Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 24
Found at i:2566198 original size:20 final size:21
Alignment explanation
Indices: 2566173--2566225 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2566163 TATTATAATG
2566173 ATTATTATTAAATCATTATTATT
1 ATTATTATTAAATC--TATTATT
2566196 ATTATTATTAAATC-ATTATT
1 ATTATTATTAAATCTATTATT
*
2566216 ATAATTATTA
1 ATTATTATTA
2566226 TTATCAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 15 0.52
23 14 0.48
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTATTAAATCTATTATT
Found at i:2566243 original size:3 final size:3
Alignment explanation
Indices: 2566142--2566229 Score: 63
Period size: 3 Copynumber: 29.7 Consensus size: 3
2566132 CTATTTAATC
* * * * * * *
2566142 ATT ATT ATA ATG ATT AATC ATT ATT ATA ATG ATT ATT ATT A-A ATC
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
2566187 ATT ATT ATT ATT ATT ATT A-A ATC ATT ATT ATA ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2566230 CAAATCATTA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (3 bp):
ATT
Found at i:2566327 original size:19 final size:19
Alignment explanation
Indices: 2566303--2566358 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2566293 AATGATTATT
2566303 ATCAAATCATTATTAAATC
1 ATCAAATCATTATTAAATC
2566322 ATCAAATC---ATTAAAT-
1 ATCAAATCATTATTAAATC
*
2566337 ATTAAAATCATTATTAAATC
1 A-TCAAATCATTATTAAATC
2566357 AT
1 AT
2566359 TATTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 1 0.03
16 13 0.42
19 16 0.52
20 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
ATCAAATCATTATTAAATC
Found at i:2566458 original size:124 final size:121
Alignment explanation
Indices: 2566087--2566487 Score: 437
Period size: 124 Copynumber: 3.3 Consensus size: 121
2566077 CATTAGTATT
* * * * *
2566087 AAATCATTATTATAAAATAATTACTAAATCATTA-T-TAAATCATTACTATTTAATCATTATTAT
1 AAATCATTAATATAAAATCATTATTAAATCATTATTATAAAT-ATTAATATTAAATCATTATTAT
* *
2566150 AATG---A-T-T-AATCATTATTATAATGATTATTATTAAATCATTATTATTATTATTATT
65 AATGATTATTATAAATCATTATTATAATGATTATTATCAAATCATTATTA--A--ATTATC
* * * * * *
2566205 AAATCATTATTATAATTATTATTATCAAATCATTATTAT---CATTAATATTAAACCATTATTAT
1 AAATCATTAATATAA-AATCATTATTAAATCATTATTATAAATATTAATATTAAATCATTATTAT
*
2566267 AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCATC
65 AATGATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTATTAAATTATC
* *
2566325 AAATCATTAAATATTAAAATCATTATTAAATCATTATTATAAATATTATTACTAAATCATTATTA
1 AAATCATT-AATA-TAAAATCATTATTAAATCATTATTATAAATATTAATATTAAATCATTATTA
* *
2566390 TAATGATTATTATAAAATCATTACTATAATGATTATTATCAAATCATTACTAAATTATC
64 TAATGATTATTAT-AAATCATTATTATAATGATTATTATCAAATCATTATTAAATTATC
* *
2566449 AAATCATTAAATATTAAATTCATTATTAAATTATTATTA
1 AAATCATT-AATA-TAAAATCATTATTAAATCATTATTA
2566488 AATCATTTTT
Statistics
Matches: 243, Mismatches: 24, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
117 23 0.09
118 15 0.06
119 15 0.06
120 14 0.06
121 25 0.10
122 4 0.02
123 2 0.01
124 145 0.60
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (121 bp):
AAATCATTAATATAAAATCATTATTAAATCATTATTATAAATATTAATATTAAATCATTATTATA
ATGATTATTATAAATCATTATTATAATGATTATTATCAAATCATTATTAAATTATC
Found at i:2566477 original size:12 final size:12
Alignment explanation
Indices: 2566460--2566494 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
2566450 AATCATTAAA
2566460 TATTAAATTCAT
1 TATTAAATTCAT
2566472 TATTAAATT-AT
1 TATTAAATTCAT
2566483 TATTAAA-TCAT
1 TATTAAATTCAT
2566494 T
1 T
2566495 TTTATTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 12 0.55
12 9 0.41
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:2566479 original size:98 final size:96
Alignment explanation
Indices: 2566078--2566487 Score: 376
Period size: 98 Copynumber: 4.2 Consensus size: 96
2566068 TTATTAAATC
* * * * **
2566078 ATTAGTATTAAATCATTATTATAA-AATAATTACTAAATCATTATTAAATCATTACTATTTAATC
1 ATTATTATTAAATCATTATTATAATGATTATTA-TAAATCATTATTAAATCATTATTATCAAATC
*
2566142 ATTATTATA-ATGATT-AATCATTATTATAATG
65 ATTATTATATATTATTAAATCATTATTATAA-G
*
2566173 ATTATTATTAAATCATTATTAT--T-ATTATTATTAAATCATTATTATAATTATTATTATCAAAT
1 ATTATTATTAAATCATTATTATAATGATTATTA-TAAATCATTATTA-AATCATTATTATCAAAT
* *
2566235 CATTATTATCATTAATATTAAACCATTATTATAATG
64 CATTATTAT-A-TATTATTAAATCATTATTATAA-G
* * * *
2566271 ATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTATTAAATCATCAAATCATTAAA
1 ATTATTATTAAATCATTATTATAATGATTATTAT-AAATCATTATTAAATCAT--TATTATCAAA
* *
2566336 T-ATTA--AAATCATTATTAAATCATTATTATAAAT
63 TCATTATTATAT-ATTATTAAATCATTATTAT-AAG
* * *
2566369 ATTATTACTAAATCATTATTATAATGATTATTATAAAATCATTACTATAATGATTATTATCAAAT
1 ATTATTATTAAATCATTATTATAATGATTATTAT-AAATCATTATTA-AATCATTATTATCAAAT
* * *
2566434 CATTACTA-A-ATTATCAAATCATTAAATATTAA-
64 CATTATTATATATTATTAAATCATT-ATTA-TAAG
*
2566466 ATTCATTATTAAATTATTATTA
1 ATT-ATTATTAAATCATTATTA
2566488 AATCATTTTT
Statistics
Matches: 265, Mismatches: 29, Indels: 39
0.80 0.09 0.12
Matches are distributed among these distances:
93 19 0.07
94 22 0.08
95 22 0.08
97 29 0.11
98 124 0.47
99 10 0.04
100 8 0.03
101 23 0.09
102 8 0.03
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (96 bp):
ATTATTATTAAATCATTATTATAATGATTATTATAAATCATTATTAAATCATTATTATCAAATCA
TTATTATATATTATTAAATCATTATTATAAG
Found at i:2566748 original size:59 final size:57
Alignment explanation
Indices: 2566680--2566839 Score: 172
Period size: 49 Copynumber: 3.1 Consensus size: 57
2566670 AATTATTATT
*
2566680 ATAATTTCATTATTATTAATAATTACTAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTA-TAAT-ATTACTAATCATTACTATCAAATCATTAAAAATTAATA
2566739 ATAATTTC------AT--TATTACTAATCATTACTATCAAATCATTAAAAATTAATA
1 ATAATTTCATTATTATAATATTACTAATCATTACTATCAAATCATTAAAAATTAATA
*
2566788 ATAATTTC------AT--TATTACTAATCATTACTATCAAATCATTAAATATTAATA
1 ATAATTTCATTATTATAATATTACTAATCATTACTATCAAATCATTAAAAATTAATA
2566837 ATA
1 ATA
2566840 GATGGGTGCC
Statistics
Matches: 99, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
49 88 0.89
50 1 0.01
52 1 0.01
53 1 0.01
59 8 0.08
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (57 bp):
ATAATTTCATTATTATAATATTACTAATCATTACTATCAAATCATTAAAAATTAATA
Found at i:2566757 original size:49 final size:49
Alignment explanation
Indices: 2566701--2566839 Score: 269
Period size: 49 Copynumber: 2.8 Consensus size: 49
2566691 ATTATTAATA
2566701 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
2566750 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
2566799 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
2566840 GATGGGTGCC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:2570956 original size:2 final size:2
Alignment explanation
Indices: 2570949--2570975 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2570939 GTTATACATG
2570949 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2570976 GGTCAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2587954 original size:15 final size:15
Alignment explanation
Indices: 2587931--2587964 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2587921 ATATTTAGCT
* *
2587931 GGGCGGGCGGATGTG
1 GGGCAGGCGGATGCG
2587946 GGGCAGGCGGATGCG
1 GGGCAGGCGGATGCG
2587961 GGGC
1 GGGC
2587965 GGGTAATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:2592575 original size:60 final size:59
Alignment explanation
Indices: 2592454--2592565 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 59
2592444 GGTCTTCCAT
* * **
2592454 TATAAGATGATGCTTTTTTGAGTCCCCGACTATTAAAAGTTACAAAATGGTCCTTTAAC
1 TATAAGATGATGCTTTGTTGAGTCACCGACTATTAAAAGTTACAAAATAATCCTTTAAC
* * *
2592513 TATAGGATGTTGCTTTGTTGAGTACATCGACTATTAAAAGTTACAAAATAATC
1 TATAAGATGATGCTTTGTTGAGT-CACCGACTATTAAAAGTTACAAAATAATC
2592566 ACTTGACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 20 0.44
60 25 0.56
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (59 bp):
TATAAGATGATGCTTTGTTGAGTCACCGACTATTAAAAGTTACAAAATAATCCTTTAAC
Found at i:2599816 original size:40 final size:38
Alignment explanation
Indices: 2599729--2599816 Score: 88
Period size: 43 Copynumber: 2.2 Consensus size: 38
2599719 AAAATATTAT
2599729 ATTTAGTTATTATTATTTTATTAGGAATTAGAGTTAAGAC
1 ATTTAGTTATTATTATTTTATT--GAATTAGAGTTAAGAC
* *
2599769 ATGTTTAGTTTATTATTATTTTATT-CATTAGTTATTTAAGAC
1 A--TTTAG-TTATTATTATTTTATTGAATTAG--AGTTAAGAC
2599811 ATTTAG
1 ATTTAG
2599817 AACTCAACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
40 11 0.27
42 14 0.34
43 16 0.39
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.52
Consensus pattern (38 bp):
