Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold512
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: 165704
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:412 original size:22 final size:22
Alignment explanation
Indices: 384--427 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
374 GGAAGGAAAA
384 TAAAGAAGAGGAGAATTGAGAG
1 TAAAGAAGAGGAGAATTGAGAG
406 TAAAGAAGAGGAGAATTGAGAG
1 TAAAGAAGAGGAGAATTGAGAG
428 AGAGAACCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (22 bp):
TAAAGAAGAGGAGAATTGAGAG
Found at i:5075 original size:26 final size:26
Alignment explanation
Indices: 5039--5089 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
5029 CTAGGTTTAT
5039 TAATTATTACTTTATTATAACAAGTC
1 TAATTATTACTTTATTATAACAAGTC
5065 TAATTATTACTTTATTATAACAAGT
1 TAATTATTACTTTATTATAACAAGT
5090 TCAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (26 bp):
TAATTATTACTTTATTATAACAAGTC
Found at i:10788 original size:2 final size:2
Alignment explanation
Indices: 10745--10776 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10735 CAGTACGTGA
10745 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
10777 GTTGGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11368 original size:27 final size:30
Alignment explanation
Indices: 11289--11374 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 30
11279 TTATATTTAT
* * *
11289 ATTAAAAAATTATTTAAATATAAA-CAAAA
1 ATTAAAAATTTATTTTAATATAAATTAAAA
11318 ATTAAAAATTTATTTTAATATAAATTAAAA
1 ATTAAAAATTTATTTTAATATAAATTAAAA
* *
11348 ATT-AAAA-TT-TTTTAGTGTAAATTAAAA
1 ATTAAAAATTTATTTTAATATAAATTAAAA
11375 TTATTAACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 16 0.31
28 2 0.04
29 26 0.51
30 7 0.14
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (30 bp):
ATTAAAAATTTATTTTAATATAAATTAAAA
Found at i:11533 original size:29 final size:29
Alignment explanation
Indices: 11481--11537 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
11471 AGAAGCACAA
*
11481 AAAATAAATTTTCTTAATTAATAAAAAGC
1 AAAATAAATTTTCTAAATTAATAAAAAGC
*
11510 AAAATAAATTTTC-AAATTTTATAAAAAG
1 AAAATAAATTTTCTAAA-TTAATAAAAAG
11538 AATTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATAAATTTTCTAAATTAATAAAAAGC
Found at i:13090 original size:19 final size:18
Alignment explanation
Indices: 13051--13096 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
13041 TAAGTACAAC
*
13051 AAAAAAAAAATAAATTCT
1 AAAAAATAAATAAATTCT
*
13069 AAAAAATAAATAATATTTT
1 AAAAAATAAATAA-ATTCT
*
13088 AAATAATAA
1 AAAAAATAA
13097 CGAAATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATAAATAAATTCT
Found at i:18341 original size:243 final size:232
Alignment explanation
Indices: 17891--18363 Score: 624
Period size: 243 Copynumber: 2.0 Consensus size: 232
17881 CAAAAATCGA
*
17891 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCATAACACATTACA
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAGAACACATTACA
* *
17956 AAAAAGAAACCTTCCAAAACTAAAATAGAAAAGAAATCCAGAACACCAAGGCCAATCCAGCACCT
66 AAAAAGAAACCTTCCAAAACTAAAATAAAAAAAAAATCCAGAACACCAAGGCCAATCCAGCACCT
* * *
18021 GGCTTAATTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTCAGAAACGGACAAATCATTCA
131 GGCGTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCAGAAACGGACAAATCATTCA
18086 AAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
196 AAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* *
18123 TTGCTTCATTGTCTTCCACTTGGCCTATCTACCAAACTACAGGAAGACAAGAAGGCAAGCAGAAT
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACT--------ACAAGAAGGCAAGCAGAAC
* * ** * *
18188 ACATTATAAAAAGGAAACCTTTTAAAATTAAAATTAAAAAAAAAAAATCTAGAACACCAAGGCCA
58 ACATTACAAAAAAGAAACCTTCCAAAACTAAAA-T--AAAAAAAAAATCCAGAACACCAAGGCC-
* * * ** *
18253 AATCCATCACCTTGCGTAGTTACCCTAAATCAATTGGGTTCAT-AAAAGAACAGCTTGGAAATGG
119 AATCCAGCACCTGGCGTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCAGAAACGG
* * *
18317 ACATATCATTCAAAAAACCTCTTTCACCAGTTTCCTTTCTAGAACTG
184 ACAAATCATTCAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTG
18364 CTTCTCAATG
Statistics
Matches: 206, Mismatches: 23, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
232 37 0.18
240 45 0.22
241 1 0.00
243 85 0.41
244 38 0.18
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (232 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATCTAACAAACTACAAGAAGGCAAGCAGAACACATTACA
AAAAAGAAACCTTCCAAAACTAAAATAAAAAAAAAATCCAGAACACCAAGGCCAATCCAGCACCT
GGCGTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCAGAAACGGACAAATCATTCA
AAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
Found at i:32017 original size:2 final size:2
Alignment explanation
Indices: 32010--32052 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
32000 AGCAGTACGT
32010 AG AG AG 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 AG AG AG
32052 A
1 A
32053 ATCTGACCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32268 original size:25 final size:25
Alignment explanation
Indices: 32235--32293 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
32225 CATTTTATTC
* *
32235 AAATATATTTTTATATTTAAATAAA
1 AAATATATTTTTAAATATAAATAAA
*
32260 AAAT-T-TATTTAAATATAAATAAA
1 AAATATATTTTTAAATATAAATAAA
32283 AAATATATTTT
1 AAATATATTTT
32294 AATAGAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 19 0.68
24 2 0.07
25 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATATTTTTAAATATAAATAAA
Found at i:32308 original size:24 final size:23
Alignment explanation
Indices: 32253--32301 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
32243 TTTTATATTT
* *
32253 AAATAAAAAATTTATTTAAATAT
1 AAATAAAAAATATATTTAAATAG
*
32276 AAATAAAAAATATATTTTAATAG
1 AAATAAAAAATATATTTAAATAG
32299 AAA
1 AAA
32302 CTCAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATAAAAAATATATTTAAATAG
Found at i:32764 original size:24 final size:25
Alignment explanation
Indices: 32693--32765 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 25
32683 TATTACATAG
*
32693 TTTTAATACATATATGTATTTT-TTA
1 TTTTAATACATATAT-TATTTTATAA
* *
32718 TTTTAATATATTATACTTCTTTTATAA
1 TTTTAATACA-TATA-TTATTTTATAA
32745 TTTTAATACATA-ATTATTTTA
1 TTTTAATACATATATTATTTTA
32766 ATTGCAGTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.17
25 10 0.25
26 11 0.28
27 12 0.30
