Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_944 ID=scaffold_944-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: 5033
ACGTcount: A:0.11, C:0.09, G:0.10, T:0.14
Warning! 2835 characters in sequence are not A, C, G, or T
Found at i:913 original size:304 final size:303
Alignment explanation
Indices: 1--1339 Score: 2181
Period size: 303 Copynumber: 4.4 Consensus size: 303
1 CTAATGCACCGGATCCC-TCCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGA
1 CTAATGCACCGGATCCCAT-CAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGA
* *
65 TGGGTGACCTCCTGGGAAGTCCTGGTGTTGCACCCCTCTCATTTTATTTCATATAATGTTTTTTT
65 TGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTT
* * *
130 TAATTGCATTTTCTCGACGTGGTGTAACTCAGTCGTTATTTGCGTTTTGTGAAATAAACAATTTG
130 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTG
*
195 AAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGTGCAACTGCGATAAGGGGCAGCCTTTAC
195 AAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTAC
* *
260 ATGAATAGATTGCGGAAGAGTTGGCGGGTGCGATCATACCAGCA
260 ATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCA
* *
304 CTAATACACCGGATCCCATCAGAACTCCGCAGTTAACCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
* *
369 GGATGACCTCCTGGGAAGTCCTCGTGTTGCACGCCTCCCATTTTATTTCATATAATGTTTTTTTT
66 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTT
*
434 AGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTCTTGTGAAATAAATAATTTGA
131 AGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGA
* * *
499 AACGATATTTGCTCGAATTTGCATTTAAATTCGAGGTGCAACTGCGATATA-GGGCATCCTTTAC
196 AACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATA-AGGGGCAGCCTTTAC
*
563 ATGAATAGATTGCGCAAGAGTTGGCGGGTGCGATCATACCAGCA
260 ATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCA
*
607 CTAACGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
*
672 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTT
66 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATG-TTTTTTT
* * * * * *
737 TAGTTGCCTTTTCTCGACATAGTGTAACTCATTCGTTATTTTCGTTTTGTGAAATGAATAATTAC
130 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATT-T
* * * * * *
802 G-AACGATATTCGGTCGAATTTACATTTAAATTCGAGGCGCAAGTGCGATCAGGGGCAACCTTGA
194 GAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTA
*
866 TATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCA
259 CATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCA
* *
911 CTAATGCACCGGATCGCATTAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
* *
976 GGGTGACCTCCTGGGAAGTCCTCGTGTTGTACCCCTCCCATTTTGTTTCATATAA--TTTTTTTT
66 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTT
1039 AGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAAT-AATCAATTTG
131 AGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAAT-AATTTG
* * * *
1103 AAACGATATTTGGTCAAATTTGCATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCATTAT
195 AAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTAC
*
1168 ATGAATAGATTGCGCAAGAGTTGACGGATGCGATCATACCAGCA
260 ATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCA
* *
1212 CTAATACACCGGATCTCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
*
1277 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCT-CCATTTTATTTCATA-GATGTTTTTTTT
66 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTT
1340 TTAGTNNNNN
Statistics
Matches: 964, Mismatches: 63, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
299 1 0.00
300 18 0.02
301 265 0.27
303 403 0.42
304 276 0.29
305 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (303 bp):
CTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTT
AGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGA
AACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTACA
TGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCA
Found at i:1286 original size:605 final size:605
Alignment explanation
Indices: 1--1340 Score: 2181
Period size: 607 Copynumber: 2.2 Consensus size: 605
*
1 CTAATGCACCGGATCCCTCCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGATCCAT-CAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
* * *
66 GGGTGACCTCCTGGGAAGTCCTGGTGTTGCACCCCTCTCATTTTATTTCATATAATG-TTTTTTT
65 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTT
* * *
130 TAATTGCATTTTCTCGACGTGGTGTAACTCAGTCGTTATTTGCGTTTTGTGAAATAAACAATTTG
130 TAATTGCATTTTCTCGACATAGTGTAACTCAGTCGTTATTTGCGTTTTGTGAAATAAACAATTCG
* * * * *
195 AAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGTGCAACTGCGATAAGGGGCAGCCTTTAC
195 AAACGATATTCGGTCGAATTTACATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAACCTTGAC
* *
260 ATGAATAGATTGCGGAAGAGTTGGCGGGTGCGATCATACCAGCACTAATACACCGGATCCCATCA
260 ATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATACACCGGATCCCATCA
325 GAACTCCGCAGTTAACCGTGCTTGGGCGAGAGTAGTACTAGGATGGATGACCTCCTGGGAAGTCC
325 GAACTCCGCAGTTAACCGTGCTTGGGCGAGAGTAGTACTAGGATGGATGACCTCCTGGGAAGTCC
*
390 TCGTGTTGCACGCCTCCCATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGG
390 TCGTGTTGCACCCCTCCCATTTTATTTCATATAA-GTTTTTTTTAGTTGCATTTTCTCGACGTGG
*
455 TGTAACTCATTCGTTATTTGCGTCTTGTGAAATAAATAATTTGAAACGATATTTGCTCGAATTTG
454 TGTAACTCATTCGTTATTTGCGTCTTGTGAAATAAATAATTTGAAACGATATTTGCTCAAATTTG
* * * *
520 CATTTAAATTCGAGGTGCAACTGCGATATAGGGCATCCTTTACATGAATAGATTGCGCAAGAGTT
519 CATTTAAATTCGAGGCGCAACTACGATATAGGGCAGCCATTACATGAATAGATTGCGCAAGAGTT
* *
585 GGCGGGTGCGATCATACCAGCA
584 GACGGATGCGATCATACCAGCA
*
607 CTAACGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGAT-CCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
672 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTT
65 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTT
* * * * * *
737 TAGTTGCCTTTTCTCGACATAGTGTAACTCATTCGTTATTTTCGTTTTGTGAAATGAATAATTAC
130 TAATTGCATTTTCTCGACATAGTGTAACTCAGTCGTTATTTGCGTTTTGTGAAATAAACAATT-C
* *
802 G-AACGATATTCGGTCGAATTTACATTTAAATTCGAGGCGCAAGTGCGATCAGGGGCAACCTTGA
194 GAAACGATATTCGGTCGAATTTACATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAACCTTGA
* * * *
866 TATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCGCATT
259 CATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATACACCGGATCCCATC
* *
931 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
324 AGAACTCCGCAGTTAACCGTGCTTGGGCGAGAGTAGTACTAGGATGGATGACCTCCTGGGAAGTC
* *
996 CTCGTGTTGTACCCCTCCCATTTTGTTTCATATAA-TTTTTTTTAGTTGCATTTTCTCGACGTGG
389 CTCGTGTTGCACCCCTCCCATTTTATTTCATATAAGTTTTTTTTAGTTGCATTTTCTCGACGTGG
* *
1060 TGTAACTCATTCGTTATTTGCGTTTTGTGAAAT-AATCAATTTGAAACGATATTTGGTCAAATTT
454 TGTAACTCATTCGTTATTTGCGTCTTGTGAAATAAAT-AATTTGAAACGATATTTGCTCAAATTT
*
1124 GCATTTAAATTCGAGGCGCAACTACGATA-AGGGGCAGCCATTATATGAATAGATTGCGCAAGAG
518 GCATTTAAATTCGAGGCGCAACTACGATATA-GGGCAGCCATTACATGAATAGATTGCGCAAGAG
1188 TTGACGGATGCGATCATACCAGCA
582 TTGACGGATGCGATCATACCAGCA
*
1212 CTAATACACCGGATCTCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1 CTAATGCACCGGATC-CATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
1277 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCT-CCATTTTATTTCATAG-ATGTTTTTTTT
65 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTT
1340 T
130 T
1341 TAGTNNNNNN
Statistics
Matches: 684, Mismatches: 44, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
603 12 0.02
