Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_581 ID=scaffold_581-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: 5510
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Found at i:401 original size:44 final size:44
Alignment explanation
Indices: 351--666 Score: 160
Period size: 44 Copynumber: 7.2 Consensus size: 44
341 ATCTTGGGAA
*
351 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
395 AGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
439 AGACAAGGCTTGGTGGC-TAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
482 AGATAAGATTTGCCATCTTCGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** ** * * * * *
526 AGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAAGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
570 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
614 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
658 AGATAAGAT
1 AGATAAGAT
667 CTACAATCTT
Statistics
Matches: 183, Mismatches: 76, Indels: 26
0.64 0.27 0.09
Matches are distributed among these distances:
42 14 0.08
43 23 0.13
44 132 0.72
45 10 0.05
46 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:656 original size:263 final size:268
Alignment explanation
Indices: 6--715 Score: 1069
Period size: 263 Copynumber: 2.6 Consensus size: 268
1 TCCCA
*
6 CTGCTGCTCTAGGGAGACCAAGGCTTGGGTGTCCTT-AATCCTGCCTCCCCACTATCTTGGAAAA
1 CTGCTGCTC-AGGGAGA-CAAGGCTTGGGTG-CCTTAAAT-CTG-CTTCCCACTATCTTGG-AAA
70 GATAAAGAATTTGCCCGTCTTCGATCTGCTCCCACTACTGCTTAGGGGAGATAAGAATCTACAAT
60 GAT-AAG-ATTTG-CCGTCTTCGATCTGCT-CCACTACTGCTTA-GGGAGATAAG-ATCTACAAT
135 CCTTCAACCTACTCCGCCTGCTGCTCAGGGAGACAAGGGCTTGGTGGCTTAAAATCTGCTTCCCA
119 -CTTCAACCTACTCCG-CTGCTGCTCAGGGAGACAA-GGCTTGGTGGCTTAAAATCTGCTTCCCA
* * *
200 CTATCTTGGAAAAGATAAGAATTACCGTCTTTGGATCTGCTCCACTACTGCTTAGGGGGGATAAG
181 CTATCTTGGAAAAGATAAGAATTACCATCTTTCGATCTGCTCCACTACTGCTTAGGGGAGATAAG
265 ATTCTACAATCTCAGCCTACTCG
246 ATTCTACAATCTCAGCCTACTCG
*
288 CTGCTGCTCAGGGAGACAAGGCTTGGGTGTCTTTAAAATCTGCTTTCCCCACTATCTTGGGAAAG
1 CTGCTGCTCAGGGAGACAAGGCTTGGGTG-CCTT-AAATCTGC-TT-CCCACTATCTT-GGAAAG
353 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
61 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
418 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC-T-AAATCTGCTTCCCACTATCTTGG-
126 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAAATCTGCTTCCCACTATCTTGGA
* * *
480 AAAGATAAGATTTGCCATC-TTCGATTTGCTCCACTACTGCTTA-GGGAGATAAGA-TCTACAAT
191 AAAGATAAGAATTACCATCTTTCGATCTGCTCCACTACTGCTTAGGGGAGATAAGATTCTACAAT
542 CTTCAGCCTACTCCG
256 C-TCAGCCTACT-CG
* *
557 CTGCTGCTCAAGGAGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAG
1 CTGCTGCTCAGGGAGACAAGGCTTGGGTGCCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAG
621 ATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACT
66 ATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACT
686 CCGCTGCTGCTCAGGGAGACAAGGC-TGGTG
131 CCGCTGCTGCTCAGGGAGACAAGGCTTGGTG
716 TCTTCGATCT
Statistics
Matches: 410, Mismatches: 11, Indels: 34
0.90 0.02 0.07
Matches are distributed among these distances:
262 5 0.01
263 101 0.25
264 11 0.03
265 2 0.00
266 8 0.02
267 11 0.03
268 24 0.06
269 47 0.11
270 16 0.04
271 23 0.06
272 1 0.00
273 11 0.03
274 19 0.05
275 15 0.04
276 9 0.02
277 10 0.02
278 13 0.03
279 16 0.04
280 23 0.06
281 14 0.03
282 29 0.07
283 2 0.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (268 bp):
CTGCTGCTCAGGGAGACAAGGCTTGGGTGCCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAG
ATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACT
CCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAAATCTGCTTCCCACTATCTTGGAAAAGA
TAAGAATTACCATCTTTCGATCTGCTCCACTACTGCTTAGGGGAGATAAGATTCTACAATCTCAG
