Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023696.1 Corchorus olitorius cultivar O-4 contig23729, 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: 29726
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:190 original size:15 final size:15
Alignment explanation
Indices: 149--237 Score: 88
Period size: 15 Copynumber: 5.8 Consensus size: 15
139 GTTTGTTACT
* *
149 TTCCGAGGAGAGTGC
1 TTCCCAGGAGAGTGA
*
164 TCTCCAAGGAGAGTGA
1 T-TCCCAGGAGAGTGA
*
180 TTCCCAGGAGAGTGC
1 TTCCCAGGAGAGTGA
* *
195 TTTCCATGGAGAGTCA
1 TTCCCA-GGAGAGTGA
*
211 TTCCAAGGAGAGTGA
1 TTCCCAGGAGAGTGA
*
226 TTCCCAAGAGAG
1 TTCCCAGGAGAG
238 AACTTTCCAT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
15 36 0.60
16 24 0.40
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.21
Consensus pattern (15 bp):
TTCCCAGGAGAGTGA
Found at i:192 original size:31 final size:31
Alignment explanation
Indices: 149--224 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
139 GTTTGTTACT
* *
149 TTCCGAGGAGAGTGCTCTCCAAGGAGAGTGA
1 TTCCAAGGAGAGTGCTCTCCAAGGAGAGTCA
* * *
180 TTCCCAGGAGAGTGCTTTCCATGGAGAGTCA
1 TTCCAAGGAGAGTGCTCTCCAAGGAGAGTCA
211 TTCCAAGGAGAGTG
1 TTCCAAGGAGAGTG
225 ATTCCCAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (31 bp):
TTCCAAGGAGAGTGCTCTCCAAGGAGAGTCA
Found at i:224 original size:46 final size:46
Alignment explanation
Indices: 166--260 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 46
156 GAGAGTGCTC
* ** *
166 TCCAAGGAGAGTGATTCCCAGGAGAGTGCTTTCCATGGAGAGTCAT
1 TCCAAGGAGAGTGATTCCCAAGAGAGAACTTTCCATGGAAAGTCAT
*
212 TCCAAGGAGAGTGATTCCCAAGAGAGAACTTTCCATGGAAAGTCTT
1 TCCAAGGAGAGTGATTCCCAAGAGAGAACTTTCCATGGAAAGTCAT
258 TCC
1 TCC
261 CTACGACCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (46 bp):
TCCAAGGAGAGTGATTCCCAAGAGAGAACTTTCCATGGAAAGTCAT
Found at i:806 original size:45 final size:45
Alignment explanation
Indices: 739--835 Score: 169
Period size: 45 Copynumber: 2.2 Consensus size: 45
729 AGCAACAGTT
739 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAG
* *
784 AATATTAGCTTTATTTTTATGAATTACCTAGAGATGAGGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAG
829 AAT-TTAG
1 AATATTAG
836 ATAATGAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 4 0.08
45 46 0.92
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAG
Found at i:1401 original size:41 final size:41
Alignment explanation
Indices: 1342--1606 Score: 359
Period size: 41 Copynumber: 6.4 Consensus size: 41
1332 CCAGGGTCGA
** * * * *
1342 ATGACTTGGTCTTGAATTGACAATCTAATTCAAAGGTCTTG
1 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* ** *
1383 ACGACTTGGTCTTGAATTGATAATAATTCGATTCAAGGGTCTCG
1 ATGACTTAATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCG
*
1427 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* *
1468 ATGACTCAATCTTGAATTGATAATTTAATTCAAAGGTCTCG
1 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
**
1509 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1550 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
*
1591 ATGACTCAATCTTGAA
1 ATGACTTAATCTTGAA
1607 CATATGAAAA
Statistics
Matches: 202, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 167 0.83
42 2 0.01
43 1 0.00
44 32 0.16
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (41 bp):
ATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
Found at i:1582 original size:123 final size:125
Alignment explanation
Indices: 1351--1606 Score: 426
Period size: 123 Copynumber: 2.1 Consensus size: 125
1341 AATGACTTGG
* *
1351 TCTTGAATTGACAATCTAATTCAAAGGTCTTGACGACTTGGTCTTGAATTGATAATAATTCGATT
1 TCTTGAATTGACAATCTAATTCAAAGGTCTCGACGACTTGGTCTTGAATTGATAAT-ATTCAATT
1416 CAAGGGTCTCGATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
65 CAAGGGTCTCGATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
* * * *
1477 TCTTGAATTGATAATTTAATTCAAAGGTCTCGATGACTTGTTCTTGAATTGATAAT-TT-AATTC
