Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013003.1 Corchorus olitorius cultivar O-4 contig13036, 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: 49367
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1060 original size:14 final size:14
Alignment explanation
Indices: 1041--1080 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1031 TGAGATTTTT
1041 AATAATAATTATTC
1 AATAATAATTATTC
* *
1055 AATAATTATTATTT
1 AATAATAATTATTC
1069 AATTAATAATTA
1 AA-TAATAATTA
1081 ATTAATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATAATTATTC
Found at i:4216 original size:15 final size:15
Alignment explanation
Indices: 4196--4228 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
4186 TATAAATAAT
4196 TGTTATGAATATACA
1 TGTTATGAATATACA
4211 TGTTATGAATATACA
1 TGTTATGAATATACA
4226 TGT
1 TGT
4229 ATATAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (15 bp):
TGTTATGAATATACA
Found at i:4346 original size:21 final size:21
Alignment explanation
Indices: 4322--4363 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4312 TTGTTCATCC
4322 CCTTGTATTTA-TGATGATGTA
1 CCTTGTATTTATTG-TGATGTA
4343 CCTTGTATTTATTGTGATGTA
1 CCTTGTATTTATTGTGATGTA
4364 TCTATGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (21 bp):
CCTTGTATTTATTGTGATGTA
Found at i:4487 original size:23 final size:23
Alignment explanation
Indices: 4461--4509 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4451 CTCTACATTC
*
4461 TCTTGTCCTTCT-CATAGTTCAAT
1 TCTTGT-CTTCTCCATACTTCAAT
*
4484 TCTTGTCTTTTCCATACTTCAAT
1 TCTTGTCTTCTCCATACTTCAAT
4507 TCT
1 TCT
4510 CTACTCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.16, C:0.27, G:0.06, T:0.51
Consensus pattern (23 bp):
TCTTGTCTTCTCCATACTTCAAT
Found at i:4726 original size:32 final size:33
Alignment explanation
Indices: 4685--4754 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4675 ACAAAGTTTA
* *
4685 TTTAACATGCATAATC-CCTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
4717 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
4750 TTTAT
1 TTTAT
4755 GATTAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 15 0.43
33 20 0.57
ACGTcount: A:0.20, C:0.30, G:0.03, T:0.47
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Found at i:6278 original size:38 final size:38
Alignment explanation
Indices: 6227--6305 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
6217 CTATATCGGG
*
6227 TGTGCAAATTTGATTG-ATGGCTCCGGAAGAGCTAGTAT
1 TGTGCAAATTTGATTGAAT-GCTCCGGAAGAGCCAGTAT
6265 TGTGCAAATTTGATTGAATGCTCCGGAAGAGCCAGTAT
1 TGTGCAAATTTGATTGAATGCTCCGGAAGAGCCAGTAT
6303 TGT
1 TGT
6306 TTTATCTGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.95
39 2 0.05
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (38 bp):
TGTGCAAATTTGATTGAATGCTCCGGAAGAGCCAGTAT
Found at i:9895 original size:21 final size:21
Alignment explanation
Indices: 9871--9912 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9861 TTGTTCATCC
9871 CCTTGTATTTA-TGATGATGTA
1 CCTTGTATTTATTG-TGATGTA
9892 CCTTGTATTTATTGTGATGTA
1 CCTTGTATTTATTGTGATGTA
9913 TTTATGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (21 bp):
CCTTGTATTTATTGTGATGTA
Found at i:10036 original size:23 final size:23
Alignment explanation
Indices: 10010--10058 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
10000 CTCTACATTC
*
10010 TCTTGTCCTTTT-CATAGTTCAAT
1 TCTTGT-CTTTTCCATACTTCAAT
10033 TCTTGTCTTTTCCATACTTCAAT
1 TCTTGTCTTTTCCATACTTCAAT
10056 TCT
1 TCT
10059 CTACTCCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.16, C:0.24, G:0.06, T:0.53
Consensus pattern (23 bp):
