Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1594534 original size:21 final size:22
Alignment explanation
Indices: 1594505--1594550 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1594495 TGTTCAGATA
** *
1594505 AGTAGTACTCCGCAACAGGTGG
1 AGTAGTACTCCAAAACAAGTGG
1594527 AGTA-TACTCCAAAACAAGTGG
1 AGTAGTACTCCAAAACAAGTGG
1594548 AGT
1 AGT
1594551 TTTAACAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAAGTGG
Found at i:1596498 original size:27 final size:27
Alignment explanation
Indices: 1596424--1596525 Score: 120
Period size: 27 Copynumber: 3.9 Consensus size: 27
1596414 AAAAGCTACC
* *
1596424 ATTTGTGTTTGTCAAAAATGATGGTTC
1 ATTTGTGTTTGTCAAAAATGGTGGTTT
* * *
1596451 CTTTGTGTTTCTAAAAAATGGTGGTTT
1 ATTTGTGTTTGTCAAAAATGGTGGTTT
*
1596478 ATTTGTGTTTGTCAAAAATGGTGGCTT
1 ATTTGTGTTTGTCAAAAATGGTGGTTT
*
1596505 A--T-TGTTTGTCAAAATTGGTGG
1 ATTTGTGTTTGTCAAAAATGGTGG
1596526 CTAATTTTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
24 18 0.28
25 1 0.02
27 46 0.71
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.45
Consensus pattern (27 bp):
ATTTGTGTTTGTCAAAAATGGTGGTTT
Found at i:1604035 original size:12 final size:12
Alignment explanation
Indices: 1604018--1604045 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1604008 TCTCTATCTC
1604018 AAGACCCTCCTG
1 AAGACCCTCCTG
1604030 AAGACCCTCCTG
1 AAGACCCTCCTG
1604042 AAGA
1 AAGA
1604046 TGAGCAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.36, G:0.18, T:0.14
Consensus pattern (12 bp):
AAGACCCTCCTG
Found at i:1605291 original size:2 final size:2
Alignment explanation
Indices: 1605286--1605315 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1605276 GAAAAAAAAA
*
1605286 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1605316 TTTAAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1605424 original size:2 final size:2
Alignment explanation
Indices: 1605419--1605458 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1605409 TTTTTTAAAG
1605419 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
1605459 AACACCAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1605587 original size:18 final size:18
Alignment explanation
Indices: 1605556--1605610 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
1605546 ATCTAATTTA
*
1605556 TAAAT-AAAAAATTTAAT
1 TAAATGAAAATATTTAAT
* *
1605573 TTAATGAAAATATTTTTAT
1 TAAATGAAAATA-TTTAAT
*
1605592 TAAATGATAATA-TTAAT
1 TAAATGAAAATATTTAAT
1605609 TA
1 TA
1605611 TTGTTTGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 10 0.33
18 5 0.17
19 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TAAATGAAAATATTTAAT
Found at i:1605892 original size:17 final size:17
Alignment explanation
Indices: 1605872--1605927 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1605862 ATTTTTAAAA
1605872 AATATTTAATATTAAGT
1 AATATTTAATATTAAGT
*
1605889 AATATTT--TATTTA-T
1 AATATTTAATATTAAGT
1605903 AAATATTTAATATTAAGT
1 -AATATTTAATATTAAGT
1605921 AATATTT
1 AATATTT
1605928 TATCAACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 1 0.03
15 12 0.36
17 19 0.58
18 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AATATTTAATATTAAGT
Found at i:1605947 original size:32 final size:32
Alignment explanation
Indices: 1605879--1605948 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1605869 AAAAATATTT
** * * *
1605879 AATATTAAGTAATATTTTATTTATAAATATTT
1 AATATTAAGTAATATTTTATCAACAAACATTA
*
1605911 AATATTAAGTAATATTTTATCAACAAGCATTA
1 AATATTAAGTAATATTTTATCAACAAACATTA
1605943 AATATT
1 AATATT
1605949 GAAATATCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (32 bp):
AATATTAAGTAATATTTTATCAACAAACATTA
Found at i:1607447 original size:6 final size:6
Alignment explanation
Indices: 1607416--1607444 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1607406 ACTTTTTTTT
1607416 TGGGGG TGGGGG TGGGGG TGGGGG -GGGGG
1 TGGGGG TGGGGG TGGGGG TGGGGG TGGGGG
1607445 GGGTTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (6 bp):
TGGGGG
Found at i:1609598 original size:16 final size:17
Alignment explanation
Indices: 1609577--1609611 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1609567 AAATATAATA
1609577 TAAATT-TTTTTAAAAT
1 TAAATTATTTTTAAAAT
*
1609593 TAAATTATTTTTTAAAT
1 TAAATTATTTTTAAAAT
1609610 TA
1 TA
1609612 TTATTGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAATTATTTTTAAAAT
Found at i:1610470 original size:21 final size:20
Alignment explanation
Indices: 1610431--1610470 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1610421 CTATGGAACA
* *
1610431 TAAATTTTATAACAAAAATT
1 TAAATTTTACAAAAAAAATT
1610451 TAAATTTTAACAAAAAAAAT
1 TAAATTTT-ACAAAAAAAAT
1610471 ACTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATTTTACAAAAAAAATT
Found at i:1611133 original size:17 final size:16
Alignment explanation
Indices: 1611094--1611134 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1611084 AATGTAAATC
*
1611094 ATTTATTGTAATTTAT
1 ATTTATTTTAATTTAT
*
1611110 CTTTATTTTAATTTAT
1 ATTTATTTTAATTTAT
1611126 GATTTATTT
1 -ATTTATTT
1611135 AACTTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (16 bp):
ATTTATTTTAATTTAT
Found at i:1612543 original size:17 final size:16
Alignment explanation
Indices: 1612521--1612563 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1612511 ATTATTAATA
*
1612521 AATTTTTAAAAATTGTT
1 AATTTTTAAAAAAT-TT
1612538 AA-TTTTAAAAAATTT
1 AATTTTTAAAAAATTT
1612553 AATATTTTAAA
1 AAT-TTTTAAA
1612564 GTGTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AATTTTTAAAAAATTT
Found at i:1613124 original size:30 final size:33
Alignment explanation
Indices: 1613056--1613130 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
1613046 AAAAATTTTT
*
1613056 TTATTTTAAATTTAATAATATTAAAAATAAATA
1 TTATTTTAAATTTAATAATAATAAAAATAAATA
1613089 TTATTTTAAATTTAATAATAATAAAAATAAATA
1 TTATTTTAAATTTAATAATAATAAAAATAAATA
1613122 TT-TTTTAAA
1 TTATTTTAAA
1613131 AATATAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 7 0.17
33 34 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TTATTTTAAATTTAATAATAATAAAAATAAATA
Found at i:1613367 original size:26 final size:27
Alignment explanation
Indices: 1613304--1613376 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 27
1613294 TTTATATTAT
*
1613304 ATTTAAAGTAAAAATAATTATTTTATAAAA
1 ATTTAAA-T-AAAATAATCA-TTTATAAAA
*
1613334 AATT--ATAAAATAATCATTT-TAAAA
1 ATTTAAATAAAATAATCATTTATAAAA
1613358 ATTTAAATAATAA-AATCAT
1 ATTTAAATAA-AATAATCAT
1613377 AACCACTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 8 0.22
25 3 0.08
26 19 0.51
27 3 0.08
28 1 0.03
30 3 0.08
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (27 bp):
ATTTAAATAAAATAATCATTTATAAAA
Found at i:1613510 original size:35 final size:33
Alignment explanation
Indices: 1613469--1613583 Score: 133
Period size: 35 Copynumber: 3.3 Consensus size: 33
1613459 AAACTTATTG
*
1613469 TAAAAGTCTTAGCGTGTCGAAAGGAATAGATGTAA
1 TAAAAGTCTT-GAGTGTCGAAAGG-ATAGATGTAA
*
1613504 TAAAAGTCTTCGGGTGTCGAAGAGGATAGATGTAA
1 TAAAAGTCTT-GAGTGTCGAA-AGGATAGATGTAA
* *
1613539 TAAAAGTCCTGAAGTG-CGAAAGGGGTAGATGTAA
1 TAAAAGTCTTG-AGTGTCGAAA-GGATAGATGTAA
1613573 TAAAAGTCTTG
1 TAAAAGTCTTG
1613584 GATGCCAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 1 0.01
