Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022802.1 Corchorus olitorius cultivar O-4 contig22835, 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: 13145
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:6578 original size:11 final size:10
Alignment explanation
Indices: 6563--6607 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
6553 CATATCCCAA
6563 TTTTCTCTTT
1 TTTTCTCTTT
6573 ATTTTCT-TTT
1 -TTTTCTCTTT
*
6583 TTTTCCCTTT
1 TTTTCTCTTT
6593 TTTTCTCTTCT
1 TTTTCTCTT-T
6604 TTTT
1 TTTT
6608 GCTTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 5 0.17
10 14 0.47
11 11 0.37
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:6622 original size:15 final size:17
Alignment explanation
Indices: 6593--6673 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 17
6583 TTTTCCCTTT
*
6593 TTTTCTCTTCTTTTTGC
1 TTTTCTCTTCTTTTTCC
6610 TTTTCT-TTC-TTTTCC
1 TTTTCTCTTCTTTTTCC
* * *
6625 TTTATATTTTCCTTTTTCT
1 TTT-TCTCTT-CTTTTTCC
6644 TTTTC-CTT-TTTTT-C
1 TTTTCTCTTCTTTTTCC
6658 TTTCTCTCTTTCTTTT
1 TTT-TCTC-TTCTTTT
6674 CCCGCTAGGC
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
14 3 0.06
15 15 0.30
16 6 0.12
17 12 0.24
18 6 0.12
19 8 0.16
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTCTCTTCTTTTTCC
Found at i:6646 original size:12 final size:12
Alignment explanation
Indices: 6615--6675 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
6605 TTTGCTTTTC
6615 TTTCTTTTCCTT
1 TTTCTTTTCCTT
* *
6627 TATATTTTCCTT
1 TTTCTTTTCCTT
6639 TTTCTTTTTCCTT
1 TTTC-TTTTCCTT
* *
6652 TTTTTCTTTCTCTC
1 TTTCT-TTTC-CTT
6666 TTTCTTTTCC
1 TTTCTTTTCC
6676 CGCTAGGCCT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 14 0.36
13 19 0.49
14 6 0.15
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTCCTT
Found at i:6655 original size:21 final size:20
Alignment explanation
Indices: 6631--6673 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
6621 TTCCTTTATA
* *
6631 TTTTCCTTTTTCTTTTTCCTT
1 TTTTCCTTTCTCTCTTT-CTT
*
6652 TTTTTCTTTCTCTCTTTCTT
1 TTTTCCTTTCTCTCTTTCTT
6672 TT
1 TT
6674 CCCGCTAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCCTTTCTCTCTTTCTT
Found at i:9915 original size:36 final size:36
Alignment explanation
Indices: 9875--9958 Score: 168
Period size: 36 Copynumber: 2.3 Consensus size: 36
9865 TTGAATATGA
9875 TGAAATTGAATGGAAGACTTATTCTTGCTCTGATTT
1 TGAAATTGAATGGAAGACTTATTCTTGCTCTGATTT
9911 TGAAATTGAATGGAAGACTTATTCTTGCTCTGATTT
1 TGAAATTGAATGGAAGACTTATTCTTGCTCTGATTT
9947 TGAAATTGAATG
1 TGAAATTGAATG
9959 ATGATTTTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (36 bp):
TGAAATTGAATGGAAGACTTATTCTTGCTCTGATTT
Found at i:13006 original size:332 final size:328
Alignment explanation
