Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 31
Found at i:433 original size:3 final size:3
Alignment explanation
Indices: 427--542 Score: 121
Period size: 3 Copynumber: 39.0 Consensus size: 3
417 TTCATTTAAA
** *
427 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AGT A-T ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
473 ATT A-T ATT ATT ATT ATT ATA ATA ATA ATAA ATT TTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
518 ATT ATT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT
543 TAATAAATAA
Statistics
Matches: 99, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
2 6 0.06
3 87 0.88
4 6 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:555 original size:28 final size:28
Alignment explanation
Indices: 427--555 Score: 124
Period size: 28 Copynumber: 4.7 Consensus size: 28
417 TTCATTTAAA
427 ATTATTATTATTAA-AATTAT-TATTATT
1 ATTATTATTA-TAATAATTATATATTATT
* *
454 ATTATTAGTAT-ATTATTATAT-TATATT
1 ATTATTATTATAATAATTATATAT-TATT
* * *
481 ATTATTATTATAATAATAATAAATTTTT
1 ATTATTATTATAATAATTATATATTATT
* *
509 ATTATTATTATTATTATTATATATTATT
1 ATTATTATTATAATAATTATATATTATT
*
537 ATTATT-TAATAAATAATTA
1 ATTATTATTAT-AATAATTA
556 CAAAACTGGA
Statistics
Matches: 81, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 7 0.09
27 27 0.33
28 45 0.56
29 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTATTATTATAATAATTATATATTATT
Found at i:5136 original size:20 final size:20
Alignment explanation
Indices: 5111--5151 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5101 AAATCGATTT
5111 GGGTTGACTCAGGTTGGTTC
1 GGGTTGACTCAGGTTGGTTC
* *
5131 GGGTTGACTTAGTTTGGTTC
1 GGGTTGACTCAGGTTGGTTC
5151 G
1 G
5152 AATTGACTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.39, T:0.39
Consensus pattern (20 bp):
GGGTTGACTCAGGTTGGTTC
Found at i:5157 original size:20 final size:20
Alignment explanation
Indices: 5114--5160 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
5104 TCGATTTGGG
**
5114 TTGACTCAGGTTGGTTCGGG
1 TTGACTCAGGTTGGTTCGAA
* *
5134 TTGACTTAGTTTGGTTCGAA
1 TTGACTCAGGTTGGTTCGAA
5154 TTGACTC
1 TTGACTC
5161 GGACCGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (20 bp):
TTGACTCAGGTTGGTTCGAA
Found at i:14422 original size:11 final size:11
Alignment explanation
Indices: 14406--14463 Score: 73
Period size: 11 Copynumber: 5.3 Consensus size: 11
14396 TTGAACATAC
14406 AAACGAACGA-T
1 AAACGAAC-ACT
14417 AAACGAACACT
1 AAACGAACACT
14428 AAACGAACACT
1 AAACGAACACT
**
14439 AAATAAACACT
1 AAACGAACACT
*
14450 AAATGAACACT
1 AAACGAACACT
14461 AAA
1 AAA
14464 TGAATGTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
10 1 0.02
11 42 0.98
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (11 bp):
AAACGAACACT
Found at i:14464 original size:11 final size:11
Alignment explanation
Indices: 14416--14467 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
14406 AAACGAACGA
*
14416 TAAACGAACAC
1 TAAATGAACAC
*
14427 TAAACGAACAC
1 TAAATGAACAC
*
14438 TAAATAAACAC
1 TAAATGAACAC
14449 TAAATGAACAC
1 TAAATGAACAC
14460 TAAATGAA
1 TAAATGAA
14468 TGTGTTTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (11 bp):
TAAATGAACAC
Found at i:15795 original size:41 final size:43
Alignment explanation
Indices: 15725--15811 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 43
15715 AATTACGACT
*
15725 ATTAATAATGAATATGAATTTGGACTAAAGACTT-G-AAAATA
1 ATTAATAATGAATATGAATTTAGACTAAAGACTTAGAAAAATA
* * *
15766 ATTAATAATGAATATGCATTTAGATTAAAGATTTAGAAAAATA
1 ATTAATAATGAATATGAATTTAGACTAAAGACTTAGAAAAATA
15809 ATT
1 ATT
15812 GTTTCCATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 30 0.75
42 1 0.03
43 9 0.22
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.34
Consensus pattern (43 bp):
ATTAATAATGAATATGAATTTAGACTAAAGACTTAGAAAAATA
Found at i:15928 original size:19 final size:20
Alignment explanation
Indices: 15889--15928 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15879 TTGTCATCGA
15889 TTTCTTTTATTTTTTACATT
1 TTTCTTTTATTTTTTACATT
15909 TTTCTTTTATTTTTTA-ATT
1 TTTCTTTTATTTTTTACATT
15928 T
1 T
15929 ATCTCATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCTTTTATTTTTTACATT
Found at i:16043 original size:13 final size:14
Alignment explanation
Indices: 16025--16053 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16015 TTATAATAGA
16025 TTTTATTTTTT-AT
1 TTTTATTTTTTGAT
16038 TTTTATTTTTTGAT
1 TTTTATTTTTTGAT
16052 TT
1 TT
16054 ATTGATCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTATTTTTTGAT
Found at i:16498 original size:30 final size:30
Alignment explanation
Indices: 16464--16524 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
16454 ATTTCGTGGA
16464 TTTCGTACCGTATCCGTTTCAATTGGAACG
1 TTTCGTACCGTATCCGTTTCAATTGGAACG
16494 TTTCGTACCGTATCCGTTTCAATTGGAACG
1 TTTCGTACCGTATCCGTTTCAATTGGAACG
16524 T
1 T
16525 GAATGAGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTCGTACCGTATCCGTTTCAATTGGAACG
Found at i:21480 original size:20 final size:20
Alignment explanation
Indices: 21446--21491 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21436 AATGATTTTC
* * *
21446 TTTTG-AAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
21465 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
21485 TTTTGAA
1 TTTTGAA
21492 TAATGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:23739 original size:42 final size:43
Alignment explanation
Indices: 23658--23747 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 43
23648 AAATAATAAA
* *
23658 TAAATATTAAGTAAATCAAAGGGGAAAAAAAATTAAAAAATG-
1 TAAATATTAAATAAATCAAAGGGGAAAAAAAAATAAAAAATGT
23700 TAAATATTAAATAAATC-AAGGGGAAAAAATAAA-ATAAAAATGT
1 TAAATATTAAATAAATCAAAGGGGAAAAAA-AAATA-AAAAATGT
23743 TAAAT
1 TAAAT
23748 TTCAAAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 13 0.30
42 25 0.58
43 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.23
Consensus pattern (43 bp):
TAAATATTAAATAAATCAAAGGGGAAAAAAAAATAAAAAATGT
Found at i:25108 original size:7 final size:7
Alignment explanation
Indices: 25098--25144 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
25088 AAACGAAAAT
25098 AAATAAA
1 AAATAAA
25105 AAAT-AA
1 AAATAAA
*
25111 ATATAAA
1 AAATAAA
*
25118 ATAATAAT
1 A-AATAAA
*
25126 AAATATA
1 AAATAAA
25133 AAATAAA
1 AAATAAA
25140 AAATA
1 AAATA
25145 CTAATAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 5 0.16
7 22 0.69
8 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAATAAA
Found at i:25109 original size:11 final size:11
Alignment explanation
Indices: 25093--25173 Score: 76
Period size: 11 Copynumber: 7.0 Consensus size: 11
25083 CCAAAAAACG
25093 AAAATAAATAA
1 AAAATAAATAA
*
25104 AAAATAAATAT
1 AAAATAAATAA
25115 AAAAT-AATAA
1 AAAATAAATAA
25125 TAAATATAAAATAA
1 -AAA-AT-AAATAA
25139 AAAATACTAATAA
1 AAAATA--AATAA
25152 AATAATAAAT-A
1 AA-AATAAATAA
*
25163 AGAATAAATAA
1 AAAATAAATAA
25174 TATCAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
10 11 0.19
11 22 0.37
12 7 0.12
13 10 0.17
14 9 0.15
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:25119 original size:18 final size:18
Alignment explanation
Indices: 25098--25163 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
25088 AAACGAAAAT
25098 AAATAAAAAATAAATATA
1 AAATAAAAAATAAATATA
*
25116 AAAT-AATAATAAATATA
1 AAATAAAAAATAAATATA
*
25133 AAATAAAAAAT-ACTAATA
1 AAATAAAAAATAAAT-ATA
*
25151 AAATAATAAATAA
1 AAATAAAAAATAA
25164 GAATAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 18 0.44
18 22 0.54
19 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAAAAATAAATATA
Found at i:25192 original size:35 final size:34
Alignment explanation
Indices: 25098--25193 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 34
25088 AAACGAAAAT
25098 AAATAAAAAATA-AATATAAAATAATAATAAATATA
1 AAATAAAAAATACAATAT-AAAT-ATAATAAATATA
*
25133 AAATAAAAAATACTA-ATAAA-ATAATAAATA-A
1 AAATAAAAAATACAATATAAATATAATAAATATA
* *
25164 GAATAAATAATATCAATATAATATATAATA
1 AAATAAAAAATA-CAATATAA-ATATAATA
25194 TAAAAAATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 11 0.21
32 12 0.23
33 4 0.08
34 4 0.08
35 20 0.38
36 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.27
Consensus pattern (34 bp):
AAATAAAAAATACAATATAAATATAATAAATATA
Found at i:25219 original size:36 final size:36
Alignment explanation
Indices: 25179--25375 Score: 157
Period size: 37 Copynumber: 5.3 Consensus size: 36
25169 AATAATATCA
* * **
25179 ATATAATATATAATATAAAAAATCATTTTTAAAACT
1 ATATAATATATAATTTTAAAAATTGTTTTTAAAACT
** * *
25215 ATATATTATATATGGTTTTAAAAATTGTTTTCAAAACC
1 ATATA--ATATATAATTTTAAAAATTGTTTTTAAAACT
*
25253 ATATAATATAT-ATTTTTAAAATTGTTTTTAAAACT
1 ATATAATATATAATTTTAAAAATTGTTTTTAAAACT
* * *
25288 ATATATTATATATATTTTCAAAA-TGTTTTCAAAAACT
1 ATATAATATATA-ATTTTAAAAATTGTTTT-TAAAACT
* * * *
25325 ATATATTATATATATATTCAAAA-TGTTTTCAAAAACT
1 ATATAATATATA-ATTTTAAAAATTGTTTT-TAAAACT
25362 ATATTACATATATA
1 ATA-TA-ATATATA
25376 TGTTTTCAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
35 30 0.22
36 17 0.12
37 54 0.39
38 30 0.22
39 6 0.04
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATAATATATAATTTTAAAAATTGTTTTTAAAACT
Found at i:25311 original size:37 final size:36
Alignment explanation
Indices: 25204--25450 Score: 212
Period size: 37 Copynumber: 6.9 Consensus size: 36
25194 TAAAAAATCA
* * *
25204 TTTTTAAAACTATATATTATATATGGTTTTAAAAATTG
1 TTTTAAAAACTATATATTATATAT-ATTTTCAAAA-TG
* * *