34 26 0.37
35 41 0.58
36 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.29, T:0.25
Consensus pattern (33 bp):
TAAAAGTCTTGAGTGTCGAAAGGATAGATGTAA
Found at i:1613573 original size:34 final size:33
Alignment explanation
Indices: 1613469--1613606 Score: 127
Period size: 35 Copynumber: 4.0 Consensus size: 33
1613459 AAACTTATTG
* *
1613469 TAAAAGTCTTAGCGTGTCGAAAGGAATAGATGTAA
1 TAAAAGTCTT-GAGTG-CGAAAGGGATAGATGTAA
*
1613504 TAAAAGTCTTCGGGTGTCG-AAGAGGATAGATGTAA
1 TAAAAGTCTT-GAGTG-CGAAAG-GGATAGATGTAA
* *
1613539 TAAAAGTCCTGAAGTGCGAAAGGGGTAGATGTAA
1 TAAAAGTCTTG-AGTGCGAAAGGGATAGATGTAA
* *
1613573 TAAAAGTCTTG-GATGCCAAAGGGGATGGATGTAA
1 TAAAAGTCTTGAG-TGCGAAA-GGGATAGATGTAA
1613607 AAGAATCTAG
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
32 1 0.01
33 6 0.07
34 38 0.43
35 43 0.49
ACGTcount: A:0.37, C:0.09, G:0.30, T:0.24
Consensus pattern (33 bp):
TAAAAGTCTTGAGTGCGAAAGGGATAGATGTAA
Found at i:1614244 original size:46 final size:47
Alignment explanation
Indices: 1614170--1614260 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 47
1614160 ATCACTCATC
*
1614170 AACTTGTAACTTTTACATGAATAAAGCTACAAATTTTTTTTATAAAT
1 AACTTGTAAATTTTACATGAATAAAGCTACAAATTTTTTTTATAAAT
*
1614217 AACTTGTAAATTTGTACA-G-ATAAAGCTACAAGTTTTTTTTATAA
1 AACTTGTAAATTT-TACATGAATAAAGCTACAAATTTTTTTTATAA
1614261 TCAATATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 24 0.59
47 13 0.32
48 4 0.10
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (47 bp):
AACTTGTAAATTTTACATGAATAAAGCTACAAATTTTTTTTATAAAT
Found at i:1614937 original size:6 final size:6
Alignment explanation
Indices: 1614926--1614953 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1614916 TGCTGTTACA
1614926 GCTACT GCTACT GCTACT GCTACT GCTA
1 GCTACT GCTACT GCTACT GCTACT GCTA
1614954 ATCATGCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (6 bp):
GCTACT
Found at i:1624235 original size:62 final size:62
Alignment explanation
Indices: 1624138--1624264 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 62
1624128 CACAAGTACT
1624138 TTCATGTCAACTGTGCATGGGTCAAAAAAGCTAGAACAAGTTAGATTAGCACTTACCAAGAC
1 TTCATGTCAACTGTGCATGGGTCAAAAAAGCTAGAACAAGTTAGATTAGCACTTACCAAGAC
* *
1624200 TTCATGTCAAGTGTGCATGGGTCACAAAAGCTAGAACAAGTTAGATTAGCACTTACCAAGAC
1 TTCATGTCAACTGTGCATGGGTCAAAAAAGCTAGAACAAGTTAGATTAGCACTTACCAAGAC
1624262 TTC
1 TTC
1624265 TTCAAGACCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (62 bp):
TTCATGTCAACTGTGCATGGGTCAAAAAAGCTAGAACAAGTTAGATTAGCACTTACCAAGAC
Found at i:1626216 original size:32 final size:32
Alignment explanation
Indices: 1626179--1626258 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
1626169 TACTTAATAT
*
1626179 TTTAATATTTAATA-TCTGTTAATAAAATATTA
1 TTTAATATTTAATATTC-ATTAATAAAATATTA
* * *
1626211 TTTAATGTTTGATGTTCATTAATAAAATATTA
1 TTTAATATTTAATATTCATTAATAAAATATTA
* *
1626243 CTTAATATTAAATATT
1 TTTAATATTTAATATT
1626259 TTATAAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTAATATTTAATATTCATTAATAAAATATTA
Found at i:1626622 original size:25 final size:25
Alignment explanation
Indices: 1626572--1626623 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1626562 AAAGTAGTTT
*
1626572 AATTAAATTAAATTTTTTACTTATA
1 AATTAAATTAAATTTTTTACTAATA
1626597 AATTAAA-TAAATATTATTTA-TAATA
1 AATTAAATTAAAT-TT-TTTACTAATA
1626622 AA
1 AA
1626624 ATATCTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 15 0.62
26 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTAAATTAAATTTTTTACTAATA
Found at i:1631891 original size:13 final size:14
Alignment explanation
Indices: 1631865--1631898 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1631855 AAATTATTTC
1631865 GTATAAATATTTAA
1 GTATAAATATTTAA
*
1631879 GTATAAGTA-TTAA
1 GTATAAATATTTAA
1631892 GTATAAA
1 GTATAAA
1631899 GATATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (14 bp):
GTATAAATATTTAA
Found at i:1631952 original size:17 final size:16
Alignment explanation
Indices: 1631924--1631958 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1631914 AACTTAAAAA
1631924 ATTTAAATATATTCAT
1 ATTTAAATATATTCAT
*
1631940 ATTTAACATATATTTAT
1 ATTTAA-ATATATTCAT
1631957 AT
1 AT
1631959 ATGATACGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAAATATATTCAT
Found at i:1632693 original size:2 final size:2
Alignment explanation
Indices: 1632686--1632712 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1632676 GAAACACGAA
1632686 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
1632713 ATACCTTTTC
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:1633657 original size:34 final size:34
Alignment explanation
Indices: 1633524--1633658 Score: 191
Period size: 34 Copynumber: 4.0 Consensus size: 34
1633514 TAGATTAAGT
* * * *
1633524 ATATTAAGTGTGTTAGGTGATATATTTGAT-AAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAA-A
*
1633558 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAAA
1633592 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAAA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAAA
* *
1633626 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAA
1633659 TAAGATATTT
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 91 0.99
35 1 0.01
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (34 bp):
ATATTAGGTGTGTTAGGTAATGTATTTGGTGAAA
Found at i:1638448 original size:34 final size:34
Alignment explanation
Indices: 1638398--1638527 Score: 181
Period size: 34 Copynumber: 3.8 Consensus size: 34
1638388 TGTGTTAAGT
* * * *
1638398 TAAGCATATTAAGTGTGTTAGGTGATATATTTGG
1 TAAGAATATTAGGTGTGTTAGGTAATGTATTTGG
*
1638432 TAAGAATATTGGGTGTGTTAGGTAATGTATTTGG
1 TAAGAATATTAGGTGTGTTAGGTAATGTATTTGG
* *
1638466 TGAGAATATTAGGTGTGTTAGGTAATGTATTTGA
1 TAAGAATATTAGGTGTGTTAGGTAATGTATTTGG
1638500 TGAA-AATATTAGGTGTGTTAGGTAATGT
1 T-AAGAATATTAGGTGTGTTAGGTAATGT
1638528 GTTAGGTGAG
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 85 0.99
35 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.29, T:0.41
Consensus pattern (34 bp):
TAAGAATATTAGGTGTGTTAGGTAATGTATTTGG
Found at i:1641417 original size:42 final size:42
Alignment explanation
Indices: 1641363--1641447 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1641353 CTTCCTCAAC
*
1641363 AACATCTCTAACATCTCAGAATCACAAACCAAACCTGTTCCT
1 AACATCTCTAACATCTCAGAATCAAAAACCAAACCTGTTCCT
*
1641405 AACATCTCTAACATCTCAGAATCAAAAACTAAACCTGTTCCT
1 AACATCTCTAACATCTCAGAATCAAAAACCAAACCTGTTCCT
1641447 A
1 A
1641448 TATGATATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.25
Consensus pattern (42 bp):
AACATCTCTAACATCTCAGAATCAAAAACCAAACCTGTTCCT
Found at i:1642877 original size:14 final size:14
Alignment explanation
Indices: 1642858--1642886 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1642848 CAAAAGCCTC
1642858 CTCGCTTGATACAG
1 CTCGCTTGATACAG
1642872 CTCGCTTGATACAG
1 CTCGCTTGATACAG
1642886 C
1 C
1642887 CGGTGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (14 bp):
CTCGCTTGATACAG
Found at i:1643730 original size:42 final size:41
Alignment explanation
Indices: 1643670--1643759 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
1643660 TTCCTTCGGT
* *
1643670 CAAACTTAATCATGTCTTTTTTTAATGGACAATTCCAGCTAC
