Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 15 of 171
Found at i:6969799 original size:21 final size:21
Alignment explanation
Indices: 6969770--6969829 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
6969760 GAATCTCGAT
*
6969770 GTTTGGGGTTTGGAGTTTAAA
1 GTTTAGGGTTTGGAGTTTAAA
* *
6969791 GTTTAGGGTTTAGAGTTTAAT
1 GTTTAGGGTTTGGAGTTTAAA
*
6969812 GTTTGAGGTTTTGG-GTTT
1 GTTT-AGGGTTTGGAGTTT
6969830 TAGGTTTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 26 0.79
22 7 0.21
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (21 bp):
GTTTAGGGTTTGGAGTTTAAA
Found at i:6974294 original size:15 final size:16
Alignment explanation
Indices: 6974276--6974313 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6974266 GTTTAAAAAT
*
6974276 AAAATAAA-TCGATTA
1 AAAATAAATTCAATTA
*
6974291 AAAATAAATTTAATTA
1 AAAATAAATTCAATTA
6974307 AAAATAA
1 AAAATAA
6974314 TAATTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATAAATTCAATTA
Found at i:6974310 original size:36 final size:36
Alignment explanation
Indices: 6974268--6974336 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
6974258 TATAAGATGT
*
6974268 TTAAAAATAA-AATAAATCGATTAAAAATAAATTTAA
1 TTAAAAATAATAATAAATCAATTAAAAA-AAATTTAA
* *
6974304 TTAAAAATAATAATTAATCAATTATAAAAAATT
1 TTAAAAATAATAATAAATCAATTAAAAAAAATT
6974337 AAAAGACGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 15 0.52
37 14 0.48
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (36 bp):
TTAAAAATAATAATAAATCAATTAAAAAAAATTTAA
Found at i:6975907 original size:22 final size:24
Alignment explanation
Indices: 6975863--6975913 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
6975853 TTCTTCCTGC
*
6975863 TTTTGTTCATAGATTTTCATTTTT
1 TTTTGTTCATAGATTTACATTTTT
*
6975887 TTTTGTT-ATAG-TTTACGTTTTT
1 TTTTGTTCATAGATTTACATTTTT
6975909 TTTTG
1 TTTTG
6975914 GTTGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.56
23 4 0.16
24 7 0.28
ACGTcount: A:0.14, C:0.06, G:0.12, T:0.69
Consensus pattern (24 bp):
TTTTGTTCATAGATTTACATTTTT
Found at i:7001230 original size:42 final size:42
Alignment explanation
Indices: 7001171--7001334 Score: 328
Period size: 42 Copynumber: 3.9 Consensus size: 42
7001161 TATTTTAAAA
7001171 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
1 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
7001213 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
1 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
7001255 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
1 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
7001297 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGT
1 AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGT
7001335 GTTTAAATTT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 122 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (42 bp):
AAGCCACTCAATATTCAAGGGAACATTAATTTATAAGTTTAT
Found at i:7007279 original size:136 final size:137
Alignment explanation
Indices: 7007121--7007375 Score: 327
Period size: 137 Copynumber: 1.9 Consensus size: 137
7007111 TGTTAAAGAT
* * * * * ** * *
7007121 TAACAATAATCACCAACCTCAAAAAT-TTCGAAGAAATTAATGTTTATAATTTATTAAATCAAAA
1 TAACAATAATCACAAACCTCAAAAATCTCCCAAAAAAATAATACTTATAATCTATAAAATCAAAA
* * * *
7007185 TGAAAATAT-ATAAAAT-TTAAAATTATATACCAATTTTTATTTTAATATCAAATAAAAGATAAA
66 TGAAAAT-TGAT-AAATCTAAAAAATATAAACCAATTTTTAATTTAATATCAAATAAAAGATAAA
7007248 CAAAGATGC
129 CAAAGATGC
* *
7007257 TAACAATAATCACAAACTTCAAAAATCTCCCAAAAAAATAATACTTATAATCTGTAAAATCAAAA
1 TAACAATAATCACAAACCTCAAAAATCTCCCAAAAAAATAATACTTATAATCTATAAAATCAAAA
*
7007322 TGAAAATTGATAAATCTAAAAAATATAAATCAATTTTTAATTTAATATCAAATA
66 TGAAAATTGATAAATCTAAAAAATATAAACCAATTTTTAATTTAATATCAAATA
7007376 TTAAATATCA
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
136 29 0.29
137 71 0.71
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (137 bp):
TAACAATAATCACAAACCTCAAAAATCTCCCAAAAAAATAATACTTATAATCTATAAAATCAAAA
TGAAAATTGATAAATCTAAAAAATATAAACCAATTTTTAATTTAATATCAAATAAAAGATAAACA
AAGATGC
Found at i:7011100 original size:31 final size:30
Alignment explanation
Indices: 7011065--7011123 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
7011055 GTTTGAAGAA
7011065 AATCAAGAAGTGAAACATTATAGAACAAACC
1 AATCAA-AAGTGAAACATTATAGAACAAACC
** *
7011096 AATCAATTGTGCAACATTATAGAACAAA
1 AATCAAAAGTGAAACATTATAGAACAAA
7011124 AATAGCTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (30 bp):
AATCAAAAGTGAAACATTATAGAACAAACC
Found at i:7013253 original size:22 final size:21
Alignment explanation
Indices: 7013227--7013271 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
7013217 AATAGGATAA
*
7013227 ATTTAATGTTA-ATTGTAAATTT
1 ATTTAATCTTACATT-T-AATTT
7013249 ATTTAATCTTACATTTAATTT
1 ATTTAATCTTACATTTAATTT
7013270 AT
1 AT
7013272 CAAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 11 0.52
23 3 0.14
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTAATCTTACATTTAATTT
Found at i:7018545 original size:22 final size:22
Alignment explanation
Indices: 7018513--7018569 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
7018503 TCACGACTTA
*
7018513 AATAATAATTTT-TAAATAATTT
1 AATAATTATTTTGTAAAT-ATTT
* *
7018535 AATAATTATTTTGTAACTTTTT
1 AATAATTATTTTGTAAATATTT
7018557 AA-AATTATTTTGT
1 AATAATTATTTTGT
7018570 GATAGAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.35
22 16 0.52
23 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
AATAATTATTTTGTAAATATTT
Found at i:7021493 original size:15 final size:15
Alignment explanation
Indices: 7021473--7021505 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
7021463 TATATTCAAA
7021473 TATTAAAAATAAT-AT
1 TATTAAAAA-AATAAT
7021488 TATTAAAAAAATAAT
1 TATTAAAAAAATAAT
7021503 TAT
1 TAT
7021506 AAATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAAAAAATAAT
Found at i:7029224 original size:14 final size:15
Alignment explanation
Indices: 7029192--7029264 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 15
7029182 TTTGATATGT
* *
7029192 TTTATATATTTTTAT
1 TTTATATATTTATAA
7029207 TTTA-ATATTTATAA
1 TTTATATATTTATAA
7029221 TTTAT-TATCTTCATTAA
1 TTTATATAT-TT-A-TAA
*
7029238 TTTTATATATTGATAA
1 -TTTATATATTTATAA
*
7029254 TATTATTTATT
1 T-TTATATATT
7029265 AAATTATCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
14 15 0.32
15 7 0.15
16 12 0.26
17 4 0.09
18 6 0.13
19 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (15 bp):
TTTATATATTTATAA
Found at i:7041700 original size:23 final size:23
Alignment explanation
Indices: 7041670--7041838 Score: 173
Period size: 23 Copynumber: 7.3 Consensus size: 23
7041660 TAGCGCGCTT
7041670 TCTGTTTAGCACTGTGTGTGCTC
1 TCTGTTTAGCACTGTGTGTGCTC
7041693 TCTGTTTAGCACTGTGTGTGCTC
1 TCTGTTTAGCACTGTGTGTGCTC
* *
7041716 TCTGTTCAGCACTATGTGTGCTC
1 TCTGTTTAGCACTGTGTGTGCTC
* * *
7041739 TCTATTCAGCAC-GTCTCGTGCTC
1 TCTGTTTAGCACTGTGT-GTGCTC
* * * *
7041762 TTTGATTAGCACTTTGTGTACTC
1 TCTGTTTAGCACTGTGTGTGCTC
*
7041785 TCTGTTTAGCACTTTGTGTGC-C
1 TCTGTTTAGCACTGTGTGTGCTC
*
7041807 TACTGTTGCCTAGCACT-TATGTGCTC
1 T-CTGTT---TAGCACTGTGTGTGCTC
7041833 TCTGTT
1 TCTGTT
7041839 CAGTACTTCG
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.03
23 97 0.79
24 2 0.02
25 11 0.09
26 9 0.07
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (23 bp):
TCTGTTTAGCACTGTGTGTGCTC
Found at i:7043386 original size:21 final size:21
Alignment explanation
Indices: 7043349--7043435 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 21
7043339 AAAAACGTAT
*
7043349 AAAAATAACATC-CAAACAAC
1 AAAAATAACATCAAAAACAAC
*
7043369 AAAAATAACATCTAAAACAGCAGC
1 AAAAATAACATC-AAAA-A-CAAC
*
7043393 AAAAAAAACGA--AAAAACAAC
1 AAAAATAAC-ATCAAAAACAAC
* *
7043413 AAAAATAGCAACAAAAACAAC
1 AAAAATAACATCAAAAACAAC
7043434 AA
1 AA
7043436 CAAAAATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.02
20 22 0.41
21 12 0.22
22 6 0.11
23 1 0.02
24 11 0.20
25 1 0.02
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAATAACATCAAAAACAAC
Found at i:7043424 original size:12 final size:12
Alignment explanation
Indices: 7043363--7043444 Score: 64
Period size: 12 Copynumber: 7.2 Consensus size: 12
7043353 ATAACATCCA
7043363 AACAACAAAAAT
1 AACAACAAAAAT
* * *
7043375 AACATCTAAAAC
1 AACAACAAAAAT
* *
7043387 AGCAGC-AAAA-
1 AACAACAAAAAT
