Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013031.1 Corchorus capsularis cultivar CVL-1 contig13052, 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: 15605
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:382 original size:198 final size:198
Alignment explanation
Indices: 5--736 Score: 937
Period size: 198 Copynumber: 3.7 Consensus size: 198
1 ATGA
* *
5 TTTAAGAGTTGACATGTGTCCTCTTAGGGAATATGTATTAATATTAAATATATAATTAATTATGA
1 TTTAAGGGTTGACATGTGTCC-CTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* * * * * *
70 AATGGGGTATGTGTCAAATTTCTTAACCCGCTTATGGCGTCCAAAATTTATACTGATAGTGTATT
65 AATGGTGTATGTGTC-AACTTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATT
* * ** *
135 GTATAATAACCCTATAAGAAAAATTATGGAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTG
129 GTATAATAATCCTATAAAAAAAATTATACAATACACCGTAAGTGGAGTTTAGCAAACTGCACGTG
*
200 CGGGG
194 CGAGG
*
205 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTAACTATG-
1 TTTAAGGGTTGACATGTGT-CCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* *
269 AATGGTGTATGTGTCAACTTCTTAACCCACTTATGGAGTCTAAAATTTACACTGACAGTGAATTG
65 AATGGTGTATGTGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATTG
* * * * * * *
334 TATAATAATCATATAAAAAAAATTATACAATATACCGTTAGCGGAGTTTAGCAGACTGCACGCGT
130 TATAATAATCCTATAAAAAAAATTATACAATACACCGTAAGTGGAGTTTAGCAAACTGCACGTGC
399 GAGG
195 GAGG
* * * *
403 TTTGAGGGTTGACACGTATTCCCTTA-GGAATATGTA-T-AT-TT-TATATTTAATTAATTATGA
1 TTTAAGGGTTGACATGT-GTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* * * * * * *
463 AATAGG-GTATGTGTCAACTCCTTAACCCGCTTATGAAGTCCAAAATTTATAATGATAGTGTGTT
65 AAT-GGTGTATGTGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATT
*
527 GTATAATAATCCTAT--AAAAAATTATACAATACACCGTAAGTGGAGTTTAGCATACTGCACGTG
129 GTATAATAATCCTATAAAAAAAATTATACAATACACCGTAAGTGGAGTTTAGCAAACTGCACGTG
590 C-ATGG
194 CGA-GG
* * *
595 TTTAAGGGTTGATATGTGTCCCCTTAAGGAATATGTATTAATATTAAGTATTTAATTAATTATGA
1 TTTAAGGGTTGACATGTGT-CCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
* *
660 AAT-GTGGTATGTTTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACATTGACAGTGTATT
65 AATGGT-GTATGTGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATT
*
724 GTATAATGATCCT
129 GTATAATAATCCT
737 TATTATAAAG
Statistics
Matches: 460, Mismatches: 59, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
191 2 0.00
192 65 0.14
193 26 0.06
194 69 0.15
195 7 0.02
196 3 0.01
197 92 0.20
198 121 0.26
199 15 0.03
200 58 0.13
201 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (198 bp):
TTTAAGGGTTGACATGTGTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
ATGGTGTATGTGTCAACTTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATTGT
ATAATAATCCTATAAAAAAAATTATACAATACACCGTAAGTGGAGTTTAGCAAACTGCACGTGCG
AGG
Found at i:1841 original size:29 final size:29
Alignment explanation
Indices: 1799--1873 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
1789 GCTAGTGTTT
1799 ATTTTATTTTATTTTTTATGTATCAAAAA
1 ATTTTATTTTATTTTTTATGTATCAAAAA
1828 ATTTTATTTTATTTTTTATGTATCAAAAA
