Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011870.1 Corchorus olitorius cultivar O-4 contig11903, 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: 30127
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1403 original size:14 final size:13
Alignment explanation
Indices: 1384--1422 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1374 AAATTGTAAA
1384 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
1397 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
1411 ATTTAAAAAATT
1 ATTTAAAAAATT
1423 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:1623 original size:123 final size:128
Alignment explanation
Indices: 1428--1665 Score: 387
Period size: 123 Copynumber: 1.9 Consensus size: 128
1418 AAATTCTAAT
1428 ATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTA
1 ATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTATAAGGATATTA
*
1493 GATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATTTGATTTTTTT
62 GATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTGATTTTTTT
1558 TA
127 TA
1560 ATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-GATATTAGATT
1 ATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATT
*
1620 TAATTAAATAAAAATTGAGTTTTTAGTTGAGTAAAACTATAAAAGT
66 TAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
1666 TTAAATAATG
Statistics
Matches: 104, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
123 55 0.53
124 2 0.02
125 2 0.02
127 2 0.02
131 32 0.31
132 11 0.11
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (128 bp):
ATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATT
TAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTGATTTTTTTTA
Found at i:4016 original size:26 final size:26
Alignment explanation
Indices: 3945--4021 Score: 136
Period size: 26 Copynumber: 3.0 Consensus size: 26
3935 ATTATTAAAA
* *
3945 TATTTTATTTAGAAAAATTAAAATTT
1 TATTTTATTTAGAAAAATTCAATTTT
3971 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTATTTAGAAAAATTCAATTTT
3997 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTCAATTT
4022 CTACAGTACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTCAATTTT
Found at i:5452 original size:15 final size:15
Alignment explanation
Indices: 5432--5462 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5422 TTGACTTCTA
5432 ATTGATGTTGAATTT
1 ATTGATGTTGAATTT
5447 ATTGATGTTGAATTT
1 ATTGATGTTGAATTT
5462 A
1 A
5463 AAATTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
ATTGATGTTGAATTT
Found at i:8462 original size:29 final size:30
Alignment explanation
Indices: 8402--8481 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
8392 GTTAAATATC
* * *
8402 CAAAAAAATCCCTTATATTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
8433 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
*
8462 CAAATTAATCCCTTATGTTT
1 CAAAATAATCCCTTATGTTT
8482 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 26 0.58
31 19 0.42
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:8623 original size:27 final size:27
Alignment explanation
Indices: 8593--8644 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
8583 ATTTGTCCCA
8593 AAAAAAACATAA-AGGATTTTTTTTATC
1 AAAAAAACATAAGA-GATTTTTTTTATC
8620 AAAAAAACATAAGAGATTTTTTTTA
1 AAAAAAACATAAGAGATTTTTTTTA
8645 GGGAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (27 bp):
AAAAAAACATAAGAGATTTTTTTTATC
Found at i:9453 original size:8 final size:7
Alignment explanation
Indices: 9425--9451 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
9415 AAAAATTGAT
9425 TTTTTTC
1 TTTTTTC
9432 TTTTTTC
1 TTTTTTC
9439 TTTTTTC
1 TTTTTTC
9446 TTTTTT
1 TTTTTT
9452 TCCTTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:9698 original size:145 final size:145
Alignment explanation
Indices: 9537--9802 Score: 374
Period size: 145 Copynumber: 1.8 Consensus size: 145
9527 AATTCCCTAA
* *
9537 AAAATGGTAAAGATAAAATAGTTATAAAAATATT-GAATTCAATTAAATAAAAATAGAA-TTTTT
1 AAAATAGTAAAAATAAAATAGTTATAAAAATATTAG-ATTCAATTAAATAAAAATA-AAGTTTTT
** * * * *
9600 GGTAAAATGAAATTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAAAAAATTCTAATA
64 AATAAAATAAAATTGTAAAAGTTCAAACAATGACATTTAAGAAATATATTTAAAAAATTCTAATA
9665 TATCTAATTTTTTAATT
129 TATCTAATTTTTTAATT
* *
9682 AAAATAGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAAAGTTTTTAA
1 AAAATAGTAAAAATAAAATAGTTATAAAAATATTAGATTCAATTAAATAAAAATAAAGTTTTTAA
** * *
9747 TTGAGTAAAATTGTAAAAGTTCAAACAATGACATTTAAGAAATATATTTGAAAAAT
66 TAAAATAAAATTGTAAAAGTTCAAACAATGACATTTAAGAAATATATTTAAAAAAT
9803 AAGGGTAAGA
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
144 2 0.02
145 102 0.97
146 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (145 bp):
AAAATAGTAAAAATAAAATAGTTATAAAAATATTAGATTCAATTAAATAAAAATAAAGTTTTTAA
TAAAATAAAATTGTAAAAGTTCAAACAATGACATTTAAGAAATATATTTAAAAAATTCTAATATA
TCTAATTTTTTAATT
Found at i:9830 original size:171 final size:174
Alignment explanation
Indices: 9637--9990 Score: 507
Period size: 181 Copynumber: 2.0 Consensus size: 174
9627 TAATGTCATT