*
7043397 AA-AACGAAAA-
1 AACAACAAAAAT
7043407 AACAACAAAAAT
1 AACAACAAAAAT
* *
7043419 AGCAACAAAAAC
1 AACAACAAAAAT
7043431 AACAACAAAAAT
1 AACAACAAAAAT
7043443 AA
1 AA
7043445 TAGTAAAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 11 0.20
12 35 0.64
ACGTcount: A:0.71, C:0.18, G:0.05, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:7043453 original size:24 final size:23
Alignment explanation
Indices: 7043362--7043444 Score: 73
Period size: 24 Copynumber: 3.7 Consensus size: 23
7043352 AATAACATCC
*
7043362 AAACAACAAAAATAACATCTAAAA
1 AAACAACAAAAATAACAAC-AAAA
* * * *
7043386 CAGCAGC-AAAA-AA-AACGAAA
1 AAACAACAAAAATAACAACAAAA
*
7043406 AAACAACAAAAATAGCAACAAAA
1 AAACAACAAAAATAACAACAAAA
7043429 ACAACAACAAAAATAA
1 A-AACAACAAAAATAA
7043445 TAGTAAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 7 0.16
21 6 0.14
22 3 0.07
23 11 0.25
24 17 0.39
ACGTcount: A:0.71, C:0.18, G:0.05, T:0.06
Consensus pattern (23 bp):
AAACAACAAAAATAACAACAAAA
Found at i:7043496 original size:32 final size:32
Alignment explanation
Indices: 7043446--7043529 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
7043436 CAAAAATAAT
*
7043446 AGTAAAAAAA-CACGAAAACAGTAACCAAAAC
1 AGTAAAAAAAGCACGAAAACAGCAACCAAAAC
* * * *
7043477 AGTAAAAAAAGTACTAAAACAGCAATCAAAAT
1 AGTAAAAAAAGCACGAAAACAGCAACCAAAAC
7043509 AGTAAAAAAAGCATC-AAAACA
1 AGTAAAAAAAGCA-CGAAAACA
7043530 ATAATATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 10 0.22
32 34 0.76
33 1 0.02
ACGTcount: A:0.64, C:0.15, G:0.10, T:0.11
Consensus pattern (32 bp):
AGTAAAAAAAGCACGAAAACAGCAACCAAAAC
Found at i:7053593 original size:25 final size:25
Alignment explanation
Indices: 7053556--7053617 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
7053546 TTAAATATTT
*
7053556 ATTTTATTTTATTTTAATATTTAAT-A
1 ATTTTA-TATATTTT-ATATTTAATGA
* *
7053582 ATTTTATATATTTTTTATTTATTGA
1 ATTTTATATATTTTATATTTAATGA
*
7053607 ATTTTTTATAT
1 ATTTTATATAT
7053618 AGTTATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 7 0.23
25 18 0.58
26 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
ATTTTATATATTTTATATTTAATGA
Found at i:7057298 original size:18 final size:18
Alignment explanation
Indices: 7057264--7057320 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
7057254 TTTTTAAAAA
*
7057264 TATAAAT-TTTGGAAATTT
1 TATAAATATTTTG-AATTT
7057282 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
* *
7057300 TTTAGAATTATTTTGTATTT
1 TATA-AA-TATTTTGAATTT
7057320 T
1 T
7057321 TTATTAAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.45
19 6 0.18
20 12 0.36
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:7057302 original size:20 final size:20
Alignment explanation
Indices: 7057279--7057324 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
7057269 ATTTTGGAAA
7057279 TTTTATAAATATTTTGAATT
1 TTTTATAAATATTTTGAATT
* * *
7057299 TTTTAGAATTATTTTGTATT
1 TTTTATAAATATTTTGAATT
7057319 TTTTAT
1 TTTTAT
7057325 TAAGGGTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTATAAATATTTTGAATT
Found at i:7059713 original size:13 final size:14
Alignment explanation
Indices: 7059695--7059723 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7059685 ACCTCTCTTC
7059695 TACTCACATG-ATT
1 TACTCACATGTATT
7059708 TACTCACATGTATT
1 TACTCACATGTATT
7059722 TA
1 TA
7059724 AGATTTCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
TACTCACATGTATT
Found at i:7069828 original size:55 final size:55
Alignment explanation
Indices: 7069744--7069886 Score: 225
Period size: 55 Copynumber: 2.6 Consensus size: 55
7069734 TAAACGTGCT
* *
7069744 ACATAACAATCGATTTAAATATATAAACAATC-TATTCAAAAGAAACCGTATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGT-TTCAAAAGAAACAGTATTCCA
7069799 ACATAACAATCGATTTAAACATATAAACAATCGTTTCAAAAGAAACAGTATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGTTTCAAAAGAAACAGTATTCCA
* * *
7069854 CCATAACAACCGATTTAAACATATAAACTATCG
1 ACATAACAATCGATTTAAACATATAAACAATCG
7069887 ATTTTTGGGA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 81 0.99
56 1 0.01
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (55 bp):
ACATAACAATCGATTTAAACATATAAACAATCGTTTCAAAAGAAACAGTATTCCA
Found at i:7071535 original size:39 final size:39
Alignment explanation
Indices: 7071476--7071553 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
7071466 TCCATGGAGA
* *
7071476 AACAATTTATGTTTATAATTAGGTTCCTCTCAATTTTGG
1 AACAATTTATGTTTAGAATTAGGTTACTCTCAATTTTGG
7071515 AACAATTTATGTTTAGAATTAGGTTACTCTCAATTTTGG
1 AACAATTTATGTTTAGAATTAGGTTACTCTCAATTTTGG
7071554 GGTCTGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (39 bp):
AACAATTTATGTTTAGAATTAGGTTACTCTCAATTTTGG
Found at i:7071587 original size:13 final size:14
Alignment explanation
Indices: 7071569--7071609 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
7071559 GTTTATTTTA
*
7071569 TTAAAAATTG-TTT
1 TTAAAAAATGATTT
7071582 TTAAAAAATGATTT
1 TTAAAAAATGATTT
*
7071596 TTAAAAAATAATTT
1 TTAAAAAATGATTT
7071610 ATTTTTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (14 bp):
TTAAAAAATGATTT
Found at i:7072179 original size:21 final size:21
Alignment explanation
Indices: 7072140--7072180 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
7072130 TTTCATAAAT
7072140 TAACTTATCATTTTAAAAAACC
1 TAACTTAT-ATTTTAAAAAACC
7072162 TAACTTAT-TTTCTAAAAAA
1 TAACTTATATTT-TAAAAAA
7072181 AAGTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (21 bp):
TAACTTATATTTTAAAAAACC
Found at i:7072778 original size:25 final size:27
Alignment explanation
Indices: 7072750--7072810 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
7072740 CGTATTTTAA
7072750 ATTA-AAATTTAATTA-GATA-TTATTT
1 ATTATAAATTTAATTATGATATTTA-TT
*
7072775 ATTATTAAATTTATTTATGATATTTATT
1 ATTA-TAAATTTAATTATGATATTTATT
7072803 ATTATAAA
1 ATTATAAA
7072811 ATATTATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 4 0.13
27 14 0.45
28 10 0.32
29 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTATAAATTTAATTATGATATTTATT
Found at i:7072781 original size:28 final size:29
Alignment explanation
Indices: 7072750--7072812 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
7072740 CGTATTTTAA
7072750 ATTAAAATTTAATTA-GATA-TTATTTATT
1 ATTAAAATTTAATTATGATATTTA-TTATT
*
7072778 ATT-AAATTTATTTATGATATTTATTATT
1 ATTAAAATTTAATTATGATATTTATTATT
7072806 A-TAAAAT
1 ATTAAAAT
7072813 ATTATTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 11 0.35
28 17 0.55
29 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (29 bp):
ATTAAAATTTAATTATGATATTTATTATT
Found at i:7073718 original size:23 final size:23
Alignment explanation
Indices: 7073688--7073858 Score: 182
Period size: 23 Copynumber: 7.3 Consensus size: 23
7073678 ACAAAGTACT
7073688 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
7073711 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
7073734 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
* * * *
7073759 GAGCACGA-GACGTGTTAAACAGA
1 GAGCAC-ACAAAGTGCTAATCAGA
* *
7073782 GAGCACACACAGTGCTAGTCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
7073805 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
7073828 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
7073853 GAGCAC
1 GAGCAC
7073859 GAGACGTGCT
Statistics
Matches: 119, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
22 1 0.01
23 93 0.78
25 24 0.20
26 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:7073740 original size:46 final size:47
Alignment explanation
Indices: 7073688--7073858 Score: 240
Period size: 46 Copynumber: 3.6 Consensus size: 47
7073678 ACAAAGTACT
*
7073688 GAGCACACAAAGTGCTAAT-CAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
* * * *
7073734 GAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGTTAAACAGA
1 GAGCACACACAGTGCTAAT-ACAGAGAGCAC-ACGAAGTGCTAATCGGA
*
7073782 GAGCACACACAGTGCTAGT-CAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
7073828 GAGCACACACAGTGCTAATAACAGAGAGCAC
1 GAGCACACACAGTGCTAAT-ACAGAGAGCAC
7073859 GAGACGTGCT
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
45 1 0.01
46 57 0.53
48 49 0.45
49 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (47 bp):
GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
Found at i:7073797 original size:94 final size:94
