Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000256.1 Hibiscus syriacus cultivar Beakdansim tig00000468_pilon, whole genome shotgun sequence
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: 102689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:52 original size:16 final size:17
Alignment explanation
Indices: 28--60 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18 TAAAATACCC
28 TTAA-ATTTTTCCCAAA
1 TTAATATTTTTCCCAAA
*
44 TTAATTTTTTTCCCAAA
1 TTAATATTTTTCCCAAA
61 AATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATATTTTTCCCAAA
Found at i:447 original size:15 final size:16
Alignment explanation
Indices: 427--461 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
417 AAAATACAAC
427 ATTCTCAATAAT-TTT
1 ATTCTCAATAATATTT
*
442 ATTCTCGATAATATTT
1 ATTCTCAATAATATTT
458 ATTC
1 ATTC
462 ATACAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTCTCAATAATATTT
Found at i:5969 original size:33 final size:33
Alignment explanation
Indices: 5932--5998 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
5922 ACAGCCCCTT
*
5932 GTTTCGGGATTTGAACATCCTTTGAAGCAAGGA
1 GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
5965 GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
1 GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
5998 G
1 G
5999 GACTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (33 bp):
GTTTCGGGATTTGAACATCCTCTGAAGCAAGGA
Found at i:10128 original size:25 final size:25
Alignment explanation
Indices: 10084--10135 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
10074 ACACTCATAA
* *
10084 AACATCATTTAAAGATCATTCATGT
1 AACATCATTTAAAGACCATTAATGT
*
10109 AACATCATTTAAATACCATTAATGT
1 AACATCATTTAAAGACCATTAATGT
10134 AA
1 AA
10136 GAATTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (25 bp):
AACATCATTTAAAGACCATTAATGT
Found at i:12598 original size:22 final size:20
Alignment explanation
Indices: 12573--12626 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
12563 ACTGAAGTGG
12573 GTATCGATACTATAGAAGGGAA
1 GTATCGATACTATAG-AGGG-A
*
12595 GTATC-AGTACTATAGTGGGA
1 GTATCGA-TACTATAGAGGGA
*
12615 GTACCGATACTA
1 GTATCGATACTA
12627 GTGCGTCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 10 0.36
21 5 0.18
22 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (20 bp):
GTATCGATACTATAGAGGGA
Found at i:13204 original size:20 final size:23
Alignment explanation
Indices: 13155--13213 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
13145 GTCGAAGGTT
13155 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
13178 CTATGTGGTCCTTC-GGAC-AAA
1 CTATGTGGTCCTTCGGGACAAAA
13199 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
13214 TGCAAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 11 0.32
21 4 0.12
22 4 0.12
23 14 0.41
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:14829 original size:13 final size:13
Alignment explanation
Indices: 14811--14858 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
14801 ATCTATGGGT
*
14811 GCATTTATGACAC
1 GCATTTATGACGC
14824 GCATTTATGACGC
1 GCATTTATGACGC
*
14837 ACATTTATGACGC
1 GCATTTATGACGC
14850 GCATTTATG
1 GCATTTATG
14859 GCTTACATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (13 bp):
GCATTTATGACGC
Found at i:14968 original size:85 final size:85
Alignment explanation
Indices: 14839--15004 Score: 251
Period size: 85 Copynumber: 2.0 Consensus size: 85
14829 TATGACGCAC
* * * *
14839 ATTTATGACGCGCATTTATGGCTTACATTGCGCGTCATTGAAGCCCCCGACATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTAAAGCCCCCGACATAAATGAAAATGA
* *
14904 CACACGTTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
* **
14924 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTAAAGCCCCCTTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTAAAGCCCCCGACATAAATGAAAATGA
14989 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
15005 GTGATTGTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTAAAGCCCCCGACATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:15040 original size:12 final size:12
