Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006998.1 Corchorus capsularis cultivar CVL-1 contig07019, 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: 50024
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:593 original size:11 final size:10
Alignment explanation
Indices: 560--595 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
550 CATTGTAAAT
560 TTAATTTTAA
1 TTAATTTTAA
570 TTAATTTTAA
1 TTAATTTTAA
*
580 TTAAATTTACA
1 TTAATTTTA-A
591 TTAAT
1 TTAAT
596 ATTGATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:859 original size:44 final size:45
Alignment explanation
Indices: 792--916 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
782 AAGGAGACTT
*
792 TGAT-AAAAAGTCATGTTGGGTTTTCAATTT-AGCCATA-CTGGCCA
1 TGATGAAAAAGCCATGTTGGGTTTTCAATTTGA-CCA-AGCTGGCCA
* **
836 TGA-GAAAAAGCCATGTTGGGTTTTCAATTTGACCAAGGTGGCTG
1 TGATGAAAAAGCCATGTTGGGTTTTCAATTTGACCAAGCTGGCCA
*
880 TGATG-AAAAGCCATGTTGGGTTTTCAATTTGAACAAG
1 TGATGAAAAAGCCATGTTGGGTTTTCAATTTGACCAAG
917 GTGGTGTGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.01
44 69 0.96
45 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (45 bp):
TGATGAAAAAGCCATGTTGGGTTTTCAATTTGACCAAGCTGGCCA
Found at i:917 original size:44 final size:42
Alignment explanation
Indices: 841--928 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 42
831 GGCCATGAGA
*
841 AAAAGCCATGTTGGGTTTTCAATTTGACCAAGGTGGCTGTGATG
1 AAAAGCCATGTTGGGTTTTCAATTTGAACAAGGTGG-TGTG-TG
885 AAAAGCCATGTTGGGTTTTCAATTTGAACAAGGTGGTGTGTG
1 AAAAGCCATGTTGGGTTTTCAATTTGAACAAGGTGGTGTGTG
927 AA
1 AA
929 GGCAAATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 4 0.09
43 4 0.09
44 35 0.81
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (42 bp):
AAAAGCCATGTTGGGTTTTCAATTTGAACAAGGTGGTGTGTG
Found at i:3500 original size:34 final size:34
Alignment explanation
Indices: 3462--3532 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
3452 TGTAACCTCC
3462 CATT-AAGGCATCCATTCATTAAAAGACATCCATT
1 CATTAAAGGCATCCATTCA-TAAAAGACATCCATT
* *
3496 CATTAAAGGCATCCATTCATGAATGACATCCATT
1 CATTAAAGGCATCCATTCATAAAAGACATCCATT
3530 CAT
1 CAT
3533 GAATCCGGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 20 0.59
35 14 0.41
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.30
Consensus pattern (34 bp):
CATTAAAGGCATCCATTCATAAAAGACATCCATT
Found at i:3508 original size:17 final size:17
Alignment explanation
Indices: 3470--3532 Score: 90
Period size: 17 Copynumber: 3.6 Consensus size: 17
3460 CCCATTAAGG
3470 CATCCATTCATTAAAAGA
1 CATCCATTCATT-AAAGA
*
3488 CATCCATTCATTAAAGG
1 CATCCATTCATTAAAGA
* *
3505 CATCCATTCATGAATGA
1 CATCCATTCATTAAAGA
3522 CATCCATTCAT
1 CATCCATTCAT
3533 GAATCCGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (17 bp):
CATCCATTCATTAAAGA
Found at i:7989 original size:2 final size:2
Alignment explanation
Indices: 7984--8016 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7974 TATATGGGCA
7984 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 A
8017 CACACACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19517 original size:30 final size:30
Alignment explanation
Indices: 19483--19540 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
