final size:21
Alignment explanation
Indices: 1129185--1129240 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
1129175 AGGGTGATTT
*
1129185 TGTATCGATACATTTCAGGTA
1 TGTATCGATACATTTCACGTA
*
1129206 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACGTA
1129226 TGTATCGATACATTT
1 TGTATCGATACATTT
1129241 ATTGTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATTTCACGTA
Found at i:1133512 original size:21 final size:22
Alignment explanation
Indices: 1133479--1133521 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1133469 ATTTTAAAAA
1133479 AAATTTAATAAATTTAAATTTT
1 AAATTTAATAAATTTAAATTTT
* *
1133501 AAATTTTA-AAATTTAATTTTT
1 AAATTTAATAAATTTAAATTTT
1133522 TTAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATTTAATAAATTTAAATTTT
Found at i:1135057 original size:2 final size:2
Alignment explanation
Indices: 1135046--1135081 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1135036 TCTCTGAAAG
1135046 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1135082 TGTATTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135369 original size:2 final size:2
Alignment explanation
Indices: 1135362--1135393 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1135352 TTCTAAACTA
1135362 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
1135394 TGGTAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1136918 original size:20 final size:19
Alignment explanation
Indices: 1136863--1136918 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1136853 AAAACCCTTA
*
1136863 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
1136883 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
1136903 AATGTATCGATACATG
1 AAAGTATCGATACATG
1136919 AAAAATATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1137014 original size:20 final size:20
Alignment explanation
Indices: 1136969--1137020 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1136959 GTAGCCAAAC
**
1136969 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
1136989 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
1137008 TTGTATCGATACA
1 TTGTATCGATACA
1137021 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:1143356 original size:20 final size:20
Alignment explanation
Indices: 1143313--1143358 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1143303 AAATCTTTTG
1143313 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1143334 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1143354 CAAAA
1 CAAAA
1143359 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1145776 original size:13 final size:13
Alignment explanation
Indices: 1145758--1145783 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1145748 TACACCAAGT
1145758 ATGTATCGATACA
1 ATGTATCGATACA
1145771 ATGTATCGATACA
1 ATGTATCGATACA
1145784 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1145781 original size:32 final size:33
Alignment explanation
Indices: 1145740--1145803 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1145730 TAGCCAAACT
**
1145740 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1145772 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1145804 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1150503 original size:20 final size:20
Alignment explanation
Indices: 1150456--1150506 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1150446 ATTCTTTTCA
*
1150456 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * * *
1150476 TGTGTCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
1150496 TGTATCGATAC
1 TGTATCGATAC
1150507 TTTTCAAGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:1157307 original size:52 final size:52
Alignment explanation
Indices: 1157159--1157287 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
1157149 CAAAATATGA
* *
1157159 AAATTTGCCTGCATGTATCGATACATTTCATAGTGCATCGATACATCTGGGC
1 AAATTTGCCTTCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1157211 ATATTTGCCTGT-ATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCT-TCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1157263 AAATTTGCCTTCATGTATCGATACA
1 AAATTTGCCTTCATGTATCGATACA
1157288 AAGATTAGCG