1 CAAACTTAATCATATC-TTTTCTAATGGACAATTCCAGCTAC
* * * * *
1643712 CAAAGTTAGTCATATCTTTTCTAATGGAGAATTCCATCTAT
1 CAAACTTAATCATATCTTTTCTAATGGACAATTCCAGCTAC
1643753 CAAACTT
1 CAAACTT
1643760 CATCTTTTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 27 0.68
42 13 0.32
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (41 bp):
CAAACTTAATCATATCTTTTCTAATGGACAATTCCAGCTAC
Found at i:1644031 original size:21 final size:21
Alignment explanation
Indices: 1644007--1644048 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1643997 AATATATTTT
1644007 TATATAAAT-TTAATTATAAAA
1 TATATAAATATT-ATTATAAAA
1644028 TATATAAATATTATTATAAAA
1 TATATAAATATTATTATAAAA
1644049 ATAACTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAAATATTATTATAAAA
Found at i:1645253 original size:25 final size:25
Alignment explanation
Indices: 1645225--1645272 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1645215 ATTAACATGA
1645225 ATATAATATAAA-TATATTAAAATTT
1 ATATAATATAAATTAT-TTAAAATTT
1645250 ATATAATATAAATTATTTAAAAT
1 ATATAATATAAATTATTTAAAAT
1645273 ATCAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATAATATAAATTATTTAAAATTT
Found at i:1645265 original size:14 final size:14
Alignment explanation
Indices: 1645225--1645310 Score: 51
Period size: 14 Copynumber: 6.2 Consensus size: 14
1645215 ATTAACATGA
1645225 ATATAATATAAA-T
1 ATATAATATAAATT
1645238 ATAT--TA-AAATTT
1 ATATAATATAAA-TT
1645250 ATATAATATAAATT
1 ATATAATATAAATT
*
1645264 ATTTAAAATATCAAATT
1 A--TATAATAT-AAATT
1645281 -TATATATATAATATT
1 ATATA-ATATAA-ATT
*
1645296 TTA-AATAT-AATT
1 ATATAATATAAATT
1645308 ATA
1 ATA
1645311 ACATAAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 23
0.69 0.04 0.27
Matches are distributed among these distances:
10 3 0.05
11 2 0.03
12 10 0.17
13 5 0.08
14 14 0.24
15 11 0.19
16 9 0.15
17 5 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAATATAAATT
Found at i:1645301 original size:29 final size:32
Alignment explanation
Indices: 1645244--1645303 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 32
1645234 AAATATATTA
1645244 AAATTTATATAATATAAATTATTTAAAATATC
1 AAATTTATATAATATAAATTATTTAAAATATC
*
1645276 AAATTTATAT-ATAT-AA-TATTTTAAATAT
1 AAATTTATATAATATAAATTATTTAAAATAT
1645304 AATTATAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.41
30 2 0.07
31 4 0.15
32 10 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (32 bp):
AAATTTATATAATATAAATTATTTAAAATATC
Found at i:1645319 original size:18 final size:18
Alignment explanation
Indices: 1645298--1645336 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1645288 ATAATATTTT
1645298 AAATATAATTATAACATA
1 AAATATAATTATAACATA
*
1645316 AAATATAATTATAATATA
1 AAATATAATTATAACATA
1645334 AAA
1 AAA
1645337 ATTAACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATTATAACATA
Found at i:1646324 original size:22 final size:21
Alignment explanation
Indices: 1646299--1646339 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1646289 GTCTAGTTAA
1646299 TAGTTATATTAATTTTTTATCT
1 TAGTT-TATTAATTTTTTATCT
*
1646321 TAGTTTTTTAATTTTTTAT
1 TAGTTTATTAATTTTTTAT
1646340 TATAAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
TAGTTTATTAATTTTTTATCT
Found at i:1647737 original size:21 final size:21
Alignment explanation
Indices: 1647711--1647752 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1647701 AAAAAATTAT
1647711 TTTTATAA-TAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
1647732 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTTATATA
1647753 AAAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:1648021 original size:59 final size:58
Alignment explanation
Indices: 1647943--1648078 Score: 204
Period size: 56 Copynumber: 2.4 Consensus size: 58
1647933 GATGAAGAGG
* *
1647943 GATGGAATTCTCCAATAAAAAAAAAGACAAAAAGAAAGAAGAAAAGATGAACTTTGATA
1 GATGGAATTCTCC-ATTAAAAAAAAGACAAAAAGAAAGAAGAAAAGATGAACTTTAATA
*
1648002 GATGGAATTCTCCATT--AAAAAAGACAAAAAGAAAGAAGAAAAGATGAAGTTTAATA
1 GATGGAATTCTCCATTAAAAAAAAGACAAAAAGAAAGAAGAAAAGATGAACTTTAATA
* *
1648058 GAAGGAATTCTCCATTGAAAA
1 GATGGAATTCTCCATTAAAAA
1648079 GATATGACTA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
56 53 0.75
58 5 0.07
59 13 0.18
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.19
Consensus pattern (58 bp):
GATGGAATTCTCCATTAAAAAAAAGACAAAAAGAAAGAAGAAAAGATGAACTTTAATA
Found at i:1649040 original size:14 final size:14
Alignment explanation
Indices: 1649021--1649049 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1649011 ATATACACCG
1649021 GCTGTATCAAGCGA
1 GCTGTATCAAGCGA
1649035 GCTGTATCAAGCGA
1 GCTGTATCAAGCGA
1649049 G
1 G
1649050 GAGGCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (14 bp):
GCTGTATCAAGCGA
Found at i:1653515 original size:2 final size:2
Alignment explanation
Indices: 1653510--1653534 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1653500 GGTATTTTTT
1653510 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
1653535 TCATTTCCTG
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:1654447 original size:34 final size:34
Alignment explanation
Indices: 1654403--1654619 Score: 242
Period size: 34 Copynumber: 6.4 Consensus size: 34
1654393 AAAAACTACT
*
1654403 ATTTAATCAACAATGGCAACCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* * * *
1654437 ATTTAGTCAACAATTGTAAGCC-ACCAAATTTTCC
1 ATTTAATCAACAATGGTAA-CCTACCAAATCTCCC
* * *
1654471 ATTTAATCAACAATGGTAAGCTACCAAATTTTCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
*
1654505 ATTTAATCAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* ** *
1654539 ATTTAGTCAACAATGACAAACC-ACCAAATCACCC
1 ATTTAATCAACAATG-GTAACCTACCAAATCTCCC
** * *
1654573 ATTTAATCAACAATGGTAAATTACTAAATC-ACC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
1654606 ATTTAATCAACAAT
1 ATTTAATCAACAAT
1654620 TCTCCCACTT
Statistics
Matches: 157, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
33 19 0.12
34 133 0.85
35 5 0.03
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.28
Consensus pattern (34 bp):
ATTTAATCAACAATGGTAACCTACCAAATCTCCC
Found at i:1654579 original size:102 final size:101
Alignment explanation
Indices: 1654403--1654619 Score: 301
Period size: 102 Copynumber: 2.1 Consensus size: 101
1654393 AAAAACTACT
* * **
1654403 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATTGTAAGCCACCAAATTT
1 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATTGCAAACCACCAAATCA
* * **
1654468 TCCATTTAATCAACAATGGTAAGCTACCAAATTTTCC
66 CCCATTTAATCAACAATGGTAAACTACCAAA-TCACC
* *
1654505 ATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAA-TGACAAACCACCAAATC
1 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATTG-CAAACCACCAAATC
* *
1654569 ACCCATTTAATCAACAATGGTAAATTACTAAATCACC
65 ACCCATTTAATCAACAATGGTAAACTACCAAATCACC
1654606 ATTTAATCAACAAT
1 ATTTAATCAACAAT
1654620 TCTCCCACTT
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 19 0.19
102 83 0.81
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.28
Consensus pattern (101 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATTGCAAACCACCAAATCA
CCCATTTAATCAACAATGGTAAACTACCAAATCACC
Found at i:1658707 original size:19 final size:19
Alignment explanation
