Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011593.1 Corchorus capsularis cultivar CVL-1 contig11614, 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: 39045
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:298 original size:33 final size:33
Alignment explanation
Indices: 239--424 Score: 192
Period size: 33 Copynumber: 5.6 Consensus size: 33
229 TCACCTAGCA
* *
239 CGTACCAAGAGAGTCTCCCCTAAGGGAGTCTCG
1 CGTAGCAAGAGAGTCTCCCCTGAGGGAGTCTCG
* * * *
272 CGTAACAAGAGAGCCTCCTCTTAGGGAGTCTCG
1 CGTAGCAAGAGAGTCTCCCCTGAGGGAGTCTCG
* * * *
305 CATAGCAAGAGAGTTTCCCTTGAAGGAGTCTCG
1 CGTAGCAAGAGAGTCTCCCCTGAGGGAGTCTCG
* * *
338 CGTAGCAAGGGAGTCTCCCCTGAAGGAATCTCG
1 CGTAGCAAGAGAGTCTCCCCTGAGGGAGTCTCG
* * * *
371 CGTAGTAAGGGAGTCTCACTTGAGGGAGTCTCG
1 CGTAGCAAGAGAGTCTCCCCTGAGGGAGTCTCG
** *
404 CGTAGTGAGGGAGTCTCCCCT
1 CGTAGCAAGAGAGTCTCCCCT
425 AACGCACAAC
Statistics
Matches: 128, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 128 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.22
Consensus pattern (33 bp):
CGTAGCAAGAGAGTCTCCCCTGAGGGAGTCTCG
Found at i:352 original size:18 final size:17
Alignment explanation
Indices: 294--420 Score: 77
Period size: 18 Copynumber: 7.6 Consensus size: 17
284 GCCTCCTCTT
*
294 AGGGAGTCTCGCATAGCA
1 AGGGAGTCTCGCGTAG-A
* * * *
312 AGAGAGTTTC-CCTTGA
1 AGGGAGTCTCGCGTAGA
328 A-GGAGTCTCGCGTAGCA
1 AGGGAGTCTCGCGTAG-A
* *
345 AGGGAGTCTCCCCT-GA
1 AGGGAGTCTCGCGTAGA
*
361 A-GGAATCTCGCGTAGTA
1 AGGGAGTCTCGCGTAG-A
* *
378 AGGGAGTCTCAC-TTG-
1 AGGGAGTCTCGCGTAGA
*
393 AGGGAGTCTCGCGTAGTG
1 AGGGAGTCTCGCGTAG-A
411 AGGGAGTCTC
1 AGGGAGTCTC
421 CCCTAACGCA
Statistics
Matches: 82, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
15 26 0.32
16 10 0.12
17 10 0.12
18 36 0.44
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.22
Consensus pattern (17 bp):
AGGGAGTCTCGCGTAGA
Found at i:694 original size:29 final size:29
Alignment explanation
Indices: 629--692 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
619 GGCGTGACGC
* *
629 TCCCCCTGT-GTTTGAATGTAAAGGTGGCG
1 TCCCCCT-TCGTTTGAATGCAAAGGGGGCG
*
658 TCCCCCTTCGTTTGAATGCAAGGGGGTGCG
1 TCCCCCTTCGTTTGAATGCAAAGGGG-GCG
688 TCCCC
1 TCCCC
693 TTTTCTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 21 0.70
30 8 0.27
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (29 bp):
TCCCCCTTCGTTTGAATGCAAAGGGGGCG
Found at i:722 original size:2 final size:2
Alignment explanation
Indices: 717--742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
707 TTTTTAAATA
717 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
743 TCTAAGGTAA
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:882 original size:25 final size:26
Alignment explanation
Indices: 826--888 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
816 AACCCTGGGG
*
826 GAGTCTTCCCTAGCGCGTGCAGCACGT
1 GAGTCTCCCCTAGCGCGT-CAGCACGT
* *
853 TAGTCTCCCCTAGCGCGT-AGCAGGT
1 GAGTCTCCCCTAGCGCGTCAGCACGT
878 GAGTCTCCCCT
1 GAGTCTCCCCT
889 GAGACGCAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 16 0.50
27 16 0.50
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (26 bp):
GAGTCTCCCCTAGCGCGTCAGCACGT
Found at i:899 original size:25 final size:23
Alignment explanation
Indices: 844--899 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
834 CCTAGCGCGT
*
844 GCAGCACGTTAGTCTCCCCTAGC
1 GCAGCACGTGAGTCTCCCCTAGC
*
867 GCGTAGCAGGTGAGTCTCCCCTGAGAC
1 GC--AGCACGTGAGTCTCCCCT-AG-C
894 GCAGCA
1 GCAGCA
900 AGAGAGCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
25 20 0.74
26 2 0.07
27 3 0.11
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.18
Consensus pattern (23 bp):
GCAGCACGTGAGTCTCCCCTAGC
Found at i:2072 original size:36 final size:36
Alignment explanation
Indices: 2012--2088 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2002 TTATGTATTA
