Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008175.1 Corchorus capsularis cultivar CVL-1 contig08196, 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: 27053
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1656 original size:4 final size:4
Alignment explanation
Indices: 1642--1677 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
1632 TCCGCCTATG
*
1642 TTTC TTTTC TTTC TTTC TTTC TTTT TTTC TTTC TTT
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1678 TAAAGATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:4725 original size:22 final size:22
Alignment explanation
Indices: 4700--4742 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4690 TAAATAAAAT
4700 ATTCATACGAAATTATGATAAC
1 ATTCATACGAAATTATGATAAC
* **
4722 ATTCCTATTAAATTATGATAA
1 ATTCATACGAAATTATGATAA
4743 TTACACTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTCATACGAAATTATGATAAC
Found at i:4751 original size:22 final size:22
Alignment explanation
Indices: 4709--4804 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
4699 TATTCATACG
4709 AAATTATGATAACATTCCTATT
1 AAATTATGATAACATTCCTATT
4731 AAATTATGAT-A-ATTACACTATT
1 AAATTATGATAACATT-C-CTATT
* *
4753 ---TT-TGATGACATT-CTAATG
1 AAATTATGATAACATTCCT-ATT
* * *
4771 AAATTTTGATAACTTTCCTATG
1 AAATTATGATAACATTCCTATT
4793 AAATTATGATAA
1 AAATTATGATAA
4805 TTACACTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
17 2 0.03
18 6 0.10
19 3 0.05
20 6 0.10
21 4 0.07
22 37 0.62
23 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (22 bp):
AAATTATGATAACATTCCTATT
Found at i:4805 original size:62 final size:62
Alignment explanation
Indices: 4708--4859 Score: 234
Period size: 62 Copynumber: 2.5 Consensus size: 62
4698 ATATTCATAC
* *
4708 GAAATTATGATAACATTCCTATTAAATTATGATAATTACACTAT-TTTTGATGACATTCTAAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATATTTT-ATGACATTCTAAT
* * *
4770 GAAATTTTGATAACTTTCCTATGAAATTATGATAATTACACTATATTTTATGACGTTCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATATTTTATGACATTCTAAT
*
4832 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACATTCCTATGAAATT
4860 TCAATAACGA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 79 0.95
63 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATATTTTATGACATTCTAAT
Found at i:4855 original size:22 final size:22
Alignment explanation
Indices: 4768--5262 Score: 178
Period size: 22 Copynumber: 22.8 Consensus size: 22
4758 TGACATTCTA
*
4768 ATGAAATTTTGATAACTTTCCT
1 ATGAAATTTTGATAACCTTCCT
*
4790 ATGAAATTATGATAA--TTACACT
1 ATGAAATTTTGATAACCTT-C-CT
* * *
4812 AT---ATTTT-ATGACGTTCTT
1 ATGAAATTTTGATAACCTTCCT
4830 ATGAAATTTTGATAACCTTCCT
1 ATGAAATTTTGATAACCTTCCT
** ** *
4852 ATGAAATTTCAATAACGATACT
1 ATGAAATTTTGATAACCTTCCT
* * * **
4874 ATGGAATTTCGAGAACCTTTTT
1 ATGAAATTTTGATAACCTTCCT
** *
4896 AT-AAATTTTTTTTAACCTTCTT
1 ATGAAA-TTTTGATAACCTTCCT
* * *
4918 ATGAAATGTTGTTAACCTCCCT
1 ATGAAATTTTGATAACCTTCCT
* *
4940 AAGGAATTTTGA-AGACC-TCACT
1 ATGAAATTTTGATA-ACCTTC-CT
*
4962 ATGAAATTTTGATAA-CTTCCAA
1 ATGAAATTTTGATAACCTTCC-T
**
4984 ATGAAATTTTGATAACCAACACT
1 ATGAAATTTTGATAACCTTC-CT
*
5007 AT-AAGATGTTGATAACC-TCCAT
1 ATGAA-ATTTTGATAACCTTCC-T
* * *
5029 AT-AATATATTGATAACC-ACGTT
1 ATGAA-ATTTTGATAACCTTC-CT
* * *
5051 ATGAAAATTTAAAAACC-TCCAT
1 ATGAAATTTTGATAACCTTCC-T
* * * *
5073 AT-AAATTGTCAGTAATC-ACACT
1 ATGAAATTTTGA-TAACCTTC-CT
* * * *
5095 CTGAAATTTTGATTATC-ACACT
1 ATGAAATTTTGATAACCTTC-CT
*
5117 ATGAAATTGTGATAACC-TCGCT
1 ATGAAATTTTGATAACCTTC-CT
5139 ATGAAATTTTGATAAACCTTCCT
1 ATGAAATTTTGAT-AACCTTCCT
* *
5162 ATAAAATTTTGATAAATCTTCCT
1 ATGAAATTTTGAT-AACCTTCCT
*
5185 ATAAAATTTTGATAACC-TCCTT
1 ATGAAATTTTGATAACCTTCC-T
* *
5207 ATGAGATCTTGATAA-----CT
1 ATGAAATTTTGATAACCTTCCT
* *
5224 A-CAAATTTTGATAACCTCCCT
1 ATGAAATTTTGATAACCTTCCT
**
5245 ATGATTTTTTGATAACCT
1 ATGAAATTTTGATAACCT
5263 CATTATTCTC
Statistics
Matches: 358, Mismatches: 81, Indels: 68
0.71 0.16 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 7 0.02
