Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014048.1 Corchorus olitorius cultivar O-4 contig14081, 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: 8687
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:516 original size:29 final size:30
Alignment explanation
Indices: 345--515 Score: 178
Period size: 30 Copynumber: 5.8 Consensus size: 30
335 TGAATGCGCG
* *
345 AAAATGACCATAATG-CCCCTA-AATGTGA
1 AAAATGACCAAAATGCCCCCTAGAATATGA
373 AAAAGTGACCAAAATG-CCCCTA-AATATGCA
1 AAAA-TGACCAAAATGCCCCCTAGAATATG-A
*
403 AAAGTGACCAAAATGCCCCCT-GAATATGCA
1 AAAATGACCAAAATGCCCCCTAGAATATG-A
* *
433 AAAATGACCAAAATGCCCCCTAGATTTTTG-
1 AAAATGACCAAAATGCCCCCTAGA-ATATGA
* *
463 AAAATGACCAAAATGCCCCCTAGATTTTTG-
1 AAAATGACCAAAATGCCCCCTAGA-ATATGA
493 AAAATGACCAAAATG-CCCCTAGA
1 AAAATGACCAAAATGCCCCCTAGA
516 TGATCCTAGC
Statistics
Matches: 131, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
28 4 0.03
29 40 0.31
30 82 0.63
31 2 0.02
32 3 0.02
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (30 bp):
AAAATGACCAAAATGCCCCCTAGAATATGA
Found at i:762 original size:13 final size:12
Alignment explanation
Indices: 744--802 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
734 ACAAATAAAT
744 AATAAAATAAAAG
1 AATAAAA-AAAAG
*
757 AATAAAAAAAAC
1 AATAAAAAAAAG
769 AA-AAAAAAAA-
1 AATAAAAAAAAG
* *
779 AACAAACAAAAAA
1 AATAAA-AAAAAG
*
792 AAGAAAAAAAA
1 AATAAAAAAAA
803 CTTGGAGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 2 0.05
11 11 0.27
12 16 0.39
13 12 0.29
ACGTcount: A:0.86, C:0.05, G:0.03, T:0.05
Consensus pattern (12 bp):
AATAAAAAAAAG
Found at i:766 original size:1 final size:1
Alignment explanation
Indices: 760--802 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
750 ATAAAAGAAT
* * * *
760 AAAAAAAACAAAAAAAAAAAACAAACAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
803 CTTGGAGCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:772 original size:17 final size:16
Alignment explanation
Indices: 731--801 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
721 AAAGAATTCC
* * *
731 AAAACAAATAAATAAT
1 AAAACAAAAAAAAAAA
* *
747 AAAATAAAAGAATAAAA
1 AAAACAAAA-AAAAAAA
764 AAAACAAAAAAAAAAA
1 AAAACAAAAAAAAAAA
780 ACAAACAAAAAAAAGAAA
1 A-AAACAAAAAAAA-AAA
798 AAAA
1 AAAA
802 ACTTGGAGCA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 14 0.31
17 27 0.60
18 4 0.09
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.07
Consensus pattern (16 bp):
AAAACAAAAAAAAAAA
Found at i:1058 original size:30 final size:30
Alignment explanation
Indices: 1022--1917 Score: 1113
Period size: 30 Copynumber: 30.0 Consensus size: 30
1012 AACTAAAGTG
* ** *
1022 ATGATCCTAAACCACCATTAAAATGAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
1052 ATGATCCTCAAACAAGATTAAAATAAAGCG
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1082 ACGATCCTCAACCAGGATTAAAATAAAGCT
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1112 ATGATCCTCAACCAGGATTAAAGTAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* **
1142 ATGATCCTCAAACAGGATTAAAAATAAAATA
1 ATGATCCTCAACCAGGATT-AAAATAAAGCA
* * *
1173 ATGATCCTCAAACAGGATTGAAATAAAGCG
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1203 ATGATCCTCAACCAGGATTAAAATAATGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * **
1233 GTGATCCTCAACCAAGATTAAAAATAAAATA
1 ATGATCCTCAACCAGGATT-AAAATAAAGCA
* * *
1264 ATGATCCTCAAACAGGATTGAAATAAAGCG
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1294 ATGATCCTCAACCAGGATTAAAATAATGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* **
1324 GTGATCCTCAACCAGGATTAAAATAAAATA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1354 ATGATCCTCAACCAGGATTAAATTGAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
1384 ACGATCCTCAAACAGGATTAAAACAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1414 ATGATCCTCAACCAGGATTAAAACAAAGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
*
1445 AT-ATCCTCAACCAGGATTAAAATAACGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* **
1474 ACGATCCTCAACCAGGATTAAAATAAAATA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1504 ATGATCCTCAACCAGGATTAAATTGAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
1534 ACGATCCTCAAACAGGATTAAAACAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1564 ATGATCCTCAACCAGGATTAAAACAAAGCAA
1 ATGATCCTCAACCAGGATTAAAATAAAGC-A
* *
1595 AT-ATCCTCAACCAGGATTAATATAACGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1624 ACGATCCTCAACCAGGATTAAAATAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1654 ATGATCCTCAACCAGGATTAAAGTAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1684 ATAATCCTCAACCAGGATTAAAATAAAGCC
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1714 ATGATCCTCAACCAGGATTAAAATAAAGTA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1744 ACGATCCTCAACCAGGATTAAAATGAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
