Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1266
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: 36445
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:8879 original size:66 final size:67
Alignment explanation
Indices: 8750--8879 Score: 165
Period size: 66 Copynumber: 1.9 Consensus size: 67
8740 GGGATGTATC
* *
8750 CCATGTGGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
8815 AGGACA
62 AGGACA
* *
8821 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
8880 TTCACCATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.17
68 1 0.02
71 20 0.37
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:12530 original size:41 final size:43
Alignment explanation
Indices: 12485--12615 Score: 128
Period size: 43 Copynumber: 3.1 Consensus size: 43
12475 GCAGGAAGCT
* *
12485 TGCTAGACTTTAAG-TCTGA-ACTCA-TTCACCGGCATT-TCGCC
1 TGCTAGACTTGAAGCTC-GATA-TCATTTCACCGGCATTATAGCC
* *
12526 TGCTAGGCTTGAAGCTCGATATCATTTCACTGGCATTATAGCC
1 TGCTAGACTTGAAGCTCGATATCATTTCACCGGCATTATAGCC
* * * *
12569 TGCTAGGCTCGAAGC-CTGATATTATCTCACCGGCATTATAGCC
1 TGCTAGACTTGAAGCTC-GATATCATTTCACCGGCATTATAGCC
12612 TGCT
1 TGCT
12616 TGGCCCGAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
41 17 0.22
42 15 0.19
43 45 0.58
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (43 bp):
TGCTAGACTTGAAGCTCGATATCATTTCACCGGCATTATAGCC
Found at i:12576 original size:43 final size:43
Alignment explanation
Indices: 12509--12632 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
12499 TCTGAACTCA
* *
12509 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAG-CTCGATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCT-GATATCAT
* *
12551 TTCACTGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATCAT
* * * *
12594 CTCACCGGCATTATAGCCTGCTTGGCCCGAAGCCCGATA
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATA
12633 ATATTATTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
42 11 0.15
43 58 0.82
44 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCTGATATCAT
Found at i:18321 original size:40 final size:40
Alignment explanation
Indices: 18069--18314 Score: 388
Period size: 40 Copynumber: 6.2 Consensus size: 40
18059 AACCCAAGTA
* *
18069 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
18108 CCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
18148 CCTTCGGGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
18188 CCTTCGAGACTTAGCCTGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
18228 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
18268 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
18308 CCTTCGG
1 CCTTCGG
18315 ATCTTAGTCC
Statistics
Matches: 191, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.07
40 178 0.93
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:26251 original size:37 final size:38
Alignment explanation
Indices: 26156--26359 Score: 299
Period size: 38 Copynumber: 5.3 Consensus size: 38
26146 AAACCCAATA
* * *
26156 CCTTCGGGATTTAGCC-GATATAGCAACTCGCACAAATG
1 CCTTC-GGACTTAGCCGGATATAGTAACTAGCACAAATG
26194 CCTTCGGGACTTAGCCGGATATAGTAACTAGCACAAATG
1 CCTTC-GGACTTAGCCGGATATAGTAACTAGCACAAATG
26233 CCTTC-GACTTAGCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGACTTAGCCGGATATAGTAACTAGCACAAATG
26270 CCTTCGGACTTAGCCCGGATATA-TAACTAGCACAAATG
1 CCTTCGGACTTAG-CCGGATATAGTAACTAGCACAAATG
*
26308 CCTTCGGACTTAGCCCGGATATA-TCACTAGCACAAATG
1 CCTTCGGACTTAG-CCGGATATAGTAACTAGCACAAATG
