Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 14 of 318
Found at i:3643399 original size:18 final size:17
Alignment explanation
Indices: 3643358--3643399 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
3643348 AATTATTCTT
3643358 ATTTAATATTAATATTA
1 ATTTAATATTAATATTA
3643375 ATATTAATATTAATATTAA
1 AT-TTAATATTAATATT-A
3643394 ATTTAA
1 ATTTAA
3643400 ATTTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.09
18 18 0.78
19 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATATTAATATTA
Found at i:3643411 original size:6 final size:6
Alignment explanation
Indices: 3643360--3643393 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3643350 TTATTCTTAT
3643360 TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
3643394 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:3643799 original size:21 final size:20
Alignment explanation
Indices: 3643765--3643806 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3643755 TTTCAAAATT
3643765 ATTTTAATTATTATATATATA
1 ATTTTAATTATTATATA-ATA
* *
3643786 ATTTTTATTTTTATATAATA
1 ATTTTAATTATTATATAATA
3643806 A
1 A
3643807 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTAATTATTATATAATA
Found at i:3650984 original size:29 final size:30
Alignment explanation
Indices: 3650937--3651004 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3650927 TGGCCCAAGA
* *
3650937 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
3650967 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
3650997 GCAAATAT
1 GTAAATAT
3651005 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:3653430 original size:46 final size:46
Alignment explanation
Indices: 3653373--3653646 Score: 406
Period size: 46 Copynumber: 6.0 Consensus size: 46
3653363 AGTGTGTTCT
* * * *
3653373 CTGAAATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
*
3653419 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
*
3653465 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
*
3653511 CTAATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
* *
3653557 CTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
* * * * *
3653603 ATGATA-GAAAATGAGTAAGACGATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGACACCATGGCA
3653647 TCATGTCAAA
Statistics
Matches: 210, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 209 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
Found at i:3655103 original size:51 final size:51
Alignment explanation
Indices: 3655032--3655258 Score: 242
Period size: 51 Copynumber: 4.5 Consensus size: 51
3655022 TCTTCAAGTT
* * * *
3655032 CTTTATTCGGGTTACTTAGGGGTGCTCCTATGTCCACTTCTCCGCAAGATA
1 CTTTATTCGGGTTACATAGGGGTTCTCCTGTGTCCACTTCTCCGCAAGCTA
* *
3655083 CTTTCTTCGGGTTACATAGGGGTTCAT-CTGTGTCCACTTCTCCGCAAGGTA
1 CTTTATTCGGGTTACATAGGGGTTC-TCCTGTGTCCACTTCTCCGCAAGCTA
* ** * * * *
3655134 CTTT-CTCTGGGTTACATAGAAGTTCACTTGTGTCCACTTCTCTGCCAGCTA
1 CTTTATTC-GGGTTACATAGGGGTTCTCCTGTGTCCACTTCTCCGCAAGCTA
* * * * * *
3655185 CTTTATCCAGGTTACATAGGGGTTCTCCTGTATTCGCTTCTCCTCAAGCTA
1 CTTTATTCGGGTTACATAGGGGTTCTCCTGTGTCCACTTCTCCGCAAGCTA
*
3655236 CTTTATTCGGGTTACTTAGGGGT
1 CTTTATTCGGGTTACATAGGGGT
3655259 GCTTCTGAGT
Statistics
Matches: 143, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
50 2 0.01
51 139 0.97
52 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (51 bp):
CTTTATTCGGGTTACATAGGGGTTCTCCTGTGTCCACTTCTCCGCAAGCTA
Found at i:3655286 original size:51 final size:50
Alignment explanation
Indices: 3655179--3655286 Score: 110
Period size: 51 Copynumber: 2.1 Consensus size: 50
3655169 ACTTCTCTGC
* * *
3655179 CAGCTACTTTATCCAGGTTACATAGGGGTTCTCCTGTATTCGCTTCTCCT
1 CAGCTACTTTATCCAGGTTACATAGGGGTGCTCCTGTAGTCGCTCCTCCT
* * * * *
3655229 CAAGCTACTTTATTCGGGTTACTTAGGGGTGCTTCTG-AGTCAGCTCCTCTTT
1 C-AGCTACTTTATCCAGGTTACATAGGGGTGCTCCTGTAGTC-GCTCCTC-CT
3655281 CAGCTA
1 CAGCTA
3655287 TTGCGCCACT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
50 4 0.09
51 41 0.87
52 2 0.04
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (50 bp):
CAGCTACTTTATCCAGGTTACATAGGGGTGCTCCTGTAGTCGCTCCTCCT
Found at i:3657208 original size:62 final size:61
Alignment explanation
Indices: 3657087--3657209 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 61
3657077 ATGTATTAAA
* *
3657087 TACTTTTTTTCATCCAGATGAAATACATACAAGATTTCCTCTTCAATTCCATTTTGCCATT
1 TACTTTTCTTCATCCAGATGAAATACATACAAGATTTCCTCTTCAACTCCATTTTGCCATT
* *
3657148 TACTTTTCTTCATCCAGATGAAATACAATTCAAGATTTCCTCTTCAACTCCTTTTTGCCATT
1 TACTTTTCTTCATCCAGATGAAATAC-ATACAAGATTTCCTCTTCAACTCCATTTTGCCATT
3657210 GTTAACACCC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
61 25 0.44
62 32 0.56
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (61 bp):
TACTTTTCTTCATCCAGATGAAATACATACAAGATTTCCTCTTCAACTCCATTTTGCCATT
Found at i:3661218 original size:16 final size:16
Alignment explanation
Indices: 3661181--3661222 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3661171 TGTTGTGACT
**
3661181 TTAATAAAAGTATTAA
1 TTAATAAAAAAATTAA
*
3661197 TT-ATAAAAAAATTAG
1 TTAATAAAAAAATTAA
3661212 TTAATAAAAAA
1 TTAATAAAAAA
3661223 TCATAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TTAATAAAAAAATTAA
Found at i:3665569 original size:18 final size:18
Alignment explanation
Indices: 3665546--3665580 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3665536 TATTTGAGCA
3665546 TTTAATCATTATGTAATG
1 TTTAATCATTATGTAATG
*
3665564 TTTAATCCTTATGTAAT
1 TTTAATCATTATGTAAT
3665581 CAACCTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTAATCATTATGTAATG
Found at i:3669997 original size:12 final size:11
Alignment explanation
Indices: 3669978--3670026 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
3669968 CAATAAGCAG
3669978 AACAAAAAAGAA
1 AACAAAAAA-AA
* *
3669990 AA-ACAAAACA
1 AACAAAAAAAA
3670000 AACAAAAAAAA
1 AACAAAAAAAA
3670011 AAGCAAAAAAAA
1 AA-CAAAAAAAA
3670023 AACA
1 AACA
3670027 CGGAAGGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 3 0.10
11 15 0.48
12 13 0.42
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (11 bp):
AACAAAAAAAA
Found at i:3670019 original size:22 final size:22
Alignment explanation
Indices: 3669978--3670018 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3669968 CAATAAGCAG
3669978 AACAAAAAAGAAAAACAAAACA
1 AACAAAAAAGAAAAACAAAACA
*
3670000 AACAAAAAA-AAAAGCAAAA
1 AACAAAAAAGAAAAACAAAA
3670019 AAAAAACACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (22 bp):
AACAAAAAAGAAAAACAAAACA
Found at i:3671988 original size:26 final size:26
Alignment explanation
Indices: 3671927--3671980 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3671917 ATAGAAGAAA
3671927 ATAAAGTGATAATCATTAACCAAAAT
1 ATAAAGTGATAATCATTAACCAAAAT
3671953 ATAAAGTGATAATCATTAACCAAAAT
1 ATAAAGTGATAATCATTAACCAAAAT
3671979 AT
1 AT
3671981 TTGTTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (26 bp):
ATAAAGTGATAATCATTAACCAAAAT
Found at i:3672689 original size:40 final size:40
Alignment explanation
Indices: 3672645--3672720 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
3672635 ACAGATATAA
* * *
3672645 TACATATTCAAGTACAATGTATATACAAATATACAAGGGT
1 TACATATACAAATACAATATATATACAAATATACAAGGGT
* * *
3672685 TACATATAGAAATACAATATATGTATAAATATACAA
1 TACATATACAAATACAATATATATACAAATATACAA
3672721 AGGTGAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (40 bp):
TACATATACAAATACAATATATATACAAATATACAAGGGT
Found at i:3673965 original size:22 final size:22
Alignment explanation
Indices: 3673920--3673965 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3673910 TATTAGCACA
* * **
3673920 AAAAAATTTAGGTACCAATTTG
1 AAAAAATGTAGATACCAAAGTG
3673942 AAAAAATGTAGATACCAAAGTG
1 AAAAAATGTAGATACCAAAGTG
3673964 AA
1 AA
3673966 GATTGAAGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (22 bp):
AAAAAATGTAGATACCAAAGTG
Found at i:3682919 original size:30 final size:31
Alignment explanation
Indices: 3682883--3682942 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3682873 TTAGCAACTC
* * *
3682883 AATGACTTGAAT-GAAATTTTTGAATAGTTT
1 AATGACTTAAATAAAAATTTTCGAATAGTTT
3682913 AATGACTTAAATAAAAATTTTCGAATAGTT
1 AATGACTTAAATAAAAATTTTCGAATAGTT
3682943 CACTGGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTTTCGAATAGTTT
Found at i:3683252 original size:7 final size:7
Alignment explanation
Indices: 3683240--3683265 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3683230 TATAACCCTA
3683240 TAAATTT
1 TAAATTT
3683247 TAAATTT
1 TAAATTT
3683254 TAAATTT
1 TAAATTT
3683261 TAAAT
1 TAAAT
3683266 GGTCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAAATTT
Found at i:3691497 original size:26 final size:27
Alignment explanation
Indices: 3691446--3691497 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3691436 TTAAAGATAG
*
3691446 ACTTAAACAAAAAAAATTCACGACCTA
1 ACTTAAACAAAAAAAATTCACAACCTA
*
3691473 ACTTAAATAAAAAAAATTCA-AACCT
1 ACTTAAACAAAAAAAATTCACAACCT
3691498 CCAAAAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.21
Consensus pattern (27 bp):
ACTTAAACAAAAAAAATTCACAACCTA
Found at i:3692008 original size:139 final size:139
Alignment explanation
Indices: 3691758--3692042 Score: 561
