Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1297
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: 31377
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:3186 original size:18 final size:19
Alignment explanation
Indices: 3163--3198 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3153 ATAAAATTAT
*
3163 TTATTTAA-GTTTAAAAAC
1 TTATTTAATATTTAAAAAC
3181 TTATTTAATATTTAAAAA
1 TTATTTAATATTTAAAAA
3199 GTTTATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TTATTTAATATTTAAAAAC
Found at i:4091 original size:55 final size:56
Alignment explanation
Indices: 4027--4142 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 56
4017 GGATTAAAGA
*
4027 AATACATCAATGTAATTTATGTATAAAATTAATTATA-ATATATATATAGATCTTT
1 AATACATCAATGTAATTCATGTATAAAATTAATTATAGATATATATATAGATCTTT
*
4082 AATACATCAATGTAATTCATGTATAGAATTAATTATAGTATATATATATAGATCTTT
1 AATACATCAATGTAATTCATGTATAAAATTAATTATAG-ATATATATATAGATCTTT
4139 AATA
1 AATA
4143 AGGTTCATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 35 0.61
57 22 0.39
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (56 bp):
AATACATCAATGTAATTCATGTATAAAATTAATTATAGATATATATATAGATCTTT
Found at i:4297 original size:2 final size:2
Alignment explanation
Indices: 4290--4326 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4280 TAGTATGGGT
*
4290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4327 TGAGTATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8051 original size:282 final size:281
Alignment explanation
Indices: 7530--8072 Score: 962
Period size: 282 Copynumber: 1.9 Consensus size: 281
7520 TCAAGAACCT
7530 TTTATGAAAAATGTTGAAAAATTTTGAAAAAAATCGTCTAGTGGGCCTGAATGGCCCAACTTGAA
1 TTTATGAAAAATGTTGAAAAATTTTGAAAAAAATCGTCTAGTGGGCCTGAATGGCCCAACTTGAA
* **
7595 TGCATTTCGTTGATTTCGTGGGTTCTTGACAGCTTGGGTTCGTAAAATCGTAACTCCCTCATCCG
66 TGCATTTCGTTGATTCCGTGGGTTCTTGACAGCTTGGGTTCGTAAAATCGTAACTCCCAAATCCG
* *
7660 GACTAGTTCGAAGGCAAATAAGATACCGTTAGAAATTGACAAAATTTATGAGAAAATACTAAAAA
131 GACTAGTTCGAAGACAAATAAGATACCGTTAAAAATTGACAAAATTTATGAGAAAATACTAAAAA
*
7725 ATTCTGAAAAAATCTTTTATTATTTTAAAATAATTATTCAACATGTAATAGTGTTGCTGCCAACT
196 ATTCTGAAAAAATCTTTTATTATTTTAAAATAATTATTCAACATGTAACAGTGTTGCTGCCAACT
7790 TCAACATGTAACAGTGTAACA
261 TCAACATGTAACAGTGTAACA
*
7811 TTTATGAAAAATGTTGAGAAAA-TTTGAAAAAAAATCGTCTAGTGGGCCTGAATGGCCTAACTTG
1 TTTATGAAAAATGTTGA-AAAATTTTG-AAAAAAATCGTCTAGTGGGCCTGAATGGCCCAACTTG
7875 AATGCATTTCGTTGATTCCGTGGGTTCTTGACAGCTTGGGTTCGTAAAATCGTAACTCCCAAATC
64 AATGCATTTCGTTGATTCCGTGGGTTCTTGACAGCTTGGGTTCGTAAAATCGTAACTCCCAAATC
*
7940 CGGACTAGTTCGAAGACAAATAAGATACCGTTAAAAATTGACACAATTTATGAGAAAATACTAAA
129 CGGACTAGTTCGAAGACAAATAAGATACCGTTAAAAATTGACAAAATTTATGAGAAAATACTAAA
* * *
8005 AAATTCTGAAAAAATCTTTTATTATTTTAAAGTGATTTTTCAACATGTAACAGTGTTGCTGCCAA
194 AAATTCTGAAAAAATCTTTTATTATTTTAAAATAATTATTCAACATGTAACAGTGTTGCTGCCAA
8070 CTT
259 CTT
8073 GAAACAGGGG
Statistics
Matches: 249, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
281 21 0.08
282 228 0.92
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (281 bp):
TTTATGAAAAATGTTGAAAAATTTTGAAAAAAATCGTCTAGTGGGCCTGAATGGCCCAACTTGAA
TGCATTTCGTTGATTCCGTGGGTTCTTGACAGCTTGGGTTCGTAAAATCGTAACTCCCAAATCCG
GACTAGTTCGAAGACAAATAAGATACCGTTAAAAATTGACAAAATTTATGAGAAAATACTAAAAA
ATTCTGAAAAAATCTTTTATTATTTTAAAATAATTATTCAACATGTAACAGTGTTGCTGCCAACT
TCAACATGTAACAGTGTAACA
Found at i:9520 original size:20 final size:21
Alignment explanation
Indices: 9495--9551 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
9485 TCAAAAACCC
9495 AAATGTATCGATACAA-TGAA
1 AAATGTATCGATACAACTGAA
*
9515 AAATGTATCGATACAACTTAA
1 AAATGTATCGATACAACTGAA
*
9536 AGCATGTATCGATACA
1 A-AATGTATCGATACA
9552 TTTCCTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 16 0.48
21 4 0.12
22 13 0.39
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (21 bp):
