Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021589.1 Corchorus olitorius cultivar O-4 contig21622, 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: 34511
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1053 original size:21 final size:21
Alignment explanation
Indices: 1014--1062 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1004 TCAATGCTTT
**
1014 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
1036 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
1057 A-GAAGC
1 AGGAAGC
1063 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:2285 original size:25 final size:26
Alignment explanation
Indices: 2251--2306 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
2241 TTTTTCAAAT
* * *
2251 ATATTTTTAAAT-TGTCATTGTTAAA
1 ATATATTTAAATATGCCATTATTAAA
*
2276 ATATATTTAACTATGCCATTATTAAA
1 ATATATTTAAATATGCCATTATTAAA
2302 ATATA
1 ATATA
2307 ATAATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATTTAAATATGCCATTATTAAA
Found at i:3013 original size:332 final size:332
Alignment explanation
Indices: 2374--3071 Score: 888
Period size: 332 Copynumber: 2.1 Consensus size: 332
2364 ATAATTTTTT
* * *
2374 AATTAGAAATTAATTCGGAAAAAGGTAGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAGTC
1 AATTAGAAATTAATTCGGAAAAA-ATAGAAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATC
* * * * *
2439 TTTTTGGCATTGAGTTATATATTTTTTATTAGTATTGTGGCCCAAAATTGAGGAGAAAGTTCTCG
65 TTTTTGGCATTGAATTATATATTTTCTATGAGTATCGTGGCCCAAAATTGAGGAGAAAATTCTCG
* * *
2504 GGTCAATTTTTGCAAAATTTTAGCTGAAATCGTATACTAACTATCACGGGTTTTGACTAAAAACG
130 GGTCAATTTTTACAAAATTTTAGCCGAAATCGTATACTAACTATCACGGGTTTTGACGAAAAACG
* ** * *
2569 CATTCTGGAGCCCCGGCTCTGTTTTACACGATTTTTGGCGCCAAGTCTCATTGAAATATCTATAT
195 CATTCTGGAGCCCCGACTCAATTTTACACGATTTTTGGCGCCAAGACTCATTGAAATAACTATAT
* * * * *
2634 CCATCTAACCAAATCTTACCCACATTGGATTTAAGGATTTGTTTTTACCAACATATGAATCATGT
260 CCATCTAACAAAATCTTACCCACATTGGATTTAAGAATTTATTTTTACCAACATATCAATCAGGT
2699 TTCGATTC
325 TTCGATTC
* * * *
2707 AATTAGGAATTAATTCGGAAAAAATTGAAAAAACGATATTATAAGCGTGA-ATAGCCTTTCAATC
1 AATTAGAAATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAGA-AGCCCTTCAATC
** *
2771 TTTTTGGTGTTGAATTATATATTTTCTATGATTATCGTGG-CCAGAAATTGA-GA-AAAATTCTT
65 TTTTTGGCATTGAATTATATATTTTCTATGAGTATCGTGGCCCA-AAATTGAGGAGAAAATTC--
* *
2833 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGACGAAAA
127 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTATACTAACTATCACGGGTTTTGACGAAAA
* * * *
2898 ACGCGTT-TCGTG-GCCCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGGAATAAC
192 ACGCATTCT-G-GAGCCCCGACTCAATTTTACACGATTTTTGGCGCCAAGACTCATTGAAATAAC
** * * * *
2961 TATATTTATCTAACAAAAT-TTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTCAA
255 TATATCCATCTAACAAAATCTT-ACCCACATTGGATTTAAGAATTTATTTTTACCAACATATCAA
* *
3025 TCCGGTTTCGATTT
319 TCAGGTTTCGATTC
*
3039 AATTAGAAATTAATTCGGGAAAAATAGAAAAAA
1 AATTAGAAATTAATTCGGAAAAAATAGAAAAAA
3072 AAACAATATT
Statistics
Matches: 313, Mismatches: 45, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
