Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 17 of 50
Found at i:8186910 original size:71 final size:71
Alignment explanation
Indices: 8186794--8186937 Score: 270
Period size: 71 Copynumber: 2.0 Consensus size: 71
8186784 AATCTAACAA
* *
8186794 AACCAGTTGACATTGTAGTTCCCAGCCTTCCTTACTTGCAAAGATTAAGTTGCAAGATAAAATTC
1 AACCAGTTGACATTATAGTTCCCAGCCTTCCTTACCTGCAAAGATTAAGTTGCAAGATAAAATTC
8186859 ATTTGC
66 ATTTGC
8186865 AACCAGTTGACATTATAGTTCCCAGCCTTCCTTACCTGCAAAGATTAAGTTGCAAGATAAAATTC
1 AACCAGTTGACATTATAGTTCCCAGCCTTCCTTACCTGCAAAGATTAAGTTGCAAGATAAAATTC
8186930 ATTTGC
66 ATTTGC
8186936 AA
1 AA
8186938 GTAGTTCATA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (71 bp):
AACCAGTTGACATTATAGTTCCCAGCCTTCCTTACCTGCAAAGATTAAGTTGCAAGATAAAATTC
ATTTGC
Found at i:8187368 original size:39 final size:39
Alignment explanation
Indices: 8187305--8187473 Score: 205
Period size: 39 Copynumber: 4.3 Consensus size: 39
8187295 AAAGAAGCTC
*
8187305 CCAGCAGAGAACAATATATCAGAAAACCATGATATGGAT
1 CCAGCAGAGAACAATATATCAGAAAACCATGATAGGGAT
* * * *
8187344 CCAGTAGAAAACAATATATTAGAAAACCATAATAGGGAT
1 CCAGCAGAGAACAATATATCAGAAAACCATGATAGGGAT
* * *
8187383 CCGGCAGAGAACAATACACCAGAAAACCATGATAGGGAT
1 CCAGCAGAGAACAATATATCAGAAAACCATGATAGGGAT
* * * * *
8187422 CCAACAGAGAACAACACATCA-AAGAAACATGGTAGGGAT
1 CCAGCAGAGAACAATATATCAGAA-AACCATGATAGGGAT
8187461 CCAGCAGAGAACA
1 CCAGCAGAGAACA
8187474 GTTCCAATGA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
38 2 0.02
39 108 0.98
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (39 bp):
CCAGCAGAGAACAATATATCAGAAAACCATGATAGGGAT
Found at i:8196545 original size:30 final size:28
Alignment explanation
Indices: 8196509--8196567 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
8196499 AAAGCAAACT
8196509 AAGGTATTCTCTACAGGGTATATCATCTAC
1 AAGGTATTCTCTACAGGGTAT-TC-TCTAC
*
8196539 AAGGTATTCTTTACAGGGTATTCTCTAC
1 AAGGTATTCTCTACAGGGTATTCTCTAC
8196567 A
1 A
8196568 GGATATAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 2 0.07
30 20 0.71
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (28 bp):
AAGGTATTCTCTACAGGGTATTCTCTAC
Found at i:8196558 original size:14 final size:14
Alignment explanation
Indices: 8196511--8196569 Score: 82
Period size: 14 Copynumber: 4.1 Consensus size: 14
8196501 AGCAAACTAA
8196511 GGTATTCTCTACAG
1 GGTATTCTCTACAG
*
8196525 GGTATATCATCTACAA
1 GGTAT-TC-TCTACAG
*
8196541 GGTATTCTTTACAG
1 GGTATTCTCTACAG
8196555 GGTATTCTCTACAG
1 GGTATTCTCTACAG
8196569 G
1 G
8196570 ATATAAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 24 0.62
15 4 0.10
16 11 0.28
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (14 bp):
GGTATTCTCTACAG
Found at i:8201549 original size:20 final size:21
Alignment explanation
Indices: 8201521--8201561 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
8201511 AGCCAACCTT
8201521 CTTTCAACTAATTAAAGCTTC
1 CTTTCAACTAATTAAAGCTTC
*
8201542 CTTT-AACTAATTGAAGCTTC
1 CTTTCAACTAATTAAAGCTTC
8201562 TCTCCCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (21 bp):
CTTTCAACTAATTAAAGCTTC
Found at i:8206780 original size:45 final size:45
Alignment explanation
Indices: 8206729--8206817 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
8206719 TGCACCTTTA
* *
8206729 AGGAACTTGATGCATTCTTTTCCTACTAACTTGTACCCCATCTTG
1 AGGAACTTGATGCATTCTGTTCCTACTAACTCGTACCCCATCTTG
* *
8206774 AGGAACTTGATGCATTCTGTTCCTGCTAGCTCGTACCCCATCTT
1 AGGAACTTGATGCATTCTGTTCCTACTAACTCGTACCCCATCTT
8206818 TATAAGGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (45 bp):
AGGAACTTGATGCATTCTGTTCCTACTAACTCGTACCCCATCTTG
Found at i:8209766 original size:13 final size:13
Alignment explanation
Indices: 8209748--8209772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8209738 AGAGAAATTG
8209748 TGATTTTATAAAA
1 TGATTTTATAAAA
8209761 TGATTTTATAAA
1 TGATTTTATAAA
8209773 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:8215952 original size:34 final size:35
Alignment explanation
Indices: 8215878--8215953 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
8215868 AAATTTAAAT
* * *
8215878 TTAAATAATCAAAAACAAATATCTCATATATCAAC
1 TTAAATAATCAAAAACAAATATCTCAAACAACAAC
*
8215913 TTAAATAATTAAAAACAAATAT-TCAAACAACAAC
1 TTAAATAATCAAAAACAAATATCTCAAACAACAAC
8215947 TTAAATA
1 TTAAATA
8215954 TTACAAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 16 0.43
35 21 0.57
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (35 bp):
TTAAATAATCAAAAACAAATATCTCAAACAACAAC
Found at i:8216177 original size:15 final size:15
Alignment explanation
Indices: 8216157--8216198 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
8216147 GTTTGTATTT
8216157 AAAGTATATATAATA
1 AAAGTATATATAATA
8216172 AAAGTATATAT-ATA
1 AAAGTATATATAATA
*
8216186 ATAGTA-ATATAAT
1 AAAGTATATATAAT
8216199 CTTTATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 10 0.40
15 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (15 bp):
AAAGTATATATAATA
Found at i:8217064 original size:41 final size:41
Alignment explanation
Indices: 8217016--8217098 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
8217006 TAGCAATAAC
8217016 TACAAACCTTTTGCAAAACGAAGGGTAAGAATTAGCAGAAG
1 TACAAACCTTTTGCAAAACGAAGGGTAAGAATTAGCAGAAG
8217057 TACAAACCTTTTGCAAAACGAAGGGTAAGAATTAGCAGAAG
1 TACAAACCTTTTGCAAAACGAAGGGTAAGAATTAGCAGAAG
8217098 T
1 T
8217099 TCATGAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (41 bp):
TACAAACCTTTTGCAAAACGAAGGGTAAGAATTAGCAGAAG
Found at i:8228058 original size:99 final size:98
Alignment explanation
Indices: 8227885--8228070 Score: 363
Period size: 99 Copynumber: 1.9 Consensus size: 98
8227875 AAGATAATAT
8227885 ATTTTTAAAGAGACACATAAGTCTCACTTGATATATAAATTAATAATCTCTTTATACATCAAAAT
1 ATTTTTAAAGAGACACATAAGTCTCACTTGATATATAAATTAATAATCTCTTTATACATCAAAAT
8227950 TATATATATATATATATATATGTATTCAATGCC
66 TATATATATATATATATATATGTATTCAATGCC
8227983 ATNTTTTAAAGAGACACATAAGTCTCACTTGATATATAAATTAATAATCTCTTTATACATCAAAA
1 AT-TTTTAAAGAGACACATAAGTCTCACTTGATATATAAATTAATAATCTCTTTATACATCAAAA
8228048 TTATATATATATATATATATATG
65 TTATATATATATATATATATATG
8228071 ACTCAATTAG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 2 0.02
99 85 0.98
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.40
Consensus pattern (98 bp):
ATTTTTAAAGAGACACATAAGTCTCACTTGATATATAAATTAATAATCTCTTTATACATCAAAAT
TATATATATATATATATATATGTATTCAATGCC
Found at i:8230287 original size:23 final size:23
Alignment explanation
Indices: 8230257--8230355 Score: 112
Period size: 23 Copynumber: 4.3 Consensus size: 23
8230247 GTTTTTGGCT
8230257 TTGCGTGACTAGTTGATAAGTCA
1 TTGCGTGACTAGTTGATAAGTCA
8230280 TTGCGTGACTAGTTGATAAGTCA
1 TTGCGTGACTAGTTGATAAGTCA
*
8230303 TTGCTTGACTAGTTTG-T-AGTCA
1 TTGCGTGACTAG-TTGATAAGTCA
* ** * *
8230325 TTGCATGTTTGGTTGATAGGTCA
1 TTGCGTGACTAGTTGATAAGTCA
*
8230348 TTACGTGA
1 TTGCGTGA
8230356 TTGGTTTAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.05
22 14 0.22
23 44 0.69
24 3 0.05
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.39
Consensus pattern (23 bp):
TTGCGTGACTAGTTGATAAGTCA
Found at i:8230425 original size:25 final size:25
Alignment explanation
Indices: 8230388--8230478 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
8230378 TGCTTGATAG
* *
8230388 GGCATTGCATGATTGTTATCTATAA
1 GGCATTGCGTGATTGTTATCTGTAA
8230413 GGCATTGCGTGATTGTTATCTGT-A
1 GGCATTGCGTGATTGTTATCTGTAA
* * * * *
8230437 GAGCATTGCGTGACTATTTTGTGTAG
1 G-GCATTGCGTGATTGTTATCTGTAA
8230463 GGCATTGCGTGATTGT
1 GGCATTGCGTGATTGT
8230479 CATTTCTTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 2 0.04
25 52 0.95
26 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.40
Consensus pattern (25 bp):
GGCATTGCGTGATTGTTATCTGTAA
Found at i:8233938 original size:43 final size:43
Alignment explanation
Indices: 8233821--8233916 Score: 192
Period size: 43 Copynumber: 2.2 Consensus size: 43
8233811 TTAAGCCTTA
8233821 TTAGGCATTGCGTGACACCACATCCTACATTGTATTGCATGAT
1 TTAGGCATTGCGTGACACCACATCCTACATTGTATTGCATGAT
8233864 TTAGGCATTGCGTGACACCACATCCTACATTGTATTGCATGAT
1 TTAGGCATTGCGTGACACCACATCCTACATTGTATTGCATGAT
8233907 TTAGGCATTG
1 TTAGGCATTG
8233917 GATGCCCCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
TTAGGCATTGCGTGACACCACATCCTACATTGTATTGCATGAT
Found at i:8236459 original size:35 final size:36
Alignment explanation
Indices: 8236420--8236497 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
8236410 CATAGCTAGA
* **
8236420 ATCATCCTGTACACTTGCACACCACACAAGGCA-AT
