Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 54
Found at i:2587532 original size:32 final size:32
Alignment explanation
Indices: 2587489--2587555 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
2587479 AAAATACATA
*
2587489 TTTACTTTCAATTCCTCATTTGGATAATAACT
1 TTTACTATCAATTCCTCATTTGGATAATAACT
*
2587521 TTTACTATCAATTCCTCATTTTGATAATAACT
1 TTTACTATCAATTCCTCATTTGGATAATAACT
2587553 TTT
1 TTT
2587556 GTATTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.49
Consensus pattern (32 bp):
TTTACTATCAATTCCTCATTTGGATAATAACT
Found at i:2588782 original size:19 final size:18
Alignment explanation
Indices: 2588750--2588785 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2588740 TTTATTTTAC
2588750 TTAAATTAAAATATATAA
1 TTAAATTAAAATATATAA
*
2588768 TTAAGATTAATATATATA
1 TTAA-ATTAAAATATATA
2588786 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TTAAATTAAAATATATAA
Found at i:2598362 original size:29 final size:29
Alignment explanation
Indices: 2598311--2598367 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2598301 AAATTTTTTA
* *
2598311 TAGTGACCAAAATGCAAATTTTGAAAAAT
1 TAGTGACCAAAATACAAACTTTGAAAAAT
*
2598340 TAGTGACCAAAATATAAACTTTGAAAAA
1 TAGTGACCAAAATACAAACTTTGAAAAA
2598368 AATTCAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (29 bp):
TAGTGACCAAAATACAAACTTTGAAAAAT
Found at i:2602941 original size:20 final size:20
Alignment explanation
Indices: 2602897--2602955 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2602887 GAAGAGAAGG
** *
2602897 GATCGATCCTTTTTCACGAGG
1 GATCGATCC-TTTTCAAAAGA
*
2602918 GATCGATCCTTTTGAAAAGA
1 GATCGATCCTTTTCAAAAGA
*
2602938 GATCGATTCTTTTCAAAA
1 GATCGATCCTTTTCAAAA
2602956 CAAAAACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 23 0.72
21 9 0.28
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (20 bp):
GATCGATCCTTTTCAAAAGA
Found at i:2604447 original size:21 final size:22
Alignment explanation
Indices: 2604407--2604448 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2604397 AACAAGTGGC
2604407 ATCATATGTACATCAACATAAA
1 ATCATATGTACATCAACATAAA
* *
2604429 ATCATAT-TCCATCATCATAA
1 ATCATATGTACATCAACATAA
2604449 TTAACCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (22 bp):
ATCATATGTACATCAACATAAA
Found at i:2610827 original size:17 final size:18
Alignment explanation
Indices: 2610805--2610842 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
2610795 GATTTTTATA
2610805 TATCTC-ATTTCATCCTT
1 TATCTCTATTTCATCCTT
2610822 TATCTCTTAATTTCATCCTT
1 TATCTC-T-ATTTCATCCTT
2610842 T
1 T
2610843 CCATTTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
20 12 0.67
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.55
Consensus pattern (18 bp):
TATCTCTATTTCATCCTT
Found at i:2614335 original size:24 final size:24
Alignment explanation
Indices: 2614276--2614386 Score: 69
Period size: 24 Copynumber: 4.6 Consensus size: 24
2614266 ATGAATGTTA
* * *
2614276 TCTGATTTCTGATTTAAATTCTAT
1 TCTGATTTCTGATATGAATTCTGT
* * ** *
2614300 TTTCATACCTGATATGAATTATGT
1 TCTGATTTCTGATATGAATTCTGT
** *
2614324 TCTGATTTCTGACCTGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * * * *
2614348 TCAGATATCTTATCTGAATTCTAT
1 TCTGATTTCTGATATGAATTCTGT
*
2614372 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
2614387 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 27, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:2616301 original size:32 final size:32
Alignment explanation
Indices: 2616239--2616301 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2616229 ATACTAATAG
*
2616239 TGTTGCATTCAGTTAATGCACAATAAAGTCAA
1 TGTTGCATTCAGTTAATGCACAAGAAAGTCAA
*
2616271 TGTTGCATTCA-TATAATGCACAAGAGAGTCA
1 TGTTGCATTCAGT-TAATGCACAAGAAAGTCA
2616302 GTATCATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (32 bp):
TGTTGCATTCAGTTAATGCACAAGAAAGTCAA
Found at i:2616990 original size:28 final size:29
Alignment explanation
Indices: 2616924--2617021 Score: 103
Period size: 28 Copynumber: 3.4 Consensus size: 29
2616914 AGATTTAATC
*
2616924 CTTTATGTACCTATTTTGACCAAAAAATA
1 CTTTATGTACTTATTTTGACCAAAAAATA
* *
2616953 CTTTAGGTACTTATTTT-AGCTAAAAAA-A
1 CTTTATGTACTTATTTTGA-CCAAAAAATA
* **
2616981 GTTTATGTACTTATTTTGGTC-AAAAATA
1 CTTTATGTACTTATTTTGACCAAAAAATA
*
2617009 CTTTATATACTTA
1 CTTTATGTACTTA
2617022 GATAAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
27 5 0.09
28 29 0.52
29 22 0.39
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (29 bp):
CTTTATGTACTTATTTTGACCAAAAAATA
Found at i:2622196 original size:120 final size:119
Alignment explanation
Indices: 2621995--2622218 Score: 283
Period size: 120 Copynumber: 1.9 Consensus size: 119
2621985 TATATTAATT
* * * *
2621995 TATATATATTTATAAATAAAGTATTTATTTATTTAGAAATATCATAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAGTATTTATTTATTTAAAAATATCATAAAAAGACATCCAGGTGCCT
* *
2622060 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATGATTAAAAATAATAA
66 TAAGACAGCTCCTTTCTT-AATATTAAAAAATAAATAAATGATTAAAAATAATAA
* *
2622115 TATATA-ATTTATAAA-ATAGGATATTTATTTATTTAAAAATATCATAAAATAGACATCCAGTTG
1 TATATATATTTATAAATA-AAG-TATTTATTTATTTAAAAATATCATAAAA-AGACATCCAGGTG
** * *
2622178 TTTTAAGACTG-TCCTTTCTTAATATTGAAAAATAAATAAAT
63 CCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAAT
2622219 ATATATTAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
118 1 0.01
119 30 0.34
120 41 0.46
121 17 0.19
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (119 bp):
TATATATATTTATAAATAAAGTATTTATTTATTTAAAAATATCATAAAAAGACATCCAGGTGCCT
TAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATGATTAAAAATAATAA
Found at i:2622312 original size:18 final size:16
Alignment explanation
Indices: 2622281--2622315 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2622271 GAATAAACAA
2622281 ATATTATTTATTATAT
1 ATATTATTTATTATAT
2622297 ATATATATTTATT-TAT
1 ATAT-TATTTATTATAT
2622313 ATA
1 ATA
2622316 AATAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTTATTATAT
Found at i:2622331 original size:12 final size:13
Alignment explanation
Indices: 2622316--2622344 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2622306 TATTTATATA
2622316 AATAAT-AAAAAT
1 AATAATAAAAAAT
2622328 AATAATAAAAAAT
1 AATAATAAAAAAT
2622341 AATA
1 AATA
2622345 TTGCAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:2623578 original size:3 final size:3
Alignment explanation
Indices: 2623570--2623658 Score: 67
Period size: 3 Copynumber: 29.7 Consensus size: 3
2623560 AATTATTTTT
* *
2623570 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
* * * * *
2623615 TTA TTA TTA TTA TAA TTA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
2623659 TTCAAATGAA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.08
3 62 0.82
4 8 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:2624132 original size:124 final size:121
Alignment explanation
Indices: 2623971--2624514 Score: 505
Period size: 110 Copynumber: 4.6 Consensus size: 121
2623961 ATCTTCTTAT
* * *
2623971 GCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAAATTCTTCT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGAT-AAGTTCTTCT
*
2624036 TATTATGAACTCTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATATAATCA
64 CATTATGAACTCTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAT-ATCA
* * *
2624095 TG-TAAAGGTTGAATAAGCTTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
1 -GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
* * * * ***
2624159 ATTATGAAC-CT-TCT-G----G-CAACGCTGATC---CATCGAATGATGA-AT-TCGA
65 ATTATGAACTCTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTG-TGATATATC-A
* * *
2624205 GCAAAAGGTTGAACAAGTTCTTCTCTTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
*
2624270 ATTATGAACT-TGAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAGTCAA
65 ATTATGAACTCT-AACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATATA-TC-A
2624329 GCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
1 GC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
* * * * *** *
2624394 ATTATGAAC-CT-TCT-G----G-CAACGCTGATC---CATCAAATGACGA-AT-TCGA
65 ATTATGAACTCTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTG-TGATATATC-A
* * *
2624440 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
2624505 ATTATGAACT
65 ATTATGAACT
2624515 TTCTCTGGAA
Statistics
Matches: 352, Mismatches: 43, Indels: 61
0.77 0.09 0.13
Matches are distributed among these distances:
109 3 0.01
110 79 0.22
111 68 0.19
112 3 0.01
113 8 0.02
114 12 0.03
115 1 0.00
116 9 0.03
117 1 0.00
118 1 0.00
119 10 0.03
120 2 0.01
121 6 0.02
122 26 0.07
123 9 0.03
124 73 0.21
125 41 0.12
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (121 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
TTATGAACTCTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATATATCA
Found at i:2624525 original size:235 final size:233
Alignment explanation
Indices: 2623971--2624527 Score: 916
Period size: 235 Copynumber: 2.4 Consensus size: 233
2623961 ATCTTCTTAT
* * * *
2623971 GCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAAATTCTTCT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG-AGTTCTTCT
* * * * *
2624036 TATTATGAACTCTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATATAATCATGTAAA
65 CATTATGAACTTTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAATCAAGAAAA
* *
2624101 GGTTGAATAAGCTTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGA
130 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGA
* *
2624166 ACCTTCTGGCAACGCTGATCCATCGAATGATGAATTCGA
195 ACCTTCTGGCAACGCTGATCCATCAAATGACGAATTCGA
*
2624205 GCAAAAGGTTGAACAAGTTCTTCTCTTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
2624270 ATTATGAACTTGAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAGTCAAGCAAAA
66 ATTATGAACTTTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAATCAAG--AAA
2624335 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
129 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
2624400 AACCTTCTGGCAACGCTGATCCATCAAATGACGAATTCGA
194 AACCTTCTGGCAACGCTGATCCATCAAATGACGAATTCGA
*
2624440 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**
2624505 ATTATGAACTTTCTCTGGAAATG
66 ATTATGAACTTTAACTGGAAATG
2624528 CTGATCCATC
Statistics
Matches: 300, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
233 63 0.21
234 51 0.17
235 186 0.62
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (233 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTAACTGGAAATGTTAATGCTGATCTATCTTCTTCTGTGATAGAATCAAGAAAAG
GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
CCTTCTGGCAACGCTGATCCATCAAATGACGAATTCGA
Found at i:2625725 original size:19 final size:17
Alignment explanation
Indices: 2625697--2625745 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
2625687 AAAATAAAAT
*
2625697 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
2625716 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
2625732 AATAAATTGAATTT
1 AATAAATTGAATTT
2625746 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:2626119 original size:14 final size:14
Alignment explanation
Indices: 2626100--2626176 Score: 79
Period size: 14 Copynumber: 5.6 Consensus size: 14
2626090 TGACCCCCTC
2626100 TTTTTTTCTTTCTT
1 TTTTTTTCTTTCTT
2626114 TTTTTTTCTTTCATT
1 TTTTTTTCTTTC-TT
*
2626129 TTTTCTT-TTTCTT
1 TTTTTTTCTTTCTT
*
2626142 TTCTTCTTC-TTCTT
1 TT-TTTTTCTTTCTT
* *
2626156 CTTTTTT-TTTCAT
1 TTTTTTTCTTTCTT
2626169 TTTTTTTC
1 TTTTTTTC
2626177 AAGCATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 18 0.34
14 27 0.51
15 8 0.15
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTTTCTT
Found at i:2637410 original size:7 final size:7
Alignment explanation
Indices: 2637398--2637422 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2637388 ATTACAAATA
2637398 ATAATTT
1 ATAATTT
2637405 ATAATTT
1 ATAATTT
2637412 ATAATTT
1 ATAATTT
2637419 ATAA
1 ATAA
2637423 AATAGGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATAATTT
Found at i:2637611 original size:18 final size:17
Alignment explanation
Indices: 2637580--2637618 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2637570 GAATAAACAA
2637580 ATAT-TATTTATTATAT
1 ATATATATTTATTATAT
2637596 ATATATATTTATT-TAT
1 ATATATATTTATTATAT
*
2637612 TTATATA
1 ATATATA
2637619 AATAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATATTTATTATAT
Found at i:2637634 original size:3 final size:3
Alignment explanation
Indices: 2637619--2637651 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2637609 TATTTATATA
*
2637619 AAT AAT AAA AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2637652 TTGCAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:2638148 original size:9 final size:11
Alignment explanation
Indices: 2638118--2638150 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
2638108 TCTCTCATTT
2638118 TTCTTTCTCTC
1 TTCTTTCTCTC
2638129 TTCTTTCTCTC
1 TTCTTTCTCTC
2638140 TTCTTTCTCTC
1 TTCTTTCTCTC
2638151 AAATGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTTTCTCTC
Found at i:2638929 original size:3 final size:3
Alignment explanation
Indices: 2638923--2638958 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2638913 ATAATATATA
*
2638923 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2638959 AATAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2638959 original size:6 final size:6
Alignment explanation
Indices: 2638902--2638967 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
2638892 AATTATTTTT
* * * * * *
2638902 TAATAA TAATAA TAATATA TATATTA TTATTA TTATTA TTATTA TTATTA
1 TAATTA TAATTA TAAT-TA TA-ATTA TAATTA TAATTA TAATTA TAATTA
*
2638952 TAATTA TAATAA TAAT
1 TAATTA TAATTA TAAT
2638968 AATATAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
6 46 0.85
7 6 0.11
8 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:2638963 original size:9 final size:9
Alignment explanation
Indices: 2638902--2638971 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
2638892 AATTATTTTT
*
2638902 TAATAATAA
1 TAATAATTA
2638911 TAATAATATA
1 TAATAAT-TA
*
2638921 TATATTATTA
1 TA-ATAATTA
* *
2638931 TTATTATTA
1 TAATAATTA
* *
2638940 TTATTATTA
1 TAATAATTA
*
2638949 TTATAATTA
1 TAATAATTA
*
2638958 TAATAATAA
1 TAATAATTA
2638967 TAATA
1 TAATA
2638972 TAAATAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
9 43 0.81
10 6 0.11
11 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATAATTA
Found at i:2639478 original size:32 final size:31
Alignment explanation
Indices: 2639407--2639481 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
2639397 CTTGCAAAAA
2639407 TTCAGTTTTTATTTCTCTATTTTTTAAAAGC
1 TTCAGTTTTTATTTCTCTATTTTTTAAAAGC
2639438 TTCAGTTTTTATTTCTCTATTTTTTAAAAGC
1 TTCAGTTTTTATTTCTCTATTTTTTAAAAGC
*
2639469 TTCAGGTTTTATT
1 TTCAGTTTTTATT
2639482 CTTCTTTTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.59
Consensus pattern (31 bp):
TTCAGTTTTTATTTCTCTATTTTTTAAAAGC
Found at i:2645617 original size:30 final size:28
Alignment explanation
Indices: 2645552--2645623 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
2645542 TTTGGTCAGT
* *
2645552 GACTAAAATACAAATTTTGAAAATTTAG
1 GACTAAAATATAAATTTGGAAAATTTAG
* *
2645580 TAGCTAAAGTATAAATTTGGAAACATTTAGG
1 GA-CTAAAATATAAATTTGGAAA-ATTTA-G
*
2645611 GACTAAACTATAA
1 GACTAAAATATAA
2645624 TTTTTAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.03
29 17 0.49
30 15 0.43
31 2 0.06
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (28 bp):
GACTAAAATATAAATTTGGAAAATTTAG
Found at i:2646721 original size:164 final size:164
Alignment explanation
Indices: 2646450--2646750 Score: 471
Period size: 164 Copynumber: 1.8 Consensus size: 164
2646440 TCTAGAATTG
* *
2646450 ATGAGATTGGAAATTTGGGTTCATAATATCTACCTATAGTATTCGTCCATAGGAAAGAAAATTTG
1 ATGAGATTGGAAATTTGAGTTCATAATATCTACCTATAGTATTCGACCATAGGAAAGAAAATTTG
** *
2646515 GGGAAAATATTGAAAAATTTCATGTGGTCTAGAATTGATATTAGGAGTATTCTACATGCTTTGGA
66 GGGAAAATATTGAAAAATTTCATACGGTCTAGAATTGATATTAGAAGTATTCTACATGCTTTGGA
2646580 GATTGATATTATAAGTATTCTACATGCTTTTATA
131 GATTGATATTATAAGTATTCTACATGCTTTTATA
* * * *
2646614 ATGAGATT-GACAATTTGAGTTTATATTCTCTATCTATAGTATTCGACCATAGGAAAGAAAATTT
1 ATGAGATTGGA-AATTTGAGTTCATAATATCTACCTATAGTATTCGACCATAGGAAAGAAAATTT
* *
2646678 GGGGAAAATGTTGAAAAATTTCCTACGGTCTAG-ATTCGATATTAGAAGTATTCTACATGCTTTG
65 GGGGAAAATATTGAAAAATTTCATACGGTCTAGAATT-GATATTAGAAGTATTCTACATGCTTTG
2646742 GAGATTGAT
129 GAGATTGAT
2646751 TTGGATCAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
163 5 0.04
164 119 0.96
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (164 bp):
ATGAGATTGGAAATTTGAGTTCATAATATCTACCTATAGTATTCGACCATAGGAAAGAAAATTTG
GGGAAAATATTGAAAAATTTCATACGGTCTAGAATTGATATTAGAAGTATTCTACATGCTTTGGA
GATTGATATTATAAGTATTCTACATGCTTTTATA
Found at i:2649583 original size:30 final size:30
Alignment explanation
Indices: 2649549--2649607 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2649539 TTTAGTCCCT
* * *
2649549 AAACTTT-TCAAAGTTTATACTTTGGTCACC
1 AAACTTTACCAAA-TTTATAATTCGGTCACC
2649579 AAACTTTACCAAATTTATAATTCGGTCAC
1 AAACTTTACCAAATTTATAATTCGGTCAC
2649608 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTCGGTCACC
Found at i:2661249 original size:16 final size:16
Alignment explanation
Indices: 2661225--2661258 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2661215 CTGCTTAAAA
2661225 TTTTGAAAATAATTTT
1 TTTTGAAAATAATTTT
* *
2661241 TTTTTAAAATTATTTT
1 TTTTGAAAATAATTTT
2661257 TT
1 TT
2661259 AATATATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTGAAAATAATTTT
Found at i:2661298 original size:20 final size:20
Alignment explanation
Indices: 2661275--2661314 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2661265 TGAAAATTCA
* *
2661275 AAATTTAGTTTTGAAATTAT
1 AAATATAGTTTTAAAATTAT
*
2661295 AAATATATTTTTAAAATTAT
1 AAATATAGTTTTAAAATTAT
2661315 TAAACAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATATAGTTTTAAAATTAT
Found at i:2663052 original size:17 final size:16
Alignment explanation
Indices: 2663032--2663065 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2663022 AAGGAAATAT
*
2663032 GAAGAAGATGGAAAAAA
1 GAAGAAGA-AGAAAAAA
2663049 GAAGAAGAAGAAAAAA
1 GAAGAAGAAGAAAAAA
2663065 G
1 G
2663066 TTGTTGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (16 bp):
GAAGAAGAAGAAAAAA
Found at i:2667173 original size:10 final size:10
Alignment explanation
Indices: 2667158--2667227 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
2667148 CCGGTTTTCA
2667158 ACCGGTTCTG
1 ACCGGTTCTG
2667168 ACCGGTT-TG
1 ACCGGTTCTG
*
2667177 ACCGGTT-TCA
1 ACCGGTTCT-G
2667187 ACCGGTTC-G
1 ACCGGTTCTG
*
2667196 AACCAGTT-TG
1 -ACCGGTTCTG
2667206 ACCGG-TCTG
1 ACCGGTTCTG
2667215 AACCGG-TCTG
1 -ACCGGTTCTG
2667225 ACC
1 ACC
2667228 CGACCCGACC
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 1 0.02
9 19 0.38
10 30 0.60