1 TCTTGAATTGACAATCTAATTCAAAGGTCTCGACGACTTGGTCTTGAATTGATAATATTCAATTC
*
1540 AAGGGTCTCGATGACTTAATCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
66 AAGGGTCTCGATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
1600 TCTTGAA
1 TCTTGAA
1607 CATATGAAAA
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
123 70 0.57
124 2 0.02
126 51 0.41
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (125 bp):
TCTTGAATTGACAATCTAATTCAAAGGTCTCGACGACTTGGTCTTGAATTGATAATATTCAATTC
AAGGGTCTCGATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
Found at i:1723 original size:16 final size:16
Alignment explanation
Indices: 1702--1736 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1692 TCTGAAAATA
1702 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
1718 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
1734 CTT
1 CTT
1737 TCTGAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:6695 original size:14 final size:16
Alignment explanation
Indices: 6677--6734 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
6667 CCATTTATTA
6677 ATATATATA-ATTAA-
1 ATATATATACATTAAT
6691 ATATATTATACATATAAT
1 ATATA-TATACAT-TAAT
* *
6709 ATTAGATATATATTAAT
1 A-TATATATACATTAAT
6726 ATATATATA
1 ATATATATA
6735 ATATTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 9 0.25
17 8 0.22
18 7 0.19
19 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATATATACATTAAT
Found at i:6747 original size:11 final size:10
Alignment explanation
Indices: 6679--6775 Score: 55
Period size: 11 Copynumber: 9.6 Consensus size: 10
6669 ATTTATTAAT
6679 ATATATAATTA
1 ATATAT-ATTA
6690 A-ATATATTATA
1 ATATATA-T-TA
6701 CATATAATATTA
1 -ATAT-ATATTA
6713 GATATATATTA
1 -ATATATATTA
6724 ATATATATATA
1 ATATATAT-TA
*
6735 ATATTTAATTA
1 ATATAT-ATTA
*
6746 AT-TCT-TT-
1 ATATATATTA
6753 ATAT-TATT-
1 ATATATATTA
6761 ATATATATT-
1 ATATATATTA
6770 ATATAT
1 ATATAT
6776 TTATAAAATT
Statistics
Matches: 73, Mismatches: 3, Indels: 22
0.74 0.03 0.22
Matches are distributed among these distances:
7 3 0.04
8 9 0.12
9 11 0.15
10 15 0.21
11 20 0.27
12 9 0.12
13 3 0.04
14 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (10 bp):
ATATATATTA
Found at i:8168 original size:87 final size:87
Alignment explanation
Indices: 8021--8184 Score: 217
Period size: 87 Copynumber: 1.9 Consensus size: 87
8011 ATATTTTTTT
* **
8021 AATATATTTCTTAAATGCAATTGTTTAAATTGTTATAATTTTACTATACTGAAAGTTCTATTTTT
1 AATATATTTCTTAAATGCAATTGTTTAAATTGTTATAATTTTACTATACTAAAAACTCTATTTTT
8086 ATTTAATTAAATCTAATTATGG
66 ATTTAATTAAATCTAATTATGG
* * * *
8108 AATATATTTCTTAAATGTC-ATTTTTTAAACTT-TTA-AACTTTTATTCTATTAAAAACTCTATT
1 AATATATTTCTTAAATG-CAATTGTTTAAA-TTGTTATAA-TTTTACTATACTAAAAACTCTATT
8170 TTTATTTAATTAAAT
63 TTTATTTAATTAAAT
8185 TCAATAGTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
86 2 0.03
87 62 0.93
88 3 0.04
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (87 bp):
AATATATTTCTTAAATGCAATTGTTTAAATTGTTATAATTTTACTATACTAAAAACTCTATTTTT
ATTTAATTAAATCTAATTATGG
Found at i:9502 original size:93 final size:93
Alignment explanation
Indices: 9391--9579 Score: 360
Period size: 93 Copynumber: 2.0 Consensus size: 93
9381 TATTTAATTA
*
9391 CTTATTTATTTATTCTCTTCCTCTGCTTTTGTTAGGCTTTTATAGTTTATACGGTCACTGTTTTT
1 CTTATTTATTTATTCTCTTCCTCTGCTTTTGTTAGGCTTTTATAGTTTACACGGTCACTGTTTTT
*
9456 GCAAACTGGTTAGTTGAATAATTGTTTG
66 GCAAACTGGTTAGTTGAATAATTGTTGG
9484 CTTATTTATTTATTCTCTTCCTCTGCTTTTGTTAGGCTTTTATAGTTTACACGGTCACTGTTTTT
1 CTTATTTATTTATTCTCTTCCTCTGCTTTTGTTAGGCTTTTATAGTTTACACGGTCACTGTTTTT
9549 GCAAACTGGTTAGTTGAATAATTGTTGG
66 GCAAACTGGTTAGTTGAATAATTGTTGG
9577 CTT
1 CTT
9580 GTTGTTGTTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (93 bp):
CTTATTTATTTATTCTCTTCCTCTGCTTTTGTTAGGCTTTTATAGTTTACACGGTCACTGTTTTT
GCAAACTGGTTAGTTGAATAATTGTTGG
Found at i:12214 original size:11 final size:11
Alignment explanation