1 ATCATCATGTACACTCCCACACCACACAAGGCATAT
* * * *
8236455 ATCATCATGTGCACTCCCACATCGCACATGGCATAT
1 ATCATCATGTACACTCCCACACCACACAAGGCATAT
8236491 ATCATCA
1 ATCATCA
8236498 GTGTGTGCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
35 26 0.74
36 9 0.26
ACGTcount: A:0.32, C:0.33, G:0.12, T:0.23
Consensus pattern (36 bp):
ATCATCATGTACACTCCCACACCACACAAGGCATAT
Found at i:8236494 original size:36 final size:36
Alignment explanation
Indices: 8236388--8236502 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
8236378 ATCTTACAGC
* *
8236388 TCATGTGCACTTCCACATCGCACATAGC-TAGAATCA
1 TCATGTGCACTTCCACATCGCACATGGCATA-TATCA
* * * * * *
8236424 TCCTGTACACTTGCACACCACACAAGGCA-ATATCA
1 TCATGTGCACTTCCACATCGCACATGGCATATATCA
*
8236459 TCATGTGCACTCCCACATCGCACATGGCATATATCA
1 TCATGTGCACTTCCACATCGCACATGGCATATATCA
8236495 TCAGTGTG
1 TCA-TGTG
8236503 TGCACTCACA
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
35 26 0.43
36 31 0.51
37 4 0.07
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (36 bp):
TCATGTGCACTTCCACATCGCACATGGCATATATCA
Found at i:8236555 original size:52 final size:52
Alignment explanation
Indices: 8236477--8236581 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
8236467 ACTCCCACAT
*
8236477 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
1 CGCACATGGCATATATCATCAATGTGTGCACTCACACAGCACACCACTATCA
8236529 CGCACATGGCATATATCATCAATGTGTGCACTCACACAGCACACCACTATCA
1 CGCACATGGCATATATCATCAATGTGTGCACTCACACAGCACACCACTATCA
8236581 C
1 C
8236582 CATCATGTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.21
Consensus pattern (52 bp):
CGCACATGGCATATATCATCAATGTGTGCACTCACACAGCACACCACTATCA
Found at i:8238546 original size:13 final size:13
Alignment explanation
Indices: 8238528--8238552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8238518 AGAGAAATTG
8238528 TGATTTTATAAAA
1 TGATTTTATAAAA
8238541 TGATTTTATAAA
1 TGATTTTATAAA
8238553 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:8242973 original size:22 final size:23
Alignment explanation
Indices: 8242878--8242978 Score: 100
Period size: 22 Copynumber: 4.5 Consensus size: 23
8242868 TCAATTTGTA
* *
8242878 ACGCAATGCCTAAAAAACTAGTC
1 ACGCAATGCCTAAAAATCTAATC
8242901 ACGCAATGCCTAAAAATC-AATC
1 ACGCAATGCCTAAAAATCTAATC
* * * * *
8242923 CCGTAATCCCT-ACAATCTAGTC
1 ACGCAATGCCTAAAAATCTAATC
*
8242945 ACACAATGCCTAAAAATC-AATC
1 ACGCAATGCCTAAAAATCTAATC
*
8242967 ATGCAATGCCTA
1 ACGCAATGCCTA
8242979 CAACCTAGAC
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
21 5 0.08
22 34 0.56
23 22 0.36
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.21
Consensus pattern (23 bp):
ACGCAATGCCTAAAAATCTAATC
Found at i:8242979 original size:44 final size:44
Alignment explanation
Indices: 8242878--8242986 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
8242868 TCAATTTGTA
* *
8242878 ACGCAATGCCTAAAAAACTAGTCACGCAATGCCTAAAAATCAATC
1 ACGCAATGCCT-ACAAACTAGTCACACAATGCCTAAAAATCAATC
* * * *
8242923 CCGTAATCCCTACAATCTAGTCACACAATGCCTAAAAATCAATC
1 ACGCAATGCCTACAAACTAGTCACACAATGCCTAAAAATCAATC
* *
8242967 ATGCAATGCCTACAACCTAG
1 ACGCAATGCCTACAAACTAG
8242987 ACACGTAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
44 45 0.85
45 8 0.15
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.20
Consensus pattern (44 bp):
ACGCAATGCCTACAAACTAGTCACACAATGCCTAAAAATCAATC
Found at i:8243078 original size:22 final size:22
Alignment explanation
Indices: 8243053--8243131 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
8243043 CTAGTCTCGT
8243053 AATGCCTACAAACTAATGACTC
1 AATGCCTACAAACTAATGACTC
*
8243075 AATGCC--CAAA-T-ATCAGTCTTGC
1 AATGCCTACAAACTAAT--GAC-T-C
*
8243097 AATGCCTACAAACTAATGACAC
1 AATGCCTACAAACTAATGACTC
*
8243119 AATGCCTAAAAAC
1 AATGCCTACAAAC
8243132 CTTTCTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 6 0.13
21 1 0.02
22 26 0.58
24 6 0.13
25 1 0.02
26 2 0.04
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22
Consensus pattern (22 bp):
AATGCCTACAAACTAATGACTC
Found at i:8243093 original size:44 final size:44
Alignment explanation
Indices: 8243030--8243124 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
8243020 CAAAGTCATG
* * *
8243030 CAATGCCTAAATACTAGTCTCGTAATGCCTACAAACTAATGACT
1 CAATGCCCAAATACTAGTCTCGCAATGCCTACAAACTAATGACA
*
8243074 CAATGCCCAAATA-TCAGTCTTGCAATGCCTACAAACTAATGACA
1 CAATGCCCAAATACT-AGTCTCGCAATGCCTACAAACTAATGACA
8243118 CAATGCC
1 CAATGCC
8243125 TAAAAACCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (44 bp):
CAATGCCCAAATACTAGTCTCGCAATGCCTACAAACTAATGACA
Found at i:8243128 original size:126 final size:125
Alignment explanation
Indices: 8242897--8243129 Score: 272
Period size: 126 Copynumber: 1.8 Consensus size: 125
8242887 CTAAAAAACT
* * *
8242897 AGTCACGCAATGCCTAAAAATCAATCCCGTAATCCCTACAATCTAGTCACACAATGCCTAAAAAT
1 AGTCACGCAATGCCTAAAAATCAATCCCGTAATCCCTACAAACTAATCACACAATGCCCAAAAAT
* *
8242962 CAATCATGCAATGCCTACAACCTAGACACGTAATATCTAAAAGCTAGTCTGGCAATGCCAA
66 CAATCATGCAATGCCTACAAACTAGACACG-AATACCTAAAAGCTAGTCTGGCAATGCCAA
* * * * * * * *
8243023 AGTCATGCAATGCCTAAATA-CTAGTCTCGTAATGCCTACAAACTAATGACTCAATGCCCAAATA
1 AGTCACGCAATGCCTAAAAATC-AATCCCGTAATCCCTACAAACTAATCACACAATGCCCAAAAA
* * *
8243087 TCAGTCTTGCAATGCCTACAAACTAATGACAC-AATGCCTAAAA
65 TCAATCATGCAATGCCTACAAACT-A-GACACGAATACCTAAAA
8243130 ACCTTTCTTT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
125 1 0.01
126 81 0.92
127 1 0.01
128 5 0.06
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.23
Consensus pattern (125 bp):
AGTCACGCAATGCCTAAAAATCAATCCCGTAATCCCTACAAACTAATCACACAATGCCCAAAAAT
CAATCATGCAATGCCTACAAACTAGACACGAATACCTAAAAGCTAGTCTGGCAATGCCAA
Found at i:8251982 original size:25 final size:25
Alignment explanation
Indices: 8251954--8252007 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
8251944 CTTTTGAAAC
8251954 TAATGTTTATTTATTGTATGAAGAT
1 TAATGTTTATTTATTGTATGAAGAT
*
8251979 TAATGTTTATTTATTGTATGGAGAT
1 TAATGTTTATTTATTGTATGAAGAT
8252004 TAAT
1 TAAT
8252008 ATTATTAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (25 bp):
TAATGTTTATTTATTGTATGAAGAT
Found at i:8252866 original size:19 final size:19
Alignment explanation
Indices: 8252807--8252866 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
8252797 ATTTTTATCT
8252807 TTTTTTTATGGTTTTTC-TA
1 TTTTTTTAT-GTTTTTCATA
**
8252826 TTTTTTTATAATTTT-ATAA
1 TTTTTTTATGTTTTTCAT-A
8252845 TTTTTTTAT-TTTTTCCATA
1 TTTTTTTATGTTTTT-CATA
8252864 TTT
1 TTT
8252867 GACTTTTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 9 0.26
19 23 0.68
20 2 0.06
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTTTTTATGTTTTTCATA
Found at i:8252888 original size:9 final size:9
Alignment explanation
Indices: 8252876--8252918 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
8252866 TGACTTTTGG
8252876 ATTTTTTAT
1 ATTTTTTAT
8252885 ATTTTTTA-
1 ATTTTTTAT
*
8252893 ATTTTCTTAA
1 ATTTT-TTAT
8252903 ATTTTTTTAT
1 A-TTTTTTAT
8252913 ATTTTT
1 ATTTTT
8252919 AGATTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 5 0.17
9 16 0.53
10 5 0.17
11 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:8254656 original size:23 final size:21
Alignment explanation
Indices: 8254610--8254657 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
8254600 ATTGACATAA
* *
8254610 TATTTAAAAAATTTATTAAGT
1 TATTTAAAAAATTTAATAAAT
8254631 TATTTAAGAAAATTTAAATAAAT
1 TATTTAA-AAAATTT-AATAAAT
8254654 TATT
1 TATT
8254658 ATTTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
TATTTAAAAAATTTAATAAAT
Found at i:8257041 original size:21 final size:21
Alignment explanation
Indices: 8257017--8257057 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8257007 TTAATTTTTA
*
8257017 AAAATTAAAATCATAGAAAAT
1 AAAATTAAAATAATAGAAAAT
* *
8257038 AAAATTCACATAATAGAAAA
1 AAAATTAAAATAATAGAAAA
8257058 AAGAAAACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAATTAAAATAATAGAAAAT
Found at i:8257092 original size:24 final size:23
Alignment explanation
Indices: 8257030--8257094 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
8257020 ATTAAAATCA
8257030 TAGAAAATAAAATTCACATAATAG
1 TAGAAAATAAAA-TCACATAATAG
* *
8257054 -AAAAAAGAAAA-CACATAATAAG
1 TAGAAAATAAAATCACATAAT-AG
8257076 TAGAAAATAAAATCACATA
1 TAGAAAATAAAATCACATA
8257095 TGATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 8 0.24
22 2 0.06
23 18 0.53
24 6 0.18
ACGTcount: A:0.65, C:0.09, G:0.08, T:0.18
Consensus pattern (23 bp):
TAGAAAATAAAATCACATAATAG
Found at i:8257739 original size:23 final size:21
