Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011910.1 Corchorus capsularis cultivar CVL-1 contig11931, 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: 24232
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:835 original size:28 final size:28
Alignment explanation
Indices: 802--863 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
792 CCGGATCGGC
802 CGGTTCAATCGGGAACCGGTCATGAATT
1 CGGTTCAATCGGGAACCGGTCATGAATT
830 CGGTTCAATCGGGAACCGGTCATGAATT
1 CGGTTCAATCGGGAACCGGTCATGAATT
858 CGGTTC
1 CGGTTC
864 CGTCACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (28 bp):
CGGTTCAATCGGGAACCGGTCATGAATT
Found at i:12067 original size:2 final size:2
Alignment explanation
Indices: 12062--12110 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
12052 TATACATAAA
* *
12062 AT AT AT AT ACT AT GT AT AT AT AT AT AT AT AT AT AT TT AT -T A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12103 AT AT AT AT
1 AT AT AT AT
12111 TGTTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12209 original size:20 final size:18
Alignment explanation
Indices: 12184--12228 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
12174 ACATATGTTT
12184 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
12204 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
12222 TACTAAT
1 TACTAAT
12229 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:12358 original size:21 final size:21
Alignment explanation
Indices: 12332--12374 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12322 GGTCTTAGGT
12332 TCAACTCTCACGGAATGTGAG
1 TCAACTCTCACGGAATGTGAG
12353 TCAACTCTCACGGAATGTGAG
1 TCAACTCTCACGGAATGTGAG
12374 T
1 T
12375 TTATTTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
TCAACTCTCACGGAATGTGAG
Found at i:12473 original size:63 final size:63
Alignment explanation
Indices: 12374--12511 Score: 260
Period size: 63 Copynumber: 2.2 Consensus size: 63
12364 GGAATGTGAG
12374 TTTATTTGTAATTTGTTTATTTATGTATTTGGTAGGTAGGTAGTTTATTTATGGGCATAGAGA
1 TTTATTTGTAATTTGTTTATTTATGTATTTGGTAGGTAGGTAGTTTATTTATGGGCATAGAGA
*
12437 TTTATTTGTAATTTGTTTATTTATGTATTTGGTAGGTAGGTAGTTTATTTATGGGTATAGAGA
1 TTTATTTGTAATTTGTTTATTTATGTATTTGGTAGGTAGGTAGTTTATTTATGGGCATAGAGA
12500 TTTATTTG-AATT
1 TTTATTTGTAATT
12512 GTAATGAGAT
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 4 0.05
63 70 0.95
ACGTcount: A:0.24, C:0.01, G:0.22, T:0.53
Consensus pattern (63 bp):
TTTATTTGTAATTTGTTTATTTATGTATTTGGTAGGTAGGTAGTTTATTTATGGGCATAGAGA
Found at i:18013 original size:29 final size:31
Alignment explanation
Indices: 17981--18047 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
17971 ATGCAATTTG
* *
17981 GGATATAACTTTAC-AAAA-CAAGCAATTAA
1 GGATATAACATTACGAAAATCAAGCAAATAA
*
18010 GGATATAACATTACGAAAATCGAGCAAATAA
1 GGATATAACATTACGAAAATCAAGCAAATAA
18041 GGATATA
1 GGATATA
18048 GTCCGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (31 bp):
GGATATAACATTACGAAAATCAAGCAAATAA
Found at i:18212 original size:31 final size:31
Alignment explanation
Indices: 18177--18282 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 31
18167 CCCTAACTGA
18177 TTATATCCTTAATTGCTCGAAATTGAAAACG
1 TTATATCCTTAATTGCTCGAAATTGAAAACG
*
18208 TTATATCCTTAATTGCTCGAAATCGAAAACG
1 TTATATCCTTAATTGCTCGAAATTGAAAACG
* ** *
18239 TTATATCCTTAATTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTCGAAATTGAAAACG
18268 TTATATCCTTAATTG
1 TTATATCCTTAATTG
18283 TTTGCGGTAG
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
29 19 0.28
30 2 0.03
31 48 0.70
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (31 bp):
TTATATCCTTAATTGCTCGAAATTGAAAACG
Found at i:18296 original size:60 final size:62
Alignment explanation
Indices: 18177--18317 Score: 160
Period size: 60 Copynumber: 2.3 Consensus size: 62
18167 CCCTAACTGA
* *
18177 TTATATCCTTAATTGCTCGAAATTGAAAACGTTATATCCTTAATTGCTCGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATTGAAAACGTTATATCCTTAATTGCTCGAAATAGAAAACG
** * * * *** *
18239 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGTTTGCGGTAGAAAATG
1 TTATATCCTTAATTGCTTGAAATTGAAAACGTTATATCCTTAATTGCTCGAAATAGAAAACG
*
18299 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
18318 CTTATCATCT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 46 0.69
61 3 0.04
62 18 0.27
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATTGAAAACGTTATATCCTTAATTGCTCGAAATAGAAAACG
Found at i:19230 original size:3 final size:3
Alignment explanation
Indices: 19222--19262 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
19212 TGAAATTAGG
19222 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19263 GAAAATACGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19345 original size:31 final size:31
Alignment explanation
Indices: 19331--19440 Score: 152
Period size: 31 Copynumber: 3.6 Consensus size: 31
19321 TTTGTTGCTG
* ***
19331 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
*
19360 CAAGCAATTAAGGATATAACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
*
19391 CGAGCAATTAAGGATATAACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
19422 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
19441 TCAGTTAGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 21 0.30
30 2 0.03
31 48 0.68
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:19623 original size:29 final size:31
Alignment explanation
Indices: 19557--19623 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
19547 TCTAACGGAC
*
19557 TATATCCTTATTTGCTCGATTTTCGTAACGT
1 TATATCCTTAATTGCTCGATTTTCGTAACGT
* *
19588 TATATCCTTAATTGCTTG-TTTT-GTAATGT
1 TATATCCTTAATTGCTCGATTTTCGTAACGT
19617 TATATCC
1 TATATCC
19624 CAAATTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGATTTTCGTAACGT
Found at i:20777 original size:32 final size:30
Alignment explanation
Indices: 20704--20777 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 30
20694 CGACATCTTA
* *
20704 TACCTCTTAAGTTTTCAAATTTAAGACAAT
1 TACCTCTAAACTTTTCAAATTTAAGACAAT
* *
20734 TAGCTACCTAAACTTTTCAAGTTTAAGACAATT
1 TACCT--CTAAACTTTTCAAATTTAAGACAA-T
20767 TACCCTCTAAA
1 TA-CCTCTAAA
20778 ATAGGGACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
30 4 0.11
32 26 0.74
33 3 0.09
34 2 0.06
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (30 bp):
TACCTCTAAACTTTTCAAATTTAAGACAAT
Found at i:21783 original size:28 final size:30
Alignment explanation
Indices: 21744--21813 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
21734 TCGATTTGAA
*
21744 GGTCCCTGTACTTAAAAAAA-G-TCAATTT
1 GGTCCCTCTACTTAAAAAAATGATCAATTT
21772 GGTCCCTCTAC-TAAAAAAATGATCAATTT
1 GGTCCCTCTACTTAAAAAAATGATCAATTT
*
21801 AGTCCCTCTACTT
1 GGTCCCTCTACTT
21814 GCAGGTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 8 0.22
28 11 0.30
29 17 0.46
30 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (30 bp):
GGTCCCTCTACTTAAAAAAATGATCAATTT
Found at i:22444 original size:2 final size:2
Alignment explanation
Indices: 22399--22427 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22389 TAGTACCTTT
22399 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 T
22428 TATTTGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22711 original size:66 final size:66
Alignment explanation
Indices: 22578--22703 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
22568 ACTATACTTT
* *
22578 TTGGTCATTTCTCAATTGACTTTAATAGAATAATGGAATTACTAAAAGATCCCTACCAAGACTTG
1 TTGGTCATTTCTCAATTGACTTTAATAGAATAATGGAATTACAAAAAAATCCCTACCAAGACTTG
22643 C
66 C
* * *
22644 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACAAAAAAATCTCTACCAAG
1 TTGGTCATTTCTCAATTGACTTTAATAGAATAATGGAATTACAAAAAAATCCCTACCAAG
22704 GTTTGCTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (66 bp):
TTGGTCATTTCTCAATTGACTTTAATAGAATAATGGAATTACAAAAAAATCCCTACCAAGACTTG
C
Found at i:23649 original size:166 final size:165
Alignment explanation
Indices: 23362--23848 Score: 575
Period size: 166 Copynumber: 2.9 Consensus size: 165
23352 AATAAACATA
* ** ** * * * *
23362 TGGAATTACTAAAAGATCCCCACCCCGGATAAATGAAGAGCGAGAGAACTATTTTTTTTTTTGTC
1 TGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGCTAGAGAACTA--ATTTTTTTCGTC
* * * *
23427 TTTTCCCACTTGGCAGATTACTTAAATGTCCTAACATTTGATTTTTAAGTGGATTAAATAACTAG
64 TTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACTA-
* *
23492 ACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTTG
128 ACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAG
* * * * ** * *
23530 TGG-ATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTTCGTCT
1 TGGAATTAATAAAAGATCCCCACCAAGGATTGATGAT-GAGCTAGAGAACTAATTTTTTTCGTCT
* * *
23594 TTTCCTACTTGGCAGATTACTTAAATATCCAAACTTTTGATTCTTAAGGGGATTAAATAAGTAAT
65 TTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACTAA-
*
23659 CTTTTTTGTCATTTCTCAA-TGTACTTGAATAGAGTAG
129 CTTTTTGGTCATTTCTCAATTG-ACTTGAATAGAGTAG
* *
23696 TGGAATTAATAAAAGATCCCCATCAAGGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTT
1 TGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTT
* * * *
23761 CAT-CTATTTGGCAGATTACTTAAATGTGCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAA
66 -TTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACT-AA
*
23825 CTTTTTGATCATTTCTCAATTGAC
129 CTTTTTGGTCATTTCTCAATTGAC
23849 AAATGACTCA
Statistics
Matches: 268, Mismatches: 44, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
165 3 0.01
166 197 0.74
167 54 0.20
168 14 0.05
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (165 bp):
TGGAATTAATAAAAGATCCCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTT
TTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGGATTAAATAACTAACT
TTTTGGTCATTTCTCAATTGACTTGAATAGAGTAG
Found at i:24208 original size:2 final size:2
Alignment explanation
Indices: 24201--24232 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24191 TCTATTAATT
24201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.