ATTTAGTTATTATTATTTTATTGAATTAGAGTTAAGAC
Found at i:2601320 original size:22 final size:23
Alignment explanation
Indices: 2601290--2601336 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2601280 AAAATATATT
2601290 TATTAATATT-TCTAATAATATAA
1 TATTAATATTGT-TAATAATATAA
*
2601313 TATT-ATATTGTTAATATTATAA
1 TATTAATATTGTTAATAATATAA
2601335 TA
1 TA
2601337 AAATAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTAATATTGTTAATAATATAA
Found at i:2601477 original size:19 final size:18
Alignment explanation
Indices: 2601453--2601521 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
2601443 ATATTATTAA
2601453 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
2601472 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
2601490 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
2601512 ATT-TTAATAA
1 ATTATTAATAA
2601522 ATATAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:2601496 original size:27 final size:27
Alignment explanation
Indices: 2601417--2601501 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
2601407 ATAAAATTTG
* *
2601417 TATTATTTAT-TAATTTCATAGAAATAA
1 TATTATTTATAT-ATTTAATATAAATAA
* *
2601444 TATTA-TTAAAT-TATTAATAATGAATAA
1 TATTATTTATATAT-TTAAT-ATAAATAA
2601471 TATTATTTATATATTTAATATTAATATAA
1 TATTATTTATATATTTAATA-TAA-ATAA
2601500 TA
1 TA
2601502 ATCTAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.16
27 18 0.40
28 12 0.27
29 7 0.16
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
TATTATTTATATATTTAATATAAATAA
Found at i:2601525 original size:34 final size:36
Alignment explanation
Indices: 2601487--2601567 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
2601477 TTATATATTT
*
2601487 AATATTAATATAATA-AT-CTAA-TAATATTTTAATA
1 AATA-TAATATAAAATATACTAATTAATATTTTAATA
**
2601521 AATATAAT-TAAAATATACTAATTAATATTTTTTTA
1 AATATAATATAAAATATACTAATTAATATTTTAATA
2601556 AATATAATATAA
1 AATATAATATAA
2601568 CACTATTACT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.10
33 6 0.15
34 8 0.20
35 19 0.47
36 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (36 bp):
AATATAATATAAAATATACTAATTAATATTTTAATA
Found at i:2601844 original size:14 final size:14
Alignment explanation
Indices: 2601822--2601856 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2601812 CAATCATCAT
*
2601822 AAAACATTTTTTAA
1 AAAATATTTTTTAA
2601836 AAAATATTTTTTAA
1 AAAATATTTTTTAA
2601850 AAAATAT
1 AAAATAT
2601857 AATTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATATTTTTTAA
Found at i:2616493 original size:150 final size:151
Alignment explanation
Indices: 2616217--2616508 Score: 577
Period size: 150 Copynumber: 1.9 Consensus size: 151
2616207 CCCCTTCTGT
2616217 GTCTGTTTCAGAGCAGAAATCTGTTGCAATGTATTTTGCATCAAGCTCCTCAACTTTTGACTGCT
1 GTCTGTTTCAGAGCAGAAATCTGTTGCAATGTATTTTGCATCAAGCTCCTCAACTTTTGACTGCT
2616282 TCAATTTGTCAATTTCAAGTTGCAACCTCCTAAGAATGAAGCTTTCATCAGCAACAAAAAAACAA
66 TCAATTTGTCAATTTCAAGTTGCAACCTCCTAAGAATGAAGCTTTCATCAGCAACAAAAAAACAA
2616347 TGTTGACAACATGAACCTATA
131 TGTTGACAACATGAACCTATA
2616368 GTCTGTTTCAGAGCAG-AATCTGTTGCAATGTATTTTGCATCAAGCTCCTCAACTTTTGACTGCT
1 GTCTGTTTCAGAGCAGAAATCTGTTGCAATGTATTTTGCATCAAGCTCCTCAACTTTTGACTGCT
2616432 TCAATTTGTCAATTTCAAGTTGCAACCTCCTAAGAATGAAGCTTTCATCAGCAACAAAAAAACAA
66 TCAATTTGTCAATTTCAAGTTGCAACCTCCTAAGAATGAAGCTTTCATCAGCAACAAAAAAACAA
2616497 TGTTGACAACAT
131 TGTTGACAACAT
2616509 CATGAACCTA
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
150 125 0.89
151 16 0.11
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (151 bp):
GTCTGTTTCAGAGCAGAAATCTGTTGCAATGTATTTTGCATCAAGCTCCTCAACTTTTGACTGCT
TCAATTTGTCAATTTCAAGTTGCAACCTCCTAAGAATGAAGCTTTCATCAGCAACAAAAAAACAA
TGTTGACAACATGAACCTATA
Found at i:2624672 original size:32 final size:32
Alignment explanation
Indices: 2624588--2624665 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
2624578 TAACTGATAC
* * * * *
2624588 GCATTATTTGAATGCGATATTGATTCTACTAT
1 GCATTATATGAATGCAATACTAACTCTACTAT
*
2624620 GCATTATCTGAATGCAATACTAACTCTACTAT
1 GCATTATATGAATGCAATACTAACTCTACTAT
2624652 GCATTATATGAATG
1 GCATTATATGAATG
2624666 ACATACTGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (32 bp):
GCATTATATGAATGCAATACTAACTCTACTAT
Found at i:2626173 original size:31 final size:32
Alignment explanation
Indices: 2626133--2626204 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
2626123 TAAATCCTAA
* *
2626133 AATGCTTAAATATTCAAATCATAGAAAATCTT
1 AATGTTTAAATACTCAAATCATAGAAAATCTT
* * *
2626165 -ATGTTTAAATACTCAAATCCTATAAAATGTT
1 AATGTTTAAATACTCAAATCATAGAAAATCTT
2626196 AATGTTTAA
1 AATGTTTAA
2626205 GTAAGTCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (32 bp):
AATGTTTAAATACTCAAATCATAGAAAATCTT
Found at i:2626508 original size:22 final size:21
Alignment explanation
Indices: 2626441--2626508 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
2626431 TGGAAATTTT
*
2626441 AAAAGAAAATG-AGAGAAG-G
1 AAAAGAATATGAAGAGAAGAG
*
2626460 AAAATGAGATAGGAAGAAGAA-ATG
1 AAAA-GA-ATATGAAG-AGAAGA-G
2626484 AAAAGAATATGAAGATGAAGAG
1 AAAAGAATATGAAGA-GAAGAG
2626506 AAA
1 AAA
2626509 TAAAAATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
19 4 0.11
20 2 0.05
21 4 0.11
22 16 0.42
23 7 0.18
24 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (21 bp):
AAAAGAATATGAAGAGAAGAG
Found at i:2631028 original size:22 final size:23
Alignment explanation
Indices: 2631003--2631046 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2630993 CACCACAGCT
*
2631003 CGTATAATTGCACCG-AGTGCCG
1 CGTAGAATTGCACCGTAGTGCCG
2631025 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGTAGTGCC
2631047 ATATATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCG
Found at i:2631321 original size:147 final size:145
Alignment explanation
Indices: 2631022--2631323 Score: 525
Period size: 147 Copynumber: 2.1 Consensus size: 145
2631012 GCACCGAGTG
* *
2631022 CCGCGTAGAATTGCACCGTAGTGCCATATATGATGTCCATAAGGACCATATAGAATTCCTTGAGA
1 CCGCGTAGAATTGCACCGTAGTGCCATATATGATGTCCATAAGGACCA-ACAGAATTCCTTAAGA
*
2631087 ATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACATGTTCCAAAGAATATA
65 ATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACATGTTCAAAAGAATATA
2631152 CATATGTCCCGAAGGA
130 CATATGTCCCGAAGGA
2631168 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACC-ACAGAATTCCTTAAGA
1 CCGCGTAGAATTGCACCGTAGTGCCATAT-ATGATGTCCATAAGGACCAACAGAATTCCTTAAGA
*
2631232 ATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCAAAAGAATA
65 ATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTT--CACATGTTCAAAAGAATA
2631297 TACATATGTCCCGAAGGA
128 TACATATGTCCCGAAGGA
2631315 CCGCGTAGA
1 CCGCGTAGA
2631324 CCCTCGACTC
Statistics
Matches: 149, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
145 58 0.39
146 29 0.19
147 62 0.42
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (145 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATATGATGTCCATAAGGACCAACAGAATTCCTTAAGAA
TCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACATGTTCAAAAGAATATAC
ATATGTCCCGAAGGA
Found at i:2632222 original size:18 final size:18
Alignment explanation
Indices: 2632201--2632235 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2632191 TCCCATCTAG
2632201 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2632219 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2632236 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2632840 original size:21 final size:21
Alignment explanation
Indices: 2632816--2632860 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2632806 TGTTGTTCGT
* *
2632816 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2632837 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2632858 TTG
1 TTG
2632861 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2640898 original size:16 final size:18
Alignment explanation
Indices: 2640867--2640901 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2640857 TATACATATC
2640867 ATATAAAATTATAATTTT
1 ATATAAAATTATAATTTT
2640885 ATAT-AAATTA-AATTTT
1 ATATAAAATTATAATTTT
2640901 A
1 A
2640902 ACTGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAAAATTATAATTTT
Found at i:2644097 original size:21 final size:21
Alignment explanation
Indices: 2643979--2644117 Score: 79
Period size: 21 Copynumber: 6.8 Consensus size: 21
2643969 AAATGACCAA
**
2643979 CAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGATTTTC
* ** *
2643999 CAGAATCGCAAATC-AATTTC
1 CAAAATCGCAACGCGATTTTC
2644019 CAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGATT-TTC
* * ** *
