Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008624.1 Hibiscus syriacus cultivar Beakdansim tig00111587_pilon, 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: 642794
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:133016 original size:30 final size:31
Alignment explanation
Indices: 132980--133202 Score: 146
Period size: 30 Copynumber: 7.4 Consensus size: 31
132970 TGTTGCATTG
*
132980 AAAATAT-TTTTTAAAATGTAAGATAAGAGT
1 AAAATATATTTTTAAAATGTAAGATAAGAAT
* * *
133010 AAAATATA-TTTTCAACT-TAAAATAAGAAT
1 AAAATATATTTTTAAAATGTAAGATAAGAAT
* * *
133039 AAAATATACTTTT-AAGTG-AAGATAAGATT
1 AAAATATATTTTTAAAATGTAAGATAAGAAT
* * *
133068 AAAAATATATTTTT-ATAT-TAAAATAAAAAT
1 -AAAATATATTTTTAAAATGTAAGATAAGAAT
* *
133098 AAAATATA--TTTAATAA-GTTAAGACAAAAAAT
1 AAAATATATTTTTAA-AATG-TAAGA-TAAGAAT
* * * *
133129 AAAAGATGTTTCTTAAAATTTAAGATAATAAT
1 AAAATATATTT-TTAAAATGTAAGATAAGAAT
*
133161 AAAATATATTTTCT-AAAT-TCAAAATAAGAAT
1 AAAATATATTTT-TAAAATGT-AAGATAAGAAT
133192 AAAATATATTT
1 AAAATATATTT
133203 GAGTGATGTC
Statistics
Matches: 152, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.02
28 1 0.01
29 39 0.26
30 45 0.30
31 37 0.24
32 15 0.10
33 8 0.05
34 4 0.03
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (31 bp):
AAAATATATTTTTAAAATGTAAGATAAGAAT
Found at i:133193 original size:31 final size:30
Alignment explanation
Indices: 132980--133202 Score: 154
Period size: 29 Copynumber: 7.4 Consensus size: 30
132970 TGTTGCATTG
* *
132980 AAAATAT-TTTT-TAAAATGTAAGATAAGAGT
1 AAAATATATTTTCT-AAAT-TAAAATAAGAAT
*
133010 AAAATATATTTTC-AACTTAAAATAAGAAT
1 AAAATATATTTTCTAAATTAAAATAAGAAT
* * * * *
133039 AAAATATACTTT-TAAGTGAAGATAAGATT
1 AAAATATATTTTCTAAATTAAAATAAGAAT
* *
133068 AAAAATATATTTT-TATATTAAAATAAAAAT
1 -AAAATATATTTTCTAAATTAAAATAAGAAT
** * *
133098 AAAATATATTTAATAAGTTAAGACA-AAAAAT
1 AAAATATATTTTCTAAATTAA-A-ATAAGAAT
* * * *
133129 AAAAGAT-GTTTCTTAAAATTTAAGATAATAAT
1 AAAATATATTTTC-T-AAA-TTAAAATAAGAAT
133161 AAAATATATTTTCTAAATTCAAAATAAGAAT
1 AAAATATATTTTCTAAATT-AAAATAAGAAT
133192 AAAATATATTT
1 AAAATATATTT
133203 GAGTGATGTC
Statistics
Matches: 151, Mismatches: 29, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
29 44 0.29
30 42 0.28
31 42 0.28
32 15 0.10
33 8 0.05
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (30 bp):
AAAATATATTTTCTAAATTAAAATAAGAAT
Found at i:133515 original size:2 final size:2
Alignment explanation
Indices: 133508--133533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
133498 AAGATAAATA
133508 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
133534 TAGAATAAAA
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:134035 original size:21 final size:21
Alignment explanation
Indices: 133988--134035 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
133978 TGGGATCGAT
*
133988 CCCTTCCCAAAAAGGATTGAC
1 CCCTTTCCAAAAAGGATTGAC
134009 CCCTTTCCAAAAAGGATTGAC
1 CCCTTTCCAAAAAGGATTGAC
134030 CCCTTT
1 CCCTTT
134036 GGTATAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.25
Consensus pattern (21 bp):
CCCTTTCCAAAAAGGATTGAC
Found at i:134076 original size:20 final size:21
Alignment explanation
Indices: 134053--134091 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
134043 TGGTCGAAAT
134053 ATTT-GAAAAAGGATCGATTC
1 ATTTGGAAAAAGGATCGATTC
* *
134073 ATTTGGCAAAATGATCGAT
1 ATTTGGAAAAAGGATCGAT
134092 CCCTTGTGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (21 bp):
ATTTGGAAAAAGGATCGATTC
Found at i:134169 original size:19 final size:20
Alignment explanation
Indices: 134130--134169 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
134120 GGCTATTTTG
*
134130 ATCCCCAATGGCTTCGAAAC
1 ATCCCCAATGGCTTAGAAAC
134150 ATCCCCAATGG-TTAGAAAC
1 ATCCCCAATGGCTTAGAAAC
134169 A
1 A
134170 ACTAGTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (20 bp):
ATCCCCAATGGCTTAGAAAC
Found at i:134940 original size:21 final size:21
Alignment explanation
Indices: 134922--134961 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
134912 TTTATAATTT
134922 AATT-TTAATAATATATAATA
1 AATTATTAATAATATATAATA
*
134942 AATTATTAATAAAAT-TAATA
1 AATTATTAATAATATATAATA
134962 GTATTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATTAATAATATATAATA
Found at i:135002 original size:27 final size:27
Alignment explanation
Indices: 134928--135007 Score: 63
Period size: 27 Copynumber: 2.9 Consensus size: 27
134918 ATTTAATTTT
*
134928 AATAATATATAATAAATTA-TTAATAAA
1 AATAATAT-TATTAAATTATTTAATAAA
* * * * * *
134955 ATTAATAGTATTTACTAATTTCATAAA
1 AATAATATTATTAAATTATTTAATAAA
*
134982 AATAATATTATTGAATTATTTGAATA
1 AATAATATTATTAAATTATTT-AATA
135008 TCTAATATAT
Statistics
Matches: 38, Mismatches: 13, Indels: 3
0.70 0.24 0.06
Matches are distributed among these distances:
26 6 0.16
27 29 0.76
28 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (27 bp):
AATAATATTATTAAATTATTTAATAAA
Found at i:135059 original size:7 final size:7
Alignment explanation
Indices: 135047--135304 Score: 509
Period size: 7 Copynumber: 37.0 Consensus size: 7
135037 AATATTCATA
135047 TTTTAAT
1 TTTTAAT
135054 TTTTAAT
1 TTTTAAT
135061 TTTTAAT
1 TTTTAAT
135068 TTTTAAT
1 TTTTAAT
135075 TTTTAAT
1 TTTTAAT
135082 TTTTAAT
1 TTTTAAT
135089 TTTTAAT
1 TTTTAAT
135096 TTTTAAT
1 TTTTAAT
135103 TTTTAAT
1 TTTTAAT
135110 TTTTAAT
1 TTTTAAT
135117 TTTTAAT
1 TTTTAAT
135124 TTTTAAT
1 TTTTAAT
135131 TTTTAAT
1 TTTTAAT
135138 TTTTAAT
1 TTTTAAT
135145 TTTTAA-
1 TTTTAAT
135151 TTTTAAT
1 TTTTAAT
135158 TTTTAAT
1 TTTTAAT
135165 TTTTAAT
1 TTTTAAT
135172 TTTTAAT
1 TTTTAAT
135179 TTTTAAT
1 TTTTAAT
135186 TTTTAAT
1 TTTTAAT
135193 TTTTAAT
1 TTTTAAT
135200 TTTTAAT
1 TTTTAAT
135207 TTTTAAT
1 TTTTAAT
135214 TTTTAAT
1 TTTTAAT
135221 TTTTAAT
1 TTTTAAT
135228 TTTTAAT
1 TTTTAAT
135235 TTTTAAT
1 TTTTAAT
135242 TTTTAAT
1 TTTTAAT
135249 TTTTAAT
1 TTTTAAT
135256 TTTTAAT
1 TTTTAAT
135263 TTTTAAT
1 TTTTAAT
135270 TTTTAAT
1 TTTTAAT
135277 TTTTAAT
1 TTTTAAT
135284 TTTTAAT
1 TTTTAAT
135291 TTTTAAT
1 TTTTAAT
135298 TTTTAAT
1 TTTTAAT
135305 AATATTTTTA
Statistics
Matches: 250, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
6 6 0.02
7 244 0.98
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:135363 original size:42 final size:37
Alignment explanation
Indices: 135310--135411 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 37
135300 TTAATAATAT
* *
135310 TTTTATTTTAATAAATTATTAGTGTAATTAATAATATATGA
1 TTTTATTTTAATAAATTATTAATATAATT--T-ATA-ATGA
135351 TTCTTATTTTAATAAATTATTAATATAATTTATAATGA
1 TT-TTATTTTAATAAATTATTAATATAATTTATAATGA
*
135389 TTTTATTTTAATAAAATA-TAATA
1 TTTTATTTTAATAAATTATTAATA
135412 ATCATAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
36 5 0.09
37 15 0.26
38 6 0.11
39 3 0.05
40 1 0.02
41 2 0.04
42 25 0.44
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (37 bp):
TTTTATTTTAATAAATTATTAATATAATTTATAATGA
Found at i:135521 original size:23 final size:23
Alignment explanation
Indices: 135482--135529 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
135472 ACATTAATCT
*
135482 AATTAAAAATTTATTTTTATG-A
1 AATTAAAAATTAATTTTTATGTA
135504 AATTAAAAATTAATTTTTATGTA
1 AATTAAAAATTAATTTTTATGTA
135527 AAT
1 AAT
135530 AGTTCTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTAAAAATTAATTTTTATGTA
Found at i:135687 original size:21 final size:23
Alignment explanation
Indices: 135645--135688 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
135635 TTTAAAAGAA
*
135645 TATATCAATCTCTAAATTAAATAG
1 TATATCAATCTCT-AATAAAATAG
135669 TATATCAA-CTCT-ATAAAATA
1 TATATCAATCTCTAATAAAATA
135689 AGTAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (23 bp):
TATATCAATCTCTAATAAAATAG
Found at i:142726 original size:27 final size:29
Alignment explanation
Indices: 142671--142749 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
142661 TACATTTATT
*
142671 ATATTATAAGATAATATATATTGTCAAAA
1 ATATTATAAGATAATATATATTGTAAAAA
142700 ATATTATAAGATAATAT-T-TT-TAAAAA
1 ATATTATAAGATAATATATATTGTAAAAA
142726 A-ATTAATATATTGATAATATATAT
1 ATATT-ATA-A--GATAATATATAT
142750 ACATTCTTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
25 3 0.07
26 9 0.21
27 3 0.07
28 1 0.02
29 25 0.58
30 1 0.02
31 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATTATAAGATAATATATATTGTAAAAA
Found at i:144196 original size:40 final size:40
Alignment explanation
Indices: 144141--144220 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
144131 TGTGTTAATG
144141 GTTGATGGTTTATTTATTTTAATTTAGATAATAAATTTAC
1 GTTGATGGTTTATTTATTTTAATTTAGATAATAAATTTAC
144181 GTTGATGGTTTATTTATTTTAATTTAGATAATAAATTTAC
1 GTTGATGGTTTATTTATTTTAATTTAGATAATAAATTTAC
144221 ATTTGATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (40 bp):
GTTGATGGTTTATTTATTTTAATTTAGATAATAAATTTAC
Found at i:145161 original size:15 final size:16
Alignment explanation
Indices: 145141--145181 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
145131 GTTTATTTCA
*
145141 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
145156 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
145172 GAATGATTCA
1 GAATGATTCA
145182 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:145271 original size:27 final size:23
Alignment explanation
Indices: 145233--145341 Score: 101
Period size: 23 Copynumber: 4.6 Consensus size: 23
145223 GATAATGGCT
145233 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAAT-T-CTT-T-TG
* *
145260 CTGAATCATTCAGTATTGTTTTG
1 CTGAATCATTCAGAATTCTTTTG
** *
145283 CTGAATCATTCAGTTTTGTTTTG
1 CTGAATCATTCAGAATTCTTTTG
** *
145306 CTGAATCATTCAGTTTTGTTTTG
1 CTGAATCATTCAGAATTCTTTTG
*
145329 CTGAATCAGTCAG
1 CTGAATCATTCAG
145342 CACTGAATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