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTTAATACATATATTATTTTATAA
Found at i:33512 original size:2 final size:2
Alignment explanation
Indices: 33505--33530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33495 GAACACAAAA
33505 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
33531 GCTTGTCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:36092 original size:45 final size:45
Alignment explanation
Indices: 36028--36128 Score: 193
Period size: 45 Copynumber: 2.2 Consensus size: 45
36018 GTAAAGAAGA
*
36028 AACAAAGCCAATCAGAGCCAAGTGAAGCACGACTCAGAGACACAC
1 AACAAAGCCTATCAGAGCCAAGTGAAGCACGACTCAGAGACACAC
36073 AACAAAGCCTATCAGAGCCAAGTGAAGCACGACTCAGAGACACAC
1 AACAAAGCCTATCAGAGCCAAGTGAAGCACGACTCAGAGACACAC
36118 AACAAAGCCTA
1 AACAAAGCCTA
36129 GTAAAGCAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.08
Consensus pattern (45 bp):
AACAAAGCCTATCAGAGCCAAGTGAAGCACGACTCAGAGACACAC
Found at i:36365 original size:14 final size:15
Alignment explanation
Indices: 36336--36369 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
36326 AGTGCCTTGC
*
36336 CTTTTCTTTTTTCTT
1 CTTTTCTTTTTCCTT
36351 CTTTT-TTTTTCCTT
1 CTTTTCTTTTTCCTT
36365 CTTTT
1 CTTTT
36370 AAAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTCTTTTTCCTT
Found at i:36603 original size:26 final size:26
Alignment explanation
Indices: 36567--36616 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
36557 TAGGGTTTAT
36567 TAATTATTACTTTATTATAACAAGCC
1 TAATTATTACTTTATTATAACAAGCC
36593 TAATTATTACTTTATTATAACAAG
1 TAATTATTACTTTATTATAACAAG
36617 TTCAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (26 bp):
TAATTATTACTTTATTATAACAAGCC
Found at i:42266 original size:2 final size:2
Alignment explanation
Indices: 42221--42252 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42211 CAGTACGTAA
42221 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
42253 GGGTTGGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43017 original size:20 final size:20
Alignment explanation
Indices: 42992--43034 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
42982 ATAAAACAAT
*
42992 ATATTTACTCAACAATTATA
1 ATATTTACTCAAAAATTATA
43012 ATATTTACTCAAAAATTATA
1 ATATTTACTCAAAAATTATA
43032 ATA
1 ATA
43035 AATATGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTTACTCAAAAATTATA
Found at i:43405 original size:24 final size:25
Alignment explanation
Indices: 43372--43419 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
43362 TTATAAGAGA
43372 ATGATAAATTATAAACTTTTATTTT
1 ATGATAAATTATAAACTTTTATTTT
* *
43397 ATGA-AAATTTTAAATTTTTATTT
1 ATGATAAATTATAAACTTTTATTT
43420 AAAAACACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
ATGATAAATTATAAACTTTTATTTT
Found at i:44486 original size:30 final size:30
Alignment explanation
Indices: 44450--44513 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
44440 GCAATAGAGC
*
44450 GTGTGATGAGTCAAACACAAGAAAAGAACA
1 GTGTGATGAGTCAAACACAAAAAAAGAACA
*
44480 GTGTGATGAGTCAAACAGAAAAAAAGAACA
1 GTGTGATGAGTCAAACACAAAAAAAGAACA
44510 GTGT
1 GTGT
44514 TCCAACCACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.11, G:0.25, T:0.16
Consensus pattern (30 bp):
GTGTGATGAGTCAAACACAAAAAAAGAACA
Found at i:45326 original size:102 final size:102
Alignment explanation
Indices: 45150--45337 Score: 270
Period size: 102 Copynumber: 1.8 Consensus size: 102
45140 GATGAATATG
* *
45150 CTGCAACCAGACATATTTGAGACACTAGTCATTATCTTACAGGACAAAGAATAAGTTAAGACACC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGACAAAGAATAAGATAAGACACC
**
45215 GGTAGACTATTTTAAACAAAAAATCTAAAAAACTATC
66 AATAGACTATTTTAAACAAAAAATCTAAAAAACTATC
* * **
45252 CTGCAACCAAACATATTTGAGACACTAGTCATTATTTTACAGGA-AATGGAATAAGATAAGATGC
1 CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGACAA-AGAATAAGATAAGACAC
* *
45316 CAATATACTATTTTAACCAAAA
65 CAATAGACTATTTTAAACAAAA
45338 TATACTAACA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
101 2 0.03
102 73 0.97
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (102 bp):
CTGCAACCAAACATATTTGAGACACTAGTCATTATCTTACAGGACAAAGAATAAGATAAGACACC
AATAGACTATTTTAAACAAAAAATCTAAAAAACTATC
Found at i:47085 original size:2 final size:2
Alignment explanation
Indices: 47080--47116 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47070 CACACATACA
47080 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
47117 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:50540 original size:600 final size:594
Alignment explanation
Indices: 49347--50545 Score: 1803
Period size: 600 Copynumber: 2.0 Consensus size: 594
49337 CAAATAATGG
* *
49347 TTTTGGTCCATTTACTACGTAAACACTACTGCTGAAATCATCCTGCAAGGTCACTGATAGAAGTC
1 TTTTGGTCCATTTACTACGTAAACACTACTGCTGAAATCATCCTGCAAGGCCACTAATAGAAGTC
49412 AATGCTGAAATAAAAAAAGACCCATATAAACTATAAAGTACTCGACATAATAAATGATCAAAGGA
66 AATGCTGAAATAAAAAAAGACCCATATAAACTATAAAGTACTCGACATAATAAATGATCAAAGGA
*
49477 ACCCAAGGCATGGAATTAATCAGCAAAATCTAAGTGCAAAACAAACTAGCATACTATTATAATCT
131 ACCCAAGGCATAGAATTAATCAGCAAAATCTAAGTGCAAAACAAACTAGCATACTATTATAATCT
*
49542 TTCCACAGGGAAAACCACATTTAAAAACAGAATTAAAAAAAAAAATCATAATCCCGGTTAAAACG
196 TTCCACAAGGAAAACCACATTTAAAAACAGAATT-AAAAAAAAAATCATAATCCCGGTTAAAACG
* * *
49607 GATTGAAGAAAACTACATTGCGTAAATAATTCTTCCCCAACCCTCCCGAAAAAAAAAAGCACAAA
260 GACTGAAGAAAACTACACTGCATAAATAATTCTTCCCCAACCCTCCCGAAAAAAAAAAGCACAAA
* *
49672 CACATTGAGCGACACTGAATAGTCAAAACAACACAAGTCAAAAAAAAAAAAAACATATGTTGTGC
325 CACATTGACCGACACAGAATAGTCAAAACAACACAAGTCAAAAAAAAAAAAAACATATGTTGTGC
*
49737 TTATATAAATGAATGACACAGGTACCTCACTAGAATCAAAGATTAGATCACTCCCCAGGAGGTAG
390 TTATATAAATGAATGACACAGGTACCTCACTAGAATCAAAGATAAGATCACTCCCCAGGAGGTAG
* *
49802 CACTGCAGCTTGCGCCCATGCAGCTAAAAAACAAACAAGGGGCCCTACCGAGACAATTCCATAAA
455 CACTGCAGCTTGCACCCACGCAGCTAAAAAACAAACAAGGGGCCCTACCGAGACAATTCCATAAA
*
49867 TAAGGAAATATGGAAATATGATCAGCACGTGCAAGTAACAAGAGCTAAAATGTTTAGATAACATA
520 TAAGGAAATATGGAAAGATGATCAGCACGTGCAAGTAACAAGAGCTAAAATGTTTAGATAACATA
49932 ACCTTCAAAA
585 ACCTTCAAAA
** * *
49942 TTTTGGTCCATTTACTGTGTAAACAGTACTGCTGACATCATCCTGCAAGGCCACTAATAGAAGTC
1 TTTTGGTCCATTTACTACGTAAACACTACTGCTGAAATCATCCTGCAAGGCCACTAATAGAAGTC
* *
50007 AATGTTGAAATAAAAAAAAGACCCATATAAACTATAAAGTACTCGATATAATAAATGATCAAA-G
66 AATGCTGAAAT-AAAAAAAGACCCATATAAACTATAAAGTACTCGACATAATAAATGATCAAAGG
