Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015539.1 Corchorus olitorius cultivar O-4 contig15572, 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: 34788
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:447 original size:24 final size:25
Alignment explanation
Indices: 397--449 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
387 CTATTAAAGT
* *
397 TATTCTCAAACTGTTGTATGCTCAG
1 TATTCTCAAACTGCTGTAGGCTCAG
* *
422 TATTC-CAAACTGCTGTAGGTTTAG
1 TATTCTCAAACTGCTGTAGGCTCAG
446 TATT
1 TATT
450 TGCCTCTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (25 bp):
TATTCTCAAACTGCTGTAGGCTCAG
Found at i:6048 original size:21 final size:22
Alignment explanation
Indices: 6008--6048 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5998 GACAAACTTG
*
6008 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
6030 TAACCC-AATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
6049 TATTATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:6384 original size:16 final size:16
Alignment explanation
Indices: 6365--6396 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6355 CCCGAAACCC
6365 GTCCAACCCGCCCATT
1 GTCCAACCCGCCCATT
*
6381 GTCCAACCTGCCCATT
1 GTCCAACCCGCCCATT
6397 TAACTACTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.47, G:0.12, T:0.22
Consensus pattern (16 bp):
GTCCAACCCGCCCATT
Found at i:7298 original size:13 final size:12
Alignment explanation
Indices: 7267--7300 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7257 CGTGTTTAAA
*
7267 TAAATTGATAAT
1 TAAATTAATAAT
7279 TAAATTAATAAT
1 TAAATTAATAAT
7291 TAAAATTAAT
1 T-AAATTAAT
7301 TAACACCGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
TAAATTAATAAT
Found at i:8076 original size:78 final size:78
Alignment explanation
Indices: 7981--8141 Score: 234
Period size: 78 Copynumber: 2.1 Consensus size: 78
7971 GTTTTCTAGT
* * * *
7981 TAAAATAGTTAAATGGTAAACTGAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAAATTTAATTAAATAAAAATAGA
8046 GTTGTTAGTTGAA-
66 GTTGTTAGTT-AAG
** *
8059 TAAAATAGTAAAATGGTAAAATAAAATTTTTATAAAAATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAAATTTAATTAAATAAAAATAGA
*
8124 GTTTTTAGTTAAG
66 GTTGTTAGTTAAG
8137 TAAAA
1 TAAAA
8142 CTATAAATCT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 2 0.03
78 72 0.97
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAAATTTAATTAAATAAAAATAGA
GTTGTTAGTTAAG
Found at i:8614 original size:21 final size:21
Alignment explanation
Indices: 8590--8635 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
8580 TCAGAAACTC
8590 AATTCACTTTGTTCATGTAGT
1 AATTCACTTTGTTCATGTAGT
***
8611 AATTTTTTTTGTTCATGTAGT
1 AATTCACTTTGTTCATGTAGT
8632 AATT
1 AATT
8636 TAAGTGGTTC
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:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (21 bp):
AATTCACTTTGTTCATGTAGT
Found at i:8636 original size:21 final size:21
Alignment explanation
Indices: 8597--8636 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
8587 CTCAATTCAC
8597 TTTGTTCATGTAGTAATTTTT
1 TTTGTTCATGTAGTAATTTTT
8618 TTTGTTCATGTAGTAATTT
1 TTTGTTCATGTAGTAATTT
8637 AAGTGGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.15, T:0.60
Consensus pattern (21 bp):
TTTGTTCATGTAGTAATTTTT
Found at i:8645 original size:21 final size:21
Alignment explanation
Indices: 8600--8646 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
8590 AATTCACTTT
*** *
8600 GTTCATGTAGTAATTTTTTTT
1 GTTCATGTAGTAATTTAAGTG
8621 GTTCATGTAGTAATTTAAGTG
1 GTTCATGTAGTAATTTAAGTG
