Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012333.1 Corchorus capsularis cultivar CVL-1 contig12354, 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: 62271
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:3774 original size:132 final size:134
Alignment explanation
Indices: 3578--3827 Score: 416
Period size: 132 Copynumber: 1.9 Consensus size: 134
3568 AAGATTCTAA
* *
3578 TATATCTAAGTTTTTTTTTAATTAATTAGTAAATAAAATGGTAAAAATAAATAATTATAAGGATA
1 TATACCTAAGTTTTTTTTTAATTAA-TAATAAATAAAATGGTAAAAATAAATAATTATAAGGATA
* *
3643 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTTAAACTGTAAAAGTATTTAAAAATTT
65 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTAAAACTATAAAAGTATTTAAAAATTT
3708 TGGAC
130 TGGAC
*
3713 TATACCTAAG-TTTTTTTTAATTAA-AAT-AGTAAAATGGTAAAAATAAAATAATTATAAGGATA
1 TATACCTAAGTTTTTTTTTAATTAATAATAAATAAAATGGTAAAAAT-AAATAATTATAAGGATA
3775 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTAAAACTATAAAAGT
65 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTAAAACTATAAAAGT
3828 TTAAACAGTG
Statistics
Matches: 109, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
131 16 0.15
132 70 0.64
134 14 0.13
135 9 0.08
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (134 bp):
TATACCTAAGTTTTTTTTTAATTAATAATAAATAAAATGGTAAAAATAAATAATTATAAGGATAT
TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTAAAACTATAAAAGTATTTAAAAATTTT
GGAC
Found at i:3920 original size:4 final size:4
Alignment explanation
Indices: 3911--3942 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
3901 TCGTACTTTT
3911 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
3943 GGATTGCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:8181 original size:15 final size:15
Alignment explanation
Indices: 8157--8215 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
8147 TGCTAGGGTG
*
8157 AATGGCGCAAACAAC
1 AATGGTGCAAACAAC
*
8172 AATGGTGCAAACCAC
1 AATGGTGCAAACAAC
* *
8187 AATGGTACGAACAAC
1 AATGGTGCAAACAAC
* *
8202 CATGGTGCGAACAA
1 AATGGTGCAAACAA
8216 TCATGTTGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:14259 original size:10 final size:10
Alignment explanation
Indices: 14244--14268 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14234 GTTGCTGCTC
14244 AATTCCAGAA
1 AATTCCAGAA
14254 AATTCCAGAA
1 AATTCCAGAA
14264 AATTC
1 AATTC
14269 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:15082 original size:13 final size:13
Alignment explanation
Indices: 15064--15098 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
15054 ATAATTATTG
15064 TTTGCTTTATTAA
1 TTTGCTTTATTAA
15077 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
15090 TCTGCTTTA
1 TTTGCTTTA
15099 GATTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:15169 original size:13 final size:13
Alignment explanation
Indices: 15153--15182 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
15143 AATTGTTTTC
15153 TTTATAATTGTTA
1 TTTATAATTGTTA
15166 TTTATAATTGTTA
1 TTTATAATTGTTA
15179 TTTA
1 TTTA
15183 CACTCCCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTATAATTGTTA
Found at i:22243 original size:22 final size:22
Alignment explanation
Indices: 22201--22246 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
22191 AGGCAACGCT
*
22201 TGGAGGCAAGTGATGAAGTCGA
1 TGGAGGCAAGTGAAGAAGTCGA
*
22223 TGGAGGCAGAG-GAAGATGTCGA
1 TGGAGGCA-AGTGAAGAAGTCGA
22245 TG
1 TG
22247 TCGATAGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.30, C:0.09, G:0.43, T:0.17
Consensus pattern (22 bp):
TGGAGGCAAGTGAAGAAGTCGA
Found at i:33494 original size:59 final size:58
Alignment explanation
Indices: 33298--33508 Score: 284
Period size: 57 Copynumber: 3.6 Consensus size: 58
33288 GTCCAAAATC
* * * * *