* *
2012 GGCGACTTAGGCCAGCGGCGTTATAGCCAAACATTG
1 GGCGACTAAGGCCAGCGGCATTATAGCCAAACATTG
* * * **
2048 GGCGACTAAGGCTAGTGGCATTATAGCTAAGTATTG
1 GGCGACTAAGGCCAGCGGCATTATAGCCAAACATTG
2084 GGCGA
1 GGCGA
2089 TCAATCTTAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (36 bp):
GGCGACTAAGGCCAGCGGCATTATAGCCAAACATTG
Found at i:4096 original size:16 final size:16
Alignment explanation
Indices: 4077--4147 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
4067 GCTTTTGTAA
4077 GTGAGTATCTCACCAG
1 GTGAGTATCTCACCAG
*
4093 GTGAGTATCTTACCAG
1 GTGAGTATCTCACCAG
*
4109 GTGAGTAT-TTACCAG
1 GTGAGTATCTCACCAG
*
4124 GTGAGTATTTCACCAG
1 GTGAGTATCTCACCAG
4140 GTGAGTAT
1 GTGAGTAT
4148 GGTATTGGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
15 15 0.29
16 37 0.71
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (16 bp):
GTGAGTATCTCACCAG
Found at i:4126 original size:31 final size:32
Alignment explanation
Indices: 4077--4147 Score: 110
Period size: 31 Copynumber: 2.2 Consensus size: 32
4067 GCTTTTGTAA
4077 GTGAGTATCTCACCAGGTGAGTATCTT-ACCAG
1 GTGAGTATCTCACCAGGTGAGTAT-TTCACCAG
*
4109 GTGAGTAT-TTACCAGGTGAGTATTTCACCAG
1 GTGAGTATCTCACCAGGTGAGTATTTCACCAG
4140 GTGAGTAT
1 GTGAGTAT
4148 GGTATTGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 2 0.05
31 27 0.73
32 8 0.22
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (32 bp):
GTGAGTATCTCACCAGGTGAGTATTTCACCAG
Found at i:4419 original size:22 final size:22
Alignment explanation
Indices: 4394--4468 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
4384 CTACACCTTC
4394 TATGAAATTTTTGTAACCACAT
1 TATGAAATTTTTGTAACCACAT
*
4416 TATGAAA-TTTTGATAATCACAT
1 TATGAAATTTTTG-TAACCACAT
* *
4438 TATGAAATTTTGGTAGCCACAT
1 TATGAAATTTTTGTAACCACAT
*
4460 TATAAAATT
1 TATGAAATT
4469 CGATAATCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 5 0.11
22 37 0.80
23 4 0.09
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTTGTAACCACAT
Found at i:4475 original size:43 final size:44
Alignment explanation
Indices: 4394--4476 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
4384 CTACACCTTC
* * *
4394 TATGAAATTTTTGTAACCACATTATGAAATTTTGATAATCACAT
1 TATGAAATTTTGGTAACCACATTATGAAAATTCGATAATCACAT
*
4438 TATGAAATTTTGGTAGCCACATTAT-AAAATTCGATAATC
1 TATGAAATTTTGGTAACCACATTATGAAAATTCGATAATC
4477 TACAAAGTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 12 0.34
44 23 0.66
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACATTATGAAAATTCGATAATCACAT
Found at i:4877 original size:53 final size:53
Alignment explanation
Indices: 4810--4912 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
4800 GTATCTTATT
4810 AAAAAAATTAAATTGGGCATAGTAAATATATAAAACCTAAAATTAAACTTAAA
1 AAAAAAATTAAATTGGGCATAGTAAATATATAAAACCTAAAATTAAACTTAAA
4863 AAAAAAATTAAATTGGGCATAGTAAATATATAAAACCTAAAATTAAACTT
1 AAAAAAATTAAATTGGGCATAGTAAATATATAAAACCTAAAATTAAACTT
4913 TTAATCATGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (53 bp):
AAAAAAATTAAATTGGGCATAGTAAATATATAAAACCTAAAATTAAACTTAAA
Found at i:5232 original size:2 final size:2
Alignment explanation
Indices: 5220--5258 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
5210 ATAGGCATAC
5220 TA TA TA T- TA TA TA TA T- TA TA TA TA CTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
5259 AATAATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5234 original size:9 final size:9
Alignment explanation
Indices: 5220--5258 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
5210 ATAGGCATAC
5220 TATATATTA
1 TATATATTA
5229 TATATATTA
1 TATATATTA
*
5238 TATATACTA
1 TATATATTA
5247 TATATA-TA
1 TATATATTA
5255 TATA
1 TATA
5259 AATAATTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (9 bp):
TATATATTA
Found at i:5364 original size:24 final size:23
