Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007711.1 Corchorus capsularis cultivar CVL-1 contig07732, 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: 53538
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2561 original size:16 final size:16
Alignment explanation
Indices: 2540--2590 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2530 CCCCTTTCTT
2540 AATTTTCTTTTTGAAG
1 AATTTTCTTTTTGAAG
** * *
2556 AATTTT-TTTGAGTAT
1 AATTTTCTTTTTGAAG
2571 AATTTTCTTTTTGAAG
1 AATTTTCTTTTTGAAG
2587 AATT
1 AATT
2591 GATTCATATT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (16 bp):
AATTTTCTTTTTGAAG
Found at i:3457 original size:253 final size:249
Alignment explanation
Indices: 2593--3578 Score: 1787
Period size: 249 Copynumber: 3.9 Consensus size: 249
2583 GAAGAATTGA
* * * *
2593 TTCATATTTTGATACTAACTCTCCTGTATTCGATGATCACATGAAATTCTGACTATCCCAAAGTT
1 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCA-ATGAAATTCTGACTATCCAAAAGTT
* * * * **
2658 GAGCCGCATCAGATCGCATATGAGAGGAAGCTCTCCCGACATTTGTTTTAATTGTTCACATTTCC
65 GAGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCC
2723 TTCTAACAACTTTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAG
130 TTCTAACAACTTTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAG
2788 AAACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
195 AAACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
2843 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
1 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
2908 AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
66 AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
2973 TCTAACAACTTTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAGA
131 TCTAACAACTTTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAGA
3038 AACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
196 AACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
3092 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
1 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
3157 AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
66 AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
3222 TCTAACAAC-TTTTTTTTGGCCCAACGATTCCTTCTAACGGAACTTAATTGCAACTTCAAACCAA
131 TCTAACAACTTTTTTTTTGG-CC-AC-ATTCCTTCTAAC--AACTTAATTGCAACTTCAAACCAA
3286 ACAGAAACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
191 ACAGAAACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
3345 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
1 TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
3410 AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
66 AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
3475 TCTAACAAC-TTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAGA
131 TCTAACAACTTTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAGA
* * *
3539 AACATAAGCAATTACTACCACTACGGTACTCAAAAGAGAA
196 AACATAAGCAATTACTACTACTACAGTACTCAAAACAGAA
3579 GAAGAAATAA
Statistics
Matches: 718, Mismatches: 13, Indels: 12
0.97 0.02 0.02
Matches are distributed among these distances:
248 76 0.11
249 344 0.48
250 50 0.07
251 14 0.02
252 2 0.00
253 232 0.32
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.33
Consensus pattern (249 bp):
TTCATATTTTGGTACTAACTCTTCTGTATTCGATGACCAATGAAATTCTGACTATCCAAAAGTTG
AGCCGCATCAGATTGCATATGACAGGAAGCTCTCCTGACATTTGTTTTCATCATTCACATTTCCT
TCTAACAACTTTTTTTTTGGCCACATTCCTTCTAACAACTTAATTGCAACTTCAAACCAAACAGA
AACATAAGCAATTACTACTACTACAGTACTCAAAACAGAATTGATCCTTCATCG
Found at i:7844 original size:1 final size:1
Alignment explanation
Indices: 7838--7869 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
7828 ATATTACTTT
7838 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7870 GCCGTAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15097 original size:30 final size:31