330 6 0.02
331 9 0.03
332 275 0.88
333 23 0.07
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (332 bp):
AATTAGAAATTAATTCGGAAAAAATAGAAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCT
TTTTGGCATTGAATTATATATTTTCTATGAGTATCGTGGCCCAAAATTGAGGAGAAAATTCTCGG
GTCAATTTTTACAAAATTTTAGCCGAAATCGTATACTAACTATCACGGGTTTTGACGAAAAACGC
ATTCTGGAGCCCCGACTCAATTTTACACGATTTTTGGCGCCAAGACTCATTGAAATAACTATATC
CATCTAACAAAATCTTACCCACATTGGATTTAAGAATTTATTTTTACCAACATATCAATCAGGTT
TCGATTC
Found at i:6195 original size:2 final size:2
Alignment explanation
Indices: 6184--6251 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
6174 ATTACCGATG
*
6184 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA 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
*
6225 TA TA TG 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 T
6252 CCTTTTTACA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7184 original size:26 final size:27
Alignment explanation
Indices: 7146--7207 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
7136 TAGTTAGGGT
* *
7146 TTCCCCTCTTCTTCTTC-CTCTACCTG
1 TTCCCCTCCTCTTCTTCTCTATACCTG
7172 TTCCCCTCCTCTTCTTCTTCTATACCTG
1 TTCCCCTCCTCTTCTTC-TCTATACCTG
7200 TTCCCCTC
1 TTCCCCTC
7208 TCCACCCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 16 0.50
28 16 0.50
ACGTcount: A:0.05, C:0.47, G:0.03, T:0.45
Consensus pattern (27 bp):
TTCCCCTCCTCTTCTTCTCTATACCTG
Found at i:7206 original size:28 final size:29
Alignment explanation
Indices: 7150--7207 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
7140 TAGGGTTTCC
*
7150 CCTCTTCTTCTTCCTCTACCTGTTCCCCT
1 CCTCTTCTTCTTCCTATACCTGTTCCCCT
7179 CCTCTTCTTCTT-CTATACCTGTTCCCCT
1 CCTCTTCTTCTTCCTATACCTGTTCCCCT
7207 C
1 C
7208 TCCACCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.05, C:0.47, G:0.03, T:0.45
Consensus pattern (29 bp):
CCTCTTCTTCTTCCTATACCTGTTCCCCT
Found at i:11358 original size:14 final size:14
Alignment explanation
Indices: 11339--11368 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11329 TTGTTGTTGC
11339 TGAACTTGAATGTT
1 TGAACTTGAATGTT
*
11353 TGAACTTGGATGTT
1 TGAACTTGAATGTT
11367 TG
1 TG
11369 TAATTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (14 bp):
TGAACTTGAATGTT
Found at i:12115 original size:54 final size:53
Alignment explanation
Indices: 12023--12127 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 53
12013 ATAATAGCTC
*
12023 CAATAAAGAACTTTTTTTTATTGGAGAAATAGTGTATATATGGCTAATTGCAG
1 CAATAAAGAACTTTTTTTTATTGGAGAAATAGTATATATATGGCTAATTGCAG
* *
12076 CAATAAAGAAC-TTTTTTTATGATGGTGAAATAGTATATATGTGGCTAATTGC
1 CAATAAAGAACTTTTTTTTAT--TGGAGAAATAGTATATATATGGCTAATTGC
12128 TTAATTAAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
52 9 0.19
53 11 0.23
54 27 0.57
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (53 bp):
CAATAAAGAACTTTTTTTTATTGGAGAAATAGTATATATATGGCTAATTGCAG
Found at i:20537 original size:16 final size:16
Alignment explanation
