Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_899 ID=scaffold_899-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: 5688
ACGTcount: A:0.12, C:0.09, G:0.11, T:0.15
Warning! 3086 characters in sequence are not A, C, G, or T
Found at i:554 original size:304 final size:302
Alignment explanation
Indices: 8--1513 Score: 2351
Period size: 302 Copynumber: 5.0 Consensus size: 302
1 TCGCATT
* *
8 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTGCTAGGATAGGTGACCTCCTGGGAAGTC
1 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
* *
73 CTCGTGTTGTACCCCTCCCATTTTATTTCATATAA-TTTTTTTTAGTTGCATTTTCTCGACGTGA
66 CTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGG
* * *
137 TGTAACTTATTCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCAAATTTG
131 TGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTG
* * *
202 CATTTAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGACTT
196 CATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTT
267 GACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATC
261 GACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATC
* ** *
309 AGAACTCCGCAGTTAAGCGTGCTTGGACGAGAGTTTTACTAGGATGGGTGACCTCCTGGGAAATC
1 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
* *
374 CTCGTGTTGCACCCCTCCCATTTTATTTCATAGAATGTTTTTTTTTAGTTGCATTTTCTCGACAT
66 CTCGTGTTGCACCCCTCCCATTTTATTTCATATAA--TTTTTTTTTAGTTGCATTTTCTCGACGT
* * * * * *
439 GGTGTAACTCATTCGTTATTTTCGTTTTGTGAAATAAATAATCTGGAACGATATTCGGTCGAATT
129 GGTGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATT
* * * * *
504 TGCATTTAAATTCGAGGCGCAAGTGCGATCAGGGGGAACCTTTATATGAATAGATTGCGCAAGAG
194 TGCATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAG
*
569 TTGACGGGTGCGATCATACCAGCACTAAATGCACCGGATCCCTTC
259 TTGACGGGTGCGATCATACCAGCACT-AATGCACCGGATCCCATC
* *
614 AGAACTCCGCAGCTAACCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
1 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
679 CTCGTGTTGCACCCCCTCCCATTTTATTTCATATAATTTTTTTTTAAGTTGCATTTTCTCGACGT
66 CTCGTGTTGCA-CCCCTCCCATTTTATTTCATATAATTTTTTTTT-AGTTGCATTTTCTCGACGT
744 GGTGTAACTCAATCGTTATTT-CGTTTTGTGTAAATAAACAAATTTAGAAAACGTATAATTT-G-
129 GGTGTAACTCAATCGTTATTTGCGTTTTGTG-AAATAAAC-AATTT-G-AAACG-AT-ATTTGGT
* * * * *
806 -G-ATTTGCATTTAAATTTGAGGCGTAAATACGATAAGGGGCAGCGTTTATATGAATAGAATGCG
188 CGAATTTGCATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCTTTATATGAATAGATTGCG
* * * *
869 CAAGAGTTGGCGGTTGCGATCATACTCAGCACTAACGCACTGGATCCCATC
253 CAAGAGTTGACGGGTGCGATCATAC-CAGCACTAATGCACCGGATCCCATC
* *
920 AGAACTCCGCAGTTAAGCGTCCCTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
1 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
* * * *
985 CTTCGTGTTGCACCCCTTCCATTTTATTTCATTTAA-TTTTTTTTAGTAGCATTTTCTTGACGTG
66 C-TCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACGTG
*
1049 GTGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACACTTTGAAACGATATTTGGTCGAATTT
130 GTGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTT
* * *
1114 GCATTTAAATTCGAGGCGCAACTCCGATAAGGGGCAGCCTTTATATGAACAGATTGCGCAAGAGC
195 GCATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGT
1179 TGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATC
260 TGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATC
* *
1222 AGAACTCCGCATTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGAAAGTC
1 AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
*
1287 CTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGG
66 CTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGG
*
1352 TGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAGCGATATTTGGTCGAATTTG
131 TGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTG
* *
1417 CATTTAAATTTGAGGCGCAACTACGATAAGGGGCAGCGTTTATATGAATAGATTGCGCAAGAGTT
196 CATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTT
1482 GACGGGTGCGATCATACCAGCACTAATGCACC