CCTACTCG
Found at i:677 original size:44 final size:44
Alignment explanation
Indices: 366--704 Score: 133
Period size: 44 Copynumber: 7.7 Consensus size: 44
356 AGATTTGCCG
*
366 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * * * * ***
410 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG-GCT-TGG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * *
452 TGGC-TAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGCCA
1 T--CTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCTACAA
* *
497 TCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
** * * * * * * * ***
541 TCTTCAGCCTACTCCGCTGCTGCTCAAGGAGACAAG-GCT-TGG
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * **
583 TGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGCCG
1 T--CTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAAGATCTACAA
*
629 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * * *
673 TCTTCAACCTACTCCGCTGCTGCTCAGGGAGA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGA
705 CAAGGCTGGT
Statistics
Matches: 202, Mismatches: 72, Indels: 42
0.64 0.23 0.13
Matches are distributed among these distances:
42 16 0.08
43 24 0.12
44 144 0.71
45 12 0.06
46 6 0.03
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
Found at i:770 original size:132 final size:132
Alignment explanation
Indices: 6--715 Score: 1034
Period size: 132 Copynumber: 5.2 Consensus size: 132
1 TCCCA
* *
6 CTGCTGCTCTAGGGAGACCAAGGCTTGGGTGTCCTT-AATCCTGCCTCCCCACTATCTTGGAAAA
1 CTGCTGCTC-AGGGAGA-CAAGGCTT-GGTG-GCTTAAAT-CTG-CTTCCCACTATCTTGG-AAA
70 GATAAAGAATTTGCCCGTCTTCGATCTGCTCCCACTACTGCTTAGGGGAGATAAGAATCTACAAT
59 GAT-AAG-ATTTG-CCGTCTTCGATCTGCT-CCACTACTGCTTA-GGGAGATAAG-ATCTACAAT
135 CCTTCAACCTACTCCG
118 -CTTCAACCTACTCCG
151 CCTGCTGCTCAGGGAGACAAGGGCTTGGTGGCTTAAAATCTGCTTCCCACTATCTTGGAAAAGAT
1 -CTGCTGCTCAGGGAGACAA-GGCTTGGTGGCTT-AAATCTGCTTCCCACTATCTTGG-AAAGAT
* * * * *
216 AAGAATTACCGTCTTTGGATCTGCTCCACTACTGCTTAGGGGGGATAAGATTCTACAATC-TCAG
62 AAGATTTGCCGTC-TTCGATCTGCTCCACTACTGCTTA-GGGAGATAAGA-TCTACAATCTTCAA
280 CCTACT-CG
124 CCTACTCCG
*
288 CTGCTGCTCAGGGAGACAAGGCTTGGGTGTCTTTAAAATCTGCTTTCCCCACTATCTTGGGAAAG
1 CTGCTGCTCAGGGAGACAAGGCTT-GGTGGC-TT-AAATCTGC-TT-CCCACTATCTT-GGAAAG
353 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
60 ATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
418 CTACTCCG
125 CTACTCCG
426 CTGCTGCTCAGGGAGACAAGGCTTGGTGGC-TAAATCTGCTTCCCACTATCTTGGAAAGATAAGA
1 CTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGA
* * *
490 TTTGCCATCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTC
66 TTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTC
555 CG
131 CG
*
557 CTGCTGCTCAAGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGA
1 CTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGA
622 TTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTC
66 TTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTC
687 CG
131 CG
689 CTGCTGCTCAGGGAGACAAGGC-TGGTG
1 CTGCTGCTCAGGGAGACAAGGCTTGGTG
716 TCTTCGATCT
Statistics
Matches: 529, Mismatches: 22, Indels: 41
0.89 0.04 0.07
Matches are distributed among these distances:
131 110 0.21
132 130 0.25
133 2 0.00
134 8 0.02
135 6 0.01
136 33 0.06
137 37 0.07
138 60 0.11
139 30 0.06
140 38 0.07
141 13 0.02
142 3 0.01
143 25 0.05
144 10 0.02
145 15 0.03
146 9 0.02
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (132 bp):
CTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGA
TTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTC
CG
Found at i:802 original size:44 final size:44
Alignment explanation
Indices: 742--1163 Score: 436
Period size: 44 Copynumber: 9.5 Consensus size: 44
732 CTCTCGGTGC
* * *
