Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019011.1 Corchorus olitorius cultivar O-4 contig19044, 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: 30920
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--33 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 CA
3 AT 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 AT A
34 AATTCATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5638 original size:21 final size:20
Alignment explanation
Indices: 5614--5661 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5604 GGATGGCATC
* *
5614 AAAGCAAAACTTAGGAAGGGG
1 AAAG-AAAACTAAAGAAGGGG
*
5635 AAAGGAAACTAAAGAAGGGG
1 AAAGAAAACTAAAGAAGGGG
5655 -AAGAAAA
1 AAAGAAAA
5662 AAACTGATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.56, C:0.06, G:0.31, T:0.06
Consensus pattern (20 bp):
AAAGAAAACTAAAGAAGGGG
Found at i:11874 original size:59 final size:58
Alignment explanation
Indices: 11782--11902 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 58
11772 TGAAGGCCGT
*
11782 TAAGTCAATATCTCTATCAGGAGAAAGTTTATGTAGAAGTTGGTTTTGGAGAAAAAAAA
1 TAAGTCAATATCTCTATCAGGAGAAAGCTTATGTAGAAGTTGGTTTTGGAG-AAAAAAA
11841 TAAGTCAATATCTCTATCAGGAGAAAGCTTATGTAGAAGTTGGTTTTGGAGAAAAAAA
1 TAAGTCAATATCTCTATCAGGAGAAAGCTTATGTAGAAGTTGGTTTTGGAGAAAAAAA
11899 TAAG
1 TAAG
11903 AACTGCTAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 11 0.18
59 50 0.82
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (58 bp):
TAAGTCAATATCTCTATCAGGAGAAAGCTTATGTAGAAGTTGGTTTTGGAGAAAAAAA
Found at i:12020 original size:14 final size:14
Alignment explanation
Indices: 12001--12064 Score: 101
Period size: 14 Copynumber: 4.4 Consensus size: 14
11991 TTACCAAGGA
12001 AATTAATTATTTTT
1 AATTAATTATTTTT
12015 AATTAATTATTTTT
1 AATTAATTATTTTT
12029 AATTAATTATTTTT
1 AATTAATTATTTTT
12043 AATTATATATTATTTTT
1 AA-T-TA-ATTATTTTT
12060 AATTA
1 AATTA
12065 CCAAGGAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
14 30 0.64
15 3 0.06
16 3 0.06
17 11 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTAATTATTTTT
Found at i:12512 original size:217 final size:214
Alignment explanation
Indices: 12072--12465 Score: 506
Period size: 219 Copynumber: 1.8 Consensus size: 214
12062 TTACCAAGGA
*
12072 AATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGTCATCTTTTGGCTTTTTTGGGTCTTTTCT
1 AATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGTCACCTTTTGGCTTTTTTGGGTCTTTTCT
** * *
12137 CACTTTTCGGATGACTAAAAAGCCCCTCTATGATTTTCCGCCCCTTCCTTTTCCTGCTACCCTTT
66 CACTTTTCAAATGACTAAAAAGCCCCTCTATGAGTTTCCGCCCCTTCCTTTTCCTGCTACCATTT
** ** *
12202 TTTGTAATTATTCATTTCACTTCCTTAATTGCTTTTAATTAATGTCCCCCCCTTTCTTTTTTCCT
131 TTTGTAATTACCCATTTCACTTCCTTAATTGCTTTTAATTAATGTCCAACCCTTTCTTTTTGCCT
* **
12267 CTCACCAACTCGATACCAGGGT
196 CTAACC-ACTAAATACC--GGT
**
12289 AATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGTCACCTTTTGGCTTTTTTTTTTTTTGTCT
1 AATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGTCACCTTTTGGC-----TTTTTTGGGTCT
* * *
12354 TTTCTCACTTTTCAAATGACT-AAAAGCTCCTCTATGAGTTT-C-CCCTTTCTTTTTCCTGCTAC
61 TTTCTCACTTTTCAAATGACTAAAAAGCCCCTCTATGAGTTTCCGCCCCTTCCTTTTCCTGCTAC
* * *
12416 CATTTTTTGTAATTACCCATTTCCCTTCCTTATTTGTTTTTAATTAATGT
126 CATTTTTTGTAATTACCCATTTCACTTCCTTAATTGCTTTTAATTAATGT
12466 TTAAGGCTTT
Statistics
