Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4664.1
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: 49184
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.30
Warning! 2002 characters in sequence are not A, C, G, or T
Found at i:1033 original size:57 final size:57
Alignment explanation
Indices: 945--1059 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
935 TACGTTCCGT
945 TCTTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGAC
1 TCTTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGAC
* *
1002 TCTTTCCCTAATATTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAATGAGAC
1 TCTTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGAC
1059 T
1 T
1060 TGCCGAGTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (57 bp):
TCTTTCCCTAATACTTCTTCTACGACTAAGTGGGGGCAAGGGTCCAACAAACGAGAC
Found at i:6707 original size:125 final size:126
Alignment explanation
Indices: 6548--6806 Score: 353
Period size: 126 Copynumber: 2.1 Consensus size: 126
6538 AGATGTTTAC
* *
6548 AAATTGGGCCCTTTGACATTTTGGCCTGATTTTCAACTAAGTATG-AAGAAATTTCTTGATTGGG
1 AAATTGGGCCCTTTGACATTTTGGCCTAATTTTCAACTAAATATGTAAG-AATTTCTTGATTGGG
* * * *
6612 -T-TAAATTTTGGTTATTGGGCCTCGCCATCAAGATTTTGGGCTCGTGATCCATCTCCTACCA
65 CTGGAAA-TTTGCTTATTGGGCCTCGCCATCAAGAATTTGGGATCGTGATCCATCTCCTACCA
* *
6673 AAATTGGGCCCTTTGACATTTTGGCCTAATTTTCAACTAAATATGTATGGATTTCTTGATTGGGC
1 AAATTGGGCCCTTTGACATTTTGGCCTAATTTTCAACTAAATATGTAAGAATTTCTTGATTGGGC
* * * * * *
6738 TGGGAATTTGCTTATTGGGCCTTGCCTTTAAGAATTTGGGATTGTGATCCATCTCCTACCG
66 TGGAAATTTGCTTATTGGGCCTCGCCATCAAGAATTTGGGATCGTGATCCATCTCCTACCA
6799 AAATTGGG
1 AAATTGGG
6807 TCGTTGACGC
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
125 57 0.49
126 58 0.50
127 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (126 bp):
AAATTGGGCCCTTTGACATTTTGGCCTAATTTTCAACTAAATATGTAAGAATTTCTTGATTGGGC
TGGAAATTTGCTTATTGGGCCTCGCCATCAAGAATTTGGGATCGTGATCCATCTCCTACCA
Found at i:6814 original size:125 final size:125
Alignment explanation
Indices: 6548--6814 Score: 333
Period size: 125 Copynumber: 2.1 Consensus size: 125
6538 AGATGTTTAC
* * *
6548 AAATTGGGCCCTTTGACATTTTGGCCTGATTTTCAACTAAGTATGAAGAAATTTCTTGATTGGGT
1 AAATTGGGCCCGTTGACATTTTGGCCTAATTTTCAACTAAATATGAAGAAATTTCTTGATTGGGT
* * * *
6613 TAAATTTTGGTTATTGGGCCTCGCCATCAAGATTTTGGGCTCGTGATCCATCTCCTACCA
66 GAAATTTTGCTTATTGGGCCTCGCCATCAAGAATTTGGGATCGTGATCCATCTCCTACCA
* * *
6673 AAATTGGGCCCTTTGACATTTTGGCCTAATTTTCAACTAAATATGTATG-GATTTCTTGATTGGG
1 AAATTGGGCCCGTTGACATTTTGGCCTAATTTTCAACTAAATATG-AAGAAATTTCTTGATTGGG
* * * * * *
6737 CTGGGAA-TTTGCTTATTGGGCCTTGCCTTTAAGAATTTGGGATTGTGATCCATCTCCTACCG
65 -T-GAAATTTTGCTTATTGGGCCTCGCCATCAAGAATTTGGGATCGTGATCCATCTCCTACCA
*
6799 AAATTGGG-TCGTTGAC
1 AAATTGGGCCCGTTGAC
6815 GCTCGTAATG
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
125 63 0.51
126 58 0.47
127 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (125 bp):
AAATTGGGCCCGTTGACATTTTGGCCTAATTTTCAACTAAATATGAAGAAATTTCTTGATTGGGT
GAAATTTTGCTTATTGGGCCTCGCCATCAAGAATTTGGGATCGTGATCCATCTCCTACCA
Found at i:6894 original size:79 final size:79
Alignment explanation
Indices: 6763--6920 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
6753 TGGGCCTTGC
6763 CTTTAAGAATTTGGGATTGTGATCCATCTCCTACCGAAATTGGGTCGTTGACGCTCGTAATGGAG
1 CTTTAAGAATTTGGGATTGTGATCCATCTCCTACCGAAATTGGGTCGTTGACGCTCGTAATGGAG
6828 ATCCAACGTGCTTT
66 ATCCAACGTGCTTT
* *
6842 CTTTAAGAATTTGGGCTTGTGATCCATCTCCTATCGAAATTGGGTCGTTGACGCTCGTAATGGAG
1 CTTTAAGAATTTGGGATTGTGATCCATCTCCTACCGAAATTGGGTCGTTGACGCTCGTAATGGAG
6907 ATCCAACGTGCTTT
66 ATCCAACGTGCTTT
6921 GGCTACAAGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (79 bp):
CTTTAAGAATTTGGGATTGTGATCCATCTCCTACCGAAATTGGGTCGTTGACGCTCGTAATGGAG
ATCCAACGTGCTTT
