Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold883
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: 34052
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:1305 original size:27 final size:26
Alignment explanation
Indices: 1265--1337 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
1255 AAAAGCCATC
*
1265 TTTT-TTTGTTAAAAATGGTGATTCTT
1 TTTTGTTTGTCAAAAATGGTGATTC-T
1291 TTTTGTTTGTCAAAAATGGTGATTCT
1 TTTTGTTTGTCAAAAATGGTGATTCT
*
1317 TTTTGTTTGTCAAAATTGGTG
1 TTTTGTTTGTCAAAAATGGTG
1338 GCATGTTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 25 0.57
27 19 0.43
ACGTcount: A:0.22, C:0.05, G:0.19, T:0.53
Consensus pattern (26 bp):
TTTTGTTTGTCAAAAATGGTGATTCT
Found at i:2904 original size:20 final size:21
Alignment explanation
Indices: 2865--2917 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2855 TTAAGTTATT
*
2865 TTTAA-AATTTTTCAAGATAA
1 TTTAATAATTTTTCAAAATAA
**
2885 TTTTTTAATTTTT-AAAATAA
1 TTTAATAATTTTTCAAAATAA
2905 TTTAATAATTTTT
1 TTTAATAATTTTT
2918 GAGTTTCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAATAATTTTTCAAAATAA
Found at i:5256 original size:18 final size:19
Alignment explanation
Indices: 5213--5271 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
5203 TATTTATTAC
*
5213 TTAAATTTATTTTAATTTTAAT
1 TTAAATTTATTTTAA--AT-AT
5235 TTAAA-TTATTTTAAATAT
1 TTAAATTTATTTTAAATAT
*
5253 TTAAATTTATTTTTAATAT
1 TTAAATTTATTTTAAATAT
5272 AGATTTAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 7 0.21
19 13 0.38
21 9 0.26
22 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATTTATTTTAAATAT
Found at i:6006 original size:29 final size:30
Alignment explanation
Indices: 5967--6025 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
5957 ATTTAAAATA
*
5967 TTTAAT-TTTTATAAATTAAAAAATTTTAT
1 TTTAATATTTAATAAATTAAAAAATTTTAT
*
5996 TTTAATATTTAAATATATTAAAAAATTTTA
1 TTTAATATTT-AATAAATTAAAAAATTTTA
6026 AAAATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 3 0.12
31 17 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTAATATTTAATAAATTAAAAAATTTTAT
Found at i:8298 original size:23 final size:22
Alignment explanation
Indices: 8267--8313 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
8257 ATTTAACTAA
*
8267 TTAACTTTTAATGAATTTA-AATT
1 TTAAATTTTAAT--ATTTATAATT
8290 TTAAATTTTAATATTTATAATT
1 TTAAATTTTAATATTTATAATT
8312 TT
1 TT
8314 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAAATTTTAATATTTATAATT
Found at i:8904 original size:20 final size:19
Alignment explanation
Indices: 8863--8902 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
8853 AGATATTAAT
8863 ATAAAATATAATTTTATAA
1 ATAAAATATAATTTTATAA
*
8882 ATAAATATATATTTATTATAA
1 ATAAA-ATATAATT-TTATAA
8903 TATTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATATAATTTTATAA
Found at i:9093 original size:13 final size:13
Alignment explanation
Indices: 9077--9101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9067 AATTGGACAT
9077 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