Alignment explanation
Indices: 7073688--7073879 Score: 357
Period size: 94 Copynumber: 2.0 Consensus size: 94
7073678 ACAAAGTACT
7073688 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
*
7073753 AACAGAGAGCACGAGACGTGTTAAACAGA
66 AACAGAGAGCACGAGACGTGCTAAACAGA
* *
7073782 GAGCACACACAGTGCTAGTCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
7073847 AACAGAGAGCACGAGACGTGCTAAACAGA
66 AACAGAGAGCACGAGACGTGCTAAACAGA
7073876 GAGC
1 GAGC
7073880 GCGCTAGTGT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (94 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
AACAGAGAGCACGAGACGTGCTAAACAGA
Found at i:7073868 original size:71 final size:71
Alignment explanation
Indices: 7073688--7073879 Score: 200
Period size: 71 Copynumber: 2.7 Consensus size: 71
7073678 ACAAAGTACT
* * *
7073688 GAGCACACAAAGTGCTAAT--CAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTA
1 GAGCACACACAGTGCTAATAACAGAGAGCACA-GACGTGCTAATCAGAGAGCACACACAGTGCTA
7073751 ATAACAGA
65 AT-ACAGA
* * * *
7073759 GAGCACGAGAC-GTG-TTA-AACAGAGAGCACACACAGTGCTAGTCAGAGAGCACACGA-AGTGC
1 GAGCAC-ACACAGTGCTAATAACAGAGAGCACAGAC-GTGCTAATCAGAGAGCACAC-ACAGTGC
*
7073820 TAAT-CGGA
63 TAATACAGA
*
7073828 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 GAGCACACACAGTGCTAATAACAGAGAGCAC-AGACGTGCTAATCAGAGAGC
7073880 GCGCTAGTGT
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
68 3 0.03
69 12 0.12
70 5 0.05
71 73 0.74
72 6 0.06
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (71 bp):
GAGCACACACAGTGCTAATAACAGAGAGCACAGACGTGCTAATCAGAGAGCACACACAGTGCTAA
TACAGA
Found at i:7073873 original size:23 final size:22
Alignment explanation
Indices: 7073699--7073879 Score: 146
Period size: 23 Copynumber: 7.7 Consensus size: 22
7073689 AGCACACAAA
* *
7073699 GTGCTAATCAGAGAGCACACGAA
1 GTGCTAAACAGAGAGCACA-GAC
* * *
7073722 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
7073744 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
* *
7073770 GTGTTAAACAGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
** *
7073792 AGTGCTAGTCAGAGAGCACACGAA
1 -GTGCTAAACAGAGAGCACA-GAC
* * *
7073816 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
7073838 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
7073864 GTGCTAAACAGAGAGC
1 GTGCTAAACAGAGAGC
7073880 GCGCTAGTGT
Statistics
Matches: 128, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.04
23 83 0.65
24 5 0.04
25 29 0.23
26 6 0.05
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACAGAC
Found at i:7080201 original size:23 final size:23
Alignment explanation
Indices: 7080171--7080341 Score: 182
Period size: 23 Copynumber: 7.3 Consensus size: 23
7080161 ACAAAGTACT
7080171 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
7080194 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
7080217 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
* * * *
7080242 GAGCACGA-GACGTGTTAAACAGA
1 GAGCAC-ACAAAGTGCTAATCAGA
* *
7080265 GAGCACACACAGTGCTAGTCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
7080288 GAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGA
*
7080311 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
7080336 GAGCAC
1 GAGCAC
7080342 GAGACGTGCT
Statistics
Matches: 119, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
22 1 0.01
23 93 0.78
25 24 0.20
26 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:7080223 original size:46 final size:47
Alignment explanation
Indices: 7080171--7080341 Score: 240
Period size: 46 Copynumber: 3.6 Consensus size: 47
7080161 ACAAAGTACT
*
7080171 GAGCACACAAAGTGCTAAT-CAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
* * * *
7080217 GAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGTTAAACAGA
1 GAGCACACACAGTGCTAAT-ACAGAGAGCAC-ACGAAGTGCTAATCGGA
*
7080265 GAGCACACACAGTGCTAGT-CAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
7080311 GAGCACACACAGTGCTAATAACAGAGAGCAC
1 GAGCACACACAGTGCTAAT-ACAGAGAGCAC
7080342 GAGACGTGCT
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
45 1 0.01
46 57 0.53
48 49 0.45
49 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (47 bp):
GAGCACACACAGTGCTAATACAGAGAGCACACGAAGTGCTAATCGGA
Found at i:7080280 original size:94 final size:94
Alignment explanation
Indices: 7080171--7080362 Score: 357
Period size: 94 Copynumber: 2.0 Consensus size: 94
7080161 ACAAAGTACT
7080171 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
*
7080236 AACAGAGAGCACGAGACGTGTTAAACAGA
66 AACAGAGAGCACGAGACGTGCTAAACAGA
* *
7080265 GAGCACACACAGTGCTAGTCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
7080330 AACAGAGAGCACGAGACGTGCTAAACAGA
66 AACAGAGAGCACGAGACGTGCTAAACAGA
7080359 GAGC
1 GAGC
7080363 GCGCTAGTGT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (94 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAAT
AACAGAGAGCACGAGACGTGCTAAACAGA
Found at i:7080351 original size:71 final size:71
Alignment explanation
Indices: 7080171--7080362 Score: 200
Period size: 71 Copynumber: 2.7 Consensus size: 71
7080161 ACAAAGTACT
* * *
7080171 GAGCACACAAAGTGCTAAT--CAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTA
1 GAGCACACACAGTGCTAATAACAGAGAGCACA-GACGTGCTAATCAGAGAGCACACACAGTGCTA
7080234 ATAACAGA
65 AT-ACAGA
* * * *
7080242 GAGCACGAGAC-GTG-TTA-AACAGAGAGCACACACAGTGCTAGTCAGAGAGCACACGA-AGTGC
1 GAGCAC-ACACAGTGCTAATAACAGAGAGCACAGAC-GTGCTAATCAGAGAGCACAC-ACAGTGC
*
7080303 TAAT-CGGA
63 TAATACAGA
*
7080311 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 GAGCACACACAGTGCTAATAACAGAGAGCAC-AGACGTGCTAATCAGAGAGC
7080363 GCGCTAGTGT
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
68 3 0.03
69 12 0.12
70 5 0.05
71 73 0.74
72 6 0.06
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (71 bp):
GAGCACACACAGTGCTAATAACAGAGAGCACAGACGTGCTAATCAGAGAGCACACACAGTGCTAA
TACAGA
Found at i:7080356 original size:23 final size:22
Alignment explanation
Indices: 7080182--7080362 Score: 146
Period size: 23 Copynumber: 7.7 Consensus size: 22
7080172 AGCACACAAA
* *
7080182 GTGCTAATCAGAGAGCACACGAA
1 GTGCTAAACAGAGAGCACA-GAC
* * *
7080205 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
7080227 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
* *
7080253 GTGTTAAACAGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
** *
7080275 AGTGCTAGTCAGAGAGCACACGAA
1 -GTGCTAAACAGAGAGCACA-GAC
* * *
7080299 GTGCTAATCGGAGAGCACACAC
1 GTGCTAAACAGAGAGCACAGAC
7080321 AGTGCTAATAACAGAGAGCACGAGAC
1 -GTGCT-A-AACAGAGAGCAC-AGAC
7080347 GTGCTAAACAGAGAGC
1 GTGCTAAACAGAGAGC
7080363 GCGCTAGTGT
Statistics
Matches: 128, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.04
23 83 0.65
24 5 0.04
25 29 0.23
26 6 0.05
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACAGAC
Found at i:7089042 original size:2 final size:2
Alignment explanation
Indices: 7089037--7089066 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7089027 GAGAGAATTC
7089037 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
7089067 CTACATTAAA
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:7093613 original size:11 final size:11
Alignment explanation
Indices: 7093597--7093629 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
7093587 CTTTTGAATA
*
7093597 ATTTAATGATT
1 ATTTAATAATT
7093608 ATTTAATAATT
1 ATTTAATAATT
7093619 ATTTAA-AATT
1 ATTTAATAATT
7093629 A
1 A
7093630 AATAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:7107201 original size:26 final size:27
Alignment explanation
Indices: 7107164--7107235 Score: 112
Period size: 26 Copynumber: 2.7 Consensus size: 27
7107154 ATTTATTTTT
7107164 AATAATTATCTACGAAACTC-GTCTTC
1 AATAATTATCTACGAAACTCTGTCTTC
* *
7107190 AATAATTGTCTACGAAA-TCTGTCTTT
1 AATAATTATCTACGAAACTCTGTCTTC
7107216 AATAATTATCTACGAAACTC
1 AATAATTATCTACGAAACTC
7107236 AAATTTCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
25 2 0.05
26 37 0.90
27 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (27 bp):
AATAATTATCTACGAAACTCTGTCTTC
Found at i:7109023 original size:23 final size:23
Alignment explanation
Indices: 7108828--7109011 Score: 203
Period size: 23 Copynumber: 7.9 Consensus size: 23
7108818 CGAAGTACTT
7108828 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
7108854 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