Indices: 12334--13145 Score: 852
Period size: 332 Copynumber: 2.5 Consensus size: 328
12324 GGCAGCGATC
* * * **
12334 ACTGAGCCTGGGCCACGAAACGTGTTTTTAGCCAAAAATCGTGATAGTTAACACACGATTTCGGC
1 ACTGAGCCGGGGCCACGAAACGCGTTTTTAGTCAAAAATCGTGAT-GTTAGTACACGATTTCGGC
* * * ** *
12399 TAAAGTTTTGCAAACATTTACCAGAAAGAATTT-TCCTCAGTTTTTGG-CTGTGATGCTCATAAA
65 TAAAATTTTGCAAA-ATTAACCAG-AA-AATTTCTCCTCAATTTTTGGCCT-CAATACTCATAAA
* * *
12462 AATATATATAATTCAACGCCAAAAAGATTAAAAGTCTTTTCACGTTTCTAATATCATTTTTCGTA
126 AATATATATAATTCAACGCCAAAAAGATTAAAAGTCTTCTCACGCTTCTAATATCATTTTTCCTA
* * * *
12527 TTTTCCGAATTAATTTCTAATTGAATCAAAACATAATTTAGATGCTCTTAAAAACAAATCCTTCA
191 TTTTCCGAATTAATTTCTAATTAAATCAAAACACAATTGAGATGCTCGTAAAAACAAATCCTTCA
* * *
12592 AACCAATGTGGGTGAGATTTGGTTATATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAAT
256 AACCAATGTGGCTGAGATTTGGTTATATGGATATAAATATTTCAATGAGACTTGACGCCAAAAAT
*
12657 CAAGGAAA
321 CAAGCAAA
* * * * * *
12665 ACAGAGCCGGGGCCCCGGAATGCGTTTTTAGTCAAAAAATTGTGATGGTTAGTACACAATTTCGG
1 ACTGAGCCGGGGCCACGAAACGCGTTTTTAGTC-AAAAATCGTGAT-GTTAGTACACGATTTCGG
* * *
12730 CTAAAATTTTGCAAAATTGACCAGGAAATTTTCTCCTCAATTTTTGGCCTCAATACTCATGAAAA
64 CTAAAATTTTGCAAAATTAACCA-GAAAATTTCTCCTCAATTTTTGGCCTCAATACTCATAAAAA
* * * *
12795 -ATATATAAGTCAACGCCAAAATGATTGAATGTCTTCTCACGCTTCTAATATCATTTTTCCTATT
128 TATATATAATTCAACGCCAAAAAGATTAAAAGTCTTCTCACGCTTCTAATATCATTTTTCCTA--
* ** * * * * **
12859 TTTTCTGAATTTTTTTCTAATTAAATTGAAATC-CGATTGAGATGCTCGTCAAAGTAAATCCTT-
191 TTTTCCGAATTAATTTCTAATTAAA-TCAAAACACAATTGAGATGCTCGTAAAAACAAATCCTTC
* * * * *
12922 AAATCCAATGTGGCTGAGATTTTGTTATATGTATATAAATATTTCAATGAGTCTTGATGTCAAAA
255 AAA-CCAATGTGGCTGAGATTTGGTTATATGGATATAAATATTTCAATGAGACTTGACGCCAAAA
***
12987 ATCTTTCAAA
319 ATCAAGCAAA
* * * *
12997 ACTGAGCCGGGACCACAAAACACGTTTTTAGTCAAAAACCGTGA---T-GTACACGATTTCGGCT
1 ACTGAGCCGGGGCCACGAAACGCGTTTTTAGTCAAAAATCGTGATGTTAGTACACGATTTCGGCT
* * * *
13058 AAATTTTTGCAAAAATTAACCA-AAAGTTTCTCCCTCAATTTTTAGCCACAATACTCATTATATA
66 AAAATTTTGC-AAAATTAACCAGAAAATTTCT-CCTCAATTTTTGGCCTCAATACTCA-TA-A-A
*
13122 TATATATATAATTCAACGCCAAAA
126 AATATATATAATTCAACGCCAAAA
Statistics
Matches: 397, Mismatches: 70, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
325 8 0.02
326 47 0.12
327 12 0.03
328 1 0.00
329 2 0.01
330 79 0.20
331 71 0.18
332 172 0.43
333 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (328 bp):
ACTGAGCCGGGGCCACGAAACGCGTTTTTAGTCAAAAATCGTGATGTTAGTACACGATTTCGGCT
AAAATTTTGCAAAATTAACCAGAAAATTTCTCCTCAATTTTTGGCCTCAATACTCATAAAAATAT
ATATAATTCAACGCCAAAAAGATTAAAAGTCTTCTCACGCTTCTAATATCATTTTTCCTATTTTC
CGAATTAATTTCTAATTAAATCAAAACACAATTGAGATGCTCGTAAAAACAAATCCTTCAAACCA
ATGTGGCTGAGATTTGGTTATATGGATATAAATATTTCAATGAGACTTGACGCCAAAAATCAAGC
AAA
Done.