Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 62
Found at i:5185089 original size:37 final size:32
Alignment explanation
Indices: 5185019--5185115 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 32
5185009 TATTATTAGC
*
5185019 ATTTTAATAATTAATTAATAATATTTTATTTTT
1 ATTTTAATAAATAATTAAT-ATATTTTATTTTT
5185052 ATTTTAATAAATAATTAATATCATTTATAGTAATTTT
1 ATTTTAATAAATAATTAATAT-ATTT-TA-T--TTTT
*
5185089 ATTTTAATAAA-ATTTAATAT-TTTTATT
1 ATTTTAATAAATAATTAATATATTTTATT
5185116 AATAAAATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
30 1 0.02
32 3 0.05
33 24 0.42
34 5 0.09
35 1 0.02
36 8 0.14
37 15 0.26
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (32 bp):
ATTTTAATAAATAATTAATATATTTTATTTTT
Found at i:5185206 original size:20 final size:20
Alignment explanation
Indices: 5185183--5185224 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5185173 TTTTAAAATT
*
5185183 TTAA-AAATATTATTAATTTA
1 TTAATAAATAATATT-ATTTA
5185203 TTAATAAATAATATTATTTA
1 TTAATAAATAATATTATTTA
5185223 TT
1 TT
5185225 GTATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATAAATAATATTATTTA
Found at i:5185220 original size:24 final size:24
Alignment explanation
Indices: 5185184--5185229 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5185174 TTTAAAATTT
5185184 TAAAAATATTATTAATT-TATTAA
1 TAAAAATATTATTAATTGTATTAA
*
5185207 TAAATAATATTATTTATTGTATT
1 TAAA-AATATTATTAATTGTATT
5185230 TGATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAAAAATATTATTAATTGTATTAA
Found at i:5186248 original size:27 final size:27
Alignment explanation
Indices: 5186217--5186269 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5186207 TAGATATAGC
* *
5186217 TGTTGAACATATTCTTTCAAAAAAAAT
1 TGTTGAACATATTATTTAAAAAAAAAT
5186244 TGTTGAACATATTATTTAAAAAAAAA
1 TGTTGAACATATTATTTAAAAAAAAA
5186270 AATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (27 bp):
TGTTGAACATATTATTTAAAAAAAAAT
Found at i:5186965 original size:40 final size:39
Alignment explanation
Indices: 5186894--5187022 Score: 197
Period size: 40 Copynumber: 3.3 Consensus size: 39
5186884 CGTGTGTATG
5186894 GCGCGGGGCAGGGGTCCGCCATACG-TCACGTAAGATATA
1 GCGCGGGGCAGGGGTCCGCCATACGCT-ACGTAAGATATA
*
5186933 GCGCGGGACAGGGGTCGCGCCATACGCTACGTAAGATATA
1 GCGCGGGGCAGGGGTC-CGCCATACGCTACGTAAGATATA
* *
5186973 GCGCGGGGCAGGGGCCACGCCATACGCCACGTAAGATATA
1 GCGCGGGGCAGGGGTC-CGCCATACGCTACGTAAGATATA
5187013 GCGCGGGGCA
1 GCGCGGGGCA
5187023 AGAGCTGCGC
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
39 15 0.18
40 67 0.81
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.37, T:0.12
Consensus pattern (39 bp):
GCGCGGGGCAGGGGTCCGCCATACGCTACGTAAGATATA
Found at i:5190584 original size:13 final size:13
Alignment explanation
Indices: 5190568--5190606 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5190558 GAAAAATTAT
*
5190568 AATAAAAAAGTCC
1 AATAAAAAAGTAC
* *
5190581 AATAAACAACTAC
1 AATAAAAAAGTAC
5190594 AATAAAAAAGTAC
1 AATAAAAAAGTAC
5190607 TAAATACAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.15
Consensus pattern (13 bp):
AATAAAAAAGTAC
Found at i:5198491 original size:117 final size:117
Alignment explanation
Indices: 5198285--5198518 Score: 468
Period size: 117 Copynumber: 2.0 Consensus size: 117
5198275 ATACCCTGTC
5198285 CCCGGTACTTTCGAAGGATTCATCTCAAAGACAGACCACTCTTCTAATTTCATCCTCCTCGACTG
1 CCCGGTACTTTCGAAGGATTCATCTCAAAGACAGACCACTCTTCTAATTTCATCCTCCTCGACTG
5198350 CCTCCGAAAGCATGATCCTGGAAGAATCTGAAATCTGAGTAAACCGGTTCCA
66 CCTCCGAAAGCATGATCCTGGAAGAATCTGAAATCTGAGTAAACCGGTTCCA
5198402 CCCGGTACTTTCGAAGGATTCATCTCAAAGACAGACCACTCTTCTAATTTCATCCTCCTCGACTG
1 CCCGGTACTTTCGAAGGATTCATCTCAAAGACAGACCACTCTTCTAATTTCATCCTCCTCGACTG
5198467 CCTCCGAAAGCATGATCCTGGAAGAATCTGAAATCTGAGTAAACCGGTTCCA
66 CCTCCGAAAGCATGATCCTGGAAGAATCTGAAATCTGAGTAAACCGGTTCCA
5198519 AACCTAAAAA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (117 bp):
CCCGGTACTTTCGAAGGATTCATCTCAAAGACAGACCACTCTTCTAATTTCATCCTCCTCGACTG
CCTCCGAAAGCATGATCCTGGAAGAATCTGAAATCTGAGTAAACCGGTTCCA
Found at i:5201180 original size:21 final size:21
Alignment explanation
Indices: 5201156--5201195 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5201146 TCATTTCCCC
*
5201156 TTCCCGATCTTCAATCCCTAA
1 TTCCCCATCTTCAATCCCTAA
* *
5201177 TTCCCCTTTTTCAATCCCT
1 TTCCCCATCTTCAATCCCT
5201196 TCTCCTGCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.40, G:0.03, T:0.40
Consensus pattern (21 bp):
TTCCCCATCTTCAATCCCTAA
Found at i:5204557 original size:12 final size:12
Alignment explanation
Indices: 5204540--5204575 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5204530 GAGTGGTCTG
**
5204540 CCTTGAATTGTT
1 CCTTGAATCCTT
5204552 CCTTGAATCCTT
1 CCTTGAATCCTT
5204564 CCTTGAATCCTT
1 CCTTGAATCCTT
5204576 AGTGTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.44
Consensus pattern (12 bp):
CCTTGAATCCTT
Found at i:5206286 original size:21 final size:20
Alignment explanation
Indices: 5206262--5206301 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5206252 ATCATTTCCC
5206262 ATTCCCGATCTTCAATCCCTA
1 ATTCCC-ATCTTCAATCCCTA
* *
5206283 ATTCCCCTTTTCAATCCCT
1 ATTCCCATCTTCAATCCCT
5206302 TCTCCTGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.40, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTCCCATCTTCAATCCCTA
Found at i:5213442 original size:27 final size:28
Alignment explanation
Indices: 5213390--5213443 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5213380 CCAAAATTAT
*
5213390 TAATAATTACAAAAATTAATATATAAAC
1 TAATAATTACAAAAATTAATAAATAAAC
5213418 TAATAA-TA-AAAAATTAAATAAATAAA
1 TAATAATTACAAAAATT-AATAAATAAA
5213444 TTATTACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 11 0.46
28 6 0.25
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
TAATAATTACAAAAATTAATAAATAAAC
Found at i:5214437 original size:8 final size:8
Alignment explanation
Indices: 5214424--5214465 Score: 57
Period size: 8 Copynumber: 4.9 Consensus size: 8
5214414 TTATGATTAT
5214424 TTTAAATA
1 TTTAAATA
5214432 TTTAAATTATA
1 TTT-AA--ATA
5214443 TTTAAATA
1 TTTAAATA
5214451 TTTAAATA
1 TTTAAATA
5214459 TTTAAAT
1 TTTAAAT
5214466 TACATATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 21 0.68
9 2 0.06
10 2 0.06
11 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAATA
Found at i:5214448 original size:19 final size:18
Alignment explanation
Indices: 5214419--5214465 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
5214409 TTTGATTATG
5214419 ATTATTTTAAATATTTAA
1 ATTATTTTAAATATTTAA
5214437 ATTATATTTAAATATTTAA
1 ATTAT-TTTAAATATTTAA
5214456 A-TA-TTTAAAT
1 ATTATTTTAAAT
5214466 TACATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.25
18 7 0.25
19 14 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTTTAAATATTTAA
Found at i:5214458 original size:27 final size:28
Alignment explanation
Indices: 5214424--5214477 Score: 92
Period size: 27 Copynumber: 1.9 Consensus size: 28
5214414 TTATGATTAT
5214424 TTTAAATATTTAAATT-ATATTTAAATA
1 TTTAAATATTTAAATTAATATTTAAATA
5214451 TTTAAATATTTAAATTACATATTTAAA
1 TTTAAATATTTAAATTA-ATATTTAAA
5214478 ACTACTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.64
29 9 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAAATATTTAAATTAATATTTAAATA
Found at i:5215278 original size:49 final size:49
Alignment explanation
Indices: 5215222--5215338 Score: 146
Period size: 49 Copynumber: 2.4 Consensus size: 49
5215212 GGAAAACGCG
* *
5215222 GCTCCTGCACCGCGCTATATGCTGATTTGGCGCCACGTGGGTATAGCAC
1 GCTCCTGCACCGCGCTATACGCTGATCTGGCGCCACGTGGGTATAGCAC
* * * * *
