Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2364
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: 26228
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Found at i:3774 original size:13 final size:13
Alignment explanation
Indices: 3756--3806 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
3746 CAGCATTCTC
3756 TGTATCGATACAT
1 TGTATCGATACAT
3769 TGTATCGATACAT
1 TGTATCGATACAT
*
3782 TGTATCGATACAG
1 TGTATCGATACAT
3795 TGTATCGATACA
1 TGTATCGATACA
3807 AAGGGTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5653 original size:21 final size:21
Alignment explanation
Indices: 5629--5672 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5619 GAGAAAGAAA
*
5629 TATGTGATTAAAAATTTTTGT
1 TATGTGATTAAAAATTATTGT
5650 TATGTGATTAAAAATTATTGT
1 TATGTGATTAAAAATTATTGT
5671 TA
1 TA
5673 AATTGCCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
TATGTGATTAAAAATTATTGT
Found at i:6150 original size:21 final size:22
Alignment explanation
Indices: 6110--6151 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6100 GATAAGTATA
6110 AATGTTTTCAAGGCTTAAAATG
1 AATGTTTTCAAGGCTTAAAATG
6132 AATGATTTTCAA-G-TTAAAAT
1 AATG-TTTTCAAGGCTTAAAAT
6152 ATATCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (22 bp):
AATGTTTTCAAGGCTTAAAATG
Found at i:6289 original size:13 final size:13
Alignment explanation
Indices: 6271--6295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6261 ATATTGCACA
6271 GTATCGATACATT
1 GTATCGATACATT
6284 GTATCGATACAT
1 GTATCGATACAT
6296 GACCAAATGT
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):
GTATCGATACATT
Found at i:6402 original size:13 final size:13
Alignment explanation
Indices: 6384--6409 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6374 TACACACAAT
6384 ATGTATCGATACA
1 ATGTATCGATACA
6397 ATGTATCGATACA
1 ATGTATCGATACA
6410 TCCCAAAATG
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:6426 original size:33 final size:32
Alignment explanation
Indices: 6366--6429 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
6356 CTTAACTGTT
* *
6366 TGTATTGATACACACAATATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
6398 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
6430 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:10153 original size:89 final size:89
Alignment explanation
Indices: 10014--10176 Score: 227
Period size: 89 Copynumber: 1.8 Consensus size: 89
10004 TATCATATCA
* * *** *
10014 TAATCGTATTTAAAGTATTTTATATTTATATAAATTTTGATGTGTGAATAACTCATATTATATAG
1 TAATCATATTTAAAGTATTTTATATTTATAGAAATTTTGATACATCAATAACTCATATTATATAG
10079 ATTTTGAGATATGTATTTGAATCT
66 ATTTTGAGATATGTATTTGAATCT
* * * * *
10103 TAATCATATTTAAAGTATTTTATATTTATAGAATTTTTTATACATCAATAATTTATATTATATAT
1 TAATCATATTTAAAGTATTTTATATTTATAGAAATTTTGATACATCAATAACTCATATTATATAG
10168 ATTTTGAGA
66 ATTTTGAGA
10177 CTTTATATAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 63 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (89 bp):
TAATCATATTTAAAGTATTTTATATTTATAGAAATTTTGATACATCAATAACTCATATTATATAG
ATTTTGAGATATGTATTTGAATCT
Found at i:10852 original size:6 final size:6
Alignment explanation
Indices: 10843--10883 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
10833 GTAAAAATCA
* *
10843 AAAATT AAAATT AAAATT AAAATT CAAAAAT AAAAAT AAAA
1 AAAATT AAAATT AAAATT AAAATT -AAAATT AAAATT AAAA
10884 ATGAAGGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (6 bp):
AAAATT
Found at i:10870 original size:26 final size:26
Alignment explanation
Indices: 10834--10885 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
10824 TAGTAATAAG
* *
10834 TAAAAATCAAAAATTAAAATTAAAAT
1 TAAAAATCAAAAATAAAAATAAAAAT
*
10860 TAAAATTCAAAAATAAAAATAAAAAT
1 TAAAAATCAAAAATAAAAATAAAAAT
10886 GAAGGCATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAATCAAAAATAAAAATAAAAAT
Found at i:10884 original size:6 final size:6
Alignment explanation
Indices: 10834--10885 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