9090 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9102 AGAGGATGTT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:9792 original size:29 final size:30
Alignment explanation
Indices: 9727--9812 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
9717 AAATAAAAAA
*
9727 AATCAAAT-AAAAAGGAGAAATTATTTTTT
1 AATCAAATAAAAAATGAGAAATTATTTTTT
**
9756 AAAAAAATAAAAAATGAGAAATTATTTTTT
1 AATCAAATAAAAAATGAGAAATTATTTTTT
* * *
9786 -TTCAAATAAGAAAGTGAGTAATT-TTTT
1 AATCAAATAA-AAAATGAGAAATTATTTT
9813 AAAAAAATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 16 0.34
30 31 0.66
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.36
Consensus pattern (30 bp):
AATCAAATAAAAAATGAGAAATTATTTTTT
Found at i:9826 original size:29 final size:28
Alignment explanation
Indices: 9749--9827 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
9739 AGGAGAAATT
9749 ATTTTTTAAAAAAATAAA-AAATGAGAA
1 ATTTTTTAAAAAAATAAAGAAATGAGAA
**** *
9776 ATTATTTTTTTTCAAAT-AAGAAAGTGAGTA
1 A-T-TTTTTAAAAAAATAAAGAAA-TGAGAA
9806 ATTTTTTAAAAAAATAAAGAAA
1 ATTTTTTAAAAAAATAAAGAAA
9828 AAAATGAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
27 1 0.03
28 12 0.32
29 19 0.50
30 6 0.16
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.35
Consensus pattern (28 bp):
ATTTTTTAAAAAAATAAAGAAATGAGAA
Found at i:9898 original size:12 final size:11
Alignment explanation
Indices: 9878--9927 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
9868 AAACCTTGAC
*
9878 TTAATATTTATT
1 TTAAAATTT-TT
9890 TTAAAATTTTT
1 TTAAAATTTTT
* *
9901 ATTTAATTTTTT
1 -TTAAAATTTTT
9913 TTAAAATTTTT
1 TTAAAATTTTT
9924 TTAA
1 TTAA
9928 TTAAATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 15 0.47
12 17 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTAAAATTTTT
Found at i:9914 original size:23 final size:25
Alignment explanation
Indices: 9878--9923 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
9868 AAACCTTGAC
9878 TTAATATTTATTTTAAAATTTTTAT
1 TTAATATTTATTTTAAAATTTTTAT
9903 TTAAT-TTT-TTTTAAAATTTTT
1 TTAATATTTATTTTAAAATTTTT
9924 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 3 0.14
25 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTAATATTTATTTTAAAATTTTTAT
Found at i:11474 original size:22 final size:23
Alignment explanation
Indices: 11419--11487 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 23
11409 GTTGAATTTA
*
11419 AATATAAATTTTATTAATTTAAATC
1 AATATAAA-ATTATT-ATTTAAATC
11444 AAGT-T-AAATTATTATTTAAAT-
1 AA-TATAAAATTATTATTTAAATC
11465 AATATAAAA-TATTTATTTTAAAT
1 AATATAAAATTA-TTA-TTTAAAT
11488 TTAATTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
20 1 0.03
21 5 0.13
22 14 0.37
23 12 0.32
24 2 0.05
25 3 0.08
26 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (23 bp):
AATATAAAATTATTATTTAAATC
Found at i:13703 original size:14 final size:15
Alignment explanation
Indices: 13680--13735 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
13670 ATTTTAGCAC
*
13680 AAGTAATTTTGACA-
1 AAGTACTTTTGACAT
* *