2644040 AAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGATTTTC
* **
2644061 CAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGATTTTC
* * *
2644082 CAGAATCGCAACGCGAATAT-
1 CAAAATCGCAACGCGATTTTC
*
2644102 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2644118 ACACATAAAT
Statistics
Matches: 88, Mismatches: 27, Indels: 8
0.72 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 39 0.44
21 46 0.52
22 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
CAAAATCGCAACGCGATTTTC
Found at i:2644110 original size:20 final size:20
Alignment explanation
Indices: 2644085--2644278 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
2644075 GATTTTCCAG
* *
2644085 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2644105 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2644125 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * * *
2644145 AATCGTAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
2644165 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2644185 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2644205 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2644225 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2644246 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2644266 AATCGCAACGCGA
1 AATCGCAACGCGA
2644279 TATTTAAAGC
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.02
20 128 0.87
21 15 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2644132 original size:40 final size:39
Alignment explanation
Indices: 2644085--2644278 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 39
2644075 GATTTTCCAG
* ** *
2644085 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * * *
2644125 AATCGCAACGCGTATCCGTAAATCGTAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* * *
2644165 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
2644205 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
2644246 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
2644279 TATTTAAAGC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 96 0.74
41 33 0.25
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:2644168 original size:60 final size:60
Alignment explanation
Indices: 2644085--2644277 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
2644075 GATTTTCCAG
* ** *
2644085 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * * *
2644145 AATCGTAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** *
2644205 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
2644266 AATCGCAACGCG
1 AATCGCAACGCG
2644278 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 77 0.69
61 33 0.30
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:2644670 original size:33 final size:33
Alignment explanation
Indices: 2644631--2644701 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2644621 TTCACTTAGA
*
2644631 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
* *
2644664 TTTCATTTCGCGTTGCTATTATCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
2644697 TTTCA
1 TTTCA
2644702 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
Found at i:2644825 original size:20 final size:20
Alignment explanation
Indices: 2644781--2644890 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
2644771 TGCAGAAGAG
*
2644781 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
2644802 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
2644822 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
2644843 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
2644857 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
2644876 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
2644891 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:2644838 original size:41 final size:38
Alignment explanation
Indices: 2644774--2644890 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
2644764 TTCAATTTGC
* *
2644774 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2644812 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
2644853 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2644886 AGAAT
1 AGAAT
2644891 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:2644860 original size:14 final size:14
Alignment explanation
Indices: 2644841--2644897 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2644831 GAGAAATGAA
2644841 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2644855 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2644874 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2644888 AATCGCAACG
1 AATCGCAACG
2644898 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2644873 original size:33 final size:33
Alignment explanation
Indices: 2644833--2644913 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2644823 CGCAACGAGA
2644833 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2644866 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
2644899 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2644914 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2644931 original size:19 final size:19
Alignment explanation
Indices: 2644909--2645036 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
2644899 GAAACCAAAA
*
2644909 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2644928 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2644942 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2644961 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2644975 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
2644995 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
2645015 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2645035 TC
1 TC
2645037 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2644950 original size:14 final size:14
Alignment explanation
Indices: 2644931--2644987 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2644921 TTTCATTTCG
2644931 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2644945 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2644964 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2644978 CGTTGCGATT
1 CGTTGCGATT
2644988 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2644956 original size:33 final size:33
Alignment explanation
Indices: 2644914--2645036 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
2644904 CAAAATCGCA
2644914 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2644947 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2644980 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
2645021 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2645037 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2644998 original size:21 final size:21
Alignment explanation
Indices: 2644972--2645036 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2644962 CGCGTTGCGA
2644972 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2644993 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2645013 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2645034 TTC
1 TTC
2645037 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2646949 original size:92 final size:93
Alignment explanation
Indices: 2646734--2647014 Score: 523
Period size: 92 Copynumber: 3.1 Consensus size: 93
2646724 TAGATTGCTT
2646734 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2646799 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2646827 AGTAAATTTTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2646892 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2646919 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2646983 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2647010 AGTAA
1 AGTAA
2647015 TGCAATCCAT
Statistics
Matches: 185, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
91 25 0.14
92 96 0.52
93 64 0.35
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2647099 original size:19 final size:19
Alignment explanation
Indices: 2647059--2647186 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2647049 TAGTTTACTT
* *
2647059 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2647079 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2647098 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2647117 TCGCAA--C-AAA--AGAA
1 TCGCAACGCGAAACCAAAA
2647131 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2647150 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
2647164 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
2647182 TCGCA
