Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015358.1 Corchorus olitorius cultivar O-4 contig15391, 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: 43506
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3340 original size:10 final size:10
Alignment explanation
Indices: 3318--3351 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
3308 ACCTCCTGTA
3318 ACATACC-TC
1 ACATACCTTC
3327 ACATACCTTC
1 ACATACCTTC
3337 ACATACCTTC
1 ACATACCTTC
3347 ACATA
1 ACATA
3352 ATTCTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (10 bp):
ACATACCTTC
Found at i:4159 original size:15 final size:16
Alignment explanation
Indices: 4126--4165 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4116 TTACTTTGCT
4126 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
4142 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
4157 TTGCTTTCT
1 TTGTTTTCT
4166 TTGAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:4467 original size:41 final size:41
Alignment explanation
Indices: 4417--4585 Score: 218
Period size: 41 Copynumber: 4.1 Consensus size: 41
4407 TCAAAAAGAA
4417 TTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
1 TTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
*
4458 TTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCCAG
1 TTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
* *** * *
4499 --TTTTTCCAAGTTTTCAATTTAAACAAAGATCGCATCCAG
1 TTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
*
4538 TCTTTTTCAAAGTTTTTCAA-TTAGGGGAAAGATCCCATCAAAG
1 TTTTTTTCAAAG-TTTTCAATTTA-GGGAAAGATCCCATC-AAG
4581 TTTTT
1 TTTTT
4586 AAAATTGAGC
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
39 34 0.31
41 52 0.47
42 18 0.16
43 6 0.05
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (41 bp):
TTTTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
Found at i:4504 original size:80 final size:82
Alignment explanation
Indices: 4419--4585 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 82
4409 AAAAAGAATT
*** *
4419 TTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTTTTTTTCAAAG-TTTTCAATTTA-G
1 TTTTTCAAAGTTTTCAATTTAAACAAAGATCCCATCAAGTCTTTTTCAAAGTTTTTCAA-TTAGG
*
4482 GGAAAGATCCCATC-CAG
65 GGAAAGATCCCATCAAAG
* * *
4499 TTTTTCCAAGTTTTCAATTTAAACAAAGATCGCATCCAGTCTTTTTCAAAGTTTTTCAATTAGGG
1 TTTTTCAAAGTTTTCAATTTAAACAAAGATCCCATCAAGTCTTTTTCAAAGTTTTTCAATTAGGG
4564 GAAAGATCCCATCAAAG
66 GAAAGATCCCATCAAAG
4581 TTTTT
1 TTTTT
4586 AAAATTGAGC
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 47 0.62
81 22 0.29
82 7 0.09
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (82 bp):
TTTTTCAAAGTTTTCAATTTAAACAAAGATCCCATCAAGTCTTTTTCAAAGTTTTTCAATTAGGG
GAAAGATCCCATCAAAG
Found at i:8183 original size:14 final size:15
Alignment explanation
Indices: 8166--8200 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
8156 TCTCTTTCTT
8166 CTTCTTCC-TTTTTC
1 CTTCTTCCGTTTTTC
8180 CTTCTTCCGTTTTTC
1 CTTCTTCCGTTTTTC
8195 CTTCTT