8642 GTTCA
1 GTTCA
8647 AATCTACTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.51
Consensus pattern (21 bp):
GTTCATGTAGTAATTTAAGTG
Found at i:10584 original size:29 final size:30
Alignment explanation
Indices: 10523--10601 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
10513 GCTAAATACC
*
10523 CAAAA-AATCCCTTATGTTTTGCTTTTGAGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGAGA
* *
10553 CAAAATAATCTCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGAGA
* *
10582 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
10602 CAAAAATGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.55
30 5 0.12
31 14 0.33
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGAGA
Found at i:11232 original size:178 final size:179
Alignment explanation
Indices: 11029--11388 Score: 524
Period size: 180 Copynumber: 2.0 Consensus size: 179
11019 TAATGTCATT
11029 TAAGAAATATATTTAGAAAATTCTAATATATCTAA-TTTTTAATTAAAATAGAAAAATGGTAAAA
1 TAAGAAATATATTTAGAAAATTCTAATATATCTAAGTTTTTAATTAAAATAGAAAAATGGTAAAA
** *
11093 ATAAAATAGTTATAAATATATTAGATTTGATTAAACAAAAATAGAGTTTTCAATTGAGAAAAATT
66 ATAAAATAGTTATAAATATATTAGATTAAATTAAACAAAAATAGAGTTTTCAATTGAGAAAAACT
* * * * *
11158 GTAAAAGTTTAAACAATGGCATTTAAGAAATATATTTGAAAAATAAGGG
131 ATAAAAATCTAAACAATGGCATTTAAGAAATATAATCGAAAAATAAGGG
** *
11207 TAAGAAATATATTTTTAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAA
1 TAAGAAATATATTTAGAAAATTCTAATATATCTAAG-TTTTTAATTAAAATAGAAAAATGGTAAA
** * * * * * *
11272 AATGCAATATTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGTGTAAAAC
65 AATAAAATAGTTATAAATATATTAGATTAAATTAAACAAAAATAGAGTTTTCAATTGAGAAAAAC
*
11337 TATAAAAATCTAAACAGTGGCATTTAAGAAATATAATCGAAAAATAAGGG
130 TATAAAAATCTAAACAATGGCATTTAAGAAATATAATCGAAAAATAAGGG
11387 TA
1 TA
11389 TAATCGACAA
Statistics
Matches: 160, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
178 33 0.21
180 127 0.79
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (179 bp):
TAAGAAATATATTTAGAAAATTCTAATATATCTAAGTTTTTAATTAAAATAGAAAAATGGTAAAA
ATAAAATAGTTATAAATATATTAGATTAAATTAAACAAAAATAGAGTTTTCAATTGAGAAAAACT
ATAAAAATCTAAACAATGGCATTTAAGAAATATAATCGAAAAATAAGGG
Found at i:11817 original size:31 final size:31
Alignment explanation
Indices: 11767--11842 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
11757 GACTAAATAT
* * * *
11767 CAAAAAAATCTCTTCTGTTTTTCT-TTTGGGA
1 CAAAATAATCCCTTATGTTTTT-TATATGGGA
11798 CAAAATAATCCCTTATGTTTTTTATATGGGA
1 CAAAATAATCCCTTATGTTTTTTATATGGGA
* *
11829 CAAATTAGTCCCTT
1 CAAAATAATCCCTT
11843 GCTGACATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (31 bp):
CAAAATAATCCCTTATGTTTTTTATATGGGA
Found at i:11983 original size:29 final size:30
Alignment explanation
Indices: 11940--12014 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
11930 TTTTGAAACG
* * *
11940 TAAGAGATTAATTTGTCCCGAAA-AAAAGA
1 TAAGGGATTATTTTGTCCCAAAACAAAAGA
*
11969 TAAGGGATTATTTTGTCCCAAAAGCAAAATA
1 TAAGGGATTATTTTGTCCCAAAA-CAAAAGA
*
12000 TAAGGGATTTTTTTG
1 TAAGGGATTATTTTG
12015 GGTATTTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 20 0.51
31 19 0.49
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (30 bp):
TAAGGGATTATTTTGTCCCAAAACAAAAGA
Found at i:12399 original size:22 final size:22
Alignment explanation
Indices: 12371--12533 Score: 82
Period size: 22 Copynumber: 7.4 Consensus size: 22
12361 GATTATCAAG
*
12371 ATTTCATAGTGTGGTTACCAAA
1 ATTTCATAGTATGGTTACCAAA
*
12393 ATTTCATA-TAAAT-GTTATCAAA
1 ATTTCATAGT--ATGGTTACCAAA
* * * *
12415 ACTTCATAGTGTAGTTATCAAA