Indices: 1658680--1658721 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1658670 TCACGTGTAC
*
1658680 AGTAACCGTATACTTGAAT
1 AGTAACCGTATACATGAAT
*
1658699 AGTACCCGTATACATGAAT
1 AGTAACCGTATACATGAAT
1658718 AGTA
1 AGTA
1658722 TCTATATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTAACCGTATACATGAAT
Found at i:1658729 original size:19 final size:19
Alignment explanation
Indices: 1658688--1658742 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
1658678 ACAGTAACCG
* *
1658688 TATACTTGAATAGTACCCG
1 TATACATGAATAGTACCCA
* *
1658707 TATACATGAATAGTATCTA
1 TATACATGAATAGTACCCA
* *
1658726 TATACGTAAATAGTACC
1 TATACATGAATAGTACC
1658743 TCGACAACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
TATACATGAATAGTACCCA
Found at i:1659085 original size:34 final size:34
Alignment explanation
Indices: 1659039--1659255 Score: 251
Period size: 34 Copynumber: 6.4 Consensus size: 34
1659029 GTAAAAACCA
*
1659039 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1659073 CCATTTAGTCAACAATGGTAAGCC-ATCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * * * *
1659107 CTATTTAATCAACAATAGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1659141 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1659175 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1659209 CCATTTAATCAACAATGGTAAGCTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1659242 CCATTTAATCAACA
1 CCATTTAATCAACA
1659256 TTTTTAACAT
Statistics
Matches: 154, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
33 18 0.12
34 131 0.85
35 5 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1659153 original size:68 final size:66
Alignment explanation
Indices: 1659037--1659255 Score: 285
Period size: 68 Copynumber: 3.2 Consensus size: 66
1659027 TGGTAAAAAC
* * *
1659037 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCATCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTA-CAA
1659102 AT
65 AT
* * * * *
1659104 CACCTATTTAATCAACAATAGTAAGCTACCAAATTTTCCATTTAATCAACAATGGTAAGCTACCA
1 CACC-ATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTA-CA
1659169 AAT
64 AAT
* * * *
1659172 CTCCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAGCTACTA
1 C-ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTAC-A
1659237 AAT
64 AAT
1659240 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1659256 TTTTTAACAT
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
67 18 0.14
68 110 0.85
69 2 0.02
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (66 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACAAA
T
Found at i:1659215 original size:102 final size:101
Alignment explanation
Indices: 1659037--1659255 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
1659027 TGGTAAAAAC
* * *
1659037 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCATCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
1659102 ATCACCTATTTAATCAACAATAGTAAGCTACCAAATT
66 ATCACCCATTTAATCAACAATAGTAAGCTACCAAA-T
** * *
1659139 TTCCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
* *
1659204 ATCACCCATTTAATCAACAATGGTAAGCTACTAAAT
66 ATCACCCATTTAATCAACAATAGTAAGCTACCAAAT
1659240 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1659256 TTTTTAACAT
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATAGTAAGCTACCAAAT
Found at i:1660449 original size:37 final size:39
Alignment explanation
Indices: 1660407--1660498 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 39
1660397 ATCGAAAAAC
*
1660407 TTATATTAATATTCA-AAATAAA-TTAAA-AAAATTATTT
1 TTATATTAATATT-ATAAATAAATTTAAATAAAAATATTT
*
1660444 TTATATTAAT-TTATAATTAAATTTAAATAAAAATATTT
1 TTATATTAATATTATAAATAAATTTAAATAAAAATATTT
*
1660482 TTATATAAATAATTATA
1 TTATATTAAT-ATTATA
1660499 TAGGTCAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
35 1 0.02
36 8 0.17
37 15 0.32
38 18 0.38
40 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (39 bp):
TTATATTAATATTATAAATAAATTTAAATAAAAATATTT
Found at i:1670984 original size:2 final size:2
Alignment explanation
Indices: 1670977--1671007 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1670967 AGTGTCCATT
1670977 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1671008 TGTTTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1671450 original size:19 final size:19
Alignment explanation
Indices: 1671426--1671462 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1671416 GTTGACTAAA
1671426 GATAGCCACCCACCATAAG
1 GATAGCCACCCACCATAAG
*
1671445 GATAGCCATCCACCATAA
1 GATAGCCACCCACCATAA
1671463 ATCTCCACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.14
Consensus pattern (19 bp):
GATAGCCACCCACCATAAG
Found at i:1675928 original size:23 final size:24
Alignment explanation
Indices: 1675878--1675929 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1675868 AAAATTAACC
* * *
1675878 ACCAATTTTGACAAACAACAAGTC
1 ACCATTTTTGACAAACAACAAATA
*
1675902 ACCATTTTTTACAAACAA-AAATA
1 ACCATTTTTGACAAACAACAAATA
1675925 ACCAT
1 ACCAT
1675930 CATATTTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (24 bp):
ACCATTTTTGACAAACAACAAATA
Found at i:1675947 original size:28 final size:27
Alignment explanation
Indices: 1675916--1675977 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
1675906 TTTTTTACAA
*
1675916 ACAAAAATAACCATCATATTTGACAAAT
1 ACAAAAA-AACCACCATATTTGACAAAT
* *
1675944 ACAAAGAAAACTACCATATTTGATAAAT
1 ACAAA-AAAACCACCATATTTGACAAAT
1675972 ACAAAA
1 ACAAAA
1675978 GGTGACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.90
29 2 0.07
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (27 bp):
ACAAAAAAACCACCATATTTGACAAAT
Found at i:1676163 original size:17 final size:18
Alignment explanation
Indices: 1676141--1676174 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1676131 CATACTTCTT
1676141 TTTTTTAATTC-TTTTTA
1 TTTTTTAATTCATTTTTA
*
1676158 TTTTTTATTTCATTTTT
1 TTTTTTAATTCATTTTT
1676175 TTAACTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTAATTCATTTTTA
Found at i:1676773 original size:21 final size:21
Alignment explanation
Indices: 1676747--1676788 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1676737 CAATCAAAAC
1676747 TTGCTTTTTATTATCTTAATA
1 TTGCTTTTTATTATCTTAATA
1676768 TTGCTTTTTATTATCTTAATA
1 TTGCTTTTTATTATCTTAATA
1676789 CGTTAGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TTGCTTTTTATTATCTTAATA
Found at i:1678107 original size:35 final size:37
Alignment explanation
Indices: 1678036--1678113 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 37
1678026 TCAAGTCCAT
*
1678036 TTAAT-AAAATGTCTCTAATTAATAATTCAAGACTAA
1 TTAATGAAAATGTCTCTAATTAATAAATCAAGACTAA
* * *
1678072 TTAATGAATATGTCTC-GATTAA-AAATCAAGCCTAA
1 TTAATGAAAATGTCTCTAATTAATAAATCAAGACTAA
1678107 TTAATGA
1 TTAATGA
1678114 GAAGATCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 18 0.49
36 10 0.27
37 9 0.24
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (37 bp):
TTAATGAAAATGTCTCTAATTAATAAATCAAGACTAA
Found at i:1678957 original size:19 final size:19
Alignment explanation
Indices: 1678921--1678960 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1678911 ACACCAATTT
* *
1678921 AATTAAAAAATTACATAAA
1 AATTAAAAAATAAAATAAA
*
1678940 AATTAAAATATAAAATAAA