1 TCGCA
2647187 TTGCGATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 6 0.07
18 9 0.10
19 37 0.40
20 13 0.14
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2647133 original size:33 final size:33
Alignment explanation
Indices: 2647094--2647186 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
2647084 ACGCGAAACC
**
2647094 AAAATCGCAACGCGAAATGAAAATCGCAAC-AA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAA
*
2647126 AAGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AA-AATCGCAACGCGAAACCAAAATCGCAACGAA
2647160 AAAATCGCAACGCGAAACC-AAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
2647187 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 10 0.18
33 43 0.77
34 3 0.05
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAA
Found at i:2647164 original size:14 final size:14
Alignment explanation
Indices: 2647145--2647171 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2647135 AACGCGAAAC
2647145 CAAAATCGCAACGA
1 CAAAATCGCAACGA
2647159 CAAAATCGCAACG
1 CAAAATCGCAACG
2647172 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:2647209 original size:19 final size:19
Alignment explanation
Indices: 2647182--2647297 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
2647172 CGAAACCAAA
*
2647182 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2647201 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2647217 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2647234 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2647250 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2647267 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2647287 TCGTGTTGCGA
1 TCGCGTTGCGA
2647298 AAGTAAACTA
Statistics
Matches: 79, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
14 15 0.19
16 11 0.14
17 11 0.14
19 30 0.38
20 12 0.15
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2647223 original size:14 final size:14
Alignment explanation
Indices: 2647204--2647260 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2647194 TTTCATTTCG
2647204 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2647218 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2647235 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2647251 CGTTGCGATT
1 CGTTGCGATT
2647261 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2647229 original size:33 final size:33
Alignment explanation
Indices: 2647187--2647279 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2647177 CCAAATCGCA
*
2647187 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2647220 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2647253 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2647280 TTAAGTTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2647774 original size:21 final size:21
Alignment explanation
Indices: 2647750--2647808 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
2647740 TCATTCCTCG
2647750 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * * *
2647771 AGAGGCCACTGTCATCATTGA
1 AGAGTCCCCTCCCACCGTTCA
2647792 AGAGTCCCCTCCCACCG
1 AGAGTCCCCTCCCACCG
2647809 ATAGAGATAG
Statistics
Matches: 25, Mismatches: 13, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2648221 original size:14 final size:14
Alignment explanation
Indices: 2648202--2648237 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2648192 ATTGTTTAAT
2648202 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2648216 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2648230 TGATTTGT
1 TGATTTGT
2648238 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2648360 original size:19 final size:19
Alignment explanation
Indices: 2648344--2648440 Score: 150
Period size: 19 Copynumber: 5.4 Consensus size: 19
2648334 AAAAATGACT
2648344 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2648363 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2648382 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2648396 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2648415 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2648434 ATCGCAA
1 ATCGCAA
2648441 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 55 0.77
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2648422 original size:52 final size:52
Alignment explanation
Indices: 2648344--2648459 Score: 223
Period size: 52 Copynumber: 2.2 Consensus size: 52
2648334 AAAAATGACT
2648344 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2648396 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2648448 ATCGCAATGCGA
1 ATCGCAATGCGA
2648460 TTTTAATTCG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2648507 original size:33 final size:33
Alignment explanation
Indices: 2648455--2648616 Score: 143
Period size: 33 Copynumber: 4.8 Consensus size: 33
2648445 AGAATCGCAA
*
2648455 TGCGATTTT-AATTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
2648487 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * *** * *
2648525 TGCGATTCTCTCGTTGCG-ATTTTAATT-TCGCAT
1 TGCGATT-T-TCATTTCGCATTGCGATTCTCTCGT
2648558 TGCGA-TTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
2648591 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
2648617 TTCATTTCCG
Statistics
Matches: 101, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
30 4 0.04
31 3 0.03
32 16 0.16
33 40 0.40
34 8 0.08
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 5 0.05
40 6 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:2648510 original size:19 final size:19
Alignment explanation
Indices: 2648449--2648669 Score: 207
Period size: 19 Copynumber: 12.7 Consensus size: 19
2648439 AACGGGAGAA
* *
2648449 TCGCAATGCGATTTT-AAT
1 TCGCATTGCGATTTTCATT
*
2648467 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2648483 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2648500 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2648519 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
2648535 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
2648552 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
2648570 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
2648587 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2648604 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2648623 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
2648641 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2648657 TCGCATTGCGATT
1 TCGCATTGCGATT
2648670 CTCGTTGCGA
Statistics
Matches: 168, Mismatches: 12, Indels: 45
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.17
16 21 0.12
17 18 0.11
18 21 0.12
19 63 0.38
20 16 0.10
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2648531 original size:52 final size:53
Alignment explanation
Indices: 2648449--2648669 Score: 353
Period size: 52 Copynumber: 4.2 Consensus size: 53
2648439 AACGGGAGAA
* *
2648449 TCGCAATGCGATTTT-AATT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
2648500 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2648552 TCGCATTGCGA-TTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
2648604 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATT
2648657 TCGCATTGCGATT
1 TCGCATTGCGATT
2648670 CTCGTTGCGA
Statistics
Matches: 160, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
51 22 0.14
52 87 0.54
53 50 0.31
54 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2648667 original size:33 final size:34
Alignment explanation
Indices: 2648486--2648681 Score: 158
Period size: 33 Copynumber: 5.7 Consensus size: 34
2648476 GATTCTCTCG
2648486 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
* *
2648524 TTGCGATTCTC-TCGTTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * *
2648557 TTGCGA-TTTCAT--TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCG-ATTTTC-ATT-TCGCA
2648590 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTT-CGCA
*
2648629 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
2648662 TTGCGA--TTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
2648682 GTAATTTCCG
Statistics
Matches: 130, Mismatches: 14, Indels: 35
0.73 0.08 0.20
Matches are distributed among these distances:
30 1 0.01
31 17 0.13
32 7 0.05
33 44 0.34
34 19 0.15
35 3 0.02
36 2 0.02
37 1 0.01
38 11 0.08
39 18 0.14
40 7 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:2650910 original size:12 final size:12
Alignment explanation
Indices: 2650893--2650917 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2650883 TCTTCGGGGA
