Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013880.1 Corchorus olitorius cultivar O-4 contig13913, 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: 41098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:684 original size:114 final size:114
Alignment explanation
Indices: 479--713 Score: 416
Period size: 114 Copynumber: 2.1 Consensus size: 114
469 GTTTTTATTT
*
479 TTTTTTTCAAAATATTAAAAGTGTTCATCTTGTTCATCTTTTATTGTTAAAAAAATAGGTGTTTG
1 TTTTTTTCAAAATATGAAAAGTGTTCATCTTGTTCATCTTTTATTGTTAAAAAAATAGGTGTTTG
* * *
544 ATCCATTGTTTAGAGTAAAATCTGAAATATGTGTGTTTTTTTATAATTC
66 ATCCATTGTTTAGAGAAAAATATGAAATATGTGTGTTTTTTGATAATTC
* *
593 TTTTTTTCAAAATCTGAAAAGTGTTCATCTTGTTCATCTTTTGTTGTTAAAAAAATAGGTGTTTG
1 TTTTTTTCAAAATATGAAAAGTGTTCATCTTGTTCATCTTTTATTGTTAAAAAAATAGGTGTTTG
658 ATCCATTGTTTAGAGAAAAATATGAAATATGTGTGTTTTTTGATAATTC
66 ATCCATTGTTTAGAGAAAAATATGAAATATGTGTGTTTTTTGATAATTC
707 TTTTTTT
1 TTTTTTT
714 GTTTGTTTAA
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (114 bp):
TTTTTTTCAAAATATGAAAAGTGTTCATCTTGTTCATCTTTTATTGTTAAAAAAATAGGTGTTTG
ATCCATTGTTTAGAGAAAAATATGAAATATGTGTGTTTTTTGATAATTC
Found at i:2658 original size:13 final size:13
Alignment explanation
Indices: 2632--2667 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2622 AAAAACTTGG
2632 TTTTGAAGAAGTGC
1 TTTTGAA-AAGTGC
2646 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
2659 TTTTTAAAA
1 TTTTGAAAA
2668 TTGGGGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:3215 original size:68 final size:67
Alignment explanation
Indices: 3103--3248 Score: 222
Period size: 68 Copynumber: 2.2 Consensus size: 67
3093 CCAATGTCAG
* *
3103 ACTCAAGTTCGAGTCAAGTTTGTCTCAATCTCAATTGAGATTTGATTTTTTTGGACTTGATGAAC
1 ACTCAAGTTCGAGTCAAGTTTGGCTCAATCTCAATCGAGATTTGA-TTTTTTGGACTTGATGAAC
3168 TAT
65 TAT
* *
3171 ACTCAAGTTCGAGTCAAGTTTGGCTTGAA-CTCAATCGAGTTTTGATTTTTTGGACTTGATGAAC
1 ACTCAAGTTCGAGTCAAGTTTGGC-TCAATCTCAATCGAGATTTGATTTTTTGGACTTGATGAAC
3235 TAT
65 TAT
*
3238 ACTCACGTTCG
1 ACTCAAGTTCG
3249 GTTCATTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
67 32 0.44
68 37 0.51
69 3 0.04
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (67 bp):
ACTCAAGTTCGAGTCAAGTTTGGCTCAATCTCAATCGAGATTTGATTTTTTGGACTTGATGAACT
AT
Found at i:3999 original size:41 final size:41
Alignment explanation
Indices: 3816--4143 Score: 272
Period size: 43 Copynumber: 7.7 Consensus size: 41
3806 CCAATAACCA
* * *
3816 AAAGTCCCCAAACACAATTATAACACAG-GAGCAATTCTCTATTCC
1 AAAGTCCTCAAACACATTTATAACACAGAGA-C-A-TCTATA-T-C
* * *
3861 AAAGTCCTCAAACACAATTATAACACAGAGGCATTTATATC
1 AAAGTCCTCAAACACATTTATAACACAGAGACATCTATATC
* *
3902 AAAAGTCC-CTAAACACATTTATAACACATGGGAATATCTAT-TCC
1 -AAAGTCCTC-AAACACATTTATAACACA-GAG-ACATCTATAT-C
*
3946 AAAGCCCTCAAACACATTTATAACACAGAGACATCTATATC
1 AAAGTCCTCAAACACATTTATAACACAGAGACATCTATATC
* * * * * *
3987 AAAGT-CTCCAAACACAATTATAGCACA-AGGGCAATTCTCTCTA
1 AAAGTCCT-CAAACACATTTATAACACAGA-GAC-A-TCTATATC
* *
4030 AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATA-C
1 AAAGTCCTCAAACACATTTATAACACAGAGACATCTATATC
* * * *
4070 TAAAGTCCCCAAACACATTTATAACACAGTGGCACCTCTATTTC
1 -AAAGTCCTCAAACACATTTATAACACAG-AG-ACATCTATATC
4114 AAAGTCCTCAAACACATTTATAACACAGAG
1 AAAGTCCTCAAACACATTTATAACACAGAG
4144 GCATTTCTCT
Statistics
Matches: 232, Mismatches: 33, Indels: 39
0.76 0.11 0.13
Matches are distributed among these distances:
40 3 0.01
41 63 0.27
42 32 0.14
43 93 0.40
44 12 0.05
45 28 0.12
46 1 0.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.23
Consensus pattern (41 bp):
AAAGTCCTCAAACACATTTATAACACAGAGACATCTATATC
Found at i:4046 original size:84 final size:85
Alignment explanation
Indices: 3814--4147 Score: 419
