Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019499.1 Corchorus olitorius cultivar O-4 contig19532, 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: 114392
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2082 original size:17 final size:19
Alignment explanation
Indices: 2045--2084 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2035 TACTGTTTTT
*
2045 AAAACTTTTTTCTTTCACC
1 AAAAATTTTTTCTTTCACC
2064 AAAAATTTTTT-TTTC-CC
1 AAAAATTTTTTCTTTCACC
2081 AAAA
1 AAAA
2085 TAATATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 4 0.20
19 10 0.50
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATTTTTTCTTTCACC
Found at i:6076 original size:25 final size:26
Alignment explanation
Indices: 6039--6094 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
6029 GGGCAGGGAG
6039 GTTAC-AATGCTTTTATT-ATTAGGAA
1 GTTACAAATGC-TTTATTGATTAGGAA
* *
6064 GTTACAAAT-CTTTATTGATTTGGAG
1 GTTACAAATGCTTTATTGATTAGGAA
6089 GTTACA
1 GTTACA
6095 TGAATGACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 18 0.67
26 3 0.11
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (26 bp):
GTTACAAATGCTTTATTGATTAGGAA
Found at i:6356 original size:149 final size:150
Alignment explanation
Indices: 6081--6533 Score: 543
Period size: 149 Copynumber: 3.0 Consensus size: 150
6071 ATCTTTATTG
* * ** * * * *
6081 ATTTGGAGGTTACATGAATGACATTATATTTGGACAGTTACGTAA-ACTTGTAACGTCTATTCAA
1 ATTTAGAGGTTACATGCACAACATCATATTTGGGCAGTTAC-AAATACTTGTAACGTCTCTTCAA
* * *
6145 GGTATTTAATAATTTGGAGGTTACATCCACATCATCATATTTGGGCAGTTACAAAT-TCTTGTAA
65 GGTATTTAATAATTTGGAGGTTACATGCACAACATCATATTTGGGCGGTTACAAATAT-TTGTAA
6209 CGTCTCTTCAAGGTATTTAATA
129 CGTCTCTTCAAGGTATTTAATA
*
6231 A-TTAGAGGTTACATGCACAACATCATATTTGGGCAGTTACAAATACTTGTAACCTCTCTTCAAG
1 ATTTAGAGGTTACATGCACAACATCATATTTGGGCAGTTACAAATACTTGTAACGTCTCTTCAAG
*** * * *
6295 GTATTCGGTAATTTGGAGGTTATATGCAGAACATCATATTTGGGCGGTTACGAATATTTGTAACG
66 GTATTTAATAATTTGGAGGTTACATGCACAACATCATATTTGGGCGGTTACAAATATTTGTAACG
*
6360 TCTCTTCAAGGTATTTACTA
131 TCTCTTCAAGGTATTTAATA
* * * *
6380 ATTTGGAGGTTACATGCACAACATCATATATTTATATTTGGGCGGTTACGAATATTTGTAACGTC
1 ATTTAGAGGTTACATGCACAACATC--------ATATTTGGGCAGTTACAAATACTTGTAACGTC
* *
6445 TCTTCAAGGTATTTACTAATTTGGAGGTTACATGCACAACATCATATATTTGGACGGTTACAAAT
58 TCTTCAAGGTATTTAATAATTTGGAGGTTACATGCACAACATC--ATATTTGGGCGGTTACAAAT
*
6510 ACTTGTAACGTCTCTTCAAGGTAT
121 ATTTGTAACGTCTCTTCAAGGTAT
6534 ATAGACTGAA
Statistics
Matches: 258, Mismatches: 32, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
148 2 0.01
149 125 0.48
150 24 0.09
158 66 0.26
160 41 0.16
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (150 bp):
ATTTAGAGGTTACATGCACAACATCATATTTGGGCAGTTACAAATACTTGTAACGTCTCTTCAAG
GTATTTAATAATTTGGAGGTTACATGCACAACATCATATTTGGGCGGTTACAAATATTTGTAACG
TCTCTTCAAGGTATTTAATA
Found at i:6392 original size:47 final size:47
Alignment explanation
Indices: 6340--6475 Score: 118
Period size: 47 Copynumber: 3.1 Consensus size: 47
6330 ATATTTGGGC
6340 GGTTACGAATATTTGTAACGTCTCTTCAAGGTATTTACTAATTTGGA
1 GGTTACGAATATTTGTAACGTCTCTTCAAGGTATTTACTAATTTGGA
* ** * *
6387 GGTTAC----A--TG-CAC--AACATCATA--TATTTA-T-ATTTGGGC
1 GGTTACGAATATTTGTAACGTCTCTTCA-AGGTATTTACTAATTT-GGA
6423 GGTTACGAATATTTGTAACGTCTCTTCAAGGTATTTACTAATTTGGA
1 GGTTACGAATATTTGTAACGTCTCTTCAAGGTATTTACTAATTTGGA
6470 GGTTAC
1 GGTTAC
6476 ATGCACAACA
Statistics
Matches: 64, Mismatches: 10, Indels: 30
0.62 0.10 0.29
Matches are distributed among these distances:
35 4 0.06
36 9 0.14
37 6 0.09
38 4 0.06
39 1 0.02
40 3 0.05
41 2 0.03
42 2 0.03
43 3 0.05
44 1 0.02
45 4 0.06
46 6 0.09
47 15 0.23
48 4 0.06
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (47 bp):
GGTTACGAATATTTGTAACGTCTCTTCAAGGTATTTACTAATTTGGA
Found at i:6469 original size:83 final size:77
Alignment explanation
Indices: 6081--6533 Score: 525
Period size: 75 Copynumber: 5.9 Consensus size: 77
6071 ATCTTTATTG
* ** * * * *
6081 ATTTGGAGGTTACATGAATGACAT--TATATTTGGACAGTTACGTAA-ACTTGTAACGTCTATTC
1 ATTTGGAGGTTACATGCACAACATCATATATTTGGGCGGTTACG-AATATTTGTAACGTCTCTTC
*
6143 AAGGTATTTAATA
65 AAGGTATTTACTA
* *
6156 ATTTGGAGGTTACAT-C-C-ACATCATCATATTTGGGCAGTTACAAAT-TCTTGTAACGTCTCTT