2650893 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2650905 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2650917 C
1 C
2650918 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2651126 original size:24 final size:24
Alignment explanation
Indices: 2651092--2651138 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2651082 CTGAAACATC
2651092 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2651116 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2651139 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2651859 original size:20 final size:20
Alignment explanation
Indices: 2651831--2652059 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
2651821 AAATTTCAGT
* * *
2651831 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2651851 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2651871 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2651891 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2651911 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2651931 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2651951 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2651971 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2651991 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2652011 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2652031 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2652051 GTTGCGATT
1 GTTGCGATT
2652060 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2654994 original size:29 final size:28
Alignment explanation
Indices: 2654962--2655017 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2654952 AATGTCTATG
2654962 TTTTTT-ATTTTAAACAATATAATTTTAA
1 TTTTTTAATTTTAAACAAT-TAATTTTAA
* *
2654990 TTTTTTAATTTTAAATAATTTATTTTAA
1 TTTTTTAATTTTAAACAATTAATTTTAA
2655018 AATTACCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTTAATTTTAAACAATTAATTTTAA
Found at i:2656649 original size:15 final size:16
Alignment explanation
Indices: 2656629--2656658 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2656619 ATATATAAAC
2656629 ATCAAAC-ATTAAAAA
1 ATCAAACTATTAAAAA
2656644 ATCAAACTATTAAAA
1 ATCAAACTATTAAAA
2656659 TAGCACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (16 bp):
ATCAAACTATTAAAAA
Found at i:2660979 original size:2 final size:2
Alignment explanation
Indices: 2660974--2660998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2660964 ATACACACTC
2660974 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2660999 AAGAAAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2666562 original size:31 final size:31
Alignment explanation
Indices: 2666519--2666584 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
2666509 CTATAGAATA
*
2666519 TTATTTTATTGAGTCATCT-GATTATTGAAAG
1 TTATTTTATTGAGTC-TCTCGATTATTAAAAG
*
2666550 TTATTTTGTTGAGTCTCTCGATTATTAAAAG
1 TTATTTTATTGAGTCTCTCGATTATTAAAAG
2666581 TTAT
1 TTAT
2666585 AAATGGTCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (31 bp):
TTATTTTATTGAGTCTCTCGATTATTAAAAG
Found at i:2676249 original size:18 final size:19
Alignment explanation
Indices: 2676226--2676268 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
2676216 CATTAATCAT
2676226 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
2676244 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
2676264 ATTCC
1 ATTCC
2676269 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:2676256 original size:20 final size:20
Alignment explanation
Indices: 2676231--2676268 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2676221 ATCATATTCC
2676231 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2676251 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2676269 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2676363 original size:16 final size:17
Alignment explanation
Indices: 2676342--2676375 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2676332 GAATAACATT
2676342 AATT-AAATAATTTAGA
1 AATTAAAATAATTTAGA
*
2676358 AATTAAAATTATTTAGA
1 AATTAAAATAATTTAGA
2676375 A
1 A
2676376 TGTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTAAAATAATTTAGA
Found at i:2678829 original size:13 final size:13
Alignment explanation
Indices: 2678825--2678867 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
2678815 CCGTTGACCC
*
2678825 GACCCGACCTGTT
1 GACCCGACCCGTT
*
2678838 GACCCGACTCGTT
1 GACCCGACCCGTT
*
2678851 GACCTGACCCGTT
1 GACCCGACCCGTT
2678864 GACC
1 GACC
2678868 GTTGACCGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.40, G:0.23, T:0.21
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2678832 original size:18 final size:18
Alignment explanation
Indices: 2678811--2678845 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2678801 CAACCCAACT
2678811 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
*
2678829 CGACCTGTTGACCCGAC
1 CGACCCGTTGACCCGAC
2678846 TCGTTGACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:2681351 original size:12 final size:12
Alignment explanation
Indices: 2681313--2681404 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
2681303 ATTTCCGAAT
2681313 TGAATTCTGTTC
1 TGAATTCTGTTC
*
2681325 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
2681337 TGAATTCTGTTC
1 TGAATTCTGTTC
*
2681349 TG-ATTCTGATC
1 TGAATTCTGTTC
*
2681360 TGGATTCTGTTC
1 TGAATTCTGTTC
* *
2681372 T-AATATCTGATA
1 TGAAT-TCTGTTC
*
2681384 TGAATTCTGTTT
1 TGAATTCTGTTC
*
2681396 TGATTTCTG
1 TGAATTCTG
2681405 ATATCTCCGT
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
10 3 0.05
11 15 0.24
12 36 0.57
13 6 0.10
14 3 0.05
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:2681390 original size:24 final size:23
Alignment explanation
Indices: 2681313--2681408 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 23
2681303 ATTTCCGAAT
* *
2681313 TGAATTCTGTTCTGATAC-GTTA
1 TGAATTCTGTTCTGATTCTGATA
*
2681335 CCTGAATTCTGTTCTGATTCTGATC
1 --TGAATTCTGTTCTGATTCTGATA
* *
2681360 TGGATTCTGTTCTAATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
2681384 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
2681408 T
1 T
2681409 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 14 0.23
24 43 0.72
25 3 0.05
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:2681594 original size:2 final size:2
Alignment explanation
Indices: 2681589--2681622 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2681579 ATATGCTTTA
2681589 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
2681623 CTTTTTACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2683589 original size:13 final size:13
Alignment explanation
Indices: 2683571--2683601 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2683561 TCACAACCCA
2683571 ACCCGACCCGTTG
1 ACCCGACCCGTTG
2683584 ACCCGACCCGTTG
1 ACCCGACCCGTTG
2683597 ACCCG
1 ACCCG
2683602 TTGACCACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:2684931 original size:18 final size:18
Alignment explanation
Indices: 2684905--2684939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2684895 TCAAAAGGAC
*
2684905 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2684923 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2684940 CCAGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2686112 original size:47 final size:47
Alignment explanation
Indices: 2686040--2686130 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
2686030 TTCAAATTGA
*
2686040 ATTCTGTTCTGATACGTTACTTGAATTATGTTCTGA-TTCTGATCTGG
1 ATTCTGTTCTGATACGATAC-TGAATTATGTTCTGATTTCTGATCTGG
* *
2686087 ATTCTGTTCTGATATCTGATA-TGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATA-C-GATACTGAATTATGTTCTGATTTCTGAT
2686131 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
47 27 0.71
48 8 0.21
49 3 0.08
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (47 bp):
ATTCTGTTCTGATACGATACTGAATTATGTTCTGATTTCTGATCTGG
Found at i:2686114 original size:24 final size:24
Alignment explanation
Indices: 2686037--2686132 Score: 99
Period size: 24 Copynumber: 4.0 Consensus size: 24
2686027 ATTTTCAAAT
*
2686037 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
* *
2686059 CTTGAATTATGTTCTGAT-TCTGATC
1 --TGAATTCTGTTCTGATATCTGATA
*
2686084 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
2686108 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
2686132 T
1 T
2686133 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 14 0.23
24 44 0.73
25 2 0.03
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:2686586 original size:27 final size:27
