Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013293.1 Corchorus capsularis cultivar CVL-1 contig13314, 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: 43425
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1622 original size:2 final size:2
Alignment explanation
Indices: 1610--1650 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1600 TTGAGTTTTA
*
1610 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1651 CAACATTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:4899 original size:20 final size:21
Alignment explanation
Indices: 4874--4912 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4864 TTTAGAAGCA
4874 ATTAATTAAAAAC-ATTAAAC
1 ATTAATTAAAAACAATTAAAC
4894 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAACAATTAA
4913 GGAAGGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAATTAAAAACAATTAAAC
Found at i:5006 original size:74 final size:74
Alignment explanation
Indices: 4919--5063 Score: 254
Period size: 74 Copynumber: 2.0 Consensus size: 74
4909 TTAAGGAAGG
* * *
4919 GAAATGTGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATAGGAGAAACTCATAGAGGGGCTTTT
4984 TAGTCATCC
66 TAGTCATCC
*
4993 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGAGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATAGGAGAAACTCATAGAGGGGCTTTT
5058 TAGTCA
66 TAGTCA
5064 CCTAAAAAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.41, C:0.09, G:0.30, T:0.21
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATAGGAGAAACTCATAGAGGGGCTTTT
TAGTCATCC
Found at i:10935 original size:16 final size:15
Alignment explanation
Indices: 10916--11026 Score: 107
Period size: 16 Copynumber: 6.9 Consensus size: 15
10906 GAACCCGTCC
10916 GACCCGAGACCCGAAT
1 GACCCGA-ACCCGAAT
*
10932 GACCCGCAACCCGGAT
1 GACCCG-AACCCGAAT
*
10948 GGCCCGAGACCCGAAT
1 GACCCGA-ACCCGAAT
10964 GACCCGTAACCC-AGAT
1 GACCCG-AACCCGA-AT
*
10980 GATCCGAAACCCGAAT
1 GACCCG-AACCCGAAT
*
10996 GACCCGTAACCCGAGT
1 GACCCG-AACCCGAAT
11012 GACCCGAAACCCGAA
1 GACCCG-AACCCGAA
11027 AAACTCGAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
15 2 0.03
16 74 0.94
17 3 0.04
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (15 bp):
GACCCGAACCCGAAT
Found at i:10954 original size:32 final size:31
Alignment explanation
Indices: 10916--11026 Score: 150
Period size: 32 Copynumber: 3.5 Consensus size: 31
10906 GAACCCGTCC
* *
10916 GACCCGAGACCCGAATGACCCGCAACCCGGAT
1 GACCCGAAACCCGAATGACCCGTAACCC-GAT
* *
10948 GGCCCGAGACCCGAATGACCCGTAACCCAGAT
1 GACCCGAAACCCGAATGACCCGTAACCC-GAT
*
10980 GATCCGAAACCCGAATGACCCGTAACCCGAGT
1 GACCCGAAACCCGAATGACCCGTAACCCGA-T
11012 GACCCGAAACCCGAA
1 GACCCGAAACCCGAA
11027 AAACTCGAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
31 2 0.03
32 69 0.97
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (31 bp):
GACCCGAAACCCGAATGACCCGTAACCCGAT
Found at i:10968 original size:48 final size:47
Alignment explanation
Indices: 10916--11026 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 47
10906 GAACCCGTCC
* * *
10916 GACCCGAGACCCGAATGACCCGCAACCCGGATGGCCCG-AGACCCGAAT
1 GACCCGA-ACCCGAATGACCCGAAACCCGAATGACCCGTA-ACCCGAAT
* *
10964 GACCCGTAACCC-AGATGATCCGAAACCCGAATGACCCGTAACCCGAGT
1 GACCCG-AACCCGA-ATGACCCGAAACCCGAATGACCCGTAACCCGAAT
11012 GACCCGAAACCCGAA
1 GACCCG-AACCCGAA
11027 AAACTCGAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
47 1 0.02
48 49 0.92
49 3 0.06
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (47 bp):
GACCCGAACCCGAATGACCCGAAACCCGAATGACCCGTAACCCGAAT
Found at i:12232 original size:16 final size:16
Alignment explanation
Indices: 12198--12300 Score: 122
Period size: 16 Copynumber: 6.5 Consensus size: 16
12188 AATCCGCCCA
*
12198 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
