Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016233.1 Corchorus olitorius cultivar O-4 contig16266, 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: 31210
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2496 original size:20 final size:21
Alignment explanation
Indices: 2458--2496 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2448 AGAGACAAAA
* *
2458 AAAAGGAAAAAATTCAAAGTC
1 AAAAGGAAAAAAATAAAAGTC
2479 AAAA-GAAAAAAATAAAAG
1 AAAAGGAAAAAAATAAAAG
2497 GAAGACAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (21 bp):
AAAAGGAAAAAAATAAAAGTC
Found at i:10527 original size:21 final size:21
Alignment explanation
Indices: 10501--10545 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
10491 ATAAGTTCTT
*
10501 ATGTCTGAGGATCATAAGTAA
1 ATGTCTGAGGATCATAAGAAA
10522 ATGTCTGAGGATCATAAGAAA
1 ATGTCTGAGGATCATAAGAAA
10543 ATG
1 ATG
10546 ATACTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (21 bp):
ATGTCTGAGGATCATAAGAAA
Found at i:16555 original size:13 final size:13
Alignment explanation
Indices: 16539--16567 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16529 TTTAACTTTG
16539 CTTTTTCATTTTT
1 CTTTTTCATTTTT
16552 CTTTTTCATTTTT
1 CTTTTTCATTTTT
16565 CTT
1 CTT
16568 CTATTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTCATTTTT
Found at i:19484 original size:22 final size:22
Alignment explanation
Indices: 19449--19859 Score: 141
Period size: 22 Copynumber: 19.0 Consensus size: 22
19439 ATGTCTGTGT
19449 GGTTATC-AAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGGA
***
19470 GGTTATCAAAATTTCATAATCT
1 GGTTATCAAAATTTCATAAGGA
* * ** *
19492 GGTTATCAAAATATGATACTGT
1 GGTTATCAAAATTTCATAAGGA
*
19514 GGTTACCAAAATTTCAT-AGGA
1 GGTTATCAAAATTTCATAAGGA
* *
19535 TGGTTTTTAAAATTTCAT-A-GA
1 -GGTTATCAAAATTTCATAAGGA
* *
19556 GTTTTTATCAAAATTT-ATAGGGATCA
1 G--GTTATCAAAATTTCATAAGG---A
* *
19582 TGTTATCAAAATTTCGT-AGGAA
1 GGTTATCAAAATTTCATAAGG-A
*
19604 GGTTATCAAAATTTCAT--GTA
1 GGTTATCAAAATTTCATAAGGA
* *
19624 GTGGT-T-AAAA-TTCATATGGA
1 G-GTTATCAAAATTTCATAAGGA
* *
19644 TCGAGTTATTAAAATTTCATAAGAA
1 --G-GTTATCAAAATTTCATAAGGA
*
19669 GGTTATCAAAA-TT--TAA-TA
1 GGTTATCAAAATTTCATAAGGA
*
19687 --TCTATCAAAATTTCATATGGA
1 GGT-TATCAAAATTTCATAAGGA
* * *
19708 GGTTATTAGAATTTCAT-AGTA
1 GGTTATCAAAATTTCATAAGGA
* *
19729 TAGTTATCAAAATTTCATAAAGA
1 -GGTTATCAAAATTTCATAAGGA
* * *
19752 GTTTATCAAATTTTTCATAA-TA
1 GGTTATCAAA-ATTTCATAAGGA
* ** *
19774 TGGTTACCAAAATTTCATCTGAA
1 -GGTTATCAAAATTTCATAAGGA
* *
19797 GGTTA-GAAAA-ATC-T-AGGAA
1 GGTTATCAAAATTTCATAAGG-A
* * *
19816 GGTTATCAAAATTTGATATTGTA
1 GGTTATCAAAATTTCATA-AGGA
*
19839 -GTTATTAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGGA
19860 AGTCTCATAA
Statistics
Matches: 284, Mismatches: 70, Indels: 72
0.67 0.16 0.17
Matches are distributed among these distances:
16 1 0.00
17 8 0.03
18 9 0.03
19 14 0.05
20 14 0.05
21 27 0.10
22 158 0.56
23 24 0.08
24 19 0.07
25 9 0.03
26 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGGA
Found at i:19617 original size:68 final size:65