5215271 GCTCCTGCCCCGCGATATACGGTGATCTGGCGCCATGTGGGTATAGTAC
1 GCTCCTGCACCGCGCTATACGCTGATCTGGCGCCACGTGGGTATAGCAC
* *
5215320 GCCCCTG-ATCGCGCTATAC
1 GCTCCTGCACCGCGCTATAC
5215339 CTGGATATCT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
48 9 0.16
49 48 0.84
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (49 bp):
GCTCCTGCACCGCGCTATACGCTGATCTGGCGCCACGTGGGTATAGCAC
Found at i:5215812 original size:107 final size:107
Alignment explanation
Indices: 5215614--5215819 Score: 353
Period size: 107 Copynumber: 1.9 Consensus size: 107
5215604 ATATATGTCT
* *
5215614 ACACTTTGCTATACGGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAATTTAGTTGAT
1 ACACTTTGCTATACAGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAATTAAGTTGAT
*
5215679 TTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TCATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
5215721 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA-TAAGTTG
1 ACACTTTGCT-ATACAGTAACATTTTAACG-TTTAATTTAATTTAAATTATTAGTAATTAAGTTG
5215785 ATTCATTT-ATGCATGATTATTAGATTAAGAATTAA
64 ATTCATTTAATGCATGATTATTAGATTAAGAATTAA
5215820 TTTTTGTAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
107 37 0.39
108 31 0.33
109 26 0.28
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (107 bp):
ACACTTTGCTATACAGTAACATTTTAACGTTTAATTTAATTTAAATTATTAGTAATTAAGTTGAT
TCATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:5217236 original size:18 final size:18
Alignment explanation
Indices: 5217209--5217251 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
5217199 CCAGCAGCCA
*
5217209 CCGCAACCATATATGATG
1 CCGCATCCATATATGATG
5217227 CCGCATCCATATATGATG
1 CCGCATCCATATATGATG
*
5217245 TCGCATC
1 CCGCATC
5217252 GCCTTTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (18 bp):
CCGCATCCATATATGATG
Found at i:5226666 original size:19 final size:19
Alignment explanation
Indices: 5226618--5226666 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
5226608 TATCACAGTC
*
5226618 ATTTTTTTTATAAAATTTT
1 ATTTTTTTCATAAAATTTT
* * *
5226637 ATTTTAATTCATATATTTTT
1 ATTTT-TTTCATAAAATTTT
5226657 ATTTTTTTCA
1 ATTTTTTTCA
5226667 ATTTAATCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTTTCATAAAATTTT
Found at i:5226986 original size:13 final size:13
Alignment explanation
Indices: 5226968--5226992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5226958 AACATTCCGT
5226968 TTTTTAAATTTAA
1 TTTTTAAATTTAA
5226981 TTTTTAAATTTA
1 TTTTTAAATTTA
5226993 TAGAAAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAAATTTAA
Found at i:5231184 original size:182 final size:186
Alignment explanation
Indices: 5230961--5231329 Score: 710
Period size: 182 Copynumber: 2.0 Consensus size: 186
5230951 GAAATTTAAA
5230961 ACTAAAAGATTTAGAGAATTTGAGTTATATAAGAGAGGAGAAGATGATTTTGGTGTGAAGAATGA
1 ACTAAAAGATTTAGAGAATTTGAGTTATATAAGAGAGGAGAAGATGATTTTGGTGTGAAGAATGA
5231026 TGGGGGTTGAGGGGGTTTATATAGGGAGGAGGAGGGGTAGTTGGGG-AAAATTGGATGGGCATTT
66 TGGGGGTTGAGGGGGTTTATATAGGGAGGAGGAGGGGTAGTTGGGGAAAAATTGGATGGGCATTT
5231090 AAGACATTTAATGAAAGACGCGT-CCCGAAGATGCGCCTTTC-CACGTGACAACCG
131 AAGACATTTAATGAAAGACGCGTCCCCGAAGATGCGCCTTTCACACGTGACAACCG
5231144 ACTAAAAGATTTAGAGAA-TTGAGTTATATAAGAGAGGAGAAGATGATTTTGGTGTGAAGAATGA
1 ACTAAAAGATTTAGAGAATTTGAGTTATATAAGAGAGGAGAAGATGATTTTGGTGTGAAGAATGA
5231208 TGGGGGTTGAGGGGGTTTATATAGGGAGGAGGAGGGGTAGTTGGGGAAAAATTGGATGGGCATTT
66 TGGGGGTTGAGGGGGTTTATATAGGGAGGAGGAGGGGTAGTTGGGGAAAAATTGGATGGGCATTT
5231273 AAGACATTTAATGAAAGACGCGTCCCCGAAGATGCGCCTTTCACACGTGACAACCG
131 AAGACATTTAATGAAAGACGCGTCCCCGAAGATGCGCCTTTCACACGTGACAACCG
5231329 A
1 A
5231330 ATCAACAATA
Statistics
Matches: 183, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
182 92 0.50
183 59 0.32
184 18 0.10
185 14 0.08
ACGTcount: A:0.32, C:0.09, G:0.34, T:0.25
Consensus pattern (186 bp):
ACTAAAAGATTTAGAGAATTTGAGTTATATAAGAGAGGAGAAGATGATTTTGGTGTGAAGAATGA
TGGGGGTTGAGGGGGTTTATATAGGGAGGAGGAGGGGTAGTTGGGGAAAAATTGGATGGGCATTT
AAGACATTTAATGAAAGACGCGTCCCCGAAGATGCGCCTTTCACACGTGACAACCG
Found at i:5236385 original size:14 final size:14
Alignment explanation
Indices: 5236356--5236399 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5236346 TACGTTTCTG
* *
5236356 TTTATATGCAGAGA
1 TTTATTTGCAGGGA
5236370 TTT-TTTCGCAGGGA
1 TTTATTT-GCAGGGA
5236384 TTTATTTGCAGGGA
1 TTTATTTGCAGGGA
5236398 TT
1 TT
5236400 ACTTCCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 21 0.81
15 3 0.12
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (14 bp):
TTTATTTGCAGGGA
Found at i:5238776 original size:23 final size:22
Alignment explanation
Indices: 5238735--5238777 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5238725 TTTGCATATA
* *
5238735 ATTTTTATTTAGGATTTTTAAT
1 ATTTTTAATTAGGAGTTTTAAT
5238757 ATTTATTAATTAGGAGTTTTA
1 ATTT-TTAATTAGGAGTTTTA
5238778 GTTTGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (22 bp):
ATTTTTAATTAGGAGTTTTAAT
Found at i:5239104 original size:3 final size:3
Alignment explanation
Indices: 5239096--5239129 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5239086 AAGAAAGGAG
5239096 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
5239130 TAATAATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:5239541 original size:14 final size:15
Alignment explanation
Indices: 5239522--5239550 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5239512 GGGTTGACGC
5239522 AAAAG-AAGAAAAAT
1 AAAAGAAAGAAAAAT
5239536 AAAAGAAAGAAAAAT
1 AAAAGAAAGAAAAAT
5239551 CCCAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (15 bp):
AAAAGAAAGAAAAAT
Found at i:5243673 original size:11 final size:12
Alignment explanation
Indices: 5243654--5243684 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
5243644 CCTTACTTAT
5243654 TTAATATTATTA
1 TTAATATTATTA
5243666 TT-ATATTATTA
1 TTAATATTATTA
5243677 TTAATATT
1 TTAATATT
5243685 TTACTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTAATATTATTA
Found at i:5247605 original size:33 final size:30
Alignment explanation
Indices: 5247514--5247623 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 30
5247504 TGCACTGAGC
* * *
5247514 GTCCTTACACACTACAGTGC-ATACTAAGT
1 GTCCTTACACACTATAGTACTGTACTAAGT
*
5247543 TTCCTTACACACTATAGTACTGTACTAAGT
1 GTCCTTACACACTATAGTACTGTACTAAGT
5247573 GTCC-TACACACTATAGTACTATATGTACTAAGT
1 GTCCTTACACACTATAGTAC----TGTACTAAGT
5247606 GTCCTTACACACTATAGT
1 GTCCTTACACACTATAGT
5247624 GCTAATCCGA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
29 32 0.46
30 11 0.16
33 14 0.20
34 13 0.19
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (30 bp):
GTCCTTACACACTATAGTACTGTACTAAGT
Found at i:5247815 original size:20 final size:20
Alignment explanation
Indices: 5247777--5247816 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
5247767 GAAATATCAT
5247777 TCATGATAAAATCATATATGC
1 TCATGATAAAATCA-ATATGC
5247798 TCATGATAAATATC-ATATG
1 TCATGATAAA-ATCAATATG
5247817 TAAATGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 10 0.56
22 3 0.17
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
TCATGATAAAATCAATATGC
Found at i:5250151 original size:30 final size:31
Alignment explanation
Indices: 5250080--5250151 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
5250070 CTTTTGGAAA
*
5250080 TATACCTTTTGTCCCTAAACTTTTTAAAAAAT
1 TATA-CTTTGGTCCCTAAACTTTTTAAAAAAT
* * * * *
5250112 AACATTTTGGTCCCTAAAC-TTTTACAAACT
1 TATACTTTGGTCCCTAAACTTTTTAAAAAAT
5250142 TATACTTTGG
1 TATACTTTGG
5250152 CCATTAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 16 0.52
31 13 0.42