13694 AAGTACTTTTAATAT
1 AAGTACTTTTGACAT
13709 AAGTAC-TTTGACAT
1 AAGTACTTTTGACAT
*
13723 ATGTA-TTTTGACA
1 AAGTACTTTTGACA
13736 CAGATATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 28 0.82
15 6 0.18
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (15 bp):
AAGTACTTTTGACAT
Found at i:13800 original size:14 final size:14
Alignment explanation
Indices: 13739--13802 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
13729 TTTGACACAG
13739 ATATTTT-AGTATAA
1 ATATTTTGA-TATAA
*
13753 AAATTTTGATA-AA
1 ATATTTTGATATAA
* *
13766 GATATTCTTGACATAG
1 -ATATT-TTGATATAA
*
13782 GTATTTTGATATAA
1 ATATTTTGATATAA
13796 ATATTTT
1 ATATTTT
13803 TGACAGAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
13 2 0.05
14 25 0.66
15 10 0.26
16 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (14 bp):
ATATTTTGATATAA
Found at i:15401 original size:21 final size:21
Alignment explanation
Indices: 15375--15419 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15365 TATAGATAAT
15375 AAAAATAGAAGAGCACAAGTA
1 AAAAATAGAAGAGCACAAGTA
* * *
15396 AAAAATATAAGAGTAGAAGTA
1 AAAAATAGAAGAGCACAAGTA
15417 AAA
1 AAA
15420 TGTACACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.64, C:0.04, G:0.18, T:0.13
Consensus pattern (21 bp):
AAAAATAGAAGAGCACAAGTA
Found at i:21221 original size:113 final size:112
Alignment explanation
Indices: 20964--21482 Score: 429
Period size: 113 Copynumber: 4.6 Consensus size: 112
20954 ATGCATATAA
* * * * * *
20964 TACGATACACTTTAACATGCATGTTGTGATGTAGATAATC-GATTTTATTATGCATCGGTGCCGT
1 TACGATACACTTTAATATGCATGTTGTAATGTAAAGAATCAG-TTTTATTATGCAT-GGTGGCAT
* *
21028 ATATACTATATATTGATACACCAA-C-AATCTACATGCATGTATGAACAG
64 ATATACTATATATTGATACA-CAAGCAAATCTACGTGCTTGTATGAACAG
* * ** *
21076 TACAATACACTTGAATATGCACATTGCAATGTAAAGAATCAGTTTTATTATGCACTGGTGGCATA
1 TACGATACACTTTAATATGCATGTTGTAATGTAAAGAATCAGTTTTATTATGCA-TGGTGGCATA
* ** *
21141 TATGCTATATATCAATACACAAGCAAATCTATGTGCTTGTAT-AGACAG
65 TATACTATATATTGATACACAAGCAAATCTACGTGCTTGTATGA-ACAG
* * * * * *
21189 TGCGATACAGTTTGATATGCATGTTGTGATGTAGAGAATAAG--TTATTATGCATTGGTGGCATA
1 TACGATACACTTTAATATGCATGTTGTAATGTAAAGAATCAGTTTTATTATGCA-TGGTGGCATA
* * * * * * *
21252 TGTACTCTACATTGGTACACAAGCAAATCTACGTGATTGTACGAATAG
65 TATACTATATATTGATACACAAGCAAATCTACGTGCTTGTATGAACAG
* ** **
21300 TACGATACACTTTAATATGCATGTTGTAATTTAAAGAATTGGTTTTATTATGTGTAGGTGGCATA
1 TACGATACACTTTAATATGCATGTTGTAATGTAAAGAATCAGTTTTATTATGCAT-GGTGGCATA
* * ** * * * * * * * *
21365 TACATTGCAAATCGATATACAAGCAAATCTACGTGCATGCACGAGCAA
65 TATACTATATATTGATACACAAGCAAATCTACGTGCTTGTATGAACAG
* * * ** * * *
21413 TATGATACACTTTAATATACATGTTGTAATATAGGGAATTAGGTTAATTATGCATTGGTGGCATA
1 TACGATACACTTTAATATGCATGTTGTAATGTAAAGAATCAGTTTTATTATGCA-TGGTGGCATA
21478 TATAC
65 TATAC
21483 ACAAGCAAAT
Statistics
Matches: 320, Mismatches: 77, Indels: 19
0.77 0.19 0.05
Matches are distributed among these distances:
111 92 0.29
112 70 0.22
113 157 0.49
114 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (112 bp):
