Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1085
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: 1639209
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.20
Warning! 665865 characters in sequence are not A, C, G, or T
File 7 of 7
Found at i:1636029 original size:32 final size:32
Alignment explanation
Indices: 1635980--1636876 Score: 1018
Period size: 32 Copynumber: 29.2 Consensus size: 32
1635970 AAAATGGTGA
* * *
1635980 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1636012 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
1636044 TTTTAAATGGGTTGCCACCAACTTCTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
1636076 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636108 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1636140 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
1636172 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1636204 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636236 TTTGAAATGGGTTGCCACCGACTTGTGTGAGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1636268 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636300 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1636332 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636364 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636396 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1636428 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636460 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636492 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
1636524 TTTGGAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1636552 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636581 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* * *
1636610 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636639 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
*
1636668 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* * * *
1636697 TTTAAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * ** *
1636726 TTTGAAAAGAG-TGCCACTAAC-T-TGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1636755 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
*
1636784 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1636812 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1636841 TTTGAAA-GAAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATG-GGTTGCCACCGACTTGTGTGGGC
1636870 TTTGAAA
1 TTTGAAA
1636877 GGGATGAACA
Statistics
Matches: 806, Mismatches: 41, Indels: 39
0.91 0.05 0.04
Matches are distributed among these distances:
28 43 0.05
29 257 0.32
30 10 0.01
31 4 0.00
32 491 0.61
33 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:1636877 original size:29 final size:29
Alignment explanation
Indices: 1636517--1636877 Score: 493
Period size: 29 Copynumber: 12.5 Consensus size: 29
1636507 CACCGACTTG
* * *
1636517 TGTGGGCTTTGGAAG-GGTGCCACTAACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
*
1636545 TGTGGGCTTTGAAA-AGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGA-AGTGCCACTGACT
*
1636574 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
*
1636603 TGTGGGCTTTGAAA-AGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGA-AGTGCCACTGACT
*
1636632 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
*
1636661 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
* *
1636690 TGTGGGCTTT-AAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGA-AGTGCCACTGACT
*
1636719 TGTGGGCTTTGAAA-AGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGA-AGTGCCACTGACT
* *
1636748 TGTAGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
*
1636777 TGTGGGCTTTGAAAG-GGTGCCACTGACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
*
1636805 TGTGGGCTTTGAAA-AGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGA-AGTGCCACTGACT
1636834 TGTGGGCTTTGAAAGAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGAAGTGCCACTGACT
1636863 TGTGGGCTTTGAAAG
1 TGTGGGCTTTGAAAG
1636878 GGATGAACAT
Statistics
Matches: 299, Mismatches: 23, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
28 42 0.14
29 253 0.85
30 4 0.01
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAGAAGTGCCACTGACT
Found at i:1638124 original size:12 final size:12
Alignment explanation
Indices: 1638117--1638148 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1638107 TATTTTTTTC
1638117 TTTTTTTTTTGT
1 TTTTTTTTTTGT
*
1638129 TTTTTGTTTTGT
1 TTTTTTTTTTGT
1638141 TTTTTTTT
1 TTTTTTTT
1638149 GGGTGTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:1638125 original size:11 final size:11
Alignment explanation
Indices: 1638099--1638148 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
1638089 GACCCTTCTA
* *
1638099 TTTTTTGCTAT
1 TTTTTTGTTTT
*
1638110 TTTTTTCTTTT
1 TTTTTTGTTTT
1638121 TTTTTTGTTTT
1 TTTTTTGTTTT
1638132 TTGTTTTGTTTT
1 TT-TTTTGTTTT
1638144 TTTTT
1 TTTTT
1638149 GGGTGTAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 23 0.68
12 11 0.32
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTGTTTT
Done.