1 ATTTCATAGTATGGTTACCAAA
** *
12437 ATTTCATACAAAGGTTACCAAA
1 ATTTCATAGTATGGTTACCAAA
** * *
12459 ATTTCATAACAAGGTTACCGAA
1 ATTTCATAGTATGGTTACCAAA
* * **
12481 ATTTCTTAGGGAT-GTTAATAAA
1 ATTTCATA-GTATGGTTACCAAA
** *
12503 ATTTCATA-TGAAAGTTAACAAA
1 ATTTCATAGT-ATGGTTACCAAA
12525 ATTTCATAG
1 ATTTCATAG
12534 GGAGGGAGGT
Statistics
Matches: 108, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
21 3 0.03
22 102 0.94
23 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
ATTTCATAGTATGGTTACCAAA
Found at i:12411 original size:44 final size:44
Alignment explanation
Indices: 12358--12466 Score: 146
Period size: 44 Copynumber: 2.5 Consensus size: 44
12348 GACAATCAAT
* * * *
12358 AAAGATTATCAAGATTTCATAGTGTGGTTACCAAAATTTCATAT
1 AAAGGTTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATAC
* * *
12402 AAATGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATAC
1 AAAGGTTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATAC
*
12446 AAAGGTTACCAAAATTTCATA
1 AAAGGTTATCAAAATTTCATA
12467 ACAAGGTTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (44 bp):
AAAGGTTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATAC
Found at i:12504 original size:66 final size:67
Alignment explanation
Indices: 12383--12532 Score: 166
Period size: 66 Copynumber: 2.3 Consensus size: 67
12373 TTCATAGTGT
* * *
12383 GGTTACCAAAATTTCATATAAATGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATA-CA
1 GGTTACCAAAATTTCATATAAAGGTTACCAAAACTTCATAGGGTAGTTATCAAAATTTCATATCA
12447 AA
66 AA
* * *
12449 GGTTACCAAAATTTCATA-ACAAGGTTACCGAAATTTCTTAGGG-ATGTTAAT-AAAATTTCATA
1 GGTTACCAAAATTTCATATA-AAGGTTACCAAAACTTCATAGGGTA-GTT-ATCAAAATTTCATA
*
12511 TGAAA
63 TCAAA
*
12516 -GTTAACAAAATTTCATA
1 GGTTACCAAAATTTCATA
12533 GGGAGGGAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
65 2 0.03
66 65 0.90
67 5 0.07
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (67 bp):
GGTTACCAAAATTTCATATAAAGGTTACCAAAACTTCATAGGGTAGTTATCAAAATTTCATATCA
AA
Found at i:12573 original size:42 final size:42
Alignment explanation
Indices: 12521--12622 Score: 195
Period size: 42 Copynumber: 2.4 Consensus size: 42
12511 TGAAAGTTAA
12521 CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
1 CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
12563 CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
1 CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
*
12605 CAAAATTTCCTAGGGAGG
1 CAAAATTTCATAGGGAGG
12623 TTAACAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (42 bp):
CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
Found at i:12632 original size:38 final size:39
Alignment explanation
Indices: 12521--12634 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 39
12511 TGAAAGTTAA
12521 CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
1 CAAAATTTCAT---GAGGGAGGTTACTAAAATTTGTGCTTAT
12563 CAAAATTTCATAGGGAGGGAGGTTACTAAAATTTGTGCTTAT
1 CAAAATTTCAT---GAGGGAGGTTACTAAAATTTGTGCTTAT
*
12605 CAAAATTTCCT-AGGGAGGTTAAC-AAAATTT
1 CAAAATTTCATGAGGGAGGTT-ACTAAAATTT
12635 TATAGGGTGG
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
38 16 0.23
39 2 0.03
42 52 0.74
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (39 bp):
CAAAATTTCATGAGGGAGGTTACTAAAATTTGTGCTTAT
Found at i:12670 original size:22 final size:22
Alignment explanation
Indices: 12601--12677 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
12591 AAATTTGTGC
* **
12601 TTATCAAAATTTCCTAGGGAGG
1 TTATGAAAATTTTATAGGGAGG
** *
12623 TTAACAAAATTTTATAGGGTGG