25242 TTTTCAAAACCATATA--ATATATATTTTTAAAATTG
1 TTTTAAAAACTATATATTATATATATTTTCAAAA-TG
*
25277 TTTTTAAAACTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
*
25313 TTTTCAAAAACTATATATTATATATATATTCAAAATG
1 TTTT-AAAAACTATATATTATATATATTTTCAAAATG
*
25350 TTTTCAAAAAC--TATATTACATATA---T----ATG
1 TTTT-AAAAACTATATATTATATATATTTTCAAAATG
* *
25378 TTTTCAAAAACTATATAGTATATACATGTTTTCAAAAT-
1 TTTT-AAAAACTATATA-T-TATATATATTTTCAAAATG
**
25416 TTTTCAAAAACCGTATATTATATATATTTTCAAAA
1 TTTT-AAAAACTATATATTATATATATTTTCAAAA
25451 ACTATATATT
Statistics
Matches: 178, Mismatches: 17, Indels: 30
0.79 0.08 0.13
Matches are distributed among these distances:
28 14 0.08
30 4 0.02
31 1 0.01
32 6 0.03
35 38 0.21
36 27 0.15
37 57 0.32
38 29 0.16
39 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATG
Found at i:25378 original size:28 final size:28
Alignment explanation
Indices: 25347--25414 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
25337 TATATTCAAA
*
25347 ATGTTTTCAAAAACTATATTA-CATATAT
1 ATGTTTTCAAAAACTATA-TAGCATATAC
*
25375 ATGTTTTCAAAAACTATATAGTATATAC
1 ATGTTTTCAAAAACTATATAGCATATAC
25403 ATGTTTTCAAAA
1 ATGTTTTCAAAA
25415 TTTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATATAGCATATAC
Found at i:25451 original size:26 final size:25
Alignment explanation
Indices: 25414--25479 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
25404 TGTTTTCAAA
*
25414 ATTTTTCAAAAACCGTATATTATAT
1 ATTTTTCAAAAACCATATATTATAT
*
25439 ATATTTTCAAAAACTATATATTATAT
1 AT-TTTTCAAAAACCATATATTATAT
* *
25465 ATGTTTCAAAGACCA
1 ATTTTTCAAAAACCA
25480 ATTTGTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 12 0.34
26 23 0.66
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (25 bp):
ATTTTTCAAAAACCATATATTATAT
Found at i:26868 original size:46 final size:46
Alignment explanation
Indices: 26801--26895 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
26791 AGACAACTTT
26801 TCTCAGCTTAAGTTGTGCTATAAATTTTCCTCTAAATGAAGGATGG
1 TCTCAGCTTAAGTTGTGCTATAAATTTTCCTCTAAATGAAGGATGG
26847 TCTCAGCTTAAGTTGTGCTATAAATTTTCCTCTAAATGAAGGATGG
1 TCTCAGCTTAAGTTGTGCTATAAATTTTCCTCTAAATGAAGGATGG
26893 TCT
1 TCT
26896 TCCTTCTCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (46 bp):
TCTCAGCTTAAGTTGTGCTATAAATTTTCCTCTAAATGAAGGATGG
Found at i:32317 original size:41 final size:42
Alignment explanation
Indices: 32270--32356 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 42
32260 CATAATAACT
* *
32270 AAATATTAAGTAAATCAAAGGGGAAAA-AATA-AAAAAATGTA
1 AAATATTAAATAAATC-AAGGGGAAAATAAAATAAAAAATGTA
* *
32311 AAATATTAAATACATCAAGGGGAAAATAAAATAAAAAATGTT
1 AAATATTAAATAAATCAAGGGGAAAATAAAATAAAAAATGTA
32353 AAAT
1 AAAT
32357 TTCAAAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 10 0.25
41 17 0.43
42 13 0.32
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.22
Consensus pattern (42 bp):
AAATATTAAATAAATCAAGGGGAAAATAAAATAAAAAATGTA
Found at i:32379 original size:2 final size:2
Alignment explanation
Indices: 32372--32438 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
32362 AAGTAATAAA
32372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32414 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
32439 AACCCAAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33711 original size:10 final size:10
Alignment explanation
Indices: 33691--33799 Score: 71
Period size: 10 Copynumber: 10.4 Consensus size: 10
33681 CCTAAAAGCG
33691 AAAATAA-AT
1 AAAATAATAT
*
33700 AAAAAAATAT
1 AAAATAATAT
33710 AAAATAATAT
1 AAAATAATAT
33720 AAAATAATA-
1 AAAATAATAT
* * *
33729 AATATAAAAGA
1 AAAATAATA-T
*
33740 AAAATATTAAT
1 AAAATAAT-AT
33751 AAAATAATAAAT
1 AAAATAAT--AT
33763 AAAAATAA-AT
1 -AAAATAATAT
*
33773 AATATCAATAT
1 AAAAT-AATAT
33784 AATATATAATAT
1 AA-A-ATAATAT
33796 AAAA
1 AAAA
33800 AATCATTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 19
0.72 0.10 0.17
Matches are distributed among these distances:
9 17 0.22
10 25 0.32
11 17 0.22
12 11 0.14
13 9 0.11
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.27
Consensus pattern (10 bp):
AAAATAATAT
Found at i:33734 original size:14 final size:14
Alignment explanation
Indices: 33715--33770 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
33705 AATATAAAAT
33715 AATATAAAATAATA
1 AATATAAAATAATA
* *
33729 AATATAAAAGAAAA
1 AATATAAAATAATA
33743 ATATTAATAAAATAATA
1 A-A-T-ATAAAATAATA
33760 AATA-AAAATAA
1 AATATAAAATAA
33771 ATAATATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 7 0.20
14 14 0.40
15 2 0.06
16 2 0.06
17 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AATATAAAATAATA
Found at i:33756 original size:31 final size:31
Alignment explanation
Indices: 33710--33799 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
33700 AAAAAAATAT
*
33710 AAAATAAT-ATAAAATAATAAATATAAAAGA
1 AAAATATTAATAAAATAATAAATATAAAAGA
*
33740 AAAATATTAATAAAATAATAAATA-AAAATA
1 AAAATATTAATAAAATAATAAATATAAAAGA
* *
33770 AATAATATCAATATAAT-ATATAATATAAAA
1 AA-AATATTAATAAAATAATA-AATATAAAA
33800 AATCATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
30 17 0.33
31 31 0.60
32 4 0.08
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (31 bp):
AAAATATTAATAAAATAATAAATATAAAAGA
Found at i:33760 original size:8 final size:8
Alignment explanation
Indices: 33696--33761 Score: 50
Period size: 7 Copynumber: 8.2 Consensus size: 8
33686 AAGCGAAAAT
*
33696 AAATAAAA
1 AAATAATA
33704 AAAT-ATA
1 AAATAATA
33711 AAATAATATA
1 AAAT-A-ATA
33721 AAATAAT-
1 AAATAATA
33728 AAAT-ATA
1 AAATAATA
*
33735 AAAGAA-A
1 AAATAATA
33742 AATATTAATA
1 AA-A-TAATA
33752 AAATAATA
1 AAATAATA
33760 AA
1 AA
33762 TAAAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
6 2 0.04
7 16 0.34
8 15 0.32
9 4 0.09
10 10 0.21
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:33820 original size:36 final size:36
Alignment explanation
Indices: 33780--34052 Score: 185
Period size: 36 Copynumber: 7.3 Consensus size: 36
33770 AATAATATCA
* * **
33780 ATATAATATATAATATAAAAAATCATTTTTAAAACT
1 ATATAATATATAATTTTAAAAATTGTTTTTAAAACT
** * *
33816 ATATATTATATATGCTTTTAAAAATTGTTTTCAAAACC
1 ATATA--ATATATAATTTTAAAAATTGTTTTTAAAACT
*
33854 ATATAATATATATTTTTAAAAATTGTTTTTAAAACT
1 ATATAATATATAATTTTAAAAATTGTTTTTAAAACT
* * *
33890 ATATATTATATATATTTTCAAAA-TGTTTTCAAAAACT
1 ATATAATATATA-ATTTTAAAAATTGTTTT-TAAAACT
* * *
33927 ATATATTATATATATGTTTTCAAAA-TGTTTTCAAAAACT
1 ATATA--ATATATA-ATTTTAAAAATTGTTTT-TAAAACT
* * * **
33966 ATATAGTATATACATGTTTTCAAAA-TATTTCAAAAACT
1 ATATAATATATA-A--TTTTAAAAATTGTTTTTAAAACT
* * *
34004 GTATATTATATATATTTTCAAAA-TGTTTTTAAAAACT
1 ATATAATATATA-ATTTTAAAAATTGTTTTT-AAAACT
*
34041 ATATATTATATA
1 ATATAATATATA
34053 TATGTTTTCA
Statistics
Matches: 198, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
36 62 0.31
37 42 0.21
38 46 0.23
39 48 0.24
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATAATATATAATTTTAAAAATTGTTTTTAAAACT
Found at i:33947 original size:39 final size:39
Alignment explanation
Indices: 33810--34065 Score: 320
Period size: 39 Copynumber: 6.8 Consensus size: 39
33800 AATCATTTTT
*
33810 AAAACTATATA-T-TATATATGCTTTTAAAAATTGTTTTC-
1 AAAACTATATATTATATATATG-TTTTCAAAA-TGTTTTCA
* * *
33848 AAAACCATATA--ATATATAT-TTTTAAAAATTGTTTT-T
1 AAAACTATATATTATATATATGTTTTCAAAA-TGTTTTCA
33884 AAAACTATATATTATATATA--TTTTCAAAATGTTTTCA
1 AAAACTATATATTATATATATGTTTTCAAAATGTTTTCA
33921 AAAACTATATATTATATATATGTTTTCAAAATGTTTTCA
1 AAAACTATATATTATATATATGTTTTCAAAATGTTTTCA
* * *
33960 AAAACTATATAGTATATACATGTTTTCAAAAT-ATTTCA
1 AAAACTATATATTATATATATGTTTTCAAAATGTTTTCA
* *
33998 AAAACTGTATATTATATATA--TTTTCAAAATGTTTTTA
1 AAAACTATATATTATATATATGTTTTCAAAATGTTTTCA
34035 AAAACTATATATTATATATATGTTTTCAAAA
1 AAAACTATATATTATATATATGTTTTCAAAA
34066 ACTATACAAT
Statistics
Matches: 195, Mismatches: 13, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
36 42 0.22
37 51 0.26
38 46 0.24
39 56 0.29
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (39 bp):
AAAACTATATATTATATATATGTTTTCAAAATGTTTTCA
Found at i:34024 original size:114 final size:112
Alignment explanation
Indices: 33810--34065 Score: 358
Period size: 114 Copynumber: 2.3 Consensus size: 112
33800 AATCATTTTT
* *
33810 AAAACTATATA-T-TATATATGCTTTTAAAAATTGTTTTCAAAACCATATAATATATATTTTTAA
1 AAAACTATATATTATATATATG-TTTTCAAAATTGTTTTCAAAACCATATAATATACATTTTTAA
* **
33873 AAATTGTTTTTAAAACTATATATTATATATATTTTCAAAATGTTTTCA
65 AAATTATTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
33921 AAAACTATATATTATATATATGTTTTCAAAA-TGTTTTCAAAAACTATATAGTATATACATGTTT
1 AAAACTATATATTATATATATGTTTTCAAAATTGTTTTC-AAAACCATATA--ATATACAT-TTT
* * *
33985 TCAAAA-TATTTCAAAAACTGTATATTATATATATTTTCAAAATGTTTTTA
62 TAAAAATTATTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCA
34035 AAAACTATATATTATATATATGTTTTCAAAA
1 AAAACTATATATTATATATATGTTTTCAAAA
34066 ACTATACAAT
Statistics
Matches: 130, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
111 18 0.14
112 19 0.15
113 8 0.06
114 77 0.59
115 8 0.06
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (112 bp):
AAAACTATATATTATATATATGTTTTCAAAATTGTTTTCAAAACCATATAATATACATTTTTAAA
AATTATTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCA
Found at i:34029 original size:75 final size:75
Alignment explanation
Indices: 33805--34065 Score: 311
Period size: 75 Copynumber: 3.5 Consensus size: 75
33795 TAAAAAATCA
* * * *
33805 TTTTTAAAACTATATAT-TATATATGCTTTTAAAAATTGTTTTC-AAAACCATATA--ATATATA
