Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_102 ID=scaffold_102-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: 15437
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.26
Warning! 1378 characters in sequence are not A, C, G, or T
Found at i:1559 original size:339 final size:342
Alignment explanation
Indices: 870--1617 Score: 852
Period size: 339 Copynumber: 2.2 Consensus size: 342
860 GATTTTGTCC
* * * * * * *
870 AGCCGAGAACCAGTCAAAAGCAGGTAAAAAACGAGCATTTCAGACCACTTTATGACCCTTTCTCT
1 AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
* * * * * *
935 GGAGCGTTTTCAGCAGATATAGCTGTGAGCGAGGGACTCGCGGAGCTTTTCCGACTGGAGAATCG
66 GGAGCGTATTCAGCAGAGATAGCTGTAAGCGAGAGACTCGCGGAGCTATTCCGACTGGAAAATCG
*
1000 CACTCAGCGGGTCATTCCCAAGCGGCATAACTTGCTTCCGGCTCGATCGGCGAATTTTCGATTTT
131 CACTCAGCGGGTCATTCCCAAGCGGCATAACTTGCTTCCGGCCCGATCGGCGAATTTTCGATTTT
* * * *
1065 GACGCTTAAAATTTAGGTAATGTAGCTGTGTTAGCCTGTTGATTTTACTCGATTTTGGACTGAGA
196 GACGCTTAAAATTTAGGTAATGTAAC-----T-CCCTGTCGATTTTACTCGATTTGGGACTGAGA
* * * *
1130 AAAAAGATTCGAGATTTCAGTCGCATTCTACGTTGCTGGAAGCGTAGAATCGATACCGCACGGTC
255 AAAAAGATTCGAGATTTCAGTCGCATCCTACGTAGCTGGAAGCGAAAAATCGATACCGCACGGTC
*
1195 CCGACTCTCGGCGAGGCTTCCTG
320 CCGACTCTCGGCGAGGCTCCCTG
* *
1218 AGCCGAGAAACAGTAAAAAACTGGTCAAAAACGAGCTTTTCTGACCACTTTTTGACTCTTTCTCT
1 AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
* *
1283 GGAGCGTATTCAGC-G-GCTAGCTCG-AAGCGAGAGACTTGCGGAGCTATTCCGACTGGAAAATC
66 GGAGCGTATTCAGCAGAGATAGCT-GTAAGCGAGAGACTCGCGGAGCTATTCCGACTGGAAAATC
* * ** * *
1345 GCACTCGGCGGGTCAATT-CCAAGCGAGC-TTACTTTTTTTCTGCCCGATCAGG-GAATTTTCGA
130 GCACTCAGCGGGTC-ATTCCCAAGCG-GCATAACTTGCTTCCGGCCCGATC-GGCGAATTTTCGA
* * *
1407 TTTTGATG-TTAAAAATTTA-GTCCATGTAAC-CCCTGTCGATTTTTCTCGATTTGGGACTGAGA
192 TTTTGACGCTT-AAAATTTAGGT-AATGTAACTCCCTGTCGATTTTACTCGATTTGGGACTGAGA
* * * *
1469 AAAAA-ATTTCTAGATTTCAGTCGCATCCTACGTAG-TTGAAGGCGAAAAATTGATTCCGCACGG
255 AAAAAGA-TTCGAGATTTCAGTCGCATCCTACGTAGCTGGAA-GCGAAAAATCGATACCGCACGG
1532 TCCCGACTCTCGGCGAGGCTCCCTG
318 TCCCGACTCTCGGCGAGGCTCCCTG
** * * * * * * *
1557 AGCTAAGAATCAGTCAAAAATTCGTCCAAAACTAGCGTTTCTGACCACTTTTTGTCTCTTT
1 AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTT
1618 TCTTCGGAGC
Statistics
Matches: 342, Mismatches: 50, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
338 5 0.01
339 151 0.44
345 4 0.01
346 104 0.30
347 9 0.03
348 69 0.20
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (342 bp):
AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCATTTCTGACCACTTTTTGACTCTTTCTCT
GGAGCGTATTCAGCAGAGATAGCTGTAAGCGAGAGACTCGCGGAGCTATTCCGACTGGAAAATCG
CACTCAGCGGGTCATTCCCAAGCGGCATAACTTGCTTCCGGCCCGATCGGCGAATTTTCGATTTT
GACGCTTAAAATTTAGGTAATGTAACTCCCTGTCGATTTTACTCGATTTGGGACTGAGAAAAAAG
ATTCGAGATTTCAGTCGCATCCTACGTAGCTGGAAGCGAAAAATCGATACCGCACGGTCCCGACT
CTCGGCGAGGCTCCCTG
Found at i:3127 original size:36 final size:36
Alignment explanation
Indices: 3078--3570 Score: 808
Period size: 36 Copynumber: 13.7 Consensus size: 36
3068 TCCGGGCGGC
*
3078 GGGG-CAGCCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAG-CCCCCTGAACCCTAAGGAGCCGAACGCG
* *
3114 GGGGTCAACCCCCTGAACCCTAAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3150 GGGGTCAGCCCCCTAAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
3186 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3222 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3258 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3294 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
3330 GGGGTCAGCCCCCTGAACCCTAAGGAGCTGGACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3366 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3402 GGGGTCAGCCCCCTGAACCCTAAGGAGCCAAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3438 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGACCGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* **
3474 GGGGTCAGCCCCCTGAACCCCAAGGAGCCGAAATCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
* *
3510 GGGGTCATCCCCCTGAACCCCAAGGAGCCGAACGCG
1 GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
*
3546 GGGGTCAGCCCCCTGAGCCCTAAGG
1 GGGGTCAGCCCCCTGAACCCTAAGG
3571 TGCTGAGGAG
Statistics
Matches: 428, Mismatches: 28, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
36 426 1.00
37 2 0.00
ACGTcount: A:0.21, C:0.37, G:0.33, T:0.09
Consensus pattern (36 bp):
GGGGTCAGCCCCCTGAACCCTAAGGAGCCGAACGCG
Found at i:11854 original size:339 final size:338
Alignment explanation
Indices: 11075--11964 Score: 897
Period size: 340 Copynumber: 2.6 Consensus size: 338
11065 TCGAAGTTCG
* * * *
11075 CCGATCGAGCCGAAAGCAA-GTTATGCCGCTTGGAAATGACCCACTGAGTACGATTTTCCAGTCG
1 CCGATCGAGCCGAAAGCAACG-GAAGCCGCTTGGAAATGACCCGCTGAGTGCGATTTTCCAGTCG
* ** *
11139 AAAAAGCTCCGCGAGTCCCTCATTTCGAGCTATCCGCTGAACACGCTCCAGAGAAAGAGTCAAAA
65 GAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGCTGAA-ACGCTCCAGAGAAAGAGTCAAAA
* * * * * * *
11204 ATTGGTCTGAAATGCTCGTGTTTGACCAGTTTTTGACTGTTTCTCGACTCAGGAAGTCTCGCCGA
