Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold680
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: 49678
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:771 original size:17 final size:17
Alignment explanation
Indices: 745--786 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
735 GGCTTACACT
*
745 TTTGGTTTGTTCGCCAC
1 TTTGGCTTGTTCGCCAC
*
762 TTTGGCTTGTTCGTCAC
1 TTTGGCTTGTTCGCCAC
779 TTTGGCTT
1 TTTGGCTT
787 ACATTTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.24, T:0.50
Consensus pattern (17 bp):
TTTGGCTTGTTCGCCAC
Found at i:4875 original size:32 final size:31
Alignment explanation
Indices: 4820--4885 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
4810 TTAAAAATAT
*
4820 AAAAAATATTTAAAATTTATTAAAAATTAGA
1 AAAAAAAATTTAAAATTTATTAAAAATTAGA
* * *
4851 AAAAAAAATTGTAAATTTTTTTAAAAATTATA
1 AAAAAAAATT-TAAAATTTATTAAAAATTAGA
4883 AAA
1 AAA
4886 TGCATCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAAAAATTTAAAATTTATTAAAAATTAGA
Found at i:4970 original size:20 final size:21
Alignment explanation
Indices: 4947--5001 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 21
4937 GATTTTTATT
4947 TTTTTATATATTTT-TTAC-AA
1 TTTTTATA-ATTTTGTTACTAA
*
4967 -TTTTATAATTTTGTTTCTAA
1 TTTTTATAATTTTGTTACTAA
4987 TTTTTAATAAATTTT
1 TTTTT-AT-AATTTT
5002 AGATGTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 2 0.07
21 4 0.14
22 2 0.07
23 6 0.21
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTATAATTTTGTTACTAA
Found at i:17900 original size:24 final size:24
Alignment explanation
Indices: 17873--17924 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17863 TTAGTAAGTC
*
17873 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17897 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17921 AAAT
1 AAAT
17925 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:34929 original size:23 final size:21
Alignment explanation
Indices: 34899--34941 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
34889 CAATTATCAT
34899 AAATTTAATTTGTATAATTAATA
1 AAATTTAA-TTGTA-AATTAATA
34922 AAATTTAATTGTAAATTAAT
1 AAATTTAATTGTAAATTAAT
34942 TTTTACCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
AAATTTAATTGTAAATTAATA
Found at i:36439 original size:16 final size:15
Alignment explanation
Indices: 36408--36437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36398 ATTTTTTTAT
*
36408 TTTTTTAATAGAAAA
1 TTTTTTAATAAAAAA
36423 TTTTTTAATAAAAAA
1 TTTTTTAATAAAAAA
36438 ATGAAAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTTTAATAAAAAA
Found at i:37328 original size:72 final size:72
Alignment explanation
Indices: 37247--37766 Score: 628
Period size: 72 Copynumber: 7.2 Consensus size: 72
37237 AAGAGTTTGA
*
37247 AACAGTTGGACCTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACC
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACC
37312 AATTTAG
66 AATTTAG
* ** * * *
37319 AACAGTTGGACTTCTCCAATAACCAAATTCGTGGTCCTAT-CC-CCTAGATTGGGGGAACATGAA
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTT-AGGCAAC-TTAA
* *
37382 -GAGTTT-G
64 CCAATTTAG
*
37389 AAACAGTTGGACCTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
1 -AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
37454 CAATTTAG
65 CAATTTAG
* * ** * *
37462 AACAGTTGGACTTCTCCAATAACCAAATTCGTGGTCCTATCCC-CCTAGACTGGGGGAACATGAA
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTA-CCTTAGGCAAC-TTAA
* *
37526 -GAGTTT-G
64 CCAATTTAG
*
37533 AAACAGTTGGACCTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
1 -AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
37598 CAATTTAG
65 CAATTTAG
* * ** * *
37606 AACAGTTGGACTTCTCCAATAACCAAATTCGTGGTCCTATCCC-CCTAGACTGGGGGAACATGAA
1 AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTA-CCTTAGGCAAC-TTAA
* *
37670 -GAGTTT-G
64 CCAATTTAG
* *
37677 AAACAGTTGGACATATCCAATAACCTAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