32 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (31 bp):
TATACTTTGGTCCCTAAACTTTTTAAAAAAT
Found at i:5250466 original size:13 final size:14
Alignment explanation
Indices: 5250448--5250486 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
5250438 ATTTTAGTTC
5250448 GTTAGAA-TTAAGA
1 GTTAGAATTTAAGA
5250461 GTTAGAATTTTAAGA
1 GTTAGAA-TTTAAGA
*
5250476 GTTAGTATTTA
1 GTTAGAATTTA
5250487 TTTTCATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 7 0.30
14 4 0.17
15 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
GTTAGAATTTAAGA
Found at i:5251334 original size:20 final size:21
Alignment explanation
Indices: 5251309--5251347 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5251299 TATAGAAATG
*
5251309 TCCCGAAGGA-CACATATATA
1 TCCCGAAAGACCACATATATA
5251329 TCCCGAAAGACCACATATA
1 TCCCGAAAGACCACATATA
5251348 AATGTCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (21 bp):
TCCCGAAAGACCACATATATA
Found at i:5251365 original size:23 final size:23
Alignment explanation
Indices: 5251275--5251365 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 23
5251265 TCCATAGGGG
*
5251275 CATATAAATTGTCTCGAAGGACCA
1 CATATAAA-TGTCCCGAAGGACCA
* *
5251299 TATAGAAATGTCCCGAAGGA-CA
1 CATATAAATGTCCCGAAGGACCA
* *
5251321 CATAT--ATATCCCGAAAGACCA
1 CATATAAATGTCCCGAAGGACCA
*
5251342 CATATAAATGTCCCTAAGGACCA
1 CATATAAATGTCCCGAAGGACCA
5251365 C
1 C
5251366 GTAGAACCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.20
21 7 0.13
22 5 0.09
23 25 0.46
24 6 0.11
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (23 bp):
CATATAAATGTCCCGAAGGACCA
Found at i:5251742 original size:17 final size:17
Alignment explanation
Indices: 5251720--5251752 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5251710 TTTTCACTTG
5251720 CATATA-TTTCACTTATT
1 CATATAGTTTCA-TTATT
5251737 CATATAGTTTCATTAT
1 CATATAGTTTCATTAT
5251753 ACCAATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (17 bp):
CATATAGTTTCATTATT
Found at i:5256870 original size:17 final size:17
Alignment explanation
Indices: 5256844--5256889 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
5256834 TCACTTAACT
* *
5256844 TATTTTACTTTTTCATA
1 TATTTCACTTATTCATA
5256861 TATTTCACTTATTCATA
1 TATTTCACTTATTCATA
5256878 TAATTTCA-TTAT
1 T-ATTTCACTTAT
5256890 ACCAATTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTCACTTATTCATA
Found at i:5279699 original size:36 final size:36
Alignment explanation
Indices: 5279600--5279712 Score: 149
Period size: 36 Copynumber: 3.2 Consensus size: 36
5279590 AATTCTTTTC
* ** *
5279600 AAGCAATACAAATTCAGA-CTTCACGGAAGAGTAGTA
1 AAGCAATGCAAATTCA-ACCTTCACAAAAGAGTAGTG
*
5279636 AAGCAATGC-AATTCAGCCTTCACAAAAGAGTAGTG
1 AAGCAATGCAAATTCAACCTTCACAAAAGAGTAGTG
*
5279671 AAGCAATGCAAATCCAACCTTCACAAAAGAGTAGTG
1 AAGCAATGCAAATTCAACCTTCACAAAAGAGTAGTG
5279707 AAGCAA
1 AAGCAA
5279713 GATCAAGATC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 30 0.44
36 38 0.56
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (36 bp):
AAGCAATGCAAATTCAACCTTCACAAAAGAGTAGTG
Found at i:5280014 original size:31 final size:32
Alignment explanation
Indices: 5279957--5280021 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
5279947 TTTTAGTTAT
* * *
5279957 AGGCCCAAATACAAGACCCAATTACAACCTGA
1 AGGCCCAAATACAAGAACAAATTACAACATGA
*
5279989 AGGCCCAAATACAA-AATAAATTACAACATGA
1 AGGCCCAAATACAAGAACAAATTACAACATGA
5280020 AG
1 AG
5280022 CCCGATTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.49, C:0.25, G:0.12, T:0.14
Consensus pattern (32 bp):
AGGCCCAAATACAAGAACAAATTACAACATGA
Found at i:5281078 original size:2 final size:2
Alignment explanation
Indices: 5281071--5281100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5281061 GTCATTAATC
5281071 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
5281101 TCTAGGGTAA
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:5286989 original size:22 final size:22
Alignment explanation
Indices: 5286949--5286990 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5286939 TAAACATTAA
* **
5286949 TTAGTTTTTAAGTTTTTTAGCC
1 TTAGATTTTAAGTGCTTTAGCC
5286971 TTAGATTTTAAGTGCTTTAG
1 TTAGATTTTAAGTGCTTTAG
5286991 TTATTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (22 bp):
TTAGATTTTAAGTGCTTTAGCC
Found at i:5288872 original size:24 final size:25
Alignment explanation
Indices: 5288828--5288875 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5288818 TCAGATGTAG
*
5288828 AAATAAAAGACATTTTATAGATGGA
1 AAATAAAAGACATTGTATAGATGGA
5288853 AAATAAAA-ACATTCGT-TAGATGG
1 AAATAAAAGACATT-GTATAGATGG
5288876 TTCCCAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (25 bp):
AAATAAAAGACATTGTATAGATGGA
Found at i:5289500 original size:18 final size:18
Alignment explanation
Indices: 5289477--5289521 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
5289467 TTTATTTTTA
5289477 TCATTTCATTG-TTAATAT
1 TCATTTCATTGCTT-ATAT
5289495 TCATTT-A-TGCTTATAT
1 TCATTTCATTGCTTATAT
5289511 TCATATTCATT
1 TCAT-TTCATT
5289522 CATTAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 7 0.30
19 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (18 bp):
TCATTTCATTGCTTATAT
Found at i:5293724 original size:13 final size:13
Alignment explanation
Indices: 5293702--5293734 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5293692 TACAATTCGA
5293702 TAAC-AAAATACT
1 TAACAAAAATACT
5293714 TAACAAAAATACT
1 TAACAAAAATACT
5293727 TAACAAAA
1 TAACAAAA
5293735 CAAGAACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (13 bp):
TAACAAAAATACT
Found at i:5294105 original size:23 final size:23
Alignment explanation
Indices: 5294073--5294146 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
5294063 TGAGTGCCAT
*
5294073 ATAG-AATGTCCTGAAGGACCGC
1 ATAGAAATGTCCCGAAGGACCGC
*
5294095 ATAGAAATGTCCCGAAGGACCAC
1 ATAGAAATGTCCCGAAGGACCGC
* * *
5294118 GTAGAATTATCCCGAAGGACCGC
1 ATAGAAATGTCCCGAAGGACCGC
*
5294141 GTAGAA
1 ATAGAA
5294147 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
22 4 0.09
23 41 0.91
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (23 bp):
ATAGAAATGTCCCGAAGGACCGC
Found at i:5299181 original size:46 final size:46
Alignment explanation
Indices: 5299114--5299408 Score: 464
Period size: 46 Copynumber: 6.4 Consensus size: 46
5299104 ATTTATTTGA
* *
5299114 ATAAATGAAAATGCATAACGGTACATTATTGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
5299160 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
5299206 ATAAATGAAAATACATAACGGTGCATTATCGGCATAAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
5299252 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
5299298 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * * * *
5299344 ATAAATGAACATGAATAACAGTGCATAATTGACATGAAAGAATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
5299390 ATAAATGAAAATACATAAC
1 ATAAATGAAAATGCATAAC
5299409 TTTGGTGCAA
Statistics
Matches: 231, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 231 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:5300025 original size:15 final size:17
Alignment explanation
Indices: 5300007--5300043 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5299997 GAAAATGAAG
5300007 AAAAAGAG-A-AAAAAT
1 AAAAAGAGAAGAAAAAT
5300022 AAAAAGAGAAGAAAAAT
1 AAAAAGAGAAGAAAAAT
5300039 AAAAA
1 AAAAA
5300044 TAAAAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAGAGAAGAAAAAT
Found at i:5300736 original size:18 final size:18
Alignment explanation
Indices: 5300713--5300770 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
5300703 ACTGCCAACG
5300713 AAGAAGAAAAGAAAGAAA