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
51 1 0.01
52 70 0.99
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTTCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1157407 original size:32 final size:32
Alignment explanation
Indices: 1157365--1157467 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
1157355 AGCTTCCTAG
* *
1157365 CGATACATTGTATGGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
1157397 TGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1157429 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1157461 CGATACA
1 CGATACA
1157468 AATCTCTGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1157414 original size:13 final size:13
Alignment explanation
Indices: 1157392--1157448 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1157382 ACAAAACTTA
*
1157392 TGTATTGATACAT
1 TGTATCGATACAT
1157405 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1157423 ATGTATCGATACAT
1 -TGTATCGATACAT
1157437 TGTATCGATACA
1 TGTATCGATACA
1157449 ACACTTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1157429 original size:19 final size:19
Alignment explanation
Indices: 1157405--1157468 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1157395 ATTGATACAT
1157405 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1157424 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1157437 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1157456 TGTATCGATACAA
1 TGTATCGATACAA
1157469 ATCTCTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 6 0.15
18 1 0.03
19 22 0.56
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1167510 original size:13 final size:13
Alignment explanation
Indices: 1167492--1167517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1167482 TACACCAAGT
1167492 ATGTATCGATACA
1 ATGTATCGATACA
1167505 ATGTATCGATACA
1 ATGTATCGATACA
1167518 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1167536 original size:34 final size:32
Alignment explanation
Indices: 1167474--1167538 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1167464 TAGCCAAACT
**
1167474 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
1167506 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
1167539 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:1169500 original size:7 final size:7
Alignment explanation
Indices: 1169488--1169547 Score: 59
Period size: 8 Copynumber: 8.0 Consensus size: 7
1169478 TTTTCCTTAG
1169488 TTTTTCT
1 TTTTTCT
1169495 TTTTTCT
1 TTTTTCT
*
1169502 TTCTTTTT
1 TT-TTTCT
1169510 TTTTTCCT
1 TTTTT-CT
1169518 CTTTTCTCT
1 -TTTT-TCT
1169527 TTTTTC-
1 TTTTTCT
1169533 TTTTTCT
1 TTTTTCT
1169540 ATTTTTCT
1 -TTTTTCT
1169548 CTCACTCTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
6 6 0.13
7 14 0.31
8 18 0.40
9 6 0.13
10 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:1169534 original size:14 final size:13
Alignment explanation
Indices: 1169488--1169547 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 13
1169478 TTTTCCTTAG
1169488 TTTTTC-TTTT-T
1 TTTTTCTTTTTCT
*
1169499 TCTTTCTTTTT-T
1 TTTTTCTTTTTCT
1169511 TTTTCCTCTTTTCTCT
1 TTTT--TCTTTT-TCT
1169527 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
1169540 ATTTTTCT
1 -TTTTTCT
1169548 CTCACTCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 3 0.07
14 19 0.46
15 1 0.02
16 5 0.12
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:1169548 original size:23 final size:21
Alignment explanation
Indices: 1169488--1169549 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
1169478 TTTTCCTTAG
1169488 TTTTTCTTTTTTCTTTCTTTTTT
1 TTTTTCTTTTTTC--TCTTTTTT
* *
1169511 TTTTCCTCTTTTCTCTTTTTT
1 TTTTTCTTTTTTCTCTTTTTT
1169532 CTTTTTCTATTTTTCTCT
1 -TTTTTCT-TTTTTCTCT
1169550 CACTCTTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.24
22 6 0.18
23 19 0.58
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTTCTCTTTTTT
Found at i:1169677 original size:25 final size:22
Alignment explanation
Indices: 1169657--1169708 Score: 52
Period size: 23 Copynumber: 2.2 Consensus size: 22
1169647 GTTTTTATTA
1169657 TCTTTATCTTTATCTTTTTTTCATT
1 TCTTTATC-TT-TCTTTTTTT-ATT
*
1169682 TCTTTTTCTTTCTTTTTTT-TT