19473 ACTGTCATAC
19483 TCATCTCCTCCTTCACATTCATTGTCTTTT
1 TCATCTCCTCCTTCACATTCATTGTCTTTT
*
19513 TCATCTTCTCCTTCACATTCATTGTCTT
1 TCATCTCCTCCTTCACATTCATTGTCTT
19541 CATGGTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.03, T:0.50
Consensus pattern (30 bp):
TCATCTCCTCCTTCACATTCATTGTCTTTT
Found at i:21981 original size:29 final size:30
Alignment explanation
Indices: 21938--22019 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
21928 GACCACTTTT
* *
21938 AAAAGAAAATGGATTTTTTTG-AATAAA-A
1 AAAAGATAAGGGATTTTTTTGTAATAAATA
* * **
21966 AAACAGATGAGGGATTTATTTGTCCTAAATA
1 AAA-AGATAAGGGATTTTTTTGTAATAAATA
21997 AAAAGATAAGGGATTTTTTTGTA
1 AAAAGATAAGGGATTTTTTTGTA
22020 TCTAAGCCTG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
28 3 0.07
29 14 0.33
30 21 0.50
31 4 0.10
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (30 bp):
AAAAGATAAGGGATTTTTTTGTAATAAATA
Found at i:30011 original size:2 final size:2
Alignment explanation
Indices: 30000--30040 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
29990 ATTAAGTACC
30000 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30040 T
1 T
30041 GTTGGTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31613 original size:32 final size:31
Alignment explanation
Indices: 31549--31717 Score: 198
Period size: 31 Copynumber: 5.4 Consensus size: 31
31539 ATGCCACGTG
* **
31549 TTTGGTACACGTGGCGTGAGA-AGTGTCACTT
1 TTTGGTACACGTAGCGTGCCACA-TGTCACTT
* *
31580 TTTGGCACACGTAGTGTTGCCACATGTCACTT
1 TTTGGTACACGTAGCG-TGCCACATGTCACTT
*
31612 TTTGGTACACGTAGTGTTGCCACATGTCACTT
1 TTTGGTACACGTAGCG-TGCCACATGTCACTT
* *
31644 TTTGGTACACGT-GACGTGCCCCATGTGACTT
1 TTTGGTACACGTAG-CGTGCCACATGTCACTT
* *
31675 TTTGGTACACATGGCGTGCCACATGTCACTT
1 TTTGGTACACGTAGCGTGCCACATGTCACTT
31706 TTTGGTACACGT
1 TTTGGTACACGT
31718 GGTATGCCAC
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
31 64 0.53
32 56 0.46
33 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.34
Consensus pattern (31 bp):
TTTGGTACACGTAGCGTGCCACATGTCACTT
Found at i:34478 original size:15 final size:15
Alignment explanation
Indices: 34458--34488 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34448 GTAATAGCCA
*
34458 ATCTATACTATCTAT
1 ATCTATACTATATAT
34473 ATCTATACTATATAT
1 ATCTATACTATATAT
34488 A
1 A
34489 AAAGTACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (15 bp):
ATCTATACTATATAT
Found at i:34776 original size:38 final size:36
Alignment explanation
Indices: 34705--34798 Score: 118
Period size: 38 Copynumber: 2.5 Consensus size: 36
34695 AATTTGCCTT
*
34705 TTTGTTTCCAACGTCTATTTAATTTTGACTTTTGTC
1 TTTGTTTCCAACGTCTATTCAATTTTGACTTTTGTC
*
34741 TTTGTTTCCAATCGTTGTATTCAATTTTG-CTTTTTGTC
1 TTTGTTTCCAA-CG-TCTATTCAATTTTGAC-TTTTGTC
*
34779 TTTGTCTCCAACGTCCTATT
1 TTTGTTTCCAACGT-CTATT
34799 TGGACTTAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
36 12 0.24
37 9 0.18
38 29 0.58
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (36 bp):
TTTGTTTCCAACGTCTATTCAATTTTGACTTTTGTC
Found at i:36694 original size:44 final size:43
Alignment explanation
Indices: 36645--36794 Score: 149
Period size: 44 Copynumber: 3.4 Consensus size: 43
36635 GTCTCTATGT