1 ATTTGGAGGTTACATGCACAACATCAT-ATATTTGGGCGGTTACGAATAT-TTGTAACGTCTCTT
*
6217 CAAGGTATTTAATA
64 CAAGGTATTTACTA
* * * * *
6231 A-TTAGAGGTTACATGCACAACATC--ATATTTGGGCAGTTACAAATACTTGTAACCTCTCTTCA
1 ATTTGGAGGTTACATGCACAACATCATATATTTGGGCGGTTACGAATATTTGTAACGTCTCTTCA
***
6293 AGGTATTCGGTA
66 AGGTATTTACTA
* *
6305 ATTTGGAGGTTATATGCAGAACATC--ATATTTGGGCGGTTACGAATATTTGTAACGTCTCTTCA
1 ATTTGGAGGTTACATGCACAACATCATATATTTGGGCGGTTACGAATATTTGTAACGTCTCTTCA
6368 AGGTATTTACTA
66 AGGTATTTACTA
6380 ATTTGGAGGTTACATGCACAACATCATATATTTATATTTGGGCGGTTACGAATATTTGTAACGTC
1 ATTTGGAGGTTACATGCACAACATC----A--TATATTTGGGCGGTTACGAATATTTGTAACGTC
6445 TCTTCAAGGTATTTACTA
60 TCTTCAAGGTATTTACTA
* * *
6463 ATTTGGAGGTTACATGCACAACATCATATATTTGGACGGTTACAAATACTTGTAACGTCTCTTCA
1 ATTTGGAGGTTACATGCACAACATCATATATTTGGGCGGTTACGAATATTTGTAACGTCTCTTCA
6528 AGGTAT
66 AGGTAT
6534 ATAGACTGAA
Statistics
Matches: 333, Mismatches: 27, Indels: 34
0.85 0.07 0.09
Matches are distributed among these distances:
72 4 0.01
74 60 0.18
75 145 0.44
76 1 0.00
77 47 0.14
79 1 0.00
83 75 0.23
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (77 bp):
ATTTGGAGGTTACATGCACAACATCATATATTTGGGCGGTTACGAATATTTGTAACGTCTCTTCA
AGGTATTTACTA
Found at i:7622 original size:13 final size:11
Alignment explanation
Indices: 7504--7617 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
7494 ATTATGTTAT
7504 TATATATAAAA
1 TATATATAAAA
* ***
7515 TATATTTGTGA
1 TATATATAAAA
7526 TATATATAAAA
1 TATATATAAAA
*
7537 TATAT-T-TAA
1 TATATATAAAA
* **
7546 T-TATTTATGA
1 TATATATAAAA
7556 TATATATAAAA
1 TATATATAAAA
*
7567 TATATGT-AAA
1 TATATATAAAA
**
7577 -ATATATAAGT
1 TATATATAAAA
* **
7587 TATATTTATGA
1 TATATATAAAA
7598 TATATATAAAA
1 TATATATAAAA
7609 TATATATAA
1 TATATATAA
7618 CAAATTTTTT
Statistics
Matches: 75, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
8 3 0.04
9 9 0.12
10 8 0.11
11 55 0.73
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (11 bp):
TATATATAAAA
Found at i:15222 original size:24 final size:24
Alignment explanation
Indices: 15190--15247 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
15180 AATGGGAATC
*
15190 GGTGGAGGAATATTCCGATTCTGA
1 GGTGGAGGAACATTCCGATTCTGA
* *
15214 GGTGGAGGAGCGTTCCGATTCTGA
1 GGTGGAGGAACATTCCGATTCTGA
15238 GGTGGAGGAA
1 GGTGGAGGAA
15248 GTGCAGGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.41, T:0.24
Consensus pattern (24 bp):
GGTGGAGGAACATTCCGATTCTGA
Found at i:15724 original size:24 final size:25
Alignment explanation
Indices: 15695--15745 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
15685 TTATATGAAC
*
15695 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
15719 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
15744 AA
1 AA
15746 ATACTCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:18008 original size:2 final size:2
Alignment explanation
Indices: 18001--18039 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17991 CAAGTAACAA
18001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18040 AAAGCCGGGC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22061 original size:18 final size:18
Alignment explanation
Indices: 22038--22073 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22028 GGGAACTATC
22038 ATAAAGAGTAATAGAAAA
1 ATAAAGAGTAATAGAAAA
22056 ATAAAGAGTAATAGAAAA
1 ATAAAGAGTAATAGAAAA
22074 GTGAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
ATAAAGAGTAATAGAAAA
Found at i:22670 original size:78 final size:75
Alignment explanation
Indices: 22541--22730 Score: 267
Period size: 78 Copynumber: 2.5 Consensus size: 75
22531 AACTATCCAA
*
22541 ATGTTGTGCATGTAACTTCCAAATTACTAAATACCTTGAAGAGACGATACAAGTATTT-GTAACC
1 ATGTTGTGCATGTAACCTCCAAATTACTAAATACCTTGAAGAGACGATACAAGTATTTAG-AACC
**
22605 GTTCAAATATG
65 GCCCAAATATG
* * *
22616 ATGTTGTGCATACATGT-ACCTCCAAATTACTAAATACCTTGAAGATACGTTACAAGTTTTTAGA
1 ATGTTGTG----CATGTAACCTCCAAATTACTAAATACCTTGAAGAGACGATACAAGTATTTAGA
22680 ACCGCCCAAATATG
62 ACCGCCCAAATATG
22694 ATGTTGTGCATGTAACCTCCAAATTACTAAATACCTT
1 ATGTTGTGCATGTAACCTCCAAATTACTAAATACCTT
22731 TAGAAAACTT
Statistics
Matches: 103, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
74 5 0.05
75 31 0.30
78 61 0.59
79 6 0.06
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (75 bp):
