Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 19 of 195
Found at i:4368052 original size:59 final size:58
Alignment explanation
Indices: 4367910--4368389 Score: 375
Period size: 59 Copynumber: 8.1 Consensus size: 58
4367900 TCAATGATTT
** * * ** *
4367910 TTTAAAATAAAAATTTGAAATAAAATATTTTTGAAGG-AAAGTTGAATGTATCAA-TTTCC
1 TTTAAAAT-AAAATTTTCAA-AAAACATTTTTG-AGGAAAAATTGAAAATATCAATTTTTC
** * * * * *
4367969 TTTTAGCATACAAATTTTAAAAAAAATATTTTTGAGGAAAAATTGAGAGTATCGATTTTTC
1 -TTTAAAATA-AAATTTT-CAAAAAACATTTTTGAGGAAAAATTGAAAATATCAATTTTTC
* * *
4368030 TTTAAAATAAAATTTTTCAAAAAAGCATTTTTGAGAAAAAATTGAAAGTATCAATTTTTA
1 TTTAAAATAAAA-TTTTCAAAAAA-CATTTTTGAGGAAAAATTGAAAATATCAATTTTTC
* * *
4368090 TTGAAAATAAAAAAAATTTT-AAAAAATGATTTTATGA--AAAAGTTGAAAATATCAATTTTTC
1 TTTAAAAT----AAAATTTTCAAAAAA-CATTTT-TGAGGAAAAATTGAAAATATCAATTTTTC
* * * * *
4368151 TTGAAAATAAAAAATTTT-AAAAAATATTTTTG-TGAAAAAGTTAAAAATATTAATTTTTC
1 TTTAAAAT--AAAATTTTCAAAAAACATTTTTGAGGAAAAA-TTGAAAATATCAATTTTTC
* * *
4368210 TTGAAAATAAAAATTTCAAGAAAACATTTTTAAGGAAAAATTGAAAATATCAATTTTTC
1 TTTAAAATAAAATTTTCAA-AAAACATTTTTGAGGAAAAATTGAAAATATCAATTTTTC
* * *
4368269 TTAAAAATAAAATTTTCAAAAAAGCATTTTCGAGAAAAAATTGAAAATATCAATTTTTC
1 TTTAAAATAAAATTTTCAAAAAA-CATTTTTGAGGAAAAATTGAAAATATCAATTTTTC
* * * * *
4368328 TCTAAAATTAAGA-TTTCAAGAAGAACATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTTC
1 TTTAAAA-TAAAATTTTCAA-AA-AACATTTTTGAGGAAAAATTGAAAATATCAATTTTTC
4368387 TTT
1 TTT
4368390 GAATAATAGT
Statistics
Matches: 353, Mismatches: 46, Indels: 43
0.80 0.10 0.10
Matches are distributed among these distances:
57 9 0.03
58 15 0.04
59 148 0.42
60 121 0.34
61 38 0.11
62 11 0.03
63 7 0.02
64 4 0.01
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (58 bp):
TTTAAAATAAAATTTTCAAAAAACATTTTTGAGGAAAAATTGAAAATATCAATTTTTC
Found at i:4368278 original size:118 final size:119
Alignment explanation
Indices: 4367991--4368385 Score: 462
Period size: 118 Copynumber: 3.3 Consensus size: 119
4367981 AATTTTAAAA
* * * * * * *
4367991 AAAATATTTTTGAGGAAAAATTGAGAGTATCGATTTTTCTTTAAAATAAAATTTTTCAAAAAAGC
1 AAAACATTTTTAAGGAAAAATTGAAAATATCAATTTTTCTTAAAAATAAAAATTTTCAAAAAAGC
* * *
4368056 ATTTTTGAGAAAAAATTGAAAGTATCAATTTTTATTGAAAATAAAAAAAATTTTAA-
66 ATTTTTGAGAAAAAATTGAAAATATCAATTTTTCTTGAAAAT---AAAAATTTCAAG
* * *
4368112 AAAATGA-TTTT-ATGAAAAAGTTGAAAATATCAATTTTTCTTGAAAATAAAAAATTTT-AAAAA
1 AAAA-CATTTTTAAGGAAAAA-TTGAAAATATCAATTTTTCTTAAAAAT-AAAAATTTTCAAAAA
* * * * *
4368174 A-TATTTTTGTGAAAAAGTTAAAAATATTAATTTTTCTTGAAAATAAAAATTTCAAG
63 AGCATTTTTGAGAAAAAATTGAAAATATCAATTTTTCTTGAAAATAAAAATTTCAAG
4368230 AAAACATTTTTAAGGAAAAATTGAAAATATCAATTTTTCTTAAAAAT-AAAATTTTCAAAAAAGC
1 AAAACATTTTTAAGGAAAAATTGAAAATATCAATTTTTCTTAAAAATAAAAATTTTCAAAAAAGC
* * *
4368294 ATTTTCGAGAAAAAATTGAAAATATCAATTTTTCTCT-AAAATTAAGATTTCAAG
66 ATTTTTGAGAAAAAATTGAAAATATCAATTTTTCT-TGAAAATAAAAATTTCAAG
* *
4368348 AAGAACATTTTTAAGGAAAAGTTGAAAGTATCAATTTT
1 AA-AACATTTTTAAGGAAAAATTGAAAATATCAATTTT
4368386 CTTTGAATAA
Statistics
Matches: 236, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
116 8 0.03
117 17 0.07
118 81 0.34
119 41 0.17
120 43 0.18
121 37 0.16
122 9 0.04
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (119 bp):
AAAACATTTTTAAGGAAAAATTGAAAATATCAATTTTTCTTAAAAATAAAAATTTTCAAAAAAGC
ATTTTTGAGAAAAAATTGAAAATATCAATTTTTCTTGAAAATAAAAATTTCAAG
Found at i:4369139 original size:24 final size:24
Alignment explanation
Indices: 4369108--4369153 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4369098 ATATACACTT
* *
4369108 TTTAAAAATACT-CTTTAATTTAA
1 TTTAAAAAAACTGCTTAAATTTAA
4369131 TTTAGAAAAAACTGCTTAAATTT
1 TTTA-AAAAAACTGCTTAAATTT
4369154 TAATATATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (24 bp):
TTTAAAAAAACTGCTTAAATTTAA
Found at i:4372525 original size:16 final size:17
Alignment explanation
Indices: 4372504--4372537 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4372494 GTATAATATT
4372504 TATAAAATAT-TTTTAA
1 TATAAAATATATTTTAA
*
4372520 TATAAATTATATTTTAA
1 TATAAAATATATTTTAA
4372537 T
1 T
4372538 TTTACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAAAATATATTTTAA
Found at i:4377597 original size:84 final size:87
Alignment explanation
Indices: 4377427--4377601 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 87
4377417 CTGGAGTTTG
4377427 AACAGCTATTGTAATTTAATTTCCTTATATATATTAATGGAAATGGAAAACTAGAAGAAATGTGT
1 AACAGCTATTGTAATTTAATTTCCTTATATATATT-AT-G-AATGGAAAACTAGAAGAAATGTGT
*
4377492 GAAATGATTGACCAAACGAGTATAA
63 AAAATGATTGACCAAACGAGTATAA
4377517 AACAGCTATTGTAATTTAATTTCCTTATATATA-T-T-AATGGAAAACTAGAAGAAATGTGTAAA
1 AACAGCTATTGTAATTTAATTTCCTTATATATATTATGAATGGAAAACTAGAAGAAATGTGTAAA
*
4377579 ATGATTGACCAAATGAGTATAA
66 ATGATTGACCAAACGAGTATAA
4377601 A
1 A
4377602 CTAACAATTT
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
84 48 0.58
87 1 0.01
89 1 0.01
90 33 0.40
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (87 bp):
AACAGCTATTGTAATTTAATTTCCTTATATATATTATGAATGGAAAACTAGAAGAAATGTGTAAA
ATGATTGACCAAACGAGTATAA
Found at i:4386469 original size:2 final size:2
Alignment explanation
Indices: 4386462--4386487 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4386452 TCCTTCCTGA
4386462 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
4386488 TGCTTGGAAC
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:4396293 original size:23 final size:22
Alignment explanation
Indices: 4396252--4396298 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
4396242 TTTTTCAATA
*
4396252 AAAATATTAATTTTAATTAATTT
1 AAAATAATAATTTTAATT-ATTT
4396275 AAAATAATAA-TTTATATTATTT
1 AAAATAATAATTTTA-ATTATTT
4396297 AA
1 AA
4396299 TAAAAATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATAATAATTTTAATTATTT
Found at i:4396300 original size:20 final size:19
Alignment explanation
Indices: 4396276--4396319 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
4396266 AATTAATTTA
* *
4396276 AAATAATAATTTATATTATT
1 AAATAAAAATCTAT-TTATT
*
4396296 TAATAAAAATCTATTTATT
1 AAATAAAAATCTATTTATT
4396315 AAATA
1 AAATA
4396320 TATATATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATAAAAATCTATTTATT
Found at i:4396324 original size:2 final size:2
Alignment explanation
Indices: 4396317--4396347 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4396307 TATTTATTAA
*
4396317 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4396348 GGGACAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4398686 original size:2 final size:2
Alignment explanation
Indices: 4398679--4398723 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4398669 TTAATCCCTT
*
4398679 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4398721 TC T
1 TC T
4398724 ATTTCATCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4403884 original size:2 final size:2
Alignment explanation
Indices: 4403877--4403904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4403867 TGCAACTACA
4403877 AC 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 AC
4403905 CTACAAGCCA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4406883 original size:2 final size:2
Alignment explanation
Indices: 4406876--4406906 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4406866 TATGAGAAGC
*
4406876 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4406907 GGATTTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4408486 original size:25 final size:26
Alignment explanation
Indices: 4408451--4408502 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
4408441 TGGTTCATTT
*
4408451 ACATTCAACCTAAAAAGAACTATACC
1 ACATTCAACCTAAAAAAAACTATACC
4408477 ACATTC-ACCTAAAAAAAACTATACC
1 ACATTCAACCTAAAAAAAACTATACC
4408502 A
1 A
4408503 ATAATAGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.52, C:0.27, G:0.02, T:0.19
Consensus pattern (26 bp):
ACATTCAACCTAAAAAAAACTATACC
Found at i:4409235 original size:21 final size:21
Alignment explanation
Indices: 4409209--4409250 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4409199 CTAACACTCT
**
4409209 AATAAACAACTTGATAAACAA
1 AATAAACAACAAGATAAACAA
*
4409230 AATAAATAACAAGATAAACAA
1 AATAAACAACAAGATAAACAA
4409251 TCTGATAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.17
Consensus pattern (21 bp):
AATAAACAACAAGATAAACAA
Found at i:4409390 original size:16 final size:16
Alignment explanation
Indices: 4409371--4409419 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
4409361 GTAGGCTTAT
*
4409371 AAAATAGCATGAAACC
1 AAAATAGCATGAAACA
4409387 AAAA-A-CAATGAAAACA
1 AAAATAGC-ATG-AAACA
4409403 AAAATAGCATGAAACA
1 AAAATAGCATGAAACA
4409419 A
1 A
4409420 TCTAATAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 1 0.04
15 4 0.14
16 18 0.64
17 4 0.14
18 1 0.04
ACGTcount: A:0.65, C:0.14, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATAGCATGAAACA
Found at i:4414821 original size:16 final size:17
Alignment explanation
Indices: 4414802--4414835 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4414792 AAAAATAATT
4414802 ATAAAA-TTAATAAAAA
1 ATAAAAGTTAATAAAAA
4414818 ATAAAATGTTAATAAAAA
1 ATAAAA-GTTAATAAAAA
4414836 TGATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAAAAGTTAATAAAAA
Found at i:4418754 original size:36 final size:37
Alignment explanation
Indices: 4418707--4418779 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 37
4418697 ACTTGATGAA
*
4418707 ATGTTATTGAAGTCGGT-AGAAGCTGTAGGAACATAC
1 ATGTTATTGAAGTCGGTGAGAAGCTATAGGAACATAC
*
4418743 ATGTTCTTGAAGTCGGTGGAAGAAGCTATAGGAACAT
1 ATGTTATTGAAGTCGGT-G-AGAAGCTATAGGAACAT
4418780 TAAGAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 16 0.50
39 16 0.50
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (37 bp):
ATGTTATTGAAGTCGGTGAGAAGCTATAGGAACATAC
Found at i:4431997 original size:18 final size:17
Alignment explanation
Indices: 4431943--4431997 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
4431933 TAATAATTTT
*
4431943 TTAAATATATAACAAAA
1 TTAAATATATAAAAAAA
* *