* * *
50071 TACCCAAGGCATAGAATTAATCTGCAAAATCTAAGTGCAAAACAAACTAGCATACTATTGTAATC
130 AACCCAAGGCATAGAATTAATCAGCAAAATCTAAGTGCAAAACAAACTAGCATACTATTATAATC
* * *
50136 TTTCCACAAGGTAAACCACATTTAAAAACAGAATT-AAAAAAAAATTATAATCCCGTTTAAAACG
195 TTTCCACAAGGAAAACCACATTTAAAAACAGAATTAAAAAAAAAATCATAATCCCGGTTAAAACG
** * ** * *** *
50200 GACTGTTGAAATCTATGCTGCATAAATAATTCTTCCCCCCACCC-CCCGCCCAAAAAAAGCCCAA
260 GACTGAAGAAAACTACACTGCATAAATAATTCTT-CCCCAACCCTCCCGAAAAAAAAAAGCACAA
****
50264 ACACATTGACCGACACAGAATAGTCAAAACAACACAAGTTTTTTTTTTTTAAAAAAAAAAACATA
324 ACACATTGACCGACACAGAATAGTCAAAACAACACAAG-------TCAAAAAAAAAAAAAACATA
* * *
50329 TGTTGTGCTTATATAATTGAATGACACAGGTACCTCCCTAGAATCAAAGATAAGATCATTCCCCA
382 TGTTGTGCTTATATAAATGAATGACACAGGTACCTCACTAGAATCAAAGATAAGATCACTCCCCA
* * * *
50394 GTAGGTAGCACTGCAGCTTGCACCCACGTAGCTAAAAAACAAACAAGGGGCTCT-CTGGAGACAA
447 GGAGGTAGCACTGCAGCTTGCACCCACGCAGCTAAAAAACAAACAAGGGGCCCTAC-CGAGACAA
* * * *
50458 TTCCATAAATAAGGAAATATGGAAAGATGATCAGCATGTGTAAGTAGCAAGAGGTAAAATGTTTA
511 TTCCATAAATAAGGAAATATGGAAAGATGATCAGCACGTGCAAGTAACAAGAGCTAAAATGTTTA
* *
50523 GATAACATAATCTTCAAAT
576 GATAACATAACCTTCAAAA
50542 TTTT
1 TTTT
50546 TTTAGCAAAA
Statistics
Matches: 542, Mismatches: 52, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
593 105 0.19
594 8 0.01
595 164 0.30
596 50 0.09
599 1 0.00
600 214 0.39
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (594 bp):
TTTTGGTCCATTTACTACGTAAACACTACTGCTGAAATCATCCTGCAAGGCCACTAATAGAAGTC
AATGCTGAAATAAAAAAAGACCCATATAAACTATAAAGTACTCGACATAATAAATGATCAAAGGA
ACCCAAGGCATAGAATTAATCAGCAAAATCTAAGTGCAAAACAAACTAGCATACTATTATAATCT
TTCCACAAGGAAAACCACATTTAAAAACAGAATTAAAAAAAAAATCATAATCCCGGTTAAAACGG
ACTGAAGAAAACTACACTGCATAAATAATTCTTCCCCAACCCTCCCGAAAAAAAAAAGCACAAAC
ACATTGACCGACACAGAATAGTCAAAACAACACAAGTCAAAAAAAAAAAAAACATATGTTGTGCT
TATATAAATGAATGACACAGGTACCTCACTAGAATCAAAGATAAGATCACTCCCCAGGAGGTAGC
ACTGCAGCTTGCACCCACGCAGCTAAAAAACAAACAAGGGGCCCTACCGAGACAATTCCATAAAT
AAGGAAATATGGAAAGATGATCAGCACGTGCAAGTAACAAGAGCTAAAATGTTTAGATAACATAA
CCTTCAAAA
Found at i:52641 original size:20 final size:20
Alignment explanation
Indices: 52584--52643 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
52574 TGAAATAAGT
* *
52584 TAAGAAAAATATGGTAATACA
1 TAAGAAAAA-ATGGTAAAATA
* ** *
52605 TAATAAATTATGTTAAAATA
1 TAAGAAAAAATGGTAAAATA
52625 TAAGAAAAAATGGTAAAAT
1 TAAGAAAAAATGGTAAAAT
52644 GTGTAAAAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.28
Consensus pattern (20 bp):
TAAGAAAAAATGGTAAAATA
Found at i:56115 original size:30 final size:29
Alignment explanation
Indices: 56081--56138 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
56071 TAAAAAATTA
*
56081 AATAAATAATAATATATTATATT-ATTTTAT
1 AATAAAAAATAATAT-TTA-ATTAATTTTAT
56111 AATAAAAAATAATATTTAATTAATTTTA
1 AATAAAAAATAATATTTAATTAATTTTA
56139 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 9 0.35
30 14 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAAAAAATAATATTTAATTAATTTTAT
Found at i:56374 original size:23 final size:23
Alignment explanation
Indices: 56348--56402 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
56338 TTAATTAAAT
*
56348 TTAAAAAAAT-TTACATTAACAAA
1 TTAAAAAAATAATA-ATTAACAAA
* *
56371 TTAAAAAAATAATATTTAACGAA
1 TTAAAAAAATAATAATTAACAAA
56394 TTAAAAAAA
1 TTAAAAAAA
56403 CTATCATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (23 bp):
TTAAAAAAATAATAATTAACAAA
Found at i:56900 original size:22 final size:21
Alignment explanation
Indices: 56875--56935 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 21
56865 AATAATTAAA
56875 TTTTAATTTATTAATATAATT-T
1 TTTTAATTTATTAA-AT-ATTAT
*
56897 TTTTAAATTTAATCAAATATTAT
1 TTTT-AATTT-ATTAAATATTAT
56920 TTTTAATTTTATTAAA
1 TTTTAA-TTTATTAAA
56936 AATAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 14 0.42
23 15 0.45
24 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAATTTATTAAATATTAT
Found at i:56952 original size:124 final size:123
Alignment explanation
Indices: 56698--57062 Score: 418
Period size: 124 Copynumber: 3.0 Consensus size: 123
56688 AAATATTATT
* * *
56698 ATAATAAAAAACTTTTTTAATTTAAAATTTTTTA-TTTT-TAAAAACATAATAATTAATATTTTA
1 ATAATAAAAAACCTTTTTATTTTAAAATTTTTTATTTTTATAAAAATATAATAATTAA-ATTTTA
* * * *
56761 ATTTGTTAATGTAA--ATTTTAAACTGAATTAAATA-T-TTTTTATTTTATTAAAAATT
65 ATTTGTTAATATAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATA
56816 ATAATAAAAAACCTTTTTATTTTAAAATTTTTTATTTTTATAAAAATATAATAATTAAATTTTAA
1 ATAATAAAAAACCTTTTTATTTTAAAATTTTTTATTTTTATAAAAATATAATAATTAAATTTTAA
* * *
56881 TTTATTAATATAATTTTTTTAAATTTAATCAAATATTATTTTTAATTTTATTAAAAATA
66 TTTGTTAATATAATTTTTTTAAACTTAATTAAATATTATTTTT-ATTTTATTAAAAATA
* * * *
56940 ATAATAATAAACCTTTTTATTTTTATTTAAAATCTTTTATTATTA-AAAAATA-ATTAA-T--AT
1 ATAATAAAAAACCTTTTTA----T-TTTAAAATTTTTTATTTTTATAAAAATATAATAATTAAAT
* *
57000 TTGAATTTGTTAATATAATTTTTTTAAAGTTAATTAAATATTA---TT-TTTTATTAAAAATA
61 TTTAATTTGTTAATATAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATA
57059 ATAA
1 ATAA
57063 ATAATACATT
Statistics
Matches: 217, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
118 32 0.15
119 40 0.18
120 17 0.08
121 18 0.08
122 1 0.00
123 5 0.02
124 73 0.34
126 1 0.00
127 4 0.02
128 8 0.04
129 18 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (123 bp):
ATAATAAAAAACCTTTTTATTTTAAAATTTTTTATTTTTATAAAAATATAATAATTAAATTTTAA
TTTGTTAATATAATTTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAATA
Found at i:57794 original size:88 final size:88
Alignment explanation
Indices: 57636--57935 Score: 308
Period size: 88 Copynumber: 3.4 Consensus size: 88
57626 AATAAATGTG
* * * * * *
57636 ATTATATCTTAAAATCGGA-T-TTTTTTAT--GAAAAAAAGTTGATTGATTGTAAATGTCATATT
1 ATTATATCTGAGAATCGGATTCTTTTTTATAAAAAAAAAAATTGATTGATTGTAAATGTCAGACT
* **
57697 GCAAAGATTAGACTAATAAATGA
66 GCAAGGATTAGACTAATGCATGA
* * ** *
57720 ATTATATCTAAGAATC-AATTCTTTTTTATAGAAAAAAAAAATTGACCGATTGTAAATGTTAGAC
1 ATTATATCTGAGAATCGGATTCTTTTTTATA-AAAAAAAAAATTGATTGATTGTAAATGTCAGAC
* *
57784 TGTAAGGATTAAACTAATGCATGA
65 TGCAAGGATTAGACTAATGCATGA
* * * *
57808 ATTATAGCTGATAATCGGATTCTTTTTTATTAAAAAAAGAAAGACTAATTGATTGTAAATGTCAG
1 ATTATATCTGAGAATCGGATTCTTTTTTA-TAAAAAAA-AAA-ATTGATTGATTGTAAATGTCAG
* *
57873 TCTGCAAGGATTAGACTAATGCATTA
63 ACTGCAAGGATTAGACTAATGCATGA
*
