Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1816
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, 764
Length: 1274
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Found at i:306 original size:78 final size:78
Alignment explanation
Indices: 53--1156 Score: 1010
Period size: 78 Copynumber: 13.7 Consensus size: 78
43 CGTGTGGCCT
* * **
53 GAGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTGAAAAACAGAAATTTAAAAGAAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTAAAAAAACAGAAATTTAAAAG-AAAT
*
118 ACCTCGGCATGTGACCC
64 ACCTCGGCATG-G-TCC
* * *
135 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAAAAATAGAAATTTAAACGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTT-AAAAAAACAGAAATTTAAAAGAA
200 ATACCTCGGCATGTGTCC
62 ATACCTCGGCATG-GTCC
* * * *
218 GAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAAAACAGAAATATAAAAAAAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAAT-TTAAAAGAAATA
*
282 CCTCGGCATGGTTC
65 CCTCGGCATGGTCC
*
296 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAACAAAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT-AAAAAAACAGAAATTTAAAAGAAA
361 TACCTCAGCGTGACCCGA-GGCTCAAC
63 TACCT---CG-G---C-ATGG-TC--C
* * *
387 TCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTT---A-AAA
1 -GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAAACAGAAATTTAAAAGAAA
* * *
448 TACCTCAGCGTGCGACCC
63 TACCTCGGCATG-G-TCC
* *
466 GAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAACAGAAATTTAAAAGAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGAAATAC
*
530 CTCGGCATGGTTC
66 CTCGGCATGGTCC
* *
543 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTT---A-AAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAAACAGAAATTTAAAAGAAAT
* * *
604 ACCTCAGCGTGCGACCC
64 ACCTCGGCATG-G-TCC
* *
621 GAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAACAGAAATTTAAAAGAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGAAATAC
*
685 CTCGGCATGGTTC
66 CTCGGCATGGTCC
* *
698 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTT---A-AAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAAACAGAAATTTAAAAGAAAT
* * *
759 ACCTCAGCGTGCGACCC
64 ACCTCGGCATG-G-TCC
* *
776 GAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAACAGAAATTTAAAAGAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGAAATAC
*
840 CTCGGCATGGTTC
66 CTCGGCATGGTCC
853 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAACAGAAATTTAAAAGA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTT---AAAAAAACAGAAATTTAAAAGA
* * **
918 AATACCTCAGCGTGACCC
61 AATACCTCGGCATGGTCC
* * ** *
936 GAGGCTCAACTCATCTCT-GTAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTTAAAAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTAAAAAAACAGAAATTTAAAAGAA
* * *
1000 ATACCTCAGCGTGCGACCC
62 ATACCTCGGCATG-G-TCC
* * * *
1019 GAGGCTCAACTCACTTCTCGCAATCTAAGTTGATTTTTTTTTGAAAAAA-A-AAATTTAAAAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTAAAAAAACAGAAATTTAAAAGAA
** * *
1082 ATACCTCAACGTGAGACCC
62 ATACCTCGGCATG-G-TCC
* * *
1101 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT--GAAAACAGAAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAA
1157 ATATTTCTTG
Statistics
Matches: 873, Mismatches: 92, Indels: 118
0.81 0.08 0.11
Matches are distributed among these distances:
75 39 0.04
76 45 0.05
77 104 0.12
78 165 0.19
79 77 0.09
80 28 0.03
81 51 0.06
82 117 0.13
83 104 0.12
84 58 0.07
85 18 0.02
87 8 0.01
88 4 0.00
89 2 0.00
91 14 0.02
92 39 0.04
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (78 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAACAGAAATTTAAAAGAAATAC
CTCGGCATGGTCC
Found at i:568 original size:155 final size:155
Alignment explanation
Indices: 389--1156 Score: 1161
Period size: 155 Copynumber: 4.9 Consensus size: 155
379 GGCTCAACTC
389 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
454 AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
66 AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
519 AAAAGAAATACCTCGGCATGGTTCG
131 AAAAGAAATACCTCGGCATGGTTCG
544 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
609 AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
66 AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
674 AAAAGAAATACCTCGGCATGGTTCG
131 AAAAGAAATACCTCGGCATGGTTCG
699 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
764 AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
66 AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
829 AAAAGAAATACCTCGGCATGGTTCG
131 AAAAGAAATACCTCGGCATGGTTCG
*
854 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAACAGAAATTTAAAAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG---AAAAAATAGAAATTT---A-AA