Alignment explanation
Indices: 15042--15120 Score: 124
Period size: 30 Copynumber: 2.6 Consensus size: 31
15032 TAGCCTAACT
*
15042 AAACCTATCCAACTTTTTTATTGCCAAAAAA
1 AAACCTATCCAACTTTTTTAGTGCCAAAAAA
*
15073 AAATCTATCCAACTTTTTT-GTGCCAAAAAA
1 AAACCTATCCAACTTTTTTAGTGCCAAAAAA
*
15103 AACCCTATCCAACTTTTT
1 AAACCTATCCAACTTTTT
15121 GCTAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 26 0.59
31 18 0.41
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (31 bp):
AAACCTATCCAACTTTTTTAGTGCCAAAAAA
Found at i:20048 original size:33 final size:33
Alignment explanation
Indices: 20011--20076 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
20001 GCATCCTCGT
*
20011 CGAAATTCAATGCTAGGAACAACGGAAACAAAA
1 CGAAATTCAATGCTAAGAACAACGGAAACAAAA
20044 CGAAATTCAATGCTAAGAACAACGGAAACAAAA
1 CGAAATTCAATGCTAAGAACAACGGAAACAAAA
20077 AAGGAATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (33 bp):
CGAAATTCAATGCTAAGAACAACGGAAACAAAA
Found at i:31162 original size:8 final size:8
Alignment explanation
Indices: 31149--31179 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
31139 AATGATGGGT
31149 TTGGGTTA
1 TTGGGTTA
31157 TTGGGTTA
1 TTGGGTTA
31165 TTGGGTTA
1 TTGGGTTA
31173 TTGGGTT
1 TTGGGTT
31180 TGGGTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.10, C:0.00, G:0.39, T:0.52
Consensus pattern (8 bp):
TTGGGTTA
Found at i:43315 original size:19 final size:20
Alignment explanation
Indices: 43291--43337 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
43281 TACTAATTAA
43291 TTATTTTA-ATATTAAATTT
1 TTATTTTATATATTAAATTT
* *
43310 TTA-TTTATATTTTATATTT
1 TTATTTTATATATTAAATTT
43329 TATATTTTA
1 T-TATTTTA
43338 CTTAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 2 0.09
21 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTATATATTAAATTT
Found at i:43325 original size:7 final size:7
Alignment explanation
Indices: 43292--43337 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
43282 ACTAATTAAT
43292 TATTTTA
1 TATTTTA
*
43299 -ATATTA
1 TATTTTA
*
43305 AATTTT-
1 TATTTTA
43311 TA-TTTA
1 TATTTTA
43317 TATTTTA
1 TATTTTA
43324 TATTTTA
1 TATTTTA
43331 TATTTTA
1 TATTTTA
43338 CTTAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 3 0.09
6 8 0.24
7 22 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTTTA
Found at i:48586 original size:111 final size:111
Alignment explanation
Indices: 48386--48609 Score: 385
Period size: 111 Copynumber: 2.0 Consensus size: 111
48376 TTGGATAAGC
* *
48386 AATTGAAGACAAATAACTCAAGAAGAGAAAGAGATTGAGTCAAGAAAACATGTATTTGAAGAGAT
1 AATTGAAGACAAATAACTCAAGAAGAGAAAGAGATTGAATCAAGAAAACATGAATTTGAAGAGAT
*
48451 GAATCAAAGGATGAATGGGCTTAAAAATTAGGGCATAGTTTCTGCA
66 GAATCAAAGGATGAACGGGCTTAAAAATTAGGGCATAGTTTCTGCA
* *
48497 AATTGAAGACAAATAACTCAAGAATAGACAGAGATTGAATCAAGAAAACATGAATTTGAAGAGAT
1 AATTGAAGACAAATAACTCAAGAAGAGAAAGAGATTGAATCAAGAAAACATGAATTTGAAGAGAT
* *
48562 GAATCAAATGATGAACGGGTTTAAAAATTAGGGCATAGTTTCTGCA
66 GAATCAAAGGATGAACGGGCTTAAAAATTAGGGCATAGTTTCTGCA
48608 AA
1 AA
48610 CCGAAGAGAA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (111 bp):
AATTGAAGACAAATAACTCAAGAAGAGAAAGAGATTGAATCAAGAAAACATGAATTTGAAGAGAT
GAATCAAAGGATGAACGGGCTTAAAAATTAGGGCATAGTTTCTGCA
Found at i:48868 original size:17 final size:17
Alignment explanation
Indices: 48846--48924 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 17
48836 TGTGTATATA
48846 TATATATATATAACAA-
1 TATATATATATAACAAT
*
48862 T-TATATATA-AACATT
1 TATATATATATAACAAT
*
48877 TAATATTTATCCACATAACAAT
1 T-ATA--TAT--ATATAACAAT
*
48899 AATATATATATAA-AAT
1 TATATATATATAACAAT
48915 TATAT-TATAT
1 TATATATATAT
48925 TATTATCGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
14 4 0.08
15 14 0.29
16 8 0.16
17 7 0.14
19 6 0.12
21 5 0.10
22 5 0.10
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATATATATAACAAT
Done.