1 TCTTTATCTTTCTTTTTTTATT
1169703 CTCTTT
1 -TCTTT
1169709 TTTCTTCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 9 0.36
24 2 0.08
25 7 0.28
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (22 bp):
TCTTTATCTTTCTTTTTTTATT
Found at i:1169693 original size:10 final size:10
Alignment explanation
Indices: 1169673--1169714 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1169663 TCTTTATCTT
1169673 TTTTTCATTTC
1 TTTTTC-TTTC
1169684 TTTTTCTTTC
1 TTTTTCTTTC
*
1169694 TTTTTTTTTC
1 TTTTTCTTTC
*
1169704 TCTTT-TTTC
1 TTTTTCTTTC
1169713 TT
1 TT
1169715 CAAGTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 5 0.18
10 17 0.61
11 6 0.21
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:1170444 original size:166 final size:165
Alignment explanation
Indices: 1170171--1170567 Score: 395
Period size: 166 Copynumber: 2.4 Consensus size: 165
1170161 AGTAAGAAAG
* * * *
1170171 AAATTGAATTTTACAAAATTGATTTAATG-GAAATTTAATAGTAATATTAGATGAATTTTAAAAA
1 AAATT-AATTTTTCAAAA-TGATTTAATGTG-AATTAAATAATAATATTTGATGAATTTTAAAAA
* * * * * ** ** *
1170235 ATTTAAATTGAGAAAAATTCTTCTGAAAACATTTATGGAGTAGAAAACTCCGTATTTCCAAAAGA
63 A-TAAAACTAAGAAAAATCCCTCCAAAAACATTTACAGAGTAGAAAACTCCGTATTTCAAAAAGA
* ** *
1170300 GGAGAATTTCAAATAAAAAAT-TTAAAACTCAAGAAAAT
127 GGAGAATTTCAAAGAAAAAATGAAAAAAATCAAGAAAAT
1170338 AAATTAATTTTTCAAAATGGATTTAATGTGAATTAAATAATAATATTTGATGAATTTTAAAGATA
1 AAATTAATTTTTCAAAAT-GATTTAATGTGAATTAAATAATAATATTTGATGAATTTTAAA-A-A
* * * * *
1170403 A-AAAACTAAGAAAAATCCCTCCAAAAATATTTACAGAGTAGAAAACTCTGTGTTTCAAAAATAT
63 ATAAAACTAAGAAAAATCCCTCCAAAAACATTTACAGAGTAGAAAACTCCGTATTTCAAAAAGAG
* * * *
1170467 GAGAGTTTCAAGGAAAAAATGAAAAAAATCATGAAGAT
128 GAGAATTTCAAAGAAAAAATGAAAAAAATCAAGAAAAT
* * * * ***
1170505 GAATGAATTCTTGAAAACTGATTTAGCATGAATTAAATAATAATATTTGATGAATTTTAAAAA
1 AAATTAATTTTTCAAAA-TGATTTAATGTGAATTAAATAATAATATTTGATGAATTTTAAAAA
1170568 TTTTAGATCG
Statistics
Matches: 190, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
165 2 0.01
166 114 0.60
167 71 0.37
168 3 0.02
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (165 bp):
AAATTAATTTTTCAAAATGATTTAATGTGAATTAAATAATAATATTTGATGAATTTTAAAAAATA
AAACTAAGAAAAATCCCTCCAAAAACATTTACAGAGTAGAAAACTCCGTATTTCAAAAAGAGGAG
AATTTCAAAGAAAAAATGAAAAAAATCAAGAAAAT
Found at i:1176969 original size:13 final size:13
Alignment explanation
Indices: 1176951--1176975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1176941 TAATGACAAT
1176951 AATAAATAAATAA
1 AATAAATAAATAA
1176964 AATAAATAAATA
1 AATAAATAAATA
1176976 TCCTTTTTCT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:1177307 original size:158 final size:156
Alignment explanation
Indices: 1177017--1177471 Score: 589
Period size: 158 Copynumber: 2.9 Consensus size: 156
1177007 ACTTTAGGGA
* * *
1177017 TACTCCAAC-CTCATCTTTCCAAAGAGATACTCCAACCTCATTTTTCTTACAAATAATCTTGAGT
1 TACTCCAACTC-CATC-TTCCAAGGAGATACTTCAACCTCATTTTTCTTACAAATAATCTTGAAT
* * * * *
1177081 TTACATTCTTAGGGGTATTCTAACTCCATCTCTCCGA-AGGAATACTCCAACCTTGTTTTTCTTG
64 TTACATTCTTAGGGGTATTCCAACTCCATCTCTCTGAGAGG-ATACTCCAACCCTATTTTTCTTA
*
1177145 CAAATAATCTTGAATTTATATTCTCGAGAG
128 CAAATAATCTTGAATTTATATTCTC-AAAG
* *
1177175 TACTCCAACTCCATCTCTCCAAGGGGATCCTTCAACCTCATTTTTCTTACAAATAATCTTGAATT
1 TACTCCAACTCCATCT-TCCAAGGAGATACTTCAACCTCATTTTTCTTACAAATAATCTTGAATT
* * *
1177240 TACATTTTTAGGGGTATTCCAACTCCATCTCTCTGAGAGGATACTCCAACCCCATTTTTGTTACA
65 TACATTCTTAGGGGTATTCCAACTCCATCTCTCTGAGAGGATACTCCAACCCTATTTTTCTTACA
1177305 AATAATCTTGAATTTATATTCTCAAAG
130 AATAATCTTGAATTTATATTCTCAAAG
** *
1177332 TACTCCAACTCCATCATTCTGAGGAAATAC-TCTAACC-CAATTTTT-TTACAAATAATCTTGAA
1 TACTCCAACTCCATC-TTCCAAGGAGATACTTC-AACCTC-ATTTTTCTTACAAATAATCTTGAA
* * * * *
1177394 TTTACATTCTCA-AGGTACTCCAACTCTATCTCTCTGAGGGGATACTCCAACCCTATTTTTCTTA
63 TTTACATTCTTAGGGGTATTCCAACTCCATCTCTCTGAGAGGATACTCCAACCCTATTTTTCTTA
*
1177458 TAAATAATCTTGAA
128 CAAATAATCTTGAA
1177472 CTCGAGGATA
Statistics
Matches: 263, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
155 59 0.22
156 30 0.11
157 37 0.14
158 133 0.51
159 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (156 bp):
TACTCCAACTCCATCTTCCAAGGAGATACTTCAACCTCATTTTTCTTACAAATAATCTTGAATTT