1 AAGAAGAAAAGAAAGAAA
*
5300731 AAGAAGAAGAGAAA-ATAA
1 AAGAAGAAAAGAAAGA-AA
5300749 AA-AATGAAAAGAGAAGGAAA
1 AAGAA-GAAAAGA-AA-GAAA
5300769 AA
1 AA
5300771 TAGAAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 3 0.09
18 23 0.70
19 2 0.06
20 4 0.12
21 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.03
Consensus pattern (18 bp):
AAGAAGAAAAGAAAGAAA
Found at i:5300752 original size:21 final size:22
Alignment explanation
Indices: 5300712--5300768 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
5300702 TACTGCCAAC
5300712 GAAGAAGA-AAAGAAAGAAAAA
1 GAAGAAGAGAAAGAAAGAAAAA
*
5300733 GAAGAAGAGAAA-ATAA-AAAAT
1 GAAGAAGAGAAAGA-AAGAAAAA
*
5300754 GAA-AAGAGAAGGAAA
1 GAAGAAGAGAAAGAAA
5300769 AATAGAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 9 0.29
21 17 0.55
22 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (22 bp):
GAAGAAGAGAAAGAAAGAAAAA
Found at i:5300865 original size:41 final size:41
Alignment explanation
Indices: 5300788--5300891 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 41
5300778 AAAACCAAAG
*
5300788 TGAAAA-CTCGAAAGGGCACTTTGACAAAAATAAATCTGAAGA
1 TGAAAACCT-GAAAGGGCACTTTGACAAAAATAAATCT-AAAA
* * * * *
5300830 -GAAAACCTGAAAGGGCGCTTTGAGAATAGTGAATCTAAAA
1 TGAAAACCTGAAAGGGCACTTTGACAAAAATAAATCTAAAA
* *
5300870 TGAAAACCTAAAAGGGTACTTT
1 TGAAAACCTGAAAGGGCACTTT
5300892 AGAGCGGATA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 3 0.06
41 46 0.90
42 2 0.04
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (41 bp):
TGAAAACCTGAAAGGGCACTTTGACAAAAATAAATCTAAAA
Found at i:5301482 original size:43 final size:43
Alignment explanation
Indices: 5301376--5301494 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 43
5301366 TAGCGTAACC
*
5301376 TTATTTTGCTCGATTCTATCACAGAAGTA-TGTAGATCAACATCG
1 TTATTTTGCTCGATTCT-TCACAGAAGAAGT-TAGATCAACATCG
* * * * *
5301420 GTATTTTGTTTGATCCTTCACAGAAGAAGTTGGATCAACAGT-G
1 TTATTTTGCTCGATTCTTCACAGAAGAAGTTAGATCAACA-TCG
* * *
5301463 TTATTTCGCTCGATTCTTCATAGAAGGAGTTA
1 TTATTTTGCTCGATTCTTCACAGAAGAAGTTA
5301495 AATTAGCATA
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
43 44 0.75
44 15 0.25
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (43 bp):
TTATTTTGCTCGATTCTTCACAGAAGAAGTTAGATCAACATCG
Found at i:5301565 original size:133 final size:132
Alignment explanation
Indices: 5301336--5301628 Score: 317
Period size: 133 Copynumber: 2.2 Consensus size: 132
5301326 TATCAATCTT
* * * *
5301336 TTGCTCTATTCTTCACATAAGGAGTTGAATTAGCGTAACCTTATTTTGCTCGATTCTATCACAGA
1 TTGCTCGATTCTTCACAGAAGGAGTTAAATTAGCATAACCTTATTTTGCTCGATTCTATCACAGA
* * * *
5301401 AGTATGTAGATCAACATCGGTATTTTGTTTGATCCTTCACAGAA-GAAGTTGGATCAACA-GTGT
66 AG-AGGTAGATCAACATCGGAATTATGTTTGATCCTCCACAGAATG-AGTTGGATCAACATGTGT
5301464 TAT-
129 TATG
* * *
5301467 TTCGCTCGATTCTTCATAGAAGGAGTTAAATTAGCATAATCTTATTTTTGTTCGATTCTATCACA
1 TT-GCTCGATTCTTCACAGAAGGAGTTAAATTAGCATAACCTTA-TTTTGCTCGATTCTATCACA
* * * * *
5301532 TGATA-AGGTAGATCAGCATTGGCAATTAT-TTTGATTCTCCACAGAATGAGTTGGATTAACATT
64 -GA-AGAGGTAGATCAACATCGG-AATTATGTTTGATCCTCCACAGAATGAGTTGGATCAACATG
*
5301595 TGTTGTG
126 TGTTATG
* *
5301602 TTACTCGATCCTTCACAGAAGGAGTTA
1 TTGCTCGATTCTTCACAGAAGGAGTTA
5301629 GATCAATGAC
Statistics
Matches: 134, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
131 2 0.01
132 35 0.26
133 60 0.45
134 34 0.25
135 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (132 bp):
TTGCTCGATTCTTCACAGAAGGAGTTAAATTAGCATAACCTTATTTTGCTCGATTCTATCACAGA
AGAGGTAGATCAACATCGGAATTATGTTTGATCCTCCACAGAATGAGTTGGATCAACATGTGTTA
TG
Found at i:5302360 original size:35 final size:34
Alignment explanation
Indices: 5302321--5302386 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
5302311 TAAATAATAA
*
5302321 TTGCATGTGATAATACATATTAAAT-ATAATTGTAT
1 TTGCATGTCAT-ATA-ATATTAAATAATAATTGTAT
*
5302356 TTGCATGTCATATAGTATTAAATAATAATTG
1 TTGCATGTCATATAATATTAAATAATAATTG
5302387 CATATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.29
34 10 0.36
35 10 0.36
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (34 bp):
TTGCATGTCATATAATATTAAATAATAATTGTAT
Found at i:5304862 original size:2 final size:2
Alignment explanation
Indices: 5304855--5304903 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5304845 TGTTGTACCT
5304855 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5304897 TA TA TA T
1 TA TA TA T
5304904 CATCCCTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5305205 original size:81 final size:81
Alignment explanation
Indices: 5305067--5305546 Score: 802
Period size: 81 Copynumber: 5.9 Consensus size: 81
5305057 AACCGTTTGT
*
5305067 TTTTACTCAACAGTATTAAACCGTTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTA
1 TTTTACTCAACGGTATTAAACC---GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTA
* *
5305132 CACAATTAGGCCATTAATC
63 CACAGTTAGGCCATTATTC
*
5305151 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTATCTTTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
5305216 AGTTAGGCCA-TATTC
66 AGTTAGGCCATTATTC
* *
5305231 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
* *
5305296 AGTTAGACCATTATTA
66 AGTTAGGCCATTATTC
5305312 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
*
5305377 AGTTAGACCATTATTC
66 AGTTAGGCCATTATTC
* *
5305393 TTTTACTCAACGGTATTAAACCGATCATCTAACTGGCATAATTGGTACCTTTCTACCAATT-GAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
*
5305457 AGTTAGGCCACTATTC
66 AGTTAGGCCATTATTC
*
5305473 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGATACCTTTCTACCAATTACAC
1 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
5305538 AGTTAGGCC
66 AGTTAGGCC
5305547 TCAAAGGCAC
Statistics
Matches: 375, Mismatches: 19, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
80 150 0.40
81 204 0.54
84 21 0.06
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (81 bp):
TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACAC
AGTTAGGCCATTATTC
Found at i:5305335 original size:161 final size:162
Alignment explanation
Indices: 5305067--5305546 Score: 820
Period size: 161 Copynumber: 3.0 Consensus size: 162
5305057 AACCGTTTGT
*
5305067 TTTTACTCAACAGTATTAAACCGTTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTA
1 TTTTACTCAACAGTATTAAACC---GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG
* *
5305132 CACAATTAGGCCATTAATCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGT
63 CACAGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGT
*
5305197 ATCTTTCTACCAATTACACAGTTAGGCCA-TATTC
128 ACCTTTCTACCAATTACACAGTTAGGCCATTATTC
5305231 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* *
5305296 AGTTAGACCATTATTATTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
*
5305361 TTTCTACCAATTACACAGTTAGACCATTATTC
131 TTTCTACCAATTACACAGTTAGGCCATTATTC
* *
5305393 TTTTACTCAACGGTATTAAACCGATCATCTAACTGGCATAATTGGTACCTTTCTACCAATTG-AC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
* *
5305457 AGTTAGGCCACTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGATACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
5305522 TTTCTACCAATTACACAGTTAGGCC
131 TTTCTACCAATTACACAGTTAGGCC
5305547 TCAAAGGCAC
Statistics
Matches: 301, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
161 214 0.71
162 65 0.22
164 22 0.07
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (162 bp):
TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACC
TTTCTACCAATTACACAGTTAGGCCATTATTC
Found at i:5305524 original size:242 final size:243
Alignment explanation
Indices: 5305067--5305543 Score: 823
Period size: 242 Copynumber: 2.0 Consensus size: 243