261 GACGGGTGCGATCATACCAGCACTAATGCACC
1514 NNNNNNNNNN
Statistics
Matches: 1099, Mismatches: 86, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
299 4 0.00
300 3 0.00
301 129 0.12
302 268 0.24
303 81 0.07
304 234 0.21
305 149 0.14
306 202 0.18
307 19 0.02
308 4 0.00
309 3 0.00
310 3 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (302 bp):
AGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
CTCGTGTTGCACCCCTCCCATTTTATTTCATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGG
TGTAACTCAATCGTTATTTGCGTTTTGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTG
CATTTAAATTCGAGGCGCAACTACGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTT
GACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATC
Found at i:5434 original size:305 final size:302
Alignment explanation
Indices: 4600--5626 Score: 1732
Period size: 305 Copynumber: 3.4 Consensus size: 302
4590 NNNNNNNNNN
*
4600 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAAGTCCTCGTGTTGTACCCCTCTCCATTTTAT
1 GAGAGTAGTACTAGGATGGGTGACCTCCTGGG-AAGTCCTCGTGTTGCACCCCTC-CCATTTTAT
*
4665 TTCATAATAATTTTTTTTTAGTTGCATTTTCTCGACGTCGTGTAACTCATTCCTTATTTGCGTTT
64 TTCAT-ATAATTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCCTTATTTGCGTTT
*
4730 TGTGAAATAAACAATTTGAAAACGATATTTGGTCAAATTTGCATTTAAATTCGAGGCGCAAAGTG
128 TGTGAAATAAACAATTTG-AAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGC-AAGTG
*
4795 CGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCCC
191 CGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCAC
*
4860 TAATGCACCGGATCCCATCAGAAACTCCGCAGTTAAGCGTGCTTGGGC
256 TAATGCACCGGATCCAATCAG-AACTCCGCAGTTAAGCGTGCTTGGGC
4908 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT
1 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT
4973 CATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCCTTATTTGCGTTTTGT
66 CATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCCTTATTTGCGTTTTGT
* * *
5038 GAAACAAACAATTTGAAATGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTTCGATA
131 GAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATA
5103 AGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATG
196 AGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATG
*
5168 CACCGGATCCAATCAGAACTCTGCAGTTAAGCGTGCTTGGGC
261 CACCGGATCCAATCAGAACTCCGCAGTTAAGCGTGCTTGGGC
5210 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT
1 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT
* * * * * * * *
5275 CATAGAATGTTTTTTTTTAGTTGCATTTTCTCGTGCGTGGTGTAACTCGTGCGTGATTGGGGTTT
66 CATATAA--TTTTTTTTTAGTTGCATTTTCTCG-ACGTGGTGTAACTCATTCCTTATTTGCGTTT
* * * * * *
5340 TGTGAAATGAATAATTAGGAACGATATTCGGTCGAATTTGCATTTAAATCCGAGGCGCAAGTGCG
128 TGTGAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCG
5405 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
193 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
* *
5470 ATGCACCGGATCCTATCAGAACTCCGCAGTCAAGCGTGCTTGGGC
258 ATGCACCGGATCCAATCAGAACTCCGCAGTTAAGCGTGCTTGGGC
*
5515 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGCCCTCGTGTTGCACCCCTCCCATTTTATTT
1 GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT
5580 CATATAA-TTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATT
66 CATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATT
5627 TCGTTTATTT
Statistics
Matches: 682, Mismatches: 34, Indels: 13
0.94 0.05 0.02
Matches are distributed among these distances:
301 14 0.02
302 119 0.17
303 88 0.13
304 62 0.09
305 332 0.49
306 14 0.02
307 21 0.03
308 32 0.05
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (302 bp):
GAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTT
CATATAATTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCCTTATTTGCGTTTTGT
GAAATAAACAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATA
AGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATG
CACCGGATCCAATCAGAACTCCGCAGTTAAGCGTGCTTGGGC
Done.