Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3564
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: 41466
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3286 original size:615 final size:606
Alignment explanation
Indices: 2125--3348 Score: 2313
Period size: 615 Copynumber: 2.0 Consensus size: 606
2115 ATCATTAAGG
*
2125 CACGCAACATCCTTGTTGCCATTGAGCATATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
1 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
*
2190 GGCCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
66 GACCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
*
2255 AAGCAGCAACAATTTCTTCATCAGTAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
131 AAGCAGCAACAATTTCTTCATCAATAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
*
2320 CACGTTTGGATATAATGCATGTCAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
196 CACGTTTGGATATAATGCATGTAAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
2385 AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
261 AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
2450 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
326 TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
*
2515 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAGCATAC
391 TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAACATAC
2580 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
456 AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
2645 CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
521 CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
2710 ACTACCACAACTCAAGCTAAT
586 ACTACCACAACTCAAGCTAAT
2731 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
1 CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
*
2796 GACCCAGTGCTTTTTGAAGAAGCAACTTGATAAACCATCACTCCCTGGAGCTTTTCGCTGGTCCA
66 GACCCAGTGCTTTTTGAAGAAGCAACCTGATAAA-C--CA-T--C---AGCTTTTCGCTGGTCCA
2861 TATGGTTAAAAGCAGCAACAATTTCTTCATCAATAAAGTCCCTGTCCAAGCAAGAGTTCATATTG
122 TATGGTTAAAAGCAGCAACAATTTCTTCATCAATAAAGTCCCTGTCCAAGCAAGAGTTCATATTG
2926 TCAGTAATGCACGTTTGGATATAATGCATGTAAGGTTCATTACAAGAAACAATGGTTGACTTAAA
187 TCAGTAATGCACGTTTGGATATAATGCATGTAAGGTTCATTACAAGAAACAATGGTTGACTTAAA
2991 AAGATCATTAAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCAT
252 AAGATCATTAAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCAT
3056 TAGAATCTTTTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAAC
317 TAGAATCTTTTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAAC
3121 GGGTGTTTCTATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCC
382 GGGTGTTTCTATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCC
3186 ACAACATACAAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTT
447 ACAACATACAAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTT
3251 TGGACCATCCACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTAT
512 TGGACCATCCACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTAT
3316 AACGCTTATACTACCACAACTCAAGCTAAT
577 AACGCTTATACTACCACAACTCAAGCTAAT
3346 CAC
1 CAC
3349 ACACCTTATC
Statistics
Matches: 603, Mismatches: 6, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
606 96 0.16
607 1 0.00
609 2 0.00
610 1 0.00
612 1 0.00
615 502 0.83
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (606 bp):
CACGCAACATCCTTGTTGCCATTGAGCACATCGTGACACAACTTTAAGACATCTTTTCCAACTAC
GACCCAGTGCTTTTTGAAGAAGCAACCTGATAAACCATCAGCTTTTCGCTGGTCCATATGGTTAA
AAGCAGCAACAATTTCTTCATCAATAAAGTCCCTGTCCAAGCAAGAGTTCATATTGTCAGTAATG
CACGTTTGGATATAATGCATGTAAGGTTCATTACAAGAAACAATGGTTGACTTAAAAAGATCATT
AAAATAGTCCCATGCAACTTTACAGATGTCCCTCTTGTCTTTTTGCCACGTCCCATTAGAATCTT
TTAACTTTTCTATATTGTGTTCTTTCTTCTGCCAGTAGCGTGCATGTGAAAATAACGGGTGTTTC
TATCACCCTCCGTGAGCCACTTAATGTGAGCCCTTTGTGCCCAATAGTCCTCATCCACAACATAC
AAGTGCCCAAGCTTGAAGCGAGCCATTTTAAGGAGGTTAGTTGTGTTATCCCTGTTTGGACCATC
CACAAGCTGATTGATCTTCCTCTTCAGACCCCATATTTGGTTCATCATTCTTTTATAACGCTTAT
ACTACCACAACTCAAGCTAAT
Found at i:12752 original size:70 final size:72
Alignment explanation
Indices: 12638--12788 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
12628 GGGGAATCAT
* *
12638 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
12702 GATATCG
66 GATATCG
***
12709 CACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
12773 GATATCG
66 GATATCG
12780 CACTTAGCA
1 CACTTAGCA
12789 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 34 0.46
71 40 0.54
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:12836 original size:104 final size:104
Alignment explanation
Indices: 12708--12930 Score: 360
Period size: 104 Copynumber: 2.2 Consensus size: 104
12698 AATGGATATC
12708 GCACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
12772 GGAT-ATCGCACTTAGCACCACCAATGAACCGAGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGAGGAATCA
12811 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* * *
12876 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGAGGAATCA
**
12915 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
12931 TTTATATACA
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
103 11 0.10
104 99 0.89
105 1 0.01
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGAGGAATCA
Found at i:13291 original size:29 final size:29
Alignment explanation
Indices: 13258--13321 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
13248 TAATCCACCA
13258 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
13287 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
13317 CCCAA
1 CCCAA
13322 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:13295 original size:30 final size:30
Alignment explanation
Indices: 13265--13321 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13255 CCACCCAACT
13265 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
13294 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
13322 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:16772 original size:19 final size:19
Alignment explanation
Indices: 16748--16784 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16738 TCAATATTTG
*
16748 GCTAGCTTATTTCTAAGTA
1 GCTAGCATATTTCTAAGTA
16767 GCTAGCATATTTCTAAGT
1 GCTAGCATATTTCTAAGT
16785 GCATGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (19 bp):
GCTAGCATATTTCTAAGTA
Found at i:19162 original size:29 final size:28
Alignment explanation
Indices: 19126--19203 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
19116 TCATGAGATT
19126 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
19156 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
19183 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
19204 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:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:38848 original size:9 final size:9
Alignment explanation
Indices: 38834--38863 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
38824 TCTGTGCCAT
38834 CAACATGGC
1 CAACATGGC
38843 CAACATGGC
1 CAACATGGC
38852 CAACATGGC
1 CAACATGGC
38861 CAA
1 CAA
38864 TGTGATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.20, T:0.10
Consensus pattern (9 bp):
CAACATGGC
Found at i:40339 original size:13 final size:13
Alignment explanation
Indices: 40317--40350 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40307 TTTTCAAGTC
* *
40317 ATGTTCTAAAGCT
1 ATGTTTTAAAGAT
40330 ATGTTTTAAAGAT
1 ATGTTTTAAAGAT
40343 ATGTTTTA
1 ATGTTTTA
40351 TGCGTGCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (13 bp):
ATGTTTTAAAGAT
Done.