ACATTCTTAGGGGTATTCCAACTCCATCTCTCTGAGAGGATACTCCAACCCTATTTTTCTTACAA
ATAATCTTGAATTTATATTCTCAAAG
Found at i:1177413 original size:77 final size:77
Alignment explanation
Indices: 1177040--1177471 Score: 476
Period size: 79 Copynumber: 5.5 Consensus size: 77
1177030 TCTTTCCAAA
* * * * *
1177040 GAGATACTCCAACCTCATTTTTCTTACAAATAATCTTGAGTTTACATTCTTAGGGGTATTCTAAC
1 GAGATACTCCAACC-CATTTTTCTTACAAATAATCTTGAATTTACATTCTCA-AGGTACTCCAAC
*
1177105 TCCATCTCTCCGAAG
64 TCCATCTCTCTG-AG
** * * *
1177120 GA-ATACTCCAACCTTGTTTTTCTTGCAAATAATCTTGAATTTATATTCTCGAGAGTACTCCAAC
1 GAGATACTCCAACC-CATTTTTCTTACAAATAATCTTGAATTTACATTCTCAAG-GTACTCCAAC
**
1177184 TCCATCTCTCCAAG
64 TCCATCTCTCTGAG
* * * * * * *
1177198 GGGATCCTTCAACCTCATTTTTCTTACAAATAATCTTGAATTTACATTTTTAGGGGTATTCCAAC
1 GAGATACTCCAACC-CATTTTTCTTACAAATAATCTTGAATTTACATTCTCA-AGGTACTCCAAC
1177263 TCCATCTCTCTGA-
64 TCCATCTCTCTGAG
* * *
1177276 GAGGATACTCCAACCCCATTTTTGTTACAAATAATCTTGAATTTATATTCTCAAAGTACTCCAAC
1 GA-GATACTCCAA-CCCATTTTTCTTACAAATAATCTTGAATTTACATTCTCAAGGTACTCCAAC
1177341 TCCATCAT-TCTGAG
64 TCCATC-TCTCTGAG
* *
1177355 GAAATACTCTAACCCAATTTTT-TTACAAATAATCTTGAATTTACATTCTCAAGGTACTCCAACT
1 GAGATACTCCAACCC-ATTTTTCTTACAAATAATCTTGAATTTACATTCTCAAGGTACTCCAACT
*
1177419 CTATCTCTCTGAG
65 CCATCTCTCTGAG
* *
1177432 GGGATACTCCAACCCTATTTTTCTTATAAATAATCTTGAA
1 GAGATACTCCAACCC-ATTTTTCTTACAAATAATCTTGAA
1177472 CTCGAGGATA
Statistics
Matches: 297, Mismatches: 45, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.00
77 71 0.24
78 55 0.19
79 165 0.56
80 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (77 bp):
GAGATACTCCAACCCATTTTTCTTACAAATAATCTTGAATTTACATTCTCAAGGTACTCCAACTC
CATCTCTCTGAG
Found at i:1180622 original size:20 final size:19
Alignment explanation
Indices: 1180597--1180666 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1180587 ACCCTGAAAA
1180597 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1180617 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
*
1180636 AGTATCGATACACA-CAATAT
1 -GTATCGATACACATTAA-AT
1180656 GTATCGATACA
1 GTATCGATACA
1180667 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1180795 original size:21 final size:22
Alignment explanation
Indices: 1180762--1180816 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
1180752 ATCACTATTT
1180762 ATCACTGTTCATGTATCGATAC
1 ATCACTGTTCATGTATCGATAC
1180784 ATCACT-TTCATGTATCGATAC
1 ATCACTGTTCATGTATCGATAC
1180805 ATCACTGTTCAT
1 ATCACTGTTCAT
1180817 ACTGTTCACG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (22 bp):
ATCACTGTTCATGTATCGATAC
Found at i:1180891 original size:13 final size:13
Alignment explanation
Indices: 1180873--1180911 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1180863 TCACTATTCA
*
1180873 TGTATCAATACAT
1 TGTATCGATACAT
*
1180886 TGTATCGATACAG
1 TGTATCGATACAT
1180899 TGTATCGATACAT
1 TGTATCGATACAT
1180912 CATAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1181025 original size:20 final size:21
Alignment explanation
Indices: 1180979--1181026 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1180969 AATTTCAAAT
*
1180979 GCATGTATCGATACATTATGA
1 GCATGTATCGATACATTAGGA
**
1181000 -TTTGTATCGATACATT-GGA
1 GCATGTATCGATACATTAGGA
1181019 GCATGTAT
1 GCATGTAT
1181027 GTGTGAAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (21 bp):
GCATGTATCGATACATTAGGA
Found at i:1186624 original size:19 final size:19
Alignment explanation
Indices: 1186575--1186658 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
1186565 CTCCCAGTTT
*
1186575 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
1186595 TATGCATCGATACAATGAA
1 CATGTATCGATACAATGAA
1186614 CATGTATCGATAC------
1 CATGTATCGATACAATGAA
*
1186627 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
*
1186646 CATGCATCGATAC
1 CATGTATCGATAC
1186659 CATGTATCGA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
13 12 0.24
19 25 0.50
20 13 0.26
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1186645 original size:32 final size:32
Alignment explanation
Indices: 1186604--1186673 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1186594 GTATGCATCG
*
1186604 ATACAATGAACATGTATCGATACCATGTATCA
1 ATACAATGAACATGCATCGATACCATGTATCA