7108876 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
7108898 AATCAGTAGGCACACGAAGTGCGG
1 AA-CAGTAAGCACACAAAGTGCGA
*
7108922 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
7108945 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
7108968 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
7108991 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
7109012 TGAACGGTAA
Statistics
Matches: 139, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.14
23 99 0.71
24 2 0.01
26 14 0.10
27 5 0.04
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.10
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:7113201 original size:329 final size:326
Alignment explanation
Indices: 7112577--7113234 Score: 1217
Period size: 329 Copynumber: 2.0 Consensus size: 326
7112567 AAATTTTAGC
7112577 CATTTGAATTCAACAATTATTTATTTTACCAAATTCAGATATTCTTTTAATAAAAAATATATGGT
1 CATTTGAATTCAACAATTATTTATTTTACCAAATTCAGATATTCTTTTAATAAAAAATATATGGT
7112642 CAGTTATATTTCAAAGGGAATATTTTACAATAGATTATAATGAAAAAATAAAAAAAATTTACATT
66 CAGTTATATTTCAAAGGGAATATTTTACAATAGATTATAATGAAAAAATAAAAAAAATTTACATT
*
7112707 TTATACTTAAATGATTGTAGAATTTGTTACATTTGAATTTTTCTTCAACGGAAATCAAAGTTGTG
131 TTATACTTAAATGATTGTAGAATTTGTTACATTTGAATTTTTCTTCAACCGAAATCAAAGTTGTG
* *
7112772 ACTTTAAAGGCTTGAAATGTCAGTTTAGATTTTCATTTCTTTTAAACTTGTGGATCAGTTTCTCA
196 ACTTTAAAGGCTTGAAATGTCAATTTAGATTTTCATTTCTTTAAAACTTGTGGATCAGTTTCTCA
*
7112837 CAAGCAGCTCACAAAGTCCATGCATCCGTCCATCCATTCAACATACATACATACATGAAGATCTG
261 CAAGCAGCTCACAAAGTCCATGCATCCATCCATCCATTCAACATACATACATACATGAAGATCTG
7112902 A
326 A
7112903 CATTTGAATTCAACAATTATTTATTTTACCAAATTCAGATATTCTTTTAATAAAAAAAATATATG
1 CATTTGAATTCAACAATTATTTATTTTACCAAATTCAGATATTCTTTTAAT--AAAAAATATATG
*
7112968 GTCAGTTATATTTCAAAGGGAATATTTTACAATAGATTATAATGAAAAAATAAAAACAATTTACA
64 GTCAGTTATATTTCAAAGGGAATATTTTACAATAGATTATAATGAAAAAATAAAAAAAATTTACA
*
7113033 TTTTATACTTAAATGATTGTAGAATTTGTTACATTTGAATTTTTTCTTCAACCGAAGTCAAAGTT
129 TTTTATACTTAAATGATTGTAGAATTTGTTACATTTGAA-TTTTTCTTCAACCGAAATCAAAGTT
7113098 GTGACTTTAAAGGCTTGAAATGTCAATTTAGATTTTCATTTCTTTAAAACTTGTGGATCAGTTTC
193 GTGACTTTAAAGGCTTGAAATGTCAATTTAGATTTTCATTTCTTTAAAACTTGTGGATCAGTTTC
* *
7113163 TCACAATCAGCTCACAAAGTCCATGCATCCATCCATCCATTCAACATGCATACATACATGAAGAT
258 TCACAAGCAGCTCACAAAGTCCATGCATCCATCCATCCATTCAACATACATACATACATGAAGAT
7113228 CTGA
323 CTGA
7113232 CAT
1 CAT
7113235 ACCCATCCCA
Statistics
Matches: 321, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
326 51 0.16
328 115 0.36
329 155 0.48
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (326 bp):
CATTTGAATTCAACAATTATTTATTTTACCAAATTCAGATATTCTTTTAATAAAAAATATATGGT
CAGTTATATTTCAAAGGGAATATTTTACAATAGATTATAATGAAAAAATAAAAAAAATTTACATT
TTATACTTAAATGATTGTAGAATTTGTTACATTTGAATTTTTCTTCAACCGAAATCAAAGTTGTG
ACTTTAAAGGCTTGAAATGTCAATTTAGATTTTCATTTCTTTAAAACTTGTGGATCAGTTTCTCA
CAAGCAGCTCACAAAGTCCATGCATCCATCCATCCATTCAACATACATACATACATGAAGATCTG
A
Found at i:7120106 original size:94 final size:94
Alignment explanation
Indices: 7119945--7120133 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
7119935 ATGCAACCTA
7119945 AGTGGTATTTTGTTGCTCTCATCAGGTTTTTTCATTTTATCAAAGAACACACATTACTCAAACCT
1 AGTGGTATTTTGTTGCTCTCATCAGGTTTTTTCATTTTATCAAAGAACACACATTACTCAAACCT
7120010 TCATTGCTTGTTTGAATAATAAGATACAC
66 TCATTGCTTGTTTGAATAATAAGATACAC
7120039 AGTGGTATTTTGTTGCTCTCATCAGGTTTTTTCATTTTATCAAAGAACACACATTACTCAAACCT
1 AGTGGTATTTTGTTGCTCTCATCAGGTTTTTTCATTTTATCAAAGAACACACATTACTCAAACCT
7120104 TCATTGCTTGTTTGAATAATAAGATACAC
66 TCATTGCTTGTTTGAATAATAAGATACAC
7120133 A
1 A
7120134 CCAACAATCT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (94 bp):
AGTGGTATTTTGTTGCTCTCATCAGGTTTTTTCATTTTATCAAAGAACACACATTACTCAAACCT
TCATTGCTTGTTTGAATAATAAGATACAC
Found at i:7126567 original size:18 final size:18
Alignment explanation
Indices: 7126527--7126565 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
7126517 AATTCTTCTT
7126527 AAAATCATTTTTGACATA
1 AAAATCATTTTTGACATA
*
7126545 AAAATTATTTTTGA-ATA
1 AAAATCATTTTTGACATA
7126562 AAAA
1 AAAA
7126566 ATAATACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATCATTTTTGACATA
Found at i:7126907 original size:12 final size:12
Alignment explanation
Indices: 7126892--7126925 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7126882 AAACTTTTCA
*
7126892 AAAATATTTTTT
1 AAAATACTTTTT
7126904 AAAATACTTTTT
1 AAAATACTTTTT
7126916 AAAAATACTT
1 -AAAATACTT
7126926 CTCAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (12 bp):
AAAATACTTTTT
Found at i:7126907 original size:13 final size:13
Alignment explanation
Indices: 7126884--7126925 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
7126874 CTTAAATCAA
*
7126884 ACTTTTCAAAAAT
1 ACTTTTTAAAAAT
*
7126897 A-TTTTTTAAAAT
1 ACTTTTTAAAAAT
7126909 ACTTTTTAAAAAT
1 ACTTTTTAAAAAT
7126922 ACTT
1 ACTT
7126926 CTCAAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (13 bp):
ACTTTTTAAAAAT
Found at i:7126932 original size:25 final size:25
Alignment explanation
Indices: 7126884--7126932 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
7126874 CTTAAATCAA
* * *
7126884 ACTTTTCAAAAATATTTTTTAAAAT
1 ACTTTTCAAAAATACTTCTCAAAAT
*
7126909 ACTTTTTAAAAATACTTCTCAAAA
1 ACTTTTCAAAAATACTTCTCAAAA
7126933 GTAATACTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (25 bp):
ACTTTTCAAAAATACTTCTCAAAAT
Found at i:7134283 original size:2 final size:2
Alignment explanation
Indices: 7134244--7134274 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7134234 ATAAAACATT
7134244 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
7134275 TGAACACACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7139635 original size:18 final size:18
Alignment explanation
Indices: 7139594--7139634 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
7139584 GTCAGAGATA
7139594 ATTTTTGAAGTTAAAAGT
1 ATTTTTGAAGTTAAAAGT
* *
7139612 ACTTTTGAA-TTAAAATT
1 ATTTTTGAAGTTAAAAGT
7139629 ATTTTT
1 ATTTTT
7139635 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (18 bp):
ATTTTTGAAGTTAAAAGT
Found at i:7139807 original size:14 final size:15
Alignment explanation
Indices: 7139777--7139814 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
7139767 TATAAAGTAT
7139777 ATATTTAAATTTATA
1 ATATTTAAATTTATA
*
7139792 ATATTTATATTT-TA
1 ATATTTAAATTTATA
7139806 ATATTTAAA
1 ATATTTAAA
7139815 ATATAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTAAATTTATA
Found at i:7139811 original size:23 final size:23
Alignment explanation
Indices: 7139774--7139835 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
7139764 AAATATAAAG
*
7139774 TATATATTTAAATTTATAATATT
1 TATATATTTAAATTTAAAATATT
7139797 TATAT-TTTAATATTTAAAATATAGTT
1 TATATATTTAA-ATTT-AAA-ATA-TT
7139823 TATATATTTAAAT
1 TATATATTTAAAT
7139836 ATAATTTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 5 0.15
23 9 0.27
24 2 0.06
25 3 0.09
26 9 0.27
27 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATATTTAAATTTAAAATATT
Found at i:7139824 original size:19 final size:19
Alignment explanation
Indices: 7139797--7139838 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
7139787 TTATAATATT
*
7139797 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATATTT-AAA
7139816 TATAGTTTATATATTTAAA
1 TATAGTTTATATATTTAAA
7139835 TATA
1 TATA
7139839 ATTTTTCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATAGTTTATATATTTAAA
Found at i:7140957 original size:23 final size:25
Alignment explanation
Indices: 7140908--7140961 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
7140898 TTAACAGTAT
7140908 AAAAATT-AAAATAACAAATATATA
1 AAAAATTAAAAATAACAAATATATA
*
7140932 AAAAATTAAAGAATAA-AAAT-TAAA
1 AAAAATTAAA-AATAACAAATATATA
7140956 AAAAAT
1 AAAAAT
7140962 AAACAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 16 0.59
25 6 0.22
26 5 0.19
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
AAAAATTAAAAATAACAAATATATA
Found at i:7140964 original size:23 final size:25
Alignment explanation
Indices: 7140908--7140964 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
7140898 TTAACAGTAT
*
7140908 AAAAATTAAAATAACAAATATATAA
1 AAAAATAAAAATAACAAATATATAA
*
7140933 AAAATTAAAGAATAA-AAAT-TA-AA
1 AAAAATAAA-AATAACAAATATATAA
7140956 AAAAATAAA
1 AAAAATAAA
