Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014777.1 Corchorus olitorius cultivar O-4 contig14810, 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: 95607
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11103 original size:23 final size:24
Alignment explanation
Indices: 11049--11097 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
11039 ATAGTCGGGA
* *
11049 AAAGAAGAATTGAAACTTTTTTTT
1 AAAGAAAAATTGAAACTTTTATTT
*
11073 AAAGAAAAATTGTAACTTTTATTT
1 AAAGAAAAATTGAAACTTTTATTT
11097 A
1 A
11098 TGAAAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (24 bp):
AAAGAAAAATTGAAACTTTTATTT
Found at i:11471 original size:14 final size:14
Alignment explanation
Indices: 11449--11485 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11439 ACTCAACACT
*
11449 AACTAACTCAAAAA
1 AACTGACTCAAAAA
*
11463 AACTGACTCAACAA
1 AACTGACTCAAAAA
11477 AACTGACTC
1 AACTGACTC
11486 CGACAGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.27, G:0.05, T:0.16
Consensus pattern (14 bp):
AACTGACTCAAAAA
Found at i:14813 original size:30 final size:30
Alignment explanation
Indices: 14779--14838 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
14769 GCATCTTTTG
*
14779 AGTCCCATAAACCTTGCAGTATCTTCACCC
1 AGTCCCATAAACCTTACAGTATCTTCACCC
* * *
14809 AGTCCGATAAGCCTTACATTATCTTCACCC
1 AGTCCCATAAACCTTACAGTATCTTCACCC
14839 GAAGCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.35, G:0.10, T:0.28
Consensus pattern (30 bp):
AGTCCCATAAACCTTACAGTATCTTCACCC
Found at i:26976 original size:21 final size:21
Alignment explanation
Indices: 26919--26964 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
26909 GAGGATGGCA
* *
26919 ATGAGCTTGAAATGGAAGGAG
1 ATGACCTTGAAATTGAAGGAG
26940 ATGACCTTGAAATTGAAGGAG
1 ATGACCTTGAAATTGAAGGAG
26961 ATGA
1 ATGA
26965 TGTTGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (21 bp):
ATGACCTTGAAATTGAAGGAG
Found at i:43330 original size:28 final size:28
Alignment explanation
Indices: 43277--43348 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
43267 TCGATTTTCC
43277 AATTACATACCAA-TTTTTTGGCACCAA
1 AATTACATACCAATTTTTTTGGCACCAA
* *
43304 AATTACACACCAATTTTTTTGGCACCAG
1 AATTACATACCAATTTTTTTGGCACCAA
43332 AATTACATACCAATTTT
1 AATTACATACCAATTTT
43349 GTCCTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 12 0.29
28 29 0.71
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (28 bp):
AATTACATACCAATTTTTTTGGCACCAA
Found at i:44615 original size:15 final size:15
Alignment explanation
Indices: 44592--44621 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44582 TTCCTCATGG
*
44592 TGTATTTCTTGATGA
1 TGTACTTCTTGATGA
44607 TGTACTTCTTGATGA
1 TGTACTTCTTGATGA
44622 GCTACACCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (15 bp):
TGTACTTCTTGATGA
Found at i:44647 original size:15 final size:15
Alignment explanation
Indices: 44597--44648 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
44587 CATGGTGTAT
44597 TTCTTGATGATG-TAC
1 TTCTTGATGA-GATAC
*
44612 TTCTTGATGAGCTAC
1 TTCTTGATGAGATAC
** *
44627 ACCTTGATGGGATAC
1 TTCTTGATGAGATAC
44642 TTCTTGA
1 TTCTTGA
44649 GATGACCCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (15 bp):
TTCTTGATGAGATAC
Found at i:44708 original size:24 final size:24
Alignment explanation
Indices: 44678--44894 Score: 164
Period size: 24 Copynumber: 9.0 Consensus size: 24
44668 GTTCAGTTTT
*
44678 AGGGATAATGCCCCCATTCCCTTT
1 AGGGATAATGCCCCCATTCCCTTC
* *
44702 AGAGATAATGCCCCCATTTCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* * *
44726 AGCGATAATGCCTCCATTCTCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* *
44750 AGGGATGATGCCACCATTCCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* * * * *
44774 ATGGCTGATGGCACCATTCCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* * * *
44798 ATGGTTGATGCCACCATTCCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* * * *
44822 ATGGTTGATGCCACCATTCCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* * * *
44846 ATGGCTGATGCCACCATTCCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
* * * **
44870 ATGGTTGATGCCAACATTCCCTTC
1 AGGGATAATGCCCCCATTCCCTTC
44894 A
1 A
44895 TGTTTGATGG
Statistics
Matches: 174, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 174 1.00
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (24 bp):
AGGGATAATGCCCCCATTCCCTTC