1 CTTCTT
8201 TCTTCCTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (15 bp):
CTTCTTCCGTTTTTC
Found at i:17181 original size:48 final size:48
Alignment explanation
Indices: 17117--17208 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
17107 ATCCCCACGG
*
17117 GAACGAAAGTCGTTTGAAATGAAGTCTCC-TCGGAATGTTAAATCGCCA
1 GAACGAAAGTCGTTTGAAATGAAGTC-CCATCGCAATGTTAAATCGCCA
*
17165 GAACGGAAGTCGTTTGAAATGAAGTCCCATCGCAATGTTAAATC
1 GAACGAAAGTCGTTTGAAATGAAGTCCCATCGCAATGTTAAATC
17209 CTTGCAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (48 bp):
GAACGAAAGTCGTTTGAAATGAAGTCCCATCGCAATGTTAAATCGCCA
Found at i:17313 original size:51 final size:51
Alignment explanation
Indices: 17233--17342 Score: 157
Period size: 51 Copynumber: 2.2 Consensus size: 51
17223 AATCTCCCTG
**
17233 CCATGTAAAATCACCTCAGGAACAACTGTCATCCAAAATGAGATCCCCTCA
1 CCATGTAAAATCACCTCAGGAACAACTGTCATCCAAAATGAGAAACCCTCA
* * * * *
17284 CCATGTAAAATCCCCTCAGGAGCAGCTGTCATCTAAGATGAGAAACCCTCA
1 CCATGTAAAATCACCTCAGGAACAACTGTCATCCAAAATGAGAAACCCTCA
17335 CCATGTAA
1 CCATGTAA
17343 TTCCCCACGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (51 bp):
CCATGTAAAATCACCTCAGGAACAACTGTCATCCAAAATGAGAAACCCTCA
Found at i:23123 original size:318 final size:317
Alignment explanation
Indices: 22535--23169 Score: 1198
Period size: 318 Copynumber: 2.0 Consensus size: 317
22525 TAAAATCCAA
22535 AAGGAAAGTACAAAAAACCAAAGGATACTTGATTCTCATGCATTTGGCCTTTAGTTTTCTTGGTT
1 AAGGAAAGTACAAAAAACCAAAGGATACTTGATTCTCATGCATTTGGCCTTTAGTTTTCTTGGTT
*
22600 TTTTGGTCATTTCAAGTCTTGTTTTTTTCGTTATTCCAGTTGATGGTTGAGGCCATTTTGGGGAC
66 TTTTGGTCATTTCAAGCCTTGTTTTTTTCGTTATTCCAGTTGATGGTTGAGGCCATTTTGGGGAC
22665 TTTGGGATAATGTTACTATTTGTGAGTCCCGTTTACATAAATAAATCATTTTCTTATTGGATTAA
131 TTTGGGATAATGTTACTATTTGTGAGTCCCGTTTACATAAATAAATCATTTTCTTATTGGATTAA
22730 TCAGATGATCCTCATACTTTTCTCCTTCATACTATTTAATCCCTCACAATTATGGGTTGGACGAT
196 TCAGATGATCCTCATACTTTTCTCCTTCATACTATTTAATCCCTCACAATTATGGGTTGGACGAT
22795 TTAACGCGTTGTCTTTTATTTTTGTATTTTTTGTTCTATTTGTCGGATCAAGGTGAT
261 TTAACGCGTTGTCTTTTATTTTTGTATTTTTTGTTCTATTTGTCGGATCAAGGTGAT
*
22852 AAGGAAAGTACAAAAAAACCAAAGGATACTTGATTCTCATGCATTTGGCCTTTGGTTTTCTTGGT
1 AAGGAAAGTAC-AAAAAACCAAAGGATACTTGATTCTCATGCATTTGGCCTTTAGTTTTCTTGGT
* *
22917 TTTTTGGTCATTTCAAGCCTTGTTTTTTTCGTTATTTCGGTTGATGGTTGAGGCCATTTTGGGGA
65 TTTTTGGTCATTTCAAGCCTTGTTTTTTTCGTTATTCCAGTTGATGGTTGAGGCCATTTTGGGGA
*
22982 CTTTGGGATAATGTTACTATTTGTGAGTCCCGTTTCCATAAATAAATCATTTTCTTATTGGATTA
130 CTTTGGGATAATGTTACTATTTGTGAGTCCCGTTTACATAAATAAATCATTTTCTTATTGGATTA
**
23047 ATCAGATGATCCTCATACTTTTCTCCTTCATGTTATTTAATCCCTCACAATTATGGGTTGGACGA
195 ATCAGATGATCCTCATACTTTTCTCCTTCATACTATTTAATCCCTCACAATTATGGGTTGGACGA
23112 TTTAACGCGTTGTCTTTTATTTTTGTATTTTTTGTTCTATTTGTCGGATCAAGGTGAT
260 TTTAACGCGTTGTCTTTTATTTTTGTATTTTTTGTTCTATTTGTCGGATCAAGGTGAT
23170 TCAAGTGTCT
Statistics
Matches: 310, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
317 11 0.04
318 299 0.96
