Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014319.1 Corchorus capsularis cultivar CVL-1 contig14340, 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: 37601
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1182 original size:18 final size:18
Alignment explanation
Indices: 1159--1193 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1149 ACATCGAGTC
1159 AATTGATAAAAATTCAGA
1 AATTGATAAAAATTCAGA
1177 AATTGATAAAAATTCAG
1 AATTGATAAAAATTCAG
1194 GTGGGGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (18 bp):
AATTGATAAAAATTCAGA
Found at i:3168 original size:219 final size:218
Alignment explanation
Indices: 2738--3177 Score: 648
Period size: 222 Copynumber: 2.0 Consensus size: 218
2728 TGGTGATTAT
2738 TATCATAGTTTTGTTTGTTTGGTTATTTCTCATTATCACCTCCTTAAAAAAACTTGACAATAATG
1 TATCATAGTTTTGTTTGTTTGGTTATTTCTCATTATCACCTCCTTAAAAAAACTTGACAATAATG
* *
2803 CAAATTAAAATATATATGGATTAGCCTACGCTGACGTTGCAGACAATTTTTTTTTAATATGAGCT
66 CAAATTAAAATATATATGGATTAACCTACGCTGACGTTGCAAACAATTTTTTTTTAATATGAGCT
* * *
2868 TATTGATAAGCCTGTTATAACTCTTAAACACATAAGAGAAAATACAAAGATAGGGTCGTAATCTC
131 TACTGATAAGCCTATTATAACTCTTAAACACATAAGAGAAAATACAAAGATAGGGTAGTAATCTC
*
2933 TATCGTCAAAAAAAAAATAGATTG
196 TATCGTC-AAAAAAAAGTAGATTG
* * * *
2957 TATCATAGTTTTGTTTGTTTGGTTATTTTTCATTATCACCTCCTT-AAAAAATTTGCCAATTATG
1 TATCATAGTTTTGTTTGTTTGGTTATTTCTCATTATCACCTCCTTAAAAAAACTTGACAATAATG
* ** * *
3021 CAAATTAAAATATATGTGGATTAACCTGTGTTGACGTTGCAAATAATTTTTTTTTTTTGAATATG
66 CAAATTAAAATATATATGGATTAACCTACGCTGACGTTGCAAACAA---TTTTTTTTT-AATATG
* * * * *
3086 AGCTTACTGATGAGTCTATTATAACTCTTAAACATATAAGAGAAGATACAAAGATGGGGTAGTAA
127 AGCTTACTGATAAGCCTATTATAACTCTTAAACACATAAGAGAAAATACAAAGATAGGGTAGTAA
3151 TCTCTATCGTCAAAAAAAAGTAGATTG
192 TCTCTATCGTCAAAAAAAAGTAGATTG
3178 GGGTTTTTAG
Statistics
Matches: 197, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
218 55 0.28
219 44 0.22
221 24 0.12
222 74 0.38
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (218 bp):
TATCATAGTTTTGTTTGTTTGGTTATTTCTCATTATCACCTCCTTAAAAAAACTTGACAATAATG
CAAATTAAAATATATATGGATTAACCTACGCTGACGTTGCAAACAATTTTTTTTTAATATGAGCT
TACTGATAAGCCTATTATAACTCTTAAACACATAAGAGAAAATACAAAGATAGGGTAGTAATCTC
TATCGTCAAAAAAAAGTAGATTG
Found at i:12992 original size:17 final size:17
Alignment explanation
Indices: 12970--13002 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12960 ATAATAAACA
12970 AAACATTTAGAAAATTT
1 AAACATTTAGAAAATTT
12987 AAACATTTAGAAAATT
1 AAACATTTAGAAAATT
13003 AACTATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (17 bp):
AAACATTTAGAAAATTT
Found at i:13438 original size:23 final size:21
Alignment explanation
Indices: 13404--13446 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
13394 GGAAGTTATC
13404 AAATTTATAATACCAGTTACTGA
1 AAATTTATAATA--AGTTACTGA
13427 AAATGTTA-AATAAGTTACTG
1 AAAT-TTATAATAAGTTACTG
13447 TCCCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.42
23 8 0.42
24 3 0.16
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATTTATAATAAGTTACTGA
Found at i:16670 original size:35 final size:35
Alignment explanation
Indices: 16631--16701 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
16621 TACTATAATA
16631 TTAAGGCTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGCTATTTTAGTAATTGACTAATTAAGATTT
*
16666 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGCTATTTTAGTAATTGACTAATTAAGATTT
16701 T
1 T
16702 GAGTTCGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.46
Consensus pattern (35 bp):
TTAAGGCTATTTTAGTAATTGACTAATTAAGATTT
Found at i:19012 original size:31 final size:31
Alignment explanation
Indices: 18957--19022 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
18947 CGGCAATTTG
* *
18957 GAAATATATTTTTTTAAAAAGGGTATAATCA
1 GAAATATATTTTTTAAAAAAGGGTACAATCA
*
18988 GAAATATA-TTTTTAAAAAAGGGGTACAATCG
1 GAAATATATTTTTTAAAAAA-GGGTACAATCA
19019 GAAA
1 GAAA
19023 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTTTAAAAAAGGGTACAATCA
Found at i:19077 original size:16 final size:14
Alignment explanation
Indices: 19077--19130 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
19067 AGATAATAGT
19077 ATAATATAATAATA
1 ATAATATAATAATA
19091 AT-ATAT-ATAATA
1 ATAATATAATAATA
19103 TATAATATAATAATA
1 -ATAATATAATAATA
19118 ATAATAT-ATAATA
1 ATAATATAATAATA
19131 TATGTATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.16
13 12 0.32
14 13 0.35