Alignment explanation
Indices: 15023--15047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15013 ATTTCGTGAA
15023 TTATATATATAT
1 TTATATATATAT
15035 TTATATATATAT
1 TTATATATATAT
15047 T
1 T
15048 GTAGATTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATATATATAT
Found at i:21969 original size:18 final size:18
Alignment explanation
Indices: 21946--21983 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21936 TCTTGTAGTG
*
21946 ACTATCTGGGGTATCGAT
1 ACTATCTAGGGTATCGAT
21964 ACTATCTAGGGTATCGAT
1 ACTATCTAGGGTATCGAT
21982 AC
1 AC
21984 CAAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (18 bp):
ACTATCTAGGGTATCGAT
Found at i:25713 original size:21 final size:21
Alignment explanation
Indices: 25687--25731 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
25677 CGTCATTTGC
*
25687 GCCTTTGCACGTTCTATTCGA
1 GCCTTTACACGTTCTATTCGA
*
25708 GCCTTTACGCGTTCTATTCGA
1 GCCTTTACACGTTCTATTCGA
25729 GCC
1 GCC
25732 GGCGCCACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (21 bp):
GCCTTTACACGTTCTATTCGA
Found at i:30315 original size:18 final size:18
Alignment explanation
Indices: 30292--30357 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
30282 ATGTTTACAA
30292 TTATCATATAATTTTCAG
1 TTATCATATAATTTTCAG
30310 TTATCATAT-ATTTAT-AG
1 TTATCATATAATTT-TCAG
* * * *
30327 TTATTAGATGATTTACAG
1 TTATCATATAATTTTCAG
30345 TTATCATATAATT
1 TTATCATATAATT
30358 ACAAATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.33
18 26 0.67
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (18 bp):
TTATCATATAATTTTCAG
Found at i:30529 original size:41 final size:41
Alignment explanation
Indices: 30484--30565 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
30474 AAGTGAGTAC
*
30484 TTATCAGTTCAGCTTTGGTACATTCGTGTATCAATGTTCAG
1 TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
30525 TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
1 TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
30566 CACCGTTGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (41 bp):
TTATCAGTTCAGCTTTGGTACATTCATGTATCAATGTTCAG
Found at i:33760 original size:21 final size:21
Alignment explanation
Indices: 33716--33761 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33706 CCTAGCTGCG
**
33716 GTGGCATCTGATATGGTTGCA
1 GTGGCATCTGATATGGAAGCA
*
33737 GTGGCATCTGATATGGAAGTA
1 GTGGCATCTGATATGGAAGCA
33758 GTGG
1 GTGG
33762 TGTCTGACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.37, T:0.30
Consensus pattern (21 bp):
GTGGCATCTGATATGGAAGCA
Found at i:33823 original size:21 final size:21
Alignment explanation
Indices: 33799--33838 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33789 AAATGGTTGT
* *
33799 GGTACCATCTGATACGGCTAC
1 GGTACCATCTAAAACGGCTAC
33820 GGTACCATCTAAAACGGCT
1 GGTACCATCTAAAACGGCT
33839 GTGGAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.23
Consensus pattern (21 bp):
GGTACCATCTAAAACGGCTAC
Found at i:41470 original size:25 final size:25
Alignment explanation
Indices: 41441--41514 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
41431 TTGGAAAATT
41441 CTTTGTGGTACTAGTACTGCTGCAA
1 CTTTGTGGTACTAGTACTGCTGCAA
*
41466 CTTTG-GAGTA-TCAGT--T-CT---T
1 CTTTGTG-GTACT-AGTACTGCTGCAA
41485 CTTTGTGGTACTAGTACTGCTGCAA
1 CTTTGTGGTACTAGTACTGCTGCAA
41510 CTTTG
1 CTTTG
41515 GAGTATCAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 20
0.63 0.03 0.34
Matches are distributed among these distances:
19 11 0.30
20 2 0.05
21 1 0.03
22 4 0.11
23 1 0.03
24 2 0.05
25 16 0.43
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.41
Consensus pattern (25 bp):
CTTTGTGGTACTAGTACTGCTGCAA
Found at i:41487 original size:44 final size:44
Alignment explanation
Indices: 41439--41526 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
41429 AGTTGGAAAA
41439 TTCTTTGTGGTACTAGTACTGCTGCAACTTTGGAGTATCAGTTC
1 TTCTTTGTGGTACTAGTACTGCTGCAACTTTGGAGTATCAGTTC
41483 TTCTTTGTGGTACTAGTACTGCTGCAACTTTGGAGTATCAGTTC
1 TTCTTTGTGGTACTAGTACTGCTGCAACTTTGGAGTATCAGTTC