33298 TCCCTTGAAGTATCACAA-AAAGAACATTTTGCTCCCTAATCTTTTTTTTCCAACTTTG
1 TCCCCTGAAGTATGA-AATAAAGGACACTTTGCCCCCTAATCTTTTTTTTCCAACTTTG
* *
33356 CCCCCTGAAATATGAAATAAAGGACACTTTGCCCCCTAATC-TTTTTTTCCAACTTT-
1 TCCCCTGAAGTATGAAATAAAGGACACTTTGCCCCCTAATCTTTTTTTTCCAACTTTG
* * *
33412 ACCTCCTGAAGTATGAAACAAAGGACACTTTGCCCCCTAATCTTTTTTTTTTCAACTTTG
1 TCC-CCTGAAGTATGAAATAAAGGACACTTTGCCCCCTAATC-TTTTTTTTCCAACTTTG
33472 TCCCCTGAAGTATGAAATAAAGGACACTTTGCCCCCT
1 TCCCCTGAAGTATGAAATAAAGGACACTTTGCCCCCT
33509 GCCGTAACAG
Statistics
Matches: 135, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
56 2 0.01
57 53 0.39
58 31 0.23
59 47 0.35
60 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.35
Consensus pattern (58 bp):
TCCCCTGAAGTATGAAATAAAGGACACTTTGCCCCCTAATCTTTTTTTTCCAACTTTG
Found at i:37766 original size:30 final size:29
Alignment explanation
Indices: 37699--37767 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
37689 GGGTCTAACT
**
37699 ATATAATTAAAATTTATTTTTTTTGGTTA
1 ATATAATTAAAATTTATTTAATTTGGTTA
*
37728 AAATAATTAAAATTTA-TTAATTTGGAATTA
1 ATATAATTAAAATTTATTTAATTTGG--TTA
*
37758 GTATAATTAA
1 ATATAATTAA
37768 CTATTCATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 7 0.21
29 15 0.45
30 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.49
Consensus pattern (29 bp):
ATATAATTAAAATTTATTTAATTTGGTTA
Found at i:50374 original size:23 final size:23
Alignment explanation
Indices: 50346--50417 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
50336 GACAATAGAC
50346 AAAGCTCTCACAAAGGAGTCCCA
1 AAAGCTCTCACAAAGGAGTCCCA
*
50369 AAAGCTCTCACAAAGGAATCCCA
1 AAAGCTCTCACAAAGGAGTCCCA
* * *
50392 AAAACTCTCACAAAGAAGTCCAA
1 AAAGCTCTCACAAAGGAGTCCCA
50415 AAA
1 AAA
50418 AAAAAAAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAGCTCTCACAAAGGAGTCCCA
Found at i:50684 original size:17 final size:17
Alignment explanation
Indices: 50655--50687 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50645 CAGTCATCAA
50655 ATATTATATATAATTAT
1 ATATTATATATAATTAT
50672 ATATGTATA-ATAATTA
1 ATAT-TATATATAATTA
50688 GTGGTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATATTATATATAATTAT
Found at i:53963 original size:21 final size:21
Alignment explanation
Indices: 53939--53978 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53929 GATATTAACG
*
53939 CAACAGCTAAAATCAAGGAGA
1 CAACAACTAAAATCAAGGAGA
53960 CAACAACTAAAATCAAGGA
1 CAACAACTAAAATCAAGGA
53979 AATAACAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (21 bp):
CAACAACTAAAATCAAGGAGA
Found at i:53985 original size:21 final size:21
Alignment explanation
Indices: 53939--53985 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
53929 GATATTAACG
* *
53939 CAACAGCTAAAATCAAGGAGA
1 CAACAACTAAAATCAAGGAAA
53960 CAACAACTAAAATCAAGGAAA
1 CAACAACTAAAATCAAGGAAA
*
53981 TAACA
1 CAACA
53986 GTTAGCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.19, G:0.13, T:0.11
Consensus pattern (21 bp):
CAACAACTAAAATCAAGGAAA
Found at i:59715 original size:21 final size:21
Alignment explanation
Indices: 59691--59730 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
59681 GACTGTTACT
59691 TCCTTGATTTTAGCTGTTGTC
1 TCCTTGATTTTAGCTGTTGTC
59712 TCCTTGATTTTAGCTGTTG
1 TCCTTGATTTTAGCTGTTG
59731 CGTTAATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (21 bp):
TCCTTGATTTTAGCTGTTGTC
Found at i:60848 original size:26 final size:26
Alignment explanation
Indices: 60784--60840 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
60774 ATGAAACCTG
*
60784 AAATTTT-TAAGAATGTAGTGTTTCT
1 AAATTTTCTAAGAATGTAGTGTTACT
60809 AAATTTTCTAAGAATGTGAG-GTTACT
1 AAATTTTCTAAGAATGT-AGTGTTACT
60835 AAATTT
1 AAATTT
60841 ATGTAGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.24
26 20 0.69
