Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1211
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: 45965
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2482 original size:28 final size:27
Alignment explanation
Indices: 2415--2487 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2405 CTTCACAATC
* *
2415 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2442 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
2470 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2488 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:2532 original size:51 final size:51
Alignment explanation
Indices: 2470--2640 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
2460 TTATTTCTGA
* * *
2470 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
2521 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
* * *
2574 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
2626 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2641 TCGTTATTTC
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 36 0.36
52 19 0.19
53 33 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:2597 original size:53 final size:51
Alignment explanation
Indices: 2294--2640 Score: 191
Period size: 51 Copynumber: 6.6 Consensus size: 51
2284 TTGAGTTGCT
* * * * * * *
2294 CAATTCTCCACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACAT
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * *
2345 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTC---AAAACAC
* * * * ** * * *
2399 CAATTTCTTCACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAATTT-TCCATAATCGGGGATACTCCAACCCCGATTTTATTTTC---AAAACAC
* * * * *
2452 CAACCCCGTTATTTC-TGA--GGGGATACTCCAACCCCGACTTTATTTTCAAAATAT
1 CAA-----TT-TTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * *
2506 CGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * *
2557 CAATTTCTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
1 CAATTT-TCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACAC
* * *
2611 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
2641 TCGTTATTTC
Statistics
Matches: 222, Mismatches: 56, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
51 72 0.32
52 19 0.09
53 45 0.20
54 26 0.12
55 39 0.18
57 7 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
Found at i:2659 original size:28 final size:30
Alignment explanation
Indices: 2623--2699 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 30
2613 ATTTTTCACA
* *
2623 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2651 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2681 A--GGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2700 GCTTTATTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 40 0.89
29 4 0.09
30 1 0.02
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:2717 original size:108 final size:107
Alignment explanation
Indices: 2360--2779 Score: 362
Period size: 108 Copynumber: 3.9 Consensus size: 107
2350 TTCTATAATC
* * * * *
2360 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGACACTC
1 GGGGATACTCCAACCCCGACTTTA-TTCC-CAAAAATACCAATTT-TTCACAATCGGGGATACTC
*
2425 CAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTCTGA
63 CAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTC-GA
** * * *
2470 GGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAAATACCAATTTTTCACAATCGGGGATACTCCAA
* * * *
2534 CCCCGGTTTTATTTTCA-C----A-ACACCAATTTCTCCTTTA-ATC--
66 CCCC-G--TTA-TTTCATCGGGGATACTCCAA---CCCCGTTATTTCGA
* * * *
2574 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAAATACCAATTTTTCACAATCGGGGATACTCCAA
*
2639 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGA
66 CCCCGTTATTTCATCGGGGATACTCCAACCCCGTTA-TTTCGA
* * *** * * *
2682 GGGGATACTCCAACCCCGGCTTTATTCCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAAATACCAATTTTTCACAATCGGGGATACTCCAA
*
2747 CCCCGTTATTT--TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTCATCG--GGGATACTCCAACCCCG
2780 ATTTTTTTTT
Statistics
Matches: 248, Mismatches: 41, Indels: 44
0.74 0.12 0.13
Matches are distributed among these distances:
101 5 0.02
102 4 0.02
104 33 0.13
105 40 0.16
106 31 0.12
107 19 0.08
108 85 0.34
109 5 0.02
110 23 0.09
111 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTCCCAAAAATACCAATTTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCGA
Found at i:9951 original size:15 final size:15
Alignment explanation
Indices: 9931--9961 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9921 ATTTCGTTTG
*
9931 GAGCTTCTTCATTTT
1 GAGCTTCATCATTTT
9946 GAGCTTCATCATTTT
1 GAGCTTCATCATTTT
9961 G
1 G
9962 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCATCATTTT
Found at i:11793 original size:21 final size:21
Alignment explanation
Indices: 11764--11808 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11754 AAGTTTTTAT
*
11764 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
11784 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
11806 TTT
1 TTT
11809 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:13915 original size:21 final size:21
Alignment explanation
Indices: 13886--13930 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13876 AAGTTTTTAT
*
13886 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