129 ATTGGTCAGAAA-ACTCGTTTTTGACCAGTTTATAACTGTATCCCGACTCAGGAAGTCTCGCCGA
* * * * *
11269 GAAATGGAACCGTGTGGAATCGATTCTACGCCTCCAAAATTCGTTAGATGCGACTGCAATCTTGA
193 GAAATGGAACCGTGCGGAATCGATTCTACGCCTCCAAAATACGTAAGATGCGACTGAAATCCTGA
** ** * * * *
11334 TTTTTTTTTTATCAGTCCAAAATCGAGTAAAATCGACAGGCGTTACATTAACCGAATTTTAAGCG
258 -TAATTTTTTATCAGTCCAAAAAAGAGAAAAATCGACAGGCATTACATCAACCAAATTTTAAGCG
*
11399 TCAAAATCGAAATTTCA
322 TCAAAAGCGAAATTTCA
** *
11416 CCGATCGAGCCGAAAGCAACTTAGGCCGCTTGGAAATGACCCGCTGAGTGCGATTTTCCAGTCGG
1 CCGATCGAGCCGAAAGCAACGGAAGCCGCTTGGAAATGACCCGCTGAGTGCGATTTTCCAGTCGG
* * * *
11481 AAAAGCTCCACAAGTCCCTCGCTTTGAACTATCCGCTGAAACGCTCCAGAGAAAGAGTCAAAAAT
66 AAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGCTGAAACGCTCCAGAGAAAGAGTCAAAAAT
* * *
11546 TGGGCAGACAAACTCGTTTTTGACCAGTTTATAACCT-TATCCCGGCTCAGGATGTCTCGCC-AT
131 TGGTCAGA-AAACTCGTTTTTGACCAGTTTATAA-CTGTATCCCGACTCAGGAAGTCTCGCCGA-
* *
11609 G-AGTCGGGACCGTGCGGAATCGATTCTACGCCTCC-AAATACG-AAGGATGCGACTGAAATCCT
193 GAAAT-GGAACCGTGCGGAATCGATTCTACGCCTCCAAAATACGTAA-GATGCGACTGAAATCCT
* * * *
11671 GA-AATTTTTTCTCAGTCCAAAAAAGAGAAAAATCGACATATGG-ATTACATCGACTAAATTTTT
256 GATAATTTTTTATCAGTCCAAAAAAGAGAAAAATCGAC--A-GGCATTACATCAACCAAATTTTA
* * * *
11734 CGGGTCAAAGGCG-AATGTTCG
318 AGCGTCAAAAGCGAAAT-TTCA
* * * * * * *
11755 CGGATTGGGCCGAAA-CCAGGGAAGCTCGCTTGGAATTGACCCGCTCAGTGCGATTTTCCAGTCG
1 CCGATCGAGCCGAAAGCAACGGAAGC-CGCTTGGAAATGACCCGCTGAGTGCGATTTTCCAGTCG
* * ** *
11819 GAAAAGCTCCGCGAGTACCTCGCTTAGAGCTATCCGCTTAAAACGCTTTAGAGAACGAGTCAAAA
65 GAAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGC-TGAAACGCTCCAGAGAAAGAGTCAAAA
* * * * * * *
11884 AGTGGTCAGAAAAGCTCTTTTTTGACCTGATTT-TGACTGTTTCTCGGCTTC-GGAAGTCTCGCC
129 ATTGGTCAGAAAA-CTCGTTTTTGACCAG-TTTATAACTGTATCCCGAC-TCAGGAAGTCTCGCC
*
11947 GAG-AATGGGAACTGTGCG
191 GAGAAAT-GGAACCGTGCG
11965 TTTGCGGTAT
Statistics
Matches: 456, Mismatches: 76, Indels: 35
0.80 0.13 0.06
Matches are distributed among these distances:
337 29 0.06
338 9 0.02
339 138 0.30
340 177 0.39
341 103 0.23
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (338 bp):
CCGATCGAGCCGAAAGCAACGGAAGCCGCTTGGAAATGACCCGCTGAGTGCGATTTTCCAGTCGG
AAAAGCTCCGCGAGTCCCTCGCTTAGAGCTATCCGCTGAAACGCTCCAGAGAAAGAGTCAAAAAT
TGGTCAGAAAACTCGTTTTTGACCAGTTTATAACTGTATCCCGACTCAGGAAGTCTCGCCGAGAA
ATGGAACCGTGCGGAATCGATTCTACGCCTCCAAAATACGTAAGATGCGACTGAAATCCTGATAA
TTTTTTATCAGTCCAAAAAAGAGAAAAATCGACAGGCATTACATCAACCAAATTTTAAGCGTCAA
AAGCGAAATTTCA
Done.