5305057 AACCGTTTGT
5305067 TTTTACTCAACAGTATTAAACCGTTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTA
1 TTTTACTCAACAGTATTAAACC--TGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTA
* *
5305132 CACAATTAGGCCATTAATCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGT
64 CACAATTAGACCATTAATCTTTTACTCAACGGTATTAAACCGATCATCTAACTGGCATAATTGGT
*
5305197 ATCTTTCTACCAATTACACAGTTAGGCCATATTCTTTTACTCAACAGTATTAAACCGTTCATCTA
129 ACCTTTCTACCAATTACACAGTTAGGCCATATTCTTTTACTCAACAGTATTAAACCGTTCATCTA
* *
5305262 ACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGACCATTATTA
194 ACTGGCATAATTGATACCTTTCTACCAATTACACAGTTAGACCATTATTA
*
5305312 TTTTACTCAACGGTATTAAACC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACA
1 TTTTACTCAACAGTATTAAACCTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACA
* *
5305376 CAGTTAGACCATTATTCTTTTACTCAACGGTATTAAACCGATCATCTAACTGGCATAATTGGTAC
66 CAATTAGACCATTAATCTTTTACTCAACGGTATTAAACCGATCATCTAACTGGCATAATTGGTAC
* *
5305441 CTTTCTACCAATT-GACAGTTAGGCCACTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAA
131 CTTTCTACCAATTACACAGTTAGGCCA-TATTCTTTTACTCAACAGTATTAAACCGTTCATCTAA
5305505 CTGGCATAATTGATACCTTTCTACCAATTACACAGTTAG
195 CTGGCATAATTGATACCTTTCTACCAATTACACAGTTAG
5305544 GCCTCAAAGG
Statistics
Matches: 221, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
241 12 0.05
242 188 0.85
245 21 0.10
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (243 bp):
TTTTACTCAACAGTATTAAACCTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTACA
CAATTAGACCATTAATCTTTTACTCAACGGTATTAAACCGATCATCTAACTGGCATAATTGGTAC
CTTTCTACCAATTACACAGTTAGGCCATATTCTTTTACTCAACAGTATTAAACCGTTCATCTAAC
TGGCATAATTGATACCTTTCTACCAATTACACAGTTAGACCATTATTA
Found at i:5305591 original size:68 final size:68
Alignment explanation
Indices: 5305491--5305656 Score: 226
Period size: 68 Copynumber: 2.4 Consensus size: 68
5305481 AACGGTATTA
* * * * *
5305491 AACCGTTCATCTAACTGGCATAATTGATACCTTTCTACCAATTA-CACAGTTAGGCCTCAAAGGC
1 AACCTTTCATCTAACTGGCTTAAATGACACCTTTCTACC-ATAAGCACAGTTAGGCCTCAAAGGC
5305555 ACTT
65 ACTT
* **
5305559 AGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCATAAGCACAGTTAGGCCTCAAAGGCA
1 AACCTTTCATCTAACTGGCTTAAATGACACCTTTCTACCATAAGCACAGTTAGGCCTCAAAGGCA
5305624 CTT
66 CTT
* *
5305627 AACCTTTCATCTAATTGGCTTATATGACAC
1 AACCTTTCATCTAACTGGCTTAAATGACAC
5305657 TTGTAATACC
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 3 0.03
68 83 0.97
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (68 bp):
AACCTTTCATCTAACTGGCTTAAATGACACCTTTCTACCATAAGCACAGTTAGGCCTCAAAGGCA
CTT
Found at i:5307952 original size:47 final size:47
Alignment explanation
Indices: 5307895--5308109 Score: 360
Period size: 47 Copynumber: 4.6 Consensus size: 47
5307885 TTATGGTTTA
5307895 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTACA-TATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTA-AGTATG
*
5307942 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
5307989 TTGATAAAATAAGCTTACGAACTTATGGAATTTAAATGGTAATTATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
*
5308036 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
5308083 TTGGTAAAATAAGCTTGCGAGCTTATG
1 TTGATAAAATAAGCTTACGAGCTTATG
5308110 AGATAAATGA
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
46 1 0.01
47 157 0.99
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (47 bp):
TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
Found at i:5308598 original size:13 final size:13
Alignment explanation
Indices: 5308580--5308616 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
5308570 TCGATCCCCC
5308580 CACTGTTCA-TCGT
1 CACTGTTCACT-GT
5308593 CACTGTTCACTGT
1 CACTGTTCACTGT
5308606 CACTGTTCACT
1 CACTGTTCACT
5308617 ATTCATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 22 0.96
14 1 0.04
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.38
Consensus pattern (13 bp):
CACTGTTCACTGT
Found at i:5309182 original size:56 final size:57
Alignment explanation
Indices: 5309057--5309215 Score: 184
Period size: 56 Copynumber: 2.8 Consensus size: 57
5309047 ATATTTTCCT
* * * *
5309057 ATAC-GAACATTCATACACTTGGTATGAATTTC-TTA-GTTAGCACA-CATTGAGCCC
1 ATACAGAA-ATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCATAGAGCCC
* *
5309111 ATACAAAAATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCA-AGTGCCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCATAGAGCCC
* *
5309167 ATACAGAAATTCATACACTTAGTATGAATATCTTACAATTTTTGCACAC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTT--TATTTTTGCACAC
5309216 TTAGTGTCAT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
54 27 0.30
55 5 0.06
56 44 0.49
57 2 0.02
58 12 0.13
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.34
Consensus pattern (57 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTTATTTTTGCACACCATAGAGCCC
Found at i:5309666 original size:94 final size:95
Alignment explanation
Indices: 5309543--5309768 Score: 249
Period size: 94 Copynumber: 2.4 Consensus size: 95
5309533 TTTGGCTCTA
* * * * * * * *
5309543 TAGTATCGATACTAC-TACCCTAGTATCGATACTTCTATACTATGGTATTGATACC-CCTTCTGG
1 TAGTATCGATACT-CTTACCATGGTATCGATACTACCATACTATGGTACTAATACCTCCTTCCGA
** ** * *
5309606 TATCGATACTGATTTTAGGTTTGATGTTGCC
65 TATCGATACAAAAATTAGATTCGATGTTGCC
*
5309637 TAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGGTACTAATACCTCTTTCCGAT
1 TAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGGTACTAATACCTCCTTCCGAT
*
5309702 ATCGATACAAAAATTAGATTCGATGTTGCT
66 ATCGATACAAAAATTAGATTCGATGTTGCC
* * *
5309732 TGGTATCGATACCCTTTATCATGGTATCGATACTACC
1 TAGTATCGATACTC-TTACCATGGTATCGATACTACC
5309769 TTGTCGGTAT
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
93 1 0.01
94 47 0.43
95 41 0.37
96 21 0.19
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (95 bp):
TAGTATCGATACTCTTACCATGGTATCGATACTACCATACTATGGTACTAATACCTCCTTCCGAT
ATCGATACAAAAATTAGATTCGATGTTGCC
Found at i:5313499 original size:20 final size:20
Alignment explanation
Indices: 5313470--5313508 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5313460 ATATTTCCAG
*
5313470 TAAAATAATTATAAATATTA
1 TAAAAGAATTATAAATATTA
*
5313490 TAAAAGAATTATAAGTATT
1 TAAAAGAATTATAAATATT
5313509 GACATATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAGAATTATAAATATTA
Found at i:5315727 original size:17 final size:17
Alignment explanation
Indices: 5315705--5315737 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5315695 TTGGTTCAGG
5315705 AAACAG-TAATACAATTA
1 AAACAGATAA-ACAATTA
5315722 AAACAGATAAACAATT
1 AAACAGATAAACAATT
5315738 GGTTCATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (17 bp):
AAACAGATAAACAATTA
Found at i:5317080 original size:34 final size:35
Alignment explanation
Indices: 5317010--5317122 Score: 108
Period size: 34 Copynumber: 3.2 Consensus size: 35
5317000 TATATATAAA
* * *
5317010 ATTTATA-TATTACATATATAAATTAT-ATAGTTTAT
1 ATTTATATTATT--ATATATAAACTATAATACTATAT
*
5317045 ATTTATATTATTATATACTATA-TATAA-ACTATAT
1 ATTTATATTATTATATA-TAAACTATAATACTATAT
* *
5317079 ATATATATTATTATGTATAAACTATAATACTATAT
1 ATTTATATTATTATATATAAACTATAATACTATAT
5317114 AGTTTATAT
1 A-TTTATAT
5317123 ATATGAACTA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
33 3 0.05
34 33 0.51
35 19 0.29
36 10 0.15
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (35 bp):
ATTTATATTATTATATATAAACTATAATACTATAT
Found at i:5317132 original size:22 final size:22
Alignment explanation
Indices: 5317101--5317184 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 22
5317091 ATGTATAAAC