4431960 TTAAAAATTTAAGAAAAA
1 TTAAATATATAA-AAAAA
4431978 TTAAATATATAAAAATAA
1 TTAAATATATAAAAA-AA
4431996 TT
1 TT
4431998 GCATAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAAATATATAAAAAAA
Found at i:4432508 original size:111 final size:111
Alignment explanation
Indices: 4432383--4432607 Score: 319
Period size: 111 Copynumber: 2.0 Consensus size: 111
4432373 AAAAAATTAG
* * * * *
4432383 TTAGATTTTCATTATTCTTTAAATATTGAAC-ATATTCATTTTAATCATGAAAAGAAATTGATA-
1 TTAGATTTTCATTATTATATAAATATTAAACAAAATTC-TTTTAATCATGAAAAGAAATTCATAT
*
4432446 TTTTTTATTTAATTACATTATTATTTCATTTAACATTGATACTCTTTT
65 TTTTTTATTTAATTACATTATTATTTCATTTAACATTGATAAT-TTTT
* *
4432494 TTAGATTTTCATTATTATATAAATATTAAACAAAATTCTTTTAATCGTGAAATGAAATTCATATT
1 TTAGATTTTCATTATTATATAAATATTAAACAAAATTCTTTTAATCATGAAAAGAAATTCATATT
* * *
4432559 TTTTTATTTAATTACATTATTATTTGATTTAATATTTATAATTTTT
66 TTTTTATTTAATTACATTATTATTTCATTTAACATTGATAATTTTT
4432605 TTA
1 TTA
4432608 AAAAAAATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
111 57 0.56
112 44 0.44
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (111 bp):
TTAGATTTTCATTATTATATAAATATTAAACAAAATTCTTTTAATCATGAAAAGAAATTCATATT
TTTTTATTTAATTACATTATTATTTCATTTAACATTGATAATTTTT
Found at i:4433723 original size:16 final size:17
Alignment explanation
Indices: 4433668--4433724 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
4433658 TTACTTTTTA
4433668 TTTTAATAATTATT-TAT
1 TTTTAATAATTATTAT-T
* *
4433685 TTTTCATAATTAATATT
1 TTTTAATAATTATTATT
*
4433702 TATTAAT-ATTATTATT
1 TTTTAATAATTATTATT
4433718 TTTTAAT
1 TTTTAAT
4433725 TAAAAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.42
17 18 0.55
18 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAATAATTATTATT
Found at i:4436583 original size:11 final size:11
Alignment explanation
Indices: 4436569--4436593 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4436559 CACTATGTTT
4436569 AGATTGAAAGG
1 AGATTGAAAGG
4436580 AGATTGAAAGG
1 AGATTGAAAGG
4436591 AGA
1 AGA
4436594 AGAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (11 bp):
AGATTGAAAGG
Found at i:4436621 original size:22 final size:23
Alignment explanation
Indices: 4436596--4436639 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4436586 AAAGGAGAAG
4436596 AAGAAA-AAGGAAAAAAAAAAAA
1 AAGAAACAAGGAAAAAAAAAAAA
*
4436618 AAGAAACCAATGAAAAAAAAAA
1 AAGAAA-CAAGGAAAAAAAAAA
4436640 TTCTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
24 13 0.68
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (23 bp):
AAGAAACAAGGAAAAAAAAAAAA
Found at i:4436803 original size:20 final size:20
Alignment explanation
Indices: 4436771--4436809 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4436761 AAAGTAAAAT
4436771 TGAAAAAAAATTAT-TTTTA
1 TGAAAAAAAATTATATTTTA
*
4436790 TGAAAAAATTATTATATTTT
1 TGAAAAAA-AATTATATTTT
4436810 TATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TGAAAAAAAATTATATTTTA
Found at i:4454450 original size:1 final size:1
Alignment explanation
Indices: 4454444--4454475 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
4454434 AAGAGGCTAG
4454444 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4454476 ATTTCTCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4461525 original size:21 final size:21
Alignment explanation
Indices: 4461501--4461540 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4461491 TGTTCAAAAT
*
4461501 TAATTGCATCTGGCTCATTAC
1 TAATTGCAGCTGGCTCATTAC
*
4461522 TAATTGTAGCTGGCTCATT
1 TAATTGCAGCTGGCTCATT
4461541 CATATCCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (21 bp):
TAATTGCAGCTGGCTCATTAC
Found at i:4465690 original size:2 final size:2
Alignment explanation
Indices: 4465683--4465708 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4465673 GTATCTTGTA
4465683 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
4465709 GCATATCTAA
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:4465981 original size:23 final size:22
Alignment explanation
Indices: 4465927--4465981 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4465917 AAAATCATGA
*
4465927 AAAGAGAAAAAAATAGGAGAACG
1 AAAG-GAAAAAAATAGGAGAAAG
*
4465950 AAAGGAAAAAAATCAGG-GAAAT
1 AAAGGAAAAAAAT-AGGAGAAAG
4465972 AAAGGAAAAA
1 AAAGGAAAAA
4465982 GAGTCTGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.05
Consensus pattern (22 bp):
AAAGGAAAAAAATAGGAGAAAG
Found at i:4468050 original size:16 final size:18
Alignment explanation
Indices: 4468015--4468057 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 18
4468005 AAATTTTTTT
4468015 ATTAAAATAATATATAAAA
1 ATTAAAA-AATATATAAAA
4468034 ATTAAAAAA-AT-TAAAA
1 ATTAAAAAATATATAAAA
4468050 ATTAAAAA
1 ATTAAAAA
4468058 TTGATGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.54
17 2 0.08
18 2 0.08
19 7 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATTAAAAAATATATAAAA
Found at i:4469000 original size:2 final size:2
Alignment explanation
Indices: 4468995--4469024 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4468985 ATATACAATC
4468995 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
4469025 GATTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4474247 original size:21 final size:23
Alignment explanation
Indices: 4474209--4474255 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
4474199 AGATGTAAAC
*
4474209 ATAATAATAATAGTAAAATGAATT
1 ATAATAATAATAGAAAAAT-AATT
4474233 ATAATAA-AA-AGAAAAATAATT
1 ATAATAATAATAGAAAAATAATT
4474254 AT
1 AT
4474256 TATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 2 0.09
24 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAATAATAATAGAAAAATAATT
Found at i:4474257 original size:24 final size:25
Alignment explanation
Indices: 4474230--4474284 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
4474220 AGTAAAATGA
4474230 ATTATA-ATAAAAAGAAAAATAATT
1 ATTATATATAAAAAGAAAAATAATT
* * *
4474254 ATTATATTTAAAAATAAATATAATT
1 ATTATATATAAAAAGAAAAATAATT
4474279 -TTATAT
1 ATTATAT
4474285 TTAATATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTATATATAAAAAGAAAAATAATT
Found at i:4474285 original size:24 final size:25
Alignment explanation
Indices: 4474237--4474288 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4474227 TGAATTATAA
4474237 TAAAAAGAAAAATAATTATTATATT
1 TAAAAAGAAAAATAATTATTATATT
* *
4474262 TAAAAATAAATATAATT-TTATATT
1 TAAAAAGAAAAATAATTATTATATT
4474286 TAA
1 TAA
4474289 TATGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TAAAAAGAAAAATAATTATTATATT
Found at i:4474839 original size:6 final size:6
Alignment explanation
Indices: 4474828--4474860 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4474818 TTAATATTAC
*
4474828 TTTCAT TTTCAT TTTCTT TTTCAT TTTCAT TTT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT
4474861 TCTCTCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTCAT
Found at i:4475297 original size:75 final size:75
Alignment explanation
Indices: 4475174--4475320 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
4475164 TGACAAGTGG
* * *
4475174 TATCAGAACTAGCCCTAAATCGTTCGACCCACGTCAAGTACCTCGAGGGAAATAGGTAGGGTGGT
1 TATCAGAACTAACCCTAAACCGTTCGACCCACGCCAAGTACCTCGAGGGAAATAGGTAGGGTGGT
4475239 CAACCTCTGA
66 CAACCTCTGA
* *
4475249 TATCAGAACTAACCCTAAACCGTTCGACCCACGCCAAGTACCTTGAGGGAAGTAGGTAGGGTGGT
1 TATCAGAACTAACCCTAAACCGTTCGACCCACGCCAAGTACCTCGAGGGAAATAGGTAGGGTGGT
4475314 CAACCTC
66 CAACCTC
4475321 CGTGACGAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (75 bp):
TATCAGAACTAACCCTAAACCGTTCGACCCACGCCAAGTACCTCGAGGGAAATAGGTAGGGTGGT
CAACCTCTGA
Found at i:4488298 original size:15 final size:16
Alignment explanation
Indices: 4488273--4488305 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4488263 TAAAATGATA
4488273 CATTTTGAAATGTTTT
1 CATTTTGAAATGTTTT
*
4488289 CATTTT-AAATTTTTT
1 CATTTTGAAATGTTTT
4488304 CA
1 CA
4488306 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (16 bp):
CATTTTGAAATGTTTT
Found at i:4493359 original size:61 final size:62
Alignment explanation
Indices: 4493222--4493350 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 62
4493212 TATAATGATA
* * * *
4493222 AATAGTAATTTTTAATTAAAATAATAAAAAATATATATTAAACTATAAAAACTTGATTAAATT
1 AATAATAA-TTTTAAATAAAATAATAAAAAATATATATCAAACTATAAAAACTTGATTAAACT
* * * *
4493285 CATAATAATTTTAAATAAAATAAT-AAAAATATATATCAAATTATAAAAATTTGATTAGACT
1 AATAATAATTTTAAATAAAATAATAAAAAATATATATCAAACTATAAAAACTTGATTAAACT
4493346 AATAA
1 AATAA
4493351 GTTATTTAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 36 0.63
62 15 0.26
63 6 0.11
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (62 bp):
AATAATAATTTTAAATAAAATAATAAAAAATATATATCAAACTATAAAAACTTGATTAAACT
Found at i:4495396 original size:16 final size:15
Alignment explanation
Indices: 4495368--4495407 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
4495358 ATATTTAGTA
*
4495368 TTAAAATTCAAAATT
1 TTAAAATTTAAAATT
4495383 TTATAAATTTAAAATT
1 TTA-AAATTTAAAATT
4495399 TTAAAATTT
1 TTAAAATTT
4495408 TTAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAATTTAAAATT
Found at i:4495411 original size:9 final size:8
Alignment explanation
Indices: 4495368--4495408 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
4495358 ATATTTAGTA
4495368 TTAAAA-T
1 TTAAAATT
*
4495375 TCAAAATT
1 TTAAAATT
4495383 TTATAAA-T
1 TTA-AAATT
4495391 TTAAAATT
1 TTAAAATT
4495399 TTAAAATT
1 TTAAAATT
4495407 TT
1 TT
4495409 TAATATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 8 0.28
8 18 0.62
9 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (8 bp):
TTAAAATT
Found at i:4495455 original size:25 final size:23
Alignment explanation
Indices: 4495393--4495457 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
4495383 TTATAAATTT
4495393 AAAATTTTAAAATTTTTAATATA
1 AAAATTTTAAAATTTTTAATATA
* *
4495416 AAAACTTAATAAAATTTTTAGAATGTA
1 AAAA-TT-TTAAAATTTTT--AATATA
*
4495443 AAAATTTTTAAATTT
1 AAAATTTTAAAATTT
4495458 AAAAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.12