57899 ATTATATTTGAGAATCGGA-T-TTTTTTATAAAAAAAAA
1 ATTATATCTGAGAATCGGATTCTTTTTTATAAAAAAAAA
57936 GAAAGACTGC
Statistics
Matches: 176, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
83 1 0.01
84 15 0.09
85 8 0.05
87 2 0.01
88 65 0.37
89 24 0.14
90 6 0.03
91 55 0.31
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (88 bp):
ATTATATCTGAGAATCGGATTCTTTTTTATAAAAAAAAAAATTGATTGATTGTAAATGTCAGACT
GCAAGGATTAGACTAATGCATGA
Found at i:57891 original size:91 final size:91
Alignment explanation
Indices: 57676--57943 Score: 289
Period size: 91 Copynumber: 3.0 Consensus size: 91
57666 AAAAAAGTTG
* * ** * *
57676 ATTGATTGTAAATGTCA-TATTGCAAAGATTAGACTAATAAATGAATTATATCTAAGAATC-AAT
1 ATTGATTGTAAATGTCAGT-CTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGAT
* *
57739 TCTTTTTTA-TAGAAAAAA-AAA-ATTG
65 TCTTTTTTATTA-AAAAAAGAAAGACTA
** * * * * * *
57764 ACCGATTGTAAATGTTAGACTGTAAGGATTAAACTAATGCATGAATTATAGCTGATAATCGGATT
1 ATTGATTGTAAATGTCAGTCTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGATT
57829 CTTTTTTATTAAAAAAAGAAAGACTA
66 CTTTTTTATTAAAAAAAGAAAGACTA
* *
57855 ATTGATTGTAAATGTCAGTCTGCAAGGATTAGACTAATGCATTAATTATATTTGAGAATCGGA-T
1 ATTGATTGTAAATGTCAGTCTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGATT
*
57919 -TTTTTTATAAAAAAAAAGAAAGACT
66 CTTTTTTAT-TAAAAAAAGAAAGACT
57944 GCAAGGATTA
Statistics
Matches: 147, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
88 46 0.31
89 25 0.17
90 21 0.14
91 55 0.37
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (91 bp):
ATTGATTGTAAATGTCAGTCTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGGATT
CTTTTTTATTAAAAAAAGAAAGACTA
Found at i:57983 original size:68 final size:68
Alignment explanation
Indices: 57874--58141 Score: 283
Period size: 68 Copynumber: 3.9 Consensus size: 68
57864 AAATGTCAGT
* * *
57874 CTGCAAGGATTAGACTAATGCATTAATTATATTTGAGAATCGGATTTTTTTATAAAAAAAAAGAA
1 CTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTTTATAAAAAAAAAGAA
57939 AGA
66 AGA
* * **
57942 CTGCAAGGATTAGATTAATGCATGAATTAAATCTGAGAATC-GTATTTTTTTATAGGAAAAAAGA
1 CTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAG-ATTTTTTTATAAAAAAAAAGA
58006 AAGA
65 AAGA
** * **
58010 CTTAAAGGATTAGACTAATGCATGAATTATATCT-AAAATCAGATTCTTTTT-TATAGGAAAAAG
1 CTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATT-TTTTTATA-AAAAAAAAG
*
58073 AAAAA
64 AAAGA
** * * * *
58078 CTATAAAGATTAGACTAATGCATAAATTGTA-CATGAGAATCAGATTTCTTTTGGTAAAAAAAAA
1 CTGCAAGGATTAGACTAATGCATGAATTATATC-TGAGAATCAGATTT-TTTT-ATAAAAAAAAA
58142 AGTTGGTTGA
Statistics
Matches: 169, Mismatches: 22, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
67 12 0.07
68 135 0.80
69 14 0.08
70 6 0.04
71 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (68 bp):
CTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTTTTTTATAAAAAAAAAGAA
AGA
Found at i:62472 original size:122 final size:120
Alignment explanation
Indices: 62216--62559 Score: 394
Period size: 122 Copynumber: 2.8 Consensus size: 120
62206 TATTATTTTT
* * *
62216 AATAAAAAATAATATTTAATTAACTTTATAAAAAAATA-TATTAGCAAATTAAAA--T-ATTAAT
1 AATAAAAAATAATATTTAATTAA-TTT-TTAAAAATTACT-TTAACAAATTAAAATTTAATT-AT
* * *
62277 TATTTTTTAATAATAAAAATTTTTAAATAAAAATAAAAAGGGTTTATTATTATTATTTTTAATAA
62 TATTTTTTAAAAATAAAAA-ATTT---T-AAAAT-AAAAGGGTTTATTATTATAATTTTTAATAA
*
62342 AATTAAAAATAATATTTAATTATATTTTTAAAAATTACTTTAACAAATTAAAATTTAATTATTAT
1 AATAAAAAATAATATTTAATTA-ATTTTTAAAAATTACTTTAACAAATTAAAATTTAATTATTAT
*
62407 GTTTTTATAAAATAAAAAATTTTAAAATAAAA-GGTTTTTTATTATAATTTTTAATAA
65 -TTTTTA-AAAATAAAAAATTTTAAAATAAAAGGGTTTATTATTATAATTTTTAATAA
* * *
62464 AATAAAAAATAATATTTAATTCA-GTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTA
1 AATAAAAAATAATATTTAATTAATTTTTAAAAA-TTACTTTAACAAATTAAAAT-TTAATTATTA
*
62528 TATTTTTAAAAATAAAAAATTTTAAATTAAAA
64 T-TTTTTAAAAATAAAAAATTTTAAAATAAAA
62560 AAAATTTATT
Statistics
Matches: 195, Mismatches: 14, Indels: 23
0.84 0.06 0.10
Matches are distributed among these distances:
120 8 0.04
121 43 0.22
122 60 0.31
123 4 0.02
124 5 0.03
125 22 0.11
126 25 0.13
127 7 0.04
128 12 0.06
129 9 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (120 bp):
AATAAAAAATAATATTTAATTAATTTTTAAAAATTACTTTAACAAATTAAAATTTAATTATTATT
TTTTAAAAATAAAAAATTTTAAAATAAAAGGGTTTATTATTATAATTTTTAATAA
Found at i:62908 original size:22 final size:23
Alignment explanation
Indices: 62866--62920 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
62856 ATAATGATAC
*
62866 ATTTTTTTAATTCTTTAAATGTT
1 ATTTTTTTAATTCTTTAAATGTG
62889 ATTTTTTTAATT-TGTT-AATGTG
1 ATTTTTTTAATTCT-TTAAATGTG
*
62911 AATTTTTTAA
1 ATTTTTTTAA
62921 AATTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (23 bp):
ATTTTTTTAATTCTTTAAATGTG
Found at i:63087 original size:111 final size:115
Alignment explanation
Indices: 62893--63174 Score: 332
Period size: 111 Copynumber: 2.4 Consensus size: 115
62883 AATGTTATTT
* *
62893 TTTTAATTTGTTAATGTGAATTTTTTAAAATTTAATTAAATATCATTTTT-ATTTTATTAAAAAA
1 TTTTAATTTGTTAATGTAAATTTTTTAAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAA
62957 TAATAATAAAAAATAC-TT-TTT-A-TTTTTA-GAAAAACATATAATTAATA
66 TAATAATAAAAAATACTTTATTTAATTTTTTATGAAAAA-A-ATAATTAATA
63004 TTTTAATTTGTTAATGT-AATTTTTTAAAATTTAATTAAATATTATTTTTTAATTTTATTAAAAA
1 TTTTAATTTGTTAATGTAAATTTTTTAAAATTTAATTAAATATTA-TTTTTAATTTTATTAAAAA
* * **
63068 A-AATAATAGTAAACT-CTTTTTAATTTAATTTTTTATTTTTAAAAAATAATTAATA
65 ATAATAATA-AAAAATAC--TTT-ATTTAATTTTTTA--TGAAAAAAATAATTAATA
*
63123 TTTTAATTTATTAATGTAAATTTTTTTAAAA-TTAATTAAATATTAGTTTTTA
1 TTTTAATTTGTTAATGTAAA-TTTTTTAAAATTTAATTAAATATTA-TTTTTA
63175 TTATAAAATA
Statistics
Matches: 149, Mismatches: 7, Indels: 21
0.84 0.04 0.12
Matches are distributed among these distances:
110 26 0.17
111 30 0.20
112 18 0.12
114 2 0.01
116 3 0.02
117 1 0.01
118 6 0.04
119 26 0.17
120 23 0.15
121 14 0.09
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (115 bp):
TTTTAATTTGTTAATGTAAATTTTTTAAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAA
TAATAATAAAAAATACTTTATTTAATTTTTTATGAAAAAAATAATTAATA
Found at i:63532 original size:17 final size:17
Alignment explanation
Indices: 63510--63556 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
63500 ATTTTATTTT
63510 TAAAAATTATTTAAATAA
1 TAAAAATTATTTAAA-AA
* *
63528 TAAAAATAATTTATAAA