12214 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
12230 ACCCGACACCCGAATG
1 ACCCGAGACCCGAATG
* *
12246 ACCCGAAACCCGAATA
1 ACCCGAGACCCGAATG
12262 ACCCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
*
12277 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
12293 ACCCGAGA
1 ACCCGAGA
12301 AAACTGCTTG
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
14 1 0.01
15 12 0.16
16 62 0.81
17 2 0.03
ACGTcount: A:0.34, C:0.39, G:0.21, T:0.06
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:12235 original size:32 final size:31
Alignment explanation
Indices: 12198--12300 Score: 136
Period size: 32 Copynumber: 3.3 Consensus size: 31
12188 AATCCGCCCA
* *
12198 ACCCGAGACCCGGTAGACCCGAGACCCGAATG
1 ACCCGAGACCCGAT-GACCCGAAACCCGAATG
* *
12230 ACCCGACACCCGAATGACCCGAAACCCGAATA
1 ACCCGAGACCCG-ATGACCCGAAACCCGAATG
12262 ACCCGA-ACCCAGATGACCCGAAACCCGAATG
1 ACCCGAGACCC-GATGACCCGAAACCCGAATG
12293 ACCCGAGA
1 ACCCGAGA
12301 AAACTGCTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
31 28 0.44
32 34 0.54
33 1 0.02
ACGTcount: A:0.34, C:0.39, G:0.21, T:0.06
Consensus pattern (31 bp):
ACCCGAGACCCGATGACCCGAAACCCGAATG
Found at i:12281 original size:31 final size:32
Alignment explanation
Indices: 12213--12298 Score: 131
Period size: 31 Copynumber: 2.7 Consensus size: 32
12203 AGACCCGGTA
*
12213 GACCCGAGACCCGAATGACCCGACACCCGAAT
1 GACCCGAAACCCGAATGACCCGACACCCGAAT
*
12245 GACCCGAAACCCGAATAACCCGA-ACCC-AGAT
1 GACCCGAAACCCGAATGACCCGACACCCGA-AT
12276 GACCCGAAACCCGAATGACCCGA
1 GACCCGAAACCCGAATGACCCGA
12299 GAAAACTGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.02
31 28 0.56
32 21 0.42
ACGTcount: A:0.35, C:0.40, G:0.20, T:0.06
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCGACACCCGAAT
Found at i:35976 original size:2 final size:2
Alignment explanation
Indices: 35969--36000 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35959 TATATGCTTC
35969 AT AT 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 AT AT
36001 CTTTTTTTGT
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):
AT
Found at i:42589 original size:62 final size:60
Alignment explanation
Indices: 42414--42777 Score: 227
Period size: 62 Copynumber: 5.8 Consensus size: 60
42404 TTAAACTTGT
* * * * *
42414 ATGCAGAGATGTGAGAAAAT-TGATCCTTTGTCTGAAAGGGCATTTGGGGAAATCAGAAATTAA
1 ATGCAGA-ATGTGA-CAAATCTGACCCTTTGTCTGAAAGGGTACTT-GGGAAAT-AGAAACTAA
* * * * * * *
42477 ATGCGGGAGTGTGACTAAAT-TGACCCTTTGTCCGACAGGGTATCCTGGGAAATTGAAACTAT
1 ATGC-AGAATGTGAC-AAATCTGACCCTTTGTCTGAAAGGGTA-CTTGGGAAATAGAAACTAA
* *
42539 ATGCGAGAATGTGACAAATCTGACCCTTTGTCTGAAAGGGTACTTAGGGAACTAGAATCTAA
1 ATGC-AGAATGTGACAAATCTGACCCTTTGTCTGAAAGGGTACTT-GGGAAATAGAAACTAA
* * * *
42601 GTGCAGGAATGTGA-AGAAACTGACCCTTTGTCTGAAAGGGTATTTTGGG-AATACTAAACTTAA
1 ATGCA-GAATGTGACA-AATCTGACCCTTTGTCTGAAAGGGTA-CTTGGGAAATA-GAAAC-TAA
* * * *** **
42664 ATGCAATAATGTGAGAAATCAG-CCCTTTGTCTGAAAGGGCGGTTTGGGAAAACTAGATCCTAA
1 ATGC-AGAATGTGACAAATCTGACCCTTTGTCTGAAAGGG-TACTTGGG-AAA-TAGAAACTAA
* * * *
42727 ATGCAAAAATGTGACGAAA-CTAACCCTTTGTCCGAAAGGGTATTTTGGGAA
1 ATGC-AGAATGTGAC-AAATCTGACCCTTTGTCTGAAAGGGTA-CTTGGGAA
42778 TCAAATGTGC
Statistics
Matches: 239, Mismatches: 43, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
61 11 0.05
62 116 0.49
63 76 0.32
64 34 0.14
65 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (60 bp):
ATGCAGAATGTGACAAATCTGACCCTTTGTCTGAAAGGGTACTTGGGAAATAGAAACTAA
Found at i:42660 original size:124 final size:125
Alignment explanation
Indices: 42342--42778 Score: 368
Period size: 124 Copynumber: 3.4 Consensus size: 125
42332 AAGTTTAACT
* * * *** *
42342 TAAATGCAAGCATGATGACGAAATTGACCCTTTGTCCGAAAGGGTATTCCAGGAA-ACCAAGATT
1 TAAATGCAGGAATG-TGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATA-C----TG