ATGTTGTGCATGTAACCTCCAAATTACTAAATACCTTGAAGAGACGATACAAGTATTTAGAACCG
CCCAAATATG
Found at i:33843 original size:440 final size:434
Alignment explanation
Indices: 32894--34149 Score: 1417
Period size: 440 Copynumber: 2.9 Consensus size: 434
32884 TCAAACAAAT
* * *
32894 TTTCAGGTCCTTCATGAAAGTCATAGATCACGCAACAACCTTTTAACCGACACTTAAACAACTTT
1 TTTCAGGCCCTTCATGAAAGTCATAGATCACGCAATAACCTTTTAACCGACACTTAAATAA--TT
* * * * * * *
32959 TGAATGGGACACATGGATAAAAATTTATATGGTATTAGATAGACCGTCAATCGAGATCACCAAAT
64 TCAATCGGACACATTGAT-AAAA-TTATACGATATTAGATAGACCGGCAATCGAGACCACCAAA-
* * * * * *
33024 TTTGGAAA-CTTTTTTTAGAA-CTGAAAGCTCAAAATTGGCTTTTGAGTCCTTAATGAAAGTTTT
126 TTTCGAAAGC-ATTTTTAGAATC-AAAACCTTAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGT
* * *
33087 AGATCATGAAATTATCTTTTAATAGACACTTGAATCAGCTTAATCGGACAAATAGAACAAAAAAT
189 AGATCATGAAATTATCTTTTAATAGACACTTGAATAACCTTGATCGGACAAATAGAACAAAAAAT
* * * * * *
33152 ATAACAATAAAAGACAAAGCGTTAACTCGTCCAACCTATAATTT-TAAAGGATTCAATAGCATAA
254 AAAAAAATTAAA-ACAAAACGTTAA-TCGTCCAACCCATAATTTGTAAAGGATTAAATAGCATAA
* * * *
33216 AGCATAAAGGTATGAGGGTCATTAGATAATTAATCCAACAAAAAATTGATTAGTTTATAGAGACG
317 AGCATAAAAGTATG-GGGTCATTTGATAAATAATCCAACAAAAAATTGATTAGTTTATAGAGACC
* *
33281 AAACATAAATATTCCCTCTTGAACCCTCCATGAAACTAATTAATCAAATTCAGC
381 AAACATAAAAATTCCCTCTTGAACCCTCCACGAAACTAATTAATCAAATTCAGC
* * ** * * * * * *
33335 TTGCGGGCCCTTCATGAAAGTCATAGATCACATAATAACCGTTCAACCGATAGTTCAATAACTTC
1 TTTCAGGCCCTTCATGAAAGTCATAGATCACGCAATAACCTTTTAACCGACACTTAAATAATTTC
*
33400 AATCGGACACATTGATCAAGAATTATACGATATTAGATAGACCGGAAATCGAGACCACCAAATTT
66 AATCGGACACATTGAT-AA-AATTATACGATATTAGATAGACCGGCAATCGAGACCACCAAATTT
* *
33465 CGAAAGCATTTTTAGAATCAAAACCTTAAAATTGGCTTTTAAGTTCTTAATGAAAGTTGTAGATC
129 CGAAAGCATTTTTAGAATCAAAACCTTAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGTAGATC
* *
33530 ATTAAATTATCTTTTAATAGACACTTGAATAACCTTGATCGGAGAAATAGAACAAAAAATAAAAA
194 ATGAAATTATCTTTTAATAGACACTTGAATAACCTTGATCGGACAAATAGAACAAAAAAT-AAAA
* * *
33595 AAATTAAAACTAAAACGTTAAGTTGTCCAACCCAGAATTTGTAAAGGATTAAATAGCATCAAGCA
258 AAATTAAAAC-AAAACGTTAA-TCGTCCAACCCATAATTTGTAAAGGATTAAATAGCATAAAGCA
** * *
33660 TAAAAGTATGGGTGTCATTTGATAAATAATCCATGGAAAAAATT-ATTTGTTTATGGAGACCAAA
321 TAAAAGTATGGG-GTCATTTGATAAATAATCCA-ACAAAAAATTGATTAGTTTATAGAGACCAAA
* *
33724 TATAAAAATTCCCTCTTGAACTCTCCACGAAAC-ATATTAATCAAATTCAGC
384 CATAAAAATTCCCTCTTGAACCCTCCACGAAACTA-ATTAATCAAATTCAGC
* * * * **
33775 TTTCAGGCCCTTGATAAAAGTCGTAGATCATGCAATAACCTTTTAACCGACACTTGGATAATTTC
1 TTTCAGGCCCTTCATGAAAGTCATAGATCACGCAATAACCTTTTAACCGACACTTAAATAATTTC
* * * * *
33840 AATCGG--ACA-TG-TGGAAATTATACAATATTAGATAGACCAGCAATCGAGACAACAAAATTTC
66 AATCGGACACATTGAT-AAAATTATACGATATTAGATAGACCGGCAATCGAGACCACCAAATTTC
* * * * *
33901 -AGAAGCATTTTTTAGAATCTAAACATTAAAATTGGGTTTTGAGTCCTTAATGAAAGTTGTAAAC
130 GA-AAGCA-TTTTTAGAATCAAAACCTTAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGTAGAT
* * * * *
33965 CATGAAATTACCTTTAAATAGACACATGAATTATCTTGATCGGACAAATAGAA-AAAAAATAAAA
193 CATGAAATTATCTTTTAATAGACACTTGAATAACCTTGATCGGACAAATAGAACAAAAAATAAAA
* * * * *
34029 GAATTAAAGCCGAAACATTTAATCGTCTAACCCATAA-TTGTAAAGGATTAAATAGCATAAAGCA
258 AAATTAAA-ACAAAAC-GTTAATCGTCCAACCCATAATTTGTAAAGGATTAAATAGCATAAAGCA
** * *
34093 TAAAAGTATGAGAATCATTTGATTAATAATCCAA-AAAAAA-TGA-TATGTTTATTGAGA
321 TAAAAGTATG-GGGTCATTTGATAAATAATCCAACAAAAAATTGATTA-GTTTATAGAGA
34150 GTAGGACCCA
Statistics
Matches: 692, Mismatches: 107, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
430 2 0.00
431 17 0.02
433 54 0.08
434 29 0.04
435 58 0.08
436 97 0.14
437 2 0.00
438 116 0.17
439 91 0.13
440 169 0.24
441 57 0.08
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (434 bp):
TTTCAGGCCCTTCATGAAAGTCATAGATCACGCAATAACCTTTTAACCGACACTTAAATAATTTC
AATCGGACACATTGATAAAATTATACGATATTAGATAGACCGGCAATCGAGACCACCAAATTTCG
AAAGCATTTTTAGAATCAAAACCTTAAAATTGGCTTTTGAGTCCTTAATGAAAGTTGTAGATCAT
GAAATTATCTTTTAATAGACACTTGAATAACCTTGATCGGACAAATAGAACAAAAAATAAAAAAA
TTAAAACAAAACGTTAATCGTCCAACCCATAATTTGTAAAGGATTAAATAGCATAAAGCATAAAA
GTATGGGGTCATTTGATAAATAATCCAACAAAAAATTGATTAGTTTATAGAGACCAAACATAAAA
ATTCCCTCTTGAACCCTCCACGAAACTAATTAATCAAATTCAGC
Found at i:37668 original size:30 final size:30
Alignment explanation
