Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_112 ID=scaffold_112-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: 12896
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:677 original size:332 final size:332
Alignment explanation
Indices: 71--803 Score: 1385
Period size: 332 Copynumber: 2.2 Consensus size: 332
61 ATGTAGGTAC
71 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
1 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
*
136 GTCAAAAACTCCAGTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATC
66 GTCAAAAACTCCACTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATC
* *
201 CAGCGGACCAGCGGACTTGCAGAGCTTTTTAGACCAGAAAATTGGACTCAGCGGGTCATTTCCAA
131 CAGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAA
266 GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
196 GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
331 GGAACCCCTGTCGATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
261 GGAACCCCTGTCGATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
396 TACATAG
326 TACATAG
*
403 TTGGAGGCGTGGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
1 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
*
468 GTCAAAAACTCCACTGTTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATC
66 GTCAAAAACTCCACTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATC
533 CAGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAA
131 CAGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAA
598 GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
196 GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
663 GGAACCCCTGTCGATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
261 GGAACCCCTGTCGATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
728 TACATAG
326 TACATAG
* * * *
735 TTGGAGGCGTAGAATCGATTCCCATTGGTTCCGAGGCTCGGCGGAGCTTCCTGAGCCGAGAAACA
1 TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
800 GTCA
66 GTCA
804 GAANNNNNNN
Statistics
Matches: 391, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
332 391 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (332 bp):
TTGGAGGCGTAGAATCGATTCCCATTGGTCCCGAGGCTCGGCGGAGCTTTCTTAGCCGAGAAACG
GTCAAAAACTCCACTATTTTTGACCGTTTCGCGAAAGTTCACCGACCGCGCGTTTTTCGCCGATC
CAGCGGACCAGCGGACTCGCAGAGCTTTTTAGACCAGAAAATCGGACTCAGCGGGTCATTTCCAA
GGGGACTTGCCCGGTTTCAGCCCGATCGGAGAACTTTCGATTTTGACCCCGAAATTTCACTCCAT
GGAACCCCTGTCGATTTTTCTCGATTTTGGAGGAGAAAAAAAATTTCGAGCTGAGTGTCGGATCT
TACATAG
Found at i:3117 original size:339 final size:341
Alignment explanation
Indices: 2427--3259 Score: 909
Period size: 339 Copynumber: 2.4 Consensus size: 341
2417 GATTTTGTCC
* * * * * * *
2427 AGCCGAGAACCAGTCAAAAGCAGGTAAAAAACGAGCATTTCAGACCACTTTATGACCCTTTCTCT
1 AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
* * *
2492 GGAGCGTTTTCAGCAGATATAGCT-GTGAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAGAATC
66 GGAGCGTTTTCAGC-G-GATAGCTCG-AAGCGAGGGACTCGCGGAGC-TTTCCGACTGGAAAATC
*
2556 GCACTCAGCGGGTC-ATTCCCAAGCGGCATAACTTGCTTCCGGCTCGATCGGCGAATTTTCGATT
127 GCACTCAGCGGGTCAATT-CCAAGCGGCATAACTTGCTTCCGGCCCGATCGGCGAATTTTCGATT
* * * * *
2620 TTGACGCTTAAAATTTAGTTAATGCCTGCTGTGTTAGCCTGTTGATTTTACTCGATTTTGGACTG
191 TTGACGCTTAAAATTTAG---AT-CC-GCTATGTAACCCTGTCGATTTTACTCGATTTGGGACTG
* * * *
2685 AGAAAAAAGATTCGAGATTTCAGTCGCATTCTACGTTGCTGGAAGCGTAGAATCGATTAAGCACG
251 AGAAAAAAGATTCGAGATTTCAGTCGCATCCTACGTAGCTGGAAGCGAAAAATCGATTAAGCACG
*
2750 GTCCCGACTCTCGGCGAGGCTTCCTG
316 GTCCCGACTCTCGGCGAGGCTCCCTG
* *
2776 AGCCGAGAAACAGTAAAAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTCTTTCTCT
1 AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
* * * *
2841 GGAGCGTATTCAGCGGCTAGCTCGAAGCGAGAGACTTGCGGAGCTATTCCGACTGGAAAATCGCA
66 GGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCT-TTCCGACTGGAAAATCGCA
* * ** * *
2906 CTCGGCGGGTCAATTCCAAGCGAGC-TTACTTTTTTTCTGCCCGATCAGG-GAATTTTCGATTTT
130 CTCAGCGGGTCAATTCCAAGCG-GCATAACTTGCTTCCGGCCCGATC-GGCGAATTTTCGATTTT
* *
2969 GATG-TTAAAAATTTAG-T-C-C-ATGTAACCCCTGTCGATTTTTCTCGATTTGGGACTGAGAAA