15 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATATAATAATA
Found at i:19086 original size:5 final size:5
Alignment explanation
Indices: 19076--19132 Score: 55
Period size: 5 Copynumber: 10.8 Consensus size: 5
19066 TAGATAATAG
19076 TATAA TATAA TAATAA TAT-A TATAATA TATAA TATAA TAATAA TA-ATA
1 TATAA TATAA T-ATAA TATAA TAT-A-A TATAA TATAA T-ATAA TATA-A
19124 TATAA TATA
1 TATAA TATA
19133 TGTATAGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
4 5 0.11
5 24 0.53
6 12 0.27
7 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:19090 original size:3 final size:3
Alignment explanation
Indices: 19077--19130 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
19067 AGATAATAGT
19077 ATA AT- ATA ATA ATA AT- ATA TATA ATA TATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA
19121 ATA TATA ATA
1 ATA -ATA ATA
19131 TATGTATAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.13
3 30 0.67
4 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:19114 original size:21 final size:21
Alignment explanation
Indices: 19069--19130 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 21
19059 GTATAGATAG
19069 ATAATAGTATAATATAATAATA
1 ATAATA-TATAATATAATAATA
19091 AT-ATATATAATAT-ATAAT-
1 ATAATATATAATATAATAATA
19109 ATAATA-ATAATAATATATAATA
1 ATAATATATAAT-ATA-ATAATA
19131 TATGTATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 7 0.20
19 10 0.29
20 8 0.23
21 8 0.23
22 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATATATAATATAATAATA
Found at i:19148 original size:5 final size:5
Alignment explanation
Indices: 19140--19178 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
19130 ATATGTATAG
19140 TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
19179 TTGATTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 27 0.84
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:19159 original size:18 final size:18
Alignment explanation
Indices: 19136--19174 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
19126 TAATATATGT
19136 ATAGTAAGATAAGATAAG
1 ATAGTAAGATAAGATAAG
19154 ATAGTAAGATAAGATAAG
1 ATAGTAAGATAAGATAAG
19172 ATA
1 ATA
19175 AGATTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (18 bp):
ATAGTAAGATAAGATAAG
Found at i:19163 original size:13 final size:13
Alignment explanation
Indices: 19145--19169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19135 TATAGTAAGA
19145 TAAGATAAGATAG
1 TAAGATAAGATAG
19158 TAAGATAAGATA
1 TAAGATAAGATA
19170 AGATAAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
TAAGATAAGATAG
Found at i:31376 original size:6 final size:6
Alignment explanation
Indices: 31361--31398 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
31351 TCTCTTTTAT
31361 TATA-C TATATC TATATC TATATC TATATC TATATC TAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TAT
31399 TAGGATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:33001 original size:14 final size:14
Alignment explanation
Indices: 32982--33014 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
32972 AAACTTTTAT
32982 TTAATTTCAATCTC
1 TTAATTTCAATCTC
32996 TTAATTTCAATCTC
1 TTAATTTCAATCTC
33010 TTAAT
1 TTAAT
33015 ATCTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAATTTCAATCTC
Found at i:33947 original size:13 final size:13
Alignment explanation
Indices: 33929--33959 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
33919 TCAAACACAA
33929 CTGAAAAGTATTT
1 CTGAAAAGTATTT
33942 CTGAAAAGTATTT
1 CTGAAAAGTATTT
33955 CTGAA
1 CTGAA
33960 TTTTCTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
CTGAAAAGTATTT
Found at i:34644 original size:2 final size:2
Alignment explanation
Indices: 34637--34664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34627 TGATAGCATC
34637 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
34665 TTTAATAACT
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:36426 original size:38 final size:38
Alignment explanation
Indices: 36375--36452 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
36365 TAAAATTACC
*
36375 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATTGTTG
1 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATAGTTG
36413 AAAAATGT-AAAGTATTAAGTAAGAATGTAAGATAGTTG
1 AAAAAT-TCAAAGTATTAAGTAAGAATGTAAGATAGTTG
36451 AA
1 AA
36453 TTTGTTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.19, T:0.29
Consensus pattern (38 bp):
AAAAATTCAAAGTATTAAGTAAGAATGTAAGATAGTTG
Done.