27 2 0.07
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (26 bp):
AAATTTTCTAAGAATGTAGTGTTACT
Found at i:61932 original size:27 final size:25
Alignment explanation
Indices: 61897--61946 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
61887 TATAATTAAG
61897 TAATAGATAACTATAAAAAAATAAAAA
1 TAATAGATAA--ATAAAAAAATAAAAA
*
61924 TAATAGATAAATAAAAAGATAAA
1 TAATAGATAAATAAAAAAATAAA
61947 TAAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
27 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (25 bp):
TAATAGATAAATAAAAAAATAAAAA
Found at i:61945 original size:12 final size:12
Alignment explanation
Indices: 61909--61973 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
61899 ATAGATAACT
*
61909 ATAAAAAAATAA
1 ATAAAAAGATAA
61921 A-AATAATAGATAA
1 ATAA-AA-AGATAA
61934 ATAAAAAGATAA
1 ATAAAAAGATAA
* * *
61946 ATAAATATATAT
1 ATAAAAAGATAA
*
61958 ATATAAAGATAA
1 ATAAAAAGATAA
61970 ATAA
1 ATAA
61974 GTATGTAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
11 2 0.05
12 29 0.71
13 8 0.20
14 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.25
Consensus pattern (12 bp):
ATAAAAAGATAA
Found at i:61952 original size:24 final size:24
Alignment explanation
Indices: 61898--61973 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
61888 ATAATTAAGT
* *
61898 AATAGATAACTATAAAAAAATAAAAA
1 AATAGATAA--ATAAAAAGATAAATA
61924 TAATAGATAAATAAAAAGATAAATA
1 -AATAGATAAATAAAAAGATAAATA
* * *
61949 AATATATATATATAAAGATAAATA
1 AATAGATAAATAAAAAGATAAATA
61973 A
1 A
61974 GTATGTAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
24 22 0.50
25 13 0.30
27 9 0.20
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.25
Consensus pattern (24 bp):
AATAGATAAATAAAAAGATAAATA
Found at i:61973 original size:36 final size:35
Alignment explanation
Indices: 61923--62010 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 35
61913 AAAAATAAAA
*
61923 ATAATAGATAAATAAAAAGATAAATAAATATATATAT
1 ATAA-AGATAAATAAAAAG-TAAACAAATATATATAT
* *
61960 ATAAAGATAAATAAGTATGTAAACAAATATATATAT
1 ATAAAGATAAATAA-AAAGTAAACAAATATATATAT
* *
61996 ATATATATAAATAAA
1 ATAAAGATAAATAAA
62011 TAATAGCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
36 38 0.86
37 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (35 bp):
ATAAAGATAAATAAAAAGTAAACAAATATATATAT
Found at i:62084 original size:17 final size:17
Alignment explanation
Indices: 62062--62101 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
62052 AGATAGATAA
*
62062 ATAATAGTATTAAATAG
1 ATAATAGTACTAAATAG
62079 ATAATAGTACTAAATAG
1 ATAATAGTACTAAATAG
62096 ATAATA
1 ATAATA
62102 ATAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (17 bp):
ATAATAGTACTAAATAG
Found at i:62104 original size:27 final size:27
Alignment explanation
Indices: 62074--62126 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
62064 AATAGTATTA
*
62074 AATAGATAATAG-TACTAAATAGATAAT
1 AATAAATAATAGTTAC-AAATAGATAAT
62101 AATAAATAATAGTTACAAATAGATAA
1 AATAAATAATAGTTACAAATAGATAA
62127 GAAAATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (27 bp):
AATAAATAATAGTTACAAATAGATAAT
Found at i:62150 original size:44 final size:45
Alignment explanation
Indices: 62054--62150 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
62044 AAAATAAAAG
* * * *
62054 ATAGATAAATAATAGTATTAAATAGATAATAGTACTAAATAGATA
1 ATAGATAAATAATAGTATCAAATAGATAAGAGAAATAAATAGATA
*
62099 ATA-ATAAATAATAGT-TACAAATAGATAAGA-AAATGAATAG-TAA
1 ATAGATAAATAATAGTAT-CAAATAGATAAGAGAAATAAATAGAT-A
62142 ATAGATAAA
1 ATAGATAAA
62151 ACAAAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.02
43 12 0.27
44 28 0.64
45 3 0.07
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (45 bp):
ATAGATAAATAATAGTATCAAATAGATAAGAGAAATAAATAGATA
Done.