Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006072.1 Corchorus capsularis cultivar CVL-1 contig06090, 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: 67792
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:166 original size:16 final size:16
Alignment explanation
Indices: 110--170 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
100 AAGGTCAAAT
110 ACCCGAACCCGAAAAA
1 ACCCGAACCCGAAAAA
* *
126 ACCTGAATCCGAAAAA
1 ACCCGAACCCGAAAAA
* * *
142 GCTCAAACCCGAAAAA
1 ACCCGAACCCGAAAAA
158 ACCCGAACCCGAA
1 ACCCGAACCCGAA
171 TCCGAAAATG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.48, C:0.34, G:0.13, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAA
Found at i:367 original size:32 final size:32
Alignment explanation
Indices: 326--396 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
316 ACCCAAACTG
*
326 AACCCGAACCCGAATTAACCTGACACAAATTC
1 AACCCGAACCCGAAGTAACCTGACACAAATTC
* *
358 AACCCGAACCCGAAGTAATCTGACCCAAATTC
1 AACCCGAACCCGAAGTAACCTGACACAAATTC
390 AACCCGA
1 AACCCGA
397 CCTGACTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.35, G:0.11, T:0.14
Consensus pattern (32 bp):
AACCCGAACCCGAAGTAACCTGACACAAATTC
Found at i:466 original size:2 final size:2
Alignment explanation
Indices: 459--491 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
449 CGTTGCCACC
459 TA TA TA TA TA TA 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 TA TA TA T
492 GTAAAAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:551 original size:2 final size:2
Alignment explanation
Indices: 544--571 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
534 TTTAGGATGA
544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
572 TTTAATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1097 original size:29 final size:30
Alignment explanation
Indices: 1028--1100 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
1018 GCTCAATTAA
**
1028 GGGCAAAACGTTTTTGGTTCGGTCTAATTTG
1 GGGCAAAACG-TTTTAATTCGGTCTAATTTG
* *
1059 GGGCACAACGTTTTAATTTGGTCT-ATTTG
1 GGGCAAAACGTTTTAATTCGGTCTAATTTG
1088 GGGCAAAACGTTT
1 GGGCAAAACGTTT
1101 CAGATTCATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.46
30 11 0.30
31 9 0.24
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (30 bp):
GGGCAAAACGTTTTAATTCGGTCTAATTTG
Found at i:1951 original size:2 final size:2
Alignment explanation
Indices: 1946--1970 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1936 ATTTTAAATT
1946 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1971 TAAGAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9480 original size:22 final size:22
Alignment explanation
Indices: 9452--9495 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
9442 AGCTGCAGAC
9452 GATTAAAAGTTTTTGATCTCAT
1 GATTAAAAGTTTTTGATCTCAT
9474 GATTAAAAGTTTTTGATCTCAT
1 GATTAAAAGTTTTTGATCTCAT
9496 CATAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
GATTAAAAGTTTTTGATCTCAT
Found at i:25010 original size:42 final size:42
Alignment explanation
Indices: 24929--25010 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
24919 GTTTTTGGGA
* * *
24929 TTGATCATCTCCATTAGTATGTTTAATTGCCGTATTTTACTT
1 TTGATCATCTCCATTAGCATGTTTAATTGCCGCACTTTACTT
* * **
24971 TTGATCGTTTCCATTAGCATGTTTAATTGTGGCACTTTAC
1 TTGATCATCTCCATTAGCATGTTTAATTGCCGCACTTTAC
25011 CGATGACTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.48
Consensus pattern (42 bp):
TTGATCATCTCCATTAGCATGTTTAATTGCCGCACTTTACTT
Found at i:25412 original size:115 final size:115
Alignment explanation
Indices: 25267--25533 Score: 498
Period size: 115 Copynumber: 2.3 Consensus size: 115
25257 CATGAATCAA
25267 ACCTATTACCCCATAACACTTGCTCTTAAAACTAGAAACTCAAATAGGCAACAAACGGAAACGTA
1 ACCTATTACCCCATAACACTTGCTCTTAAAACTAGAAACTCAAATAGGCAACAAACGGAAACGTA
25332 CATAATAAATCAAATAGGATTGTCAAATCTCTAATTTCATCTATCAAGTT