Indices: 37553--37657 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
37543 CGCCCGTAGG
37553 GAGAGAGAGGCTCAGTTGCAGAGGGAGAGA
1 GAGAGAGAGGCTCAGTTGCAGAGGGAGAGA
*
37583 GAGAGAGAGGCTCAGTTGTAGAGGGAGAGA
1 GAGAGAGAGGCTCAGTTGCAGAGGGAGAGA
* ** * *
37613 GAG-GCTGCTGCTCA-TATTCAGAGGGAGAGG
1 GAGAG-AGAGGCTCAGT-TGCAGAGGGAGAGA
37643 GAGAGAGAGGCTCAG
1 GAGAGAGAGGCTCAG
37658 ATTTTGAGGG
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
29 2 0.03
30 58 0.95
31 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.45, T:0.13
Consensus pattern (30 bp):
GAGAGAGAGGCTCAGTTGCAGAGGGAGAGA
Found at i:40302 original size:11 final size:11
Alignment explanation
Indices: 40268--40315 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
40258 TTGAAACAAT
40268 TCTTC-AATAG
1 TCTTCAAATAG
40278 TCTTC--A-AG
1 TCTTCAAATAG
40286 TCTTCAAATTA-
1 TCTTCAAA-TAG
40297 TCTTCAAATAG
1 TCTTCAAATAG
40308 TCTTCAAA
1 TCTTCAAA
40316 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 8 0.24
11 16 0.48
12 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:45147 original size:30 final size:30
Alignment explanation
Indices: 45086--45149 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
45076 AAGTTCGTGT
* *
45086 TTGATGACTTATTGAAGATAATTTGAAGAA
1 TTGAAGACTTATTGAAGATAATTTCAAGAA
*
45116 TTGAAGAC-TATTGAAGAATTATTTCAAGAA
1 TTGAAGACTTATTGAAG-ATAATTTCAAGAA
45146 TTGA
1 TTGA
45150 GGATTGAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (30 bp):
TTGAAGACTTATTGAAGATAATTTCAAGAA
Found at i:46844 original size:17 final size:17
Alignment explanation
Indices: 46824--46861 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
46814 AATACTAACA
46824 AATACATAATAA-ATAAT
1 AATAC-TAATAATATAAT
*
46841 AATACTAATAATATTAT
1 AATACTAATAATATAAT
46858 AATA
1 AATA
46862 ATACTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
AATACTAATAATATAAT
Found at i:47197 original size:20 final size:21
Alignment explanation
Indices: 47169--47211 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
47159 CAAAACTGTC
* *
47169 AAAAGGGGGCGGTAAGTAGCA
1 AAAAGGGGACGGTAAATAGCA
47190 AAAAGGGGACGGTAAATAGCA
1 AAAAGGGGACGGTAAATAGCA
47211 A
1 A
47212 CTCCCATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.37, T:0.09
Consensus pattern (21 bp):
AAAAGGGGACGGTAAATAGCA
Found at i:50987 original size:178 final size:178
Alignment explanation
Indices: 50723--51060 Score: 477
Period size: 178 Copynumber: 1.9 Consensus size: 178
50713 CTGATTAAGG
*
50723 TGATTTAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * * *
50788 AATTTAATGTTTCAAGTATAAAAAATGCTTTCGAAA-AATTTGTTGTTTCGGTTAACGGGAATAG
66 AATTTAATGTTTCAAGTATAAAAAATGC-TTCCAAAGAATTAGTTATTTCGGTTAAAGGAAATAG
*
50852 ACGGT-TCACTTAATATTATATAACTTT-TGCTCCAGATGTATAATTGAGA
130 ACGGTCT-ACTTAATATTACATAA-TTTGTGCTCCAGATGTATAATTGAGA
* * * * * *
50901 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGGCTCGAAAATTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
*
50966 AATTTAATG-TTCGAAGTATAAAAATTGCTTCCAAAGAATTAGTTATTTCGGTTAAAGGAAATAG
66 AATTTAATGTTTC-AAGTATAAAAAATGCTTCCAAAGAATTAGTTATTTCGGTTAAAGGAAATAG
*
51030 ATGGTCTACTTAATATTACATAATTTGTGCT
130 ACGGTCTACTTAATATTACATAATTTGTGCT
51061 TATGGTGGAA
Statistics
Matches: 141, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
177 12 0.09
178 128 0.91
179 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTATTTCGGTTAAAGGAAATAGA
CGGTCTACTTAATATTACATAATTTGTGCTCCAGATGTATAATTGAGA
Found at i:54704 original size:3 final size:3
Alignment explanation
Indices: 54696--54721 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54686 ACAAATTGGG
54696 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
54722 CGGGCCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:55993 original size:14 final size:14
Alignment explanation
Indices: 55974--56001 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55964 GAAGCTTTGG
55974 ATTTTATGTTATGA
1 ATTTTATGTTATGA
55988 ATTTTATGTTATGA
1 ATTTTATGTTATGA
56002 GACACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
ATTTTATGTTATGA
Found at i:59055 original size:37 final size:38
Alignment explanation
Indices: 59014--59089 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
