Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021105.1 Corchorus olitorius cultivar O-4 contig21138, 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: 20335
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:901 original size:16 final size:16
Alignment explanation
Indices: 880--910 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
870 TGGATGTTCT
*
880 TTTTTTTTCCTATTTC
1 TTTTTTTTCATATTTC
896 TTTTTTTTCATATTT
1 TTTTTTTTCATATTT
911 AAAACAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCATATTTC
Found at i:2082 original size:21 final size:20
Alignment explanation
Indices: 2052--2100 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2042 TAAAACTATC
2052 TAAGATTACTAAAAAGCTTAA
1 TAAG-TTACTAAAAAGCTTAA
* *
2073 TAAAGTTACTAAAATGCTTAC
1 T-AAGTTACTAAAAAGCTTAA
2094 TAAGTTA
1 TAAGTTA
2101 TATATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
TAAGTTACTAAAAAGCTTAA
Found at i:2397 original size:22 final size:22
Alignment explanation
Indices: 2360--2411 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2350 GCTTACAAGA
*
2360 TTACT-AAAATTTTAATAAAGG
1 TTACTAAAAATTGTAATAAAGG
2381 TTACTAAAAATTGTAATAAAGG
1 TTACTAAAAATTGTAATAAAGG
2403 TTACTAAAA
1 TTACTAAAA
2412 CGTTTAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (22 bp):
TTACTAAAAATTGTAATAAAGG
Found at i:2744 original size:20 final size:22
Alignment explanation
Indices: 2699--2746 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
2689 AAAACACTCA
2699 ATAAGGTTACTAAAAAAAACTTC
1 ATAAGGTTACT-AAAAAAACTTC
*
2722 ATAAGGTTACT-ATAAAA-TTC
1 ATAAGGTTACTAAAAAAACTTC
2742 ATAAG
1 ATAAG
2747 TTAACGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
23 11 0.46
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (22 bp):
ATAAGGTTACTAAAAAAACTTC
Found at i:2756 original size:20 final size:21
Alignment explanation
Indices: 2714--2757 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
2704 GTTACTAAAA
*
2714 AAAACTTCATAAGGTTACTAT
1 AAAACTTCATAAGGTTACGAT
2735 AAAA-TTCATAA-GTTAACGAT
1 AAAACTTCATAAGGTT-ACGAT
2755 AAA
1 AAA
2758 TCTTACAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAACTTCATAAGGTTACGAT
Found at i:2972 original size:85 final size:86
Alignment explanation
Indices: 2820--2988 Score: 313
Period size: 86 Copynumber: 2.0 Consensus size: 86
2810 TAAGATCACT
*
2820 AAAAATCTTAAATGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAATTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAATTTAAT
2885 GAAAAATTTATAAGCTTACCA
66 GAAAAATTTATAAGCTTACCA
*
2906 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTT-AAAAACTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAATTTAAT
2970 GAAAAATTTATAAGCTTAC
66 GAAAAATTTATAAGCTTAC
2989 GAAGATAATT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
85 37 0.46
86 44 0.54
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (86 bp):
AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAACTTTTAAATTTAAT
GAAAAATTTATAAGCTTACCA
Found at i:3050 original size:21 final size:20
Alignment explanation