Found at i:10273 original size:12 final size:12
Alignment explanation
Indices: 10253--10282 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10243 GGAGTAACAA
*
10253 AAAAATCGAAAG
1 AAAATTCGAAAG
10265 AAAATTCGAAAG
1 AAAATTCGAAAG
10277 AAAATT
1 AAAATT
10283 TGATTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.13, T:0.17
Consensus pattern (12 bp):
AAAATTCGAAAG
Found at i:10323 original size:12 final size:13
Alignment explanation
Indices: 10289--10322 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
10279 AATTTGATTG
10289 AAAAAAAAATTCA
1 AAAAAAAAATTCA
10302 AAAAAAAAATTCA
1 AAAAAAAAATTCA
10315 AAAAAAAA
1 AAAAAAAA
10323 TCGAGCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:11429 original size:18 final size:18
Alignment explanation
Indices: 11403--11488 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
11393 AAATTGAAAG
*
11403 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
* *
11421 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAAACGA
** * *
11439 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
11457 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
11478 AAAAGAAAAAG
1 AAAAGAAAAAG
11489 CGAAAAAAGA
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
18 31 0.62
19 5 0.10
20 8 0.16
21 6 0.12
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:11431 original size:6 final size:6
Alignment explanation
Indices: 11399--11488 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
11389 AAAGAAATTG
* * * **
11399 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCA-AA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* * *
11446 AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
11489 CGAAAAAAGA
Statistics
Matches: 63, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
5 4 0.06
6 47 0.75
7 8 0.13
8 4 0.06
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:11468 original size:14 final size:13
Alignment explanation
Indices: 11449--11486 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
11439 AAAAGTGAGA
11449 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
11461 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
11476 GAAAAAGAAAA
1 GAAAAAGAAAA
11487 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:11483 original size:13 final size:12
Alignment explanation
Indices: 11385--11486 Score: 50
Period size: 12 Copynumber: 8.0 Consensus size: 12
11375 AGAAAGAGAT
*
11385 TGAAAAAGAAAT
1 TGAAAAAGAAAA
11397 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
11407 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
11418 CGAAAAAGAAAA
1 TGAAAAAGAAAA
*
11430 AGAAATCAA-AAAA
1 TGAAA--AAGAAAA
11443 GTGAGAGAAAAAGAAAA
1 -T----GAAAAAGAAAA
11460 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
11474 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
11487 AGCGAAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.10
11 8 0.11
12 17 0.24
13 14 0.20
14 12 0.17
15 2 0.03
16 3 0.04
17 4 0.06
18 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:11500 original size:21 final size:21
Alignment explanation
Indices: 11450--11500 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
11440 AAAGTGAGAG
*
11450 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
11471 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
11492 AAAAAGAAA
1 AAAAAGAAA
11501 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:15138 original size:11 final size:11
Alignment explanation
Indices: 15122--15161 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
15112 CATAGACTCG
15122 TGAAAAAAAAT
1 TGAAAAAAAAT
15133 TGAAAAAAAA-
1 TGAAAAAAAAT
15143 T-AAAAAAAAT
1 TGAAAAAAAAT
15153 TGAAAAAAA
1 TGAAAAAAA
15162 GAAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