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:2667182 original size:19 final size:20
Alignment explanation
Indices: 2667138--2667227 Score: 80
Period size: 19 Copynumber: 4.6 Consensus size: 20
2667128 GCTGCTGGAA
* * *
2667138 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
2667158 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
2667177 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
*
2667197 ACCAGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
*
2667216 ACCGGTCTGACC
1 ACCGGTTTGACC
2667228 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
18 3 0.05
19 32 0.55
20 15 0.26
21 8 0.14
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.28
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:2667218 original size:29 final size:29
Alignment explanation
Indices: 2667155--2667227 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
2667145 TAACCGGTTT
* *
2667155 TCAACCGGTTCTGACCGGTTTGACCGGTT
1 TCAACCGGTTCTGACCAGTTTGACCGGTC
2667184 TCAACCGGTTC-GAACCAGTTTGACCGGTC
1 TCAACCGGTTCTG-ACCAGTTTGACCGGTC
*
2667213 TGAACCGG-TCTGACC
1 TCAACCGGTTCTGACC
2667228 CGACCCGACC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.26
Consensus pattern (29 bp):
TCAACCGGTTCTGACCAGTTTGACCGGTC
Found at i:2667249 original size:22 final size:22
Alignment explanation
Indices: 2667241--2667283 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2667231 CCCGACCGTT
*
2667241 GACCCGACCTGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2667263 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
2667284 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:2667283 original size:17 final size:17
Alignment explanation
Indices: 2667223--2667271 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
2667213 TGAACCGGTC
2667223 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
2667240 TGACCCGACCTGACCGT
1 TGACCCGACCCGACCGT
2667257 TGACCCGACCCGACC
1 TGACCCGACCCGACC
2667272 CGACCGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2672025 original size:16 final size:16
Alignment explanation
Indices: 2672004--2672034 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2671994 AATGTTAAGC
2672004 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
2672020 GCTGAATGATTCAAA
1 GCTGAATGATTCAAA
2672035 GGCTCTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:2672045 original size:18 final size:16
Alignment explanation
Indices: 2672004--2672038 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2671994 AATGTTAAGC
*
2672004 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAG
2672020 GCTGAATGATTCAAAG
1 GCTGAATGATTCAAAG
2672036 GCT
1 GCT
2672039 CTGAATGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (16 bp):
GCTGAATGATTCAAAG
Found at i:2673299 original size:37 final size:37
Alignment explanation
Indices: 2673245--2673316 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
2673235 GTGCAACTAG
2673245 AACTCTCGCAAGACGAAATGCTTTTCACCTTGGAAGA
1 AACTCTCGCAAGACGAAATGCTTTTCACCTTGGAAGA
* **
2673282 AACTCTCGCAAGGCGAAATGCTTTTCTTCTTGGAA
1 AACTCTCGCAAGACGAAATGCTTTTCACCTTGGAA
2673317 CAACTCTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (37 bp):
AACTCTCGCAAGACGAAATGCTTTTCACCTTGGAAGA
Found at i:2673701 original size:43 final size:43
Alignment explanation
Indices: 2673640--2673725 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2673630 GTAAATATAT
2673640 CGGTTCATCAAGTTGAAGTCGAGTATCTATACGAACATTAAAC
1 CGGTTCATCAAGTTGAAGTCGAGTATCTATACGAACATTAAAC
2673683 CGGTTCATCAAGTTGAAGTCGAGTATCTATACGAACATTAAAC
1 CGGTTCATCAAGTTGAAGTCGAGTATCTATACGAACATTAAAC
2673726 AAACCATATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (43 bp):
CGGTTCATCAAGTTGAAGTCGAGTATCTATACGAACATTAAAC
Found at i:2681070 original size:24 final size:24
Alignment explanation
Indices: 2681040--2681095 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2681030 TAGAAGTTCG
2681040 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
2681064 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
2681088 ATTGAAGC
1 ATTGAAGC
2681096 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:2686598 original size:24 final size:24
Alignment explanation
Indices: 2686571--2686680 Score: 93
Period size: 24 Copynumber: 4.6 Consensus size: 24
2686561 GTAAACGGAG
*
2686571 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * *
2686595 ATATAAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
2686619 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
2686642 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
2686666 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
2686681 TAAAATATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.24
24 48 0.71
25 2 0.03
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:2686626 original size:12 final size:11
Alignment explanation
Indices: 2686604--2686663 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
2686594 CATATAAGAT
2686604 ATCAGAACAGA
1 ATCAGAACAGA
*
2686615 ATCCAGATCAGA
1 AT-CAGAACAGA
2686627 ATCAGAACAGA
1 ATCAGAACAGA
*
2686638 ATTCAGGTAAC-GT
1 A-TCA-G-AACAGA
2686651 ATCAGAACAGA
1 ATCAGAACAGA
2686662 AT
1 AT
2686664 TCAATTCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.08
11 15 0.38
12 16 0.40
13 3 0.08
14 3 0.08
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (11 bp):
ATCAGAACAGA
Found at i:2686654 original size:47 final size:48
Alignment explanation
Indices: 2686573--2686663 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
2686563 AAACGGAGAT
*
2686573 ATCAGAAATCAAAACAGAATTCATATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
* *
2686621 ATCAG-AATCAGAACAGAATTCAGGTAACG-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAAT
2686664 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 33 0.85
48 6 0.15
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:2689114 original size:13 final size:13
Alignment explanation
Indices: 2689098--2689133 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2689088 GTCAACGGGT
*
2689098 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
2689111 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2689124 CGGGTCGGGT
1 CGGGTCGGGT
2689134 TATGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:2690868 original size:13 final size:13
Alignment explanation
Indices: 2690850--2690874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2690840 AGTGGCACCT
2690850 TATATACCATTAA
1 TATATACCATTAA
2690863 TATATACCATTA
1 TATATACCATTA
2690875 TGTATTTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATACCATTAA
Found at i:2690933 original size:46 final size:45
Alignment explanation
Indices: 2690880--2691002 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 45
2690870 CATTATGTAT
* *
2690880 TTTCATTTGTGGCATCCTTTCATGCCAATTATGCGCTGTTATATA
1 TTTCATTTGTGGCATCCTTTCATACCAATTATGCGCGGTTATATA
* * * *
2690925 TATTCATTTATGGCATTCTTCCATACCAATTATGCGCGGTTATACA
1 T-TTCATTTGTGGCATCCTTTCATACCAATTATGCGCGGTTATATA
*
2690971 TTTCCATTTGTGGCATCCTTTCATATCAATTA
1 TTT-CATTTGTGGCATCCTTTCATACCAATTA
2691003 GAATGATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
45 3 0.05
46 63 0.95
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (45 bp):
TTTCATTTGTGGCATCCTTTCATACCAATTATGCGCGGTTATATA
Found at i:2691160 original size:81 final size:81
Alignment explanation
Indices: 2691080--2691733 Score: 941
Period size: 81 Copynumber: 8.1 Consensus size: 81
2691070 AGGCATTTAG
* * * *
2691080 TCTTTTACCCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAAGGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* ** *
2691145 ACAGTTAGGCTTTTAG
66 ACAGCTAGGCCATTAA
* * *
2691161 TCTTTTATTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAATTGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
2691226 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
2691242 TCTTTTACTCAAAGGTATTTAACCTTTAATCTAGCTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
2691307 ACAGCTAGG-CATTAA
66 ACAGCTAGGCCATTAA
* * * *
2691322 TCTTTTACTCAAAGGTATTTAACCTTTTATCTAAATAGCATAATTGACACCTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* **
2691387 ACAGCTAGACGGTTAA
66 ACAGCTAGGCCATTAA
* *
2691403 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
2691468 ACAGCTAAGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
2691484 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGTATAATTGACATCTTTCTATCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
2691549 AAAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
2691565 TCTTTTACTCAAAGGTATTTAAACTTTCATCTAATTGGCATAATTGACACATTTCTGTCCAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
2691630 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
2691646 TCTTTTACTAAAAGGTATGTAACCTTTCATCTAACTGGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
2691711 ACAGATAGGCCATTAA
66 ACAGCTAGGCCATTAA
2691727 TCTTTTA
1 TCTTTTA
2691734 TTTTAGAACA
Statistics
Matches: 512, Mismatches: 60, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
80 74 0.14
81 438 0.86
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:2691885 original size:55 final size:55
Alignment explanation
Indices: 2691826--2692033 Score: 319
Period size: 55 Copynumber: 3.8 Consensus size: 55
2691816 AGTAGTACCA
* * *
2691826 ATACAGTAATACATAAACTTATTATGGATTTCTTAGTTTTGCACACACAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* * *
