Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold562
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: 31143
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13495 original size:12 final size:12
Alignment explanation
Indices: 13480--13506 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13470 TTCTTTTTGC
13480 TTTTCAAAGGCT
1 TTTTCAAAGGCT
13492 TTTTCAAAGGCT
1 TTTTCAAAGGCT
13504 TTT
1 TTT
13507 GCAAGTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:19944 original size:20 final size:20
Alignment explanation
Indices: 19911--19985 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
19901 AACTTAAGCC
*
19911 AAGCTCAATCGAGCTAAAGT
1 AAGCTAAATCGAGCTAAAGT
*
19931 AAGCTAAATTGAGCTCAAACG-
1 AAGCTAAATCGAGCT-AAA-GT
** * *
19952 -AGCTAAATTAAGCTCATGT
1 AAGCTAAATCGAGCTAAAGT
19971 AAGCTAAATCGAGCT
1 AAGCTAAATCGAGCT
19986 GGGAAAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 38 0.86
21 3 0.07
22 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
AAGCTAAATCGAGCTAAAGT
Found at i:19984 original size:30 final size:30
Alignment explanation
Indices: 19911--19985 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
19901 AACTTAAGCC
19911 AAGCTCAATCGAGCTAAAGTAAGCTAAATT
1 AAGCTCAATCGAGCTAAAGTAAGCTAAATT
* * * *
19941 GAGCTCAAACGAGCTAAATTAAGCT-CATGT
1 AAGCTCAATCGAGCTAAAGTAAGCTAAAT-T
*
19971 AAGCTAAATCGAGCT
1 AAGCTCAATCGAGCT
19986 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (30 bp):
AAGCTCAATCGAGCTAAAGTAAGCTAAATT
Found at i:21836 original size:12 final size:12
Alignment explanation
Indices: 21803--21883 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
21793 TTTCCACTCG
21803 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
21814 AGCTCTCTTTCA
1 ATTTCTTTTTCA
21826 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
21839 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
21852 --TTCTCTTTCA
1 ATTTCTTTTTCA
21862 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
21874 ATCTCTTTTT
1 ATTTCTTTTT
21884 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:21844 original size:21 final size:20
Alignment explanation
Indices: 21818--21873 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
21808 TTTTCAAGCT
21818 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
21839 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
21854 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
21874 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:21944 original size:15 final size:16
Alignment explanation
Indices: 21913--21959 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
21903 TTTTGAAATC
**
21913 TCATTTTCACATT-TT
1 TCATTTTCATTTTCTT
*
21928 TCTTTTTCA-TTTCTT
1 TCATTTTCATTTTCTT
21943 TCATTTTCATTTTCTT
1 TCATTTTCATTTTCTT
21959 T
1 T
21960 ATTCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.07
15 18 0.67
16 7 0.26
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (16 bp):
TCATTTTCATTTTCTT
Found at i:21953 original size:28 final size:29
Alignment explanation
Indices: 21913--21969 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
21903 TTTTGAAATC
21913 TCATTTTCACATTTTTCTTT-TTCATTTCTT
1 TCATTTT-ACA-TTTTCTTTATTCATTTCTT
*
21943 TCATTTT-CATTTTCTTTATTCTTTTCT
1 TCATTTTACATTTTCTTTATTCATTTCT
21970 CGCTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 8 0.32
28 10 0.40
30 7 0.28
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.68
Consensus pattern (29 bp):
TCATTTTACATTTTCTTTATTCATTTCTT
Found at i:22360 original size:30 final size:30
Alignment explanation
Indices: 22326--22422 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
22316 AGCTCACTCC
22326 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
22356 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
22386 CAGCTCAACTTTAGCTCACGGGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
22416 TAGCTCA
1 TAGCTCA
22423 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:23354 original size:22 final size:20
Alignment explanation
Indices: 23322--23370 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
23312 GCCGAATTTA
23322 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
23345 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
23365 TGAACA
1 TGAACA
23371 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:24146 original size:11 final size:11
Alignment explanation
Indices: 24129--24171 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
24119 GGAAATTCGA
24129 AAAAAAAAATT
1 AAAAAAAAATT
* *
24140 TAAAAAAAATC
1 AAAAAAAAATT
*