** *
36645 GGTTATCAAAATTTCATAAGATGATTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAGATGATTACCAAAATTTCAT-AGGA
* * *
36689 GGTTATCAAAATTCCAT-AGTGTGCTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAAG-ATGATTACCAAAATTTCATA-GGA
* * * * *
36733 AGTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAATGT
1 GGTTATCAAAATTTCATAAGATGATTACCAAAATTTCAT-AGGA
*
36777 GGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATA
36795 GGATCAGGTT
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
43 3 0.03
44 82 0.94
45 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGATTACCAAAATTTCATAGGA
Found at i:36701 original size:22 final size:21
Alignment explanation
Indices: 36645--36815 Score: 117
Period size: 22 Copynumber: 7.7 Consensus size: 21
36635 GTCTCTATGT
*
36645 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
36666 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
36689 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
36711 GCTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* **
36733 AGTTATCAAAATTTCATAATA
1 GGTTATCAAAATTTCATAGGA
* * *
36754 TGGTTACCAAAATTTCATAATGT
1 -GGTTATCAAAATTTCAT-AGGA
*
36777 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
*
36801 GGTTATTAAAATTTC
1 GGTTATCAAAATTTC
36816 TTAAGTTTGG
Statistics
Matches: 114, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
21 5 0.04
22 91 0.80
23 5 0.04
24 13 0.11
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:36759 original size:66 final size:68
Alignment explanation
Indices: 36641--36829 Score: 181
Period size: 66 Copynumber: 2.8 Consensus size: 68
36631 TCTTGTCTCT
* * * * * * * * *
36641 ATGTGGTTATCAAAATTTCATAAGA-TGATTATTATAATTTCATGAGGA-GGTTATCAAAATTCC
1 ATGTGCTTACCAAAATTTCATAGGACAGGTTATCAAAATTTCATAAGTATGGTTATCAAAATTCC
36704 ATA
66 ATA
* * *
36707 GTGTGCTTACCAAAATTTCATATGGA-A-GTTATCAAAATTTCATAA-TATGGTTACCAAAATTT
1 ATGTGCTTACCAAAATTTCATA-GGACAGGTTATCAAAATTTCATAAGTATGGTTATCAAAATTC
36769 CATA
65 CATA
* * * *
36773 ATGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAAGTTTGGTTAT
1 ATGTGCTTACCAAAATTTCATAGGA-CAGGTTATCAAAATTTCATAAGTATGGTTAT
36830 TGAAATTTCA
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
65 4 0.04
66 69 0.70
67 3 0.03
68 16 0.16
69 7 0.07
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (68 bp):
ATGTGCTTACCAAAATTTCATAGGACAGGTTATCAAAATTTCATAAGTATGGTTATCAAAATTCC
ATA
Found at i:36811 original size:24 final size:23
Alignment explanation
Indices: 36784--36843 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
36774 TGTGGTTACC
36784 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG-TCAGGTTATT
* * **
36808 AAAATTTCTTAAGTTTGGTTATT
1 AAAATTTCATAGGTCAGGTTATT
*
36831 GAAATTTCATAGG
1 AAAATTTCATAGG
36844 GTGGTTAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (23 bp):
AAAATTTCATAGGTCAGGTTATT
Found at i:36911 original size:22 final size:22
Alignment explanation
Indices: 36886--37283 Score: 159
Period size: 22 Copynumber: 17.9 Consensus size: 22
36876 ACCAAAGAGA
*
36886 TTATCAAAATGTT-ATAGCGAGG
1 TTATCAAAAT-TTCATAGTGAGG
*
36908 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
36930 TTAACAAAATTTCATTAG-AAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