1 TAAAAATTATTTAAAAA
*
63545 TATAAATTATTT
1 TAAAAATTATTT
63557 TTAAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAAATTATTTAAAAA
Found at i:64324 original size:22 final size:22
Alignment explanation
Indices: 64294--64341 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
64284 TATTTTTTTA
*
64294 TAAATTTTGATATATTATATCAT
1 TAAATTTTGATATATAATAT-AT
* *
64317 TAAA-TTTGTTTTATAATATAT
1 TAAATTTTGATATATAATATAT
64338 TAAA
1 TAAA
64342 ATTAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 12 0.55
23 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TAAATTTTGATATATAATATAT
Found at i:65615 original size:18 final size:18
Alignment explanation
Indices: 65552--65655 Score: 53
Period size: 17 Copynumber: 6.1 Consensus size: 18
65542 AAAATATTAT
* *
65552 ATATTTTTATAAATTTTA
1 ATATATTTATTAATTTTA
*
65570 ATATA-TTAATAA-TTT-
1 ATATATTTATTAATTTTA
* * *
65585 ATTTAATGA-TAATTTTA
1 ATATATTTATTAATTTTA
*
65602 ATATATTTATTAATTTATG
1 ATATATTTATTAATTT-TA
*
65621 TTATATTTATT--TTTT-
1 ATATATTTATTAATTTTA
*
65636 ATAT-TATATTATATTTTA
1 ATATATTTATTA-ATTTTA
65654 AT
1 AT
65656 GATTTTATCT
Statistics
Matches: 65, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
14 5 0.08
15 10 0.15
16 9 0.14
17 18 0.28
18 12 0.18
19 11 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATATATTTATTAATTTTA
Found at i:65627 original size:19 final size:18
Alignment explanation
Indices: 65603--65650 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
65593 ATAATTTTAA
*
65603 TATATTTATTAATTTATGT
1 TATATTTATT-ATTTATAT
*
65622 TATATTTATTTTTTATAT
1 TATATTTATTATTTATAT
65640 TATATTATATT
1 TATATT-TATT
65651 TTAATGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TATATTTATTATTTATAT
Found at i:73573 original size:2 final size:2
Alignment explanation
Indices: 73561--73593 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
73551 AACAAAGTCC
*
73561 AT AT A- AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73594 TACATAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75215 original size:27 final size:27
Alignment explanation
Indices: 75183--75235 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
75173 TCTATAAGAT
75183 GCTAAGCTACATTAACCAAATCTAAAA
1 GCTAAGCTACATTAACCAAATCTAAAA
75210 GCTAAGCTACATTAACCAAATCTAAA
1 GCTAAGCTACATTAACCAAATCTAAA
75236 TTACAATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
GCTAAGCTACATTAACCAAATCTAAAA
Found at i:75299 original size:26 final size:26
Alignment explanation
Indices: 75263--75315 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
75253 TTGGGAAAAA
75263 TTTTTAGAAGAAAGGATACATTCAAC
1 TTTTTAGAAGAAAGGATACATTCAAC
75289 TTTTTAGAAGAAAGGATACATTCAAC
1 TTTTTAGAAGAAAGGATACATTCAAC
75315 T
1 T
75316 AATGCAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (26 bp):
TTTTTAGAAGAAAGGATACATTCAAC
Found at i:77411 original size:118 final size:119
Alignment explanation
Indices: 77255--77492 Score: 379
Period size: 119 Copynumber: 2.0 Consensus size: 119
77245 ACCATACATG
* * * *
77255 ATTATAGACCAAGCAATACTGACACGAATTGAAAGATAAAAAGTACTCATA-CCCATGCTCTAAC
1 ATTACAGACCAAGCAATAATGACACGAATTGAAAGATAAAAAGTACCCACACCCCATGCTCTAAC
* * *
77319 CGGGCAATGCCTGCGGGGCAATTTATTTTTCAAACAAACAAAAGCCATAAAGGA
66 CAGGCAATGCCTGCAGAGCAATTTATTTTTCAAACAAACAAAAGCCATAAAGGA
* * *
77373 ATTACAGACTAAGTAATAATGACACGAATTGACAGATAAAAAGTACCCACACCCCATGCTCTAAC
1 ATTACAGACCAAGCAATAATGACACGAATTGAAAGATAAAAAGTACCCACACCCCATGCTCTAAC
77438 CAGGCAATGCCTGCAGAGCAATTTATTTTTCAAACAAACAAAAGCCATAAAGGA
66 CAGGCAATGCCTGCAGAGCAATTTATTTTTCAAACAAACAAAAGCCATAAAGGA
77492 A
1 A
77493 AAATAATAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
118 44 0.40
119 65 0.60
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21
Consensus pattern (119 bp):
ATTACAGACCAAGCAATAATGACACGAATTGAAAGATAAAAAGTACCCACACCCCATGCTCTAAC
CAGGCAATGCCTGCAGAGCAATTTATTTTTCAAACAAACAAAAGCCATAAAGGA
Found at i:80736 original size:18 final size:17
Alignment explanation
Indices: 80708--80741 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
80698 GTTTAATTAG
*
80708 ATTAATAAATTTTTAAA
1 ATTAATAAATTATTAAA
80725 ATTAATTAAATTATTAA
1 ATTAA-TAAATTATTAA
80742 TTATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAATAAATTATTAAA
Found at i:81228 original size:15 final size:14
Alignment explanation
Indices: 81208--81247 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
81198 TTTAAATTTC
81208 ATAAATTATTTTTAA
1 ATAAATT-TTTTTAA
*
81223 ATAAATTTTTATAA
1 ATAAATTTTTTTAA
*
81237 ATTAATTTTTT
1 ATAAATTTTTT
81248 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATAAATTTTTTTAA
Found at i:81248 original size:15 final size:15
Alignment explanation
Indices: 81211--81256 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
81201 AAATTTCATA
81211 AATTATTTT-TAAA-T
1 AATT-TTTTATAAATT
*
81225 AAATTTTTATAAATT
1 AATTTTTTATAAATT
*
81240 AATTTTTTATTAATT
1 AATTTTTTATAAATT
81255 AA
1 AA
81257 AATAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTTTTATAAATT
Found at i:81254 original size:25 final size:25
Alignment explanation
Indices: 81199--81271 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 25
81189 CACATATATT
*
81199 TTAAATTTCATAAATTATTTTTAAA
1 TTAATTTTCATAAATTATTTTTAAA
* * *
81224 TAAATTTTTATAAATTAATTTTT-TA
1 TTAATTTTCATAAATT-ATTTTTAAA
***
81249 TTAATTAAAATAAA-TATTTTTAA
1 TTAATTTTCATAAATTATTTTTAA
81272 TATATTTTAC
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
23 6 0.16
24 1 0.03
25 24 0.65
26 6 0.16
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAATTTTCATAAATTATTTTTAAA
Found at i:81291 original size:24 final size:23
Alignment explanation
Indices: 81257--81302 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
81247 TATTAATTAA
81257 AATAAATATTTTTAATATATTTTAC
1 AATAAATATTTTTAA-AT-TTTTAC
81282 AATAAA-ATTTTTAAATTTTTA
1 AATAAATATTTTTAAATTTTTA
81303 AATGGTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 8 0.38
25 6 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAAATATTTTTAAATTTTTAC
Found at i:81982 original size:17 final size:16
Alignment explanation
Indices: 81947--81990 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
81937 ATTTTATAAA
81947 TAATTT-ATAT-TATT
1 TAATTTAATATATATT
81961 TAATTTAATATATATT
1 TAATTTAATATATATT
81977 TAAATTTAA-ATATA