Alignment explanation
Indices: 5337--5384 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5327 TTTGATTTAG
*
5337 AATTTGTAATTTTGATTTAGACTT
1 AATTTGTAATTTTAATTTA-ACTT
* *
5361 AATTTTTATTTTTAATTTAACTT
1 AATTTGTAATTTTAATTTAACTT
5384 A
1 A
5385 TATGATGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.58
Consensus pattern (23 bp):
AATTTGTAATTTTAATTTAACTT
Found at i:9749 original size:27 final size:26
Alignment explanation
Indices: 9719--9785 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 26
9709 AGGGTCCACG
9719 GGGGCATTTTGGTCATTTTTGCACCC
1 GGGGCATTTTGGTCATTTTTGCACCC
9745 AGGGGCATTTTGGTCATTTTTGCACCC
1 -GGGGCATTTTGGTCATTTTTGCACCC
*
9772 GAGGGCATCTTGGT
1 G-GGGCATTTTGGT
9786 AAATCAGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.13, C:0.21, G:0.30, T:0.36
Consensus pattern (26 bp):
GGGGCATTTTGGTCATTTTTGCACCC
Found at i:9869 original size:55 final size:55
Alignment explanation
Indices: 9784--10020 Score: 431
Period size: 55 Copynumber: 4.3 Consensus size: 55
9774 GGGCATCTTG
9784 GTAAATCAGTAATTAAGTAAAAAGCA-ATTAATCAGAGTCAAAGTAATAGTAATCA
1 GTAAATCAGTAATTAAGTAAAAAG-AGATTAATCAGAGTCAAAGTAATAGTAATCA
*
9839 GTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAAGTAATAGTAATCA
1 GTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCA
*
9894 GTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCA
1 GTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCA
*
9949 GTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAATAATCA
1 GTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCA
10004 GTAAATCAGTAATTAAG
1 GTAAATCAGTAATTAAG
10021 AGTTAAAATG
Statistics
Matches: 176, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
54 1 0.01
55 175 0.99
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (55 bp):
GTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCA
Found at i:9992 original size:26 final size:26
Alignment explanation
Indices: 9853--9994 Score: 76
Period size: 26 Copynumber: 5.2 Consensus size: 26
9843 ATCAGTAATT
*
9853 AAGTAAAAGGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
* * * *
9879 AAGTAATAGTAATCAG-TAAATCAGTAAT-T
1 AAGTAA-A--AA-GAGATTAATCAG-AGTCA
9908 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
** * * *
9934 AAGTAGTAGTAATCAG-TAAATCAGTAAT-T
1 AAGTA--A--AAAGAGATTAATCAG-AGTCA
9963 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
9989 AAGTAA
1 AAGTAA
9995 TAATAATCAG
Statistics
Matches: 83, Mismatches: 19, Indels: 28
0.64 0.15 0.22
Matches are distributed among these distances:
25 10 0.12
26 33 0.40
27 2 0.02
28 2 0.02
29 26 0.31
30 10 0.12
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (26 bp):
AAGTAAAAAGAGATTAATCAGAGTCA
Found at i:10305 original size:43 final size:42
Alignment explanation
Indices: 10255--10594 Score: 256
Period size: 43 Copynumber: 7.7 Consensus size: 42
10245 GTAATTAGTA
10255 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
* * **
10298 AAGAGTAAAATATTAGTCAGTAAAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * * **
10340 AAGAGTAAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGT-AAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
** * **
10383 AAGAGTAAAA-AGGCGATCAGTAAAGAGTAAAAAACTAATCAAC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* * *
10426 AAGAAGTAAAA-ACGTAATCAGTGAAAAGCAAAAGGCAATCAGTA-
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * * *
10470 AAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT--AAAA--AG--TAAAA-GGTAATCA--AC
*
10521 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
10564 AAGAGTAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
10595 GAATAATCAG
Statistics
Matches: 237, Mismatches: 42, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.00
42 31 0.13
43 129 0.54
44 22 0.09
45 13 0.05