5317101 TATAATACTATATAGTTTATATA
1 TATAA-ACTATATAGTTTATATA
* *
5317124 TATGAACTAT-T-G--AACTATA
1 TATAAACTATATAGTTTA-TATA
*
5317143 TATAAACTACATAGTTTAT-TAA
1 TATAAACTATATAGTTTATAT-A
*
5317165 TATAAATTATATAGTTTATA
1 TATAAACTATATAGTTTATA
5317185 GATAGTAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
18 1 0.02
19 12 0.26
20 2 0.04
21 3 0.06
22 24 0.51
23 5 0.11
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (22 bp):
TATAAACTATATAGTTTATATA
Found at i:5317146 original size:2 final size:2
Alignment explanation
Indices: 5316994--5317126 Score: 66
Period size: 2 Copynumber: 67.5 Consensus size: 2
5316984 AAAATTGAAG
* * * *
5316994 TA TA TA TA TA TA TA -A AA TT TA TA TA T- TA CA TA TA TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
5317033 TA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA AA CTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * *
5317076 TA TA TA TA TA T- TA T- TA TG TA TA AA CTA TA -A TA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA
5317118 TA TA TA TA T
1 TA TA TA TA T
5317127 GAACTATTGA
Statistics
Matches: 98, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
1 8 0.08
2 82 0.84
3 8 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5317595 original size:65 final size:63
Alignment explanation
Indices: 5317476--5317685 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
5317466 TTTTTCAGAG
* * *
5317476 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
5317538 ATT
61 ATT
* *
5317541 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
5317605 T
63 T
* * * * *
5317606 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
5317670 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
5317686 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:5317685 original size:17 final size:19
Alignment explanation
Indices: 5317657--5317705 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5317647 TATTTTGAAA
5317657 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
5317675 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
5317694 CACCGATGCACT
1 CATCGATGCACT
5317706 AAGGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:5318453 original size:29 final size:29
Alignment explanation
Indices: 5318419--5318483 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
5318409 TCAACATTAT
5318419 ACTATATATACTATATAATTTACATATGA
1 ACTATATATACTATATAATTTACATATGA
* *
5318448 ATTATATATACTATATAGTTTACATATGA
1 ACTATATATACTATATAATTTACATATGA
5318477 ACTATAT
1 ACTATAT
5318484 GTATAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (29 bp):
ACTATATATACTATATAATTTACATATGA
Found at i:5318494 original size:13 final size:13
Alignment explanation
Indices: 5318476--5318520 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
5318466 TTTACATATG
5318476 AACTATATGTATA
1 AACTATATGTATA
5318489 AACTATATGTATA
1 AACTATATGTATA
*
5318502 AACTATATATATA
1 AACTATATGTATA
5318515 AACTAT
1 AACTAT
5318521 GTAAACTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (13 bp):
AACTATATGTATA
Found at i:5318521 original size:24 final size:23
Alignment explanation
Indices: 5318469--5318532 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
5318459 TATATAGTTT
*
5318469 ACATATG--AACTATATGTATAA
1 ACATATGTAAACTATATATATAA
5318490 ACTATATGTATAAACTATATATATAA
1 AC-ATATG--TAAACTATATATATAA
5318516 AC-TATGTAAACTATATA
1 ACATATGTAAACTATATA
5318533 GTTTACATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.05
22 16 0.43
24 4 0.11
26 15 0.41
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (23 bp):
ACATATGTAAACTATATATATAA
Found at i:5318566 original size:18 final size:18
Alignment explanation
Indices: 5318545--5318670 Score: 60
Period size: 20 Copynumber: 6.6 Consensus size: 18
5318535 TTACATATGA
*
5318545 ATTATATATATATAGTTT
1 ATTATATATATATAGTAT
* *
5318563 ATTAGTGAAATATATA-AACT
1 ATTA-T-ATATATATAGTA-T
*
5318583 ATTTATATAATATATACTAT
1 A-TTATAT-ATATATAGTAT
* *
5318603 A-TATATAAAGTATAGTTT
1 ATTATATATA-TATAGTAT
*
5318621 ATTTATATACTACATAGTAT
1 A-TTATATA-TATATAGTAT
*
5318641 AGTTGATATTTATACTA-TAT
1 A-TT-ATATATATA-TAGTAT
5318661 ATTATATATA
1 ATTATATATA
5318671 AACTATATAT
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
17 2 0.02
18 22 0.27
19 4 0.05
20 42 0.52
21 11 0.14
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (18 bp):
ATTATATATATATAGTAT
Found at i:5318571 original size:26 final size:26
Alignment explanation
Indices: 5318527--5318578 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5318517 CTATGTAAAC
*
5318527 TATATAGTTTACATATGAATTATATA
1 TATATAGTTTACATATGAAATATATA
*
5318553 TATATAGTTTA-TTAGTGAAATATATA
1 TATATAGTTTACATA-TGAAATATATA
5318579 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (26 bp):
TATATAGTTTACATATGAAATATATA
Found at i:5318594 original size:20 final size:18
Alignment explanation
Indices: 5318574--5318688 Score: 58
Period size: 18 Copynumber: 6.3 Consensus size: 18
5318564 TTAGTGAAAT
* *
5318574 ATATAAACTATTTATATA
1 ATATATACTATATATATA
5318592 ATATATACTATATATATA
1 ATATATACTATATATATA
* *
5318610 A-AGTATAGTTTATTTATATA
1 ATA-TATA--CTATATATATA
* * *
5318630 CTACATAGTATAGT-TGAT-
1 ATATATACTATA-TAT-ATA
*
5318648 ATTTATACTATATAT-TA
1 ATATATACTATATATATA
*
5318665 TATATAAACTATATATATA
1 -ATATATACTATATATATA
*
5318684 GTATA
1 ATATA
5318689 ATTTACATAC
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
16 1 0.01
17 2 0.03
18 51 0.71
19 5 0.07
20 12 0.17
21 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATATACTATATATATA
Found at i:5318655 original size:25 final size:25
Alignment explanation
Indices: 5318611--5318666 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
5318601 ATATATATAA
*
5318611 AGTATAGTTTATTTATATACTACAT
1 AGTATAGTTGATTTATATACTACAT
*
5318636 AGTATAGTTGATATT-TATACTATAT
1 AGTATAGTTGAT-TTATATACTACAT
*
5318661 ATTATA
1 AGTATA
5318667 TATAAACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (25 bp):
AGTATAGTTGATTTATATACTACAT
Found at i:5318683 original size:29 final size:28
Alignment explanation
Indices: 5318646--5318710 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
5318636 AGTATAGTTG
* *
5318646 ATATTTATACTATATATTATATATA-AACT
1 ATATATATACTATA-ATT-TACATACAACT
*
5318675 ATATATATAGTATAATTTACATACGAACT
1 ATATATATACTATAATTTACATAC-AACT
5318704 ATATATA
1 ATATATA
5318711 AAAACTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 5 0.16
28 3 0.10
29 23 0.74
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (28 bp):
ATATATATACTATAATTTACATACAACT
Found at i:5318787 original size:18 final size:18
Alignment explanation
Indices: 5318757--5318870 Score: 87
Period size: 18 Copynumber: 6.2 Consensus size: 18
5318747 TATAAAACTA
*
5318757 TATAG-TTATATATGAAC
1 TATAGTTTACATATGAAC
*
5318774 TATAGTTTACATATAAAC
1 TATAGTTTACATATGAAC
5318792 TATAGTTGATATTTACATATGAAC
1 TATA---G---TTTACATATGAAC
5318816 TATAGTTTACATATGAAC
1 TATAGTTTACATATGAAC
*
5318834 TATA---T--ATATAAAC
1 TATAGTTTACATATGAAC
5318847 TATATAGTTTACATATGAAC
1 --TATAGTTTACATATGAAC
5318867 TATA
1 TATA
5318871 TAAACTATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 27
0.71 0.05 0.25
Matches are distributed among these distances:
13 7 0.09
15 5 0.06
17 5 0.06
18 36 0.46
20 7 0.09
21 2 0.03
24 16 0.21
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (18 bp):
TATAGTTTACATATGAAC
Found at i:5318847 original size:13 final size:13
Alignment explanation
Indices: 5318826--5318905 Score: 58
Period size: 13 Copynumber: 6.1 Consensus size: 13
5318816 TATAGTTTAC
*
5318826 ATATGAACTATAT
1 ATATAAACTATAT