AAATGTATCGATACAACTGAA
Found at i:10655 original size:21 final size:20
Alignment explanation
Indices: 10631--10673 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
10621 ATATAAAATA
*
10631 ATTTAATTAATAAATAAATTT
1 ATTTAATAAATAAAT-AATTT
* *
10652 ATTTGATAAATTAATAATTT
1 ATTTAATAAATAAATAATTT
10672 AT
1 AT
10674 AAATTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTAATAAATAAATAATTT
Found at i:11510 original size:17 final size:17
Alignment explanation
Indices: 11490--11527 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
11480 TATAATTTAA
*
11490 TTTATATATTA-AAATAT
1 TTTATAT-TTATAAAAAT
11507 TTTATATTTATAAAAAT
1 TTTATATTTATAAAAAT
11524 TTTA
1 TTTA
11528 ATAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATATTTATAAAAAT
Found at i:11833 original size:14 final size:14
Alignment explanation
Indices: 11790--11833 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
11780 TAAATTTTAA
11790 ATATATATTATATTT
1 ATATATATT-TATTT
*
11805 -TATTTATTTTATTT
1 ATATATA-TTTATTT
11819 ATATATATTTATTT
1 ATATATATTTATTT
11833 A
1 A
11834 ATTATGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATATATTTATTT
Found at i:11843 original size:24 final size:22
Alignment explanation
Indices: 11798--11843 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
11788 AAATATATAT
*
11798 TATATTTTATTTATTTTATTTA
1 TATATTTTATTTATTATATTTA
*
11820 TATATATTTATTTAATTATGTTTA
1 TATAT-TTTATTT-ATTATATTTA
11844 GCGTAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATATTTTATTTATTATATTTA
Found at i:12173 original size:22 final size:21
Alignment explanation
Indices: 12146--12198 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
12136 TTATATTTCG
*
12146 TTTAAAATTA-AAGTAATTAT
1 TTTAAAATTATAAATAATTAT
12166 TTAATAAAATTATTAAATAATTAT
1 TT--TAAAATTA-TAAATAATTAT
12190 TTTAAAATT
1 TTTAAAATT
12199 TGTATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.07
22 15 0.54
24 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTAAAATTATAAATAATTAT
Found at i:12206 original size:24 final size:24
Alignment explanation
Indices: 12152--12198 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
12142 TTCGTTTAAA
12152 ATTAAAGTAATTATTTAATAAAATT
1 ATTAAAGTAATTATTT-ATAAAATT
12177 ATTAAA-TAATTATTT-TAAAATT
1 ATTAAAGTAATTATTTATAAAATT
12199 TGTATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
24 9 0.41
25 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTAAAGTAATTATTTATAAAATT
Found at i:12554 original size:24 final size:24
Alignment explanation
Indices: 12504--12550 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
12494 ATTATCATAA
12504 TTAATATTTTTATTAAATTTTAAAT
1 TTAATATTTTTATT-AATTTTAAAT
12529 TTAA-ATTTTTATT-ATTTTAAAT
1 TTAATATTTTTATTAATTTTAAAT
12551 ATTTTAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
24 9 0.41
25 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATATTTTTATTAATTTTAAAT
Found at i:13306 original size:2 final size:2
Alignment explanation
Indices: 13299--13333 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
13289 GTAATTTAAC
*
13299 TA TA TA TA TA TA TA TA TA TA TA CA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
13334 CACACAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:13819 original size:21 final size:21
Alignment explanation
Indices: 13794--13838 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
13784 TATTTTTATT
* *
13794 TAAAT-TTTATATTAAAATATA
1 TAAATATTAATATAAAAATA-A
13815 TAAATATTAATATAAAAATAA
1 TAAATATTAATATAAAAATAA
13836 TAA
1 TAA
13839 TTTAGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAAATAA
Found at i:17590 original size:32 final size:32
Alignment explanation
Indices: 17539--17619 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 32
17529 ATATGGTTAA
17539 AAATAATTAAAATATAAAATTTATAT-AATAT