Alignment explanation
Indices: 8257709--8257765 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
8257699 TACGAAAAAN
8257709 ATATATAATATATAATAATATAA
1 ATATATAATATATAA-AA-ATAA
* *
8257732 ATATATAAAAAATAAAAATAA
1 ATATATAATATATAAAAATAA
*
8257753 AGATAATAATATA
1 ATAT-ATAATATA
8257766 AATTGAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.25
22 8 0.29
23 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATATAATATATAAAAATAA
Found at i:8257745 original size:17 final size:17
Alignment explanation
Indices: 8257703--8257751 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
8257693 GAAATTTACG
8257703 AAAAANATATATAATATAT
1 AAAAA-ATATA-AATATAT
*
8257722 -AATAATATAAATATAT
1 AAAAAATATAAATATAT
*
8257738 AAAAAATAAAAATA
1 AAAAAATATAAATA
8257752 AAGATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 16 0.62
18 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATAAATATAT
Found at i:8264840 original size:2 final size:2
Alignment explanation
Indices: 8264835--8264885 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
8264825 GTCTGTGTGT
8264835 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8264877 AG AG AG AG A
1 AG AG AG AG A
8264886 TCAGAGGTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8271213 original size:36 final size:36
Alignment explanation
Indices: 8271166--8271262 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 36
8271156 ATAGCGTCAC
8271166 ATTTACCCAAGGAATCTGCTGATTCAGCGCCATCAA
1 ATTTACCCAAGGAATCTGCTGATTCAGCGCCATCAA
8271202 ATTTACCCAAGGAATCTGCTGATTCAGCGCCATCAA
1 ATTTACCCAAGGAATCTGCTGATTCAGCGCCATCAA
* * *
8271238 ATTTACCCCAGAAATCTACTGATTC
1 ATTTACCCAAGGAATCTGCTGATTC
8271263 GGTGCTCCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (36 bp):
ATTTACCCAAGGAATCTGCTGATTCAGCGCCATCAA
Found at i:8274756 original size:13 final size:13
Alignment explanation
Indices: 8274738--8274762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8274728 TACAAGATAA
8274738 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
8274751 TTAGAGAGAGAA
1 TTAGAGAGAGAA
8274763 GCTCTCAAGT
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:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:8275004 original size:14 final size:14
Alignment explanation
Indices: 8274987--8275035 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
8274977 GAGGTGTACA
8274987 AGAATAGGTATAAG
1 AGAATAGGTATAAG
* * *
8275001 AGAAGAAGCTATACG
1 AGAA-TAGGTATAAG
*
8275016 AGAATAGGTACAAG
1 AGAATAGGTATAAG
8275030 AGAATA
1 AGAATA
8275036 AGCTATACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.51, C:0.06, G:0.27, T:0.16
Consensus pattern (14 bp):
AGAATAGGTATAAG
Found at i:8275018 original size:15 final size:15
Alignment explanation
Indices: 8274995--8275062 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
8274985 CAAGAATAGG
* *
8274995 TATAAGAGAAGAAGC
1 TATACGAGAATAAGC
*
8275010 TATACGAGAAT-AGG
1 TATACGAGAATAAGC
* *
8275024 TACAAGAGAATAAGC
1 TATACGAGAATAAGC
8275039 TATAC-ATGAATAAG-
1 TATACGA-GAATAAGC
8275053 TATACGAGAA
1 TATACGAGAA
8275063 CAAGATAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 20 0.48
15 22 0.52
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (15 bp):
TATACGAGAATAAGC
Found at i:8275020 original size:29 final size:28
Alignment explanation
Indices: 8274987--8275062 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
8274977 GAGGTGTACA
8274987 AGAATAGGTATAAGAGAAGAAGCTATAC
1 AGAATAGGTATAAGAGAAGAAGCTATAC
* *
8275015 GAGAATAGGTACAAGAGAATAAGCTATAC
1 -AGAATAGGTATAAGAGAAGAAGCTATAC
* *
8275044 ATGAATAAGTATACGAGAA
1 A-GAATAGGTATAAGAGAA
8275063 CAAGATAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (28 bp):
AGAATAGGTATAAGAGAAGAAGCTATAC
Found at i:8275366 original size:26 final size:26
Alignment explanation
Indices: 8275330--8275388 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
8275320 AAGTAATACT
8275330 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
8275356 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
8275382 TGAAGTA
1 TGAAGTA
8275389 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (26 bp):
TGAAGTAGCGCTTCACTTGTTCTGCG
Found at i:8338067 original size:19 final size:19
Alignment explanation
Indices: 8338040--8338085 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
8338030 AGGAGACAAG
*
8338040 ATAAAATTTT-TAGAATAAA
1 ATAATATTTTATA-AATAAA
8338059 ATAATATTTTATAAATAAA
1 ATAATATTTTATAAATAAA
8338078 ATAATATT
1 ATAATATT
8338086 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATTTTATAAATAAA
Found at i:8340926 original size:15 final size:14
Alignment explanation
Indices: 8340899--8340945 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
8340889 TTCTATCACA
8340899 AATGTTAAATGATG
1 AATGTTAAATGATG
8340913 AATGTTAGAATGATG
1 AATGTTA-AATGATG
*
8340928 AATGTTAATTGATG
1 AATGTTAAATGATG
8340942 AATG
1 AATG
8340946 CTACTCGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 17 0.55
15 14 0.45
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.36
Consensus pattern (14 bp):
AATGTTAAATGATG
Found at i:8351083 original size:8 final size:8
Alignment explanation
Indices: 8351070--8351189 Score: 59
Period size: 8 Copynumber: 14.4 Consensus size: 8
8351060 TTACAAAAAG
8351070 ATATATAA
1 ATATATAA
*
8351078 ATATATAT
1 ATATATAA
*
8351086 ATAAATAA
1 ATATATAA
* *
8351094 ATAAATAT
1 ATATATAA
8351102 ATATA-AA
1 ATATATAA
8351109 ATATA-AA
1 ATATATAA
8351116 ATATAACTAA
1 ATAT-A-TAA
* * *
8351126 TTAAATACG
1 ATATATA-A
8351135 ATATATAA
1 ATATATAA
*
8351143 GATTTTATATA
1 -A-TATATA-A
8351154 ATA-ATTAA
1 ATATA-TAA
8351162 ATATATAA
1 ATATATAA
8351170 ATAGT-TAA
1 ATA-TATAA
8351178 ATAATATAA
1 AT-ATATAA
8351187 ATA
1 ATA
8351190 GAAAGGAGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 24
0.69 0.11 0.19
Matches are distributed among these distances:
7 12 0.14
8 45 0.52
9 18 0.21
10 10 0.12
11 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:8351099 original size:20 final size:19
Alignment explanation
Indices: 8351074--8351120 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
8351064 AAAAAGATAT
8351074 ATAAATATATATATAAATAA
1 ATAAATATATATA-AAATAA
*
8351094 ATAAATATATATAAAATAT
1 ATAAATATATATAAAATAA
8351113 A-AAATATA
1 ATAAATATA
8351121 ACTAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 13 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATATATATAAAATAA
Found at i:8351103 original size:18 final size:17
Alignment explanation
Indices: 8351080--8351120 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
8351070 ATATATAAAT
8351080 ATATATATAAATAAATAA
1 ATATATATAAA-AAATAA
*
8351098 ATATATATAAAATATAA
1 ATATATATAAAAAATAA
8351115 A-ATATA
1 ATATATA
8351121 ACTAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATATATAAAAAATAA
Found at i:8351719 original size:8 final size:9
Alignment explanation
Indices: 8351701--8351770 Score: 54
Period size: 9 Copynumber: 7.3 Consensus size: 9
8351691 TCCTTCTTTC
8351701 TATTTATAT
1 TATTTATAT
8351710 TATTTAATTAT
1 TATTT-A-TAT
8351721 TATTTGATAT
1 TATTT-ATAT
* *
8351731 TCTATATAT
1 TATTTATAT
8351740 GGTATTTA-AT
1 --TATTTATAT
8351750 TATTTATAT
1 TATTTATAT
8351759 T-TTATATAT
1 TATT-TATAT
8351768 TAT
1 TAT
8351771 ATTTTATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
8 8 0.16
9 18 0.37
10 10 0.20
11 13 0.27
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TATTTATAT
Found at i:8351773 original size:28 final size:27
Alignment explanation
Indices: 8351703--8351774 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
8351693 CTTCTTTCTA
*
8351703 TTTATATTATTTAATTATTATTTGATAT
1 TTTATA-TATTTATTTATTATTTGATAT
* *
8351731 TCTATATATGGTATTTAATTATTT-ATAT
1 TTTATATAT-TTATTT-ATTATTTGATAT
8351759 TTTATATATTATATTT
1 TTTATATATT-TATTT
8351775 TATGAATCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
27 3 0.08
28 26 0.72
29 7 0.19
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTATATATTTATTTATTATTTGATAT
Found at i:8365368 original size:2 final size:2
Alignment explanation
Indices: 8365361--8365385 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8365351 TAATTTAATC
8365361 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
8365386 GTTAGCCTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8366203 original size:47 final size:47
Alignment explanation
Indices: 8366133--8366235 Score: 179
Period size: 47 Copynumber: 2.2 Consensus size: 47
