Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5745.1
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: 18432
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.30
Warning! 953 characters in sequence are not A, C, G, or T
Found at i:4073 original size:40 final size:40
Alignment explanation
Indices: 4018--4098 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
4008 GTTTCTCGTG
* *
4018 ACTTGACAACTCGATCTTGGTCCGCACGCAACCCCGTATC
1 ACTTGACAACTCGATCTTGGTCCACACGCAACCCCCTATC
4058 ACTTGACAACTCGATCTTGGTCCACACGCAACCCCCTATC
1 ACTTGACAACTCGATCTTGGTCCACACGCAACCCCCTATC
4098 A
1 A
4099 GCAGCTAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.22
Consensus pattern (40 bp):
ACTTGACAACTCGATCTTGGTCCACACGCAACCCCCTATC
Found at i:8201 original size:15 final size:15
Alignment explanation
Indices: 8181--8219 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
8171 CTCACTCTCA
8181 TTTTCTTTTAGTTCT
1 TTTTCTTTTAGTTCT
*
8196 TTTTCTTTTATTTCT
1 TTTTCTTTTAGTTCT
8211 TTTTCTTTT
1 TTTTCTTTT
8220 TCTCTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTAGTTCT
Found at i:8218 original size:21 final size:21
Alignment explanation
Indices: 8192--8244 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
8182 TTTCTTTTAG
* *
8192 TTCTTTTTCTTTTATTTCTTT
1 TTCTTTTTCTCTCATTTCTTT
8213 TTCTTTTTCTCTCATTTCTTT
1 TTCTTTTTCTCTCATTTCTTT
*
8234 TT-TTCTTCTCT
1 TTCTTTTTCTCT
8245 TAATTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (21 bp):
TTCTTTTTCTCTCATTTCTTT
Found at i:8250 original size:21 final size:21
Alignment explanation
Indices: 8205--8251 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
8195 TTTTTCTTTT
* *
8205 ATTTCTTTTTCTTTTTCTCTC
1 ATTTCTTTTTCTTCTTCTCTA
8226 ATTTCTTTTT-TTCTTCTCTTA
1 ATTTCTTTTTCTTCTTCTC-TA
8247 ATTTC
1 ATTTC
8252 ATTCAAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTCTTTTTCTTCTTCTCTA
Found at i:9101 original size:29 final size:31
Alignment explanation
Indices: 9049--9121 Score: 105
Period size: 29 Copynumber: 2.4 Consensus size: 31
9039 CAATCACTCT
* *
9049 TTTTTTTTTCAATTTTGAATTTTTTTTCTTC
1 TTTTTTTTTCAAATCTGAATTTTTTTTCTTC
9080 TTTTTTTTT-AAATCTGAA-TTTTTTTCTTC
1 TTTTTTTTTCAAATCTGAATTTTTTTTCTTC
9109 TTTTTTTCTTCAA
1 TTTTTTT-TTCAA
9122 TACTAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 18 0.47
30 9 0.24
31 11 0.29
ACGTcount: A:0.15, C:0.11, G:0.03, T:0.71
Consensus pattern (31 bp):
TTTTTTTTTCAAATCTGAATTTTTTTTCTTC
Found at i:9177 original size:11 final size:11
Alignment explanation
Indices: 9161--9189 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
9151 AATACAAACT
9161 TTTTTTTTGAA
1 TTTTTTTTGAA
9172 TTTTTTTTGAA
1 TTTTTTTTGAA
9183 TTTTTTT
1 TTTTTTT
9190 CAAGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:9197 original size:11 final size:10
Alignment explanation
Indices: 9162--9208 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
9152 ATACAAACTT
9162 TTTTTTTGAA
1 TTTTTTTGAA
9172 TTTTTTTTGAA
1 -TTTTTTTGAA
*
9183 TTTTTTTCAA
1 TTTTTTTGAA
9193 GTTTTTTT--A