Period size: 84 Copynumber: 3.9 Consensus size: 85
3804 ACCCAATAAC
* *
3814 CAAAAGTCCCCAAACACAATTATAACACAGGAGCAATTCTCTATTCCAAAGTCCTCAAACACAAT
1 CAAAAGTCCCCAAACACAATTATAACACAGG-GCAATTCTAT-TTCCAAAGTCCTCAAACACATT
*
3879 TATAACACAGAGGCATTTATAT
64 TATAACACAGAGGCATCTATAT
* * *
3901 CAAAAGTCCCTAAACACATTTATAACACATGGG-AATATCTA-TTCCAAAGCCCTCAAACACATT
1 CAAAAGTCCCCAAACACAATTATAACACA-GGGCAAT-TCTATTTCCAAAGTCCTCAAACACATT
*
3964 TATAACACAGAGACATCTATAT
64 TATAACACAGAGGCATCTATAT
* * * * *
3986 C-AAAGTCTCCAAACACAATTATAGCACAAGGGCAATTCTCTCT-AAAAGTCCTCAAACACATTT
1 CAAAAGTCCCCAAACACAATTATAACAC-AGGGCAATTCTATTTCCAAAGTCCTCAAACACATTT
*
4049 ATAACACAGAGGCATCCATA-
65 ATAACACAGAGGCATCTATAT
* * **
4069 CTAAAGTCCCCAAACACATTTATAACACAGTGGCACCTCTATTT-CAAAGTCCTCAAACACATTT
1 CAAAAGTCCCCAAACACAATTATAACACAG-GGCAATTCTATTTCCAAAGTCCTCAAACACATTT
4133 ATAACACAGAGGCAT
65 ATAACACAGAGGCAT
4148 TTCTCTTTAT
Statistics
Matches: 215, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
83 3 0.01
84 130 0.60
85 46 0.21
86 3 0.01
87 31 0.14
88 2 0.01
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (85 bp):
CAAAAGTCCCCAAACACAATTATAACACAGGGCAATTCTATTTCCAAAGTCCTCAAACACATTTA
TAACACAGAGGCATCTATAT
Found at i:4221 original size:2 final size:2
Alignment explanation
Indices: 4214--4248 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4204 ATTCCTATCT
* *
4214 TA TA TA TA TA TA TA TA TA TA TA CA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4249 GTACATATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4250 original size:10 final size:10
Alignment explanation
Indices: 4214--4261 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
4204 ATTCCTATCT
*
4214 TATATATATA
1 TATATGTATA
*
4224 TATATATATA
1 TATATGTATA
*
4234 TACATGTATA
1 TATATGTATA
*
4244 TATATGTACA
1 TATATGTATA
4254 TATCATGT
1 TAT-ATGT
4262 GCACCACGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 29 0.88
11 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (10 bp):
TATATGTATA
Found at i:4253 original size:16 final size:16
Alignment explanation
Indices: 4214--4254 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4204 ATTCCTATCT
* *
4214 TATATATATATATATA
1 TATATACATGTATATA
4230 TATATACATGTATATA
1 TATATACATGTATATA
*
4246 TATGTACAT
1 TATATACAT
4255 ATCATGTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
TATATACATGTATATA
Found at i:7344 original size:32 final size:32
Alignment explanation
Indices: 7303--7363 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
7293 AAATATGTTT
** * *
7303 GAAAAATAAGGGTATAATGGTTGATTCAATTA
1 GAAAAATAAGAATATAATAGTCGATTCAATTA
7335 GAAAAATAAGAATATAATAGTCGATTCAA
1 GAAAAATAAGAATATAATAGTCGATTCAA
7364 AAGTTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (32 bp):
GAAAAATAAGAATATAATAGTCGATTCAATTA
Found at i:15169 original size:13 final size:13
Alignment explanation
Indices: 15144--15171 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15134 ATTAATTAAA
15144 AAAATTATTAAGG
1 AAAATTATTAAGG
15157 AAAATTATTAAGG
1 AAAATTATTAAGG
15170 AA
1 AA
15172 TGTGATAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (13 bp):
AAAATTATTAAGG
Found at i:17068 original size:21 final size:19
Alignment explanation
Indices: 17044--17101 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
17034 GCTGTTCTAA
*
17044 TAATCTCATCTGTACAGTG
1 TAATCTCATTTGTACAGTG
*
17063 CCTAATCTAATTTGTACAGTG
1 --TAATCTCATTTGTACAGTG
17084 TAATCTCATTTGTACAGT
1 TAATCTCATTTGTACAGT
17102 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (19 bp):
TAATCTCATTTGTACAGTG
Found at i:17089 original size:19 final size:20
Alignment explanation
Indices: 17044--17107 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
