Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022985.1 Corchorus olitorius cultivar O-4 contig23018, 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: 90620
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:2134 original size:14 final size:14
Alignment explanation
Indices: 2115--2143 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2105 ATCTCTATTA
2115 TTGGTACTGCTAAG
1 TTGGTACTGCTAAG
2129 TTGGTACTGCTAAG
1 TTGGTACTGCTAAG
2143 T
1 T
2144 AACGCACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.38
Consensus pattern (14 bp):
TTGGTACTGCTAAG
Found at i:6159 original size:86 final size:86
Alignment explanation
Indices: 6028--6200 Score: 321
Period size: 86 Copynumber: 2.0 Consensus size: 86
6018 GGGACCATCA
6028 CTTCCCTTCCGATATGGGTTCTCGTTAGTTGGAATGTTTTTGTTTTATAAACAAATAATAAAAGG
1 CTTCCCTTCCGATATGGGTTCTCGTTAGTTGGAATGTTTTTGTTTTATAAACAAATAATAAAAGG
6093 AAAGTA-ATGATACGCCATTGC
66 AAAG-AGATGATACGCCATTGC
*
6114 CTTCCCTTCCGATATGGGTTCTCGTTGGTTGGAATGTTTTTGTTTTATAAACAAATAATAAAAGG
1 CTTCCCTTCCGATATGGGTTCTCGTTAGTTGGAATGTTTTTGTTTTATAAACAAATAATAAAAGG
6179 AAAGAGATGATACGCCATTGC
66 AAAGAGATGATACGCCATTGC
6200 C
1 C
6201 CATTGATGTG
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 1 0.01
86 84 0.99
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (86 bp):
CTTCCCTTCCGATATGGGTTCTCGTTAGTTGGAATGTTTTTGTTTTATAAACAAATAATAAAAGG
AAAGAGATGATACGCCATTGC
Found at i:13584 original size:2 final size:2
Alignment explanation
Indices: 13579--13607 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13569 CTGCAAAATA
13579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13608 AAGGTTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13892 original size:45 final size:48
Alignment explanation
Indices: 13820--13912 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 48
13810 AAAAAAAACG
*
13820 TCATAGTGCTATCAAGAAATAAAGG-TT-TGTAATCCCTTTATGTTAA
1 TCATAGTGCTATCAAGAAACAAAGGTTTATGTAATCCCTTTATGTTAA
*
13866 TCATAGTTCTATC-AGAAACAAAGGTTTATGTAATCCCTTTATGTTAA
1 TCATAGTGCTATCAAGAAACAAAGGTTTATGTAATCCCTTTATGTTAA
13913 CATCTTACTG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 10 0.23
46 14 0.33
47 19 0.44
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (48 bp):
TCATAGTGCTATCAAGAAACAAAGGTTTATGTAATCCCTTTATGTTAA
Found at i:14187 original size:2 final size:2
Alignment explanation
Indices: 14180--14221 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
14170 CCAGACTTAA
14180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
14222 AACATGACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14929 original size:34 final size:35
Alignment explanation
Indices: 14891--14962 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 35
14881 TTTTTAAAAT
*
14891 TAAAAAATAAGAAGGGTATTTTAGATATTTCA-AA
1 TAAAAAATAAGAAAGGTATTTTAGATATTTCAGAA
14925 TAAAAAATAAGAAAGGTATTTTAGATATTTCAGAA
1 TAAAAAATAAGAAAGGTATTTTAGATATTTCAGAA
14960 TAA
1 TAA
14963 GGTTTTGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 31 0.86
35 5 0.14
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (35 bp):
TAAAAAATAAGAAAGGTATTTTAGATATTTCAGAA
Found at i:15090 original size:53 final size:53
Alignment explanation
Indices: 15014--15168 Score: 296
Period size: 51 Copynumber: 3.0 Consensus size: 53
15004 AAAAATAAAG
15014 ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATTAATAT
1 ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATTAATAT
15067 ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATT-A-AT
1 ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATTAATAT
15118 ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATTAAT
1 ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATTAAT
15169 TAGCTATAGC
Statistics
Matches: 100, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
51 50 0.50
52 2 0.02
53 48 0.48