59004 TGAATAGGTA
59014 TAAACTACC-AAAAACTGTCTTTTATCTGATAGATACC
1 TAAACTACCAAAAAACTGTCTTTTATCTGATAGATACC
*
59051 TAAACTACCAAAAAACTGTCTTTTATCTTATAGATACC
1 TAAACTACCAAAAAACTGTCTTTTATCTGATAGATACC
59089 T
1 T
59090 TTTATTTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 9 0.24
38 28 0.76
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (38 bp):
TAAACTACCAAAAAACTGTCTTTTATCTGATAGATACC
Found at i:65062 original size:31 final size:31
Alignment explanation
Indices: 65027--65098 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
65017 TAATTTCTGA
65027 CAAATGATTTGGCAGTGAAATTCACAAAAGG
1 CAAATGATTTGGCAGTGAAATTCACAAAAGG
65058 CAAATGATTTGGCAGTGAAATTCACAAAAGG
1 CAAATGATTTGGCAGTGAAATTCACAAAAGG
*
65089 CAAATAATTT
1 CAAATGATTT
65099 CTGACAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.25
Consensus pattern (31 bp):
CAAATGATTTGGCAGTGAAATTCACAAAAGG
Found at i:68421 original size:33 final size:33
Alignment explanation
Indices: 68384--68477 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 33
68374 GCGTAGACGA
68384 TAGCGCGGATGGCCGGGCATGTGGCTCGGATGG
1 TAGCGCGGATGGCCGGGCATGTGGCTCGGATGG
* * * *
68417 TAGCGCTGATGGCTGGGCATGAGGCTCGGGTGG
1 TAGCGCGGATGGCCGGGCATGTGGCTCGGATGG
* * *
68450 TTG-G-GTCATGGCCGGGCATGTGTCTCGG
1 TAGCGCG-GATGGCCGGGCATGTGGCTCGG
68478 CGCAGCTCGG
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
32 19 0.38
33 31 0.62
ACGTcount: A:0.11, C:0.20, G:0.47, T:0.22
Consensus pattern (33 bp):
TAGCGCGGATGGCCGGGCATGTGGCTCGGATGG
Found at i:70921 original size:15 final size:16
Alignment explanation
Indices: 70895--70936 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
70885 GCAGAGGGTT
70895 AAGAAGAACAATTAAA-
1 AAGAA-AACAATTAAAC
70911 AAGAAAACAATTAAAC
1 AAGAAAACAATTAAAC
*
70927 TAGAAAACAA
1 AAGAAAACAA
70937 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12
Consensus pattern (16 bp):
AAGAAAACAATTAAAC
Found at i:72355 original size:19 final size:18
Alignment explanation
Indices: 72322--72357 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
72312 TTGAAATAAT
72322 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
72340 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
72358 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:87707 original size:2 final size:2
Alignment explanation
Indices: 87700--87733 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
87690 GAAAATTGGA
*
87700 AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
87734 ATAAGCCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:92695 original size:17 final size:17
Alignment explanation
Indices: 92673--92708 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
92663 GATCGGGTTC
92673 GGGTCATTTTGGGTCTG
1 GGGTCATTTTGGGTCTG
*
92690 GGGTCATTTTGGGTTTG
1 GGGTCATTTTGGGTCTG
92707 GG
1 GG
92709 TCGTTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.08, G:0.44, T:0.42
Consensus pattern (17 bp):
GGGTCATTTTGGGTCTG
Found at i:95486 original size:3 final size:3
Alignment explanation
Indices: 95478--95526 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
95468 CTAAACAGAT
95478 ATA ATA ATA ATA 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
95526 A
1 A
95527 ATTGCTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:100672 original size:24 final size:24
Alignment explanation
Indices: 100603--100673 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
100593 ACCACGTTTA
* * * *
100603 ATGGTAGGCGCGCTGCCACTTCGG
1 ATGGTGGGTGCGCTTCCACTTCAG
* *
100627 ATGGGGGGGTGTGC-TCCTACTTCAG
1 AT-GGTGGGTGCGCTTCC-ACTTCAG
100652 ATGGTGGGTGCGCTTCCACTTC
1 ATGGTGGGTGCGCTTCCACTTC
100674 TGCTGGTGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.11, C:0.25, G:0.37, T:0.27
Consensus pattern (24 bp):
ATGGTGGGTGCGCTTCCACTTCAG
Found at i:100968 original size:28 final size:28
Alignment explanation
Indices: 100937--101028 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
100927 TTGTCTTCGA
*
100937 GAGCATACTACCTCTTCCCTATCTTTGG
1 GAGCGTACTACCTCTTCCCTATCTTTGG
*
100965 GAGCGTACTACCTCTTCGCTATCTTTGG
1 GAGCGTACTACCTCTTCCCTATCTTTGG
* * *
100993 GAGCGTACTACCGCTT-CCTGGTCATTGG
1 GAGCGTACTACCTCTTCCCT-ATCTTTGG
101021 GAGCGTAC
1 GAGCGTAC
