Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2488
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: 42700
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:4479 original size:13 final size:13
Alignment explanation
Indices: 4461--4499 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
4451 ACAAAATTCT
* *
4461 TTGTATTGATATA
1 TTGTATCGATACA
4474 TTGTATCGATACA
1 TTGTATCGATACA
4487 TTGTATCGATACA
1 TTGTATCGATACA
4500 AGGGTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4646 original size:22 final size:21
Alignment explanation
Indices: 4608--4648 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4598 ATCAAATCTT
* *
4608 CTTCAAATTTCTTATTTTTCA
1 CTTCAAAATACTTATTTTTCA
4629 CTTCAAAATACTTCATTTTT
1 CTTCAAAATACTT-ATTTTT
4649 TTATCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (21 bp):
CTTCAAAATACTTATTTTTCA
Found at i:6912 original size:13 final size:13
Alignment explanation
Indices: 6894--6918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6884 GATTATGCTT
6894 TGTATCGATACAA
1 TGTATCGATACAA
6907 TGTATCGATACA
1 TGTATCGATACA
6919 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6931 original size:19 final size:21
Alignment explanation
Indices: 6903--6959 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
6893 TTGTATCGAT
6903 ACAA-TGTATCGATACATGT-
1 ACAATTGTATCGATACATGTG
*
6922 TC-ATTGTATCGATACAT-TG
1 ACAATTGTATCGATACATGTG
6941 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
6960 AAACTGACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 15 0.47
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
ACAATTGTATCGATACATGTG
Found at i:6949 original size:20 final size:21
Alignment explanation
Indices: 6902--6958 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
6892 TTTGTATCGA
6902 TACAA-TGTATCGATACA-TG
1 TACAATTGTATCGATACATTG
*
6921 TTC-ATTGTATCGATACATTG
1 TACAATTGTATCGATACATTG
6941 -ACAATTGTATCGATACAT
1 TACAATTGTATCGATACAT
6959 GAAACTGACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.45
20 17 0.52
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
TACAATTGTATCGATACATTG
Found at i:7023 original size:13 final size:13
Alignment explanation
Indices: 7005--7034 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
6995 GATACATGGC
7005 ACATTGTATCGAT
1 ACATTGTATCGAT
7018 ACATTGTATCGAT
1 ACATTGTATCGAT
7031 ACAT
1 ACAT
7035 GATGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:7032 original size:33 final size:32
Alignment explanation
Indices: 6988--7056 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
6978 CTACCACTGT
*
6988 TTGTATTGATACATG-GCACATTGTATCGATACA
1 TTGTATCGATACATGAG-A-ATTGTATCGATACA
*
7021 TTGTATCGATACATGATGAATTGTGTCGATACA
1 TTGTATCGATACATGA-GAATTGTATCGATACA
7054 TTG
1 TTG
7057 CTTCTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTGTATCGATACA
Found at i:7814 original size:13 final size:13
Alignment explanation
Indices: 7796--7852 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
7786 CATAAAGTGT
7796 TGTATCGATACAA
1 TGTATCGATACAA
7809 TGTATCGATACATAA
1 TGTATCGATAC--AA
7824 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
7841 TGTATCGATACA
1 TGTATCGATACA
7853 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7831 original size:32 final size:32
Alignment explanation
Indices: 7776--7873 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
7766 TTCAACGATT
7776 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
7809 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
7841 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
7873 T
1 T
7874 TTAAGCTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:7833 original size:19 final size:18
Alignment explanation
Indices: 7774--7871 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
7764 ATTTCAACGA
7774 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
7793 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
7809 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
7825 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
7841 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
7857 TTTTGTATCGATACA
1 -TTTGTATCGATACA
7872 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:7932 original size:13 final size:13
Alignment explanation
Indices: 7914--7938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7904 ATTACTCAAA
7914 TGTATCGATACAT
1 TGTATCGATACAT
7927 TGTATCGATACA
1 TGTATCGATACA
7939 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7988 original size:32 final size:33
Alignment explanation
Indices: 7947--8023 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
7937 CACTGATCTT
7947 TGTATCGATACA-TGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTGCAGGCAAATTTGCCCAGA
*
7979 TGTATCGATACATTGCAGGCAAATTTGGCCAGA
1 TGTATCGATACATTGCAGGCAAATTTGCCCAGA
8012 TGTATCGATACA
1 TGTATCGATACA
8024 CTATTAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 12 0.28
33 31 0.72
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (33 bp):
TGTATCGATACATTGCAGGCAAATTTGCCCAGA
Found at i:11585 original size:17 final size:17
Alignment explanation
Indices: 11546--11587 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
11536 AATATTTGAG
*
11546 CCAAAAT-AATCTAAAT
1 CCAAAATAAATCTAAAC
**
11562 CTGAAATAAATCTAAAC
1 CCAAAATAAATCTAAAC
11579 CCAAAATAA
1 CCAAAATAA
11588 CCAAAATCCA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (17 bp):
CCAAAATAAATCTAAAC