1 TTTTAAAAACTATATATATATATATG-TTTTCAAAA-TGATTTCAAAAACTATATATTATATATA
*
33866 TTTTTAAAAATTG
64 TTTTTCAAAA-TG
* * *
33879 TTTTTAAAACTATATAT-TATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATG
1 TTTTAAAAACTATATATATATATATGTTTTCAAAATGATTTCAAAAACTATATATTATATATAT-
33943 TTTTCAAAATG
65 TTTTCAAAATG
* *
33954 TTTTCAAAAACTATATAGTATATACATGTTTTCAAAAT-ATTTCAAAAACTGTATATTATATATA
1 TTTT-AAAAACTATATA-TATATATATGTTTTCAAAATGATTTCAAAAACTATATATTATATATA
34018 -TTTTCAAAATG
64 TTTTTCAAAATG
34029 TTTTTAAAAACTATATATTATATATATGTTTTCAAAA
1 -TTTTAAAAACTATATA-TATATATATGTTTTCAAAA
34066 ACTATACAAT
Statistics
Matches: 168, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
72 7 0.04
73 18 0.11
74 24 0.14
75 55 0.33
76 23 0.14
77 25 0.15
78 16 0.10
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (75 bp):
TTTTAAAAACTATATATATATATATGTTTTCAAAATGATTTCAAAAACTATATATTATATATATT
TTTCAAAATG
Found at i:34078 original size:28 final size:28
Alignment explanation
Indices: 34026--34079 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
34016 TATTTTCAAA
* * *
34026 ATGTTTTTAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATACAATATATAT
34054 ATGTTTTCAAAAACTATACAATATAT
1 ATGTTTTCAAAAACTATACAATATAT
34080 GTTTTCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATACAATATATAT
Found at i:34090 original size:63 final size:60
Alignment explanation
Indices: 33993--34128 Score: 191
Period size: 63 Copynumber: 2.2 Consensus size: 60
33983 TTTCAAAATA
** *
33993 TTTCAAAAACTGTATATTATATATATTTTCAAAATGTTTTTAAAAACTATATATTATATATATG
1 TTTCAAAAAC--TATACAATATATATTTTCAAAATGTTTTCAAAAACTATATA-T-TATATATG
*
34057 TTTTCAAAAACTATACAATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATG
1 -TTTCAAAAACTATACAATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATG
34118 TTTCAAAAACT
1 TTTCAAAAACT
34129 GATTTTTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
60 11 0.16
61 8 0.12
62 1 0.01
63 37 0.55
65 10 0.15
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (60 bp):
TTTCAAAAACTATACAATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATG
Found at i:35321 original size:2 final size:2
Alignment explanation
Indices: 35314--35338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35304 AAAAAGGAAA
35314 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
35339 CATCAAAGTA
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:35661 original size:2 final size:2
Alignment explanation
Indices: 35617--35645 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35607 ATAAAAAATA
35617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35646 AAGTTATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36037 original size:169 final size:175
Alignment explanation
Indices: 35824--36148 Score: 556
Period size: 178 Copynumber: 1.9 Consensus size: 175
35814 TATTAAAGAA
35824 ATATATATATAATAATAAAATATAGTAAAAAAAATCAAATGAAAATAATTTAAAA-A-ATATATA
1 ATATATATATAATAATAAAATATAGTAAAAAAAATCAAATGAAAATAATTTAAAATATATATATA
35887 TATACGTATAATAATAACATG-AAAAT-AAAT-T-AATAAAATATCCATATAATAAATAAAGGGA
66 TATACGTATAATAATAACATGAAAAATAAAATATGAATAAAATATCCATATAATAAATAAAGGGA
35948 CTAATATAGATTTTTAAAAAGCTCTTAATTAGGAAAGAAATATAT
131 CTAATATAGATTTTTAAAAAGCTCTTAATTAGGAAAGAAATATAT
35993 ATATATATAATAATAATAAAATATAGT-AAAAAAATCAAATGAAAATAATTTAAAATATATATAT
1 ATATATAT-ATAATAATAAAATATAGTAAAAAAAATCAAATGAAAATAATTTAAAATATATATAT
*
36057 ATATACGTATAATAATAACATGAAAAATAAAAATAAATGAATAAAATATCTATATAATAAATAAA
65 ATATACGTATAATAATAACATGAAAAAT-AAAAT--ATGAATAAAATATCCATATAATAAATAAA
36122 GGGACTAATATAGATTTTTAAAAAGCT
127 GGGACTAATATAGATTTTTAAAAAGCT
36149 ATTCCCCTCC
Statistics
Matches: 145, Mismatches: 1, Indels: 11
0.92 0.01 0.07
Matches are distributed among these distances:
169 36 0.25
170 19 0.13
171 28 0.19
172 5 0.03
174 4 0.03
177 1 0.01
178 52 0.36
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (175 bp):
ATATATATATAATAATAAAATATAGTAAAAAAAATCAAATGAAAATAATTTAAAATATATATATA
TATACGTATAATAATAACATGAAAAATAAAATATGAATAAAATATCCATATAATAAATAAAGGGA
CTAATATAGATTTTTAAAAAGCTCTTAATTAGGAAAGAAATATAT
Found at i:36527 original size:35 final size:35
Alignment explanation
Indices: 36482--36549 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
36472 AAAAACCCTA
36482 TTTAGACTAGTATTTGAGTCCTAATCCAACTCTAT
1 TTTAGACTAGTATTTGAGTCCTAATCCAACTCTAT
36517 TTTAGACTAGTATTTGAGTCCTAATCCAACTCT
1 TTTAGACTAGTATTTGAGTCCTAATCCAACTCT
36550 TCTTTTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.40
Consensus pattern (35 bp):
TTTAGACTAGTATTTGAGTCCTAATCCAACTCTAT
Found at i:37225 original size:106 final size:106
Alignment explanation
Indices: 37033--37766 Score: 958
Period size: 106 Copynumber: 7.0 Consensus size: 106
37023 TGTATTGTTC
* ** ** * *
37033 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTTG-CTCTGGAACTGGAAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAA-TTGACTCTAAAATTGGGAAATTGTTTGTTGAC
* * * * * *
37097 AGCCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
37139 TGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTAAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTGTTGACA
* *
37204 ACCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
37245 CGAGTCCAATATCCTTCGCTGTGAAGTTGGAATTGGCTCTGAAATTAGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTGTTGACA
37310 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG--GTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
37349 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGAC-CTTAAAATTGGGATATTGTTTATTGAT
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTC-TAAAATTGGGAAATTGTTTGTTGAC
**
37413 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCCGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
37455 CGAGTCCAATATCCTTCG--CT--A-TTG-----G-CTCTAAAATTGGGAGATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTGTTGACA
37509 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
37550 TGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTGTTGACA
*
37615 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
37656 CGAGTCCAACATCCTTTGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTAACA
1 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTGTTGACA
*
37721 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
37762 CGAGT
1 CGAGT
37767 GGCGCGATAT
Statistics
Matches: 555, Mismatches: 57, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
95 80 0.14
96 2 0.00
97 1 0.00
99 1 0.00
100 2 0.00
101 3 0.01
102 1 0.00
103 1 0.00
104 94 0.17
105 4 0.01
106 366 0.66
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:37595 original size:305 final size:306
Alignment explanation
Indices: 37177--37755 Score: 973
Period size: 305 Copynumber: 1.9 Consensus size: 306
37167 GAAATTGACC
*
37177 CTAAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTCG
1 CTAAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
** *
37242 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTGGAATTGGCTCTGAAATTAGGAAATTATTTGTTG
66 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAATTAGGAAATTATTTGTTG
* *
37307 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCTCGAGTCCAATATCCTTCGATGT
131 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCCCGAGTCCAACATCCTTCGATGT
* * *
37371 GAAGTTGAAATTGAC-CTTAAAATTGGGATATTGTTTATTGATAACCAGCCGTCCCTTCGTTGTG
196 GAAGTTGAAATTGACTC-TAAAATTGGGAAATTGTTTATTAACAACCAGCCGTCCCTTCGTTGTG
37435 AAGTTGAACTTGTGCCGTCTCGAGTCCAATATCCTTCGCTATTGGCT
260 AAGTTGAACTTGTGCCGTCTCGAGTCCAATATCCTTCGCTATTGGCT
* * *
37482 CTAAAATTGGGAGATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1 CTAAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
* *
37547 TCTTGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAATTGGGAAATTATTTGTTG
66 TCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAATTAGGAAATTATTTGTTG
*
37612 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAACATCCTTTGATG
131 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCCCGAGTCCAACATCCTTCGATG
* *
37677 TGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTGTTAACAACCAGCCGTCCCTTCGTTGTG
195 TGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTATTAACAACCAGCCGTCCCTTCGTTGTG
37742 AAGTTGAACTTGTG
260 AAGTTGAACTTGTG
37756 TTGTCCCGAG
Statistics
Matches: 254, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
305 159 0.63
307 94 0.37
308 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (306 bp):
CTAAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCG
TCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAAATTAGGAAATTATTTGTTG
ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCCCGAGTCCAACATCCTTCGATGT
GAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTATTAACAACCAGCCGTCCCTTCGTTGTGA
AGTTGAACTTGTGCCGTCTCGAGTCCAATATCCTTCGCTATTGGCT
Found at i:38902 original size:74 final size:76
Alignment explanation
Indices: 38762--38902 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 76
38752 TTATTTTGTT
* * * * *
38762 CTTTTTGTTCTTTTTTCCCTTTTTCATTTTTTTCAATTTAGGGCGCCCTTTCAGGTTTTCGCCCT
1 CTTTTTGTTCTTTTTTCCCTTTTTCA-TTTCTCCAACTTAGGACGCCCTTTCAGGTTTTCACCCT
38827 AAACGTTTTTCA
65 AAACGTTTTTCA
** * *
38839 CTTTTTGTTCTTTTTT-GTTTTTTC-TTTCTCCAACTTAGGACGCCCTTTCGGGTTTTCATCCTA
1 CTTTTTGTTCTTTTTTCCCTTTTTCATTTCTCCAACTTAGGACGCCCTTTCAGGTTTTCACCCTA
38902 A
66 A
38903 GCGAAGTATT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
74 33 0.60
76 6 0.11
77 16 0.29