41527 CCGCTCCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (44 bp):
TTCTTTGTGGTACTAGTACTGCTGCAACTTTGGAGTATCAGTTC
Found at i:48144 original size:23 final size:23
Alignment explanation
Indices: 48118--48175 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
48108 TCTCTATGTA
48118 TGAACCTATAAAGAACATGTTTG
1 TGAACCTATAAAGAACATGTTTG
*
48141 TGAACCCTA-AATGAACATGTTTG
1 TGAA-CCTATAAAGAACATGTTTG
*
48164 TGAACATATAAA
1 TGAACCTATAAA
48176 TGAATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 3 0.10
23 23 0.77
24 4 0.13
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (23 bp):
TGAACCTATAAAGAACATGTTTG
Found at i:48229 original size:30 final size:32
Alignment explanation
Indices: 48190--48273 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
48180 TATATTTGCT
*
48190 AAAAGTAAATAAACGAACATGAACAC-AT-TC
1 AAAAATAAATAAACGAACATGAACACGATATC
* *
48220 AAAAATAAATAAATGAACATGAACACGATATT
1 AAAAATAAATAAACGAACATGAACACGATATC
* *
48252 AAAAA-AATTAAACGAAAATGAA
1 AAAAATAAATAAACGAACATGAA
48274 ACGTATGTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 24 0.52
31 16 0.35
32 6 0.13
ACGTcount: A:0.62, C:0.11, G:0.10, T:0.18
Consensus pattern (32 bp):
AAAAATAAATAAACGAACATGAACACGATATC
Found at i:48522 original size:43 final size:42
Alignment explanation
Indices: 48472--48780 Score: 316
Period size: 43 Copynumber: 7.2 Consensus size: 42
48462 TGTAAAATAA
* **
48472 AAACGCCGCAAAAAGTCAAGATCTATAGCCACGTTTTT-GACAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGA-AC
* *
48515 AAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* *
48558 AAACGCTGCAAAAGGTCGAGATCTATATCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAC
* *
48601 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTATTGAAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
48643 AAACACCACAAAAGGTTAGATCTATAGCGGCGTTTGTAT-TAAA
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTT-T-TGGAAC
* * *
48686 AAATGCCGCAAAAGGTCAGATCTATAACGGTGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* * * * * *
48729 AAATGCCACAAAAGGTTAGATTTATAGCAGCGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
*
48772 AAATGCCGC
1 AAACGCCGC
48781 TAATTACCAT
Statistics
Matches: 224, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.00
42 71 0.32
43 131 0.58
44 21 0.09
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:48645 original size:128 final size:128
Alignment explanation
Indices: 48472--48780 Score: 347
Period size: 128 Copynumber: 2.4 Consensus size: 128
48462 TGTAAAATAA
* * *
48472 AAACGCCGCAAAAAGTCAAGATCTATAGCCA-CGTTTTTGACACAAACGCCGCAAAAGGTCGGAT
1 AAACGCCGCAAAAGGTC-AGATCTATAG-CAGCGTTTTTGAAACAAACGCCGCAAAAGGTCAGAT
* * * *
48536 CTATAGCGGCATTTTTGGA-T-ACAAACGCTGCAAAAGGTCGAGATCTATATCGGCGTTTTTGGA
64 CTATAGCGGC--GTTTGGATTAAAAAACGCCGCAAAAGGTC-AGATCTATAACGGCGTTTTTGGA
48599 -AC
126 TAC
* * * * *
48601 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTATTGAAACAAACACCACAAAAGGTTAGATCT
1 AAACGCCGCAAAAGGTCAGATCTATAGCAGCGTTTTTGAAACAAACGCCGCAAAAGGTCAGATCT
* * *
48666 ATAGCGGCGTTTGTATTAAAAAATGCCGCAAAAGGTCAGATCTATAACGGTGTTTTTGGATAC
66 ATAGCGGCGTTTGGATTAAAAAACGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGATAC
* * * * * *
48729 AAATGCCACAAAAGGTTAGATTTATAGCAGCGTTTTTTGATACAAATGCCGC
1 AAACGCCGCAAAAGGTCAGATCTATAGCAGCG-TTTTTGAAACAAACGCCGC
48781 TAATTACCAT
Statistics
Matches: 150, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
126 5 0.03
127 23 0.15
128 92 0.61
129 30 0.20
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (128 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCAGCGTTTTTGAAACAAACGCCGCAAAAGGTCAGATCT
ATAGCGGCGTTTGGATTAAAAAACGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGATAC
Found at i:51869 original size:18 final size:20
Alignment explanation
Indices: 51830--51872 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
51820 ACTAAATGGT
*
51830 AGTTAGTTTGTTAAACGAGC
1 AGTTAGCTTGTTAAACGAGC
51850 AGTTAGCTTGTT-AA-GAGC
1 AGTTAGCTTGTTAAACGAGC
51868 AGTTA
1 AGTTA
51873 TGTGCTGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (20 bp):