23 59 0.76
24 1 0.01
25 2 0.03
26 1 0.01
27 15 0.19
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (23 bp):
CTGAATCATTCAGAATTCTTTTG
Found at i:145288 original size:23 final size:23
Alignment explanation
Indices: 145258--145341 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
145248 TGTACTTCTG
*
145258 TGCTGAATCATTCAGTATTGTTT
1 TGCTGAATCATTCAGTTTTGTTT
145281 TGCTGAATCATTCAGTTTTGTTT
1 TGCTGAATCATTCAGTTTTGTTT
145304 TGCTGAATCATTCAGTTTTGTTT
1 TGCTGAATCATTCAGTTTTGTTT
*
145327 TGCTGAATCAGTCAG
1 TGCTGAATCATTCAG
145342 CACTGAATCA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.46
Consensus pattern (23 bp):
TGCTGAATCATTCAGTTTTGTTT
Found at i:145409 original size:22 final size:22
Alignment explanation
Indices: 145381--145436 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
145371 CGCGCTGAAT
145381 GCTGAACGGTTCAACATTCAAC
1 GCTGAACGGTTCAACATTCAAC
145403 GCTGAACGGTTCAACATTCAAC
1 GCTGAACGGTTCAACATTCAAC
*
145425 GCTGAATGGTTC
1 GCTGAACGGTTC
145437 CATTCAGAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
GCTGAACGGTTCAACATTCAAC
Found at i:145633 original size:29 final size:31
Alignment explanation
Indices: 145585--145642 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
145575 AGAATTAGAA
*
145585 AAATGATTTTGAAGTGTCAAATTTAGAAAAC
1 AAATGATTTTGAAGTGTCAAAATTAGAAAAC
145616 AAAT-ATTTTG-AGTGTCAAAATTAGAAA
1 AAATGATTTTGAAGTGTCAAAATTAGAAA
145643 TTTTAGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 16 0.62
30 6 0.23
31 4 0.15
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (31 bp):
AAATGATTTTGAAGTGTCAAAATTAGAAAAC
Found at i:150018 original size:57 final size:56
Alignment explanation
Indices: 149934--150178 Score: 188
Period size: 57 Copynumber: 4.3 Consensus size: 56
149924 AGTTCCTAGA
* * * *
149934 TTGAAGCACAACAATGCTCAACCGTTTATTAAAAGCACAGAGGTACCAATTTATAGG
1 TTGAAGCACAACGATGCTCAATCATTTATTAAAAGCACAGAGGTGCCAATTT-TAGG
* * ** * * * * *
149991 CTGAAGCACAACGATGCTAAATTGTTTATTAGAAGTATAGAGGTGCAAATTTCTAGA
1 TTGAAGCACAACGATGCTCAATCATTTATTAAAAGCACAGAGGTGCCAATTT-TAGG
* * * * * * * *
150048 TTGGAGTAGAATGATGCTCAATCATTTATTTAAAGCACAAACGTGCCAGATTTTTGG
1 TTGAAGCACAACGATGCTCAATCATTTATTAAAAGCACAGAGGTGCCA-ATTTTAGG
* * * *
150105 TTGAAGCACGACGATGCTTAATCATTTATT-AAAGCACAGAGGTTCTAGATTGTT-GG
1 TTGAAGCACAACGATGCTCAATCATTTATTAAAAGCACAGAGGTGCCA-ATT-TTAGG
* *
150161 TTAAAGCACAACGGTGCT
1 TTGAAGCACAACGATGCT
150179 TATAAATTTA
Statistics
Matches: 144, Mismatches: 42, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
56 34 0.24
57 106 0.74
58 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (56 bp):
TTGAAGCACAACGATGCTCAATCATTTATTAAAAGCACAGAGGTGCCAATTTTAGG
Found at i:150161 original size:56 final size:57
Alignment explanation
Indices: 150060--150180 Score: 154
Period size: 56 Copynumber: 2.1 Consensus size: 57
150050 GGAGTAGAAT
* * * *
150060 GATGCTCAATCATTTATTTAAAGCACAAACGTGCCAGATTTTTGGTTGAAGCACGAC
1 GATGCTTAATCATTTATTTAAAGCACAAACGTGCCAGATTGTTGGTTAAAGCACAAC
* * * *
150117 GATGCTTAATCATTTA-TTAAAGCACAGAGGTTCTAGATTGTTGGTTAAAGCACAAC
1 GATGCTTAATCATTTATTTAAAGCACAAACGTGCCAGATTGTTGGTTAAAGCACAAC
*
150173 GGTGCTTA
1 GATGCTTA
150181 TAAATTTAGC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
56 40 0.73
57 15 0.27
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (57 bp):
GATGCTTAATCATTTATTTAAAGCACAAACGTGCCAGATTGTTGGTTAAAGCACAAC
Found at i:158716 original size:37 final size:37
Alignment explanation
Indices: 158675--158746 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
158665 TGAATAAAAC
* * *
158675 TCGACTCCATTTAACTTCAAGTAATAATTTTATAAAT
1 TCGACTCCAATTAACTACAAGTAATAATTTCATAAAT
* *
158712 TCGACTCGAATTAACTACAAGTTATAATTTCATAA
1 TCGACTCCAATTAACTACAAGTAATAATTTCATAA
158747 CTCGACCCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (37 bp):
TCGACTCCAATTAACTACAAGTAATAATTTCATAAAT
Found at i:158890 original size:2 final size:2
Alignment explanation
Indices: 158883--158907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
158873 AAGTCCCTCA
158883 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 T
158908 ATATATATAT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:161481 original size:31 final size:31
Alignment explanation
Indices: 161443--161578 Score: 134
Period size: 31 Copynumber: 4.4 Consensus size: 31
161433 TCTTATTTCC
* *
161443 AAGTGACCAAAACTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAAAGA
*
161474 AAGTGACCAAAACTTAATAAAACGATAAAGA
1 AAGTGACCAAAACTTAATAAAACAATAAAGA
* * * *
161505 AAGTAACCAAAAGTGT-A-CAAA-TATGAAAGGA
1 AAGTGACCAAAACT-TAATAAAACAAT-AAA-GA
* **
161536 AAGTGACTAAAACTTAATAAAATGATAAAGA
1 AAGTGACCAAAACTTAATAAAACAATAAAGA
161567 AAGTGACCAAAA
1 AAGTGACCAAAA
161579 GTGTACAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
29 2 0.02
30 7 0.08
31 68 0.79
32 7 0.08
33 2 0.02
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.18
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAAAGA
Found at i:161549 original size:62 final size:62
Alignment explanation
Indices: 161474--161611 Score: 249
Period size: 62 Copynumber: 2.2 Consensus size: 62
161464 ACAATAACGT
161474 AAGTGACCAAAACTTAATAAAACGATAAAGAAAGTAACCAAAAGTGTACAAATATGAAAGGA
1 AAGTGACCAAAACTTAATAAAACGATAAAGAAAGTAACCAAAAGTGTACAAATATGAAAGGA
* * *
161536 AAGTGACTAAAACTTAATAAAATGATAAAGAAAGTGACCAAAAGTGTACAAATATGAAAGGA
1 AAGTGACCAAAACTTAATAAAACGATAAAGAAAGTAACCAAAAGTGTACAAATATGAAAGGA
161598 AAGTGACCAAAACT
1 AAGTGACCAAAACT
161612 AAATCCACTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (62 bp):
AAGTGACCAAAACTTAATAAAACGATAAAGAAAGTAACCAAAAGTGTACAAATATGAAAGGA
Found at i:161600 original size:31 final size:31
Alignment explanation
Indices: 161503--161609 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
161493 AAACGATAAA
*
161503 GAAAGTAACCAAAAGTGTACAAATATGAAAG
1 GAAAGTGACCAAAAGTGTACAAATATGAAAG
* * * *
161534 GAAAGTGACTAAAACT-TA-ATAAAATGATAAA
1 GAAAGTGACCAAAAGTGTACA-AATATGA-AAG
161565 GAAAGTGACCAAAAGTGTACAAATATGAAAG
1 GAAAGTGACCAAAAGTGTACAAATATGAAAG
161596 GAAAGTGACCAAAA
1 GAAAGTGACCAAAA
161610 CTAAATCCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
29 1 0.02
30 8 0.13
31 45 0.71
32 8 0.13
33 1 0.02
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (31 bp):
GAAAGTGACCAAAAGTGTACAAATATGAAAG
Found at i:163146 original size:64 final size:64
Alignment explanation
Indices: 163009--163170 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
162999 TTGTTCAAGG
* * * * * *
163009 TGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAC
1 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCAC
* * ** *
163073 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATTAAATGGGATTTA-
1 TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCA-TCAC
* *
163137 TGTACCGATGCA-TAGATAGTGCATCGATGCACCC
1 TGTATCGATGCACAAG-TAGTGCATCGATGCACCC
163171 ATCAAGGGAT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.02
64 79 0.95
65 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (64 bp):
TGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCAC
Found at i:167560 original size:64 final size:64
Alignment explanation
Indices: 167485--167606 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
167475 ATTGTTCAAG
* ** * **
167485 GTGTATCGATGCACATGAAGTTTATCGATGCACTCTTTTAAAATAAAAACATCAAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCA
* * * *
167549 GTGTATTGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATG
167607 GGATTTATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCA
Found at i:173033 original size:3 final size:3
Alignment explanation
Indices: 173027--173088 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
173017 CTCCTACTAC
*
173027 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
173075 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
173089 GTGACAGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:181415 original size:16 final size:18
Alignment explanation
Indices: 181394--181438 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
181384 AACATTCCCA
181394 GTAATCTTA-TTCC-CTG
1 GTAATCTTATTTCCACTG
181410 GTAATCTTACATTTCCACTG
1 GTAATCTT--ATTTCCACTG
181430 GTAATCTTA
1 GTAATCTTA
181439 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 2 0.08
19 4 0.16
20 11 0.44
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (18 bp):
GTAATCTTATTTCCACTG
Found at i:181432 original size:20 final size:19
Alignment explanation
Indices: 181403--181442 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
181393 AGTAATCTTA
181403 TTCCCTGGTAATCTTACAT
1 TTCCCTGGTAATCTTACAT
181422 TTCCACTGGTAATCTTACAT
1 TTCC-CTGGTAATCTTACAT
181442 T
1 T
181443 CCGTGAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (19 bp):
TTCCCTGGTAATCTTACAT
Found at i:194569 original size:22 final size:22
Alignment explanation
Indices: 194544--194586 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
194534 GCGACATACG
194544 TCCCCATCTCCGACGAAATCCA
1 TCCCCATCTCCGACGAAATCCA
* *
194566 TCCCCATCTCTGGCGAAATCC
1 TCCCCATCTCCGACGAAATCC
194587 GTCTATCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCCA
Found at i:197193 original size:21 final size:21
Alignment explanation
Indices: 197114--197191 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
197104 TTCACCTGTC
197114 ATCGTTCAAGAGGCCTCTCC-T
1 ATCGTTCAAGAGGCCTC-CCAT
*
197135 ATCGTTCAAGAGGCCTCTCAT
1 ATCGTTCAAGAGGCCTCCCAT
*
197156 ATCGTTCAAGAAGCC-CCCAT
1 ATCGTTCAAGAGGCCTCCCAT
*
197176 CATCCTTCAAGAGGCC
1 -ATCGTTCAAGAGGCC
197192 CCTTCCACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 5 0.10
21 45 0.90
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCTCCCAT
Found at i:198618 original size:13 final size:14
Alignment explanation
Indices: 198593--198625 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
198583 AAATTGATGT
198593 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
198607 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
198620 ATTTGT
1 ATTTGT
198626 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:202283 original size:40 final size:40
Alignment explanation
Indices: 202239--202338 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
202229 TTGCGAAATT
*
202239 AAAATTCGTGTTGCAAATTC-GAAAATTGAGTTACGAAAAC
1 AAAATTCGTGTTGCAAATTCAG-AAATCGAGTTACGAAAAC
** * ***
202279 AAAATTCACGTTGCGAATTCAGAAATCGAGTTACGAATTT
1 AAAATTCGTGTTGCAAATTCAGAAATCGAGTTACGAAAAC
*
202319 GAAATTCAGTGTTGCAAATT
1 AAAATTC-GTGTTGCAAATT
202339 TGGAAAATCG
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 37 0.79
41 10 0.21
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (40 bp):
AAAATTCGTGTTGCAAATTCAGAAATCGAGTTACGAAAAC
Found at i:202919 original size:23 final size:23
Alignment explanation
Indices: 202893--202936 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
202883 CAAAAGGTAG
*
202893 AGATAAATATGCCGCAAAGACAT
1 AGATAAATATGCCACAAAGACAT
*
202916 AGATAAATATGTCACAAAGAC
1 AGATAAATATGCCACAAAGAC
202937 GGACTTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (23 bp):
AGATAAATATGCCACAAAGACAT
Found at i:204539 original size:19 final size:19
Alignment explanation
Indices: 204515--204554 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
204505 TCTTTTAATT
204515 TATTTTT-TCATTAAAATAA
1 TATTTTTATCATTAAAA-AA
*
204534 TATTTTTATTATTAAAAAA
1 TATTTTTATCATTAAAAAA
204553 TA
1 TA
204555 AAAAATATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTTATCATTAAAAAA
Found at i:212127 original size:31 final size:31
Alignment explanation
Indices: 212089--212213 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
212079 CCCGAAGGAC
* * *
212089 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
212120 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
212151 CTGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
212182 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
212213 C
1 C
212214 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:216635 original size:31 final size:31
Alignment explanation
Indices: 216612--216784 Score: 285
Period size: 31 Copynumber: 5.6 Consensus size: 31
216602 TCCATAGATT
*
216612 CCGAAGAACCTAGGT-AATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAAT-AGTCCATATGTC
* *
216643 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAATAGTCCATATGTC
*
216674 CCAAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAATAGTCCATATGTC
216705 CCGAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAATAGTCCATATGTC
216736 CCGAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAATAGTCCATATGTC
*
216767 CCAAAGAACATAGGTAAA
1 CCGAAGAACATAGGTAAA
216785 CCCTCGACCC
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 133 0.99
32 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAATAGTCCATATGTC
Found at i:219965 original size:23 final size:24
Alignment explanation
Indices: 219931--219982 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
219921 CTCGAGATAC
*
219931 AGAACTTGAAACATAAGAGTGGGT
1 AGAACTTGAAACATAAGAATGGGT
219955 AGAAC-TGAAACATAAGAATGGGT
1 AGAACTTGAAACATAAGAATGGGT
*
219978 TGAAC
1 AGAAC
219983 CGTTGTGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (24 bp):
AGAACTTGAAACATAAGAATGGGT
Found at i:222815 original size:30 final size:30
Alignment explanation
Indices: 222780--222861 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
222770 AAATAAAATT
* *
222780 ACATAAAATA-AAGACCCAAAATATAGAATA
1 ACATAAAATACAACACCAAAAAT-TAGAATA
* *
222810 ACATAAAATACCACACCAAAAATTATAATA
1 ACATAAAATACAACACCAAAAATTAGAATA
* *
222840 ACATAAAATATAATACCAAAAA
1 ACATAAAATACAACACCAAAAA
222862 ATACAATATG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 35 0.80
31 9 0.20
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.18
Consensus pattern (30 bp):
ACATAAAATACAACACCAAAAATTAGAATA
Found at i:222853 original size:15 final size:15
Alignment explanation
Indices: 222767--222905 Score: 59
Period size: 15 Copynumber: 9.3 Consensus size: 15
222757 TTGACAAAAT
* *
222767 ATAAAATAAAATTAC
1 ATAAAATACAATAAC
* *
222782 ATAAAATA-AAGACCC
1 ATAAAATACAATA-AC
*
222797 A-AAATATAGAATAAC
1 ATAAA-ATACAATAAC
* * *
222812 ATAAAATACCACACC
1 ATAAAATACAATAAC
*
222827 A-AAAATTATAATAAC
1 ATAAAA-TACAATAAC
* *
222842 ATAAAATATAATACC
1 ATAAAATACAATAAC
* **
222857 AAAAAATACAATATG
1 ATAAAATACAATAAC
* *
222872 AGAAAATACAATTAC
1 ATAAAATACAATAAC
* * *
222887 AAAAAATATAATTAC
1 ATAAAATACAATAAC
222902 ATAA
1 ATAA
222906 TTATGTTTCA
Statistics
Matches: 93, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
14 9 0.10
15 74 0.80
16 10 0.11
ACGTcount: A:0.63, C:0.12, G:0.03, T:0.22
Consensus pattern (15 bp):
ATAAAATACAATAAC
Found at i:224375 original size:23 final size:23
Alignment explanation
Indices: 224302--224368 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
224292 TAAATACACC
224302 GAAGTGCCACGTAGAATTGCACT
1 GAAGTGCCACGTAGAATTGCACT
224325 GAAGTGCCACGTAGAATTGCACT
1 GAAGTGCCACGTAGAATTGCACT
*
224348 GAAGTGCCGCGTAGAATTGCA
1 GAAGTGCCACGTAGAATTGCA
224369 TCGAAGTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (23 bp):
GAAGTGCCACGTAGAATTGCACT
Found at i:229421 original size:23 final size:23
Alignment explanation
Indices: 229389--229491 Score: 125
Period size: 23 Copynumber: 4.5 Consensus size: 23
229379 CTCATATAAA
*
229389 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
229412 TACACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
** * * *
229435 TGTGCCGAAGTGTCTCTTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
229458 TGTACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
229481 TGCACTGAAGT
1 TGCACCGAAGT
229492 TCCATATAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:230618 original size:17 final size:20
Alignment explanation
Indices: 230576--230623 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 20
230566 ATAAATCATG
230576 AATCATATACAAAGCATATC
1 AATCATATACAAAGCATATC
*
230596 AA-CATATA-ACA-CATAT-
1 AATCATATACAAAGCATATC
230612 AATCATAT-CAAA
1 AATCATATACAAA
230624 CTATTCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.08
17 12 0.50
18 2 0.08
19 6 0.25
20 2 0.08
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.25
Consensus pattern (20 bp):
AATCATATACAAAGCATATC
Found at i:236695 original size:17 final size:17
Alignment explanation
Indices: 236653--236696 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
236643 ATACATTATT
236653 AATTATAAAATATAAAAA
1 AATT-TAAAATATAAAAA
* * *
236671 AATCTAAAATATAATAG
1 AATTTAAAATATAAAAA
236688 AATTTAAAA
1 AATTTAAAA
236697 GTTTTAGAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AATTTAAAATATAAAAA
Found at i:246474 original size:2 final size:2
Alignment explanation
Indices: 246469--246494 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
246459 ACTAAATAAC
246469 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
246495 GATAAAATTA
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:246913 original size:13 final size:13
Alignment explanation
Indices: 246895--246920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
246885 TAAATATATA
246895 AAATTATAAAAAT
1 AAATTATAAAAAT
246908 AAATTATAAAAAT
1 AAATTATAAAAAT
246921 TGTCGCTAGG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTATAAAAAT
Found at i:253032 original size:31 final size:31
Alignment explanation
Indices: 252997--253060 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
252987 CCACAGCCTG
*
252997 CAAAAGTCGAGTCAATTAGAAATTCTGCATT
1 CAAAAGTCGAGTCAATTAGAAATTCGGCATT
253028 CAAAAGTCGAGTCAATTAGAAATTCGGCATT
1 CAAAAGTCGAGTCAATTAGAAATTCGGCATT
253059 CA
1 CA
253061 CAATAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (31 bp):
CAAAAGTCGAGTCAATTAGAAATTCGGCATT
Found at i:254251 original size:30 final size:31
Alignment explanation
Indices: 254213--254280 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
254203 CGTTAACAAC
* * * *
254213 TCAGTGACCTAAAA-ACTAATTTTATTAAGT
1 TCAGTGACCAAAAATACTAAATGTATAAAGT
*
254243 TTAGTGACCAAAAATACTAAATGTATAAAGT
1 TCAGTGACCAAAAATACTAAATGTATAAAGT
254274 TCAGTGA
1 TCAGTGA
254281 GGAAATTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (31 bp):
TCAGTGACCAAAAATACTAAATGTATAAAGT
Found at i:254707 original size:21 final size:20
Alignment explanation
Indices: 254683--254740 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
254673 TTTTATAATC
* *
254683 TAAAAATAAAATTTAAAAGTA
1 TAAAAATAAAA-ATAAAAATA
254704 TAAAAATATAAAATAAAAATA
1 TAAAAATA-AAAATAAAAATA
* *
254725 TAAAATTAAAACTAAA
1 TAAAAATAAAAATAAA
254741 TTTAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.22
21 22 0.69
22 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAATA
Found at i:254719 original size:13 final size:13
Alignment explanation
Indices: 254703--254735 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
254693 ATTTAAAAGT
254703 ATAAAAATATAAA
1 ATAAAAATATAAA
254716 ATAAAAATATAAA
1 ATAAAAATATAAA
254729 ATTAAAA
1 A-TAAAA
254736 CTAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAAAATATAAA
Found at i:259110 original size:2 final size:2
Alignment explanation
Indices: 259103--259132 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
259093 CCTATTATTA
*
259103 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
259133 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:259321 original size:3 final size:3
Alignment explanation