36952 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
36974 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
36996 TTATCAAAATTTCATA-TAAAGG
1 TTATCAAAATTTCATAGT-GAGG
* *
37018 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
37043 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
37065 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
37086 TTATCAAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
**
37111 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * *
37133 TTATCAAAATTTCAAAGCGAGA
1 TTATCAAAATTTCATAGTGAGG
* * * * *
37155 TTATCAAAATTACGTAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
37177 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * **
37199 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* **
37221 TTATCAAAATTCCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
37243 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
37265 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
37284 GTATTTCTGG
Statistics
Matches: 281, Mismatches: 73, Indels: 44
0.71 0.18 0.11
Matches are distributed among these distances:
20 9 0.03
21 22 0.08
22 205 0.73
23 10 0.04
24 2 0.01
25 23 0.08
26 6 0.02
27 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:37008 original size:44 final size:43
Alignment explanation
Indices: 36886--37651 Score: 130
Period size: 44 Copynumber: 17.8 Consensus size: 43
36876 ACCAAAGAGA
* * *
36886 TTATCAAAATGTTATAGCGAGGTTAT-AAGAATTTCATAGTGTGG
1 TTATCAAAATTTTATAG-GAGGTTATCAA-AATTTCATAGGGAGG
* * * * *
36930 TTAACAAAATTTCATTAGAAGGTTA-CTAATATTTCATGGGGAGG
1 TTATCAAAATTTTA-TAGGAGGTTATC-AAAATTTCATAGGGAGG
* ***
36974 TTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATATAAAGG
1 TTATCAAAATTTTATAG-GAGGTTATCAAAATTTCATAGGGAGG
* * *
37018 TTAT-AAAAGTCTCAATTTCATAAGGA-G-TACCAAAATTTGATA-GAAGG
1 TTATCAAAA---T---TTT-AT-AGGAGGTTATCAAAATTTCATAGGGAGG
* * * *
37065 TTATC-AAATCTCATA-GAGTGATTATCAAAATTTCATAGAGATCAGA
1 TTATCAAAATTTTATAGGAG-G-TTATCAAAATTTCATAG-G--GAGG
* ** * * *
37111 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGA
1 TTATCAAAATTTTATAG-GAGGTTATCAAAATTTCATAGGGAGG
* * * * *
37155 TTATCAAAATTACGTA-ATGTGATTATCAGAATTTCATAGAGG-GG
1 TTATCAAAATT--TTATAGGAGGTTATCAAAATTTCATAG-GGAGG
* * * * **
37199 TCAACAAAATTTTATAAAGAGGTTATCAAAATTCCATAAAGAGG
1 TTATCAAAATTTTAT-AGGAGGTTATCAAAATTTCATAGGGAGG
* * * * *
37243 TTATC-AAATTTTCAAAATGTGATTA-CAAAAATTTCATA--GTGG
1 TTATCAAAATTTT--ATAGGAGGTTATC-AAAATTTCATAGGGAGG
* ** *
37285 -TAT-----TTCTGGA-GAGGTTATCAAAATTTCATA-GTATGG
1 TTATCAAAATTTTATAGGAGGTTATCAAAATTTCATAGGGA-GG
* ** * * *
37321 TTA-CCAAA---T-TAGGAAGGTTATTTAACTTTTATTATGGA-G
1 TTATCAAAATTTTATAGG-AGGTTATCAAAATTTCA-TAGGGAGG
* * * * **
37360 TAATCAAAATTTCA-GGGAGGATATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTTATAGGAGGTTATCAAAATTTCATAG-GGAGG
* * * * *
37402 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATG
1 TTATCAAAATTTTATAGGA-GGTTATCAAAATTTCATAGGGAGG
* * * * **
37445 TGGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG
1 T-TATCAAAATTTTATA-GGAGGTTATCAAAATTTCATAGGGAGG
* ** * * *
37490 TCATCAAAAAATCATAGGGAGGTTATCAGAA-TT--T--GTA-G
1 TTATCAAAATTTTATA-GGAGGTTATCAAAATTTCATAGGGAGG