101029 CACCGCTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 2 0.04
28 55 0.96
ACGTcount: A:0.16, C:0.29, G:0.23, T:0.32
Consensus pattern (28 bp):
GAGCGTACTACCTCTTCCCTATCTTTGG
Found at i:101048 original size:28 final size:28
Alignment explanation
Indices: 100957--101049 Score: 107
Period size: 28 Copynumber: 3.3 Consensus size: 28
100947 CCTCTTCCCT
*
100957 ATCTTTGGGAGCGTACTACCTCTTCGCT-
1 ATCTTTGGGAGCGTACTACCGCTTCG-TG
*
100985 ATCTTTGGGAGCGTACTACCGCTTCCTG
1 ATCTTTGGGAGCGTACTACCGCTTCGTG
* * * *
101013 GTCATTGGGAGCGTACCACCGCTTTGTG
1 ATCTTTGGGAGCGTACTACCGCTTCGTG
*
101041 AACTTTGGG
1 ATCTTTGGG
101050 TGCGCTCCCT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.02
28 53 0.98
ACGTcount: A:0.15, C:0.26, G:0.27, T:0.32
Consensus pattern (28 bp):
ATCTTTGGGAGCGTACTACCGCTTCGTG
Found at i:101252 original size:29 final size:29
Alignment explanation
Indices: 101220--101294 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
101210 ATGCAACGTC
*
101220 CTCTTCCAAGATGGTGTG-TGCACGGCGCT
1 CTCTTCCAAGATGGTG-GATGCACGACGCT
* *
101249 CTCTTCCAAGATGGCGGATGTACGACGCT
1 CTCTTCCAAGATGGTGGATGCACGACGCT
101278 CTCTTCCAAGATGGTGG
1 CTCTTCCAAGATGGTGG
101295 GCGCTACCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (29 bp):
CTCTTCCAAGATGGTGGATGCACGACGCT
Found at i:101328 original size:27 final size:27
Alignment explanation
Indices: 101298--101440 Score: 126
Period size: 27 Copynumber: 5.2 Consensus size: 27
101288 ATGGTGGGCG
* * *
101298 CTACCATTTCGTGAACTTTGGGGAGTA
1 CTACCAATTCGAGAGCTTTGGGGAGTA
** * *
101325 CTACCACCTCGAGAGCTTGGAGGGCGTA
1 CTACCAATTCGAGAGCTTTG-GGGAGTA
* *
101353 CTACCAATTCGCGAGCTTTGGGGTGTA
1 CTACCAATTCGAGAGCTTTGGGGAGTA
** * *
101380 CTACCACCTCGAGAGCTTGGAGGGCGTA
1 CTACCAATTCGAGAGCTTTG-GGGAGTA
*
101408 CTACCAATTCGCGAGCTTTGGGGCA-TA
1 CTACCAATTCGAGAGCTTTGGGG-AGTA
101435 CTACCA
1 CTACCA
101441 CCTCGCGGTC
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
27 48 0.52
28 44 0.48
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (27 bp):
CTACCAATTCGAGAGCTTTGGGGAGTA
Found at i:101355 original size:28 final size:28
Alignment explanation
Indices: 101322--101633 Score: 215
Period size: 28 Copynumber: 11.2 Consensus size: 28
101312 ACTTTGGGGA
* *
101322 GTACTACCACCTCGAGAGCTTGGAGGGC
1 GTACTACCACTTCGCGAGCTTGGAGGGC
* * *
101350 GTACTACCAATTCGCGAGCTTTG-GGGT
1 GTACTACCACTTCGCGAGCTTGGAGGGC
* *
101377 GTACTACCACCTCGAGAGCTTGGAGGGC
1 GTACTACCACTTCGCGAGCTTGGAGGGC
* *
101405 GTACTACCAATTCGCGAGCTTTG-GGGC
1 GTACTACCACTTCGCGAGCTTGGAGGGC
* * *
101432 ATACTACCACCTCGCG-GTCTTTGG-GAGC
1 GTACTACCACTTCGCGAG-C-TTGGAGGGC
* * * * * *
101460 GCATTACCTCTTTGCGATCCTT-GAGAGC
1 GTACTACCACTTCGCGA-GCTTGGAGGGC
** * * *
101488 GTACTTTCACCTCGAGAGCTTGGAGGGA
1 GTACTACCACTTCGCGAGCTTGGAGGGC
* * * *
101516 GTACTACCATTTCGTGAACTTTGA-GGC
1 GTACTACCACTTCGCGAGCTTGGAGGGC
* * *
101543 GTACTACCACTTTGCGATCCTT-GAGGGT
1 GTACTACCACTTCGCGA-GCTTGGAGGGC
* ** *
101571 GTACTACCACCTCAAGAGCTTGGAGCGC
1 GTACTACCACTTCGCGAGCTTGGAGGGC
*
101599 GTACTACCAATTCGCGAGCTTGGAGGGC
1 GTACTACCACTTCGCGAGCTTGGAGGGC
*
101627 ATACTAC
1 GTACTAC
101634 GATTTCATGA
Statistics
Matches: 211, Mismatches: 63, Indels: 20
0.72 0.21 0.07
Matches are distributed among these distances:
26 1 0.00
27 65 0.31
28 144 0.68
29 1 0.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (28 bp):
GTACTACCACTTCGCGAGCTTGGAGGGC
Found at i:101375 original size:55 final size:55
Alignment explanation
Indices: 101298--101552 Score: 246
Period size: 55 Copynumber: 4.6 Consensus size: 55
101288 ATGGTGGGCG
* *
101298 CTACCATTTCGTGAACTTTGGGGAGTACTACCACCTCGAGAGCTTGGAGGGCGTA
1 CTACCAATTCGCGAACTTTGGGGAGTACTACCACCTCGAGAGCTTGGAGGGCGTA
* *
101353 CTACCAATTCGCGAGCTTTGGGGTGTACTACCACCTCGAGAGCTTGGAGGGCGTA
1 CTACCAATTCGCGAACTTTGGGGAGTACTACCACCTCGAGAGCTTGGAGGGCGTA
* * * *
101408 CTACCAATTCGCGAGCTTTGGGGCA-TACTACCACCTCGCG-GTCTTTGG-GAGCGCA
1 CTACCAATTCGCGAACTTTGGGG-AGTACTACCACCTCGAGAG-C-TTGGAGGGCGTA
* ** * * * * * ** *
101463 TTACCTCTTTGCGATCCTTGAGAGCGTACTTTCACCTCGAGAGCTTGGAGGGAGTA
1 CTACCAATTCGCGAACTTTG-GGGAGTACTACCACCTCGAGAGCTTGGAGGGCGTA
* * * *
101519 CTACCATTTCGTGAACTTTGAGGCGTACTACCAC
1 CTACCAATTCGCGAACTTTGGGGAGTACTACCAC
101553 TTTGCGATCC
Statistics