2691881 ATACAGAAATTCATAAACTTATTATGCATTTCTTAGTTTTGGACACACGGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
2691936 ATACTGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAGTGCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
* *
2691991 ATACTGAAATTCATAAACTTATTATGAATTTCCTAG-TTTGCAC
1 ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCAC
2692034 GTATAGTGCC
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 7 0.05
55 135 0.95
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (55 bp):
ATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCC
Found at i:2692223 original size:14 final size:14
Alignment explanation
Indices: 2692199--2692237 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2692189 TTTGTCTATA
*
2692199 TTGCAGAGATTT-T
1 TTGCAGGGATTTAT
2692212 TATGCAGGGATTTAT
1 T-TGCAGGGATTTAT
2692227 TTGCAGGGATT
1 TTGCAGGGATT
2692238 ACTTCCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (14 bp):
TTGCAGGGATTTAT
Found at i:2699388 original size:3 final size:3
Alignment explanation
Indices: 2699380--2699412 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2699370 TCCTATTTAA
*
2699380 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2699413 AAATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2708934 original size:12 final size:12
Alignment explanation
Indices: 2708919--2708983 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
2708909 TTTGACTTGA
2708919 TTCTGTTATGAT
1 TTCTGTTATGAT
* *
2708931 TTCTGATCTGGA-
1 TTCTGTTAT-GAT
*
2708943 TTCTATTATGAT
1 TTCTGTTATGAT
* * *
2708955 ATCTGTTTTGAA
1 TTCTGTTATGAT
*
2708967 TTCTGTTTTGAT
1 TTCTGTTATGAT
2708979 TTCTG
1 TTCTG
2708984 ATATCTCCAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 36 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:2708946 original size:24 final size:24
Alignment explanation
Indices: 2708904--2708985 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
2708894 ATATTTTATC
* *
2708904 TGATTTTTGA-CTTGATTCTGTTA
1 TGATTTCTGATCTGGATTCTGTTA
*
2708927 TGATTTCTGATCTGGATTCTATTA
1 TGATTTCTGATCTGGATTCTGTTA
* * * * *
2708951 TGATATCTGTTTTGAATTCTGTTT
1 TGATTTCTGATCTGGATTCTGTTA
2708975 TGATTTCTGAT
1 TGATTTCTGAT
2708986 ATCTCCATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
23 9 0.19
24 38 0.81
ACGTcount: A:0.18, C:0.10, G:0.17, T:0.55
Consensus pattern (24 bp):
TGATTTCTGATCTGGATTCTGTTA
Found at i:2709652 original size:135 final size:135
Alignment explanation
Indices: 2709410--2709681 Score: 499
Period size: 135 Copynumber: 2.0 Consensus size: 135
2709400 CTGAGCTTTC
*
2709410 TGAAGCTCACTCTATTACTCGCTATTGCAGGTTAAAAGGATTACACCAGTGCATCTATCGACTTC
1 TGAAGCTCACTCTATTACTCGCTATTGCAGGTTAAAAAGATTACACCAGTGCATCTATCGACTTC
*
2709475 AGTAAAAGAGTTCTTCCGGCGTTATTTGCTGAGTATGGTACATGTGATTAGGGGGCATGTAAATG
66 AGTAAAAGAGTTCTTCCGGCGTTATTTGCTGAGTATGATACATGTGATTAGGGGGCATGTAAATG
2709540 TATTT
131 TATTT
*
2709545 TGAAGCTCACTCTATTACTCGCTATTGCAGGTTAAAAAGATTACACGAGTGCATCTATCGACTTC
1 TGAAGCTCACTCTATTACTCGCTATTGCAGGTTAAAAAGATTACACCAGTGCATCTATCGACTTC
* *
2709610 AGTAAAAGAGTTCTTCCGGCGTTATTTGCTGAGTATGATACATGTGATTATGGGGCATGTAATTG
66 AGTAAAAGAGTTCTTCCGGCGTTATTTGCTGAGTATGATACATGTGATTAGGGGGCATGTAAATG
2709675 TATTT
131 TATTT
2709680 TG
1 TG
2709682 TTTTATATAT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 132 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (135 bp):
TGAAGCTCACTCTATTACTCGCTATTGCAGGTTAAAAAGATTACACCAGTGCATCTATCGACTTC
AGTAAAAGAGTTCTTCCGGCGTTATTTGCTGAGTATGATACATGTGATTAGGGGGCATGTAAATG
TATTT
Found at i:2714355 original size:14 final size:13
Alignment explanation
Indices: 2714330--2714367 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2714320 TAATAATAAT
*
2714330 ATTATTATTTTTA
1 ATTATTAATTTTA
2714343 ATTAATTAATTTTA
1 ATT-ATTAATTTTA
2714357 ATT-TTAATTTT
1 ATTATTAATTTT
2714368 TTCAGGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTATTAATTTTA
Found at i:2716488 original size:131 final size:131
Alignment explanation
Indices: 2716250--2716527 Score: 351
Period size: 131 Copynumber: 2.1 Consensus size: 131
2716240 GGGAGGTCAT
* * * * * * * *
2716250 TTAT-TATTATCATTTTCTCTCGAATTAATATTGATTTTTGAGATGGAATAGTGATATCTCTTCA
1 TTATATATTATCATTTTCACTCGAATTAATAATAAATTTTAAGACGGAATAATGATATATCTTCA
* * * * *
2716314 TTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTAGAAATT
66 TTTCAATTGGAACAATAAATGACTGCTTTAAGGCATGAAAGGTCATTTATTCTCGATTAGAAATC
*
2716379 G
131 A
* * *
2716380 TTATATATTATCATTTTCACTCGAATTGATAATAAATTTTAAGACGTAATAATGATATATTTTCA
1 TTATATATTATCATTTTCACTCGAATTAATAATAAATTTTAAGACGGAATAATGATATATCTTCA
* * * *
2716445 TTTCAATTGGAATAATAAATGATTGTTTTAAGGCATGAAAGGTCATTTATTCTCGATTGGAAATC
66 TTTCAATTGGAACAATAAATGACTGCTTTAAGGCATGAAAGGTCATTTATTCTCGATTAGAAATC
2716510 A
131 A
*
2716511 TTAGATATTATCATTTT
1 TTATATATTATCATTTT
2716528 TTCTCTTAAA
Statistics
Matches: 125, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
130 4 0.03
131 121 0.97
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (131 bp):
TTATATATTATCATTTTCACTCGAATTAATAATAAATTTTAAGACGGAATAATGATATATCTTCA
TTTCAATTGGAACAATAAATGACTGCTTTAAGGCATGAAAGGTCATTTATTCTCGATTAGAAATC
A
Found at i:2721408 original size:31 final size:31
Alignment explanation
Indices: 2721372--2721480 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 31
2721362 CAGTCGCTGC
*
2721372 TGGTAATTCCTTGTATAGGTCCAGCACTGAT
1 TGGTAATTCCTTGTATAGGTTCAGCACTGAT
* * * * *
2721403 TGGTAATTCCTATCTCTGGAAGGTTTAGTCGCTG-C
1 TGGTAATTCCT-TGTAT---AGGTTCAG-CACTGAT
* *
2721438 TGGTAATTCCTTGTATAGGTTCAGTACTTAT
1 TGGTAATTCCTTGTATAGGTTCAGCACTGAT
2721469 TGGTAATTCCTT
1 TGGTAATTCCTT
2721481 ATGGACCTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
30 2 0.03
31 30 0.51
32 3 0.05
34 3 0.05
35 17 0.29
36 4 0.07
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
TGGTAATTCCTTGTATAGGTTCAGCACTGAT
Found at i:2723750 original size:35 final size:35
Alignment explanation
Indices: 2723704--2723772 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
2723694 CCAAATATAG
* *
2723704 TTTAATGGGATAGACAATTGATAATTACGTATTTT
1 TTTAATGGGATAAACAATTGATAATTAAGTATTTT
2723739 TTTAATGGGATAAACAATTGATAATTAAGTATTT
1 TTTAATGGGATAAACAATTGATAATTAAGTATTT
2723773 CTATAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (35 bp):
TTTAATGGGATAAACAATTGATAATTAAGTATTTT
Found at i:2742409 original size:17 final size:18
Alignment explanation
Indices: 2742370--2742416 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2742360 TGTTTTTGAG
2742370 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
2742388 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
2742405 GGAATTGGAATC
1 GGAATTGGAATC
2742417 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:2742932 original size:7 final size:7
Alignment explanation
Indices: 2742920--2742951 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2742910 GGTATTTTTC
2742920 ACCCTAA
1 ACCCTAA
2742927 ACCCTAA
1 ACCCTAA
2742934 ACCCTAA
1 ACCCTAA
2742941 ACCCTAA
1 ACCCTAA
2742948 ACCC
1 ACCC
2742952 GAACCCGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.47, G:0.00, T:0.12
Consensus pattern (7 bp):
ACCCTAA
Found at i:2746229 original size:41 final size:41
Alignment explanation
Indices: 2746169--2746376 Score: 238
Period size: 41 Copynumber: 5.1 Consensus size: 41
2746159 TACTTTAGTT
* * *
2746169 TTCAACTTGATTCGGTCATGGTAGCATAAAATAGTTCACCA
1 TTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCA
2746210 TTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCA
1 TTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCA
* * *
2746251 ATCAACTTGATTCGATTATGGTAGCATACAATAATTCATCA
1 TTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCA
* * * * * * * * **
2746292 ATCAA-TTCAATTCAATCAAGGCATCATATAATAGTTCATTA
1 TTCAACTT-GATTCGATCATGGTAGCATACAATAATTCACCA
* *
2746333 TTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCA
1 TTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCA
2746374 TTC
1 TTC
2746377 GATTCAATTC
Statistics
Matches: 139, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
40 2 0.01
41 135 0.97
42 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (41 bp):
TTCAACTTGATTCGATCATGGTAGCATACAATAATTCACCA
Found at i:2746257 original size:82 final size:82
Alignment explanation
Indices: 2746105--2746389 Score: 257
Period size: 82 Copynumber: 3.5 Consensus size: 82
2746095 TTACAAATAT
* * * * * * * * * * ****
2746105 TGGTAGCATGCAATAATTCACCATTCGATTAAATTTAGTCAAGGAAACATGCAATACTTTAGTTT
1 TGGTAGCATACAATAATTCACCATTCAATTCAATTCAATCAAGGCAGCATACAATAATTCACCAA
*
2746170 TCAACTTGATTCGGTCA
66 TCAACTTGATTCGATCA
* * * * * *
2746187 TGGTAGCATAAAATAGTTCACCATTCAACTT-GATTCGATCATGGTAGCATACAATAATTCACCA
1 TGGTAGCATACAATAATTCACCATTCAA-TTCAATTCAATCAAGGCAGCATACAATAATTCACCA
*
2746251 ATCAACTTGATTCGATTA
65 ATCAACTTGATTCGATCA
* * * * * ** *
2746269 TGGTAGCATACAATAATTCATCAATCAATTCAATTCAATCAAGGCATCATATAATAGTTCATTAT
1 TGGTAGCATACAATAATTCACCATTCAATTCAATTCAATCAAGGCAGCATACAATAATTCACCAA
*
2746334 TCAATTTGATTCGATCA
66 TCAACTTGATTCGATCA
* *
2746351 TGGTAGCATGCAATAATTCACCATTCGATTCAATTCAAT
1 TGGTAGCATACAATAATTCACCATTCAATTCAATTCAAT
2746390 TCAATCAAGG
Statistics
Matches: 161, Mismatches: 40, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
81 2 0.01
82 157 0.98
83 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (82 bp):
TGGTAGCATACAATAATTCACCATTCAATTCAATTCAATCAAGGCAGCATACAATAATTCACCAA
TCAACTTGATTCGATCA