ACGTcount: A:0.11, C:0.23, G:0.12, T:0.53
Consensus pattern (76 bp):
CTTTTTGTTCTTTTTTCCCTTTTTCATTTCTCCAACTTAGGACGCCCTTTCAGGTTTTCACCCTA
AACGTTTTTCA
Found at i:46045 original size:18 final size:18
Alignment explanation
Indices: 46014--46054 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
46004 AATGTGTTAG
*
46014 ATAAACAAGGTAAAGAAA
1 ATAAACAAGATAAAGAAA
* *
46032 ATAAATAAGATAAAGAGA
1 ATAAACAAGATAAAGAAA
46050 ATAAA
1 ATAAA
46055 ATAAAAGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.15
Consensus pattern (18 bp):
ATAAACAAGATAAAGAAA
Found at i:46288 original size:39 final size:40
Alignment explanation
Indices: 46245--46321 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
46235 TCACTTCACC
*
46245 GAAAGTGG-GAGACTTTAGTAAAAAATAAGACAAAAAGAG
1 GAAAGTGGAGAGACTTTAGTAAAAAATAAAACAAAAAGAG
* *
46284 GAAAGTGGAAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGG-AGAGACTTTAGTAAAAAATAAAACAAAAA
46322 AATGGGCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 8 0.24
41 25 0.76
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.17
Consensus pattern (40 bp):
GAAAGTGGAGAGACTTTAGTAAAAAATAAAACAAAAAGAG
Found at i:46491 original size:2 final size:2
Alignment explanation
Indices: 46441--46475 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46431 ATAAAAAATA
46441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46476 AAGTTATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46658 original size:2 final size:2
Alignment explanation
Indices: 46651--46684 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46641 AATATTAAAG
46651 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
46685 TAAAATATAG
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:46950 original size:17 final size:18
Alignment explanation
Indices: 46917--46952 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46907 ATATATACGT
*
46917 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
46935 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
46952 A
1 A
46953 AATATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:46965 original size:176 final size:182
Alignment explanation
Indices: 46657--47003 Score: 580
Period size: 176 Copynumber: 1.9 Consensus size: 182
46647 AAAGATATAT
*
46657 ATATATATATATATATATATATATATATTAAAATATAGTAAAAAAATCAAATGAAAATAATTTAA
1 ATATATATATATATATATATATATATAATAAAATATAGTAAAAAAATCAAATGAAAATAATTT--
*
46722 AATATATATATATATACGTATAATGATAACATGAAGAATAAAAATAAATGAATAAAATATCCATA
64 AATATATATATATATACGTATAATAATAACATGAAGAATAAAAATAAATGAATAAAATATCCATA
* *
46787 TAATAAATAAAGGGATTAATATAGATTTTTAAAAAGCTCTTGGTTAGGAAAGAA
129 TAATAAATAAAGGGACTAATATAGATTTTTAAAAAACTCTTGGTTAGGAAAGAA
46841 ATATATATATATATATATA-ATA-ATAATAAAATATAGTAAAAAAATCAAATGAAAATAATTT-A
1 ATATATATATATATATATATATATATAATAAAATATAGTAAAAAAATCAAATGAAAATAATTTAA
* *
46903 -A-A-ATATATATACGTATAATAATAACATGAATAATAAAAATAAATGAATAAAATATTCATATA
66 TATATATATATATACGTATAATAATAACATGAAGAATAAAAATAAATGAATAAAATATCCATATA
46965 ATAAATAAAGGGACTAATATAGATTTTTAAAAAACTCTT
131 ATAAATAAAGGGACTAATATAGATTTTTAAAAAACTCTT
47004 CCCATTCTTT
Statistics
Matches: 157, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
176 94 0.60
177 1 0.01
178 1 0.01
179 1 0.01
182 38 0.24
183 3 0.02
184 19 0.12
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (182 bp):
ATATATATATATATATATATATATATAATAAAATATAGTAAAAAAATCAAATGAAAATAATTTAA
TATATATATATATACGTATAATAATAACATGAAGAATAAAAATAAATGAATAAAATATCCATATA
ATAAATAAAGGGACTAATATAGATTTTTAAAAAACTCTTGGTTAGGAAAGAA
Found at i:47370 original size:35 final size:35
Alignment explanation
Indices: 47331--47402 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
47321 CTAAAAAACC
*
47331 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAATATTTGAGTCCTAATCCAACT
*
47366 CTATTTTTGACTAATATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAATATTTGAGTCCTAATCCAACT
47401 CT
1 CT
47403 TCTTTTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (35 bp):
CTATTTTAGACTAATATTTGAGTCCTAATCCAACT
Found at i:52668 original size:18 final size:18
Alignment explanation
Indices: 52641--52676 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52631 TTTAATTATT
* *
52641 TTCTTTTCTTTTCTTTTA
1 TTCTTATCTTTTATTTTA
52659 TTCTTATCTTTTATTTTA
1 TTCTTATCTTTTATTTTA
52677 GAAACAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (18 bp):
TTCTTATCTTTTATTTTA
Found at i:60105 original size:21 final size:21
Alignment explanation
Indices: 60081--60120 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60071 GTTTTCAATA
*
60081 AAAGTTTTTCTTTTTTTTTTC
1 AAAGTTTTTCTTTTGTTTTTC
*
60102 AAAGTTTTTGTTTTGTTTT
1 AAAGTTTTTCTTTTGTTTT
60121 GTTTTTGTTT
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:0.15, C:0.05, G:0.10, T:0.70
Consensus pattern (21 bp):
AAAGTTTTTCTTTTGTTTTTC
Found at i:65034 original size:31 final size:33
Alignment explanation
Indices: 64999--65062 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
64989 TGATTTTGAA
*
64999 AAAATTGAAAGTTTATGTACTAAA-ACA-AATT
1 AAAATTGAAAGTTTAGGTACTAAATACACAATT
* *
65030 AAAATTGATAGTTTAGGTATTAAATACACAATT
1 AAAATTGAAAGTTTAGGTACTAAATACACAATT
65063 TACCCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 21 0.75
32 3 0.11
33 4 0.14
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34
Consensus pattern (33 bp):
AAAATTGAAAGTTTAGGTACTAAATACACAATT
Found at i:69048 original size:67 final size:67
Alignment explanation
Indices: 68940--69073 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
68930 TACTTTTGCA
68940 CGGACGAAACAAGGTTAATTTGCTTTACTTGGTTTACATCTCTTTCTGCAACATTTCTGTGCATA
1 CGGACGAAACAAGGTTAATTTGCTTTACTTGGTTTACATCTCTTTCTGCAACATTTCTGTGCATA
69005 TG
66 TG
*
69007 CGGACGAAACAAGGTTAATTTGCTTTATTTGGTTTACATCTCTTTCTGCAACATTTCTGTGCATA
1 CGGACGAAACAAGGTTAATTTGCTTTACTTGGTTTACATCTCTTTCTGCAACATTTCTGTGCATA
69072 TG
66 TG
69074 TGAACCAATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (67 bp):
CGGACGAAACAAGGTTAATTTGCTTTACTTGGTTTACATCTCTTTCTGCAACATTTCTGTGCATA
TG
Found at i:69892 original size:2 final size:2
Alignment explanation
Indices: 69885--69914 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69875 TTGCTTCTTC
69885 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
69915 CAAAACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71396 original size:20 final size:20
Alignment explanation
Indices: 71373--71438 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
71363 AATTTGTAAA
*
71373 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
71393 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
71413 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
71433 TCGCAA
1 TCGCAA
71439 AGCGCGTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:71618 original size:21 final size:22
Alignment explanation
Indices: 71593--71642 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
71583 CTACGGCGAC
71593 ATCCGTCCCCA-CTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
* *
71614 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACAAA
71636 ATCCGTC
1 ATCCGTC
71643 TATCTCCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.22, C:0.46, G:0.14, T:0.18
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:71637 original size:22 final size:21
Alignment explanation
Indices: 71586--71642 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
71576 TCACTCTCTA
*
71586 CGGCGACATCCGTCCCCACTC
1 CGGCGAAATCCGTCCCCACTC
* *
71607 CGACAAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCA-CTC
71629 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
71643 TATCTCCATC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.21, C:0.46, G:0.18, T:0.16
Consensus pattern (21 bp):
CGGCGAAATCCGTCCCCACTC
Found at i:72086 original size:20 final size:20
Alignment explanation
Indices: 72051--72153 Score: 118
Period size: 20 Copynumber: 5.2 Consensus size: 20
72041 ATATCGCAAC
*
72051 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
72070 GCGATTTTCATTTTCGCTTT
1 GCGATTTTCATTTTCGCGTT
***
72090 GCGATTTTCATTTTCTTATT
1 GCGATTTTCATTTTCGCGTT
* *
72110 GAGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
* *
72130 GTGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
72150 GCGA
1 GCGA
72154 ATTTAAGTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
19 8 0.12
20 61 0.88
ACGTcount: A:0.13, C:0.15, G:0.19, T:0.53
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:74130 original size:4 final size:4
Alignment explanation
Indices: 74121--74166 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
74111 TTTTTCGACA
* * * *
74121 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
74167 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:74361 original size:21 final size:21
Alignment explanation
Indices: 74337--74407 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
74327 CCTCCTATCA
*
74337 TTCAAGAGGCTCCTCTCATAG
1 TTCAAGAGGCCCCTCTCATAG
* *
74358 TTCAAGAGCCCCCTCCCACTA-
1 TTCAAGAGGCCCCTCTCA-TAG
* *
74379 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCTCATAG
74400 TTCAAGAG
1 TTCAAGAG
74408 ATCCCTCCCA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.02
21 38 0.93
22 2 0.05
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCATAG
Found at i:74382 original size:42 final size:42
Alignment explanation
Indices: 74336--74418 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
74326 GCCTCCTATC