Indices: 3026--3064 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3016 GTTTTACCAA
*
3026 TTACAATAAAATTTAAATAGT
1 TTACAA-AAAAGTTAAATAGT
*
3047 TTACTAAAAAGTTAAATA
1 TTACAAAAAAGTTAAATA
3065 AGATTACCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
TTACAAAAAAGTTAAATAGT
Found at i:3077 original size:21 final size:19
Alignment explanation
Indices: 3032--3080 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
3022 CCAATTACAA
* *
3032 TAAAATTTAAATAGTTTAC
1 TAAAAGTTAAATAGATTAC
3051 TAAAAAGTTAAATAAGATTACC
1 T-AAAAGTTAAAT-AGATTA-C
3073 TAAAAGTT
1 TAAAAGTT
3081 TTCAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 12 0.48
22 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (19 bp):
TAAAAGTTAAATAGATTAC
Found at i:3510 original size:26 final size:28
Alignment explanation
Indices: 3474--3525 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
3464 TAAGGTGACT
3474 AAAAAACTTT-ATAAGG-CCAAAAAAGG
1 AAAAAACTTTAATAAGGTCCAAAAAAGG
*
3500 AAAAAAGTTTAATAAGGTCCAAAAAA
1 AAAAAACTTTAATAAGGTCCAAAAAA
3526 AAAGCTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 6 0.26
28 8 0.35
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (28 bp):
AAAAAACTTTAATAAGGTCCAAAAAAGG
Found at i:8783 original size:42 final size:42
Alignment explanation
Indices: 8736--8830 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
8726 ATGTGGCTAT
*
8736 AGAGAAGGACACTCCCATAGTTGACACTGA-TGCTGCGGTTAG
1 AGAGAAGGACACTCCCACAGTTGACA-TGATTGCTGCGGTTAG
* * * * * *
8778 GGAGAAGGACATTCCCGCAGTTGAGATTATTGTTGCGGTTAG
1 AGAGAAGGACACTCCCACAGTTGACATGATTGCTGCGGTTAG
8820 AGAGAAGGACA
1 AGAGAAGGACA
8831 TCGACATTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (42 bp):
AGAGAAGGACACTCCCACAGTTGACATGATTGCTGCGGTTAG
Found at i:9052 original size:27 final size:27
Alignment explanation
Indices: 9015--9143 Score: 145
Period size: 27 Copynumber: 4.8 Consensus size: 27
9005 AGAAAGATGT
* * *
9015 TCCCGTAGTTGGCACTCATGCTGAAAT
1 TCCCGCAGTTGGGACTCATGCTGAAAC
* * *
9042 TCCCGCAGTTGGGACTCACGC-CATAGC
1 TCCCGCAGTTGGGACTCATGCTGA-AAC
*
9069 -CTCCGCAGTTGGGACTCATGCTGAAGC
1 TC-CCGCAGTTGGGACTCATGCTGAAAC
9096 TCCCGCAGTTGGGACTCATGCTGAAAC
1 TCCCGCAGTTGGGACTCATGCTGAAAC
* *
9123 TCCCACGGTTGGGACTCATGC
1 TCCCGCAGTTGGGACTCATGC
9144 CAAAGCCTCC
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.02
27 83 0.95
28 2 0.02
ACGTcount: A:0.19, C:0.31, G:0.26, T:0.23
Consensus pattern (27 bp):
TCCCGCAGTTGGGACTCATGCTGAAAC
Found at i:9162 original size:81 final size:81
Alignment explanation
Indices: 9015--9175 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 81
9005 AGAAAGATGT
* * * * * *
9015 TCCCGTAGTTGGCACTCATGCTGAAATTCCCGCAGTTGGGACTCACGCCATAGCCTCCGCAGTTG
1 TCCCGCAGTTGGCACTCATGCTGAAACTCCCACAGTTGGGACTCACGCCAAAGCCTCCACAATTG
9080 GGACTCATGCTGAAGC
66 GGACTCATGCTGAAGC
* * * *
9096 TCCCGCAGTTGGGACTCATGCTGAAACTCCCACGGTTGGGACTCATGCCAAAGCCTCCATAATTG
1 TCCCGCAGTTGGCACTCATGCTGAAACTCCCACAGTTGGGACTCACGCCAAAGCCTCCACAATTG
* *
9161 GGATTTATGCTGAAG
66 GGACTCATGCTGAAG
9176 GACTCATGCC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (81 bp):
TCCCGCAGTTGGCACTCATGCTGAAACTCCCACAGTTGGGACTCACGCCAAAGCCTCCACAATTG