1 TTATGAAAATTTTATAGGGAGG
12645 TTATGAAAATTTTAT-GGAGAGG
1 TTATGAAAATTTTATAGG-GAGG
12667 TTATCGAAAAT
1 TTAT-GAAAAT
12678 ACATAGAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 2 0.04
22 38 0.83
23 6 0.13
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.35
Consensus pattern (22 bp):
TTATGAAAATTTTATAGGGAGG
Found at i:12762 original size:19 final size:20
Alignment explanation
Indices: 12714--12769 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
12704 TCTCATAGAA
12714 AGGTTATCAAAA-TTTATGG
1 AGGTTATCAAAATTTTATGG
*
12733 TGTGATTATCAAAATTTTAT-G
1 AG-G-TTATCAAAATTTTATGG
12754 AGGTTATCAAAATTTT
1 AGGTTATCAAAATTTT
12770 CATAGTGCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 14 0.44
20 2 0.06
21 11 0.34
22 5 0.16
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (20 bp):
AGGTTATCAAAATTTTATGG
Found at i:12848 original size:22 final size:22
Alignment explanation
Indices: 12823--12882 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
12813 TATAGGCAAA
12823 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTCACACTAAGG
* * * **
12845 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCACACTAAGG
*
12867 TTACCAAAATTTCACA
1 TTATCAAAATTTCACA
12883 ATGTCGTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCACACTAAGG
Found at i:12891 original size:22 final size:22
Alignment explanation
Indices: 12851--12902 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
12841 AAGGTTATCG
* * *
12851 AAATTTCATAGTGTGGTTACCA
1 AAATTTCACAATGTCGTTACCA
*
12873 AAATTTCACAATGTCGTTATCA
1 AAATTTCACAATGTCGTTACCA
12895 AATATTTC
1 AA-ATTTC
12903 TACATTGGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
AAATTTCACAATGTCGTTACCA
Found at i:15525 original size:21 final size:21
Alignment explanation
Indices: 15500--15582 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
15490 TATCTTAGAT
15500 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
15521 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
15542 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
15564 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
15583 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:15533 original size:25 final size:25
Alignment explanation
Indices: 15502--15550 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
15492 TCTTAGATAT
*
15502 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
15527 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
15551 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:21548 original size:26 final size:23
Alignment explanation
Indices: 21519--21565 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 23
21509 TTTAAGAAAA
21519 ACGCAGAAACAAATATTTTTTTTATT
1 ACGCA-AAA-AAAT-TTTTTTTTATT
*
21545 ACGCAAAAAACTTTTTTTTTA
1 ACGCAAAAAAATTTTTTTTTA
21566 GAAAAAACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 3 0.15
26 5 0.25
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
ACGCAAAAAAATTTTTTTTTATT
Found at i:21676 original size:34 final size:33
Alignment explanation
Indices: 21607--21685 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
21597 GGAAAATCAA
*
21607 TTTTTTTTTAGAAAAAACGCAGAAAACAGAAAT
1 TTTTTTTTTAGAAAAAACACAGAAAACAGAAAT
* ***
21640 TTTTTTTTATAGAAAAAACACAGAAAATATTTAT
1 TTTTTTTT-TAGAAAAAACACAGAAAACAGAAAT
21674 TTTTTTTTTAGA
1 TTTTTTTTTAGA
21686 TCAGAAACGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 12 0.30
34 28 0.70
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (33 bp):
TTTTTTTTTAGAAAAAACACAGAAAACAGAAAT