24 2 0.06
25 17 0.50
26 2 0.06
27 9 0.26
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
AAAATTTTAAAATTTTTAATATA
Found at i:4495463 original size:17 final size:18
Alignment explanation
Indices: 4495421--4495465 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
4495411 ATATAAAAAC
4495421 TTAATAAAATTTTTAGAAT
1 TTAA-AAAATTTTTAGAAT
*
4495440 GT-AAAAATTTTTA-AAT
1 TTAAAAAATTTTTAGAAT
4495456 TTAAAAAATT
1 TTAAAAAATT
4495466 AAATGTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 1 0.04
19 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAAAAAATTTTTAGAAT
Found at i:4495478 original size:16 final size:14
Alignment explanation
Indices: 4495450--4495492 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
4495440 GTAAAAATTT
4495450 TTAAATTTAAAAAA
1 TTAAATTTAAAAAA
4495464 TTAAATGTTACAAAAA
1 TTAAAT-TTA-AAAAA
*
4495480 TATAATTTTAAAA
1 T-TAAATTTAAAA
4495493 CATCGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 9 0.36
17 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (14 bp):
TTAAATTTAAAAAA
Found at i:4496156 original size:14 final size:14
Alignment explanation
Indices: 4496136--4496168 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4496126 GAAATGTTAA
4496136 TTTTAATA-AAATT
1 TTTTAATATAAATT
4496149 TATTTAATATAAATT
1 T-TTTAATATAAATT
4496164 TTTTA
1 TTTTA
4496169 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 11 0.61
15 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:4496210 original size:6 final size:6
Alignment explanation
Indices: 4496184--4496225 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
4496174 TTTTTCAATC
* *
4496184 ATAATT ATAATA ATATTTT ATAATT ATAATT ATAATT ATAAT
1 ATAATT ATAATT ATA-ATT ATAATT ATAATT ATAATT ATAAT
4496226 AATTATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:4497067 original size:21 final size:22
Alignment explanation
Indices: 4497025--4497073 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
4497015 TTTAAAATTA
*
4497025 TCAAATATCTAAAAATTGAATG
1 TCAAATATCTAAAAATTAAATG
*
4497047 TCAAATAT-TACAAATTAAATG
1 TCAAATATCTAAAAATTAAATG
4497068 TCAAAT
1 TCAAAT
4497074 TTAACATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (22 bp):
TCAAATATCTAAAAATTAAATG
Found at i:4503336 original size:24 final size:23
Alignment explanation
Indices: 4503295--4503348 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
4503285 TTAAATTAAT
*
4503295 ATAAATTTTTTATTATAATTATA
1 ATAAATTTTTTATCATAATTATA
*
4503318 ATAATTTTTTTAATCATAATTATA
1 ATAAATTTTTT-ATCATAATTATA
4503342 ATAAATT
1 ATAAATT
4503349 CATTCAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATAAATTTTTTATCATAATTATA
Found at i:4516848 original size:2 final size:2
Alignment explanation
Indices: 4516803--4516829 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4516793 TAATGTTGAT
4516803 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 T
4516830 GCAGCTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4520064 original size:2 final size:2
Alignment explanation
Indices: 4520057--4520081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4520047 ATGGTCTTTT
4520057 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 T
4520082 TTTTTTTTTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4522048 original size:240 final size:241
Alignment explanation
Indices: 4521587--4522071 Score: 658
Period size: 240 Copynumber: 2.0 Consensus size: 241
4521577 TAATTCTTTA
* *
4521587 TTTCTTTAGTTTCTTTCATTTTTGAAACAAAAATTATATCATATATCATATATAATATTATATTA
1 TTTCTTTAGTTTCTTTCATTTTTGAAACAAAAATCATATCATATATCATACATAATATTATATTA
* ** ** *
4521652 TAACACACATAGAAATATGATAAGGTCTATTTACACGGATGCTTAAATGGATGGTTTCTTTTTCC
66 CAACACACATAGAAATATGATAAGGTCTATTTACACAAACACTTAAATGGATAGTTTCTTTTTCC
* * *
4521717 AACATGTGAAAAAATTCTTACATTTTCTCTTTATAATGATATGTAAGATATTTCCTAATTTAAGC
131 AACATGTGAAAAAATTCTTAAAATTTCTCTCTATAATGATATGTAAGATATTTCCTAATTTAAGC
*
4521782 TATTTATCAAAAAATATATATTAAAAATTATTTAATTATCC-AAAC
196 TATTTATCAAAAAATATATATTAAAAAGTATTTAATTATCCAAAAC
** *
4521827 TTTCTTTAGTTTCTTTCATTTTTGAAATTAAAATCATATCATATATCATACATATTATTATATTA
1 TTTCTTTAGTTTCTTTCATTTTTGAAACAAAAATCATATCATATATCATACATAATATTATATTA
* * * * * *
4521892 CAACATATATA-AAATTTGATAAGGTC-AGTTTACATAAACACTTAGATGGATAGTTT-TTTTTT
66 CAACACACATAGAAATATGATAAGGTCTA-TTTACACAAACACTTAAATGGATAGTTTCTTTTTC
* * *
4521954 CAACATGT-ACGAAAATTTTTAAAATTTCTCTCTATAATGATATGTAAGATATTTTCTAATTTTA
130 CAACATGTGA-AAAAATTCTTAAAATTTCTCTCTATAATGATATGTAAGATATTTCCTAA-TTTA
*
4522018 AGTTATTTATCAAAAAATAT-TAATTTAAAAAGTATTTAATTATCCAAAAC
193 AGCTATTTATCAAAAAATATAT-A-TTAAAAAGTATTTAATTATCCAAAAC
4522068 TTTC
1 TTTC
4522072 AAATTTAAGT
Statistics
Matches: 214, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
237 1 0.00
238 58 0.27
239 59 0.28
240 88 0.41
241 8 0.04
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.43
Consensus pattern (241 bp):
TTTCTTTAGTTTCTTTCATTTTTGAAACAAAAATCATATCATATATCATACATAATATTATATTA
CAACACACATAGAAATATGATAAGGTCTATTTACACAAACACTTAAATGGATAGTTTCTTTTTCC
AACATGTGAAAAAATTCTTAAAATTTCTCTCTATAATGATATGTAAGATATTTCCTAATTTAAGC
TATTTATCAAAAAATATATATTAAAAAGTATTTAATTATCCAAAAC
Found at i:4522279 original size:74 final size:72
Alignment explanation
Indices: 4522155--4522353 Score: 196
Period size: 72 Copynumber: 2.8 Consensus size: 72
4522145 TACATTTCCA
* * * *
4522155 AATAATCT-AATATATAT-TTTTCAATTTAAAATTTTCAAATA-ATGATATATTATCTTTTAAAA
1 AATAATATAAATATATATCTTTTAAATTTAAAAATTTCAAATATATGA-ATATTA--TTATAAAA
*
4522217 TAGGTTTTC-T
63 T-GGATTTCTT
* *
4522227 AATAATATAAATATATATCTTTTAAATCTAAAAATTTCAAATATAGTG-ATATTATTATAAAGTG
1 AATAATATAAATATATATCTTTTAAATTTAAAAATTTCAAATATA-TGAATATTATTATAAAATG
4522291 GATTTCTT
65 GATTTCTT
* * * *
4522299 AATAATTTAAATATATGTCTTTTTAAATTTGAAAATTT-AAA-ATATGAATTTTATT
1 AATAATATAAATATATATC-TTTTAAATTTAAAAATTTCAAATATATGAATATTATT
4522354 TTTAGAGATT
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
70 2 0.02
71 16 0.15
72 35 0.32
73 25 0.23
74 27 0.25
75 1 0.01
76 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.47
Consensus pattern (72 bp):
AATAATATAAATATATATCTTTTAAATTTAAAAATTTCAAATATATGAATATTATTATAAAATGG
ATTTCTT
Found at i:4524141 original size:23 final size:24
Alignment explanation
Indices: 4524102--4524162 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
4524092 ATTTACACAC
*
4524102 ATATATATA-AATTAAAAATGAAA
1 ATATATATATAATTAAAAATAAAA
4524125 AT-TATATATAATTAAAAATAAAA
1 ATATATATATAATTAAAAATAAAA
4524148 ATAATATATATAATT
1 AT-ATATATATAATT
4524163 TTTGTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 6 0.18
23 17 0.50
25 11 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATATATAATTAAAAATAAAA
Found at i:4525230 original size:108 final size:107
Alignment explanation
Indices: 4525074--4525377 Score: 287
Period size: 108 Copynumber: 2.8 Consensus size: 107
4525064 TGTTTGTTCG
* * * *
4525074 AACAAATGCCTTATTTGATGCTTTTTTCAGAAT-TCTTGCAAAAACATTAAAAAAGGCATTTCTT
1 AACAAATG-CTTATTTGAT-TTTTTTTCAAAATAT-TTACAAAAGCATTAAAAAAGGCATTTCTT
*
4525138 TAAACAAA-GTCTTATTTGACCCATTCAAATAAGGTGTTTTCCTTT-
63 TAAACAAACGTCTTATTTAACCCATTCAAATAAGGTG-TTT-CTTTA
* * *
4525183 TATAAATGTCTTATTTGATTTTTTTTCAAAATATTTACAAAAGCATTAAATAAA-GCGTTTCTTT
1 AACAAATG-CTTATTTGATTTTTTTTCAAAATATTTACAAAAGCATTAAA-AAAGGCATTTCTTT
* **
4525247 GAACAAACGTCTTATTTAACCTGTTCAAATAAGGTGTTTCTTTA
64 AAACAAACGTCTTATTTAACCCATTCAAATAAGGTGTTTCTTTA
* * * *
4525291 AACAAATGCCTAGTTTGATTTTTTTTCCCACATATTTAC-AAAGTCCATTCAAATAAGGCATTTT
1 AACAAATGCTTA-TTTGATTTTTTTT-CAAAATATTTACAAAAG--CATT-AAAAAAGGCA-TTT
**
4525355 CTTTTTACAAAC-TCTTTATTTAA
60 CTTTAAACAAACGTC-TTATTTAA
4525378 TAGACAATCT
Statistics
Matches: 162, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
107 7 0.04
108 66 0.41
109 55 0.34
110 6 0.04
111 7 0.04
112 21 0.13
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (107 bp):
AACAAATGCTTATTTGATTTTTTTTCAAAATATTTACAAAAGCATTAAAAAAGGCATTTCTTTAA
ACAAACGTCTTATTTAACCCATTCAAATAAGGTGTTTCTTTA
Found at i:4527989 original size:14 final size:14
Alignment explanation
Indices: 4527968--4528003 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4527958 ACTAAAATTC
4527968 ATAATAAAAATAATA
1 ATAATAAAAA-AATA
4527983 A-AATAAAAAAATA
1 ATAATAAAAAAATA
4527996 ATAATAAA
1 ATAATAAA
4528004 CCTATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAATAAAAAAATA
Found at i:4527994 original size:16 final size:17
Alignment explanation
Indices: 4527968--4527999 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4527958 ACTAAAATTC
4527968 ATAATAAAAATAATAAA
1 ATAATAAAAATAATAAA
4527985 ATAA-AAAAATAATAA
1 ATAATAAAAATAATAA
4528000 TAAACCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAATAAAAATAATAAA
Found at i:4528175 original size:21 final size:19
Alignment explanation
Indices: 4528149--4528197 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
4528139 TTATTTGAAC
4528149 TTTAGATTTAACCCATTTGAT
1 TTTAGATTT-A-CCATTTGAT
*
4528170 TTTAGATTTATCATTTGAT
1 TTTAGATTTACCATTTGAT
*
4528189 TTTATATTT
1 TTTAGATTT
4528198 TGGACTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 1 0.04
21 9 0.35
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (19 bp):
TTTAGATTTACCATTTGAT
Found at i:4529545 original size:17 final size:19
Alignment explanation
Indices: 4529519--4529557 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
4529509 CGTAATTTGT
4529519 TTTTGGTATTT-TTT-TTA
1 TTTTGGTATTTATTTATTA
*
4529536 TTTTGTTATTTATTTATTA
1 TTTTGGTATTTATTTATTA
4529555 TTT
1 TTT
4529558 CTCTTGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (19 bp):
TTTTGGTATTTATTTATTA
Found at i:4529687 original size:57 final size:58
Alignment explanation
Indices: 4529625--4529996 Score: 371
Period size: 58 Copynumber: 6.5 Consensus size: 58
4529615 TTGGAATACT
*
4529625 AATTTTTCCTT-AATAAAAAGTATTTCAAAAAAATATTTAAAG-AAAAGTTGAAGTGTC
1 AATTTTTCCTTAAATAAAAA-TATTTCAAAAAAATATTTAAAGAAAAAGTTGAAGTATC
* * * ** * *
4529682 AA-TTTTCTTTAAATAAAAAAATATTTCACAAAAATGTTTTGAGAAAAAGTTGAAATATT