Matches: 157, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
217 47 0.30
219 62 0.39
220 1 0.01
221 18 0.11
222 29 0.18
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (214 bp):
AATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGTCACCTTTTGGCTTTTTTGGGTCTTTTCT
CACTTTTCAAATGACTAAAAAGCCCCTCTATGAGTTTCCGCCCCTTCCTTTTCCTGCTACCATTT
TTTGTAATTACCCATTTCACTTCCTTAATTGCTTTTAATTAATGTCCAACCCTTTCTTTTTGCCT
CTAACCACTAAATACCGGT
Found at i:13406 original size:16 final size:16
Alignment explanation
Indices: 13382--13425 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
13372 ATTTTCGGGT
13382 ACCCGAACCCGAAATG
1 ACCCGAACCCGAAATG
* *
13398 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
13414 ACCCGAACCCGA
1 ACCCGAACCCGA
13426 TCAACCCGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.41, G:0.14, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:14166 original size:23 final size:24
Alignment explanation
Indices: 14109--14166 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
14099 TACATATTTA
*
14109 ATTTATGTTAATTTAAAGTTTAAAT
1 ATTTAAGTTAATTT-AAGTTTAAAT
***
14134 ATTGCGGTTAATTT-AGTTTAAAT
1 ATTTAAGTTAATTTAAGTTTAAAT
14157 ATTTAAGTTA
1 ATTTAAGTTA
14167 TATATTAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 16 0.59
25 11 0.41
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTTAAGTTAATTTAAGTTTAAAT
Found at i:14227 original size:2 final size:2
Alignment explanation
Indices: 14216--14258 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
14206 TTTTGATTCT
*
14216 TA TA TA -A TA TA TG TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14256 TA T
1 TA T
14259 TTGTTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15109 original size:17 final size:17
Alignment explanation
Indices: 15077--15110 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15067 CGAACCGCTT
*
15077 GACCCGAAACCGAAAAC
1 GACCCGAAACCAAAAAC
*
15094 GACCCGAACCCAAAAAC
1 GACCCGAAACCAAAAAC
15111 CCGAGATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.38, G:0.15, T:0.00
Consensus pattern (17 bp):
GACCCGAAACCAAAAAC
Found at i:15121 original size:68 final size:68
Alignment explanation
Indices: 15024--15172 Score: 205
Period size: 68 Copynumber: 2.2 Consensus size: 68
15014 AAAGAACTGT
* * * *
15024 AACGACCCGAATCC-GAAACCCAAGGTTCAAACCCGAAATTATCCGAACCGCT-TGACCCGAAAC
1 AACGACCCGAACCCAAAAACCCAAGATTCAAACCCGAAATTATCCGAACCG-TATGAACCGAAAC
15087 CGAA
65 CGAA
* *
15091 AACGACCCGAACCCAAAAACCCGAGATTCAAACCCGAAATTATCCGAACCGTATGAACTGAAACC
1 AACGACCCGAACCCAAAAACCCAAGATTCAAACCCGAAATTATCCGAACCGTATGAACCGAAACC
15156 GAA
66 GAA
*
15159 AGCGACCC-AACCCA
1 AACGACCCGAACCCA
15173 TAATTGACCC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 20 0.27
68 53 0.73
ACGTcount: A:0.40, C:0.34, G:0.15, T:0.11
Consensus pattern (68 bp):
AACGACCCGAACCCAAAAACCCAAGATTCAAACCCGAAATTATCCGAACCGTATGAACCGAAACC
GAA
Found at i:15197 original size:15 final size:17
Alignment explanation
Indices: 15162--15199 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
15152 AACCGAAAGC
15162 GACCC-AACCCATAATT
1 GACCCGAACCCATAATT
15178 GACCCGAACCCA-AA-T
1 GACCCGAACCCATAATT
15193 GACCCGA
1 GACCCGA
15200 CATTTGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.13, T:0.11
Consensus pattern (17 bp):
GACCCGAACCCATAATT
Found at i:15660 original size:35 final size:37