Found at i:22076 original size:151 final size:152
Alignment explanation
Indices: 21802--22105 Score: 490
Period size: 151 Copynumber: 2.0 Consensus size: 152
21792 GCTAAAATTT
*
21802 ATGATCGGTCGTCAGCAATCATAAAAATAATTCCCAACAAAATCCTAACTAAATAGATAGGGTAA
1 ATGATCGGTCGTCAGCAATCATAAAAATAATTCCCAACAAAATCCTAACTAAATAGATAGGGCAA
* * *
21867 GTAGGGGTCGATCCCACAGAGAAGGGTGCTAGACTTTATCCGAAAATTCAATCTTTAAAATCTC-
66 GTAGAGGTCGATCCCACAGAGAAGGGTGCTAGACTTTATCCAAAAATTCAATCCTTAAAATCTCT
21931 TAAAA-AACAACACAGAAAGCAG
131 TAAAACAA-AACACAGAAAGCAG
* *
21953 ATGATCGGTCGTCAGCAATCATAAAAATAATTCCCCACAAAATCCTAACTATAGTAGATAGGGCA
1 ATGATCGGTCGTCAGCAATCATAAAAATAATTCCCAACAAAATCCTAACTA-AATAGATAGGGCA
*
22018 AGTAGAGGTCGATTCCACAGAGAAGGGTG-TAGACTTTATCCAAAAATAT-AATCCTTAAAATCT
65 AGTAGAGGTCGATCCCACAGAGAAGGGTGCTAGACTTTATCCAAAAAT-TCAATCCTTAAAATCT
22081 CTTAAAACAAAACACAGAAAGCAG
129 CTTAAAACAAAACACAGAAAGCAG
22105 A
1 A
22106 GGTTGAAAGA
Statistics
Matches: 142, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
151 81 0.57
152 59 0.42
153 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (152 bp):
ATGATCGGTCGTCAGCAATCATAAAAATAATTCCCAACAAAATCCTAACTAAATAGATAGGGCAA
GTAGAGGTCGATCCCACAGAGAAGGGTGCTAGACTTTATCCAAAAATTCAATCCTTAAAATCTCT
TAAAACAAAACACAGAAAGCAG
Found at i:22137 original size:15 final size:16
Alignment explanation
Indices: 22113--22152 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
22103 AGAGGTTGAA
*
22113 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
22128 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
22144 AGAAAACAA
1 AGAAAACAA
22153 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:26337 original size:67 final size:67
Alignment explanation
Indices: 26229--26647 Score: 393
Period size: 67 Copynumber: 6.3 Consensus size: 67
26219 TTTACTCTCT
* *
26229 ATTTCC-AAAATACCCTTTCGGTAGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTAGTATTT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTTGCATTTAAGTTTAGTATTT
26292 TC
66 TC
* *
26294 AAATTTCC-AAAATACCCTTTCGGTCGAAGGGTCATTTCCGTC-TTTTGCATTTAAATGTAGTAT
1 --ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTTGCATTTAAGTTTAGTAT
26357 TTTC
64 TTTC
* * * * *
26361 ATTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTT-TGTCATCCTTGCATTTGAGTTTAGTAC
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTCCGTCAT-TTTGCATTTAAGTTTAGTA-
*
26425 TTTTG
63 TTTTC
* * *
26430 ATTTCCAAAAATACCCTTTCGGT-GAAAGGGTCAGTTT-CATCATTTCCGCATTTCAGTTTA-T-
1 ATTTCCAAAAATACCCTTTCGGTCG-AAGGGTCA-TTTCCGTCATTT-TGCATTTAAGTTTAGTA
*
26491 TTTAC
63 TTTTC
* *
26496 -TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTT-CATCAAGTTTTTGCATTTAAGTCTAGT
1 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTC-A--TTTTGCATTTAAGTTTAGT
*
26559 -CTTTC
62 ATTTTC
* * * *
26564 -TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTGCATTTCAGTTTA-T-T
1 ATTTCCAAA-AATACCCTTTCGGTCGAAGGGTCATTTCCGTCATT-TTGCATTTAAGTTTAGTAT
* *
26626 CTAC
64 TTTC
26630 -TTTCCAAAAATACCCTTT
1 ATTTCCAAAAATACCCTTT
26648 TGGTGAAAAT
Statistics
Matches: 302, Mismatches: 34, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
65 54 0.18
66 45 0.15
67 90 0.30
68 36 0.12
69 77 0.25
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (67 bp):
ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCATTTTGCATTTAAGTTTAGTATTT
TC
Found at i:26524 original size:65 final size:65
Alignment explanation
Indices: 26230--26723 Score: 390
Period size: 65 Copynumber: 7.4 Consensus size: 65
26220 TTACTCTCTA
* *
