Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014134.1 Corchorus capsularis cultivar CVL-1 contig14155, 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: 11928
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1039 original size:49 final size:48
Alignment explanation
Indices: 972--1650 Score: 588
Period size: 49 Copynumber: 13.9 Consensus size: 48
962 CAATTTTCGG
* *
972 TTTTCACCTGCTACTTT-CCAAAATGCCCTTCCCGGACGGAATGCATTTA
1 TTTT-ACCTGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* *
1021 TTGTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCGCTGGT-
1 TT-TTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACT--TA
* * * * *
1071 TTTTACCTG-TTTTTCCTAAAACGCCCTTCCCGAACGGAAGGCTC-TA
1 TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * ** * * * * *
1117 GTTTTGCCCGCTTTTTCTTAAAATTCCCTTCTCAGACGGAAGCCATTTA
1 -TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * ** *
1166 TTTTTGCTTGCTATTTCCCAAAATGCCCTTCCTAGACGGAAGCCA-TTCA
1 -TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT-A
* * **
1215 TCTTTATCTGCTATTTCCCAAAATGCCCTTCCCAGACGGAAGGCACATGC
1 T-TTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCAC-TTA
* *
1265 TTTTATCTACTA-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTGT-
1 TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCA-CT-TA
** * *
1313 TTTTATATGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTG
1 TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
1361 TCTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACTTGT
1 T-TTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT-A
* * *
1411 TTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACTTGT
1 TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT-A
** * * * *
1460 TTTTATATGTTATTTCCCAAAATGCCCTTCCCAGACGGAAGCCAATTA
1 TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * *
1508 TTTT-CGCTTGTTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCAGTAA
1 TTTTAC-C-TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
1557 TCTTTACCTGCT-TTGTCTCAAAATGCCCTTCCCGGACGGAAAGCACTAA
1 T-TTTACCTGCTATT-TCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* *
1606 TTTTTACCTG-T-TTTCCCTAAAACGCCCTTCCCGGATGGAAGGCAC
1 -TTTTACCTGCTATTTCCC-AAAATGCCCTTCCCGGACGGAAGGCAC
1651 CATCCTCTTA
Statistics
Matches: 535, Mismatches: 70, Indels: 51
0.82 0.11 0.08
Matches are distributed among these distances:
45 1 0.00
47 11 0.02
48 137 0.26
49 372 0.70
50 11 0.02
51 3 0.01
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
Found at i:1302 original size:146 final size:146
Alignment explanation
Indices: 972--1646 Score: 589
Period size: 146 Copynumber: 4.6 Consensus size: 146
962 CAATTTTCGG
* * * * **
972 TTTTCACCTGCTACTTTCCAAAATGCCCTTCCCGGACGGAATGCATTTATTGTTACCTGCTATTT
1 TTTT-ACCTGCTA-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTATATGCTATTT
* * * ** ** * * * * *
1037 TCCAAAATGCCCTTCCCGGACGGAAGGCGCTGGTTTTTACCTG-TTTTTCCTAAAACGCCCTTCC
64 CCCAAAATGCCCTTCCCAGACGGAAGCCATTCATCTTTATCTGCTATTTCCCAAAATGCCCTTCC
* *
1101 CGAACGGAAGGCTC-TAG-
129 CGGACGGAAGGCACAT-GC
* * * ** * * * * * *
1118 TTTTGCCCGCTTTTTCTTAAAATTCCCTTCTCAGACGGAAGCCATTTATTTTTGCT-TGCTATTT
1 TTTTACCTGC-TATTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTT-ATATGCTATTT
*
1182 CCCAAAATGCCCTTCCTAGACGGAAGCCATTCATCTTTATCTGCTATTTCCCAAAATGCCCTTCC
64 CCCAAAATGCCCTTCCCAGACGGAAGCCATTCATCTTTATCTGCTATTTCCCAAAATGCCCTTCC