1 T-AATTTAATATATA
81991 AAAATATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 10 0.37
17 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTAATATATATT
Found at i:82372 original size:12 final size:12
Alignment explanation
Indices: 82355--82379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82345 GTATCCGATG
82355 ACAGGTTACTCA
1 ACAGGTTACTCA
82367 ACAGGTTACTCA
1 ACAGGTTACTCA
82379 A
1 A
82380 ATGACAAGGG
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACAGGTTACTCA
Found at i:84231 original size:16 final size:17
Alignment explanation
Indices: 84210--84251 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
84200 TTGGATTGAA
84210 TTTTAATTTTAATTT-T
1 TTTTAATTTTAATTTAT
*
84226 TTTTAATTTTTATTTAT
1 TTTTAATTTTAATTTAT
*
84243 ATTTAATTT
1 TTTTAATTT
84252 ATTTTAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTAATTTTAATTTAT
Found at i:84354 original size:24 final size:23
Alignment explanation
Indices: 84296--84362 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
84286 ATTTTTATTT
* *
84296 AAATTATTAAAAATTTATAAATAA
1 AAATAATTAAAAA-TTATTAATAA
** *
84320 ATTTAAATAAAAATTATTAATAAA
1 AAATAATTAAAAATTATTAAT-AA
*
84344 AAATAATTAAAAATAATTA
1 AAATAATTAAAAATTATTA
84363 TTTTATATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATAATTAAAAATTATTAATAA
Found at i:84728 original size:22 final size:23
Alignment explanation
Indices: 84682--84730 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
84672 AATAACAAGC
84682 TTTCATTTCTTTAACCATTTATT
1 TTTCATTTCTTTAACCATTTATT
**
84705 TTTCATTT-TTTCCCCATTT-TT
1 TTTCATTTCTTTAACCATTTATT
84726 TTTCA
1 TTTCA
84731 AATTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 8 0.33
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTCATTTCTTTAACCATTTATT
Found at i:84736 original size:21 final size:22
Alignment explanation
Indices: 84696--84737 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
84686 ATTTCTTTAA
**
84696 CCATTTATTTTTCATTTTTTCC
1 CCATTTATTTTTCAAATTTTCC
84718 CCATTT-TTTTTCAAATTTTC
1 CCATTTATTTTTCAAATTTTC
84738 TTTTTTGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (22 bp):
CCATTTATTTTTCAAATTTTCC
Found at i:95458 original size:12 final size:12
Alignment explanation
Indices: 95413--95450 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
95403 TCAAAATAAT
95413 TTTAATTTTTAA
1 TTTAATTTTTAA
95425 TTTAA-TTTTAA
1 TTTAATTTTTAA
* *
95436 ATAAATTTTTAA
1 TTTAATTTTTAA
95448 TTT
1 TTT
95451 TTAATTTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAATTTTTAA
Found at i:95466 original size:30 final size:29
Alignment explanation
Indices: 95412--95471 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
95402 ATCAAAATAA
*
95412 TTTTAATTTTTAATTTAATTTTAAATAAAT
1 TTTTAATTTTTAATTTAATATTAAA-AAAT
95442 TTTTAATTTTTAATTT-ATAATTAAAAAAT
1 TTTTAATTTTTAATTTAAT-ATTAAAAAAT
95471 T
1 T
95472 AAAAAAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTAATTTTTAATTTAATATTAAAAAAT
Found at i:105688 original size:27 final size:27
Alignment explanation
Indices: 105665--105716 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
105655 ATTAATTTTG
* *
105665 TTAATTTTTAATTAATATTAAATTATT
1 TTAATTTGTAATTAAAATTAAATTATT
*
105692 TTAATTTGTACTTAAAATT-AATTAT
1 TTAATTTGTAATTAAAATTAAATTAT
105717 GAATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAATTTGTAATTAAAATTAAATTATT
Found at i:106247 original size:24 final size:24
Alignment explanation
Indices: 106220--106289 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
106210 AATAAAAATT
106220 AGCCACCAA-TTTTGACAAACAACA
1 AGCCA-CAATTTTTGACAAACAACA
* *
106244 AGCCATAATTTTTGACAAACAAAA
1 AGCCACAATTTTTGACAAACAACA
106268 AGGAACCACAATTTTTGACAAA
1 A-G--CCACAATTTTTGACAAA
106290 TACAAAGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.05
24 20 0.51
25 1 0.03
27 16 0.41
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACAATTTTTGACAAACAACA
Found at i:106288 original size:27 final size:27
Alignment explanation
Indices: 106229--106318 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
106219 TAGCCACCAA
* *
106229 TTTTGACAAACAACAA-G--CCATAAT
1 TTTTGACAAACAAAAAGGAACCACAAT
106253 TTTTGACAAACAAAAAGGAACCACAAT
1 TTTTGACAAACAAAAAGGAACCACAAT
* * * *
106280 TTTTGACAAATACAAAGTAACCACCAT
1 TTTTGACAAACAAAAAGGAACCACAAT
*
106307 TGTTGACAAACA
1 TTTTGACAAACA
106319 CATGGTGGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 15 0.27
25 1 0.02
27 39 0.71
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (27 bp):
TTTTGACAAACAAAAAGGAACCACAAT
Found at i:106337 original size:24 final size:25
Alignment explanation
Indices: 106306--106363 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
106296 GTAACCACCA
*
106306 TTGTTGACAAACAC-ATGGTGGTTT
1 TTGTTGACAAACACAAGGGTGGTTT
106330 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGTTT
106356 TTGTTGAC
1 TTGTTGAC
106364 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGTTT
Found at i:109362 original size:27 final size:27
Alignment explanation
Indices: 109324--109391 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
109314 ACAAGTCATA
109324 ATTTTTGACAAACAAAAAGAAACCACC
1 ATTTTTGACAAACAAAAAGAAACCACC
* * *
109351 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGAAACCACC
*
109378 ATTATTGACAAACA
1 ATTTTTGACAAACA
109392 CATGATGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGAAACCACC
Found at i:110837 original size:4 final size:4
Alignment explanation
Indices: 110830--110863 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
110820 TTATTTATAT
110830 TACA TACA TA-A GTACA TACA TACA TACA TACA TA
1 TACA TACA TACA -TACA TACA TACA TACA TACA TA
110864 TATATATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.04
4 26 0.93
5 1 0.04
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:116555 original size:7 final size:7
Alignment explanation
Indices: 116543--116574 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
116533 CACTGCTTGT
116543 CATTTTC
1 CATTTTC
116550 CATTTTC
1 CATTTTC
116557 CATTTTC
1 CATTTTC
116564 CATTTTC
1 CATTTTC
116571 CATT
1 CATT
116575 ACTGAGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
CATTTTC
Found at i:118399 original size:2 final size:2
Alignment explanation
Indices: 118347--118383 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