* *
74336 ATTCAAGAGGCTCCTCTCATAGTTCAAGAGCCCCCTCCCACT
1 ATTCAAGAGGCCCCTCTCATAGTTCAAGAGACCCCTCCCACT
* * *
74378 ATTCAAGAGGCCCCTGTCATCGTTCAAGAGATCCCTCCCAC
1 ATTCAAGAGGCCCCTCTCATAGTTCAAGAGACCCCTCCCAC
74419 CGTTTAAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (42 bp):
ATTCAAGAGGCCCCTCTCATAGTTCAAGAGACCCCTCCCACT
Found at i:74422 original size:21 final size:21
Alignment explanation
Indices: 74357--74428 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
74347 TCCTCTCATA
* *
74357 GTTCAAGAGCCCCCTCCCACT
1 GTTCAAGAGACCCCTCCCACC
* * ** *
74378 ATTCAAGAGGCCCCTGTCATC
1 GTTCAAGAGACCCCTCCCACC
*
74399 GTTCAAGAGATCCCTCCCACC
1 GTTCAAGAGACCCCTCCCACC
*
74420 GTTTAAGAG
1 GTTCAAGAG
74429 CCTGATTCAC
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (21 bp):
GTTCAAGAGACCCCTCCCACC
Found at i:74428 original size:42 final size:42
Alignment explanation
Indices: 74335--74428 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
74325 CGCCTCCTAT
* *
74335 CATTCAAGAGGCTCCTCTCATAGTTCAAGAGCCCCCTCCCAC
1 CATTCAAGAGGCCCCTCTCATAGTTCAAGAGACCCCTCCCAC
* * * *
74377 TATTCAAGAGGCCCCTGTCATCGTTCAAGAGATCCCTCCCAC
1 CATTCAAGAGGCCCCTCTCATAGTTCAAGAGACCCCTCCCAC
* *
74419 CGTTTAAGAG
1 CATTCAAGAG
74429 CCTGATTCAC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.23
Consensus pattern (42 bp):
CATTCAAGAGGCCCCTCTCATAGTTCAAGAGACCCCTCCCAC
Found at i:75895 original size:64 final size:64
Alignment explanation
Indices: 75785--75942 Score: 271
Period size: 64 Copynumber: 2.5 Consensus size: 64
75775 TTAATTGAAT
75785 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
* * * *
75850 TTTAATTAATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
75914 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
75943 GCTAAATTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 84 0.95
65 4 0.05
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:76082 original size:20 final size:20
Alignment explanation
Indices: 76036--76083 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
76026 ACGATTTTCT
*
76036 CGTTGCGATAGTCAAATTCG
1 CGTTGCGAAAGTCAAATTCG
** *
76056 CAATGCGAAAGTCAAATTGG
1 CGTTGCGAAAGTCAAATTCG
76076 CGTTGCGA
1 CGTTGCGA
76084 TTTTCACGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAAATTCG
Found at i:77290 original size:18 final size:18
Alignment explanation
Indices: 77267--77303 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
77257 ATTTATATAT
77267 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
77285 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
77303 A
1 A
77304 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:77722 original size:24 final size:25
Alignment explanation
Indices: 77674--77722 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
77664 CATTATTTTC
*
77674 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
77699 CAAATAATGTA-CCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
77723 TAATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:77844 original size:29 final size:29
Alignment explanation
Indices: 77811--77871 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
77801 GCGAATTAAC
*
77811 GCGAAAGTAAAATTCGCGTTGCGATTGTT
1 GCGAAAGTAAAATTCGCATTGCGATTGTT
* *
77840 GCGAAAGTCAAATTCGCATTGCGATTTTT
1 GCGAAAGTAAAATTCGCATTGCGATTGTT
77869 GCG
1 GCG
77872 TTGCGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (29 bp):
GCGAAAGTAAAATTCGCATTGCGATTGTT
Found at i:80447 original size:24 final size:24
Alignment explanation
Indices: 80413--80466 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
80403 CTGAAACATC
80413 ATCAAAATCTGAGTATTAACCAAG
1 ATCAAAATCTGAGTATTAACCAAG
* * *
80437 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTAACCAAG
80461 ATCAAA
1 ATCAAA
80467 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTAACCAAG
Found at i:81557 original size:19 final size:20
Alignment explanation
Indices: 81533--81632 Score: 116
Period size: 20 Copynumber: 5.0 Consensus size: 20
81523 ATCAGATTGT
*
81533 CCAGGGGGTACAGA-TCCTC
1 CCAGGGGGTACAGATTCCCC
*
81552 CCA-GGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
*
81572 CCA-GGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
81591 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
81611 CCTAGGGGGTACCGATTCCCC
1 CC-AGGGGGTACAGATTCCCC
81632 C
1 C
81633 TGTCTAACGG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.13
19 11 0.16
20 32 0.46
21 17 0.25
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:81609 original size:40 final size:40
Alignment explanation
Indices: 81533--81632 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
81523 ATCAGATTGT
* *
81533 CCAGGGGGTACAGA-TCCTCCCAGGGGAACAGATTCCCCC
1 CCAGGGGGTACCGATTCCCCCCAGGGGAACAGATTCCCCC
81572 CCA-GGGGTACCGATTCCCCCCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACCGATTCCCCCCA-GGGGAACAGATTCCCCC
*
81612 CTAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
81633 TGTCTAACGG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
38 9 0.16
39 10 0.18
40 19 0.35
41 17 0.31
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (40 bp):
CCAGGGGGTACCGATTCCCCCCAGGGGAACAGATTCCCCC
Found at i:81633 original size:20 final size:20
Alignment explanation
Indices: 81575--81633 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
81565 TTCCCCCCCA
*
81575 GGGGTACCGATTCCCCCCAG
1 GGGGTACCGATTCCCCCTAG
* *
81595 GGGGAACAGATTCCCCCCTAG
1 GGGGTACCGATT-CCCCCTAG
81616 GGGGTACCGATTCCCCCT
1 GGGGTACCGATTCCCCCT
81634 GTCTAACGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.17, C:0.37, G:0.29, T:0.17
Consensus pattern (20 bp):
GGGGTACCGATTCCCCCTAG
Found at i:82804 original size:19 final size:20
Alignment explanation
Indices: 82780--82827 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
82770 AACGATTTTC
*
82780 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
*
82799 TTTTGAAAGCAAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
82819 TTTTGAAAA
1 TTTTGAAAA
82828 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:84319 original size:19 final size:19
Alignment explanation
Indices: 84284--84336 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
84274 AGATTGTCCA
*
84284 AGGGGTATAGA-TCCCCCC
1 AGGGGTACAGATTCCCCCC
84302 AGGGGTACAGATTCCCCCC
1 AGGGGTACAGATTCCCCCC
*
84321 AGGGGGAACAGATTCC
1 A-GGGGTACAGATTCC
84337 TCCCTGGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
20 13 0.42
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (19 bp):
AGGGGTACAGATTCCCCCC
Found at i:84355 original size:21 final size:20
Alignment explanation
Indices: 84285--84358 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 20
84275 GATTGTCCAA
*
84285 GGGGTATAGA-TCCCCCCA-
1 GGGGTACAGATTCCCCCCAG
84303 GGGGTACAGATTCCCCCCAG
1 GGGGTACAGATTCCCCCCAG
* **
84323 GGGGAACAGATTCCTCCCTGG
1 GGGGTACAGATTCC-CCCCAG
*
84344 GGGGTACCGATTCCC
1 GGGGTACAGATTCCC
84359 ACTGTCTAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 9 0.19
19 8 0.17
20 14 0.30
21 16 0.34
ACGTcount: A:0.19, C:0.32, G:0.31, T:0.18
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCAG
Found at i:85176 original size:19 final size:20
Alignment explanation
Indices: 85153--85302 Score: 184
Period size: 19 Copynumber: 7.7 Consensus size: 20
85143 ACTAAAACCT
* *
85153 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* *
85172 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
85192 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
85211 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
85230 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
85249 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTC-GA
*
85270 GTTGCGAATTTGGAAA-TCGC
1 GTTGCGAATTT-GAAATTCGA
*
85290 GTTGCAAATTTGA
1 GTTGCGAATTTGA
85303 CTTATGGGTT
Statistics
Matches: 118, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
19 68 0.58
20 33 0.28
21 13 0.11
22 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:85265 original size:57 final size:60
Alignment explanation
Indices: 85153--85299 Score: 187
Period size: 58 Copynumber: 2.5 Consensus size: 60
85143 ACTAAAACCT
* *
85153 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA-
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCAG
* *
85211 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAG
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCAG
* *
85269 TGTTGCGAATTTGGAAA-TCGCGTTGCAAATT
1 -GTTGCGAATTT-GAAATTCGAGTTGCGAATT
85300 TGACTTATGG
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
57 20 0.26
58 26 0.33
59 19 0.24
60 13 0.17
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (60 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCAG
Found at i:85333 original size:20 final size:20
Alignment explanation
Indices: 85310--85356 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
85300 TGACTTATGG
*
85310 GTTGCGAAATTAGAGTTCGC
1 GTTGCGAAATTAGAGATCGC
*
85330 GTTGCG-AATTTGAGATCGC
1 GTTGCGAAATTAGAGATCGC
*
85349 ATTGCGAA
1 GTTGCGAA
85357 TTTATTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (20 bp):
GTTGCGAAATTAGAGATCGC
Found at i:85782 original size:26 final size:26
Alignment explanation
Indices: 85753--85809 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
85743 GTATATATTA
85753 ATATAATATCATTA-TAT-TAATAAACT
1 ATATAAT-TCATTACTATAT-ATAAACT
*
85779 ATATAGTTCATTACTATATATAAACT
1 ATATAATTCATTACTATATATAAACT
85805 ATATA
