Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009250.1 Corchorus capsularis cultivar CVL-1 contig09271, 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: 32069
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:10751 original size:23 final size:25
Alignment explanation
Indices: 10699--10765 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
10689 TGACAGGTAT
*
10699 AAAGAAAATCTCATTATATAACTCAAA
1 AAAGAAAATCTCATTATACAACT--AA
10726 AAAGAAAATCTCATTATACAA-TAA
1 AAAGAAAATCTCATTATACAACTAA
* *
10750 AAA-TAAATCTCTTTAT
1 AAAGAAAATCTCATTAT
10766 GTCCGAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 11 0.30
24 5 0.14
26 1 0.03
27 20 0.54
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAGAAAATCTCATTATACAACTAA
Found at i:10889 original size:40 final size:40
Alignment explanation
Indices: 10844--10920 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
10834 ACAAGCATCT
10844 AATTAACCAATAACAAATTAACTAAACTCACATTCTAACA
1 AATTAACCAATAACAAATTAACTAAACTCACATTCTAACA
10884 AATTAACCAATAACAAATTAACTAAACTCACATTCTA
1 AATTAACCAATAACAAATTAACTAAACTCACATTCTA
10921 TTAGAATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (40 bp):
AATTAACCAATAACAAATTAACTAAACTCACATTCTAACA
Found at i:11853 original size:17 final size:17
Alignment explanation
Indices: 11815--11847 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11805 CTCATAGTAC
*
11815 CTAGGTAGTATGAGGTA
1 CTAGGTAGCATGAGGTA
11832 CTAGGTAGCATGAGGT
1 CTAGGTAGCATGAGGT
11848 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (17 bp):
CTAGGTAGCATGAGGTA
Found at i:12436 original size:156 final size:155
Alignment explanation
Indices: 12199--12561 Score: 346
Period size: 156 Copynumber: 2.3 Consensus size: 155
12189 AGACTTCTCA
* * ** *
12199 CCTCAAATTGTCCTTAGATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCGAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGAGCT-AAA
** * * *
12264 CTTTGCCAAGGTACTTAGAATATTTCCAT-GAGACTAT-GGAAAAAATCCCAATTGAAACCGTAC
65 CTTTGCCAAGGTACTTAGAATATCACCATAGAGA-TATGGGAAAAAAT-CCAAGTAAAACCGAAC
* * *
12327 TCTCCTTG-ATGGTGAACTAGGTTTCCACC
128 TCT-CTAGCATAGAGAACTAGGTTT-CACC
* *
12356 CCT-GAGTTGTCCTTAAATGAAAAATTAGCATAAGTTTTTCATTCTAAGTCCAACAAG-GCT-AA
1 CCTCGAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAA-AAGAGCTAAA
* * * *
12418 -TTTTCCACCA-GTAGACTTAGATTATCACCATATAGATATGGGAAAAAATCGAAGTAAAACCGA
65 CTTTGCCA--AGGT--ACTTAGAATATCACCATAGAGATATGGGAAAAAATCCAAGTAAAACCGA
* * * *
12481 ACTCTCTAGCATAGAGAAGTTGGTTTGACT
126 ACTCTCTAGCATAGAGAACTAGGTTTCACC
* * *
12511 CCTCGAATTGTCCTTAATTGAAAAACTAGCATAAGTTTTTAATACTAAGTC
1 CCTCGAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC
12562 TGTTTGAGAT
Statistics
Matches: 169, Mismatches: 28, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
153 6 0.04
154 4 0.02
155 9 0.05
156 133 0.79
157 17 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (155 bp):
CCTCGAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCCAAAAGAGCTAAAC
TTTGCCAAGGTACTTAGAATATCACCATAGAGATATGGGAAAAAATCCAAGTAAAACCGAACTCT
CTAGCATAGAGAACTAGGTTTCACC
Found at i:13611 original size:38 final size:38
Alignment explanation
Indices: 13561--13634 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
13551 CCTAGTTAAA
13561 TAAATAATAAGATTTTATATGATAAATCTTAAATTTAT
1 TAAATAATAAGATTTTATATGATAAATCTTAAATTTAT
13599 TAAATAATAAGATTTTATATGATAAATCTTAAATTT
1 TAAATAATAAGATTTTATATGATAAATCTTAAATTT
13635 TAGTATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (38 bp):
TAAATAATAAGATTTTATATGATAAATCTTAAATTTAT
Found at i:15061 original size:17 final size:17
Alignment explanation
Indices: 15040--15074 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
15030 TTTGTTTTAA
15040 CTTTTTT-T-TTCTTTT
1 CTTTTTTATATTCTTTT
15055 CTTTTTTATATTCTTTT
1 CTTTTTTATATTCTTTT
15072 CTT
1 CTT
15075 CTCTCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 1 0.06
17 10 0.56
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTTATATTCTTTT
Found at i:16315 original size:105 final size:108
Alignment explanation
Indices: 16184--16381 Score: 278
Period size: 105 Copynumber: 1.9 Consensus size: 108
16174 TTAAGGGTGA
* * ***
16184 AAAATACATGAAATTAAAATCATGAAACCAC-AAAATTTCGTAAAAATTTTACACAAATCGATTA
1 AAAATACATGAAATTAAAATCATGAAACCACAAAAATCTCATAAAAATCCAACA-AAATCGATTA
16248 AA-TTTTT-TTA-ATATCTTGAATAATCTACTATAATAACTGTG
65 AATTTTTTATTATATATCTTGAATAATCTACTATAATAACTGTG
* * * *
16289 AAAATACATGAAATTAAAATCTTGAAACCACAAAAATCTCATTAATATCCAATAAAATCGATTAA
1 AAAATACATGAAATTAAAATCATGAAACCACAAAAATCTCATAAAAATCCAACAAAATCGATTAA
16354 ATTTTTTATTATATATCTTGAATAATCT
66 ATTTTTTATTATATATCTTGAATAATCT
16382 TGAAACAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
105 42 0.52
106 19 0.24
107 3 0.04
108 16 0.20
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.35
Consensus pattern (108 bp):
AAAATACATGAAATTAAAATCATGAAACCACAAAAATCTCATAAAAATCCAACAAAATCGATTAA
ATTTTTTATTATATATCTTGAATAATCTACTATAATAACTGTG
Found at i:17009 original size:18 final size:18
Alignment explanation
Indices: 16986--17037 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
16976 AACATAAGAT
*
16986 TCAGACTTGAAAAGAAAC
1 TCAGACTAGAAAAGAAAC
* *
17004 TCAGACTCG-AAAGGAAC
1 TCAGACTAGAAAAGAAAC
*
17021 TGAGACTAGAAAAGAAA
1 TCAGACTAGAAAAGAAA
17038 TTGACACGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.13
Consensus pattern (18 bp):
TCAGACTAGAAAAGAAAC
Found at i:18178 original size:13 final size:13
Alignment explanation
Indices: 18160--18186 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18150 TGATCTCTCG
18160 TTTATAGATAAGA
1 TTTATAGATAAGA
18173 TTTATAGATAAGA
1 TTTATAGATAAGA
18186 T
1 T
18187 ACGGATCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTATAGATAAGA
Found at i:21005 original size:105 final size:105
Alignment explanation
Indices: 20823--21138 Score: 569
Period size: 105 Copynumber: 3.0 Consensus size: 105
20813 TTGGTCACAT
** *
20823 TTACAAGATTCCCATTATCCATTTGCTCACTGTCAAACTTCTTTTGTTCAGATTCCATAGTAAGC