* * * * * *
37528 TTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATATGGAGG
1 TTATCAAAATTTTAT-AGGAGGTTATCAAAATTTCATAGGGAGG
* * * *
37572 TTTATCAAAATTTTATAGGAAGATTTATGAAAAATTCATAGCGAGG
1 -TTATCAAAATTTTATAGG-AG-GTTATCAAAATTTCATAGGGAGG
* * * *
37618 TTATCACAATTTCATAGTGTGATTATCAAAATTT
1 TTATCAAAATTTTATAG-GAGGTTATCAAAATTT
37652 TAGAGTGTGA
Statistics
Matches: 521, Mismatches: 131, Indels: 140
0.66 0.17 0.18
Matches are distributed among these distances:
34 16 0.03
35 2 0.00
36 2 0.00
37 6 0.01
38 27 0.05
39 21 0.04
40 9 0.02
41 10 0.02
42 46 0.09
43 26 0.05
44 225 0.43
45 44 0.08
46 27 0.05
47 36 0.07
48 14 0.03
49 5 0.01
50 3 0.01
51 2 0.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTTATAGGAGGTTATCAAAATTTCATAGGGAGG
Found at i:37430 original size:22 final size:21
Alignment explanation
Indices: 37362--37651 Score: 105
Period size: 22 Copynumber: 13.5 Consensus size: 21
37352 TTATGGAGTA
** *
37362 ATCAAAATTTCAGGGA-GGAT
1 ATCAAAATTTCATAGAGGGTT
***
37382 ATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAG-AGGGTT
*
37404 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCAT-AGAGGGTT
37426 ATCAAAATTTCATAGTATGTGG--
1 ATCAAAATTTCATAG-A-G-GGTT
37448 ATCAAAATTTCATAG-GGAGATT
1 ATCAAAATTTCATAGAGG-G-TT
* *
37470 AACAAAATTTCATA-ATGAGGTC
1 ATCAAAATTTCATAGA-G-GGTT
** *
37492 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
* *
37514 ATCAGAATTT-GT--A--GTT
1 ATCAAAATTTCATAGAGGGTT
* **
37530 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGAGGGTT
* *
37552 ATCAAAATTTTATATGGAGGTTT
1 ATCAAAATTTCATA--GAGGGTT
* **
37575 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATA-G-AGGGTT
* * *
37598 ATGAAAAATTCATAGCGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
* * *
37620 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGAG-GGTT
37642 ATCAAAATTT
1 ATCAAAATTT
37652 TAGAGTGTGA
Statistics
Matches: 202, Mismatches: 44, Indels: 46
0.69 0.15 0.16
Matches are distributed among these distances:
16 11 0.05
17 1 0.00
18 1 0.00
19 2 0.01
20 14 0.07
21 5 0.02
22 126 0.62
23 39 0.19
24 3 0.01
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATAGAGGGTT
Found at i:37598 original size:23 final size:23
Alignment explanation
Indices: 37528--37604 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
37518 GAATTTGTAG
* * * *
37528 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
*
37550 TTATCAAAATTTTATATGG-AGGT
1 TTATCAAAATTTTATA-GGAAGAT
37573 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
37596 TTATGAAAA
1 TTATCAAAA
37605 ATTCATAGCG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 17 0.38
23 28 0.62
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:37658 original size:22 final size:22
Alignment explanation
Indices: 37618--37664 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
37608 CATAGCGAGG
* *
37618 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
37640 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
37662 TTA
1 TTA
37665 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:37734 original size:22 final size:22
Alignment explanation
Indices: 37717--37828 Score: 93
Period size: 22 Copynumber: 5.0 Consensus size: 22