AGTTAGCTTGTTAAACGAGC
Found at i:54529 original size:63 final size:63
Alignment explanation
Indices: 54430--54553 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
54420 CAAGTCAGTT
* *
54430 ACCAAATACCACCACCGTGCATGAAGAAGATGGTAATGCAG-AAGTACATAATGAAGCCGAGTC
1 ACCAAATACCACCACCGCGCATGAAGAAGATGGTAATGCAGCAA-TACATAATGAAGACGAGTC
* * *
54493 ACCAAATATCATCACCGCGCATGAAGAAG-TGAGTAATGCAGCAATTCATAATGAAGACGAG
1 ACCAAATACCACCACCGCGCATGAAGAAGATG-GTAATGCAGCAATACATAATGAAGACGAG
54554 ATGATTAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.93
64 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (63 bp):
ACCAAATACCACCACCGCGCATGAAGAAGATGGTAATGCAGCAATACATAATGAAGACGAGTC
Found at i:56498 original size:18 final size:20
Alignment explanation
Indices: 56459--56501 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
56449 ACTAAATGGT
*
56459 AGTTAGTTTGTTAAACGAGC
1 AGTTAGCTTGTTAAACGAGC
56479 AGTTAGCTTGTT-AA-GAGC
1 AGTTAGCTTGTTAAACGAGC
56497 AGTTA
1 AGTTA
56502 TGTGCTGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (20 bp):
AGTTAGCTTGTTAAACGAGC
Found at i:56645 original size:33 final size:33
Alignment explanation
Indices: 56600--56662 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
56590 TTTTCTAACA
* *
56600 AAGACTACTTGACTGTAAGAATACGACAGCTGC
1 AAGACTACTTGACGGCAAGAATACGACAGCTGC
* *
56633 AAGACTATTTGACGGCAAGAATACGGCAGC
1 AAGACTACTTGACGGCAAGAATACGACAGC
56663 GTCGAGAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (33 bp):
AAGACTACTTGACGGCAAGAATACGACAGCTGC
Found at i:57059 original size:39 final size:40
Alignment explanation
Indices: 56931--57065 Score: 122
Period size: 39 Copynumber: 3.4 Consensus size: 40
56921 TTGCGGCATT
*
56931 TTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGTG
1 TTTTACATAAACGCCATTAAAGTACGCATTTTTAGCAGTG
* * *
56971 TTTTTACGA-AAACGCCGCTATATAA-TA-GGA-TATTACGC-GT-
1 -TTTTAC-ATAAACGCC-AT-TA-AAGTACGCATTTTTA-GCAGTG
57011 TTTTACATAAACGCCATTAAAGTACGCATTTTTAGCAGTG
1 TTTTACATAAACGCCATTAAAGTACGCATTTTTAGCAGTG
57051 TTTT-CATAAAACGCC
1 TTTTACAT-AAACGCC
57066 GCATATATTC
Statistics
Matches: 75, Mismatches: 7, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
36 2 0.03
37 4 0.05
38 6 0.08
39 22 0.29
40 11 0.15
41 19 0.25
42 5 0.07
43 4 0.05
44 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (40 bp):
TTTTACATAAACGCCATTAAAGTACGCATTTTTAGCAGTG
Found at i:57126 original size:80 final size:82
Alignment explanation
Indices: 56896--57114 Score: 275
Period size: 80 Copynumber: 2.7 Consensus size: 82
56886 CATTTTTACA
* * ** *
56896 AAAACGCCACTATATATCTAGTCTATTGCGGCATTTTTTACATAAACGCCACTAAAGTACGCATT
1 AAAACGCCGCTATATA-ATAGAATATTGCGGCGTTTTTTACATAAACGCCACTAAAGTACGCATT
*
56961 TTTAGCAGTGTTTTTACG
65 TTTAGCAGTGTTTTCACG
* * *
56979 AAAACGCCGCTATATAATAGGATATTAC-GCG-TTTTTACATAAACGCCATTAAAGTACGCATTT
1 AAAACGCCGCTATATAATAGAATATTGCGGCGTTTTTTACATAAACGCCACTAAAGTACGCATTT
*
57042 TTAGCAGTGTTTTCA-T
66 TTAGCAGTGTTTTCACG
* * * *
57058 AAAACGCCGC-ATATATTCGAATATTGCGGTGTTTTTTACATAAACGACACTAAAGTA
1 AAAACGCCGCTATATAATAGAATATTGCGGCGTTTTTTACATAAACGCCACTAAAGTA
57115 TGAGCTTTTA
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
78 13 0.11
79 12 0.10
80 68 0.58
81 2 0.02
82 8 0.07
83 15 0.13
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (82 bp):
AAAACGCCGCTATATAATAGAATATTGCGGCGTTTTTTACATAAACGCCACTAAAGTACGCATTT
TTAGCAGTGTTTTCACG
Found at i:60333 original size:73 final size:73
Alignment explanation
Indices: 60214--60360 Score: 251
Period size: 73 Copynumber: 2.0 Consensus size: 73
60204 CTTTACACCG
* *
60214 AAAACACTTTAGTTGCTCTTGTTTGTTTACCCTCAGCTTTCCTACTTGGTCCTTGGCTTTC-CTA
1 AAAACACTCTAGTTGCTCCTGTTTGTTTACCCTCAGCTTTCCTACTTGGTCCTTGGCTTTCGC-A
60278 CCGAGCTTT
65 CCGAGCTTT
*
60287 AAAACACTCTAGTTGCTCCTGTTTGTTTACCCTCGGCTTTCCTACTTGGTCCTTGGCTTTCGCAC
1 AAAACACTCTAGTTGCTCCTGTTTGTTTACCCTCAGCTTTCCTACTTGGTCCTTGGCTTTCGCAC
60352 CGAGCTTT
66 CGAGCTTT
60360 A
1 A
60361 CTTGATTTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 69 0.99