1 AATTTTTCCTTAAAT--AAAAATATTTCAAAAAAATATTTAAAGAAAAAGTTGAAGTATC
* * *
4529741 AATTTTT-CTTAAATAAAAATTTTTTCAAAAAAATGTTTTAAGGAAAAA-TTGAAGTA-C
1 AATTTTTCCTTAAATAAAAA-TATTTCAAAAAAAT-ATTTAAAGAAAAAGTTGAAGTATC
** * * *
4529798 AAAATTTCCTTAAATAAGAAATATTTCAAAAAAATATTT-GAGAAAAAATTAAAGTATC
1 AATTTTTCCTTAAATAA-AAATATTTCAAAAAAATATTTAAAGAAAAAGTTGAAGTATC
* * *
4529856 AAATTTT-CTT-AA-AAAAATATTTC-AAAAAATATTTTAAGAAAAAGTTGAATTATC
1 AATTTTTCCTTAAATAAAAATATTTCAAAAAAATATTTAAAGAAAAAGTTGAAGTATC
4529910 AATTTTT--TTAAAATAAAAATATTTC-AAAAAATATTT-AAGAAAAAGTTGAAGTATC
1 AATTTTTCCTT-AAATAAAAATATTTCAAAAAAATATTTAAAGAAAAAGTTGAAGTATC
*
4529965 AA-TTTTCCTTAAAACAAAAATAATTTCAAAAA
1 AATTTTTCCTT-AAATAAAAAT-ATTTCAAAAA
4529997 GATTTGAGGA
Statistics
Matches: 264, Mismatches: 32, Indels: 37
0.79 0.10 0.11
Matches are distributed among these distances:
53 13 0.05
54 34 0.13
55 24 0.09
56 49 0.19
57 33 0.12
58 70 0.27
59 37 0.14
60 4 0.02
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.35
Consensus pattern (58 bp):
AATTTTTCCTTAAATAAAAATATTTCAAAAAAATATTTAAAGAAAAAGTTGAAGTATC
Found at i:4530061 original size:109 final size:106
Alignment explanation
Indices: 4529628--4530079 Score: 312
Period size: 111 Copynumber: 4.0 Consensus size: 106
4529618 GAATACTAAT
* * *
4529628 TTTTCCTTAATAAAAAGTATTTCAAAAAA-ATATTTAA-AGAAAAGTTGAAGTGTCAATTTTCTT
1 TTTT-CTTAA-AAAAA-TATTTCAAAAAAGAT-TTTAAGA-AAAAGTTGAAATATCAATTTTC-C
* *
4529691 TAAATAAAAAAATATTTCACAAAAATGTTTTGAGAAAAAGTTGAAA-TATTAA
60 TAAA-ATAAAAATATTTCA-AAAAA---TTTGAGAAAAAGTT-AAAGTATCAA
* * *
4529743 TTTTTCTTAAATAAAAATTTTTTCAAAAAA-ATGTTTTAAGGAAAAA-TTGAAGTA-CAAAATTT
1 -TTTTCTT-AA-AAAAA-TATTTCAAAAAAGA--TTTTAA-GAAAAAGTTGAAATATC-AATTTT
* *
4529805 CCTTAAATAAGAAATATTTCAAAAAAATATTTGAGAAAAAATTAAAGTATCAAA
58 CCTAAAATAA-AAATATTTC--AAAAA-ATTTGAGAAAAAGTTAAAGTATC-AA
* * **
4529859 TTTTCTTAAAAAAATATTTCAAAAAATATTTTAAGAAAAAGTTGAATTATCAATTTTTTTAAAAT
1 TTTTCTTAAAAAAATATTTCAAAAAAGATTTTAAGAAAAAGTTGAAATATCAATTTTCCTAAAAT
* *
4529924 AAAAATATTTCAAAAAATATTTAAGAAAAAGTTGAAGTATCAA
66 AAAAATATTTC-AAAAA-ATTTGAGAAAAAGTTAAAGTATCAA
* * *
4529967 TTTTCCTTAAAACAAAAATAATTTC-AAAAAGA-TTTGAGGAAAAGTTTAAATATCAATTTCTCC
1 TTTT-CTT--AA-AAAAAT-ATTTCAAAAAAGATTTTAAGAAAAAGTTGAAATATCAATTT-TCC
* * * * *
4530030 TAAAAT-GAAATTTTTC-AAGAATTTGAGGAAAAAGTCAAAGTATCGA
60 TAAAATAAAAATATTTCAAAAAATTTGA-GAAAAAGTTAAAGTATCAA
4530076 TTTT
1 TTTT
4530080 TCTTTGAAAT
Statistics
Matches: 282, Mismatches: 32, Indels: 51
0.77 0.09 0.14
Matches are distributed among these distances:
108 11 0.04
109 53 0.19
110 15 0.05
111 58 0.21
112 31 0.11
113 11 0.04
114 5 0.02
115 29 0.10
116 39 0.14
117 22 0.08
118 7 0.02
119 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (106 bp):
TTTTCTTAAAAAAATATTTCAAAAAAGATTTTAAGAAAAAGTTGAAATATCAATTTTCCTAAAAT
AAAAATATTTCAAAAAATTTGAGAAAAAGTTAAAGTATCAA
Found at i:4534009 original size:8 final size:8
Alignment explanation
Indices: 4533988--4534020 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
4533978 TGAAGTAAAT
4533988 AAAAT-AA
1 AAAATGAA
*
4533995 AATATGAA
1 AAAATGAA
4534003 AAAATGAA
1 AAAATGAA
4534011 AAAATGAA
1 AAAATGAA
4534019 AA
1 AA
4534021 TGAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (8 bp):
AAAATGAA
Found at i:4534966 original size:20 final size:22
Alignment explanation
Indices: 4534936--4534975 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4534926 GTATCATTAT
4534936 TATACAAAATTTT-AACTTTCG
1 TATACAAAATTTTCAACTTTCG
4534957 TATA-AAAATTTTCAACTTT
1 TATACAAAATTTTCAACTTT
4534976 TGAATCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (22 bp):
TATACAAAATTTTCAACTTTCG
Found at i:4535211 original size:43 final size:43
Alignment explanation
Indices: 4535163--4535252 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
4535153 AATCATAACA
* * * *
4535163 AAATTTTATATGAATCTCCAAAGTTTTTGAATTAGAATCTTTG
1 AAATTTTAGATGAAACTCCAAAATTTTTGAATGAGAATCTTTG
* * *
4535206 AAATTTTGGATGAAACTCTAAAATTTTTTAATGAGAATCTTTG
1 AAATTTTAGATGAAACTCCAAAATTTTTGAATGAGAATCTTTG
4535249 AAAT
1 AAAT
4535253 ATTGAATCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (43 bp):
AAATTTTAGATGAAACTCCAAAATTTTTGAATGAGAATCTTTG
Found at i:4535212 original size:23 final size:23
Alignment explanation
Indices: 4535186--4535252 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
4535176 ATCTCCAAAG
4535186 TTTTTGAATTAGAATCTTTGAAA
1 TTTTTGAATTAGAATCTTTGAAA
* * * *
4535209 -TTTTGGA-T-GAAACTCTAAAA
1 TTTTTGAATTAGAATCTTTGAAA
* *
4535229 TTTTTTAATGAGAATCTTTGAAA
1 TTTTTGAATTAGAATCTTTGAAA
4535252 T
1 T
4535253 ATTGAATCAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
20 9 0.29
21 6 0.19
22 6 0.19
23 10 0.32
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (23 bp):
TTTTTGAATTAGAATCTTTGAAA
Found at i:4535472 original size:17 final size:17
Alignment explanation
Indices: 4535452--4535538 Score: 97
Period size: 17 Copynumber: 5.2 Consensus size: 17
4535442 AACCTTCCAT
4535452 TCTTGCGAATCTGAAAA
1 TCTTGCGAATCTGAAAA
* *
4535469 TCTTTCGAATCT-TAAA
1 TCTTGCGAATCTGAAAA
* *
4535485 TCTTGCAAATCTAAAAA
1 TCTTGCGAATCTGAAAA
** *
4535502 TCTTATGAA-CTTAAAA
1 TCTTGCGAATCTGAAAA
4535518 TCTTGCGAATCTGAAAA
1 TCTTGCGAATCTGAAAA
4535535 TCTT
1 TCTT
4535539 ATAAATCTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
16 26 0.46
17 30 0.54
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (17 bp):
TCTTGCGAATCTGAAAA
Found at i:4535490 original size:33 final size:33
Alignment explanation
Indices: 4535452--4535540 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
4535442 AACCTTCCAT
4535452 TCTTGCGAATCTGAAAATCTT-TCGAATCTT-AAA
1 TCTTGCGAATCTGAAAATCTTAT-GAA-CTTAAAA
* *
4535485 TCTTGCAAATCTAAAAATCTTATGAACTTAAAA
1 TCTTGCGAATCTGAAAATCTTATGAACTTAAAA
4535518 TCTTGCGAATCTGAAAATCTTAT
1 TCTTGCGAATCTGAAAATCTTAT
4535541 AAATCTAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 3 0.06
33 46 0.92
34 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (33 bp):
TCTTGCGAATCTGAAAATCTTATGAACTTAAAA
Found at i:4537497 original size:58 final size:56
Alignment explanation
Indices: 4537381--4537826 Score: 293
Period size: 56 Copynumber: 8.0 Consensus size: 56
4537371 ATTTTTCCTT
* * ** * * *
4537381 AATAAAAATTATTTCAAAAAAAT-ATTTGAGGGAAAGTTGAAGTATTAATTTTCATTA
1 AATAAAAAATATTTC-AAAAAATGTTTTGAGAAAAAGTTAAAGTATCAATTTT-TTTA
4537438 AATAAAAAAATATTTCAAAAAAATGTTTTGAGAAAAAGTTAAAGTATCAATTTTTTTA
1 AAT-AAAAAATATTTC-AAAAAATGTTTTGAGAAAAAGTTAAAGTATCAATTTTTTTA
* * * *
4537496 AAT-AAAAATATTCCAAAAAAATGTTTTGAGTAAAAA-TTGAAGTATAAATTTTCCTTA
1 AATAAAAAATATTTC-AAAAAATGTTTTGAG-AAAAAGTTAAAGTATCAATTTT-TTTA
* * * * * *
4537553 AATAAGAAATATTGCAAAAAAAATATTTT-AGGAAAAA-TTGAAA-TATTAATCTTTGT-
1 AATAAAAAATATTTC--AAAAAATGTTTTGA-GAAAAAGTT-AAAGTATCAATTTTTTTA
* * * * * *
4537609 --TAAAAAATATTTCAAATAATGTTTTAAGGAAAAGTTGAATTATCAATTTTTCTAA
1 AATAAAAAATATTTCAAAAAATGTTTTGAGAAAAAGTTAAAGTATCAATTTTT-TTA
* * *
4537664 AATAAAAAATATTTCAAAAAATG-TTTAAGAAAAAATGT-AATTATCAATTTTTCTTA
1 AATAAAAAATATTTCAAAAAATGTTTTGAGAAAAAGT-TAAAGTATCAATTTTT-TTA
*
4537720 AA-ACAAAAATAATTTC-AAAAA-GATTTGAGGAAAAAGTTGAAA-TATCAATTTTTTTTTA
1 AATA-AAAAAT-ATTTCAAAAAATGTTTTGA-GAAAAAGTT-AAAGTATCAA--TTTTTTTA
* * **
4537778 AAT-GAAAAT-TTTC-AAGAAT-TTAAG-GAAAAAGTTAAAGTATCAATTTTTT
1 AATAAAAAATATTTCAAAAAATGTTTTGAGAAAAAGTTAAAGTATCAATTTTTT
4537827 CTTGAAATTA
Statistics
Matches: 322, Mismatches: 40, Indels: 60
0.76 0.09 0.14
Matches are distributed among these distances:
51 6 0.02
52 20 0.06
53 27 0.08
54 11 0.03
55 12 0.04
56 86 0.27
57 59 0.18
58 57 0.18
59 44 0.14
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (56 bp):
AATAAAAAATATTTCAAAAAATGTTTTGAGAAAAAGTTAAAGTATCAATTTTTTTA
Found at i:4537687 original size:57 final size:58
Alignment explanation
Indices: 4537370--4537772 Score: 347
Period size: 56 Copynumber: 7.1 Consensus size: 58
4537360 TTGGAATACT
* * * *
4537370 AATTTTTCCTT-AATAAAAATTATTTCAAAAAAAT-ATTTGAGGGAAAGTTGAAGTATT
1 AATTTTT-CTTAAATAAAAAATATTTCAAAAAAATGTTTTGAGGAAAAGTTGAAGTATC
* *
4537427 AA-TTTTCATTAAATAAAAAAATATTTCAAAAAAATGTTTTGAGAAAAAGTTAAAGTATC
1 AATTTTTC-TTAAAT-AAAAAATATTTCAAAAAAATGTTTTGAGGAAAAGTTGAAGTATC
* * * *
4537486 AATTTTT-TTAAAT-AAAAATATTCCAAAAAAATGTTTTGAGTAAAAATTGAAGTATA
1 AATTTTTCTTAAATAAAAAATATTTCAAAAAAATGTTTTGAGGAAAAGTTGAAGTATC
* * * * * * *
4537542 AATTTTCCTTAAATAAGAAATATTGCAAAAAAAATATTTT-AGGAAAAATTGAAATATT
1 AATTTTTCTTAAATAAAAAATATTTC-AAAAAAATGTTTTGAGGAAAAGTTGAAGTATC
* * * * *
4537600 AATCTTT-GT---TAAAAAATATTTC-AAATAATGTTTTAAGGAAAAGTTGAATTATC
1 AATTTTTCTTAAATAAAAAATATTTCAAAAAAATGTTTTGAGGAAAAGTTGAAGTATC
* * ** *
4537653 AATTTTTCTAAAATAAAAAATATTTC-AAAAAATG-TTT-AAGAAAAAATGTAATTATC
1 AATTTTTCTTAAATAAAAAATATTTCAAAAAAATGTTTTGAGGAAAAGTTG-AAGTATC
* *
4537709 AATTTTTCTTAAA-ACAAAAATAATTTC--AAAAA-GATTTGAGGAAAAAGTTGAAATATC
1 AATTTTTCTTAAATA-AAAAAT-ATTTCAAAAAAATGTTTTGAGG-AAAAGTTGAAGTATC
4537766 AATTTTT
1 AATTTTT
4537773 TTTTAAATGA
Statistics
Matches: 287, Mismatches: 40, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
52 10 0.03
53 21 0.07
54 11 0.04
55 11 0.04
56 86 0.30
57 52 0.18
58 60 0.21
59 32 0.11
60 4 0.01
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (58 bp):
AATTTTTCTTAAATAAAAAATATTTCAAAAAAATGTTTTGAGGAAAAGTTGAAGTATC
Found at i:4537786 original size:57 final size:54
Alignment explanation
Indices: 4537444--4537840 Score: 187
Period size: 57 Copynumber: 7.1 Consensus size: 54
4537434 ATTAAATAAA
**
4537444 AAAATATTTCAAAAAAATGTTTTGAGAAAAAGTT-AAAGTATCAA-TTTTTTT-AAAT
1 AAAATATTTC-AAAAAAT-TTAAG-GAAAAAGTTGAAA-TATCAATTTTTTTTAAAAT
* * * * * **
4537499 AAAAATATTCCAAAAAAATGTTTTGAGTAAAAA-TTGAAGTATAAATTTTCCTT-AAAT
1 -AAAATATTTC-AAAAAA---TTTAAGGAAAAAGTTGAAATATCAATTTTTTTTAAAAT
* * * * *
4537556 AAGAAATATTGCAAAAAAAATATTTTAGGAAAAA-TTGAAATATTAATCTTTGTT--AA-
1 -A-AAATATTTC---AAAAA-ATTTAAGGAAAAAGTTGAAATATCAATTTTTTTTAAAAT
* * *
4537612 AAAATATTTCAAATAATGTTTTAAGG-AAAAGTTGAATTATCAA-TTTTTCTAAAAT
