Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014247.1 Corchorus olitorius cultivar O-4 contig14280, 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: 48172
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4661 original size:2 final size:2
Alignment explanation
Indices: 4649--4679 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4639 ATTGAATTCC
4649 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4680 GCAATTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8261 original size:39 final size:39
Alignment explanation
Indices: 8184--8261 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
8174 TCCCTCCTGA
* *
8184 ACCTCCTGCCCCAATCAGGGCCAGTCCTCCTCCTCCACC
1 ACCTCCTGCCCCAATCAAGGCCAGTCCTCCTCCACCACC
*
8223 ACCTCCTGTCCCAAGT-AAGGCCAGTCCTCCTCCACCACC
1 ACCTCCTGCCCCAA-TCAAGGCCAGTCCTCCTCCACCACC
8262 TCCCCCCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.18, C:0.51, G:0.13, T:0.18
Consensus pattern (39 bp):
ACCTCCTGCCCCAATCAAGGCCAGTCCTCCTCCACCACC
Found at i:18468 original size:27 final size:27
Alignment explanation
Indices: 18418--18472 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
18408 GAGAGTGTCG
* *
18418 AATCTTAAATATAGAGAAACTCTTTCA
1 AATCTTAAATATAGAAAAAATCTTTCA
18445 AATCTTAAATAT-GAAAAAAATCTTTCA
1 AATCTTAAATATAG-AAAAAATCTTTCA
18472 A
1 A
18473 TAACTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (27 bp):
AATCTTAAATATAGAAAAAATCTTTCA
Found at i:23326 original size:15 final size:16
Alignment explanation
Indices: 23306--23343 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
23296 TGTGTGTGTG
*
23306 TTGTTTTT-GTTTTTT
1 TTGTTTTTAATTTTTT
23321 TTGTTTTTAATTTTTT
1 TTGTTTTTAATTTTTT
*
23337 TTATTTT
1 TTGTTTT
23344 AATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (16 bp):
TTGTTTTTAATTTTTT
Found at i:27214 original size:31 final size:30
Alignment explanation
Indices: 27176--27339 Score: 124
Period size: 31 Copynumber: 5.4 Consensus size: 30
27166 AAAGGCTAAT
27176 TGCTCAAATAAGGGCCTAACGTTTTCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTT-CAAAA
* * **
27207 TGCTCAAATAAGGGTCCGATC-TTTT-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTTCAAAA
*
27236 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTTC-AAAA
* * **
27267 TGCTCAAATAAGGGCCCGATC-TTTT-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTTCAAAA
* *
27296 TGAC-CAAATAAAGGCCTAACGTTATCGAAAA
1 TG-CTCAAATAAGGGCCTAACGTTTTC-AAAA
27327 TGCTCAAATAAGG
1 TGCTCAAATAAGG
27340 ACCTGACATC
Statistics
Matches: 100, Mismatches: 21, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
28 8 0.08
29 32 0.32
30 6 0.06
31 46 0.46
32 8 0.08
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTCAAAA
Found at i:27273 original size:60 final size:60
Alignment explanation
Indices: 27180--27339 Score: 275
Period size: 60 Copynumber: 2.7 Consensus size: 60
27170 GCTAATTGCT
* * * *
27180 CAAATAAGGGCCTAACGTTTTCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
27240 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
27300 CAAATAAAGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
27340 ACCTGACATC
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:27424 original size:31 final size:30
Alignment explanation
Indices: 27385--27549 Score: 142
Period size: 31 Copynumber: 5.5 Consensus size: 30
27375 CGATGCCAGA
*
27385 CCCTTATTTGAGCATTTTGGCAAACATTAGG
1 CCCTTATTTGAGCATTTT-GAAAACATTAGG
* ** * **
27416 CCTTTATTTG-GCCAAATT-AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTGAAAACATTAGG
27445 CCCTTATTTGAGCATTTTCGAAAACATTAGG
1 CCCTTATTTGAGCATTTT-GAAAACATTAGG
** * *
27476 CCCTTATTTG-GTCAAATT-AAAAGATT-GAA
1 CCCTTATTTGAG-CATTTTGAAAACATTAG-G
27505 CCCTTATTTGAGCATTTTGAGAAACATTAGG
1 CCCTTATTTGAGCATTTTGA-AAACATTAGG
27536 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
27550 ATTAGCCATA
Statistics
Matches: 103, Mismatches: 21, Indels: 20
0.72 0.15 0.14
Matches are distributed among these distances:
28 1 0.01
29 41 0.40
30 5 0.05
31 55 0.53
32 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGAAAACATTAGG
Found at i:27483 original size:60 final size:59