74 1 0.01
ACGTcount: A:0.15, C:0.29, G:0.16, T:0.40
Consensus pattern (73 bp):
AAAACACTCTAGTTGCTCCTGTTTGTTTACCCTCAGCTTTCCTACTTGGTCCTTGGCTTTCGCAC
CGAGCTTT
Found at i:66221 original size:3 final size:3
Alignment explanation
Indices: 66206--66264 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
66196 TATTTATATA
* * **
66206 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
66250 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
66265 TTACAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:66273 original size:26 final size:27
Alignment explanation
Indices: 66206--66275 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 27
66196 TATTTATATA
*
66206 AATAA-TAAAAATAATAATAATGAAAT
1 AATAATTAAAAATAATAATAATAAAAT
66232 AATAATTAAAGCAATAATAATAATAAAAT
1 AATAATTAAA--AATAATAATAATAAAAT
*
66261 AAT-ATTACAAATAAT
1 AATAATTAAAAATAAT
66276 GATTAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 11 0.28
27 4 0.10
28 5 0.13
29 19 0.49
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (27 bp):
AATAATTAAAAATAATAATAATAAAAT
Found at i:66341 original size:29 final size:29
Alignment explanation
Indices: 66292--66353 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
66282 AATAAAAGGA
* *
66292 ATTAAAAATATAGTAT-TAAAATGTAAAAT
1 ATTAAAAATATAATATCAAAAATG-AAAAT
66321 ATTAAAAATA-AATAGTCAAAAATGAAAAT
1 ATTAAAAATATAATA-TCAAAAATGAAAAT
66350 -TTAA
1 ATTAA
66354 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTAAAAATATAATATCAAAAATGAAAAT
Found at i:67577 original size:3 final size:3
Alignment explanation
Indices: 67563--67654 Score: 98
Period size: 3 Copynumber: 31.0 Consensus size: 3
67553 GCCTGAAGTG
* * * *
67563 TAA TAA -AA TAA TAA TAT TAT TAA TAA TAA TAA TAT TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
67610 TAA TAA TAA TAG TAA TAA AAA TAA AAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
67655 AAAACCAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
2 3 0.04
3 70 0.95
4 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:68180 original size:113 final size:112
Alignment explanation
Indices: 67997--68748 Score: 1227
Period size: 113 Copynumber: 6.7 Consensus size: 112
67987 AGAATCATGC
* *
67997 AAAAGATTGAATAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
68062 TATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCA
65 TATGAACTCAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
*
68111 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
68176 ATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCG
66 ATGAACTC-ACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
* *
68224 AAAAGTTGAATAAGTTCTTCTCATTATGAACTTGTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
68289 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTC-ACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
68337 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
68402 ATGAACTGGACCTAGTAATGGTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACT-CACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
*
68450 AGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
68515 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTC-ACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
*
68563 AGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
68628 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTC-ACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
68676 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCATT-AGATGAGTTCTTCTCAT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCAT
68740 TATGAACTC
65 TATGAACTC
68749 TTCCAGAAAT
Statistics
Matches: 606, Mismatches: 28, Indels: 9
0.94 0.04 0.01
Matches are distributed among these distances:
113 598 0.99
114 8 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (112 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
Found at i:69209 original size:22 final size:22
Alignment explanation
Indices: 69184--69238 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
69174 GATAAAGCTT