1 AAAATATTTCAAA-AA--ATTTAAGGAAAAAGTTGAAATATCAATTTTTTTTAAAAT
* * * *
4537667 AAAAAATATTTCAAAAAATGTTTAA-GAAAAA-ATGTAATTATCAATTTTTCTTAAAACA
1 --AAAATATTTCAAAAAA--TTTAAGGAAAAAGTTG-AAATATCAATTTTTTTTAAAA-T
* *
4537725 AAAATAATTTCAAAAAGATTTGAGGAAAAAGTTGAAATATCAATTTTTTTTTAAAT
1 AAAAT-ATTTCAAAAA-ATTTAAGGAAAAAGTTGAAATATCAATTTTTTTTAAAAT
* *
4537781 GAAAAT-TTTC-AAGAATTTAAGGAAAAAGTT-AAAGTATCAATTTTTTCTTGAAATT
1 -AAAATATTTCAAAAAATTTAAGGAAAAAGTTGAAA-TATCAATTTTTT-TT-AAAAT
4537836 AAAAT
1 AAAAT
4537841 TTTTTAAGAA
Statistics
Matches: 270, Mismatches: 40, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
51 3 0.01
52 13 0.05
53 43 0.16
54 20 0.07
55 11 0.04
56 52 0.19
57 81 0.30
58 39 0.14
59 1 0.00
60 6 0.02
61 1 0.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (54 bp):
AAAATATTTCAAAAAATTTAAGGAAAAAGTTGAAATATCAATTTTTTTTAAAAT
Found at i:4537868 original size:55 final size:53
Alignment explanation
Indices: 4537762--4537868 Score: 133
Period size: 55 Copynumber: 2.0 Consensus size: 53
4537752 AAAGTTGAAA
* * *
4537762 TATCAATTTTTTTTTAAATGAAAATTTTCAAGAATTTAAGGAAAAAGTTAAAG
1 TATCAATTTTTTTTGAAATGAAAATTTTCAAGAATTTAAGAAAAAAATTAAAG
* * * *
4537815 TATCAATTTTTTCTTGAAATTAAAATTTTTTAAGAATTTCATAAAAAAATTAAA
1 TATCAATTTTTT-TTGAAATGAAAA-TTTTCAAGAATTTAAGAAAAAAATTAAA
4537869 TAAATATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 12 0.27
54 10 0.22
55 23 0.51
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (53 bp):
TATCAATTTTTTTTGAAATGAAAATTTTCAAGAATTTAAGAAAAAAATTAAAG
Found at i:4540344 original size:61 final size:61
Alignment explanation
Indices: 4540218--4540365 Score: 160
Period size: 61 Copynumber: 2.4 Consensus size: 61
4540208 ATATAAGGGG
* * * * *
4540218 TATTATAATAATTTTGATCAATTATAGTGTAAAGGCTTTTTTGTAAGTATAGTATGAAGGG
1 TATTATAATAATTTTGATCAATTATAGTGTAAAGACCTTTCTATAAGTATAGTATGAAGGA
*
4540279 TATTATAATAATTTTGATCAATTATAGTAG-AAGAGACCTTTCTATAATTAT-G-AT-AAGATGA
1 TATTATAATAATTTTGATCAATTATAGT-GTAA-AGACCTTTCTATAAGTATAGTATGAAG--GA
* *
4540340 TATTATAATAATTTTAATTAATTATA
1 TATTATAATAATTTTGATCAATTATA
4540366 AAAAGATGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
59 3 0.04
60 2 0.03
61 56 0.75
62 14 0.19
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (61 bp):
TATTATAATAATTTTGATCAATTATAGTGTAAAGACCTTTCTATAAGTATAGTATGAAGGA
Found at i:4541772 original size:164 final size:164
Alignment explanation
Indices: 4541501--4541828 Score: 611
Period size: 164 Copynumber: 2.0 Consensus size: 164
4541491 CTCAAAATTT
4541501 ATTATAGGTGTTTTACACATTTCAGGTGTTTTATACGTTATCTCATCATCAGCAACAAAAGTCTA
1 ATTATAGGTGTTTTACACATTTCAGGTGTTTTATACGTTATCTCATCATCAGCAACAAAAGTCTA
*
4541566 TCTTGATTTGAACATTCTAAAGACTACTCAACTAAAATCAGGCATGTATCATTATATTCAACGTT
66 TCTTGATTTGAACATTCTAAAGACTACTCAACTAAAATCAGGCATATATCATTATATTCAACGTT
* *
4541631 TGCTGCTCAAACTTACATTATATATGTACTTACA
131 TGCTACTCAAACTTACAATATATATGTACTTACA
*
4541665 ATTATAGGTTTTTTACACATTTCAGGTGTTTTATACGTTATCTCATCATCAGCAACAAAAGTCTA
1 ATTATAGGTGTTTTACACATTTCAGGTGTTTTATACGTTATCTCATCATCAGCAACAAAAGTCTA
*
4541730 TCTTGATTTGAACATTCTAAAGACTACTCAACTAAAATCAGGCATATATCATTATATTCAATGTT
66 TCTTGATTTGAACATTCTAAAGACTACTCAACTAAAATCAGGCATATATCATTATATTCAACGTT
4541795 TGCTACTCAAACTTACAATATATATGTACTTACA
131 TGCTACTCAAACTTACAATATATATGTACTTACA
4541829 TGTATTTAAT
Statistics
Matches: 159, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
164 159 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (164 bp):
ATTATAGGTGTTTTACACATTTCAGGTGTTTTATACGTTATCTCATCATCAGCAACAAAAGTCTA
TCTTGATTTGAACATTCTAAAGACTACTCAACTAAAATCAGGCATATATCATTATATTCAACGTT
TGCTACTCAAACTTACAATATATATGTACTTACA
Found at i:4544461 original size:11 final size:11
Alignment explanation
Indices: 4544460--4544771 Score: 123
Period size: 11 Copynumber: 27.5 Consensus size: 11
4544450 TTATATTAAT
4544460 ATAATATTAT-
1 ATAATATTATA
*
4544470 ATAAATAATATA
1 AT-AATATTATA
* * *
4544482 CTATTAATATA
1 ATAATATTATA
4544493 AT-ATATTGATAA
1 ATAATATT-AT-A
4544505 ATAATATTATA
1 ATAATATTATA
4544516 AT-ATATTAATAA
1 ATAATATT-AT-A
4544528 ATAATATTATA
1 ATAATATTATA
4544539 AT-ATATTCATAA
1 ATAATATT-AT-A
4544551 ATAATATTATA
1 ATAATATTATA
* * *
4544562 TTAATA-AACA
1 ATAATATTATA
*
4544572 ATATTATTAT-
1 ATAATATTATA
* *
4544582 ATATTAATA-A
1 ATAATATTATA
*
4544592 ATACTATTATAA
1 ATAATATTAT-A
4544604 ATAAATATATACTA
1 AT-AATAT-TA-TA
4544618 AT-ATATTAATA
1 ATAATATT-ATA
* *
4544629 TTAATA-AATA
1 ATAATATTATA
4544639 AT-ATATTATTA
1 ATAATATTA-TA
*
4544650 ATACATAATATA
1 ATA-ATATTATA
* * *
4544662 CTATTAATATA
1 ATAATATTATA
*
4544673 A-GATATTAATAA
1 ATAATATT-AT-A
*
4544685 ATAATATTAAGAA
1 ATAATATT-A-TA
4544698 ATAATATTATA
1 ATAATATTATA
4544709 AT-ATATTAATAA
1 ATAATATT-AT-A
*
4544721 ATAATATAATA
1 ATAATATTATA
4544732 ATAAATATTAT-
1 AT-AATATTATA
4544743 -TAAT-TTAATTA
1 ATAATATT-A-TA
4544754 ATAAATATTATA
1 AT-AATATTATA
4544766 ATAATA
1 ATAATA
4544772 CATGAACAAA
Statistics
Matches: 231, Mismatches: 33, Indels: 75
0.68 0.10 0.22
Matches are distributed among these distances:
8 2 0.01
9 7 0.03
10 51 0.22
11 64 0.28
12 51 0.22
13 48 0.21
14 7 0.03
15 1 0.00
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (11 bp):
ATAATATTATA
Found at i:4544558 original size:23 final size:23
Alignment explanation
Indices: 4544558--4544838 Score: 107
Period size: 23 Copynumber: 11.9 Consensus size: 23
4544548 TAAATAATAT
* *
4544558 TATATTAATAAACAATATTATTA
1 TATATTAATAAATAATATTATAA
*
4544581 TATATTAATAAATACTATTATAA
1 TATATTAATAAATAATATTATAA
* * * *
4544604 -ATA--AATATATACTAATATAT
1 TATATTAATAAATAATATTATAA
4544624 TAATATTAATAAATAATATATTATTAA
1 T-ATATTAATAAAT-A-ATATTA-TAA
* * * *
4544651 TACA-TAATATACTATTAATATAA
1 TATATTAATA-AATAATATTATAA
* *
4544674 GATATTAATAAATAATATTAAGAAA
1 TATATTAATAAATAATATT-A-TAA
4544699 TAATATT-AT-AAT-ATATTAATAA
1 T-ATATTAATAAATAATATT-ATAA
4544721 -ATAATATAAT-AATAAATATTATTAA
1 TAT-AT-TAATAAAT-AATATTA-TAA
* * *
4544746 TTTAATTAATAAATATTATAATAA
1 TAT-ATTAATAAATAATATTATAA
* * * *
4544770 TACATGAACAAATAATA-TATCA
1 TATATTAATAAATAATATTATAA
* *
4544792 T-TAATAAATAACATACTATTAATATAA
1 TAT-ATTAATAA-ATA--A-TATTATAA
*
4544819 TATATTAATAAATATTATTA
1 TATATTAATAAATAATATTA
4544839 ATAAATAATA
Statistics
Matches: 192, Mismatches: 39, Indels: 54
0.67 0.14 0.19
Matches are distributed among these distances:
20 16 0.08
21 2 0.01
22 19 0.10
23 61 0.32
24 24 0.12
25 29 0.15
26 25 0.13
27 15 0.08
28 1 0.01
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (23 bp):
TATATTAATAAATAATATTATAA
Found at i:4544679 original size:49 final size:48
Alignment explanation
Indices: 4544456--4544850 Score: 129
Period size: 46 Copynumber: 8.1 Consensus size: 48
4544446 AATATTATAT
* *
4544456 TAATATAATATTATATAAATAATATACTATTAATATAATATATTGATAAA
1 TAATATATTATTA-AT-AATAATATACTATTAATATAATATATTAATAAA
* * * *
4544506 T-A-ATATTA-TAATATATTAATA-AATAATATTATAATATATTCATAAA
1 TAATATATTATTAATA-A-TAATATACTATTAATATAATATATTAATAAA
* * *
4544552 TAATAT-TATATTAATAAACAATATTATTATATATTAATAAATACTATT-ATAAA
1 TAATATAT-TATTAAT-AATAATA-TACTAT-TAAT-AT-AATA-TATTAATAAA
* * * *
4544605 TAA-ATATATACTAATATATTAATATTAATAAATAATAT-AT-TATTAATACA
1 TAATATAT-TATTAATA-A-TAATA-TACT-ATTAATATAATATATTAATAAA
* * *
4544655 TAATATACTATTAAT-AT-A-AGA-TATTAATA-AATAATATTAAGAAA
1 TAATATATTATTAATAATAATATACTATTAATATAAT-ATATTAATAAA
* * * *
4544699 TAATATTATAATATATTAATAA-ATAATA-TAATAATAAATATTATTAATTTAAT
1 TAATA-TATTAT-TAATAATAATATACTATTAAT-AT-AATA-TATTAA--TAAA
* * *
4544752 TAATAAATATTA-TAATAATACATGA-ACAAATAATAT-AT-CATTAATAAA
1 TAAT--ATATTATTAATAATA-AT-ATACTATTAATATAATATATTAATAAA
* *
4544800 TAACATACTATTAAT-AT-A-ATA-TATTAATA-AATATTATTAATAAA
1 TAATATATTATTAATAATAATATACTATTAATATAATA-TATTAATAAA
4544844 TAATATA
1 TAATATA
4544851 AAGAATAATA
Statistics
Matches: 263, Mismatches: 38, Indels: 94
0.67 0.10 0.24
Matches are distributed among these distances:
42 17 0.06
43 2 0.01
44 30 0.11
45 6 0.02
46 36 0.14
47 16 0.06
48 27 0.10
49 13 0.05
50 24 0.09
51 18 0.07
52 14 0.05
53 30 0.11
54 23 0.09
55 7 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (48 bp):
TAATATATTATTAATAATAATATACTATTAATATAATATATTAATAAA
Found at i:4544800 original size:18 final size:17
Alignment explanation
Indices: 4544437--4544850 Score: 196
Period size: 18 Copynumber: 24.9 Consensus size: 17
4544427 ATAATTTTAC
4544437 TTAATAAATAATATTATA
1 TTAATAAATAATA-TATA
4544455 TTAAT--ATAATAT-TA
1 TTAATAAATAATATATA
4544469 -T-ATAAATAATATACTA
1 TTAATAAATAATATA-TA
4544485 TTAAT--ATAATATATTGA
1 TTAATAAATAATATA-T-A
* *
4544502 TAAATAATATTATAATATA
1 TTAATAA-ATAAT-ATATA
4544521 TTAATAAATAATATTATAA
1 TTAATAAATAATA-TAT-A
4544540 TATATTCATAAATAATATTATA
1 T-TA---ATAAATAATA-TATA
*
4544562 TTAATAAACAATAT-TA
1 TTAATAAATAATATATA
4544578 TTATATATTAATAA-ATACTA
1 TTA-ATA--AATAATATA-TA
4544598 TT-ATAAATAA-ATATA
1 TTAATAAATAATATATA
* *
4544613 -TACTAATATATTA-ATA
1 TTAATAA-ATAATATATA
4544629 TTAATAAATAATATATTA
1 TTAATAAATAATATA-TA
*
4544647 TTAATACATAATATACTA
1 TTAATAAATAATATA-TA
*
4544665 TTAAT--AT-A-AGATA
1 TTAATAAATAATATATA
4544678 TTAATAAATAATAT-TAA
1 TTAATAAATAATATAT-A
** *
4544695 GAAATAATATTATAATATA
1 TTAATAA-ATAAT-ATATA
4544714 TTAATAAATAATATA-A
1 TTAATAAATAATATATA
*
4544730 -TAATAAATATTAT-TAA
1 TTAATAAATAATATAT-A
* *
4544746 TT--TAATTAATAAATA
1 TTAATAAATAATATATA
*
4544761 TT-AT-AAT-A-ATACA
1 TTAATAAATAATATATA
* *
4544774 TGAACAAATAATATATCA
1 TTAATAAATAATATAT-A
*
4544792 TTAATAAATAACATACTA
1 TTAATAAATAATATA-TA
4544810 TTAAT--AT-A-ATATA
1 TTAATAAATAATATATA
4544823 TTAAT--A-AATAT-TA
1 TTAATAAATAATATATA
4544836 TTAATAAATAATATA
1 TTAATAAATAATATA
4544851 AAGAATAATA
Statistics
Matches: 309, Mismatches: 34, Indels: 107
0.69 0.08 0.24
Matches are distributed among these distances:
12 2 0.01
13 28 0.09
14 19 0.06
15 38 0.12
16 57 0.18
17 32 0.10
18 78 0.25
19 22 0.07
20 12 0.04
21 5 0.02
22 2 0.01
23 14 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
TTAATAAATAATATATA
Found at i:4544922 original size:19 final size:20
Alignment explanation