Indices: 259315--259360 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
259305 ACTCTTGTGT
259315 TTA TTA TTA TTA TT- TATA TTA TTA TTA TTA -TA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
259360 T
1 T
259361 ATATATTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 3 0.08
3 32 0.82
4 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:259336 original size:15 final size:15
Alignment explanation
Indices: 259319--259368 Score: 84
Period size: 15 Copynumber: 3.3 Consensus size: 15
259309 TTGTGTTTAT
259319 TATTATTATT-TATA
1 TATTATTATTATATA
259333 TTATTATTATTATATA
1 -TATTATTATTATATA
259349 TATTATTATTATATA
1 TATTATTATTATATA
259364 TATTA
1 TATTA
259369 CTAACCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATATA
Found at i:259338 original size:18 final size:18
Alignment explanation
Indices: 259315--259366 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
259305 ACTCTTGTGT
*
259315 TTATTATTATTATTTATA
1 TTATTATTATTATATATA
259333 TTATTATTATTATATATA
1 TTATTATTATTATATATA
259351 TTATTATTA-TATATAT
1 TTATTATTATTATATAT
259367 TACTAACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATTATTATATATA
Found at i:259859 original size:15 final size:14
Alignment explanation
Indices: 259833--259863 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
259823 TATCTCCGTA
259833 TTATTTTTTTTATT
1 TTATTTTTTTTATT
259847 TTATTTGTTTTTATT
1 TTATTT-TTTTTATT
259862 TT
1 TT
259864 CTCATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (14 bp):
TTATTTTTTTTATT
Found at i:264135 original size:91 final size:93
Alignment explanation
Indices: 263955--264141 Score: 247
Period size: 91 Copynumber: 2.0 Consensus size: 93
263945 ACTCTTGTTC
* * *
263955 TTCTTCTTCTTCTTCTTCTTAACTTTAAAAGATTCTCATTCTTGAATCTAAGTAACTTAAATGTT
1 TTCTTCTTCATATTCTTCTTAACTTTAAAAGA-T-TCATTCTTGAATCTAAGTAACTCAAATGTT
** *
264020 CATATGTTGGCTAACTCATACATTTGTGCA
64 CATATGCGGGCTAACTCATACATTTATGCA
264050 TTCTTCTTCATATTCTTCTTAACTTT-AAA-A-T-ATTCTTGAATCTAAGTGTAACTCAAATGTT
1 TTCTTCTTCATATTCTTCTTAACTTTAAAAGATTCATTCTTGAATCTAA--GTAACTCAAATGTT
*
264111 CATATGCGGGCTAACTCATTCATTTATGCA
64 CATATGCGGGCTAACTCATACATTTATGCA
264141 T
1 T
264142 ATTACTACTC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
89 14 0.17
90 1 0.01
91 40 0.48
93 1 0.01
94 3 0.04
95 24 0.29
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (93 bp):
TTCTTCTTCATATTCTTCTTAACTTTAAAAGATTCATTCTTGAATCTAAGTAACTCAAATGTTCA
TATGCGGGCTAACTCATACATTTATGCA
Found at i:266589 original size:21 final size:20
Alignment explanation
Indices: 266565--266603 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
266555 TTCTCCTGGT
266565 TCAGCATCTCTGCTTTCTTCC
1 TCAGCATCTC-GCTTTCTTCC
* *
266586 TCAGCTTCTCGTTTTCTT
1 TCAGCATCTCGCTTTCTT
266604 TCATTATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.08, C:0.33, G:0.10, T:0.49
Consensus pattern (20 bp):
TCAGCATCTCGCTTTCTTCC
Found at i:270718 original size:55 final size:55
Alignment explanation
Indices: 270656--271106 Score: 293
Period size: 51 Copynumber: 8.6 Consensus size: 55
270646 CAATTGGCGG
* *
270656 GTCTGCTCTCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAACGT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* * * * *
270711 GTCTGCTCTCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAATGG
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* *
270766 GTCTGCTCCCTATTCTTTCAAAGAGTATAAGACTCG----ATCTTCAATAAACGT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
** * * * ** *
270817 GTCCACTCTCTATTCCTTCAGAGAGTATAGGACT----CAATATTCAACGAACTT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* * * * ** *
270868 GTCCGCTCTCTATTCCTTCACAGAGTATAGGACT----CAATCTTCAACGAACTT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* * * * ** *
270919 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* * * * ** *
270970 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* * * * ** *
271021 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
* * * *
271072 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTC
271107 AATCTTCAAC
Statistics
Matches: 366, Mismatches: 27, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
51 284 0.78
55 82 0.22
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (55 bp):
GTCTGCTCTCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGT
Found at i:270842 original size:51 final size:51
Alignment explanation
Indices: 270770--271116 Score: 586
Period size: 51 Copynumber: 6.8 Consensus size: 51
270760 AAATGGGTCT
* * * * ** *
270770 GCTCCCTATTCTTTCAAAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* * *
270821 ACTCTCTATTCCTTCAGAGAGTATAGGACTCAATATTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
* *
270872 GCTCTCTATTCCTTCACAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
270923 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
270974 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
271025 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
271076 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
271117 AAACGAGTTT
Statistics
Matches: 281, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 281 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:271448 original size:17 final size:17
Alignment explanation
Indices: 271416--271448 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
271406 TATCTTCATC
271416 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
271433 TCAAT-CTTCAACTATC
1 TCAATGCTTCAA-TATC
271449 ATTGGGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.39
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:272498 original size:27 final size:27
Alignment explanation
Indices: 272468--272593 Score: 82
Period size: 27 Copynumber: 4.6 Consensus size: 27
272458 TTGAACCCTC
272468 CTTTTATTTCTCTTTTTTCA-TTTTTCT
1 CTTTTATTT-TCTTTTTTCATTTTTTCT
** *
272495 CTTTTCCTTTCTTTTTCCATTTTTTCT
1 CTTTTATTTTCTTTTTTCATTTTTTCT
* *
272522 CTTTTTTTTTTCATTTTTTTCGTTTTTTCCAT
1 C-TTTTATTTTC--TTTTTTCATTTTTT-C-T
*
272554 CATTTT-TTCTT-TTTTCTCATTTTTTCT
1 C-TTTTATT-TTCTTTTTTCATTTTTTCT
*
272581 -TCTT-TTTTCTTTT
1 CTTTTATTTTCTTTT
272594 ATTTCTTCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
24 2 0.03
25 9 0.11
26 9 0.11
27 16 0.20
28 9 0.11
29 12 0.15
30 12 0.15
31 3 0.04
32 8 0.10
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.75
Consensus pattern (27 bp):
CTTTTATTTTCTTTTTTCATTTTTTCT
Found at i:272529 original size:20 final size:20
Alignment explanation
Indices: 272496--272588 Score: 79
Period size: 20 Copynumber: 4.7 Consensus size: 20
272486 CATTTTTCTC
272496 TTTTC-CTTTCTTTTTCCATT
1 TTTTCTCTTT-TTTTTCCATT
*
272516 TTTTCTCTTTTTTTTTTCATT
1 TTTTCTC-TTTTTTTTCCATT
*
272537 TTTT-TC-GTTTTTTCCATCAT
1 TTTTCTCTTTTTTTTCCAT--T
*
272557 TTTT-TCTTTTTTCT-CATT
1 TTTTCTCTTTTTTTTCCATT
272575 TTTTCTTCTTTTTT
1 TTTTC-TCTTTTTT
272589 CTTTTATTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
18 14 0.23
20 25 0.41
21 19 0.31
22 3 0.05
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTTCTCTTTTTTTTCCATT
Found at i:272530 original size:21 final size:21
Alignment explanation
Indices: 272496--272588 Score: 74
Period size: 21 Copynumber: 4.6 Consensus size: 21
272486 CATTTTTCTC
*
272496 TTTTC-CTTTCTTTTTCCATT
1 TTTTCTCTTTTTTTTTCCATT
*
272516 TTTTCTCTTTTTTTTTTCATT
1 TTTTCTCTTTTTTTTTCCATT
*
272537 TTTT-TC--GTTTTTTCCATCAT
1 TTTTCTCTTTTTTTTTCCAT--T
*
272557 TTTT-TC-TTTTTTCT-CATT
1 TTTTCTCTTTTTTTTTCCATT
272575 TTTTCTTCTTTTTT
1 TTTTC-TCTTTTTT
272589 CTTTTATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
18 14 0.23
20 19 0.32
21 27 0.45
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.75
Consensus pattern (21 bp):
TTTTCTCTTTTTTTTTCCATT
Found at i:272587 original size:11 final size:10
Alignment explanation
Indices: 272506--272590 Score: 65
Period size: 10 Copynumber: 8.7 Consensus size: 10
272496 TTTTCCTTTC
272506 TTTTTC-CAT
1 TTTTTCTCAT
*
272515 TTTTTCTCTTT
1 TTTTTCTC-AT
*
272526 TTTTTTTCAT
1 TTTTTCTCAT
*
272536 TTTTT-TCGT
1 TTTTTCTCAT
272545 TTTTTC-CAT
1 TTTTTCTCAT
272554 CATTTTT-TC-T
1 --TTTTTCTCAT
272564 TTTTTCTCAT
1 TTTTTCTCAT
272574 TTTTTCTTC-T
1 TTTTTC-TCAT
272584 TTTTTCT
1 TTTTTCT
272591 TTTATTTCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
8 5 0.08
9 19 0.31
10 22 0.35
11 16 0.26
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (10 bp):
TTTTTCTCAT
Found at i:272589 original size:20 final size:20
Alignment explanation
Indices: 272506--272603 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 20
272496 TTTTCCTTTC
*
272506 TTTTTC-CATTTTTTCTCTTT
1 TTTTTCTCATTTTTTCT-TCT
*
272526 TTTTTTTCA-TTTTT-TTCGT
1 TTTTTCTCATTTTTTCTTC-T
*
272545 TTTTTC-CATCATTTT-TTCT
1 TTTTTCTCAT-TTTTTCTTCT
272564 TTTTTCTCATTTTTTCTTCT
1 TTTTTCTCATTTTTTCTTCT
272584 TTTTTCT--TTTATTTCTTCT
1 TTTTTCTCATTT-TTTCTTCT
272603 T
1 T
272604 CAAGCAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.09
19 27 0.41
20 31 0.47
21 2 0.03
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTTCTCATTTTTTCTTCT
Found at i:272591 original size:10 final size:10
Alignment explanation
Indices: 272556--272603 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
272546 TTTTCCATCA
272556 TTTT-TTCTT
1 TTTTCTTCTT
272565 TTTTC-TCATT
1 TTTTCTTC-TT
272575 TTTTCTTCTT
1 TTTTCTTCTT
272585 TTTTCTT-TT
1 TTTTCTTCTT
*
272594 ATTTCTTCTT
1 TTTTCTTCTT
272604 CAAGCAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 14 0.41
10 18 0.53
11 2 0.06
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:272603 original size:39 final size:37
Alignment explanation
Indices: 272488--272603 Score: 94
Period size: 39 Copynumber: 3.0 Consensus size: 37
272478 TCTTTTTTCA
*