* *
69184 TCATCATTGAAAAGAG-AATCTG
1 TCATCTTTGAAAAG-GTAATCTA
*
69206 TCATCTTTAAAAAGGTAATCTA
1 TCATCTTTGAAAAGGTAATCTA
69228 TCATCTTTGAA
1 TCATCTTTGAA
69239 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGGTAATCTA
Found at i:69688 original size:54 final size:53
Alignment explanation
Indices: 69606--69761 Score: 179
Period size: 54 Copynumber: 2.9 Consensus size: 53
69596 AGAATAGCAG
* * *
69606 GTTCGTAAAACATTTGACAGCGCATTCATTCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAA-ATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCTCAGAC
* * *
69660 GTTCGTAAAATATTTGAGAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAC
1 GTTCGTAAAA-ATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCTCAGAC
* * * *
69714 GTTCATAAAGAGTTTGACAACACATTCA-TCTTTTTCTGTGGCTGCTGC
1 GTTCGTAAA-AATTTGACAACACATTCATTC-TTTCCTGTGGCTTCTGC
69762 CAAGATTTCT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 84 0.98
55 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (53 bp):
GTTCGTAAAAATTTGACAACACATTCATTCTTTCCTGTGGCTTCTGCTCAGAC
Found at i:72097 original size:114 final size:114
Alignment explanation
Indices: 71897--72118 Score: 381
Period size: 114 Copynumber: 1.9 Consensus size: 114
71887 ACGATCATGC
* * * *
71897 AATTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAA
*
71962 GAACAGTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACA
* *
72011 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAAATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAA
72076 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
72119 CGAGAACGTG
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACA
Found at i:73788 original size:32 final size:32
Alignment explanation
Indices: 73747--73808 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
73737 GAAGAAATGA
*
73747 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTCG
73779 TTGTTATGCTCATCTGGTAGAGATACTTCT
1 TTGTTATGCTCATCTGGTAGAGATACTTCT
73809 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTGGTAGAGATACTTCTCG
Found at i:74439 original size:14 final size:14
Alignment explanation
Indices: 74416--74464 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
74406 TGATTCAATT
* *
74416 TTTTTCTTTTTTCC
1 TTTTTATTTTTTCA
*
74430 TTTTTATTTTTTTTA
1 TTTTTA-TTTTTTCA
74445 TTTTTATTTCTTTCA
1 TTTTTATTT-TTTCA
74460 TTTTT
1 TTTTT
74465 TTCATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTTTTCA
Found at i:74440 original size:15 final size:15
Alignment explanation
Indices: 74422--74492 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
74412 AATTTTTTTC
*
74422 TTTTTTCCTTTTTAT
1 TTTTTTCATTTTTAT
*
74437 TTTTTTTATTTTTAT
1 TTTTTTCATTTTTAT
*
74452 TTCTTTCATTTTT-T
1 TTTTTTCATTTTTAT
* *
74466 TCATTTT--TTTTCAT
1 T-TTTTTCATTTTTAT
74480 TTTTTTCATTTTT
1 TTTTTTCATTTTT
74493 CCTCTTTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
13 8 0.19
14 4 0.09
15 31 0.72
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCATTTTTAT
Found at i:74479 original size:19 final size:19
Alignment explanation
Indices: 74455--74510 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 19
74445 TTTTTATTTC
74455 TTTCATTTTTTTCATTTTT
1 TTTCATTTTTTTCATTTTT
74474 TTTCATTTTTTTCATTTTT
1 TTTCATTTTTTTCATTTTT
**
74493 CCTC-TTTTTTTC-TTTTT
1 TTTCATTTTTTTCATTTTT
74510 T
1 T
74511 CCTTTCTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 5 0.15
18 8 0.24
19 21 0.62
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCATTTTTTTCATTTTT
Found at i:74492 original size:10 final size:9
Alignment explanation
Indices: 74413--74510 Score: 76
Period size: 9 Copynumber: 10.8 Consensus size: 9
74403 TCTTGATTCA
74413 ATTTTTTTC
1 ATTTTTTTC
*
74422 -TTTTTTCC
1 ATTTTTTTC
* *
74430 TTTTTATTTT
1 ATTTT-TTTC
* *
74440 TTTTATTTTT
1 ATTT-TTTTC
*
74450 ATTTCTTTC
1 ATTTTTTTC
74459 ATTTTTTTC
1 ATTTTTTTC
74468 ATTTTTTTTC
1 A-TTTTTTTC
74478 ATTTTTTTC
1 ATTTTTTTC
*
74487 ATTTTTCCTC
1 ATTTTT-TTC
74497 -TTTTTTTC
1 ATTTTTTTC
74505 -TTTTTT
1 ATTTTTT
74511 CCTTTCTTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
