Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022416.1 Corchorus olitorius cultivar O-4 contig22449, 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: 80817
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2745 original size:24 final size:26
Alignment explanation
Indices: 2706--2761 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
2696 TTTAATGACA
2706 AAAAAAGCATTATATATATGAAAAAT
1 AAAAAAGCATTATATATATGAAAAAT
2732 AAAAAAGCATTATATATATGAAAAAT
1 AAAAAAGCATTATATATATGAAAAAT
2758 AAAA
1 AAAA
2762 GGAGTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAAAAGCATTATATATATGAAAAAT
Found at i:2762 original size:24 final size:24
Alignment explanation
Indices: 2700--2762 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 24
2690 CGGAGGTTTA
*
2700 ATGACAAA-AAAAGCATTATATAT
1 ATGAAAAATAAAAGCATTATATAT
2723 ATGAAAAATAAAAAAGCATTATATAT
1 ATGAAAAAT--AAAAGCATTATATAT
2749 ATGAAAAATAAAAG
1 ATGAAAAATAAAAG
2763 GAGTTTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 7 0.19
24 5 0.14
26 24 0.67
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (24 bp):
ATGAAAAATAAAAGCATTATATAT
Found at i:13112 original size:2 final size:2
Alignment explanation
Indices: 13105--13151 Score: 60
Period size: 2 Copynumber: 22.5 Consensus size: 2
13095 TAGTATGTGA
13105 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AGT AT -T AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT A-T
13149 AT A
1 AT A
13152 ATGTTTGGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 1 0.02
2 34 0.83
3 6 0.15
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14403 original size:31 final size:31
Alignment explanation
Indices: 14363--14422 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
14353 AAATTATTAG
* *
14363 GGGGTCAATACTATAAAACTTTCATTTTAAA
1 GGGGCCAATACAATAAAACTTTCATTTTAAA
*
14394 GGGGCCAATACAATAAATCTTTCATTTTA
1 GGGGCCAATACAATAAAACTTTCATTTTA
14423 GTGAGATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (31 bp):
GGGGCCAATACAATAAAACTTTCATTTTAAA
Found at i:17164 original size:20 final size:18
Alignment explanation
Indices: 17128--17166 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
17118 CTTAGTTAAC
*
17128 TTGACACGCCTTATTTTT
1 TTGACACACCTTATTTTT
*
17146 TTGACACACCTTACTTTT
1 TTGACACACCTTATTTTT
17164 TTG
1 TTG
17167 TAATCTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (18 bp):
TTGACACACCTTATTTTT
Found at i:18212 original size:14 final size:14
Alignment explanation
Indices: 18179--18222 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
18169 TCTTGAAAGC
18179 AAAAAAAAAAAA-A
1 AAAAAAAAAAAACA
18192 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
* * *
18206 TACAAAAATAAACA
1 AAAAAAAAAAAACA
18220 AAA
1 AAA
18223 CCGAGTGGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.89, C:0.07, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:18213 original size:1 final size:1
Alignment explanation
Indices: 18179--18203 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
18169 TCTTGAAAGC
18179 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
18204 CATACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22111 original size:12 final size:12
Alignment explanation
Indices: 22094--22126 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
22084 TACTACTTCC
22094 TCTTCACGATCA
1 TCTTCACGATCA
22106 TCTTCACGATCA
1 TCTTCACGATCA
22118 TCTTCACGA
1 TCTTCACGA
22127 ACCCAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (12 bp):
TCTTCACGATCA
Found at i:28780 original size:25 final size:25
Alignment explanation
Indices: 28752--28800 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28742 TCGAACATGA
28752 AGCTTGTAAAAAAAAAATAACAGGG
1 AGCTTGTAAAAAAAAAATAACAGGG
28777 AGCTTGTAAAAAAAAAATAACAGG
1 AGCTTGTAAAAAAAAAATAACAGG
28801 ATCAATTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.16
Consensus pattern (25 bp):
AGCTTGTAAAAAAAAAATAACAGGG
Found at i:35894 original size:64 final size:64
Alignment explanation
Indices: 35793--35915 Score: 246
Period size: 64 Copynumber: 1.9 Consensus size: 64
35783 AATTGGCACG
35793 ATTAAATCTCCTATTCTCAATTTTGGATCAATTTAGTCCCTTATTGGATGGACGTTAGTTGCCA
1 ATTAAATCTCCTATTCTCAATTTTGGATCAATTTAGTCCCTTATTGGATGGACGTTAGTTGCCA
35857 ATTAAATCTCCTATTCTCAATTTTGGATCAATTTAGTCCCTTATTGGATGGACGTTAGT
1 ATTAAATCTCCTATTCTCAATTTTGGATCAATTTAGTCCCTTATTGGATGGACGTTAGT
35916 AACGTGAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (64 bp):
ATTAAATCTCCTATTCTCAATTTTGGATCAATTTAGTCCCTTATTGGATGGACGTTAGTTGCCA
Found at i:52929 original size:13 final size:13
Alignment explanation