8366123 CTTTTGCTGA
*
8366133 CCTCACCCTAAACAAACTCTAAGCCTCTCCAAACTGTTACAACCTTT
1 CCTCACCCTAAACAAACTCTAAGCCTCTCCAAACTGCTACAACCTTT
* *
8366180 GCTCACCCTAAACAAACTCTAAGCCTCTCCAAACTGCTGCAACCTTT
1 CCTCACCCTAAACAAACTCTAAGCCTCTCCAAACTGCTACAACCTTT
8366227 CCTCACCCT
1 CCTCACCCT
8366236 CTTGCTGACA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.29, C:0.41, G:0.06, T:0.24
Consensus pattern (47 bp):
CCTCACCCTAAACAAACTCTAAGCCTCTCCAAACTGCTACAACCTTT
Found at i:8366853 original size:15 final size:15
Alignment explanation
Indices: 8366815--8366864 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
8366805 AATAAGAACA
8366815 AAAAT-AAATATAAA-
1 AAAATGAAATA-AAAT
* *
8366829 AAATATGAAATTAAGT
1 AAA-ATGAAATAAAAT
8366845 AAAATGAAATAAAAT
1 AAAATGAAATAAAAT
8366860 AAAAT
1 AAAAT
8366865 AACATATGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 3 0.10
15 19 0.66
16 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAATGAAATAAAAT
Found at i:8377392 original size:43 final size:43
Alignment explanation
Indices: 8377331--8377424 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
8377321 CTCCCTCAGT
*
8377331 TGGGTCATCATCAGCTCATGTGCACTCCTACACCACACATGGC
1 TGGGTCATCATCAGCTCATGTGCACTCCTACACCACACATAGC
** *
8377374 TGGGTCATCATCAGCTCATGTGCACTTTTACACCGCACATAGC
1 TGGGTCATCATCAGCTCATGTGCACTCCTACACCACACATAGC
8377417 TGGGTCAT
1 TGGGTCAT
8377425 AATTATCACA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (43 bp):
TGGGTCATCATCAGCTCATGTGCACTCCTACACCACACATAGC
Found at i:8378249 original size:20 final size:21
Alignment explanation
Indices: 8378226--8378269 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
8378216 AAGAAGAAGA
*
8378226 AGAAGAAATTGCTGGAAA-TT
1 AGAAGAAATTGCTAGAAACTT
* *
8378246 AGAATAAGTTGCTAGAAACTT
1 AGAAGAAATTGCTAGAAACTT
8378267 AGA
1 AGA
8378270 TATTTATGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (21 bp):
AGAAGAAATTGCTAGAAACTT
Found at i:8380112 original size:35 final size:35
Alignment explanation
Indices: 8380042--8380112 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
8380032 ATTTGCAGTA
* *
8380042 AGTAGGTATTAACAGATTGTCATAAAACTTTCAGC
1 AGTAAGTATTAACAGATTGTCATAAAACTTCCAGC
* * * *
8380077 AGTAAGTATTGACAGATTTTCATCAAAGTTCCAGC
1 AGTAAGTATTAACAGATTGTCATAAAACTTCCAGC
8380112 A
1 A
8380113 ACTGTCAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (35 bp):
AGTAAGTATTAACAGATTGTCATAAAACTTCCAGC
Found at i:8382813 original size:16 final size:17
Alignment explanation
Indices: 8382782--8382818 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
8382772 TGGTACACAC
8382782 ATTCTTTATATTATTTT
1 ATTCTTTATATTATTTT
8382799 ATTCTTTAT-TTATTTT
1 ATTCTTTATATTATTTT
8382815 ATTC
1 ATTC
8382819 ACTGAGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTCTTTATATTATTTT
Found at i:8392369 original size:43 final size:43
Alignment explanation
Indices: 8392279--8392370 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
8392269 GTTCACGATC
* * * *
8392279 GGTCATCATCATCTCATGTGGACTCCTACACTGCACATGGCTG
1 GGTCATCATCAGCTCATGTGCACTCCTACACCGCACATGGCTA
*
8392322 GGTCATCATCAGCTCATGTGCACTCCTACACCGCACGTAGG-TA
1 GGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT-GGCTA
8392365 GGTCAT
1 GGTCAT
8392371 AATTATCACA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 41 0.95
44 2 0.05
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (43 bp):
GGTCATCATCAGCTCATGTGCACTCCTACACCGCACATGGCTA
Found at i:8402263 original size:3 final size:3
Alignment explanation
Indices: 8402255--8402295 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
8402245 GTTCAAATTA
* *
8402255 AAT AAT AAT AAT AAC AAC AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
8402296 AACAGTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:8411140 original size:2 final size:2
Alignment explanation
Indices: 8411133--8411160 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8411123 TTTATAATTA
8411133 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
8411161 TATTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8417465 original size:19 final size:19
Alignment explanation
Indices: 8417441--8417478 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
8417431 ACTTCTAAAT
8417441 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
8417460 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
8417479 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:8449939 original size:9 final size:8
Alignment explanation
Indices: 8449931--8450007 Score: 64
Period size: 9 Copynumber: 8.6 Consensus size: 8
8449921 TTTTTATTTA
8449931 ATTTTTTT
1 ATTTTTTT
8449939 ATTTATTGTT
1 ATTT-TT-TT
8449949 ATTTTATTT
1 ATTTT-TTT
*
8449958 ATTTATTT
1 ATTTTTTT
8449966 ATTTTATTT
1 ATTTT-TTT
8449975 ATTTTATTT
1 ATTTT-TTT
*
8449984 AATTTAATTTA
1 -ATTT--TTTT
8449995 ATTTTTTT
1 ATTTTTTT
8450003 ATTTT
1 ATTTT
8450008 ATTTGAGTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
8 19 0.33
9 21 0.36
10 15 0.26
11 2 0.03
12 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.75
Consensus pattern (8 bp):
ATTTTTTT
Found at i:8449943 original size:4 final size:4
Alignment explanation
Indices: 8449919--8450011 Score: 71
Period size: 4 Copynumber: 21.0 Consensus size: 4
8449909 CCCATTTTTA
*
8449919 ATTT -TTT ATTT AATTT TTTT ATTT ATTGTT ATTTT ATTT ATTT ATTT
1 ATTT ATTT ATTT -ATTT ATTT ATTT A-T-TT A-TTT ATTT ATTT ATTT
*
8449966 ATTTT ATTT ATTTT ATTT AATTT AATTT AATTT TTTT ATTTT ATTT
1 A-TTT ATTT A-TTT ATTT -ATTT -ATTT -ATTT ATTT A-TTT ATTT
8450012 GAGTGTCTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
3 3 0.04
4 35 0.45
5 34 0.44
6 5 0.06
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:8449957 original size:5 final size:5
Alignment explanation
Indices: 8449922--8450011 Score: 72
Period size: 5 Copynumber: 19.6 Consensus size: 5
8449912 ATTTTTAATT
*
8449922 TTTTA -TTTA ATTT- TTTTA -TTTA TTGTTA TTTTA -TTTA -TTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
* * *
8449967 TTTTA -TTTA TTTTA -TTTA ATTTA ATTTA ATTT- TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
8450012 GAGTGTCTAC
Statistics
Matches: 75, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
4 34 0.45
5 36 0.48
6 5 0.07
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:8449957 original size:23 final size:22
Alignment explanation
Indices: 8449913--8450011 Score: 96
Period size: 23 Copynumber: 4.4 Consensus size: 22
8449903 GCCATCCCCA
* *
8449913 TTTTTAATT-TTTTATTTAATT
1 TTTTTATTTATTTTATTTTATT
8449934 TTTTTATTTATTGTTATTTTATT
1 TTTTTATTTATT-TTATTTTATT
*
8449957 TATTTATTTATTTTA-TTTATT
1 TTTTTATTTATTTTATTTTATT
*
8449978 TTATTTAATTTAATTTAATTTT-TT
1 TT-TTT-ATTT-ATTTTATTTTATT
8450002 TATTTTATTT
1 T-TTTTATTT
8450012 GAGTGTCTAC
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
21 15 0.23
22 8 0.12
23 28 0.42
24 11 0.17
25 4 0.06
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTTTATTTATTTTATTTTATT
Found at i:8449971 original size:32 final size:31
Alignment explanation
Indices: 8449923--8450011 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 31
8449913 TTTTTAATTT
*
8449923 TTTATTTAATTTTTTTATTTATTGTTATTTTA
1 TTTATTTAATTTTTTTATTTATT-TTATTTAA
8449955 TTTATTT-ATTTATTTTATTTATTTTATTTAA
1 TTTATTTAATTT-TTTTATTTATTTTATTTAA
8449986 TTTAATTTAATTTTTTTATTTTATTT
1 TTT-ATTTAATTTTTTTA-TTTATTT
8450012 GAGTGTCTAC
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
31 14 0.27
32 27 0.52
33 11 0.21
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (31 bp):
TTTATTTAATTTTTTTATTTATTTTATTTAA
Found at i:8451558 original size:23 final size:22
Alignment explanation
Indices: 8451519--8451561 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8451509 AAAAATCAAT
**
8451519 AAAAAAAATTAAAAAAGAAACA
1 AAAAAAAAGGAAAAAAGAAACA
8451541 AAAAAAAAGGAAAGAAAGAAA
1 AAAAAAAAGGAAA-AAAGAAA
8451562 AATTTTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (22 bp):
AAAAAAAAGGAAAAAAGAAACA
Found at i:8452601 original size:38 final size:38
Alignment explanation
Indices: 8452446--8452822 Score: 494
Period size: 38 Copynumber: 10.0 Consensus size: 38
8452436 GAAAAAAATA
** *
8452446 TTTCGTTATCTCAGTTTTGAGGAGTTCATTTTT-AAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
8452483 TTTCGTTGCCTCAGCTTTGAGGAGTTCA-TTTTAAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
* *
8452520 TTTCGTTGCCTCAGCTTTAAGGTGTTCA-TTTTAAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