5318839 ATATAAACTATAT
1 ATATAAACTATAT
* *
5318852 AGTTTACA-TATGAACT
1 A-TATAAACTAT--A-T
5318868 ATATAAACTAT-T
1 ATATAAACTATAT
* *
5318880 -TATATAGTATAT
1 ATATAAACTATAT
5318892 ATATAAACTATAT
1 ATATAAACTATAT
5318905 A
1 A
5318906 AACTATTTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
11 8 0.16
12 2 0.04
13 27 0.53
14 4 0.08
15 5 0.10
16 5 0.10
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:5318884 original size:33 final size:33
Alignment explanation
Indices: 5318816--5318920 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 33
5318806 ACATATGAAC
* **
5318816 TATAGTTTACATATGAACTATATATA-TAAACTA
1 TATAGTTTACATATGAACTATATAAACT-ATTTA
5318849 TATAGTTTACATATGAACTATATAAACTATTTA
1 TATAGTTTACATATGAACTATATAAACTATTTA
* * *
5318882 TATAGTATATATATAAACTATATAAACTATTTA
1 TATAGTTTACATATGAACTATATAAACTATTTA
5318915 TATAGT
1 TATAGT
5318921 ATATATCTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (33 bp):
TATAGTTTACATATGAACTATATAAACTATTTA
Found at i:5318961 original size:13 final size:13
Alignment explanation
Indices: 5318943--5318980 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
5318933 ATATACTATA
5318943 CTATATTTATATG
1 CTATATTTATATG
5318956 CTATATTTATATG
1 CTATATTTATATG
*
5318969 CTATAATTATAT
1 CTATATTTATAT
5318981 ATATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (13 bp):
CTATATTTATATG
Found at i:5319049 original size:28 final size:27
Alignment explanation
Indices: 5319004--5319172 Score: 80
Period size: 28 Copynumber: 6.4 Consensus size: 27
5318994 TATATATAGT
5319004 ATAAT-ATAGTTTACATATGAACTATATA
1 ATAATAATA-TTTA-ATATGAACTATATA
*
5319032 ATAATAAATATTTAATAT--AGTATAT-
1 ATAAT-AATATTTAATATGAACTATATA
5319057 ATACAT-ATA-TT-ATAT--ACTATATA
1 ATA-ATAATATTTAATATGAACTATATA
*
5319080 TTAATATACATATAATTAATATGAACTATATA
1 AT-A-ATA-ATAT--TTAATATGAACTATATA
* *
5319112 TATAATACTATATT-ATATAAACTATAT-
1 -ATAATAATAT-TTAATATGAACTATATA
*
5319139 AT-AT-ATAGTTACATATGAACTATAT-
1 ATAATAATATTTA-ATATGAACTATATA
5319164 ATAA-AATAT
1 ATAATAATAT
5319173 GGTATATAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 38
0.70 0.07 0.24
Matches are distributed among these distances:
22 10 0.09
23 5 0.04
24 8 0.07
25 19 0.17
26 17 0.15
28 21 0.19
29 9 0.08
30 10 0.09
31 3 0.03
32 9 0.08
33 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (27 bp):
ATAATAATATTTAATATGAACTATATA
Found at i:5319070 original size:15 final size:15
Alignment explanation
Indices: 5319046--5319308 Score: 86
Period size: 15 Copynumber: 16.9 Consensus size: 15
5319036 TAAATATTTA
*
5319046 ATATAGTATATATAC
1 ATATATTATATATAC
5319061 ATATA-T-TATATAC
1 ATATATTATATATAC
5319074 TATATATTA-ATATAC
1 -ATATATTATATATAC
5319089 ATATAATTA-ATATGA-
1 ATAT-ATTATATAT-AC
5319104 ACTATA-TATATAATAC
1 A-TATATTATAT-ATAC
*
5319120 -TATATTATATAAAC
1 ATATATTATATATAC
5319134 -TATATATATATAGTTAC
1 ATATAT-TATATA--TAC
*
5319151 ATATGAACTATATATA-
1 ATAT--ATTATATATAC
* *
5319167 AAATATGGTATATAAAC
1 ATATAT--TATATATAC
*
5319184 -TATACTTATATAGTTC
1 ATATA-TTATATA-TAC
* *
5319200 AT-TAGTATATATAA
1 ATATATTATATATAC
*
5319214 ACTATATGGTATATAAAC
1 A-TATAT--TATATATAC
*
5319232 -TATATTATATAGTTC
1 ATATATTATATA-TAC
* *
5319247 AT-TAGTATATATAA
1 ATATATTATATATAC
*
5319261 ACTATATATATATAGTTC
1 A-TATAT-TATATA-TAC
* *
5319279 AT-TAGTATATATAA
1 ATATATTATATATAC
5319293 ACTATATATATATATA
1 A-TATAT-TATATATA
5319309 GTTCATTAGT
Statistics
Matches: 186, Mismatches: 27, Indels: 68
0.66 0.10 0.24
Matches are distributed among these distances:
13 7 0.04
14 37 0.20
15 66 0.35
16 36 0.19
17 21 0.11
18 12 0.06
19 6 0.03
20 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (15 bp):
ATATATTATATATAC
Found at i:5319117 original size:18 final size:16
Alignment explanation
Indices: 5318874--5319143 Score: 88
Period size: 15 Copynumber: 16.8 Consensus size: 16
5318864 AACTATATAA
* *
5318874 ACTATTTATATAGTAT
1 ACTATATATATAATAT
* *
5318890 A-TATATAAACTATATAA
1 ACTATATATA-TA-ATAT
*
5318907 ACTATTTATATAGTATAT
1 ACTATATATATA--ATAT
*
5318925 ATCTATATATATACTAT
1 A-CTATATATATAATAT
5318942 ACTATAT-T-T-ATAT
1 ACTATATATATAATAT
* **
5318955 GCTATATTTATATGCTAT
1 ACTATA--TATATAATAT
* *
5318973 AATTATATATATAAATTT
1 -ACTATATATAT-AATAT
*
5318991 AC-ATATATATAGTAT
1 ACTATATATATAATAT
*
5319006 A--ATATAGTTTACATAT
1 ACTATATA-TATA-ATAT
5319022 GAACTATATA-ATAATA-
1 --ACTATATATATAATAT
* *
5319038 AATATTTAATATAGTATAT
1 ACTATAT-ATATA--ATAT
* *
5319057 A-TACATATATTATAT
1 ACTATATATATAATAT
5319072 ACTATATAT-TAATAT
1 ACTATATATATAATAT
5319087 AC-ATATA-ATTAATAT
1 ACTATATATA-TAATAT
5319102 GAACTATATATAT-A-AT
1 --ACTATATATATAATAT
*
5319118 ACTATAT-TAT-ATAA
1 ACTATATATATAATAT
5319132 ACTATATATATA
1 ACTATATATATA
5319144 TAGTTACATA
Statistics
Matches: 190, Mismatches: 31, Indels: 66
0.66 0.11 0.23
Matches are distributed among these distances:
13 12 0.06
14 31 0.16
15 37 0.19
16 32 0.17
17 26 0.14
18 31 0.16
19 16 0.08
20 5 0.03
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
ACTATATATATAATAT
Found at i:5319142 original size:32 final size:32
Alignment explanation
Indices: 5318867--5319342 Score: 110
Period size: 32 Copynumber: 14.8 Consensus size: 32
5318857 ACATATGAAC
* * *
5318867 TATATAAACTATTTATATAGTATATATA-TAAAC
1 TATATAAACTATATATATA-TATA-ATACTATAT
*
5318900 TATATAAACTATTTATATAGTAT-ATATCTATA-
1 TATATAAACTATATATATA-TATAATA-CTATAT
* *
5318932 TATAT--ACTATACTATATTTAT-ATGCTATAT
1 TATATAAACTATA-TATATATATAATACTATAT
**
5318962 T-TATATGCTATAATTATATATATAAATTTAC-ATAT
1 TATATAAACTAT-A-TATATATAT-AA--TACTATAT
* * *
5318997 ATATAGTATAA-TATAGTTTACATATGA-ACTATAT
1 -TATA-TA-AACTATA-TATATATATAATACTATAT
* *
5319031 AATAATAAA-TATTTAATATAGTATATATACATATAT
1 TAT-ATAAACTATAT-ATATA-TATA-ATAC-TATAT
5319067 TATAT--ACTATATAT-TA-AT-ATAC-ATA-
1 TATATAAACTATATATATATATAATACTATAT
*
5319092 TA-ATTAA-TATGAACTATATATATAATACTATAT
1 TATATAAACTAT--A-TATATATATAATACTATAT
5319125 TATATAAACTATATATATATAGT--TACATATGAACT
1 TATATAAACTATATATATATA-TAATAC-TAT--A-T
**
5319160 ATATATAAA--ATAT-GGTATATAA-ACTATACT
1 -TATATAAACTATATATATATATAATACTATA-T
**
5319190 TATAT-AGTTCAT-TAGTATATATAA-ACTATAT
1 TATATAAACT-ATATA-TATATATAATACTATAT
*
5319221 GGTATATAAACTATAT-TATATAGT--TCATTAGTA-
1 --TATATAAACTATATATATATA-TAAT-ACTA-TAT
*
5319254 TATATAAACTATATATATATAGT--TCATTAGTA-
1 TATATAAACTATATATATATA-TAAT-ACTA-TAT
* *
5319286 TATATAAACTATATATATATATAGTTC-ATTAGT
1 TATATAAACTATATATATATATAATACTA-TA-T
5319319 ATATATAAACTATATA-ATATATAA
1 -TATATAAACTATATATATATATAA
5319343 ATTAACATTA
Statistics
Matches: 347, Mismatches: 34, Indels: 124
0.69 0.07 0.25
Matches are distributed among these distances:
24 2 0.01
25 5 0.01
26 4 0.01
27 1 0.00
28 8 0.02
29 15 0.04
30 19 0.05
31 41 0.12
32 99 0.29
33 67 0.19
34 40 0.12
35 12 0.03
36 19 0.05
37 10 0.03
38 5 0.01
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (32 bp):
TATATAAACTATATATATATATAATACTATAT
Found at i:5319164 original size:2 final size:2
Alignment explanation
Indices: 5318880--5319145 Score: 96
Period size: 2 Copynumber: 132.0 Consensus size: 2
5318870 ATAAACTATT
* * *
5318880 TA TA TA GTA TA TA TA TA AA CTA TA TA AA CTA TT TA TA TA GTA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA
* * * *
5318924 TA TC TA TA TA TA TA CTA TA CTA TA TT TA TA TGC TA TA TT TA TA
1 TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA T-A TA TA TA TA TA
* * * *
5318967 TGC TA TA -A T- TA TA TA TA TA AA TT TA CA TA TA TA TA GTA TA -A
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
5319008 TA TA GTT TA CA TA TGA -A CTA TA TA -A TA -A TA AA TA TT TA -A