66 CATAATAAATCAAATAGGATTGTCAAATCTCTAATTTCATCTATCAAGTT
25382 ACCTATTACCCCATAACACTTGCTCTTAAAACTAGAAACTCAAATAGGCAACAAACGGAAACGTA
1 ACCTATTACCCCATAACACTTGCTCTTAAAACTAGAAACTCAAATAGGCAACAAACGGAAACGTA
25447 CATAATAAATCAAATAGGATTGTCAAATCTCTAATTTCATCTATCAAGTT
66 CATAATAAATCAAATAGGATTGTCAAATCTCTAATTTCATCTATCAAGTT
* * * *
25497 ACTTGTTACCCCATAACACCTGCTCTTGAAACTAGAA
1 ACCTATTACCCCATAACACTTGCTCTTAAAACTAGAA
25534 GCTAGAAACT
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 148 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (115 bp):
ACCTATTACCCCATAACACTTGCTCTTAAAACTAGAAACTCAAATAGGCAACAAACGGAAACGTA
CATAATAAATCAAATAGGATTGTCAAATCTCTAATTTCATCTATCAAGTT
Found at i:25967 original size:19 final size:19
Alignment explanation
Indices: 25943--25984 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
25933 TGAATTATAT
25943 ATATGTTTCATTTTTTGGA
1 ATATGTTTCATTTTTTGGA
*
25962 ATATGTTTGATTTTTTGGA
1 ATATGTTTCATTTTTTGGA
25981 ATAT
1 ATAT
25985 TCCAAGTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (19 bp):
ATATGTTTCATTTTTTGGA
Found at i:31663 original size:148 final size:149
Alignment explanation
Indices: 31388--31689 Score: 500
Period size: 148 Copynumber: 2.0 Consensus size: 149
31378 CTCAGTCTAT
* *
31388 TTCCTGGTCAGTTCAGAAATCTCAAATCTGACCTCTTTCCCAAAGTTTCCCACCTTCCAAAGCTT
1 TTCCTGGTCAGTTCAGAAATCTCAAATCTGACCTCTTTCCCAAAGTTACCCACCTCCCAAAGCTT
*
31453 CAGAGTTTATATATCACTGGTTGCAAAGACCTCACTTCTTTGTCTGAAGAAACAGGGACATTGAA
66 CAGAGTTTATATATCACCGGTTGCAAAGACCTCACTTCTTTGTCTGAAGAAACAGGGACATTGAA
**
31518 AAGCTTGTCCTCTCTCTGG
131 AAGCTTGTCCTCTCTAGGG
* *
31537 TTCCTGGTCATTTCAGACATCTCAAATCT-ACCTCTTTCCCAAAGTTACCCACCTCCCAAAGCTT
1 TTCCTGGTCAGTTCAGAAATCTCAAATCTGACCTCTTTCCCAAAGTTACCCACCTCCCAAAGCTT
* *
31601 CAGAGTTTATATATCACCGGTTGCAAAGCCCTCACTTCTTTGTCTGAAGAAGA-AGGGTCATTGA
66 CAGAGTTTATATATCACCGGTTGCAAAGACCTCACTTCTTTGTCTGAAGAA-ACAGGGACATTGA
31665 AAAGCTTGTCCTCTCTAGGG
130 AAAGCTTGTCCTCTCTAGGG
31685 TTCCT
1 TTCCT
31690 CTCTGTTCAA
Statistics
Matches: 143, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
148 115 0.80
149 28 0.20
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (149 bp):
TTCCTGGTCAGTTCAGAAATCTCAAATCTGACCTCTTTCCCAAAGTTACCCACCTCCCAAAGCTT
CAGAGTTTATATATCACCGGTTGCAAAGACCTCACTTCTTTGTCTGAAGAAACAGGGACATTGAA
AAGCTTGTCCTCTCTAGGG
Found at i:41627 original size:12 final size:12
Alignment explanation
Indices: 41610--41636 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41600 GTTTATATCA
41610 AAGAGAAAAATC
1 AAGAGAAAAATC
41622 AAGAGAAAAATC
1 AAGAGAAAAATC
41634 AAG
1 AAG
41637 CACCAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.19, T:0.07
Consensus pattern (12 bp):
AAGAGAAAAATC
Found at i:41738 original size:27 final size:27
Alignment explanation
Indices: 41700--41755 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
41690 CAAATCAAGT
41700 TACAAGTCTTCCTTTTTACATGTCTAA
1 TACAAGTCTTCCTTTTTACATGTCTAA
41727 TACAAGTCTTCCTTTTTACATGTCTAA
1 TACAAGTCTTCCTTTTTACATGTCTAA
41754 TA
1 TA
41756 ATGTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (27 bp):
TACAAGTCTTCCTTTTTACATGTCTAA
Found at i:46389 original size:3 final size:3
Alignment explanation
Indices: 46383--46472 Score: 63
Period size: 3 Copynumber: 29.7 Consensus size: 3
46373 TCTTCTTTCC
** * * * * * *
46383 CTT CTT CTT CAC CTT CTT CAT CTT CTT CCT CCT CCT CAT CTT CCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
46431 CCT CTT CTT CTT CTT CTC CTT CTC CTT CTT CCTT CTT TTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CT
46473 CCTCAAGTCC
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.54
Consensus pattern (3 bp):
CTT
Found at i:57431 original size:14 final size:13
Alignment explanation
Indices: 57408--57441 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
57398 TAATATAAAC
57408 AATAATTAATAGT
1 AATAATTAATAGT
57421 AATAGATTAATAGT
