Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_501 ID=scaffold_501-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: 9350
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.20
Warning! 2972 characters in sequence are not A, C, G, or T
Found at i:8583 original size:118 final size:117
Alignment explanation
Indices: 8376--8617 Score: 349
Period size: 118 Copynumber: 2.1 Consensus size: 117
8366 ATAGTGTACA
* * *
8376 GATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTCCATTGCAGCGGAGCAGATTAAAGCTGACGG
1 GATTAAAGCTAAAGGCAGCAAATCTTGTTTCCCTCCATTGAAGCAGAGCAGATTAAAGCTGACGG
* * *
8441 CAGCCAATCTTATCTGCCTGGTGTTAAGACTTGAAATAGTTGAAGTGCAACG
66 CAGCCAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGCAACG
** * * *
8493 GATTAAAGCTATGGGCAGCGAATCTTGTTTCCCTAGCATTGAAGCAGAGCAGATTAAAGCTGAGG
1 GATTAAAGCTAAAGGCAGCAAATCTTGTTTCCCT-CCATTGAAGCAGAGCAGATTAAAGCTGACG
* * *
8558 GCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGGAGCG
65 GCAGCCAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGCAACG
8611 GATTAAA
1 GATTAAA
8618 ACTGTGGACA
Statistics
Matches: 110, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
117 30 0.27
118 80 0.73
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (117 bp):
GATTAAAGCTAAAGGCAGCAAATCTTGTTTCCCTCCATTGAAGCAGAGCAGATTAAAGCTGACGG
CAGCCAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGCAACG
Found at i:8650 original size:118 final size:118
Alignment explanation
Indices: 8411--8641 Score: 318
Period size: 118 Copynumber: 2.0 Consensus size: 118
8401 TGTTTCCCTC
* * * *
8411 CATTGCAGCGGAGCAGATTAAAGCTGACGGCAGCCAATCTTATCTGCCTGGTGTTAAGACTTGAA
1 CATTGAAGCAGAGCAGATTAAAGCTGACGGCAGCCAATCTTATCTCCCTAGTGTTAAGACTTGAA
* * * * * *
8476 ATAGTTGAAGTGCAACGGATTAAAGCTATGGGCAGCGAATCTTGTTTCCCTAG
66 ATAGCTGAAGTGCAACGGATTAAAACTATGGACAGCGAATCCTATCTCCCTAG
* *
8529 CATTGAAGCAGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAA
1 CATTGAAGCAGAGCAGATTAAAGCTGACGGCAGCCAATCTTATCTCCCTAGTGTTAAGACTTGAA
* * * *
8594 ATAGCTGAAGTGGAGCGGATTAAAACTGTGGACAGTGAATCCTATCTC
66 ATAGCTGAAGTGCAACGGATTAAAACTATGGACAGCGAATCCTATCTC
8642 GTTGGCATTA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
118 97 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (118 bp):
CATTGAAGCAGAGCAGATTAAAGCTGACGGCAGCCAATCTTATCTCCCTAGTGTTAAGACTTGAA
ATAGCTGAAGTGCAACGGATTAAAACTATGGACAGCGAATCCTATCTCCCTAG
Found at i:8685 original size:118 final size:118
Alignment explanation
Indices: 8424--8697 Score: 280
Period size: 118 Copynumber: 2.3 Consensus size: 118
8414 TGCAGCGGAG
* * * * * *
8424 CAGATTAAAGCTGACGGCAGCCAATCTTATCTGCCTGGTGTTAAGACTTGAAATAGTTGAAGTGC
1 CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGC
* * * * * *
8489 AACGGATTAAAGCTATGGGCAGCGAATCTTGTTTCCCTAGCATTGAAGCAGAG
66 AACGGATTAAAACTATGGACAGCGAATCCTATCTCCCTAGCATTGAAGCAGAA
* * *
8542 CAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGG
1 CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGC
* * * ** * **
8607 AGCGGATTAAAACTGTGGACAGTGAATCCTATCTCGTTGGCATT-ATAGTGGAA
66 AACGGATTAAAACTATGGACAGCGAATCCTATCTCCCTAGCATTGA-AGCAGAA
* * * * *
8660 CAGATTGAAGCTAAAGGTAGTGAATCTTGTTTCCCTAG
1 CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAG
8698 AGTTGCAGCG
Statistics
Matches: 128, Mismatches: 27, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
117 1 0.01
118 127 0.99
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (118 bp):
CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGC
AACGGATTAAAACTATGGACAGCGAATCCTATCTCCCTAGCATTGAAGCAGAA
Found at i:8805 original size:169 final size:169
Alignment explanation
Indices: 8484--9346 Score: 1199
Period size: 169 Copynumber: 5.1 Consensus size: 169
8474 AAATAGTTGA
* * ** * * *
8484 AGTGCAACGGATTAAAGCTATGGGCAGCGAATCTTGTTTCCCTAGCATTGAAGCAGAGCAGATTA
1 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTA
* *
8549 AAGCTGAGGGCAGCGAATCTTATCTCCCTAGTGTTAAGACTTGAAATAGCTGAAGTGGAGCGGAT
66 AAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGAT
* * * *
8614 TAAAACTGTGGACAGTGAATCCTATCTCGTTGGCATTAT
131 TAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAT
* *
8653 AGTGGAACAGATTGAAGCTAAAGGTAGTGAATCTTGTTTCCCTAG-AGTTGCAGCGGAGCAGATT
1 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCA-TTGCAGCGGAGCAGATT
* *
8717 AAAGCTGAAGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCAGAAGTGGAGCGGA
65 AAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGA
* *
8782 CTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCTTTAT
130 TTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAT
* * * ** * *
8822 AGTGGAACAGATTAAAGTTAAAGGTAGCAAATCTTCTTTCCCTATTATTGTAGTGGAGCAGATTA
1 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTA
* * * *
8887 AATCTGAGGGCAGCGGATCTTGTCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGAAT
66 AAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGAT
* * * *
8952 TAAAGATGTGGGCAGTGAATCCTATCTCGTTGGGATTAT
131 TAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAT
* * * *
8991 AGTGGAACATATTAAAGCTAAAGGTAGCGAATCTTGTTTCCATAGCATTGTAGCGGAGCAGATTC
1 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTA
* * *
9056 AAGCTGAGGGCAGCGATTCTTTTCTCCCTGGCGTTAAGACTTAAAATAGCTGAAGTGGAGCGGAT
66 AAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGAT
*
9121 TAAAGCTGTGGGTAGCGAATCCTATCTCTTTGGCATTAT
131 TAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAT
* * * * * * *
9160 AGTAGAATAAATTAAAGCTAAAGGTGGCGAATCTCGTTTCCCTAGCATTGCATCGAAGCAGATTA
1 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTA
* * * * *
9225 AAACTGAGGGTAGCGAATCTTTTCTCCCTGGCGTTAAGACTTGAAATAGCTAAAGT-GATGTGGA
66 AAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGA-GCGGA
*
9289 TTAAAGCTTTGGGCAGCGAATCCTATCTCTTTGGCATTAT
130 TTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAT
9329 AGTGGAACAGATTAAAGC
1 AGTGGAACAGATTAAAGC
9347 GAAA
Statistics
Matches: 611, Mismatches: 80, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
168 3 0.00
169 607 0.99
170 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (169 bp):
AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTA
AAGCTGAGGGCAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGAT
TAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAT
Done.