Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2542
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: 30071
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1573 original size:15 final size:15
Alignment explanation
Indices: 1549--1588 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1539 TTTAAATTGG
*
1549 ATTTCCTTATCATGA
1 ATTTCTTTATCATGA
* *
1564 ATTTCTTTATCTTGG
1 ATTTCTTTATCATGA
1579 ATTTCTTTAT
1 ATTTCTTTAT
1589 TCTAGGCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTTCTTTATCATGA
Found at i:4085 original size:27 final size:27
Alignment explanation
Indices: 4055--4108 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
4045 TGTCATGTGA
* *
4055 AATTAAATGGCAAATTATTGTTACATG
1 AATTAAATGGCAAATTACTATTACATG
* **
4082 AATTGAATGTTAAATTACTATTACATG
1 AATTAAATGGCAAATTACTATTACATG
4109 GGTAGTATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (27 bp):
AATTAAATGGCAAATTACTATTACATG
Found at i:9041 original size:27 final size:26
Alignment explanation
Indices: 8993--9052 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
8983 GCGAGGCTGC
*
8993 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
9020 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
9046 CAGATAT
1 CAGATAT
9053 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:9823 original size:27 final size:27
Alignment explanation
Indices: 9800--9857 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
9790 ATTGGTAGTC
9800 CTACCCTACAGGGGTATTTCGGTAACT
1 CTACCCTACAGGGGTATTTCGGTAACT
* * *
9827 CTACCTTATAGGGGTATTTCGGTAATT
1 CTACCCTACAGGGGTATTTCGGTAACT
9854 CTAC
1 CTAC
9858 AACTTATCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (27 bp):
CTACCCTACAGGGGTATTTCGGTAACT
Found at i:16492 original size:27 final size:26
Alignment explanation
Indices: 16444--16524 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
16434 GCGAGGCTGC
*
16444 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
16471 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
16497 CATATATATATGTGGCGAAGCCACCAGA
1 C--AGATAT-TGTGACGAAGCCACCAGA
16525 TTGCAGCGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.05
27 21 0.48
28 5 0.11
29 16 0.36
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:17262 original size:27 final size:27
Alignment explanation
Indices: 17232--17291 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
17222 TTACCCTCTG
*
17232 GGGGTAAATCGGTAGTCCTACCCTACA
1 GGGGTAAATCGGTAATCCTACCCTACA
** * * *
17259 GGGGTATTTCGGTAATTCTACCTTATA
1 GGGGTAAATCGGTAATCCTACCCTACA
17286 GGGGTA
1 GGGGTA
17292 TTTCAGTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (27 bp):
GGGGTAAATCGGTAATCCTACCCTACA
Found at i:17292 original size:27 final size:27
Alignment explanation
Indices: 17240--17306 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
17230 TGGGGGTAAA
* *
17240 TCGGTAGTCCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* *
17267 TCGGTAATTCTACCTTATAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
*
17294 TCAGTAATTCTAC
1 TCGGTAATTCTAC
17307 AACTTATCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (27 bp):
TCGGTAATTCTACCCTACAGGGGTATT
Found at i:18644 original size:18 final size:18
Alignment explanation
Indices: 18595--18644 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
18585 GTTTTCAATT
18595 TTCTTTTT-CTTCTCACA
1 TTCTTTTTCCTTCTCACA
*
18612 TTCTTTTTCAC-TCTC-GA
1 TTCTTTTTC-CTTCTCACA
18629 TCTCTTTTTCCTTCTC
1 T-TCTTTTTCCTTCTC
18645 TTTTTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.39
18 16 0.57
19 1 0.04
ACGTcount: A:0.08, C:0.32, G:0.02, T:0.58
Consensus pattern (18 bp):
TTCTTTTTCCTTCTCACA
Found at i:18664 original size:18 final size:18
Alignment explanation
Indices: 18612--18726 Score: 69
Period size: 18 Copynumber: 6.4 Consensus size: 18
18602 TCTTCTCACA
**
18612 TTCTTTTTCACTCTCGAT
1 TTCTTTTTCACTCTCTTT
*
18630 CTCTTTTTC-CTTCTCTTT
1 TTCTTTTTCAC-TCTCTTT
*
18648 TTCTTTTTCACTATCTTT
1 TTCTTTTTCACTCTCTTT
**
18666 TTCAATTTCA-T-T-TTT
1 TTCTTTTTCACTCTCTTT
* *
18681 CTT-TTTCTCATTCTCTTT
1 -TTCTTTTTCACTCTCTTT
*
18699 TTGCTTTTTTTCACACTCTTT
1 TT-C--TTTTTCACTCTCTTT
18720 TTCTTTT
1 TTCTTTT
18727 GTTTCTTTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
15 7 0.09
16 4 0.05
17 5 0.07
18 42 0.57
19 1 0.01
20 1 0.01
21 14 0.19
ACGTcount: A:0.09, C:0.24, G:0.02, T:0.65
Consensus pattern (18 bp):
TTCTTTTTCACTCTCTTT
Found at i:18731 original size:21 final size:20
Alignment explanation
Indices: 18676--18731 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
18666 TTCAATTTCA
* **
18676 TTTTTCTTTTTCTCATTCTC
1 TTTTTCTTTTTTTCACACTC
18696 TTTTTGCTTTTTTTCACACTC
1 TTTTT-CTTTTTTTCACACTC
18717 TTTTTCTTTTGTTTC
1 TTTTTCTTTT-TTTC
18732 TTTTTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.05, C:0.21, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTCTTTTTTTCACACTC
Found at i:22692 original size:28 final size:29
Alignment explanation
Indices: 22661--22720 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
22651 AAAGTGATTT
*
22661 TTGACAACAA-TGTCAATT-AGGGATTAAA
1 TTGACAA-AAGTGTAAATTGAGGGATTAAA
*
22689 TTGACAAAAGTGTAAATTGAGGGGTTAAA
1 TTGACAAAAGTGTAAATTGAGGGATTAAA
22718 TTG
1 TTG
22721 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 14 0.50
29 12 0.43
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (29 bp):
TTGACAAAAGTGTAAATTGAGGGATTAAA
Found at i:25381 original size:68 final size:67
Alignment explanation
Indices: 25309--25458 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
25299 CATCATGTGT
* * * *
25309 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
25371 ATGTAG
62 ATGTAG
** * *
25377 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
25442 AG
66 AG
25444 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
25459 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:25414 original size:64 final size:64
Alignment explanation
Indices: 25333--25516 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
25323 AGACATTATG
* *
25333 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
25397 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
25462 AA
63 AA
* * * *
25464 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
25517 CAAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29813 original size:68 final size:67
Alignment explanation
Indices: 29741--29890 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
29731 CATCATGTGT
* * * *
29741 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
29803 ATGTAG
62 ATGTAG
** * *
29809 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
29874 AG
66 AG
29876 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
29891 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:29846 original size:64 final size:64
Alignment explanation
Indices: 29765--29948 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
29755 AGACATTATG
* *
29765 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
29829 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29894 AA
63 AA
* * * *
29896 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
29949 CAACTATATG
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Done.