8452557 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
* * *
8452595 TCTCGTTGCCTCAGCTATAAGGAGTTCATTTTTAAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
* * *
8452633 TCTCGTTGCCTCAGCTTTGAGGAGTTC-GTTTAAAGAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAA-AAG
* * *
8452671 TTTCATTGCCTCAGCTTTGAAGAGTTCATTTTTTAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
* * * *
8452709 TTCCGTTACCTCAACCTTGAGGAGTTCATTTTTAAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
8452747 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTT-AAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
* * ** * *
8452784 TTTCATTACCTCAATTTTGAGGAGTTTATTCTTAAAAG
1 TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
8452822 T
1 T
8452823 GTCATTACCT
Statistics
Matches: 298, Mismatches: 37, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
36 4 0.01
37 126 0.42
38 164 0.55
39 4 0.01
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (38 bp):
TTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG
Found at i:8452883 original size:20 final size:20
Alignment explanation
Indices: 8452855--8452910 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
8452845 GTTCATTTAA
* *
8452855 AAAAAAAAAGACAAAACAAC
1 AAAAAAAAACAAAAAACAAC
*
8452875 AAAACAAAACAAAAAACAAC
1 AAAAAAAAACAAAAAACAAC
8452895 AAAAAAACAA-AAAAAA
1 AAAAAAA-AACAAAAAA
8452911 AGTAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAAAAACAAC
Found at i:8452895 original size:23 final size:22
Alignment explanation
Indices: 8452855--8452911 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 22
8452845 GTTCATTTAA
*
8452855 AAAAAAAAAGACAAAACAACAAAAC
1 AAAAAAAAA-AC--AACAAAAAAAC
8452880 AAAACAAAAAACAACAAAAAAAC
1 AAAA-AAAAAACAACAAAAAAAC
8452903 AAAAAAAAA
1 AAAAAAAAA
8452912 GTAAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 14 0.47
25 6 0.20
26 5 0.17
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAACAACAAAAAAAC
Found at i:8452897 original size:28 final size:27
Alignment explanation
Indices: 8452853--8452928 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
8452843 AAGTTCATTT
*
8452853 AAAAAAAAAAAGACAAAACAACAAAACA
1 AAAAAAAAAAAGACAAAAAAACAAAA-A
*
8452881 AAACAAAAAACA-ACAAAAAAACAAAAA
1 AAA-AAAAAAAAGACAAAAAAACAAAAA
* *
8452908 AAAAGTAAAAAA-ATAAAAAAA
1 AAAA-AAAAAAAGACAAAAAAA
8452929 TAATAATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.02
27 17 0.41
28 16 0.39
29 7 0.17
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAAAGACAAAAAAACAAAAA
Found at i:8452907 original size:8 final size:8
Alignment explanation
Indices: 8452853--8452909 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
8452843 AAGTTCATTT
8452853 AAAAAA-A
1 AAAAAACA
*
8452860 AAAAGACA
1 AAAAAACA
*
8452868 AAACAACAA
1 AAAAAAC-A
8452877 AACAAAACAA
1 AA-AAAAC-A
8452887 AAAACAACA
1 AAAA-AACA
8452896 AAAAAACA
1 AAAAAACA
8452904 AAAAAA
1 AAAAAA
8452910 AAGTAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 5 0.12
8 16 0.38
9 10 0.24
10 11 0.26
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:8452907 original size:18 final size:17
Alignment explanation
Indices: 8452856--8452927 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
8452846 TTCATTTAAA
8452856 AAAAAAAAGACAAAACAAC
1 AAAAAAAA-ACAAAA-AAC
*
8452875 AAAACAAAACAAAAAAC
1 AAAAAAAAACAAAAAAC
*
8452892 AACAAAAAAACAAAAAAA
1 AA-AAAAAAACAAAAAAC
*
8452910 AAGTAAAAAAATAAAAAA
1 AA--AAAAAAACAAAAAA
8452928 ATAATAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 5 0.11
18 21 0.46
19 20 0.43
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:8454106 original size:14 final size:14
Alignment explanation
Indices: 8454087--8454116 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
8454077 TTTGGATTAC
8454087 TTATTGGGTTATGA
1 TTATTGGGTTATGA
8454101 TTATTGGGTTATGA
1 TTATTGGGTTATGA
8454115 TT
1 TT
8454117 GTGGTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (14 bp):
TTATTGGGTTATGA
Found at i:8454454 original size:16 final size:17
Alignment explanation
Indices: 8454433--8454465 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
8454423 TACATGACAT
8454433 TAAATAAATAA-AAAAA
1 TAAATAAATAATAAAAA
8454449 TAAATAAATAATAAAAA
1 TAAATAAATAATAAAAA
8454466 ATCTAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAATAAATAATAAAAA
Found at i:8454796 original size:9 final size:8
Alignment explanation
Indices: 8454774--8454845 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
8454764 GAAACTTAGA
8454774 ATAAAAAT
1 ATAAAAAT
8454782 ATAAAAAT
1 ATAAAAAT
8454790 ATAAAAAAT
1 AT-AAAAAT
*
8454799 AATAATAAGAA
1 -ATAA-AA-AT
8454810 ATAAAAAT
1 ATAAAAAT
*
8454818 A-GAAAAT
1 ATAAAAAT
*
8454825 ATAATAAT
1 ATAAAAAT
8454833 A-AAAATAT
1 ATAAAA-AT
8454841 ATAAA
1 ATAAA
8454846 GTAAAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
7 9 0.18
8 20 0.39
9 13 0.25
10 8 0.16
11 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:8454804 original size:3 final size:3
Alignment explanation
Indices: 8454796--8454879 Score: 50
Period size: 3 Copynumber: 28.3 Consensus size: 3
8454786 AAATATAAAA
* * * *
8454796 AAT AAT AAT AAGA AAT AAA AAT AGAA AAT -AT AAT AAT AAA AAT ATAT
1 AAT AAT AAT AA-T AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT
* * *
8454843 AA- AGT AAA AAT AA- AAT AAT AAT TA- AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
8454880 CTAAAAATAG
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
2 6 0.10
3 47 0.78
4 7 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:8454811 original size:13 final size:12
Alignment explanation
Indices: 8454782--8454888 Score: 71
Period size: 11 Copynumber: 8.8 Consensus size: 12
8454772 GAATAAAAAT
8454782 ATAAAAAT-AT-
1 ATAAAAATAATA
8454792 A-AAAAATAATA
1 ATAAAAATAATA
*
8454803 ATAAGAAATAAAA
1 ATAA-AAATAATA
8454816 ATAGAAAATATAATA
1 AT--AAAA-ATAATA
8454831 ATAAAAATATATAA
1 ATAAAAATA-AT-A
8454845 AGTAAAAATAA-A
1 A-TAAAAATAATA
* *
8454857 ATAATAATTA-A
1 ATAAAAATAATA
*
8454868 ATAATAATAATA
1 ATAAAAATAATA
*
8454880 CTAAAAATA
1 ATAAAAATA
8454889 GTTAACTGCA
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
9 6 0.08
10 3 0.04
11 18 0.23
12 15 0.19
13 15 0.19
14 5 0.06
15 17 0.22
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:8454814 original size:28 final size:27
Alignment explanation
Indices: 8454773--8454860 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 27
8454763 AGAAACTTAG
* *
8454773 AATAA-AAATATAAAAATATAAAAAAT
1 AATAATAAAAATAAAAATAGAAAAAAT
*
8454799 AATAATAAGAAATAAAAATAGAAAATAT
1 AATAATAA-AAATAAAAATAGAAAAAAT
* *
8454827 AATAATAAAAATATATAA-AGTAAAAAT
1 AATAATAAAAATA-AAAATAGAAAAAAT
8454854 AA-AATAA
1 AATAATAA
8454861 TAATTAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.19
27 16 0.30
28 27 0.51
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (27 bp):
AATAATAAAAATAAAAATAGAAAAAAT
Found at i:8454817 original size:6 final size:6
Alignment explanation
Indices: 8454793--8454888 Score: 61
Period size: 6 Copynumber: 15.2 Consensus size: 6
8454783 TAAAAATATA
*
8454793 AAAAAT AATAAT AAGAAAT AAAAAT AGAAAAT ATAATAAT AAAAAT ATATAAAGT
1 AAAAAT AAAAAT AA-AAAT AAAAAT A-AAAAT A-AA-AAT AAAAAT A-A-AAA-T
* * * * *
8454848 AAAAAT -AAAAT AATAAT -TAAAT AATAAT AATACT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
8454889 GTTAACTGCA
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
5 8 0.11
6 34 0.48
7 19 0.27
8 8 0.11
9 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (6 bp):
AAAAAT
Found at i:8454840 original size:49 final size:49
Alignment explanation
Indices: 8454773--8454888 Score: 123
Period size: 49 Copynumber: 2.4 Consensus size: 49
8454763 AGAAACTTAG
* *
8454773 AATAAAAAT-ATAAAAATATAAAAAATAATAATAAGAAATAA-AAATAGAA-
1 AATAATAATAATAAAAATATAAAAAATAAAAAT-A-AAATAATAAATA-AAT
* * *
8454822 AAT-ATAATAATAAAAATATATAAAGTAAAAATAAAATAATAATTAAAT
1 AATAATAATAATAAAAATATAAAAAATAAAAATAAAATAATAAATAAAT
*
8454870 AATAATAATACTAAAAATA
1 AATAATAATAATAAAAATA
8454889 GTTAACTGCA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
47 8 0.14
48 12 0.21
49 37 0.65
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.25
Consensus pattern (49 bp):
AATAATAATAATAAAAATATAAAAAATAAAAATAAAATAATAAATAAAT
Found at i:8454854 original size:21 final size:19
Alignment explanation
Indices: 8454773--8454884 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 19
8454763 AGAAACTTAG
8454773 AATAAAAAT-AT-AA-AAA
1 AATAAAAATAATAAATAAA
*
8454789 TATAAAAAATAAT-AATAAGA