46 2 0.01
47 4 0.02
49 8 0.03
50 9 0.04
51 18 0.08
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:10423 original size:22 final size:22
Alignment explanation
Indices: 10245--10608 Score: 209
Period size: 22 Copynumber: 16.5 Consensus size: 22
10235 GGGTAAAATG
* *
10245 GTAATTAGTAAAGAGTAAAATA
1 GTAATCAGTAAAGAGTAAAAAA
* * *
10267 GTAATCAGTAAAAAGTAAGAAG
1 GTAATCAGTAAAGAGTAAAAAA
*
10289 GTAATCA--ACAAGAGTAAAATA
1 GTAATCAGTA-AAGAGTAAAAAA
* * * *
10310 TTAGTCAGTAAAAAGT-AAATA
1 GTAATCAGTAAAGAGTAAAAAA
10331 GTAATCAGT-AAGAGTAAAAAAA
1 GTAATCAGTAAAGAGT-AAAAAA
* *
10353 GTAATAAGT-AAGAAGT-AAAAG
1 GTAATCAGTAAAG-AGTAAAAAA
* *
10374 GAAATCAGT-AAGAGTAAAAAG
1 GTAATCAGTAAAGAGTAAAAAA
**
10395 GCGATCAGTAAAGAGTAAAAAA
1 GTAATCAGTAAAGAGTAAAAAA
* *
10417 CTAATCA--ACAAGAAGTAAAAAC
1 GTAATCAGTA-AAG-AGTAAAAAA
* *
10439 GTAATCAGTGAAA-AG-CAAAAG
1 GTAATCAGT-AAAGAGTAAAAAA
* * *
10460 GCAATCAGTAAAAAGTAAAAGA
1 GTAATCAGTAAAGAGTAAAAAA
*
10482 GTAATCAGTAAAAAAGGAGCAGAAAATA
1 GTAATCAGT---AAA-GAGTA-AAAA-A
**
10510 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAGT-AAAGAGTAAAAAA
* * *
10533 GTAATCAGTAAAAAGTAAGAAG
1 GTAATCAGTAAAGAGTAAAAAA
*
10555 GTAATCA--ACAAGAGTAAAATA
1 GTAATCAGTA-AAGAGTAAAAAA
*
10576 GTAATCAGTACAA-AGTAAAGAA
1 GTAATCAGTA-AAGAGTAAAAAA
10598 -TAATCAGTAAA
1 GTAATCAGTAAA
10609 ATAGTGATGC
Statistics
Matches: 268, Mismatches: 50, Indels: 50
0.73 0.14 0.14
Matches are distributed among these distances:
20 16 0.06
21 92 0.34
22 110 0.41
23 17 0.06
24 5 0.02
25 8 0.03
26 7 0.03
27 3 0.01
28 10 0.04
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (22 bp):
GTAATCAGTAAAGAGTAAAAAA
Found at i:10491 original size:15 final size:15
Alignment explanation
Indices: 10473--10528 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
10463 ATCAGTAAAA
10473 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
10488 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
10502 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
10516 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
10529 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:10549 original size:116 final size:114
Alignment explanation
Indices: 10398--10609 Score: 246
Period size: 116 Copynumber: 1.8 Consensus size: 114
10388 TAAAAAGGCG
* ** *
10398 ATCAGTAAAGAGTAAAAAACTAATCAACAAGAAGTAAAAACGTAATCAGTGAAAAGCAAAA-GGC
1 ATCAGTAAAGAGTAAAAAACTAATCAACAAAAAGTAAAAACGTAATCA-ACAAAAGCAAAATAGC
*
10462 AATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTA
65 AATCAGTAAAAAGT-AAAGAATAATCAGTAAAAAAGGAGCAGAAAATAGTA
*** ** * * * * *
10513 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGT
1 ATCAGT-AAAGAGTAAAAAACTAATCAACAAAAAGTAAAAACGTAATCAACAAAAGCAAAATAGC
*
10578 AATCAGTACAAAGTAAAGAATAATCAGTAAAA
65 AATCAGTAAAAAGTAAAGAATAATCAGTAAAA
10610 TAGTGATGCT
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
115 31 0.39
116 48 0.61
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.17
Consensus pattern (114 bp):
ATCAGTAAAGAGTAAAAAACTAATCAACAAAAAGTAAAAACGTAATCAACAAAAGCAAAATAGCA
ATCAGTAAAAAGTAAAGAATAATCAGTAAAAAAGGAGCAGAAAATAGTA
Found at i:14335 original size:63 final size:63
Alignment explanation
Indices: 14141--14340 Score: 201
Period size: 63 Copynumber: 3.2 Consensus size: 63
14131 AGACAATGTG
* * * *
14141 TTATTCAGTAGTTGGTGGTATTTTCAGACTATATGTTTAATTATGTACTCGGAGTTTATGGTA
1 TTATTCAGCAGTAGATGGTATTTTCAGACTATGTGTTTAATTATGTACTCGGAGTTTATGGTA
* ** * * * * *
14204 TTATTCGGCAGGGGATGGTGTTTCCAGACTATGT-TATT-ATTCAATG--CTTGTAGTTCATGGT
1 TTATTCAGCAGTAGATGGTATTTTCAGACTATGTGT-TTAATT--ATGTACTCGGAGTTTATGGT
14265 A
63 A
* * * *
14266 TTATTCAGCAGTAGATGCTATTTTCAAACTATGTGTTTAATTATGTACTCGGAATTTATGATA
1 TTATTCAGCAGTAGATGGTATTTTCAGACTATGTGTTTAATTATGTACTCGGAGTTTATGGTA
14329 TTATTCAGCAGT
1 TTATTCAGCAGT