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (53 bp):
ATATATATATATATAATTACATATTCAATTACACAAAACCATTTGATTAATAT
Found at i:15875 original size:16 final size:16
Alignment explanation
Indices: 15854--15887 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
15844 AATATGAAAA
*
15854 TAAAATCTGGTTGGAT
1 TAAAATCTGGTTAGAT
15870 TAAAATCTGGTTAGAT
1 TAAAATCTGGTTAGAT
15886 TA
1 TA
15888 CATATTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (16 bp):
TAAAATCTGGTTAGAT
Found at i:31500 original size:15 final size:15
Alignment explanation
Indices: 31480--31514 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31470 AAGCAGTACA
*
31480 AGAGAAGAAACATAT
1 AGAGAAGAAACAGAT
*
31495 AGAGAAGCAACAGAT
1 AGAGAAGAAACAGAT
31510 AGAGA
1 AGAGA
31515 TTACTATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.09, G:0.26, T:0.09
Consensus pattern (15 bp):
AGAGAAGAAACAGAT
Found at i:38239 original size:45 final size:45
Alignment explanation
Indices: 38188--38277 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
38178 TCTGCTTGCA
*
38188 GTTTTGTCGATTTCGCTAGCCAATCAAGAAGAATCAATGCGGATG
1 GTTTTGTCGACTTCGCTAGCCAATCAAGAAGAATCAATGCGGATG
*
38233 GTTTTGTTGACTTCGCTAGCCAATCAAGAAGAATCAATGCGGATG
1 GTTTTGTCGACTTCGCTAGCCAATCAAGAAGAATCAATGCGGATG
38278 TGACGATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (45 bp):
GTTTTGTCGACTTCGCTAGCCAATCAAGAAGAATCAATGCGGATG
Found at i:40646 original size:21 final size:22
Alignment explanation
Indices: 40617--40658 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40607 GTTTATAATA
*
40617 TTCTTGGGTCA-TCGGGTTACC
1 TTCTCGGGTCATTCGGGTTACC
*
40638 TTCTCGGGTTATTCGGGTTAC
1 TTCTCGGGTCATTCGGGTTAC
40659 GAGTTTATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTACC
Found at i:43743 original size:12 final size:12
Alignment explanation
Indices: 43711--43754 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
43701 ACCACATTAG
43711 CTGCTTCATACT
1 CTGCTTCATACT
*
43723 CTGC--AATACT
1 CTGCTTCATACT
43733 CTGCTTCATACT
1 CTGCTTCATACT
43745 CTGCTTCATA
1 CTGCTTCATA
43755 GTCAACCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (12 bp):
CTGCTTCATACT
Found at i:46325 original size:26 final size:27
Alignment explanation
Indices: 46281--46333 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
46271 CAGATTTTAA
46281 GGAACCGACTCCCAACTTGAAATCTCT
1 GGAACCGACTCCCAACTTGAAATCTCT
46308 GGAACCGAC-CCCAACTTGAAATCTCT
1 GGAACCGACTCCCAACTTGAAATCTCT
46334 TATACTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (27 bp):
GGAACCGACTCCCAACTTGAAATCTCT
Found at i:83252 original size:22 final size:22
Alignment explanation
Indices: 83140--83264 Score: 73
Period size: 22 Copynumber: 5.7 Consensus size: 22
83130 GAAATATTTT
*
83140 TATGAAATTTTGACAA-CT-AC
1 TATGAAATTTTGATAATCTAAC
* *
83160 TTTATTAAATTTTGATAATC-ACGC
1 --TATGAAATTTTGATAATCTA-AC
* * *
83184 TATGCAATTCTGATAAT-TACC
1 TATGAAATTTTGATAATCTAAC
* * *
83205 TAT-AATATTGTGATAAACT-CC
1 TATGAA-ATTTTGATAATCTAAC
83226 ATATGAAATTTTGATAATCTAAC
1 -TATGAAATTTTGATAATCTAAC
*
83249 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
83265 AACTTTTTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 18
0.71 0.12 0.16
Matches are distributed among these distances:
20 1 0.01
21 15 0.19
22 59 0.74
23 4 0.05
24 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTAAC
Found at i:83313 original size:20 final size:20
Alignment explanation
Indices: 83279--83317 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
83269 TTTTATGAAA
83279 TTTTGTAACCTTCCTATGAT
1 TTTTGTAACCTTCCTATGAT
83299 TTTTGATAACC-TCCTATGA
1 TTTTG-TAACCTTCCTATGA
83318 GATTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTTGTAACCTTCCTATGAT
Found at i:83323 original size:21 final size:19
Alignment explanation
Indices: 83272--83343 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 19
83262 TAAAACTTTT
83272 TATGAAATTTTGTAACCTTCC