1 ATATA
85810 TTATATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.21
26 21 0.75
27 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATAATTCATTACTATATATAAACT
Found at i:85816 original size:33 final size:33
Alignment explanation
Indices: 85778--86009 Score: 275
Period size: 33 Copynumber: 7.2 Consensus size: 33
85768 ATTAATAAAC
*
85778 TATATAGTTCATTACTATATATAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAT
*
85811 TATATAATAT-ATTAGTATATATAAACTATAT-T
1 TATATAGT-TCATTAGTATATATAAACTATATAT
* *
85843 GTATATAGTTCATTATTATATATAAATTATATAT
1 -TATATAGTTCATTAGTATATATAAACTATATAT
*
85877 TATATAGTTCATTAGTATATATAAATTATATAGT
1 TATATAGTTCATTAGTATATATAAACTATATA-T
*
85911 TCATATTGTTCATTAGTATATATAAAC-------
1 T-ATATAGTTCATTAGTATATATAAACTATATAT
* *
85938 TATATAGTTCATTAGTTTATATAAACTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAT
* *
85971 TATATAGTTCATTAGTATATATTAACTATATAA
1 TATATAGTTCATTAGTATATATAAACTATATAT
86004 TATATA
1 TATATA
86010 TATATAAATT
Statistics
Matches: 173, Mismatches: 13, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
26 23 0.13
27 1 0.01
32 2 0.01
33 120 0.69
34 4 0.02
35 23 0.13
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (33 bp):
TATATAGTTCATTAGTATATATAAACTATATAT
Found at i:85855 original size:66 final size:65
Alignment explanation
Indices: 85733--86009 Score: 281
Period size: 66 Copynumber: 4.4 Consensus size: 65
85723 TATTAATAGA
* * * *
85733 TATATATAAAGTATATATTAATATAA-TATCA-T-TATATTAA-TA-A-ACTATATAGTTCATTA
1 TATATATAAACTATATATT-ATATAATTATTAGTATATATAAACTATATAGTATATAGTTCATTA
*
85792 C
65 G
*
85793 TATATATAAACTATATATTATATAATATATTAGTATATATAAACTATATTGTATATAGTTCATTA
1 TATATATAAACTATATATTATATAAT-TATTAGTATATATAAACTATATAGTATATAGTTCATTA
*
85858 T
65 G
* * * *
85859 TATATATAAATTATATATTATATAGTTCATTAGTATATATAAATTATATAGTTCATATTGTTCAT
1 TATATATAAACTATATATTATATAATT-ATTAGTATATATAAACTATATAG-T-ATATAGTTCAT
85924 TAG
63 TAG
* * *
85927 TATATATAAAC--TATA-TA-GT--TCATTAGTTTATATAAACTATATAGTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAATTATTAGTATATATAAACTATATAGTATATAGTTCATTAG
* *
85986 TATATATTAACTATATAATATATA
1 TATATATAAACTATATATTATATA
86010 TATATAAATT
Statistics
Matches: 182, Mismatches: 20, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
59 29 0.16
60 19 0.10
61 29 0.16
62 4 0.02
63 8 0.04
64 3 0.02
65 4 0.02
66 63 0.35
67 1 0.01
68 22 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (65 bp):
TATATATAAACTATATATTATATAATTATTAGTATATATAAACTATATAGTATATAGTTCATTAG
Found at i:85932 original size:26 final size:26
Alignment explanation
Indices: 85913--85971 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
85903 TATATAGTTC
*
85913 ATATTGTTCATTAGTATATATAAACT
1 ATATAGTTCATTAGTATATATAAACT
*
85939 ATATAGTTCATTAGTTTATATAAACT
1 ATATAGTTCATTAGTATATATAAACT
85965 ATATAGT
1 ATATAGT
85972 ATATAGTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (26 bp):
ATATAGTTCATTAGTATATATAAACT
Found at i:86011 original size:22 final size:22
Alignment explanation
Indices: 85986--86029 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85976 AGTTCATTAG
*
85986 TATATATTAACTATATAATATA
1 TATATATAAACTATATAATATA
* *
86008 TATATATAAATTATATAGTATA
1 TATATATAAACTATATAATATA
86030 CACTAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATATATAAACTATATAATATA
Found at i:86247 original size:29 final size:30
Alignment explanation
Indices: 86214--86274 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
86204 TTCATATAAT
*
86214 ATACATTATATATTATTAA-TTATGCATAC
1 ATACATTATATATTAATAAGTTATGCATAC
86243 ATACATTATATATTAATAAGTTATGCATAC
1 ATACATTATATATTAATAAGTTATGCATAC
86273 AT
1 AT
86275 TGTACAGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (30 bp):
ATACATTATATATTAATAAGTTATGCATAC
Found at i:91628 original size:13 final size:14
Alignment explanation
Indices: 91602--91634 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
91592 TTCTTATATT
91602 TTTAAATTATTTAA
1 TTTAAATTATTTAA
91616 TTTAAATTA-TTAA
1 TTTAAATTATTTAA
91629 TTTAAA
1 TTTAAA
91635 AAATTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAAATTATTTAA
Found at i:92854 original size:20 final size:20
Alignment explanation
Indices: 92806--92867 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
92796 AACTTAAATC
*
92806 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
92826 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
92844 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
92863 AAAAT
1 AAAAT
92868 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:92894 original size:28 final size:25
Alignment explanation
Indices: 92863--92927 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 25
92853 TATATGATAT
92863 AAAATTAAATATCTATAATATAATATTAA
1 AAAATTAAATAT-T-TAAT-TAAT-TTAA
*
92892 AAAATT-AATATTTAATTTATTTAA
1 AAAATTAAATATTTAATTAATTTAA
92916 AAAA-TAAATATT
1 AAAATTAAATATT
92928 AAAATTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
23 1 0.03
24 14 0.41
25 3 0.09
26 4 0.12
27 1 0.03
28 5 0.15
29 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AAAATTAAATATTTAATTAATTTAA
Found at i:92965 original size:22 final size:19
Alignment explanation
Indices: 92915--92971 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
92905 AATTTATTTA
*
92915 AAAAATAAATATTAAAATT
1 AAAATTAAATATTAAAATT
*
92934 AAAATCAAATATTATATAATAT
1 AAAATTAAATATTA-A-AAT-T
92956 AAAATTAAATA-TAAAA
1 AAAATTAAATATTAAAA
92972 CCTCTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 14 0.44
20 2 0.06
21 5 0.16
22 11 0.34
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTAAATATTAAAATT
Found at i:99072 original size:3 final size:3
Alignment explanation
Indices: 99038--99093 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
99028 GTTGAAAAGA
* * *
99038 TAT TAT TAAT TAT GAT TAT GAT TAT GAT TAT TAT TAT TAAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
99085 TAAT TAT TA
1 T-AT TAT TA
99094 ATTACATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 35 0.80
4 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:99082 original size:10 final size:10
Alignment explanation
Indices: 99038--99093 Score: 69
Period size: 10 Copynumber: 5.5 Consensus size: 10
99028 GTTGAAAAGA
99038 TATTATTAAT
1 TATTATTAAT
*
99048 TATGATTATGAT
1 TATTATTA--AT
*
99060 TATGATT-AT
1 TATTATTAAT
99069 TATTATTAAT
1 TATTATTAAT
99079 TATTATTAAT
1 TATTATTAAT
99089 TATTA
1 TATTA
99094 ATTACATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 8 0.20
10 24 0.59
12 9 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (10 bp):
TATTATTAAT
Found at i:104940 original size:25 final size:24
Alignment explanation
Indices: 104884--104930 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
104874 AGGATAAGAG
104884 CAAAGAAAAAGCAAAGAGAGAAAAT
1 CAAAGAAAAA-CAAAGAGAGAAAAT
104909 CAAAGAAAAA-AAAGAGAGAAAA
1 CAAAGAAAAACAAAGAGAGAAAA
104931 AAGTCAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.55
25 10 0.45
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (24 bp):
CAAAGAAAAACAAAGAGAGAAAAT
Found at i:106962 original size:16 final size:16
Alignment explanation
Indices: 106941--106996 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
106931 GATCAAGAAA
106941 ACATACATCAACACAT
1 ACATACATCAACACAT
106957 ACATACATCAACACAT
1 ACATACATCAACACAT
* *
106973 ACGTACATTAACACAT
1 ACATACATCAACACAT
*
106989 ATATACAT
1 ACATACAT
106997 GTTACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (16 bp):
ACATACATCAACACAT
Found at i:107394 original size:37 final size:37
Alignment explanation
Indices: 107351--107474 Score: 146
Period size: 36 Copynumber: 3.4 Consensus size: 37
107341 ACAAAGTGCC
*
107351 GTCTCGCTAGAGACAATTTTTCTTAAAAACAAATTTT
1 GTCTCGCTTGAGACAATTTTTCTTAAAAACAAATTTT
*
107388 GTCTCGCTTGAGAC-AGTTTTCTCTAAAAA-AAATTTT
1 GTCTCGCTTGAGACAATTTTTCT-TAAAAACAAATTTT
* * * * *
107424 GTCTCGTTTGAGAAAATTTAT-TTCAAAACAAATTTC
1 GTCTCGCTTGAGACAATTTTTCTTAAAAACAAATTTT
*
107460 GTCTCACTTGAGACA
1 GTCTCGCTTGAGACA
107475 GTTTCCCTCG
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
35 5 0.07
36 45 0.62
37 23 0.32
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (37 bp):
GTCTCGCTTGAGACAATTTTTCTTAAAAACAAATTTT
Found at i:107489 original size:36 final size:35
Alignment explanation
Indices: 107351--107496 Score: 130
Period size: 36 Copynumber: 4.0 Consensus size: 35
107341 ACAAAGTGCC
* * *
107351 GTCTCGCTAGAGACAATTTTTCTTAAAAACAAATTTT
1 GTCTCGCTTGAGAC-AGTTTTC-TCAAAACAAATTTT
*
107388 GTCTCGCTTGAGACAGTTTTCTCTAAAAAAAATTTT
1 GTCTCGCTTGAGACAGTTTTCTC-AAAACAAATTTT
* * * * *
107424 GTCTCGTTTGAGAAAATTTATTTCAAAACAAATTTC
1 GTCTCGCTTGAGACAGTTT-TCTCAAAACAAATTTT
* *
107460 GTCTCACTTGAGACAGTTTCCCTCGAAACACAAATTT
1 GTCTCGCTTGAGACAGTTT-TCTC-AAA-ACAAATTT
107497 CAAAGTTGTT
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
35 1 0.01
36 60 0.68
37 19 0.22
38 8 0.09
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (35 bp):
GTCTCGCTTGAGACAGTTTTCTCAAAACAAATTTT
Found at i:107621 original size:99 final size:98
Alignment explanation
Indices: 107446--107625 Score: 254
Period size: 99 Copynumber: 1.8 Consensus size: 98
107436 AAAATTTATT
* * *
107446 TCAAAACAAATTTCGTCTCACTTGAGACAGTTTCCCTCGAAACACAAATTTCAAAGTTGTTTTAC
1 TCAAAACAAATTTCGTCTCACTTGAGAAAGTTTCCCTCAAAACACAAATTTCAAAGTTGTTTCAC
*
107511 TTGAAACAAAATTGATCTCACTTGAGATTGTTC
66 TGGAAACAAAATTGATCTCACTTGAGATTGTTC
* * * * *