14341 GTATGATGTG
Statistics
Matches: 107, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
61 3 0.03
62 46 0.43
63 55 0.51
64 3 0.03
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (63 bp):
TTATTCAGCAGTAGATGGTATTTTCAGACTATGTGTTTAATTATGTACTCGGAGTTTATGGTA
Found at i:14357 original size:63 final size:62
Alignment explanation
Indices: 14168--14362 Score: 182
Period size: 63 Copynumber: 3.1 Consensus size: 62
14158 GTATTTTCAG
* * * * *
14168 ACTATATGTTTAATTATGTACTCGGAGTTTATGGTATTATTCGGCAGGGGATGGTGTTTCCAG
1 ACTATGTGTTTAATTATGTACTCGGAGTTTATGGTATTATTCAGCA-GTGATGATGTTTCCAA
* * * * * *
14231 ACTATGT-TATT-ATTCAATG--CTTGTAGTTCATGGTATTATTCAGCAGTAGATGCTATTTTCA
1 ACTATGTGT-TTAATT--ATGTACTCGGAGTTTATGGTATTATTCAGCAGT-GATGATGTTTCCA
14292 A
62 A
* * *
14293 ACTATGTGTTTAATTATGTACTCGGAATTTATGATATTATTCAGCAGTGTATGATGTGTCCAA
1 ACTATGTGTTTAATTATGTACTCGGAGTTTATGGTATTATTCAGCAGTG-ATGATGTTTCCAA
14356 ACTATGT
1 ACTATGT
14363 ATGGATGTCA
Statistics
Matches: 104, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
61 4 0.04
62 46 0.44
63 51 0.49
64 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (62 bp):
ACTATGTGTTTAATTATGTACTCGGAGTTTATGGTATTATTCAGCAGTGATGATGTTTCCAA
Found at i:20652 original size:49 final size:53
Alignment explanation
Indices: 20591--20689 Score: 161
Period size: 50 Copynumber: 1.9 Consensus size: 53
20581 ATTATGCCTA
20591 AAAAAAACTGGGCCT-AAAAAAGAAAGAGGTCACAA-AA-AGAAA-GAAAAAG
1 AAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCACAAGAAGAGAAATGAAAAAG
*
20640 AAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCGCAAGAAGAGAAATGAAA
1 AAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCACAAGAAGAGAAATGAAA
20690 CATAAGGAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 15 0.33
50 19 0.42
51 2 0.04
52 5 0.11
53 4 0.09
ACGTcount: A:0.61, C:0.10, G:0.22, T:0.07
Consensus pattern (53 bp):
AAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCACAAGAAGAGAAATGAAAAAG
Found at i:21864 original size:26 final size:27
Alignment explanation
Indices: 21803--21872 Score: 99
Period size: 26 Copynumber: 2.6 Consensus size: 27
21793 ATTAGGGTTG
*
21803 CCCGGGGGCATTTTGGTCATTTTTGCA
1 CCCGAGGGCATTTTGGTCATTTTTGCA
21830 CCC-AGGGGCATTTTGGTCA-TTTTGCA
1 CCCGA-GGGCATTTTGGTCATTTTTGCA
*
21856 CCCGAGGGCATCTTGGT
1 CCCGAGGGCATTTTGGT
21873 AAATTGGTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.13, C:0.24, G:0.30, T:0.33
Consensus pattern (27 bp):
CCCGAGGGCATTTTGGTCATTTTTGCA
Found at i:22515 original size:24 final size:24
Alignment explanation
Indices: 22483--22621 Score: 107
Period size: 25 Copynumber: 5.5 Consensus size: 24
22473 TAGTATTACA
* *
22483 ATTCCTTTTTTACATAAATAATAG
1 ATTCATTTTTTACACAAATAATAG
* * *
22507 ATTCATTTTTCTATAAACAAATATTACA
1 ATTCA-TTTT-T-TACACAAATAATA-G
*
22535 ATTCCTTTTTTACACAAATAATAG
1 ATTCATTTTTTACACAAATAATAG
* * *
22559 ATTCATTTTTCTATAAACAAATATTACA
1 ATTCA-TTTT-T-TACACAAATAATA-G
*
22587 ATTCCTTTTTTACACAAATAATAG
1 ATTCATTTTTTACACAAATAATAG
*
22611 ATACATTTTTT
1 ATTCATTTTTT
22622 CTATAAACAA
Statistics
Matches: 88, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
24 17 0.19
25 30 0.34
26 4 0.05
27 29 0.33
28 8 0.09
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTCATTTTTTACACAAATAATAG
Found at i:22533 original size:52 final size:52
Alignment explanation
Indices: 22476--22665 Score: 323
Period size: 52 Copynumber: 3.7 Consensus size: 52
22466 TATCATTTAG
*
22476 TATTACAATTCCTTTTTTACATAAATAATAGATTCATTTTTCTATAAACAAA
1 TATTACAATTCCTTTTTTACACAAATAATAGATTCATTTTTCTATAAACAAA
22528 TATTACAATTCCTTTTTTACACAAATAATAGATTCATTTTTCTATAAACAAA
1 TATTACAATTCCTTTTTTACACAAATAATAGATTCATTTTTCTATAAACAAA
*
22580 TATTACAATTCCTTTTTTACACAAATAATAGATACATTTTTTCTATAAAC-AA
1 TATTACAATTCCTTTTTTACACAAATAATAGATTCA-TTTTTCTATAAACAAA
*