Indices: 20502--20545 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20492 AAAATATTGC
* *
20502 TATATGTATGTATGGTA
1 TATAT-TATATATAGTA
20519 TATATTATATATAGTA
1 TATATTATATATAGTA
*
20535 TATACTATATA
1 TATATTATATA
20546 GATATAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (16 bp):
TATATTATATATAGTA
Found at i:20543 original size:14 final size:15
Alignment explanation
Indices: 20525--20561 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20515 GGTATATATT
20525 ATATATAGTATATA-
1 ATATATAGTATATAG
*
20539 CTATATAG-ATATAG
1 ATATATAGTATATAG
20553 ATATATAGT
1 ATATATAGT
20562 CAATTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (15 bp):
ATATATAGTATATAG
Found at i:22699 original size:79 final size:78
Alignment explanation
Indices: 22563--22719 Score: 278
Period size: 79 Copynumber: 2.0 Consensus size: 78
22553 GTCAAAAAGT
22563 ATTTTTCATTCTTAACTCCTTATAATTTTTTTTATCATTTATGAATTACATAAGCATATTGATAT
1 ATTTTTCATTCTTAACTCCTTATAATTTTTTTTATCATTTATGAATTACATAAGCATATTGATAT
22628 ATTCAATAATATA
66 ATTCAATAATATA
* * *
22641 ATTTTTCCTTCTTAACTCCTTATAATTTTTTTTTATCATTTATGAATTATATAAGCATATTGGTA
1 ATTTTTCATTCTTAACTCCTTATAA-TTTTTTTTATCATTTATGAATTACATAAGCATATTGATA
22706 TATTCAATAATATA
65 TATTCAATAATATA
22720 TGATTATGCA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 24 0.32
79 51 0.68
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (78 bp):
ATTTTTCATTCTTAACTCCTTATAATTTTTTTTATCATTTATGAATTACATAAGCATATTGATAT
ATTCAATAATATA
Found at i:23661 original size:34 final size:34
Alignment explanation
Indices: 23617--23682 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
23607 CTTTCTTGGC
* *
23617 TTTTTGTTTTGCGTAT-GTGTTGCATTAAAAGTTT
1 TTTTTGTTTTG-GCATCATGTTGCATTAAAAGTTT
*
23651 TTTTTTTTTTGGCATCATGTTGCATTAAAAGT
1 TTTTTGTTTTGGCATCATGTTGCATTAAAAGT
23683 CTAAAACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.55
Consensus pattern (34 bp):
TTTTTGTTTTGGCATCATGTTGCATTAAAAGTTT
Found at i:25194 original size:19 final size:19
Alignment explanation
Indices: 25170--25216 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
25160 CTACAAACTT
25170 GCTCCGTGCAAAAAACCAA
1 GCTCCGTGCAAAAAACCAA
25189 GCTCCGTGCAAAAAACCAA
1 GCTCCGTGCAAAAAACCAA
25208 GCTCCGTGC
1 GCTCCGTGC
25217 TTATTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.34, C:0.34, G:0.19, T:0.13
Consensus pattern (19 bp):
GCTCCGTGCAAAAAACCAA
Found at i:33539 original size:29 final size:29
Alignment explanation
Indices: 33472--33576 Score: 97
Period size: 29 Copynumber: 3.7 Consensus size: 29
33462 AGGATCACCT
* * * **
33472 AGGGGAATTTTGGTCATTTTTAAAAACCC
1 AGGGGCATTTTAGTCATTTTTCAAATTCC
* * **
33501 AGGGGTATTTTGGTCATTTTTCACGTTCC
1 AGGGGCATTTTAGTCATTTTTCAAATTCC
* *
33530 AGGGGCATTTTAGTCA-TTTGCATATT-C
1 AGGGGCATTTTAGTCATTTTTCAAATTCC
33557 AGGGGCATTTTAGTCATTTT
1 AGGGGCATTTTAGTCATTTT
33577 AAGTTCACAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 17 0.27
28 10 0.16
29 37 0.58
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (29 bp):
AGGGGCATTTTAGTCATTTTTCAAATTCC
Done.