10824 TAGTAATAAG
* * *
10834 TAAAAA TCAAAAA TTAAAAT TAAAAT TAAAAT TCAAAAA TAAAAA TAAAAA
1 TAAAAA T-AAAAA -TAAAAA TAAAAA TAAAAA T-AAAAA TAAAAA TAAAAA
10885 T
1 T
10886 GAAGGCATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 26 0.63
7 14 0.34
8 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (6 bp):
TAAAAA
Found at i:10884 original size:12 final size:13
Alignment explanation
Indices: 10834--10885 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
10824 TAGTAATAAG
10834 TAAAAATCAAAAA
1 TAAAAATCAAAAA
* * *
10847 TTAAAATTAAAAT
1 TAAAAATCAAAAA
*
10860 TAAAATTCAAAAA
1 TAAAAATCAAAAA
10873 TAAAAAT-AAAAA
1 TAAAAATCAAAAA
10885 T
1 T
10886 GAAGGCATGG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
12 6 0.19
13 25 0.81
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAAATCAAAAA
Found at i:10918 original size:35 final size:35
Alignment explanation
Indices: 10878--11012 Score: 261
Period size: 35 Copynumber: 3.9 Consensus size: 35
10868 AAAAATAAAA
10878 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
10913 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
*
10948 ATAAAAATGGAGGCATGGAATGATGGGCATGGAAT
1 ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
10983 ATAAAAATGAAGGCATGGAATGATGGGCAT
1 ATAAAAATGAAGGCATGGAATGATGGGCAT
11013 AAAAAATGAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 98 1.00
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.20
Consensus pattern (35 bp):
ATAAAAATGAAGGCATGGAATGATGGGCATGGAAT
Found at i:10928 original size:21 final size:20
Alignment explanation
Indices: 10903--11003 Score: 73
Period size: 21 Copynumber: 5.5 Consensus size: 20
10893 TGGAATGATG
10903 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
*
10924 GGCATGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
10938 GGCATGGAATATAAAAATGGA
1 GGCATGGAATATAAAAAT-GA
*
10959 GGCATGG-A-AT---GATG-
1 GGCATGGAATATAAAAATGA
10973 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATG-A
10994 GGCATGGAAT
1 GGCATGGAAT
11004 GATGGGCATA
Statistics
Matches: 62, Mismatches: 4, Indels: 28
0.66 0.04 0.30
Matches are distributed among these distances:
14 14 0.23
15 3 0.05
16 9 0.15
19 9 0.15
20 3 0.05
21 24 0.39
ACGTcount: A:0.43, C:0.06, G:0.32, T:0.20
Consensus pattern (20 bp):
GGCATGGAATATAAAAATGA
Found at i:12554 original size:79 final size:79
Alignment explanation
Indices: 12421--13090 Score: 1072
Period size: 79 Copynumber: 8.4 Consensus size: 79
12411 TTTAATTTTC
* *
12421 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
12486 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
12500 TTAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGAGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
12565 TTATCTCTAAAACA
66 TTATTTCTAAAACA
*
12579 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGATGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
12644 TTATCTCTAAAACA
66 TTATTTCTAAAACA
12658 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
12723 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* *
12737 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCCGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
12802 TTATTTCTAAAACA
66 TTATTTCTAAAACA
*
12816 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
12881 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* *
12895 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
12960 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * **
12974 TCAATTTCTCACAATCGGGGATACTCTAACCCCGTTATTT-TAATGGGGATACTCCAACCCCGGC
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGA-GGGGATACTCCAACCCCGG-
** *
13038 CCTTATTTCTAAAGCA
64 TTTTATTTCTAAAACA
* *
13054 TCAAATTTTTTTTATAATCGGGGATACTCTAACCCCG
1 TC-AA--TTTTTCATAATCGGGGATACTCCAACCCCG
13091 ATTTTATTTT
Statistics
Matches: 553, Mismatches: 33, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
78 1 0.00
79 508 0.92
80 15 0.03
81 2 0.00
83 27 0.05