* * * * *
42406 AAACTTGTATGCAGAGATGTGAGAAAAT-TGATCCTTTGTCTGAAAGGGCATTTGGGGAAATCAG
60 AAACTTATATGCAGA-ATGTGA-AAAATCTGACCCTTTGTCTGAAAGGGCACTTAGGGAACT-AG
42470 AAAT-
122 -AATC
* * * * * ** *
42474 TAAATGCGGGAGTGTGACTAAATTGACCCTTTGTCCGACAGGGTATCCTGGGAA-ATTGAAAC-T
1 TAAATGCAGGAATGTGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTGAAACTT
* *
42537 ATATGCGAGAATGTGACAAATCTGACCCTTTGTCTGAAAGGGTACTTAGGGAACTAGAATC
66 ATATGC-AGAATGTGAAAAATCTGACCCTTTGTCTGAAAGGGCACTTAGGGAACTAGAATC
* * *
42598 TAAGTGCAGGAATGTGAAGAAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACT-AAACTT
1 TAAATGCAGGAATGTGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTGAAACTT
* * * * ** *
42662 AAATGCAATAATGTGAGAAATCAG-CCCTTTGTCTGAAAGGGCGGTTTGGGAAAACTAG-ATCC
66 ATATGC-AGAATGTGAAAAATCTGACCCTTTGTCTGAAAGGGCACTTAGGG--AACTAGAAT-C
** *
42724 TAAATGCAAAAATGTGACGAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAAT
1 TAAATGCAGGAATGTGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAT
42779 CAAATGTGCT
Statistics
Matches: 253, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
123 3 0.01
124 76 0.30
125 64 0.25
126 64 0.25
131 36 0.14
132 10 0.04
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (125 bp):
TAAATGCAGGAATGTGACGAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAATACTGAAACTT
ATATGCAGAATGTGAAAAATCTGACCCTTTGTCTGAAAGGGCACTTAGGGAACTAGAATC
Found at i:42904 original size:65 final size:65
Alignment explanation
Indices: 42546--43070 Score: 367
Period size: 65 Copynumber: 8.0 Consensus size: 65
42536 TATATGCGAG
* * * *** * * * *
42546 AATGTGACAAATCTGACCCTTTGTCTGAAAGGGTACTTAGGG--AACTAGAATCTAAGTGC-AGG
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
* * ** * *
42608 AATGTGA-AGAAACTGACCCTTTGTCTGAAAGGGTATTTTGGGAATACTA-AACTTAAATGCAA-
1 AATGTGACA-AAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAG
*
42670 T
65 A
* * * * * *
42671 AATGTGAGAAATC-AGCCCTTTGTCTGAAAGGGCGGTTTGGGAAAACTAGATCCTAAATGCAA-A
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
* ** * *
42734 AATGTGACGAAACTAACCCTTTGTCCGAAAGGGTATTTTGGGAATCAAATGTGCT-GAACTTAGA
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGG-A--AAA----CTAGAACCTAAA
*
42798 T--AATGG
59 TGCAA-GA
* * * ** * *
42804 AATGTGACAGAACTAGCCTTTTGTTTG-AAGGGCGTTTTGGGAAAACTAGAGCCTCAATGCAAGA
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
*
42868 AATTTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
* * * **
42933 AATTTTACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGGAATTGAAAATGCT-GAACTTTG
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTT--GG----GAAAA--CTAGAACCTAA
* * *
42997 ATAC-TGG
58 ATGCAAGA
* * *
43004 AATGTTACAAAACTAACCCTTTGTTCGAAAGGGCGTTTTAGGAAAACTAGAACCTAAATGCAAGA
1 AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
43069 AA
1 AA
43071 GTTGATTCTT
Statistics
Matches: 366, Mismatches: 67, Indels: 57
0.75 0.14 0.12
Matches are distributed among these distances:
61 1 0.00
62 68 0.19
63 47 0.13
64 59 0.16
65 84 0.23
66 3 0.01
67 5 0.01
68 3 0.01
69 13 0.04
70 28 0.08
71 45 0.12
72 8 0.02
73 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (65 bp):
AATGTGACAAAACTAACCCTTTGTCCGAAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAAGA
Found at i:43338 original size:27 final size:27
Alignment explanation
Indices: 43261--43338 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
43251 ATTAGGGTCG
* * *
43261 TCCAAGGGTATTTTGGTCATTTTCGCG
1 TCCAGGGGTATTTTGGTCATTTTTGCA
*
43288 CCCAGGGGTATTTTGGTCATTTTTGCA
1 TCCAGGGGTATTTTGGTCATTTTTGCA
* *
43315 TCCAGGGGCATTTTGGTAATTTTT
1 TCCAGGGGTATTTTGGTCATTTTT
43339 ACACTCGTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.42
Consensus pattern (27 bp):
TCCAGGGGTATTTTGGTCATTTTTGCA
Done.