Found at i:2746425 original size:87 final size:82
Alignment explanation
Indices: 2746169--2746454 Score: 279
Period size: 82 Copynumber: 3.4 Consensus size: 82
2746159 TACTTTAGTT
* * ** * * * * * * *
2746169 TTCAACTTGATTCGGTCATGGTAGCATAAAATAGTTCACCATTCAACTT-GATTCGATCATGGTA
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAATTCATCAATCAA-TTCAATTCAATCAAGGCA
* * *
2746233 GCATACAATAATTCACCA
65 GCATATAATAGTTCATCA
* * * * *
2746251 ATCAACTTGATTCGATTATGGTAGCATACAATAATTCATCAATCAATTCAATTCAATCAAGGCAT
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAATTCATCAATCAATTCAATTCAATCAAGGCAG
*
2746316 CATATAATAGTTCATTA
66 CATATAATAGTTCATCA
*
2746333 TTCAATTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGATTCAATTCAATTCAATCAA
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAATT---CA-TC-AATCAATTCAATTCAATCAA
2746398 GGCAGCATATACA-AGTTCATCA
61 GGCAGCATATA-ATAGTTCATCA
* *
2746420 TTCAATTTTAATTCGGTCATGGTAGCATGCAATAA
1 TTCAA-TTTGATTCGATCATGGTAGCATGCAATAA
2746455 CCAATTTATC
Statistics
Matches: 171, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
81 2 0.01
82 95 0.56
85 2 0.01
86 2 0.01
87 42 0.25
88 28 0.16
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (82 bp):
TTCAATTTGATTCGATCATGGTAGCATGCAATAATTCATCAATCAATTCAATTCAATCAAGGCAG
CATATAATAGTTCATCA
Found at i:2755222 original size:4 final size:4
Alignment explanation
Indices: 2755215--2755239 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2755205 AAATTAATTA
2755215 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2755240 TTTAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2755886 original size:13 final size:13
Alignment explanation
Indices: 2755868--2755900 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2755858 AGCATTGTGA
*
2755868 AAAGAAAATAATG
1 AAAGAAAATAAAG
2755881 AAAGAAAATAAAG
1 AAAGAAAATAAAG
2755894 AAAGAAA
1 AAAGAAA
2755901 GATGGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:2758058 original size:21 final size:21
Alignment explanation
Indices: 2758024--2758063 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2758014 CAAACATCGT
*
2758024 TTTTTGTCAAATAAATAAGTA
1 TTTTTCTCAAATAAATAAGTA
*
2758045 TTTTTCTCAGATAAATAAG
1 TTTTTCTCAAATAAATAAG
2758064 CTAAAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTTCTCAAATAAATAAGTA
Found at i:2760519 original size:161 final size:161
Alignment explanation
Indices: 2760261--2760607 Score: 421
Period size: 161 Copynumber: 2.2 Consensus size: 161
2760251 CATTTTAGAA
* * * ** * *
2760261 TACAAACGCCGCAATATATTT-ATATTAATAATTATTTTTTAGAAACATGTTCTATATTTAGCGG
1 TACAAACGCCACAATATGTTTGATATTAATAATGATTTTGCAGAAACATCTTCGATATTTAGCGG
* * * * * ** * * *
2760325 TGTTTTCTACCACAAACGCCGCAATATAATAAATATTTTGCAGCGTTTGTAGTAACAAACACCGT
66 CGTTTTCGACCACAAACGACACAATAGAATAAATATTTCACAGCATTTGTAGTAAAAAACACCAT
2760390 AATATATTTGATATATAGCGGCGTTTTTAGT
131 AATATATTTGATATATAGCGGCGTTTTTAGT
* * *
2760421 TACAAATGCCACAATATGTTTGATATTAATAATCGA-TTTGCAGAAGCATCTTCGATATTTATCG
1 TACAAACGCCACAATATGTTTGATATTAATAAT-GATTTTGCAGAAACATCTTCGATATTTAGCG
* * ***
2760485 GCGTTTTCGACCACAAATGACACAATAGAATAAATATTTCACGGCATTTGTAGTAAAAAATGTCA
65 GCGTTTTCGACCACAAACGACACAATAGAATAAATATTTCACAGCATTTGTAGTAAAAAACACCA
*
2760550 TAATATATTTGATATATAGTGGCGTTTTTAGT
130 TAATATATTTGATATATAGCGGCGTTTTTAGT
2760582 TACAAACGCCACAATA-GATTTGATAT
1 TACAAACGCCACAATATG-TTTGATAT
2760608 ATAGCGGCGT
Statistics
Matches: 157, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
160 19 0.12
161 137 0.87
162 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (161 bp):
TACAAACGCCACAATATGTTTGATATTAATAATGATTTTGCAGAAACATCTTCGATATTTAGCGG
CGTTTTCGACCACAAACGACACAATAGAATAAATATTTCACAGCATTTGTAGTAAAAAACACCAT
AATATATTTGATATATAGCGGCGTTTTTAGT
Found at i:2766039 original size:19 final size:19
Alignment explanation
Indices: 2766011--2766047 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2766001 ATCGGGAAAG
*
2766011 GGTATCGATACCAAATCAT
1 GGTATCGATACAAAATCAT
*
2766030 GGTATTGATACAAAATCA
1 GGTATCGATACAAAATCA
2766048 AAGGAAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
GGTATCGATACAAAATCAT
Found at i:2772168 original size:15 final size:15
Alignment explanation
Indices: 2772130--2772170 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2772120 CTTTCTTTTA
*
2772130 TTCTCTTTTTTCCTT
1 TTCTCTTTTTTCCAT
* *
2772145 TTTTGTTTTTTCCAT
1 TTCTCTTTTTTCCAT
2772160 TTCTCTTTTTT
1 TTCTCTTTTTT
2772171 TGAAACTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (15 bp):
TTCTCTTTTTTCCAT
Found at i:2773777 original size:28 final size:27
Alignment explanation
Indices: 2773737--2773794 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
2773727 AATATCTAGG
**
2773737 GTACCTAAAAAATTCAAAGAAAAATAA
1 GTACCTAAAAAATAAAAAGAAAAATAA
* *
2773764 GTACGTAATAAAATAAAAATAAAAATAA
1 GTACCTAA-AAAATAAAAAGAAAAATAA
2773792 GTA
1 GTA
2773795 AAACTTATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.21
Consensus pattern (27 bp):
GTACCTAAAAAATAAAAAGAAAAATAA
Found at i:2773900 original size:22 final size:22
Alignment explanation
Indices: 2773867--2773927 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
2773857 TGGTCGATCC
*
2773867 TTAATCTCAAAATAAATTGTCA
1 TTAATCTCAAAATAAATTATCA
* * * *
2773889 TTGATCTAAAAATAAACTATCC
1 TTAATCTCAAAATAAATTATCA
2773911 TTAATCTCAAAATAAAT
1 TTAATCTCAAAATAAAT
2773928 AAATAAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (22 bp):
TTAATCTCAAAATAAATTATCA
Found at i:2776185 original size:44 final size:46
Alignment explanation
Indices: 2776065--2776236 Score: 233
Period size: 45 Copynumber: 3.8 Consensus size: 46
2776055 ATCCAATATT
*
2776065 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATT-ATCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
2776112 TTACCATTTATTCTCATAAGCTCATAAGCTTATTTTACC-ATATAC
1 TTACCATTTATTATCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
2776157 TTACCATTTATT-TCATAAGCTCGTAAGCTTATTTTACCAACATAT
1 TTACCATTTATTATCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
2776202 TTGCCA-TTATTTTCGTAAGCTCGTAAGCTTATTTT
1 TTACCATTTATTATCATAAGCTCGTAAGCTTATTTT
2776237 CATGCTTGCC
Statistics
Matches: 114, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
44 30 0.26
45 48 0.42
46 24 0.21
47 12 0.11
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (46 bp):
TTACCATTTATTATCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:2778969 original size:224 final size:223
Alignment explanation
Indices: 2778550--2778997 Score: 853
Period size: 224 Copynumber: 2.0 Consensus size: 223
2778540 AGGATTCACT
2778550 CATTGTTTCTCAAAGTGTTTCAGGTAAAAGAAAACACTCAAGCTAGAACCAAACATGACATTACC
1 CATTGTTTCTCAAAGTGTTTCAGGTAAAAGAAAACACTCAAGCTAGAACCAAACATGACATTACC
2778615 ATAAGATTTTAAGTAAATCAAGTCTCCATCACTAAAGTGAACAACATGCATTAATCAAAGGGTCT
66 ATAAGATTTTAAGTAAATCAAGTCTCCATCACTAAAGTGAACAACATGCATTAATCAAAGGGTCT
*
2778680 TTAAAAAGGGTGTAATGGGGGGGTTAGGTTAAGGTAGGTAAAAAGAACAAAAAATGGTGAATATC
131 TTAAAAAGGGTGTAAT-GGGGGCTTAGGTTAAGGTAGGTAAAAAGAACAAAAAATGGTGAATATC
2778745 AAGACAATAGATGCAAAACATATCAGCCC
195 AAGACAATAGATGCAAAACATATCAGCCC
2778774 CATTGTTTCTCAAAGTGTTTCAGGTAAAAGAAAACACTCAAGCTAGAACCAAACATGACATTACC
1 CATTGTTTCTCAAAGTGTTTCAGGTAAAAGAAAACACTCAAGCTAGAACCAAACATGACATTACC
2778839 ATAAGATTTTAAGTAAATCAAGTCTCCATCACTAAAGTGAACAACATGCATTAATCAAAGGGTCT
66 ATAAGATTTTAAGTAAATCAAGTCTCCATCACTAAAGTGAACAACATGCATTAATCAAAGGGTCT
2778904 TTAAAAAGGGTGTAAT-GGGGCTTAGGTTAAGGTAGGTAAAAAGAACAAAAATATGGTGAAATAT
131 TTAAAAAGGGTGTAATGGGGGCTTAGGTTAAGGTAGGTAAAAAGAACAAAAA-ATGGTG-AATAT
2778968 CAAGACAATAGATGCAAAACATATCAGCCC
194 CAAGACAATAGATGCAAAACATATCAGCCC
2778998 AAACAATGCA
Statistics
Matches: 221, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
222 34 0.15
223 6 0.03
224 181 0.82
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (223 bp):
CATTGTTTCTCAAAGTGTTTCAGGTAAAAGAAAACACTCAAGCTAGAACCAAACATGACATTACC
ATAAGATTTTAAGTAAATCAAGTCTCCATCACTAAAGTGAACAACATGCATTAATCAAAGGGTCT
TTAAAAAGGGTGTAATGGGGGCTTAGGTTAAGGTAGGTAAAAAGAACAAAAAATGGTGAATATCA
AGACAATAGATGCAAAACATATCAGCCC
Found at i:2780051 original size:12 final size:12
Alignment explanation
Indices: 2780034--2780076 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2780024 CCTTAGTACC
*
2780034 TAAAAATTAAAA
1 TAAAAAATAAAA
2780046 TAAAAAATAAAA
1 TAAAAAATAAAA
*
2780058 TAAAGAAATGAAA
1 TAAA-AAATAAAA
2780071 TGAAAA
1 T-AAAA
2780077 GAAAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 15 0.56
13 9 0.33
14 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:2781510 original size:22 final size:22
Alignment explanation
Indices: 2781480--2781543 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
2781470 AATTTTAGTG
*
2781480 CAGAGGGAATCGATACCCCCTTGA
1 CAGA-GGAATCGATACCCCC-TCA
* *
2781504 -AGAGGAACCGATTCCCCC-CA
1 CAGAGGAATCGATACCCCCTCA
*
2781524 CAGGGGAATCGATACCCCCT
1 CAGAGGAATCGATACCCCCT
2781544 GAGGGTTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 13 0.41
23 3 0.09
ACGTcount: A:0.28, C:0.34, G:0.23, T:0.14
Consensus pattern (22 bp):
CAGAGGAATCGATACCCCCTCA
Found at i:2783152 original size:18 final size:18
Alignment explanation
Indices: 2783129--2783169 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2783119 AGAACAGCAT
*
2783129 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
2783147 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
2783165 GAGGA
1 GAGGA
