Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016563.1 Corchorus olitorius cultivar O-4 contig16596, 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: 59744
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9984 original size:224 final size:219
Alignment explanation
Indices: 9532--10119 Score: 878
Period size: 224 Copynumber: 2.7 Consensus size: 219
9522 CTTGTTATTA
* ** * *
9532 CTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGACATTGACATTTTTTCTTA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGATTTACA-TTTTTC-TA
9597 TATACCCAAAATTGGCTTTAAACGT-TCTTTAATCCATA-TTTTCATCCTAATTAATTGAATAAA
64 TATACCCAAAATTGGCTTTAAACGTGT-TTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
* * * * * *
9660 CCAAGTCTAAATGAATTTAGTGTCATCTAATAATTAAATAACATGCAAAATTCAGTATCCCCAAA
128 CCCAGTCTATATGAATTTAATGTCATCTAATAATTAAAAAAAATGCAAAATTCAGTATCCCAAAA
*
9725 GTGATATACTTTATACCCAAATCATTT
193 GTAATATACTTTATACCCAAATCATTT
* *
9752 CTCATCATCCCCACATAATCATATGCATCATCCCCAAATTTTTTAGAGATTTACATTTTTCCTCA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGATTTACATTTTT-CT-A
* *
9817 TATACCCAAAATTGGCTTTAAAAAGTGTTTTAATCCATATTTTTCATCCTAATTAATTGAATATA
64 TATACCCAAAATTGGCTTT-AAACGTGTTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
*
9882 CCCAGTCTATATGATTTTTAATGTCATCTAATAATTAAACAAAAATGCAAAATTCAGTATCCCAA
128 CCCAGTCTATATGA-ATTTAATGTCATCTAATAATTAAA-AAAAATGCAAAATTCAGTATCCCAA
9947 AAGTAATATACTTTATACCCAAATCATTT
191 AAGTAATATACTTTATACCCAAATCATTT
* *
9976 CTCATCATCACCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGATTTGCA-TTTTCTATA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGATTTACATTTTTCTATA
* *
10040 TACCC-AAATTGGCTTCAAACGTGTTTTAATCCATATTTTTCATCTTAATTAATTGAATAAACCC
66 TACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCC
*
10104 CGTCTATATGAATTTA
131 AGTCTATATGAATTTA
10120 GCGCCATCTA
Statistics
Matches: 334, Mismatches: 27, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
218 4 0.01
219 61 0.18
220 79 0.24
221 24 0.07
222 39 0.12
223 26 0.08
224 101 0.30
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (219 bp):
CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGAGATTTACATTTTTCTATA
TACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCC
AGTCTATATGAATTTAATGTCATCTAATAATTAAAAAAAATGCAAAATTCAGTATCCCAAAAGTA
ATATACTTTATACCCAAATCATTT
Found at i:10824 original size:65 final size:65
Alignment explanation
Indices: 10737--10872 Score: 209
Period size: 65 Copynumber: 2.1 Consensus size: 65
10727 CAAAATTTGG
* *
10737 CATCCCCAAACTGATATACTCTATACCCAAATTATTTCTCATCATCCCTAAATAATCATAAGCAC
1 CATCCCCAAACTGATATACTCTATACCCAAATTAATTCTCATCATCCCCAAATAATCATAAGCAC
* * * * *
10802 CATCCCCAGAGTGATATGCTCTATACCCAAATTAATTCTTATCATCCCCAAATAATCATAAGCAT
1 CATCCCCAAACTGATATACTCTATACCCAAATTAATTCTCATCATCCCCAAATAATCATAAGCAC
10867 CATCCC
1 CATCCC
10873 AAATTCATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (65 bp):
CATCCCCAAACTGATATACTCTATACCCAAATTAATTCTCATCATCCCCAAATAATCATAAGCAC
Found at i:11050 original size:286 final size:285
Alignment explanation
Indices: 10521--11086 Score: 875
Period size: 286 Copynumber: 2.0 Consensus size: 285
10511 ATTCAGCATT
* *
10521 CCCAAAGTGATATACTCCATAGCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCACCATC
1 CCCAAAGTGATATACTCCATACCCAAATCAATTCTCATCATCCCCAAATAATCATAAGCACCATC
* *
10586 CCCAAATTCATTAGAGATTGACATTTGTTCTTATATACCCAAAATTGTCTTTAAACGTGCTTTAA
66 CCCAAATTCATTAGAGATTGACATTTGTTCTTATATACCCAAAATTGGCTTTAAAAGTGCTTTAA
*
10651 TCCATACATTTATCCTGATTAATTGAATAAACCCCATCTATATGAATTGAGTGTCATCTAATAAT
131 TCCATACATTTATCCTAATTAATTGAATAAACCCCATCTATATGAATTGAGTGTCATCTAATAAT
** *
10716 GAAACAAAATGCAAAATTTGGCATCCCCAAACTGATATACTCTATACCCAAATTATTTCTCATCA
196 GAAACAAAATGCAAAATTCAGCATCCCCAAACTGATATACTCTATACCCAAATCATTTCTCATCA
*
10781 TCCCTAAATAATCATAAGCACCATC
261 TCCCCAAATAATCATAAGCACCATC
* * * * * *
10806 CCCAGAGTGATATGCTCTATACCCAAATTAATTCTTATCATCCCCAAATAATCATAAGCATCAT-
1 CCCAAAGTGATATACTCCATACCCAAATCAATTCTCATCATCCCCAAATAATCATAAGCACCATC
*
10870 CCCAAATTCATTAGAGATTGACATTTTTTCTTTATATACCCAAAATTGGCTTTAAAAAGTGCTTT
66 CCCAAATTCATTAGAGATTGACATTTGTTC-TTATATACCCAAAATTGGCTTT-AAAAGTGCTTT
* * * *
10935 AATTCATA-TTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTAGTGTCATCTAAT
129 AATCCATACATTT-ATCCTAATTAATTGAATAAACCCCATCTATATGAATTGAGTGTCATCTAAT
* * * *
10999 AATGAAACAAAATGCAAAATTCAGTATCCTCAAACTGCTATACTTTATACCCAAATCATTTCTCA
193 AATGAAACAAAATGCAAAATTCAGCATCCCCAAACTGATATACTCTATACCCAAATCATTTCTCA
11064 TCATCCCCAAATAATCATAAGCA
258 TCATCCCCAAATAATCATAAGCA
11087 ACGTACCCAA
Statistics
Matches: 254, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
284 29 0.11
285 80 0.31
286 145 0.57
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.33
Consensus pattern (285 bp):
CCCAAAGTGATATACTCCATACCCAAATCAATTCTCATCATCCCCAAATAATCATAAGCACCATC
CCCAAATTCATTAGAGATTGACATTTGTTCTTATATACCCAAAATTGGCTTTAAAAGTGCTTTAA
TCCATACATTTATCCTAATTAATTGAATAAACCCCATCTATATGAATTGAGTGTCATCTAATAAT
GAAACAAAATGCAAAATTCAGCATCCCCAAACTGATATACTCTATACCCAAATCATTTCTCATCA
TCCCCAAATAATCATAAGCACCATC
Found at i:20276 original size:21 final size:20
Alignment explanation
Indices: 20250--20291 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
20240 ACATATCACG
20250 CCATGTGTACCAAAAAAGTGA
1 CCATGTGTACC-AAAAAGTGA
**
20271 CCATGTGTTTCAAAAAGTGA
1 CCATGTGTACCAAAAAGTGA
20291 C
1 C
20292 ACGTGGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
CCATGTGTACCAAAAAGTGA
Found at i:20705 original size:11 final size:11
Alignment explanation
Indices: 20685--20728 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
20675 ATGTATATTC
*
20685 ATAATAAATTT
1 ATAATTAATTT
20696 ATAATTAATTT
1 ATAATTAATTT
20707 ATAATT-ATTT
1 ATAATTAATTT
*
20717 GATAATTTATTT
1 -ATAATTAATTT
20729 TATATAGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:26826 original size:19 final size:18
Alignment explanation
Indices: 26794--26829 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26784 ATGAAAAATC
*
26794 AAAAAGAAAGAAAGAAGG
1 AAAAAGAAAAAAAGAAGG
26812 AAAAAGAAACAAAAGAAG
1 AAAAAGAAA-AAAAGAAG
26830 TTAGTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAGAAGG
Found at i:35314 original size:4 final size:4
Alignment explanation
Indices: 35305--35332 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35295 CACAAACAGG
35305 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
35333 CTATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:35643 original size:29 final size:30
Alignment explanation
Indices: 35601--35657 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
35591 CACATATGAA
*
35601 AATAAATATTCTAAACAAAC-AGTAACAAC
1 AATAAATAATCTAAACAAACAAGTAACAAC
*
35630 AATAAATAATCTAAATAAACAAGTAACA
1 AATAAATAATCTAAACAAACAAGTAACA
35658 CACTTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.21
Consensus pattern (30 bp):
AATAAATAATCTAAACAAACAAGTAACAAC
Found at i:43575 original size:3 final size:3
Alignment explanation
Indices: 43569--43634 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
43559 ACGACGAGAG
* * * * * *
43569 AGA AGA AGA AGA AGA CGA AGA CGT AGA AGA TGA AGA AGA CGA AGA GGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
43617 GGA GGA GGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA
43635 GCCGAGGCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.53, C:0.05, G:0.39, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:46239 original size:80 final size:81
Alignment explanation
Indices: 46102--46252 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 81
46092 CTTGGAAAAA
* * *
46102 GTTTACAATAGTAAAGTTAACACTGTAATTTTATCTTCAGATGAACAACTATATGGTGCGTTCTT
1 GTTTACAATAGTAAAGTTAACACTGTAATCTTATCTTCAGATGAACAACTATATGGTGCATCCTT
46167 GTAGGATATGTCAAAG
66 GTAGGATATGTCAAAG
* * * * *
46183 GTTTACAATATTGAA-TTAACTACTGTAA-CTTATCTTGAGATGAACAATTATGTGGTGCATCCT
1 GTTTACAATAGTAAAGTTAAC-ACTGTAATCTTATCTTCAGATGAACAACTATATGGTGCATCCT
46246 TGTAGGA
65 TGTAGGA
46253 CATGATGAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 41 0.67
81 20 0.33
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (81 bp):
GTTTACAATAGTAAAGTTAACACTGTAATCTTATCTTCAGATGAACAACTATATGGTGCATCCTT
GTAGGATATGTCAAAG
Found at i:59663 original size:18 final size:19
Alignment explanation
Indices: 59613--59649 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59603 TTATTTTTGA
* *
59613 ATTTTTAAATAAAAAATTG
1 ATTTTTTAAGAAAAAATTG
59632 ATTTTTTAAGAAAAAATT
1 ATTTTTTAAGAAAAAATT
59650 ACTTTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATTTTTTAAGAAAAAATTG
Done.