*
1186636 ATACAATGAACATGCATCGATACCATGTATCG
1 ATACAATGAACATGCATCGATACCATGTATCA
1186668 ATACAA
1 ATACAA
1186674 AGCATAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (32 bp):
ATACAATGAACATGCATCGATACCATGTATCA
Found at i:1187505 original size:42 final size:42
Alignment explanation
Indices: 1187393--1187492 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
1187383 AAATAAAAAT
* *
1187393 AATTTTTCCCCTTTTGTCAAATGCCAAAATTTATTTTTCAAA
1 AATTTCTCCCTTTTTGTCAAATGCCAAAATTTATTTTTCAAA
1187435 AATTTCTCCCTTTTTGTCAAATGCCAAAATTTATTTTTCAAA
1 AATTTCTCCCTTTTTGTCAAATGCCAAAATTTATTTTTCAAA
1187477 AATTTCTCCTCTTTTT
1 AATTTCTCC-CTTTTT
1187493 TCTTATAGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 49 0.89
43 6 0.11
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (42 bp):
AATTTCTCCCTTTTTGTCAAATGCCAAAATTTATTTTTCAAA
Found at i:1188677 original size:28 final size:28
Alignment explanation
Indices: 1188596--1188677 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1188586 TTTTGGAGAT
*
1188596 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1188624 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1188652 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1188678 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1188820 original size:51 final size:51
Alignment explanation
Indices: 1188660--1188830 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1188650 GAAATAACGA
* * *
1188660 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
1188712 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1188765 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1188816 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1188831 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1188876 original size:27 final size:28
Alignment explanation
Indices: 1188813--1188888 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1188803 AAAATAAAGT
*
1188813 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1188841 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1188868 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1188889 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1192548 original size:32 final size:32
Alignment explanation
Indices: 1192477--1192551 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
1192467 TTTATGGGTG
*
1192477 GTTTTGAATGAAAAATTTGATGGAAAAAGATCTA
1 GTTTTG-ATGAAAAATTTGATGAAAAAAGA-CTA
* * *
1192511 TTTTTGATGAAGATTTTGATGAAAAATAGA-TA
1 GTTTTGATGAAAAATTTGATGAAAAA-AGACTA
1192543 GTTTTGATG
1 GTTTTGATG
1192552 TGAAAATGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 10 0.29
33 17 0.49
34 8 0.23
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.39
Consensus pattern (32 bp):
GTTTTGATGAAAAATTTGATGAAAAAAGACTA
Found at i:1192568 original size:21 final size:20
Alignment explanation
Indices: 1192523--1192570 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1192513 TTTGATGAAG
1192523 ATTTTGATGAAAAATAGATA
1 ATTTTGATGAAAAATAGATA
* *
1192543 GTTTTGATGTGAAAAT-GATGA
1 ATTTTGATG-AAAAATAGAT-A
1192564 ATTTTGA
1 ATTTTGA
1192571 AAAATGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTTGATGAAAAATAGATA
Found at i:1198983 original size:13 final size:13
Alignment explanation
Indices: 1198965--1198991 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1198955 ACAATTGAGT
1198965 ATGTATCGATACA
1 ATGTATCGATACA
1198978 ATGTATCGATACA
1 ATGTATCGATACA
1198991 A
1 A
1198992 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1204370 original size:32 final size:33
Alignment explanation
Indices: 1204329--1204392 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1204319 TAGCCAAACT
** *
1204329 TGTATCGATACA-CAAAGTATGTATTGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
1204361 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
1204393 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:1206448 original size:19 final size:19
Alignment explanation
Indices: 1206404--1206448 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1206394 AATTTAAAAC
*
1206404 ATAAAAAGACAATCATAAA
1 ATAAAAAGACAATAATAAA
*
1206423 ATTAAAAGA-AGATAATAAA
1 ATAAAAAGACA-ATAATAAA