1 AATTAAAAAATAAAATAAA
1678959 AA
1 AA
1678961 ACATATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AATTAAAAAATAAAATAAA
Found at i:1679583 original size:21 final size:21
Alignment explanation
Indices: 1679557--1679598 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1679547 AAAAAATTAT
1679557 TTTTAT-AGTAATATTTATATA
1 TTTTATAAGTAA-ATTTATATA
*
1679578 TTTTATAATTAAATTTATATA
1 TTTTATAAGTAAATTTATATA
1679599 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTATAAGTAAATTTATATA
Found at i:1679889 original size:41 final size:41
Alignment explanation
Indices: 1679844--1679953 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 41
1679834 AAAGATGAAG
* *
1679844 TTTGATAGATGGAATTCTCCATTAAAAAAGACATGACTAAC
1 TTTGATAGATGGAATTCTCCATTAAAAAAGAAACGACTAAC
* * * * *
1679885 TTTGATAGCTGAAATTGTCCATTAAAAAAGAAACGATTAAG
1 TTTGATAGATGGAATTCTCCATTAAAAAAGAAACGACTAAC
** * *
1679926 TTTGACCGAAGGAATTCTCTATTAAAAA
1 TTTGATAGATGGAATTCTCCATTAAAAA
1679954 TAAAGATAAG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (41 bp):
TTTGATAGATGGAATTCTCCATTAAAAAAGAAACGACTAAC
Found at i:1680624 original size:17 final size:16
Alignment explanation
Indices: 1680602--1680633 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
1680592 TGATATGAAT
1680602 ATATAAATTTATTAATA
1 ATATAAA-TTATTAATA
1680619 ATATAAATTATTAAT
1 ATATAAATTATTAAT
1680634 GTATCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAAATTATTAATA
Found at i:1681536 original size:2 final size:2
Alignment explanation
Indices: 1681529--1681564 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1681519 ATTCTTCGGA
1681529 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
1681565 TGATAACATT
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:1682748 original size:16 final size:16
Alignment explanation
Indices: 1682729--1682791 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 16
1682719 TCTCCTCATA
1682729 TTATATTTTTAATAA-
1 TTATATTTTTAATAAT
*
1682744 TT-TATTTTTAAAAAT
1 TTATATTTTTAATAAT
* *
1682759 ATATTTTTTTAA-AAT
1 TTATATTTTTAATAAT
* *
1682774 TTA-ATCTTTATTAAT
1 TTATATTTTTAATAAT
1682789 TTA
1 TTA
1682792 ATAATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
14 16 0.42
15 14 0.37
16 8 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTTTTAATAAT
Found at i:1682751 original size:14 final size:14
Alignment explanation
Indices: 1682730--1682766 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1682720 CTCCTCATAT
*
1682730 TATATTTTTAATAA
1 TATATTTTTAAAAA
*
1682744 TTTATTTTTAAAAA
1 TATATTTTTAAAAA
1682758 TATATTTTT
1 TATATTTTT
1682767 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATTTTTAAAAA
Found at i:1682797 original size:23 final size:22
Alignment explanation
Indices: 1682766--1682817 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1682756 AATATATTTT
1682766 TTTAAAATTTAATCTTTATTAA-
1 TTTAAAATTT-ATCTTTATTAAG
* *
1682788 TTTAATAATTTTTTTTTATTAAG
1 TTTAA-AATTTATCTTTATTAAG
1682811 TTTAAAA
1 TTTAAAA
1682818 ATATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTAAAATTTATCTTTATTAAG
Found at i:1683039 original size:19 final size:19
Alignment explanation
Indices: 1682991--1683042 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
1682981 AGTCTAACTC
*
1682991 ATTTTTTAA-TTAAATTTA
1 ATTTTTTAAGTTTAATTTA
*
1683009 ATTATTTT--GTTTAATTTT
1 ATT-TTTTAAGTTTAATTTA
1683027 ATTTTTTAAGTTTAAT
1 ATTTTTTAAGTTTAAT
1683043 ATTTTTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.14
18 13 0.46
19 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
ATTTTTTAAGTTTAATTTA
Found at i:1683397 original size:15 final size:16
Alignment explanation
Indices: 1683365--1683401 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1683355 CGGTTGAAAG
*
1683365 AAATTTAAATCGTTTT
1 AAATTTAAATCATTTT
1683381 AAATTTAAAT-ATTTT
1 AAATTTAAATCATTTT
1683396 AAATTT
1 AAATTT
1683402 GAATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
AAATTTAAATCATTTT
Found at i:1685250 original size:24 final size:23
Alignment explanation
Indices: 1685221--1685272 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
1685211 TGATAATTTT
*
1685221 AAATAT-GATATAATAAAATAATTA
1 AAATATAG-TATAATAAAAT-ATAA
*
1685245 AAATATAGTATAATATAATATAA
1 AAATATAGTATAATAAAATATAA
1685268 AAATA
1 AAATA
1685273 ATATGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 16 0.64
25 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATATAGTATAATAAAATATAA
Found at i:1685256 original size:5 final size:5
Alignment explanation
Indices: 1685222--1685285 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
1685212 GATAATTTTA
* * * *
1685222 AATAT GATAT AATA- AA-AT AATTAA AATAT AGTAT AATAT AATAT AAAAAT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT -AATAT
1685272 AATAT GAATAT AAT
1 AATAT -AATAT AAT
1685286 TTAAATAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 29 0.63
6 12 0.26
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:1685281 original size:22 final size:21
Alignment explanation
Indices: 1685228--1685301 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
1685218 TTTAAATATG
1685228 ATATAATA-AA-ATAATTAAA
1 ATATAATATAATATAATTAAA
*
1685247 ATATAGTATAATATAATATAAA
1 ATATAATATAATATAAT-TAAA
*
1685269 A-ATAATATGAATATAATTTAA
1 ATATAATAT-AATATAATTAAA
1685290 ATA-AAT-TAATAT
1 ATATAATATAATAT
1685302 TTATATAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 12 0.26
20 3 0.06
21 18 0.38
22 14 0.30
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
ATATAATATAATATAATTAAA
Found at i:1685292 original size:11 final size:11
Alignment explanation
Indices: 1685228--1685292 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 11
1685218 TTTAAATATG
1685228 ATATAATA-AA
1 ATATAATATAA
*
1685238 ATA-ATTA-AA
1 ATATAATATAA
*
1685247 ATATAGTAT-A
1 ATATAATATAA
1685257 ATATAATATAA
1 ATATAATATAA
* *
1685268 AAATAATATGA
1 ATATAATATAA
*
1685279 ATATAATTTAA
1 ATATAATATAA
1685290 ATA
1 ATA
1685293 AATTAATATT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
9 8 0.18
10 15 0.34
11 21 0.48
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1685835 original size:11 final size:11
Alignment explanation
Indices: 1685819--1685862 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
1685809 AAATATAATT
1685819 ATATAAATATA
1 ATATAAATATA
*
1685830 ATATAAAAATTTA
1 ATAT--AAATATA
1685843 ATA-AAATATA
1 ATATAAATATA
1685853 ATATAAATAT
1 ATATAAATAT
1685863 CTAAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 9 0.32
11 10 0.36
13 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1685914 original size:18 final size:16
Alignment explanation
Indices: 1685891--1685955 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
1685881 ATATAATATG
1685891 AATTATTAATATATTAA
1 AATTATTAATATATT-A
*
1685908 AATTTATAAATATA-TA
1 AA-TTATTAATATATTA
1685924 AATTATTTAATATA-T-
1 AATTA-TTAATATATTA
*
1685939 AATT-TTAATATAATA
1 AATTATTAATATATTA
1685954 AA
1 AA
1685956 ATACATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
13 8 0.19
14 1 0.02
15 9 0.21
16 11 0.26
17 3 0.07
18 10 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTATTAATATATTA
Found at i:1685947 original size:47 final size:47