GGACTCATGCTGAAGC
Found at i:9216 original size:27 final size:27
Alignment explanation
Indices: 9175--9230 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
9165 TTATGCTGAA
9175 GGACTCATGCCGAAGCTCCCGCAGTTG
1 GGACTCATGCCGAAGCTCCCGCAGTTG
*
9202 GGACTCATGCTGAAGCTCCCGCAGTTG
1 GGACTCATGCCGAAGCTCCCGCAGTTG
9229 GG
1 GG
9231 TTTTGTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.30, G:0.32, T:0.20
Consensus pattern (27 bp):
GGACTCATGCCGAAGCTCCCGCAGTTG
Found at i:17346 original size:56 final size:56
Alignment explanation
Indices: 17260--17374 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
17250 AAAAAACTTA
*
17260 TATAGAGTTGCTAATTTTCCATGTGATTAATATAAGTAGAGAGCATTTCGAGAACG
1 TATAGAGCTGCTAATTTTCCATGTGATTAATATAAGTAGAGAGCATTTCGAGAACG
*
17316 TATAGAGCTGCTAATTTTCCATGTGATTAATATAAGTAGAGAGCATTTCGAGATCG
1 TATAGAGCTGCTAATTTTCCATGTGATTAATATAAGTAGAGAGCATTTCGAGAACG
17372 TAT
1 TAT
17375 GTACTCTGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (56 bp):
TATAGAGCTGCTAATTTTCCATGTGATTAATATAAGTAGAGAGCATTTCGAGAACG
Found at i:18154 original size:178 final size:178
Alignment explanation
Indices: 17789--18170 Score: 466
Period size: 178 Copynumber: 2.1 Consensus size: 178
17779 CCATAAACAT
** * * * * * * *
17789 AAATTATGCAATATTAAGTAGACCGTCTATTTTCGTTAACCGAAACAACTAATTCTTTGGAATCA
1 AAATTATATAATATTAAATAGATCGTCTATTCTCGTTAACCAAAACAACAAATTCTTCGGAAGCA
* * *
17854 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
66 TTTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
* * * *
17919 AGTCTTTCAAGAGACACTTTAATAATCTCAATCAGACATCTGGAGCAA
131 AATCTTTCAAGAGACACTTTAATAACCTCAATCAGACAACCGGAGCAA
*
17967 AAGTTATATAATATTAAATAGATCGTCTATTCTCGTTAACCAAAACAACAAATAT-TTCGGAAGC
1 AAATTATATAATATTAAATAGATCGTCTATTCTCGTTAACCAAAACAACAAAT-TCTTCGGAAGC
* * *
18031 ATTTTTGATA-CTTAAAACATTAAATTTAGTTTTTGAGTTCTTCATGAAAGTTGTAGATCATTAA
65 ATTTTTGATACCTT-AAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAA
* * * * * *
18095 ACAATCTTTTAATAGACA-TTTAAATCACCTTAATCGGATAACCGGAG-AGA
129 ACAATCTTTCAAGAGACACTTT-AATAACCTCAATCAGACAACCGGAGCA-A
18145 AAATTATATAATATTAAATAGATCGT
1 AAATTATATAATATTAAATAGATCGT
18171 TTAGTCAAAC
Statistics
Matches: 173, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
177 7 0.04
178 165 0.95
179 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (178 bp):
AAATTATATAATATTAAATAGATCGTCTATTCTCGTTAACCAAAACAACAAATTCTTCGGAAGCA
TTTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
AATCTTTCAAGAGACACTTTAATAACCTCAATCAGACAACCGGAGCAA
Found at i:18435 original size:11 final size:11
Alignment explanation
Indices: 18419--18449 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
18409 AATCGTGTTT
18419 AAATTAAAAGA
1 AAATTAAAAGA
18430 AAATTAAAAGA
1 AAATTAAAAGA
18441 AAATTAAAA
1 AAATTAAAA
18450 TAATTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAATTAAAAGA
Found at i:18627 original size:21 final size:22
Alignment explanation
Indices: 18587--18627 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18577 GACAAACTCG
*