Found at i:17193 original size:18 final size:17
Alignment explanation
Indices: 17165--17205 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
17155 GTATTGAACT
*
17165 ATTTTTTATTTTTTAAA
1 ATTTTTTATTTATTAAA
17182 ATTTTCTTATTTATTAAA
1 ATTTT-TTATTTATTAAA
*
17200 CTTTTT
1 ATTTTT
17206 AATCAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTATTTATTAAA
Found at i:19438 original size:8 final size:8
Alignment explanation
Indices: 19427--19462 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
19417 ATTTGTGTTT
19427 TATTTATA
1 TATTTATA
19435 TATTTATA
1 TATTTATA
19443 TATTTATA
1 TATTTATA
19451 TTTATTTATA
1 --TATTTATA
19461 TA
1 TA
19463 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.69
10 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTATA
Found at i:19470 original size:16 final size:16
Alignment explanation
Indices: 19435--19485 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
19425 TTTATTTATA
*
19435 TATTTATATATTTATATT
1 TATTTATATAATT-T-TT
19453 TATTTATATAATTTTT
1 TATTTATATAATTTTT
19469 TA-TTATAATATATTTTT
1 TATTTAT-ATA-ATTTTT
19486 ATCATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
17 7 0.23
18 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATATAATTTTT
Found at i:19475 original size:13 final size:14
Alignment explanation
Indices: 19425--19487 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 14
19415 TAATTTGTGT
19425 TTTATTTA-TAT-A
1 TTTATTTATTATAA
*
19437 TTTATATATT-TATA
1 TTTATTTATTATA-A
19451 TTTATTTA-TATAA
1 TTTATTTATTATAA
19464 TTT-TTTATTATAA
1 TTTATTTATTATAA
*
19477 TATATTT-TTAT
1 TTTATTTATTAT
19488 CATATTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 12 0.29
13 17 0.40
14 13 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTATTATAA
Found at i:21721 original size:15 final size:14
Alignment explanation
Indices: 21699--21739 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
21689 GTAATTATAT
21699 AATAAATAAAATAC
1 AATAAATAAAATAC
*
21713 AATTAAATAAAATAT
1 AA-TAAATAAAATAC
*
21728 AATGAATAAAAT
1 AATAAATAAAAT
21740 TGTATATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (14 bp):
AATAAATAAAATAC
Found at i:22220 original size:21 final size:21
Alignment explanation
Indices: 22192--22249 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
22182 TAACATTAGG
*
22192 TTAT-TAAAAATTGCATT-TT
1 TTATCTAAAAAATGCATTCTT
22211 TTCATCTAAAAAATGCATTCTT
1 TT-ATCTAAAAAATGCATTCTT
**
22233 TTATCTAACTAATGCAT
1 TTATCTAAAAAATGCAT
22250 CATTTCATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 25 0.76
22 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (21 bp):
TTATCTAAAAAATGCATTCTT
Found at i:22852 original size:13 final size:13
Alignment explanation
Indices: 22834--22859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22824 TACACCAAGT
22834 ATGTATCGATACA
1 ATGTATCGATACA
22847 ATGTATCGATACA
1 ATGTATCGATACA
22860 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:22857 original size:32 final size:33
Alignment explanation
Indices: 22816--22879 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
22806 TAGCCAAACT
* **
22816 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
22848 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
22880 TTGGATTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:28551 original size:21 final size:21
Alignment explanation
Indices: 28527--28569 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28517 AATAGCCAAA
28527 ATGGCATACTTGTATCGATAC
1 ATGGCATACTTGTATCGATAC
*
28548 ATGGCATACTTGTATTGATAC
1 ATGGCATACTTGTATCGATAC
28569 A
1 A
28570 ATCTTCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (21 bp):
ATGGCATACTTGTATCGATAC
Found at i:32652 original size:22 final size:20
Alignment explanation
Indices: 32619--32664 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
32609 TCTTTGGACA
32619 TAAAATTTTTATCAAATTAT
1 TAAAATTTTTATCAAATTAT
* *
32639 CTAAAGTTTCTTATTAAATTAT
1 -TAAAATTT-TTATCAAATTAT
32661 TAAA
1 TAAA
32665 TAAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAAATTTTTATCAAATTAT
Found at i:34993 original size:21 final size:21
Alignment explanation
Indices: 34969--35011 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34959 AAAGTTGCCT
*
34969 TTTTTTCATCCAAAAAATGCA
1 TTTTTCCATCCAAAAAATGCA
**
34990 TTTTTCCATCCAACCAATGCA
1 TTTTTCCATCCAAAAAATGCA
35011 T
1 T
35012 CATTTTACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (21 bp):
TTTTTCCATCCAAAAAATGCA
Found at i:38367 original size:21 final size:21
Alignment explanation
Indices: 38349--38408 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
38339 TATTAAAAGT
*
38349 TGCATTTTTTCATCCAAAAAA
1 TGCATTCTTTCATCCAAAAAA
**
38370 TGCATTCTTTCATCCAACTAA
1 TGCATTCTTTCATCCAAAAAA
38391 TGCA-TCATTTCATCCAAA
1 TGCATTC-TTTCATCCAAA
38409 GATACCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 2 0.06
21 32 0.94
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (21 bp):
TGCATTCTTTCATCCAAAAAA
Found at i:41977 original size:20 final size:20
Alignment explanation
Indices: 41954--42028 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
41944 AAGTACCCAG
41954 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
41974 ATGTATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
* *
41994 ATGTATCGATACATTCTTCG
1 ATGTATCGATACATTTTTCA
*
42014 ATGTATTGATACATT
1 ATGTATCGATACATT
42029 CTATCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Done.