Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013768.1 Corchorus capsularis cultivar CVL-1 contig13789, 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: 28875
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Found at i:114 original size:45 final size:46
Alignment explanation
Indices: 62--166 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 46
52 GGAAGAAGAA
*
62 AAGGAAAAAATTTAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
1 AAGGAAAAAATTGAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
* *
108 AA-GAAAAGGAA--GAAGAAAAGAAATTGATAAAAGCAGAAAACGGAG
1 AAGGAAAA--AATTGAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
153 AAGGAAAGAAATTG
1 AAGGAAA-AAATTG
167 GGGAAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
45 40 0.80
46 6 0.12
47 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.23, T:0.10
Consensus pattern (46 bp):
AAGGAAAAAATTGAAGAAAAGAAATTGATAAAAACAGAAAACAGAG
Found at i:147 original size:21 final size:21
Alignment explanation
Indices: 76--147 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
66 AAAAAATTTA
*
76 AGAAAAGAAATTGATAAAAAC
1 AGAAAAGAAATTGATAAAAGC
* *
97 AGAAAACAGAGAA--GAAAAGGAAGA
1 AG-AAA-AGA-AATTGATAA--AAGC
121 AGAAAAGAAATTGATAAAAGC
1 AGAAAAGAAATTGATAAAAGC
142 AGAAAA
1 AGAAAA
148 CGGAGAAGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
21 13 0.33
22 10 0.26
23 10 0.26
24 6 0.15
ACGTcount: A:0.67, C:0.04, G:0.21, T:0.08
Consensus pattern (21 bp):
AGAAAAGAAATTGATAAAAGC
Found at i:1189 original size:180 final size:180
Alignment explanation
Indices: 887--1248 Score: 724
Period size: 180 Copynumber: 2.0 Consensus size: 180
877 AAATGCTATG
887 ATCGCAAACCCTCTCATAACCTTGAATTTATAACAAAGTCAAGGATAAAGGAAAGATTCCTAATT
1 ATCGCAAACCCTCTCATAACCTTGAATTTATAACAAAGTCAAGGATAAAGGAAAGATTCCTAATT
952 CATATTTGGAACTTGTTGGTTAATCTAATATCTCTTAATCCAGGACCTTTTTATAAGAATTATAG
66 CATATTTGGAACTTGTTGGTTAATCTAATATCTCTTAATCCAGGACCTTTTTATAAGAATTATAG
1017 TGAAGACATCATTGTTTATTAGGAATATACAAACAAATGAAAATTAAAAA
131 TGAAGACATCATTGTTTATTAGGAATATACAAACAAATGAAAATTAAAAA
1067 ATCGCAAACCCTCTCATAACCTTGAATTTATAACAAAGTCAAGGATAAAGGAAAGATTCCTAATT
1 ATCGCAAACCCTCTCATAACCTTGAATTTATAACAAAGTCAAGGATAAAGGAAAGATTCCTAATT
1132 CATATTTGGAACTTGTTGGTTAATCTAATATCTCTTAATCCAGGACCTTTTTATAAGAATTATAG
66 CATATTTGGAACTTGTTGGTTAATCTAATATCTCTTAATCCAGGACCTTTTTATAAGAATTATAG
1197 TGAAGACATCATTGTTTATTAGGAATATACAAACAAATGAAAATTAAAAA
131 TGAAGACATCATTGTTTATTAGGAATATACAAACAAATGAAAATTAAAAA
1247 AT
1 AT
1249 AAATGAAAAT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (180 bp):
ATCGCAAACCCTCTCATAACCTTGAATTTATAACAAAGTCAAGGATAAAGGAAAGATTCCTAATT
CATATTTGGAACTTGTTGGTTAATCTAATATCTCTTAATCCAGGACCTTTTTATAAGAATTATAG
TGAAGACATCATTGTTTATTAGGAATATACAAACAAATGAAAATTAAAAA
Found at i:2086 original size:12 final size:11
Alignment explanation
Indices: 2069--2121 Score: 70
Period size: 12 Copynumber: 4.5 Consensus size: 11
2059 ACTATCGTTA
2069 TTGTCATCCTGC
1 TTGTCATCCT-C
2081 TTGTCATCCTC
1 TTGTCATCCTC
2092 TTGGTCATCCTC
1 TT-GTCATCCTC
2104 TTTGTCATCCTCC
1 -TTGTCATCCT-C