118337 ATTTTAAAGT
118347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118384 TAACTGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:119740 original size:16 final size:16
Alignment explanation
Indices: 119721--119777 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
119711 AATTGGTATT
119721 ATTTTTAATTAATTAA
1 ATTTTTAATTAATTAA
* *
119737 ATTTTAAATTATTTATA
1 ATTTTTAATTAATTA-A
* *
119754 ATTTATATTTAAATTAAA
1 ATTTTTAATT-AATT-AA
119772 ATTTTT
1 ATTTTT
119778 GTATATTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 9 0.29
19 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTAATTAATTAA
Found at i:119793 original size:28 final size:28
Alignment explanation
Indices: 119725--119803 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
119715 GGTATTATTT
119725 TTAATTAATTAAATTTTAAATTATTTATAA
1 TTAA-TAATTAAA-TTTAAATTATTTATAA
* * * *
119755 TTTATATTTAAATTAAAATT-TTTGTATA
1 TTAATAATTAAATTTAAATTATTTATA-A
*
119783 TTAATAATTAATTTTAAATTA
1 TTAATAATTAAATTTAAATTA
119804 AATATTTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
27 5 0.13
28 24 0.62
29 7 0.18
30 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATAATTAAATTTAAATTATTTATAA
Found at i:121002 original size:39 final size:40
Alignment explanation
Indices: 120929--121005 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
120919 AACATTAAAA
120929 AAATAAAAATTATTTTTATATAAATATTTGTAATTCAATTT
1 AAATAAAAATTATTTTTATATAAATA-TTGTAATTCAATTT
* *
120970 AAATAAAATTTTTTTATTATATAAATA-T-TAATTCAA
1 AAATAAAAATTATTT-TTATATAAATATTGTAATTCAA
121006 GCCTTGTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 8 0.24
40 1 0.03
41 13 0.39
42 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (40 bp):
AAATAAAAATTATTTTTATATAAATATTGTAATTCAATTT
Found at i:121991 original size:24 final size:25
Alignment explanation
Indices: 121933--121992 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
121923 GAATATTCGG
* *
121933 TTAATTAATATTTATAAATATTAAT
1 TTAATTATTATTTAAAAATATTAAT
* *
121958 TAAAAT-TTATTTAAAAATA-TAAT
1 TTAATTATTATTTAAAAATATTAAT
121981 TTAATTATTATT
1 TTAATTATTATT
121993 AATTTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
25 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATTATTATTTAAAAATATTAAT
Found at i:122513 original size:2 final size:2
Alignment explanation
Indices: 122506--122533 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
122496 AATCATGAAA
122506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122534 TTAAACTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123176 original size:2 final size:2
Alignment explanation
Indices: 123169--123196 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
123159 ACTGAAAGTT
123169 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123197 ATTTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:124942 original size:2 final size:2
Alignment explanation
Indices: 124935--124959 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
124925 AAATAAAAAC
124935 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
124960 AAAAAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:125244 original size:27 final size:28
Alignment explanation
Indices: 125214--125270 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
125204 AATTTAAAAA
* * *
125214 ATTATTCAAATTTAATAAATTA-TTATT
1 ATTATTAAAATTTAAAAAATAATTTATT
125241 ATTATTAAAATTTAAAAAATAATTTATT
1 ATTATTAAAATTTAAAAAATAATTTATT
125269 AT
1 AT
125271 ATATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTATTAAAATTTAAAAAATAATTTATT
Found at i:127910 original size:24 final size:24
Alignment explanation
Indices: 127841--127912 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
127831 TTAAAAATTA
*
127841 ATTTTTAAATTAAATATGATTTTATT
1 ATTTTTAAATTATATAT--TTTTATT
* * *
127867 ATTTTTATATCTCTAAATTTTTATT
1 ATTTTTAAAT-TATATATTTTTATT
127892 A-TTTTAAATATATATATTTTT
1 ATTTTTAAAT-TATATATTTTT
127913 GACATTTTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 16 0.43
25 8 0.22
26 9 0.24
27 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTTTAAATTATATATTTTTATT
Found at i:134459 original size:18 final size:19
Alignment explanation
Indices: 134429--134466 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
134419 TATAATTAAA
134429 TTTATATAAAAAT-ATATT
1 TTTATATAAAAATAATATT
134447 TTTAT-TAATAAATAATATT
1 TTTATATAA-AAATAATATT
134466 T
1 T
134467 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 9 0.50
19 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATATAAAAATAATATT
Found at i:134470 original size:31 final size:31
Alignment explanation
Indices: 134410--134470 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
134400 AACATATTAT
*
134410 TATATTTATTATAATTAAATTTATATAAAAA
1 TATATTTATTATAATTAAATATATATAAAAA
*
134441 TATATTT-TTATTAA-TAAATAATATTTAAAA
1 TATATTTATTA-TAATTAAAT-ATATATAAAA
134471 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TATATTTATTATAATTAAATATATATAAAAA
Found at i:135454 original size:2 final size:2
Alignment explanation
Indices: 135447--135472 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
135437 TTACCTCATA
135447 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
135473 TTTTAAAGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:135545 original size:2 final size:2
Alignment explanation
Indices: 135532--135565 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
135522 ATCTCCTTTT
*
135532 TA TA TA TT TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
135566 TGTTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:141886 original size:51 final size:52
Alignment explanation
Indices: 141830--141934 Score: 194
Period size: 51 Copynumber: 2.0 Consensus size: 52
141820 TTCCTTTAAG
141830 TTAACTAAATTTTAATGCTTTGATAGTA-TTTTTTTATCAAACATGATTTAC
1 TTAACTAAATTTTAATGCTTTGATAGTATTTTTTTTATCAAACATGATTTAC
141881 TTAACTAAATTTTAATGCTTTGATAGTATTTTTTTTTATCAAACATGATTTAC
1 TTAACTAAATTTTAATGCTTTGATAGTA-TTTTTTTTATCAAACATGATTTAC
141934 T
1 T
141935 CCTGTTGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 28 0.54
53 24 0.46
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (52 bp):
TTAACTAAATTTTAATGCTTTGATAGTATTTTTTTTATCAAACATGATTTAC