22632 -ATTACAATTCC-TTTTTACACAAATAATAAATTCA
1 TATTACAATTCCTTTTTTACACAAATAATAGATTCA
22666 CTTTCCCATA
Statistics
Matches: 133, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
50 21 0.16
51 11 0.08
52 88 0.66
53 13 0.10
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.42
Consensus pattern (52 bp):
TATTACAATTCCTTTTTTACACAAATAATAGATTCATTTTTCTATAAACAAA
Found at i:22544 original size:28 final size:28
Alignment explanation
Indices: 22507--22647 Score: 113
Period size: 25 Copynumber: 5.4 Consensus size: 28
22497 TAAATAATAG
*
22507 ATTCATTTTTCTATAAACAAATATTACA
1 ATTCCTTTTTCTATAAACAAATATTACA
* * *
22535 ATTCC-TTTT-T-TACACAAATAATA-G
1 ATTCCTTTTTCTATAAACAAATATTACA
*
22559 ATTCATTTTTCTATAAACAAATATTACA
1 ATTCCTTTTTCTATAAACAAATATTACA
* * *
22587 ATTCC-TTTT-T-TACACAAATAATA-G
1 ATTCCTTTTTCTATAAACAAATATTACA
* *
22611 ATACATTTTTTCTATAAAC-AA-ATTACA
1 ATTC-CTTTTTCTATAAACAAATATTACA
22638 ATTCCTTTTT
1 ATTCCTTTTT
22648 ACACAAATAA
Statistics
Matches: 85, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
24 7 0.08
25 26 0.31
26 15 0.18
27 25 0.29
28 12 0.14
ACGTcount: A:0.39, C:0.16, G:0.01, T:0.44
Consensus pattern (28 bp):
ATTCCTTTTTCTATAAACAAATATTACA
Found at i:24487 original size:30 final size:30
Alignment explanation
Indices: 24453--24539 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
24443 TTTTTGTATA
24453 AAAGATTGAACTTTTAAGTAATTAGTAAAT
1 AAAGATTGAACTTTTAAGTAATTAGTAAAT
24483 AAAGA-TGTAACCTTTT--G----TA-T--A-
1 AAAGATTG-AA-CTTTTAAGTAATTAGTAAAT
24504 AAAGATTGAACTTTTAAGTAATTAGTAAAT
1 AAAGATTGAACTTTTAAGTAATTAGTAAAT
24534 AAAGAT
1 AAAGAT
24540 GTAACCTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 26
0.63 0.00 0.37
Matches are distributed among these distances:
20 5 0.11
21 7 0.16
22 4 0.09
24 1 0.02
25 2 0.05
26 2 0.05
27 1 0.02
29 4 0.09
30 13 0.30
31 5 0.11
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.36
Consensus pattern (30 bp):
AAAGATTGAACTTTTAAGTAATTAGTAAAT
Found at i:24519 original size:51 final size:51
Alignment explanation
Indices: 24439--24801 Score: 425
Period size: 51 Copynumber: 7.2 Consensus size: 51
24429 TTGATTTATA
* *
24439 TAACTTTTTGTATAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGATG
1 TAACCTTTTGTATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
*
24490 TAACCTTTTGTATAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGATG
1 TAACCTTTTGTATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
* **
24541 TAACCTTTTGTATAAAAGATTGAACTTTTAAGTAATTAGTTCATAAAGATG
1 TAACCTTTTGTATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
* * * * *
24592 TAGCCTTTTG-ACTAAAAGATTGATTTTTTTTTAGTAATTAGTAAGTAAAAATGG
1 TAACCTTTTGTA-TAAAAGATTGA--ATTTTTAAGTAATTAGTAAATAAAGAT-G
* * * *
24646 T-ACC-TTTG-AGCAAAAGATTTAATTTTTAAGTAATTAGTAAATAAGGATA
1 TAACCTTTTGTA-TAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
* * * *
24695 T-ACCCTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAGGATA
1 TAACCTTTTGTATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
* * *
24745 T-ACCCTTTGAATAAAAGATTGAGTTTTTAAGTAATTAGTAAATAAA-ATG
1 TAACCTTTTGTATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
*
24794 TCACCTTT
1 TAACCTTT
24802 GAATTAGAAG
Statistics
Matches: 278, Mismatches: 27, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
49 7 0.03
50 113 0.41
51 120 0.43
52 14 0.05
53 22 0.08
54 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (51 bp):
TAACCTTTTGTATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG
Found at i:25574 original size:55 final size:55
Alignment explanation
Indices: 25515--25875 Score: 645
Period size: 55 Copynumber: 6.6 Consensus size: 55
25505 ATGGGATCAG
* *
25515 AGTAATAGTAGTCAGCAAATCAGTAATTAAGTAAAAAGCA-ATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAG-AGATTAATCAGAGTCAA