* * *
919 ATACCTCAGCGT--GACCCGAGGCTCAACTCATCTCT-GTAATATGAGTTGATTTTTTTTTTGAA
59 ATACCTCAGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-----TTTTTGAA
* * * **
981 AAATAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCG
119 AAACAGAAATTTAAAAGAAATACCTCGGCATG-G-TTCG
* * *
1020 AGGCTCAACTCACTTCTCGCAATCTAAGTTGATTTTTTTTTGAAAAAA-A-AAATTTAAAAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAAAATAGAAATTT---A-AAA
* * * *
1083 TACCTCAACGTGAGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAG
60 TACCTCAGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG
*
1147 AAATTGAAAA
125 AAATTTAAAA
1157 ATATTTCTTG
Statistics
Matches: 576, Mismatches: 18, Indels: 33
0.92 0.03 0.05
Matches are distributed among these distances:
155 350 0.61
158 14 0.02
159 13 0.02
160 36 0.06
161 7 0.01
162 14 0.02
163 24 0.04
164 38 0.07
165 28 0.05
166 44 0.08
168 8 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (155 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAATACCTC
AGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT
AAAAGAAATACCTCGGCATGGTTCG
Found at i:836 original size:310 final size:312
Alignment explanation
Indices: 53--1156 Score: 1320
Period size: 310 Copynumber: 3.4 Consensus size: 312
43 CGTGTGGCCT
* * *
53 GAGGCTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTG-AAAAACAGAAATTTAAAAGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTT---A-AAAA
* * * * *
117 TACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTAAAAAA
62 TACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTT--GAAA
* * * *
182 AATAGAAATTTAAACGAAATACCTCGGCATGTGTCCGAGGTTCAACTCACCTCTCGCAATATGAG
122 AACAGAAATTTAAAAGAAATACCTCGGCATG-GTTCGAGGCTCAACTCACCTCTCGCAATATGAG
** * * * **
247 TTGA---TTTAAAAAAAACAGAAATATAAAAAAAAATACCTCGGCATGG-TTCGAGGCTCAACTC
186 TTGATTTTTTTGAAAAAACAGAAAT-T----TAAAATACCTCAGCGTGGACCCGAGGCTCAACTC
* * *
308 ACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAACAAAAATTTAAAAGAAATACCTCAGCGTG
246 ACCTCTCGCAATATGAGTTGA-TTTTTTG--AAAAACAGAAATTTAAAAGAAATACCTCGGCATG
373 ACCCGAGGCTCAACTC
308 ----GA---T----TC
389 -AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTT-AAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAAATACC
*
452 TCAGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
66 TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
517 TTAAAAGAAATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
131 TTAAAAGAAATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
582 TGAAAAAATAGAAATTTAAAATACCTCAGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATAT
196 TGAAAAAACAGAAATTTAAAATACCTCAGCGTG-GACCCGAGGCTCAACTCACCTCTCGCAATAT
647 GAGTTGA-TTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGG-TTC
260 GAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGGATTC
698 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTT-AAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAAATACC
*
762 TCAGCGTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
66 TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
827 TTAAAAGAAATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
131 TTAAAAGAAATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
892 TGAAAAAAAAACAGAAATTTAAAAGAAATACCTCAGCGT-GACCCGAGGCTCAACTCATCTCT-G
196 TG---AAAAAACAGAAATTT---A-AAATACCTCAGCGTGGACCCGAGGCTCAACTCACCTCTCG
* * * * **
955 TAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTTAAAAGAAATACCTCAGCGTGCGACCC
254 CAATATGAGTTGA----TTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATG-GATTC
* * *
1019 GAGGCTCAACTCACTTCTCGCAATCTAAGTTGATTTTTTTTTGAAAAAA-A-AAATTTAAAAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAAAATAGAAATTT--AA-AA
* * *
1082 ATACCTCAACGTGAGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACA
61 ATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
*
1146 GAAATTGAAAA
126 GAAATTTAAAA
1157 ATATTTCTTG
Statistics
Matches: 699, Mismatches: 42, Indels: 66
0.87 0.05 0.08
Matches are distributed among these distances:
309 2 0.00
310 195 0.28
313 15 0.02
314 13 0.02
315 21 0.03
316 1 0.00
317 15 0.02
319 37 0.05
320 1 0.00
321 68 0.10
322 1 0.00
323 34 0.05
324 18 0.03
325 124 0.18
326 32 0.05
327 1 0.00
328 20 0.03
331 50 0.07
335 38 0.05
336 13 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (312 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGAAATTTAAAAATACC
TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
TTAAAAGAAATACCTCGGCATGGTTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
TGAAAAAACAGAAATTTAAAATACCTCAGCGTGGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGGATTC
Done.