Indices: 52911--52937 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52901 GGGGGGAGGA
52911 CAGGACCAATGTG
1 CAGGACCAATGTG
52924 CAGGACCAATGTG
1 CAGGACCAATGTG
52937 C
1 C
52938 TGATTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (13 bp):
CAGGACCAATGTG
Found at i:58191 original size:21 final size:21
Alignment explanation
Indices: 58165--58205 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
58155 GGAACTCCTC
58165 TTCTTCCCATGTTTGCCTTTG
1 TTCTTCCCATGTTTGCCTTTG
*
58186 TTCTTCCCATGTTTGTCTTT
1 TTCTTCCCATGTTTGCCTTT
58206 CTTCATGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.27, G:0.12, T:0.56
Consensus pattern (21 bp):
TTCTTCCCATGTTTGCCTTTG
Found at i:58313 original size:51 final size:50
Alignment explanation
Indices: 58232--58381 Score: 246
Period size: 51 Copynumber: 2.9 Consensus size: 50
58222 GCCGCTGGAA
* *
58232 CAGGGGGTTGCGGAACAGGCTTTTCAAACTTTTTCCTGAACTTGTACGTTC
1 CAGGAGGTTGCGGAAAAGGCTTTTCAAACTTTTTCC-GAACTTGTACGTTC
58283 CAGGAGGTTGCGGAAAAGGCTTTTCAAACTTTTCTCCGAACTTGTACGTTC
1 CAGGAGGTTGCGGAAAAGGCTTTTCAAACTTTT-TCCGAACTTGTACGTTC
*
58334 CAGGAGGTTGCGGAAAAGGCTTTTCAAACTTTTCCCCGAACTTGTACG
1 CAGGAGGTTGCGGAAAAGGCTTTTCAAACTTTT-TCCGAACTTGTACG
58382 AGAAATTCAG
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
51 92 0.97
52 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (50 bp):
CAGGAGGTTGCGGAAAAGGCTTTTCAAACTTTTTCCGAACTTGTACGTTC
Found at i:71579 original size:48 final size:48
Alignment explanation
Indices: 71518--71669 Score: 223
Period size: 48 Copynumber: 3.1 Consensus size: 48
71508 GTCTTCTCCT
* * *
71518 CCGCCTTCGACCACTTCCACAGCCCCCAGTCCACCTAAATCATCACCG
1 CCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCACCG
* *
71566 CCGCCTTCAACCACTTCCTCATCCCCAAGTCCACCTAAATCATCACCTTCT
1 CCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCA-C--CG
*
71617 CCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCAACG
1 CCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCACCG
71665 CCGCC
1 CCGCC
71670 ACCGTCTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
48 47 0.51
49 1 0.01
51 45 0.48
ACGTcount: A:0.23, C:0.49, G:0.07, T:0.20
Consensus pattern (48 bp):
CCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCACCG
Found at i:71636 original size:51 final size:48
Alignment explanation
Indices: 71515--71661 Score: 222
Period size: 51 Copynumber: 3.0 Consensus size: 48
71505 ACCGTCTTCT
* * *
71515 CCTCCGCCTTCGACCACTTCCACAGCCCCCAGTCCACCTAAATCATCA
1 CCTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCA
* *
71563 CCGCCGCCTTCAACCACTTCCTCATCCCCAAGTCCACCTAAATCATCA
1 CCTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCA
71611 CCTTCTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCA
1 -C--CTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCA
71662 ACGCCGCCAC
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
48 43 0.48
49 1 0.01
51 45 0.51
ACGTcount: A:0.23, C:0.49, G:0.06, T:0.22
Consensus pattern (48 bp):
CCTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCA
Found at i:71717 original size:66 final size:66
Alignment explanation
Indices: 71615--71738 Score: 221
Period size: 66 Copynumber: 1.9 Consensus size: 66
71605 TCATCACCTT
* *
71615 CTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCAACGCCGCCACCGTCTTCT
1 CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCAACGCCACCACCGTCTTCT
71680 C
66 C
*
71681 CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCACCGCCACCACC
1 CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCAACGCCACCACC
71739 CTCTCCTTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.21, C:0.52, G:0.06, T:0.20
Consensus pattern (66 bp):
CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCAACGCCACCACCGTCTTCT
C
Found at i:71764 original size:66 final size:65
Alignment explanation
Indices: 71615--71759 Score: 213
Period size: 66 Copynumber: 2.2 Consensus size: 65
71605 TCATCACCTT
* *
71615 CTCCGCCTTCAACCACTTCCTCATCCCCCAGTCCACCTAAATCATCAACGCCGCCACCGTCTTCT
1 CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCAACGCCACCACCG-CTTCT
71680 C
65 C
*
71681 CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCACCGCCACCACC-C-TCTC
1 CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCAACGCCACCACCGCTTCTC
* * *
71744 CTTCTCCTTCCACCAC
1 CTCCGCCTTCAACCAC
71760 CACTTTCTCA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
63 17 0.23
64 1 0.01
66 55 0.75
ACGTcount: A:0.19, C:0.53, G:0.06, T:0.22
Consensus pattern (65 bp):
CTCCGCCTTCAACCACTTCCTCATCCCCCAGCCCACCTAAATCATCAACGCCACCACCGCTTCTC
Done.