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:15566 original size:25 final size:25
Alignment explanation
Indices: 15532--15581 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
15522 AGAGTAGCAT
15532 GAACTTGATGTTTTCATCAAATTGG
1 GAACTTGATGTTTTCATCAAATTGG
15557 GAACTTGATGTTTTCATCAAATTGG
1 GAACTTGATGTTTTCATCAAATTGG
15582 TCATCCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (25 bp):
GAACTTGATGTTTTCATCAAATTGG
Found at i:16854 original size:92 final size:90
Alignment explanation
Indices: 16729--17049 Score: 240
Period size: 92 Copynumber: 3.5 Consensus size: 90
16719 CCTAGTCTTC
* * * * *
16729 AAAAAAA-TTCAAACTTTCTCTTATATGATTTTATCTTTAGGGAAACTCTATCTCCATTACTCCG
1 AAAAAAATTTCAAATTTTCCCTTGTATAATTTTATCTTTAGGGAAACTCTATCTCCACTACTCCG
*
16793 AAGGGATACTTCAACACCATTCTACT
66 AAGGGATACTTCAAC-CCGTTCTACT
* * * * * * *
16819 AAAAAAATTTCAAATTTTCCCTTTGTATAATTTTATCTTTGGGGATATTTTAACCCCACGACTCC
1 AAAAAAATTTCAAATTTTCCC-TTGTATAATTTTATCTTTAGGGAAACTCTATCTCCACTACTCC
* * * *
16884 -AAGGGAATACTTTAGCTTCGGTCT--T
65 GAAGGG-ATACTTCAAC-CCGTTCTACT
* * * * *
16909 AAAAAAAGTTT-AAATTTTCTCTTGTATGATTTTATCCTTGGGGAAACTCCAT-TCTCACTACTC
1 AAAAAAA-TTTCAAATTTTCCCTTGTATAATTTTATCTTTAGGGAAACTCTATCTC-CACTACTC
* * * * *
16972 CGAGGGGATAATCCAACCTCGTTCAACC
64 CGAAGGGATACTTCAACC-CGTTCTACT
* * * * *
17000 AAACAAATTTTAAATTTTCCCTTCTTGTAATTTTATCTTTAGGGATACTC
1 AAAAAAATTTCAAATTTTCCCTT-GTATAATTTTATCTTTAGGGAAACTC
17050 CAACCCTACT
Statistics
Matches: 175, Mismatches: 45, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
88 1 0.01
89 42 0.24
90 31 0.18
91 36 0.21
92 65 0.37
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (90 bp):
AAAAAAATTTCAAATTTTCCCTTGTATAATTTTATCTTTAGGGAAACTCTATCTCCACTACTCCG
AAGGGATACTTCAACCCGTTCTACT
Found at i:17737 original size:146 final size:146
Alignment explanation
Indices: 17461--17728 Score: 351
Period size: 146 Copynumber: 1.8 Consensus size: 146
17451 AGTGATTATC
* * * * *
17461 GTGCATTCATATTTTAAAAATTCATTTTTCAATAAAATTTACAAGGTAACATTCCGTGTTGACAG
1 GTGCATTAATATTTTAAAAATTCATTTTCCAATAAAATTTACAAGGCAACATTCCATGTAGACAG
* ** * * * *
17526 CTTTCTAGTGTTTAATACGAAATATCTAATATTTTAAACCCAACTCAGACATTATTTAAAAAAAA
66 CTCTCTAGTGCCTAATACGAAATATCCAAAATTTCAAACCCAACACAGACATTATTTAAAAAAAA
17591 AAGGAAAAATTCCTAT
131 AAGGAAAAATTCCTAT
* * *
17607 GTGCATTAATATTTTAAAAATTCATTTTCCAATAAAATTTAGAAGGCAACATTTCATGCTAG-TA
1 GTGCATTAATATTTTAAAAATTCATTTTCCAATAAAATTTACAAGGCAACATTCCATG-TAGACA
* *
17671 TCTCTCTAGTGCCTAATAC-AGAATATCCAAAATTTCAAACCCAACACAGATATTATTT
65 GCTCTCTAGTGCCTAATACGA-AATATCCAAAATTTCAAACCCAACACAGACATTATTT
17729 TTTAAAAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
145 1 0.01
146 100 0.97
147 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (146 bp):
GTGCATTAATATTTTAAAAATTCATTTTCCAATAAAATTTACAAGGCAACATTCCATGTAGACAG
CTCTCTAGTGCCTAATACGAAATATCCAAAATTTCAAACCCAACACAGACATTATTTAAAAAAAA
AAGGAAAAATTCCTAT
Found at i:20309 original size:2 final size:2
Alignment explanation
Indices: 20302--20364 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
20292 ATATTTATTT
* * * * *
20302 TA TA TA TA TA TT TA TA T- TA TA TT TA TA TT TT TA T- TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20342 TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
20365 TATTTTATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:20314 original size:17 final size:17
Alignment explanation
Indices: 20292--20372 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
20282 TAAATTTTAA
20292 ATATTTATTTTATATAT
1 ATATTTATTTTATATAT
* *
20309 ATATTTATATTATATTT
1 ATATTTATTTTATATAT
*
20326 ATATTT-TTATTATATTT
1 ATATTTATT-TTATATAT
* *
20343 ATATATA-TATATATAT
1 ATATTTATTTTATATAT
*
20359 ACATATTATTTTAT
1 ATAT-TTATTTTAT
20373 TTATTTTTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
16 10 0.20
17 37 0.73
18 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTATTTTATATAT
Found at i:20317 original size:6 final size:6
Alignment explanation