Period size: 139 Copynumber: 2.1 Consensus size: 139
3691748 GAGTTACCAT
3691758 AATTTTTGAAGAGGTTAAATGGCAGACTTACCATTTTTAGGACCCCTTTGTTTACGCCCTCGTTG
1 AATTTTTGAAGAGGTTAAATGGCAGACTTACCATTTTTAGGACCCCTTTGTTTACGCCCTCGTTG
3691823 CCATGCTTAAACTCTTCAATTTCTGTAGTTTAATTTGTTCACAACTGTTCATGACTCTTATCATG
66 CCATGCTTAAACTCTTCAATTTCTGTAGTTTAATTTGTTCACAACTGTTCATGACTCTTATCATG
3691888 ACCACACTA
131 ACCACACTA
3691897 AATTTTTGAAGAGGTTAAATGGCAGACTTACCATTTTTAGGACCCCTTTGTTTACGCCCTCGTTG
1 AATTTTTGAAGAGGTTAAATGGCAGACTTACCATTTTTAGGACCCCTTTGTTTACGCCCTCGTTG
3691962 CCATGCTTAAACTCTTCAATTTCTGTAGTTTAATTTGTTCACAACTGTTCATGACTCTTATCATG
66 CCATGCTTAAACTCTTCAATTTCTGTAGTTTAATTTGTTCACAACTGTTCATGACTCTTATCATG
3692027 ACCACACTA
131 ACCACACTA
*
3692036 AAATTTT
1 AATTTTT
3692043 AAGCTCTCAA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 145 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (139 bp):
AATTTTTGAAGAGGTTAAATGGCAGACTTACCATTTTTAGGACCCCTTTGTTTACGCCCTCGTTG
CCATGCTTAAACTCTTCAATTTCTGTAGTTTAATTTGTTCACAACTGTTCATGACTCTTATCATG
ACCACACTA
Found at i:3692634 original size:37 final size:37
Alignment explanation
Indices: 3692584--3692655 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
3692574 TCATTGTTAA
*
3692584 TTCAACTGCTGCAAAAGATATGGTTGGTTGATTCATT
1 TTCAACTGCTGCAAAAGATATGGTTGATTGATTCATT
3692621 TTCAACTGCTGCAAAAGATATGGTTGATTGATTCA
1 TTCAACTGCTGCAAAAGATATGGTTGATTGATTCA
3692656 CTAAAGTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (37 bp):
TTCAACTGCTGCAAAAGATATGGTTGATTGATTCATT
Found at i:3698735 original size:12 final size:12
Alignment explanation
Indices: 3698720--3698757 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
3698710 GAAAATAAAG
3698720 ACAAAAAAAGAA
1 ACAAAAAAAGAA
3698732 ACAAAGAAAAGAA
1 ACAAA-AAAAGAA
3698745 A-AGAAAAAAGAA
1 ACA-AAAAAAGAA
3698757 A
1 A
3698758 AGCAAATGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (12 bp):
ACAAAAAAAGAA
Found at i:3698746 original size:18 final size:17
Alignment explanation
Indices: 3698716--3698759 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
3698706 TATTGAAAAT
3698716 AAAGACAAA-AAAAGAAA
1 AAAGA-AAAGAAAAGAAA
3698733 CAAAGAAAAGAAAAGAAA
1 -AAAGAAAAGAAAAGAAA
3698751 AAAGAAAAG
1 AAAGAAAAG
3698760 CAAATGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.80, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAAGAAA
Found at i:3699550 original size:8 final size:8
Alignment explanation
Indices: 3699537--3699564 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3699527 AATAGGGTAT
3699537 TATATTCA
1 TATATTCA
3699545 TATATTCA
1 TATATTCA
3699553 TATATTCA
1 TATATTCA
3699561 TATA
1 TATA
3699565 ATTAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATTCA
Found at i:3699600 original size:20 final size:19
Alignment explanation
Indices: 3699561--3699616 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 19
3699551 CATATATTCA
3699561 TATAATTAAATCAAGTTAT
1 TATAATTAAATCAAGTTAT
3699580 TATAATTACAATCAA-TATATT
1 TATAATTA-AATCAAGT-TA-T
3699601 CATATAATTAAATCAA
1 --TATAATTAAATCAA
3699617 AATCAAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 9 0.28
20 8 0.25
21 1 0.03
22 6 0.19
23 8 0.25
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (19 bp):
TATAATTAAATCAAGTTAT
Found at i:3699656 original size:48 final size:47
Alignment explanation
Indices: 3699568--3699660 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 47
3699558 TCATATAATT
* *
3699568 AAATCAAGTTATTATAATTACAATCAATATATTCATATAATTAAATCA
1 AAATCAAGTTATTATAATTACAATAAATATATT-AGATAATTAAATCA
3699616 AAATCAAGTTATTATAATTTACAAATAAATGA-ATT-GATAATTAAA
1 AAATCAAGTTATTATAA-TTAC-AATAAAT-ATATTAGATAATTAAA
3699661 ATATATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
48 26 0.65
49 4 0.10
50 9 0.22
51 1 0.03
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (47 bp):
AAATCAAGTTATTATAATTACAATAAATATATTAGATAATTAAATCA
Found at i:3707679 original size:93 final size:93
Alignment explanation
Indices: 3707567--3707737 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
3707557 GCCCATAAGT
* *
3707567 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3707632 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
3707660 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3707725 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3707738 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:3707734 original size:46 final size:46
Alignment explanation
Indices: 3707559--3707734 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
3707549 TGTAACCCGC
* *
3707559 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
3707605 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
3707651 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
3707698 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
3707735 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:3710128 original size:15 final size:15
Alignment explanation
Indices: 3710096--3710163 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
3710086 CAAAGATAAC
3710096 AAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
3710109 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
3710124 GAGAAATCCAGAATA
1 AAGAAATCCAGAATA
3710139 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
3710154 AAGAAATCCA
1 AAGAAATCCA
3710164 AGATACGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.12
14 3 0.06
15 39 0.80
16 1 0.02
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:3713166 original size:46 final size:46
Alignment explanation
Indices: 3713099--3713269 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 46
3713089 TGTAACCCGC
* * *
3713099 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * * *
3713145 CCATAAGTGAACTCGG-----ACTCAACGAGTTCGGATACCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACA-TTTGCAT
* *** *
3713186 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
3713233 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3713270 TGCTCAACCA
Statistics
Matches: 98, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
41 19 0.19
42 10 0.10
46 47 0.48
47 22 0.22
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:3713288 original size:46 final size:45
Alignment explanation
Indices: 3713195--3713280 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
3713185 TACATCTCTC
* *
3713195 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
*
3713241 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCAT
3713281 CCTAGTGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 9 0.24
46 28 0.76
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:3721203 original size:3 final size:3
Alignment explanation
Indices: 3721195--3721228 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3721185 ATAAACTTTT
3721195 AGA AGA AGA AGA AGA AGA AGA AGA A-A A-A AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3721229 CATAATTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3731684 original size:18 final size:18
Alignment explanation
Indices: 3731661--3731697 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3731651 TATGTATTAT
3731661 TTATTTAAAACTGTTTCA
1 TTATTTAAAACTGTTTCA
* *
3731679 TTATTTTAAATTGTTTCA
1 TTATTTAAAACTGTTTCA
3731697 T
1 T
3731698 ATACCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (18 bp):
TTATTTAAAACTGTTTCA
Found at i:3733950 original size:10 final size:10
Alignment explanation
Indices: 3733937--3733969 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3733927 CATCATGTTG
3733937 CATTGCATTA
1 CATTGCATTA
3733947 CATTGCATTA
1 CATTGCATTA
*
3733957 CA-TGCATCA
1 CATTGCATTA
3733966 CATT
1 CATT
3733970 AATTAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (10 bp):
CATTGCATTA
Found at i:3738574 original size:16 final size:16
Alignment explanation
Indices: 3738551--3738589 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3738541 TTAATCAAAA
3738551 AGAA-AAAGAGAAA-G
1 AGAAGAAAGAGAAAGG
3738565 AGGAAGAAAGAGAAAGG
1 A-GAAGAAAGAGAAAGG
3738582 AGAAGAAA
1 AGAAGAAA
3738590 TAAAATTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 3 0.14
16 16 0.73
17 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AGAAGAAAGAGAAAGG
Found at i:3746547 original size:65 final size:65
Alignment explanation
Indices: 3746436--3746561 Score: 191
Period size: 65 Copynumber: 1.9 Consensus size: 65
3746426 AGATAACTCA
* *
3746436 TTTCTTTAAAGCAAATTTAGATAACACACTTATTTAAAATGGCTTTACCTCTTTAAGGTAACATG
1 TTTCTTTAAAGCAAATCTAGATAACACACTTATTTAAAATGACTTTACCTCTTTAAGGTAACATG
* * *
3746501 TTTCTTTAAAGCAGAA-CTAGATAGCACACTTCTTTAAAGTGACTTTACCTCTTTAAGGTAA
1 TTTCTTTAAAGCA-AATCTAGATAACACACTTATTTAAAATGACTTTACCTCTTTAAGGTAA
3746562 TACATTTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 53 0.96
66 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (65 bp):
TTTCTTTAAAGCAAATCTAGATAACACACTTATTTAAAATGACTTTACCTCTTTAAGGTAACATG
Found at i:3746574 original size:65 final size:65
Alignment explanation
Indices: 3746429--3746575 Score: 188
Period size: 65 Copynumber: 2.3 Consensus size: 65
3746419 TCCTTAAAGA
* * *
3746429 TAACTCATTTCTTTAAAGCAAATTTAGATAACACACTTATTTAAAATGGCTTTACCTCTTTAAGG