8 15 0.20
9 35 0.47
10 24 0.32
11 1 0.01
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:74529 original size:27 final size:26
Alignment explanation
Indices: 74499--74552 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
74489 TTTTCCTCTT
*
74499 TTTTTCTTTTTTCCTTTCTTTGTTGGA
1 TTTTTC-TTTTTCCTTTCTTTGCTGGA
74526 TTTTTCTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTCCTTTCTTTGCTGGA
74552 T
1 T
74553 GAGTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTCCTTTCTTTGCTGGA
Found at i:79228 original size:19 final size:18
Alignment explanation
Indices: 79188--79242 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
79178 TTAATACCTG
79188 AATAAAATAA-AAAAATATT
1 AATAAAATAATAAAAA-A-T
79207 AATAAAATAATATAAAAAT
1 AATAAAATAATA-AAAAAT
*
79226 AATAAGA-AATAAAAAAT
1 AATAAAATAATAAAAAAT
79243 TTGAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.18
18 4 0.12
19 17 0.52
20 2 0.06
21 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATAATAAAAAAT
Found at i:80075 original size:3 final size:3
Alignment explanation
Indices: 80060--80118 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
80050 TATTTATATA
* * **
80060 AAT AAT AAA AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
80104 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
80119 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:80127 original size:26 final size:28
Alignment explanation
Indices: 80068--80129 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
80058 TAAATAATAA
*
80068 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
80098 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
80123 AAATAAT
1 AAATAAT
80130 GATTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 6 0.20
28 3 0.10
29 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:80195 original size:29 final size:29
Alignment explanation
Indices: 80146--80207 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
80136 AATAAAAGGA
* *
80146 ATTAAAAATATAGTAT-TAAAATGTAAAAT
1 ATTAAAAATATAATATCAAAAATG-AAAAT
80175 ATTAAAAATA-AATAGTCAAAAATGAAAAT
1 ATTAAAAATATAATA-TCAAAAATGAAAAT
80204 -TTAA
1 ATTAA
80208 TGATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTAAAAATATAATATCAAAAATGAAAAT
Found at i:80360 original size:2 final size:2
Alignment explanation
Indices: 80353--80391 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
80343 GATATTTACC
80353 TA TA TA TA 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 TA TA TA TA T
80392 GCTGATAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81435 original size:3 final size:3
Alignment explanation
Indices: 81421--81512 Score: 98
Period size: 3 Copynumber: 31.0 Consensus size: 3
81411 GCCTGAAGTG
* * * *
81421 TAA TAA -AA TAA TAA TAT TAA TAA TAT TAA TAA TAT TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
81468 TAA TAA TAA TAG TAA TAA AAA TAA AAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
81513 AAAACCAAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 3 0.04
3 68 0.94
4 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:81817 original size:46 final size:46
Alignment explanation
Indices: 81767--81893 Score: 184
Period size: 46 Copynumber: 2.7 Consensus size: 46
81757 TAAATTTAAT
*
81767 TTTTATTTATGGCATTCTTTCATGCCTTAATTCATCATTTCATGCA
1 TTTTATTTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCA
* * *
81813 TTTTATTTATGGCATCCTTTCATGCCTTGATGCATCATTTCATGCC
1 TTTTATTTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCA
*
81859 TTTTATTTATGGCA-TCATTTCATGCCAATAATGCA
1 TTTTATTTATGGCATTC-TTTCATGCC-TTAATGCA
81894 CCCATATGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
45 1 0.01
46 65 0.90
47 6 0.08
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.46
Consensus pattern (46 bp):
TTTTATTTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCA
Found at i:81884 original size:26 final size:26
Alignment explanation
Indices: 81799--81884 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