1 -AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAAC
37742 CAATTTAG
65 CAATTTAG
37750 AACAGTTGGACTTATCC
1 AACAGTTGGACTTATCC
37767 TTTAATCAAA
Statistics
Matches: 373, Mismatches: 56, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
70 7 0.02
71 68 0.18
72 275 0.74
73 23 0.06
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (72 bp):
AACAGTTGGACTTATCCAATAACCAAATTCGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACC
AATTTAG
Found at i:37403 original size:143 final size:144
Alignment explanation
Indices: 37212--37762 Score: 1061
Period size: 144 Copynumber: 3.8 Consensus size: 144
37202 TATTACGGTT
37212 CTAT-CCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
1 CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
37276 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
66 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
37341 CCAAATTCGTGGTC
131 CCAAATTCGTGGTC
*
37355 CTAT-CCCCTAGATTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
1 CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
37419 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
66 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
37484 CCAAATTCGTGGTC
131 CCAAATTCGTGGTC
37498 CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
1 CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
37563 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
66 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
37628 CCAAATTCGTGGTC
131 CCAAATTCGTGGTC
* *
37642 CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACATATCCAATAACCTAATT
1 CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
37707 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTT
66 CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTT
37763 ATCCTTTAAT
Statistics
Matches: 403, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
143 146 0.36
144 257 0.64
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (144 bp):
CTATCCCCCTAGACTGGGGGAACATGAAGAGTTTGAAACAGTTGGACCTATCCAATAACCAAATT
CGTGGTCCTATCCCTCCTACCTTAGGCAACTTAACCAATTTAGAACAGTTGGACTTCTCCAATAA
CCAAATTCGTGGTC
Found at i:40870 original size:17 final size:17
Alignment explanation
Indices: 40844--40885 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
40834 GGCTTACACT
*
40844 TTTGGTTTGTTCGCCAC
1 TTTGGCTTGTTCGCCAC
*
40861 TTTGGCTTGTTCGTCAC
1 TTTGGCTTGTTCGCCAC
40878 TTTGGCTT
1 TTTGGCTT
40886 ACATTTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.24, T:0.50
Consensus pattern (17 bp):
TTTGGCTTGTTCGCCAC
Found at i:42016 original size:30 final size:30
Alignment explanation
Indices: 41959--42016 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
41949 AGAAGTTGAT
* **
41959 TTAAATTTTGAAATATGAAAATTAAAAGGA
1 TTAAATTTTCAAATATGAAAAGGAAAAGGA
41989 TTAAA-TTTCAAATATGTAAAAGGAAAAG
1 TTAAATTTTCAAATATG-AAAAGGAAAAG
42017 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (30 bp):
TTAAATTTTCAAATATGAAAAGGAAAAGGA
Found at i:44968 original size:30 final size:32
Alignment explanation
Indices: 44932--45007 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
44922 ATAACCCTAT
*
44932 TTAAAAATATAAAAAAAT-ATT-TAAATTTTA
1 TTAAAAATATAAAAAAATAATTGTAAAATTTA
* *
44962 TTAAAAAT-TAGAAAAATAATTGTAAAATTTC
1 TTAAAAATATAAAAAAATAATTGTAAAATTTA
44993 TTAAAAATTATAAAA
1 TTAAAAA-TATAAAA
45008 TGCATCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 8 0.21
30 11 0.29
31 14 0.37
32 1 0.03
33 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (32 bp):
TTAAAAATATAAAAAAATAATTGTAAAATTTA
Found at i:48657 original size:18 final size:19
Alignment explanation
Indices: 48636--48680 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
48626 GCCATTCCTG
48636 GAGAGTTCGA-CAAATTTA
1 GAGAGTTCGACCAAATTTA
*
48654 GAGAGTAC-ACCAAATTTA
1 GAGAGTTCGACCAAATTTA
*
48672 GGGAGTTCG
1 GAGAGTTCG
48681 CCGGTCGTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (19 bp):
GAGAGTTCGACCAAATTTA
Done.