Alignment explanation
Indices: 1685847--1685986 Score: 122
Period size: 47 Copynumber: 2.8 Consensus size: 47
1685837 AATTTAATAA
*
1685847 AATATAATATAAATATC-TAAATATTTTATAATTTATATAATATGAATTATT
1 AATATAATA-AAATA-CATAAATA---TATAAATTATATAATATGAATTATT
* ** * *
1685898 AATATATTAAAATTTATAAATATATAAATTATTTAATATATAATT-TT
1 AATATAATAAAATACATAAATATATAAATTATATAATAT-GAATTATT
*
1685945 AATATAATAAAATACATAAATATAATATATATATATATATAT
1 AATATAATAAAATACATAAATAT-ATAAAT-TATATA-ATAT
1685987 ATATGTGTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
47 37 0.51
48 9 0.12
49 5 0.07
50 14 0.19
51 8 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (47 bp):
AATATAATAAAATACATAAATATATAAATTATATAATATGAATTATT
Found at i:1687430 original size:21 final size:21
Alignment explanation
Indices: 1687404--1687445 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1687394 TAAAAATTAT
1687404 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
1687425 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTTATATA
1687446 AAAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:1687746 original size:41 final size:41
Alignment explanation
Indices: 1687671--1687809 Score: 145
Period size: 41 Copynumber: 3.3 Consensus size: 41
1687661 AGAAAGATAC
*
1687671 AGACAAGA-TGAAGTTTGATAGATGGAATTCTCCATTAAAAA
1 AGACAAGACT-AAATTTGATAGATGGAATTCTCCATTAAAAA
* * * * * *
1687712 AGATAGGACTAACTTTGATAGATAGAATTGTCCATTAAAAG
1 AGACAAGACTAAATTTGATAGATGGAATTCTCCATTAAAAA
* *
1687753 ATACAAGATTAAATTTGATAGATGGAATTCTCCATTAACAAAAA
1 AGACAAGACTAAATTTGATAGATGGAATTCTCCATT---AAAAA
1687797 AGGACAAGACTAA
1 A-GACAAGACTAA
1687810 CTTTCTCGGC
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
41 62 0.81
42 1 0.01
44 5 0.06
45 9 0.12
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (41 bp):
AGACAAGACTAAATTTGATAGATGGAATTCTCCATTAAAAA
Found at i:1688338 original size:22 final size:22
Alignment explanation
Indices: 1688308--1688374 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1688298 TATGAACACG
*
1688308 ATAACAATAATTAAAATATAAT
1 ATAAAAATAATTAAAATATAAT
*
1688330 ATAAAAATAA-TATAATATAAAT
1 ATAAAAATAATTAAAATAT-AAT
* *
1688352 ATATAAATTTATTAATAATATAA
1 ATA-AAAATAATTAA-AATATAA
1688375 ATTATAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 7 0.19
22 15 0.42
23 5 0.14
24 4 0.11
25 5 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAAATAATTAAAATATAAT
Found at i:1689458 original size:19 final size:19
Alignment explanation
Indices: 1689405--1689461 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
1689395 TTTAATCTAA
* *
1689405 TTAATAAATTAAGCTCAA-
1 TTAATAATTTGAGCTCAAT
* * * *
1689423 ATAATGATATGAACTCAAT
1 TTAATAATTTGAGCTCAAT
1689442 TTAATAATTTGAGCTCAAT
1 TTAATAATTTGAGCTCAAT
1689461 T
1 T
1689462 AACAACTCAA
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.37
Consensus pattern (19 bp):
TTAATAATTTGAGCTCAAT
Found at i:1689560 original size:21 final size:21
Alignment explanation
Indices: 1689534--1689584 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1689524 AAGTTTCAAT
* *
1689534 TAAAAAATTAAACTTAATTAA
1 TAAAAAATTAAACGTAACTAA
* * *
1689555 TAAAAAAATCATCGTAACTAA
1 TAAAAAATTAAACGTAACTAA
1689576 TAAAAAATT
1 TAAAAAATT
1689585 TAAAATAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAACGTAACTAA
Found at i:1691181 original size:29 final size:29
Alignment explanation
Indices: 1691139--1691198 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1691129 AAATAAAAAC
1691139 AATACTTTTAATGTCAATATACATGAGAT
1 AATACTTTTAATGTCAATATACATGAGAT
1691168 AATACTTTTAATGTCAATATACATGAGAT
1 AATACTTTTAATGTCAATATACATGAGAT
1691197 AA
1 AA
1691199 CGATCAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (29 bp):
AATACTTTTAATGTCAATATACATGAGAT
Found at i:1691414 original size:16 final size:16
Alignment explanation
Indices: 1691367--1691405 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1691357 CAATTGAAAG
*
1691367 AAATTTAAATCGTTTT
1 AAATTTAAATCATTTT
1691383 AAATTTAAATCATTTT
1 AAATTTAAATCATTTT
1691399 AAATTTA
1 AAATTTA
1691406 CATTATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (16 bp):
AAATTTAAATCATTTT
Found at i:1691454 original size:16 final size:16
Alignment explanation
Indices: 1691435--1691469 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1691425 TTTTTATTTA
1691435 TAAAATTAAATTAATT
1 TAAAATTAAATTAATT
* *
1691451 TAAATTTAAATTATTT
1 TAAAATTAAATTAATT
1691467 TAA
1 TAA
1691470 GTTATCCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAAATTAAATTAATT
Found at i:1691747 original size:8 final size:8
Alignment explanation
Indices: 1691734--1691763 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1691724 AAAAAGGCCT
1691734 TTTTTTTG
1 TTTTTTTG
1691742 TTTTTTTG
1 TTTTTTTG
1691750 TTTTTTT-
1 TTTTTTTG
1691757 TTTTTTT
1 TTTTTTT
1691764 TTGGCAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1691755 original size:15 final size:14
Alignment explanation
Indices: 1691733--1691765 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1691723 CAAAAAGGCC
1691733 TTTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
1691747 TTGTTTTTT-TTTTT
1 TT-TTTTTTGTTTTT
1691761 TTTTT
1 TTTTT
1691766 GGCAGAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 9 0.50
15 6 0.33
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (14 bp):
TTTTTTTTGTTTTT
Found at i:1691755 original size:16 final size:15
Alignment explanation
Indices: 1691734--1691763 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1691724 AAAAAGGCCT
1691734 TTTTTTTGTTTTTTTG
1 TTTTTTT-TTTTTTTG
1691750 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
1691764 TTGGCAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:1691755 original size:17 final size:17
Alignment explanation
Indices: 1691733--1691766 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1691723 CAAAAAGGCC
1691733 TTTTTTTTGTTTTTTTG
1 TTTTTTTTGTTTTTTTG
*
1691750 TTTTTTTTTTTTTTTTG
1 TTTTTTTTGTTTTTTTG
1691767 GCAGAGAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTTG
Found at i:1693294 original size:17 final size:16
Alignment explanation
Indices: 1693274--1693322 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
1693264 TTTAAATACG
1693274 ATATAAAAATAATTAAA
1 ATATAAAAATAA-TAAA
* *
1693291 ATAT-TAAATAATATA
1 ATATAAAAATAATAAA
1693306 ATAT-AAAA-AATAAA
1 ATATAAAAATAATAAA
1693320 ATA
1 ATA
1693323 AATACAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.29
15 10 0.36
16 6 0.21
17 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAAAATAATAAA
Found at i:1693335 original size:23 final size:22
Alignment explanation
Indices: 1693287--1693335 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1693277 TAAAAATAAT
* * *
1693287 TAAAATATTAAATAATATAATA
1 TAAAAAATAAAATAATACAATA
1693309 TAAAAAATAAAATAAATACAATA
1 TAAAAAATAAAAT-AATACAATA
1693332 TAAA
1 TAAA
1693336 TATGTCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATAAAATAATACAATA
Found at i:1695695 original size:21 final size:21
Alignment explanation
Indices: 1695657--1695710 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1695647 ATAATAAAAT
*
1695657 ATTAAAAAT-TAT-TTTTAT-
1 ATTAAAATTATATATTTTATA
1695675 ATTAATAATTATATATTTTATA