1 TAACACATTTCTTTAAAGCAAATCTAGATAACACACTTATTTAAAATGACTTTACCTCTTTAAGG
** * * *
3746494 TAACATGTTTCTTTAAAGCAGAA-CTAGATAGCACACTTCTTTAAAGTGACTTTACCTCTTTAAG
1 TAACACATTTCTTTAAAGCA-AATCTAGATAACACACTTATTTAAAATGACTTTACCTCTTTAAG
3746558 G
65 G
* *
3746559 TAATACATTTATTTAAA
1 TAACACATTTCTTTAAA
3746576 CATGTTTATT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
65 67 0.97
66 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (65 bp):
TAACACATTTCTTTAAAGCAAATCTAGATAACACACTTATTTAAAATGACTTTACCTCTTTAAGG
Found at i:3752323 original size:42 final size:42
Alignment explanation
Indices: 3752277--3752358 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
3752267 TTGGGACACA
3752277 GCCATGTGACCT-AAGTCAGCGAGTTACACGGGCTAG-GACAAG
1 GCCATGTG-CCTCAAGTCAGCGAGTTACACGGG-TAGAGACAAG
* *
3752319 GCCATGTGTCTCAAGTCAGTGAGTTACACGGGTAGAGACA
1 GCCATGTGCCTCAAGTCAGCGAGTTACACGGGTAGAGACA
3752359 CGAGTTGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (42 bp):
GCCATGTGCCTCAAGTCAGCGAGTTACACGGGTAGAGACAAG
Found at i:3755118 original size:27 final size:27
Alignment explanation
Indices: 3755088--3755141 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3755078 CAGGAAAGTT
*
3755088 TATTTTTTAAGGAAAATAGATATGCAA
1 TATTTTTGAAGGAAAATAGATATGCAA
3755115 TATTTTTGAAGGAAAATAGATATGCAA
1 TATTTTTGAAGGAAAATAGATATGCAA
3755142 AGCCAGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (27 bp):
TATTTTTGAAGGAAAATAGATATGCAA
Found at i:3755429 original size:24 final size:24
Alignment explanation
Indices: 3755397--3755460 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
3755387 GTTGCCACAC
*
3755397 CCACTGCCACAACCACCACAACCG
1 CCACCGCCACAACCACCACAACCG
*
3755421 CCACCGCCACAACCGCCACAACCG
1 CCACCGCCACAACCACCACAACCG
3755445 CCACCGCCACAACCAC
1 CCACCGCCACAACCAC
3755461 TGTTCTCCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.31, C:0.58, G:0.09, T:0.02
Consensus pattern (24 bp):
CCACCGCCACAACCACCACAACCG
Found at i:3755435 original size:9 final size:9
Alignment explanation
Indices: 3755402--3755448 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
3755392 CACACCCACT
3755402 GCCACAACC
1 GCCACAACC
*
3755411 ACCACAACC
1 GCCACAACC
3755420 G-C-C-ACC
1 GCCACAACC
3755426 GCCACAACC
1 GCCACAACC
3755435 GCCACAACC
1 GCCACAACC
3755444 GCCAC
1 GCCAC
3755449 CGCCACAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 2 0.06
9 25 0.76
ACGTcount: A:0.32, C:0.57, G:0.11, T:0.00
Consensus pattern (9 bp):
GCCACAACC
Found at i:3755588 original size:12 final size:12
Alignment explanation
Indices: 3755568--3755599 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3755558 TATGCTTCCA
3755568 CAACCACCCCCG
1 CAACCACCCCCG
*
3755580 CACCCACCCCCG
1 CAACCACCCCCG
3755592 CAACCACC
1 CAACCACC
3755600 ACCACAGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.69, G:0.06, T:0.00
Consensus pattern (12 bp):
CAACCACCCCCG
Found at i:3755677 original size:117 final size:117
Alignment explanation
Indices: 3755544--3755766 Score: 374
Period size: 117 Copynumber: 1.9 Consensus size: 117
3755534 AGAGCCACAA
* *
3755544 CTGCCGCTATTCACTATGCTTCCACAACCACCCCCGCACCCACCCCCGCAACCACCACCACAGCC
1 CTGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCACCCCCGCAACCACCACCACAACC
*
3755609 ACCACTCTTCACCATGTTTCCACATCCAGCACCACAACCACCGGCACCGCAG
66 ACCACTCTTCACCACGTTTCCACATCCAGCACCACAACCACCGGCACCGCAG
* ** *
3755661 CTGCCGCTATTCACTATGCTTCCACAACCACCCCCACATCCACTGCCGCAACCACTACCACAACC
1 CTGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCACCCCCGCAACCACCACCACAACC
*
3755726 ACCACTCTTCACCACGTTTCCACATCCAGCGCCACAACCAC
66 ACCACTCTTCACCACGTTTCCACATCCAGCACCACAACCAC
3755767 TGCAGCCACC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 98 1.00
ACGTcount: A:0.26, C:0.50, G:0.09, T:0.15
Consensus pattern (117 bp):
CTGCCGCTATTCACTATGCTTCCACAACCACCCCCACACCCACCCCCGCAACCACCACCACAACC
ACCACTCTTCACCACGTTTCCACATCCAGCACCACAACCACCGGCACCGCAG
Found at i:3757107 original size:38 final size:38
Alignment explanation
Indices: 3757056--3757133 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
3757046 TCGGAAGTAA
*
3757056 GCTTAAAGTTAATTGCCAACATTTAACTTGGTGTGGAT
1 GCTTAAAGTTAATTGCCAACATTTAACTTGGTGTGAAT
*
3757094 GCTTAAAGTTAATTGCCAACATTTAGCTTGGTGTGAAT
1 GCTTAAAGTTAATTGCCAACATTTAACTTGGTGTGAAT
3757132 GC
1 GC
3757134 ATGTATATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (38 bp):
GCTTAAAGTTAATTGCCAACATTTAACTTGGTGTGAAT
Found at i:3759789 original size:17 final size:17
Alignment explanation
Indices: 3759764--3759798 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3759754 GTAAGGATTG
* *
3759764 AAATTTAAAAATTAAAA
1 AAATATAAAAACTAAAA
3759781 AAATATAAAAACTAAAA
1 AAATATAAAAACTAAAA
3759798 A
1 A
3759799 TGACCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATATAAAAACTAAAA
Found at i:3764900 original size:3 final size:3
Alignment explanation
Indices: 3764892--3764942 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3764882 TTCTTAATTC
3764892 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3764940 ATT
1 ATT
3764943 TTAAAAAAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3766535 original size:132 final size:132
Alignment explanation
Indices: 3766293--3766773 Score: 617
Period size: 132 Copynumber: 3.7 Consensus size: 132
3766283 ATTATTCATT
* *
3766293 TAAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * *
3766358 GCTGGGTTGC-AGTTTCGCGTTTACTCAAAATAATCGAATATCCCTTCAAAATTTCACCCATGTC
66 GCTGGGTTGCGA-TTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTC
*
3766422 TCC
130 TTC
* * * * *
3766425 TAAAGATTCTTTAAAACGAAGGCGAGGTTTGATATTTGGCAGTTCGCGAAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * **
3766490 GTTGGGTTGCGATTTCTCGTTTGCTCAAAATGATCGAATATCCCTTCAAAATTTCGTTCATGTCT
66 GCTGGGTTGCGATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTCT
3766555 TC
131 TC
* *
3766557 TAAAAATCCTTTAAAACGAAGGCGATG-TTCGATATTTGACAATTCGCGGAATCGTGCCCTAACG
1 TAAAAATTCTTTAAAACGAAGGCGA-GATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
* * * * * * **
3766621 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAGTGTCCCTTTAGAATTTCGTTCATGTC
65 TGCTGGGTTGCGATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTC
3766686 TTC
130 TTC
* ** * * * **
3766689 TAAAAACTCTTTAAAACGAAGGTAATACTCGATGTTTGGCAATTCG-GGAATCGTGCCCTATTGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
*
3766753 GCTGGGTTGCGATTTCCCGTT
66 GCTGGGTTGCGATTTCTCGTT
3766774 CGTTCAATGA
Statistics
Matches: 307, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
131 35 0.11
132 270 0.88
133 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (132 bp):
TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
GCTGGGTTGCGATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTCT
TC
Found at i:3776548 original size:46 final size:45
Alignment explanation
Indices: 3776498--3776672 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
3776488 TGGTTGAGCA
3776498 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
3776544 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
3776590 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
3776636 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3776673 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 98 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:3776652 original size:92 final size:92
Alignment explanation
Indices: 3776495--3776665 Score: 315
Period size: 92 Copynumber: 1.9 Consensus size: 92
3776485 GGATGGTTGA
* *
3776495 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3776560 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
3776587 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3776652 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3776666 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:3785887 original size:46 final size:45
Alignment explanation
Indices: 3785837--3786010 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
3785827 TGGTTGAGCA
3785837 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
3785883 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
3785929 TCCG-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
3785974 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3786011 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 1 0.01
45 31 0.29
46 67 0.62
47 1 0.01
48 3 0.03
49 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:3785997 original size:91 final size:92
Alignment explanation
Indices: 3785834--3786003 Score: 306
Period size: 91 Copynumber: 1.9 Consensus size: 92
3785824 GGATGGTTGA
* *
3785834 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3785899 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
3785926 GCATCCG-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3785990 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3786004 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 68 0.91
92 7 0.09
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:3795188 original size:46 final size:45
Alignment explanation
Indices: 3795138--3795312 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