1 AAATAATTAAAATATAAAATTTATATAAATAT
* *
17570 AAATTATTAATATATTAAAATTTATATAAATAT
1 AAATAATTAAAATA-TAAAATTTATATAAATAT
* *
17603 AAATATTTTAAATATAA
1 AAATAATTAAAATATAA
17620 TTATAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 12 0.29
32 15 0.36
33 15 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATAATTAAAATATAAAATTTATATAAATAT
Found at i:17602 original size:18 final size:17
Alignment explanation
Indices: 17548--17610 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 17
17538 AAAATAATTA
17548 AAATATAAAATTTATAT
1 AAATATAAAATTTATAT
17565 -AATAT-AAA-TTAT-T
1 AAATATAAAATTTATAT
17578 AATATATTAAAATTTATAT
1 AA-ATA-TAAAATTTATAT
17597 AAATATAAATATTT
1 AAATATAAA-ATTT
17611 TAAATATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.13
15 6 0.15
16 6 0.15
17 7 0.18
18 11 0.28
19 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATAAAATTTATAT
Found at i:17647 original size:17 final size:16
Alignment explanation
Indices: 17546--17646 Score: 68
Period size: 16 Copynumber: 6.4 Consensus size: 16
17536 TAAAAATAAT
*
17546 TAAAATATAAAATTTA
1 TAAAATATAAAATATA
* *
17562 TATAATATAAATTAT-
1 TAAAATATAAAATATA
* *
17577 TAATATATTAAAATTTA
1 TAAAATA-TAAAATATA
*
17594 TATAAATAT-AAATATT
1 TA-AAATATAAAATATA
*
17610 TTAAATAT--AAT-TA
1 TAAAATATAAAATATA
*
17623 TAATATAATAAAATATA
1 TAAAAT-ATAAAATATA
17640 TAAAATA
1 TAAAATA
17647 AAATAGATAC
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
13 5 0.08
14 5 0.08
15 11 0.17
16 28 0.44
17 10 0.16
18 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATAAAATATA
Found at i:17651 original size:44 final size:49
Alignment explanation
Indices: 17538--17651 Score: 143
Period size: 46 Copynumber: 2.4 Consensus size: 49
17528 AATATGGTTA
*
17538 AAAATA-ATTAAAATATAAA-ATTTATATAATATAAATTATTAATATATT
1 AAAATATA-TAAAATATAAATATTTATATAATATAAATTATTAATATAAT
*
17586 AAAATTTATATAAATATAAATATTT-TA-AATAT-AATTA-TAATATAAT
1 AAAATATATA-AAATATAAATATTTATATAATATAAATTATTAATATAAT
17632 AAAATATATAAAATA-AAATA
1 AAAATATATAAAATATAAATA
17652 GATACATAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
44 5 0.08
45 5 0.08
46 17 0.28
47 5 0.08
48 12 0.20
49 12 0.20
50 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (49 bp):
AAAATATATAAAATATAAATATTTATATAATATAAATTATTAATATAAT
Found at i:17831 original size:23 final size:24
Alignment explanation
Indices: 17797--17842 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17787 AATTAAAAAA
17797 ATATATCA-TTTTATTTAATTATG
1 ATATATCATTTTTATTTAATTATG
*
17820 ATATAT-ATTTTTTATTTATTTAT
1 ATATATCA-TTTTTATTTAATTAT
17843 TATTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 6 0.30
24 13 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
ATATATCATTTTTATTTAATTATG
Found at i:22349 original size:11 final size:10
Alignment explanation
Indices: 22333--22392 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
22323 TTAAAATTTT
22333 AATATAAATAA
1 AATAT-AATAA
*
22344 AATATATTATA
1 AATATAATA-A
* *
22355 AATATGATTAT
1 AATAT-AATAA
22366 AATATAATAA
1 AATATAATAA
22376 AATAT-ATAA
1 AATATAATAA
22385 AA-ATAATA
1 AATATAATA
22393 TGAATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 2 0.05
9 9 0.21
10 11 0.26
11 16 0.38
12 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AATATAATAA
Found at i:22398 original size:29 final size:29
Alignment explanation
Indices: 22302--22404 Score: 78
Period size: 32 Copynumber: 3.7 Consensus size: 29
22292 TAAAATTTAT
*
22302 ATAATATGAAT-TATTAAAATAT-T-AAA
1 ATAATATGAATATAATAAAATATATAAAA
*
22328 AT--T-TTAATATAAATAAAATATATTATAAA
1 ATAATATGAATAT-AATAAAATATA-TA-AAA
*
22357 TATGATTAT-AATATAATAAAATATATAAAA
1 -AT-AATATGAATATAATAAAATATATAAAA
22387 ATAATATGAATAT-ATAAA
1 ATAATATGAATATAATAAA
22405 TTTGTAATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 22
