Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1479
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: 23672
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2437 original size:93 final size:93
Alignment explanation
Indices: 2325--2496 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
2315 GCCCATAAGT
* *
2325 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2390 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
2418 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
2483 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
2497 CAAACATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:2492 original size:46 final size:46
Alignment explanation
Indices: 2317--2492 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
2307 TGTAACCCGC
* *
2317 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
2363 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
2409 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
2456 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
2493 TGCCCAAACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:4913 original size:30 final size:30
Alignment explanation
Indices: 4869--4957 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
4859 CAAAGATAAT
4869 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
4898 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
4928 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
4958 CGATATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:4917 original size:15 final size:15
Alignment explanation
Indices: 4869--4948 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
4859 CAAAGATAAT
*
4869 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
4883 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
4898 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
4913 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
4928 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
4943 AAGAAA
1 AAGAAA
4949 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:4957 original size:15 final size:15
Alignment explanation
Indices: 4880--4957 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
4870 AGAAAACCGA
4880 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
4895 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
4909 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
4924 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
4940 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
4955 ATA
1 ATA
4958 CGATATTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:7087 original size:20 final size:20
Alignment explanation
Indices: 7040--7087 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
7030 AGTAAGCTCG
7040 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
7060 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
7080 GTTGAGCT
1 GTTGAGCT
7088 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:9466 original size:93 final size:93
Alignment explanation
Indices: 9354--9525 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
9344 GCCCATAAGT
* *
9354 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
9419 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
9447 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
9512 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
9526 CAAACATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:9521 original size:46 final size:46
Alignment explanation
Indices: 9346--9521 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
9336 TGTAATCCGC
* *
9346 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
9392 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
9438 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
9485 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
9522 TGCCCAAACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 69 0.63
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:11488 original size:33 final size:33
Alignment explanation
Indices: 11446--11511 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
11436 CCGGCTAAGC
11446 CCAAAAAGCTTCTAATCTCGGTTACATTTTTAA
1 CCAAAAAGCTTCTAATCTCGGTTACATTTTTAA
11479 CCAAAAAGCTTCTAATCTCGGTTACATTTTTAA
1 CCAAAAAGCTTCTAATCTCGGTTACATTTTTAA
11512 GTGGTTTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (33 bp):
CCAAAAAGCTTCTAATCTCGGTTACATTTTTAA
Found at i:16430 original size:29 final size:28
Alignment explanation
Indices: 16394--16471 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
16384 TCATGAGATT
16394 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
16424 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
16451 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
16472 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:16735 original size:171 final size:173
Alignment explanation
Indices: 16424--16747 Score: 580
Period size: 171 Copynumber: 1.9 Consensus size: 173
16414 AAATTGTACA
*
16424 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
16489 TGTGCGAACCCAATATATATTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGAT
66 TGTGCGAACCCAATATATATTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAAT
16554 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
16597 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGC-CGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
16661 TGTGCGAACCCAATATATATTT-TATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
66 TGTGCGAACCCAATATATATTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAAT
16725 TTTGGACAGCGGAAAAGGTAAGT
131 TTTGGACAGCGGAAAAGGTAAGT
16748 ACCTTGAGTT
Statistics
Matches: 145, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
171 62 0.43
172 43 0.30
173 40 0.28
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (173 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAAT
TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Done.