Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1390
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: 1860
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:320 original size:110 final size:102
Alignment explanation
Indices: 108--509 Score: 428
Period size: 105 Copynumber: 3.7 Consensus size: 102
98 GTTTTTACGC
* * * *
108 AAAAATAAATCAAATTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
1 AAAAATAAATCAATTTATAAAAAAAAAAAAAAAATTTAGAATACCAAAACGGCGTCATTTTGATA
173 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCA
66 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCA
* *
210 AAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTG
1 AAAAATAAATCAATTTATAAAAAA-AAAA-AAAAAA-TTTAGAATACCAAAACGGCGTCATTTTG
* * *
275 TTCAAAACGAAATAATTTTGCGGCGTTTTTATGAAAAAA-GCCGCAAAAAATACA
63 ATAAAAATGAAAT-A----GCGGCGTTTTTAT-AAAAAACGCCG---------CA
* * *
329 AAAAATAAATCAATTTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
1 AAAAATAAATCAATTTATAAAAAAAAAAAAAAAATTTAGAATACCAAAACGGCGTCATTTTGATA
*
394 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGTA
66 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCA
** * **
431 AAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATAGTAAAACAGCGTTGTTTTG
1 AAAAATAAATCAATTTATAAAAAA-AAAA-AAAAAA-TTTAGAATACCAAAACGGCGTCATTTTG
* *
496 TTCAAAATGAAATA
63 ATAAAAATGAAATA
510 ATTTTGCGGC
Statistics
Matches: 250, Mismatches: 28, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
102 48 0.19
103 6 0.02
104 12 0.05
105 67 0.27
106 1 0.00
110 23 0.09
111 23 0.09
115 1 0.00
116 34 0.14
117 6 0.02
118 3 0.01
119 26 0.10
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.26
Consensus pattern (102 bp):
AAAAATAAATCAATTTATAAAAAAAAAAAAAAAATTTAGAATACCAAAACGGCGTCATTTTGATA
AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCA
Found at i:423 original size:111 final size:116
Alignment explanation
Indices: 208--476 Score: 323
Period size: 116 Copynumber: 2.4 Consensus size: 116
198 AAAAACGCCG
* *
208 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTT
1 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATACCAAAACGGCGTCATTT
* * *
273 TGTTCAAAACGAAATAATTTTGCGGCGTTTTTATGAAAAAAGCCGCAAAAAATA
66 TGATAAAAACGAAATAA---TGCGGCGTTTTTATAAAAAAAGCCGCAAAAAATA
* * *
327 CAAAAAATAAATCAATTTATAAAAAA-TAAA-AAAAAA-TTTAGCATACCAAAACGGTGTCATTT
1 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATACCAAAACGGCGTCATTT
* *
389 TGATAAAAATGAAAT-A-GCGGCGTTTTTATAAAAAACGCCG-------T-
66 TGATAAAAACGAAATAATGCGGCGTTTTTATAAAAAAAGCCGCAAAAAATA
430 -AAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATA
1 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATA
477 GTAAAACAGC
Statistics
Matches: 135, Mismatches: 12, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
102 25 0.19
103 3 0.02
104 7 0.05
105 8 0.06
111 22 0.16
115 1 0.01
116 34 0.25
117 6 0.04
118 3 0.02
119 26 0.19
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.26
Consensus pattern (116 bp):
CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTAGAATACCAAAACGGCGTCATTT
TGATAAAAACGAAATAATGCGGCGTTTTTATAAAAAAAGCCGCAAAAAATA
Found at i:496 original size:221 final size:221
Alignment explanation
Indices: 108--525 Score: 773
Period size: 221 Copynumber: 1.9 Consensus size: 221
98 GTTTTTACGC
108 AAAAATAAATCAAATTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
1 AAAAATAAATCAAATTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
173 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAA
66 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAA
* *
238 ATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAACGAAATAATTTTGCGGCGTTT
131 ATAAAAAATTTTAGAATAGCAAAACAGCGTCGTTTTGTTCAAAACGAAATAATTTTGCGGCGCTT
303 TTATGAAAAAAGCCGCAAAAAATACA
196 TTATGAAAAAAGCCGCAAAAAATACA
*
329 AAAAATAAATCAATTTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
1 AAAAATAAATCAAATTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
*
394 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGTAAAAAATAAATCAATTTATAAAAAACAAA
66 AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAA
* * *
459 ATAAAAAATTTTAGAATAGTAAAACAGCGTTGTTTTGTTCAAAATGAAATAATTTTGCGGCGCTT
131 ATAAAAAATTTTAGAATAGCAAAACAGCGTCGTTTTGTTCAAAACGAAATAATTTTGCGGCGCTT
524 TT
196 TT
526 GTAAAAACAC
Statistics
Matches: 190, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
221 190 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (221 bp):
AAAAATAAATCAAATTATAAAAAATAAAAAAAAATTTAGCATACCAAAACGGTGTCATTTTGATA
AAAATGAAATAGCGGCGTTTTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAA
ATAAAAAATTTTAGAATAGCAAAACAGCGTCGTTTTGTTCAAAACGAAATAATTTTGCGGCGCTT
TTATGAAAAAAGCCGCAAAAAATACA
Done.