193 GACGCTT-AAAATTTAGATCCGCTATGTAA-CCCTGTCGATTTTACTCGATTTGGGACTGAGAAA
* * * **
3029 AAA-ATTTCTAGATTTCAGTCGCATCCTACGTAG-TTGAAGGCGAAAAATTGATTCCGCACGGTC
256 AAAGA-TTCGAGATTTCAGTCGCATCCTACGTAGCTGGAA-GCGAAAAATCGATTAAGCACGGTC
3092 CCGACTCTCGGCGAGGCTCCCTG
319 CCGACTCTCGGCGAGGCTCCCTG
** * * * * * * *
3115 AGCTAAGAATCAGTCAAAAATTCGTCCAAAACTAGCGTTTCTGACCACTTTTTGTCTCTTTCT-T
1 AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
* * ** * *
3179 CGGAGCGTTTTCAACGGATAACTCGTTGCGAGGGACTCGAGGTGCTTTCTCGACTGGAAAATC-C
66 -GGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTTC-CGACTGGAAAATCGC
3243 ACTCAGCGGGTCAATTC
129 ACTCAGCGGGTCAATTC
3260 GTCAAATTGT
Statistics
Matches: 412, Mismatches: 61, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
338 30 0.07
339 201 0.49
341 1 0.00
343 1 0.00
346 3 0.01
347 98 0.24
348 9 0.02
349 69 0.17
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (341 bp):
AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
GGAGCGTTTTCAGCGGATAGCTCGAAGCGAGGGACTCGCGGAGCTTTCCGACTGGAAAATCGCAC
TCAGCGGGTCAATTCCAAGCGGCATAACTTGCTTCCGGCCCGATCGGCGAATTTTCGATTTTGAC
GCTTAAAATTTAGATCCGCTATGTAACCCTGTCGATTTTACTCGATTTGGGACTGAGAAAAAAGA
TTCGAGATTTCAGTCGCATCCTACGTAGCTGGAAGCGAAAAATCGATTAAGCACGGTCCCGACTC
TCGGCGAGGCTCCCTG
Found at i:4672 original size:36 final size:36
Alignment explanation
Indices: 4623--5840 Score: 1902
Period size: 36 Copynumber: 33.7 Consensus size: 36
4613 TCCGGGCGGC
*
4623 GGGG-CAGCCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAG-CCCCCTGAACCCTAAGGAGCCGAACGCG
* *
4659 GGGGTCAACCCCCTGAACCCTAAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
4695 GGGGTCAGCCCCCT-AATCCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAA-CCCTAAGGAGCCGAACGCG
*
4731 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
4767 GGGGTCATCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
4803 GGGGTCATCCCCCTGAACCCCAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* * *
4839 GGGGTCAGCCCCCTGAACCCCAAGAAGCCGAACACG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
**
4875 GGGGTCAGCCCCCTGAACCCTTTGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
4911 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* * *
4947 GGGGTCAGCCCCCTGAATCGTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
4983 GGGGTCAGCCCCCTGAACCCTAGGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5019 GGGGTCAGCCCCCTGAACCCCAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5055 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5091 GGGGTCAGCCTCAACCCCCTGAACCCTTAGGAGCCGGACGCG
1 GGGGTCAG------CCCCCTGAACCCTAAGGAGCCGAACGCG
5133 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5169 GGGATCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5205 GGGGTCAG-CCCCTGAACCCTAAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5240 GGGGTCAGCCCCCTGAACCCTAAGGAGCTGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5276 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
5312 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5348 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5384 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5420 GGGGTCAGCCCCCTGAACCCTGAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5456 GGGGTCAGCCCCCTGAACCCTGAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5492 GGGGTAAGCCCCCTGAACCCTAAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5528 GGGGTCAGCCCCCTGAACCCTAAGGAGCCAAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
5564 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5600 GGGGTCATCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5636 GGGGTCATCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* * *
5672 GGGGTCATCCCCCTGAACCCCAAGGATCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5708 GGGGTCAGCCCCCTGAACCCCAAGGAGCCGAACACG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5744 GGGGTCATCCCCCTGAACCCCAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
5780 GGGGTCATCCCCCTGAACCCCAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