3795128 TGGTTGAGCA
3795138 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
3795184 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
3795230 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
3795276 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3795313 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 98 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:3795292 original size:92 final size:92
Alignment explanation
Indices: 3795135--3795305 Score: 315
Period size: 92 Copynumber: 1.9 Consensus size: 92
3795125 GGATGGTTGA
* *
3795135 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3795200 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
3795227 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3795292 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3795306 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:3802717 original size:46 final size:46
Alignment explanation
Indices: 3802667--3802842 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
3802657 TGGTTGAGCA
3802667 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
3802713 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
3802758 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3802806 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3802843 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.58
47 27 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3802823 original size:93 final size:93
Alignment explanation
Indices: 3802664--3802835 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
3802654 GGATGGTTGA
* * *
3802664 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACGCCCGAACTCGTTGAGT
*
3802729 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
3802757 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACGCCCGAACTCGTTGAGT
3802822 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3802836 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:3807431 original size:45 final size:45
Alignment explanation
Indices: 3807382--3807575 Score: 114
Period size: 45 Copynumber: 4.4 Consensus size: 45
3807372 TTCCCTGAGA
3807382 TTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGGCTTCCTGAAG
1 TTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGGCTTCCTGAAG
** ** * * *
3807427 TTGCAGT-GAGACAGATTTAAG-CCACCAACCTA-GCTCCCT-AAGG
1 TTGCAGTGGAG-CAGATCGAAGACGGCGAATCTAGGCTTCCTGAA-G
* * ** * * *
3807470 TTGTAGTGGAGCAG-GCTGAAGATTG-TAGATCT-TGTTTCCCTGAAG
1 TTGCAGTGGAGCAGATC-GAAGACGGCGA-ATCTAGGCTT-CCTGAAG
* * * *
3807515 TTGTAGTGAAGCAGATCGAAGACGGTGAATCTAGGCTTCCTGATG
1 TTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGGCTTCCTGAAG
* *
3807560 TTGCAGCGAAGCAGAT
1 TTGCAGTGGAGCAGAT
3807576 TTAAGCCACC
Statistics
Matches: 109, Mismatches: 28, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
42 2 0.02
43 20 0.18
44 18 0.17
45 62 0.57
46 7 0.06
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (45 bp):
TTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGGCTTCCTGAAG
Found at i:3807690 original size:132 final size:132
Alignment explanation
Indices: 3807363--3807766 Score: 562
Period size: 133 Copynumber: 3.0 Consensus size: 132
3807353 CGAATCCTAC
* * * * *
3807363 AGATCCTGTTTCCCTGAGATTGCAGTGGAGCAGATCGAAGACGGCGAATCTAGGCTTCCTGAAGT
1 AGATCTTGTTTCCCTGAGATTGTAGTGGAACAGATCGAAGACGGTGAATCTAGGCTTCCTGATGT
*
3807428 TGCAGTGAGACAGATTTAAGCCACCAACCTAGCTCCCTAAGGTTGTAGTGGAGCAGGCTGAAGAT
66 TGCAGTGAG-CAGATTTAAGCCACCAACCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGAT
3807493 TGT
130 TGT
3807496 AGATCTTGTTTCCCTGA-AGTTGTAGT-GAAGCAGATCGAAGACGGTGAATCTAGGCTTCCTGAT
1 AGATCTTGTTTCCCTGAGA-TTGTAGTGGAA-CAGATCGAAGACGGTGAATCTAGGCTTCCTGAT
* * *
3807559 GTTGCAGCGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGTTGAA-
64 GTTGCAGTG-AGCAGATTTAAGCCACCAACCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAG
3807623 ATTGT
128 ATTGT
* * *
3807628 AGATTTTGTTTCCCTGAGATTGTAGTGGAACAGATCAAAGACAGTGAATCTAGGCTTCCTGATGT
1 AGATCTTGTTTCCCTGAGATTGTAGTGGAACAGATCGAAGACGGTGAATCTAGGCTTCCTGATGT
* * * * * * *
3807693 TGCAATGCAGCAGATTTAAGTCATCACCCTAGCTCCCTAAAGTTGCAGTGGAGTAGGCTGACGAT
66 TGCAGTG-AGCAGATTTAAGCCACCAACCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGAT
*
3807758 TGC
130 TGT
3807761 AGATCT
1 AGATCT
3807767 CGTCTCCAAT
Statistics
Matches: 241, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
132 116 0.48
133 123 0.51
134 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (132 bp):
AGATCTTGTTTCCCTGAGATTGTAGTGGAACAGATCGAAGACGGTGAATCTAGGCTTCCTGATGT
TGCAGTGAGCAGATTTAAGCCACCAACCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATT
GT
Found at i:3810982 original size:132 final size:132
Alignment explanation
Indices: 3810740--3811220 Score: 606
Period size: 132 Copynumber: 3.7 Consensus size: 132
3810730 ATTATTCATT
* *
3810740 TAAAAATTCTTTAAAACGAAGACGAGATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* *
3810805 GCTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACCCATGTCT
66 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTCT
*
3810870 CC
131 TC
* * * * *
3810872 TAAAGATTCTTTAAAATGAAGGCGAGGTTTGATATTTGGCAGTTCGCGGAATCGTGCCCTAACGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * * ***
3810937 GTTGGGTTGCGATTTCTCGTTTGCTCAAAATGATCGAATATCCCTTCAAAATTTTGTTCATGTCT
66 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTCT
3811002 TC
131 TC
* * * * *
3811004 TAAAAATCCTTTAAAACGAAGGCGATG-TTCGATATTTGACAATTTGCGAAACCGTGCCCTAACG
1 TAAAAATTCTTTAAAACGAAGGCGA-GATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
* * * * **
3811068 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATGTCCCTTTAGAATTTCGTTCATGTC
65 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTC
3811133 TTC
130 TTC
* ** * * * *
3811136 TAAAAACTCTTTAAAACGAAGGTAATACTCGATGTTTGGCAATTCG-GGAATCGTGCCCTATCGT
1 TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * *
3811200 GTTGGGTTGCGATTTCCCGTT
66 GCTGGGTTGCAATTTCTCGTT
3811221 CGTTCAATGA
Statistics
Matches: 301, Mismatches: 46, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
131 33 0.11
132 267 0.89
133 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (132 bp):
TAAAAATTCTTTAAAACGAAGGCGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATGTCT
TC
Found at i:3813371 original size:11 final size:11
Alignment explanation
Indices: 3813347--3813379 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
3813337 TTAATTTAAT
3813347 ATAAAATCAAAA
1 ATAAAAT-AAAA
3813359 ATAAAATAAAA
1 ATAAAATAAAA
3813370 AT-AAATAAAA
1 ATAAAATAAAA
3813380 TAAGATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 6 0.29
12 7 0.33
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:3815151 original size:22 final size:21
Alignment explanation
Indices: 3815112--3815152 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3815102 CTGCTCTCAA
*
3815112 ATTGATGATTTAACTGTTGAG
1 ATTGATGATTTAAATGTTGAG
*
3815133 ATTGATGTTTTTAAATGTTG
1 ATTGATG-ATTTAAATGTTG
3815153 GCCGACGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (21 bp):
ATTGATGATTTAAATGTTGAG
Found at i:3825962 original size:25 final size:25
Alignment explanation
Indices: 3825932--3825979 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3825922 TTTAGCCTGG
*
3825932 ATAAGCTTCCTAATACATGGCTCAC
1 ATAAGCATCCTAATACATGGCTCAC
**
3825957 ATAAGCATCCTGTTACATGGCTC
1 ATAAGCATCCTAATACATGGCTC
3825980 GAGAGAGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (25 bp):
ATAAGCATCCTAATACATGGCTCAC
Found at i:3829053 original size:18 final size:18
Alignment explanation
Indices: 3829030--3829068 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3829020 GCATTGTTAG
3829030 TTAATGAGAAATGAAAAA
1 TTAATGAGAAATGAAAAA
3829048 TTAATGAGAAATGAAAAA
1 TTAATGAGAAATGAAAAA
3829066 TTA
1 TTA
3829069 TCATAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (18 bp):
TTAATGAGAAATGAAAAA
Found at i:3829376 original size:30 final size:29
Alignment explanation
Indices: 3829321--3829388 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
3829311 TGGTTTAATG
* *
3829321 TGTAATTATATATATGAACTTTGATTTTA
1 TGTAATTTTATATATGAACTTTGATTTGA
*
3829350 TGTAATTTTATATATGAAATTTTGATTTGA
1 TGTAATTTTATATATG-AACTTTGATTTGA
*
3829380 TCTAATTTT
1 TGTAATTTT
3829389 TGTGAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.54
Consensus pattern (29 bp):
TGTAATTTTATATATGAACTTTGATTTGA
Found at i:3831807 original size:3 final size:3
Alignment explanation
Indices: 3831799--3831947 Score: 173
Period size: 3 Copynumber: 49.3 Consensus size: 3
3831789 ATAAATAAAT
* * * *
3831799 ATA ATA ATA ATA AT- ATA AAA ATA ATG ATA TTG ATA CATA A-A TATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA -AT-A
3831845 ATA TATA CATA GA-A AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3831891 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3831938 ATA ATA ATA A
1 ATA ATA ATA A
3831948 AAGTTTTAAA
Statistics
Matches: 127, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
2 8 0.06
3 106 0.83
4 12 0.09
5 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3832005 original size:4 final size:4