0.71 0.03 0.25
Matches are distributed among these distances:
23 4 0.06
24 2 0.03
25 9 0.15
26 2 0.03
27 1 0.02
28 9 0.15
29 10 0.16
30 5 0.08
31 2 0.03
32 11 0.18
33 6 0.10
34 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
ATAATATGAATATAATAAAATATATAAAA
Found at i:22921 original size:33 final size:33
Alignment explanation
Indices: 22854--22920 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
22844 TGATGATACT
*
22854 AATAAACCTCAATGATTTTATCTCCAAAATAAA
1 AATAAACCTCAATGATCTTATCTCCAAAATAAA
*
22887 AATAAACCTCAA-GGTCTTATC-CCAAAAATAAA
1 AATAAACCTCAATGATCTTATCTCC-AAAATAAA
22919 AA
1 AA
22921 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 2 0.06
32 17 0.55
33 12 0.39
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.25
Consensus pattern (33 bp):
AATAAACCTCAATGATCTTATCTCCAAAATAAA
Found at i:23056 original size:6 final size:6
Alignment explanation
Indices: 23045--23071 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23035 ATATTTTATA
23045 TAAATT TAAATT TAAATT TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAA
23072 TTAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:23457 original size:11 final size:11
Alignment explanation
Indices: 23421--23498 Score: 57
Period size: 13 Copynumber: 6.3 Consensus size: 11
23411 TTATGGTTAG
23421 ATAATAAAAAT
1 ATAATAAAAAT
23432 ATAATGTAAAAAT
1 ATAA--TAAAAAT
*
23445 AATAAAAATATAAT
1 -ATAATAA-A-AAT
*
23459 ATAATATAAAT
1 ATAATAAAAAT
23470 ATTAATATAAAAT
1 A-TAATA-AAAAT
23483 ATAATATAAAAAT
1 AT-A-ATAAAAAT
23496 ATA
1 ATA
23499 TATGTATTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
11 8 0.15
12 10 0.19
13 26 0.48
14 10 0.19
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:23470 original size:22 final size:22
Alignment explanation
Indices: 23423--23498 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
23413 ATGGTTAGAT
* *
23423 AATAAAAATATAATGTAA-AAA
1 AATAAAAATATAATATAATATA
23444 TAATAAAAATATAATATAATATA
1 -AATAAAAATATAATATAATATA
**
23467 AATATTAATAT-A-A-AATATA
1 AATAAAAATATAATATAATATA
23486 ATATAAAAATATA
1 A-ATAAAAATATA
23499 TATGTATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 7 0.16
20 9 0.20
21 1 0.02
22 26 0.58
23 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
AATAAAAATATAATATAATATA
Found at i:23477 original size:12 final size:12
Alignment explanation
Indices: 23451--23492 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
23441 AAATAATAAA
23451 AATAT-AATA-T
1 AATATAAATATT
23461 AATATAAATATT
1 AATATAAATATT
23473 AATATAAA-ATAT
1 AATATAAATAT-T
23485 AATATAAA
1 AATATAAA
23493 AATATATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.17
11 6 0.21
12 18 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATATAAATATT
Found at i:23501 original size:24 final size:24
Alignment explanation
Indices: 23427--23501 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 24
23417 TTAGATAATA
*
23427 AAAATATAATGTAAAAATA-ATA-
1 AAAATATAATATAAAAATATATAT
23449 AAAATATAATATAATATAAATATTAATAT
1 AAAATATAATAT-A-A-AAATA-T-ATAT
23478 AAAATATAATATAAAAATATATAT
1 AAAATATAATATAAAAATATATAT
23502 GTATTAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
22 11 0.24
23 1 0.02
24 5 0.11
25 6 0.13
26 5 0.11
27 1 0.02
28 4 0.09
29 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (24 bp):
AAAATATAATATAAAAATATATAT
Found at i:23511 original size:29 final size:30
Alignment explanation
Indices: 23444--23501 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
23434 AATGTAAAAA
*
23444 TAATA-AAAATATAATAT-AATATAAATAT
1 TAATATAAAATATAATATAAAAATAAATAT
*
23472 TAATATAAAATATAATATAAAAATATATAT
1 TAATATAAAATATAATATAAAAATAAATAT
23502 GTATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 12 0.46
30 9 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
TAATATAAAATATAATATAAAAATAAATAT