TACGATACACTTTAATATGCATGTTGTAATGTAAAGAATCAGTTTTATTATGCATGGTGGCATAT
ATACTATATATTGATACACAAGCAAATCTACGTGCTTGTATGAACAG
Found at i:21389 original size:224 final size:223
Alignment explanation
Indices: 20962--21482 Score: 525
Period size: 224 Copynumber: 2.3 Consensus size: 223
20952 CGATGCATAT
* * ** * * *
20962 AATACGATACACTTTAACATGCATGTTGTGATGTAGATAATCGATTTTATTATGCATCGGTGCCG
1 AATACGATACACTTTAATATGCATGTTGTGATGTAGAGAAT--AAGTTATTATGCATTGGTGGCA
* *
21027 TATATACTATATATTGATACACCAACAATCTACATGCATGTATGAACAGTACAATACACTTGAAT
64 TATATACTATACATTGATACACCAACAATCTACATGCATGTACGAACAGTACAATACACTTGAAT
21092 ATGCACATTGCAATGTAAAGAATCAGTTTTATTATGCACTGGTGGCATATATGCTATATATCAAT
129 ATGCACATTGCAATGTAAAGAATCAGTTTTATTATGCACTGGTGGCATATATGCTATATATCAAT
* * *
21157 ACACAAGCAAATCTATGTGCTTGTATAGA-C
194 ACACAAGCAAATCTACGTGCATGCA-AGAGC
* * * *
21187 AGTGCGATACAGTTTGATATGCATGTTGTGATGTAGAGAATAAGTTATTATGCATTGGTGGCATA
1 AATACGATACACTTTAATATGCATGTTGTGATGTAGAGAATAAGTTATTATGCATTGGTGGCATA
* * * * * * *
21252 TGTACTCTACATTGGTACA-CAAGCAAATCTACGTG-ATTGTACGAATAGTACGATACACTTTAA
66 TATACTATACATTGATACACCAA-C-AATCTACATGCA-TGTACGAACAGTACAATACACTTGAA
** * * ** **
21315 TATGCATGTTGTAATTTAAAGAATTGGTTTTATTATG-TGTAGGTGGCATATACATTGC-A-A-A
128 TATGCACATTGCAATGTAAAGAATCAGTTTTATTATGCACT-GGTGGCATAT--A-TGCTATATA
* * *
21376 TCGATATACAAGCAAATCTACGTGCATGCACGAGC
189 TCAATACACAAGCAAATCTACGTGCATGCAAGAGC
* * * * * *
21411 AATATGATACACTTTAATATACATGTTGTAATATAGGGAATTAGGTTAATTATGCATTGGTGGCA
1 AATACGATACACTTTAATATGCATGTTGTGATGTAGAGAA-TAAGTT-ATTATGCATTGGTGGCA
21476 TATATAC
64 TATATAC
21483 ACAAGCAAAT
Statistics
Matches: 241, Mismatches: 45, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
222 3 0.01
223 39 0.16
224 130 0.54
225 41 0.17
226 25 0.10
227 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (223 bp):
AATACGATACACTTTAATATGCATGTTGTGATGTAGAGAATAAGTTATTATGCATTGGTGGCATA
TATACTATACATTGATACACCAACAATCTACATGCATGTACGAACAGTACAATACACTTGAATAT
GCACATTGCAATGTAAAGAATCAGTTTTATTATGCACTGGTGGCATATATGCTATATATCAATAC
ACAAGCAAATCTACGTGCATGCAAGAGC
Found at i:24632 original size:2 final size:2
Alignment explanation
Indices: 24627--24662 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24617 ATATATAGAA
24627 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
24663 GTTTTACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27708 original size:16 final size:16
Alignment explanation
Indices: 27678--27708 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27668 TCACAAATAC
*
27678 AAAATAATTTAAATTA
1 AAAAAAATTTAAATTA
27694 AAAAAAATTTAAATT
1 AAAAAAATTTAAATT
27709 TAATATGACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAAAATTTAAATTA
Found at i:30531 original size:16 final size:16
Alignment explanation
Indices: 30510--30541 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30500 TAGAAGTTGG
*
30510 AAAATTAAATTTAAAA
1 AAAATTAAATATAAAA
30526 AAAATTAAATATAAAA
1 AAAATTAAATATAAAA
30542 GTTTCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAAATATAAAA
Done.