Indices: 4544878--4544924 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
4544868 TTATTTTAAG
*
4544878 TATTTTTTATATTAACATAA
1 TATTTTTAATATTAACATAA
*
4544898 TA-TTTTAATATTAA-ATAT
1 TATTTTTAATATTAACATAA
4544916 TATTTTTAA
1 TATTTTTAA
4544925 AATATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 17 0.71
20 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTAATATTAACATAA
Found at i:4544968 original size:16 final size:16
Alignment explanation
Indices: 4544899--4545002 Score: 53
Period size: 17 Copynumber: 6.6 Consensus size: 16
4544889 TTAACATAAT
*
4544899 ATTTTAATATTAAATA
1 ATTTTAATAATAAATA
*
4544915 TTATTTTTAA-AATATAATT
1 --A-TTTTAATAATA-AATA
*
4544934 ATTTTAGA-ACATTAATA
1 ATTTTA-ATA-ATAAATA
4544951 ATTTTAATAATAAATA
1 ATTTTAATAATAAATA
*
4544967 A-TTT--CAAT--AT-
1 ATTTTAATAATAAATA
4544977 ATTTTAATAATAAATA
1 ATTTTAATAATAAATA
4544993 ATTTTTAATA
1 A-TTTTAATA
4545003 TTTTAATAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 25
0.68 0.07 0.25
Matches are distributed among these distances:
10 1 0.01
11 5 0.07
13 6 0.09
15 5 0.07
16 14 0.21
17 21 0.31
18 6 0.09
19 9 0.13
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (16 bp):
ATTTTAATAATAAATA
Found at i:4544980 original size:26 final size:26
Alignment explanation
Indices: 4544947--4545012 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
4544937 TTAGAACATT
4544947 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
4544972 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
4544998 TA-ATATTTTAATAAT
1 AATATATTTTAATAAT
4545013 TATATTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 17 0.45
26 21 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:4545362 original size:22 final size:23
Alignment explanation
Indices: 4545337--4545381 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4545327 ATAGAATACG
4545337 TTTA-GTTTGAGAAAATATTTTT
1 TTTATGTTTGAGAAAATATTTTT
* *
4545359 TTTATTTTTTAGAAAATATTTTT
1 TTTATGTTTGAGAAAATATTTTT
4545382 AATTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (23 bp):
TTTATGTTTGAGAAAATATTTTT
Found at i:4545386 original size:21 final size:22
Alignment explanation
Indices: 4545346--4545388 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4545336 GTTTAGTTTG
*
4545346 AGAAAATATTTTTTTTATTTTTT
1 AGAAAATA-TTTTTTAATTTTTT
4545369 AGAAAATA-TTTTTAATTTTT
1 AGAAAATATTTTTTAATTTTT
4545389 GTTTTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
AGAAAATATTTTTTAATTTTTT
Found at i:4545809 original size:2 final size:2
Alignment explanation
Indices: 4545797--4545830 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4545787 GCAATTTTAA
4545797 AT AT A- AT AT 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 AT AT AT AT AT A
4545831 AAAGATTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4547045 original size:22 final size:22
Alignment explanation
Indices: 4547014--4547063 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
4547004 TGGTAATTTC
*
4547014 TGATAAAATTTTAGTACCCTTT
1 TGATAAAATTTTAGTAACCTTT
* *
4547036 TGATATAATTTTAGTAATCTTT
1 TGATAAAATTTTAGTAACCTTT
4547058 TGATAA
1 TGATAA
4547064 CTTATGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (22 bp):
TGATAAAATTTTAGTAACCTTT
Found at i:4547613 original size:74 final size:74
Alignment explanation
Indices: 4547481--4547623 Score: 171
Period size: 74 Copynumber: 1.9 Consensus size: 74
4547471 GTTACTGATT
* * * *
4547481 ATTTGTTATAAAATTATAATTGATTTACTATTAATTTATCAATAATTTACTACAAAGTTATCAAT
1 ATTTGTTATAAAATTATAATTGATTTACAATTAAATTATCAATAACTTACCACAAAGTTATCAAT
4547546 AATTAACTA
66 AATTAACTA
* * * * ** *
4547555 ATTTGTTATTAAATTAT-CTCTTATTTACAATTAAATTATTAATAACTTACCATTAAGTTATTAA
1 ATTTGTTATAAAATTATAAT-TGATTTACAATTAAATTATCAATAACTTACCACAAAGTTATCAA
4547619 TAATT
65 TAATT
4547624 TACATCTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
73 1 0.02
74 56 0.98
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.47
Consensus pattern (74 bp):
ATTTGTTATAAAATTATAATTGATTTACAATTAAATTATCAATAACTTACCACAAAGTTATCAAT
AATTAACTA
Found at i:4547859 original size:45 final size:43
Alignment explanation
Indices: 4547766--4547907 Score: 126
Period size: 45 Copynumber: 3.3 Consensus size: 43
4547756 TATTATCAAG
* * * *
4547766 TTATCATTAATTTATACTAAATTATATATGATTTACTATTAAG
1 TTATCATTAATTTATACTAAATTATAAATGATTAACTACTAAA
** *
4547809 TTATCATTAATTTCATTTTAAATTTTCAAATGATTAACTACTAAA
1 TTATCATTAATTT-ATACTAAATTAT-AAATGATTAACTACTAAA
* * ** * *
4547854 TTATCATTAATTTACTAATAAGTTATTTATAATTTACTACTAAA
1 TTATCATTAATTTA-TACTAAATTATAAATGATTAACTACTAAA
4547898 TT-T-ATTAATT
1 TTATCATTAATT
4547908 AATTATTATT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
42 7 0.09
43 14 0.17
44 26 0.32
45 34 0.42
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (43 bp):
TTATCATTAATTTATACTAAATTATAAATGATTAACTACTAAA
Found at i:4547879 original size:22 final size:22
Alignment explanation
Indices: 4547561--4547923 Score: 179
Period size: 22 Copynumber: 16.5 Consensus size: 22
4547551 ACTAATTTGT
*
4547561 TATTAAATTATC-TCTTATTTAC
1 TATTAAATTATCAT-TAATTTAC
* * * *
4547583 AATTAAATTATTAATAACTTAC
1 TATTAAATTATCATTAATTTAC
* * * *
4547605 CATTAAGTTATTAATAATTTAC
1 TATTAAATTATCATTAATTTAC
*
4547627 -ATCTAAATTATCAATAATTTAC
1 TAT-TAAATTATCATTAATTTAC
* *
4547649 TATTATATTATTATGT-ATTTAC
1 TATTAAATTATCAT-TAATTTAC
** *
4547671 TATTATGTTATCATTGATTTAC
1 TATTAAATTATCATTAATTTAC
* * *
4547693 TACTTAATTTTTGATT-ATTTAC
1 TA-TTAAATTATCATTAATTTAC
** * *
4547715 TACAAAATTAACA-TAGATTTAT
1 TATTAAATTATCATTA-ATTTAC
* * *
4547737 TATTAAATTAACAATAATTTAT
1 TATTAAATTATCATTAATTTAC
* *
4547759 TATCAAGTTATCATTAATTTA-
1 TATTAAATTATCATTAATTTAC
* *
4547780 TACTAAATTAT-ATATGATTTAC
1 TATTAAATTATCAT-TAATTTAC
*
4547802 TATTAAGTTATCATTAATTT-C
1 TATTAAATTATCATTAATTTAC
* * * * *
4547823 ATTTTAAATTTTCAAATGATTAAC
1 -TATTAAATTATC-ATTAATTTAC
*
4547847 TACTAAATTATCATTAATTTAC
1 TATTAAATTATCATTAATTTAC
* * *
4547869 TAATAAGTTAT-TTATAATTTAC
1 TATTAAATTATCAT-TAATTTAC
* * *
4547891 TACTAAATTTATTAATTAA-TTAT
1 TATTAAA-TTA-TCATTAATTTAC
4547914 TATTAAATTA
1 TATTAAATTA
4547924 AAGCTGATTT
Statistics
Matches: 263, Mismatches: 59, Indels: 38
0.73 0.16 0.11
Matches are distributed among these distances:
20 3 0.01
21 24 0.09
22 188 0.71
23 42 0.16
24 5 0.02
25 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (22 bp):
TATTAAATTATCATTAATTTAC
Found at i:4548053 original size:14 final size:15
Alignment explanation
Indices: 4548034--4548068 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4548024 ATGACCCATT
4548034 TTATTTTTA-GTTTA
1 TTATTTTTATGTTTA
*
4548048 TTATTTTTATTTTTA
1 TTATTTTTATGTTTA
4548063 TTATTT
1 TTATTT
4548069 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTATTTTTATGTTTA
Found at i:4548057 original size:6 final size:6
Alignment explanation
Indices: 4548032--4548070 Score: 51
Period size: 6 Copynumber: 6.0 Consensus size: 6
4548022 AAATGACCCA
4548032 TTTTAT TTTTAGT TTATTAT TTTTAT TTTTAT TATTTAT
1 TTTTAT TTTTA-T TT-TTAT TTTTAT TTTTAT T-TTTAT
4548071 ATATATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 16 0.53
7 11 0.37
8 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:4548163 original size:27 final size:27
Alignment explanation
Indices: 4548072--4548166 Score: 113
Period size: 27 Copynumber: 3.5 Consensus size: 27
4548062 ATTATTTATA
* *
4548072 TATATATTATCTAATAATATATATTTTA
1 TATAT-TTATCTATTAATATATATTTTT
* *
4548100 T-TAGTTATCCATTAATAT-TATTTTT
1 TATATTTATCTATTAATATATATTTTT
*
4548125 TATTATTTATCTATTAATGTATATTTTT
1 TA-TATTTATCTATTAATATATATTTTT
4548153 TATATTTATCTATT
1 TATATTTATCTATT
4548167 TTTTATTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
25 7 0.12
26 12 0.21
27 28 0.49
28 10 0.18
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TATATTTATCTATTAATATATATTTTT
Found at i:4549123 original size:15 final size:16
Alignment explanation
Indices: 4549091--4549125 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4549081 AAGTATCAAT
*
4549091 TTTTCTTAAAAATAAG
1 TTTTCTAAAAAATAAG
4549107 TTTTCTAAAAAAT-AG
1 TTTTCTAAAAAATAAG
4549122 TTTT
1 TTTT
4549126 AAGAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (16 bp):
TTTTCTAAAAAATAAG
Found at i:4549270 original size:116 final size:117
Alignment explanation
Indices: 4549057--4549327 Score: 349
Period size: 118 Copynumber: 2.3 Consensus size: 117
4549047 ATTTCAAAAC
* *
4549057 AAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAAAAAATAG
1 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTCCTAAAAAATAG
*
4549122 TTTTAAGAAAAAGTTGAAAGTATCAATTTTTT-TTGAAAAT-AAGTTTTCTA-A
66 TTTTAAGAAAAAGTTGAAAGTATCAATTTTTTCTCGAAAATAAAG-TTTC-AGA
*
4549173 AAAATATTTTTGAGGAAAAGTTGAAAGTATTAA-TTTTCTTTAAAAATAA-TTTCCTAAAAAAGG
1 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAGTTTCCTAAAAAA--
** * * *
4549236 TTTTTTTTTATAAAAAGTTGAAAGTATCAA-TTTTTCTCGAAATTAAAGTTTCAGA
63 -TAGTTTTAAGAAAAAGTTGAAAGTATCAATTTTTTCTCGAAAATAAAGTTTCAGA
*
4549291 AAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTT
1 AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
4549328 TTTGTACAAA
Statistics
Matches: 136, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
115 16 0.12
116 41 0.30
117 30 0.22
118 46 0.34
119 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (117 bp):
AAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTCCTAAAAAATAG
TTTTAAGAAAAAGTTGAAAGTATCAATTTTTTCTCGAAAATAAAGTTTCAGA
Found at i:4549322 original size:57 final size:58
Alignment explanation
Indices: 4549057--4549327 Score: 318
Period size: 58 Copynumber: 4.7 Consensus size: 58
4549047 ATTTCAAAAC
* *
4549057 AAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTCTAA
1 AAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAA
* *
4549115 AAAATAGTTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTTGAAAATAAGTTTTCTAA
1 AAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAA
* * * * *