19 5 0.01
20 4 0.01
21 25 0.07
22 233 0.65
23 69 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTTCCT
Found at i:5163 original size:23 final size:22
Alignment explanation
Indices: 5115--5221 Score: 110
Period size: 23 Copynumber: 4.8 Consensus size: 22
5105 GATTATCACA
*
5115 CTATGAAATTGTGAT-AACCTC
1 CTATGAAATTTTGATAAACCTC
5136 GCTATGAAATTTTGATAAACCTTC
1 -CTATGAAATTTTGATAAACC-TC
* *
5160 CTATAAAATTTTGATAAATCTTC
1 CTATGAAATTTTGATAAA-CCTC
*
5183 CTATAAAATTTTGAT-AACCTC
1 CTATGAAATTTTGATAAACCTC
* *
5204 CTTATGAGATCTTGATAA
1 C-TATGAAATTTTGATAA
5222 CTACAAATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.05
22 27 0.37
23 39 0.53
24 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAAACCTC
Found at i:5303 original size:22 final size:21
Alignment explanation
Indices: 5274--5355 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 21
5264 ATTATTCTCC
*
5274 CTATGAAATTTTGATAACCCA
1 CTATGAAATTTTGATAACCAA
* *
5295 CTTATGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAAC-CAA
**
5318 CTATGAAATTTTGATAACCTT
1 CTATGAAATTTTGATAACCAA
5339 CATATGAAATTTTGATA
1 C-TATGAAATTTTGATA
5356 TCCTCCCCGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.04
22 47 0.92
23 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCAA
Found at i:5505 original size:22 final size:22
Alignment explanation
Indices: 5480--5557 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
5470 AATCACATTT
*
5480 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
*
5502 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
5524 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
*
5546 TGAAATTTTGAT
1 TGAAAATTTGAT
5558 CACATTATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.07
22 40 0.87
23 3 0.07
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:6593 original size:38 final size:37
Alignment explanation
Indices: 6500--6596 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 37
6490 ATCTAAATCC
* * *
6500 AAATAGGACGCTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** * *
6537 AAATACAACGATTAGAAACAAAGACAAAATGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGCAAAATT
6575 ATAATAGGACGTTGGAAACAAA
1 A-AATAGGACGTTGGAAACAAA
6597 AAGCCAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
37 8 0.17
38 33 0.69
39 7 0.15
ACGTcount: A:0.55, C:0.12, G:0.19, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:6753 original size:30 final size:31
Alignment explanation
Indices: 6719--6786 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
6709 TAATAGCAAG
6719 TTAGAAATATATTTTTAAAAA-AA-GGTACAA
1 TTAGAAATATA-TTTTAAAAATAAGGGTACAA
6749 TTAGAAATATATTTTAAAAATAAGGGTACAA
1 TTAGAAATATATTTTAAAAATAAGGGTACAA
6780 TTAGAAA
1 TTAGAAA
6787 ACATAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 9 0.25
30 13 0.36
31 14 0.39
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (31 bp):
TTAGAAATATATTTTAAAAATAAGGGTACAA
Found at i:8668 original size:18 final size:18
Alignment explanation
Indices: 8642--8676 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8632 AAGATGGTAA
8642 ATTACTACTACCTAATTG
1 ATTACTACTACCTAATTG
* *
8660 ATTATTACTACTTAATT
1 ATTACTACTACCTAATT
8677 ATAATTACGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTACTACTACCTAATTG
Found at i:12709 original size:22 final size:22
Alignment explanation
Indices: 12681--12820 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 22
12671 TGTCTCTATG
*
12681 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
12703 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
12726 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
12747 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
12769 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** * *
12793 TGGTTATTGAAATTTCATGGGG
1 TGGTTATCAAAATTTCATAGGA
12815 TGGTTA
1 TGGTTA
12821 ATTATCACCA
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
21 3 0.03