Alignment explanation
Indices: 3831998--3832022 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3831988 ACAACACGAT
3831998 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
3832023 ATGTTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3832087 original size:21 final size:22
Alignment explanation
Indices: 3832063--3832108 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3832053 TAAGAAAAAT
*
3832063 AATAATGAAA-ATAA-ATATAGA
1 AATAA-GAAATATAATAAATAGA
3832084 AAT-AGAAATATAATAAATAGA
1 AATAAGAAATATAATAAATAGA
3832105 AATA
1 AATA
3832109 TAATAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (22 bp):
AATAAGAAATATAATAAATAGA
Found at i:3832103 original size:15 final size:15
Alignment explanation
Indices: 3832083--3832126 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
3832073 ATAAATATAG
3832083 AAATAGAAATATAAT
1 AAATAGAAATATAAT
3832098 AAATAGAAATATAAT
1 AAATAGAAATATAAT
3832113 AAATAGAAATATAA
1 AAATAGAAATATAA
3832127 ATAGATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:3832126 original size:12 final size:14
Alignment explanation
Indices: 3832071--3832139 Score: 69
Period size: 15 Copynumber: 5.2 Consensus size: 14
3832061 ATAATAATGA
*
3832071 AAATA-AATAT-AG
1 AAATAGAATATAAT
3832083 AAATAGAAATATAAT
1 AAATAG-AATATAAT
3832098 AAATAGAAATATAAT
1 AAATAG-AATATAAT
3832113 AAATAGAA-AT-AT
1 AAATAGAATATAAT
3832125 AAATAG-ATA-AAT
1 AAATAGAATATAAT
3832137 AAA
1 AAA
3832140 AATTAGATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
11 1 0.02
12 19 0.37
13 2 0.04
14 7 0.14
15 22 0.43
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (14 bp):
AAATAGAATATAAT
Found at i:3832148 original size:15 final size:14
Alignment explanation
Indices: 3832073--3832159 Score: 65
Period size: 15 Copynumber: 6.0 Consensus size: 14
3832063 AATAATGAAA
3832073 ATAAATATAGAAATAG
1 ATAAATA-A-AAATAG
3832089 A-AATATAATAAATAG
1 ATAA-ATAA-AAATAG
3832104 A-AATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
3832119 --AAATATAAATAG
1 ATAAATAAAAATAG
3832131 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
3832146 ATAAATAATAATAG
1 ATAAATAAAAATAG
3832160 TATTAGAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
12 6 0.10
13 3 0.05
14 13 0.21
15 37 0.59
16 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:3832153 original size:27 final size:26
Alignment explanation
Indices: 3832095--3832153 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
3832085 ATAGAAATAT
3832095 AATAAATAGAAATATAATAAATAGAA
1 AATAAATAGAAATATAATAAATAGAA
3832121 ATATAAATAGATAA-ATAA-AAATTAGATA
1 A-ATAAATAGA-AATATAATAAA-TAGA-A
3832149 AATAA
1 AATAA
3832154 TAATAGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 4 0.14
27 21 0.72
28 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (26 bp):
AATAAATAGAAATATAATAAATAGAA
Found at i:3832170 original size:21 final size:21
Alignment explanation
Indices: 3832141--3832185 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
3832131 ATAAATAAAA
3832141 ATTAGAT-AAATAATAATAGT
1 ATTAGATAAAATAATAATAGT
3832161 ATTAGAATAACAAATAATAATAGT
1 ATTAG-AT-A-AAATAATAATAGT
3832185 A
1 A
3832186 ATAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
24 14 0.67
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (21 bp):
ATTAGATAAAATAATAATAGT
Found at i:3832684 original size:10 final size:9
Alignment explanation
Indices: 3832669--3832717 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
3832659 TAACTAATTT
3832669 AATAAATTAA
1 AATAAA-TAA
3832679 AATAAAATAA
1 AAT-AAATAA
3832689 AATAAATAA
1 AATAAATAA
*
3832698 AA-ACA-AA
1 AATAAATAA
3832705 AATAAA-AA
1 AATAAATAA
3832713 AATAA
1 AATAA
3832718 TATTTTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 4 0.11
8 11 0.31
9 8 0.23
10 9 0.26
11 3 0.09
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (9 bp):
AATAAATAA
Found at i:3832694 original size:20 final size:21
Alignment explanation
Indices: 3832669--3832717 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
3832659 TAACTAATTT
* *
3832669 AATAAATTAAAA-TAAAATAA
1 AATAAATAAAAACAAAAATAA
3832689 AATAAATAAAAACAAAAATAA
1 AATAAATAAAAACAAAAATAA
3832710 AA-AAATAA
1 AATAAATAA
3832718 TATTTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (21 bp):
AATAAATAAAAACAAAAATAA
Found at i:3836012 original size:22 final size:22
Alignment explanation
Indices: 3835959--3836000 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3835949 AGTTAACGAC
3835959 TAAATTTAAATTAATAAAAAAA
1 TAAATTTAAATTAATAAAAAAA
*
3835981 TAAGTGTTAAATTAA-AAAAA
1 TAAAT-TTAAATTAATAAAAA
3836001 TGTAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
TAAATTTAAATTAATAAAAAAA
Found at i:3836387 original size:20 final size:22
Alignment explanation
Indices: 3836334--3836388 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
3836324 TCAAAGTTTG
3836334 AAATCTCAAGACAATGACTCTT
1 AAATCTCAAGACAATGACTCTT
* ** *
3836356 ATATCTTGAGACAA-GTC-CTT
1 AAATCTCAAGACAATGACTCTT
3836376 AAATCTCAAGACA
1 AAATCTCAAGACA
3836389 TTAGATTGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 13 0.50
21 2 0.08
22 11 0.42
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (22 bp):
AAATCTCAAGACAATGACTCTT
Found at i:3836907 original size:191 final size:189
Alignment explanation
Indices: 3836579--3836950 Score: 584
Period size: 191 Copynumber: 2.0 Consensus size: 189
3836569 GAAATTTTAA
* **
3836579 GTATGTCGTTCAATATTGTTGTCATTTCTACATCAAAAGTTTAAAATTTTAAGAATATATATTAA
1 GTATGTCGTTCAATATTGTTGTCATTTCTACATCAAAAGTTCAAAACCTTAAGAATATATATTAA
3836644 ATTATGACACACTCACAATATGGGATAAACAAGCAATATATGTCGATTTTTTTATTGGCAAAAAA
66 ATTATGACACACTCACAATATGGGATAAACAAGCAATATATGTCGATTTTTTTATTGGCAAAAAA
3836709 GAGGTCATTTTTTTTTCAAGATTTAGAAAATAGGCTGATTTTAGAGAGAGTGTGTGAAAAC
131 GAGGTCATTTTTTTTTCAAGATTTAGAAAATAGGCTGATTTT-GA-AGAGTGTGTGAAAAC
* * *
3836770 GTATGTCGTTCGATATTGTTGTCATATT-TGCATCAAAAGTTCAAAACCTTAAGAATATATATTG
1 GTATGTCGTTCAATATTGTTGTCAT-TTCTACATCAAAAGTTCAAAACCTTAAGAATATATATTA
* * * * *
3836834 AATTATGGCACACTCATAATATGGGCTAAACAGGCAATATATGTTGATTTTTTTATTGGCAAAAA
65 AATTATGACACACTCACAATATGGGATAAACAAGCAATATATGTCGATTTTTTTATTGGCAAAAA
* * *
3836899 ATAGGTCATTTTTTTTTCAAGATTTAGGAAATATGCTGATTTTGAAGAGTGT
130 AGAGGTCATTTTTTTTTCAAGATTTAGAAAATAGGCTGATTTTGAAGAGTGT
3836951 ACTGGGCACA
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
189 7 0.04
190 2 0.01
191 155 0.93
192 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (189 bp):
GTATGTCGTTCAATATTGTTGTCATTTCTACATCAAAAGTTCAAAACCTTAAGAATATATATTAA
ATTATGACACACTCACAATATGGGATAAACAAGCAATATATGTCGATTTTTTTATTGGCAAAAAA
GAGGTCATTTTTTTTTCAAGATTTAGAAAATAGGCTGATTTTGAAGAGTGTGTGAAAAC
Found at i:3838126 original size:17 final size:17
Alignment explanation
Indices: 3838097--3838132 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3838087 ACCACCGACT
3838097 TGTTAAGGGTTTTTTTG
1 TGTTAAGGGTTTTTTTG
3838114 TGTT-AGGGTTTTTTTG
1 TGTTAAGGGTTTTTTTG
3838130 TGT
1 TGT
3838133 GAGAATTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.61
Consensus pattern (17 bp):
TGTTAAGGGTTTTTTTG
Found at i:3839753 original size:46 final size:46
Alignment explanation
Indices: 3839686--3839856 Score: 197
Period size: 46 Copynumber: 3.7 Consensus size: 46
3839676 AACCCGCCCC
* *
3839686 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCA
* * *
3839732 TAAGTGAACTCGGATTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCATCCA
* * *
3839780 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCA
3839825 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
3839857 AATGCTCAAC
Statistics
Matches: 103, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 57 0.55
47 27 0.26
48 3 0.03
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCA
Found at i:3839799 original size:93 final size:93
Alignment explanation
Indices: 3839691--3839861 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3839681 GCCCCTAAGT
* * *
3839691 GAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGATTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3839756 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGAATGCCTAGTTACATTTCAC
*
3839784 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3839849 CGAGTTCGAATGC
66 CGAGTTCGAATGC
3839862 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGAATGCCTAGTTACATTTCAC
Found at i:3846247 original size:22 final size:22
Alignment explanation
Indices: 3846221--3846264 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3846211 TACGAAACTC
3846221 GAAATCAAGATCCGTAAATTTT
1 GAAATCAAGATCCGTAAATTTT
3846243 GAAATCAAGATCCGTAAATTTT
1 GAAATCAAGATCCGTAAATTTT
3846265 TCCTAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (22 bp):
GAAATCAAGATCCGTAAATTTT
Found at i:3855452 original size:45 final size:45
Alignment explanation
Indices: 3855388--3855477 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3855378 TAGCTAAGAG
3855388 AATATTGTTAAAATCTCCTCCAACCAGCCAAGGTAATGAATTGTT
1 AATATTGTTAAAATCTCCTCCAACCAGCCAAGGTAATGAATTGTT
3855433 AATATTGTTAAAATCTCCTCCAACCAGCCAAGGTAATGAATTGTT
1 AATATTGTTAAAATCTCCTCCAACCAGCCAAGGTAATGAATTGTT
3855478 CCTTCCCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (45 bp):
