Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1554
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: 30074
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:1523 original size:32 final size:35
Alignment explanation
Indices: 1448--1513 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 35
1438 ACCAATTCTA
*
1448 TATATAACATATACCAAATCATATCATTTCATAAGT
1 TATA-AACATATACCAAAACATATCATTTCATAAGT
1484 TATAAACATA-A-CAAAACATAT-ATTTCATAA
1 TATAAACATATACCAAAACATATCATTTCATAA
1514 TCTCAAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 9 0.31
33 9 0.31
34 1 0.03
35 6 0.21
36 4 0.14
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (35 bp):
TATAAACATATACCAAAACATATCATTTCATAAGT
Found at i:2691 original size:27 final size:27
Alignment explanation
Indices: 2653--2820 Score: 169
Period size: 27 Copynumber: 6.2 Consensus size: 27
2643 TAAGTTGTAG
* * *
2653 AATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCTCGATTTATAA
*
2680 AATTACCAAAATACCC-CTGGTTTATAA
1 AATTACCAAAATACCCTC-GATTTATAA
* *
2707 AATTACCAAAAAACCC-CTGATTTGTAA
1 AATTACCAAAATACCCTC-GATTTATAA
* **
2734 AATTACTAAAATACCCTCGACCTATAA
1 AATTACCAAAATACCCTCGATTTATAA
** *
2761 AATTACTGAAATACCCTCGACTTATAA
1 AATTACCAAAATACCCTCGATTTATAA
* * *
2788 GATTACCAAAGTACCCTCGATTTACAA
1 AATTACCAAAATACCCTCGATTTATAA
2815 AATTAC
1 AATTAC
2821 TGTTTTACCC
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 119 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCTCGATTTATAA
Found at i:2810 original size:81 final size:81
Alignment explanation
Indices: 2647--2797 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 81
2637 AGTGGATAAG
* * *** **
2647 TTGTAGAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTGGTTTATAAAATTA
1 TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTA
2712 CCAAAAAACCCCTGAT
66 CCAAAAAACCCCTGAT
** *
2728 TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACTGAAATA-CCCTCGACTTATAAGATT
1 TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCT-GACTTATAAAATT
2792 ACCAAA
65 ACCAAA
2798 GTACCCTCGA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 4 0.07
81 55 0.93
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (81 bp):
TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTA
CCAAAAAACCCCTGAT
Found at i:2817 original size:81 final size:81
Alignment explanation
Indices: 2653--2821 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 81
2643 TAAGTTGTAG
* *** **
2653 AATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTGGTTTATAAAATTACCAAAA
1 AATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTACCAAAA
**
2718 AACCCCTGATTTGTAA
66 AACCCCTGATTTACAA
** *
2734 AATTACTAAAATACCCTCGACCTATAAAATTACTGAAATA-CCCTCGACTTATAAGATTACCAAA
1 AATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCT-GACTTATAAAATTACCAAA
**
2798 GTA-CCCTCGATTTACAA
65 AAACCCCT-GATTTACAA
2815 AATTACT
1 AATTACT
2822 GTTTTACCCT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
80 8 0.11
81 65 0.89
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (81 bp):
AATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTACCAAAA
AACCCCTGATTTACAA
Found at i:2856 original size:27 final size:28
Alignment explanation
Indices: 2732--2858 Score: 120
Period size: 27 Copynumber: 4.7 Consensus size: 28
2722 CCTGATTTGT
* *
2732 AAAATTACTA-AAATACCCTCGACCTAT
1 AAAATTACTAGAAATACCCTCGACTTAC
*
2759 AAAATTACT-GAAATACCCTCGACTTAT
1 AAAATTACTAGAAATACCCTCGACTTAC
* * * *
2786 AAGATTACCA-AAGTACCCTCGATTTAC
1 AAAATTACTAGAAATACCCTCGACTTAC
*** *
2813 AAAATTACT-GTTTTACCCTCGATTTAC
1 AAAATTACTAGAAATACCCTCGACTTAC
2840 AAAATTA-TAGAAATACCCT
1 AAAATTACTAGAAATACCCT
