Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024887.1 Corchorus olitorius cultivar O-4 contig24920, 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: 33054
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:162 original size:21 final size:21
Alignment explanation
Indices: 132--171 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
122 CTAAAAACAG
*
132 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
153 GACAACTCCTGCCCAGGAC
1 GACAACTCCTGCCCAGGAC
172 CTGGTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:225 original size:71 final size:71
Alignment explanation
Indices: 124--314 Score: 294
Period size: 71 Copynumber: 2.7 Consensus size: 71
114 ATTGAAGCCT
* *
124 AAAAA-CAGGACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
188 CGGAAG
66 CGGAAG
* * *
194 AAAAATCAGAACAACTCTTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
259 CGGAAG
66 CGGAAG
* * *
265 AAAATTCAGAACAAGTCCTGTCCAGGATTTGGACAACTCCTGCCCAGGAC
1 AAAAATCAGAACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGAC
315 TTGTTGCGGA
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 5 0.05
71 85 0.78
72 19 0.17
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (71 bp):
AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAA
CGGAAG
Found at i:230 original size:21 final size:21
Alignment explanation
Indices: 204--245 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
194 AAAAATCAGA
*
204 ACAACTCTTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
225 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
246 GTCTGTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
ACAACTCCTGCCCAGGACTTG
Found at i:5165 original size:21 final size:21
Alignment explanation
Indices: 5139--5213 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 21
5129 ATTTAACGTG
* *
5139 TTGACTATCAAACTTTGGGTT
1 TTGACTATCAAAATTTGGGAT
5160 TTGACTATCAAAATTTGGGAT
1 TTGACTATCAAAATTTGGGAT
*
5181 TTGACCATC--AA--TGGGAT
1 TTGACTATCAAAATTTGGGAT
5198 TTGACTATCAAAATTT
1 TTGACTATCAAAATTT
5214 AATTAATTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 14 0.30
19 4 0.09
21 28 0.61
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGACTATCAAAATTTGGGAT
Found at i:5197 original size:17 final size:17
Alignment explanation
Indices: 5175--5208 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5165 TATCAAAATT
5175 TGGGATTTGACCATCAA
1 TGGGATTTGACCATCAA
*
5192 TGGGATTTGACTATCAA
1 TGGGATTTGACCATCAA
5209 AATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (17 bp):
TGGGATTTGACCATCAA
Found at i:5331 original size:21 final size:21
Alignment explanation
Indices: 5306--5513 Score: 274
Period size: 21 Copynumber: 9.9 Consensus size: 21
5296 TCAAATCTCA
* *
5306 TTGATGGTCAACCCCCAAATT
1 TTGATAGTCAAACCCCAAATT
*
5327 TTGATAGTCAAACCCCAAAGT
1 TTGATAGTCAAACCCCAAATT
* *
5348 TTGATGGTCAACCCCCAAATT
1 TTGATAGTCAAACCCCAAATT
*
5369 TTGATAGTC-AACACCCAAAGT
1 TTGATAGTCAAAC-CCCAAATT
*
5390 TTGATTGTCAAACCCCAAATT
1 TTGATAGTCAAACCCCAAATT
*
5411 TTGATAGTCAAACCCCAAAGT
1 TTGATAGTCAAACCCCAAATT
* *
5432 TTGATGGTCAACCCCCAAATT
1 TTGATAGTCAAACCCCAAATT
*
5453 TTGATAGTCAAACCCCAAAAT
1 TTGATAGTCAAACCCCAAATT
* * *
5474 TTGATGGTCAACCCCCGAATT
1 TTGATAGTCAAACCCCAAATT
5495 TTGATAGTCAAACCCCAAA
1 TTGATAGTCAAACCCCAAA
5514 GTTTCATATA
Statistics
Matches: 159, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 2 0.01
21 154 0.97
22 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (21 bp):
TTGATAGTCAAACCCCAAATT
Found at i:5359 original size:42 final size:42
Alignment explanation
Indices: 5306--5517 Score: 372
Period size: 42 Copynumber: 5.0 Consensus size: 42
5296 TCAAATCTCA
5306 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
5348 TTGATGGTCAACCCCCAAATTTTGATAGTC-AACACCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAAC-CCCAAAGT