AATATTGTTAAAATCTCCTCCAACCAGCCAAGGTAATGAATTGTT
Found at i:3860866 original size:47 final size:44
Alignment explanation
Indices: 3860754--3860876 Score: 131
Period size: 47 Copynumber: 2.7 Consensus size: 44
3860744 ATGCGTGCTG
* *
3860754 ATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCCA
* * * * *
3860798 ATGCGTGTCCCAAACACGTCTTACACTGGC-TATCTCTGTCGAGGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCACAACTCT-T--A-GCCA
*
3860845 ATGCATGTCCCAGACATGTCTTACTCTGGCAC
1 ATGCATGTCCCAGACATGTCTTACACTGGCAC
3860877 TCATAATATG
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
43 5 0.08
44 27 0.44
46 1 0.02
47 29 0.47
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (44 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCCA
Found at i:3872258 original size:46 final size:46
Alignment explanation
Indices: 3872182--3872617 Score: 537
Period size: 46 Copynumber: 9.8 Consensus size: 46
3872172 TGATGTCATA
* * ** * *
3872182 GTATCTTTCAACTATGGTTTTACTTGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTAC-TCATTTCATATCAGGTTGCCATG
* *** *
3872228 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
* *
3872275 GTATCTTTCAACCATCGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
3872321 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
3872367 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
3872413 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
3872459 GTATCTTTCAACCATGGTCTTA--CA---C--A-CAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
3872497 GTATCTTTCAACTATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
3872543 GTATCTTTCAACCATGGTCTTA--CA---C--A-CAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
3872581 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
3872618 AGAGCACACT
Statistics
Matches: 352, Mismatches: 20, Indels: 36
0.86 0.05 0.09
Matches are distributed among these distances:
38 66 0.19
39 2 0.01
40 4 0.01
41 2 0.01
43 2 0.01
44 4 0.01
45 3 0.01
46 231 0.66
47 38 0.11
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:3872501 original size:38 final size:38
Alignment explanation
Indices: 3872450--3872606 Score: 233
Period size: 38 Copynumber: 3.9 Consensus size: 38
3872440 TTCATATCAC
3872450 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
*
3872488 GTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAG
3872534 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
3872572 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
3872607 TTTCATATCA
Statistics
Matches: 109, Mismatches: 2, Indels: 16
0.86 0.02 0.13
Matches are distributed among these distances:
38 67 0.61
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 32 0.29
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:3872545 original size:84 final size:84
Alignment explanation
Indices: 3872404--3872617 Score: 410
Period size: 84 Copynumber: 2.5 Consensus size: 84
3872394 TTCATATCAC
*
3872404 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
3872469 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
*
3872488 GTTGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
3872553 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
3872572 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
3872618 AGAGCACACT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 127 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (84 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:3877257 original size:21 final size:21
Alignment explanation
Indices: 3877226--3877277 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
3877216 AAGGCCTATG
*
3877226 ACACGGGCATGTCCCATGGCC
1 ACACAGGCATGTCCCATGGCC
* *
3877247 ATACAGGCATGTCCCTTGGCC
1 ACACAGGCATGTCCCATGGCC
3877268 ACACAGGCAT
1 ACACAGGCAT
3877278 CTGGGTTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (21 bp):
ACACAGGCATGTCCCATGGCC
Found at i:3877311 original size:109 final size:109
Alignment explanation
Indices: 3877170--3877380 Score: 271
Period size: 109 Copynumber: 1.9 Consensus size: 109
3877160 CATGGGTGTG
** * * *
3877170 TGGGTTGGTTGTGTGACCCAAGTTAGTGAGTTACACGGGGTCGGACAAGGCCT-ATGACACGGGC
1 TGGGTTGGCCGTGTAACCCAAGTCAGTAAGTTACACGGGGTCGGACAAGGCCTGA-GACACGGGC
*
3877234 ATGTCCCATGGCCATACAGGCATGTCCCTTGGCCACACAGGCATC
65 ATGTCCCATGGCCACACAGGCATGTCCCTTGGCCACACAGGCATC
* * ** ** *
3877279 TGGGTTGGCCGTGTAACCCAAGTCAGTAAGTTATATGGGGTCGGACCCGGCCTGAGACATTGGCG
1 TGGGTTGGCCGTGTAACCCAAGTCAGTAAGTTACACGGGGTCGGACAAGGCCTGAGACACGGGCA
**
3877344 TGTCCCATGGCCACACAGGTGTGTCCCTTGGCCACAC
66 TGTCCCATGGCCACACAGGCATGTCCCTTGGCCACAC
3877381 GGGTGTGTGA
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
109 85 0.99
110 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (109 bp):
TGGGTTGGCCGTGTAACCCAAGTCAGTAAGTTACACGGGGTCGGACAAGGCCTGAGACACGGGCA
TGTCCCATGGCCACACAGGCATGTCCCTTGGCCACACAGGCATC
Found at i:3877386 original size:19 final size:21
Alignment explanation
Indices: 3877343--3877388 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3877333 AGACATTGGC
3877343 GTGTCCCATGGCCACACAGGT
1 GTGTCCCATGGCCACACAGGT
* *
3877364 GTGTCCCTTGGCCACACGGGT
1 GTGTCCCATGGCCACACAGGT
3877385 GTGT
1 GTGT
3877389 GACCTCTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.33, T:0.24
Consensus pattern (21 bp):
GTGTCCCATGGCCACACAGGT
Found at i:3878089 original size:18 final size:18
Alignment explanation
Indices: 3878066--3878105 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3878056 GAGCCTTTAG
*
3878066 TGTTAAATAAATAACTAT
1 TGTTAAATAAACAACTAT
*
3878084 TGTTAAATAAACAACTTT
1 TGTTAAATAAACAACTAT
3878102 TGTT
1 TGTT
3878106 GAGTAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TGTTAAATAAACAACTAT
Found at i:3880020 original size:40 final size:39
Alignment explanation
Indices: 3879855--3880038 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
3879845 AAATTGAATG
* * *
3879855 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
3879895 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
3879935 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
3879975 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
3880014 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
3880039 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:3880063 original size:80 final size:81
Alignment explanation
Indices: 3879895--3880083 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
3879885 GCTGGAAATT
* * * *
3879895 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
3879960 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
3879976 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
3880039 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
3880055 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
3880084 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:3888139 original size:40 final size:39
Alignment explanation
Indices: 3887974--3888157 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
3887964 AAATTGAATG
* * *
3887974 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
3888014 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
3888054 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
3888094 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
3888133 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
3888158 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:3888182 original size:80 final size:81
Alignment explanation
Indices: 3888014--3888202 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
3888004 GCTGGAAATT
* * * *
3888014 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
3888079 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
3888095 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
3888158 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
3888174 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
3888203 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:3901086 original size:40 final size:37
Alignment explanation
Indices: 3901020--3901154 Score: 170
Period size: 35 Copynumber: 3.7 Consensus size: 37
3901010 CATGGCAAAG
3901020 TGTGAAATGTAGGTATGGTA--TCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
3901055 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATT-TC--ATCCATACTGAGT
** * *
3901095 TAAGAAATGTAGGTATGGCATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
*
3901130 TGTAAAATGTAGGTATGGTATTTCA
1 TGTGAAATGTAGGTATGGTATTTCA
3901155 ATGAGGAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
35 50 0.58
38 2 0.02
39 2 0.02
40 32 0.37
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
Found at i:3905254 original size:21 final size:21
Alignment explanation
Indices: 3905230--3905272 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3905220 CACTGAATTA
*
3905230 GGCCCATTT-TTGTCTGTTTTT
1 GGCCCATTTCTTG-CTCTTTTT
3905251 GGCCCATTTCTTGCTCTTTTT
1 GGCCCATTTCTTGCTCTTTTT
3905272 G
1 G
3905273 CCTTCCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.05, C:0.23, G:0.19, T:0.53
Consensus pattern (21 bp):
GGCCCATTTCTTGCTCTTTTT
Found at i:3906825 original size:20 final size:20