2783170 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.27, G:0.29, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:2786276 original size:52 final size:52
Alignment explanation
Indices: 2786198--2786301 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
2786188 ATAACGATTA
2786198 TCCTGAAGTGATCAGTGAACATAATATGAAGAATCACGTCTTTTTAAAGAAG
1 TCCTGAAGTGATCAGTGAACATAATATGAAGAATCACGTCTTTTTAAAGAAG
2786250 TCCTGAAGTGATCAGTGAACATAATATGAAGAATCACGTCTTTTTAAAGAAG
1 TCCTGAAGTGATCAGTGAACATAATATGAAGAATCACGTCTTTTTAAAGAAG
2786302 CCAATGTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (52 bp):
TCCTGAAGTGATCAGTGAACATAATATGAAGAATCACGTCTTTTTAAAGAAG
Found at i:2787249 original size:38 final size:38
Alignment explanation
Indices: 2787151--2787270 Score: 106
Period size: 38 Copynumber: 3.2 Consensus size: 38
2787141 TTTGTCTCAC
* * * * *
2787151 TTGAGACTCGTTTCCCTT-AGAAC-AAAATTTGTCTTCT
1 TTGAGACTCATTTCTCTTGA-AACAAAAATATATCTCCT
2787188 TTGAGA-TCATTTCTCTTGAAACAAAAAT-TCATCTCCT
1 TTGAGACTCATTTCTCTTGAAACAAAAATAT-ATCTCCT
* * *
2787225 TTCAGACTCATTTGC-CTTGCAACAAAAATATATCTCCC
1 TTGAGACTCATTT-CTCTTGAAACAAAAATATATCTCCT
2787263 TTGAGACT
1 TTGAGACT
2787271 TGTTCCCTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
36 13 0.19
37 22 0.32
38 32 0.46
39 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (38 bp):
TTGAGACTCATTTCTCTTGAAACAAAAATATATCTCCT
Found at i:2787612 original size:38 final size:38
Alignment explanation
Indices: 2787435--2787613 Score: 107
Period size: 38 Copynumber: 4.7 Consensus size: 38
2787425 GACTTGATTA
* * * * *
2787435 CCTTGAAGCACAAATTTTATCTCCCATGAGATTCGTTTT
1 CCTTGAAACACAAA-TTTATTTCCCTTGAGACTCATTTT
* * * *
2787474 CCTTGGAATA-AAATTT-TGTCTCACTTGAGACTC-GTTT
1 CCTTGAAACACAAATTTAT-T-TCCCTTGAGACTCATTTT
* ** ** * *
2787511 CACTTGAAACACTAATCCATTTCAATT-ATGACTTATTTC
1 C-CTTGAAACACAAATTTATTTCCCTTGA-GACTCATTTT
* *
2787550 CCTTAAAACACAAATTT-TCCTCCCTTGAGACTCATTTT
1 CCTTGAAACACAAATTTAT-TTCCCTTGAGACTCATTTT
2787588 CCTTGAAACACAAATTTATTTCCCTT
1 CCTTGAAACACAAATTTATTTCCCTT
2787614 ATGAAACAAA
Statistics
Matches: 102, Mismatches: 28, Indels: 21
0.68 0.19 0.14
Matches are distributed among these distances:
36 1 0.01
37 9 0.09
38 75 0.74
39 16 0.16
40 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (38 bp):
CCTTGAAACACAAATTTATTTCCCTTGAGACTCATTTT
Found at i:2787882 original size:37 final size:37
Alignment explanation
Indices: 2787776--2787883 Score: 126
Period size: 37 Copynumber: 2.9 Consensus size: 37
2787766 ATAATTTTGC
* * ** *
2787776 CTCCCTTAAGACTATTTTTCTTGAAACAAAAATTTGT
1 CTCCCTTAAGACTATTTTCCTTGACACAAATTTTTAT
* * *
2787813 TTCCCTTAAGACAATTTTCCTTAACACAAATTTTTAT
1 CTCCCTTAAGACTATTTTCCTTGACACAAATTTTTAT
* *
2787850 CTCCCTTAAGACTATTTCCCTTGACACTAATTTT
1 CTCCCTTAAGACTATTTTCCTTGACACAAATTTT
2787884 GTCTTTCTTG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (37 bp):
CTCCCTTAAGACTATTTTCCTTGACACAAATTTTTAT
Found at i:2788372 original size:22 final size:22
Alignment explanation
Indices: 2788335--2788396 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
2788325 CTTGAAACAA
2788335 TTCCAATCTCCCTTTGAGACAT
1 TTCCAATCTCCCTTTGAGACAT
2788357 TTCCAATCTCCCTTTGAGACAT
1 TTCCAATCTCCCTTTGAGACAT
*
2788379 TTCCAATCTCTC-TTGAGA
1 TTCCAATCTCCCTTTGAGA
2788397 TAAATATGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 6 0.15
22 33 0.85
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.37
Consensus pattern (22 bp):
TTCCAATCTCCCTTTGAGACAT
Found at i:2789833 original size:73 final size:73
Alignment explanation
Indices: 2789712--2789859 Score: 201
Period size: 73 Copynumber: 2.0 Consensus size: 73
2789702 AGATAATTCC
* *
2789712 TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAATTATTAAAACTAAACTACCTAAGACAA
1 TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAATTATTAAAACTAAAATACCTAAAACAA
2789777 AGATAAAA
66 AGATAAAA
* * * *
2789785 TAAAATAATAT-TCTAAATCCTAATTAAAATAC-TAACATCTATTTAAACTAAAATGCCTAAAAC
1 TAAAATAATATCT-TAAATCCTAATTAAAACACTTAAAAT-TATTAAAACTAAAATACCTAAAAC
*
2789848 GAAGATAAAA
64 AAAGATAAAA
2789858 TA
1 TA
2789860 TAATGTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
72 6 0.09
73 60 0.91
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (73 bp):
TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAATTATTAAAACTAAAATACCTAAAACAA
AGATAAAA
Found at i:2794379 original size:14 final size:15
Alignment explanation
Indices: 2794362--2794390 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2794352 ATATAATGAC
2794362 AAATTTT-GTAACTA
1 AAATTTTAGTAACTA
2794376 AAATTTTAGTAACTA
1 AAATTTTAGTAACTA
2794391 TGACATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
AAATTTTAGTAACTA
Found at i:2796559 original size:22 final size:22
Alignment explanation
Indices: 2796507--2796559 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
2796497 TTTTTATCCC
*
2796507 TTAATTATTTTATTTTACTAACT
1 TTAATT-TTTTATTTTACTAAAT
**
2796530 TTTGTTTTTTATTTCTAC-AAAT
1 TTAATTTTTTATTT-TACTAAAT
2796552 TTAATTTT
1 TTAATTTT
2796560 GGGTCTTTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (22 bp):
TTAATTTTTTATTTTACTAAAT
Found at i:2798177 original size:89 final size:90
Alignment explanation
Indices: 2798020--2798291 Score: 361
Period size: 89 Copynumber: 3.0 Consensus size: 90
2798010 ACCTTGGGTC
* * * * * *
2798020 TATAGGGTTACCCTAAGAACACAACAAAGGGAACCAACCTAAGGATATACCTTGAGGCCTATTGG
1 TATA-GGTTACCTTAAGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTATGGG
2798085 CCTACCCAAGGATATCCTTAGATCCG
65 CCTACCCAAGGATATCCTTAGATCCG
* * * * *
2798111 TATA-GTTACCTTAAGCACATAGTAAAGGAAACCAACCTAAGTATATGCTTTGGGGCCTATGGGC
1 TATAGGTTACCTTAAGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTATGGGC
*
2798175 CTACCTAAGGATATCCTTAGAT-C-
66 CTACCCAAGGATATCCTTAGATCCG
*
2798198 TATAGGGTTACCTTAAGCACACAGCAAAGGTAACCAACCTAAGGATATACCTTGGGGCCTATGGG
1 TATA-GGTTACCTTAAGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTATGGG
* * *
2798263 CCTACGCAAGGGTATCCTTATATCCG
65 CCTACCCAAGGATATCCTTAGATCCG
2798289 TAT
1 TAT
2798292 GGACTTACCA
Statistics
Matches: 155, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
87 4 0.03
88 1 0.01
89 142 0.92
90 1 0.01
91 7 0.05
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (90 bp):
TATAGGTTACCTTAAGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTATGGGC
CTACCCAAGGATATCCTTAGATCCG
Found at i:2806775 original size:20 final size:20
Alignment explanation
Indices: 2806750--2806878 Score: 181
Period size: 20 Copynumber: 6.5 Consensus size: 20
2806740 TTTCCCTCGA
2806750 ATTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCTGGGTC
2806770 ATTTGTAAAGCCT-TCGGGTC
1 ATTTGTAAAGCCTCT-GGGTC
2806790 ATTTGTAAAGCCT-TAGGGTC
1 ATTTGTAAAGCCTCT-GGGTC
*
2806810 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCTGGGTC
*
2806830 ATTTGTAAAGCCTATGGGTC
1 ATTTGTAAAGCCTCTGGGTC
* * *
2806850 ATTTGTAAAGCCTCCGAGTA
1 ATTTGTAAAGCCTCTGGGTC
2806870 ATTTGTAAA
1 ATTTGTAAA
2806879 TCCTTAAGGT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 98 0.99
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATTTGTAAAGCCTCTGGGTC
Found at i:2806794 original size:40 final size:39
Alignment explanation
Indices: 2806750--2806883 Score: 205
Period size: 40 Copynumber: 3.4 Consensus size: 39
2806740 TTTCCCTCGA
*
2806750 ATTTGTAAAGCCTCTGGGTCATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCT-TGGGTCATTTGTAAAGCCTCCGGGTC
2806790 ATTTGTAAAGCCTTAGGGTCATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTT-GGGTCATTTGTAAAGCCTCCGGGTC
* *
2806830 ATTTGTAAAGCCTATGGGTCATTTGTAAAGCCTCCGAGTA
1 ATTTGTAAAGCCT-TGGGTCATTTGTAAAGCCTCCGGGTC
*
2806870 ATTTGTAAATCCTT
1 ATTTGTAAAGCCTT
2806884 AAGGTCATCT
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 2 0.02
40 85 0.97
41 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (39 bp):
ATTTGTAAAGCCTTGGGTCATTTGTAAAGCCTCCGGGTC
Found at i:2806849 original size:60 final size:60
Alignment explanation
Indices: 2806750--2806862 Score: 201
Period size: 60 Copynumber: 1.9 Consensus size: 60
2806740 TTTCCCTCGA
*
2806750 ATTTGTAAAGCCTCTGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTAGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTAGGGTC
2806810 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTAT-GGGTCATTTGTAAAGCCT
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCT-TCGGGTCATTTGTAAAGCCT
2806863 CCGAGTAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (60 bp):
ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTAGGGTC
Found at i:2807072 original size:36 final size:36
Alignment explanation
Indices: 2807023--2807196 Score: 195
Period size: 36 Copynumber: 4.8 Consensus size: 36
2807013 TTTTCAAGTC
* *
2807023 AATTCAGCCTTCACGGAAGAGTAGTGAAGAAAATCA
1 AATTCAACCTTCACGGAAGAGTAGTGAAGTAAATCA
* *
2807059 AATTCAACTTTCACGGAAGAGTAGTGAAGTCAATCA
1 AATTCAACCTTCACGGAAGAGTAGTGAAGTAAATCA
** * * * **
2807095 TTTTCAGCCTTCACAGAAGAGTGGTGAACCAAATCA
1 AATTCAACCTTCACGGAAGAGTAGTGAAGTAAATCA
* * *
2807131 AATTCAACCTTCACGGAAAAGTAGTGAAGTCAATCG
1 AATTCAACCTTCACGGAAGAGTAGTGAAGTAAATCA
** *
2807167 TTTTCAACCTTCACAGAAGAGTAGTGAAGT
1 AATTCAACCTTCACGGAAGAGTAGTGAAGT
2807197 TATTCAACCT
Statistics
Matches: 111, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 111 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (36 bp):
AATTCAACCTTCACGGAAGAGTAGTGAAGTAAATCA
Found at i:2807130 original size:72 final size:72
Alignment explanation
Indices: 2807025--2807194 Score: 268