604 21 0.03
605 262 0.38
606 113 0.17
607 275 0.40
608 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (605 bp):
CTAATGCACCGGATCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATG
GGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTTT
AATTGCATTTTCTCGACATAGTGTAACTCAGTCGTTATTTGCGTTTTGTGAAATAAACAATTCGA
AACGATATTCGGTCGAATTTACATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAACCTTGACA
TGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATACACCGGATCCCATCAG
AACTCCGCAGTTAACCGTGCTTGGGCGAGAGTAGTACTAGGATGGATGACCTCCTGGGAAGTCCT
CGTGTTGCACCCCTCCCATTTTATTTCATATAAGTTTTTTTTAGTTGCATTTTCTCGACGTGGTG
TAACTCATTCGTTATTTGCGTCTTGTGAAATAAATAATTTGAAACGATATTTGCTCAAATTTGCA
TTTAAATTCGAGGCGCAACTACGATATAGGGCAGCCATTACATGAATAGATTGCGCAAGAGTTGA
CGGATGCGATCATACCAGCA
Found at i:4728 original size:303 final size:302
Alignment explanation
Indices: 4180--5032 Score: 1429
Period size: 303 Copynumber: 2.8 Consensus size: 302
4170 NNNNNNNNNN
*
4180 GATATTTGGTCGAATTTGC-TTTAAAATTTGAGGGCGCAACTGCGATAAGGGCAGCCTTTATATG
1 GATATTTGGTCGAATTTGCATTT-AAATTCGA-GGCGCAACTGCGATAAGGGCAGCCTTTATATG
* *
4244 AATAGATTGCGCAAGAGTTATCGGGTGCGATCAAACCAGCACTAATGCACCGGATCCCATCAGAA
64 AATAGATTGCGCAAGAGTTAACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAA
4309 CTCCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTC
129 CT-CCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTC
* *
4374 GTGTTGCACCCCTCCCATTTTATGTCATTTAATGTTTTTTTTAGTTGCATTTGCTCGACGTGGTG
193 GTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTGCTCGACGTGGTG
* *
4439 TAACTCATTCGTTATTTTCGTTGTGTGAAATAAATAATTTGAAAC
258 TAACTCATTCGTTATTTGCGTTGTGTGAAATAAACAATTTGAAAC
*
4484 GATATTTGCTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGGCAGCCTTTATATGA
1 GATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAA-GGGCAGCCTTTATATGA
*
4549 ATAGATTGCGCAAGAGTTAACGTGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAAC
65 ATAGATTGCGCAAGAGTTAACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAAC
* *
4614 TCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGATGATCTCCTGGGAAGTCCTCGT
130 TCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGT
* *
4679 GTTGCACGCCTCCCATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTA
195 GTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTGCTCGACGTGGTGTA
*
4744 ACTCATTCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAAC
260 ACTCATTCGTTATTTGCGTTGTGTGAAATAAACAATTTGAAAC
* * * *
4787 GATATTTGGTCGAATTTGCATTTAAATTCGAGGTGCAACTGCGATATTGGGCATCCTTTACATGA
1 GATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATA-AGGGCAGCCTTTATATGA
**
4852 ATAGATTGCGCAAGAGTTGGCGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAAC
65 ATAGATTGCGCAAGAGTTAACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAAC
* *
4917 TCCGCAGTTAACCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCTT
130 TCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGT
* *
4982 GTTGCACCCCTCCCATTTTATTTCATAGAATCTTTTTTTTTAGTTGCATTT
195 GTTGCACCCCTCCCATTTTATTTCATATAAT-GTTTTTTTTAGTTGCATTT
5033 T
Statistics
Matches: 516, Mismatches: 29, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
303 390 0.76
304 123 0.24
305 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (302 bp):
GATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGCGATAAGGGCAGCCTTTATATGAA
TAGATTGCGCAAGAGTTAACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACT
CCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
TTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTTAGTTGCATTTGCTCGACGTGGTGTAA
CTCATTCGTTATTTGCGTTGTGTGAAATAAACAATTTGAAAC
Done.