1 AAT-AAAAATAATAAATAA-A
8454809 AATAAAAATAGA-AAATATAA
1 AATAAAAATA-ATAAATA-AA
8454829 TAATAAAAATATATAAAGTAAA
1 -AATAAAAATA-ATAAA-TAAA
*
8454851 AAT-AAAATAATAATTAAA
1 AATAAAAATAATAAATAAA
* *
8454869 TAATAATAATACTAAA
1 -AATAAAAATAATAAA
8454885 AATAGTTAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.03
17 6 0.08
18 8 0.10
19 16 0.21
20 23 0.30
21 15 0.19
22 5 0.06
23 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (19 bp):
AATAAAAATAATAAATAAA
Found at i:8454860 original size:16 final size:15
Alignment explanation
Indices: 8454773--8454888 Score: 53
Period size: 15 Copynumber: 7.3 Consensus size: 15
8454763 AGAAACTTAG
*
8454773 AATAAAA-ATATAAA
1 AATAAAATAAATAAA
*
8454787 AATATAAA-AAATAAT
1 AATA-AAATAAATAAA
8454802 AATAAGAAATAAAAATAGAA
1 AAT-A-AAAT--AAATA-AA
*
8454822 AATATAAT-AATAAA
1 AATAAAATAAATAAA
*
8454836 AAT-ATATAAAGTAAA
1 AATAAAATAAA-TAAA
8454851 AATAAAAT-AATAATTA
1 AATAAAATAAATAA--A
8454867 AATAATAATAATACTAAA
1 AATAA-AATAA-A-TAAA
8454885 AATA
1 AATA
8454889 GTTAACTGCA
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.03
14 14 0.18
15 24 0.30
16 13 0.16
17 3 0.04
18 9 0.11
19 7 0.09
20 7 0.09
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAAAATAAATAAA
Found at i:8454888 original size:9 final size:9
Alignment explanation
Indices: 8454773--8454888 Score: 69
Period size: 9 Copynumber: 12.1 Consensus size: 9
8454763 AGAAACTTAG
8454773 AATAAAAAT
1 AATAAAAAT
8454782 -ATAAAAAT
1 AATAAAAAT
8454790 -ATAAAAAAT
1 AAT-AAAAAT
8454799 AATAATAAGA-
1 AATAA-AA-AT
8454809 AATAAAAAT
1 AATAAAAAT
*
8454818 AGAAAATATAAT
1 A-ATAA-A-AAT
8454830 AATAAAAAT
1 AATAAAAAT
*
8454839 ATATAAAGTAAA
1 A-ATAAA--AAT
8454851 AAT-AAAAT
1 AATAAAAAT
8454859 AATAATTAAAT
1 AATAA--AAAT
*
8454870 AATAATAAT
1 AATAAAAAT
*
8454879 ACTAAAAAT
1 AATAAAAAT
8454888 A
1 A
8454889 GTTAACTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
8 16 0.19
9 27 0.31
10 20 0.23
11 16 0.19
12 7 0.08
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.25
Consensus pattern (9 bp):
AATAAAAAT
Found at i:8456575 original size:211 final size:211
Alignment explanation
Indices: 8456211--8456631 Score: 718
Period size: 211 Copynumber: 2.0 Consensus size: 211
8456201 TAAATTTCAA
* * *
8456211 TGCAAATGACTTGGATTTCTTAGAATTGTTAGAGTTTTGATTCTTTTCAAATTTATTGAAATTCT
1 TGCAAATGACTTGCATTTCATAGAATTGTTAGAGTTTTGATTCTTTTCAAAATTATTGAAATTCT
* *
8456276 GACTCACAAAATTCACATTAGAATATGAGGACTAAAATAATGCATCTCGTATACATGCTTCACAT
66 GACTCACAAAATTCACATTAGAATATAAGGACTAAAATAATGCATCACGTATACATGCTTCACAT
*
8456341 TCTATTTGCATTTAAGCCATGAATTATTCTACTAATAAAGAATCAATAAAATATAGAAACTTCTT
131 TCTATTTGCATCTAAGCCATGAATTATTCTACTAATAAAGAATCAATAAAATATAGAAACTTCTT
8456406 TCTGTAATTATTCCAG
196 TCTGTAATTATTCCAG
8456422 TGCAAATGACTTGCATTTCATAGAATTGTTAGAGTTTTGATTCTTTTCAAAATTATTGAAATTCT
1 TGCAAATGACTTGCATTTCATAGAATTGTTAGAGTTTTGATTCTTTTCAAAATTATTGAAATTCT
* * *
8456487 GACTCACAAAATTCACATTGGAATCA-AAGGACTGAAATAGTGCATCACGTATACATGCTTCACA
66 GACTCACAAAATTCACATTAGAAT-ATAAGGACTAAAATAATGCATCACGTATACATGCTTCACA
* * *
8456551 TTCTATTTGCATCTAAGCCATGAATTGTTCTACTAATAACGAATCAATAAAATATAGAACCTTCT
130 TTCTATTTGCATCTAAGCCATGAATTATTCTACTAATAAAGAATCAATAAAATATAGAAACTTCT
8456616 TTCTGTAATTATTCCA
195 TTCTGTAATTATTCCA
8456632 AGATTAAGTT
Statistics
Matches: 197, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
211 196 0.99
212 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (211 bp):
TGCAAATGACTTGCATTTCATAGAATTGTTAGAGTTTTGATTCTTTTCAAAATTATTGAAATTCT
GACTCACAAAATTCACATTAGAATATAAGGACTAAAATAATGCATCACGTATACATGCTTCACAT
TCTATTTGCATCTAAGCCATGAATTATTCTACTAATAAAGAATCAATAAAATATAGAAACTTCTT
TCTGTAATTATTCCAG
Found at i:8456745 original size:13 final size:13
Alignment explanation
Indices: 8456727--8456755 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8456717 ACTTATAGTT
8456727 CATGTACTTAATC
1 CATGTACTTAATC
8456740 CATGTACTTAATC
1 CATGTACTTAATC
8456753 CAT
1 CAT
8456756 AAGGCACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (13 bp):
CATGTACTTAATC
Found at i:8457476 original size:18 final size:18
Alignment explanation
Indices: 8457429--8457476 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
8457419 AATTTTTAAT
8457429 AATTATATTT-GTTAAAA
1 AATTATATTTAGTTAAAA
* *
8457446 ATATTTTTATTTATTTAAAA
1 A-A-TTATATTTAGTTAAAA
8457466 AATTATATTTA
1 AATTATATTTA
8457477 AATATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 8 0.32
20 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTATATTTAGTTAAAA
Found at i:8460053 original size:22 final size:22
Alignment explanation
Indices: 8460028--8460069 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8460018 GAAGGAAGAT
* *
8460028 TTGATACCATGAATTTGATGCA
1 TTGATACAATCAATTTGATGCA
8460050 TTGATACAATCAATTTGATG
1 TTGATACAATCAATTTGATG
8460070 ATGACTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
TTGATACAATCAATTTGATGCA
Found at i:8464549 original size:19 final size:19
Alignment explanation
Indices: 8464509--8464570 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
8464499 TGTTTTTCAA
* *
8464509 TATTAGTAGA-ATATTATTT
1 TATTAGTAGATA-ATAATAT
8464528 TATTAGTAGATAATAATAT
1 TATTAGTAGATAATAATAT
*
8464547 TATTTTATGTTGATAATAATAT
1 TA--TTA-GTAGATAATAATAT
8464569 TA
1 TA
8464571 GTAGAATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.47
20 1 0.03
21 3 0.08
22 15 0.42
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
TATTAGTAGATAATAATAT
Found at i:8464564 original size:22 final size:24
Alignment explanation
Indices: 8464518--8464570 Score: 83
Period size: 22 Copynumber: 2.3 Consensus size: 24
8464508 ATATTAGTAG
8464518 AATATTATTTTATTAGTAGATAAT
1 AATATTATTTTATTAGTAGATAAT
*
8464542 AATATTATTTTA-T-GTTGATAAT
1 AATATTATTTTATTAGTAGATAAT
8464564 AATATTA
1 AATATTA
8464571 GTAGAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 15 0.54
23 1 0.04
24 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (24 bp):
AATATTATTTTATTAGTAGATAAT
Found at i:8478980 original size:30 final size:30
Alignment explanation
Indices: 8478944--8479006 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
8478934 CTTTGTCGGA
*
8478944 TCTGCCATACCATTTTCCATCCTCGAGTCT
1 TCTGCCATACCATTTTCCATCATCGAGTCT
*
8478974 TCTGCCATACCGTTTTCCATCATCGAGTCT
1 TCTGCCATACCATTTTCCATCATCGAGTCT
8479004 TCT
1 TCT
8479007 CTGATAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.35, G:0.11, T:0.38
Consensus pattern (30 bp):
TCTGCCATACCATTTTCCATCATCGAGTCT
Found at i:8480584 original size:16 final size:16
Alignment explanation
Indices: 8480559--8480597 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
8480549 CATGAAAATC
*
8480559 TATTAATTAATTAAGA
1 TATTAATTAATCAAGA
*
8480575 TATTATTTAATCAAGA
1 TATTAATTAATCAAGA
*
8480591 AATTAAT
1 TATTAAT
8480598 AATATATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (16 bp):
TATTAATTAATCAAGA
Found at i:8486111 original size:316 final size:316
Alignment explanation
Indices: 8485527--8486155 Score: 906
Period size: 316 Copynumber: 2.0 Consensus size: 316
8485517 TTCACAACTG
** * * * ***
8485527 GTTGGATTTTTACAATTGGTGTGAATGCTATTTCTTGGGATTCTAAGAAACAATTTGGTTAAGTG
1 GTTGGATTTTTACAATTGGTGCAAATGCTATTTCTTAGGATTCTAAGAAACAATTTGATCAAACA
* * * * *
8485592 GACTCCAACATGGCGACTAAATTTATAGCTTTAGTATCTGTCACCCGAGAAGTAGAATGGTCGAG
66 GACTCCAACATGGCGACTAAATTTATAACTTTAGTATCTGCCACCCAAGAAGCAAAATGGTCGAG
**
8485657 AGATTTACTTTATGAAATTTTGTTGTGGCCTAAACCAATGGCACTAATCTTGATACATTATGACA
131 AGATTTACTTTATGAAATTTCATTGTGGCCTAAACCAATGGCACTAATCTTGATACATTATGACA
* * *
8485722 ATGAAGCAACAGTATCAAAGGCACATAATCAAGCAAACAATGGAAAGAGTCGATAAAATGGACTT
196 ATGAAGCAACAGTATCAAAGGCACAAAACCAAGCAAACAATGGAAAGAGTCGATAAAATAGACTT
* *
8485787 TAACATAGCATTGTAAGACAAAGAATTAGTGATAGTATAGTCACTATAAGTTACTT
261 CAACATAGCATTGTAAGACAAAGAATTAGTGATAGCATAGTCACTATAAGTTACTT
* *
8485843 GTTGGATTTTTACAATTGGTGCAAATGTTGTTTCTTAGGATTGC-AAGAAACAATCTT-ATCAAA
1 GTTGGATTTTTACAATTGGTGCAAATGCTATTTCTTAGGATT-CTAAGAAACAAT-TTGATCAAA
* * *
8485906 CAGACTCC-ACTATGGC-AGCTGAATTTATAACTTTAGTATTTGCCACCCAATAAGCAAAATGGT
64 CAGACTCCAAC-ATGGCGA-CTAAATTTATAACTTTAGTATCTGCCACCCAAGAAGCAAAATGGT
* *
8485969 TGAGAGATTTACTTTATGAAATTTCATTGTGGCCTAAACCAATGGCACTAATCTTGATACATTGT
127 CGAGAGATTTACTTTATGAAATTTCATTGTGGCCTAAACCAATGGCACTAATCTTGATACATTAT
* * * *
8486034 GACAATGAAGCAACGGTATCAAAGGCATAAAACCAAGCATACAATGGAAAGAGTCGATAAATTAG
192 GACAATGAAGCAACAGTATCAAAGGCACAAAACCAAGCAAACAATGGAAAGAGTCGATAAAATAG
*