24151 GAAAAAAAATT
1 AAAAAAAAATT
24162 AAAAAAAAAT
1 AAAAAAAAAT
24172 CGAAGTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:24155 original size:22 final size:22
Alignment explanation
Indices: 24130--24175 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
24120 GAAATTCGAA
*
24130 AAAAAAAATTTAAAAAAAATCG
1 AAAAAAAATTAAAAAAAAATCG
24152 AAAAAAAATTAAAAAAAAATCG
1 AAAAAAAATTAAAAAAAAATCG
24174 AA
1 AA
24176 GTATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAAAAAATTAAAAAAAAATCG
Found at i:25098 original size:5 final size:5
Alignment explanation
Indices: 25088--25149 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
25078 AAGAGAAAAC
* *
25088 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA AAA-GA
25135 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
25150 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 35 0.73
6 10 0.21
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:25118 original size:26 final size:26
Alignment explanation
Indices: 25088--25149 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
25078 AAGAGAAAAC
25088 AAAGAAAAGAAAAGAAAAAGAAA-AA
1 AAAGAAAAGAAAAGAAAAAGAAATAA
* * *
25113 GCAAGAGAAGAAAAGAAAATGAAATAA
1 -AAAGAAAAGAAAAGAAAAAGAAATAA
25140 AAAGAAAAGA
1 AAAGAAAAGA
25150 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAAAAAGAAATAA
Found at i:25150 original size:31 final size:30
Alignment explanation
Indices: 25076--25151 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
25066 TACATTCTTG
* *
25076 TAAAGAGAAAACA-AAGAAAAGAAAAGAAA
1 TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
25105 -AAGAAA-AAGCAAGAGAAGAAAAGAAAATGAAA
1 TAA-AAAGAA--AAGAGAAGAAAAGAAAA-GAAA
25137 TAAAAAGAAAAGAGA
1 TAAAAAGAAAAGAGA
25152 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 3 0.08
31 18 0.47
32 7 0.18
33 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.04
Consensus pattern (30 bp):
TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
Found at i:25229 original size:11 final size:12
Alignment explanation
Indices: 25197--25227 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25187 TTGAGAGAAC
25197 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25209 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25221 TTGAAAA
1 TTGAAAA
25228 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:25245 original size:11 final size:12
Alignment explanation
Indices: 25230--25261 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25220 TTTGAAAAGC
25230 AAAAAGAAAATG
1 AAAAAGAAAATG
25242 AAAAAGAAAATG
1 AAAAAGAAAATG
25254 -AAAAGAAA
1 AAAAAGAAA
25262 TTTGAGAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:27395 original size:30 final size:30
Alignment explanation
Indices: 27361--27457 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
27351 AGCTCACTCC
27361 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
27391 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
27421 CAGCTCAACTTTAGCTCACGGGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
27451 TAGCTCA
1 TAGCTCA
27458 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:28385 original size:22 final size:20
Alignment explanation
Indices: 28353--28401 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
28343 GCCGAATTTA
28353 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
28376 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
28396 TGAACA
1 TGAACA
28402 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:29869 original size:33 final size:33
Alignment explanation
Indices: 29817--29884 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
29807 TTAAACTTGA
29817 TTTTTTTTGCTCACCTTTTTTCT-CTTTTTCTTT
1 TTTTTTTTGCTCACCTTTTTTCTACTTTTT-TTT
* *
29850 TTTTTTTTGCTCGA-TTTTTTTTTACTTTTTTTT
1 TTTTTTTTGCTC-ACCTTTTTTCTACTTTTTTTT
29883 TT
1 TT
29885 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.76
Consensus pattern (33 bp):
TTTTTTTTGCTCACCTTTTTTCTACTTTTTTTT
Found at i:29879 original size:12 final size:13
Alignment explanation
Indices: 29864--29932 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 13
29854 TTTTGCTCGA
*
29864 TTTTTTTTT-ACT
1 TTTTTTTTTGAAT
29876 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
* *
29889 TTTTTTTCAATCAA-
1 TTTTTTT--TTGAAT
*
29903 ATTTTTTTTGAA-
1 TTTTTTTTTGAAT
*
29915 TTTCTTTTTGAAT
1 TTTTTTTTTGAAT
29928 TTTTT
1 TTTTT
29933 GTTACTCCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
12 22 0.50
13 13 0.30
14 6 0.14
15 3 0.07
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Done.