7140965 CAAAAACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 10 0.36
24 2 0.07
25 11 0.39
26 5 0.18
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (25 bp):
AAAAATAAAAATAACAAATATATAA
Found at i:7151681 original size:17 final size:18
Alignment explanation
Indices: 7151659--7151699 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
7151649 TATTTATATT
7151659 TATTTTAT-TTTTTAAAA
1 TATTTTATATTTTTAAAA
*
7151676 TATTTTATAATTTTTAAAT
1 TATTTTAT-ATTTTTAAAA
7151695 TATTT
1 TATTT
7151700 GTTGAAGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTATATTTTTAAAA
Found at i:7164955 original size:2 final size:2
Alignment explanation
Indices: 7164950--7164977 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7164940 AAAAATTTTA
7164950 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
7164978 TTTAAAAGTT
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:7173335 original size:15 final size:16
Alignment explanation
Indices: 7173301--7173339 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
7173291 TAGTAAAAAT
*
7173301 ATAATTTTATTATTTTA
1 ATAA-TTTATTATGTTA
7173318 ATAATTTA-TATGTTA
1 ATAATTTATTATGTTA
7173333 ATAATTT
1 ATAATTT
7173340 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATAATTTATTATGTTA
Found at i:7173778 original size:34 final size:34
Alignment explanation
Indices: 7173735--7173827 Score: 161
Period size: 34 Copynumber: 2.7 Consensus size: 34
7173725 AGAATATGAA
7173735 AGGTTAAGGAAGATGGAAGGTTAAAGGTC-AAGAG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAG-G
7173769 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
*
7173803 AAGTTAAGGAAGATGGAAGGTTAAA
1 AGGTTAAGGAAGATGGAAGGTTAAA
7173828 AGATGAAAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
34 54 0.95
35 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.37, T:0.18
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAGG
Found at i:7177906 original size:23 final size:24
Alignment explanation
Indices: 7177859--7177903 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
7177849 CGACTAGTTA
7177859 ATAGAGACTTTCAATTTACAATTC
1 ATAGAGACTTTCAATTTACAATTC
7177883 ATAGA-ACTTTCAATTT-CAATT
1 ATAGAGACTTTCAATTTACAATT
7177904 TCACTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (24 bp):
ATAGAGACTTTCAATTTACAATTC
Found at i:7180289 original size:12 final size:12
Alignment explanation
Indices: 7180272--7180307 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
7180262 TCCTCGATCG
7180272 TGACCACGACCA
1 TGACCACGACCA
7180284 TGACCACGACCA
1 TGACCACGACCA
* *
7180296 TGTCCTCGACCA
1 TGACCACGACCA
7180308 CGACTACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.42, G:0.17, T:0.14
Consensus pattern (12 bp):
TGACCACGACCA
Found at i:7181532 original size:17 final size:17
Alignment explanation
Indices: 7181497--7181538 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
7181487 ATAAAAAGTA
*
7181497 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
7181515 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
7181532 GTTAAAG
1 GTTAAAG
7181539 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:7181559 original size:34 final size:34
Alignment explanation
Indices: 7181513--7181605 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 34
7181503 AGAATATGAA
* **
7181513 AGGTTAAAGAAGATGGAAGGTTAAAGGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAAG
* *
7181547 AGGTTAAGGAAGATGAAAGGTAAAAGGTCAAAAG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAAG
* *
7181581 AAGTTAAGAAAGATGGAAGGTTAAA
1 AGGTTAAGGAAGATGGAAGGTTAAA
7181606 AAATGAAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.47, C:0.02, G:0.33, T:0.17
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAAAG
Found at i:7197902 original size:14 final size:15
Alignment explanation
Indices: 7197868--7197906 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
7197858 AATTAGAGTG
* *
7197868 ATTAAATTAAAAAAA
1 ATTAAAATAATAAAA
7197883 ATTAAAATAATAAAA
1 ATTAAAATAATAAAA
7197898 A-TAAAATAA
1 ATTAAAATAA
7197907 ATTCTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATTAAAATAATAAAA
Found at i:7211280 original size:22 final size:23
Alignment explanation
Indices: 7211255--7211299 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
7211245 GATTTAGCAG
*
7211255 CCTTTCATTTATTT-TTAATTTT
1 CCTTTCATTCATTTATTAATTTT
* *
7211277 CCTTTTATTCATTTATTGATTTT
1 CCTTTCATTCATTTATTAATTTT
7211300 TTTAATCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (23 bp):
CCTTTCATTCATTTATTAATTTT
Found at i:7219647 original size:20 final size:20
Alignment explanation
Indices: 7219622--7219665 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
7219612 ATTTAACATG
* *
7219622 TATCGATACCATGCTCAAGC
1 TATCGATACCATCCTCAAGA
*
7219642 TATCGATACCTTCCTCAAGA
1 TATCGATACCATCCTCAAGA
7219662 TATC
1 TATC
7219666 AGTACTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (20 bp):
TATCGATACCATCCTCAAGA
Found at i:7221410 original size:16 final size:15
Alignment explanation
Indices: 7221369--7221415 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 15
7221359 AATTTTTATG
7221369 TTTTTTA-ATTTTAA
1 TTTTTTATATTTTAA
*
7221383 TTTTTAAGATATTTATAA
1 TTTTT--TATATTT-TAA
7221401 TTTTTTATATTTTAA
1 TTTTTTATATTTTAA
7221416 AAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.19
15 3 0.11
16 7 0.26
17 4 0.15
18 8 0.30
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTTTATATTTTAA
Found at i:7223191 original size:90 final size:90
Alignment explanation
Indices: 7222668--7223179 Score: 774
Period size: 90 Copynumber: 5.7 Consensus size: 90
7222658 GACCCATCGA
* * * ** *
7222668 TTGTGCATCGACTAGAGCAGGAGAAACAGTTTGCACGCTAGTAGCTGAGCCAGTTGAAGGGATCC
1 TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
* * *
7222733 CTGAAGCTGTGGAAGGCTGCAAGGT
66 CTGAAGCAGTAGAACGCTGCAAGGT
*
7222758 TTGTGAATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
1 TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
* *
7222823 CTGAAGCAGT-GAAAGGCTGCAAGTT
66 CTGAAGCAGTAG-AACGCTGCAAGGT
** * * *
7222848 TTGCACATTGACTACAGCAGATGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAGGGGATCC
1 TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
7222913 CTGAAGCAGTAGAACGCTGCAAGGT
66 CTGAAGCAGTAGAACGCTGCAAGGT
* * *
7222938 TTGTGCATTGACTACAGCAGGTGAAACGGTTTGCATAGTATAAGCTGAGCCAGTTGAAGGGATCC
1 TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
*
7223003 CTGAAGCAGTAGAACGCTGCAATGT
66 CTGAAGCAGTAGAACGCTGCAAGGT
*
7223028 TTGTGCGTTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
1 TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
* *
7223093 CTGAAGCAGTAGAACACTGCAATGT
66 CTGAAGCAGTAGAACGCTGCAAGGT
* *
7223118 TTGTGCATTAACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTAAGCCAGTTGAAGGGA
1 TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGA
7223180 GACCAGAAGC
Statistics
Matches: 388, Mismatches: 32, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
89 1 0.00
90 386 0.99
91 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (90 bp):
TTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGAAGGGATCC
CTGAAGCAGTAGAACGCTGCAAGGT
Found at i:7238256 original size:42 final size:42
Alignment explanation
Indices: 7238194--7238363 Score: 252
Period size: 42 Copynumber: 4.0 Consensus size: 42
7238184 TTAAATCATT
*
7238194 ATCTCCATCATCCTTAGCTTTCCTACTAGAGGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGAGGATCTAGTACC
7238236 A-CATCCATCATCCTTAGCTTTCCTACTAGAGGATCTAGTACC
1 ATC-TCCATCATCCTTAGCTTTCCTACTAGAGGATCTAGTACC
* * * *
7238278 ATCTCCGTCATCCTTAGCTTTCCTTCCAGACGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGAGGATCTAGTACC
** *
7238320 ATCTCCATCATCCTTAGCTTTCCTACTAGACAACCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGAGGATCTAGTACC
7238362 AT
1 AT
7238364 TCGCCATACC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.01
42 114 0.98
43 1 0.01
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.32
Consensus pattern (42 bp):
ATCTCCATCATCCTTAGCTTTCCTACTAGAGGATCTAGTACC
Found at i:7239254 original size:16 final size:17
Alignment explanation
Indices: 7239223--7239255 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7239213 TATTTATAGT
*
7239223 AATTTTATTTTTATATA
1 AATTTTATTTTAATATA
7239240 AATTTT-TTTTAATATA