26230 TTTCC-AAAATACCCTTTCGGTAGAAGGGTCATTTTCGTC-TTT-TGCATTTAAGTTTAGTATTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCATTTCTGCATTTAAG-TT--TATTT
*
26292 TCAAA
63 T--AC
*
26297 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTCCGTC-TTT-TGCATTTAAATGTAGTATT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTT-CGTCATTTCTGCATTT-AA-GT-TTATT
26358 TT-C
62 TTAC
* * * * * *
26361 ATTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTTTGTCA-TCCTTGCATTTGAGTTTAGTAC
1 -TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCATTTC-TGCATTTAAG-TT--TA-
26425 TTTTGA-
60 TTTT-AC
* * *
26431 TTTCCAAAAATACCCTTTCGGT-GAAAGGGTCAGTTTCATCATTTCCGCATTTCAGTTTATTTTA
1 TTTCCAAAAATACCCTTTCGGTCG-AAGGGTCAGTTTCGTCATTTCTGCATTTAAGTTTATTTTA
26495 C
65 C
* * *
26496 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCAAGTTTTTGCATTTAAGTCTAGTCT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTC-A-TTTCTGCATTTAAGTTTA-T-T
26561 TT-C
62 TTAC
* * * *
26564 TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCA-ATTCTGTCA-TTCTTGCATTTCAGTTTATTC
1 TTTCCAAA-AATACCCTTTCGGTCGAAGGGTCAGTTTC-GTCATTTC-TGCATTTAAGTTTATTT
26627 TAC
63 TAC
* ** ** * *
26630 TTTCCAAAAATACCCTTTTGGT-GAAAATGTCAGTTTCAACATTTCCT-CATTTCAGTTTATTCT
1 TTTCCAAAAATACCCTTTCGGTCG-AAGGGTCAGTTTCGTCATTT-CTGCATTTAAGTTTATTTT
26693 AC
64 AC
*
26695 TTTCCAAAAATGCCCTTTCGGTCGAAGGG
1 TTTCCAAAAATACCCTTTCGGTCGAAGGG
26724 CGAACTTTGT
Statistics
Matches: 356, Mismatches: 38, Indels: 68
0.77 0.08 0.15
Matches are distributed among these distances:
64 1 0.00
65 111 0.31
66 56 0.16
67 82 0.23
68 28 0.08
69 76 0.21
70 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (65 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCATTTCTGCATTTAAGTTTATTTTAC
Found at i:26664 original size:199 final size:199
Alignment explanation
Indices: 26297--26723 Score: 591
Period size: 199 Copynumber: 2.1 Consensus size: 199
26287 TATTTTCAAA
* *
26297 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAATGTAGTATTTTC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAATCTAGTACTTTC
* * *
26361 ATTTCCCAAAATACCCTTTCGGTCAAAGGGTCAATTTTGTCATCCTTGCATTTGAGTTTAGTACT
66 ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATCCTTGCATTTCAGTTTA-TACT
* * *
26426 TTTGATTTCCAAAAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTCCGCATTTCAGTTTAT
130 TCTGATTTCCAAAAATACCCTTTCGGTGAAAAGGTCAGTTTCAACATTTCCGCATTTCAGTTTAT
*
26491 TTTAC
195 TCTAC
*
26496 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCATCAAGT-TTTTGCATTTAAGTCTAGT-
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTC--C--GTCTTTTGCATTTAAATCTAGTA
*
26559 CTTTC-TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATTCTTGCATTTCAG-TT
61 CTTTCATTTCCAAA-AATACCCTTTCGGTCAAAGGGTCAATTCTGTCATCCTTGCATTTCAGTTT
* * *
26622 -TA-TTCT-ACTTTCCAAAAATACCCTTTTGGTGAAAATGTCAGTTTCAACATTTCCTCATTTCA
125 ATACTTCTGA-TTTCCAAAAATACCCTTTCGGTGAAAAGGTCAGTTTCAACATTTCCGCATTTCA
26684 GTTTATTCTAC
189 GTTTATTCTAC
*
26695 TTTCCAAAAATGCCCTTTCGGTCGAAGGG
1 TTTCCAAAAATACCCTTTCGGTCGAAGGG
26724 CGAACTTTGT
Statistics
Matches: 205, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
198 1 0.00
199 95 0.46
200 28 0.14
201 4 0.02
202 9 0.04
203 49 0.24
204 17 0.08
205 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (199 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAATCTAGTACTTTC
ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAATTCTGTCATCCTTGCATTTCAGTTTATACTT
CTGATTTCCAAAAATACCCTTTCGGTGAAAAGGTCAGTTTCAACATTTCCGCATTTCAGTTTATT
CTAC
Done.