25570 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
25625 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
25680 AGTAATGGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
25735 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
25790 AGTAGTAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
25845 GGTAATAGTAATCAGTAAATC-GATAATTAAG
1 AGTAATAGTAATCAGTAAATCAG-TAATTAAG
25876 AGTTAAAATG
Statistics
Matches: 297, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
54 2 0.01
55 295 0.99
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (55 bp):
AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
Found at i:26116 original size:22 final size:22
Alignment explanation
Indices: 26059--26447 Score: 229
Period size: 22 Copynumber: 17.8 Consensus size: 22
26049 AATAGCATGC
* * *
26059 AATCAATAAAAAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
26081 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
26101 AATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
*
26123 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
**
26145 AATCA--ACAAGAGTAAAATATT
1 AATCAGTA-AAGAGTAAAATGGT
* * *
26166 AGTCAGTAAAAAGT-AAATAGT
1 AATCAGTAAAGAGTAAAATGGT
**
26187 AATCAGT-AAGAGTAAAAAAGT
1 AATCAGTAAAGAGTAAAATGGT
* *
26208 AATAAGT-AAGAAGTAAAA-GGA
1 AATCAGTAAAG-AGTAAAATGGT
* *
26229 AATCAGT-AAGAGTAAAAAGGC
1 AATCAGTAAAGAGTAAAATGGT
* * *
26250 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAATGGT
* *
26272 AATCAG-CAAGAAGTAAAAAGGT
1 AATCAGTAAAG-AGTAAAATGGT
* *
26294 AATCAGTGAAA-AGCAAAA-GGC
1 AATCAGT-AAAGAGTAAAATGGT
*
26315 AATCAGTAAAAAGTAAAA-GAGT
1 AATCAGTAAAGAGTAAAATG-GT
* *
26337 AATCAGTAAAAAAGGAGCAGAAAATAGT
1 AATCAGT---AAA-GAG--TAAAATGGT
26365 AATCAGTAAAAGAGTAAAATGGT
1 AATCAGT-AAAGAGTAAAATGGT
*
26388 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAGAGTAA-AATGGT
*
26410 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAGAGTAAAATGGT
26431 AATCAGTACAA-AGTAAA
1 AATCAGTA-AAGAGTAAA
26448 GAATAATCAG
Statistics
Matches: 294, Mismatches: 45, Indels: 56
0.74 0.11 0.14
Matches are distributed among these distances:
20 33 0.11
21 96 0.33
22 115 0.39
23 23 0.08
24 2 0.01
25 6 0.02
26 6 0.02
28 13 0.04
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:26158 original size:43 final size:42
Alignment explanation
Indices: 26109--26447 Score: 263
Period size: 43 Copynumber: 7.7 Consensus size: 42
26099 GTAATTAGTA
26109 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
* * **
26152 AAGAGTAAAATATTAGTCAGTAAAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * * **
26194 AAGAGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
** * * *
26236 AAGAGTAAAA-AGGCGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* * *
26279 AAGAAGTAAAA-AGGTAATCAGTGAAAAGCAAAAGGCAATCAGTA-
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * * *
26323 AAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT--AAAA--AG--TAAAA-GGTAATCA--AC
*
26374 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
26417 AAGAGTAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
26448 GAATAATCAG
Statistics
Matches: 240, Mismatches: 39, Indels: 35
0.76 0.12 0.11
Matches are distributed among these distances:
41 2 0.01
42 64 0.27
43 98 0.41
44 23 0.10
45 12 0.05
46 2 0.01
47 4 0.02
49 8 0.03
50 9 0.04
51 18 0.08
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:26344 original size:15 final size:15
Alignment explanation
Indices: 26326--26381 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
26316 ATCAGTAAAA
26326 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
26341 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
26355 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
26369 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