1 ATTAA-AATTATATATTTTATA
*
1695697 ATTAAATTTATATA
1 ATTAAAATTATATA
1695711 AAAATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 3 0.10
21 14 0.47
22 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTAAAATTATATATTTTATA
Found at i:1695785 original size:11 final size:11
Alignment explanation
Indices: 1695769--1695807 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
1695759 TTGAATATAA
1695769 AAATTTAAATT
1 AAATTTAAATT
1695780 AAATTTAAATT
1 AAATTTAAATT
1695791 AAATTTAAATT
1 AAATTTAAATT
1695802 -AATTTA
1 AAATTTA
1695808 TTAAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 6 0.21
11 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:1695787 original size:6 final size:6
Alignment explanation
Indices: 1695769--1695801 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1695759 TTGAATATAA
1695769 AAATTT AAA-TT AAATTT AAA-TT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
1695802 AATTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:1696047 original size:8 final size:8
Alignment explanation
Indices: 1696036--1696090 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
1696026 TATTAAATAT
1696036 TTAAAAAA
1 TTAAAAAA
*
1696044 TTAAAAAT
1 TTAAAAAA
* *
1696052 TTTATAAA
1 TTAAAAAA
1696060 TTAAAAAA
1 TTAAAAAA
*
1696068 TTAAAAAT
1 TTAAAAAA
* *
1696076 TTTATAAA
1 TTAAAAAA
1696084 TTAAAAA
1 TTAAAAA
1696091 TTTTAATTTA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1696048 original size:16 final size:16
Alignment explanation
Indices: 1696027--1696074 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1696017 AAGATATATT
*
1696027 ATTAAATATTTAAAAA
1 ATTAAAAATTTAAAAA
* *
1696043 ATTAAAAATTTTATAA
1 ATTAAAAATTTAAAAA
*
1696059 ATTAAAAAATTAAAAA
1 ATTAAAAATTTAAAAA
1696075 TTTTATAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAAAATTTAAAAA
Found at i:1696064 original size:24 final size:24
Alignment explanation
Indices: 1696036--1696090 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1696026 TATTAAATAT
1696036 TTAAAAAATTAAAAATTTTATAAA
1 TTAAAAAATTAAAAATTTTATAAA
1696060 TTAAAAAATTAAAAATTTTATAAA
1 TTAAAAAATTAAAAATTTTATAAA
1696084 TTAAAAA
1 TTAAAAA
1696091 TTTTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAAAATTAAAAATTTTATAAA
Found at i:1696084 original size:16 final size:16
Alignment explanation
Indices: 1696065--1696095 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1696055 ATAAATTAAA
1696065 AAATTAAAAATTTTAT
1 AAATTAAAAATTTTAT
1696081 AAATTAAAAATTTTA
1 AAATTAAAAATTTTA
1696096 ATTTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTAAAAATTTTAT
Found at i:1696935 original size:16 final size:17
Alignment explanation
Indices: 1696905--1696949 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
1696895 TGATAAAAAT
1696905 AATTTAAATATAATTTA
1 AATTTAAATATAATTTA
1696922 AATTTAAA-ATAATTT-
1 AATTTAAATATAATTTA
*
1696937 AATATAAATATAA
1 AATTTAAATATAA
1696950 AAATTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 7 0.27
16 11 0.42
17 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAATATAATTTA
Found at i:1696956 original size:19 final size:19
Alignment explanation
Indices: 1696932--1696977 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1696922 AATTTAAAAT
1696932 AATTTAAT-ATAAATATAAA
1 AATTTAATAAT-AATATAAA
*
1696951 AATTTATTAATAATATAAA
1 AATTTAATAATAATATAAA
1696970 AATATTAA
1 AAT-TTAA
1696978 CATATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTAATAATAATATAAA
Found at i:1697045 original size:23 final size:23
Alignment explanation
Indices: 1697002--1697046 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1696992 CGATTTTAAT
* * *
1697002 ATATCAAAGTATATGATCATGAC
1 ATATCAAAATATATAAACATGAC
1697025 ATATCAAAATATATAAACATGA
1 ATATCAAAATATATAAACATGA
1697047 TATAAATAAA
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:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (23 bp):
ATATCAAAATATATAAACATGAC
Found at i:1700271 original size:10 final size:10
Alignment explanation
Indices: 1700248--1700340 Score: 55
Period size: 11 Copynumber: 9.0 Consensus size: 10
1700238 TACGATATGA
*
1700248 AAAAAATAATT
1 AAAATATAA-T
*
1700259 AAAATTTAAT
1 AAAATATAAT
*
1700269 AAAATTTAATT
1 AAAATATAA-T
* *
1700280 AAAAAATAAC
1 AAAATATAAT
1700290 ATAAATATAAT
1 A-AAATATAAT
*
1700301 AAAAATATATT
1 -AAAATATAAT
*
1700312 AAAAT-TTAT
1 AAAATATAAT
*
1700321 ATAATATAAT
1 AAAATATAAT
1700331 ATAAAT-TAAT
1 A-AAATATAAT
1700341 TATAAATATC
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
9 6 0.09
10 24 0.38
11 33 0.52
12 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATATAAT
Found at i:1701112 original size:2 final size:2
Alignment explanation
Indices: 1701105--1701133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1701095 CCCAAACTAA
1701105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1701134 GTTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1703460 original size:15 final size:15
Alignment explanation
Indices: 1703432--1703470 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1703422 CTCTTTTTTT
*
1703432 TTATTTAATTTTTTAA
1 TTATTT-ATCTTTTAA
*
1703448 TTATTTATCTTTTAG
1 TTATTTATCTTTTAA
1703463 TTATTTAT
1 TTATTTAT
1703471 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTTATCTTTTAA
Found at i:1704520 original size:16 final size:15
Alignment explanation
Indices: 1704491--1704538 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1704481 GATTTATAAA
1704491 TAAATTTTAAAAAAT
1 TAAATTTTAAAAAAT
*
1704506 TAAATTTTAAAAAAA
1 TAAATTTTAAAAAAT
*
1704521 T-AA-TTTAAAATAT
1 TAAATTTTAAAAAAT
1704534 TAAAT
1 TAAAT
1704539 AATTTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 9 0.32
14 4 0.14
15 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATTTTAAAAAAT
Found at i:1705728 original size:17 final size:18
Alignment explanation
Indices: 1705708--1705750 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1705698 AAAATTAAAT
*
1705708 TAATTTTAAATAT-TTTA
1 TAATTTTAAATATGATTA
*
1705725 TAATTTTTAATATGATTA
1 TAATTTTAAATATGATTA
1705743 T-ATTTTAA
1 TAATTTTAA
1705751 TAAGTTGTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TAATTTTAAATATGATTA
Found at i:1707894 original size:2 final size:2
Alignment explanation
Indices: 1707887--1707916 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1707877 ATTCATGAAG
1707887 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1707917 AAGATTGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1708781 original size:12 final size:12
Alignment explanation
Indices: 1708758--1708792 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1708748 TTTATATCAG
*
1708758 TTTTATTCTTTT
1 TTTTATTATTTT
1708770 TTTT-TTATTTT
1 TTTTATTATTTT
1708781 TTTTATTATTTT
1 TTTTATTATTTT
1708793 GCATGAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:1708934 original size:21 final size:21
Alignment explanation
Indices: 1708908--1708957 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1708898 AATAAAAAAG
* *
1708908 GAATTTGGCAAGCATATTTAT
1 GAATTTGGCAAGAATATTGAT
*
1708929 GAATTTGGCATGAATATTGAT
1 GAATTTGGCAAGAATATTGAT
*
1708950 TAATTTGG
1 GAATTTGG
1708958 ACCATTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (21 bp):
