Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_425 ID=scaffold_425-JGI_221_v2.0
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: 7158
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:2626 original size:7 final size:7
Alignment explanation
Indices: 2616--2660 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
2606 GATAAAAGAG
2616 ATGAAAA
1 ATGAAAA
2623 ATG-AAA
1 ATGAAAA
2629 ATGAAAA
1 ATGAAAA
2636 ATGAAAAA
1 ATG-AAAA
2644 ATGAAAA
1 ATGAAAA
2651 A-GTAAAA
1 ATG-AAAA
2658 ATG
1 ATG
2661 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.21
7 19 0.56
8 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:2634 original size:13 final size:13
Alignment explanation
Indices: 2616--2642 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2606 GATAAAAGAG
2616 ATGAAAAATGAAA
1 ATGAAAAATGAAA
2629 ATGAAAAATGAAA
1 ATGAAAAATGAAA
2642 A
1 A
2643 AATGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:2646 original size:15 final size:14
Alignment explanation
Indices: 2616--2660 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
2606 GATAAAAGAG
2616 ATGAAAAATG-AAA
1 ATGAAAAATGAAAA
2629 ATGAAAAATGAAAAA
1 ATGAAAAATG-AAAA
2644 ATGAAAAA-GTAAAA
1 ATGAAAAATG-AAAA
2658 ATG
1 ATG
2661 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:4264 original size:50 final size:50
Alignment explanation
Indices: 4210--4675 Score: 341
Period size: 50 Copynumber: 9.4 Consensus size: 50
4200 GCAGCGGAAC
*
4210 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *** * * * ** ** *
4260 AGATTAAAGCTACAACAACGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * *
4310 AGATTAAAGTCACATCGGTGAATCTTGGTTCCCCGACAATGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *** * * * ** *
4360 AGATTAAAGCTACAACAACGAATCTTAC-TCCTCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCC-CCGAC-ATTGCAGTTAAAA
*
4410 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * **** ** *
4460 AGATTAAAGCTACAACAGCGAATGTTACTTCCCTGGTGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
4510 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** ** *
4560 AGATTAAAGCTACAACAGTG-A-CTTACTT-CTCAAGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGA-CATTGCAGTTAAAA
* * * *
4608 AGATTAACGCCACAACGGCGAA-CTTTGTTTCCCCAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATC-TTGCTTCCCCGACATTGCAGTTAAAA
*
4658 AGACTAAAGCCACAACGG
1 AGATTAAAGCCACAACGG
4676 CGGATCTTAC
Statistics
Matches: 303, Mismatches: 105, Indels: 16
0.71 0.25 0.04
Matches are distributed among these distances:
47 3 0.01
48 31 0.10
49 7 0.02
50 254 0.84
51 8 0.03
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:4355 original size:100 final size:100
Alignment explanation
Indices: 4182--4718 Score: 776
Period size: 100 Copynumber: 5.4 Consensus size: 100
4172 TTGCATCAGG
* * * *
4182 TCTTATTTCCCTGGTGGTGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
*
4247 ATTGCAGTTAAAAAGATTAAAGCTACAACAACGAA
66 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
* * *
4282 TCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGTCACATCGGTGAATCTTGGTTCCCCGAC
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
* *
4347 AATGCAGTTAAAAAGATTAAAGCTACAACAACGAA
66 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
*
4382 TCTTAC-TCCTCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
1 TCTTACTTCC-CAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
4446 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
65 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
* * *
4482 TGTTACTTCCCTGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
*
4547 ATTGCAGTTAAAAAGATTAAAGCTACAACAGTG-A
66 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
* * * * * * *
4581 -CTTACTTCTCAAGCGGTGCAGTGGAACAGATTAACGCCACAACGGCGAA-CTTTGTTTCCCCAA
1 TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATC-TTGCTTCCCCGA
* * * *
4644 CATTGCAGTTAAAAAGACTAAAGCCACAACGGCGGA
65 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
*
4680 TCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGAAGC
1 TCTTAC-TTCCCAGGCGGTGCAGTGGAACAGATTAAAGC
4719 TACAACAACA
Statistics
Matches: 396, Mismatches: 35, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
97 1 0.00
98 81 0.20
99 5 0.01
100 278 0.70
101 31 0.08
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (100 bp):
TCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGAC
ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAA
Done.