37707 TCTCAATATA
* *
37717 TCATATGGAGGTTATCAACATC
1 TCATATGGAGGTTATCAAAATT
**
37739 TCATAGTGTTGGTTATCAAAATT
1 TCATA-TGGAGGTTATCAAAATT
*
37762 TCAT-TGGGAAGTTATCAAAATT
1 TCATAT-GGAGGTTATCAAAATT
*
37784 TCATATCGAGGTCT-TCAAAATT
1 TCATATGGAGGT-TATCAAAATT
* * * *
37806 CCTTAGGGAGGTTAACAAAATT
1 TCATATGGAGGTTATCAAAATT
37828 T
1 T
37829 AATAAGAAGG
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
21 2 0.03
22 49 0.70
23 19 0.27
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (22 bp):
TCATATGGAGGTTATCAAAATT
Found at i:40350 original size:21 final size:21
Alignment explanation
Indices: 40326--40369 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40316 TAATTAATAC
40326 TTTAAATATATAGAATGATGA
1 TTTAAATATATAGAATGATGA
40347 TTTAAATATATAGAATGATGA
1 TTTAAATATATAGAATGATGA
40368 TT
1 TT
40370 GATAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTAAATATATAGAATGATGA
Found at i:40476 original size:15 final size:15
Alignment explanation
Indices: 40428--40481 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
40418 ATCTATAAAA
40428 ATAAATAATTAAAT-T
1 ATAAATAA-TAAATGT
*
40443 AAAAATAATAAATGT
1 ATAAATAATAAATGT
*
40458 ATAATTAAT-AATGT
1 ATAAATAATAAATGT
40472 AATAAATAAT
1 -ATAAATAAT
40482 TGAAAATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.30
15 23 0.70
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
ATAAATAATAAATGT
Found at i:47235 original size:108 final size:110
Alignment explanation
Indices: 47044--47268 Score: 348
Period size: 108 Copynumber: 2.1 Consensus size: 110
47034 CCACAATTGT
* *
47044 TTAAAATAACATTTCGAGTTTAAGTCTTATAGATACAAAAAAACATTCATTAAAAGAATTATACC
1 TTAAAATAACATTTCGAGTTTAAGTCTTACAAATACAAAAAAACATTCATTAAAAGAATTATACC
*
47109 TCATAATAGATTGCTTGATCTAGAACAAAATTAGTC-ATAAACCC
66 TCATAATAGATTGCTTGATCTAAAACAAAATTAGTCTATAAACCC
* * *
47153 TTAAAATAACATTTCGAGTTTGAGTCTTACAAATAC-AGAAAGCATTCATTAAAAGAAATT-TAC
1 TTAAAATAACATTTCGAGTTTAAGTCTTACAAATACAAAAAAACATTCATTAAAAG-AATTATAC
* *
47216 CTCATAATAGATTGTTTGATCTAAAACAAAATTAGTCTGTAAACCC
65 CTCATAATAGATTGCTTGATCTAAAACAAAATTAGTCTATAAACCC
47262 TTAAAAT
1 TTAAAAT
47269 GAAGATACGT
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
108 55 0.52
109 51 0.48
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (110 bp):
TTAAAATAACATTTCGAGTTTAAGTCTTACAAATACAAAAAAACATTCATTAAAAGAATTATACC
TCATAATAGATTGCTTGATCTAAAACAAAATTAGTCTATAAACCC
Found at i:47490 original size:91 final size:91
Alignment explanation
Indices: 47335--47521 Score: 356
Period size: 91 Copynumber: 2.1 Consensus size: 91
47325 TCCTTGGAAA
47335 TAATATGAACAACAATATAGCTGCCTTGGAGGTTTAATTGCTTTAGATTTCCTCAAATATCTCTA
1 TAATATGAACAACAATATAGCTGCCTTGGAGGTTTAATTGCTTTAGATTTCCTCAAATATCTCTA
*
47400 GTTACACACTATATCAAGGTAAATAC
66 GCTACACACTATATCAAGGTAAATAC
*
47426 TAATATGAACAACAATATAGCTGCTTTGGAGGTTTAATTGCTTTAGATTTCCTCAAATATCTCTA
1 TAATATGAACAACAATATAGCTGCCTTGGAGGTTTAATTGCTTTAGATTTCCTCAAATATCTCTA
47491 GCTACACACTATATCAAGGTAAATAC
66 GCTACACACTATATCAAGGTAAATAC
47517 TAATA
1 TAATA
47522 GAGCTGAATT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (91 bp):
TAATATGAACAACAATATAGCTGCCTTGGAGGTTTAATTGCTTTAGATTTCCTCAAATATCTCTA
GCTACACACTATATCAAGGTAAATAC
Done.