Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1855
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: 36888
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9827 original size:12 final size:12
Alignment explanation
Indices: 9803--9840 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
9793 CTTCAAAAAA
9803 TTTTGAA-TTTT
1 TTTTGAATTTTT
9814 TTTTGAATTTTT
1 TTTTGAATTTTT
9826 TTTTGAATTTTT
1 TTTTGAATTTTT
9838 TTT
1 TTT
9841 CAAATTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTGAATTTTT
Found at i:9847 original size:12 final size:11
Alignment explanation
Indices: 9803--9840 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
9793 CTTCAAAAAA
9803 TTTTGAATTTT
1 TTTTGAATTTT
9814 TTTTGAATTTTT
1 TTTTGAA-TTTT
9826 TTTTGAATTTT
1 TTTTGAATTTT
9837 TTTT
1 TTTT
9841 CAAATTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTGAATTTT
Found at i:13873 original size:29 final size:29
Alignment explanation
Indices: 13840--13899 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
13830 ATAACCAAAC
* *
13840 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
13869 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
13898 CT
1 CT
13900 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:13892 original size:15 final size:15
Alignment explanation
Indices: 13846--13893 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
13836 AAACCTACAA
*
13846 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
13861 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
13875 AAACTTCATATCCAT
1 AAACTTCATATCCAT
13890 AAAC
1 AAAC
13894 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:14835 original size:30 final size:30
Alignment explanation
Indices: 14801--14897 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
14791 TAAACTAAAA
14801 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
14831 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
14861 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
14891 TGAGCTA
1 TGAGCTA
14898 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:17078 original size:30 final size:30
Alignment explanation
Indices: 17007--17089 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
16997 CTTTTGTTTC
* *
17007 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
*
17038 AATTT-ATTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
17067 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
17090 GCTTTTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 4 0.09
30 32 0.74
31 7 0.16
ACGTcount: A:0.14, C:0.20, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:17089 original size:18 final size:18
Alignment explanation
Indices: 17043--17095 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
17033 TCTCAAATTT
* *
17043 ATTTTCGTTCTCTTTTTC
1 ATTTTCATTTTCTTTTTC
* *
17061 AATCTCATTTTCTTTTTC
1 ATTTTCATTTTCTTTTTC
*
17079 ATTTTCTTTTTGCTTTT
1 ATTTTCATTTT-CTTTT
17096 CAAAGGCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.09, C:0.19, G:0.04, T:0.68
Consensus pattern (18 bp):
ATTTTCATTTTCTTTTTC
Found at i:17096 original size:12 final size:12
Alignment explanation
Indices: 17065--17089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17055 TTTTTCAATC
17065 TCATTTTCTTTT
1 TCATTTTCTTTT
17077 TCATTTTCTTTT
1 TCATTTTCTTTT
17089 T
1 T
17090 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:17168 original size:5 final size:5
Alignment explanation
Indices: 17158--17220 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
17148 CTCTTGCCTC
*
17158 TCTTT TCTTT T-TATT TCTTTT TCTTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT
17206 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
17221 ATTTTCTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.58
6 12 0.24
7 5 0.10
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:17178 original size:15 final size:15
Alignment explanation
Indices: 17158--17216 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
17148 CTCTTGCCTC
17158 TCTTTTCTTTTTATT
1 TCTTTTCTTTTTATT
*
17173 TCTTTTTCTTTTTCTT
1 TC-TTTTCTTTTTATT
*
17189 T-TTCTTCTTTTGCTTTT
1 TCTT-TTCTTTT--TATT
17206 TCTTTTCTTTT
1 TCTTTTCTTTT
17217 CTTTATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 13 0.35
17 11 0.30
18 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
TCTTTTCTTTTTATT
Found at i:17180 original size:6 final size:6
Alignment explanation
Indices: 17171--17220 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
17161 TTTCTTTTTA
17171 TTTCTT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
17220 T
1 T
17221 ATTTTCTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.25
6 19 0.47
7 5 0.12
8 5 0.12
9 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:17182 original size:21 final size:21
Alignment explanation
Indices: 17160--17220 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
17150 CTTGCCTCTC
17160 TTTTCTTTTTATTTCTTTTTCT
1 TTTTCTTTTT-TTTCTTTTTCT
* *
17182 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCTTTTTCT
17203 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTT-TTTTCTTT
17221 ATTTTCTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTTTTCTTTTTCT
Found at i:17199 original size:31 final size:30
Alignment explanation
Indices: 17162--17220 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
17152 TGCCTCTCTT
17162 TTCTTTT-TATTTCTTTTTCTTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTC-TTTTCTTTTTC
*
17193 TTCTTTTGCTTTTTCTTTTCTTTTCTTT
1 TTCTTTT-CTATTTCTTTTCTTTTCTTT
17221 ATTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 15 0.60
32 5 0.20
33 5 0.20
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (30 bp):
TTCTTTTCTATTTCTTTTCTTTTCTTTTTC
Found at i:18149 original size:13 final size:13
Alignment explanation
Indices: 18131--18188 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