8486099 ACTTCGACATAGCATTGTAAGACAAAGAATTAGTGATAGCATAGTCACTATAAGTTA
257 ACTTCAACATAGCATTGTAAGACAAAGAATTAGTGATAGCATAGTCACTATAAGTTA
8486156 TGTGAGGCCT
Statistics
Matches: 277, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
315 3 0.01
316 271 0.98
317 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (316 bp):
GTTGGATTTTTACAATTGGTGCAAATGCTATTTCTTAGGATTCTAAGAAACAATTTGATCAAACA
GACTCCAACATGGCGACTAAATTTATAACTTTAGTATCTGCCACCCAAGAAGCAAAATGGTCGAG
AGATTTACTTTATGAAATTTCATTGTGGCCTAAACCAATGGCACTAATCTTGATACATTATGACA
ATGAAGCAACAGTATCAAAGGCACAAAACCAAGCAAACAATGGAAAGAGTCGATAAAATAGACTT
CAACATAGCATTGTAAGACAAAGAATTAGTGATAGCATAGTCACTATAAGTTACTT
Found at i:8498141 original size:21 final size:21
Alignment explanation
Indices: 8498115--8498158 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
8498105 AACCCAATTT
*
8498115 CTATCAACGAATCACACATGC
1 CTATCAACCAATCACACATGC
*
8498136 CTATCAACCAATCACGCATGC
1 CTATCAACCAATCACACATGC
8498157 CT
1 CT
8498159 TGTCACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.20
Consensus pattern (21 bp):
CTATCAACCAATCACACATGC
Found at i:8499630 original size:25 final size:25
Alignment explanation
Indices: 8499596--8499726 Score: 120
Period size: 25 Copynumber: 5.2 Consensus size: 25
8499586 TCATTAATAG
8499596 GGCATTACGTGACTGTTATCTGTAT
1 GGCATTACGTGACTGTTATCTGTAT
8499621 GGCATTACGTGACTGTTATCTGTAT
1 GGCATTACGTGACTGTTATCTGTAT
* ** * *
8499646 CGCATTACGTGACCATAATATGTA-
1 GGCATTACGTGACTGTTATCTGTAT
** * *
8499670 GGTCATTGTGTGACAGTTATCTATAT
1 GG-CATTACGTGACTGTTATCTGTAT
* * * * *
8499696 AGCATTGCATGAATTTTATCTGTAT
1 GGCATTACGTGACTGTTATCTGTAT
8499721 GGCATT
1 GGCATT
8499727 GCATGACCAT
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
24 1 0.01
25 81 0.98
26 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (25 bp):
GGCATTACGTGACTGTTATCTGTAT
Found at i:8501795 original size:15 final size:16
Alignment explanation
Indices: 8501775--8501807 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
8501765 CACACAAAAA
8501775 CATAAAAA-CATAAAC
1 CATAAAAAGCATAAAC
8501790 CATAAAAAGCATAAAC
1 CATAAAAAGCATAAAC
8501806 CA
1 CA
8501808 ATATACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.64, C:0.21, G:0.03, T:0.12
Consensus pattern (16 bp):
CATAAAAAGCATAAAC
Found at i:8504920 original size:49 final size:48
Alignment explanation
Indices: 8504847--8504945 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 48
8504837 TCATAATTGC
*
8504847 AAAAACAAATAACATTATAATAAATTTAACCATTGAAAGTAACAAGAA
1 AAAAACAAATAACATTATAATAAATTTAACCATTAAAAGTAACAAGAA
8504895 ANAAAACAAATAACATTATAATAAATTTAACCATTAAAAGTAACAAGAA
1 A-AAAACAAATAACATTATAATAAATTTAACCATTAAAAGTAACAAGAA
8504944 AA
1 AA
8504946 TTAAAAGCTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 2 0.04
49 47 0.96
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.22
Consensus pattern (48 bp):
AAAAACAAATAACATTATAATAAATTTAACCATTAAAAGTAACAAGAA
Found at i:8507441 original size:2 final size:2
Alignment explanation
Indices: 8507436--8507489 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
8507426 TCTATGTATG
8507436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8507478 TA TA TA TA TA TA
1 TA TA TA TA TA TA
8507490 ATCTTCATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8507600 original size:42 final size:43
Alignment explanation
Indices: 8507537--8507634 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
8507527 ATATGGACTC
* *
8507537 CCCACTAGCACAT-GGCTGGGTCATAATCAGCTTATGCGCACT
1 CCCACTCGCACATAGGCTGGGTCAGAATCAGCTTATGCGCACT
* * *
8507579 CCCACTCGCACATAGTC-GGGTCAGCATCGGCTTATGCGCACT
1 CCCACTCGCACATAGGCTGGGTCAGAATCAGCTTATGCGCACT
8507621 CCCACTCGCACATA
1 CCCACTCGCACATA
8507635 ACCGAGTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 48 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.21
Consensus pattern (43 bp):
CCCACTCGCACATAGGCTGGGTCAGAATCAGCTTATGCGCACT
Found at i:8507693 original size:2 final size:2
Alignment explanation
Indices: 8507688--8507714 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8507678 CATATATTCG
8507688 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8507715 CAAAATGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8510480 original size:42 final size:42
Alignment explanation
Indices: 8510398--8510482 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
8510388 TCGTAAATAG
* * *
8510398 GGTCATCGCACTCAACATCTTTTAAGATAACAATTATGGCAT
1 GGTCATCGCACTCAACATCTTCTAACACAACAATTATGGCAT
* * *
8510440 GGTCATCGCACTGAACATCTTCTAACACAACAGTTGTGGCAT
1 GGTCATCGCACTCAACATCTTCTAACACAACAATTATGGCAT
8510482 G
1 G
8510483 TTCTGTACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
GGTCATCGCACTCAACATCTTCTAACACAACAATTATGGCAT
Found at i:8511594 original size:22 final size:22
Alignment explanation
Indices: 8511564--8511606 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
8511554 TAACAAAGTA
* *
8511564 TCACGCAATGCCTAATATCTAT
1 TCACACAATACCTAATATCTAT
8511586 TCACACAATACCTAATATCTA
1 TCACACAATACCTAATATCTA
8511607 GTCATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.30
Consensus pattern (22 bp):
TCACACAATACCTAATATCTAT
Found at i:8515039 original size:29 final size:30
Alignment explanation
Indices: 8514995--8515062 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
8514985 GTAACAAGGG
* *
8514995 TTTATTTAATTTAAAAT-AAA-AATATAAAA
1 TTTATTTAACTCAAAATAAAAGAATAT-AAA
*
8515024 TTTATTTAACTCAAAATAAAAGAATATGAA
1 TTTATTTAACTCAAAATAAAAGAATATAAA
8515054 TTTATTTAA
1 TTTATTTAA
8515063 ATTTTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 15 0.44
30 14 0.41
31 5 0.15
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
TTTATTTAACTCAAAATAAAAGAATATAAA
Found at i:8517791 original size:6 final size:6
Alignment explanation
Indices: 8517741--8517793 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
8517731 GGCTATTGTC
* * *
8517741 TGCTGT TGCGGTGT CTGCTGA TGCTGA TGCTGG TGCTGT TGCTGT TGCTGT
1 TGCTGT TGC--TGT -TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT
8517792 TG
1 TG
8517794 TAGCTGTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 33 0.80
7 2 0.05
8 3 0.07
9 3 0.07
ACGTcount: A:0.04, C:0.17, G:0.38, T:0.42
Consensus pattern (6 bp):
TGCTGT
Found at i:8524577 original size:3 final size:3
Alignment explanation
Indices: 8524569--8524634 Score: 114
Period size: 3 Copynumber: 22.0 Consensus size: 3
8524559 TATGGAGGAA
* *
8524569 CTG CTG CTG CTG CTG CTG CTG CTG CTG TTG CTG TTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
8524617 CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG
8524635 TTGTTGATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.36
Consensus pattern (3 bp):
CTG
Found at i:8541280 original size:28 final size:29
Alignment explanation
Indices: 8541235--8541289 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
8541225 TTTGATTCGA
8541235 AATAAAAATATTAAAATTTGA-TTAAATGT
1 AATAAAAATATTAAAATTT-ATTTAAATGT
8541264 AATAAAAA-A-TAATAATTTATTTAAAT
1 AATAAAAATATTAA-AATTTATTTAAAT
8541290 TTTTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 4 0.17
28 12 0.50
29 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (29 bp):
AATAAAAATATTAAAATTTATTTAAATGT
Found at i:8543510 original size:24 final size:24
Alignment explanation
Indices: 8543460--8543507 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
8543450 TCTTCTTTCA
*
8543460 ATTTGTATTATTATTTTTATTTAT
1 ATTTGTATTATTATTTTCATTTAT
8543484 ATTTGT-TTATT-TTTTCATTTAT
1 ATTTGTATTATTATTTTCATTTAT
8543506 AT
1 AT
8543508 ATTATTTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.52
23 5 0.22
24 6 0.26
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (24 bp):
ATTTGTATTATTATTTTCATTTAT
Found at i:8545295 original size:21 final size:21
Alignment explanation
Indices: 8545271--8545347 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
8545261 AGACATTTCA
*
8545271 CAAAGTCTTGATACTTGGATT
1 CAAAGTCTTGATACTTGGTTT
8545292 CAAAGTCTTGATACTTGGTTT
1 CAAAGTCTTGATACTTGGTTT
*
8545313 CAAAATCTTGATACTTGGTTT
1 CAAAGTCTTGATACTTGGTTT
8545334 CAAAGTCTTGATAC
1 CAAAGTCTTGATAC
8545348 ATAACTTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (21 bp):
CAAAGTCTTGATACTTGGTTT
Found at i:8545366 original size:42 final size:42
Alignment explanation
Indices: 8545271--8545367 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
8545261 AGACATTTCA
***
8545271 CAAAGTCTTGATACTTGGATTCAAAGTCTTGATACTTGGTTT
1 CAAAGTCTTGATACTTGGATTCAAAGTCTTGATACTAACTTT
* *