Alignment explanation
Indices: 3906800--3906960 Score: 128
Period size: 20 Copynumber: 8.1 Consensus size: 20
3906790 TGTATACACT
3906800 TCGGTGCCCCTATTTGCACA
1 TCGGTGCCCCTATTTGCACA
* * *
3906820 TCGGTGCCCTTGTTAGCACA
1 TCGGTGCCCCTATTTGCACA
* * *
3906840 TCAGTGCCCTTGTTTGCACA
1 TCGGTGCCCCTATTTGCACA
* *
3906860 TCAGTGCCCCTATTAGCACA
1 TCGGTGCCCCTATTTGCACA
** * *
3906880 TTTGTGCCACTGTTTGCACA
1 TCGGTGCCCCTATTTGCACA
* *
3906900 TCGATGCCCCTATTTCCACA
1 TCGGTGCCCCTATTTGCACA
* * *
3906920 T-GCGTGCCCCTGTTTGTACT
1 TCG-GTGCCCCTATTTGCACA
*
3906940 TTGGTGCCCCTGA-TTGCACA
1 TCGGTGCCCCT-ATTTGCACA
3906960 T
1 T
3906961 ATATGCCTCT
Statistics
Matches: 111, Mismatches: 27, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
19 1 0.01
20 109 0.98
21 1 0.01
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.33
Consensus pattern (20 bp):
TCGGTGCCCCTATTTGCACA
Found at i:3906847 original size:40 final size:40
Alignment explanation
Indices: 3906803--3906960 Score: 158
Period size: 40 Copynumber: 4.0 Consensus size: 40
3906793 ATACACTTCG
* * *
3906803 GTGCCCCTATTTGCACATCGGTGCCCTTGTTAGCACATCA
1 GTGCCCCTGTTTGCACATCGGTGCCCCTATTAGCACATCA
* * **
3906843 GTGCCCTTGTTTGCACATCAGTGCCCCTATTAGCACATTT
1 GTGCCCCTGTTTGCACATCGGTGCCCCTATTAGCACATCA
* * **
3906883 GTGCCACTGTTTGCACATCGATGCCCCTATTTCCACATGC-
1 GTGCCCCTGTTTGCACATCGGTGCCCCTATTAGCACAT-CA
* * *
3906923 GTGCCCCTGTTTGTACTTTGGTGCCCCTGATT-GCACAT
1 GTGCCCCTGTTTGCACATCGGTGCCCCT-ATTAGCACAT
3906961 ATATGCCTCT
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 93 0.97
41 3 0.03
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.33
Consensus pattern (40 bp):
GTGCCCCTGTTTGCACATCGGTGCCCCTATTAGCACATCA
Found at i:3906908 original size:60 final size:60
Alignment explanation
Indices: 3906803--3906930 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
3906793 ATACACTTCG
* * * *
3906803 GTGCCCCTATTTGCACATCGGTGCCCTTGTTAGCACATCAGTGCCCTTGTTTGCACAT-C
1 GTGCCCCTATTAGCACATCGGTGCCCTTGTTAGCACATCAGTGCCCCTATTTCCACATGC
** *
3906862 AGTGCCCCTATTAGCACATTTGTGCCAC-TGTTTGCACATC-GATGCCCCTATTTCCACATGC
1 -GTGCCCCTATTAGCACATCGGTGCC-CTTGTTAGCACATCAG-TGCCCCTATTTCCACATGC
3906923 GTGCCCCT
1 GTGCCCCT
3906931 GTTTGTACTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.02
60 55 0.95
61 2 0.03
ACGTcount: A:0.16, C:0.34, G:0.19, T:0.31
Consensus pattern (60 bp):
GTGCCCCTATTAGCACATCGGTGCCCTTGTTAGCACATCAGTGCCCCTATTTCCACATGC
Found at i:3907595 original size:3 final size:3
Alignment explanation
Indices: 3907587--3907615 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3907577 GTTCAAAATG
3907587 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3907616 TGGTTAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3909720 original size:12 final size:12
Alignment explanation
Indices: 3909703--3909754 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
3909693 ATAATATTTA
3909703 TATTATTACTAT
1 TATTATTACTAT
*
3909715 TATTATTATTAT
1 TATTATTACTAT
* *
3909727 CATTATTAGTA-
1 TATTATTACTAT
3909738 TATT-TCTACTAT
1 TATTAT-TACTAT
3909750 TATTA
1 TATTA
3909755 GCATTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.22
12 24 0.75
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:3909753 original size:3 final size:3
Alignment explanation
Indices: 3909646--3909734 Score: 58
Period size: 3 Copynumber: 29.0 Consensus size: 3
3909636 TTTTATATAT
* * *
3909646 TTA TTA TTA TTA TTG TTA TTTA TTA TTA TTA TTA -CA CTT- GTA TGTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA T-TA
* * *
3909692 TATA ATA TT- TATA TTA TTA CTA TTA TTA TTA TTA TCA TTA TTA
1 T-TA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3909735 GTATATTTCT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
2 3 0.05
3 54 0.82
4 9 0.14
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3909819 original size:2 final size:2
Alignment explanation
Indices: 3909781--3909806 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3909771 AATTAATACT
3909781 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
3909807 CTTTCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3910051 original size:27 final size:26
Alignment explanation
Indices: 3910021--3910129 Score: 93
Period size: 28 Copynumber: 4.2 Consensus size: 26
3910011 TATTATGTAC
*
3910021 ATTTTTAATACTATA-TATATTGTATGT
1 ATTTTTAATA-TATATTATA-TGTATAT
*
3910048 ATTTTCAATAACTATATTATATGTATAT
1 ATTTTTAAT-A-TATATTATATGTATAT
* *
3910076 ACTTTAAATAT-TA-T-TATGTA-AT
1 ATTTTTAATATATATTATATGTATAT
3910098 CATTTTTAATATATATATATATGTATAT
1 -ATTTTTAATATATAT-TATATGTATAT
3910126 ATTT
1 ATTT
3910130 ATGAAGTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
22 2 0.03
23 15 0.22
24 3 0.04
25 2 0.03
26 2 0.03
27 19 0.28
28 21 0.31
29 4 0.06
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (26 bp):
ATTTTTAATATATATTATATGTATAT
Found at i:3910130 original size:25 final size:25
Alignment explanation
Indices: 3909914--3910130 Score: 91
Period size: 25 Copynumber: 8.6 Consensus size: 25
3909904 TTTGATTATG
* *
3909914 TATATATATATTTTTCAATAT-TATA
1 TATATGTATATATTT-AATATATATA
* * *
3909939 T-TATTTAGATTATTT-ATATATCATC
1 TATATGTATA-TATTTAATATAT-ATA
* *
3909964 T-TATGTATATATTT-TTGATATTATC
1 TATATGTATATATTTAAT-ATA-TATA
* * *
3909989 TCATACGTATATTTTTAATA-A-CTA
1 T-ATATGTATATATTTAATATATATA
* *
3910013 T-TATGTACATTTTTAATACTATATA
1 TATATGTATATATTTAATA-TATATA
*
3910038 TAT-TGTATGTATTTTCAATA-ACTATA
1 TATATGTATATA-TTT-AATATA-TATA
3910064 TTATATGTATATACTTTAA-ATAT-TA
1 -TATATGTATATA-TTTAATATATATA
*
3910089 T-TATGTAATCATTTTTAATATATATA
1 TATATGT-AT-ATATTTAATATATATA
3910115 TATATGTATATATTTA
1 TATATGTATATATTTA
3910131 TGAAGTATTG
Statistics
Matches: 147, Mismatches: 22, Indels: 46
0.68 0.10 0.21
Matches are distributed among these distances:
22 15 0.10
23 9 0.06
24 24 0.16
25 44 0.30
26 17 0.12
27 27 0.18
28 11 0.07
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (25 bp):
TATATGTATATATTTAATATATATA
Found at i:3910168 original size:3 final size:3
Alignment explanation
Indices: 3910162--3910215 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
3910152 TAAAAAAAAA
3910162 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3910210 TAT TAT
1 TAT TAT
3910216 ATGTTTTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3910354 original size:2 final size:2
Alignment explanation
Indices: 3910305--3910345 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3910295 TTTTTAATAC
* *
3910305 TA TA TC TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3910346 TTCATATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3910393 original size:17 final size:18
Alignment explanation
Indices: 3910371--3910404 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3910361 TGTATATGTT
3910371 TTTTTATATA-TATTATA
1 TTTTTATATACTATTATA
3910388 TTTTTATATACTATTAT
1 TTTTTATATACTATTAT
3910405 GTATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATATACTATTATA
Found at i:3910424 original size:22 final size:22
Alignment explanation
Indices: 3910369--3910465 Score: 71
Period size: 22 Copynumber: 4.4 Consensus size: 22
3910359 TGTGTATATG
*
3910369 TTTTTTTATA-TA-TAT-TATA
1 TTTTTATATATTATTATGTATA
*
3910388 TTTTTATATACTATTATGTATA
1 TTTTTATATATTATTATGTATA
3910410 TATTTTA-ATATTATTA-GTTATA
1 T-TTTTATATATTATTATG-TATA
*
3910432 TACCTTTTATACTATT-GTATGTATA
1 T---TTTTATA-TATTATTATGTATA
3910457 TTTTTATAT
1 TTTTTATAT
3910466 TGTATATTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
19 9 0.14
20 2 0.03
21 5 0.08
22 25 0.39
23 5 0.08
24 5 0.08
25 8 0.12
26 5 0.08
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTTATATATTATTATGTATA
Found at i:3921593 original size:75 final size:73
Alignment explanation
Indices: 3921506--3921651 Score: 229
Period size: 75 Copynumber: 2.0 Consensus size: 73
3921496 CTAATGTTTT
* * *
3921506 ATTTCTGTTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
3921571 TATTTTCG
66 TATTTTCG
* *
3921579 ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGA
1 ATTTCTG--TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGA
3921644 GGTATTTT
64 GGTATTTT
3921652 AAATTTCTAC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 7 0.11
75 59 0.89
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (73 bp):
ATTTCTGTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
TATTTTCG
Found at i:3921667 original size:75 final size:75
Alignment explanation
Indices: 3921513--3921668 Score: 224
Period size: 75 Copynumber: 2.1 Consensus size: 75
3921503 TTTATTTCTG
* * * *
3921513 TTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTA
* *
3921578 GATTTCTGTC
66 AATTTCTCTC
* *
3921588 TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTA
1 TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTA
3921653 AATTTCTACT-
66 AATTTCT-CTC
3921663 TTTCAA
1 TTTCAA
3921669 TTCCTGTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 71 0.99
76 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (75 bp):
TTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTA
AATTTCTCTC
Found at i:3921735 original size:90 final size:85
Alignment explanation