26346 CCTTCGGATCTTAG
1 CCTTCGGA-CTTAG
26360 TCGTTATCAT
Statistics
Matches: 158, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
37 37 0.23
38 82 0.52
39 39 0.25
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (38 bp):
CCTTCGGACTTAGCCGGATATAGTAACTAGCACAAATG
Found at i:29998 original size:39 final size:39
Alignment explanation
Indices: 29955--30186 Score: 287
Period size: 39 Copynumber: 6.0 Consensus size: 39
29945 ATCCGAAGAA
29955 ATTTGTGCTAGTGA-TATATCCGGTCTAAGTCCCGAAGGC
1 ATTTGTGCTAGTGACTATATCCGG-CTAAGTCCCGAAGGC
* * *
29994 ATTTGTGCTAGTTACTAT-TTCGGTCTAGGTCCCGAAGGC
1 ATTTGTGCTAGTGACTATATCCGG-CTAAGTCCCGAAGGC
*
30033 ATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGC
1 ATTTGTGCTAGTGACTATATCC-GGCTAAGTCCCGAAGGC
30073 ATTTGTGCTAGTGACTATATCCAGGCTAAGT-CCGAAGGC
1 ATTTGTGCTAGTGACTATATCC-GGCTAAGTCCCGAAGGC
* *
30112 ATCTGTGCTAGTTACTATATCCGGGCTAAGT-CCGAAGGC
1 ATTTGTGCTAGTGACTATATCC-GGCTAAGTCCCGAAGGC
* ** *
30151 ATTTG-GCGAG-GTTTATATCCGGCTAAATCCCGAAGG
1 ATTTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGG
30187 TACTTGGGTT
Statistics
Matches: 173, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
36 7 0.04
37 14 0.08
38 4 0.02
39 98 0.57
40 48 0.28
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (39 bp):
ATTTGTGCTAGTGACTATATCCGGCTAAGTCCCGAAGGC
Found at i:30077 original size:79 final size:79
Alignment explanation
Indices: 29940--30155 Score: 305
Period size: 79 Copynumber: 2.7 Consensus size: 79
29930 TGTAACCGGA
** * *
29940 CTAAGATCCGAAGAAATTTGTGCTAGTGA-TATATCCGGTCTAAGTCCCGAAGGCATTTGTGCTA
1 CTAAG-TCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA
* *
30004 GTTACTAT-TTC-GG
65 GTGACTATATCCAGG
*
30017 TCTAGGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT
1 -CTAAGT-CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT
30082 AGTGACTATATCCAGG
64 AGTGACTATATCCAGG
*
30098 CTAAGTCCGAAGGCATCTGTGCTAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTTG
1 CTAAGTCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
30156 GCGAGGTTTA
Statistics
Matches: 125, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
77 1 0.01
78 36 0.29
79 79 0.63
80 7 0.06
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (79 bp):
CTAAGTCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG
TGACTATATCCAGG
Found at i:30148 original size:118 final size:115
Alignment explanation
Indices: 29955--30186 Score: 319
Period size: 118 Copynumber: 2.0 Consensus size: 115
29945 ATCCGAAGAA
* * *
29955 ATTTGTGCTAGTGATATATCCGGTCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATTTCGGTCT
1 ATTTGTGCTAGTGATATATCCGGTCTAAGTCCCGAAGGCATCTGTGCTAGTTACTATTCCGGGCT
* * *
30020 AGGTCCCGAAGGCATTTGTGCTA-GTTACTATATCCGGGCTAAGTCCCGAAGGC
66 AAGTCCCGAAGGCATTTG-GCGAGGTT--TATATCC-GGCTAAATCCCGAAGGC
30073 ATTTGTGCTAGTGACTATATCCAGG-CTAAGT-CCGAAGGCATCTGTGCTAGTTACTATATCCGG
1 ATTTGTGCTAGTGA-TATATCC-GGTCTAAGTCCCGAAGGCATCTGTGCTAGTTACTAT-TCCGG
30136 GCTAAGT-CCGAAGGCATTTGGCGAGGTTTATATCCGGCTAAATCCCGAAGG
63 GCTAAGTCCCGAAGGCATTTGGCGAGGTTTATATCCGGCTAAATCCCGAAGG
30187 TACTTGGGTT
Statistics
Matches: 104, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
115 15 0.14
116 7 0.07
117 3 0.03
118 55 0.53
119 22 0.21
120 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (115 bp):
ATTTGTGCTAGTGATATATCCGGTCTAAGTCCCGAAGGCATCTGTGCTAGTTACTATTCCGGGCT
AAGTCCCGAAGGCATTTGGCGAGGTTTATATCCGGCTAAATCCCGAAGGC
Done.