Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_162 ID=scaffold_162-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: 10690
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.27
Warning! 301 characters in sequence are not A, C, G, or T
Found at i:1761 original size:19 final size:20
Alignment explanation
Indices: 1717--1762 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1707 AATGTCTCTT
*
1717 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
1736 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
1755 TATGCATT
1 TATGCATT
1763 AAACACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 12 0.52
20 10 0.43
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:8115 original size:132 final size:132
Alignment explanation
Indices: 7956--9029 Score: 1743
Period size: 132 Copynumber: 8.1 Consensus size: 132
7946 TTAGACAGCA
* ** * * * *
7956 GAGCAGATCAAAGATGGCAAATTTTACCTTTCTGTGGTTACAGTGGAGAACATTGAAGCCAGTAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
* ** *
8021 TTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8086 TG
131 TG
* * * * *
8088 GAGCAGATCAAAGATGGAAAATTTTACCACCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
*
8153 TTCTACTTCCCTGGGCAGTAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8218 TG
131 TG
*
8220 GAGCAGATCAAAGATGGCAGATTTTACCTCTCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
* ** *
8285 TTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8350 TG
131 TG
* * *
8352 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAATAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
* *
8417 TTCTACTTCCCTGGGCAGTAGTGGAATAGATTGAAGATTTTGGATCTTTTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8482 TG
131 TG
* *
8484 GAGCAGATCAAAGATGGCATATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCTAATAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
8549 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8614 TG
131 TG
* * * *
8616 GAGCAGATCAAAGATGGTAGATTTTACCTCCCTAAGGTTGCAGTGTAGTACATTGAAGCCAGTAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
8681 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8746 TG
131 TG
* * *
8748 GAGCAGATCAAAGATGGAAAATTTTACCTCCCTGAGGTTGTAGTGGAGTACATTGAAGCCAATAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
*
8813 TTCTACTTCCCTGGGCAGCAGTGGAACAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
8878 TG
131 TG
* * *
8880 GAGTAGATCAAAGATGGTAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAA
1 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
* * * **
8945 TTCTACTTCCCTCGGCAGCAGCGAAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
9010 TG
131 TG
9012 GAGCAGATCAAAGATGGC
1 GAGCAGATCAAAGATGGC
9030 NNNNNNNNNN
Statistics
Matches: 877, Mismatches: 65, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 877 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (132 bp):
GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAATAA
TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAG
TG
Found at i:8647 original size:44 final size:44
Alignment explanation
Indices: 8167--8912 Score: 207
Period size: 44 Copynumber: 17.0 Consensus size: 44
8157 ACTTCCCTGG
* ** * * **
8167 GCAGTAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* ** * * *
8211 GCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCTCTGAG
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCT-AA
** * * **** * * **
8256 GTTGCAGTGGAGTACATTGAAGCCAATA-ATTCTACTTCCCTGG
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* * * * * *
8299 GCAGCAGCGGAATAGATTGAAGAT-TTCAGATCTTGCCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGT-AGATTTTACCTCCCTAA
* ** *
8343 GCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCT--
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
** * ** * * **
8385 GTGGTTACAGTGGAGTACATTGAAG-TCAATA-ATTCTACTTCCCTGG
1 GCAG-T--AGTGGAGTAGATTGAAGAT-GGTAGATTTTACCTCCCTAA
* ** * *
8431 GCAGTAGTGGAATAGATTGAAGATTTTGGATCTTT-TCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGAT-TTTACCTCCCTAA
* ** * * *
8475 GCAGTAGTGGAGCAGATCAAAGATGGCATATTTTACCTCCCTGAG
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCT-AA
** * * * ** * * **
8520 GTTGCAGTGGAGTACATTGAAGCTAATA-ATTCTACTTCCCTGG
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* * ** * * **
8563 GCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* **
8607 GCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTACCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
** * * * *** * * **
8651 GGTTGCAGTGTAGTACATTGAAGCCAGTA-ATTCTACTTCCCTGG
1 -GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* * ** * * **
8695 GCAGCAGTGGAATAGATTGAAGATTTTGGATCTTGTCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* ** * * *
8739 GCAGTAGTGGAGCAGATCAAAGATGGAAAATTTTACCTCCCTGAG
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCT-AA
** * **** * * **
8784 GTTGTAGTGGAGTACATTGAAGCCAATA-ATTCTACTTCCCTGG
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
* ** ** * * **
8827 GCAGCAGTGGAACAGATTGAAGATTTTGGATCTTGTCTCCCTAA
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
**
8871 GCAGTAGTGGAGTAGATCAAAGATGGTAGATTTTACCTCCCT
1 GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCT
8913 GAGGTTGCAG
Statistics
Matches: 466, Mismatches: 216, Indels: 40
0.65 0.30 0.06
Matches are distributed among these distances:
42 3 0.01
43 96 0.21
44 278 0.60
45 87 0.19
46 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
GCAGTAGTGGAGTAGATTGAAGATGGTAGATTTTACCTCCCTAA
Found at i:9568 original size:132 final size:132
Alignment explanation
Indices: 9331--9603 Score: 420
Period size: 132 Copynumber: 2.1 Consensus size: 132
9321 NNNNNNNNNN
* * * * **
9331 GAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAACAGATTGAAGATTTTGGATCTTGTCTCC
1 GAAGCCAGTAATTCTACTTCCCTCGGCAGCAGCGAAACAGATTGAAGATTTCAGATCTTGTCTCC
* * *
9396 CTAAGCAGTAGTGGAGTAGATCAAAGATGGTAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACA
66 CTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACA
9461 TT
131 TT
*
9463 GAAGCCAGTAATTCTACTTCCCTCGGCAGCAGCGAAATAGATTGAAGATTTCAGATCTTGTCTCC
1 GAAGCCAGTAATTCTACTTCCCTCGGCAGCAGCGAAACAGATTGAAGATTTCAGATCTTGTCTCC
* * * *
9528 CTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGGTTTTACCTCCCTGTGTTTACAGTGGAGTACA
66 CTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACA
9593 TT
131 TT
9595 GAAGCCAGT
1 GAAGCCAGT
9604 TACCCTATTT
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 127 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (132 bp):
GAAGCCAGTAATTCTACTTCCCTCGGCAGCAGCGAAACAGATTGAAGATTTCAGATCTTGTCTCC
CTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACA
TT
Done.