TCTTGTCTTTTCCATACTTCAAT
Found at i:15362 original size:8 final size:8
Alignment explanation
Indices: 15351--15429 Score: 64
Period size: 8 Copynumber: 10.6 Consensus size: 8
15341 TGCAAGTATT
15351 TATATCTA
1 TATATCTA
*
15359 TATATGTA
1 TATATCTA
15367 TATATCTA
1 TATATCTA
* *
15375 T-T-TTTT
1 TATATCTA
15381 TATA-C-A
1 TATATCTA
15387 TATATCTA
1 TATATCTA
15395 TATATC--
1 TATATCTA
15401 TATA-CTA
1 TATATCTA
*
15408 TCTATCTA
1 TATATCTA
15416 TATATACTA
1 TATAT-CTA
15425 TATAT
1 TATAT
15430 AAAAGTAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
5 1 0.02
6 11 0.20
7 6 0.11
8 29 0.53
9 8 0.15
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.52
Consensus pattern (8 bp):
TATATCTA
Found at i:15486 original size:31 final size:31
Alignment explanation
Indices: 15448--15509 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
15438 GAGTTTTGTA
*
15448 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
15479 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTGAATCACCTATTATACCCTTATT
15510 TTTTGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTATT
Found at i:17256 original size:31 final size:31
Alignment explanation
Indices: 17218--17279 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
17208 GAGTTTTGTA
17218 AAACTTTTGAATCGCCTATTAAACCCTTATT
1 AAACTTTTGAATCGCCTATTAAACCCTTATT
*
17249 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTAAACCCTTATT
17280 TTTTAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTAAACCCTTATT
Found at i:17417 original size:93 final size:93
Alignment explanation
Indices: 17315--17499 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
17305 TTGTTTAAAT
*
17315 TTTTATAGTTTTAGTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* * *
17380 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTAATTTTACCATATTACTAATTTAC
* *
17408 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
17473 TTTTAATTTTACGATATTACTAATTTA
66 TTTTAATTTTACCATATTACTAATTTA
17500 ATAAAAAAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTAATTTTACCATATTACTAATTTAC
Found at i:18834 original size:42 final size:43
Alignment explanation
Indices: 18783--18876 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
18773 AGTGCATTAT
* *
18783 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
18824 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
18869 CTAATATT
1 CTAATATT
18877 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
45 36 0.80
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:20230 original size:57 final size:56
Alignment explanation
Indices: 20151--20263 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 56
20141 TAGAATATTA
*
20151 TAAAATGGTAAAATAAGGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAG
1 TAAAATGGTAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAG
*
20207 TAAAATGGTAAAAATAAAGTAATTATAAAGATATTATATTTAATTGAATAAAAATAG
1 TAAAATGGT-AAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAG
20264 AGTTTTTAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 9 0.17
57 45 0.83
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (56 bp):
TAAAATGGTAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAG
Found at i:23187 original size:13 final size:12
Alignment explanation
Indices: 23169--23213 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
23159 ATTTTATTAC
23169 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
23182 TGTTTTATAAAT
1 TGTTTTATAAAT
*
23194 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
23208 TGTTTT
1 TGTTTT