Matches: 160, Mismatches: 33, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
54 1 0.01
55 122 0.76
56 36 0.22
57 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.26
Consensus pattern (55 bp):
CTACCAATTCGCGAACTTTGGGGAGTACTACCACCTCGAGAGCTTGGAGGGCGTA
Found at i:101795 original size:28 final size:28
Alignment explanation
Indices: 101763--101833 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
101753 GTCTTTGGGA
* * *
101763 GCATATTACCGCTTTGCGATCCTTAAGG
1 GCATACTACCCCTTTGCAATCCTTAAGG
* *
101791 GCATACTACCCCTTTGTAATCCTTGAGG
1 GCATACTACCCCTTTGCAATCCTTAAGG
* *
101819 GCGTACTACACCTTT
1 GCATACTACCCCTTT
101834 TTTTTTATGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.32
Consensus pattern (28 bp):
GCATACTACCCCTTTGCAATCCTTAAGG
Found at i:102750 original size:58 final size:57
Alignment explanation
Indices: 102561--102750 Score: 308
Period size: 58 Copynumber: 3.3 Consensus size: 57
102551 TAGGTTGCAC
* *
102561 GACCGAGGGATGCTCGTTTCTCTTTTTACACGAGTGGGGGATGCCCACTAGGTCGTGT
1 GACCGAGGGATGCTCGTTT-TCTTATTGCACGAGTGGGGGATGCCCACTAGGTCGTGT
* *
102619 GACCGGGGGATGCTCAATTTTCTTATTGCACGAGTGGGGGATGCCCACTAGGTCGTGT
1 GACCGAGGGATGCTC-GTTTTCTTATTGCACGAGTGGGGGATGCCCACTAGGTCGTGT
102677 GACCGAGGGATGCTCGCTTTTCTTATTGCACGAGTGGGGGATGCCCACTAGGTCGTGT
1 GACCGAGGGATGCTCG-TTTTCTTATTGCACGAGTGGGGGATGCCCACTAGGTCGTGT
*
102735 GACCGAGGGGTGCTCG
1 GACCGAGGGATGCTCG
102751 GTCGTTCTTG
Statistics
Matches: 123, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
58 120 0.98
59 3 0.02
ACGTcount: A:0.16, C:0.22, G:0.35, T:0.27
Consensus pattern (57 bp):
GACCGAGGGATGCTCGTTTTCTTATTGCACGAGTGGGGGATGCCCACTAGGTCGTGT
Found at i:102804 original size:12 final size:12
Alignment explanation
Indices: 102787--102817 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
102777 CTAATCAAAA
102787 TAGCATGATGCT
1 TAGCATGATGCT
102799 TAGCATGATGCT
1 TAGCATGATGCT
*
102811 TTGCATG
1 TAGCATG
102818 GCCATTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (12 bp):
TAGCATGATGCT
Found at i:102879 original size:2 final size:2
Alignment explanation
Indices: 102872--102897 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
102862 ATACATAACG
102872 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
102898 CATAATGGTA
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):
AT
Found at i:105939 original size:30 final size:30
Alignment explanation
Indices: 105903--106000 Score: 187
Period size: 30 Copynumber: 3.3 Consensus size: 30
105893 TGTTGGGTTA
*
105903 GGGTTAGGTGATGGTATTTATAATGATGTT
1 GGGTTAGGTGATGGTATTTATAAGGATGTT
105933 GGGTTAGGTGATGGTATTTATAAGGATGTT
1 GGGTTAGGTGATGGTATTTATAAGGATGTT
105963 GGGTTAGGTGATGGTATTTATAAGGATGTT
1 GGGTTAGGTGATGGTATTTATAAGGATGTT
105993 GGGTTAGG
1 GGGTTAGG
106001 GTTTCAAGAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (30 bp):
GGGTTAGGTGATGGTATTTATAAGGATGTT
Found at i:106152 original size:18 final size:15
Alignment explanation
Indices: 106126--106173 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
106116 GAAGATAATT
106126 CAGAAGAAGAAGATG
1 CAGAAGAAGAAGATG
* *
106141 CAGATATGGAAGATGATT
1 CAGA-A--GAAGAAGATG
106159 CAGAAGAAGAAGATG
1 CAGAAGAAGAAGATG
106174 TCGACTGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.46
16 1 0.04
17 1 0.04
18 12 0.46
ACGTcount: A:0.48, C:0.06, G:0.31, T:0.15
Consensus pattern (15 bp):
CAGAAGAAGAAGATG
Found at i:109516 original size:31 final size:29
Alignment explanation
Indices: 109458--109521 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 29
109448 TGTGGGGTTT
*
109458 ATTTGTCCCAAAAAATAGATAAGGGGCCG
1 ATTTGTCCCAAAAAATAGATAAGGGGCCA
*
109487 ATTTGTCCCAAAATAAATAG-TTAGAGGGCCA
1 ATTTGTCCC-AAA-AAATAGATAAG-GGGCCA
109518 ATTT
1 ATTT
109522 TTGCCTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.30
30 6 0.20
31 15 0.50
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (29 bp):
ATTTGTCCCAAAAAATAGATAAGGGGCCA
Found at i:111631 original size:23 final size:23
Alignment explanation
Indices: 111601--111645 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
111591 TCCCAATAAT
111601 AAAAAATGAAAAAAAAAAAGAAG
1 AAAAAATGAAAAAAAAAAAGAAG
**
111624 AAAAAATGAAAATGAAAAAGAA
1 AAAAAATGAAAAAAAAAAAGAA