Found at i:146936 original size:25 final size:25
Alignment explanation
Indices: 146903--146955 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
146893 ATCTATGTTT
146903 GATACATATTTGAAAATGAATATAA
1 GATACATATTTGAAAATGAATATAA
146928 GATACATATTTGAAAATGAATATAA
1 GATACATATTTGAAAATGAATATAA
146953 GAT
1 GAT
146956 GTGATCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (25 bp):
GATACATATTTGAAAATGAATATAA
Found at i:149575 original size:2 final size:2
Alignment explanation
Indices: 149568--149592 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
149558 CATGATAATT
149568 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
149593 TAATGATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:150346 original size:29 final size:30
Alignment explanation
Indices: 150291--150350 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
150281 ATATAAAAAT
*
150291 TATAAAAAATTAATTTTATATTAATATTTA
1 TATAAAAAAATAATTTTATATTAATATTTA
*
150321 TATAAAAATAATAATTTTTTA-T-ATATTTA
1 TATAAAAA-AATAATTTTATATTAATATTTA
150350 T
1 T
150351 TTTATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 9 0.33
31 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATAAAAAAATAATTTTATATTAATATTTA
Found at i:157162 original size:3 final size:3
Alignment explanation
Indices: 157148--157219 Score: 56
Period size: 3 Copynumber: 24.3 Consensus size: 3
157138 AACAGATATA
* * * * * *
157148 AAG AAG ATG AAG AAG GAG AA- AAG CAG AGG TAG AAG AAG AAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
157195 AAG GAG AAG AGG AAG AGG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
157220 TGGAGGGATC
Statistics
Matches: 50, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.56, C:0.01, G:0.40, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:158037 original size:2 final size:2
Alignment explanation
Indices: 158030--158065 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
158020 ATTCATGCCA
158030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
158066 CCATATCAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159629 original size:3 final size:3
Alignment explanation
Indices: 159621--159678 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
159611 GTGCTTTCTC
159621 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
159668 TAT TAT ATAT T
1 TAT TAT -TAT T
159679 CAAATAGTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:160060 original size:28 final size:28
Alignment explanation
Indices: 159983--160060 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
159973 AATGATGGAT
*
159983 ATGATATGAAAAATATATTAAAGATAAC
1 ATGATATAAAAAATATATTAAAGATAAC
* *
160011 ATGATATAAAAAATA-ACATAAAGATAAT
1 ATGATATAAAAAATATA-TTAAAGATAAC
* *
160039 AT-ATATACATAAATATTTTAAA
1 ATGATATA-AAAAATATATTAAA
160061 ATTTATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
27 6 0.15
28 35 0.85
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
ATGATATAAAAAATATATTAAAGATAAC
Found at i:160110 original size:17 final size:16
Alignment explanation
Indices: 160057--160111 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
160047 ATAAATATTT
*
160057 TAAAATTTATATAATA
1 TAAAATTTATAAAATA
*
160073 T-AAA-TTATTAACATA
1 TAAAATTTA-TAAAATA
160088 TCAAAATTTATAAAAATA
1 T-AAAATTTAT-AAAATA
160106 TAAAAT
1 TAAAAT
160112 ACTTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 1 0.03
17 9 0.29
18 9 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATTTATAAAATA
Found at i:160168 original size:47 final size:49
Alignment explanation
Indices: 160069--160170 Score: 113
Period size: 48 Copynumber: 2.1 Consensus size: 49
160059 AAATTTATAT
* * *
160069 AATATAAATTATTAACATATCAAAATTTATAAAAATATAAAATACTTTA
1 AATATAAATTATTAACATATCAAAATATATAAAAATATAAAATACATAA
* *
160118 AATA-AAATTA-TAACATGAT-AAAATATACTATAAATATAATATA-ATAA
1 AATATAAATTATTAACAT-ATCAAAATATA-TAAAAATATAAAATACATAA
160165 AATATA
1 AATATA
160171 TAAATATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
47 19 0.42
48 22 0.49
49 4 0.09
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (49 bp):
AATATAAATTATTAACATATCAAAATATATAAAAATATAAAATACATAA
Found at i:161953 original size:21 final size:21
Alignment explanation
Indices: 161914--161982 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
161904 TTTAAAAATT
161914 TTATTTATTTATGTAATATTTATA
1 TTATTT-TTTAT-T-ATATTTATA
161938 TTATTTTTTATTATATTT-TAA
1 TTATTTTTTATTATATTTAT-A
*
161959 TTATTTTATA-TATATTTATA
1 TTATTTTTTATTATATTTATA
161979 TTAT
1 TTAT
161983 ATAATCATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 13 0.31
21 17 0.40
22 1 0.02
23 5 0.12
24 6 0.14
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (21 bp):
TTATTTTTTATTATATTTATA
Found at i:161974 original size:11 final size:11
Alignment explanation
Indices: 161861--161984 Score: 52
Period size: 11 Copynumber: 11.6 Consensus size: 11
161851 TTTAAAATAT
161861 TATATATTTTA
1 TATATATTTTA
* *
161872 AATAAATTTTA
1 TATATATTTTA
*
161883 -ATATA-TTAA
1 TATATATTTTA
*
161892 TAATTTATTTTA
1 T-ATATATTTTA
* *
161904 TTTAAAAATTTTA
1 --TATATATTTTA
161917 T-T-TA-TTTA
1 TATATATTTTA
*
161925 TGTA-ATATTTA
1 TATATAT-TTTA
*
161936 TAT-TATTTTT
1 TATATATTTTA
161946 TATTATATTTTA
1 TA-TATATTTTA
161958 -AT-TATTTTA
1 TATATATTTTA
161967 TATATA-TTTA
1 TATATATTTTA
161977 TATTATAT
1 TA-TATAT
161985 AATCATGTCT
Statistics
Matches: 83, Mismatches: 14, Indels: 31
0.65 0.11 0.24
Matches are distributed among these distances:
8 5 0.06
9 13 0.16
10 18 0.22
11 30 0.36
12 9 0.11
13 7 0.08
14 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (11 bp):
TATATATTTTA
Found at i:163742 original size:15 final size:15
Alignment explanation
Indices: 163719--163748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
163709 CAAATGAAAT
*
163719 AAAATGAAAAGTTTA
1 AAAAAGAAAAGTTTA
163734 AAAAAGAAAAGTTTA
1 AAAAAGAAAAGTTTA
163749 CACCGATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
AAAAAGAAAAGTTTA
Found at i:165414 original size:9 final size:9
Alignment explanation
Indices: 165400--165429 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
165390 CCATTTCATA
165400 TTTTTTTCT
1 TTTTTTTCT
165409 TTTTTTTCT
1 TTTTTTTCT
165418 TTTTCTTTCT
1 TTTT-TTTCT
165428 TT
1 TT
165430 CTTTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTCT
Done.