742 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
** * * *
786 ATAAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* *
831 AGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * *
875 AGGAAGACAGGATCTGCCATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * * * *
919 ACGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* * *
964 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * * * * *
1008 AGGAAGATAGGATCTGGTACCTTTGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * * *
1052 ATGAAGACAATATCTGCTTTCTTCGATCTACTTCAGCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CACCAATAT
* * *
1097 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
*
1141 AGGAAGACAAGATTTGCTATCTT
1 AGGAAGACAAGATCTGCTATCTT
1164 TACGGATCTG
Statistics
Matches: 304, Mismatches: 65, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
43 3 0.01
44 205 0.67
45 96 0.32
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
Found at i:844 original size:89 final size:89
Alignment explanation
Indices: 742--1163 Score: 431
Period size: 89 Copynumber: 4.8 Consensus size: 89
732 CTCTCGGTGC
* * ** *
742 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATC
*
807 TTCGATCTACTTCGCCACCAGTAT
66 TTCGATCTACTTCGCCACCAATAT
* * * * *
831 AGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCCAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATACAGGAAGACAAGATCTGCTAT
* * *
895 CTTCGATCTACTTC-ACGCCAATAC
65 CTTCGATCTACTTCGCCACCAATAT
* * * * * **
919 ACGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-AT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTGCTAT
* *
983 CTTCGATCCACTTCGCTACCAATAT
65 CTTCGATCTACTTCGCCACCAATAT
* * * * * * * * *
1008 AGGAAGATAGGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATC
*
1073 TTCGATCTACTTCAG-CACCAGTAT
66 TTCGATCTACTTC-GCCACCAATAT
* * * * *
1097 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAAGATTTGCTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATACAGGAAGACAAGATCTGCTAT
1161 CTT
65 CTT
1164 TACGGATCTG
Statistics
Matches: 268, Mismatches: 58, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
88 86 0.32
89 180 0.67
90 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (89 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATC
TTCGATCTACTTCGCCACCAATAT
Found at i:889 original size:133 final size:133
Alignment explanation
Indices: 742--1163 Score: 702
Period size: 133 Copynumber: 3.2 Consensus size: 133
732 CTCTCGGTGC
* *
742 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
*
807 TTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
872 TAT
131 TAT
* * * *
875 AGGAAGACAGGATCTGCCATCTTCGATCTACTTCACGCCAATACACGAAGATAAGATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
940 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
1005 TAT
131 TAT
* * * * * *
1008 AGGAAGATAGGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
1073 TTCGATCTACTTCAG-CACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCA
66 TTCGATCTACTTC-GCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCA
1137 ATAT
130 ATAT
*
1141 AGGAAGACAAGATTTGCTATCTT
1 AGGAAGACAAGATCTGCTATCTT
1164 TACGGATCTG
Statistics
Matches: 268, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
133 267 1.00
134 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (133 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
TAT
Found at i:4822 original size:24 final size:24
Alignment explanation
Indices: 4793--4838 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4783 ATCATCTTTT
* *
4793 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
4817 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
4839 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Done.