18121 CATTAAACAC
*
18131 TTTTTTCAGATTT
1 TTTTTTCAAATTT
18144 TTTTTTCGAAATTT
1 TTTTTTC-AAATTT
**
18158 TTTTTTTGAA-TT
1 TTTTTTCAAATTT
18170 TTTTTTCAAATTT
1 TTTTTTCAAATTT
18183 TTTTTT
1 TTTTTT
18189 ACTTGTATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 10 0.26
13 17 0.45
14 11 0.29
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTTTCAAATTT
Found at i:18171 original size:11 final size:12
Alignment explanation
Indices: 18131--18187 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
18121 CATTAAACAC
*
18131 TTTTTTCAGATTT
1 TTTTTTCA-AATT
18144 TTTTTTCGAAATTT
1 TTTTTTC-AAA-TT
**
18158 TTTTTTTGAATT
1 TTTTTTCAAATT
18170 TTTTTTCAAATT
1 TTTTTTCAAATT
18182 TTTTTT
1 TTTTTT
18188 TACTTGTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
12 18 0.49
13 10 0.27
14 9 0.24
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTTTCAAATT
Found at i:19931 original size:30 final size:30
Alignment explanation
Indices: 19897--19979 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
19887 TAAACTAAAA
19897 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * * *
19927 TGAGCTGAGGC-TAAACTCCTAAGCTGACGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
19957 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
19980 TTGAAAGCGA
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
29 2 0.05
30 33 0.87
31 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:20728 original size:14 final size:14
Alignment explanation
Indices: 20709--20753 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
20699 AACTCATCTT
*
20709 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
20723 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
20736 AATTTAATTTAATG
1 AGTTTAATTTAATG
20750 AGTT
1 AGTT
20754 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:21761 original size:29 final size:29
Alignment explanation
Indices: 21728--21787 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
21718 ATAACCAAAC
*
21728 CTACAAAAAATTTATATCCATAAACCCAT
1 CTACAAAAAATTCATATCCATAAACCCAT
* *
21757 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAAATTCATATCCATAAACCCAT
21786 CT
1 CT
21788 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAAATTCATATCCATAAACCCAT
Found at i:21780 original size:15 final size:14
Alignment explanation
Indices: 21741--21785 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
21731 CAAAAAATTT
21741 ATATCCATAAACCC
1 ATATCCATAAACCC
* * *
21755 ATCTACATAAACTTC
1 ATATCCATAAAC-CC
21770 ATATCCATAAACCC
1 ATATCCATAAACCC
21784 AT
1 AT
21786 CTTTGAATCC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (14 bp):
ATATCCATAAACCC
Found at i:22062 original size:17 final size:19
Alignment explanation
Indices: 22030--22064 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
22020 AAAAAATTTC
22030 AAACAAAAATTCTGAAAAA
1 AAACAAAAATTCTGAAAAA
22049 AAAC-AAAA-TCTGAAAA
1 AAACAAAAATTCTGAAAA
22065 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (19 bp):
AAACAAAAATTCTGAAAAA
Found at i:23135 original size:18 final size:18
Alignment explanation
Indices: 23112--23161 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
23102 TGAAAGAAAA
*
23112 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
23130 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
23148 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
23162 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:23140 original size:24 final size:24
Alignment explanation
Indices: 23108--23186 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
23098 GAAATGAAAG
*
23108 AAAAGAAAAAGAGATTGAGAGTGA
1 AAAAGAAAAAGAGATTGAGAGAGA
* * *
23132 AAAAGAAAATGAGATTGAAAAAGA
1 AAAAGAAAAAGAGATTGAGAGAGA
* * *
23156 GAATGAAAAAGAGTTTGAGAGAGA
1 AAAAGAAAAAGAGATTGAGAGAGA
*
23180 GAAAGAA
1 AAAAGAA
23187 TGTGAACAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (24 bp):
AAAAGAAAAAGAGATTGAGAGAGA
Found at i:27328 original size:14 final size:14
Alignment explanation
Indices: 27309--27353 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
27299 AACTCATCTT
*
27309 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
27323 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
27336 AATTTAATTTAATG
1 AGTTTAATTTAATG
27350 AGTT
1 AGTT
27354 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:28358 original size:29 final size:29
Alignment explanation
Indices: 28325--28384 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
28315 ATAACCAAAC
*
28325 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
28354 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
28383 CT
1 CT
28385 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:28377 original size:15 final size:15
Alignment explanation
Indices: 28331--28378 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
28321 AAACCTACAA
*
28331 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
28346 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
28360 AAACTTCATATCCAT
1 AAACTTCATATCCAT
28375 AAAC
1 AAAC
28379 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:30432 original size:20 final size:20
Alignment explanation
Indices: 30386--30432 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
30376 AGCTTGTTTC
*
30386 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
30406 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
30426 CAGCTCA
1 CAGCTCA
30433 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31847 original size:10 final size:11
Alignment explanation
Indices: 31826--31861 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
31816 CAAAAAAATC
31826 AAAATTCAAAA
1 AAAATTCAAAA
31837 AAAATTCAAAA
1 AAAATTCAAAA
* *
31848 AAAAGTGAAAA
1 AAAATTCAAAA
31859 AAA
1 AAA
31862 TCGAGCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAATTCAAAA
Done.