*
1247 CAGACGGAAGGCACATGC
129 CGGACGGAAGGCACATGC
* * * *
1265 TTTTATCTACTATTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTGTTTTTATATGCTATTTCC
1 TTTTACCTGCTATTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTATATGCTATTTCC
* * * *
1330 CAAAATGCCCTTCCCGGACGGAAGGCA-CCTGTCTTTATCTGCTATTTCCCAAAATGCCCTTCCC
66 CAAAATGCCCTTCCCAGACGGAAGCCATTC-ATCTTTATCTGCTATTTCCCAAAATGCCCTTCCC
* * *
1394 GGACGGAAGGTACTTGT
130 GGACGGAAGGCACATGC
* * * *
1411 TTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACTTGTTTTTATATGTTATTTC
1 TTTTACCTGCTA-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTATATGCTATTTC
** * * *
1476 CCAAAATGCCCTTCCCAGACGGAAGCCAATT-AT-TTTCGCTTGTTTTTTCCTAAAATGCCCTTC
65 CCAAAATGCCCTTCCCAGACGGAAGCC-ATTCATCTTTATC-TGCTATTTCCCAAAATGCCCTTC
*
1539 CCGGACGGAAGGCAGTAAT-C
128 CCGGACGGAAGGCA--CATGC
* * * * **
1559 -TTTACCTGCTTTGTCTCAAAATGCCCTTCCCGGACGGAAAGCACTAATTTTTACCTG-T-TTTC
1 TTTTACCTGCTAT-TCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTATATGCTATTTC
* * *
1621 CCTAAAACGCCCTTCCCGGATGGAAG
65 CC-AAAATGCCCTTCCCAGACGGAAG
1647 GCACCATCCT
Statistics
Matches: 431, Mismatches: 83, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
145 84 0.19
146 184 0.43
147 161 0.37
148 1 0.00
149 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (146 bp):
TTTTACCTGCTATTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTATATGCTATTTCC
CAAAATGCCCTTCCCAGACGGAAGCCATTCATCTTTATCTGCTATTTCCCAAAATGCCCTTCCCG
GACGGAAGGCACATGC
Found at i:5705 original size:14 final size:15
Alignment explanation
Indices: 5673--5724 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
5663 CAAGAGACGT
5673 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATGG
*
5688 TTTTCAAGAAAA-GG
1 TTTTCAAAAAAATGG
*
5702 TTTTC--GAAAATGAG
1 TTTTCAAAAAAATG-G
5716 TTTTCAAAA
1 TTTTCAAAA
5725 GATTTTCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 1 0.03
14 13 0.42
15 11 0.35
16 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (15 bp):
TTTTCAAAAAAATGG
Found at i:7393 original size:37 final size:37
Alignment explanation
Indices: 7311--7393 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
7301 AGAAAATTCA
7311 CAAAGATC-AACAATCGACCACGGATTGGTCTCTCCT
1 CAAAGATCAAACAATCGACCACGGATTGGTCTCTCCT
* *
7347 C-ACGTATCAAACAA-CTGACCACGGATTGGT-TGCTTCT
1 CAAAG-ATCAAACAATC-GACCACGGATTGGTCT-CTCCT
7384 CAAAGATCAA
1 CAAAGATCAA
7394 CAAAATTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
35 2 0.05
36 6 0.15
37 29 0.74
38 2 0.05
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (37 bp):
CAAAGATCAAACAATCGACCACGGATTGGTCTCTCCT
Found at i:7576 original size:38 final size:38
Alignment explanation
Indices: 7534--7606 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
7524 CTCTTAGCAA
*
7534 TAATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAG
1 TAATCAAAGTTGACTGGAAACAAGTCATCTTTCAACAG
7572 TAATCAAAGTTGACTGGAAACAAGTCATCTTTCAA
1 TAATCAAAGTTGACTGGAAACAAGTCATCTTTCAA
7607 GTTATCAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (38 bp):
TAATCAAAGTTGACTGGAAACAAGTCATCTTTCAACAG
Found at i:7799 original size:73 final size:74
Alignment explanation
Indices: 7618--7817 Score: 287
Period size: 73 Copynumber: 2.7 Consensus size: 74
7608 TTATCAGAGA
*
7618 TCATCTTTTCAATAAGTTATCAA-AGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACG
1 TCATC-TTTCAA-CAGTTATCAAGA-TTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACG
7682 ACTGGAAACAGG
63 ACTGGAAACAGG
* * * * * *
7694 TCGTCTTTCAGCACTTATTAGGTTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTT-CGACT
1 TCATCTTTCAACAGTTATCAAGATTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACT
7758 GGAAACAGG
66 GGAAACAGG
*
7767 TCATCTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCA
1 TCATCTTTCAACAGTTATCAAGATTGACTGGAAACAGGTCATCTTTCAGCA
7818 GTTTTCGGTT
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
73 58 0.53
74 42 0.39
75 5 0.05
76 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (74 bp):
TCATCTTTCAACAGTTATCAAGATTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGACT
GGAAACAGG
Found at i:7820 original size:38 final size:37
Alignment explanation
Indices: 7632--7820 Score: 213
Period size: 38 Copynumber: 5.1 Consensus size: 37
7622 CTTTTCAATA
*
7632 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGC
1 AGTTATCAAA-TCGACTGGAAACAGGTCATCTTTCAGC
* ** *
7670 AATTATCTTA-CGACTGGAAACAGGTCGTCTTTCAGC
1 AGTTATCAAATCGACTGGAAACAGGTCATCTTTCAGC
* * ** *
7706 ACTTATTAGGTTTGACTGGAAACAGGTCATCTTTCAGC
1 AGTTATCA-AATCGACTGGAAACAGGTCATCTTTCAGC
* * *
7744 AATTATC--TTCGACTGGAAACAGGTCATCTTTCAAC
1 AGTTATCAAATCGACTGGAAACAGGTCATCTTTCAGC
7779 AGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
1 AGTTATCAA-ATCGACTGGAAACAGGTCATCTTTCAGC
7817 AGTT
1 AGTT
7821 TTCGGTTGCT
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
35 32 0.25
36 29 0.23
38 66 0.52
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (37 bp):
AGTTATCAAATCGACTGGAAACAGGTCATCTTTCAGC
Found at i:7864 original size:8 final size:8
Alignment explanation
Indices: 7851--7902 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
7841 GGCATTCCAA
7851 CAACTTTT
1 CAACTTTT
7859 CAACTTTT
1 CAACTTTT
*
7867 AAAACTTTTT
1 -CAAC-TTTT
*
7877 CAA-TTTA
1 CAACTTTT
7884 CAACTTTT
1 CAACTTTT
*
7892 CAACATTT
1 CAACTTTT
7900 CAA
1 CAA
7903 TACAAAACTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 21 0.58
9 5 0.14
10 4 0.11
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (8 bp):
CAACTTTT
Found at i:7888 original size:16 final size:17
Alignment explanation
Indices: 7850--7895 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
7840 GGGCATTCCA
7850 ACAAC-TTTTCAACTTTT
1 ACAACTTTTTCAAC-TTT
*
7867 AAAACTTTTTCAA-TTT
1 ACAACTTTTTCAACTTT
7883 ACAAC-TTTTCAAC
1 ACAACTTTTTCAAC
7896 ATTTCAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 4 0.16
18 7 0.28
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (17 bp):
ACAACTTTTTCAACTTT
Found at i:8067 original size:47 final size:46
Alignment explanation
Indices: 7924--8070 Score: 195
Period size: 47 Copynumber: 3.1 Consensus size: 46
7914 TCAATTTAAA
* *
7924 ACTTCCATGTGAGTCAGCAATCCTTCGAACCAAGTTGGTCATTCCTC
1 ACTTCCATGTGAGTCAGAAATCCTTCG-ACCAAGTTGGTCTTTCCTC
* *
7971 ACTTCCATGTGAGTCAGAAATCGTTCCGACCCAAGTTGGTCTTCCCTC
1 ACTTCCATGTGAGTCAGAAATCCTT-CGA-CCAAGTTGGTCTTTCCTC
* * *
8019 ACTTCCGTGTGAGTCAGAAATCCTTCGACCAAAGTTTGTCTTTTCTC
1 ACTTCCATGTGAGTCAGAAATCCTTCGACC-AAGTTGGTCTTTCCTC
8066 ACTTC
1 ACTTC
8071 TATGCAAAGT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 2 0.02
47 45 0.51
48 41 0.47
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (46 bp):
ACTTCCATGTGAGTCAGAAATCCTTCGACCAAGTTGGTCTTTCCTC
Found at i:8181 original size:33 final size:33