Alignment explanation
Indices: 2686546--2686616 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
2686536 GGTAGTTCTG
* *
2686546 TATTACTGAGCTTTTCAAAGCTCACTC
1 TATTACTCACCTTTTCAAAGCTCACTC
2686573 TATTACTCACCTTTTCAAAGCTCACTC
1 TATTACTCACCTTTTCAAAGCTCACTC
2686600 TATTACTCACCTTTTCA
1 TATTACTCACCTTTTCA
2686617 GGTTAAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.30, G:0.06, T:0.39
Consensus pattern (27 bp):
TATTACTCACCTTTTCAAAGCTCACTC
Found at i:2689217 original size:2 final size:2
Alignment explanation
Indices: 2689210--2689246 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2689200 GTACAAAACT
2689210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2689247 CACCTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2689643 original size:23 final size:24
Alignment explanation
Indices: 2689617--2689662 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2689607 ATAGATTTAA
2689617 ATATAATATAT-TTTTTTATTTTT
1 ATATAATATATATTTTTTATTTTT
** *
2689640 ATATGTTCTATATTTTTTATTTT
1 ATATAATATATATTTTTTATTTT
2689663 GATGATATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
ATATAATATATATTTTTTATTTTT
Found at i:2696246 original size:15 final size:15
Alignment explanation
Indices: 2696226--2696272 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
2696216 GTAGGACCAT
2696226 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
2696241 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
2696256 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
2696271 TA
1 TA
2696273 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:2696434 original size:12 final size:12
Alignment explanation
Indices: 2696417--2696463 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
2696407 TATCATGTTC
* *
2696417 TCATATTACATG
1 TCATATCACATA
2696429 TCATATCACATA
1 TCATATCACATA
2696441 TCATATCACATA
1 TCATATCACATA
2696453 TCATATCACAT
1 TCATATCACAT
2696464 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:2696860 original size:19 final size:19
Alignment explanation
Indices: 2696836--2696887 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
2696826 TATTGTTGGG
2696836 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
2696855 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
2696874 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2696888 CGATTGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:2696988 original size:64 final size:63
Alignment explanation
Indices: 2696855--2697015 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 63
2696845 TGCACTCCTT
* *
2696855 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGAG
* *
2696919 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATT--AATG
2696982 AG
62 AG
**
2696984 -TGCATCGATGCACTACCAATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
2697016 ATTCATATAA
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
63 2 0.02
64 78 0.90
65 4 0.05
66 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGAG
Found at i:2703236 original size:15 final size:15
Alignment explanation
Indices: 2703216--2703277 Score: 115
Period size: 15 Copynumber: 4.1 Consensus size: 15
2703206 GTAGGACCAT
2703216 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
2703231 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
2703246 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
2703261 TACATCTCGAAGGAC
1 TACATCCCGAAGGAC
2703276 TA
1 TA
2703278 TTATACCCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:2703439 original size:12 final size:12
Alignment explanation
Indices: 2703422--2703468 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
2703412 TATCATGTTC
* *
2703422 TCATATTACATG
1 TCATATCACATA
2703434 TCATATCACATA
1 TCATATCACATA
2703446 TCATATCACATA
1 TCATATCACATA
2703458 TCATATCACAT
1 TCATATCACAT
2703469 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:2703883 original size:64 final size:64
Alignment explanation
Indices: 2703775--2703916 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 64
2703765 TAATGAAGGT
* * * **
2703775 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATCAAAGGCATTCGATGT-GTCACTATTAATGGG
* * * ** *
2703839 ATGCATCGATGCACTCCTTATGCATCGATGCA-CTGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATC-AAAGGCATTCGATGTGTCACTATTAATGGG
2703903 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2703917 GAATTGCATT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.03
64 63 0.97
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATCAAAGGCATTCGATGTGTCACTATTAATGGG
Found at i:2704924 original size:23 final size:23
Alignment explanation
Indices: 2704890--2704958 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2704880 CATTATTATA
2704890 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
2704913 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
2704936 TGGCACTTCGGTACAATTATACG
1 TGGCACTACGGTGCAATTCTACG
2704959 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:2705339 original size:16 final size:16
Alignment explanation
Indices: 2705288--2705340 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2705278 TGTATGTGAT
2705288 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
2705306 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
2705322 ATATGATATATGTGTG
1 ATATGATATATGTGTG
2705338 ATA
1 ATA
2705341 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:2708260 original size:18 final size:18
Alignment explanation
Indices: 2708237--2708284 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2708227 AAATTGTCCT
*
2708237 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
2708255 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
2708272 TATTTATATATTT
1 TA-TTATATATTT
2708285 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:2709041 original size:21 final size:20
Alignment explanation
Indices: 2709015--2709066 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
2709005 TATAGCACAG
* *
2709015 CCTCTTTCCTCTTTCCTCTTT
1 CCTCTTTCCTCTTTCAT-TTC
2709036 CCTCTTTCCTCTTTCATTTC
1 CCTCTTTCCTCTTTCATTTC
2709056 CCTC-TTCCTCT
1 CCTCTTTCCTCT
2709067 CTCACACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 7 0.24
20 6 0.21
21 16 0.55
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (20 bp):
CCTCTTTCCTCTTTCATTTC
Found at i:2709063 original size:7 final size:7
Alignment explanation
Indices: 2709015--2709050 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
2709005 TATAGCACAG
2709015 CCTCTTT
1 CCTCTTT
2709022 CCTCTTT
1 CCTCTTT
2709029 CCTCTTT
1 CCTCTTT
2709036 CCTCTTT
1 CCTCTTT
2709043 CCTCTTT
1 CCTCTTT
2709050 C
1 C
2709051 ATTTCCCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
CCTCTTT
Found at i:2718506 original size:17 final size:16
Alignment explanation
Indices: 2718480--2718513 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2718470 ATATAATAAG
*
2718480 AAAGAGAACAAGAGTTT
1 AAAGAAAACAAGA-TTT
2718497 AAAGAAAACAAGATTT
1 AAAGAAAACAAGATTT
2718513 A
1 A
2718514 GAAGTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (16 bp):
AAAGAAAACAAGATTT
Found at i:2721076 original size:14 final size:14
Alignment explanation
Indices: 2721057--2721088 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2721047 TGATGTTCAC
2721057 TAGTTTTTTTCTAA
1 TAGTTTTTTTCTAA
2721071 TAG-TTTTTTCTAA
1 TAGTTTTTTTCTAA
2721084 TAGTT
1 TAGTT
2721089 ATAGATGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.62
Consensus pattern (14 bp):
TAGTTTTTTTCTAA
Found at i:2723778 original size:29 final size:29
Alignment explanation
Indices: 2723736--2723792 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2723726 AATAAAAAAT
2723736 TATTTACTAACTCTTGAAACTTTAATAAC
1 TATTTACTAACTCTTGAAACTTTAATAAC
*
2723765 TATTTTCTAACTCTTGAAACTTTAATAA
1 TATTTACTAACTCTTGAAACTTTAATAA
2723793 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.44
Consensus pattern (29 bp):
TATTTACTAACTCTTGAAACTTTAATAAC
Found at i:2732756 original size:24 final size:24
Alignment explanation
Indices: 2732721--2732782 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2732711 TTGATATTAT
2732721 AATAT-TTATAAATATATACTT-TCA
1 AATATGTT-TAAATATATACTTGT-A
* *
2732745 AATATGTTTAAATATATAGTTGTG
1 AATATGTTTAAATATATACTTGTA
2732769 AATATGTTTAAATA
1 AATATGTTTAAATA
2732783 ATTAAATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (24 bp):
AATATGTTTAAATATATACTTGTA
Found at i:2732792 original size:24 final size:24
Alignment explanation