2859 TGTAAGGTAG
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 81 0.99
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (28 bp):
AAAATTACTAGAAATACCCTCGACTTAC
Found at i:2857 original size:54 final size:54
Alignment explanation
Indices: 2732--2858 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 54
2722 CCTGATTTGT
* *
2732 AAAATTACTAAAATACCCTCGACCTATAAAATTACTGAAATACCCTCGACTTAT
1 AAAATTACTAAAATACCCTCGACCTACAAAATTACTGAAATACCCTCGACTTAC
* * * ** *** *
2786 AAGATTACCAAAGTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTAC
1 AAAATTACTAAAATACCCTCGACCTACAAAATTACTGAAATACCCTCGACTTAC
2840 AAAATTA-TAGAAATACCCT
1 AAAATTACTA-AAATACCCT
2859 TGTAAGGTAG
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
53 1 0.02
54 57 0.98
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (54 bp):
AAAATTACTAAAATACCCTCGACCTACAAAATTACTGAAATACCCTCGACTTAC
Found at i:2926 original size:27 final size:27
Alignment explanation
Indices: 2849--2929 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
2839 CAAAATTATA
* *
2849 GAAATACCCTTGTAAGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
2876 GAAATACCCCTGTAGGATAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
2903 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
2930 ATTTTTCCCC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:4917 original size:43 final size:42
Alignment explanation
Indices: 4847--5007 Score: 184
Period size: 43 Copynumber: 3.8 Consensus size: 42
4837 GAAAAGCTCG
* * *
4847 TACGATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAAA
1 TACGATGCCAACATCCCAGACGTGGTCTTACATGAAATCAAA
***
4889 TATCGATGCCATTGTCCCAGACAG-GGTCTTACATGAAATCAAA
1 TA-CGATGCCAACATCCCAGAC-GTGGTCTTACATGAAATCAAA
4932 TACGATGCCAACATCCCAGACGTGGTCTTACACAT-AAATCATAA
1 TACGATGCCAACATCCCAGACGTGGTCTT--ACATGAAATCA-AA
*
4976 GT-TGATGCCAACATCCCAGACGTGGTCTTACA
1 -TACGATGCCAACATCCCAGACGTGGTCTTACA
5008 CGATAACACA
Statistics
Matches: 104, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.26
43 42 0.40
44 33 0.32
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
TACGATGCCAACATCCCAGACGTGGTCTTACATGAAATCAAA
Found at i:18099 original size:16 final size:16
Alignment explanation
Indices: 18078--18109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18068 CATGCATTGA
*
18078 ACATAATGAACATAAT
1 ACATAATCAACATAAT
18094 ACATAATCAACATAAT
1 ACATAATCAACATAAT
18110 CTTGCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (16 bp):
ACATAATCAACATAAT
Found at i:20355 original size:39 final size:39
Alignment explanation
Indices: 20298--20388 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
20288 GCATGATACT
* *
20298 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCAGACTTGAGGTCCGCAGGCTACATGC
*
20337 TGGAAACATATCCAGACTTGAGGTCCGCAGGCTATATGC
1 TGGAAACATATCCAGACTTGAGGTCCGCAGGCTACATGC
* *
20376 CGGAAATATATCC
1 TGGAAACATATCC
20389 GGGCTTAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.22
Consensus pattern (39 bp):
TGGAAACATATCCAGACTTGAGGTCCGCAGGCTACATGC
Found at i:28228 original size:39 final size:39
Alignment explanation
Indices: 28169--28279 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
28159 GCATGATACT
* *
28169 TGGAAACGTATCCGGACTTGAGGTCCGCAGCCTACGTGC
1 TGGAAACATATCCGGGCTTGAGGTCCGCAGCCTACGTGC
* * *
28208 TGGAAACATATCTGGGCTTGAGGTCCGCAGGCTATGTGC
1 TGGAAACATATCCGGGCTTGAGGTCCGCAGCCTACGTGC
* * *
28247 T-GAAATATATCCGGGCTTAAAGTCCCGCAGCCT
1 TGGAAACATATCCGGGCTTGAGGT-CCGCAGCCT
28280 TTATGCTAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
38 18 0.30
39 43 0.70
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGGCTTGAGGTCCGCAGCCTACGTGC
Done.