1206442 ATAAAAA
1 ATAAAAA
1206449 TGATTGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (19 bp):
ATAAAAAGACAATAATAAA
Found at i:1212426 original size:20 final size:22
Alignment explanation
Indices: 1212389--1212432 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1212379 CAAATTTGAT
1212389 AAAATTATCTTATTAAGGGGGA
1 AAAATTATCTTATTAAGGGGGA
1212411 AAAATTAT-TT-TTAAGGGGGA
1 AAAATTATCTTATTAAGGGGGA
1212431 AA
1 AA
1212433 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 2 0.09
22 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (22 bp):
AAAATTATCTTATTAAGGGGGA
Found at i:1213241 original size:13 final size:13
Alignment explanation
Indices: 1213223--1213248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1213213 CAATTTTTTG
1213223 TGTATCGATACAT
1 TGTATCGATACAT
1213236 TGTATCGATACAT
1 TGTATCGATACAT
1213249 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1217923 original size:15 final size:15
Alignment explanation
Indices: 1217903--1217933 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1217893 ATTTCGTTTG
*
1217903 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1217918 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1217933 G
1 G
1217934 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1219769 original size:21 final size:21
Alignment explanation
Indices: 1219740--1219784 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1219730 AAGTTTTCAT
*
1219740 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1219760 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1219782 TTT
1 TTT
1219785 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1221667 original size:13 final size:13
Alignment explanation
Indices: 1221649--1221674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1221639 CAATTTTTTG
1221649 TGTATCGATACAT
1 TGTATCGATACAT
1221662 TGTATCGATACAT
1 TGTATCGATACAT
1221675 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1221758 original size:20 final size:21
Alignment explanation
Indices: 1221713--1221765 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1221703 CTGCCAAGAA
* **
1221713 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTGTAAC
1221734 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTGTAAC
1221754 ATGTATCGATAC
1 ATGTATCGATAC
1221766 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTGTAAC
Found at i:1222648 original size:13 final size:13
Alignment explanation
Indices: 1222630--1222655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1222620 TACACAAAGT
1222630 ATGTATCGATACA
1 ATGTATCGATACA
1222643 ATGTATCGATACA
1 ATGTATCGATACA
1222656 CCAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1222653 original size:32 final size:33
Alignment explanation
Indices: 1222612--1222675 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1222602 TAGCCAAACT
**
1222612 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
1222644 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
1222676 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:1224233 original size:32 final size:32
Alignment explanation
Indices: 1224185--1224521 Score: 304
Period size: 32 Copynumber: 10.5 Consensus size: 32
1224175 GCACTTATCG
* *
1224185 ACCTCAATCCTCAAAGAGTAGGATGCTTACCA
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
* * * ***
1224217 ACCTTACTCCTCAAAGAGTAGGGCACTTACCA
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
* * * *
1224249 GCCTTAGTCCTTAAATAGCAAGGCA--CTTACCA
1 ACCTCAGTCCTCAAAGAGC-AGG-ATGCTTACCA
* * * **
1224281 ACCTTAGTCCTCAAAGTGTAGGATGCTTATTA
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
* *
1224313 ACCTCAGTCCTCAAAGAGCAAGATGCTTACCG
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
* *
1224345 ACCTCAATACTCAAAGAGCAGGATGCTTACCA
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
***
1224377 ACCTCAGTCCTCAAAGAGCAGGGCACTTACCA
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
* * *
1224409 ATCTCAATCCTCAAAGAGCAAGATGCTTACCA
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
*
1224441 ACCTCAGTCCTCAAAGAGCAAGGCAT--TTACAA
1 ACCTCAGTCCTCAAAGAGC-AGG-ATGCTTACCA
* * * * * *
1224473 ACATCAATCCTCAAAGTGCAAGATGCCTACCT