GAATTTGGCAAGAATATTGAT
Found at i:1709992 original size:5 final size:5
Alignment explanation
Indices: 1709984--1710028 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
1709974 AGAAAATAAA
*
1709984 AAAAG AAAAAG AAAAG AAAAG AAAAG AAAAG AAAGG AAAAAG AAA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAA
1710029 TATAGCAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 27 0.75
6 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1710010 original size:15 final size:16
Alignment explanation
Indices: 1709984--1710028 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
1709974 AGAAAATAAA
1709984 AAAAGAAAAAGAAAAG
1 AAAAGAAAAAGAAAAG
1710000 AAAAG-AAAAGAAAAG
1 AAAAGAAAAAGAAAAG
*
1710015 AAAGGAAAAAGAAA
1 AAAAGAAAAAGAAA
1710029 TATAGCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:1710766 original size:2 final size:2
Alignment explanation
Indices: 1710754--1710783 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1710744 AACTATCAAT
*
1710754 TA TA TA AA 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
1710784 ACATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1711274 original size:12 final size:11
Alignment explanation
Indices: 1711257--1711298 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
1711247 TCTTTCTTTC
1711257 TTGTTTTTGGTT
1 TTGTTTTT-GTT
1711269 TTGTTTTTGTT
1 TTGTTTTTGTT
1711280 TT-TTTTT-TT
1 TTGTTTTTGTT
*
1711289 TTTTTTTTGT
1 TTGTTTTTGT
1711299 GTCTTAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.14
10 10 0.36
11 6 0.21
12 8 0.29
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTGTTTTTGTT
Found at i:1711276 original size:6 final size:6
Alignment explanation
Indices: 1711257--1711296 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1711247 TCTTTCTTTC
*
1711257 TTGTTT TTGGTT TTGTTT TTGTTT TT-TTT TT-TTT TT-TTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT T
1711297 GTGTCTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTGTTT
Found at i:1714134 original size:11 final size:11
Alignment explanation
Indices: 1714118--1714165 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
1714108 ATAAATTAAA
1714118 TTTTATTATAT
1 TTTTATTATAT
*
1714129 TTTTATTTTTAT
1 TTTTA-TTATAT
1714141 TTTTAATTA-ATT
1 TTTT-ATTATA-T
1714153 TTTTATTATAT
1 TTTTATTATAT
1714164 TT
1 TT
1714166 AAAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 13 0.42
12 17 0.55
13 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:1714165 original size:12 final size:12
Alignment explanation
Indices: 1714118--1714165 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
1714108 ATAAATTAAA
1714118 TTTTATTATA-T
1 TTTTATTATATT
*
1714129 TTTTATTTTTATT
1 TTTTA-TTATATT
*
1714142 TTTAATTA-ATT
1 TTTTATTATATT
1714153 TTTTATTATATT
1 TTTTATTATATT
1714165 T
1 T
1714166 AAAAATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 15 0.50
12 10 0.33
13 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATTATATT
Found at i:1714281 original size:6 final size:6
Alignment explanation
Indices: 1714270--1714306 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
1714260 ATAAATAAGA
1714270 TTATTT TTATTT TTATTTT TTATTTT TTATTT TTATT
1 TTATTT TTATTT TTA-TTT TTA-TTT TTATTT TTATT
1714307 ATATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:1714289 original size:7 final size:7
Alignment explanation
Indices: 1714273--1714303 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1714263 AATAAGATTA
1714273 TTTTTA-
1 TTTTTAT
1714279 TTTTTAT
1 TTTTTAT
1714286 TTTTTAT
1 TTTTTAT
1714293 TTTTTAT
1 TTTTTAT
1714300 TTTT
1 TTTT
1714304 ATTATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:1714313 original size:14 final size:13
Alignment explanation
Indices: 1714269--1714314 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1714259 AATAAATAAG
1714269 ATTATTTTTATTT
1 ATTATTTTTATTT
1714282 -TTATTTTTTATTT
1 ATTA-TTTTTATTT
*
1714295 TTTATTTTTATTAT
1 ATTATTTTTATT-T
1714309 ATTATT
1 ATTATT
1714315 ATTACGGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.10
13 17 0.59
14 9 0.31
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:1714744 original size:21 final size:20
Alignment explanation
Indices: 1714718--1714766 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
1714708 AATTACGATT
1714718 TAATTTAAATTTTAATATTTA
1 TAATTTAAATTTTAATA-TTA
** *
1714739 TAATTTTTTATTTTTATATTA
1 TAA-TTTAAATTTTAATATTA
1714760 TAATTTA
1 TAATTTA
1714767 CTTGATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATTTAAATTTTAATATTA
Found at i:1715851 original size:1 final size:1
Alignment explanation
Indices: 1715845--1715869 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1715835 ATCAAATCTT
1715845 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1715870 GGCCTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1716927 original size:78 final size:79
Alignment explanation
Indices: 1716772--1716935 Score: 303
Period size: 78 Copynumber: 2.1 Consensus size: 79
1716762 TAAATTAATT
1716772 TATTTTAAATAACTATTTATATAATAAAAATATTTTAAAAAATTAATTAAAATTATAATAATAAT
1 TATTTTAAATAACTATTTATATAATAAAAATATTTTAAAAAATTAATTAAAATTATAATAATAAT
1716837 TATTATTATACAAG
66 TATTATTATACAAG
* *
1716851 TATTTTGAATAACTATTTATATAATAAAAATATTTT-AAAAATTAATTAAAATTATAATAATTAT
1 TATTTTAAATAACTATTTATATAATAAAAATATTTTAAAAAATTAATTAAAATTATAATAATAAT
1716915 TATTATTATACAAG
66 TATTATTATACAAG
1716929 TATTTTA
1 TATTTTA
1716936 GATTTTTAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
78 47 0.57
79 35 0.43
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (79 bp):
TATTTTAAATAACTATTTATATAATAAAAATATTTTAAAAAATTAATTAAAATTATAATAATAAT
TATTATTATACAAG
Found at i:1717589 original size:19 final size:19
Alignment explanation
Indices: 1717548--1717615 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
1717538 GATTTGATTC
* *
1717548 ATTTAAATATTTAAAAATTT
1 ATTTTAATATTT-AAAATAT
*
1717568 ATTTTATTATTTAAAATAT
1 ATTTTAATATTTAAAATAT
**
1717587 ATTAAAATA-TTAAAATAT
1 ATTTTAATATTTAAAATAT
*
1717605 ATTTTTATATT
1 ATTTTAATATT
1717616 AATATTTATA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 15 0.39
19 13 0.34
20 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATATTTAAAATAT
Found at i:1717594 original size:29 final size:29
Alignment explanation
Indices: 1717539--1717594 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1717529 TTTTATTTAG
*
1717539 ATTTGATTCATTTAAATATTTAAAAATTT
1 ATTTGATTCATTTAAATATATAAAAATTT
* *
1717568 ATTTTATT-ATTTAAAATATATTAAAAT
1 ATTTGATTCATTT-AAATATATAAAAAT
1717595 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
ATTTGATTCATTTAAATATATAAAAATTT
Found at i:1717614 original size:18 final size:18
Alignment explanation
Indices: 1717574--1717640 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
1717564 ATTTATTTTA
*
1717574 TTAT-TTAAAATATATTA
1 TTATATTAAAATATATTT
**
1717591 AAATATTAAAATATATTT
1 TTATATTAAAATATATTT
1717609 TTATATTAATATTTATATATTT
1 TTATATTAA-A---ATATATTT
1717631 TTATAATTAA
1 TTAT-ATTAA
1717641 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 2 0.05
18 19 0.49
19 1 0.03
22 12 0.31
23 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATTAAAATATATTT
Done.