Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010941.1 Corchorus capsularis cultivar CVL-1 contig10962, 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: 8109
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Found at i:600 original size:2 final size:2
Alignment explanation
Indices: 593--626 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
583 ATTATAAGAT
* *
593 TA TA TA TA TA TA TA TA TA TA TA TT TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
627 AAAGATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2047 original size:2 final size:2
Alignment explanation
Indices: 2040--2065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2030 ATAATCACCC
2040 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2066 ATCCAACTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5545 original size:38 final size:35
Alignment explanation
Indices: 5481--5557 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
5471 AATTTGGCTT
5481 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTG-C-TTTGTC
**
5518 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTC
5554 TTTG
1 TTTG
5558 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (35 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTGTC
Found at i:5731 original size:19 final size:21
Alignment explanation
Indices: 5689--5730 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
5679 TCCTTTACTA
5689 TTATTTTGTGAATTTAATATT
1 TTATTTTGTGAATTTAATATT
5710 TTATTTT-T-AATTTCAATATT
1 TTATTTTGTGAATTT-AATATT
5730 T
1 T
5731 AAATGTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TTATTTTGTGAATTTAATATT
Found at i:5960 original size:22 final size:21
Alignment explanation
Indices: 5898--6039 Score: 95
Period size: 22 Copynumber: 6.2 Consensus size: 21
5888 GTCTCTATGT
*
5898 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
*
5919 TGATTATCATTATAATTTCATCAGGA
1 -GGTTATCA--A-AATTTCAT-AGGA
*
5945 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
5967 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * * *
5991 GGTTATTAAAATCTCTTAGGTC
1 GGTTATCAAAATTTCATAGG-A
**
6013 GGTTATTGAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
6034 TGGTTA
1 -GGTTA
6040 ATTATCACAA
Statistics
Matches: 95, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
21 3 0.03
22 56 0.59
23 1 0.01
24 17 0.18
25 15 0.16
26 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:6017 original size:46 final size:46
Alignment explanation
Indices: 5944--6034 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
5934 TTTCATCAGG
*
5944 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
1 AGGTTATCAAAATCTCATAGTGTGGTTACCAAAATTTCATAGGATC
* * ***
5990 AGGTTATTAAAATCTCTTAG-GTCGGTTATTGAAATTTCATAGGAT
1 AGGTTATCAAAATCTCATAGTGT-GGTTACCAAAATTTCATAGGAT
6035 GGTTAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (46 bp):
AGGTTATCAAAATCTCATAGTGTGGTTACCAAAATTTCATAGGATC
Found at i:6100 original size:22 final size:22
Alignment explanation
Indices: 6075--6133 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
6065 ATCAAAGATA
*
6075 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
6097 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
6119 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
6134 TAAATATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:6198 original size:22 final size:21
Alignment explanation
Indices: 6150--6456 Score: 124
Period size: 22 Copynumber: 13.8 Consensus size: 21
6140 TTTCATGGGG
** *
6150 AGGTTATCAAAATTTTTTAGTG
1 AGGTTATCAAAATTTCATAG-A
*
6172 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
6194 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
6219 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
6241 AGGTTATC-AAATCTCATA-A
1 AGGTTATCAAAATTTCATAGA
* *
6260 AGTGATTATCGAAATTTCACAGA
1 AG-G-TTATCAAAATTTCATAGA
6283 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
6308 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
6328 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
6352 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
6372 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
6395 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
6417 GAGGTTATCAAAATTTCATA-A
1 -AGGTTATCAAAATTTCATAGA
*
6438 AGAGTTTATCAAATTTTCA
1 AG-G-TTATCAAAATTTCA
6457 AAATGTGATT
Statistics
Matches: 216, Mismatches: 42, Indels: 54
0.69 0.13 0.17
Matches are distributed among these distances:
19 3 0.01
20 13 0.06
21 27 0.12
22 130 0.60
23 6 0.03
24 7 0.03
25 20 0.09
26 6 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:6381 original size:44 final size:44
Alignment explanation
Indices: 6288--6478 Score: 165
Period size: 44 Copynumber: 4.4 Consensus size: 44
6278 ACAGAGATCG
* * * *
6288 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
6332 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
6375 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * *
6419 GGTTATCAAAATTTCATAA-AGAGTTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
6463 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
6479 TAGTGGTATT
Statistics
Matches: 114, Mismatches: 29, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
43 15 0.13
44 98 0.86
45 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:6393 original size:66 final size:66
Alignment explanation
Indices: 6309--6456 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