Alignment explanation
Indices: 27384--27545 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 59
27374 TCGATGCCAG
* * *
27384 ACCCTTATTTGAGCATTTTGGCAAACATTAGGCCTTTATTTGGCCAAATTAAAAGATCGG
1 ACCCTTATTTGAGCATTTT-GAAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
* * *
27444 GCCCTTATTTGAGCATTTTCGAAAACATTAGGCCCTTATTTGGTCAAATTAAAAGATTGA
1 ACCCTTATTTGAGCATTTT-GAAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
27504 ACCCTTATTTGAGCATTTTGAGAAACATTAGGCCCTTATTTG
1 ACCCTTATTTGAGCATTTTGA-AAACATTAGGCCCTTATTTG
27546 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 2 0.02
60 91 0.98
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (59 bp):
ACCCTTATTTGAGCATTTTGAAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:29510 original size:48 final size:48
Alignment explanation
Indices: 29458--29556 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
29448 TGTCCTTTGT
*
29458 AAAAGTTTGAAAGGAAAATGGGTATAATGTCATTGTTTAAGGGATATC
1 AAAAGTTTGAAAGGAAAATGGGTATAATGTCATTGTTTAAAGGATATC
*
29506 AAAAGTTTGAAGGGAAAATGGGTATAATGTCATTGTTTAAAGGATATC
1 AAAAGTTTGAAAGGAAAATGGGTATAATGTCATTGTTTAAAGGATATC
29554 AAA
1 AAA
29557 TTCCTTACAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (48 bp):
AAAAGTTTGAAAGGAAAATGGGTATAATGTCATTGTTTAAAGGATATC
Found at i:33774 original size:17 final size:17
Alignment explanation
Indices: 33752--33787 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
33742 CATTAGTAAT
*
33752 TGAAGTGAAGATAGAGC
1 TGAAGTGAAGAAAGAGC
33769 TGAAGTGAAGAAAGAGC
1 TGAAGTGAAGAAAGAGC
33786 TG
1 TG
33788 GTAATTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.36, T:0.17
Consensus pattern (17 bp):
TGAAGTGAAGAAAGAGC
Found at i:47138 original size:320 final size:320
Alignment explanation
Indices: 46576--47238 Score: 877
Period size: 320 Copynumber: 2.1 Consensus size: 320
46566 AAATTTTGCT
* * * *
46576 AAAATTGACCCGAAAAATTTTCCTCAATTTTTTTTGCCACACTACTCAGAAAAAATATATAATTC
1 AAAACTGACCCGAAAATTTTTCCTCAA-TTTTTTTGCAACAATACTCAGAAAAAATATATAATTC
* ***
46641 AAAGCCAAAAAGAGTAAATGTTTTTTTCACGCTTCTAATATCATTTTCCAACTTTTTTCCGAATT
65 AAAGCCAAAAAGAGTAAACGGGATTTTCACGCTTCTAATATCATTTTCCAAC-TTTTTCCGAATT
* * *
46706 AATTTCTAATTAAATCGAAACAAGATTCAGATTCTAGAAAAAGCAAATCCTTAAACCAATGTGGC
129 AATTTCTAATTAAATCGAAACAAGATTCAAATACTAGAAAAAGCAAATCCTTAAACAAATGTGGC
*
46771 TGAGATTTGGTTACATGAATATAGATATTTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAATTG
194 TGAGATTTGGTTACATGAATATAGAAATTTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAATTG
*
46836 AGCCGGGCTCCGGAACGCGTTGTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTA
259 AGCCGGGCTCCGGAACGCGTTGTTAGCAAAAAACCATGATGGTTAGTACACGATTTCGGCTA
* * *
46898 AAAACTGACCCGAAAATTTTTTTCTCAA-TTTTTTGCAACAATTCTGAGAAAAAATATATAATTC
1 AAAACTGACCCGAAAA-TTTTTCCTCAATTTTTTTGCAACAATACTCAGAAAAAATATATAATTC
* * ** * * *
46962 AACGCCAAAAGGA-TTGACGGGATTTTCATGCTTCTAAATATCGTTTTTCC-A-TTTTTCTGAAT
65 AAAGCCAAAAAGAGTAAACGGGATTTTCACGCTTCT-AATATC-ATTTTCCAACTTTTTCCGAAT
* * * * * *
47024 TAATTTCTAGTTTAATTGAAACAAGATTCAAATACTCGTAAAAA-CAAATTCTTATATCAAATGT
128 TAATTTCTAATTAAATCGAAACAAGATTCAAATACTAG-AAAAAGCAAATCCTTA-AACAAATGT
* * * * *
47088 GGCTGAGATTTGGTTAGATGAATATAGAAATTTTAAGGAGTCTTTGCGCCCAAAATCATGTAAAA
191 GGCTGAGATTTGGTTACATGAATATAGAAATTTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAA
* * *
47153 TTGAGCCGGGCTCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTTGGCTA
256 TTGAGCCGGGCTCCGGAACGCGTTGTTAGCAAAAAACCATGATGGTTAGTACACGATTTCGGCTA
* *
47218 AAAACCGACCCGAAAAGTTTT
1 AAAACTGACCCGAAAATTTTT
47239 GATTCAATTT
Statistics
Matches: 297, Mismatches: 39, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
319 55 0.19
320 162 0.55
321 50 0.17
322 21 0.07
323 9 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (320 bp):
AAAACTGACCCGAAAATTTTTCCTCAATTTTTTTGCAACAATACTCAGAAAAAATATATAATTCA
AAGCCAAAAAGAGTAAACGGGATTTTCACGCTTCTAATATCATTTTCCAACTTTTTCCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAAATACTAGAAAAAGCAAATCCTTAAACAAATGTGGCTG
AGATTTGGTTACATGAATATAGAAATTTCAAGAAGCCTTTGCGCCCAAAATCATCTAAAATTGAG
CCGGGCTCCGGAACGCGTTGTTAGCAAAAAACCATGATGGTTAGTACACGATTTCGGCTA
Done.