Indices: 12198--12235 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12188 GACAGAAAGT
12198 AAAAAAAA-AA
1 AAAAAAAATAA
12208 AAAAAAAATAA
1 AAAAAAAATAA
*
12219 AAAAAAACTAA
1 AAAAAAAATAA
12230 AAAAAA
1 AAAAAA
12236 CTAAAAAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.92, C:0.03, G:0.00, T:0.05
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:12242 original size:11 final size:10
Alignment explanation
Indices: 12197--12243 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
12187 CGACAGAAAG
12197 TAAAAAAAAA
1 TAAAAAAAAA
12207 -AAAAAAAAA
1 TAAAAAAAAA
12216 TAAAAAAAAA
1 TAAAAAAAAA
*
12226 CTAAAAAAAAC
1 -TAAAAAAAAA
12237 TAAAAAA
1 TAAAAAA
12244 GCTTTTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.26
10 16 0.47
11 9 0.26
ACGTcount: A:0.87, C:0.04, G:0.00, T:0.09
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:26619 original size:15 final size:15
Alignment explanation
Indices: 26599--26636 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
26589 GACTTTTTTG
*
26599 TGACAATGCTTAAAA
1 TGACAATACTTAAAA
26614 TGACAACTACTTAAAA
1 TGACAA-TACTTAAAA
26630 TG-CAATA
1 TGACAATA
26637 TCTAATGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 9 0.43
16 10 0.48
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (15 bp):
TGACAATACTTAAAA
Found at i:26905 original size:27 final size:27
Alignment explanation
Indices: 26863--26933 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
26853 AGTGGACTTA
** *
26863 AAATGACCAACGTGCCCCTGAATAT-G
1 AAATGACCAAAATGCCCCTGAAAATAG
*
26889 CAAATGACCAAAATG-CCCTTAAAATAG
1 -AAATGACCAAAATGCCCCTGAAAATAG
26916 AAATGACCAAAATGCCCC
1 AAATGACCAAAATGCCCC
26934 CCTAGGTGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAAAATAG
Found at i:29470 original size:31 final size:31
Alignment explanation
Indices: 29432--29519 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
29422 TCAATACAGT
*
29432 TTTTCAATTCTGTTTTACATTTCTTTTTTAC
1 TTTTCAATTCTGTTTTACATTTCTGTTTTAC
* * *
29463 TTTTCAATACTGTTTTCCAATTT-TGTTTTAT
1 TTTTCAATTCTGTTTTAC-ATTTCTGTTTTAC
*
29494 TTTTCAATAT-TGTTTTGCATTTCTGT
1 TTTTCAAT-TCTGTTTTACATTTCTGT
29520 AAAGGCTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.08
31 40 0.83
32 4 0.08
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (31 bp):
TTTTCAATTCTGTTTTACATTTCTGTTTTAC
Found at i:29496 original size:18 final size:18
Alignment explanation
Indices: 29475--29509 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29465 TTCAATACTG
*
29475 TTTTCCAATTTTGTTTTA
1 TTTTCCAATATTGTTTTA
*
29493 TTTTTCAATATTGTTTT
1 TTTTCCAATATTGTTTT
29510 GCATTTCTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.09, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTCCAATATTGTTTTA
Found at i:29575 original size:31 final size:28
Alignment explanation
Indices: 29534--29602 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
29524 GCTAAATACC
*
29534 CAAAAAAATCCCGTATGTTTTTCTTTTCGGA
1 CAAAATAATCCCGTATG-TTTT-TTTT-GGA
*
29565 CAAAATAATCCCTTATGTTTTTTTTGGA
1 CAAAATAATCCCGTATGTTTTTTTTGGA
*
29593 CAAATTAATC
1 CAAAATAATC
29603 TCTTACGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.34
29 4 0.11
30 4 0.11
31 15 0.43
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (28 bp):
CAAAATAATCCCGTATGTTTTTTTTGGA
Found at i:29588 original size:28 final size:29
Alignment explanation
Indices: 29534--29613 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 29
29524 GCTAAATACC
* *
29534 CAAAAAAATCCCGTATGTTTTTCTTTTCGGA
1 CAAAATAATCCCTTATG--TTTCTTTTCGGA
*
29565 CAAAATAATCCCTTATGTTT-TTTTTGGA
1 CAAAATAATCCCTTATGTTTCTTTTCGGA
* * *
29593 CAAATTAATCTCTTACGTTTC
1 CAAAATAATCCCTTATGTTTC
29614 AAAAGTGAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 24 0.57
29 3 0.07
31 15 0.36
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (29 bp):
CAAAATAATCCCTTATGTTTCTTTTCGGA
Done.