1 AATA-ATTAATAGT
*
57435 AACAATT
1 AATAATT
57442 TGGGAGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (13 bp):
AATAATTAATAGT
Found at i:57622 original size:2 final size:2
Alignment explanation
Indices: 57609--57643 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
57599 TACGACATAG
*
57609 TA TA TA TG TA TA TA 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 TA TA TA TA T
57644 TAATCAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58946 original size:107 final size:105
Alignment explanation
Indices: 58825--59088 Score: 345
Period size: 107 Copynumber: 2.5 Consensus size: 105
58815 TAAAAATATA
* * * *
58825 TTAATTTGGAGCTAAATTTAATGACATTAGTTTTATATTTTAATTCTAAAACCCTGTAACGATAA
1 TTAATTTGGGGCTAAACTTAATGACATTA-TTTTATATTTTAATTCTAAAACCCTATAACAATAA
58890 ATTATTAATTTTGGAATTTACCCTTAAAATTAAATTAAAATT
65 ATTATTAATTTTGGAATTTACCCTT-AAATTAAATTAAAATT
* * *
58932 TTAATTTGGGGCTAATTAACTTAGTGATATTAATTT-T-TTTTAATTCTAAAACCCTATAACAAT
1 TTAATTTGGGGCT-A--AACTTAATGACATTATTTTATATTTTAATTCTAAAACCCTATAACAAT
*
58995 AAATTATTAATTTTTGAATTTACCCTTAAATTAAATTAAAATT
63 AAATTATTAATTTTGGAATTTACCCTTAAATTAAATTAAAATT
* * *
59038 TTAATTTGGGACTAAACTTAATGGCATTAATTTGATA-TTTAATTTCTAAAA
1 TTAATTTGGGGCTAAACTTAATGACATT-ATTTTATATTTTAA-TTCTAAAA
59089 AGAATAAAAA
Statistics
Matches: 136, Mismatches: 14, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
103 11 0.08
104 3 0.02
105 7 0.05
106 36 0.26
107 62 0.46
108 2 0.01
109 3 0.02
110 12 0.09
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (105 bp):
TTAATTTGGGGCTAAACTTAATGACATTATTTTATATTTTAATTCTAAAACCCTATAACAATAAA
TTATTAATTTTGGAATTTACCCTTAAATTAAATTAAAATT
Found at i:60053 original size:15 final size:16
Alignment explanation
Indices: 60033--60070 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
60023 CGTTCAAATG
60033 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
60048 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
60065 T-GGGTC
1 TCGGGTC
60071 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:60144 original size:16 final size:16
Alignment explanation
Indices: 60123--60154 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60113 GAACCTCGGG
*
60123 TTTTCGGGTTTGGGTC
1 TTTTCGGGTTCGGGTC
60139 TTTTCGGGTTCGGGTC
1 TTTTCGGGTTCGGGTC
60155 GTAACAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.38, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTC
Found at i:61371 original size:15 final size:15
Alignment explanation
Indices: 61351--61402 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
61341 GGTTAATATG
*
61351 TCGGGTTGATTGGGT
1 TCGGGTTGTTTGGGT
61366 TCGGGTCAT-TTTGGGT
1 TCGGGT--TGTTTGGGT
* *
61382 TCGGGTCGTTTGGAT
1 TCGGGTTGTTTGGGT
61397 TCGGGT
1 TCGGGT
61403 ACCCAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 18 0.58
16 12 0.39
17 1 0.03
ACGTcount: A:0.06, C:0.12, G:0.42, T:0.40
Consensus pattern (15 bp):
TCGGGTTGTTTGGGT
Found at i:61381 original size:16 final size:15
Alignment explanation
Indices: 61360--61402 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
61350 GTCGGGTTGA
*
61360 TTGGGTTCGGGTCATT
1 TTGGGTTCGGGTC-GT
61376 TTGGGTTCGGGTCGT
1 TTGGGTTCGGGTCGT
*
61391 TTGGATTCGGGT
1 TTGGGTTCGGGT
61403 ACCCAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.05, C:0.12, G:0.42, T:0.42
Consensus pattern (15 bp):
TTGGGTTCGGGTCGT
Found at i:63251 original size:27 final size:28
Alignment explanation
Indices: 63202--63260 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
63192 GTATATAAAT
*
63202 ATTTGATTTAATTTGTATCTAT-ATTTA
1 ATTTGATTTAATTTGTATATATAATTTA
* *
63229 ATTTGATTTAATTTTTTTATATAAATTTA
1 ATTTGATTTAATTTGTATATAT-AATTTA
63258 ATT
1 ATT
63261 ATATGCATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
29 8 0.30
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTTGATTTAATTTGTATATATAATTTA
Done.