Indices: 2732745--2732792 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2732735 TATACTTTCA
**
2732745 AATATGTTTAAATATATAGTTGTG
1 AATATGTTTAAATATATAAATGTG
2732769 AATATGTTTAAATA-ATTAAATGTG
1 AATATGTTTAAATATA-TAAATGTG
2732793 TATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (24 bp):
AATATGTTTAAATATATAAATGTG
Found at i:2735762 original size:21 final size:20
Alignment explanation
Indices: 2735677--2735833 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
2735667 AATGACCAAT
** *
2735677 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
2735696 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
2735716 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
2735736 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
2735757 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
2735778 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
2735799 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
2735819 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
2735834 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:2735843 original size:20 final size:20
Alignment explanation
Indices: 2735800--2735992 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
2735790 CGATTTTCCA
* ** *
2735800 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2735820 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2735840 AAATCGC-ACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2735859 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2735879 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2735899 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2735919 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2735939 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2735959 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2735980 AAATCGCAACGCG
1 AAATCGCAACGCG
2735993 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.11
20 112 0.78
21 15 0.10
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2736414 original size:33 final size:33
Alignment explanation
Indices: 2736375--2736445 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2736365 TTCACTTAGA
*
2736375 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2736408 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2736441 TTTCA
1 TTTCA
2736446 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2736569 original size:20 final size:20
Alignment explanation
Indices: 2736527--2736634 Score: 104
Period size: 21 Copynumber: 5.7 Consensus size: 20
2736517 CAGAAGAGTT
*
2736527 GCAACGAGATAAATGAAAATC
1 GCAACGAGA-GAATGAAAATC
***
2736548 GCAACGAGAGAATGACTGTC
1 GCAACGAGAGAATGAAAATC
2736568 GCAACGAGAGAAATGAAAATC
1 GCAACGAGAG-AATGAAAATC
2736589 GCAAC--GAG-A-G--AATC
1 GCAACGAGAGAATGAAAATC
*
2736603 GCAACGCGA-AATGAAAATC
1 GCAACGAGAGAATGAAAATC
2736622 GCAACGAGAGAAT
1 GCAACGAGAGAAT
2736635 CACAACGCGA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 2 0.03
19 15 0.21
20 20 0.28
21 21 0.30
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
GCAACGAGAGAATGAAAATC
Found at i:2736584 original size:41 final size:37
Alignment explanation
Indices: 2736527--2736634 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 37
2736517 CAGAAGAGTT
*
2736527 GCAACGAGATAAATGAAAATCGCAACGAGAGAATGACTGTC
1 GCAACGAGAGAAATGAAAATCGCAACGAGAGAAT-A---TC
2736568 GCAACGAGAGAAATGAAAATCGCAACGAGAG-A-ATC
1 GCAACGAGAGAAATGAAAATCGCAACGAGAGAATATC
*
2736603 GCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 GCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
2736635 CACAACGCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
33 23 0.37
34 1 0.02
35 7 0.11
38 1 0.02
40 1 0.02
41 30 0.48
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (37 bp):
GCAACGAGAGAAATGAAAATCGCAACGAGAGAATATC
Found at i:2736604 original size:14 final size:14
Alignment explanation
Indices: 2736585--2736641 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2736575 GAGAAATGAA
2736585 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2736599 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2736618 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2736632 AATCACAACG
1 AATCGCAACG
2736642 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2736617 original size:33 final size:33
Alignment explanation
Indices: 2736577--2736657 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2736567 CGCAACGAGA
*
2736577 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
2736610 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
**
2736643 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2736658 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:2736675 original size:19 final size:19
Alignment explanation
Indices: 2736653--2736780 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
2736643 GAAACCAAAA
*
2736653 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2736672 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2736686 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2736705 TCGCGTTGC-A-ATTC---
1 TCGCGTTGCGATTTTCATT
*
2736719 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
2736739 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
2736759 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2736779 TC
1 TC
2736781 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 18 0.21
15 1 0.01
16 6 0.07
17 6 0.07
18 1 0.01
19 20 0.24
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2736694 original size:14 final size:14
Alignment explanation
Indices: 2736675--2736731 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2736665 TTTCATTTCG
2736675 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2736689 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
2736708 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
2736722 CGTTGCGATT
1 CGTTGCGATT
2736732 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2736700 original size:33 final size:33
Alignment explanation
Indices: 2736658--2736780 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
2736648 CAAAATCGCA
2736658 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2736691 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2736724 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
2736765 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2736781 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.56
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 2 0.03
40 2 0.03
41 21 0.27
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2736742 original size:21 final size:21
Alignment explanation
Indices: 2736716--2736780 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2736706 CGCGTTGCAA
2736716 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2736737 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2736757 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2736778 TTC
1 TTC
2736781 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2738622 original size:92 final size:91
Alignment explanation
Indices: 2738465--2738652 Score: 351
Period size: 92 Copynumber: 2.1 Consensus size: 91
2738455 TAGATTGCTT
2738465 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2738530 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 -TTGTCTTTGTTTTGTCTTTTGGTTG-A
2738557 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2738622 TTGTCTTTGTTTTGTCTTTTGGTTGA
66 TTGTCTTTGTTTTGTCTTTTGGTTGA
2738648 AGTAA
1 AGTAA
2738653 TGCAATCCAT
Statistics
Matches: 95, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
91 15 0.16
92 80 0.84
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (91 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2738739 original size:19 final size:20
Alignment explanation
Indices: 2738699--2738745 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
2738689 TAGTTTACTT
* *
2738699 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTGAAAA
2738719 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTGAAAA
2738738 TCGCAACG
1 TCGCAACG
2738746 ACAGAATCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTGAAAA
Found at i:2738774 original size:19 final size:19
Alignment explanation
Indices: 2738699--2738775 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
2738689 TAGTTTACTT
* *
2738699 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
