Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold578
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: 32314
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.27
Warning! 6548 characters in sequence are not A, C, G, or T
Found at i:1072 original size:9 final size:9
Alignment explanation
Indices: 1058--1223 Score: 100
Period size: 9 Copynumber: 19.3 Consensus size: 9
1048 TTTTTATGTA
1058 TTATGTAAG
1 TTATGTAAG
1067 TTATGTAAG
1 TTATGTAAG
*
1076 TAATGT-A-
1 TTATGTAAG
1083 TTATGTAAG
1 TTATGTAAG
*
1092 TTGTGTATA-
1 TTATGTA-AG
*
1101 ATAT-TAA-
1 TTATGTAAG
*
1108 TTATGTGAG
1 TTATGTAAG
*
1117 TTGTGT-A-
1 TTATGTAAG
* *
1124 TAATGTCAG
1 TTATGTAAG
*
1133 TTAAG-AAGG
1 TTATGTAA-G
1142 TTATGT-A-
1 TTATGTAAG
*
1149 TAATGTAAG
1 TTATGTAAG
**
1158 TTATGCCAG
1 TTATGTAAG
* *
1167 TTATTTAAT
1 TTATGTAAG
1176 TTATGTAAG
1 TTATGTAAG
* *
1185 TTATTTAAT
1 TTATGTAAG
*
1194 TTTTGTAAG
1 TTATGTAAG
1203 TTATGTAAG
1 TTATGTAAG
1212 TTATGTAAG
1 TTATGTAAG
1221 TTA
1 TTA
1224 CTTAATTTGT
Statistics
Matches: 116, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
7 18 0.16
8 10 0.09
9 87 0.75
10 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1110 original size:25 final size:23
Alignment explanation
Indices: 1053--1155 Score: 91
Period size: 25 Copynumber: 4.2 Consensus size: 23
1043 ATATATTTTT
*
1053 ATGTATTATGTAAGTTATGTAAGTA
1 ATGTATTATGTAAGTTGTGT-A-TA
1078 ATGTATTATGTAAGTTGTGTATA
1 ATGTATTATGTAAGTTGTGTATA
* *
1101 ATATTAATTATGTGAGTTGTGTATA
1 AT-GT-ATTATGTAAGTTGTGTATA
* *
1126 ATGTCAGTTAAG-AAGGTTATGTATA
1 ATGT-A-TTATGTAA-GTTGTGTATA
1151 ATGTA
1 ATGTA
1156 AGTTATGCCA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
23 4 0.06
24 6 0.09
25 56 0.85
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (23 bp):
ATGTATTATGTAAGTTGTGTATA
Found at i:1186 original size:18 final size:18
Alignment explanation
Indices: 1165--1231 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
1155 AAGTTATGCC
1165 AGTTATTTAATTTATGTA
1 AGTTATTTAATTTATGTA
*
1183 AGTTATTTAATTTTTGTA
1 AGTTATTTAATTTATGTA
* *
1201 AGTTATGTAAGTTATGTA
1 AGTTATTTAATTTATGTA
*
1219 AGTTACTTAATTT
1 AGTTATTTAATTT
1232 GTGATACCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (18 bp):
AGTTATTTAATTTATGTA
Found at i:5407 original size:188 final size:188
Alignment explanation
Indices: 5085--5483 Score: 602
Period size: 188 Copynumber: 2.1 Consensus size: 188
5075 TAATACTATG
* * * * * * *
5085 ATTTAGCGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTT
1 ATTTTGCGGCGTTTTCCAATAAACACCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
* * * *
5150 TGGTTAAGAAATATTGCGGCGCTTTTCAGTACTCGCCGCTACTACTGTACTTTAGCAGCGTTTTA
66 TGGTTAAGAAATATTGCGGCACTTTTCACTACTCGCCGCTAATACTATACTTTAGCAGCGTTTTA
*
5215 ATATAAGTGCCACTAATGCTACTATACATCAAGACCAAAGCGCTACGTTTTGGTTAAT
131 ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTACGTTTTGGTTAAT
*
5273 CTTTTGCGGCGTTTTCCAATAAACACCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 ATTTTGCGGCGTTTTCCAATAAACACCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
* *
5338 TGGTTAAGAAATCTTGCGGCACTTTTCACTACTCGCCGCTAATACTATGA-TTTAGCGGCGTTTT
66 TGGTTAAGAAATATTGCGGCACTTTTCACTACTCGCCGCTAATACTAT-ACTTTAGCAGCGTTTT
* * *
5402 AATATAAGCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
130 AATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTACGTTTTGGTTAAT
* *
5461 ATTTTGCGGCGCTTTACAATAAA
1 ATTTTGCGGCGTTTTCCAATAAA
5484 TGTCGCTAAT
Statistics
Matches: 189, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
188 188 0.99
189 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (188 bp):
ATTTTGCGGCGTTTTCCAATAAACACCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
TGGTTAAGAAATATTGCGGCACTTTTCACTACTCGCCGCTAATACTATACTTTAGCAGCGTTTTA
ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCGCTACGTTTTGGTTAAT
Found at i:5636 original size:114 final size:114
Alignment explanation
Indices: 5298--5760 Score: 502
Period size: 114 Copynumber: 4.1 Consensus size: 114
5288 CCAATAAACA
* * *
5298 CCACTAAGCCTAATATACCG-CAAGACCAAACTCTGCGTTTTGGTTAAGAAATCTTGCGGCACTT
1 CCACTAATCCTAATATA-CGTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTT
* * *
5362 TTCACTACTCGCCGCTAATACTATGATTTAGCGGCGTTTTAATATAAGCG