111646 AATGAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (23 bp):
AAAAAATGAAAAAAAAAAAGAAG
Found at i:112070 original size:25 final size:25
Alignment explanation
Indices: 112042--112116 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
112032 AAAATATAAT
* *
112042 AAAATAAAAT-AAATCAAAGTCAACC
1 AAAATAAAATCAAATCAAAATCAA-A
112067 AAAA-AAAATCAAATCAAAATCAAA
1 AAAATAAAATCAAATCAAAATCAAA
*
112091 AAAATCAAATCAAATCAAAATCAAA
1 AAAATAAAATCAAATCAAAATCAAA
112116 A
1 A
112117 GAGAATGGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
24 9 0.20
25 36 0.80
ACGTcount: A:0.69, C:0.15, G:0.01, T:0.15
Consensus pattern (25 bp):
AAAATAAAATCAAATCAAAATCAAA
Found at i:112082 original size:5 final size:5
Alignment explanation
Indices: 112072--112115 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
112062 CAACCAAAAA
*
112072 AAATC AAATC AAAATC AAA-A AAATC AAATC AAATC AAAATC AAA
1 AAATC AAATC -AAATC AAATC AAATC AAATC AAATC -AAATC AAA
112116 AGAGAATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 3 0.09
5 21 0.62
6 10 0.29
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (5 bp):
AAATC
Found at i:112104 original size:20 final size:19
Alignment explanation
Indices: 112029--112110 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 19
112019 AAGAAATTAA
*
112029 AAAAAAAT-ATAATAAAAT-
1 AAAAAAATCA-AATCAAATC
*
112047 AAAATAAATCAAAGTC-AACC
1 AAAA-AAATCAAA-TCAAATC
112067 AAAAAAAATCAAATCAAAATC
1 -AAAAAAATCAAATC-AAATC
112088 AAAAAAATCAAATCAAATC
1 AAAAAAATCAAATCAAATC
112107 AAAA
1 AAAA
112111 TCAAAAGAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.07
19 19 0.35
20 24 0.44
21 7 0.13
ACGTcount: A:0.71, C:0.12, G:0.01, T:0.16
Consensus pattern (19 bp):
AAAAAAATCAAATCAAATC
Found at i:112793 original size:50 final size:50
Alignment explanation
Indices: 112707--112806 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
112697 AGTTTTACAA
* * * * *
112707 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCATTCCATTTGTGAGTCCAAAATAAAAATTCGCTTTTCAAAG
112757 TAAAATTGCATTCCATTTGTGAGTCCAAAATAAAAATTCGCTTTTCAAAG
1 TAAAATTGCATTCCATTTGTGAGTCCAAAATAAAAATTCGCTTTTCAAAG
112807 GACATTGAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (50 bp):
TAAAATTGCATTCCATTTGTGAGTCCAAAATAAAAATTCGCTTTTCAAAG
Found at i:113354 original size:79 final size:79
Alignment explanation
Indices: 113260--113409 Score: 255
Period size: 79 Copynumber: 1.9 Consensus size: 79
113250 CAAGTTATCA
* *
113260 AAGTTGACTGCACATTGGTCCTCTTTCATCATTAATCAAGAAATTTTCAGTTACAACATCAGACT
1 AAGTTGACCGCACATTGGTCCTCTTTCATCATCAATCAAGAAATTTTCAGTTACAACATCAGACT
113325 CAGAGTTATTTTTC
66 CAGAGTTATTTTTC
* * *
113339 AAGTTGACCGCACATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAGATT
1 AAGTTGACCGCACATTGGTCCTCTTTCATCATCAATCAAGAAATTTTCAGTTACAACATCAGACT
113404 CAGAGT
66 CAGAGT
113410 CATTGTCCCA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (79 bp):
AAGTTGACCGCACATTGGTCCTCTTTCATCATCAATCAAGAAATTTTCAGTTACAACATCAGACT
CAGAGTTATTTTTC
Found at i:113616 original size:50 final size:50
Alignment explanation
Indices: 113482--113600 Score: 202
Period size: 50 Copynumber: 2.4 Consensus size: 50
113472 TCCGAATGCT
113482 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
* *
113532 CAGGCTTTTCCACAAGGCAAACTCGTTTCCATACGAGTCGATTATCAACA
1 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
**
113582 TGGGCTTTTCCACAAGCCA
1 CAGGCTTTTCCACAAGCCA
113601 CATCCGGTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (50 bp):
CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
Found at i:113701 original size:50 final size:50
Alignment explanation
Indices: 113628--113833 Score: 376
Period size: 50 Copynumber: 4.1 Consensus size: 50
113618 TGCATTACCT
113628 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
113678 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGCCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
113728 TTTTGAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
* *
113778 TTTTAAGATTGAGTTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
113828 TTTTAA
1 TTTTAA
113834 TATGTTAGAT
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 150 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
Done.