13906 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
13928 TTT
1 TTT
13931 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:16096 original size:20 final size:20
Alignment explanation
Indices: 16071--16119 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
16061 AAGCCAATGT
**
16071 ATCGATACAATTTTTTGTGC
1 ATCGATACAATACTTTGTGC
*
16091 ATCGATAC-ATACTTTGTGT
1 ATCGATACAATACTTTGTGC
16110 ATCGATACAA
1 ATCGATACAA
16120 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
ATCGATACAATACTTTGTGC
Found at i:16991 original size:35 final size:34
Alignment explanation
Indices: 16946--17020 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
16936 AAAATTCTTT
*
16946 ATAAAAAAAGAAGTTACATCTTAGCCTTTAAAAG
1 ATAAAAAAAGAAGTTACATCGTAGCCTTTAAAAG
* *
16980 ATAAGAAAAAGAGGTTATATCGTAGCCTTTAAAAG
1 ATAA-AAAAAGAAGTTACATCGTAGCCTTTAAAAG
17015 ATAAAA
1 ATAAAA
17021 GTTTGTTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 6 0.16
35 31 0.84
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (34 bp):
ATAAAAAAAGAAGTTACATCGTAGCCTTTAAAAG
Found at i:19095 original size:25 final size:23
Alignment explanation
Indices: 19038--19096 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 23
19028 TGTTTTAGAG
*
19038 ATAAGTTCAAATGTTTTTCAAGCA
1 ATAA-TTCAAATGTTTTTCAAGAA
*
19062 ATAAATCAAATGTTTTTCAAGTAAA
1 ATAATTCAAATGTTTTTCAAG--AA
19087 ATAATTCAAA
1 ATAATTCAAA
19097 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.53
24 4 0.13
25 10 0.33
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (23 bp):
ATAATTCAAATGTTTTTCAAGAA
Found at i:19348 original size:32 final size:32
Alignment explanation
Indices: 19312--19372 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
19302 GTAAACTGTC
* *
19312 TCGATACATTAAGTCCAATGGCTATAATTGTA
1 TCGATACATTAAGTCCAACGGCTAGAATTGTA
* *
19344 TCGATACATTGAGTCTAACGGCTAGAATT
1 TCGATACATTAAGTCCAACGGCTAGAATT
19373 TCAAATGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (32 bp):
TCGATACATTAAGTCCAACGGCTAGAATTGTA
Found at i:20765 original size:9 final size:9
Alignment explanation
Indices: 20747--20777 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20737 GTCAACCATC
20747 AATGATGAT
1 AATGATGAT
*
20756 AATGAAGAT
1 AATGATGAT
20765 AATGATGAT
1 AATGATGAT
20774 AATG
1 AATG
20778 GTGAAGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:25621 original size:13 final size:13
Alignment explanation
Indices: 25603--25628 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25593 CAATTTTTTG
25603 TGTATCGATACAT
1 TGTATCGATACAT
25616 TGTATCGATACAT
1 TGTATCGATACAT
25629 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:28200 original size:13 final size:13
Alignment explanation
Indices: 28182--28218 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
28172 ATAATCACCC
28182 TGTATCGATACAG
1 TGTATCGATACAG
*
28195 TGTATCGATACAT
1 TGTATCGATACAG
28208 TGTATCGATAC
1 TGTATCGATAC
28219 CAAGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:34396 original size:32 final size:32
Alignment explanation
Indices: 34354--34416 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
34344 TACAAGCTAA
**
34354 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
*
34386 TGTATTGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
34417 AGTTTGGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:34805 original size:12 final size:12
Alignment explanation
Indices: 34788--34813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34778 ACAATTTTCT
34788 AATCCCTTCAAA
1 AATCCCTTCAAA
34800 AATCCCTTCAAA
1 AATCCCTTCAAA
34812 AA
1 AA
34814 CCCACATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (12 bp):
AATCCCTTCAAA
Found at i:37229 original size:52 final size:52
Alignment explanation
Indices: 37150--37258 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
37140 TAGCCTAAGT
* *
37150 GAATTGTATCGATACATGGTAAATTGTATCGATACATTAAGTCCAATGACTA
1 GAATTGTATCGATACATGATAAATTGTACCGATACATTAAGTCCAATGACTA
* * * * *
37202 TAATTGTATCGATACATTATGAATTGTACCGATACATTGAGTCCAATGGCTA
1 GAATTGTATCGATACATGATAAATTGTACCGATACATTAAGTCCAATGACTA
37254 GAATT
1 GAATT
37259 TCAAATGCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (52 bp):
GAATTGTATCGATACATGATAAATTGTACCGATACATTAAGTCCAATGACTA
Found at i:37300 original size:20 final size:20
Alignment explanation
Indices: 37263--37301 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37253 AGAATTTCAA
*
37263 ATGCATTGTATTGATACATT
1 ATGCATTGTATCGATACATT
* *
37283 ATGCGTTGTATCGGTACAT
1 ATGCATTGTATCGATACAT
37302 AGGAGCATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
ATGCATTGTATCGATACATT
Found at i:42522 original size:36 final size:35
Alignment explanation
Indices: 42475--42593 Score: 144
Period size: 34 Copynumber: 3.5 Consensus size: 35
42465 AGTGATTGAG
42475 AGGTTCTATCTTAGCCTT-TGAAAAAGATAAGGAGAA
1 AGGTTCTATCTTAGCCTTGTGAAAAAGAT-AGG-GAA
42511 AGGTTCTATCTTAG-CTTGTGAAAAA-ATAGGGAA
1 AGGTTCTATCTTAGCCTTGTGAAAAAGATAGGGAA
* *
42544 GAGGTTCTATTTTA-TCTTGTG-AAAAGATAGGG--
1 -AGGTTCTATCTTAGCCTTGTGAAAAAGATAGGGAA
42576 AGGTTCTATCTTAGCCTT
1 AGGTTCTATCTTAGCCTT
42594 CAAAAGATAG
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
31 12 0.16
32 3 0.04
33 7 0.09
34 27 0.36
35 5 0.07
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
AGGTTCTATCTTAGCCTTGTGAAAAAGATAGGGAA
Done.