Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1305
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: 2081
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:404 original size:72 final size:72
Alignment explanation
Indices: 159--589 Score: 453
Period size: 72 Copynumber: 6.0 Consensus size: 72
149 ATTGCGGTGT
* * * * * *
159 TTTTACAGAAGTGCCGCTAATGCCAGTACATCTGAAACCAAAACGATGCGTTTTGG-T-TTTTTT
1 TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTTTTT
222 GTGGCGC
66 GTGGCGC
* * * * *
229 TTTTACAGAAGCGCCGCTAATGCCACTACAGCTCATATCAAAACGATGCGTTTTGGTTTGTTTTT
1 TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGG-TTATTTTT
*
294 TGTGGCGA
65 TGTGGCGC
* * * **
302 TTATACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTATTCCTT
1 TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTTTTT
**
367 GCCGCGC
66 GTGGCGC
* * * *
374 TTTTATGGAAGCGCCGCTAATGCAACTACATCCCAAATCAAAACGATGTGTTTTGATTATTTTTT
1 TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTTTTT
* *
439 GCGACGC
66 GTGGCGC
** * * * * *
446 TTTTGTGGAATCGCCGCTAATGCCACAACA--TCAAATCAAATCGAAGTGTTTGGGTTATTTTTT
1 TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTA-TTTTT
*
509 TGTGGCGT
65 TGTGGCGC
* * *
517 TTTTACGGAATCGCCGCTAATGCTACTACATCTCAAATCAAAACGATGCG-TTTGG--ATTTTTA
1 TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTTTT-
*
579 TGCGGCGC
65 TGTGGCGC
587 TTT
1 TTT
590 ATCGAAAACG
Statistics
Matches: 303, Mismatches: 51, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
69 5 0.02
70 82 0.27
71 36 0.12
72 102 0.34
73 78 0.26
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (72 bp):
TTTTACGGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGATGTGTTTTGGTTATTTTTT
GTGGCGC
Found at i:437 original size:143 final size:144
Alignment explanation
Indices: 162--574 Score: 467
Period size: 143 Copynumber: 2.9 Consensus size: 144
152 GCGGTGTTTT
* * * * * *
162 TACAGAAGTGCCGCTAATGCCAGTACATCTGAAACCAAAACGATGCGTTTTGGTT-TTTTTGTGG
1 TACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTATTTTTGTGG
* * * * *
226 CGCTTTTACAGAAGCGCCGCTAATGCCACTACAGCTCATATCAAAACGATGCGTTTTGGTTTG-T
66 CGCTTTTACGGAAGCGCCGCTAATGCAACTACATCTCAAATCAAAACGATGCGTTTT-GATTGAT
* *
290 TTTTTGTGGCGATTA
130 TTTTTGCGACGATTA
* **
305 TACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTATTCCTTGCC
1 TACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTATT-TTTGTG
* * *
370 GCGCTTTTATGGAAGCGCCGCTAATGCAACTACATCCCAAATCAAAACGATGTGTTTTGATT-AT
65 GCGCTTTTACGGAAGCGCCGCTAATGCAACTACATCTCAAATCAAAACGATGCGTTTTGATTGAT
* *
434 TTTTTGCGACGCTTT
130 TTTTTGCGACGATTA
*** * * * *
449 TGTGGAATCGCCGCTAATGCCACAACA--TCAAATCAAATCGAAGTGTTTGGGTTATTTTTTTGT
1 TACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTA--TTTTTGT
* * * *
512 GGCGTTTTTACGGAATCGCCGCTAATGCTACTACATCTCAAATCAAAACGATGCGTTTGGATT
64 GGCGCTTTTACGGAAGCGCCGCTAATGCAACTACATCTCAAATCAAAACGATGCGTTTTGATT
575 TTTATGCGGC
Statistics
Matches: 227, Mismatches: 38, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