2738719 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2738738 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2738752 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2738771 TCGCA
1 TCGCA
2738776 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 19 0.41
20 12 0.26
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2738793 original size:19 final size:19
Alignment explanation
Indices: 2738771--2738924 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
2738761 GAAACCAAAA
*
2738771 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2738790 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2738806 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
2738823 TCACATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2738839 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2738856 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2738875 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
2738894 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2738914 TCGTGTTGCGA
1 TCGCGTTGCGA
2738925 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 15 0.14
16 11 0.10
17 11 0.10
19 60 0.55
20 12 0.11
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2738812 original size:14 final size:14
Alignment explanation
Indices: 2738793--2738849 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2738783 TTTCATTTCG
2738793 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2738807 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
2738824 CACATTGCGATTCTGT
1 --CGTTGCGATTCTTT
2738840 CGTTGCGATT
1 CGTTGCGATT
2738850 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2738818 original size:33 final size:33
Alignment explanation
Indices: 2738776--2738906 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
2738766 CAAAATCGCA
2738776 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* * *
2738809 TTGCGATTTTCATTTCACATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
2738842 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TT--CTT-TCG
*
2738880 TTGCGATTATCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2738907 TTAAGTTTCG
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
33 53 0.62
35 2 0.02
36 2 0.02
37 1 0.01
38 27 0.32
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:2739440 original size:21 final size:20
Alignment explanation
Indices: 2739381--2739440 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
2739371 CTCGAGAGTC
*
2739381 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * *
2739401 CCACTGTCATCATT-GAGAGG
1 CC-CTCCCACCATTCAAGAGG
2739421 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
2739441 CCCGATTCAC
Statistics
Matches: 28, Mismatches: 9, Indels: 5
0.67 0.21 0.12
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:2740848 original size:14 final size:14
Alignment explanation
Indices: 2740829--2740864 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2740819 ATTGTTTAAT
2740829 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2740843 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2740857 TGATTTGT
1 TGATTTGT
2740865 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2741025 original size:20 final size:19
Alignment explanation
Indices: 2740971--2741035 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
2740961 AAAAATGATT
2740971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2740990 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2741009 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2741029 ATCGCAA
1 ATCGCAA
2741036 CGAGAGAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2741072 original size:19 final size:19
Alignment explanation
Indices: 2741044--2741194 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
2741034 AACGAGAGAA
* *
2741044 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
2741063 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2741079 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2741096 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2741115 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2741131 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2741148 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
2741166 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2741182 TCGCATTGCGATT
1 TCGCATTGCGATT
2741195 CTCTCGTTGC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
14 23 0.21
16 16 0.15
17 12 0.11
18 3 0.03
19 42 0.39
20 12 0.11
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2741107 original size:52 final size:52
Alignment explanation
Indices: 2741044--2741163 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
2741034 AACGAGAGAA
*
2741044 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
2741096 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2741148 TCCGCATTGCGATTTT
1 T-CGCATTGCGATTTT
2741164 CATGTTGGGA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 51 0.78
53 14 0.22
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2741216 original size:33 final size:33
Alignment explanation
Indices: 2741101--2741208 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
2741091 TCATTTCGCA
2741101 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2741134 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
2741168 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
2741201 TTGCGATT
1 TTGCGATT
2741209 GTAATTTCCG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2744384 original size:20 final size:20
Alignment explanation
Indices: 2744356--2744583 Score: 219
Period size: 20 Copynumber: 11.5 Consensus size: 20
2744346 AAAATTCAGT
* * *
2744356 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2744376 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2744396 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2744416 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2744436 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2744456 G-TGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
2744475 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
2744495 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2744515 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2744535 GTTGTGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
2744555 GTTGCGATTT-CATATTCGC
1 GTTGCGATTTACGGATTCGC
2744574 GTTGCGATTT
1 GTTGCGATTT
2744584 TGGAAAATCG
Statistics
Matches: 178, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
19 32 0.18
20 145 0.81
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2744575 original size:79 final size:79
Alignment explanation
Indices: 2744378--2744583 Score: 231
Period size: 79 Copynumber: 2.6 Consensus size: 79
2744368 AGATTCTCGT
* * * * *
2744378 TGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCG
1 TGCGATATACGGA-TACGCGTTGCGATTTACACATTCGCGTTGCGATTTACGGATTAACGTTGCG
2744442 ATTTACGGATACGCG
65 ATTTACGGATACGCG
* * *
2744457 TGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGA-TACACGTTGCG
1 TGCGATATACGGATACGCGTTGCGATTTACACATTCGCGTTGCGATTTACGGATTA-ACGTTGCG
2744521 ATTTACGGATACGCG
65 ATTTACGGATACGCG
* * * * *
2744536 TTGTGATTTATGTG-TTCGCGTTGCGATTT-CATATTCGCGTTGCGATTT
1 -TGCGATATACG-GATACGCGTTGCGATTTACACATTCGCGTTGCGATTT
2744584 TGGAAAATCG
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
78 4 0.04
79 81 0.76
80 21 0.20
81 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (79 bp):
TGCGATATACGGATACGCGTTGCGATTTACACATTCGCGTTGCGATTTACGGATTAACGTTGCGA
TTTACGGATACGCG
Found at i:2744600 original size:21 final size:21
Alignment explanation
Indices: 2744570--2744651 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
2744560 GATTTCATAT
*
2744570 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2744591 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2744612 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2744633 TCGCGTTGCGA-TTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2744652 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 6 0.13
21 41 0.87
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2747901 original size:21 final size:22
Alignment explanation
Indices: 2747864--2747907 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2747854 TTATATTATA
2747864 AATTTTAATAATATA-TTATTT
1 AATTTTAATAATATATTTATTT
*
2747885 AATTTTATTAA-ATTATTTATTT
1 AATTTTAATAATA-TATTTATTT
2747907 A
1 A
2747908 TTGAACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 12 0.60
22 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTTTAATAATATATTTATTT
Done.