107544 TCAAAACAAATTTCGTCTCACTTGAGATAATTTTTCTTTAAAACACAAATTCTGAAA-TTGTTTC
1 TCAAAACAAATTTCGTCTCACTTGAGA-AAGTTTCCCTCAAAACACAAATT-TCAAAGTTGTTTC
107608 ACTGGAAACAAAATTGAT
64 ACTGGAAACAAAATTGAT
107626 AAACCATTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
98 27 0.38
99 40 0.56
100 4 0.06
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (98 bp):
TCAAAACAAATTTCGTCTCACTTGAGAAAGTTTCCCTCAAAACACAAATTTCAAAGTTGTTTCAC
TGGAAACAAAATTGATCTCACTTGAGATTGTTC
Found at i:107761 original size:103 final size:103
Alignment explanation
Indices: 107640--107849 Score: 271
Period size: 103 Copynumber: 2.0 Consensus size: 103
107630 CATTGAGATT
* * * *
107640 GTTTCCCTGTAAACAAGTTTTATCACCCTTGAGAGAGTTTCTCTTGAAACACAATTATTTAAGTC
1 GTTTCCCTGTAAACAAGTTTTATCACCCTTGAGACAGTTTCTCTTGAAAAAAAAGTATTTAAGTC
*
107705 TGTTTCCCTTGAAACGAA-TTTTGTCTCCCTCGAGACA
66 TGTTTCCCTTGAAACAAAGTTTTGTCTCCCTCGAGACA
* * * * *
107742 GTTTCCCT-TAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAAGTCTTTGAG
1 GTTTCCCTGT-AAAC-AAGTTTTATCACCCTTGAGACAGTTTCTCTTGAAAAAAAAGTATTTAAG
* * *
107806 TCTGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
64 TCTGTTTCCCTTGAAACAAAGTTTTGTCTCCCTCGAGACA
107846 GTTT
1 GTTT
107850 TTCTTGGAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 1 0.01
102 12 0.13
103 58 0.63
104 21 0.23
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (103 bp):
GTTTCCCTGTAAACAAGTTTTATCACCCTTGAGACAGTTTCTCTTGAAAAAAAAGTATTTAAGTC
TGTTTCCCTTGAAACAAAGTTTTGTCTCCCTCGAGACA
Found at i:107768 original size:37 final size:37
Alignment explanation
Indices: 107706--107803 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
107696 ATTTAAGTCT
* *
107706 GTTTCCCTTGAAACGAA-TTTTGTCTCCCTCGAGACA
1 GTTTCCCTTAAAACAAAGTTTTGTCTCCCTCGAGACA
* *
107742 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTAAAACAAAGTTTTGTCTCCCTCGAGACA
* *
107779 GTTTCTCTTGAAAAAAAAGTCTTTG
1 GTTTCCCTT-AAAACAAAGT-TTTG
107804 AGTCTGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
36 15 0.28
37 25 0.47
38 9 0.17
39 4 0.08
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
GTTTCCCTTAAAACAAAGTTTTGTCTCCCTCGAGACA
Found at i:107905 original size:21 final size:21
Alignment explanation
Indices: 107881--107925 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
107871 GTCTGTTTCT
*
107881 CTTGAAACATGTTTTGTCTCC
1 CTTGAAACAAGTTTTGTCTCC
107902 CTTGAAACAAGTTTTGTCTCC
1 CTTGAAACAAGTTTTGTCTCC
107923 CTT
1 CTT
107926 TAGATAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.42
Consensus pattern (21 bp):
CTTGAAACAAGTTTTGTCTCC
Found at i:107915 original size:66 final size:67
Alignment explanation
Indices: 107742--107916 Score: 255
Period size: 67 Copynumber: 2.6 Consensus size: 67
107732 CCTCGAGACA
* * * *
107742 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAAGTCTTTGAGT
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAAAAAAAGTATTTGAGT
107807 CT
66 CT
*
107809 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGGAAAAAAA-TATTTGAGT
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAAAAAAAGTATTTGAGT
107873 CT
66 CT
* * *
107875 GTTTCTCTTGAAAC-ATGTTTTGTCTCCCTTGAAACAAGTTTT
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC-AGTTTT
107917 GTCTCCCTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
65 18 0.18
66 30 0.30
67 51 0.52
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (67 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGAAAAAAAAGTATTTGAGT
CT
Found at i:107957 original size:153 final size:154
Alignment explanation
Indices: 107745--108059 Score: 377
Period size: 153 Copynumber: 2.1 Consensus size: 154
107735 CGAGACAGTT
* * *
107745 TCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAAAGTCTTTGAGTCTG
1 TCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAAAAAAGTCTTTGAGTATG
* * * * ** * *
107810 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGGAAA-A-AAATATTTGAGT
66 TTTCCCTTAAAACAAA-TTTTGTCTCCCTTGAGACAATTTCCCTT-GAAACACAAACATTTAAGT
* **
107873 CTGTTTCTCTTGAAACATGTTTTGTC
129 CTGTTTCCCTTGAAACAAATTTTGTC
* * *
107899 TCCCTTGAAAC-AAGTTTTGTCTCCCTTTAGATAGTTTCTCTTGAAACACAAA-TCTTTGAGTAT
1 TCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA-AAAAAGTCTTTGAGTAT
* * *
107962 GTTTCCCTTAAAACGAATTTTGTTTCCCTTGAGACAATTTCCCTTGAAACACAAACCTTTAAGTC
65 GTTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAACATTTAAGTC
*
108027 TGTTTCCCTTGAAATAAATTTTGTC
130 TGTTTCCCTTGAAACAAATTTTGTC
*
108052 TCTCTTGA
1 TCCCTTGA
108060 GATAGTTTCT
Statistics
Matches: 136, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
151 4 0.03
152 24 0.18
153 94 0.69
154 14 0.10
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (154 bp):
TCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAAAAAAGTCTTTGAGTATG
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAACATTTAAGTCT
GTTTCCCTTGAAACAAATTTTGTC
Found at i:107965 original size:87 final size:86
Alignment explanation
Indices: 107815--107998 Score: 219
Period size: 87 Copynumber: 2.1 Consensus size: 86
107805 GTCTGTTTCT
* * *
107815 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTGGAAAAAAATATTTGAGTCTGTTTC
1 CTTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGGAAAAAAATATTTGAGTATGTTTC
* * *
107880 TCTTGAAAC-ATGTTTTGTCTCC
65 CCTTAAAACGA-ATTTTGTCTCC
* * *
107902 CTTGAAACAAGTTTTGTCTCCCTTTAGATAGTTTCTCTT-GAAACACAAATCTTTGAGTATGTTT
1 CTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGGAAA-A-AAATATTTGAGTATGTTT
*
107966 CCCTTAAAACGAATTTTGTTTCC
64 CCCTTAAAACGAATTTTGTCTCC
*
107989 CTTGAGACAA
1 CTTGAAACAA
107999 TTTCCCTTGA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
85 4 0.05
86 28 0.34
87 50 0.60
88 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (86 bp):
CTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGGAAAAAAATATTTGAGTATGTTTCC
CTTAAAACGAATTTTGTCTCC
Found at i:108008 original size:66 final size:65
Alignment explanation
Indices: 107899--108078 Score: 234
Period size: 66 Copynumber: 2.7 Consensus size: 65
107889 ATGTTTTGTC
* * *
107899 TCCCTTGAAACAAGTTTTGTCTCCCTTTAGATAGTTTCTCTTGAAACACAAATCTTTGAGTATGT
1 TCCCTTGAAACAA-TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAACCTTTAAGTATGT
107964 T
65 T
* * * * * *
107965 TCCCTTAAAACGAATTTTGTTTCCCTTGAGACAATTTCCCTTGAAACACAAACCTTTAAGTCTGT
1 TCCCTTGAAAC-AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAACCTTTAAGTATGT
108030 T
65 T
* *
108031 TCCCTTGAAATAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TCCCTTGAAA-CAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
108079 AATCCCTAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
66 94 0.98
67 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (65 bp):
TCCCTTGAAACAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAACCTTTAAGTATGTT
Found at i:108320 original size:130 final size:132
Alignment explanation
Indices: 108080--108437 Score: 398
Period size: 130 Copynumber: 2.7 Consensus size: 132
108070 CTTGAAACAA
* * * *
108080 ATCCCTAAAGATGGCATATCATCTTCATCGCGTAGGAACTGCGTCATCCATCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATAT-ATCCTCATCGCGTAGGAACCGTGTCATCCCT-GACCAGACCTCCT
* * * **
108145 CATCATGTAGGAGCCGCGTCAACCTTAGATAATCAGTTGTCCTCATCACGTAAGAACCGT-TT-T
64 CATCACGTAGGAGCCGTGTCACCCTTAGATAATCAGCCGTCCTCATCACGTAAGAACCGTGTTAT
108208 -ATC
129 CATC
* * *
108211 ATCCCTAAAGATGGCCTGTAGTCCTCATCACGTAGGAACCGTGTCATCCCTGACCAGACCTCCTC
1 ATCCCTAAAGATGGCATATA-TCCTCATCGCGTAGGAACCGTGTCATCCCTGACCAGACCTCCTC
* * * * *
108276 ATCACGTAGGAGTCGTGTCACCCCTAGATAATCAGCCGTTCTCATCGCGTAGGAACCGTGTTATC
65 ATCACGTAGGAGCCGTGTCACCCTTAGATAATCAGCCGTCCTCATCACGTAAGAACCGTGTTATC
108341 ATC
130 ATC
* * * ** * * * * *
108344 ATTCTTAAATATGGTCATCCATCCTCATCGTGTAGGAACCGTGTCATCCACCGACCAAATCTCTT
1 ATCCCTAAAGATGG-CATATATCCTCATCGCGTAGGAACCGTGTCATCC-CTGACCAGACCTCCT
*
108409 CATCACGTAAGAGCCGTGTCACCCTTAGA
64 CATCACGTAGGAGCCGTGTCACCCTTAGA
108438 CGACCAGAAC
Statistics
Matches: 189, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
130 64 0.34
131 44 0.23
132 1 0.01
133 40 0.21
134 40 0.21
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (132 bp):
ATCCCTAAAGATGGCATATATCCTCATCGCGTAGGAACCGTGTCATCCCTGACCAGACCTCCTCA
TCACGTAGGAGCCGTGTCACCCTTAGATAATCAGCCGTCCTCATCACGTAAGAACCGTGTTATCA
TC
Found at i:108625 original size:3 final size:3
Alignment explanation
Indices: 108619--108683 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
108609 TTTAAAAAAA
108619 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
108667 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
108684 ATTACATTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:110520 original size:15 final size:15
Alignment explanation
Indices: 110500--110530 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
110490 CTCTTTTCAT
*
110500 TTTCATTTTGTTTTA
1 TTTCATTTTATTTTA
110515 TTTCATTTTATTTTA
1 TTTCATTTTATTTTA
110530 T
1 T
110531 CTTTGCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTCATTTTATTTTA
Found at i:110832 original size:33 final size:33
Alignment explanation
Indices: 110792--110859 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
110782 GAATGATCGT
110792 AATTTAAATATATTTTTGAGTTTGTAATTTCCC
1 AATTTAAATATATTTTTGAGTTTGTAATTTCCC
*
110825 AATTTAAATATATTTTTGAGTTTGTAATTTTCC
1 AATTTAAATATATTTTTGAGTTTGTAATTTCCC
110858 AA
1 AA
110860 CATTTAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.51
Consensus pattern (33 bp):