10 2 0.07
11 17 0.63
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (11 bp):
TGAAAAAAAAT
Found at i:15149 original size:18 final size:19
Alignment explanation
Indices: 15123--15169 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
15113 ATAGACTCGT
15123 GAAAAAAAATTGAAAAAAAA
1 GAAAAAAAATTG-AAAAAAA
*
15143 TAAAAAAAATTGAAAAAAA
1 GAAAAAAAATTGAAAAAAA
15162 GAAAAAAA
1 GAAAAAAA
15170 TTGTATACGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (19 bp):
GAAAAAAAATTGAAAAAAA
Found at i:15172 original size:18 final size:20
Alignment explanation
Indices: 15124--15161 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15114 TAGACTCGTG
15124 AAAAAAAATTGAAAAAAAAT
1 AAAAAAAATTGAAAAAAAAT
15144 AAAAAAAATTGAAAAAAA
1 AAAAAAAATTGAAAAAAA
15162 GAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAAAAAATTGAAAAAAAAT
Found at i:20759 original size:51 final size:51
Alignment explanation
Indices: 20693--20795 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
20683 TGATAGTAAG
* *
20693 CAGGAATAAAACGCTTTCTCATTATTGCTTTCATTTCCGCCCATGTAGACA
1 CAGGAATAAAACGCTTCCTCATTATGGCTTTCATTTCCGCCCATGTAGACA
* *
20744 CAGGAATGAATCGCTTCCTCATTATGGCTTTCATTTCCGCCCATGTAGACA
1 CAGGAATAAAACGCTTCCTCATTATGGCTTTCATTTCCGCCCATGTAGACA
20795 C
1 C
20796 GGGACGTTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (51 bp):
CAGGAATAAAACGCTTCCTCATTATGGCTTTCATTTCCGCCCATGTAGACA
Found at i:23123 original size:14 final size:14
Alignment explanation
Indices: 23088--23130 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
23078 ACAACAAAAG
*
23088 AAAG-TGAAAATAA
1 AAAGATGAAAAGAA
*
23101 AATGA-GAAAAGAA
1 AAAGATGAAAAGAA
23114 AAAGATGAAAAGAA
1 AAAGATGAAAAGAA
23128 AAA
1 AAA
23131 AAGAAGAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (14 bp):
AAAGATGAAAAGAA
Found at i:23127 original size:19 final size:19
Alignment explanation
Indices: 23044--23129 Score: 52
Period size: 20 Copynumber: 4.5 Consensus size: 19
23034 ATGAAAATGC
23044 AAAAGAAAAGAAAAATGA-G
1 AAAAGAAAAGAAAAA-GATG
* * **
23063 AAAAAGAAAGGAAAAACAAC
1 -AAAAGAAAAGAAAAAGATG
** *
23083 AAAAG-AAAGTGAAA-ATA
1 AAAAGAAAAGAAAAAGATG
23100 AAATGAGAAAAGAAAAAGATG
1 AAA--AGAAAAGAAAAAGATG
23121 AAAAGAAAA
1 AAAAGAAAA
23130 AAAGAAGAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
17 4 0.08
18 6 0.12
19 14 0.28
20 21 0.42
21 5 0.10
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAGATG
Found at i:23754 original size:34 final size:34
Alignment explanation
Indices: 23716--23782 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
23706 TTAAATGCAT
* *
23716 CTTTAATTAATGTCTTGCATTAT-TGATCTACATC
1 CTTTAATT-ATGACATGCATTATGTGATCTACATC
*
23750 CTTTAATTATGACATGCATTATGTGTTCTACAT
1 CTTTAATTATGACATGCATTATGTGATCTACAT
23783 TTAATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.46
Consensus pattern (34 bp):
CTTTAATTATGACATGCATTATGTGATCTACATC
Found at i:26343 original size:40 final size:40
Alignment explanation
Indices: 26299--26374 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
26289 ATGAACTTTA
26299 ACTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGG
1 ACTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGG
*
26339 ACTTTGTTAAACTCATCTTAGTTAATAATTGAGTTG
1 ACTTTATTAAACTCATCTTAGTTAATAATTGAGTTG
26375 TTGGGCTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (40 bp):
ACTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGG
Found at i:31561 original size:13 final size:13
Alignment explanation
Indices: 31543--31567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31533 AATATTTACA
31543 TAAAAATTTAAAC
1 TAAAAATTTAAAC
31556 TAAAAATTTAAA
1 TAAAAATTTAAA
31568 AAAAAAATAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATTTAAAC
Done.