1 ATTTTATTTTATTTTTTATGTATCAAAAA
1857 ATTTTATTTTATTTTTT
1 ATTTTATTTTATTTTTT
1874 GATAGAATGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (29 bp):
ATTTTATTTTATTTTTTATGTATCAAAAA
Found at i:2870 original size:109 final size:109
Alignment explanation
Indices: 2738--3012 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 109
2728 AAAAAAATTA
2738 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
*
2801 AAAAAATTTTAATATATCCAATTTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
2846 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
2911 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
2955 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
3013 CTATAATAGT
Statistics
Matches: 156, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 6 0.04
109 118 0.76
110 3 0.02
111 1 0.01
114 28 0.18
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:4630 original size:13 final size:13
Alignment explanation
Indices: 4612--4636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4602 AACGGCTTTG
4612 GCTTAATAATTAT
1 GCTTAATAATTAT
4625 GCTTAATAATTA
1 GCTTAATAATTA
4637 AGCAACCTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
GCTTAATAATTAT
Found at i:6716 original size:22 final size:22
Alignment explanation
Indices: 6664--6761 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
6654 ATTTTAGTTG
*
6664 ATCAAAATTTCATAAGATGGTT
1 ATCAAAATTTCATAGGATGGTT
* *
6686 ATTATAATTTCATGAGGA-GGTT
1 ATCAAAATTTCAT-AGGATGGTT
* *
6708 ATCAAAATTCCATAGTATGGTT
1 ATCAAAATTTCATAGGATGGTT
*
6730 ACCAAAATTTCATAGGATCAGGTT
1 ATCAAAATTTCATAGGAT--GGTT
*
6754 ATTAAAAT
1 ATCAAAAT
6762 CTCTTAGGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.05
22 44 0.73
23 3 0.05
24 10 0.17
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGATGGTT
Found at i:6860 original size:22 final size:22
Alignment explanation
Indices: 6835--6877 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6825 GGTTATCAAA
6835 GAGATTATCAA-AATGTCATAGC
1 GAGATTAT-AAGAATGTCATAGC
*
6857 GAGATTATAAGAATTTCATAG
1 GAGATTATAAGAATGTCATAG
6878 TGTGGTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
GAGATTATAAGAATGTCATAGC
Found at i:7016 original size:22 final size:22
Alignment explanation
Indices: 6969--7223 Score: 161
Period size: 22 Copynumber: 11.6 Consensus size: 22
6959 TAAGTAGTAC
*
6969 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATTTCATAG-AGTGATTAT
*
6990 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
7011 CCAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAG-T--GATTAT
**
7036 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
7057 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
* * *
7079 CAAAATTTCAAAGCGAGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
7101 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GTGATTAT
* * *
7123 CAGAATTTCATAGAAG-GATCAA
1 CAAAATTTCATAG-AGTGATTAT
* * *
7145 CAAAATTTTATAAAG-AAGTTAT
1 CAAAATTTCATAGAGTGA-TTAT
* * *
7167 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
* *
7189 CAAATTTTCA-AAATGTGATTA-