*
1774 ATTATCCTCAACCAGGATTAAAAT-----A
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1799 ATGATCCTCAAACAGGATTAAAATGAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * * **
1829 ATGATCCTCAAACAGGATTTAAATGACTCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* *
1859 ATGATCCTCAAACAGGATTAGAATAAAGCA
1 ATGATCCTCAACCAGGATTAAAATAAAGCA
* * *
1889 AGGATCCTCAAACATGATTAAAATAAAGC
1 ATGATCCTCAACCAGGATTAAAATAAAGC
1918 TGATAAAGCA
Statistics
Matches: 748, Mismatches: 107, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
25 23 0.03
29 4 0.01
30 664 0.89
31 57 0.08
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.21
Consensus pattern (30 bp):
ATGATCCTCAACCAGGATTAAAATAAAGCA
Found at i:2285 original size:36 final size:36
Alignment explanation
Indices: 2246--2757 Score: 589
Period size: 35 Copynumber: 14.4 Consensus size: 36
2236 CAGATCGCCT
* *
2246 TGAAATAAACTGAAGAAAAGATCGCCCTGGATCAAT
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
**
2282 TGAAATAAACTGAAGAAAAGATAGCCCTGGATCAAC
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
*
2318 TGAAATAAACTGAAG-AAAGACCGCCCTGGGTCAAC
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
*
2353 TGAAATAAACTGAAG-AAAGACCGCCCTGGGTCAAC
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* **
2388 TGAAATAAACTGAAGAAAGGGTCGCCCTGGATCAA-
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2423 TTAATATAAACTGAAG-AAAGACCGCCCTGGGTCAAC
1 TGAA-ATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2459 TGAAATAAACTGAAGAAAGGATCGCCCTGGATCAA-
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2494 TTAATATAAACTGAAG-AAAGACCGCCCTGGGTCAAC
1 TGAA-ATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2530 TGAAATAAACTGAAGAAAGGATCGCCCTGGATCAA-
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* * *
2565 TTAATATAAACTGAAGAAAGGATCGCCCTGGATCAA-
1 TGAA-ATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2601 TTAATATAAACTGAAG-AAAGACCGCCCTGGGTCAAC
1 TGAA-ATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2637 TGAAATAAACTGAAGAAATA-ATCGCCCTGAATCAAC
1 TGAAATAAACTGAAGAAA-AGACCGCCCTGGATCAAC
* * * * * * *
2673 TTAAGTGAATTGAAG-AAAGACCACCCTGGGTCAGC
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
* *
2708 TGAAATAAACTGAA-TAAAGACCGCCCTGGGTCAAC
1 TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
*
2743 TGAAATGAACTGAAG
1 TGAAATAAACTGAAG
2758 CATCTGAAAT
Statistics
Matches: 412, Mismatches: 50, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.00
35 210 0.51
36 200 0.49
37 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.18
Consensus pattern (36 bp):
TGAAATAAACTGAAGAAAAGACCGCCCTGGATCAAC
Found at i:2364 original size:71 final size:69
Alignment explanation
Indices: 2246--2757 Score: 630
Period size: 71 Copynumber: 7.2 Consensus size: 69
2236 CAGATCGCCT
**
2246 TGAAATAAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGAAGAAAAGATAGCCCTG
1 TGAAATAAACTGAAG-AAAGATCGCCCTGGATCAA-TGAAATAAACTGAAG-AAAGACCGCCCTG
*
2311 GATCAAC
63 GGTCAAC
* *
2318 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGG
1 TGAAATAAACTGAAGAAAGATCGCCCTGGATCAA-TGAAATAAACTGAAGAAAGACCGCCCTGGG
2383 TCAAC
65 TCAAC
* *
2388 TGAAATAAACTGAAGAAAGGGTCGCCCTGGATCAATTAATATAAACTGAAGAAAGACCGCCCTGG
1 TGAAATAAACTGAAGAAA-GATCGCCCTGGATCAATGAA-ATAAACTGAAGAAAGACCGCCCTGG
2453 GTCAAC
64 GTCAAC
*
2459 TGAAATAAACTGAAGAAAGGATCGCCCTGGATCAATTAATATAAACTGAAGAAAGACCGCCCTGG
1 TGAAATAAACTGAAGAAA-GATCGCCCTGGATCAATGAA-ATAAACTGAAGAAAGACCGCCCTGG
2524 GTCAAC
64 GTCAAC
* *
2530 TGAAATAAACTGAAGAAAGGATCGCCCTGGATCAATTAATATAAACTGAAGAAAGGATCGCCCTG
1 TGAAATAAACTGAAGAAA-GATCGCCCTGGATCAATGAA-ATAAACTGAAGAAA-GACCGCCCTG
*
2595 GATCAA-
63 GGTCAAC
* * * * *
2601 TTAATATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAATAATCGCCCTG
1 TGAA-ATAAACTGAAGAAAGATCGCCCTGGATCAA-TGAAATAAACTGAAGAAA-GACCGCCCTG
**
2666 AATCAAC
63 GGTCAAC
* * * * * * * * *
2673 TTAAGTGAATTGAAGAAAGACCACCCTGGGTCAGCTGAAATAAACTGAATAAAGACCGCCCTGGG
1 TGAAATAAACTGAAGAAAGATCGCCCTGGATCA-ATGAAATAAACTGAAGAAAGACCGCCCTGGG
2738 TCAAC
65 TCAAC
*
2743 TGAAATGAACTGAAG
1 TGAAATAAACTGAAG
2758 CATCTGAAAT
Statistics
Matches: 400, Mismatches: 33, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
70 63 0.16
71 287 0.72
72 50 0.12
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.18
Consensus pattern (69 bp):
TGAAATAAACTGAAGAAAGATCGCCCTGGATCAATGAAATAAACTGAAGAAAGACCGCCCTGGGT
CAAC
Found at i:4672 original size:2 final size:2
Alignment explanation
Indices: 4665--4691 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4655 GAACAATAGA
4665 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 A
4692 CATAATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.