Found at i:24117 original size:22 final size:21
Alignment explanation
Indices: 24092--24133 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
24082 ATTTTAAAAA
24092 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
24112 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
24133 A
1 A
24134 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:24927 original size:20 final size:19
Alignment explanation
Indices: 24904--24957 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
24894 GTATAAAAAA
*
24904 TAATTTTTATCAATTTAAT
1 TAATTTTTATCAATTAAAT
**
24923 CTAATATTTTATTTATTAAAT
1 -TAAT-TTTTATCAATTAAAT
24944 TAATTTTTTATCAA
1 TAA-TTTTTATCAA
24958 CTCACAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTTTTATCAATTAAAT
Found at i:25162 original size:22 final size:22
Alignment explanation
Indices: 25122--25169 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
25112 AAAGATGAAT
*
25122 ATTTTTTAAATATAATTATTAA
1 ATTTTTTAAATATAATTATAAA
* * *
25144 ATTTTTTAATTTTATTTATAAA
1 ATTTTTTAAATATAATTATAAA
25166 ATTT
1 ATTT
25170 ATAAAACTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTTTAAATATAATTATAAA
Found at i:25470 original size:20 final size:21
Alignment explanation
Indices: 25429--25471 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
25419 CCGATAAGAT
*
25429 TTTAAATATATATTTTATTAA
1 TTTAAATATATATTTTAATAA
*
25450 TTTAAATTTATA-TTTAATAA
1 TTTAAATATATATTTTAATAA
25470 TT
1 TT
25472 AAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAAATATATATTTTAATAA
Found at i:27664 original size:19 final size:17
Alignment explanation
Indices: 27622--27674 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 17
27612 TACTATTTAA
27622 ATATATTAAAATATTATTT
1 ATATATT-AAAT-TTATTT
*
27641 TTATATTAATATTTATATT
1 ATATATTAA-ATTTAT-TT
27660 ATATAATTAAATTTA
1 ATAT-ATTAAATTTA
27675 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 18 0.62
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTAAATTTATTT
Found at i:27961 original size:15 final size:14
Alignment explanation
Indices: 27936--27965 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
27926 AATTAATTTT
27936 AATTAAAAAATAAA
1 AATTAAAAAATAAA
27950 AATTATAAAAATAAA
1 AATTA-AAAAATAAA
27965 A
1 A
27966 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATTAAAAAATAAA
Found at i:29869 original size:16 final size:16
Alignment explanation
Indices: 29844--29895 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 16
29834 TTTTAAGTCT
*
29844 TATATATTATTAAAAA
1 TATATTTTATTAAAAA
29860 TATATTTTATTAAAAATCA
1 TATATTTTATT-AAAA--A
29879 TATATTTTTATTAAAAA
1 TATA-TTTTATTAAAAA
29896 ATTATAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
19 9 0.29
20 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATTTTATTAAAAA
Found at i:29895 original size:21 final size:21
Alignment explanation
Indices: 29859--29919 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
29849 ATTATTAAAA
29859 ATATA-TTTTATT-AAAAATC
1 ATATATTTTTATTAAAAAATC
*
29878 ATATATTTTTATTAAAAAATT
1 ATATATTTTTATTAAAAAATC
29899 ATA-ACTTATTTGATTAAAAAA
1 ATATA-TT-TTT-ATTAAAAAA
29920 ATTATAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 5 0.14
20 8 0.22
21 11 0.31
22 3 0.08
23 9 0.25
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATATTTTTATTAAAAAATC
Found at i:29901 original size:19 final size:18
Alignment explanation
Indices: 29850--29901 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 18
29840 GTCTTATATA
29850 TTATTAAAAA-TATA-TT
1 TTATTAAAAATTATATTT
29866 TTATTAAAAATCATATATTT
1 TTATTAAAAAT--TATATTT
29886 TTATTAAAAAATTATA
1 TTATT-AAAAATTATA
29902 ACTTATTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 10 0.32
19 8 0.26
20 7 0.23
21 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTAAAAATTATATTT
Done.