272488 TTTTTCTC-TTTTCCTTTCTTTTTCCATTTT-TTCTCTT-T
1 TTTTTCTCATTTT--TTTCTTTTTTC-TTTTATT-TCTTCT
* ** * *
272526 TTTTTTTCATTTTTTTCGTTTTTTCCATCATTTTTTCT
1 TTTTTCTCATTTTTTTC-TTTTTTCTTTTATTTCTTCT
272564 TTTTTCTCATTTTTTCTTCTTTTTTCTTTTATTTCTTCT
1 TTTTTCTCA-TTTTT-TTCTTTTTTCTTTTATTTCTTCT
272603 T
1 T
272604 CAAGCAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
37 8 0.13
38 24 0.39
39 26 0.43
40 3 0.05
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (37 bp):
TTTTTCTCATTTTTTTCTTTTTTCTTTTATTTCTTCT
Found at i:282308 original size:45 final size:46
Alignment explanation
Indices: 282242--282337 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
282232 GTTATCCACA
*
282242 AAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC-TTATTCAG
1 AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTC-G
* *
282288 AAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
282334 AAAA
1 AAAA
282338 AACGAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 27 0.60
46 12 0.27
47 6 0.13
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (46 bp):
AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:289277 original size:25 final size:25
Alignment explanation
Indices: 289249--289307 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
289239 CGTGGCAATG
289249 GCGGTGGCTGTACATGGAACCGACA
1 GCGGTGGCTGTACATGGAACCGACA
* * *
289274 GCGGCGGCTGTACTTGGAACCGACG
1 GCGGTGGCTGTACATGGAACCGACA
*
289299 GCGATGGCT
1 GCGGTGGCT
289308 ATAGGCATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.17
Consensus pattern (25 bp):
GCGGTGGCTGTACATGGAACCGACA
Found at i:290240 original size:140 final size:139
Alignment explanation
Indices: 289788--290328 Score: 727
Period size: 140 Copynumber: 3.9 Consensus size: 139
289778 GAAATGTTAG
* * *
289788 TGCTG-TTCCAACTCCGTATGCGATGGAAACAAGTTAAGGTTGAACAAGTTCTTCTCATTATGAA
1 TGCTGATT-CAACTCCATATGCGAT-GAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAA
* **
289852 CTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAAATCTCCACTTAAAATGTTGATCCCTC
64 CTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTC
289917 GAGTGAGGTGT
129 GAGTGAGGTGT
* * *
289928 TGTTGATTCAACTCCATATGCGATGAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAACT
1 TGCTGATTCAACTCCATATGCGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
* ** * *
289993 TC-TCAT--TTTGTCGGATGAGTTCTTCTCATTATGAACTCT--TCTGGAAATATTGATTCACCT
66 TCTTC-TCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA-TC-CCT
*
290053 C-ATTCTGAGGTGT
128 CGA--GTGAGGTGT
* * * *
290066 TGCTGATTTAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTTTCATTATGAACT
1 TGCTGATTCAACTCCATATGCGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
* * * * *
290131 TCTTCTCTCTCTGTCGGATGAGTTATTCACATTATGAACTCTCCACTGGAAATGTCGATCCCTCG
66 TCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCG
290196 AGTGAGGTGT
130 AGTGAGGTGT
*
290206 TGCTGATTCAACTCCATATGTGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
1 TGCTGATTCAACTCCATATGCGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
*
290271 TCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAT
66 TCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAT
290329 TGGTTCATCC
Statistics
Matches: 351, Mismatches: 37, Indels: 27
0.85 0.09 0.07
Matches are distributed among these distances:
135 10 0.03
136 3 0.01
137 33 0.09
138 73 0.21
139 84 0.24
140 100 0.28
141 34 0.10
142 3 0.01
143 11 0.03
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (139 bp):
TGCTGATTCAACTCCATATGCGATGAATCAAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACT
TCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGA
GTGAGGTGT
Found at i:291043 original size:54 final size:56
Alignment explanation
Indices: 290969--291085 Score: 132
Period size: 55 Copynumber: 2.1 Consensus size: 56
290959 GGTAAATTTT
* *** * * *
290969 GCTTC-TTCAAAAGATCCATTTATAGTTATCAAGAAACCC-TTAAAATTAGGCTTA
1 GCTTCTTTCAAAAGATCCATTTAAAAACATCAAGAAACCCATGAAAATAAAGCTTA
*
291023 GCTTCTTTCAAAAG-TTCATTTAAAAACATCAAGAAACCCATGAAAATAAAGCTTA
1 GCTTCTTTCAAAAGATCCATTTAAAAACATCAAGAAACCCATGAAAATAAAGCTTA
*
291078 GTTTCTTT
1 GCTTCTTT
291086 GAAATCTCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
54 25 0.48
55 27 0.52
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (56 bp):
GCTTCTTTCAAAAGATCCATTTAAAAACATCAAGAAACCCATGAAAATAAAGCTTA
Found at i:293162 original size:16 final size:16
Alignment explanation
Indices: 293131--293210 Score: 87
Period size: 15 Copynumber: 5.1 Consensus size: 16
293121 TTATAACTTC
*
293131 TTTCTTTCTT-TTCTT
1 TTTCTTTTTTCTTCTT
293146 TTTCTTTTTTCTTCTT
1 TTTCTTTTTTCTTCTT
293162 TCTTCTTTTTT-TTCTTT
1 T-TTCTTTTTTCTTC-TT
293179 TTTCTTTTTTTCTT-TT
1 TTTC-TTTTTTCTTCTT
*
293195 TTTCATTTTTC-TCTT
1 TTTCTTTTTTCTTCTT
293210 T
1 T
293211 ATTTCATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.02
15 18 0.32
16 18 0.32
17 18 0.32
18 2 0.04
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTTCTTCTT
Found at i:293175 original size:32 final size:31
Alignment explanation
Indices: 293131--293210 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 31
293121 TTATAACTTC
*
293131 TTTCTTTCTTTTCTTTTTC-TTTTTTCTTCTT
1 TTTCTTTTTTTTCTTTTTCTTTTTTTCTT-TT
293162 TCTTCTTTTTTTTCTTTTTTCTTTTTTTCTTTT
1 T-TTCTTTTTTTTC-TTTTTCTTTTTTTCTTTT
* *
293195 TTTCATTTTTCTCTTT
1 TTTCTTTTTTTTCTTT
293211 ATTTCATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 4 0.09
32 21 0.49
33 9 0.21
34 9 0.21
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (31 bp):
TTTCTTTTTTTTCTTTTTCTTTTTTTCTTTT
Found at i:293203 original size:8 final size:7
Alignment explanation
Indices: 293139--293234 Score: 74
Period size: 7 Copynumber: 13.6 Consensus size: 7
293129 TCTTTCTTTC
293139 TTTTC-T
1 TTTTCTT
293145 TTTTCTT
1 TTTTCTT
293152 TTTTCTT
1 TTTTCTT
*
293159 CTTTC-T
1 TTTTCTT
*
293165 TCTT-TT
1 TTTTCTT
293171 TTTTCTT
1 TTTTCTT
293178 TTTTCTTT
1 TTTTC-TT
293186 TTTTCTTT
1 TTTTC-TT
293194 TTTTCATT
1 TTTTC-TT
293202 TTTCTCTT
1 TTT-TCTT
*
293210 TATTTC-A
1 T-TTTCTT
*
293217 TTTTGTT
1 TTTTCTT
*
293224 TTTGCTT
1 TTTTCTT
293231 TTTT
1 TTTT
293235 TTTGTGTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
6 15 0.21
7 28 0.39
8 25 0.35
9 4 0.06
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:293215 original size:17 final size:16
Alignment explanation
Indices: 293144--293220 Score: 75
Period size: 17 Copynumber: 4.7 Consensus size: 16
293134 CTTTCTTTTC
*
293144 TTTTTCTTTTTTCTTCT
1 TTTTTCATTTTTC-TCT
* * *
293161 TTCTTCTTTTTTTTCT
1 TTTTTCATTTTTCTCT
*
293177 TTTTTC-TTTTTTTCTT
1 TTTTTCATTTTTCTC-T
293193 TTTTTCATTTTTCTCT
1 TTTTTCATTTTTCTCT
293209 TTATTTCATTTT
1 TT-TTTCATTTT
293221 GTTTTTGCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.15
16 18 0.34
17 27 0.51
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCATTTTTCTCT
Found at i:293838 original size:65 final size:65
Alignment explanation
Indices: 293717--293950 Score: 229
Period size: 65 Copynumber: 3.7 Consensus size: 65
293707 TTTATCAAAG
* **
293717 TGATGCATCGATGCACCA-ATCCATGCATCGATGCACCATGA--ATTAAATTG-AACATCGAATG
1 TGATGCATCGATGCA-CATAGCCATGCATCGATGCA-C-TGAGGATTTTA-TGAAACATCGAATG
293778 CATT
62 CATT
*
293782 TCATGCATCGATGCACATA-CCATGCATCGATGCACTGAGGATTTTATGAAAGCATCGAATGCAT
1 TGATGCATCGATGCACATAGCCATGCATCGATGCACTGAGGATTTTATGAAA-CATCGAATGCAT
293846 T
65 T
** * *
293847 TGATGCATAAATG-A-ATAAGCCATGCATCGATGCACTTAGGCTATTT-TGAAACATCGAATGCA
1 TGATGCATCGATGCACAT-AGCCATGCATCGATGCACTGAGGAT-TTTATGAAACATCGAATGCA
*
293909 CT
64 TT
* *
293911 TGATGCATCGATGCAC-TTG--ATGCATCGATGCACTAAGGAT
1 TGATGCATCGATGCACATAGCCATGCATCGATGCACTGAGGAT
293951 CCAACGGTCA
Statistics
Matches: 145, Mismatches: 14, Indels: 23
0.80 0.08 0.13
Matches are distributed among these distances:
62 22 0.15
63 5 0.03
64 49 0.34
65 66 0.46
66 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACATAGCCATGCATCGATGCACTGAGGATTTTATGAAACATCGAATGCATT
Found at i:293926 original size:17 final size:17
Alignment explanation
Indices: 293898--293944 Score: 85
Period size: 17 Copynumber: 2.7 Consensus size: 17
293888 TATTTTGAAA
293898 CATCGAATGCACTTGATG
1 CATCG-ATGCACTTGATG
293916 CATCGATGCACTTGATG
1 CATCGATGCACTTGATG
293933 CATCGATGCACT
1 CATCGATGCACT
293945 AAGGATCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (17 bp):
CATCGATGCACTTGATG
Found at i:293932 original size:9 final size:9
Alignment explanation
Indices: 293904--293944 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
293894 GAAACATCGA
*
293904 ATGCACTTG
1 ATGCACTCG
293913 ATGCA-TCG
1 ATGCACTCG
*
293921 ATGCACTTG
1 ATGCACTCG
293930 ATGCA-TCG
1 ATGCACTCG
293938 ATGCACT
1 ATGCACT
293945 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (9 bp):
ATGCACTCG
Found at i:303248 original size:2 final size:2
Alignment explanation
Indices: 303241--303356 Score: 232
Period size: 2 Copynumber: 58.0 Consensus size: 2
303231 ACAACAAGGG
303241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
303283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
303325 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
303357 TTTGAAAGGA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 114 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304349 original size:21 final size:20
Alignment explanation
Indices: 304325--304364 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
304315 ATGCACGTTG
*
304325 ATATTCAATGTATATCATGCA
1 ATATACAATGTATAT-ATGCA
*
304346 ATATACGATGTATATATGC
1 ATATACAATGTATATATGC
304365 TAATGCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
ATATACAATGTATATATGCA
Found at i:307708 original size:3 final size:3
Alignment explanation