26382 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:26402 original size:116 final size:114
Alignment explanation
Indices: 26251--26462 Score: 273
Period size: 116 Copynumber: 1.8 Consensus size: 114
26241 TAAAAAGGCG
* ** *
26251 ATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAAAGGTAATCAGTGAAAAGCAAAA-GGC
1 ATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCA-ACAAAAGCAAAATAGC
*
26315 AATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTA
65 AATCAGTAAAAAGT-AAAGAATAATCAGTAAAAAAGGAGCAGAAAATAGTA
* * * * * * *
26366 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGT
1 ATCAGT-AAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCAACAAAAGCAAAATAGC
*
26431 AATCAGTACAAAGTAAAGAATAATCAGTAAAA
65 AATCAGTAAAAAGTAAAGAATAATCAGTAAAA
26463 TAGTGATGCT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
115 31 0.38
116 51 0.62
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (114 bp):
ATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGTAAAAAGGTAATCAACAAAAGCAAAATAGCA
ATCAGTAAAAAGTAAAGAATAATCAGTAAAAAAGGAGCAGAAAATAGTA
Found at i:26460 original size:94 final size:93
Alignment explanation
Indices: 26180--26438 Score: 218
Period size: 94 Copynumber: 2.9 Consensus size: 93
26170 AGTAAAAAGT
* * * * * * *
26180 AAATAGTAATCAGT--AAGAGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCAGTAAGAGTA
1 AAATAGTAATCAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGAAAAAGTA
** *
26243 AAA-AGGCGATCAGT---AAA-GAG--TA
66 AAAGA-GTAATCAGTAAAAAAGGAGAAGA
* * *
26265 AAA-AGCTAATCAGCAAGA-AGTAAAAAGGTAATCAGTGAAAAGCAAAAGGCAATCAGTAAAAAG
1 AAATAG-TAATCAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAG-AAAAAG
*
26328 TAAAAGAGTAATCAGTAAAAAAGGAGCAGA
64 TAAAAGAGTAATCAGTAAAAAAGGAGAAGA
* * * *
26358 AAATAGTAATCAGTAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCA-ACAAGAG
1 AAATAGTAATCAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAA-AAGGCAATCAGA-AAAAG
*
26422 TAAAATAGTAATCAGTA
64 TAAAAGAGTAATCAGTA
26439 CAAAGTAAAG
Statistics
Matches: 138, Mismatches: 21, Indels: 21
0.77 0.12 0.12
Matches are distributed among these distances:
84 2 0.01
85 10 0.07
86 32 0.23
87 17 0.12
88 1 0.01
90 3 0.02
91 3 0.02
93 15 0.11
94 46 0.33
95 9 0.07
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.17
Consensus pattern (93 bp):
AAATAGTAATCAGTAAAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCAGAAAAAGTA
AAAGAGTAATCAGTAAAAAAGGAGAAGA
Found at i:34070 original size:21 final size:21
Alignment explanation
Indices: 34044--34085 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
34034 GATTCTTTCA
34044 ATACTCAATTACAGGAACTAC
1 ATACTCAATTACAGGAACTAC
34065 ATACTCAATTACAGGAACTAC
1 ATACTCAATTACAGGAACTAC
34086 GCGCAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
ATACTCAATTACAGGAACTAC
Found at i:34536 original size:34 final size:34
Alignment explanation
Indices: 34448--34537 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 34
34438 CTTTTGCCAG
*
34448 GGCTCTCAAAGTGTGCTTTGGCCCTTCTCAATTT
1 GGCTCTCAAAGTGCGCTTTGGCCCTTCTCAATTT
* *
34482 GTGAATCCTCAAAGTGCGCTTTGGCCCTTCTTAATTT
1 G-G-CT-CTCAAAGTGCGCTTTGGCCCTTCTCAATTT
*
34519 GGCTCTCGAAGTGCGCTTT
1 GGCTCTCAAAGTGCGCTTT
34538 AACTCAGGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
34 15 0.31
35 2 0.04
36 2 0.04
37 29 0.60
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.37
Consensus pattern (34 bp):
GGCTCTCAAAGTGCGCTTTGGCCCTTCTCAATTT
Found at i:37262 original size:13 final size:13
Alignment explanation
Indices: 37244--37269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37234 ATGTTGGAGG
37244 GTTTTCTTTAATT
1 GTTTTCTTTAATT
37257 GTTTTCTTTAATT
1 GTTTTCTTTAATT
37270 TTCTTGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
GTTTTCTTTAATT
Done.