81789 TGCCTTAATT
*
81799 CATCATTTCATGCATTTTATTTATGG
1 CATCATTTCATGCCTTTTATTTATGG
* *
81825 CATCCTTTCATGCC-----TTGAT-G
1 CATCATTTCATGCCTTTTATTTATGG
81845 CATCATTTCATGCCTTTTATTTATGG
1 CATCATTTCATGCCTTTTATTTATGG
81871 CATCATTTCATGCC
1 CATCATTTCATGCC
81885 AATAATGCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 14 0.29
21 4 0.08
25 4 0.08
26 27 0.55
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (26 bp):
CATCATTTCATGCCTTTTATTTATGG
Found at i:81929 original size:45 final size:45
Alignment explanation
Indices: 81866--81995 Score: 215
Period size: 45 Copynumber: 2.9 Consensus size: 45
81856 GCCTTTTATT
* *
81866 TATGGCATCATTTCATGCCAATAATGCACCCATATGCATTTCAGA
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTTCAGA
*
81911 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTTCAGC
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTTCAGA
* *
81956 TATGTCATCCTTTCATGCTAATAATGCACCCATATGCATT
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATT
81996 ATTCTTGTAT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (45 bp):
TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTTCAGA
Found at i:89030 original size:44 final size:45
Alignment explanation
Indices: 88907--89030 Score: 205
Period size: 45 Copynumber: 2.8 Consensus size: 45
88897 TATAAAATCT
88907 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
88952 CTTACCATTTATTCTATAAGCTCGAAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
88997 CTTATCA-TTATCCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
89031 GAATACTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 24 0.33
45 48 0.67
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:91864 original size:16 final size:16
Alignment explanation
Indices: 91840--91934 Score: 52
Period size: 16 Copynumber: 5.6 Consensus size: 16
91830 ATCTATTTTA
*
91840 ATTACTATATTTATAT
1 ATTATTATATTTATAT
91856 ATTATTATATTT-TAATT
1 ATTATTATATTTAT-A-T
91873 ATTTATTATATTTA-AT
1 A-TTATTATATTTATAT
*
91889 AATTAATAT-TGTTAATGAAT
1 -ATTATTATAT-TT-AT--AT
* *
91909 ATTATTTTATTTATTT
1 ATTATTATATTTATAT
*
91925 ATTATAATAT
1 ATTATTATAT
91935 ATTTTTTCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
15 2 0.03
16 30 0.49
17 5 0.08
18 13 0.21
19 8 0.13
20 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:92022 original size:3 final size:3
Alignment explanation
Indices: 92001--92079 Score: 58
Period size: 3 Copynumber: 25.7 Consensus size: 3
91991 CTCTATTTTA
*
92001 ATT ATT A-T ATTT ATAT ATT ATT A-T ATT -TCA ATT ATTT ATT ATT ATT
1 ATT ATT ATT A-TT AT-T ATT ATT ATT ATT AT-T ATT A-TT ATT ATT ATT
*
92047 ATT ATT ATT AGT ATT ATT A-T ATTT ATTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT AT
92080 AATATAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
2 7 0.11
3 41 0.65
4 15 0.24
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:96700 original size:19 final size:19
Alignment explanation
Indices: 96676--96713 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
96666 TAACTCGAAA
96676 TTAATTCAAATTAAATTTT
1 TTAATTCAAATTAAATTTT
*
96695 TTAATTCAAATTTAATTTT
1 TTAATTCAAATTAAATTTT
96714 ACCCGCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATTCAAATTAAATTTT
Found at i:97179 original size:2 final size:2
Alignment explanation
Indices: 97172--97214 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
97162 ATTTTATCAA
97172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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 AT AT AT
97213 AT
1 AT
97215 CAATCACGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:97487 original size:3 final size:3
Alignment explanation
Indices: 97481--97555 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
97471 CTAGTTTTTT
* * *
97481 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA ATA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
97529 ATA ATA TTA TTA TTA TTA TT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
97556 AGATACAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Done.