8545313 CAAAATCTTGATACTTGGTTTCAAAGTCTTGATACATAACTTT
1 CAAAGTCTTGATACTTGGATTCAAAGTCTTGATAC-TAACTTT
*
8545356 -AAAGTTTTGATA
1 CAAAGTCTTGATA
8545368 TCTGGCATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (42 bp):
CAAAGTCTTGATACTTGGATTCAAAGTCTTGATACTAACTTT
Found at i:8545566 original size:20 final size:20
Alignment explanation
Indices: 8545543--8545585 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
8545533 AATCATCCTT
8545543 AATGGCTACAAAGCTTCTCC
1 AATGGCTACAAAGCTTCTCC
** * *
8545563 AATGTTTACAAGGTTTCTCC
1 AATGGCTACAAAGCTTCTCC
8545583 AAT
1 AAT
8545586 TATAAAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
AATGGCTACAAAGCTTCTCC
Found at i:8546022 original size:28 final size:28
Alignment explanation
Indices: 8545917--8546009 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
8545907 CAATGTTGTA
* * *
8545917 AAGGTTTTGCCTGATCCTTGAAAAAGCT
1 AAGGTTTTGCTTAATCCTTGAAAAGGCT
** * *** *
8545945 AACCTTTTACCCGATCCTTAAAAAGGCT
1 AAGGTTTTGCTTAATCCTTGAAAAGGCT
*
8545973 AAGGTTTTGCTTAATCTTTGAAAAGGCT
1 AAGGTTTTGCTTAATCCTTGAAAAGGCT
*
8546001 GAGGTTTTG
1 AAGGTTTTG
8546010 TCTGCTCCTT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (28 bp):
AAGGTTTTGCTTAATCCTTGAAAAGGCT
Found at i:8546072 original size:34 final size:34
Alignment explanation
Indices: 8546030--8546117 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
8546020 GAAGAGGCAT
* * *
8546030 TGTGTGGGTTATGCTTGCTTCCGTGAAAAAGTAG
1 TGTGTGGGTTATGCTTGATCCCATGAAAAAGTAG
* *
8546064 TGTGTGGGTTATGCTTGATCCCATGAAAAAGCAA
1 TGTGTGGGTTATGCTTGATCCCATGAAAAAGTAG
* *
8546098 TGTG-AGGTTATACTTGATCC
1 TGTGTGGGTTATGCTTGATCC
8546118 TTTCGAAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 14 0.30
34 33 0.70
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (34 bp):
TGTGTGGGTTATGCTTGATCCCATGAAAAAGTAG
Found at i:8546151 original size:37 final size:33
Alignment explanation
Indices: 8546070--8546161 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 33
8546060 GTAGTGTGTG
** *
8546070 GGTTATGCTTGATCCCATGAAAAAGCAATGTGA
1 GGTTATGCTTGATCCTTTGAAAAAGCAATGTAA
* *
8546103 GGTTATACTTGATCCTTTCGAAAAGGCAATGTATAAA
1 GGTTATGCTTGATCCTTT-GAAAAAGCAATG--T-AA
8546140 GGTTATGCTTGATCC-TTGAAAA
1 GGTTATGCTTGATCCTTTGAAAA
8546162 GACAGATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
33 15 0.31
34 11 0.22
35 5 0.10
36 3 0.06
37 15 0.31
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32
Consensus pattern (33 bp):
GGTTATGCTTGATCCTTTGAAAAAGCAATGTAA
Found at i:8547022 original size:157 final size:156
Alignment explanation
Indices: 8546811--8547123 Score: 617
Period size: 157 Copynumber: 2.0 Consensus size: 156
8546801 CTTGTTTGTT
8546811 CATTTTCCTTGTTTTTTTTTTAAGTGAAATTTTTTTTTTAAAGCTTGTCATCAAACTCAAAAGCT
1 CATTTTCCTTGTTTTTTTTTTAAGTGAAATTTTTTTTTTAAAGCTTGTCATCAAACTCAAAAGCT
8546876 CAAATTACTGAAAAGAATTTTTAAAATTCAATTCACCCCATTCTTGAATATTTTTTCATCATTTT
66 CAAATTACTGAAAAGAATTTTTAAAATTCAATTCACCCCATTCTTGAATATTTTTTCATCATTTT
8546941 TATTAAGCTAACCGATCTAACAAAAG
131 TATTAAGCTAACCGATCTAACAAAAG
8546967 NCATTTTCCTTGTTTTTTTTTTAAGTGAAATTTTTTTTTTAAAGCTTGTCATCAAACTCAAAAGC
1 -CATTTTCCTTGTTTTTTTTTTAAGTGAAATTTTTTTTTTAAAGCTTGTCATCAAACTCAAAAGC
8547032 TCAAATTACTGAAAAGAATTTTTAAAATTCAATTCACCCCATTCTTGAATATTTTTTCATCATTT
65 TCAAATTACTGAAAAGAATTTTTAAAATTCAATTCACCCCATTCTTGAATATTTTTTCATCATTT
8547097 TTATTAAGCTAACCGATCTAACAAAAG
130 TTATTAAGCTAACCGATCTAACAAAAG
8547124 ATATTGAAGT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (156 bp):
CATTTTCCTTGTTTTTTTTTTAAGTGAAATTTTTTTTTTAAAGCTTGTCATCAAACTCAAAAGCT
CAAATTACTGAAAAGAATTTTTAAAATTCAATTCACCCCATTCTTGAATATTTTTTCATCATTTT
TATTAAGCTAACCGATCTAACAAAAG
Found at i:8552620 original size:20 final size:20
Alignment explanation
Indices: 8552584--8552621 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8552574 TCATAACTAG
*
8552584 GAAATGTTTATGGTTTATTA
1 GAAATGTTTATGATTTATTA
8552604 GAAA-GTTTATGAATTTAT
1 GAAATGTTTATG-ATTTAT
8552622 GCTCCTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
GAAATGTTTATGATTTATTA
Found at i:8553895 original size:39 final size:38
Alignment explanation
Indices: 8553794--8553895 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 38
8553784 ATCTGTGAGA
* *
8553794 AGTCCAAGATAGTGGGGATCATACCATTATTTGAGAAT
1 AGTCCAAGATAGTGGAGATCATACCATTATTTCAGAAT
* * *
8553832 ATGTCCAAGGTAATGGAGACCATACCATTATTTCAGAAGT
1 A-GTCCAAGATAGTGGAGATCATACCATTATTTCAGAA-T
* *
8553872 AGTCCTAGATAGTTGAGATCATAC
1 AGTCCAAGATAGTGGAGATCATAC
8553896 TATTGTTGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 49 0.94
40 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (38 bp):
AGTCCAAGATAGTGGAGATCATACCATTATTTCAGAAT
Found at i:8565633 original size:27 final size:27
Alignment explanation
Indices: 8565602--8565655 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
8565592 AGAGCATGAA
*
8565602 AATTTATT-AATTAATGTATAAATTAAT
1 AATTTATTAAATT-ATATATAAATTAAT
*
8565629 AATTTATTAAATTATATATTAATTAAT
1 AATTTATTAAATTATATATAAATTAAT
8565656 CAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AATTTATTAAATTATATATAAATTAAT
Found at i:8572490 original size:8 final size:8
Alignment explanation
Indices: 8572466--8572510 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
8572456 CTCAAAGGCC
*
8572466 TATATATC
1 TATATATA
*
8572474 TATACATA
1 TATATATA
*
8572482 TATCTATA
1 TATATATA
8572490 TATATATA
1 TATATATA
*
8572498 TATATATG
1 TATATATA
8572506 TATAT
1 TATAT
8572511 TAATGGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (8 bp):
TATATATA
Found at i:8572504 original size:6 final size:6
Alignment explanation
Indices: 8572466--8572510 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
8572456 CTCAAAGGCC
* * * *
8572466 TATATA TCTATA CATATA TCTATA TATATA TATATA TATGTA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TAT
8572511 TAATGGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:8573318 original size:6 final size:6
Alignment explanation
Indices: 8573299--8573332 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
8573289 TGGCGTGGGT
* *
8573299 GGGAAA GGGGAA GGGAAA GGGAAA GGGGAA GGGA
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GGGA
8573333 GTTAAAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:8580891 original size:21 final size:21
Alignment explanation
Indices: 8580861--8580900 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8580851 CTAAACTTAA
*
8580861 ATTAATTTAAAGC-AAAATAAT
1 ATTAAATTAAA-CTAAAATAAT
8580882 ATTAAATTAAACTAAAATA
1 ATTAAATTAAACTAAAATA
8580901 CTTAAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
ATTAAATTAAACTAAAATAAT
Found at i:8583107 original size:42 final size:41
Alignment explanation
Indices: 8583050--8583133 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
8583040 TTATTATTTG
*
8583050 TTCATTACTTAACTTAGGAAAAATATTTTTACTTAGATTTAT
1 TTCATTACTTAACTTAGG-AAAATATCTTTACTTAGATTTAT
* * * *
8583092 TTCATTATTTGACTTAGGAAGATATCTTTACTTTGATTTAT
1 TTCATTACTTAACTTAGGAAAATATCTTTACTTAGATTTAT
8583133 T
1 T
8583134 CTTAGTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 21 0.57
42 16 0.43
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.50
Consensus pattern (41 bp):
TTCATTACTTAACTTAGGAAAATATCTTTACTTAGATTTAT
Found at i:8585034 original size:35 final size:35
Alignment explanation
Indices: 8584994--8585077 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
8584984 CGGTGTGGGC
**
8584994 AGGAGTACATGTGATGATATTGAAATGTGCATGTA
1 AGGAGTACACATGATGATATTGAAATGTGCATGTA
* * *
8585029 GGGAGTGCACATGATGATATTGAAATGTGCTTGTA
1 AGGAGTACACATGATGATATTGAAATGTGCATGTA
8585064 AGGAGTACACATGA
1 AGGAGTACACATGA
8585078 GCTGAGTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (35 bp):
AGGAGTACACATGATGATATTGAAATGTGCATGTA
Found at i:8586634 original size:19 final size:19
Alignment explanation
Indices: 8586610--8586647 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
8586600 CCATTTGACT
*
8586610 TATTGGAGTATGGTTTGAG
1 TATTGGAGTATGATTTGAG
8586629 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
8586648 GTTGAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:8587718 original size:19 final size:19
Alignment explanation
Indices: 8587691--8587728 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
8587681 CCATTTGACT
*
8587691 TATTGGAGTATGATTTGAG
1 TATTCGAGTATGATTTGAG
8587710 TATTCGAGTATGATTTGAG
1 TATTCGAGTATGATTTGAG
8587729 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTCGAGTATGATTTGAG
Done.