2117 TTGTC
1 TTGTC
2122 CTTCTTGATC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.08
12 32 0.84
13 3 0.08
ACGTcount: A:0.08, C:0.34, G:0.13, T:0.45
Consensus pattern (11 bp):
TTGTCATCCTC
Found at i:3037 original size:11 final size:11
Alignment explanation
Indices: 3021--3066 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
3011 CCGTAGCAAC
*
3021 TTGCTACGAGT
1 TTGCTACGAAT
*
3032 TTGCTATGAAT
1 TTGCTACGAAT
3043 TTGCTACGAAT
1 TTGCTACGAAT
*
3054 TTGCTACGCAT
1 TTGCTACGAAT
3065 TT
1 TT
3067 TGCAATTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (11 bp):
TTGCTACGAAT
Found at i:6256 original size:11 final size:11
Alignment explanation
Indices: 6240--6290 Score: 102
Period size: 11 Copynumber: 4.6 Consensus size: 11
6230 TTGACATTTA
6240 GCTACGGACCT
1 GCTACGGACCT
6251 GCTACGGACCT
1 GCTACGGACCT
6262 GCTACGGACCT
1 GCTACGGACCT
6273 GCTACGGACCT
1 GCTACGGACCT
6284 GCTACGG
1 GCTACGG
6291 CTACGGAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (11 bp):
GCTACGGACCT
Found at i:8756 original size:22 final size:21
Alignment explanation
Indices: 8702--8755 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
8692 TTCGTATGAG
8702 GGTTATCAAAATTTCATAGTCAA
1 GGTTAT-AAAATTTCATAG-CAA
8725 -GTTACTAAAATTTCATAAG-AA
1 GGTTA-TAAAATTTCAT-AGCAA
8746 GGTTATAAAA
1 GGTTATAAAA
8756 ACTCAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 7 0.25
22 18 0.64
23 3 0.11
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGCAA
Found at i:8934 original size:22 final size:21
Alignment explanation
Indices: 8909--9034 Score: 81
Period size: 22 Copynumber: 5.7 Consensus size: 21
8899 CTGTGGAGTA
*
8909 ATCAAAATTTCATAGGGAAGAT
1 ATCAAAATTTCATA-GGAAGTT
* * *
8931 ATCAACATTTTATATGAAGGTT
1 ATCAAAATTTCATAGGAA-GTT
*
8953 ATCAAAATTTTAATAAGGAAGTT
1 ATCAAAA-TTTCAT-AGGAAGTT
* **
8976 ATCAAAATTTCACAGTTTAGTT
1 ATCAAAATTTCATAG-GAAGTT
* * * *
8998 TTTAAGATTTCATAGGAGGGTT
1 ATCAAAATTTCATAGGA-AGTT
*
9020 ATCAAAAATTCATAG
1 ATCAAAATTTCATAG
9035 TGTGCCTCAA
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
21 5 0.06
22 53 0.69
23 15 0.19
24 4 0.05
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAAGTT
Found at i:8979 original size:23 final size:22
Alignment explanation
Indices: 8909--8985 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
8899 CTGTGGAGTA
* * *
8909 ATCAAAATTTCATAGGGAAGAT
1 ATCAAAATTTTATAAGGAAGTT
* *
8931 ATCAACATTTTAT-ATGAAGGTT
1 ATCAAAATTTTATAAGGAA-GTT
8953 ATCAAAATTTTAATAAGGAAGTT
1 ATCAAAATTTT-ATAAGGAAGTT
8976 ATCAAAATTT
1 ATCAAAATTT
8986 CACAGTTTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.07
22 23 0.51
23 15 0.33
24 4 0.09
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTTATAAGGAAGTT
Found at i:13986 original size:49 final size:50
Alignment explanation
Indices: 13867--14220 Score: 402
Period size: 50 Copynumber: 7.2 Consensus size: 50
13857 TTTTACCTGC
*
13867 ATACCCTTCCCGGGCGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
*
13917 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTATTTTCC-AAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