142 25 0.11
143 107 0.47
144 41 0.18
145 54 0.24
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (144 bp):
TACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTATTTTTGTGG
CGCTTTTACGGAAGCGCCGCTAATGCAACTACATCTCAAATCAAAACGATGCGTTTTGATTGATT
TTTTGCGACGATTA
Found at i:547 original size:215 final size:214
Alignment explanation
Indices: 166--562 Score: 521
Period size: 215 Copynumber: 1.8 Consensus size: 214
156 TGTTTTTACA
* * * ** *
166 GAAGTGCCGCTAATGCCAGTACATCTGAAACCAAAACGATGCGTTTTGGTTTTTTTGTGGCGCTT
1 GAAGCGCCGCTAATGCAACTACATCCCAAACCAAAACGATGCGTTTTGATTTTTTTGTGGCGCTT
* * * *
231 TTACAGAAGCGCCGCTAATGCCACTACAGCTCATATCAAAACGATGCGTTTTGGTTTGTTTTTTG
66 TTACAGAAGCGCCGCTAATGCCACAACA-CTCAAATCAAAACGAAGCGTTTGGGTTTGTTTTTTG
296 TGGCGATTATACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTA
130 TGGCGATTATACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTA
361 TTCCTTGCCGCGCTTTTATG
195 TTCCTTGCCGCGCTTTTATG
* *
381 GAAGCGCCGCTAATGCAACTACATCCCAAATCAAAACGATGTGTTTTGATTATTTTT-TGCGACG
1 GAAGCGCCGCTAATGCAACTACATCCCAAACCAAAACGATGCGTTTTGATT-TTTTTGTG-G-CG
*** * * *
445 CTTTTGTGGAATCGCCGCTAATGCCACAACA-TCAAATCAAATCGAAGTGTTTGGGTTAT-TTTT
63 CTTTTACAGAAGCGCCGCTAATGCCACAACACTCAAATCAAAACGAAGCGTTTGGGTT-TGTTTT
* * * * *
508 TTGTGGCGTTTTTACGGAATCGCCGCTAATGCTACTACATCTCAAATCAAAACGA
127 TTGTGGCGATTATACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGA
563 TGCGTTTGGA
Statistics
Matches: 155, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
215 120 0.77
216 7 0.05
217 28 0.18
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (214 bp):
GAAGCGCCGCTAATGCAACTACATCCCAAACCAAAACGATGCGTTTTGATTTTTTTGTGGCGCTT
TTACAGAAGCGCCGCTAATGCCACAACACTCAAATCAAAACGAAGCGTTTGGGTTTGTTTTTTGT
GGCGATTATACAGAAGCGCCGCTAATGCCACTACATCTCAAATCAAAACGAAGTGTTTTGGTTAT
TCCTTGCCGCGCTTTTATG
Found at i:699 original size:41 final size:39
Alignment explanation
Indices: 654--744 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
644 GGTTTTTTGT
*
654 GGCGTTTTCTCCAGAATCGCCGCTAAAT-TCATATTATTAGC
1 GGCGTTTTCT-CAGAATCGCCGCT-AATCTC-TATTATTAGA
* * *
695 GGCGTTTACTTAGAATCGCCGCTAATGCTCTATTTTTAGA
1 GGCGTTTTCTCAGAATCGCCGCTAAT-CTCTATTATTAGA
735 GGCGTTTTCT
1 GGCGTTTTCT
745 TTGATTGGCC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 29 0.67
41 11 0.26
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (39 bp):
GGCGTTTTCTCAGAATCGCCGCTAATCTCTATTATTAGA
Found at i:739 original size:40 final size:39
Alignment explanation
Indices: 666--772 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 39
656 CGTTTTCTCC
* *
666 AGAATCGCCGCTAAAT-TCATATTATTAGCGGCGTTTACTT
1 AGAATCGCCGCT-AATCTC-TATTTTTAGAGGCGTTTACTT
*
706 AGAATCGCCGCTAATGCTCTATTTTTAGAGGCGTTTTCTT
1 AGAATCGCCGCTAAT-CTCTATTTTTAGAGGCGTTTACTT
* * * *
746 TGATTGGCCGCTAATACTCGATTTTTA
1 AGAATCGCCGCTAAT-CTCTATTTTTA
773 CCGGCGTCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
39 3 0.05
40 52 0.91
41 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (39 bp):
AGAATCGCCGCTAATCTCTATTTTTAGAGGCGTTTACTT
Done.