AATTTAAATATATTTTTGAGTTTGTAATTTCCC
Found at i:111702 original size:18 final size:16
Alignment explanation
Indices: 111670--111700 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
111660 AATATTGAAA
111670 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
111686 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
111701 AAAATTAGAA
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:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:111773 original size:14 final size:14
Alignment explanation
Indices: 111754--111781 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
111744 AAGTGAAAGA
111754 ATAGTTATATAATT
1 ATAGTTATATAATT
111768 ATAGTTATATAATT
1 ATAGTTATATAATT
111782 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:113072 original size:137 final size:138
Alignment explanation
Indices: 112861--113196 Score: 482
Period size: 137 Copynumber: 2.4 Consensus size: 138
112851 TATTTGATTC
* * *
112861 ATTTAGTCCTTTAATTTAGGAAAATTCTTAATTTGGTC-TTCGTTTTTGCTCGAGGTTCCATTTT
1 ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAGTCATT-GTTTTTGCTCGAGGTTCCATTTA
* * * *
112925 AATTATTCGATTCAATAACTGATTAAAATTAATTAGTATTAAT-ATTAGGGCCTTCACTTTAGAC
65 AATTATTCGATTCAATAACTGACTAAAATGAACTAG-ATTAATAATTAGAGCCTTCACTTTAGAC
112989 TTAATTT-AA
129 TTAATTTCAA
* *
112998 ATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTAGTCATTGCTTTTGCTCGAGGTTCCATTTAA
1 ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAGTCATTGTTTTTGCTCGAGGTTCCATTTAA
* * *
113063 ATTATTCGATTCAATAATTGACTAAAATGAACTAGGTTAATAATTAGAGCCTTCACTTTAGGCTT
66 ATTATTCGATTCAATAACTGACTAAAATGAACTAGATTAATAATTAGAGCCTTCACTTTAGACTT
*
113128 AATTTCAT
131 AATTTCAA
* *
113136 ATTTAGTCCTTTAATTTAGGAGAATTCTTAA-TTAGTTCATCGTTTTTGCTCAAGGTTCCAT
1 ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAG-TCATTGTTTTTGCTCGAGGTTCCAT
113197 AATCGATTGC
Statistics
Matches: 178, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
136 5 0.03
137 118 0.66
138 55 0.31
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (138 bp):
ATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTAGTCATTGTTTTTGCTCGAGGTTCCATTTAA
ATTATTCGATTCAATAACTGACTAAAATGAACTAGATTAATAATTAGAGCCTTCACTTTAGACTT
AATTTCAA
Found at i:114818 original size:37 final size:37
Alignment explanation
Indices: 114773--114850 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
114763 TATAGGATAA
*
114773 ATAT-AAAAAGAAAATAG-ATAAATAAATGAGTAAAAT
1 ATATAAAAAAGAAAA-AGCATAAATAAATAAGTAAAAT
* * *
114809 ATATAAAAAAGTAAAAGCATATATATATAAGTAAAAT
1 ATATAAAAAAGAAAAAGCATAAATAAATAAGTAAAAT
114846 A-ATAA
1 ATATAA
114851 TAATAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 10 0.28
37 26 0.72
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.24
Consensus pattern (37 bp):
ATATAAAAAAGAAAAAGCATAAATAAATAAGTAAAAT
Found at i:114832 original size:20 final size:20
Alignment explanation
Indices: 114807--114844 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
114797 AATGAGTAAA
114807 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
114827 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
114845 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:116300 original size:105 final size:105
Alignment explanation
Indices: 116113--116622 Score: 868
Period size: 105 Copynumber: 4.9 Consensus size: 105
116103 GCATTGTTCA
* * ** *
116113 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
116173 CAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
116213 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
116278 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
116318 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
116383 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
116423 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
116488 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
116528 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
116593 CAGCGGTCCCTTCGTCGTGAAGTTGAACTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTT
116623 TGACTTGAAT
Statistics
Matches: 389, Mismatches: 16, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
100 37 0.10
101 1 0.00
102 1 0.00
104 5 0.01
105 345 0.89
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:117313 original size:67 final size:66
Alignment explanation
Indices: 117192--117349 Score: 187
Period size: 68 Copynumber: 2.4 Consensus size: 66
117182 AAGATATCTG
* * **
117192 TTGTTT-AATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAA-GAGAAACTGTCTCAAGGGAAACAAAAATATGTTTTAAGGGAAATAAATTCAAAG-
*
117256 TTT
64 GTT
* *
117259 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAA-AAAAAT-TGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGA-AACAAAAATATGTTTTAAGGGAAATAAATTCAAAG
117322 GTT
64 GTT
*
117325 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
117350 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 27 0.34
69 4 0.05
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAAATATGTTTTAAGGGAAATAAATTCAAAGGT
T
Found at i:117361 original size:65 final size:67
Alignment explanation
Indices: 117193--117375 Score: 178
Period size: 65 Copynumber: 2.7 Consensus size: 67
117183 AGATATCTGT
* **
117193 TGTTT-AATGAGAAACGGTCTCAAG-G-GAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAG
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGAAA-AAAA-T-TGTTTTAAGGGAAATAAATTCAAAG
*
117255 ATTTTG
62 AGTTTG
* * *
117261 TGTTTCAAGAGTAACTGTCTCAAGGGAGAAAAAAATTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTGTTTTAAGGGAAATAAATTCAAAGAGTT
117325 T-
66 TG
* * ** * *
117326 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTGTTTTAAGGGAAA
117376 CTGTCTTAAG
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
65 41 0.42
66 3 0.03
67 22 0.23
68 20 0.21
69 7 0.07
70 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.30
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:117376 original size:36 final size:36
Alignment explanation
Indices: 117325--117448 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
117315 TTCAAAGGTT
*
117325 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* *
117361 TTGTTTCAAGAGAAACTGTCTTAAGAGAGAC-AAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* * *
117396 CTTAGTTCCAAGGGAAACTATCTCAAGAGAGACGAAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
*
117434 TTATTTCAAGGGAAA
1 TTGTTTCAAGGGAAA
117449 TGTTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
Found at i:117970 original size:18 final size:18
Alignment explanation
Indices: 117943--117978 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
117933 TGTTGAATCC
* *
117943 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
117961 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
117979 TGAATCTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:118447 original size:29 final size:29
Alignment explanation
Indices: 118405--118467 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
118395 TTGGCATTTG
118405 ATGCTCAAAGGATTGATGGGGTAGCTTGC
1 ATGCTCAAAGGATTGATGGGGTAGCTTGC
118434 ATGCTCAAAGGATTGATGGGGTAGCTTGC
1 ATGCTCAAAGGATTGATGGGGTAGCTTGC
118463 ATGCT
1 ATGCT
118468 TCTCTACTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (29 bp):
ATGCTCAAAGGATTGATGGGGTAGCTTGC
Found at i:119077 original size:20 final size:21
Alignment explanation
Indices: 119053--119114 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
119043 TTTTTTGTTC
*
119053 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
119074 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
119094 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
119115 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:119125 original size:22 final size:22
Alignment explanation
Indices: 119071--119123 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
119061 ATTTTTGTTC
119071 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
119092 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
119115 TTTCTTTTT
1 TTTCTTTTT
119124 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:122397 original size:24 final size:23
Alignment explanation
Indices: 122366--122424 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
122356 AAATGAGTAA
*
122366 AATATATAAAAAAGTAAAAGCAT
1 AATATATAAAAAAGTAAAAGAAT
* * *
122389 ATATATATATATAAGTAAAATAAT
1 A-ATATATAAAAAAGTAAAAGAAT
122413 AATA-ATAAAAAA
1 AATATATAAAAAA
122425 ATCAAAAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 19 0.66
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
AATATATAAAAAAGTAAAAGAAT
Found at i:124804 original size:17 final size:17
Alignment explanation
Indices: 124782--124835 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
124772 CGATTTGCAT
124782 AAAGTAGATGTGCATGG
1 AAAGTAGATGTGCATGG
*
124799 AAAGTATATGTGCATGG
1 AAAGTAGATGTGCATGG
**
124816 AAAGTAGATGCACATGG
1 AAAGTAGATGTGCATGG
124833 AAA
1 AAA
124836 TTATACCGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (17 bp):
AAAGTAGATGTGCATGG
Found at i:133671 original size:14 final size:14
Alignment explanation
Indices: 133652--133678 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
133642 ATACGGCGTC
133652 TTGAGAAAGATGAT
1 TTGAGAAAGATGAT
133666 TTGAGAAAGATGA
1 TTGAGAAAGATGA
133679 GGAGGTTTAA
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:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (14 bp):
TTGAGAAAGATGAT
Done.