4549173 AAAATATTTTTGAGGAAAAGTTGAAAGTATTAA-TTTTCTTTAAAAATAA-TTTCCTAA
1 AAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAGTTTTCTAA
* * * * *
4549230 AAAAGGTTTTTTTTTATAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAG-TTTC-AGA
1 AAAA---TATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAGTTTTCTA-A
*
4549291 AAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTT
1 AAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTT
4549328 TTTGTACAAA
Statistics
Matches: 182, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
57 44 0.24
58 93 0.51
60 30 0.16
61 15 0.08
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (58 bp):
AAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAA
Found at i:4560915 original size:43 final size:43
Alignment explanation
Indices: 4560849--4561052 Score: 275
Period size: 43 Copynumber: 4.7 Consensus size: 43
4560839 AGCTTTGTTT
* *
4560849 AAGTTGTTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTCA
1 AAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCA
* *
4560892 AAGTCGTTGAACCTCTGTTTAGAGGAGCTTTTTTTATTTTTTCA
1 AAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA-TTTTTCA
* * *
4560936 AAGTCGTTGAGCCTCTGTTTAGAGAAACTTTATTTATTTTCCA
1 AAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCA
* *
4560979 AAGTCATTTAGCCTCTGTTTAGAGGCA-CTTTATTTATTTTTCA
1 AAGTCGTTGAGCCTCTGTTTAGAGG-AGCTTTATTTATTTTTCA
* * *
4561022 AAGTCGTTGAGCTTTTGTTTAGAAGAGCTTT
1 AAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
4561053 GATCAAAATT
Statistics
Matches: 140, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 99 0.71
44 40 0.29
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (43 bp):
AAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCA
Found at i:4560922 original size:78 final size:79
Alignment explanation
Indices: 4560769--4560914 Score: 206
Period size: 78 Copynumber: 1.8 Consensus size: 79
4560759 TTTACTTTCA
* * *
4560769 AAGTTGTGATGCCTCTGTTTAGAAGAACTTTGTTTATTTTTTTCAAAGTCATTGAGCCTCTGTTT
1 AAGTTGTGATGCCTCTATTTAGAAGAACTTTATTTA-TTTTTTCAAAGTCATTGAACCTCTGTTT
4560834 AGAAAAGCTTTGTTT
65 AGAAAAGCTTTGTTT
* * *
4560849 AAGTTGTTGA-GCCTCTATTTAGAGGAGCTTTATTTA-TTTTTCAAAGTCGTTGAACCTCTGTTT
1 AAGTTG-TGATGCCTCTATTTAGAAGAACTTTATTTATTTTTTCAAAGTCATTGAACCTCTGTTT
4560912 AGA
65 AGA
4560915 GGAGCTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
78 28 0.47
80 28 0.47
81 3 0.05
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (79 bp):
AAGTTGTGATGCCTCTATTTAGAAGAACTTTATTTATTTTTTCAAAGTCATTGAACCTCTGTTTA
GAAAAGCTTTGTTT
Found at i:4561000 original size:87 final size:86
Alignment explanation
Indices: 4560849--4561044 Score: 268
Period size: 87 Copynumber: 2.3 Consensus size: 86
4560839 AGCTTTGTTT
* * * * * *
4560849 AAGTTGTTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAACCTCTGTTTAG
1 AAGTCGTTGAGCCTCTGTTTAGAGAAACTTTATTTATTTTCCAAAGTCATTGAACCTCTGTTTAG
*
4560914 AGG-AGCTTTTTTTATTTTTTCA
66 AGGCA-CTTTATTTA-TTTTTCA
* *
4560936 AAGTCGTTGAGCCTCTGTTTAGAGAAACTTTATTTATTTTCCAAAGTCATTTAGCCTCTGTTTAG
1 AAGTCGTTGAGCCTCTGTTTAGAGAAACTTTATTTATTTTCCAAAGTCATTGAACCTCTGTTTAG
4561001 AGGCACTTTATTTATTTTTCA
66 AGGCACTTTATTTATTTTTCA
* *
4561022 AAGTCGTTGAGCTTTTGTTTAGA
1 AAGTCGTTGAGCCTCTGTTTAGA
4561045 AGAGCTTTGA
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
86 28 0.29
87 68 0.70
88 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (86 bp):
AAGTCGTTGAGCCTCTGTTTAGAGAAACTTTATTTATTTTCCAAAGTCATTGAACCTCTGTTTAG
AGGCACTTTATTTATTTTTCA
Found at i:4561020 original size:130 final size:123
Alignment explanation
Indices: 4560780--4561053 Score: 329
Period size: 130 Copynumber: 2.2 Consensus size: 123
4560770 AGTTGTGATG
*
4560780 CCTCTGTTTAGAAGAACTTTGTTTATTTTTTTCAAAGTCATTGAGCCTCTGTTTAGAAAAGCTTT
1 CCTCTGTTTAGAAGAGCTTTGTTTATTTTTTTCAAAGTCATTGAGCCTCTGTTTAGAAAAGCTTT
**
4560845 GTTTAAGTTGTTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAA
66 GTTTAAGTCATTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAA
* * *
4560903 CCTCTGTTTAGAGGAGCTTTTTTTA-TTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGAAA-CTT
1 CCTCTGTTTAGAAGAGCTTTGTTTATTTTTTTCAAAGTCATTGAGCCTCTGTTTAGA-AAAGC--
* * *
4560966 TATTTATTTTCCAAAGTCATTTAGCCTCTGTTTAGAGGCA-CTTTATTTATTTTTCAAAGTCGTT
63 --TTT-GTTT---AAGTCATTGAGCCTCTATTTAGAGG-AGCTTTATTTATTTTTCAAAGTCGTT
*
4561030 GAG
121 GAA
* *
4561033 CTTTTGTTTAGAAGAGCTTTG
1 CCTCTGTTTAGAAGAGCTTTG
4561054 ATCAAAATTT
Statistics
Matches: 127, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
122 31 0.24
123 25 0.20
126 3 0.02
127 3 0.02
130 64 0.50
131 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (123 bp):
CCTCTGTTTAGAAGAGCTTTGTTTATTTTTTTCAAAGTCATTGAGCCTCTGTTTAGAAAAGCTTT
GTTTAAGTCATTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAA
Found at i:4561268 original size:15 final size:15
Alignment explanation
Indices: 4561248--4561283 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
4561238 ATGGCCCATT
4561248 TTATTTTTAGTTTTA
1 TTATTTTTAGTTTTA
*
4561263 TTATTTTTATTTTTA
1 TTATTTTTAGTTTTA
4561278 TTATTT
1 TTATTT
4561284 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTATTTTTAGTTTTA
Found at i:4561300 original size:16 final size:18
Alignment explanation
Indices: 4561279--4561317 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4561269 TTATTTTTAT
4561279 TATTTATAT-AT-ATATA
1 TATTTATATAATAATATA
*
4561295 TATTTATCTAATAATATA
1 TATTTATATAATAATATA
4561313 TATTT
1 TATTT
4561318 TTTATTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTATATAATAATATA
Found at i:4561329 original size:28 final size:28
Alignment explanation
Indices: 4561298--4561375 Score: 113
Period size: 27 Copynumber: 2.8 Consensus size: 28
4561288 ATATATATAT
*
4561298 TTATCTAATAATATATATTTTTTATTAG
1 TTATCTATTAATATATATTTTTTATTAG
* *
4561326 TTATCCATTAATAT-TATTTTTTATTAT
1 TTATCTATTAATATATATTTTTTATTAG
*
4561353 TTATCTATTAATGTATATTTTTT
1 TTATCTATTAATATATATTTTTT
4561376 TATTTATCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATCTATTAATATATATTTTTTATTAG
Found at i:4561339 original size:26 final size:26
Alignment explanation
Indices: 4561310--4561383 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 26
4561300 ATCTAATAAT
*
4561310 ATATATTTTTTATTAGTTATCCATTA
1 ATATATTTTTTATTATTTATCCATTA
*
4561336 ATATTATTTTTTATTATTTATCTATTA
1 ATA-TATTTTTTATTATTTATCCATTA
*
4561363 ATGTATATTTTT-TTATTTATC
1 ATATAT-TTTTTATTATTTATC
4561384 TGTTCTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 15 0.35
27 28 0.65
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (26 bp):
ATATATTTTTTATTATTTATCCATTA
Found at i:4562137 original size:3 final size:3
Alignment explanation
Indices: 4562131--4562200 Score: 97
Period size: 3 Copynumber: 23.0 Consensus size: 3
4562121 TTTTTCTTAT
* *
4562131 TTA TTA TTA TTA TT- TCTT TTA GTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4562176 TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA
4562201 GATTAGAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.02
3 56 0.92
4 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4562205 original size:18 final size:16
Alignment explanation
Indices: 4562127--4562247 Score: 99
Period size: 15 Copynumber: 7.6 Consensus size: 16
4562117 TTTTTTTTTC
4562127 TTATTTATTATTATTA
1 TTATTTATTATTATTA
* *
4562143 TTTCTTTTAGTATTATTA
1 -TT-ATTTATTATTATTA
4562161 TTA-TTATTATTATTA
1 TTATTTATTATTATTA
4562176 TTA-TTATTATTATTA
1 TTATTTATTATTATTA
**
4562191 TTATTTATTAGATTAGAA
1 TTATTTATT--ATTATTA
* *
4562209 TTATTTAGTATT-CT-
1 TTATTTATTATTATTA
*
4562223 TTATTTTATTTTTATT-
1 TTA-TTTATTATTATTA
4562239 TTATTTATT
1 TTATTTATT
4562248 TATTTATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 3 0.03
15 42 0.49
16 12 0.14
17 4 0.05
18 25 0.29
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATTTATTATTATTA
Found at i:4562395 original size:68 final size:67
Alignment explanation
Indices: 4562322--4562513 Score: 226
Period size: 68 Copynumber: 3.0 Consensus size: 67
4562312 GTTGAAAGTA
4562322 TCAATTTTTCTTGAAAATAAGTTTTCTAAAAATTATTTTTGAGTAAAAGTTGAAAGTATCAATTT
1 TCAATTTTTCTTGAAAATAAGTTTTCTAAAAA-TATTTTTGAGTAAAAGTTGAAAGTATCAATTT
4562387 TTT
65 TTT
* * * *
4562390 TCAATTTTTTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAGGAAAAGTTGAAAGTATCAA---
1 TCAATTTTTCTTGAAAATAAGTTTTCT-AAAAATATTTTTGAGTAAAAGTTGAAAGTATCAATTT
4562452 TTT
65 TTT
*
4562455 TC-------CTTGAAAATAAGTTTTTTTAAAAATATTTTTGA-TGAAAAGTTGAAAGTATCAATT
1 TCAATTTTTCTTGAAAATAAG-TTTTCTAAAAATATTTTTGAGT-AAAAGTTGAAAGTATCAATT
4562512 TT
64 TT
4562514 CTTTAAAAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
58 41 0.38
59 5 0.05
61 1 0.01
65 5 0.05
68 52 0.48
69 5 0.05
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (67 bp):
TCAATTTTTCTTGAAAATAAGTTTTCTAAAAATATTTTTGAGTAAAAGTTGAAAGTATCAATTTT
TT
Found at i:4562397 original size:126 final size:125
Alignment explanation
Indices: 4562267--4562513 Score: 338
Period size: 126 Copynumber: 2.0 Consensus size: 125
4562257 TTTCAAAATG
* * *
4562267 ATTTTCTTT-AAATAAAATTTCAAAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTT
1 ATTTTCTTTAAAATAAAATTTC-AAAAAA-ATAGTGTTAAGAAAAAGTTGAAAGTATCAATTTTC
4562331 CTTGAAAATAAG-TTTTCTAAAAATTATTTTTGA-GTAAAAGTTGAAAGTATCAATTTTTTTCA
64 CTTGAAAATAAGTTTTTCTAAAAA-TATTTTTGATG-AAAAGTTGAAAGTATCAATTTTTTTCA
* ** * * *
4562393 ATTTTTTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 ATTTTCTTT-AAAATAAAATTTCAAAAAAATAGTGTTAAGAAAAAGTTGAAAGTATCAATTTTCC
*
4562458 TTGAAAATAAGTTTTTTTAAAAATATTTTTGATGAAAAGTTGAAAGTATCAATTTT
65 TTGAAAATAAGTTTTTCTAAAAATATTTTTGATGAAAAGTTGAAAGTATCAATTTT
4562514 CTTTAAAAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
126 81 0.76
127 16 0.15
128 10 0.09
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (125 bp):
ATTTTCTTTAAAATAAAATTTCAAAAAAATAGTGTTAAGAAAAAGTTGAAAGTATCAATTTTCCT
TGAAAATAAGTTTTTCTAAAAATATTTTTGATGAAAAGTTGAAAGTATCAATTTTTTTCA
Found at i:4562455 original size:58 final size:58
Alignment explanation
