Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1250
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: 20143
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1327 original size:47 final size:45
Alignment explanation
Indices: 1257--1429 Score: 179
Period size: 47 Copynumber: 3.7 Consensus size: 45
1247 AACCCGCCCC
* *
1257 TAAGTGAACTCGGACTCAGCTCAACGAGCTCGGGCGTTCGTATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTATCCA
* * *
1303 TAAGTGAACTCAGGACTCAACTCAACGAGTTCGGATGCCTAGT-TACA
1 TAAGTGAACTC-GGACTCAACTCAACGAGTTCGG--GCTTCGTATCCA
* * * * *
1350 TTTCA-CGAACTCGTACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTATCCA
1397 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1430 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
45 3 0.03
46 40 0.39
47 47 0.46
48 9 0.09
49 4 0.04
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGTATCCA
Found at i:4404 original size:93 final size:93
Alignment explanation
Indices: 4297--4467 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
4287 GCCCCTAAGT
* *
4297 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
4362 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
4390 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
4455 CGAGTTCGGATGC
66 CGAGTTCGGATGC
4468 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:4464 original size:46 final size:46
Alignment explanation
Indices: 4292--4464 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
4282 AACCCGCCCC
* * *
4292 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
4338 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
4386 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
4431 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
4465 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:4909 original size:30 final size:30
Alignment explanation
Indices: 4875--4934 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4865 ATTTAATACG
4875 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
4905 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
4935 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:7442 original size:93 final size:93
Alignment explanation
Indices: 7335--7505 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
7325 GCCCCTAAGT
* *
7335 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
7400 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
7428 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
7493 CGAGTTCGGATGC
66 CGAGTTCGGATGC
7506 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:7502 original size:46 final size:46
Alignment explanation
Indices: 7330--7502 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
7320 AACCCGCCCC
* * *
7330 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
7376 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
7424 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
7469 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
7503 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:7952 original size:30 final size:30
Alignment explanation
Indices: 7918--7977 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
7908 ATTTAATACG
7918 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
7948 AACTTTTGTATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
7978 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:11521 original size:24 final size:24
Alignment explanation
Indices: 11430--11514 Score: 152
Period size: 24 Copynumber: 3.5 Consensus size: 24
11420 GAAATGATTT
*
11430 TGGCACTATGTGTGCGAATTTGAA
1 TGGCACTATGTGTGCGAATTTGTA
11454 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGTA
*
11478 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGAATTTGTA
11502 TGGCACTATGTGT
1 TGGCACTATGTGT
11515 ACGGATTGGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.36
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGTA
Found at i:11535 original size:24 final size:24
Alignment explanation
Indices: 11430--11536 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 24
11420 GAAATGATTT
* * * *
11430 TGGCACTATGTGTGCGAATTTGAA
1 TGGCAATATGTGTACGGATTGGAA
* * * * *
11454 TGGCACTATGTGTGCGAATTTGTA
1 TGGCAATATGTGTACGGATTGGAA
* * * *
11478 TGGCACTATGTGTGCGGATTTGTA
1 TGGCAATATGTGTACGGATTGGAA
*
11502 TGGCACTATGTGTACGGATTGGAA
1 TGGCAATATGTGTACGGATTGGAA
*
11526 TGTCAATATGT
1 TGGCAATATGT
11537 ATGTGAATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (24 bp):
TGGCAATATGTGTACGGATTGGAA
Found at i:11536 original size:48 final size:48
Alignment explanation
Indices: 11430--11545 Score: 133
Period size: 48 Copynumber: 2.4 Consensus size: 48
11420 GAAATGATTT
* * * *
11430 TGGCACTATGTGTGCGAATTTGAATGGCACTATGTGTGCGAATTTGTA
1 TGGCAATATGTGTGCGAATTTGAATGGCACTATGTGTACGAATTGGAA
* * * *
11478 TGGCACTATGTGTGCGGATTTGTATGGCACTATGTGTACGGATTGGAA
1 TGGCAATATGTGTGCGAATTTGAATGGCACTATGTGTACGAATTGGAA
* * *
11526 TGTCAATATGTATGTGAATT
1 TGGCAATATGTGTGCGAATT
11546 ACTAAGGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.36
Consensus pattern (48 bp):
TGGCAATATGTGTGCGAATTTGAATGGCACTATGTGTACGAATTGGAA
Found at i:11555 original size:72 final size:72
Alignment explanation
Indices: 11430--11566 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
11420 GAAATGATTT
* * * * ** *
11430 TGGCACTATGTGTGCGAATTTGAATGGCACTATGTGTGCGAATTTGTATGGCACTATGTGTGCGG
1 TGGCACTATGTGTACGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
11495 ATTTGTA
66 ATTTGTA
* * * *
11502 TGGCACTATGTGTACGGATTGGAATGTCAATATGTATGTGAATTACTAAGGCACTATTTGTGCGG
1 TGGCACTATGTGTACGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
11567 GTTAACATGG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.35
Consensus pattern (72 bp):
TGGCACTATGTGTACGAATTGGAATGGCAATATGTATGCGAATTACTAAGGCACTATGTGTGCGG
ATTTGTA
Found at i:17785 original size:17 final size:17
Alignment explanation
Indices: 17759--17792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17749 TATATAATTG
*
17759 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
17776 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
17793 TTAAGTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:18986 original size:24 final size:24
Alignment explanation
Indices: 18959--19070 Score: 116
Period size: 24 Copynumber: 4.7 Consensus size: 24
18949 GAAATGATTT
*
18959 TGGCACAATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGTA
*
18983 TGGCACTATGTGTGCGGATTTGTA
1 TGGCACTATGTGTGCGAATTTGTA
* * *
19007 TGGCACTATGTGTGCGGATTGGAA
1 TGGCACTATGTGTGCGAATTTGTA
* * * * **
19031 TGTCAATATGTATGTGAATTACTA
1 TGGCACTATGTGTGCGAATTTGTA
*
19055 AGGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
19071 GGTTAACATG
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGTA
Done.