Found at i:44761 original size:48 final size:48
Alignment explanation
Indices: 44680--44969 Score: 285
Period size: 48 Copynumber: 6.0 Consensus size: 48
44670 TCAGTTTTAG
* * * * * *
44680 GGATAATGCCCCCATTCCCTTTAGAGATAATGCCCCCATTTCCTTCA-
1 GGATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
* *
44727 GCGATAATGCCTCCATTCTCTTCAGGGATGATGCCACCATTCCCTTCAT
1 G-GATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
* * * * *
44776 GGCTGATGGCACCATTCCCTTCATGGTTGATGCCACCATTCCCTTCAT
1 GGATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
* * * *
44824 GGTTGATGCCACCATTCCCTTCATGGCTGATGCCACCATTCCCTTCAT
1 GGATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
* * * * ** * *
44872 GGTTGATGCCAACATTCCCTTCATGTTTGATGGCACCATTCTCTTCAT
1 GGATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
* * * * * *
44920 GGCTGATGTCAGCATTCCCTTCATGGCTGATGCCACCATTCCCTTCAT
1 GGATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
44968 GG
1 GG
44970 CTGATGCTCG
Statistics
Matches: 212, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
47 1 0.00
48 210 0.99
49 1 0.00
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (48 bp):
GGATAATGCCACCATTCCCTTCAGGGATGATGCCACCATTCCCTTCAT
Found at i:44983 original size:24 final size:24
Alignment explanation
Indices: 44733--44976 Score: 353
Period size: 24 Copynumber: 10.2 Consensus size: 24
44723 TTCAGCGATA
* * * *
44733 ATGCCTCCATTCTCTTCAGGGATG
1 ATGCCACCATTCCCTTCATGGCTG
44757 ATGCCACCATTCCCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
* *
44781 ATGGCACCATTCCCTTCATGGTTG
1 ATGCCACCATTCCCTTCATGGCTG
*
44805 ATGCCACCATTCCCTTCATGGTTG
1 ATGCCACCATTCCCTTCATGGCTG
44829 ATGCCACCATTCCCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
*
44853 ATGCCACCATTCCCTTCATGGTTG
1 ATGCCACCATTCCCTTCATGGCTG
* **
44877 ATGCCAACATTCCCTTCATGTTTG
1 ATGCCACCATTCCCTTCATGGCTG
* *
44901 ATGGCACCATTCTCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
* *
44925 ATGTCAGCATTCCCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
44949 ATGCCACCATTCCCTTCATGGCTG
1 ATGCCACCATTCCCTTCATGGCTG
44973 ATGC
1 ATGC
44977 TCGCATTACC
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 199 1.00
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.32
Consensus pattern (24 bp):
ATGCCACCATTCCCTTCATGGCTG
Found at i:52009 original size:18 final size:16
Alignment explanation
Indices: 51985--52018 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
51975 GTACACTAAT
*
51985 AAAG-AGAGAAAGAAA
1 AAAGAAGAGAAAAAAA
52000 AAAGAAGAGAAAAAAA
1 AAAGAAGAGAAAAAAA
52016 AAA
1 AAA
52019 CAGAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAGAGAAAAAAA
Found at i:52015 original size:15 final size:16
Alignment explanation
Indices: 51985--52026 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
51975 GTACACTAAT
51985 AAAG-AGAGAAAGAAA
1 AAAGAAGAGAAAGAAA
52000 AAAGAAGAGAAA-AAA
1 AAAGAAGAGAAAGAAA
52015 AAA-ACAGAGAAA
1 AAAGA-AGAGAAA
52027 TGGAAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.04
15 17 0.68
16 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAGAGAAAGAAA
Found at i:52272 original size:2 final size:2
Alignment explanation
Indices: 52265--52289 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52255 TAAATGCTGC
52265 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52290 TTAAAACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52625 original size:10 final size:10
Alignment explanation
Indices: 52610--52640 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
52600 AAATGGCCAA
52610 AGAGAAAGAG
1 AGAGAAAGAG
52620 AGAGAAAGAG
1 AGAGAAAGAG
*
52630 AGAGAGAGAG
1 AGAGAAAGAG
52640 A
1 A
52641 TAGGGAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AGAGAAAGAG
Found at i:54432 original size:29 final size:28
Alignment explanation
Indices: 54396--54494 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
54386 GTCAAAATGC
54396 TCAAATAAGGTCCCGATCTTTTAATTTGG
1 TCAAATAAGG-CCCGATCTTTTAATTTGG
* * ** *
54425 TCAAATAAAGG-CCTAACGTTATTGAAAATGC
1 TCAAAT-AAGGCCCGATC-TT-TT-AATTTGG
*
54456 TCAAAGAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAA-GGCCCGATCTTTTAATTTGG
*
54485 CCAAATAAGG
1 TCAAATAAGG
54495 GCCTAACATT
Statistics
Matches: 51, Mismatches: 13, Indels: 13
0.66 0.17 0.17
Matches are distributed among these distances:
28 6 0.12
29 18 0.35
30 10 0.20
31 13 0.25
32 4 0.08