Indices: 4562390--4562632 Score: 213
Period size: 58 Copynumber: 4.1 Consensus size: 58
4562380 TCAATTTTTT
*
4562390 TCAATTTTTTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAGGAAAAGTTGAAAGTA
1 TCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAGGAAAAGTTGAAAGTA
* * * * * *
4562448 TCAATTTTCCTTGAAAATAAGTTTTTTTAAAAATATTTTTGATGAAAAGTTGAAAGTA
1 TCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAGGAAAAGTTGAAAGTA
* * ** * *
4562506 TCAATTTTCTTTAAAAATAA-TTTCCTAAAAAAGGTTTTTTTTTTTAGGAAAAGTTGAAAGTA
1 TCAATTTTCTTTGAAAATAAGTTTTCTAAAAAA-----TAGTGTTGAGGAAAAGTTGAAAGTA
* * * ** * * *
4562568 TCAATTTTCCTCGAAATTAAAATTTCAAAAAAATA-TTTTG-GAAAAAAGTTGAAAGTA
1 TCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAG-GAAAAGTTGAAAGTA
*
4562625 TTAATTTT
1 TCAATTTT
4562633 TCTTGTACAA
Statistics
Matches: 152, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.01
57 34 0.22
58 70 0.46
62 38 0.25
63 9 0.06
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (58 bp):
TCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATAGTGTTGAGGAAAAGTTGAAAGTA
Found at i:4563299 original size:21 final size:21
Alignment explanation
Indices: 4563274--4563332 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
4563264 TAATTTACTA
**
4563274 TTAAGTTATCAATAATTATTT
1 TTAAGTTATCAATAATTACAT
* *
4563295 TTAAGTTAT-ATTGATTACAT
1 TTAAGTTATCAATAATTACAT
*
4563315 TTAAGTTTTCAATAATTA
1 TTAAGTTATCAATAATTA
4563333 ATTATTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
TTAAGTTATCAATAATTACAT
Found at i:4565579 original size:26 final size:26
Alignment explanation
Indices: 4565550--4565602 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
4565540 ATAATTGAAT
4565550 ATGTTTTTATCCATTTATTTAAATGG
1 ATGTTTTTATCCATTTATTTAAATGG
*
4565576 ATGTTTTTATCCATTTATTTAATTGG
1 ATGTTTTTATCCATTTATTTAAATGG
4565602 A
1 A
4565603 GATTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (26 bp):
ATGTTTTTATCCATTTATTTAAATGG
Found at i:4574571 original size:18 final size:21
Alignment explanation
Indices: 4574548--4574590 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
4574538 TCAATCAAGT
4574548 AAAATTTTAT-AA-AA-TTTA
1 AAAATTTTATCAATAATTTTA
4574566 AAAATTTTATCAATAATTTTA
1 AAAATTTTATCAATAATTTTA
4574587 AAAA
1 AAAA
4574591 AATCAAACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 2 0.09
21 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTTTATCAATAATTTTA
Found at i:4575595 original size:4 final size:4
Alignment explanation
Indices: 4575586--4575612 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4575576 GAGTTCTTCA
4575586 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
4575613 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:4576211 original size:85 final size:85
Alignment explanation
Indices: 4576101--4576275 Score: 289
Period size: 85 Copynumber: 2.1 Consensus size: 85
4576091 AACCCTGGAA
*
4576101 GATTTTATTCATTTTAGCTCTATATTAGGAAATGTTTTAATTGTGAGTTGTCGT-AGTGCAATAT
1 GATTTTATTCATTTTAGCTCTATATTAGGAAATGTTTGAATTGTGAGTTGTCGTGA-TGCAATAT
*
4576165 AGCCTAGGAGAACACATTTTT
65 AGCATAGGAGAACACATTTTT
* * *
4576186 TATTTTATTCGTTTTAGCTTTATATTAGGAAATGTTTGAATTGTGAGTTGTCGTGATGCAATATA
1 GATTTTATTCATTTTAGCTCTATATTAGGAAATGTTTGAATTGTGAGTTGTCGTGATGCAATATA
4576251 GCATAGGAGAACACATTTTT
66 GCATAGGAGAACACATTTTT
4576271 GATTT
1 GATTT
4576276 GATGCATAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 82 0.99
86 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (85 bp):
GATTTTATTCATTTTAGCTCTATATTAGGAAATGTTTGAATTGTGAGTTGTCGTGATGCAATATA
GCATAGGAGAACACATTTTT
Found at i:4608810 original size:15 final size:15
Alignment explanation
Indices: 4608787--4608821 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4608777 ATATTTAACG
4608787 ATTTGGGTATGAAAC
1 ATTTGGGTATGAAAC
* *
4608802 ATTTTGGTATGAATC
1 ATTTGGGTATGAAAC
4608817 ATTTG
1 ATTTG
4608822 ATTTGACTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (15 bp):
ATTTGGGTATGAAAC
Found at i:4614806 original size:43 final size:43
Alignment explanation
Indices: 4614741--4614886 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
4614731 CTTCTACCCA
* *
4614741 ATCATGGCCCTATACAAGGGTGGCTCATAACATCCTATGCCTG
1 ATCATGACCCTATACAATGGTGGCTCATAACATCCTATGCCTG
* *
4614784 ATCATGACCCTATACAATGGTGGCTCTTAACATCTTATGTCC-G
1 ATCATGACCCTATACAATGGTGGCTCATAACATCCTATG-CCTG
** * * *
4614827 ATCATGACTTTATACAATGGTGGCTCATATCATTCTATGCTTG
1 ATCATGACCCTATACAATGGTGGCTCATAACATCCTATGCCTG
* *
4614870 GTCATAACCCTATACAA
1 ATCATGACCCTATACAA
4614887 AATTAACTCA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 83 0.97
44 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (43 bp):
ATCATGACCCTATACAATGGTGGCTCATAACATCCTATGCCTG
Found at i:4617323 original size:31 final size:31
Alignment explanation
Indices: 4617288--4617375 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
4617278 AAATGATCTT
*
4617288 TATACTCATATGAAATTTAAAATTTAGTCCC
1 TATACTCATATGAAATTTAAAATTTACTCCC
* *
4617319 TATACTCACACGAAATTTAAAATTTACTCCC
1 TATACTCATATGAAATTTAAAATTTACTCCC
* * *
4617350 AATATTTATATGAAATTTAAAATTTA
1 TATACTCATATGAAATTTAAAATTTA
4617376 ATCCTTCTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.39
Consensus pattern (31 bp):
TATACTCATATGAAATTTAAAATTTACTCCC
Found at i:4618480 original size:18 final size:18
Alignment explanation
Indices: 4618457--4618496 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4618447 ATTTTAATAT
4618457 TTTTAAAAAATT-AAAAAA
1 TTTT-AAAAATTCAAAAAA
*
4618475 TTTTAAAAATTCAAAATA
1 TTTTAAAAATTCAAAAAA
4618493 TTTT
1 TTTT
4618497 TGTATTAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAATTCAAAAAA
Found at i:4618544 original size:31 final size:31
Alignment explanation
Indices: 4618509--4618590 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
4618499 TATTAGAGGG
*
4618509 ATTAAATTTTAAATTTGGTGCCAATACAAAA
1 ATTAAATTTTAAATTTCGTGCCAATACAAAA
* * * **
4618540 ATTAAATTTCAAATTTCGTGCGAATATAATT
1 ATTAAATTTTAAATTTCGTGCCAATACAAAA
*
4618571 ACTAAATTTTAAATTTCGTG
1 ATTAAATTTTAAATTTCGTG
4618591 TGAATATATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
ATTAAATTTTAAATTTCGTGCCAATACAAAA
Found at i:4624078 original size:2 final size:2
Alignment explanation
Indices: 4624071--4624102 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4624061 ATTTTGATCC
4624071 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
4624103 CTACTTTATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4625016 original size:22 final size:21
Alignment explanation
Indices: 4624973--4625016 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
4624963 TACAATATAT
4624973 ATTTTTTATAATGTCACGAATA
1 ATTTTTTATAATGTCAC-AATA
4624995 ATTTTTTAATAATAGTCA-AATA
1 ATTTTTT-ATAAT-GTCACAATA
4625017 TTAAATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTTTTTATAATGTCACAATA
Found at i:4625073 original size:32 final size:31
Alignment explanation
Indices: 4625031--4625101 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
4625021 ATGTAATATT
* ** *
4625031 TTAATGTGATATTTAAATTATATATTTATTAA
1 TTAATATGATATTTAAAAAAT-TATTTACTAA
4625063 TTAATATGATATTTAAAAAATTATTTACTAA
1 TTAATATGATATTTAAAAAATTATTTACTAA
4625094 TTACATAT
1 TTA-ATAT
4625102 CATTATTGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (31 bp):
TTAATATGATATTTAAAAAATTATTTACTAA
Found at i:4625294 original size:29 final size:29
Alignment explanation
Indices: 4625251--4625320 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
4625241 TAAATTATTT
*
4625251 TAAATTATAATAAATATTTAATATAATATC-
1 TAAATTATAA-AAATATATAATATAATA-CA
*
4625281 TAAATTTTAAAAATATATAATATAATACA
1 TAAATTATAAAAATATATAATATAATACA
4625310 TAAATTATAAA
1 TAAATTATAAA
4625321 TTTATTAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 26 0.72
30 9 0.25
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAATTATAAAAATATATAATATAATACA
Found at i:4625429 original size:32 final size:32
Alignment explanation
Indices: 4625393--4625470 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 32
4625383 ATAAATAATT
*
4625393 TTTAAATATCATATTAATTAATAAATTTAT-AA
1 TTTAAATAT-ATATTAATTAAAAAATTTATAAA
*
4625425 TTTAAATAT-TA-T-ATTAAAAAATTTTTAAA
1 TTTAAATATATATTAATTAAAAAATTTATAAA
4625454 TTTAAATATAATATTAA
1 TTTAAATAT-ATATTAA
4625471 ATGTTTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 12 0.31
29 12 0.31
30 2 0.05
31 2 0.05
32 10 0.26
33 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
TTTAAATATATATTAATTAAAAAATTTATAAA
Found at i:4625467 original size:29 final size:29
Alignment explanation
Indices: 4625374--4625471 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
4625364 AAATGATGAC
* * * *
4625374 ATATGATATATAAATAATTTTTAAATAT-C
1 ATATTATAT-TAAAAAATTTTTAAATTTAA
* *
4625403 ATATTA-ATTAATAAATTTAT-AATTTAA
1 ATATTATATTAAAAAATTTTTAAATTTAA
4625430 ATATTATATTAAAAAATTTTTAAATTTAA
1 ATATTATATTAAAAAATTTTTAAATTTAA
*
4625459 ATATAATATTAAA
1 ATATTATATTAAA
4625472 TGTTTATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
26 4 0.07
27 15 0.26
28 14 0.25
29 24 0.42
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATTATATTAAAAAATTTTTAAATTTAA
Found at i:4626060 original size:14 final size:15
Alignment explanation
Indices: 4626043--4626076 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
4626033 ATTATGTATT
4626043 TAAAATAATT-TCAA
1 TAAAATAATTATCAA
4626057 T-AAATAATTATCAA
1 TAAAATAATTATCAA
4626071 TAAAAT
1 TAAAAT
4626077 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 6 0.33
15 4 0.22
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATAATTATCAA
Found at i:4626709 original size:15 final size:14
Alignment explanation
Indices: 4626689--4626735 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
4626679 AAATATATTT
*
4626689 ATAAATTATAATTAA
1 ATAAATT-TAAATAA
4626704 ATAAATTTAAATAA
1 ATAAATTTAAATAA
*
4626718 ACAAATCTTAAATAA
1 ATAAAT-TTAAATAA
4626733 ATA
1 ATA
4626736 TAAATGAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAATTTAAATAA
Done.