1 TTACAAGATTCCCATTATTGATTTGCTCACTGTCAAACTTCTTATGTTCAGATTCCATAGTAAGC
20888 CCATCAGAAACCAAAACTGATCCATCATTTGCATCCTCAA
66 CCATCAGAAACCAAAACTGATCCATCATTTGCATCCTCAA
*
20928 TTACAAGATTCCCATTATTGATTTGCTCACTGTCAAACTTCTTATGTTCAGATTCCATAGTGAGC
1 TTACAAGATTCCCATTATTGATTTGCTCACTGTCAAACTTCTTATGTTCAGATTCCATAGTAAGC
*
20993 CCATCAGAAACCAAAACTGATCCATCATTGGCATCCTCAA
66 CCATCAGAAACCAAAACTGATCCATCATTTGCATCCTCAA
*
21033 TTACAAGATTCCCATTATTGATTTGCTCACTGTCAAACTTCTTATGTTCGGATTCCATAGTAAGC
1 TTACAAGATTCCCATTATTGATTTGCTCACTGTCAAACTTCTTATGTTCAGATTCCATAGTAAGC
*
21098 CCATCAGAAACCAGAACTGATCCATCATTTGCATCCTCAA
66 CCATCAGAAACCAAAACTGATCCATCATTTGCATCCTCAA
21138 T
1 T
21139 ATGACTAGGA
Statistics
Matches: 202, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 202 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (105 bp):
TTACAAGATTCCCATTATTGATTTGCTCACTGTCAAACTTCTTATGTTCAGATTCCATAGTAAGC
CCATCAGAAACCAAAACTGATCCATCATTTGCATCCTCAA
Found at i:22175 original size:29 final size:29
Alignment explanation
Indices: 22102--22178 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
22092 CAACTAATGT
*
22102 CCAAATTGGGCCTAAACCTTTCCAAACTTG
1 CCAAATTGGGCCTAAACCTTT-CAAACTAG
* *
22132 CTCAATTTGAGCCTAAACCTTT-AAAC-AG
1 C-CAAATTGGGCCTAAACCTTTCAAACTAG
22160 AACCAAATTGGGCCTAAAC
1 --CCAAATTGGGCCTAAAC
22179 GTTAGCAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 18 0.46
30 2 0.05
31 18 0.46
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (29 bp):
CCAAATTGGGCCTAAACCTTTCAAACTAG
Found at i:22353 original size:31 final size:31
Alignment explanation
Indices: 22315--22389 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
22305 TGGTTCTGTT
22315 TAAAGGTTTAGGCTCAAATTGAGCAAGTTTG
1 TAAAGGTTTAGGCTCAAATTGAGCAAGTTTG
22346 TAAAGGTTTAGGCTCAAATTGAGCAAGTTTG
1 TAAAGGTTTAGGCTCAAATTGAGCAAGTTTG
22377 TAAAGGTTTAGGC
1 TAAAGGTTTAGGC
22390 CCAATTTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (31 bp):
TAAAGGTTTAGGCTCAAATTGAGCAAGTTTG
Found at i:27028 original size:30 final size:30
Alignment explanation
Indices: 26974--27035 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
26964 TTTAATTTTC
26974 CCCAAGTTCAGTTCATAAATAAAGGCAAAG
1 CCCAAGTTCAGTTCATAAATAAAGGCAAAG
* * * *
27004 CCCAGGTTGAGTTGATAGATAAAGGCAAAG
1 CCCAAGTTCAGTTCATAAATAAAGGCAAAG
27034 CC
1 CC
27036 GTTGTAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (30 bp):
CCCAAGTTCAGTTCATAAATAAAGGCAAAG
Found at i:31612 original size:3 final size:3
Alignment explanation
Indices: 31604--31633 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31594 CCACCCGAAA
31604 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
31634 TATCCCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32025 original size:2 final size:2
Alignment explanation
Indices: 32018--32069 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
32008 AGCCAAATGA
32018 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32060 AG AG AG AG AG
1 AG AG AG AG AG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.