Indices: 307695--307753 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
307685 TTTTTATCCA
* *
307695 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
307743 TAT TAT TAT TA
1 TAT TAT TAT TA
307754 ATAAATATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:307768 original size:14 final size:14
Alignment explanation
Indices: 307749--307789 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
307739 TTATTATTAT
307749 TATTAATAAATATA
1 TATTAATAAATATA
307763 TATTAAATAAATATA
1 TATT-AATAAATATA
*
307778 TATAAATAAATA
1 TATTAATAAATA
307790 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:307773 original size:15 final size:15
Alignment explanation
Indices: 307749--307789 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
307739 TTATTATTAT
307749 TATT-AATAAATATA
1 TATTAAATAAATATA
307763 TATTAAATAAATATA
1 TATTAAATAAATATA
307778 TA-TAAATAAATA
1 TATTAAATAAATA
307790 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:308221 original size:19 final size:19
Alignment explanation
Indices: 308197--308237 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
308187 ACCCCAACCT
308197 GAAAAAAAAAATG-GAGACA
1 GAAAAAAAAAA-GAGAGACA
*
308216 GAAAAAAAAGAGAGAGACA
1 GAAAAAAAAAAGAGAGACA
308235 GAA
1 GAA
308238 CCGGAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.02
Consensus pattern (19 bp):
GAAAAAAAAAAGAGAGACA
Found at i:320655 original size:16 final size:17
Alignment explanation
Indices: 320636--320681 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
320626 CTATTTCAAG
*
320636 TTCAATTTATT-GGAGA
1 TTCAATTTATTGGGAAA
320652 TTCAATTTATTTTGGGAAA
1 TTCAATTTA--TTGGGAAA
320671 TTCAATTTATT
1 TTCAATTTATT
320682 CTTCTATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 13 0.50
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (17 bp):
TTCAATTTATTGGGAAA
Found at i:321661 original size:82 final size:81
Alignment explanation
Indices: 321438--322026 Score: 881
Period size: 82 Copynumber: 7.4 Consensus size: 81
321428 GATGAATGTG
321438 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAA-
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
*
321502 ATGAATTTGCCAATAGC
66 ATGAATTTGTC-ATAGC
321519 ATCTTCTGG-AGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
321583 ATGAATTTGTCAATAGC
66 ATGAATTTGTC-ATAGC
*
321600 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAGAACAATCATTGAGTTTAGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
321665 ATGAATTTGTCAATAGC
66 ATGAATTTGTC-ATAGC
321682 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
321747 ATGAA--TGTCATAGC
66 ATGAATTTGTCATAGC
* * *
321761 ATCTT-AGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAGTTTAGAA
*
321824 GATGAATGTGTTCATAGC
65 GATGAATTTG-TCATAGC
321842 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAATCAATCATTGAG-TTAGA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAA-CAATCATTGAGTTTAGA
*
321905 TGATG---TT-TCATAGC
64 AGATGAATTTGTCATAGC
* * *
321919 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC----TGG-CAGACCAATCATTGA-ATTGGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
*
321978 ATGAATGTGTTCATAGC
66 ATGAATTTG-TCATAGC
321995 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
322027 TCAGTAGGAA
Statistics
Matches: 478, Mismatches: 16, Indels: 33
0.91 0.03 0.06
Matches are distributed among these distances:
71 18 0.04
72 7 0.01
74 1 0.00
76 39 0.08
77 45 0.09
78 55 0.12
79 11 0.02
80 60 0.13
81 46 0.10
82 177 0.37
83 19 0.04
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (81 bp):
ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
ATGAATTTGTCATAGC
Found at i:321844 original size:160 final size:161
Alignment explanation
Indices: 321438--322026 Score: 886
Period size: 160 Copynumber: 3.7 Consensus size: 161
321428 GATGAATGTG
*
321438 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAA-
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAATTTAGAAG
* *
321502 ATGAATTTGCCAATAGCATCTTCTGG-AGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
66 ATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
321566 ATCATTGAGTTTAGAAGATGAATTTGTCAATAGC
131 ATCATTGAGTTTAGAAGATGAA--TGTC-ATAGC
* *
321600 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAGAACAATCATTGAGTTTAGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAATTTAGAAG
*
321665 ATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
66 ATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
321730 ATCATTGAGTTTAGAAGATGAATGTCATAGC
131 ATCATTGAGTTTAGAAGATGAATGTCATAGC
* *
321761 ATCTT-AGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAGAACCAATCATTGAATTTGGAA
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAATTTAGAA
321824 GATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
65 GATGAATGTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
* *
321887 ATCAATCATTGAG-TTAGATGATG--TTTCATAGC
128 A-CAATCATTGAGTTTAGAAGATGAATGTCATAGC
* *
321919 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC----TGG-CAGACCAATCATTGAA-TTGGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAATTTAGAAG
321978 ATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 ATGAATGTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
322027 TCAGTAGGAA
Statistics
Matches: 409, Mismatches: 11, Indels: 23
0.92 0.02 0.05
Matches are distributed among these distances:
153 56 0.14
154 11 0.03
155 7 0.02
158 13 0.03
159 30 0.07
160 113 0.28
161 27 0.07
162 67 0.16
163 25 0.06
164 60 0.15
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (161 bp):
ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAATTTAGAAG
ATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
ATCATTGAGTTTAGAAGATGAATGTCATAGC
Found at i:321865 original size:242 final size:239
Alignment explanation
Indices: 321438--322026 Score: 873
Period size: 242 Copynumber: 2.5 Consensus size: 239
321428 GATGAATGTG
321438 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAA-
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
*
321502 ATGAATTTGCCAATAGCATCTTCTGG-AGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
66 ATGAA-TTGTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
* *
321566 ATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
129 ATCATTGAATTTAGAAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
321631 TCTGG-TTGGAAAGAA-CAATCATTGAGTTTAGAAGATGAATTTGTCAATAGC
194 TCTGGTTTGG-AAGAATCAATCATTGAG-TTAGAAGATG---TT-TC-ATAGC
321682 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
*
321747 ATGAA-TGTCATAGCATCTT-AGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAGAACCAA
66 ATGAATTGTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAA
*
321809 TCATTGAATTTGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
130 TCATTGAATTTAGAAGATGAATGTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
* *
321873 TCTGGTTTGGCAGAATCAATCATTGAGTTAGATGATGTTTCATAGC
194 TCTGGTTTGGAAGAATCAATCATTGAGTTAGAAGATGTTTCATAGC
* * *
321919 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC----TGG-CAGACCAATCATTGA-ATTGGAAG
1 ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
321978 ATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
66 ATGAAT-TG-TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
322027 TCAGTAGGAA
Statistics
Matches: 324, Mismatches: 11, Indels: 29
0.89 0.03 0.08
Matches are distributed among these distances:
231 11 0.03
232 14 0.04
233 5 0.02
234 12 0.04
235 25 0.08
237 38 0.12
238 2 0.01
239 2 0.01
241 7 0.02
242 119 0.37
243 20 0.06
244 64 0.20
245 5 0.02
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (239 bp):
ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAGTTTAGAAG
ATGAATTGTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAAT
CATTGAATTTAGAAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGAAGAATCAATCATTGAGTTAGAAGATGTTTCATAGC
Found at i:322949 original size:109 final size:109
Alignment explanation
Indices: 322739--323018 Score: 462
Period size: 110 Copynumber: 2.6 Consensus size: 109
322729 TCGAATCCAC
322739 TTGATGGATCATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAA
1 TTGATGGATCATTTTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAAGAA
322803 GTTCATAATGAGAAGAATTTTTCAACCTTTTACTGAAT-CATCAT
65 GTTCATAATGAGAAGAATTTTTCAACCTTTTACTGAATCCATCAT
322847 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAAT-G-AGAACTCATCTGAAGAAGGAAGAAGAA
1 TTGATGGATCA-TTTTTCCAGAGAAAGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAA
322910 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCAT
65 GTTCATAATGAGAAGAATTT-TTCAACCTTTTAC-TGAATCCATCAT
*
322957 TTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-AAGAAGAAAGAA
1 TTGATGGATCAT-TTTTCCAGAGAAAGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAAGAA
323019 TTGTTCAACC
Statistics
Matches: 162, Mismatches: 1, Indels: 14
0.92 0.01 0.08
Matches are distributed among these distances:
106 22 0.14
107 25 0.15
108 24 0.15
109 29 0.18
110 39 0.24
112 12 0.07
113 11 0.07
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (109 bp):
TTGATGGATCATTTTTCCAGAGAAAGTTCATAATAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAATTTTTCAACCTTTTACTGAATCCATCAT
Found at i:323124 original size:26 final size:25
Alignment explanation
Indices: 323079--323127 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
323069 GTTCATAATG
323079 AGAAGAACTCATATGAAGAAGAAGA
1 AGAAGAACTCATATGAAGAAGAAGA
*
323104 AGAAGAAGTTCATAATG-AGAAGAA
1 AGAAGAA-CTCAT-ATGAAGAAGAA
323128 CTTGTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 11 0.52
27 3 0.14
ACGTcount: A:0.55, C:0.06, G:0.24, T:0.14
Consensus pattern (25 bp):
AGAAGAACTCATATGAAGAAGAAGA