*
13966 ATACCCTTCCCGGGTTGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
* *
14016 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTACTATTTTCCAAAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
** ** * * *
14066 ACGCCCTTCCCGGACGGAAGGCACTGA-TTTT---TGCCTTTTTTCCTAAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTG-CTTTTTTCCAAAA
** * * * *
14113 ACGCCCTTCCCGGATGGAAGGCA-CTAATCTTTACCTG--TTTTTCCCAAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACT-TTTACCTGCTTTTTTCCAAAA
* * ** * *
14161 ATGCCCTTCCAGGACGGAAGGCACTTA-TTTTACTTGCTTTTTTCCAAAA
1 ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
*
14210 ATGCCCTTCCC
1 ATACCCTTCCC
14221 AGACGAAAGA
Statistics
Matches: 267, Mismatches: 27, Indels: 21
0.85 0.09 0.07
Matches are distributed among these distances:
46 2 0.01
47 41 0.15
48 34 0.13
49 73 0.27
50 115 0.43
51 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (50 bp):
ATACCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAA
Found at i:13990 original size:99 final size:98
Alignment explanation
Indices: 13867--14220 Score: 434
Period size: 99 Copynumber: 3.6 Consensus size: 98
13857 TTTTACCTGC
* *
13867 ATACCCTTCCCGGGCGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGT
1 ATACCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGT
13932 GGAAGGCATTTACTTTTACCTGCTATTTTCCAAA
65 GGAAGGCATTTACTTTTACCTGCTATTTTCCAAA
*** *
13966 ATACCCTTCCCGGGTTGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGT
1 ATACCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGT
*
14031 GGAAGGCATTTACTTTTACCTACTATTTTCCAAA
65 GGAAGGCATTTACTTTTACCTGCTATTTTCCAAA
* * **
14065 A-ACGCCCTTCCCGGACGGAAGGCACTGATTTT---TGCCTTTTTTCCTAAAACGCCCTTCCCGG
1 ATA--CCCTTCCCGGACGGAAGGCACTTATTTTACCTG-CTTTTTTCCAAAAATACCCTTCCCGG
* * *
14126 ATGGAAGGCA-CTAATCTTTACCTG-T-TTTTCCCAAA
63 GTGGAAGGCATTTACT-TTTACCTGCTATTTT-CCAAA
* * * *
14161 ATGCCCTTCCAGGACGGAAGGCACTTATTTTACTTGCTTTTTTCCAAAAATGCCCTTCCC
1 ATACCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTTTTTTCCAAAAATACCCTTCCC
14221 AGACGAAAGA
Statistics
Matches: 226, Mismatches: 20, Indels: 20
0.85 0.08 0.08
Matches are distributed among these distances:
95 30 0.13
96 12 0.05
97 61 0.27
98 3 0.01
99 101 0.45
100 19 0.08
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (98 bp):
ATACCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGTG
GAAGGCATTTACTTTTACCTGCTATTTTCCAAA
Found at i:14237 original size:49 final size:49
Alignment explanation
Indices: 13870--14378 Score: 410
Period size: 49 Copynumber: 10.4 Consensus size: 49
13860 TACCTGCATA
* * *
13870 CCCTTCCCGGGCGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAAATA
1 CCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATG
** * * *
13920 CCCTTCCCGGGTGGAAGGCATTTACTTTTACCTGCTATTTTCC-AAAATA
1 CCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATG
*** * *
13969 CCCTTCCCGGGTTGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAAATA
1 CCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATG
** * * * *
14019 CCCTTCCCGGGTGGAAGGCATTTACTTTTACCTACTATTTTCCAAAAACG
1 CCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATG
* * *
14069 CCCTTCCCGGACGGAAGGCACTGATTTT---TGCCTTTTTTCCTAAAACG
1 CCCTTCCCGGACGGAAGGCACTTATTTTACCTG-CTTTTTTCCAAAAATG
* * *
14116 CCCTTCCCGGATGGAAGGCACTAATCTTTACCTG--TTTTTCCCAAAATG
1 CCCTTCCCGGACGGAAGGCACTTAT-TTTACCTGCTTTTTTCCAAAAATG
* *
14164 CCCTTCCAGGACGGAAGGCACTTATTTTACTTGCTTTTTTCCAAAAATG
1 CCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTTTTTTCCAAAAATG
* * * * ** * *
14213 CCCTTCCCAGACGAAAGACGCTTATTTTAACCCAC-TTTTTCCCAAAGTG
1 CCCTTCCCGGACGGAAGGCACTTATTTT-ACCTGCTTTTTTCCAAAAATG
* * * ** * * *
14262 CCCTTCCCGTACGGAAGTCACTAACTTTTAGTTGC-TTTTTCCTAACACG
1 CCCTTCCCGGACGGAAGGCACTTA-TTTTACCTGCTTTTTTCCAAAAATG
* * **
14311 CCCTTCCCGGACGGAAGGC-GTTAGTTTT-GCTCGCTTTTTT-TTAAAATG
1 CCCTTCCCGGACGGAAGGCACTTA-TTTTACCT-GCTTTTTTCCAAAAATG
* *
14359 CCCTTTCCGGACGAAAGGCA
1 CCCTTCCCGGACGGAAGGCA
14379 AGTTCACTTT
Statistics
Matches: 386, Mismatches: 60, Indels: 27
0.82 0.13 0.06
Matches are distributed among these distances:
46 1 0.00
47 46 0.12
48 67 0.17
49 151 0.39
50 119 0.31
51 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (49 bp):
CCCTTCCCGGACGGAAGGCACTTATTTTACCTGCTTTTTTCCAAAAATG
Found at i:14350 original size:98 final size:95
Alignment explanation
Indices: 13870--14378 Score: 282
Period size: 99 Copynumber: 5.2 Consensus size: 95
13860 TACCTGCATA
* * * * * * ** **
13870 CCCTTCCCGGGCGGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGTGGA
1 CCCTTCCAGGACGGAAGGCA-CTAATTTTACTTGCTTTTTTCCTAAAACGCCCTTCCCGGACGGA
* *
13935 AGGCATTTACTTTT-ACCTGCTATTTT-CCAAAATA
65 AGGC-GTTA-TTTTCACCT--T-TTTTCCCAAAATG
* *** * * * * ** **
13969 CCCTTCCCGGGTTGAAGGCATTTACTTTTACCTGCTTTTTTCCAAAAATACCCTTCCCGGGTGGA
1 CCCTTCCAGGACGGAAGGCA-CTAATTTTACTTGCTTTTTTCCTAAAACGCCCTTCCCGGACGGA
* * *
14034 AGGCATTTACTTTT-ACCTACTATTTTCCAAAAACG
65 AGGC-GTTA-TTTTCACCT--T-TTTTCCCAAAATG
* * *
14069 CCCTTCCCGGACGGAAGGCACTGA-TTT--TTGCCTTTTTTCCTAAAACGCCCTTCCCGGATGGA
1 CCCTTCCAGGACGGAAGGCACTAATTTTACTTG-CTTTTTTCCTAAAACGCCCTTCCCGGACGGA
* *
14131 AGGCACTAATCTTT-ACCTGTTTTTCCCAAAATG
65 AGGC-GTTAT-TTTCACCT-TTTTTCCCAAAATG
* * * * *
14164 CCCTTCCAGGACGGAAGGCACTTATTTTACTTGCTTTTTTCCAAAAATGCCCTTCCCAGACGAAA
1 CCCTTCCAGGACGGAAGGCACTAATTTTACTTGCTTTTTTCCTAAAACGCCCTTCCCGGACGGAA
* * * *
14229 GACGCTTATTTTAACCCACTTTTTCCCAAAGTG
66 GGCG-TTATTTTCA-CC-TTTTTTCCCAAAATG
* * * * *
14262 CCCTTCCCGTACGGAAGTCACTAACTTTTAGTTGC-TTTTTCCTAACACGCCCTTCCCGGACGGA
1 CCCTTCCAGGACGGAAGGCACTAA-TTTTACTTGCTTTTTTCCTAAAACGCCCTTCCCGGACGGA
* **
14326 AGGCGTTAGTTTTGCTCGCTTTTTT-TTAAAATG
65 AGGCGTTA-TTTT-CAC-CTTTTTTCCCAAAATG
*
14359 CCCTTTCC-GGACGAAAGGCA
1 CCC-TTCCAGGACGGAAGGCA
14379 AGTTCACTTT
Statistics
Matches: 341, Mismatches: 54, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
95 33 0.10
96 10 0.03
97 94 0.28
98 83 0.24
99 99 0.29
100 22 0.06
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (95 bp):
CCCTTCCAGGACGGAAGGCACTAATTTTACTTGCTTTTTTCCTAAAACGCCCTTCCCGGACGGAA
GGCGTTATTTTCACCTTTTTTCCCAAAATG
Done.