5816 GGGGTCAGCCCCCTGAGCCCTAAGG
1 GGGGTCAGCCCCCTGAACCCTAAGG
5841 TGCTGAGGAG
Statistics
Matches: 1110, Mismatches: 62, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
35 36 0.03
36 1037 0.93
37 4 0.00
42 33 0.03
ACGTcount: A:0.21, C:0.37, G:0.33, T:0.09
Consensus pattern (36 bp):
GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
Found at i:8308 original size:339 final size:338
Alignment explanation
Indices: 7503--8418 Score: 922
Period size: 340 Copynumber: 2.7 Consensus size: 338
7493 ATTCCGCAGG
* * * * * *
7503 TTTTTAGCGTCAAAATCGAAAGTTCGCCGATCGAGCCGAAAGCAA-GTTATGCCGCTTGGAAATG
1 TTTTAAGCGTCAAAAGCGAAATTTCACCGATCGAGCCGAAAGCAACG-GAAGCCGCTTGGAAATG
* * * ** *
7567 ACCCACTGAGTACGATTTTCCAGTCGAAAAAGCTCCGCGAGTCCCTCATTTCGAGCTATCCGCTG
65 ACCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGCTG
* * * * *
7632 AACACGCTCCAGAGAAAGAGTCAAAAATTGGTCTGAAATGCTCGTGTTTGACCAGTTTTTGACTG
130 AA-ACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGAAA-ACTCGTTTTTGACCAGTTTATAACTG
* * * *
7697 TTTCTCGACTCAGGAAGTCTCGCCGAGAAATGGAACCGTGTGGAATCGATTCTACGCCTCCAAAA
193 TATCCCGACTCAGGAAGTCTCGCCGAGAAATGGAACCGTGCGGAATCGATTCTAAGCCTCCAAAA
* * * * ** ** *
7762 TTCGTTAGATGCGACTGCAATCTTGATTTTTTTTTTATCAGTCCAAAATCGAGTAAAATCGACAG
258 TACGTAAGATGCGACTGAAATCCTGA-TAATTTTTTATCAGTCCAAAAAAGAGAAAAATCGACAG
* * *
7827 GCGTTACATTAACCGAA
322 GCATTACATCAACCAAA
* ** *
7844 TTTTAAGCGTCAAAATCGAAATTTCACCGATCGAGCCGAAAGCAACTTAGGCCGCTTGGAAATGA
1 TTTTAAGCGTCAAAAGCGAAATTTCACCGATCGAGCCGAAAGCAACGGAAGCCGCTTGGAAATGA
* * * *
7909 CCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCACAAGTCCCTCGCTTTGAACTATCCGCTGA
66 CCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGCTGA
*
7974 AACGCTCCAGAGAAAGAGTCAAAAATTGGGCAGACAAACTCGTTTTTGACCAGTTTATAACCT-T
131 AACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGA-AAACTCGTTTTTGACCAGTTTATAA-CTGT
* * * *
8038 ATCCCGGCTCAGGATGTCTCGCC-ATG-AGTCGGGACCGTGCGGAATCGATTCTAAGCCTCC-AA
194 ATCCCGACTCAGGAAGTCTCGCCGA-GAAAT-GGAACCGTGCGGAATCGATTCTAAGCCTCCAAA
*
8100 ATACG-AAGGATGCGACTGAAATCCTGA-AATTTTTTCTCAGTCCAAAAAAGAGAAAAATCGACA
257 ATACGTAA-GATGCGACTGAAATCCTGATAATTTTTTATCAGTCCAAAAAAGAGAAAAATCGAC-
* *
8163 TATGG-ATTACATCGACTAAA
320 -A-GGCATTACATCAACCAAA
** * * * * * * * * *
8183 TTTTTCGGGTCAAAGGCG-AATGTTCGCGGATTGGGCCGAAA-CCAGGGAAGCTCGCTTGGAATT
1 TTTTAAGCGTCAAAAGCGAAAT-TTCACCGATCGAGCCGAAAGCAACGGAAGC-CGCTTGGAAAT
* *
8246 GACCCGCTCAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTACCTCGCTTAGAGCTATCCGCT
64 GACCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGC-
* ** * * *
8311 TAAAACGCTTTAGAGAACGAGTCAAAAAGTGGTCAGAAAAGCTCGTTTTTGACCAGATTT-TGAC
128 TGAAACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGAAAA-CTCGTTTTTGACCAG-TTTATAAC
* * * *
8375 TGTTTCTCGGCTTC-GGAAGTCTCGCCGAG-AATCGGAACTGTGCG
191 TGTATCCCGAC-TCAGGAAGTCTCGCCGAGAAAT-GGAACCGTGCG
8419 TTTGCGGTAT
Statistics
Matches: 481, Mismatches: 77, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
337 29 0.06
338 9 0.02
339 138 0.29
340 179 0.37
341 126 0.26
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (338 bp):
TTTTAAGCGTCAAAAGCGAAATTTCACCGATCGAGCCGAAAGCAACGGAAGCCGCTTGGAAATGA
CCCGCTGAGTGCGATTTTCCAGTCGGAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGCTGA
AACGCTCCAGAGAAAGAGTCAAAAATTGGTCAGAAAACTCGTTTTTGACCAGTTTATAACTGTAT
CCCGACTCAGGAAGTCTCGCCGAGAAATGGAACCGTGCGGAATCGATTCTAAGCCTCCAAAATAC
GTAAGATGCGACTGAAATCCTGATAATTTTTTATCAGTCCAAAAAAGAGAAAAATCGACAGGCAT
TACATCAACCAAA
Found at i:12233 original size:43 final size:43
Alignment explanation
Indices: 12172--12257 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
12162 CGCACATTTT
12172 GGCAACTTTGCATCAAGTAGGCTTCAGCCCTACCGGAGCTATC
1 GGCAACTTTGCATCAAGTAGGCTTCAGCCCTACCGGAGCTATC
*
12215 GGCAACTTTGCATCAAGTAGGCTTCAGCCCTACCGGATCTATC
1 GGCAACTTTGCATCAAGTAGGCTTCAGCCCTACCGGAGCTATC
12258 CTTGGAGCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.24
Consensus pattern (43 bp):
GGCAACTTTGCATCAAGTAGGCTTCAGCCCTACCGGAGCTATC
Done.