1 CAAAATTTCATAGA-GTGATTAT
7210 CAAAAATTTCATAG
1 C-AAAATTTCATAG
7224 TGGTATTTCT
Statistics
Matches: 183, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
19 2 0.01
20 10 0.05
21 28 0.15
22 120 0.66
23 4 0.02
24 6 0.03
25 13 0.07
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:7085 original size:68 final size:64
Alignment explanation
Indices: 6969--7107 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 64
6959 TAAGTAGTAC
* *
6969 CAAAATTTGATAGAAGGTTATCAAATCTCATAGAGTGATTATCCAAATTTCATAGAGATCG-GAT
1 CAAAATTTGATAGAAGATTATCAAATCTCATAGAGTGATTATCAAAATTTCA-A-AG--CGAGAT
7033 TAT
62 TAT
* *
7036 CAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAGATT
1 CAAAATTTGATAG-AAGATTATC-AAATCTCATAGAG-TGATTATCAAAATTTCAAAGCGAGATT
7099 AT
63 AT
7101 CAAAATT
1 CAAAATT
7108 ACATAATGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
64 2 0.03
65 13 0.20
66 6 0.09
67 17 0.27
68 24 0.38
69 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (64 bp):
CAAAATTTGATAGAAGATTATCAAATCTCATAGAGTGATTATCAAAATTTCAAAGCGAGATTAT
Found at i:7136 original size:88 final size:88
Alignment explanation
Indices: 7030--7223 Score: 223
Period size: 88 Copynumber: 2.2 Consensus size: 88
7020 ATAGAGATCG
* * ** ** *
7030 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGC
1 GATTATCAAAATTTCATAGAAAGATCAACAAAATTTCATAAAGAAGTTATCAAAATTTCATAA-A
*
7093 GAGATTATCAAAATTACATAATGT
65 GAGATTATCAAAATTACAAAATGT
* * *
7117 GATTATCAGAATTTCATAGAAGGATCAACAAAATTTTATAAAGAAGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAAAGATCAACAAAATTTCATAAAGAAGTTATCAAAATTTCATAAAG
* * *
7182 AGGTTATCAAATTTTCAAAATGT
66 AGATTATCAAAATTACAAAATGT
7205 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
7224 TGGTATTTCT
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
87 14 0.16
88 73 0.82
89 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (88 bp):
GATTATCAAAATTTCATAGAAAGATCAACAAAATTTCATAAAGAAGTTATCAAAATTTCATAAAG
AGATTATCAAAATTACAAAATGT
Found at i:7340 original size:19 final size:19
Alignment explanation
Indices: 7304--7351 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
7294 TTATGGAGTA
7304 ATCAAAATTTCAATGAGGAT
1 ATCAAAA-TTCAATGAGGAT
7324 ATCAAAATTC-ATGGAGGAT
1 ATCAAAATTCAAT-GAGGAT
*
7343 AACAAAATT
1 ATCAAAATT
7352 TCATACGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAATGAGGAT
Found at i:7371 original size:22 final size:21
Alignment explanation
Indices: 7304--7880 Score: 168
Period size: 22 Copynumber: 26.7 Consensus size: 21
7294 TTATGGAGTA
*
7304 ATCAAAATTTCA-ATG-AGGAT
1 ATCAAAATTTCATA-GAAGGTT
* *
7324 ATCAAAA-TTCAT-GGAGGAT
1 ATCAAAATTTCATAGAAGGTT
*
7343 AACAAAATTTCATACGAAGGTT
1 ATCAAAATTTCATA-GAAGGTT
* *
7365 ATCAAAATTTCATAGTTTAGTTT
1 ATCAAAATTTCATAG--AAGGTT
* *
7388 A-CAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCA-TAGAAGGTT
* * *
7409 ATCAAAATTTTATAGTATGTAT
1 ATCAAAATTTCATAGAAGGT-T
* *
7431 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATA-GAAGGTT
*
7453 AACAAAATTTCATA-ATGAGGTT
1 ATCAAAATTTCATAGA--AGGTT
** *
7475 ATCAAAAAGTCATAGGGAGGTT