18587 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
18609 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
18628 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:19648 original size:162 final size:161
Alignment explanation
Indices: 19448--20065 Score: 598
Period size: 162 Copynumber: 3.7 Consensus size: 161
19438 GACATTTAAG
** * *
19448 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTTAAAAATTCTAATATATAAAATTTTTTTAATTAAATTAGTAAAATGATAAAAATA
19513 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTTGCTTTTTGCCAA
66 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTTGCTTTTTGCC-A
19578 AAAATAGAGTTTTTAGTTGAGTAAAACTATAA
130 AAAATAGAGTTTTTAGTTGAGTAAAACTATAA
* * * *
19610 AAATATATTTTAAAAGTTCTACTATATAAAATTTTTTTAATTAAAATAGTAAAATGATAAAAATT
1 AAATATATTTTAAAAATTCTAATATATAAAATTTTTTTAATTAAATTAGTAAAATGATAAAAATA
** * * * * ** *
19675 AAATATTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTTT-AGTAGAATAATTG-TA
66 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTTG-CTTTTTGCCA
* ** **** * *
19738 AAAGTTTA-TTTCTTAAAAAAACTGTAAAATTTAAACAA
130 AAAATAGAGTTT-TT-AGTTGA--GTAAAA-CT--ATAA
* * *
19776 TGTCATTTAAGAAATATATTTTAAAAATTATAATATATCTAAGTTTTTTT-ATTAAATTAGTAAA
1 ----A-------AATATATTTTAAAAATTCTAATATAT-AAAATTTTTTTAATTAAATTAGTAAA
* * *
19840 TTGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAATATAGAGTTTTTAGTTT
54 ATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA--AT
** *
19905 TTTTTTTTTAGCCAAAAATAGAGTTTTTTTGTTGAGTAAAACTATAA
117 TTGCTTTTT-GCCAAAAATAGAG-TTTTTAGTTGAGTAAAACTATAA
* * *
19952 AAATATATTTAAAAAATTCTAATATATATAATTTTTTTAATTGAAA-TAGTAAAATGGTAAAAAT
1 AAATATATTTTAAAAATTCTAATATATAAAATTTTTTTAATT-AAATTAGTAAAATGATAAAAAT
* * *
20016 TAAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
65 AAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
20066 GTTGAGTAAA
Statistics
Matches: 360, Mismatches: 67, Indels: 55
0.75 0.14 0.11
Matches are distributed among these distances:
159 3 0.01
160 8 0.02
161 5 0.01
162 106 0.29
163 6 0.02
164 9 0.03
165 89 0.25
166 6 0.02
170 1 0.00
172 1 0.00
176 3 0.01
177 90 0.25
178 10 0.03
179 9 0.03
180 2 0.01
181 7 0.02
182 2 0.01
183 3 0.01
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (161 bp):
AAATATATTTTAAAAATTCTAATATATAAAATTTTTTTAATTAAATTAGTAAAATGATAAAAATA
AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTTGCTTTTTGCCAA
AAATAGAGTTTTTAGTTGAGTAAAACTATAA
Found at i:20209 original size:2 final size:2
Alignment explanation
Indices: 20172--20303 Score: 135
Period size: 2 Copynumber: 66.0 Consensus size: 2
20162 GTACTTTTTA
* * * *
20172 AT AT A- AT AT AG AT AT AC AT AT -T AT CT AT AT AGT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
20213 AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT CT AT ACT TT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
20255 AT AT AGT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20298 AT AT AT
1 AT AT AT
20304 GTTGAGCACC
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
1 3 0.03
2 100 0.93
3 5 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.