1 TATG-AATTTTGTAACC-TCC
*
83293 TATGATTTTTGATAACCTCC
1 TATGAATTTTG-TAACCTCC
*
83313 TATGAGATTTTGTTAATCTCCC
1 TATGA-ATTTTG-TAACCT-CC
83335 TAT-AATTTT
1 TATGAATTTT
83344 TTTATACTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 19 0.43
21 20 0.45
22 5 0.11
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (19 bp):
TATGAATTTTGTAACCTCC
Found at i:85267 original size:21 final size:21
Alignment explanation
Indices: 85243--85290 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
85233 TAGTATAGAT
*
85243 ATATATATATATAACATA-ACA
1 ATATATAT-TATAACATATAAA
*
85264 ATATATATTATACCATATAAA
1 ATATATATTATAACATATAAA
85285 ATATAT
1 ATATAT
85291 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATATTATAACATATAAA
Found at i:86072 original size:29 final size:29
Alignment explanation
Indices: 86040--86141 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 29
86030 TCCTTAGACA
86040 TTATATTTTATACGATTTTCCCTTCAACT
1 TTATATTTTATACGATTTTCCCTTCAACT
***
86069 TTATATCTTTTATACGA-AAGCCC-TCAAACAT
1 TTATA--TTTTATACGATTTTCCCTTC-AAC-T
* *
86100 TTATATTTTATACGATTTTGACCCTTGAAAT
1 TTATATTTTATACGATTTT--CCCTTCAACT
86131 TT-TATTTTATA
1 TTATATTTTATA
86142 AAATTAGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
29 17 0.30
30 15 0.26
31 19 0.33
32 5 0.09
33 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (29 bp):
TTATATTTTATACGATTTTCCCTTCAACT
Found at i:86762 original size:95 final size:95
Alignment explanation
Indices: 86651--86837 Score: 356
Period size: 95 Copynumber: 2.0 Consensus size: 95
86641 AACTTAATCA
*
86651 ATGATGAGAAAATGCATGTTTGTTGTAGTGGTGAAATAAAAATGTGAGGGTATTGGTTTAAGAAA
1 ATGATGAGAAAATGCATGTTTGTTGTAGTGGTGAAATAAAAATGTAAGGGTATTGGTTTAAGAAA
*
86716 ATGATATACTAATTGTTTTTCATCCTCGGG
66 ATAATATACTAATTGTTTTTCATCCTCGGG
86746 ATGATGAGAAAATGCATGTTTGTTGTAGTGGTGAAATAAAAATGTAAGGGTATTGGTTTAAGAAA
1 ATGATGAGAAAATGCATGTTTGTTGTAGTGGTGAAATAAAAATGTAAGGGTATTGGTTTAAGAAA
86811 ATAATATACTAATTGTTTTTCATCCTC
66 ATAATATACTAATTGTTTTTCATCCTC
86838 AGGCAACAGC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.36
Consensus pattern (95 bp):
ATGATGAGAAAATGCATGTTTGTTGTAGTGGTGAAATAAAAATGTAAGGGTATTGGTTTAAGAAA
ATAATATACTAATTGTTTTTCATCCTCGGG
Found at i:88775 original size:6 final size:6
Alignment explanation
Indices: 88749--88788 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
88739 TTGTACAAGC
* *
88749 TTTATT TTTACT TTTACT TTTATTT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT TTT
88789 TACAACAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:88776 original size:13 final size:13
Alignment explanation
Indices: 88760--88791 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
88750 TTATTTTTAC
88760 TTTTACTTTTATT
1 TTTTACTTTTATT
*
88773 TTTTATTTTTATT
1 TTTTACTTTTATT
88786 TTTTAC
1 TTTTAC
88792 AACAAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTACTTTTATT
Found at i:89447 original size:40 final size:41
Alignment explanation
Indices: 89370--89450 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 41
89360 AGGTACTTTT
89370 TTTCTTTCTCACTCCCGCTCTTATTTCTTTAAAGTTGTAGAA
1 TTTCTTTCTCACTCCCGCTC-TATTTCTTTAAAGTTGTAGAA
*
89412 TTTCTTTCTCACTTCCGCTC-ATTTCTTTAAAGTTGTAGA
1 TTTCTTTCTCACTCCCGCTCTATTTCTTTAAAGTTGTAGA
89451 TTAGATGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 19 0.50
42 19 0.50
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (41 bp):
TTTCTTTCTCACTCCCGCTCTATTTCTTTAAAGTTGTAGAA
Found at i:90510 original size:22 final size:23
Alignment explanation
Indices: 90482--90525 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
90472 CAGTAGTCAA
90482 GGACGGATCTGA-GTGGGGGCAG
1 GGACGGATCTGATGTGGGGGCAG
90504 GGACGGATCTGATGTGGGGGCA
1 GGACGGATCTGATGTGGGGGCA
90526 CGTGCCCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.18, C:0.14, G:0.52, T:0.16
Consensus pattern (23 bp):
GGACGGATCTGATGTGGGGGCAG
Done.