1 AATTTTATTTTAATATA
7239256 TTAAGGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTATTTTAATATA
Found at i:7239524 original size:21 final size:20
Alignment explanation
Indices: 7239470--7239525 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
7239460 CTTTAAAAAT
7239470 ATTATTTATATTTATTAATATA
1 ATTATTTATATTT-TTAATA-A
*
7239492 ATATAATT-TATTTTTAATAA
1 AT-TATTTATATTTTTAATAA
7239512 ATTATTTAATATTT
1 ATTATTT-ATATTT
7239526 CAATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 11 0.38
22 7 0.24
23 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTTATATTTTTAATAA
Found at i:7239658 original size:36 final size:37
Alignment explanation
Indices: 7239573--7239658 Score: 85
Period size: 36 Copynumber: 2.4 Consensus size: 37
7239563 ATATATTAAT
7239573 TGAAT-TTTATTTATAATAATATTTTTCTAATAAATA
1 TGAATATTTATTTATAATAATATTTTTCTAATAAATA
*
7239609 T--ATATTATAATTTAT-A-AATA-TTTTATAGTATAAATA
1 TGAATATT-T-ATTTATAATAATATTTTTCTA--ATAAATA
7239645 TGAATATTTATTTA
1 TGAATATTTATTTA
7239659 AATTTTATTC
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
34 8 0.19
35 6 0.14
36 16 0.38
37 7 0.17
38 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (37 bp):
TGAATATTTATTTATAATAATATTTTTCTAATAAATA
Found at i:7239694 original size:22 final size:22
Alignment explanation
Indices: 7239642--7239702 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
7239632 TATAGTATAA
* *
7239642 ATATGAATATTTATTTAAATTT
1 ATATTAATATTTGTTTAAATTT
7239664 -TATTCAATATTTGTTT-AATTAT
1 ATATT-AATATTTGTTTAAATT-T
7239686 ATATTAATATTATGTTT
1 ATATTAATATT-TGTTT
7239703 GTTTGTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 7 0.21
22 17 0.52
23 9 0.27
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (22 bp):
ATATTAATATTTGTTTAAATTT
Found at i:7242271 original size:6 final size:6
Alignment explanation
Indices: 7242260--7242298 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
7242250 TGATCAAAAT
* * *
7242260 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
7242299 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:7264378 original size:117 final size:117
Alignment explanation
Indices: 7264167--7264406 Score: 471
Period size: 117 Copynumber: 2.1 Consensus size: 117
7264157 CTTTCAAAGT
*
7264167 CATGATGCATTTTCTTTTTACAGACATTTACACGAAGTATAAGCAAACATGCATTTTATACATCA
1 CATGTTGCATTTTCTTTTTACAGACATTTACACGAAGTATAAGCAAACATGCATTTTATACATCA
7264232 TATTCCATCAAAATACAAAAATACAAAATACATATCAAACCATGCTTGGGGA
66 TATTCCATCAAAATACAAAAATACAAAATACATATCAAACCATGCTTGGGGA
7264284 CATGTTGCATTTTCTTTTTACAGACATTTACACGAAGTATAAGCAAACATGCATTTTATACATCA
1 CATGTTGCATTTTCTTTTTACAGACATTTACACGAAGTATAAGCAAACATGCATTTTATACATCA
7264349 TATTCCATCAAAATACAAAAATACAAAATACATATCAAACCATGCTTGGGGA
66 TATTCCATCAAAATACAAAAATACAAAATACATATCAAACCATGCTTGGGGA
7264401 CATGTT
1 CATGTT
7264407 TTCCAAAACA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 122 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (117 bp):
CATGTTGCATTTTCTTTTTACAGACATTTACACGAAGTATAAGCAAACATGCATTTTATACATCA
TATTCCATCAAAATACAAAAATACAAAATACATATCAAACCATGCTTGGGGA
Found at i:7267413 original size:2 final size:2
Alignment explanation
Indices: 7267406--7267440 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7267396 TGGGAGGAGG
7267406 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
7267441 CATGGATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7274689 original size:6 final size:6
Alignment explanation
Indices: 7274678--7274704 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7274668 CCCTCCCTTT
7274678 AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAA
7274705 TAGCACCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:7284240 original size:24 final size:24
Alignment explanation
Indices: 7284188--7284250 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
7284178 ATAAAACTAA
* *
7284188 AATATAATTA-AAAGTATATATTT
1 AATATAATTATAAATTATATAATT
7284211 AA-ATAATTATAAATTA-ATTAATT
1 AATATAATTATAAATTATA-TAATT
7284234 AATATAATATATAAATT
1 AATATAAT-TATAAATT
7284251 GAAATTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.24
23 13 0.38
24 5 0.15
25 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATAATTATAAATTATATAATT
Found at i:7293552 original size:1 final size:1
Alignment explanation
Indices: 7293546--7293580 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
7293536 GAAATTTTCC
*
7293546 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7293581 CCTCTCGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:7297955 original size:2 final size:2
Alignment explanation
Indices: 7297948--7297976 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7297938 TACATTGATA
7297948 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 A
7297977 AAAGATACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7304003 original size:7 final size:7
Alignment explanation
Indices: 7303992--7304030 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
7303982 CATTGCCTCT
*
7303992 TTTATTT
1 TTTATTC
*
7303999 TTTA-TA
1 TTTATTC
7304005 TTTATTC
1 TTTATTC
7304012 TTTATTC
1 TTTATTC
7304019 TTTATTC
1 TTTATTC
7304026 TTTAT
1 TTTAT
7304031 CTTCATGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTC
Found at i:7316369 original size:30 final size:29
Alignment explanation
Indices: 7316302--7316372 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
7316292 AAATAAATTT
*
7316302 AAATTTTTATTTTCAATTTTTAAAAAGTTC
1 AAATTTTT-TTTTCAAATTTTAAAAAGTTC
* * *
7316332 AATTTTTTTTTTCAAATTTTAAGAGGTTC
1 AAATTTTTTTTTCAAATTTTAAAAAGTTC
*
7316361 AAAATTTTTTTT
1 AAATTTTTTTTT
7316373 AATCAACTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (29 bp):
AAATTTTTTTTTCAAATTTTAAAAAGTTC
Found at i:7319327 original size:3 final size:3
Alignment explanation
Indices: 7319277--7319313 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
7319267 TTCAAAACAA
7319277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
7319314 TACTTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7319432 original size:10 final size:12
Alignment explanation
Indices: 7319403--7319430 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7319393 TTGTATATTC
7319403 TTTATAAATTTT
1 TTTATAAATTTT
7319415 TTTATAAATTTT
1 TTTATAAATTTT
7319427 TTTA
1 TTTA
7319431 AAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATAAATTTT
Found at i:7328209 original size:22 final size:21
Alignment explanation
Indices: 7328174--7328273 Score: 93
Period size: 20 Copynumber: 4.9 Consensus size: 21
7328164 TACTAAAAAC
*
7328174 ATTAAAAATTGTAAATAATAT
1 ATTAAATATTGTAAATAATAT
*
7328195 ATATATATATTGTAAATAAT-T
1 AT-TAAATATTGTAAATAATAT
*
7328216 ATTAAATATTGTTAA-AATAT
1 ATTAAATATTGTAAATAATAT
* *
7328236 -TTTAA-ATTGTAAAAAAGT-T
1 ATTAAATATTGTAAATAA-TAT
*
7328255 ATTAAAAATTGTAAATAAT
1 ATTAAATATTGTAAATAAT
7328274 TAACAAATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.11
19 10 0.15
20 18 0.28
21 15 0.23
22 15 0.23
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
ATTAAATATTGTAAATAATAT
Found at i:7328266 original size:39 final size:42
Alignment explanation
Indices: 7328174--7328273 Score: 127
Period size: 39 Copynumber: 2.5 Consensus size: 42
7328164 TACTAAAAAC
* *
7328174 ATTAAAAATTGTAAATAATATATATATATATTGTAAATAATT
1 ATTAAAAATTGTAAATAATATATATATAAATTGTAAAAAATT
* *
7328216 ATTAAATATTGTTAA-AATAT-T-T-TAAATTGTAAAAAAGTT
1 ATTAAAAATTGTAAATAATATATATATAAATTGTAAAAAA-TT
7328255 ATTAAAAATTGTAAATAAT
1 ATTAAAAATTGTAAATAAT
7328274 TAACAAATCG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
38 12 0.24
39 16 0.32
40 4 0.08
41 5 0.10
42 13 0.26
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (42 bp):
ATTAAAAATTGTAAATAATATATATATAAATTGTAAAAAATT
Found at i:7328522 original size:19 final size:19
Alignment explanation
Indices: 7328491--7328646 Score: 81
Period size: 19 Copynumber: 8.1 Consensus size: 19
7328481 CCACTGATTC
*
7328491 ACAATTTTAAATAATTTTT
1 ACAATTTTTAATAATTTTT
*
7328510 ACAGTTTTTAATAATTATTT
1 ACAATTTTTAATAATT-TTT
* * * *
7328530 GCAAACTTTTAATAAATTTC
1 AC-AATTTTTAATAATTTTT
* *
7328550 ACAATATTTGATAATTTTT
1 ACAATTTTTAATAATTTTT
* *
7328569 ACAAATTTT-A-AATTGTGT
1 ACAATTTTTAATAATT-TTT
7328587 --AATTTTTAATAACTTCTTTT
1 ACAATTTTTAATAA--T-TTTT
*
7328607 ACAAATTTTAA-ATATTTTT