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (317 bp):
AAGGAAAGTACAAAAAACCAAAGGATACTTGATTCTCATGCATTTGGCCTTTAGTTTTCTTGGTT
TTTTGGTCATTTCAAGCCTTGTTTTTTTCGTTATTCCAGTTGATGGTTGAGGCCATTTTGGGGAC
TTTGGGATAATGTTACTATTTGTGAGTCCCGTTTACATAAATAAATCATTTTCTTATTGGATTAA
TCAGATGATCCTCATACTTTTCTCCTTCATACTATTTAATCCCTCACAATTATGGGTTGGACGAT
TTAACGCGTTGTCTTTTATTTTTGTATTTTTTGTTCTATTTGTCGGATCAAGGTGAT
Found at i:23956 original size:30 final size:31
Alignment explanation
Indices: 23892--23957 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
23882 TAGTGGGCCA
* * *
23892 CCAAGATACTTTACACACACTAAAAAGTGGC
1 CCAATATACTTCACACACACTAAAAAGAGGC
*
23923 CCAATATACTTCACACACACT-CAAAGAGGC
1 CCAATATACTTCACACACACTAAAAAGAGGC
23953 CCAAT
1 CCAAT
23958 GAAATTCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.18
Consensus pattern (31 bp):
CCAATATACTTCACACACACTAAAAAGAGGC
Found at i:23966 original size:30 final size:31
Alignment explanation
Indices: 23904--23969 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
23894 AAGATACTTT
* *
23904 ACACACACTAAAAAGTGGCCCAATATACTTC
1 ACACACACTAAAAAGAGGCCCAATATAATTC
*
23935 ACACACACT-CAAAGAGGCCCAATGA-AATTC
1 ACACACACTAAAAAGAGGCCCAAT-ATAATTC
23965 ACACA
1 ACACA
23970 TACATTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.44, C:0.30, G:0.11, T:0.15
Consensus pattern (31 bp):
ACACACACTAAAAAGAGGCCCAATATAATTC
Found at i:31032 original size:15 final size:15
Alignment explanation
Indices: 30981--31031 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
30971 AACATATATA
*
30981 ATATAAATATTCCAC
1 ATATAAATATTTCAC
*
30996 ATATAAATACTTCAC
1 ATATAAATATTTCAC
*
31011 ATATAAGTATTTCAC
1 ATATAAATATTTCAC
*
31026 ACATAA
1 ATATAA
31032 GAGGGTCACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (15 bp):
ATATAAATATTTCAC
Found at i:32005 original size:11 final size:11
Alignment explanation
Indices: 31991--32021 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31981 TAAAGGAAAA
31991 GGCTAGGAAGG
1 GGCTAGGAAGG
32002 GGCTAGGAAGG
1 GGCTAGGAAGG
*
32013 AGCTAGGAA
1 GGCTAGGAA
32022 AGATCCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.10, G:0.48, T:0.10
Consensus pattern (11 bp):
GGCTAGGAAGG
Found at i:32320 original size:65 final size:65
Alignment explanation
Indices: 32216--32340 Score: 214
Period size: 65 Copynumber: 1.9 Consensus size: 65
32206 AACTGGTCTT
* * * *
32216 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGTAGAAAGTTTGAATCGTCCA
1 ACCCATCCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAAAAAGTTGGAATCGTCCA
32281 ACCCATCCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAAAAAGTTGGAATC
1 ACCCATCCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAAAAAGTTGGAATC
32341 AATAGCAAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (65 bp):
ACCCATCCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAAAAAGTTGGAATCGTCCA
Found at i:32560 original size:21 final size:21
Alignment explanation
Indices: 32542--32667 Score: 218
