Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold905
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: 4455
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.29
Warning! 738 characters in sequence are not A, C, G, or T
Found at i:197 original size:45 final size:44
Alignment explanation
Indices: 62--197 Score: 123
Period size: 45 Copynumber: 3.1 Consensus size: 44
52 GATTAGTGAT
* *
62 GATAACAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAA
1 GATAACAGATCTTGCCTTCCTG-ATAGACAGTGGAGCAGATCGAA
* * * * * * * *
107 GACACCA-ACCTCGCCTCCCTCG-GAGACAGTGGAGCAGGTTGAA
1 GATAACAGATCTTGCCTTCCT-GATAGACAGTGGAGCAGATCGAA
* *
150 GATAGCAGATCTTGCCTTCCTGTATAGACAGTGGAGCAGATCAAA
1 GATAACAGATCTTGCCTTCCTG-ATAGACAGTGGAGCAGATCGAA
195 GAT
1 GAT
198 GGTGAATTTT
Statistics
Matches: 68, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
43 22 0.32
44 20 0.29
45 26 0.38
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (44 bp):
GATAACAGATCTTGCCTTCCTGATAGACAGTGGAGCAGATCGAA
Found at i:344 original size:132 final size:132
Alignment explanation
Indices: 179--1030 Score: 1130
Period size: 132 Copynumber: 6.6 Consensus size: 132
169 CTGTATAGAC
* *
179 AGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCC
1 AGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * *
243 AGTAATTCTACTTCCCTGGTCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGACTCCCCAAGC
65 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGC
308 AGT
130 AGT
* * *
311 AGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCACTGTGGTTA-AGTGGAGAACATTGAAGCC
1 AGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * * * * * *
374 AGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATATTGCCTTCCTGCAT
65 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCT-AAG
* **
439 AAAC
129 CAGT
* * *
443 AGTGGAGCAAATCAAAGATGGC-GAATTTTACCTCCATGTGGTTACAGAGGAGTACATTGAAGCC
1 AGTGGAGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
* * *
507 AGAAATTATACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGC
65 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGC
572 AGT
130 AGT
* * *
575 AGTGGAACATATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
* *
640 GTAATTCTACTTCCCTAGGCAGCAATGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCA
66 GTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCA
705 GT
131 GT
* * *
707 AGTGGAACAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGACA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
* * ** * * *
772 GTAATTCTA-TCTCCCTGGGCAACAGTGGAATAAATTGAAGATTACAGATTTTATCTCCCTAAAC
66 GTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGC
836 AGT
130 AGT
*
839 AGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCC-GTGGTTACAGTGGAGTACATTGAAGCC
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTC-CCTGTGGTTACAGTGGAGTACATTGAAGCC
*
903 AATAATTCTACTTCCCT-GG--GC--------A-ATTGAAGATTTTAGATCTTGTCTCCCTAAGC
65 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGC
956 AGT
130 AGT
* *
959 AGTGGAACATATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
1024 GT-ATTCT
66 GTAATTCT
1031 TATCTCCCTA
Statistics
Matches: 644, Mismatches: 68, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
119 7 0.01
120 90 0.14
121 1 0.00
129 1 0.00
131 75 0.12
132 396 0.61
133 74 0.11
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
AGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCA
GT
Found at i:1039 original size:120 final size:120
Alignment explanation
Indices: 804--1023 Score: 361
Period size: 120 Copynumber: 1.8 Consensus size: 120
794 CAGTGGAATA
* *
804 AATTGAAGATTACAGATTTTATCTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTA
1 AATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGTGGAACAAATCAAAGATGGCAGATTTTA
869 CCTCTCCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGC
66 CCTCTCCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGC
** * * *
924 AATTGAAGATTTTAGATCTTGTCTCCCTAAGCAGTAGTGGAACATATCAAAGATGGCAGATTTTA
1 AATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGTGGAACAAATCAAAGATGGCAGATTTTA
989 CCTC-CCTGTGGTTACAGTGGAGTACATTGAAGCCA
66 CCTCTCC-GTGGTTACAGTGGAGTACATTGAAGCCA
1024 GTATTCTTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
119 2 0.02
120 90 0.98
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (120 bp):
AATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGTGGAACAAATCAAAGATGGCAGATTTTA
CCTCTCCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGC
Found at i:2600 original size:16 final size:16
Alignment explanation
Indices: 2579--2612 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2569 TATTGTACAC
*
2579 ATATATATGTATTTGA
1 ATATATATGTATGTGA
2595 ATATATATGTATGTGA
1 ATATATATGTATGTGA
2611 AT
1 AT
2613 TTTCATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
ATATATATGTATGTGA
Done.