Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold853
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: 57871
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:462 original size:22 final size:22
Alignment explanation
Indices: 434--476 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
424 TTTGAAACCA
434 TACCATTTCGTACCAAATCCCT
1 TACCATTTCGTACCAAATCCCT
*
456 TACCATTTCGTACCAATTCCC
1 TACCATTTCGTACCAAATCCC
477 AAATACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.33
Consensus pattern (22 bp):
TACCATTTCGTACCAAATCCCT
Found at i:2754 original size:27 final size:27
Alignment explanation
Indices: 2717--2921 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
2707 TAAATTGTAC
*
2717 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2744 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
2771 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2797 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
2825 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2852 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
2880 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2907 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2922 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2778 original size:54 final size:54
Alignment explanation
Indices: 2718--2921 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
2708 AAATTGTACA
* * *
2718 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
2772 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
2826 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
2881 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
2922 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:10894 original size:27 final size:27
Alignment explanation
Indices: 10857--11061 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
10847 TAAATTGTAC
*
10857 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10884 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
10911 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
10937 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
10965 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
10992 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
11020 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
11047 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
11062 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:10918 original size:54 final size:54
Alignment explanation
Indices: 10858--11061 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
10848 AAATTGTACA
* * *
10858 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
10912 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
10966 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
11021 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
11062 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:12633 original size:21 final size:21
Alignment explanation
Indices: 12588--12648 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
12578 TTTGAACCAT
* *
12588 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
12610 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
12631 TACTATTTCGAACCAATT
1 TACCATTTCGTACCAATT
12649 TTCAAATACC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:16095 original size:23 final size:22
Alignment explanation
Indices: 16044--16095 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
16034 CCTCGTCTTT
*
16044 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
16066 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
16089 TTCTTTT
1 TTCTTTT
16096 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:20463 original size:22 final size:22
Alignment explanation
Indices: 20435--20478 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20425 TTTTGAACCA
20435 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
20457 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
20479 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:22445 original size:22 final size:22
Alignment explanation
Indices: 22394--22459 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
22384 GGTATTTGGG
* *
22394 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
22415 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
22437 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
22460 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:24147 original size:28 final size:30
Alignment explanation
Indices: 24088--24147 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
24078 CAAAAAAATC
* ***
24088 AAAAAAAATTCGAAAAATAAATTGATTGAA
1 AAAAAAAATTCGAAAAATAAAGTGAAAAAA
24118 AAAAAAAATTC-AAAAA-AAAGTGAAAAAA
1 AAAAAAAATTCGAAAAATAAAGTGAAAAAA
24146 AA
1 AA
24148 TTGAGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 10 0.38
29 5 0.19
30 11 0.42
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (30 bp):
AAAAAAAATTCGAAAAATAAAGTGAAAAAA
Found at i:24149 original size:39 final size:39
Alignment explanation
Indices: 24079--24183 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 39
24069 TTGGAGTAAC
*
24079 AAAAAAA-TCAAAAAAAATTCGAAAAATAAATTGATTG-AAA
1 AAAAAAATTCAAAAAAAAGT-GAAAAATAAATTGA--GCAAA
24119 AAAAAAATTCAAAAAAAAGTGAAAAA-AAATTGAGCAAA
1 AAAAAAATTCAAAAAAAAGTGAAAAATAAATTGAGCAAA
24157 AAAAATCAAGTT-AAAAAAAAGTGAAAA
1 AAAAA--AA-TTCAAAAAAAAGTGAAAA
24184 GTCTTGCGAG
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
37 1 0.02
38 8 0.14
39 7 0.12
40 30 0.51
41 13 0.22
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.16
Consensus pattern (39 bp):
AAAAAAATTCAAAAAAAAGTGAAAAATAAATTGAGCAAA
Found at i:29703 original size:21 final size:21
Alignment explanation
Indices: 29678--29740 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
29668 ATTTAAGGAA
29678 GAATTTCGGCATTCATCAATG
1 GAATTTCGGCATTCATCAATG
* * **
29699 GAATTTGGTGCAAT-A-CCGTG
1 GAATTTCG-GCATTCATCAATG
*
29719 CAATTTCGGCATTCATCAATG
1 GAATTTCGGCATTCATCAATG
29740 G
1 G
29741 TCCTTTTAGT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
19 4 0.14
20 10 0.34
21 11 0.38
22 4 0.14
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (21 bp):
GAATTTCGGCATTCATCAATG
Found at i:34420 original size:20 final size:22
Alignment explanation
Indices: 34395--34439 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
34385 TCCTTTTTGC
34395 CTTTTTCATTTTCATTTTCT-T
1 CTTTTTCATTTTCATTTTCTCT
34416 CTTTTTCACTTTT-ATTTT-TCT
1 CTTTTTCA-TTTTCATTTTCTCT
34437 CTT
1 CTT
34440 CTCAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTTTCATTTTCATTTTCTCT
Found at i:37641 original size:15 final size:16
Alignment explanation
Indices: 37602--37642 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
37592 AACAACACTC
37602 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
37618 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
37632 CTTTCTTTTTC
1 CTTTCTTTTTC
37643 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:37837 original size:17 final size:15
Alignment explanation
Indices: 37800--37838 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
37790 TATGTCCCAC
37800 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
37816 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
37833 TCATTT
1 TCATTT
37839 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:38767 original size:27 final size:29
Alignment explanation
Indices: 38736--38804 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 29
38726 TTTCAATCAC
**
38736 TCTTTTTTTTTTCAATTTTG-A-TTTTTT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTT
38763 TCTTTTTTTTTT-AATTCCGAATTTTTTT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTT
38791 TCTTCTTTTTTTTC
1 TCTT-TTTTTTTTC
38805 TTCAATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 5 0.14
27 13 0.36
28 10 0.28
29 8 0.22
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (29 bp):
TCTTTTTTTTTTCAATTCCGAATTTTTTT
Found at i:38865 original size:11 final size:11
Alignment explanation
Indices: 38849--38878 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
38839 AATACAAACT
38849 TTTTTTTTGAA
1 TTTTTTTTGAA
38860 TTTTTTTTGAA
1 TTTTTTTTGAA
38871 TTTTTTTT
1 TTTTTTTT
38879 ACAATACCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:45338 original size:21 final size:22
Alignment explanation
Indices: 45309--45360 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
45299 TCTCTATCGC
* *
45309 TTTCCTTTTTGCCTTTTTCA-T
1 TTTCATTTTTACCTTTTTCACT
* *
45330 TTTCATTTTCATCTTTTTCACT
1 TTTCATTTTTACCTTTTTCACT
45352 TTT-ATTTTT
1 TTTCATTTTT
45361 CTCTTCTCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTTACCTTTTTCACT
Found at i:49928 original size:29 final size:29
Alignment explanation
Indices: 49894--49966 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
49884 ATGTATTAGT
* *
49894 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
49923 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
49952 TTAGGACATATTTAA
1 TTAGGACATATTTAA
49967 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:52957 original size:22 final size:22
Alignment explanation
Indices: 52927--52970 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52917 TTTGGTATTT
52927 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
52949 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
52971 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:55054 original size:22 final size:22
Alignment explanation
Indices: 55026--55069 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55016 TTTTGAACCA
55026 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
55048 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
55070 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Done.