Found at i:323200 original size:116 final size:113
Alignment explanation
Indices: 323064--323383 Score: 397
Period size: 116 Copynumber: 2.8 Consensus size: 113
323054 GATCCCCAGC
*
323064 GGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 GGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
* * * *
323129 TTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGA-TCAACATTGCCA
66 TTGTTCAACTTTTT-GATTGAATTCATCACTGGATGGATTCAAC-TT-CCA
323179 GGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG--GAAGAAGAAGTTCATAATGAGAAG
1 GGAA-AGTTCATAATGAGAAGAA--CTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAG
* * **
323242 AATTTGTTCAACCTTTT-ATTGAATTCATCACTGGATGGATTCTTCTTCCA
63 AACTTGTTCAACTTTTTGATTGAATTCATCACTGGATGGATTCAACTTCCA
*
323292 GAGAAAGTTCATAATGAGAAGAACTCCATCT---GAAGAAGAAGAAGAAGTTCAT-ATAAGAAGA
1 G-GAAAGTTCATAATGAGAAGAACT-CATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGA
*
323353 ACTTGTTCAACTTTTTGAAT-AATTCTATCAC
64 ACTTGTTCAACTTTTTGATTGAATTC-ATCAC
323384 AGAAGGAGAT
Statistics
Matches: 182, Mismatches: 13, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
109 4 0.02
110 27 0.15
111 24 0.13
112 5 0.03
113 22 0.12
114 24 0.13
115 7 0.04
116 56 0.31
118 13 0.07
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (113 bp):
GGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACTTTTTGATTGAATTCATCACTGGATGGATTCAACTTCCA
Found at i:323330 original size:317 final size:304
Alignment explanation
Indices: 322760--323331 Score: 853
Period size: 317 Copynumber: 1.8 Consensus size: 304
322750 TTTTTCCAGA
* *
322760 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAGTTCATAATGAGAAGAATTTTT
1 GAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAGAAGTTCATAATGAGAAGAATTGTT
*** *
322825 CAACCTTTTACTGAATCATCATTTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAACTC
66 CAACCTTTTACTGAATCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAACTC
322890 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
131 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
* *
322955 ATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAGAAAGAAT
196 ACTGGATGGAT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAGAAAGAAT
323020 TGTTCAACCTTTTACATGAATCCATTACTTGATGGATCCCCAGCG
260 TGTTCAACCTTTTACATGAATCCATTACTTGATGGATCCCCAGCG
323065 GAAAGTTCATAATGAGAAGAACTCATATGAAGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACT
1 GAAAGTTCATAATGAGAAGAACTCATATGAAGAAG--GAAG-AGAAGTTCATAATGAGAAGAA-T
** **
323130 TGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAAT
62 TGTTCAACCTTTT--ACTGAA-TCATCATTTGATGGATCAACATTGCCAGAGAA-AGTTCATAAT
323194 GAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
123 --G-AGAA--CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
*
323259 A-TTGAATTCATCACTGGATGGAT-TCTTCTTCCAGAGAAAGTTCATAATGAGAAGAACTCCATC
183 ACTTGAATCCATCACTGGATGGATATCTT-TTCCAGAGAAAGTTCATAATGAGAAGAACT-CATC
323322 TGAAGAAGAA
246 T-AAGAAGAA
323332 GAAGAAGTTC
Statistics
Matches: 238, Mismatches: 13, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
305 34 0.14
307 4 0.02
308 21 0.09
309 11 0.05
311 7 0.03
312 34 0.14
314 5 0.02
315 34 0.14
316 24 0.10
317 64 0.27
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (304 bp):
GAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAGAAGTTCATAATGAGAAGAATTGTT
CAACCTTTTACTGAATCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAACTC
ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATC
ACTGGATGGATATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAGAAAGAATT
GTTCAACCTTTTACATGAATCCATTACTTGATGGATCCCCAGCG
Found at i:323602 original size:3 final size:3
Alignment explanation
Indices: 323589--323640 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
323579 TTTTTATCCA
*
323589 TAT TTT TAT TAT TAT TAT TA- TAT TAT TAT TA- TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
323633 TAT TAT TA
1 TAT TAT TA
323641 AATATATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.86
4 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:323645 original size:23 final size:23
Alignment explanation
Indices: 323600--323651 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
323590 ATTTTTATTA
*
323600 TTATTATTATATTATTATTATAT
1 TTATTATTATATTATTATAATAT
323623 TTATTATTATTATTATTA-AATAT
1 TTATTATTA-TATTATTATAATAT
*
323646 ATATTA
1 TTATTA
323652 AATAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATTATTATAATAT
Found at i:323672 original size:14 final size:15
Alignment explanation
Indices: 323639--323672 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
323629 TTATTATTAT
323639 TAAATATATATTAAA
1 TAAATATATATTAAA
323654 T-AATATATA-TAAA
1 TAAATATATATTAAA
323667 TAAATA
1 TAAATA
323673 ATTACAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 12 0.67
15 1 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:324091 original size:15 final size:15
Alignment explanation
Indices: 324071--324102 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
324061 CCCAACCTGA
324071 AAAAAAAAAAGACAG
1 AAAAAAAAAAGACAG
*
324086 AAAAAAAAGAGACAG
1 AAAAAAAAAAGACAG
324101 AA
1 AA
324103 CGGAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGACAG
Found at i:324122 original size:22 final size:19
Alignment explanation
Indices: 324070--324139 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 19
324060 CCCCAACCTG
*
324070 AAAAAAAAAA-AGA-CAGA
1 AAAAAAAAAACAGAGAAGA
* *
324087 AAAAAAAGAGACAGAACGGAGA
1 AAAAAAA-AAACAG-A-GAAGA
324109 AAAGAAAAAAACAGAGAAGA
1 AAA-AAAAAAACAGAGAAGA
324129 AAAAAAAAAAC
1 AAAAAAAAAAC
324140 TACTAAACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 7 0.16
18 2 0.05
19 10 0.23
20 8 0.19
21 1 0.02
22 11 0.26
23 4 0.09
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAACAGAGAAGA
Found at i:324600 original size:148 final size:146
Alignment explanation
Indices: 324333--324627 Score: 506
Period size: 148 Copynumber: 2.0 Consensus size: 146
324323 ACGGTCCGAT
324333 CTACATTTAGATGTAAAAAAAAAATTTTCCGGCCACCGAAGACGGCCGGCGGCGGGGTGGTTGAT
1 CTACATTTAGATGTAAAAAAAAAATTTTCCGGCCACCGAAGACGGCCGGCGGCGGGGTGGTTGAT
324398 GGCGGACGAACGCCGGCTAACGGCTGCCGGCCGGCTGGGCTTCTCTCTGTTTTAGAGAGAAGC-G
66 GGCGGACGAACGCCGGCTAACGGCTGCCGGCCGGCTGGGCTTCTCTCTGTTTT--AGAGAAGCAG
324462 AGAAAATTTCTCTCTCTC
129 AGAAAATTTCTCTCTCTC
*
324480 CTACATTTAGATGT-AAAAAAAAATTTTCCGGCCACCAGAAGACGG-TGGCCGGCGGCGGTGGTT
1 CTACATTTAGATGTAAAAAAAAAATTTTCCGGCCACC-GAAGACGGCCGG-CGGCGG-GGTGGTT
324543 GATGGCGGACGAACGCCGGCTAACGGCTGCCGGCCGGCTGGGCTTCTCTCTGTTTTAGAGAAGCG
63 GATGGCGGACGAACGCCGGCTAACGGCTGCCGGCCGGCTGGGCTTCTCTCTGTTTTAGAGAAGC-
324608 AGAGAAAATTTCTCTCTCTC
127 AGAGAAAATTTCTCTCTCTC
324628 AGAGAAGAGA
Statistics
Matches: 142, Mismatches: 1, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
146 32 0.23
147 28 0.20
148 82 0.58
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (146 bp):
CTACATTTAGATGTAAAAAAAAAATTTTCCGGCCACCGAAGACGGCCGGCGGCGGGGTGGTTGAT
GGCGGACGAACGCCGGCTAACGGCTGCCGGCCGGCTGGGCTTCTCTCTGTTTTAGAGAAGCAGAG
AAAATTTCTCTCTCTC
Found at i:331512 original size:27 final size:26
Alignment explanation
Indices: 331485--331551 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
331475 TATCAAGTTA
* *
331485 AAAAATATTTTTTATATTAACTT-ATT
1 AAAAATATTTTAT-TATTAAATTAATT
*
331511 AAATATATTTTATTATTAAATTAATTT
1 AAAAATATTTTATTATTAAATTAA-TT
331538 AAAAATATTTTATT
1 AAAAATATTTTATT
331552 TTTATTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.23
26 12 0.34
27 15 0.43
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AAAAATATTTTATTATTAAATTAATT
Found at i:331514 original size:24 final size:24
Alignment explanation
Indices: 331464--331534 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
331454 TTAAATTAAT
* * *
331464 AATATTTTATATATCAAGTTAAAA
1 AATATTTTTTATATTAACTTAAAA
**
331488 AATATTTTTTATATTAACTTATTA
1 AATATTTTTTATATTAACTTAAAA
* *
331512 AATATATTTTATTATTAAATTAA
1 AATATTTTTTA-TATTAACTTAA
331535 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 29 0.76
25 9 0.24
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (24 bp):
AATATTTTTTATATTAACTTAAAA
Found at i:334685 original size:27 final size:30
Alignment explanation
Indices: 334636--334691 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 30
334626 AAAAATTGAG
334636 TTATTTAAATATTATTTTATAAATCAAATC
1 TTATTTAAATATTATTTTATAAATCAAATC
*
334666 TTATTT-AAT-TT-TTTTTTAAATCAAAT
1 TTATTTAAATATTATTTTATAAATCAAAT
334692 TGAATTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 14 0.56
28 2 0.08
29 3 0.12
30 6 0.24
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (30 bp):
TTATTTAAATATTATTTTATAAATCAAATC
Found at i:335573 original size:150 final size:150
Alignment explanation
Indices: 335280--335580 Score: 554
Period size: 150 Copynumber: 2.0 Consensus size: 150
335270 TGTGAGACGC
335280 CTGCATGGGTTGGGAGTGGGAAAAATAGCGGTGGGTTCGCTGCCACCGTTGGGCTGTCTCCCCGT
1 CTGCATGGGTTGGGAGTGGGAAAAATAGCGGTGGGTTCGCTGCCACCGTTGGGCTGTCTCCCCGT
335345 TAACCGCACAGACCTCGTTTCAACGGTGGCGATCCAACTCGGAACGCTCTTGTTGATCTCCACAA
66 TAACCGCACAGACCTCGTTTCAACGGTGGCGATCCAACTCGGAACGCTCTTGTTGATCTCCACAA
335410 CCAGCTGCTCTTCAGGCGCT
131 CCAGCTGCTCTTCAGGCGCT
335430 CTGCATGGGTTGGGAGTGGGAAAAATAGCGGTGGGTTCGCTGCC-CCG-TGGGCTGTCTCCCCGT
1 CTGCATGGGTTGGGAGTGGGAAAAATAGCGGTGGGTTCGCTGCCACCGTTGGGCTGTCTCCCCGT
335493 TAACACCGCACAGACCTCGTTTCAACGGT-GCGATCCAACTCGGAACGCTCTTGTTGATCTCCAC
66 T-A-ACCGCACAGACCTCGTTTCAACGGTGGCGATCCAACTCGGAACGCTCTTGTTGATCTCCAC
335557 AACCAGCTGCTCCTTCAGGCGCT
129 AACCAGCTGCT-CTTCAGGCGCT
335580 C
1 C
335581 ACCAATATCA
Statistics
Matches: 148, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
148 17 0.11
149 50 0.34