* *
5390 TTGATTGTCAAACCCCAAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
*
5432 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAAT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
*
5474 TTGATGGTCAACCCCCGAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
5516 TT
1 TT
5518 CATATATTTC
Statistics
Matches: 161, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
41 3 0.02
42 155 0.96
43 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
Found at i:9458 original size:23 final size:23
Alignment explanation
Indices: 9410--9460 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
9400 CTTGGTTGTT
*
9410 AAAAACTCAAAATTCTATCATTA
1 AAAAACTCAAAATTCTATCATAA
* *
9433 AAAAACATTAAAATTCTATTA-AA
1 AAAAAC-TCAAAATTCTATCATAA
9456 AAAAA
1 AAAAA
9461 GAGAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAACTCAAAATTCTATCATAA
Found at i:9459 original size:24 final size:23
Alignment explanation
Indices: 9410--9460 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
9400 CTTGGTTGTT
**
9410 AAAAACTCAAAATTCTATCATTA
1 AAAAACTCAAAATTCTATCAAAA
* *
9433 AAAAACATTAAAATTCTATTAAAA
1 AAAAAC-TCAAAATTCTATCAAAA
9457 AAAA
1 AAAA
9461 GAGAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAACTCAAAATTCTATCAAAA
Found at i:11024 original size:3 final size:3
Alignment explanation
Indices: 11016--11064 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
11006 ACGCCAACAC
11016 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11064 A
1 A
11065 CCCCAAGCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17925 original size:24 final size:24
Alignment explanation
Indices: 17897--17955 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
17887 TGAGAGGGGT
17897 CGTGGCCGTAGTACCTCCACTGGG
1 CGTGGCCGTAGTACCTCCACTGGG
17921 CGTGGCCGTAGTACCTCCACTGGG
1 CGTGGCCGTAGTACCTCCACTGGG
17945 CGTGGCCGTAG
1 CGTGGCCGTAG
17956 CTCATCGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.12, C:0.32, G:0.36, T:0.20
Consensus pattern (24 bp):
CGTGGCCGTAGTACCTCCACTGGG
Found at i:19005 original size:10 final size:10
Alignment explanation
Indices: 18992--19034 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
18982 ATAAGTATAT
18992 TCCATAAAAA
1 TCCATAAAAA
*
19002 TCCAAAAAAA
1 TCCATAAAAA
** *
19012 GACATAAACA
1 TCCATAAAAA
19022 TCCATAAAAA
1 TCCATAAAAA
19032 TCC
1 TCC
19035 CAAAATATAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.58, C:0.23, G:0.02, T:0.16
Consensus pattern (10 bp):
TCCATAAAAA
Found at i:21359 original size:26 final size:26
Alignment explanation
Indices: 21311--21360 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
21301 AGCTTGAATA
* **
21311 AAAAATAATAATTAATTTTAGTAAAT
1 AAAAATAATAAGTAATTACAGTAAAT
*
21337 AAAAATTATAAGTAATTACAGTAA
1 AAAAATAATAAGTAATTACAGTAA
21361 TATATAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (26 bp):
AAAAATAATAAGTAATTACAGTAAAT
Found at i:21642 original size:33 final size:33
Alignment explanation
Indices: 21600--21673 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
21590 TGACCGGCGG
21600 CGGCGCCCCCAGGAGGCGCCGCCGATATGCCAA
1 CGGCGCCCCCAGGAGGCGCCGCCGATATGCCAA
* *
21633 CGGCGCCCCCAGGAGGCGCCGCTGATATGCCGA
1 CGGCGCCCCCAGGAGGCGCCGCCGATATGCCAA
*
21666 CGCCGCCC
1 CGGCGCCC
21674 AACTTGGGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.15, C:0.45, G:0.34, T:0.07
Consensus pattern (33 bp):
CGGCGCCCCCAGGAGGCGCCGCCGATATGCCAA
Found at i:23124 original size:3 final size:3
Alignment explanation
Indices: 23116--23155 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
23106 TTATGGAATA
* *
23116 ATT ATT ATT AAT ATT -TT TTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
23156 AAGTCAGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:31470 original size:32 final size:32