Indices: 20292--20358 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
20282 TAAATTTTAA
* *
20292 ATATTT AT-TTT ATATAT ATATTT ATA-TT ATATTT ATATTT TTA-TT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
* *
20337 ATATTT ATATAT ATATAT ATAT
1 ATATTT ATATTT ATATTT ATAT
20359 ACATATTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
5 14 0.26
6 39 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:20393 original size:46 final size:46
Alignment explanation
Indices: 20302--20396 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
20292 ATATTTATTT
** * * *
20302 TATATATATATTTATATTATATTTATATTTTTATTATATTTATATA
1 TATATATATATACATATTATATTTATATTTTTACTATAATAATATA
20348 TATATATATATACATATTAT-TTTATTTATTTTT-CTATAATAATATA
1 TATATATATATACATATTATATTTA--TATTTTTACTATAATAATATA
20394 TAT
1 TAT
20397 TTTTTGTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 4 0.10
46 31 0.74
47 7 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (46 bp):
TATATATATATACATATTATATTTATATTTTTACTATAATAATATA
Found at i:21104 original size:19 final size:18
Alignment explanation
Indices: 21060--21105 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
21050 TATTATTAAC
*
21060 CAAAATTAAAATTAAAAAA
1 CAAAA-TAAAATCAAAAAA
*
21079 TAAAATAAAATCACAAAAA
1 CAAAATAAAATCA-AAAAA
21098 CAAAATAA
1 CAAAATAA
21106 GATAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
CAAAATAAAATCAAAAAA
Found at i:21360 original size:12 final size:11
Alignment explanation
Indices: 21341--21371 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
21331 TATTTTAAAA
21341 TATTTTTTATT
1 TATTTTTTATT
21352 TATTATTTTATT
1 TATT-TTTTATT
21364 TATTTTTT
1 TATTTTTT
21372 GTACCGCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:21673 original size:14 final size:14
Alignment explanation
Indices: 21654--21701 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
21644 ATTTTTTTGA
21654 TAATTTAAATTTTT
1 TAATTTAAATTTTT
21668 TAATTT--ATTTTT
1 TAATTTAAATTTTT
*
21680 T-ATTTCAAAATTTT
1 TAATTT-AAATTTTT
21694 TAATTTAA
1 TAATTTAA
21702 GTTATAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
11 4 0.14
12 7 0.24
14 14 0.48
15 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTTAAATTTTT
Found at i:22391 original size:30 final size:29
Alignment explanation
Indices: 22348--22413 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
22338 AACTTTTATG
*
22348 TATATTATAAATTTTTAATT-TTATTAAAT
1 TATATTATAAATTTTT-ATTATTAATAAAT
22377 TATATTATTAAATTTTTATTATTAATAAAT
1 TATATTA-TAAATTTTTATTATTAATAAAT
*
22407 TAAATTA
1 TATATTA
22414 CTTTATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TATATTATAAATTTTTATTATTAATAAAT
Found at i:22398 original size:14 final size:14
Alignment explanation
Indices: 22350--22401 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
22340 CTTTTATGTA
22350 TATTA-TAAATTTT
1 TATTATTAAATTTT
*
22363 TAATTTTATTAAA-TTA
1 T-A--TTATTAAATTTT
22379 TATTATTAAATTTT
1 TATTATTAAATTTT
22393 TATTATTAA
1 TATTATTAA
22402 TAAATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.28
14 12 0.38
15 1 0.03
16 6 0.19
17 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATTAAATTTT
Found at i:23923 original size:16 final size:16
Alignment explanation
Indices: 23904--23934 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23894 AAATTTTTGA
*
23904 ATCATTTTGAGTTTAG
1 ATCATTTTAAGTTTAG
23920 ATCATTTTAAGTTTA
1 ATCATTTTAAGTTTA
23935 ATTAGTCATT
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:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (16 bp):
ATCATTTTAAGTTTAG
Found at i:24929 original size:33 final size:33
Alignment explanation
Indices: 24882--24944 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
24872 AATAATATGT
24882 ATATATATATATATATATATTACCTTTTTAATA
1 ATATATATATATATATATATTACCTTTTTAATA
*
24915 ATATGTATATATATATATATTACCTTTTTA
1 ATATATATATATATATATATTACCTTTTTA
24945 TGTCTTGTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (33 bp):
ATATATATATATATATATATTACCTTTTTAATA
Done.