Alignment explanation
Indices: 8138--8473 Score: 127
Period size: 33 Copynumber: 10.3 Consensus size: 33
8128 CTTTAGTTTC
8138 CGACCTCAGACAGGTCTTTCTCAATTTCAATAT
1 CGACCTCAGACAGGTCTTTCTCAATTTCAATAT
* * * *
8171 CGACCACAGACCGGTC-TTCTTCAA-TTCCAGA-
1 CGACCTCAGACAGGTCTTTC-TCAATTTCAATAT
**
8202 CCTCCT-AGA-A-GTCTTTCTCAATTTCAATTAT
1 CGACCTCAGACAGGTCTTTCTCAATTTCAA-TAT
* *
8233 CAAAGTTGACCTCAGACAGGTCTTTTCTCAATTTCAAAAG
1 C------GACCTCAGACAGGTC-TTTCTCAATTTCAATAT
* * * * *
8273 CGACCACAGACTGGTCTATTTCTCAGATATTTAGTTT
1 CGACCTCAGACAGGTC--TTTCTCA-AT-TTCAATAT
* * *
8310 CAGGCCTCAAATAGGTCTTTCTCAATTTCAATAT
1 C-GACCTCAGACAGGTCTTTCTCAATTTCAATAT
* * * *
8344 TGACCGCAGACTGGTC---CT--A-TTCAATTT
1 CGACCTCAGACAGGTCTTTCTCAATTTCAATAT
* *
8371 CAGACCTCAAACA-TTCTTTCTCAATTTCAATAT
1 C-GACCTCAGACAGGTCTTTCTCAATTTCAATAT
* * * *
8404 TGACCGCAGACTGGTC---CT--A-TTCAATTT
1 CGACCTCAGACAGGTCTTTCTCAATTTCAATAT
* *
8431 CAGACCTCAAACA-TTCTTTCTCAATTTCAATAT
1 C-GACCTCAGACAGGTCTTTCTCAATTTCAATAT
*
8464 CGACCACAGA
1 CGACCTCAGA
8474 TTGGTCCTAT
Statistics
Matches: 212, Mismatches: 57, Indels: 69
0.63 0.17 0.20
Matches are distributed among these distances:
27 18 0.08
28 25 0.12
29 7 0.03
30 12 0.06
31 4 0.02
32 25 0.12
33 45 0.21
34 18 0.08
35 9 0.04
36 9 0.04
37 7 0.03
38 13 0.06
39 1 0.00
40 5 0.02
41 14 0.07
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (33 bp):
CGACCTCAGACAGGTCTTTCTCAATTTCAATAT
Found at i:8394 original size:27 final size:27
Alignment explanation
Indices: 8364--8459 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
8354 CTGGTCCTAT
8364 TCAATTTCAGACCTCAAACATTCTTTC
1 TCAATTTCAGACCTCAAACATTCTTTC
* * *
8391 TCAATTTCAATATTGACCGCAGAC-TGGTCCTAT-
1 TCAATTTC---A--GACCTCAAACAT--T-CTTTC
8424 TCAATTTCAGACCTCAAACATTCTTTC
1 TCAATTTCAGACCTCAAACATTCTTTC
8451 TCAATTTCA
1 TCAATTTCA
8460 ATATCGACCA
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
26 3 0.06
27 18 0.34
28 8 0.15
29 1 0.02
30 2 0.04
31 1 0.02
32 8 0.15
33 9 0.17
34 3 0.06
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.36
Consensus pattern (27 bp):
TCAATTTCAGACCTCAAACATTCTTTC
Found at i:8401 original size:60 final size:60
Alignment explanation
Indices: 8307--8499 Score: 314
Period size: 60 Copynumber: 3.2 Consensus size: 60
8297 AGATATTTAG
* * *
8307 TTTCAGGCCTCAAATAGGTCTTTCTCAATTTCAATATTGACCGCAGACTGGTCCTATTCAA
1 TTTCAGACCTCAAACA-TTCTTTCTCAATTTCAATATTGACCGCAGACTGGTCCTATTCAA
8368 TTTCAGACCTCAAACATTCTTTCTCAATTTCAATATTGACCGCAGACTGGTCCTATTCAA
1 TTTCAGACCTCAAACATTCTTTCTCAATTTCAATATTGACCGCAGACTGGTCCTATTCAA
* * * *
8428 TTTCAGACCTCAAACATTCTTTCTCAATTTCAATATCGACCACAGATTGGTCCTATCCAA
1 TTTCAGACCTCAAACATTCTTTCTCAATTTCAATATTGACCGCAGACTGGTCCTATTCAA
8488 TTTCAGACCTCA
1 TTTCAGACCTCA
8500 GACGGGTCAT
Statistics
Matches: 125, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
60 111 0.89
61 14 0.11
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (60 bp):
TTTCAGACCTCAAACATTCTTTCTCAATTTCAATATTGACCGCAGACTGGTCCTATTCAA
Found at i:8942 original size:27 final size:27
Alignment explanation
Indices: 8889--8943 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
8879 TAAGTCGCAT
*
8889 AGGGGCATTTTGGTCAATTTCACGTTC
1 AGGGGCATTTTGGTCAATTTCAAGTTC
* *
8916 AGGGGCATTTTGGTCATTTTTAAGTTC
1 AGGGGCATTTTGGTCAATTTCAAGTTC
8943 A
1 A
8944 CTTTTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGGTCAATTTCAAGTTC
Done.