1 ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
1224505 ACCTCAGTCCTCAAAGA
1 ACCTCAGTCCTCAAAGA
1224522 ACATAACATT
Statistics
Matches: 243, Mismatches: 54, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
30 3 0.01
31 5 0.02
32 228 0.94
33 5 0.02
34 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (32 bp):
ACCTCAGTCCTCAAAGAGCAGGATGCTTACCA
Found at i:1227502 original size:79 final size:80
Alignment explanation
Indices: 1227409--1227899 Score: 511
Period size: 79 Copynumber: 6.2 Consensus size: 80
1227399 ATTTTTGGGA
* * *
1227409 TACTCTAACTCCATCTCTTCGAGA-GGATACTCTAACCTTGTTTTTCTTACAAATAATCTT-AAG
1 TACTCCAACTCCATCTCTTCGAGAGGGATACTCTAACCCTATTTTTCTTACAAATAATCTTGAA-
* *
1227472 TTTATATTCTCGAGGC
65 TTTACATTCTCGAGGG
* * * *
1227488 TACTCCAACTCCATCTC-TCTAAAGGGATACTCTAATCCC-ATTTTTCTTACAAATAATTTTAAA
1 TACTCCAACTCCATCTCTTCGAGAGGGATACTCTAA-CCCTATTTTTCTTACAAATAATCTTGAA
* *
1227551 TTTATATTCTTGAGGG
65 TTTACATTCTCGAGGG
* * ** *
1227567 TACTCTAACTCCATCTCTCCGA-AGGGATACTCTAACCCCGTTTTTCTTGCAAATAATCTTGAAT
1 TACTCCAACTCCATCTCTTCGAGAGGGATACTCTAACCCTATTTTTCTTACAAATAATCTTGAAT
1227631 TTACATTCTCGAGGG
66 TTACATTCTCGAGGG
* * *
1227646 TACTCCAACTCCATCTCATT-GAG-GAGATACTTTAACCCTATTTTTCTTACGAATAATCTTGAA
1 TACTCCAACTCCATCTC-TTCGAGAGGGATACTCTAACCCTATTTTTCTTACAAATAATCTTGAA
* * *
1227709 GTTACATTATCGGGGG
65 TTTACATTCTCGAGGG
* * ** * * * *
1227725 TAATCCAACTCTATAGCTCCGAGA-GGATAC-CTCAACCCTGTTTTTCTTACAAATAATATTAAA
1 TACTCCAACTCCATCTCTTCGAGAGGGATACTCT-AACCCTATTTTTCTTACAAATAATCTTGAA
* *
1227788 TTTACATTCTTGGGGG
65 TTTACATTCTCGAGGG
** * *
1227804 TACTCCAACTCCATC-CTTTTA-AGGGAATACTCAAACCTTATTTTTCTTACAAATAATCTTGAA
1 TACTCCAACTCCATCTCTTCGAGAGGG-ATACTCTAACCCTATTTTTCTTACAAATAATCTTGAA
* *
1227867 TTTACATTCTTGGGGG
65 TTTACATTCTCGAGGG
1227883 TAC-CCAACTCCATCTCT
1 TACTCCAACTCCATCTCT
1227900 CCGATGAATA
Statistics
Matches: 345, Mismatches: 53, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
77 1 0.00
78 25 0.07
79 311 0.90
80 8 0.02
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (80 bp):
TACTCCAACTCCATCTCTTCGAGAGGGATACTCTAACCCTATTTTTCTTACAAATAATCTTGAAT
TTACATTCTCGAGGG
Found at i:1227701 original size:158 final size:156
Alignment explanation
Indices: 1227409--1227943 Score: 602
Period size: 158 Copynumber: 3.4 Consensus size: 156
1227399 ATTTTTGGGA
* * **
1227409 TACTCTAACTCCATCTCTTCGAGAGGATACTCTAACCTTGTTTTTCTTACAAATAATCTT-AAGT
1 TACTCCAACTCCATCTCTCCGAGAGGATACTCTAACCCCGTTTTTCTTACAAATAATCTTGAA-T
* *
1227473 TTATATTCTCGAGGCTACTCCAACTCCATCTCTCTAAAGGGATACTCTAATCCC-ATTTTTCTTA
65 TTACATTCTCGAGGGTACTCCAACTCCATCTCT-T-AAGGGATACTCTAA-CCCTATTTTTCTTA
* * * *
1227537 CAAATAATTTTAAATTTATATTCTTGAGGG
127 CAAATAATCTTGAATTTACATTCTTGGGGG
* *
1227567 TACTCTAACTCCATCTCTCCGA-AGGGATACTCTAACCCCGTTTTTCTTGCAAATAATCTTGAAT
1 TACTCCAACTCCATCTCTCCGAGA-GGATACTCTAACCCCGTTTTTCTTACAAATAATCTTGAAT
* *
1227631 TTACATTCTCGAGGGTACTCCAACTCCATCTCATTGAGGAGATACTTTAACCCTATTTTTCTTAC
65 TTACATTCTCGAGGGTACTCCAACTCCATCTC-TTAAGG-GATACTCTAACCCTATTTTTCTTAC
* * * *
1227696 GAATAATCTTGAAGTTACATTATCGGGGG
128 AAATAATCTTGAATTTACATTCTTGGGGG
* * ** * * *
1227725 TAATCCAACTCTATAGCTCCGAGAGGATAC-CTCAACCCTGTTTTTCTTACAAATAATATTAAAT
1 TACTCCAACTCCATCTCTCCGAGAGGATACTCT-AACCCCGTTTTTCTTACAAATAATCTTGAAT
* * * * *
1227789 TTACATTCTTGGGGGTACTCCAACTCCATCCTTTTAAGGGAATACTCAAACCTTATTTTTCTTAC
65 TTACATTCTCGAGGGTACTCCAACTCCAT-CTCTTAAGGG-ATACTCTAACCCTATTTTTCTTAC
1227854 AAATAATCTTGAATTTACATTCTTGGGGG
128 AAATAATCTTGAATTTACATTCTTGGGGG
* *
1227883 TAC-CCAACTCCATCTCTCCGATGA--ATACTCCAACCCC-TTTTT-TTCCATAAATAATCTTGA
1 TACTCCAACTCCATCTCTCCGA-GAGGATACTCTAACCCCGTTTTTCTT--ACAAATAATCTTGA
1227943 A
63 A
1227944 CTCGAGGATA
Statistics
Matches: 319, Mismatches: 45, Indels: 28
0.81 0.11 0.07
Matches are distributed among these distances:
154 2 0.01
155 5 0.02
156 21 0.07
157 26 0.08
158 259 0.81
159 6 0.02
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (156 bp):
TACTCCAACTCCATCTCTCCGAGAGGATACTCTAACCCCGTTTTTCTTACAAATAATCTTGAATT
TACATTCTCGAGGGTACTCCAACTCCATCTCTTAAGGGATACTCTAACCCTATTTTTCTTACAAA
TAATCTTGAATTTACATTCTTGGGGG
Found at i:1227850 original size:237 final size:237