1 ACAATTTTTAATA-ATTTTT
*
7328626 AACAA-TATTAATAATTATTT
1 -ACAATTTTTAATAATT-TTT
7328646 A
1 A
7328647 TAATATTTCT
Statistics
Matches: 103, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
16 6 0.06
17 5 0.05
18 5 0.05
19 46 0.45
20 19 0.18
21 13 0.13
22 9 0.09
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (19 bp):
ACAATTTTTAATAATTTTT
Found at i:7328687 original size:23 final size:23
Alignment explanation
Indices: 7328643--7328702 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
7328633 TTAATAATTA
*
7328643 TTTATAATATTTCTTTTTTACAAGT
1 TTTA-AATATTT-TTTTATACAAGT
*
7328668 TTTAAATATTTTTTTATACAATT
1 TTTAAATATTTTTTTATACAAGT
*
7328691 TTTATATATTTT
1 TTTAAATATTTT
7328703 AAAATGTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 21 0.66
24 7 0.22
25 4 0.12
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTAAATATTTTTTTATACAAGT
Found at i:7330584 original size:6 final size:6
Alignment explanation
Indices: 7330573--7330599 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7330563 CGGAGTTACG
7330573 TTCCTC TTCCTC TTCCTC TTCCTC TTC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTC
7330600 ATCTCCGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCCTC
Found at i:7334545 original size:13 final size:13
Alignment explanation
Indices: 7334527--7334552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7334517 CCTTTTGACA
7334527 AGGCACACATCTT
1 AGGCACACATCTT
7334540 AGGCACACATCTT
1 AGGCACACATCTT
7334553 GCACACACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (13 bp):
AGGCACACATCTT
Found at i:7352018 original size:1 final size:1
Alignment explanation
Indices: 7352007--7352038 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
7351997 GGTTGGTATG
*
7352007 CCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7352039 TTTTACTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:7353690 original size:3 final size:3
Alignment explanation
Indices: 7353684--7353722 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
7353674 CTTCTTCCCG
*
7353684 CCA CCA CC- CACA CCA CCA CCA CCA CCA CCA CCC CCA CCA
1 CCA CCA CCA C-CA CCA CCA CCA CCA CCA CCA CCA CCA CCA
7353723 GTTCCACTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:7355026 original size:2 final size:2
Alignment explanation
Indices: 7355021--7355058 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7355011 GTTGGGAGTG
7355021 TA TA TA TA TA 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 TA TA TA TA TA
7355059 GAGTGGAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7367811 original size:2 final size:2
Alignment explanation
Indices: 7367804--7367830 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7367794 GCTCTCCCCA
7367804 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
7367831 TTCAGTCTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:7377236 original size:23 final size:22
Alignment explanation
Indices: 7377196--7377238 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
7377186 TGAAAATTAA
*
7377196 ATTAAAAATTAAAAAAATATCT
1 ATTAAAAAATAAAAAAATATCT
*
7377218 ATTAATAAAATAAATAAATAT
1 ATTAA-AAAATAAAAAAATAT
7377239 TAAACTTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATTAAAAAATAAAAAAATATCT
Found at i:7378365 original size:30 final size:30
Alignment explanation
Indices: 7378331--7378388 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
7378321 CTTTTATTGA
7378331 GTTGGT-TCTACCAATCAATCAGATATCATT
1 GTTGGTGT-TACCAATCAATCAGATATCATT
*
7378361 GTTGGTGTTACCAATCAATCATATATCA
1 GTTGGTGTTACCAATCAATCAGATATCA
7378389 ATTCTGTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (30 bp):
GTTGGTGTTACCAATCAATCAGATATCATT
Found at i:7386138 original size:31 final size:30
Alignment explanation
Indices: 7386103--7386169 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
7386093 ATTAATAAAA
7386103 ATAAAA-TTACATTTTAATATTCTTAAAAATG
1 ATAAAAGTTACA-TTTAATATT-TTAAAAATG
** * *
7386134 ATAAAAGTTTGATTTAATCTTTTAAAAATT
1 ATAAAAGTTACATTTAATATTTTAAAAATG
7386164 ATAAAA
1 ATAAAA
7386170 ATATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 14 0.45
31 14 0.45
32 3 0.10
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
ATAAAAGTTACATTTAATATTTTAAAAATG
Found at i:7390028 original size:12 final size:13
Alignment explanation
Indices: 7390006--7390046 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
7389996 TTAAATTTTG
7390006 TTTTGATTCAATT
1 TTTTGATTCAATT
* *
7390019 TTTTTA-TCAATG
1 TTTTGATTCAATT
7390031 TTTTGATTCAATT
1 TTTTGATTCAATT
7390044 TTT
1 TTT
7390047 ACAAACAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTGATTCAATT
Found at i:7390041 original size:13 final size:13
Alignment explanation
Indices: 7390004--7390046 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
7389994 CATTAAATTT
7390004 TGTTTTGATTCAA
1 TGTTTTGATTCAA
* *
7390017 TTTTTTTA-TCAA
1 TGTTTTGATTCAA
7390029 TGTTTTGATTCAA
1 TGTTTTGATTCAA
7390042 T-TTTT
1 TGTTTT
7390047 ACAAACAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (13 bp):
TGTTTTGATTCAA
Found at i:7416278 original size:22 final size:22
Alignment explanation
Indices: 7416240--7416281 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7416230 TACTTTCATC
*
7416240 TATTTTCAAATTAATTAATTTT
1 TATTTTCAAAGTAATTAATTTT
7416262 TATTTT-AAAGTAGATTAATT
1 TATTTTCAAAGTA-ATTAATT
7416282 CCCATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTTCAAAGTAATTAATTTT
Found at i:7419110 original size:3 final size:3
Alignment explanation
Indices: 7419102--7419136 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7419092 TAGACGAGGT
7419102 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
7419137 TACTTGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7421268 original size:17 final size:17
Alignment explanation
Indices: 7421246--7421280 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
7421236 GAGTGGAAAT
7421246 CATTGGTGTACATACTC
1 CATTGGTGTACATACTC
7421263 CATTGGTGTACATACTC
1 CATTGGTGTACATACTC
7421280 C
1 C
7421281 CTTAGCACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (17 bp):
CATTGGTGTACATACTC
Found at i:7423715 original size:19 final size:18
Alignment explanation
Indices: 7423688--7423724 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
7423678 TAAAAAATGG
*
7423688 TAATCATAAATTAAATAAT
1 TAATAATAAATT-AATAAT
7423707 TAATAATAAATTAATAAT
1 TAATAATAAATTAATAAT
7423725 GAGGTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATAAATTAATAAT
Found at i:7439896 original size:20 final size:20
Alignment explanation
Indices: 7439860--7439897 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7439850 ATAATTTTAG
*
7439860 TTTCATACTTTATATCAAAT
1 TTTCATACTGTATATCAAAT
7439880 TTTCAT-CTGTATAATCAA
1 TTTCATACTGTAT-ATCAA
7439898 TAAATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTCATACTGTATATCAAAT
Found at i:7441663 original size:23 final size:24
Alignment explanation
Indices: 7441636--7441681 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
7441626 TTAAAAATAA
7441636 TATTA-TAATA-AATAATAATATTT
1 TATTATTAATATAATAA-AATATTT
7441659 TATTATTTAATATAATAAAATAT
1 TATTA-TTAATATAATAAAATAT
7441682 AAGAGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
25 10 0.50
26 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATTAATATAATAAAATATTT
Found at i:7448121 original size:27 final size:24
Alignment explanation
Indices: 7448075--7448123 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
7448065 AGAGAAATGT
7448075 AAATGTGATATATGAAATTATGAG
1 AAATGTGATATATGAAATTATGAG
*
7448099 AAATGATGTTATATGAGATATTATG
1 AAATG-TGATATATGA-A-ATTATG
7448124 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 1 0.05
27 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (24 bp):
AAATGTGATATATGAAATTATGAG
Found at i:7450326 original size:21 final size:23
Alignment explanation
Indices: 7450276--7450347 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 23
7450266 ATTATAACAA
*
7450276 TATT-AAATTTATTATAAATATT
1 TATTAAAATGTATTATAAATATT
**
7450298 TAAAAAAATGTATTA-AAAT-TT
1 TATTAAAATGTATTATAAATATT
* *
7450319 TATTAAAAT-AATTAT-AATA-A
1 TATTAAAATGTATTATAAATATT
7450339 TATTAAAAT
1 TATTAAAAT
7450348 CATATAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 16 0.40
21 9 0.22