9637 TAAGAAATATATTTAAAAAATTCTAATATATCTAA-TTTTTTAATTAAAATAG-TA-AAAATAAA
1 TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGATATAAAATAAA
* * * *
9699 ATAGTTATAAATATATTAGATTTAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAATTGTAAA
66 ATAGTTAAAAATATATTAGATTAAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAACTATAAA
* * * *
9764 AGTTCAAACAATGACATTTAAGAAATATATTTGAAAAATAAGGG
131 AATTCAAACAATAACATTTAAGAAATATAATCGAAAAATAAGGG
9808 TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATAGTTA
1 TAAGAAATATATTTAAAAAATTCTAATATATCTAAG-TTTTTTAATTAAAATAG----ATA--TA
* * * *
9873 AAATAAAATATTTAAAAATATATTAGATTAAATTAAATGAAAATAGAGTTTTTAGTTGAGTAAAA
59 AAATAAAATAGTTAAAAATATATTAGATTAAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAA
*
9938 CTATAAAAATTTAAACAATAACATTTAAGAAATATAATCGAAAAATAAGGG
124 CTATAAAAATTCAAACAATAACATTTAAGAAATATAATCGAAAAATAAGGG
9989 TA
1 TA
9991 TAATCGTGAT
Statistics
Matches: 160, Mismatches: 13, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
171 35 0.22
173 17 0.11
178 2 0.01
181 106 0.66
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (174 bp):
TAAGAAATATATTTAAAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGATATAAAATAAA
ATAGTTAAAAATATATTAGATTAAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAACTATAAA
AATTCAAACAATAACATTTAAGAAATATAATCGAAAAATAAGGG
Found at i:11998 original size:31 final size:31
Alignment explanation
Indices: 11933--11999 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
11923 ATCAAAAAAC
*
11933 CCCTTATGTTTTTCTTTTGGGAGCTAATAAT
1 CCCTTATGTTTTTCTTTTGGGAGCAAATAAT
*
11964 CCCTTATGTTTTT-TTTATGGGA-CAAATTAGT
1 CCCTTATGTTTTTCTTT-TGGGAGCAAA-TAAT
11995 CCCTT
1 CCCTT
12000 GCTGACGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (31 bp):
CCCTTATGTTTTTCTTTTGGGAGCAAATAAT
Found at i:12192 original size:31 final size:29
Alignment explanation
Indices: 12126--12205 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
12116 CTCATTTTTT
* * *
12126 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
12155 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
12186 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
12206 GGTATTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:15628 original size:25 final size:26
Alignment explanation
Indices: 15586--15637 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
15576 CAAAAAAAAG
15586 AAATCCAAACTCTAGTAAATTTAATC
1 AAATCCAAACTCTAGTAAATTTAATC
*
15612 AAATCC-AAGTCTAGTAAATTTAATC
1 AAATCCAAACTCTAGTAAATTTAATC
15637 A
1 A
15638 TTTCCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATCCAAACTCTAGTAAATTTAATC
Found at i:15766 original size:41 final size:41
Alignment explanation
Indices: 15709--15791 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
15699 AATATAGAAG
*
15709 TCCTAAGAAATGTGAACTTTTCCTCAATTTTTGCTAAAAAT
1 TCCTAAGAAACGTGAACTTTTCCTCAATTTTTGCTAAAAAT
15750 TCCTAAGAAACGTGAACTTTTCCTCAATTTTTGCTAAAAAT
1 TCCTAAGAAACGTGAACTTTTCCTCAATTTTTGCTAAAAAT
15791 T
1 T
15792 TGAGGTATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (41 bp):
TCCTAAGAAACGTGAACTTTTCCTCAATTTTTGCTAAAAAT
Found at i:18110 original size:41 final size:40
Alignment explanation
Indices: 18065--18144 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
18055 TGTTTTTTTT
*
18065 TTTTATCTCACCTAGGGTTTA-ATGTGTTTTTTGAGGGTTTC
1 TTTTATCTCACCTAGGGTTTATAT-TGTTTGTT-AGGGTTTC
*
18106 TTTTATCTCACTTAGGGTTTATATTGTTTGTTAGGGTTT
1 TTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGGTTT
18145 GGGTTTCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 7 0.19
41 27 0.75
42 2 0.06
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (40 bp):
TTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGGTTTC
Found at i:20228 original size:3 final size:3
Alignment explanation
Indices: 20220--20245 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20210 CTATAGCTTT
20220 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20246 TTTTGCTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:25778 original size:12 final size:12
Alignment explanation
Indices: 25761--25792 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
25751 AATGACTCCT
25761 ATATCCAAGGAA
1 ATATCCAAGGAA
25773 ATATCCAAGGAA
1 ATATCCAAGGAA
25785 ATATCCAA
1 ATATCCAA
25793 ATCCCGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (12 bp):
ATATCCAAGGAA
Found at i:27408 original size:51 final size:50
Alignment explanation
Indices: 27336--27436 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 50
27326 AAATTTTGTT
*
27336 TTTAATTTTGAGTCTTGCGTTTTTGAAAAAAAAAATTTGAT-TTTTGCGTC
1 TTTAATTTTGAGTCTTGCGTTTTTGAAAAAAAAAAGTTG-TGTTTTGCGTC
*
27386 TTTAATTTCTTAGTCTTGCGTTTTTGAAAAAAAAAAGTTGTGTTTTGCGTC
1 TTTAATTT-TGAGTCTTGCGTTTTTGAAAAAAAAAAGTTGTGTTTTGCGTC
27437 AAGAAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 9 0.19
51 38 0.81
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.48
Consensus pattern (50 bp):
TTTAATTTTGAGTCTTGCGTTTTTGAAAAAAAAAAGTTGTGTTTTGCGTC
Done.