Alignment explanation
Indices: 1227409--1227899 Score: 595
Period size: 237 Copynumber: 2.1 Consensus size: 237
1227399 ATTTTTGGGA
* * *
1227409 TACTCTAACTCCATCTCTTCGAGAGGATACTCTAACCTTGTTTTTCTTACAAATAATCTTAAGTT
1 TACTCCAACTCCATCTCTTCGAGAGGATACTCTAACCCTATTTTTCTTACAAATAATCTTAAGTT
* * * *
1227474 TATATTCTCGAGGCTACTCCAACTCCATCTCTCTAAAGGGATACTCTAATCCCATTTTTCTTACA
66 TACATTATCGAGGCTAATCCAACTCCATCTCTCGAAAGGGATACTCTAATCCCATTTTTCTTACA
* * * *
1227539 AATAATTTTAAATTTATATTCTTGAGGGTACTCTAACTCCATCTCTCCGAAGGGATACTCTAACC
131 AATAATATTAAATTTACATTCTTGAGGGTACTCCAACTCCATCTCTCCGAAGGGATACTCAAACC
* *
1227604 CCGTTTTTCTTGCAAATAATCTTGAATTTACATTCTCGAGGG
196 CCATTTTTCTTACAAATAATCTTGAATTTACATTCTCGAGGG
* *
1227646 TACTCCAACTCCATCTCATT-GAG-GAGATACTTTAACCCTATTTTTCTTACGAATAATCTTGAA
1 TACTCCAACTCCATCTC-TTCGAGAG-GATACTCTAACCCTATTTTTCTTACAAATAATCTT-AA
* * * * *
1227709 G-TTACATTATCGGGGGTAATCCAACTCTATAGCTC-CGAGA-GGATAC-CTCAA-CCCTGTTTT
63 GTTTACATTATCGAGGCTAATCCAACTCCAT--CTCTCGAAAGGGATACTCT-AATCCC-ATTTT
* ***
1227769 TCTTACAAATAATATTAAATTTACATTCTTGGGGGTACTCCAACTCCATC-CTTTTAAGGGAATA
124 TCTTACAAATAATATTAAATTTACATTCTTGAGGGTACTCCAACTCCATCTCTCCGAAGGG-ATA
** * *
1227833 CTCAAACCTTATTTTTCTTACAAATAATCTTGAATTTACATTCTTGGGGG
188 CTCAAACCCCATTTTTCTTACAAATAATCTTGAATTTACATTCTCGAGGG
1227883 TAC-CCAACTCCATCTCT
1 TACTCCAACTCCATCTCT
1227900 CCGATGAATA
Statistics
Matches: 218, Mismatches: 28, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
235 1 0.00
236 26 0.12
237 180 0.83
238 8 0.04
239 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (237 bp):
TACTCCAACTCCATCTCTTCGAGAGGATACTCTAACCCTATTTTTCTTACAAATAATCTTAAGTT
TACATTATCGAGGCTAATCCAACTCCATCTCTCGAAAGGGATACTCTAATCCCATTTTTCTTACA
AATAATATTAAATTTACATTCTTGAGGGTACTCCAACTCCATCTCTCCGAAGGGATACTCAAACC
CCATTTTTCTTACAAATAATCTTGAATTTACATTCTCGAGGG
Found at i:1230296 original size:21 final size:21
Alignment explanation
Indices: 1230272--1230348 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1230262 AATTTATCCA
1230272 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
**
1230293 AATGTATCGATACATTTGCGG
1 AATGTATCGATACATTTGTAG
* * * *
1230314 AATTTAACGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
1230335 AATGTATCGATACA
1 AATGTATCGATACA
1230349 GGGTCCCAAC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1230408 original size:19 final size:19
Alignment explanation
Indices: 1230384--1230451 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
1230374 AATTCAACAA
1230384 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1230403 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
* *
1230418 --TGTATTGATACATTAGT
1 TTTGTATCGATACATAAGT
*
1230435 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1230452 TTAGCTACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
13 10 0.26
15 1 0.03
17 2 0.05
19 26 0.67
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1230428 original size:32 final size:32
Alignment explanation
Indices: 1230386--1230448 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1230376 TTCAACAATT
*
1230386 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
* *
1230418 TGTATTGATACATTAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1230449 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1230496 original size:20 final size:20
Alignment explanation
Indices: 1230471--1230525 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1230461 GCCAAGGAAA
*
1230471 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
1230491 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
1230511 TGTATCGATACATTT
1 TGTATCGATACATTT
1230526 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:1233063 original size:31 final size:28
Alignment explanation
Indices: 1232980--1233049 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
1232970 CTTCACAATC
*
1232980 GGGGATACTCCAACCCCGTTGATCAT-C--
1 GGGGATACTCCAACCCCGTT-AT-TTCCGA
1233007 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
1233035 GGGGATACTCCAACC
1 GGGGATACTCCAACC
1233050 TCGACTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 20 0.51
28 15 0.38
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Done.