Alignment explanation
Indices: 19515--19682 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 65
19505 TGATACTGTG
* * * * ** *
19515 GTTACCAAAATTTCATAGGATGGTTTTTAAAATTTCATAG-AGTTTTTATCAAAATTTATAGGGA
1 GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-GTAG-TGGT-T-AAAATTCATAGGGA
19579 TC-A
62 TCGA
* *
19582 TGTTATCAAAATTTCGTAGGAAGGTTATCAAAATTTCATGTAGTGGTTAAAATTCATATGGATCG
1 -GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATGTAGTGGTTAAAATTCATAGGGATCG
19647 A
65 A
* *
19648 GTTATTAAAATTTCATAAGAAGGTTATCAAAATTT
1 GTTATCAAAATTTCATAGGAAGGTTATCAAAATTT
19683 AATATCTATC
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
65 46 0.53
66 2 0.02
67 3 0.03
68 35 0.41
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (65 bp):
GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATGTAGTGGTTAAAATTCATAGGGATCGA
Found at i:19694 original size:17 final size:17
Alignment explanation
Indices: 19672--19704 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19662 ATAAGAAGGT
19672 TATCAAAATTTAATATC
1 TATCAAAATTTAATATC
*
19689 TATCAAAATTTCATAT
1 TATCAAAATTTAATAT
19705 GGAGGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
TATCAAAATTTAATATC
Found at i:19932 original size:22 final size:22
Alignment explanation
Indices: 19871--19955 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 22
19861 GTCTCATAAA
* * *
19871 GTAGTTATCAAACTTTCATAGA
1 GTAGTTATCAAAATTTGATAGT
*
19893 GATTAGATTACCAAAATTTGATAGT
1 G--TAG-TTATCAAAATTTGATAGT
*
19918 GTGGTTATCAAAATTTGATAGT
1 GTAGTTATCAAAATTTGATAGT
*
19940 GTAGTTATTAAAATTT
1 GTAGTTATCAAAATTT
19956 CATATGGAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
22 32 0.62
23 2 0.04
24 3 0.06
25 15 0.29
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (22 bp):
GTAGTTATCAAAATTTGATAGT
Found at i:19943 original size:104 final size:104
Alignment explanation
Indices: 19816--20020 Score: 356
Period size: 104 Copynumber: 2.0 Consensus size: 104
19806 AATCTAGGAA
* * *
19816 GGTTATCAAAATTTGATATTGTAGTTATTAAAATTTCATAAGGAAGTCTCATAAAGTAGTTATCA
1 GGTTATCAAAATTTGATAGTGTAGTTATTAAAATTTCATAAGGAAGTCTCATAAACTAATTATCA
*
19881 AACTTTCATAGAGATTAGATTACCAAAATTTGATAGTGT
66 AACTTTCATAGAGATTAGATTACCAAAATTTCATAGTGT
*
19920 GGTTATCAAAATTTGATAGTGTAGTTATTAAAATTTCATATGGAAGTCTCATAAACTAATTATCA
1 GGTTATCAAAATTTGATAGTGTAGTTATTAAAATTTCATAAGGAAGTCTCATAAACTAATTATCA
*
19985 AACTTTCATAGAGATTATATTACCAAAATTTCATAG
66 AACTTTCATAGAGATTAGATTACCAAAATTTCATAG
20021 GAAGGCATAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (104 bp):
GGTTATCAAAATTTGATAGTGTAGTTATTAAAATTTCATAAGGAAGTCTCATAAACTAATTATCA
AACTTTCATAGAGATTAGATTACCAAAATTTCATAGTGT
Found at i:20103 original size:22 final size:21
Alignment explanation
Indices: 20076--20177 Score: 104
Period size: 22 Copynumber: 4.9 Consensus size: 21
20066 ATTTTTCAGT
20076 GGTTATCGAAATTTCATATGAA
1 GGTTATCGAAATTTCATA-GAA
*
20098 GGTTAT--AAATTTCATAGTAT
1 GGTTATCGAAATTTCATAG-AA
* * *
20118 TGTTATCAAAATTTCATAAAGA
1 GGTTATCGAAATTTCATAGA-A
*
20140 GGTTATCGACATTTCAT--AA
1 GGTTATCGAAATTTCATAGAA