22 71 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:12881 original size:22 final size:21
Alignment explanation
Indices: 12856--13225 Score: 140
Period size: 22 Copynumber: 16.7 Consensus size: 21
12846 ATCAAAGATA
*
12856 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
12878 TTAT-AAGAATTTCATAGTATGG
1 TTATCAA-AATTTCATAGGA-GG
*
12900 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
12922 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
*
12944 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
* **
12966 TTAT-AAAAGTCTCAATTTTATAAGG
1 TTATCAAAA-TTTC-A---TAGGAGG
* * * *
12991 AATACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
13013 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
*
13033 ATTATCGAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAG-GA--GG
* *
13058 ATTATCAAAATTT-ATATGAAGA
1 -TTATCAAAATTTCATA-GGAGG
**
13080 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
13102 ATATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * * *
13124 TTATCAAAATTACACAATGTGA
1 TTATCAAAATTTCA-TAGGAGG
* *
13146 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * ** *
13168 TCAACAACATTTTGTAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
13190 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
13212 TTATCAAATTTTCA
1 TTATCAAAATTTCA
13226 AAATGTGATT
Statistics
Matches: 261, Mismatches: 59, Indels: 56
0.69 0.16 0.15
Matches are distributed among these distances:
19 2 0.01
20 9 0.03
21 31 0.12
22 172 0.66
23 11 0.04
24 6 0.02
25 19 0.07
26 7 0.03
27 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:13491 original size:44 final size:44
Alignment explanation
Indices: 13419--13827 Score: 221
Period size: 44 Copynumber: 9.4 Consensus size: 44
13409 CATAAGAGCG
* * *
13419 TTATAAAAATTTCATAGT-ATGTAGATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGA
* * * *
13463 TTAACAAAATTTCATAATGAGGTTATCAAAAAATT-ATAGGGAGC
1 TTATCAAAATTTCATAGTGAGGTTATC-AAAATTTCATAGGGAGA
* * *
13507 TTATCAAAA-TT--T-GT-A-GTTATCAAGATTTCATA-AGAAA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA
* * * **
13544 TTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGAAAGA
1 -TTATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGGAGA
* * * *
13590 TTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGTGA
1 -TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA
* * * * * *
13635 TTATCAAAAGTTCAGAGTGTGATTA-CTAACAA-TTCATATGGAGG
1 TTATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCATAGGGAGA
* * * ** * * * * *
13679 TTTTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA
* * * * *
13723 TTATCAACATCTCATAGTGTTGGTTATCAAAATTTCAT-TGGAAA
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGGAGA
* * * * * *
13767 GTTATCAAAATTTCATATTGAGGTTTTCAAAATTCCTTAGAGAGG
1 -TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA
* *
13812 TTAACAAAATTCCATA
1 TTATCAAAATTTCATA
13828 AGAAGGTTAA
Statistics
Matches: 276, Mismatches: 70, Indels: 38
0.72 0.18 0.10
Matches are distributed among these distances:
37 7 0.03
38 18 0.07
39 3 0.01
40 1 0.00
41 2 0.01
42 1 0.00
43 5 0.02
44 138 0.50
45 77 0.28
46 24 0.09
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGA
Found at i:13595 original size:46 final size:45
Alignment explanation
Indices: 13522--13629 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
13512 AAAATTTGTA
* * *
13522 GTTATCAAGATTTCATA-AGAA-ATTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGA-AAGATTTATCAAAATTTCATAGCGAG
*
13566 GTTTATCAAAATTTTATAGAAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATCAAAATTTCATAGAAAGATTTATCAAAATTTCATAGCGAG
*
13612 GTTATCACAATTTCATAG
1 GTTATCAAAATTTCATAG
13630 TGTGATTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 1 0.02
45 31 0.56
46 23 0.42
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (45 bp):
GTTATCAAAATTTCATAGAAAGATTTATCAAAATTTCATAGCGAG
Found at i:13796 original size:22 final size:22
Alignment explanation
Indices: 13304--13836 Score: 160