6299 TTTATAGAAA
* ** * * *
6309 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAT
6373 GT
65 GT
* * * *
6375 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
*
6440 A
66 T
* *
6441 GTTTATCAAATTTTCA
1 GATTATCAAAATTTCA
6457 AAATGTGATT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
T
Found at i:6453 original size:21 final size:22
Alignment explanation
Indices: 6210--6456 Score: 148
Period size: 22 Copynumber: 11.3 Consensus size: 22
6200 TAAAAGTCTC
* *
6210 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
6230 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * *
6250 AATCTCATAAAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
* *
6272 AATTTCACAGAGATCGGATTATCAA
1 AATTTCATAAAGA--GG-TTATCAA
*
6297 AATTT-ATAGAA-AGATTATCAA
1 AATTTCATA-AAGAGGTTATCAA
** **
6318 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
6340 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATAA-AGAGGTTATCAA
* * * * *
6362 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
* * * *
6384 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
*
6406 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
6428 AATTTCATAAAGAGTTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
6450 ATTTTCA
1 AATTTCA
6457 AAATGTGATT
Statistics
Matches: 167, Mismatches: 48, Indels: 22
0.70 0.20 0.09
Matches are distributed among these distances:
19 1 0.01
20 18 0.11
21 22 0.13
22 108 0.65
23 2 0.01
24 4 0.02
25 12 0.07
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:6587 original size:20 final size:20
Alignment explanation
Indices: 6562--6612 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
6552 TTATGGAGTA
6562 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
6582 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
6601 ATCAAAATTTCA
1 ATCAAAATTTCA
6613 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:6716 original size:22 final size:22
Alignment explanation
Indices: 6562--7178 Score: 276
Period size: 22 Copynumber: 28.6 Consensus size: 22
6552 TTATGGAGTA
*
6562 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
*
6582 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
6601 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
6623 ATTAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * **
6645 TTCAAATTTTCA-AAAGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
6667 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
6689 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
6711 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
6733 ATCGAAAA-ATCATAGGGAGGTT
1 ATC-AAAATTTCATAGGGAGGTT
*
6755 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * **
6771 ATCAAGATTTCATAAGAAAATT
1 ATCAAAATTTCATAGGGAGGTT
*
6793 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
6816 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* ** *
6839 ATCAAAATTTTATAGAAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
**
6862 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
6884 ATCACAATTTGATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
6906 ATCAAAATTT--T-GTGA--TT
1 ATCAAAATTTCATAGGGAGGTT
*
6923 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
6945 TTTAAATTTTCATAATGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
6967 ATCAAAATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
6989 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
7012 ATCAAAATTTCGTTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
**
7034 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
7057 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
7078 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * ***
7100 AAAAAAAATT-ATAAAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
7121 CTCAAAATTGCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* *
7143 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
7165 ATCAAAATTTCATA
1 ATCAAAATTTCATA
7179 ATGGGATCAT
Statistics
Matches: 445, Mismatches: 118, Indels: 66
0.71 0.19 0.10
Matches are distributed among these distances:
16 10 0.02
17 11 0.02
18 3 0.01
19 23 0.05
20 14 0.03
21 28 0.06
22 269 0.60
23 87 0.20
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:6819 original size:23 final size:23
Alignment explanation
Indices: 6791--6916 Score: 139
Period size: 23 Copynumber: 5.6 Consensus size: 23
6781 CATAAGAAAA
6791 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
6814 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
** *
6837 TTATCAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* **
6860 TTATCAAAATTTCATAACGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
6882 TTATCACAATTTGATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
6904 TTATCAAAATTTT
1 TTATCAAAATTTT
6917 GTGATTACTA
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
21 1 0.01
22 26 0.30
23 60 0.69
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:7035 original size:45 final size:44
Alignment explanation
Indices: 6954--7047 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
6944 TTTTAAATTT
* *
6954 TCATAATGTGGTTATCAAAATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
* * * *
6998 TCATAGTGTTGGTTATCAAAATTTCGT-TGGGAAGTTATCAAAATT
1 TCATAATG-TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATC
7043 TCATA
1 TCATA
7048 TTGAGGTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
Done.