1 ATCAAAATTTCATA-GAAGGTT
*
7497 ATCAAAA-TT--T-GTA-GTT
1 ATCAAAATTTCATAGAAGGTT
* *
7513 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGAAGGTT
* *
7535 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-GAAGG-TT
* * *
7558 ATCAAAATTTTATGGGAAGACTT
1 ATCAAAATTTCAT-AGAAG-GTT
*
7581 ATCAAAATTTCATAGCAAGATT
1 ATCAAAATTTCATAG-AAGGTT
* * *
7603 ATCACAATTTTATAG-TGTGATT
1 ATCAAAATTTCATAGAAG-G-TT
* *
7625 ATCAAAATTTCAGAG-TGTGATT
1 ATCAAAATTTCATAGAAG-G-TT
*
7647 A-CTAACAA-TTCATATAGAGGTT
1 ATC-AA-AATTTCATAGA-AGGTT
* * * *
7669 TTTAAATTTTCATA-ACGTGGTT
1 ATCAAAATTTCATAGA--AGGTT
* * *
7691 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATA-GAAGGTT
* * *
7713 ATCAACATCTCATA-ATTTTGGTT
1 ATCAAAATTTCATAGA---AGGTT
7736 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA--GAAGGT-T
* * *
7759 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATA-GAAGGTT
* *
7780 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT-AGAAGGTT
** * *
7802 AAAAAAAATT-ATTAAAAGGTT
1 ATCAAAATTTCA-TAGAAGGTT
* * * **
7823 CTCGAAATTCCATAGTATCGTT
1 ATCAAAATTTCATAG-AAGGTT
*
7845 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATA-GAAGGTT
7867 ATCAAAATTTCATA
1 ATCAAAATTTCATA
7881 ATGGGATAAT
Statistics
Matches: 410, Mismatches: 96, Indels: 100
0.68 0.16 0.17
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
18 1 0.00
19 17 0.04
20 13 0.03
21 32 0.08
22 266 0.65
23 67 0.16
24 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATAGAAGGTT
Found at i:7397 original size:44 final size:44
Alignment explanation
Indices: 7345--7636 Score: 197
Period size: 44 Copynumber: 6.7 Consensus size: 44
7335 TGGAGGATAA
*
7345 CAAAATTTCATACGAAGGTTATCAAAATTTCATAGTTTAGTTTA-
1 CAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-TTAGTTTAT
* * * * *
7389 CAAAATTTCACAAGAGGGTTATCAAAATTTTATAG-TATGTATAT
1 CAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-GTTTAT
* * * * * *
7433 CAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTAT
1 CAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGTTTAT
** *
7477 CAAAAAGTCATAGGGAGGTTATCAAAA-TT--T-G-TAG-TTAT
1 CAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGTTTAT
* * * * **
7515 CAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-GTTTAT
* * * ** *
7560 CAAAATTTTATGGGAAGACTTATCAAAATTTCATAGCAAGATTAT
1 CAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTTAGTTTAT
* * * *
7605 CACAATTTTATAGTG-TGATTATCAAAATTTCA
1 CAAAATTTCATAG-GAAGGTTATCAAAATTTCA
7637 GAGTGTGATT
Statistics
Matches: 193, Mismatches: 43, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
38 25 0.13
39 4 0.02
41 2 0.01
42 3 0.02
43 7 0.04
44 100 0.52
45 34 0.18
46 18 0.09
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGTTTAT
Found at i:7500 original size:66 final size:63
Alignment explanation
Indices: 7304--7636 Score: 209
Period size: 66 Copynumber: 5.2 Consensus size: 63
7294 TTATGGAGTA
* * * * * * *
7304 ATCAAAATTTCAATGAGGA--TATCAAAA-TTCAT-GGAGGATAACAAAATTTCATACGAAGGTT
1 ATCAAAATTTC-ATG-GGAGTTAACAAAATTTCATAAGAGGTTATCAAAATTTTATAGGGAGGTT