22 6 0.15
23 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
TATTAAAATGTATTATAAATATT
Found at i:7451568 original size:189 final size:188
Alignment explanation
Indices: 7451272--7451618 Score: 411
Period size: 189 Copynumber: 1.8 Consensus size: 188
7451262 ATAATTGAAT
*
7451272 TTATCTACAACATAATATATAAAGATATTTTAGTTGACCGTTAAAATCATTATTACTATCAATCA
1 TTATCTACAACATAATATATAAAGATATTTTAATTGACCGTTAAAATCATTATTACTATCAATCA
* * * *
7451337 CTAAAATAAACATATATCTTGATCGATAATTTTTTAAAATAAATTCACAA-GTATATTTTAAC-G
66 CTAAAATAAACAAATATCTTAATCGATAATTATTTAAAATAAATCCACAATG-ATATTTT-ACTG
**
7451400 ACCTTTAAAATCA-TTATTATTTTCAATAATCAAAAAAATATTTTTTTATCCATAAACAAAG
129 ACAGTTAAAAT-AGTTATT-TTTTCAATAATCAAAAAAATATTTTTTTATCCATAAACAAAG
* * * * * **
7451461 TTATTTACAACA-AAGTCTATAATGATATTTTAATTGATCGTTAAAATCGTTATTA-TCATTGAT
1 TTATCTACAACATAA-TATATAAAGATATTTTAATTGACCGTTAAAATCATTATTACT-ATCAAT
* * *
7451524 CACTAAAGCT-AACAAATATTTTAATCGACTGATTATTT-AAATAAATCCACAATGATATTTTAC
64 CACTAAA-ATAAACAAATATCTTAATCGA-TAATTATTTAAAATAAATCCACAATGATATTTTAC
7451587 TTGACAGTTAAAATAGTTATTTTTTCAATAAT
127 -TGACAGTTAAAATAGTTATTTTTTCAATAAT
7451619 TAAACCGTAC
Statistics
Matches: 133, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
188 5 0.04
189 104 0.78
190 24 0.18
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (188 bp):
TTATCTACAACATAATATATAAAGATATTTTAATTGACCGTTAAAATCATTATTACTATCAATCA
CTAAAATAAACAAATATCTTAATCGATAATTATTTAAAATAAATCCACAATGATATTTTACTGAC
AGTTAAAATAGTTATTTTTTCAATAATCAAAAAAATATTTTTTTATCCATAAACAAAG
Found at i:7457530 original size:2 final size:2
Alignment explanation
Indices: 7457523--7457547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7457513 TATAATGGTA
7457523 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
7457548 AAACAATCTA
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:7470408 original size:6 final size:6
Alignment explanation
Indices: 7470397--7470446 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
7470387 AAGCCTTGGA
7470397 CTATTC CTATTC CTATTC CTATTC CTATTC CTATTC CTATTC CTATTC
1 CTATTC CTATTC CTATTC CTATTC CTATTC CTATTC CTATTC CTATTC
7470445 CT
1 CT
7470447 TGGAAAAGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (6 bp):
CTATTC
Found at i:7470908 original size:37 final size:38
Alignment explanation
Indices: 7470839--7470911 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
7470829 TATTATTTAT
**
7470839 AAATAACTTATAATTCATAACATTATGTATTTAAAACA
1 AAATAACTTATAATTCATAACATTATAAATTTAAAACA
*
7470877 AAATAA-TT-TAATTCAATAATATTATAAATTTAAAA
1 AAATAACTTATAATTC-ATAACATTATAAATTTAAAA
7470912 TATTAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 19 0.61
38 6 0.19
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (38 bp):
AAATAACTTATAATTCATAACATTATAAATTTAAAACA
Found at i:7470921 original size:36 final size:35
Alignment explanation
Indices: 7470881--7470972 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 35
7470871 AAAACAAAAT
* * *
7470881 AATTTAATTCAATAATATTATAAATTTAAAATATTA
1 AATTTACTTCAATAATATTATAAAATTAAAA-ATAA
* **
7470917 AATTTACTTAAATAACGTTATAAAATTAAAAATAA
1 AATTTACTTCAATAATATTATAAAATTAAAAATAA
**
7470952 AACATACTTCAATAATATTAT
1 AATTTACTTCAATAATATTAT
7470973 GAACGAAAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
35 19 0.42
36 26 0.58
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (35 bp):
AATTTACTTCAATAATATTATAAAATTAAAAATAA
Found at i:7473715 original size:24 final size:23
Alignment explanation
Indices: 7473671--7473715 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
7473661 TATTAAAATA
* * *
7473671 ATAAAAAATATATTTTTATTATC
1 ATAAAAAATACAATTTAATTATC
7473694 ATAAAAATATACAATTTAATTA
1 ATAAAAA-ATACAATTTAATTA
7473716 CGGTCTTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAAAAATACAATTTAATTATC
Found at i:7484824 original size:21 final size:22
Alignment explanation
Indices: 7484784--7484825 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
7484774 AATAACTATA
*
7484784 TAATTATAGTAATTAAATTCAT
1 TAATTATAGTAATGAAATTCAT
*
7484806 TAATT-TAGTAATGATATTCA
1 TAATTATAGTAATGAAATTCA
7484826 CAAAGAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
TAATTATAGTAATGAAATTCAT
Found at i:7490709 original size:4 final size:4
Alignment explanation
Indices: 7490700--7490729 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
7490690 CAAAGGTGGA
7490700 GGGT GGGT GGGT GGGT GGGT GGGT GGGT GG
1 GGGT GGGT GGGT GGGT GGGT GGGT GGGT GG
7490730 TAGGGCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.77, T:0.23
Consensus pattern (4 bp):
GGGT
Found at i:7496774 original size:69 final size:69
Alignment explanation
Indices: 7496663--7496801 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
7496653 GTTAAATGAA
7496663 TCCAATCACGTTTAATAATTGATATTACCAAACTTGCCGCATTGTTCTTTTGCCCTTGTCTTCAC
1 TCCAATCACGTTTAATAATTGATATTACCAAACTTGCCGCATTGTTCTTTTGCCCTTGTCTTCAC
7496728 TTCT
66 TTCT
7496732 TCCAATCACGTTTAATAATTGATATTACCAAACTTGCCGCATTGTTCTTTTGCCCTTGTCTTCAC
1 TCCAATCACGTTTAATAATTGATATTACCAAACTTGCCGCATTGTTCTTTTGCCCTTGTCTTCAC
7496797 TTCT
66 TTCT
7496801 T
1 T
7496802 TGTGGAAGGT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (69 bp):
TCCAATCACGTTTAATAATTGATATTACCAAACTTGCCGCATTGTTCTTTTGCCCTTGTCTTCAC
TTCT
Found at i:7496866 original size:24 final size:26
Alignment explanation
Indices: 7496848--7496907 Score: 61
Period size: 30 Copynumber: 2.2 Consensus size: 26
7496838 TTTTATTATT
*
7496848 TTAATAATTT-TT-ATTTTTATTATTT
1 TTAAAAATTTATTAATTTTTATTA-TT
7496873 TTAAAAAATTTAATTAAATTTTTATTATT
1 TT-AAAAATTT-ATT-AATTTTTATTATT
7496902 TTAAAA
1 TTAAAA
7496908 GTTGAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 2 0.07
26 7 0.24
28 6 0.21
29 4 0.14
30 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTAAAAATTTATTAATTTTTATTATT
Found at i:7496921 original size:29 final size:29
Alignment explanation
Indices: 7496860--7496932 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
7496850 AATAATTTTT
* *
7496860 ATTTTTATTATTTTTAAAAAATTTAATTAA
1 ATTTTTATTA-TTTTAAAAAATTGAAATAA
*
7496890 ATTTTTATTATTTT-AAAAGTTGAAATATA
1 ATTTTTATTATTTTAAAAAATTGAAATA-A
7496919 ATTTTATCATTATT
1 ATTTT-T-ATTATT
7496933 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.27
29 10 0.27
30 11 0.30
31 6 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTTTTATTATTTTAAAAAATTGAAATAA
Found at i:7537092 original size:11 final size:11
Alignment explanation
Indices: 7537076--7537134 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
7537066 AAATAAACCC
7537076 TAATCTAATAT
1 TAATCTAATAT
*
7537087 TAATCTAACAT
1 TAATCTAATAT
*
7537098 TAATTTCTAATGT
1 TAA--TCTAATAT
7537111 TAATCTAATAT
1 TAATCTAATAT
*
7537122 TTATCCTAATAT
1 TAAT-CTAATAT
7537134 T
1 T
7537135 GTCGTCGGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 23 0.57
12 8 0.20
13 9 0.22
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (11 bp):
TAATCTAATAT
Found at i:7545063 original size:30 final size:29
Alignment explanation
Indices: 7545023--7545081 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
7545013 ATGATAACAA
*
7545023 TTAAATATAAAAAAT-AGAAATATTAAATTT
1 TTAAAAATAAAAAATAAG-AA-ATTAAATTT
*
7545053 TTAAAAATAAAAATTAAGAAATTAAATTT
1 TTAAAAATAAAAAATAAGAAATTAAATTT
7545082 CAAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 15 0.58
31 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAAAAATAAAAAATAAGAAATTAAATTT
Found at i:7554406 original size:23 final size:23
Alignment explanation
Indices: 7554376--7554445 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
7554366 TTTCTTTTTA
*
7554376 TCCGTAATTTTTCTGTTTCCTTC
1 TCCGTAATTTTTCTGTTTCTTTC
* *
7554399 TCTGTAATTTTTCTATTTCTTTC
1 TCCGTAATTTTTCTGTTTCTTTC
7554422 TCCGTAATTTTTCTGTTTCTTTC
1 TCCGTAATTTTTCTGTTTCTTTC
7554445 T
1 T
7554446 TTGTTTTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.10, C:0.21, G:0.07, T:0.61
Consensus pattern (23 bp):
TCCGTAATTTTTCTGTTTCTTTC
Found at i:7554453 original size:13 final size:13
Alignment explanation
Indices: 7554437--7554462 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7554427 AATTTTTCTG
7554437 TTTCTTTCTTTGT
1 TTTCTTTCTTTGT
7554450 TTTCTTTCTTTGT
1 TTTCTTTCTTTGT
7554463 AATTTTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTTGT
Done.