1 -TTTTTTTGAA
9202 TTTTTTT
1 TTTTTTT
9209 ACAATACCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 9 0.26
11 17 0.50
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:10227 original size:86 final size:86
Alignment explanation
Indices: 10082--10252 Score: 333
Period size: 86 Copynumber: 2.0 Consensus size: 86
10072 ATGCAATGTG
*
10082 AATTTATGAAAGGGAATTTTCACCCTTGCAATGCACGAAGGGATGCTTGGAAAATAGCAACTAGC
1 AATTTATGAAAGGGAATTTTCACCCTTGCAATGCACGAAGGGATGCTTGGAAAATAGCAACCAGC
10147 AGCCCACTCTCTTTAATGCAA
66 AGCCCACTCTCTTTAATGCAA
10168 AATTTATGAAAGGGAATTTTCACCCTTGCAATGCACGAAGGGATGCTTGGAAAATAGCAACCAGC
1 AATTTATGAAAGGGAATTTTCACCCTTGCAATGCACGAAGGGATGCTTGGAAAATAGCAACCAGC
10233 AGCCCACTCTCTTTAATGCA
66 AGCCCACTCTCTTTAATGCA
10253 GGTCTTCTTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (86 bp):
AATTTATGAAAGGGAATTTTCACCCTTGCAATGCACGAAGGGATGCTTGGAAAATAGCAACCAGC
AGCCCACTCTCTTTAATGCAA
Found at i:13760 original size:94 final size:94
Alignment explanation
Indices: 13599--13786 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
13589 AAGTGTTATA
13599 TACAAGGAGTGGCCGGCCATGCCTTTAAATAGGCCTCAAGTAATCCTAATCTAACAAGTAACTAA
1 TACAAGGAGTGGCCGGCCATGCCTTTAAATAGGCCTCAAGTAATCCTAATCTAACAAGTAACTAA
13664 TAAAACTAAACCTAATTAATAGAATAAAT
66 TAAAACTAAACCTAATTAATAGAATAAAT
13693 TACAAGGAGTGGCCGGCCATGCCTTTAAATAGGCCTCAAGTAATCCTAATCTAACAAGTAACTAA
1 TACAAGGAGTGGCCGGCCATGCCTTTAAATAGGCCTCAAGTAATCCTAATCTAACAAGTAACTAA
* *
13758 TAAAATTAAACCTACTTAATAGAATAAAT
66 TAAAACTAAACCTAATTAATAGAATAAAT
13787 AAAGGAAAAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (94 bp):
TACAAGGAGTGGCCGGCCATGCCTTTAAATAGGCCTCAAGTAATCCTAATCTAACAAGTAACTAA
TAAAACTAAACCTAATTAATAGAATAAAT
Found at i:14406 original size:10 final size:10
Alignment explanation
Indices: 14380--14430 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
14370 TTTAACTTAG
14380 TTCAGCTC-A
1 TTCAGCTCAA
*
14389 CTCGAGCTCAA
1 TTC-AGCTCAA
*
14400 GTCAGCTC-A
1 TTCAGCTCAA
14409 TTCAAGCTCAA
1 TTC-AGCTCAA
14420 TTCAGCTCAA
1 TTCAGCTCAA
14430 T
1 T
14431 ATTAACCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 5 0.14
10 23 0.66
11 7 0.20
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:14406 original size:20 final size:20
Alignment explanation
Indices: 14381--14428 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
14371 TTAACTTAGT
*
14381 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCAAGCTCAAG
* *
14401 TCAGCTCATTCAAGCTCAAT
1 TCAGCTCACTCAAGCTCAAG
14421 TCAGCTCA
1 TCAGCTCA
14429 ATATTAACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (20 bp):
TCAGCTCACTCAAGCTCAAG
Found at i:15149 original size:22 final size:21
Alignment explanation
Indices: 15120--15167 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
15110 AAGCATAAAC
*
15120 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAGTT-GTG
* *
15141 TGAACATTTTTATTAGTTGTG
1 TGAACATTTTAATGAGTTGTG
15162 TGAACA
1 TGAACA
15168 CATAGGTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAGTTGTG
Done.