Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold754
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: 30057
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:1137 original size:40 final size:40
Alignment explanation
Indices: 1092--1269 Score: 285
Period size: 39 Copynumber: 4.5 Consensus size: 40
1082 ACTACTTGCT
*
1092 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1132 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACT-GCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1171 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAA-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
1210 CAAATGCCTTCGGGACTTAG-CCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
1249 CAAATGCCTTCGGGAC-TAGCC
1 CAAATGCCTTCGGGACTTAGCC
1270 GGTTATCATC
Statistics
Matches: 131, Mismatches: 3, Indels: 9
0.92 0.02 0.06
Matches are distributed among these distances:
37 1 0.01
38 14 0.11
39 81 0.62
40 35 0.27
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:9140 original size:40 final size:40
Alignment explanation
Indices: 9088--9272 Score: 293
Period size: 40 Copynumber: 4.6 Consensus size: 40
9078 ACTACTTGCT
* *
9088 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TATAGTAACTAGCA
9128 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
9168 CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
9208 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCA
*
9248 CAAATGCCTTCGGGACTTTGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
9273 TTATCATCCA
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.01
40 134 0.98
41 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:17215 original size:40 final size:40
Alignment explanation
Indices: 17117--17339 Score: 274
Period size: 40 Copynumber: 5.6 Consensus size: 40
17107 TCCTCGTTCA
* * ** *
17117 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
17156 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
17196 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
17236 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * *
17276 AATGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
17316 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
17340 CAGCATTCAA
Statistics
Matches: 165, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
39 38 0.23
40 118 0.72
41 9 0.05
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:17266 original size:80 final size:79
Alignment explanation
Indices: 17117--17339 Score: 304
Period size: 80 Copynumber: 2.8 Consensus size: 79
17107 TCCTCGTTCA
* * * * *
17117 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
17182 TAACAACTCGCACG
66 TAACAACTCGCACG
17196 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
17261 TTAACAACTCGCACG
65 TTAACAACTCGCACG
* * * * * * *
17276 AATGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
17340 CAGCATTCAA
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
79 38 0.29
80 86 0.67
81 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACG
Found at i:25037 original size:40 final size:38
Alignment explanation
Indices: 24939--25194 Score: 243
Period size: 40 Copynumber: 6.6 Consensus size: 38
24929 TCCTCGTTCA
* * * ** *
24939 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAA-TCGCAC
*
24978 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAA-TCGCAC
25017 GAATGCCTTCGGGACTTAACCCGGATTTAAC--TCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAATCGCAC
*
25054 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAA-TCGCAC
*
25094 GAATGCCTTCGGGACTTAACCCGGATTTATC--TCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAATCGCAC
* * * * * *
25131 AAAGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACA-ATCGCAC
* *
25171 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25195 CAGCATTCAA
Statistics
Matches: 191, Mismatches: 16, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
35 3 0.02
36 21 0.11
37 44 0.23
39 33 0.17
40 87 0.46
41 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (38 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAATCGCAC
Found at i:25061 original size:37 final size:37
Alignment explanation
Indices: 24939--25155 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 37
24929 TCCTCGTTCA
* * * *
24939 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGG-ATT--TAACTCGCACG
*
24978 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAAC---TCGCACG
25018 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACG
25055 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-TT--TAACTCGCACG
*
25095 AATGCCTTCGGGACTTAACCCGGATTTATCTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACG
* *
25131 AAAGCCTTC-GGATCTTAATCCGGAT
1 AATGCCTTCGGGA-CTTAACCCGGAT
25156 ATATTCACTT
Statistics
Matches: 163, Mismatches: 7, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
35 3 0.02
36 23 0.14
37 40 0.25
38 4 0.02
39 29 0.18
40 64 0.39
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (37 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACG
Found at i:25080 original size:77 final size:76
Alignment explanation
Indices: 24939--25194 Score: 300
Period size: 77 Copynumber: 3.3 Consensus size: 76
24929 TCCTCGTTCA
* * * * *
24939 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAACCCGG-ATT--TAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
25004 TAACAATTCGCACG
63 TAACAATTCGCACG
25018 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCAC-AATGCCTTCGGGACTTAACCCGGATTTA
* *
25083 ATAACTCGCACG
65 ACAATTCGCACG
* * * *
25095 AATGCCTTCGGGACTTAACCCGGATTTATCTCGCACAAAGCCTTC-GGATCTTAATCCGGATATA
1 AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACAATGCCTTCGGGA-CTTAACCCGGATTTA
* * *
25159 TTCACTTAGCAC-
65 -ACAATTCGCACG
* *
25171 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25195 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
75 3 0.02
76 52 0.33
77 78 0.50
78 2 0.01
79 21 0.13
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (76 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAA
CAATTCGCACG
Found at i:25178 original size:116 final size:113
Alignment explanation
Indices: 24937--25194 Score: 297
Period size: 116 Copynumber: 2.2 Consensus size: 113
24927 GCTCCTCGTT
* * *
24937 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
* *
25002 TTTAACAATTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACTCGCA
65 TTTAAC-A-TCGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACTAGCA
* * * *
25053 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGG
* * *
25118 ATTTATC-TCGCAC-AAAGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
64 ATTTAACATCGCACGAAAGCCTTCGGGA-CTTAACCCGG--AT-TTAAC-TAGCA
25170 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
25195 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
112 3 0.02
113 17 0.14
114 6 0.05
115 2 0.02
116 58 0.48
117 35 0.29
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (113 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACATCGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACTAGCA
Found at i:28748 original size:40 final size:40
Alignment explanation
Indices: 28646--28790 Score: 159
Period size: 40 Copynumber: 3.6 Consensus size: 40
28636 TACTCGAATG
* *
28646 ATATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* * *
28687 ACAATCCGGACTAAAAT--CGAAGGCATTTGTGCTAGCGACT
1 A-TATCCGGGCT-AAGTCCCGAAGGCATTTGTGCTAGCGACT
* * *
28727 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
28767 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
28791 CTTGTGCGAG
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
38 3 0.03
39 8 0.09
40 50 0.57
41 16 0.18
42 7 0.08
43 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Done.