Period size: 72 Copynumber: 2.4 Consensus size: 72
2807015 TTCAAGTCAA
* * * *
2807025 TTCAGCCTTCACGGAAGAGTAGTGAAGAAAATCAAATTCAACTTTCACGGAAGAGTAGTGAAGTC
1 TTCAGCCTTCACAGAAGAGTAGTGAACAAAATCAAATTCAACCTTCACGGAAAAGTAGTGAAGTC
2807090 AATCATT
66 AATCATT
* *
2807097 TTCAGCCTTCACAGAAGAGTGGTGAACCAAATCAAATTCAACCTTCACGGAAAAGTAGTGAAGTC
1 TTCAGCCTTCACAGAAGAGTAGTGAACAAAATCAAATTCAACCTTCACGGAAAAGTAGTGAAGTC
*
2807162 AATCGTT
66 AATCATT
*
2807169 TTCAACCTTCACAGAAGAGTAGTGAA
1 TTCAGCCTTCACAGAAGAGTAGTGAA
2807195 GTTATTCAAC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (72 bp):
TTCAGCCTTCACAGAAGAGTAGTGAACAAAATCAAATTCAACCTTCACGGAAAAGTAGTGAAGTC
AATCATT
Found at i:2810585 original size:24 final size:24
Alignment explanation
Indices: 2810530--2810607 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
2810520 AACAAAAAAG
*
2810530 GTAGTATCGGTACAACT--ACTAA
1 GTAGTATCGGTACTACTACACTAA
2810552 G-AGTATCGGTACTACTACACTAA
1 GTAGTATCGGTACTACTACACTAA
2810575 GTAGTATCGGTACTACTACACTAA
1 GTAGTATCGGTACTACTACACTAA
2810599 GTAGTATCG
1 GTAGTATCG
2810608 ATGCCAATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
21 14 0.27
22 1 0.02
23 6 0.12
24 31 0.60
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (24 bp):
GTAGTATCGGTACTACTACACTAA
Found at i:2810710 original size:74 final size:76
Alignment explanation
Indices: 2810577--2810740 Score: 199
Period size: 74 Copynumber: 2.2 Consensus size: 76
2810567 TACACTAAGT
* *
2810577 AGTATCGGTACTACTACACTAAGTAGTATCGATGCCAATATATAGTATCAATACCATTTTAGCAT
1 AGTATCGGTACTACTACACTAAGTAGTATCGATGACAATAAATAGTATCAATACCATTTTAGCAT
2810642 TATGTTTTGAC
66 TATGTTTTGAC
* *** *
2810653 AGTATCGGTACTACT-TACTAAGTAGTATCGAT-ATTGTAAATAGTAT-AGGTACCATTTTAGCA
1 AGTATCGGTACTACTACACTAAGTAGTATCGATGACAATAAATAGTATCA-ATACCATTTTAGCA
* *
2810715 TTTTGTTTTGAT
65 TTATGTTTTGAC
* *
2810727 GGTATCAGTACTAC
1 AGTATCGGTACTAC
2810741 ATAGCAGTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 1 0.01
74 44 0.58
75 16 0.21
76 15 0.20
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (76 bp):
AGTATCGGTACTACTACACTAAGTAGTATCGATGACAATAAATAGTATCAATACCATTTTAGCAT
TATGTTTTGAC
Found at i:2811005 original size:3 final size:3
Alignment explanation
Indices: 2810992--2811025 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2810982 CTATGCTTTA
*
2810992 ATT ATTT ATT ATT ATT CTT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2811026 TTCTTAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2811209 original size:14 final size:14
Alignment explanation
Indices: 2811180--2811218 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2811170 ATATGCTCTT
2811180 AATAAT-ATTATTA
1 AATAATAATTATTA
*
2811193 AATAATAATTTTTA
1 AATAATAATTATTA
2811207 AATAAATAATTA
1 AAT-AATAATTA
2811219 ATTTAGGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 9 0.41
15 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAATAATTATTA
Found at i:2814972 original size:22 final size:22
Alignment explanation
Indices: 2814945--2814987 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2814935 TAAAATATAT
* *
2814945 TTTTAGTTATCATAACCAATTA
1 TTTTAGTTATAATAACAAATTA
2814967 TTTTAGTTATAATAACAAATT
1 TTTTAGTTATAATAACAAATT
2814988 TAAATAAAAA
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:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
TTTTAGTTATAATAACAAATTA
Found at i:2815111 original size:32 final size:32
Alignment explanation
Indices: 2815066--2815193 Score: 141
Period size: 32 Copynumber: 3.9 Consensus size: 32
2815056 TTTCTTCTAA
* *
2815066 TATTTTGTGAAAATAAAAAATTGTGACAAATT
1 TATTTAGTCAAAATAAAAAATTGTGACAAATT
2815098 TATTTAGTCAAAATAAAAAATTGTGACAAATT
1 TATTTAGTCAAAATAAAAAATTGTGACAAATT
* * * *
2815130 TATTTAATCAAAATAACAATTTGTAACAAATAT
1 TATTTAGTCAAAATAAAAAATTGTGACAAAT-T
* **
2815163 TAATTT-CTCATCATAAAAAAATTGTGACAAA
1 T-ATTTAGTCAAAAT-AAAAAATTGTGACAAA
2815194 AAAATATTCT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
32 57 0.70
33 7 0.09
34 17 0.21
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (32 bp):
TATTTAGTCAAAATAAAAAATTGTGACAAATT
Found at i:2815247 original size:32 final size:32
Alignment explanation
Indices: 2815077--2815248 Score: 136
Period size: 32 Copynumber: 5.2 Consensus size: 32
2815067 ATTTTGTGAA
* *
2815077 AATAAAAAATTGTGACAAATTTATTTAGTCAA
1 AATAAAAAATTGTGACAAAATTATTTAGTCAC
* * *
2815109 AATAAAAAATTGTGACAAATTTATTTAATCAA
1 AATAAAAAATTGTGACAAAATTATTTAGTCAC
* * * *
2815141 AATAACAATTTGTAACAAATATTAATTT-CTCATC
1 AATAAAAAATTGTGACAAA-ATT-ATTTAGTCA-C
* *
2815175 -ATAAAAAAATTGTGACAAAAAAATATTCT-TTCAC
1 AAT-AAAAAATTGTGAC--AAAATTATT-TAGTCAC
2815209 AATAAAAAATTGT-ATCAAAATTATTTAGTCAC
1 AATAAAAAATTGTGA-CAAAATTATTTAGTCAC
*
2815241 AGTAAAAA
1 AATAAAAA
2815249 GTTATAAAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
31 1 0.01
32 66 0.57
33 8 0.07
34 29 0.25
35 8 0.07
36 3 0.03
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.33
Consensus pattern (32 bp):
AATAAAAAATTGTGACAAAATTATTTAGTCAC
Found at i:2817046 original size:21 final size:21
Alignment explanation
Indices: 2817020--2817066 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2817010 GCTTTGGAAT
*
2817020 TTTTCCTGGGATGCAACCAGC
1 TTTTCCTGGGATGCAACCAAC
*
2817041 TTTTCCTGGGATGTAACCAAC
1 TTTTCCTGGGATGCAACCAAC
2817062 TTTTC
1 TTTTC
2817067 TTGTGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TTTTCCTGGGATGCAACCAAC
Found at i:2818523 original size:22 final size:22
Alignment explanation
Indices: 2818498--2818542 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2818488 GATGAAATTG
*
2818498 AAAACATAGAATAA-AATAAAAT
1 AAAACA-AGAAAAATAATAAAAT
*
2818520 AAAATAAGAAAAATAATAAAAT
1 AAAACAAGAAAAATAATAAAAT
2818542 A
1 A
2818543 TTAAATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (22 bp):
AAAACAAGAAAAATAATAAAAT
Found at i:2819052 original size:12 final size:12
Alignment explanation
Indices: 2819035--2819059 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2819025 TTTGGAATTG
2819035 AGCCTTCGCCTT
1 AGCCTTCGCCTT
2819047 AGCCTTCGCCTT
1 AGCCTTCGCCTT
2819059 A
1 A
2819060 AAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.40, G:0.16, T:0.32
Consensus pattern (12 bp):
AGCCTTCGCCTT
Found at i:2819363 original size:82 final size:84
Alignment explanation
Indices: 2819273--2819452 Score: 235
Period size: 82 Copynumber: 2.2 Consensus size: 84
2819263 GATAATTCTT
* * *
2819273 AAAATAATATCTTAAATCCTAATTAAAACACT-TA-CTATTTAAACTAAACTACCTAAAACAAAG
1 AAAATAATATCCTAAATCCTAATTAAAACACTACATCTATTTAAACTAAAATACCTAAAACAAAG
2819336 ATAAAATAAAATAATATTC
66 ATAAAATAAAATAATATTC
* * *
2819355 AAAATAATATCCTAAATCCTAATTAAAATACTAACATCTATTTTACCTAAAATACCTAAAACAAA
1 AAAATAATATCCTAAATCCTAATTAAAACACT-ACATCTATTTAAACTAAAATACCTAAAACAAA
* *
2819420 GATAAAAT---ATAATGTTT
65 GATAAAATAAAATAATATTC
*
2819437 AAAATATTATCCTAAA
1 AAAATAATATCCTAAA
2819453 ACTTGAGTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 52 0.60
84 1 0.01
85 33 0.38
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (84 bp):
AAAATAATATCCTAAATCCTAATTAAAACACTACATCTATTTAAACTAAAATACCTAAAACAAAG
ATAAAATAAAATAATATTC
Found at i:2820489 original size:2 final size:2
Alignment explanation
Indices: 2820482--2820520 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2820472 GAGAAAATGT
2820482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2820521 GAATTTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2823584 original size:133 final size:137
Alignment explanation
Indices: 2823339--2823743 Score: 451
Period size: 133 Copynumber: 2.9 Consensus size: 137
2823329 GGCAATTAAT
* * * * *
2823339 TATCACAAAAAATGTACATTTCTCATAAGCAAAATAATGCATCATGGCAGAAACTTTTCAGTGCC
1 TATCACAAAAAACGTGCATTTCTCATAGGCAAAATAATGCACCAT-GCAAAAACTTTTCAGTGCC
* * * * * *
2823404 CAATTAATTATTTTTAGCAACTTTTTAATGATATATCAACTTATTTCAGCAAACTTCTCAGTG-T
65 CAATTAATTATCTTCAACAACTTTTCAATGATATATCAACTCATTTCAGCAAACTTTTCAGTGAT
*
2823468 -TGA-T-A
130 ATCACTCA
* * *
2823473 TATCACAAAAAA-GTGCATTTCTCATAGGAAAAATAATGCACCATGACAAAAACTTTTCATTTCC
1 TATCACAAAAAACGTGCATTTCTCATAGGCAAAATAATGCACCATG-CAAAAACTTTTCAGTGCC
* *
2823537 CAATTAATTATCTTCAACAACTTTTCAATGATATATCAACTCATTTCAGCATACTTTTTAGTGCT
65 CAATTAATTATCTTCAACAACTTTTCAATGATATATCAACTCATTTCAGCAAACTTTTCA--G-T
2823602 GATATATCACTTCA
127 G--ATATCAC-TCA
* * *
2823616 TATCACAAAAAACGTGCATTTCTCATAGGCAAAATAATGTACCATCGCATAAACTTTTCAGTGGC
1 TATCACAAAAAACGTGCATTTCTCATAGGCAAAATAATGCACCAT-GCAAAAACTTTTCAGTGCC
* * * * * * *
2823681 CAATTATTTGTCTTCAATAACTTCTCAGTGACATATCAACTCATTTCAGTAAACTTTTCAGTG
65 CAATTAATTATCTTCAACAACTTTTCAATGATATATCAACTCATTTCAGCAAACTTTTCAGTG
2823744 GCCAATTAAT
Statistics
Matches: 227, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
132 1 0.00
133 95 0.42
134 12 0.05
135 1 0.00
136 2 0.01
139 1 0.00
140 2 0.01
141 2 0.01
142 2 0.01
143 13 0.06
144 95 0.42
145 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (137 bp):
TATCACAAAAAACGTGCATTTCTCATAGGCAAAATAATGCACCATGCAAAAACTTTTCAGTGCCC
AATTAATTATCTTCAACAACTTTTCAATGATATATCAACTCATTTCAGCAAACTTTTCAGTGATA
TCACTCA
Found at i:2823709 original size:32 final size:32
Alignment explanation
Indices: 2823667--2823775 Score: 96
Period size: 32 Copynumber: 3.4 Consensus size: 32
2823657 CCATCGCATA
* *
2823667 AACTTTTCAGTGGCCAATTATTTGTCTTCAAT
1 AACTTCTCAGTGGCCAATTAATTGTCTTCAAT
* * ** *
2823699 AACTTCTCAGT-GACATATCAACTCAT-TTCAGT
1 AACTTCTCAGTGGCCA-ATTAA-TTGTCTTCAAT
*
2823731 AAACTTTTCAGTGGCCAATTAATTGTCTTCAAT