65 TTCACTACTCGCCGCTAATACTATGCTTTAGCGGCATTTTTATATAAGCG
* * * * * * *
5412 CCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTT-A-ATATTTTGCGGCGCTT
1 CCACTAATCCTAATATACGTCAAGACCAAA-CTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTT
* * * * * * ***
5475 TACAATAAAT-GTCGCTAATACTATGCTTTACCAGCATTTTCCGATAAGCG
65 TTCACT-ACTCGCCGCTAATACTATGCTTTAGCGGCATTTTTATATAAGCG
* *
5525 CCACTAATCCTAATATACGTCAAGACCGAACTCTGCGTTTTGGTTAAGAAATATTGCGACGCTTT
1 CCACTAATCCTAATATACGTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTTT
* * * *
5590 TCACTACTCGCCGCTAATACTATTCTGTAGCGGCGTTTTTTTATAAGCG
66 TCACTACTCGCCGCTAATACTATGCTTTAGCGGCATTTTTATATAAGCG
* * * * ** *
5639 CCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATGTATTGAGGCGCTTT
1 CCACTAATCCTAATATACGTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTTT
** * * * *
5704 TTGCGACTCGCCGCTAATTCTATGCTTTAGCGGCATTTTTAAATATGCG
66 TCACTACTCGCCGCTAATACTATGCTTTAGCGGCATTTTTATATAAGCG
5753 CCACTAAT
1 CCACTAAT
5761 ACTTTCTTTA
Statistics
Matches: 283, Mismatches: 60, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
112 14 0.05
113 78 0.28
114 177 0.63
115 14 0.05
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (114 bp):
CCACTAATCCTAATATACGTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTTT
TCACTACTCGCCGCTAATACTATGCTTTAGCGGCATTTTTATATAAGCG
Found at i:11009 original size:14 final size:15
Alignment explanation
Indices: 10981--11011 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
10971 ACATAAATCG
10981 TAAACCCCTAACCCT
1 TAAACCCCTAACCCT
10996 TAAACCCC-AACCCT
1 TAAACCCCTAACCCT
11010 TA
1 TA
11012 TAACTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAACCCCTAACCCT
Found at i:13699 original size:11 final size:9
Alignment explanation
Indices: 13672--13704 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
13662 TGTGTAACTA
13672 TAATATAAT
1 TAATATAAT
13681 TAATATAAT
1 TAATATAAT
13690 TAATAT-A-
1 TAATATAAT
13697 TAATATAA
1 TAATATAA
13705 CAAGTGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.26
8 2 0.09
9 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATATAAT
Found at i:15716 original size:21 final size:21
Alignment explanation
Indices: 15690--15732 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
15680 GTGGGATTCT
15690 AACTTTTTATTAATTAAACTA
1 AACTTTTTATTAATTAAACTA
*
15711 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTAATTAAACTA
15732 A
1 A
15733 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTAATTAAACTA
Found at i:26855 original size:59 final size:59
Alignment explanation
Indices: 26787--26898 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
26777 AATAAAATAA
** *
26787 TTTAATTATATATATTTTTAAAAAAACTATTCCATTTT-TGTTTTAAATGTTTTGAAAAT
1 TTTAATTATATATATTTAAAAAAAAACTATTCCATTTTAT-TTTTAAACGTTTTGAAAAT
*
26846 TTTAATTATATATATTTAAAAAAAAACTATTCTATTTTATTTTTAAACGTTTT
1 TTTAATTATATATATTTAAAAAAAAACTATTCCATTTTATTTTTAAACGTTTT
26899 ATTTAAAGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 47 0.98
60 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (59 bp):
TTTAATTATATATATTTAAAAAAAAACTATTCCATTTTATTTTTAAACGTTTTGAAAAT
Found at i:28954 original size:23 final size:23
Alignment explanation
Indices: 28922--29130 Score: 158
Period size: 22 Copynumber: 9.1 Consensus size: 23
28912 TATGTAAAGA
28922 GTAT-ATTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* *
28944 GTATAGTTGGTTGTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* * * *
28967 TTATATATATGGTGGTGTTTTGCA-A
1 GTATA-AT-TGGTTGTG-TTTGGAGG
* * * ***
28992 GTACATTTGGTTATGTTCAAAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
29015 GTA-AATTGGTTGTGTTTGGAAG
1 GTATAATTGGTTGTGTTTGGAGG
* *
29037 GTATACTTGGTTGTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
29060 TTATATATATGGTTGTGTTTGGAGG
1 GTATA-AT-TGGTTGTGTTTGGAGG
* * *
29085 GTA-AATTGGCTGTGTTTCGAGA
1 GTATAATTGGTTGTGTTTGGAGG
*
29107 GTA-AATTGGTTGTGTTTGGGGG
1 GTATAATTGGTTGTGTTTGGAGG
29129 GT
1 GT
29131 GATAGCTTTA
Statistics
Matches: 142, Mismatches: 37, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
22 56 0.39
23 51 0.36
24 4 0.03
25 27 0.19
26 4 0.03
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTTGGAGG
Done.