23214 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:31883 original size:128 final size:131
Alignment explanation
Indices: 31699--31948 Score: 391
Period size: 128 Copynumber: 1.9 Consensus size: 131
31689 CTTGCAGGCT
*
31699 ACTCATAGCTTTCTTTTTTCTTTTTTTTTGTTTCCCACCCAGTATCCAAAGTTTTGCTCT-GAGT
1 ACTCATAGCTTTCTTTTTTC--TTTTTTTGTTTCCCACCCAGTATCCAAAGCTTTGCT-TAGAGT
* *
31763 AATCTAGATTCGACCAGGGTTGCGCACCTCGGTATGGTGGGTGAGTTTACCAACGGGGTCGCGCA
63 AATCCAGATTCGACCAGGGTCGCGCACCTCGGTATGGTGGGTGAGTTTACCAACGGGGTCGCGCA
31828 CCTC
128 CCTC
*
31832 ACTCATAGCTTTC-TTTTTC-TTTTTT-TTTCCCACCCGGTATCCAAAGCTTTGCTTAGAGTAAT
1 ACTCATAGCTTTCTTTTTTCTTTTTTTGTTTCCCACCCAGTATCCAAAGCTTTGCTTAGAGTAAT
* *
31894 CCGGATTTGACCAGGGTCGCGCACCTCGGTATGGTGGGTGAGTTTACCAACGGGG
66 CCAGATTCGACCAGGGTCGCGCACCTCGGTATGGTGGGTGAGTTTACCAACGGGG
31949 GCGGCTGCAT
Statistics
Matches: 110, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
127 1 0.01
128 84 0.76
129 6 0.05
132 6 0.05
133 13 0.12
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (131 bp):
ACTCATAGCTTTCTTTTTTCTTTTTTTGTTTCCCACCCAGTATCCAAAGCTTTGCTTAGAGTAAT
CCAGATTCGACCAGGGTCGCGCACCTCGGTATGGTGGGTGAGTTTACCAACGGGGTCGCGCACCT
C
Found at i:32946 original size:29 final size:29
Alignment explanation
Indices: 32898--32975 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
32888 CATCAGCCTG
* * *
32898 AGGGGGCAAAACGTCACAAAATTGAAGTTT
1 AGGGGACAAAATGTC-CAAAATTGAAGTTC
**
32928 AGGGGTTAAAATGTCCAAAATTGAAGTTC
1 AGGGGACAAAATGTCCAAAATTGAAGTTC
32957 AGGGGACAAAATGTCCAAA
1 AGGGGACAAAATGTCCAAA
32976 CGCTACAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.21
Consensus pattern (29 bp):
AGGGGACAAAATGTCCAAAATTGAAGTTC
Found at i:44044 original size:16 final size:17
Alignment explanation
Indices: 44023--44064 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
44013 TGCCAATTGA
*
44023 TATTTTTTCTT-TATCT
1 TATTTTATCTTATATCT
44039 TATTTTATCTTACTATCT
1 TATTTTATCTTA-TATCT
*
44057 TATCTTAT
1 TATTTTAT
44065 TATTTTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
18 12 0.55
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTATCTTATATCT
Found at i:45806 original size:107 final size:104
Alignment explanation
Indices: 45634--45895 Score: 382
Period size: 107 Copynumber: 2.5 Consensus size: 104
45624 AGTTTAGCCT
*
45634 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
45699 AATAATTTATTATTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA--TATTATTACAGGGTTTTAGAAATAAAATACAAAAC
* *
45741 TAATTTCACTAAGTTTAGCCCCAAATTTAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * * *
45806 AATAATATTGTTACATGGTTTTAGAAATAAAATATATAAC
65 AATAATATTATTACAGGGTTTTAGAAATAAAATACAAAAC
** *
45846 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
45896 TAGAAAAATT
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 29 0.20
104 14 0.10
105 33 0.23
107 66 0.46
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTATTACAGGGTTTTAGAAATAAAATACAAAAC
Found at i:49351 original size:12 final size:12
Alignment explanation
Indices: 49333--49367 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
49323 GTTTTATTTC
*
49333 CTTTTCCCTTTT
1 CTTTTTCCTTTT
49345 -TTTTTCCTTTT
1 CTTTTTCCTTTT
49356 CTTTTTCCTTTT
1 CTTTTTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTTTCCTTTT
Found at i:49367 original size:18 final size:17
Alignment explanation
Indices: 49324--49361 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
49314 AAAATTTCTG
*
49324 TTTTATTTCCTTTTCCCT
1 TTTTTTTTCCTTTT-CCT
49342 TTTTTTTTCCTTTT-CT
1 TTTTTTTTCCTTTTCCT
49358 TTTT
1 TTTT
49362 CCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCCTTTTCCT
Done.