1 -AACTTCTCAGTGGCCAATTAATTGTCTTCAAT
*
2823764 AACTTCTTAGTG
1 AACTTCTCAGTG
2823776 ACACATCAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
31 3 0.05
32 30 0.53
33 21 0.37
34 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (32 bp):
AACTTCTCAGTGGCCAATTAATTGTCTTCAAT
Found at i:2823742 original size:33 final size:32
Alignment explanation
Indices: 2823699--2823808 Score: 91
Period size: 33 Copynumber: 3.4 Consensus size: 32
2823689 TGTCTTCAAT
*
2823699 AACTTCTCAGTGACATATCAACTCATTTCAGTA
1 AACTTTTCAGTGACA-ATCAACTCATTTCAGTA
* * ** *
2823732 AACTTTTCAGTGGCCAATTAA-TTGTCTTCAAT-
1 AACTTTTCAGT-GACAATCAACTCAT-TTCAGTA
2823764 AACTTCTT-AGTGACACATCAACTCATTTCAGTA
1 AACTT-TTCAGTGACA-ATCAACTCATTTCAGTA
*
2823797 AACTTTTTAGTG
1 AACTTTTCAGTG
2823809 TTGGTATATC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
31 3 0.05
32 21 0.36
33 32 0.54
34 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (32 bp):
AACTTTTCAGTGACAATCAACTCATTTCAGTA
Found at i:2823745 original size:65 final size:65
Alignment explanation
Indices: 2823665--2823808 Score: 252
Period size: 65 Copynumber: 2.2 Consensus size: 65
2823655 TACCATCGCA
* *
2823665 TAAACTTTTCAGTGGCCAATTATTTGTCTTCAATAACTTCTCAGTGACATATCAACTCATTTCAG
1 TAAACTTTTCAGTGGCCAATTAATTGTCTTCAATAACTTCTCAGTGACACATCAACTCATTTCAG
*
2823730 TAAACTTTTCAGTGGCCAATTAATTGTCTTCAATAACTTCTTAGTGACACATCAACTCATTTCAG
1 TAAACTTTTCAGTGGCCAATTAATTGTCTTCAATAACTTCTCAGTGACACATCAACTCATTTCAG
*
2823795 TAAACTTTTTAGTG
1 TAAACTTTTCAGTG
2823809 TTGGTATATC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 75 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (65 bp):
TAAACTTTTCAGTGGCCAATTAATTGTCTTCAATAACTTCTCAGTGACACATCAACTCATTTCAG
Found at i:2823895 original size:16 final size:16
Alignment explanation
Indices: 2823874--2823915 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
2823864 ACCATGTCAG
2823874 AAACTTTTCAGTTCAC
1 AAACTTTTCAGTTCAC
2823890 AAACTTTTCAGTTCAC
1 AAACTTTTCAGTTCAC
2823906 AAACTTTTCA
1 AAACTTTTCA
2823916 TCAACCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (16 bp):
AAACTTTTCAGTTCAC
Found at i:2825596 original size:30 final size:30
Alignment explanation
Indices: 2825533--2825598 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2825523 AGAATTGGAA
* * * *
2825533 GAACCGGCTGAAAATCGGGAAAACTGGGGT
1 GAACCGACTGAAAACCGGCAAAACCGGGGT
**
2825563 GAACCGACTGAAAACCGGCAAAACCGGTTT
1 GAACCGACTGAAAACCGGCAAAACCGGGGT
2825593 GAACCG
1 GAACCG
2825599 CCGATTCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.30, T:0.12
Consensus pattern (30 bp):
GAACCGACTGAAAACCGGCAAAACCGGGGT
Found at i:2825845 original size:24 final size:24
Alignment explanation
Indices: 2825816--2825895 Score: 142
Period size: 24 Copynumber: 3.3 Consensus size: 24
2825806 TAGAAGTTCG
* *
2825816 ATTGAAGCCTAAAATTCGAGCTCA
1 ATTGAAGCCTGAAATTTGAGCTCA
2825840 ATTGAAGCCTGAAATTTGAGCTCA
1 ATTGAAGCCTGAAATTTGAGCTCA
2825864 ATTGAAGCCTGAAATTTGAGCTCA
1 ATTGAAGCCTGAAATTTGAGCTCA
2825888 ATTGAAGC
1 ATTGAAGC
2825896 GAAAGAATAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (24 bp):
ATTGAAGCCTGAAATTTGAGCTCA
Found at i:2831503 original size:19 final size:19
Alignment explanation
Indices: 2831479--2831547 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
2831469 AATCCAAAAT
2831479 GGGTATCGATACCGTGGAA
1 GGGTATCGATACCGTGGAA
2831498 GGGTATCGATACCGTGGAA
1 GGGTATCGATACCGTGGAA
*
2831517 GGGTATCGATACCATGGAA
1 GGGTATCGATACCGTGGAA
2831536 GGGTATCGATAC
1 GGGTATCGATAC
2831548 TACCGGCATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
GGGTATCGATACCGTGGAA
Found at i:2832209 original size:13 final size:14
Alignment explanation
Indices: 2832192--2832224 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2832182 GAAGCTATAA
*
2832192 GAATATGTCTATGT
1 GAATATGACTATGT
2832206 -AATATGACTATGT
1 GAATATGACTATGT
2832219 GAATAT
1 GAATAT
2832225 ATGACAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (14 bp):
GAATATGACTATGT
Found at i:2833715 original size:73 final size:73
Alignment explanation
Indices: 2833635--2833781 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
2833625 TTTGTTTATG
**
2833635 ATGCAAATATTAAAGTTGAATATTGATATTCATTTTGAGACGTCTAAATTGAAGTAATAAGTCGT
1 ATGCAAATATTAAAGTTGAATATTGATATTCATTTTGAGACACCTAAATTGAAGTAATAAGTCGT
2833700 TAAAGTGA
66 TAAAGTGA
** * *
2833708 ATGCAAATATTAAAGTTGAATATTGATATTCATTTTGAGACACCTTGATTGGAGTAATAAGTTGT
1 ATGCAAATATTAAAGTTGAATATTGATATTCATTTTGAGACACCTAAATTGAAGTAATAAGTCGT
2833773 TAAAGTGA
66 TAAAGTGA
2833781 A
1 A
2833782 CTTAGTTATG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (73 bp):
ATGCAAATATTAAAGTTGAATATTGATATTCATTTTGAGACACCTAAATTGAAGTAATAAGTCGT
TAAAGTGA
Found at i:2837751 original size:17 final size:17
Alignment explanation
Indices: 2837729--2837761 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2837719 ATTTACCTAC
2837729 CTTTTTCTTTGGTCTAT
1 CTTTTTCTTTGGTCTAT
2837746 CTTTTTCTTTGGTCTA
1 CTTTTTCTTTGGTCTA
2837762 ATATAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.12, T:0.64
Consensus pattern (17 bp):
CTTTTTCTTTGGTCTAT
Found at i:2838811 original size:29 final size:29
Alignment explanation
Indices: 2838778--2838965 Score: 184
Period size: 29 Copynumber: 6.4 Consensus size: 29
2838768 TTTGTCTCCT
* * *
2838778 TTTATTATAATTTATAAAAGGTTTTATCC
1 TTTATTGTAATTTATAAAAGGTTTTGTAC
*
2838807 TTTATTGTAATTTATAAATA-GTTTTGTAT
1 TTTATTGTAATTTATAAA-AGGTTTTGTAC
**
2838836 TTTATTGTAATTTATAAATTGTTTTGTAC
1 TTTATTGTAATTTATAAAAGGTTTTGTAC
**
2838865 TTTATTGTAATTTATAAATTGTTTTGTAC
1 TTTATTGTAATTTATAAAAGGTTTTGTAC
* * * *
2838894 TTTATTGTAGTTTATAACAA-ATTTCGTCC
1 TTTATTGTAATTTATAA-AAGGTTTTGTAC
* **
2838923 TTTATTATAATTTATAAAATAATTTTGT-C
1 TTTATTGTAATTTATAAAA-GGTTTTGTAC
2838952 TTTTATTGTAATTT
1 -TTTATTGTAATTT
2838966 GATGATTTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.01
29 116 0.84
30 20 0.14
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (29 bp):
TTTATTGTAATTTATAAAAGGTTTTGTAC
Found at i:2838860 original size:58 final size:57
Alignment explanation
Indices: 2838777--2838965 Score: 234
Period size: 58 Copynumber: 3.2 Consensus size: 57
2838767 ATTTGTCTCC
* *
2838777 TTTTATTATAATTTATAAAAGGTTTTATCCTTTATTGTAATTTATAAATAGTTTTGTA
1 TTTTATTGTAATTTATAAAA-GTTTTGTCCTTTATTGTAATTTATAAATAGTTTTGTA
* * *
2838835 TTTTATTGTAATTTATAAATTGTTTTGTACTTTATTGTAATTTATAAATTGTTTTGTA
1 TTTTATTGTAATTTATAAA-AGTTTTGTCCTTTATTGTAATTTATAAATAGTTTTGTA
* * * * * * *
2838893 CTTTATTGTAGTTTATAACAAATTTCGTCCTTTATTATAATTTATAAAATAATTTTGTC
1 TTTTATTGTAATTTATAA-AAGTTTTGTCCTTTATTGTAATTTAT-AAATAGTTTTGTA
2838952 TTTTATTGTAATTT
1 TTTTATTGTAATTT
2838966 GATGATTTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
58 88 0.79
59 23 0.21
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (57 bp):
TTTTATTGTAATTTATAAAAGTTTTGTCCTTTATTGTAATTTATAAATAGTTTTGTA
Found at i:2838897 original size:87 final size:88
Alignment explanation
Indices: 2838746--2838965 Score: 230
Period size: 87 Copynumber: 2.5 Consensus size: 88
2838736 TTATGCTAAA
* * * * * *
2838746 TTTATTGTATTTTATAAAAAAATTTGTCTCCTTTTATTATAATTTATAAAAGGTTTTATCCTTTA
1 TTTATTATAATTTATAAAATAATTT-TGT-CTTTTATTGTAATTTATAAAAGGTTTTATACTTTA
* * *
2838811 TTGTAATTTATAA-ATAGTTTTGTAT
64 TTGTAATTTATAACA-AATTTCGTAC
* ** ** *
2838836 TTTATTGTAATTTAT-AAATTGTTTTGTAC-TTTATTGTAATTTATAAATTGTTTTGTACTTTAT
1 TTTATTATAATTTATAAAATAATTTTGT-CTTTTATTGTAATTTATAAAAGGTTTTATACTTTAT
* *
2838899 TGTAGTTTATAACAAATTTCGTCC
65 TGTAATTTATAACAAATTTCGTAC
2838923 TTTATTATAATTTATAAAATAATTTTGTCTTTTATTGTAATTT
1 TTTATTATAATTTATAAAATAATTTTGTCTTTTATTGTAATTT
2838966 GATGATTTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
87 61 0.56
88 27 0.25
89 6 0.06
90 14 0.13
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.56
Consensus pattern (88 bp):
TTTATTATAATTTATAAAATAATTTTGTCTTTTATTGTAATTTATAAAAGGTTTTATACTTTATT
GTAATTTATAACAAATTTCGTAC
Found at i:2840632 original size:22 final size:22
Alignment explanation
Indices: 2840607--2840648 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2840597 TTACTGCGTT
2840607 GACCCTTGACCACCGTTGACCC
1 GACCCTTGACCACCGTTGACCC
* **
2840629 GACCTTTGACCGGCGTTGAC
1 GACCCTTGACCACCGTTGAC
2840649 TGACAGTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.38, G:0.24, T:0.21
Consensus pattern (22 bp):
GACCCTTGACCACCGTTGACCC
Found at i:2843837 original size:8 final size:8
Alignment explanation
Indices: 2843824--2843849 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2843814 GTATTCATAA
2843824 ATGATTTT
1 ATGATTTT
2843832 ATGATTTT
1 ATGATTTT
2843840 ATGATTTT
1 ATGATTTT
2843848 AT
1 AT
2843850 ATGTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATGATTTT
Found at i:2844096 original size:18 final size:19
Alignment explanation
Indices: 2844073--2844111 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2844063 AAATCTTTTA
*
2844073 TTTAAATTTCA-TTTTGTT
1 TTTAAATTTCACTTTTCTT
2844091 TTTAAATTTCACTTTTCTT
1 TTTAAATTTCACTTTTCTT
2844110 TT
1 TT
2844112 AAAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTAAATTTCACTTTTCTT
Found at i:2849159 original size:7 final size:7
Alignment explanation
Indices: 2849147--2849173 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2849137 ATTTAGTTTT
2849147 ATAAATC
1 ATAAATC
2849154 ATAAATC
1 ATAAATC
2849161 ATAAATC
1 ATAAATC
2849168 ATAAAT
1 ATAAAT
2849174 TTTCTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAAATC
Done.