150 81 0.55
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (150 bp):
CTGCATGGGTTGGGAGTGGGAAAAATAGCGGTGGGTTCGCTGCCACCGTTGGGCTGTCTCCCCGT
TAACCGCACAGACCTCGTTTCAACGGTGGCGATCCAACTCGGAACGCTCTTGTTGATCTCCACAA
CCAGCTGCTCTTCAGGCGCT
Found at i:344320 original size:82 final size:82
Alignment explanation
Indices: 344183--344348 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 82
344173 TACGCTCACG
344183 TTGTTGTTGCATGTATGCACATCAATGTTGACCCATGCTTATATGCTGATGACTGTTATAACATG
1 TTGTTGTTGCATGTATGCACATCAATGTTGACCCATGCTTATATGCTGATGACTGTTATAACATG
344248 CACAACTATGAGCAACA
66 CACAACTATGAGCAACA
*
344265 TTGTTGTTGCATGTATGCACATCAATGTTGACCCATGCTTATATGCTGATGACTGTTATAGCATG
1 TTGTTGTTGCATGTATGCACATCAATGTTGACCCATGCTTATATGCTGATGACTGTTATAACATG
344330 CACAACTATGAGCAACA
66 CACAACTATGAGCAACA
344347 TT
1 TT
344349 TACAGTTGTG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (82 bp):
TTGTTGTTGCATGTATGCACATCAATGTTGACCCATGCTTATATGCTGATGACTGTTATAACATG
CACAACTATGAGCAACA
Found at i:345819 original size:74 final size:75
Alignment explanation
Indices: 345740--345908 Score: 261
Period size: 75 Copynumber: 2.3 Consensus size: 75
345730 GTTCCATGTC
* ** *
345740 ATTTTTTTT-AAATTTGTTAAAAATTTCTGCAAGTTTCATATTATTTTTAACTTCGAAATTTTAA
1 ATTTTTTTTAAAATTTATTAAAAATTTCTAAAAGTTTCATATTATTTTTAACTTCAAAATTTTAA
*
345804 AATTTTTAAT
66 AAATTTTAAT
*
345814 ATTTTTTTTAAAATTTATTAAAAATTTCTAAAATTTTCATATTATTTTTAACTTCAAAATTTTAA
1 ATTTTTTTTAAAATTTATTAAAAATTTCTAAAAGTTTCATATTATTTTTAACTTCAAAATTTTAA
345879 AAATTTTAAT
66 AAATTTTAAT
*
345889 ATTTTTTTCAAAATTT-TTAA
1 ATTTTTTTTAAAATTTATTAA
345909 TTACACTAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 13 0.15
75 74 0.85
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.54
Consensus pattern (75 bp):
ATTTTTTTTAAAATTTATTAAAAATTTCTAAAAGTTTCATATTATTTTTAACTTCAAAATTTTAA
AAATTTTAAT
Found at i:349244 original size:20 final size:20
Alignment explanation
Indices: 349217--349380 Score: 97
Period size: 20 Copynumber: 8.2 Consensus size: 20
349207 CGCGAATTTG
349217 TAAA-TCGCAACACAGA-AGT
1 TAAATTCGCAACAC-GATAGT
**
349236 TAAATTCGCAATGCGATAGT
1 TAAATTCGCAACACGATAGT
* * *
349256 CAAATTCACAACGCGATAGT
1 TAAATTCGCAACACGATAGT
*
349276 TAAATTTGCAACA-GAATAGT
1 TAAATTCGCAACACG-ATAGT
* * *
349296 CAAATTCGCAACGCGA-ATTT
1 TAAATTCGCAACACGATA-GT
349316 GTAAA-TCGCAACACAGA-AGT
1 -TAAATTCGCAACAC-GATAGT
* * *
349336 CAAATTCGTAACGCGATAGT
1 TAAATTCGCAACACGATAGT
* * * *
349356 CAAATTCACAACGCGAAAGT
1 TAAATTCGCAACACGATAGT
349376 TAAAT
1 TAAAT
349381 GTTTTTACAC
Statistics
Matches: 113, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.12
20 93 0.82
21 7 0.06
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (20 bp):
TAAATTCGCAACACGATAGT
Found at i:349277 original size:40 final size:41
Alignment explanation
Indices: 349233--349369 Score: 133
Period size: 40 Copynumber: 3.4 Consensus size: 41
349223 GCAACACAGA
* *
349233 AGTTAAATTCGCAATGC-GATAGTCAAATTCACAACGCGAT
1 AGTTAAATTCGCAACGCAGATAGTCAAATTCGCAACGCGAT
*
349273 AGTTAAATTTGCAA--CAGAATAGTCAAATTCGCAACGCGA-
1 AGTTAAATTCGCAACGCAG-ATAGTCAAATTCGCAACGCGAT
* * *
349312 ATTTGTAAA-TCGCAACACAGA-AGTCAAATTCGTAACGCGAT
1 A-GT-TAAATTCGCAACGCAGATAGTCAAATTCGCAACGCGAT
* *
349353 AGTCAAATTCACAACGC
1 AGTTAAATTCGCAACGC
349370 GAAAGTTAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
38 1 0.01
39 5 0.06
40 65 0.81
41 6 0.08
42 3 0.04
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (41 bp):
AGTTAAATTCGCAACGCAGATAGTCAAATTCGCAACGCGAT
Found at i:349329 original size:100 final size:100
Alignment explanation
Indices: 349195--349380 Score: 327
Period size: 100 Copynumber: 1.9 Consensus size: 100
349185 AACCAAGTTT
* * *
349195 TCAATTTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTTAAATTCGCAATGCGATAGTCAAA
1 TCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAA
*
349260 TTCACAACGCGATAGTTAAATTTGCAACAGAATAG
66 TTCACAACGCGAAAGTTAAATTTGCAACAGAATAG
*
349295 TCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGTAACGCGATAGTCAAA
1 TCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAA
349360 TTCACAACGCGAAAGTTAAAT
66 TTCACAACGCGAAAGTTAAAT
349381 GTTTTTACAC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 81 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (100 bp):
TCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAA
TTCACAACGCGAAAGTTAAATTTGCAACAGAATAG
Found at i:349911 original size:20 final size:20
Alignment explanation
Indices: 349886--349938 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
349876 GTGATTTTAG
349886 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
349906 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
349926 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
349939 ATTTAAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:349949 original size:20 final size:20
Alignment explanation
Indices: 349879--349949 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
349869 TCACAACGTG
*
349879 ATTTTAGTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* *
349899 TTTTCATTTTCGCGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
* * *
349919 TTTTCATTTTCGTGTTGCGA
1 ATTTCAGTTTCGCGTTGCGA
*
349939 ATTTAAGTTTC
1 ATTTCAGTTTC
349950 AGAAACTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.14, C:0.15, G:0.20, T:0.51
Consensus pattern (20 bp):
ATTTCAGTTTCGCGTTGCGA
Found at i:351923 original size:12 final size:12
Alignment explanation
Indices: 351906--351947 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
351896 TTTTTCGGCA
*
351906 TTATTTATTTAT
1 TTATTTATTAAT
*
351918 TTATTTACTAAT
1 TTATTTATTAAT
*
351930 TTATGTATTAAT
1 TTATTTATTAAT
351942 TTATTT
1 TTATTT
351948 TCAGCGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:352131 original size:21 final size:21
Alignment explanation
Indices: 352090--352187 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
352080 GATGCACCTA
* * *
352090 TCATCATTCAAGAGACGCCTC
1 TCATCGTTCAAGAGGCCCCTC
352111 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* * *
352132 TCATC-ATCGAATAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
352153 ACACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
352174 TCATCGTTCAAGAG
1 TCATCGTTCAAGAG
352188 ATCCTGCCCG
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:352137 original size:42 final size:43
Alignment explanation
Indices: 352086--352188 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 43
352076 GCCCGATGCA
* *
352086 CCTATCATCATTCAAGAGA-CGCCTC-CTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGAGCCCCTCAC-ACCGTTCAAGAGGCC
* *
352128 CCTCTCATCA-TCGAATA-AGCCCCTCACACCGTTCAAGAGGCC
1 CCTATCATCATTC-AAGAGAGCCCCTCACACCGTTCAAGAGGCC
*
352170 CCTATCATCGTTCAAGAGA
1 CCTATCATCATTCAAGAGA
352189 TCCTGCCCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
41 3 0.06
42 42 0.86
43 4 0.08
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (43 bp):
CCTATCATCATTCAAGAGAGCCCCTCACACCGTTCAAGAGGCC
Found at i:353667 original size:61 final size:62
Alignment explanation
Indices: 353567--353707 Score: 187
Period size: 67 Copynumber: 2.2 Consensus size: 62
353557 TTTTACATTG
*
353567 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* * *
353627 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA---TTTTT-CTTGATTAATTGATTTG
353692 TA
61 TA
353694 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
353708 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
60 17 0.24
61 18 0.26
65 4 0.06
67 31 0.44
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:354150 original size:39 final size:39
Alignment explanation
Indices: 354096--354182 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
354086 TCAAGTTGTA
354096 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
*
354135 GATTTTGATTTCCTTTTGCTTGACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
354174 GATTTTGAT
1 GATTTTGAT
354183 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:357799 original size:20 final size:20
Alignment explanation
Indices: 357774--357814 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
357764 AATTTTGGGT
357774 TGAAGAACTTAGTTGATTAC
1 TGAAGAACTTAGTTGATTAC
357794 TGAAGAACTTAGTTGATTAC
1 TGAAGAACTTAGTTGATTAC
357814 T
1 T
357815 ACCCCGCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
TGAAGAACTTAGTTGATTAC
Found at i:359000 original size:21 final size:20
Alignment explanation
Indices: 358974--359017 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
358964 GATTTCTGGG
* *
358974 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
358995 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
359015 CAA
1 CAA
359018 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:359883 original size:32 final size:32
Alignment explanation
Indices: 359842--359937 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
359832 GAGTCGAGGG
359842 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
359874 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
359905 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
359937 T
1 T
359938 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:360018 original size:29 final size:30
Alignment explanation
Indices: 359929--360021 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
359919 AAGGAACATA
359929 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
359959 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* *
359989 TGGACAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
360018 TGGA
1 TGGA
360022 TAGGTCCTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
29 18 0.30
30 43 0.70
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Done.