Alignment explanation
Indices: 31429--31491 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
31419 ACTATCCTCC
31429 GTTAATGGAAGAGTTAACAAGATGGATCTTTA
1 GTTAATGGAAGAGTTAACAAGATGGATCTTTA
31461 GTTAATGGAAGAGTTAACAAGATGGATCTTT
1 GTTAATGGAAGAGTTAACAAGATGGATCTTT
31492 TGGTCATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (32 bp):
GTTAATGGAAGAGTTAACAAGATGGATCTTTA
Found at i:31744 original size:103 final size:101
Alignment explanation
Indices: 31628--31881 Score: 316
Period size: 103 Copynumber: 2.4 Consensus size: 101
31618 AATTTTTCTA
31628 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGTGAATTAGTTATATAGTTTATT
1 ACCCTTAAAATAAAA---TAATTTTAATTTGGGCTAAACTTAGTGAATTAGTTATATAGTTTATT
*
31693 TCTAAAACCCCATAAT-AAT-ATTATTAATTATGGAATTT
63 TCTAAAACCCCAT-ATCAATAATTATTAATTATGAAATTT
* * *
31731 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAAT--AATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATAGTTTA
* *
31796 TTTCTAAAACCCTATATCAATAAATTATTAATTTTGAAATTT
61 TTTCTAAAACCCCATATCAAT-AATTATTAATTATGAAATTT
**
31838 ACCCTTAAAATAAAA-AAAATTAATTTGGGACTAAACTTAGTGAA
1 ACCCTTAAAATAAAATAATTTTAATTTGGG-CTAAACTTAGTGAA
31882 ATTAAGGGCT
Statistics
Matches: 134, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
101 1 0.01
102 5 0.04
103 43 0.32
104 21 0.16
105 32 0.24
106 4 0.03
107 28 0.21
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (101 bp):
ACCCTTAAAATAAAATAATTTTAATTTGGGCTAAACTTAGTGAATTAGTTATATAGTTTATTTCT
AAAACCCCATATCAATAATTATTAATTATGAAATTT
Found at i:31971 original size:29 final size:31
Alignment explanation
Indices: 31939--32003 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
31929 GCAATTTGGA
31939 ATATAACGTTAC-AAAA-CAAGCAATTAAGG
1 ATATAACGTTACGAAAAGCAAGCAATTAAGG
* *
31968 ATATAATGTTACGAAAAGCGAGCAATTAAGG
1 ATATAACGTTACGAAAAGCAAGCAATTAAGG
31999 ATATA
1 ATATA
32004 GTCCGTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.34
30 4 0.12
31 17 0.53
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (31 bp):
ATATAACGTTACGAAAAGCAAGCAATTAAGG
Found at i:32191 original size:30 final size:31
Alignment explanation
Indices: 32122--32201 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
32112 CCCTAACTGA
* * *
32122 TTATATCCTTAATTGCTTTAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCAAAAAAG
**
32153 CCATATCCTTAATTGCTTGAAAT-AAAAAAG
1 TTATATCCTTAATTGCTTGAAATCAAAAAAG
*
32183 TTATATCCTTAATTTCTTG
1 TTATATCCTTAATTGCTTG
32202 TGGCAGCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 21 0.51
31 20 0.49
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCAAAAAAG
Found at i:32918 original size:29 final size:29
Alignment explanation
Indices: 32882--32953 Score: 135
Period size: 29 Copynumber: 2.4 Consensus size: 29
32872 CATGGAAGGG
32882 ATTAAGGATATAACGTTACAAAACAAGCA
1 ATTAAGGATATAACGTTACAAAACAAGCA
32911 ATTAAGGATATAACGTTACAAAACAAGCA
1 ATTAAGGATATAACGTTACAAAACAAGCA
32940 ATTAAAGGATATAA
1 ATT-AAGGATATAA
32954 TGTTTTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 32 0.76
30 10 0.24
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (29 bp):
ATTAAGGATATAACGTTACAAAACAAGCA
Found at i:32990 original size:31 final size:31
Alignment explanation
Indices: 32905--33015 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
32895 CGTTACAAAA
* ***
32905 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* **
32934 CAAGCAATTAAAGGATATAATGTTTTTTATTT
1 CAAGCAATT-AAGGATATAACGTTTTCGATTT
* *
32966 CAAGCAATTAACGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
32997 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
33016 TCAGTTAGGA
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
29 9 0.14
30 11 0.17
31 36 0.55
32 10 0.15
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Done.