17034 GCTGTTCTAA
*
17044 TAATCTCATCTGTACAGTGCC
1 TAATCTCATTTGTACAGTG-C
*
17065 TAATCTAATTTGTACAGTG-
1 TAATCTCATTTGTACAGTGC
17084 TAATCTCATTTGTACAGTTGC
1 TAATCTCATTTGTACAG-TGC
17105 TAA
1 TAA
17108 ACAGTGTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.42
20 2 0.05
21 20 0.53
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (20 bp):
TAATCTCATTTGTACAGTGC
Found at i:24348 original size:21 final size:21
Alignment explanation
Indices: 24283--24348 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
24273 AAGGATCAAG
24283 ATTTGAGTTGAGTATTT-TTA
1 ATTTGAGTTGAGTATTTCTTA
** * *
24303 ATTT-A-CAGAGAATATTCTATG
1 ATTTGAGTTGAGTAT-TTCT-TA
24324 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
24345 ATTT
1 ATTT
24349 ACAGAGAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 9
0.66 0.16 0.18
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
20 5 0.15
21 10 0.30
22 5 0.15
23 5 0.15
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.50
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:25323 original size:16 final size:16
Alignment explanation
Indices: 25302--25333 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25292 ATTATCCAAT
25302 TTGATTACCAAACAAC
1 TTGATTACCAAACAAC
25318 TTGATTACCAAACAAC
1 TTGATTACCAAACAAC
25334 GAAAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
TTGATTACCAAACAAC
Found at i:25769 original size:93 final size:93
Alignment explanation
Indices: 25667--25836 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
25657 TTATTTAAAT
* *
25667 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTACATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
25732 TTTTATTTTTACCATTTTACCATTTTAC
66 TTTTATTTTTACCATTTTACCATTTTAC
* *
25760 TTTTATAGTTTTACTCAACTTAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
25825 TTTTATTTTTAC
66 TTTTATTTTTAC
25837 AATATTACTA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACCATTTTAC
Found at i:26424 original size:16 final size:16
Alignment explanation
Indices: 26403--26448 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
26393 CAGGTAATTT
26403 TTTCAGGTCATTCGGA
1 TTTCAGGTCATTCGGA
* *
26419 TTTCAGATC-TTCTAGA
1 TTTCAGGTCATTC-GGA
26435 -TTCAGGTCATTCGG
1 TTTCAGGTCATTCGG
26449 GTCTAAGGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (16 bp):
TTTCAGGTCATTCGGA
Found at i:26508 original size:16 final size:16
Alignment explanation
Indices: 26484--26514 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26474 TTGGCCTTAG
26484 GTCACTCGGGTTTTGA
1 GTCACTCGGGTTTTGA
*
26500 GTCATTCGGGTTTTG
1 GTCACTCGGGTTTTG
26515 GGTTTTTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.32, T:0.42
Consensus pattern (16 bp):
GTCACTCGGGTTTTGA
Found at i:29321 original size:12 final size:11
Alignment explanation
Indices: 29294--29327 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29284 GTGTTTAGTT
29294 AAAGGAAAAAA
1 AAAGGAAAAAA
*
29305 AAAGGAAAAGGA
1 AAAGGAAAA-AA
29317 AAAGGAAAAAA
1 AAAGGAAAAAA
29328 GAAAACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAGGAAAAAA
Found at i:40525 original size:42 final size:44
Alignment explanation
Indices: 40474--40567 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
40464 AGTGCGTTAC
*
40474 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAAT-AAAT
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAAT
40515 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAAT
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAAT
40561 -TAATATT
1 CTAATATT
40568 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 33 0.70
46 4 0.09
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAAT
Done.