Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020143.1 Corchorus olitorius cultivar O-4 contig20176, 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: 21374
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:290 original size:3 final size:3
Alignment explanation
Indices: 284--316 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
274 TTAGGAGGAA
284 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
317 TTTGGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:993 original size:28 final size:28
Alignment explanation
Indices: 933--985 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
923 CCTATCATGA
* *
933 AAAATTACCGTTTTGCCCTTTGTCGAAT
1 AAAATTACCGTTTTGCCCTCTGTAGAAT
961 AAAATTACCGTTTTGCCC-CTGTAGA
1 AAAATTACCGTTTTGCCCTCTGTAGA
986 CCTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (28 bp):
AAAATTACCGTTTTGCCCTCTGTAGAAT
Found at i:2942 original size:23 final size:23
Alignment explanation
Indices: 2912--2957 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2902 CCGTCTATAT
2912 TTAC-TTTTAAAATAAAATAATAA
1 TTACTTTTTAAAATAAAA-AATAA
*
2935 TTACTTTTTTAAATAAAAAATAA
1 TTACTTTTTAAAATAAAAAATAA
2958 AATTTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TTACTTTTTAAAATAAAAAATAA
Found at i:3106 original size:29 final size:30
Alignment explanation
Indices: 3062--3119 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
3052 CTAATTAATA
* *
3062 TATACATATAAATTATTCAATTTTATTATG
1 TATAAATATAAATTATTCAATTATATTATG
*
3092 TATAAATAT-AATTATTTAATTATATTAT
1 TATAAATATAAATTATTCAATTATATTAT
3120 ATTATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (30 bp):
TATAAATATAAATTATTCAATTATATTATG
Found at i:5965 original size:21 final size:22
Alignment explanation
Indices: 5933--5988 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
5923 CAGGTTGAAG
*
5933 AAGAAGAAAAAAGA-AAAGGGAA
1 AAGAA-AAAAAAGACAAAAGGAA
5955 AAGAAAAAAAA-ACAAAAGGAA
1 AAGAAAAAAAAGACAAAAGGAA
*
5976 AGGAAAAGAAAAG
1 AAGAAAA-AAAAG
5989 CTAAACGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 19 0.66
22 9 0.31
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAGACAAAAGGAA
Found at i:5987 original size:22 final size:22
Alignment explanation
Indices: 5933--5987 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
5923 CAGGTTGAAG
* *
5933 AAGAAGAAAAAAGAAAAGGGAA
1 AAGAAAAAAAAACAAAAGGGAA
5955 AAGAAAAAAAAACAAAA-GGAA
1 AAGAAAAAAAAACAAAAGGGAA
* *
5976 AGGAAAAGAAAA
1 AAGAAAAAAAAA
5988 GCTAAACGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAAAACAAAAGGGAA
Found at i:7277 original size:25 final size:24
Alignment explanation
Indices: 7249--7333 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 24
7239 ATCCGTTTAG
7249 TATTAAATACTATATATTATTTATT
1 TATTAAATA-TATATATTATTTATT
*
7274 TATTTTGAACTCAT-TAT-TTA-TTATT
1 TA--TT-AAAT-ATATATATTATTTATT
*
7299 TA--AAATATATTTATTATTTATT
1 TATTAAATATATATATTATTTATT
7321 TATT-AATATATAT
1 TATTAAATATATAT
7334 TATATCTAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 20
0.66 0.06 0.28
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 3 0.06
22 7 0.15
23 8 0.17
25 9 0.19
26 3 0.06
27 5 0.11
28 4 0.09
29 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (24 bp):
TATTAAATATATATATTATTTATT
Found at i:7315 original size:21 final size:24
Alignment explanation
Indices: 7286--7336 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
7276 TTTTGAACTC
7286 ATTATT-TATTATTTA-AAATATAT
1 ATTATTAT-TTATTTATAAATATAT
*
7309 -TTATTATTTATTTATTAATATAT
1 ATTATTATTTATTTATAAATATAT
7332 ATTAT
1 ATTAT
7337 ATCTAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 12 0.50
23 8 0.33
24 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTATTTATTTATAAATATAT
Found at i:7334 original size:25 final size:25
Alignment explanation
Indices: 7286--7334 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
7276 TTTTGAACTC
7286 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATTTAAAATATATTT
*
7311 ATTATTTATT-TATTAATATATATT
1 ATTATTTATTAT-TTAAAATATATT
7335 ATATCTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTATTTATTATTTAAAATATATTT
Found at i:12524 original size:3 final size:3
Alignment explanation
Indices: 12516--12562 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
12506 GACACTTTAT
12516 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
12563 GATTTTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12799 original size:2 final size:2
Alignment explanation
Indices: 12794--12839 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12784 CATATATATC
12794 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12836 TG TG
1 TG TG
12840 CATGATTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18524 original size:26 final size:28
Alignment explanation
Indices: 18480--18531 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
18470 ATTGAGCTTT
18480 TTTTTTGGACCTTATTAAACTTTTTTCC
1 TTTTTTGGACCTTATTAAACTTTTTTCC
*
18508 TTTTTTGG-CCTTA-TAAAGTTTTTT
1 TTTTTTGGACCTTATTAAACTTTTTT
18532 AGTCACCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 5 0.22
28 8 0.35
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTTTTGGACCTTATTAAACTTTTTTCC
Found at i:19112 original size:85 final size:86
Alignment explanation
Indices: 19017--19185 Score: 313
Period size: 86 Copynumber: 2.0 Consensus size: 86
19007 AATTATCTTC
19017 GTAAGCTTATAAATTTTTCATTAAACTTAAAAG-TTTTTAAATAGTTTTCTTAAATTTATTCAAT
1 GTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
*
19081 CACCTCGTTTAAGATTTTTTG
66 CACCTCATTTAAGATTTTTTG
*
19102 GTAAGCTTATAAATTTTTCATTAAATTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
1 GTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
19167 CACCTCATTTAAGATTTTT
66 CACCTCATTTAAGATTTTT
19186 AGTGATCTTA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
85 32 0.40
86 49 0.60
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.49
Consensus pattern (86 bp):
GTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
CACCTCATTTAAGATTTTTTG
Found at i:19199 original size:21 final size:22
Alignment explanation
Indices: 19175--19229 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
19165 ATCACCTCAT
* *
19175 TTAAGATTTTTAGTGATCTTA-
1 TTAAGATTTTTAGAGACCTTAC
*
19196 TTAACATATTTTAGAGACCTTAC
1 TTAAGAT-TTTTAGAGACCTTAC
19219 TTAAG-TTTTTA
1 TTAAGATTTTTA
19230 TTTAGTGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (22 bp):
TTAAGATTTTTAGAGACCTTAC
Found at i:19282 original size:20 final size:22
Alignment explanation
Indices: 19259--19306 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
19249 TTATCGTTAA
19259 CTTATGAA-TT-TTATAGTAAC
1 CTTATGAAGTTCTTATAGTAAC
*
19279 CTTATGAAGTTTCTTTTAGTAAC
1 CTTATGAAG-TTCTTATAGTAAC
19302 CTTAT
1 CTTAT
19307 TGAGTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
22 2 0.08
23 14 0.58
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (22 bp):
CTTATGAAGTTCTTATAGTAAC
Found at i:19640 original size:20 final size:22
Alignment explanation
Indices: 19593--19643 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 22
19583 TTACTAAACG
*
19593 TTTTAGTAACCTTTATTACAAT
1 TTTTAGTAACCTTTATTACAAA
19615 TTTTAGTAACC-TTATTA-AAA
1 TTTTAGTAACCTTTATTACAAA
19635 TTTTAGTAA
1 TTTTAGTAA
19644 TCTTGTAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 11 0.39
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (22 bp):
TTTTAGTAACCTTTATTACAAA
Done.