Period size: 22 Copynumber: 24.3 Consensus size: 22
13294 CAAATTAGGA
* * *
13304 AGGTTATTAAACTTTTATTATGG
1 AGGTTATCAAAATTTCA-TATGG
* *
13327 A-GTAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATATGG
* *
13346 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGG
** * **
13368 AACTTAACAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATA-TGG
* *
13391 A-GTTTTCAAAATTAATTTCATA-AG
1 AGGTTATC--AA--AATTTCATATGG
* *
13415 AGCGTTATAAAAATTTCATA-GT
1 AG-GTTATCAAAATTTCATATGG
* * *
13437 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATATGG
* *
13460 AGATTAACAAAATTTCATAAT-G
1 AGGTTATCAAAATTTCAT-ATGG
* *
13482 AGGTTATCAAAAAATT-ATAGGG
1 AGGTTATC-AAAATTTCATATGG
* *
13504 AGCTTATCAAAA--T--T-TGT
1 AGGTTATCAAAATTTCATATGG
* * *
13521 A-GTTATCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCATATGG
** * *
13542 AATTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATATGG
* *
13564 AGGTTTATCAAAATTTTATA-GAA
1 AGG-TTATCAAAATTTCATATG-G
*
13587 AGATTTATCAAAATTTCATA-GCG
1 AG-GTTATCAAAATTTCATATG-G
*
13610 AGGTTATCACAATTTCATAGTGTG
1 AGGTTATCAAAATTTCATA-TG-G
* *
13634 A--TTATCAAAAGTTCAGAGTGTG
1 AGGTTATCAAAATTTCATA-TG-G
13656 A--TTA-CTAACAA-TTCATATGG
1 AGGTTATC-AA-AATTTCATATGG
* * * **
13676 AGGTTTTTAAATTTTCATAACG
1 AGGTTATCAAAATTTCATATGG
* * *
13698 TGGTTATCAATATATCATATGG
1 AGGTTATCAAAATTTCATATGG
* * *
13720 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATA-TGG
*
13743 TGGTTATCAAAATTTCAT-TGG
1 AGGTTATCAAAATTTCATATGG
* *
13764 AAAGTTATCAAAATTTCATATTG
1 -AGGTTATCAAAATTTCATATGG
* * *
13787 AGGTTTTCAAAATTCCTTA-GAG
1 AGGTTATCAAAATTTCATATG-G
* * * *
13809 AGGTTAACAAAATTCCATAAGA
1 AGGTTATCAAAATTTCATATGG
13831 AGGTTA
1 AGGTTA
13837 AAAAAAATTT
Statistics
Matches: 377, Mismatches: 96, Indels: 75
0.69 0.18 0.14
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
19 5 0.01
20 15 0.04
21 15 0.04
22 238 0.63
23 71 0.19
24 8 0.02
26 13 0.03
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGG
Found at i:13837 original size:22 final size:22
Alignment explanation
Indices: 13794--13842 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
13784 TTGAGGTTTT
*
13794 CAAAATTCCTTAGAGAGGTTAA
1 CAAAATTCCTAAGAGAGGTTAA
13816 CAAAATTCCATAAGA-AGGTTAA
1 CAAAATTCC-TAAGAGAGGTTAA
*
13838 AAAAA
1 CAAAA
13843 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAAATTCCTAAGAGAGGTTAA
Found at i:16760 original size:1 final size:1
Alignment explanation
Indices: 16754--16788 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
16744 AAGAAAATTT
16754 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16789 GGATGCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17378 original size:2 final size:2
Alignment explanation
Indices: 17371--17411 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
17361 GATTAAAGAG
17371 CA CA CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
17412 AGAAAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20382 original size:21 final size:22
Alignment explanation
Indices: 20356--20400 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
20346 TAATATTGAA
20356 TTGCTAAATACCGCCCC-ATTT
1 TTGCTAAATACCGCCCCAATTT
**
20377 TTGCTATTTACCGCCCCAATTT
1 TTGCTAAATACCGCCCCAATTT
20399 TT
1 TT
20401 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (22 bp):
TTGCTAAATACCGCCCCAATTT
Found at i:23140 original size:4 final size:4
Alignment explanation
Indices: 23133--23157 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
23123 AATTTTTCCC
23133 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
23158 TTCTAAGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:25814 original size:15 final size:15
Alignment explanation
Indices: 25796--25830 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25786 CTTTTTTCAG
**
25796 TCTTTTTTTTTTTTT
1 TCTTTTTTTCCTTTT
25811 TCTTTTTTTCCTTTT
1 TCTTTTTTTCCTTTT
25826 TCTTT
1 TCTTT
25831 CGTAGCTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TCTTTTTTTCCTTTT
Done.