Indices: 3921594--3921973 Score: 341
Period size: 88 Copynumber: 4.4 Consensus size: 85
3921584 TGTCTTTCAA
* * *
3921594 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTAAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGTTGAGGTATTTTAAATTTC
3921659 TACTTTTCAATTCCTGTTTTTC
66 T-CTTTTCAATT-CTGTTTTTC
* * *
3921681 AAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTCAAT
1 ---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGTTGAGGTATTTTAAAT
* *
3921746 TTCT-GTTT--A---TATTTTTC
63 TTCTCTTTTCAATTCTGTTTTTC
* *
3921763 AAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCACATGTCGAGGTATTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGT-AC--GTTGAGGTATTTT-AAA
* *
3921827 -ATCTGCTTTTCAAAATCTG-TTTTC
62 TTTCT-CTTTTC-AATTCTGTTTTTC
* * * *
3921851 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGT-ACGT--TGAGGTATTTTAAAT
* *
3921915 TTCTGTTTTTAATGTCTGTTTTT-
63 TTCTCTTTTCAAT-TCTGTTTTTC
* * **
3921938 AAAGATTCAATTCATATTGCGAGAAATGAGTTGAGC
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
3921974 TCAAGATCAC
Statistics
Matches: 242, Mismatches: 29, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
78 3 0.01
79 38 0.16
81 15 0.06
82 9 0.04
83 3 0.01
86 6 0.02
87 13 0.05
88 94 0.39
89 1 0.00
90 60 0.25
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (85 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGTTGAGGTATTTTAAATTTC
TCTTTTCAATTCTGTTTTTC
Found at i:3921790 original size:79 final size:81
Alignment explanation
Indices: 3921519--3921973 Score: 338
Period size: 88 Copynumber: 5.4 Consensus size: 81
3921509 TCTGTTTCAA
* * *
3921519 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAAGA-CACGTTGAGGTATTTTCGATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCACGTTGAGGTATTTTCAATTT
* ***
3921583 CTG-----TCT-TTCAA
65 CTGTTTAATATGTTTTC
* * * *
3921594 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG-GCACGCTGAGGTATTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCACGTTGAGGTATTTTCAATTT
* *
3921658 CTACTTTTCAATTCCTGTTTTTC
65 CT--GTTT-AA-T-ATG-TTTTC
*
3921681 AAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGAT-ACGTTGAGGTATTTTCAA
1 ---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGATCACGTTGAGGTATTTTCAA
3921745 TTTCTGTTT-ATAT-TTTTC
62 TTTCTGTTTAATATGTTTTC
* * * **
3921763 AAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCAC--GTTGAGGTATTTTCAATT
*
3921828 TCTGCTTTTCAAAATCTGTTTTC
64 TCTG--TTT---AATATGTTTTC
* * *
3921851 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGT--TGAGGTATTTTCAATT
* *
3921916 TCTGTTTTTAATGTCTGTTTTT
64 TCTG--TTTAA--TATGTTTTC
* * **
3921938 AAAGATTCAATTCATATTGCGAGAAATGAGTTGAGC
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
3921974 TCAAGATCAC
Statistics
Matches: 311, Mismatches: 37, Indels: 51
0.78 0.09 0.13
Matches are distributed among these distances:
75 59 0.19
78 3 0.01
79 38 0.12
81 19 0.06
82 5 0.02
83 3 0.01
84 2 0.01
85 5 0.02
86 3 0.01
87 16 0.05
88 98 0.32
90 60 0.19
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (81 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATCACGTTGAGGTATTTTCAATTTC
TGTTTAATATGTTTTC
Found at i:3921857 original size:14 final size:14
Alignment explanation
Indices: 3921819--3921854 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3921809 TGTCGAGGTA
3921819 TTTTCAAAATCTGC
1 TTTTCAAAATCTGC
3921833 TTTTCAAAATCTG-
1 TTTTCAAAATCTGC
3921846 TTTTCAAAA
1 TTTTCAAAA
3921855 ATCAACTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (14 bp):
TTTTCAAAATCTGC
Found at i:3921911 original size:169 final size:166
Alignment explanation
Indices: 3921513--3921923 Score: 475
Period size: 169 Copynumber: 2.5 Consensus size: 166
3921503 TTTATTTCTG
* * *
3921513 TTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGTTGAGGTATTTTC
* *
3921578 GATTTCTG---TCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACG
65 AATTTCTGTTTTATTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACG
* *
3921640 CTGAGGTATTTTAAATTTCTACTTTTCAATTCCTGTT
130 CTGAGGTATTTTAAATATCTACTTTTCAAATCCTGTT
*
3921677 TTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGAT-ACGTTGAGGTATTT
1 TTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACGTTGAGGTATTT
*** * *
3921741 TCAATTTCTGTTTATATTTTTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGT
63 TCAATTTCTGTTT-TATTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGG-
*
3921805 CACATG-TCGAGGTATTTTCAAA-ATCTGCTTTTCAAAAT-CTG-T
126 CAC--GCT-GAGGTATTTT-AAATATCTACTTTTC-AAATCCTGTT
* *
3921847 TTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGAGCTATTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACGT--TGAGGTATTT
3921910 TCAATTTCTGTTTT
63 TCAATTTCTGTTTT
3921924 TAATGTCTGT
Statistics
Matches: 214, Mismatches: 18, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
164 4 0.02
165 63 0.29
166 3 0.01
167 40 0.19
168 4 0.02
169 65 0.30
170 6 0.03
171 23 0.11
172 6 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (166 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGTTGAGGTATTTTCA
ATTTCTGTTTTATTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCACGC
TGAGGTATTTTAAATATCTACTTTTCAAATCCTGTT
Found at i:3923073 original size:23 final size:25
Alignment explanation
Indices: 3923047--3923093 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3923037 TATCATTCAT
*
3923047 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
3923070 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
3923094 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:3923414 original size:46 final size:46
Alignment explanation
Indices: 3923354--3923619 Score: 325
Period size: 46 Copynumber: 6.0 Consensus size: 46
3923344 TTTGACGTGA
* * * * * * *
3923354 TGCCATAGTGTCTTTCAGCTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
3923400 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
3923446 TGCCACGGTATCTTTCAACCATGGTCTTACACATCTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3923492 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3923530 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3923576 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
3923620 AGAGCACACT
Statistics
Matches: 195, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
38 32 0.16
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 149 0.76
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:3923585 original size:84 final size:84
Alignment explanation
Indices: 3923444--3923608 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 84
3923434 TTCATGTCAC
3923444 GTTGCCACGGTATCTTTCAACCATGGTCTTACACATCTCATATCAAGTTGCCATGGTATCTTTCA
1 GTTGCCACGGTATCTTTCAACCATGGTCTTACACATCTCATATCAAGTTGCCATGGTATCTTTCA
3923509 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
* * *
3923528 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCACGGTATCTTTCAACCATGGTCTTACACATCTCATATCAAGTTGCCATGGTATCTTTCA
3923593 ACCATGGTCTTACACA
66 ACCATGGTCTTACACA
3923609 TTTCATATCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (84 bp):
GTTGCCACGGTATCTTTCAACCATGGTCTTACACATCTCATATCAAGTTGCCATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:3926489 original size:40 final size:41
Alignment explanation
Indices: 3926444--3926610 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 41
3926434 CGGAATATAA
*
3926444 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
3926484 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
3926524 CCGGATGT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
3926564 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
3926603 CCGGATAT
1 CCGGATAT
3926611 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 17 0.16
40 87 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:3927459 original size:17 final size:19
Alignment explanation
Indices: 3927436--3927481 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
3927426 AAGAAGCATG
3927436 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
3927454 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
3927472 AATCATGCTC
1 AATCATGCTC
3927482 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:3934544 original size:13 final size:14
Alignment explanation
Indices: 3934520--3934549 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3934510 CACCTGTTTG
3934520 CGACGATATGCTGA
1 CGACGATATGCTGA
3934534 CGACG-TATGCTGA
1 CGACGATATGCTGA
3934547 CGA
1 CGA
3934550 GATCCACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (14 bp):
CGACGATATGCTGA
Found at i:3935723 original size:26 final size:26
Alignment explanation
Indices: 3935654--3935762 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
3935644 CATGAAATTC
3935654 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3935680 TTATCATG-AACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3935705 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
3935731 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3935757 TTATCA
1 TTATCA
3935763 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 25 0.31
26 55 0.69
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Done.