Period size: 21 Copynumber: 6.0 Consensus size: 21
32532 ATTCCAATTT
*
32542 GCTTGAAACCTTCTCCAATGA
1 GCTTGGAACCTTCTCCAATGA
*
32563 GCTTGGAACCTTCTCTAATGA
1 GCTTGGAACCTTCTCCAATGA
32584 GCTTGGAACCTTCTCCAATGA
1 GCTTGGAACCTTCTCCAATGA
32605 GCTTGGAACCTTCTCCAATGA
1 GCTTGGAACCTTCTCCAATGA
32626 GCTTGGAACCTTCTCCAATGA
1 GCTTGGAACCTTCTCCAATGA
32647 GCTTGGAA-CTTGCTCCAATGA
1 GCTTGGAACCTT-CTCCAATGA
32668 ACTCCTAGCA
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
20 3 0.03
21 98 0.97
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (21 bp):
GCTTGGAACCTTCTCCAATGA
Found at i:34530 original size:33 final size:32
Alignment explanation
Indices: 34460--34597 Score: 107
Period size: 33 Copynumber: 4.2 Consensus size: 32
34450 ATGATCAACC
** *
34460 AAAACAAATTTGTTTTCATCACAATTAGCATCC-
1 AAAACAAATTTG-TTTCATCACAAACAACA-CCT
34493 AAAACATAATTTGTTTCATCACAAACAACACCT
1 AAAACA-AATTTGTTTCATCACAAACAACACCT
* * *
34526 AAAACAGATTTAGTGTCATCACAAACAACACTT
1 AAAACAAATTT-GTTTCATCACAAACAACACCT
** ** * * *
34559 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAAATTT-GTTTCATCACAAACAACACCT
34592 AAAACA
1 AAAACA
34598 CTCTTTGCAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
32 6 0.07
33 75 0.86
34 6 0.07
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (32 bp):
AAAACAAATTTGTTTCATCACAAACAACACCT
Found at i:36962 original size:65 final size:65
Alignment explanation
Indices: 36851--36980 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 65
36841 GGAAAAACTA
* * * * *
36851 GTCCTACCCATGCATGGGGTACCCTTGGCTTACCCACGCCTGGGCTAGTGTAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTAGGCTAGTGCAGAAAGTTGGAATC
*
36916 GTCCAACCCATGCATGTGGTACCCTTGGCCTACCCACGCCTAGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTAGGCTAGTGCAGAAAGTTGGAATC
36981 AATAGCAAGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTAGGCTAGTGCAGAAAGTTGGAATC
Found at i:37307 original size:21 final size:21
Alignment explanation
Indices: 37174--37295 Score: 208
Period size: 21 Copynumber: 5.8 Consensus size: 21
37164 CTTAGGCAAT
*
37174 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
37195 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
37216 TCCAATGAGCTTGAAACTTTC
1 TCCAATGAGCTTGGAACCTTC
37237 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
37258 TCCAATGAGCTTGGAATCTTC
1 TCCAATGAGCTTGGAACCTTC
37279 TCCAATGAGCTTGGAAC
1 TCCAATGAGCTTGGAAC
37296 TTGCTTCAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 94 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:40123 original size:22 final size:22
Alignment explanation
Indices: 40097--40149 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
40087 GATTAAAACT
40097 AACAATTAA-AATTAACT-AAGAA
1 AACAATTAAGAA--AACTAAAGAA
* *
40119 AACAATCAAGAAAATTAAAGAA
1 AACAATTAAGAAAACTAAAGAA
40141 AACAATTAA
1 AACAATTAA
40150 TAAGAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (22 bp):
AACAATTAAGAAAACTAAAGAA
Done.