Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3217
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: 33531
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:1256 original size:27 final size:27
Alignment explanation
Indices: 1223--1351 Score: 104
Period size: 27 Copynumber: 4.7 Consensus size: 27
1213 AATTGTTACA
*
1223 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGAT
** *
1250 GCACTAAGTGTGCGAAATGA-AATGAT
1 GCACTAAGTGTGCGATTTGACTATGAT
* * *
1276 GCACTAA-TGTGCGA-ATGACCATGCAG
1 GCACTAAGTGTGCGATTTGACTATG-AT
* *
1302 GCCACTAAGTGTGCGAGTTTGATTACCG-T
1 G-CACTAAGTGTGCGA-TTTGACTA-TGAT
1331 AGCACTAAGTGTGCGATTTGA
1 -GCACTAAGTGTGCGATTTGA
1352 TTTATAGCAC
Statistics
Matches: 83, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
24 4 0.05
25 10 0.12
26 13 0.16
27 24 0.29
28 12 0.14
29 14 0.17
30 5 0.06
31 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGAT
Found at i:1367 original size:26 final size:27
Alignment explanation
Indices: 1304--1367 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
1294 CCATGCAGGC
1304 CACTAAGTGTGCGAGTTTGATTACCGTAG
1 CACTAAGTGTGCGAGTTTGATTA-C-TAG
1333 CACTAAGTGTGCGA-TTTGATTTA-TAG
1 CACTAAGTGTGCGAGTTTGA-TTACTAG
*
1359 CACTGAGTG
1 CACTAAGTG
1368 AGCGGACTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 11 0.33
28 5 0.15
29 17 0.52
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (27 bp):
CACTAAGTGTGCGAGTTTGATTACTAG
Found at i:9013 original size:27 final size:27
Alignment explanation
Indices: 8983--9133 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
8973 ATATTGAGTC
* *
8983 CGCACACTCAGTGCTATATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
9010 CGCACACTTAGTGCTACGTAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
9038 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
9065 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
9092 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
9119 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9134 GTACAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 82 0.79
28 22 0.21
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:11852 original size:44 final size:43
Alignment explanation
Indices: 11645--12379 Score: 272
Period size: 44 Copynumber: 16.7 Consensus size: 43
11635 CCAAGCCTTG
* * * * * *
11645 TCTCCCTAAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGTAGATCTTA
* * *
11689 TCTCCCTAAGTAGTAGTTGAGCAGATCGAAGACG-ACGAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGTA-G-ATCTTA
* * ** * *
11733 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACGTAGATCTTA
* * * * * *
11777 TCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGTAGATCTTA
* **
11821 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGTAG-ATCTTA
* * ** * *
11865 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACGTAGATCTTA
* * * * * *
11909 TCTCCCTAAGCAGCAGCGGAGAAGGTTGAAAATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGTAGATCTTA
* **
11953 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGTAG-ATCTTA
* * * * *
11997 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-C-TAACAAGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGT-A-GA-TCTTA
* * * * *
12041 TCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGTAGATCTTA
* * *
12085 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC-GTAGATCTTA
* * ** *
12129 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTA
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACGTAGATCTTA
* * * * *
12173 TCTCCCTAAACAGTAGCGGAGAAGGTTGAAGATTGTAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGTAGATCTTA
* **
12217 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGTAG-ATCTTA
* * ** * *
12261 TCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ACGTAGATCTTA
* * * **
12305 TCTCCCTAAGCAGTAGCGGAGAAGGTTGAAGATTATAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-CGTAGATCTTA
* *
12349 TCTCCCTAAGCAGTAGCGGAGCAGATCGAAG
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAG
12380 TCGGCGAATC
Statistics
Matches: 494, Mismatches: 138, Indels: 118
0.66 0.18 0.16
Matches are distributed among these distances:
42 25 0.05
43 47 0.10
44 364 0.74
45 32 0.06
46 24 0.05
47 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (43 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGTAGATCTTA
Found at i:11871 original size:132 final size:132
Alignment explanation
Indices: 11634--12445 Score: 1435
Period size: 132 Copynumber: 6.2 Consensus size: 132
11624 CAGATCGGTA
*
11634 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * *
11699 TAGTAGTTGAGCAGATCGAAGACGACGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
11764 CC
131 CC
*
11766 ACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
11831 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
11896 CC
131 CC
*
11898 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAAATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
11963 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
*
12028 CT
131 CC
*
12030 AACAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
*
12095 CAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
12160 CC
131 CC
* * *
12162 ACCAAGCCTTATCTCCCTAAACAGTAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
12227 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
12292 CC
131 CC
* *
12294 ACCAAGCCTTGTCTCCCTAAGCAGTAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAG
1 ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * * *
12359 CAGTAGCGGAGCAGATCGAAGTCGGCGAATCTTATCTTTCCAAGACAGTGGGAAGTAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
12424 CC
131 CC
** *
12426 ACCAAATCTTATCTCCCTAA
1 ACCAAGCCTTGTCTCCCTAA
12446 AGTTGCAATG
Statistics
Matches: 653, Mismatches: 27, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 653 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (132 bp):
ACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
CC
Found at i:19503 original size:19 final size:20
Alignment explanation
Indices: 19479--19521 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19469 AGCTTGAATG
19479 ATATA-TATAAA-AATTATAA
1 ATATATTATAAATAATTA-AA
*
19498 ATATATTTTAAATAATTAAA
1 ATATATTATAAATAATTAAA
19518 ATAT
1 ATAT
19522 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATATTATAAATAATTAAA
Found at i:26930 original size:23 final size:24
Alignment explanation
Indices: 26885--26931 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
26875 CAATTAGAAA
*
26885 AGAAAATCATAATAAGAAATAACAGG
1 AGAAAAACATAATAAG--ATAACAGG
26911 AGAAAAACATAATAAG-TAACA
1 AGAAAAACATAATAAGATAACA
26932 ATATGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
26 15 0.75
ACGTcount: A:0.64, C:0.09, G:0.13, T:0.15
Consensus pattern (24 bp):
AGAAAAACATAATAAGATAACAGG
Done.