20159 GGTTATCGAAATTTCATAG
1 GGTTATCGAAATTTCATAG
20178 TGTCATTATC
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
19 18 0.27
20 17 0.26
21 1 0.02
22 30 0.45
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
GGTTATCGAAATTTCATAGAA
Found at i:20123 original size:42 final size:40
Alignment explanation
Indices: 20076--20176 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 40
20066 ATTTTTCAGT
*
20076 GGTTATCGAAATTTCAT-ATGAAGGTTAT-AAATTTCATAGTA
1 GGTTATCGAAATTTCATAAAG-AGGTTATCAAATTTCATA--A
* * *
20117 TTGTTATCAAAATTTCATAAAGAGGTTATCGACATTTCATAA
1 -GGTTATCGAAATTTCATAAAGAGGTTATC-AAATTTCATAA
20159 GGTTATCGAAATTTCATA
1 GGTTATCGAAATTTCATA
20177 GTGTCATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
41 16 0.32
42 23 0.46
43 2 0.04
44 9 0.18
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (40 bp):
GGTTATCGAAATTTCATAAAGAGGTTATCAAATTTCATAA
Found at i:20187 original size:63 final size:63
Alignment explanation
Indices: 20033--20198 Score: 171
Period size: 63 Copynumber: 2.6 Consensus size: 63
20023 AGGCATAGTG
* ** *
20033 AGGTTATCAAATTTTCCTAGTGATATTATCAAAATTT--TTCAGTGGTTATCGAAATTTCATATG
1 AGGTTATCAAA-TTTCATAGTG-TATTATCAAAATTTCATAAAGAGGTTATCGAAATTTCA-ATG
20096 A
63 A
* * *
20097 AGGTTAT-AAATTTCATAGTATTGTTATCAAAATTTCATAAAGAGGTTATCGACATTTC-AT-A
1 AGGTTATCAAATTTCATAGT-GTATTATCAAAATTTCATAAAGAGGTTATCGAAATTTCAATGA
*
20158 AGGTTATCGAAATTTCATAGTGTCATTATCAAAATTCCATA
1 AGGTTATC-AAATTTCATAGTGT-ATTATCAAAATTTCATA
20199 GGGAAGTTAG
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
61 8 0.09
62 24 0.28
63 30 0.35
64 24 0.28
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (63 bp):
AGGTTATCAAATTTCATAGTGTATTATCAAAATTTCATAAAGAGGTTATCGAAATTTCAATGA
Found at i:20217 original size:63 final size:61
Alignment explanation
Indices: 20096--20217 Score: 136
Period size: 63 Copynumber: 2.0 Consensus size: 61
20086 ATTTCATATG
** * * * * *
20096 AAGGTTATAAATTTCATAGTATTGTTATCAAAATTTCATAAAGAGGTTATCGACATTTCAT
1 AAGGTTATAAATTTCATAGTATCATTATCAAAATTCCATAAAGAAGTTAGCAAAATTTCAT
* **
20157 AAGGTTATCGAAATTTCATAGTGTCATTATCAAAATTCCATAGGGAAGTTAGCAAAATTTC
1 AAGGTTAT--AAATTTCATAGTATCATTATCAAAATTCCATAAAGAAGTTAGCAAAATTTC
20218 TTGGTATTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
61 8 0.16
63 41 0.84
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (61 bp):
AAGGTTATAAATTTCATAGTATCATTATCAAAATTCCATAAAGAAGTTAGCAAAATTTCAT
Found at i:27814 original size:19 final size:19
Alignment explanation
Indices: 27790--27831 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
27780 AAACGACAGA
*
27790 AAAACCAAGATAATCAATC
1 AAAACCAAGATAATAAATC
27809 AAAACCAAGATAATAAATC
1 AAAACCAAGATAATAAATC
27828 AAAA
1 AAAA
27832 TGTCAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.17, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAACCAAGATAATAAATC
Found at i:31177 original size:2 final size:2
Alignment explanation
Indices: 31172--31210 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31162 ACATGCGGAC
31172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.