Alignment explanation
Indices: 15614--15691 Score: 142
Period size: 35 Copynumber: 2.2 Consensus size: 37
15604 TTTCATTCAT
15614 ATATATATATATATTTACACACACAGAGTACA-TT-C
1 ATATATATATATATTTACACACACAGAGTACATTTCC
15649 ATATATATATATATTTACACACACAGAGTACATTTCC
1 ATATATATATATATTTACACACACAGAGTACATTTCC
15686 ATATAT
1 ATATAT
15692 CAACTTGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 32 0.78
36 2 0.05
37 7 0.17
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (37 bp):
ATATATATATATATTTACACACACAGAGTACATTTCC
Found at i:20302 original size:2 final size:2
Alignment explanation
Indices: 20295--20325 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20285 TTCAGAAAGA
20295 AT 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 AT A
20326 CAAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24411 original size:28 final size:27
Alignment explanation
Indices: 24346--24411 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
24336 TTTAGCGTCT
* *
24346 AAGGGCAAAATTGTAATTTAGTCAATC
1 AAGGGCAAAATTGTAATTTAGCCAACC
* * *
24373 AGGGGGTAAAATTGTAATTTTAGCCGACC
1 A-AGGGCAAAATTGTAA-TTTAGCCAACC
24402 AAGGGCAAAA
1 AAGGGCAAAA
24412 CAATAATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 1 0.03
28 20 0.67
29 9 0.30
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (27 bp):
AAGGGCAAAATTGTAATTTAGCCAACC
Found at i:25067 original size:5 final size:5
Alignment explanation
Indices: 25039--25085 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
25029 ATTTCATTTC
** *
25039 TTATT ATTATT TT-TT TCCTT TTATT TTATT TTATT TTATT TTGTT TT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
25086 CCTTTTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
4 3 0.08
5 28 0.78
6 5 0.14
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:29024 original size:15 final size:15
Alignment explanation
Indices: 28995--29035 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28985 TACTTTGCTT
28995 TGTTTTCTAGTTTAAC
1 TGTTTTCT-GTTTAAC
*
29011 TGTTTTCTGTTTAAT
1 TGTTTTCTGTTTAAC
*
29026 TGCTTTCTGT
1 TGTTTTCTGT
29036 CAATCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (15 bp):
TGTTTTCTGTTTAAC
Found at i:29415 original size:23 final size:22
Alignment explanation
Indices: 29388--29465 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 22
29378 TTTTTTTGTG
29388 TTTTGCGTCGAAAAAAAAAATTT
1 TTTTGCGTC-AAAAAAAAAATTT
29411 TTTTGCGTCATAAAAAAAAAATTT
1 TTTTGCGTC--AAAAAAAAAATTT
* *
29435 GTTTCTGCGTCATAAAAAAAA-GT
1 -TTT-TGCGTCAAAAAAAAAATTT
29458 TTTTGCGT
1 TTTTGCGT
29466 TTTTCTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
21 5 0.10
22 3 0.06
23 10 0.20
24 22 0.45
25 3 0.06
26 6 0.12
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TTTTGCGTCAAAAAAAAAATTT
Found at i:29443 original size:26 final size:25
Alignment explanation
Indices: 29386--29455 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 25
29376 TTTTTTTTTG
*
29386 TGTTTTGCGTC-GAAAAAAAAAATT
1 TGTTTTGCGTCATAAAAAAAAAATT
29410 T-TTTTGCGTCATAAAAAAAAAATT
1 TGTTTTGCGTCATAAAAAAAAAATT
29434 TGTTTCTGCGTCATAAAAAAAA
1 TGTTT-TGCGTCATAAAAAAAA
29456 GTTTTTGCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 9 0.21
24 14 0.33
25 3 0.07
26 16 0.38
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (25 bp):
TGTTTTGCGTCATAAAAAAAAAATT
Done.