** * * * *
7365 ATCAAAATTTCATAGTTTAGTTTACAAAATTTCACAAGAGGGTTATCAAAATTTTATA-GTATGT
1 ATCAAAATTTCAT-G-GGAGTTAACAAAATTTCATAAGA-GGTTATCAAAATTTTATAGGGAGGT
7429 AT
63 -T
** *
7431 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAGTCATAGGGAGGT
1 ATCAAAATTTCAT-GGGAG-TTAACAAAATTTCATAA-GAGGTTATCAAAATTTTATAGGGAGGT
7496 T
63 T
* * * *
7497 ATCAAAA-TT--T-GTAGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATGGGAGTTAACAAAATTTCATAAG-AGGTTATCAAAATTTTATAGGGAGG-TT
* * * * * *
7558 ATCAAAATTTTATGGGAAGACTTATCAAAATTTCAT-AGCAAGATTATCACAATTTTATAGTGTG
1 ATCAAAATTTCATGGG-AG--TTAACAAAATTTCATAAG--AGGTTATCAAAATTTTATAGGGAG
*
7622 ATT
61 GTT
7625 ATCAAAATTTCA
1 ATCAAAATTTCA
7637 GAGTGTGATT
Statistics
Matches: 215, Mismatches: 37, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
59 1 0.00
60 38 0.18
61 25 0.12
62 2 0.01
63 7 0.03
64 5 0.02
65 11 0.05
66 71 0.33
67 21 0.10
68 34 0.16
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (63 bp):
ATCAAAATTTCATGGGAGTTAACAAAATTTCATAAGAGGTTATCAAAATTTTATAGGGAGGTT
Found at i:7561 original size:23 final size:23
Alignment explanation
Indices: 7533--7634 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
7523 CATAAGAAAG
*
7533 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGA
*
7556 TTATCAAAATTTTAT-GGGAAGA
1 TTATCAAAATTTTATAGGGAGGA
* * *
7578 CTTATCAAAATTTCATA-GCAAGA
1 -TTATCAAAATTTTATAGGGAGGA
* * *
7601 TTATCACAATTTTATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGA
7623 TTATCAAAATTT
1 TTATCAAAATTT
7635 CAGAGTGTGA
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
22 32 0.48
23 34 0.52
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGA
Found at i:13685 original size:195 final size:195
Alignment explanation
Indices: 13353--13716 Score: 692
Period size: 195 Copynumber: 1.9 Consensus size: 195
13343 TTTATCAGAC
*
13353 TCATTAAAGCGATCTTCTTTTGCCATGTGCAAAAATTGCCACCATCAAAGCGATTTAGTTTGACA
1 TCATTAAAGCGATCTTCTTTTGCCATCTGCAAAAATTGCCACCATCAAAGCGATTTAGTTTGACA
*
13418 AAATTAGAAGGCAATTCTCCAAATGTTCCACTTGTTGCAGGCCTTAAGATTGTTATAAATATAGA
66 AAATTAGAAGGCAATTCTCCAAATGTTCCACTTATTGCAGGCCTTAAGATTGTTATAAATATAGA
*
13483 TAAATCTGCAAATGGAAATTGACTCTAGTACGGAGCCACAGACTCATTAAAGCGATCTTCTTGGT
131 TAAATCTGCAAATGGAAATTGACTCCAGTACGGAGCCACAGACTCATTAAAGCGATCTTCTTGGT
13548 TCATTAAAGCGATCTTCTTTTGCCATCTGCAAAAATTGCCACCATCAAAGCGATTTAGTTTGACA
1 TCATTAAAGCGATCTTCTTTTGCCATCTGCAAAAATTGCCACCATCAAAGCGATTTAGTTTGACA
*
13613 AAATTAGAAGGCAATTCTCCAAATGTTCCATTTATTGCAGGCCTTAAGATTGTTATAAATATAGA
66 AAATTAGAAGGCAATTCTCCAAATGTTCCACTTATTGCAGGCCTTAAGATTGTTATAAATATAGA
13678 TAAATCTGCAAATGGAAATTGACTCCAGTACGGAGCCAC
131 TAAATCTGCAAATGGAAATTGACTCCAGTACGGAGCCAC
13717 TAAGGAGCAA
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 165 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (195 bp):
TCATTAAAGCGATCTTCTTTTGCCATCTGCAAAAATTGCCACCATCAAAGCGATTTAGTTTGACA
AAATTAGAAGGCAATTCTCCAAATGTTCCACTTATTGCAGGCCTTAAGATTGTTATAAATATAGA
TAAATCTGCAAATGGAAATTGACTCCAGTACGGAGCCACAGACTCATTAAAGCGATCTTCTTGGT
Done.