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (28 bp):
TCAAATAAGGCCCGATCTTTTAATTTGG
Found at i:54460 original size:60 final size:60
Alignment explanation
Indices: 54389--54528 Score: 226
Period size: 60 Copynumber: 2.3 Consensus size: 60
54379 AACGTTTGTC
* * * *
54389 AAAATGCTCAAATAAGGTCCCGATCTTTTAATTTGGTCAAATAAAGGCCTAACGTTATTG
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACATTATCG
* *
54449 AAAATGCTCAAAGAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACATTATCG
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACATTATCG
54509 AAAATGCTCAAATAAGGGCC
1 AAAATGCTCAAATAAGGGCC
54529 TGACATCAGT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACATTATCG
Found at i:54610 original size:31 final size:31
Alignment explanation
Indices: 54572--54735 Score: 94
Period size: 31 Copynumber: 5.4 Consensus size: 31
54562 TATGTCAGGT
*
54572 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGACAAACGTTAGGC
** * *
54603 CCTTATTTG-GCCAAATT-AAAAGACCG--A-TC
1 CCTTATTTGAG-CATTTTGACAA-A-CGTTAGGC
* * *
54632 CCTTATTTGAGCATTTTGGCAAATGTTAGGT
1 CCTTATTTGAGCATTTTGACAAACGTTAGGC
* ** * *
54663 CATTATTTG-GCCAAATT-A-AAA-GATCGAGC
1 CCTTATTTGAG-CATTTTGACAAACGTTAG-GC
*
54692 CCTTATTTGAGCATTTTGACAAACATTAGGC
1 CCTTATTTGAGCATTTTGACAAACGTTAGGC
54723 CCTTATTTGAGCA
1 CCTTATTTGAGCA
54736 ATTAGCCTAA
Statistics
Matches: 94, Mismatches: 25, Indels: 28
0.64 0.17 0.19
Matches are distributed among these distances:
28 4 0.04
29 31 0.33
30 11 0.12
31 44 0.47
32 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTGACAAACGTTAGGC
Found at i:54669 original size:60 final size:60
Alignment explanation
Indices: 54572--54731 Score: 248
Period size: 60 Copynumber: 2.7 Consensus size: 60
54562 TATGTCAGGT
* *
54572 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGATC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCATTATTTGGCCAAATTAAAAGACCGAGC
* * *
54632 CCTTATTTGAGCATTTTGGCAAATGTTAGGTCATTATTTGGCCAAATTAAAAGATCGAGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCATTATTTGGCCAAATTAAAAGACCGAGC
* * *
54692 CCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCATTATTTG
54732 AGCAATTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCCATTATTTGGCCAAATTAAAAGACCGAGC
Found at i:79634 original size:19 final size:19
Alignment explanation
Indices: 79579--79636 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
79569 TGCTGCTCTA
*
79579 ATAATCTCATCTGTAC-GT
1 ATAATCTCATCTATACAGT
* * *
79597 ACCTAATCTAATTTTTACAGT
1 A--TAATCTCATCTATACAGT
79618 ATAATCTCATCTATACAGT
1 ATAATCTCATCTATACAGT
79637 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 12 0.39
21 3 0.10
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (19 bp):
ATAATCTCATCTATACAGT
Found at i:86401 original size:11 final size:11
Alignment explanation
Indices: 86385--86412 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
86375 GTTCCAAATA
86385 ATATATAGTAT
1 ATATATAGTAT
86396 ATATATAGTAT
1 ATATATAGTAT
86407 ATATAT
1 ATATAT
86413 GAGCCAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (11 bp):
ATATATAGTAT
Found at i:86952 original size:10 final size:10
Alignment explanation
Indices: 86937--86968 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
86927 GTCTACCACA
86937 TCATCCGTGG
1 TCATCCGTGG
86947 TCATCCGTGG
1 TCATCCGTGG
86957 TCATCCGTGG
1 TCATCCGTGG
86967 TC
1 TC
86969 CCGACCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.31, G:0.28, T:0.31
Consensus pattern (10 bp):
TCATCCGTGG
Found at i:89798 original size:24 final size:24
Alignment explanation
Indices: 89766--89825 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
89756 GTAATGCTAG
89766 TGATTCAAGTGATGACTGGACCGA
1 TGATTCAAGTGATGACTGGACCGA
*
89790 TGATTCAAGTGATGACTGGACTGA
1 TGATTCAAGTGATGACTGGACCGA
89814 TGATTCAAGTGA
1 TGATTCAAGTGA
89826 AGATGGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (24 bp):
TGATTCAAGTGATGACTGGACCGA
Found at i:93279 original size:26 final size:25
Alignment explanation
Indices: 93233--93291 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
93223 TACCTGCCCT
* *
93233 ATAATCATATTAAAAATTATAATTA
1 ATAATAATATTAAAAATTATAAGTA
93258 ATAATAATATATAAAAATTATAAGTA
1 ATAATAATAT-TAAAAATTATAAGTA
*
93284 GTAATAAT
1 ATAATAAT
93292 TGTGAAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (25 bp):
ATAATAATATTAAAAATTATAAGTA
Done.