1 TA TA -TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
5319047 TA TA GTA TA TA TA CA TA TA T- TA TA TA CTA TA TA T- TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
5319088 CA TA TA -A T- TA -A TA TGA -A CTA TA TA TA TA -A TA CTA TA T-
1 TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA -TA TA TA
*
5319125 TA TA TA AA CTA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA
5319146 GTTACATATG
Statistics
Matches: 194, Mismatches: 36, Indels: 68
0.65 0.12 0.23
Matches are distributed among these distances:
1 16 0.08
2 152 0.78
3 26 0.13
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5319179 original size:25 final size:25
Alignment explanation
Indices: 5319098--5319187 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 25
5319088 CATATAATTA
* *
5319098 ATATGAACTATATATATAATACTATATT
1 ATATAAACTATATATA-AA-A-TATGTT
*
5319126 ATATAAACTATATAT-ATATA-GTT
1 ATATAAACTATATATAAAATATGTT
* *
5319149 ACATATGAACTATATATAAAATATGGT
1 --ATATAAACTATATATAAAATATGTT
5319176 ATATAAACTATA
1 ATATAAACTATA
5319188 CTTATATAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 26 0.51
26 5 0.10
27 2 0.04
28 14 0.27
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.39
Consensus pattern (25 bp):
ATATAAACTATATATAAAATATGTT
Found at i:5319184 original size:50 final size:50
Alignment explanation
Indices: 5319089--5319245 Score: 191
Period size: 50 Copynumber: 3.2 Consensus size: 50
5319079 ATTAATATAC
* **
5319089 ATATAATTA-ATATGAACTATATATATAATACTATATTATATAAACTATATAT
1 ATATAGTTACATATGAACTATATATA-AATA-TATGGTATATAAACTATAT-T
5319141 ATATAGTTACATATGAACTATATATAAA-ATATGGTATATAAACTATACTT
1 ATATAGTTACATATGAACTATATATAAATATATGGTATATAAACTATA-TT
*
5319191 ATATAGTT-CAT-T--AGTATATATAAACTATATGGTATATAAACTATATT
1 ATATAGTTACATATGAACTATATATAAA-TATATGGTATATAAACTATATT
5319238 ATATAGTT
1 ATATAGTT
5319246 CATTAGTATA
Statistics
Matches: 97, Mismatches: 4, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
46 11 0.11
47 10 0.10
48 20 0.21
49 3 0.03
50 25 0.26
51 2 0.02
52 10 0.10
53 16 0.16
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (50 bp):
ATATAGTTACATATGAACTATATATAAATATATGGTATATAAACTATATT
Found at i:5319258 original size:47 final size:47
Alignment explanation
Indices: 5319108--5319267 Score: 220
Period size: 47 Copynumber: 3.3 Consensus size: 47
5319098 ATATGAACTA
*
5319108 TATATATAATACTATAT--TATATAAACTATATATATATAGTTACATATGAAC
1 TATATATAA-ACTATATGGTATATAAACTATAT-TATATAGTT-CAT-T--AG
5319159 TATATATAAA--ATATGGTATATAAACTATACTTATATAGTTCATTAG
1 TATATATAAACTATATGGTATATAAACTATA-TTATATAGTTCATTAG
5319205 TATATATAAACTATATGGTATATAAACTATATTATATAGTTCATTAG
1 TATATATAAACTATATGGTATATAAACTATATTATATAGTTCATTAG
5319252 TATATATAAACTATAT
1 TATATATAAACTATAT
5319268 ATATATAGTT
Statistics
Matches: 103, Mismatches: 1, Indels: 14
0.87 0.01 0.12
Matches are distributed among these distances:
46 11 0.11
47 32 0.31
48 24 0.23
49 3 0.03
50 23 0.22
51 10 0.10
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (47 bp):
TATATATAAACTATATGGTATATAAACTATATTATATAGTTCATTAG
Found at i:5319301 original size:34 final size:32
Alignment explanation
Indices: 5319223--5319341 Score: 204
Period size: 34 Copynumber: 3.7 Consensus size: 32
5319213 AACTATATGG
5319223 TATATAAACTATAT-TATATAGTTCATTAGTA
1 TATATAAACTATATATATATAGTTCATTAGTA
5319254 TATATAAACTATATATATATAGTTCATTAGTA
1 TATATAAACTATATATATATAGTTCATTAGTA
5319286 TATATAAACTATATATATATATAGTTCATTAGTA
1 TATATAAAC--TATATATATATAGTTCATTAGTA
5319320 TATATAAACTATATAATATATA
1 TATATAAACTATAT-ATATATA
5319342 AATTAACATT
Statistics
Matches: 84, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
31 14 0.17
32 31 0.37
33 7 0.08
34 32 0.38
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (32 bp):
TATATAAACTATATATATATAGTTCATTAGTA
Found at i:5319383 original size:50 final size:50
Alignment explanation
Indices: 5319285--5319382 Score: 155
Period size: 48 Copynumber: 2.0 Consensus size: 50
5319275 GTTCATTAGT
*
5319285 ATATATAAACTATATATATATATAGTTCATTAGTATATATAAACTATATA
1 ATATATAAACTATACATATATATAGTTCATTAGTATATATAAACTATATA
* *
5319335 ATATATAAATTA-ACAT-TATATAGTTCATTAGTATATATAACCTATATA
1 ATATATAAACTATACATATATATAGTTCATTAGTATATATAAACTATATA
5319383 TTAATTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 31 0.69
49 3 0.07
50 11 0.24
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (50 bp):
ATATATAAACTATACATATATATAGTTCATTAGTATATATAAACTATATA
Found at i:5319403 original size:113 final size:114
Alignment explanation
Indices: 5319174--5319416 Score: 331
Period size: 113 Copynumber: 2.2 Consensus size: 114
5319164 ATAAAATATG
* ** *
5319174 GTATATAAACTATA-CT-TATATAGTTCATTAGTATATATAAACTATATGGTATATAAACTATAT
1 GTATATAAACTATATATATATATAGTTCATTAGTATATATAAACTATATAATATATAAACTACAT
*
5319237 TATATAGTTCATTAGTATATATAAACTATATATATATAGTTCATTAGTA
66 TATATAGTTCATTAGTATATATAAACTATATATATATAGTTCATTAATA
*
5319286 -TATATAAACTATATATATATATAGTTCATTAGTATATATAAACTATATAATATATAAATTAACA
1 GTATATAAACTATATATATATATAGTTCATTAGTATATATAAACTATATAATATATAAACT-ACA
*
5319350 TTATATAGTTCATTAGTATATATAACCTATATAT-TA-A-TT-ATTAATAAA
65 TTATATAGTTCATTAGTATATATAAACTATATATATATAGTTCATTAAT--A
5319398 GTATATATAAC-ATATATAT
1 GTATATA-AACTATATATAT
5319417 TAATTGAAAG
Statistics
Matches: 117, Mismatches: 7, Indels: 13
0.85 0.05 0.09
Matches are distributed among these distances:
110 5 0.04
111 15 0.13
112 3 0.03
113 56 0.48
114 38 0.32
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (114 bp):
GTATATAAACTATATATATATATAGTTCATTAGTATATATAAACTATATAATATATAAACTACAT
TATATAGTTCATTAGTATATATAAACTATATATATATAGTTCATTAATA
Found at i:5319487 original size:21 final size:20
Alignment explanation
Indices: 5319462--5319550 Score: 53
Period size: 21 Copynumber: 4.3 Consensus size: 20
5319452 AAACAAATTT
5319462 TAAATATGAAGCTTAAATTAA
1 TAAAT-TGAAGCTTAAATTAA
*
5319483 TAAATTGTAA-CATTAAATTTGGAC
1 TAAATTG-AAGC-TTAAA-TT--AA
*
5319507 TAAATTGAAG---AAATT-T
1 TAAATTGAAGCTTAAATTAA
5319523 TAAATATGAAGCTTAAATTAA
1 TAAAT-TGAAGCTTAAATTAA
*
5319544 TATATTG
1 TAAATTG
5319551 CATCATTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 23
0.66 0.05 0.29
Matches are distributed among these distances:
16 5 0.09
17 5 0.09
19 2 0.04
20 13 0.25
21 16 0.30
22 2 0.04
23 2 0.04
24 8 0.15
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.37
Consensus pattern (20 bp):
TAAATTGAAGCTTAAATTAA
Found at i:5319521 original size:61 final size:61
Alignment explanation
Indices: 5319447--5319593 Score: 231
Period size: 61 Copynumber: 2.4 Consensus size: 61
5319437 TATAAGGATC
* *
5319447 AAATTAAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGTAACATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
* * *
5319508 AAATTGAAGAAATTTTAAATATGAAGCTTAAATTAATATATTGCATCATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
*
5319569 AAATTGAACAAATTTAAAACTATGA
1 AAATTGAACAAATTTTAAA-TATGA
5319594 GACAACGCTA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 73 0.94
62 5 0.06
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
Found at i:5319967 original size:91 final size:92
Alignment explanation
Indices: 5319814--5319983 Score: 220
Period size: 91 Copynumber: 1.8 Consensus size: 92
5319804 TTCATCCGTG
* *
5319814 TTCATTCCAAAAACCCTCATTTGATTTTCAAAAACACCAAACCCAAACCATTTCATG-TTTTTTT
1 TTCATCCCAAAAACCCTCATTTGATCTTCAAAAACACCAAACCCAAACCATTT-ATGTTTTTTTT
5319878 -ATCAAACACCCATAATTTCAACCCTTT
65 CATCAAACACCCATAATTTCAACCCTTT
* * * * *
5319905 TTCATCCCAAAAATCTTCCTTTGATCTTCAGAAACACCAAAACCCAAACTATTT-TGTGTTTTTT
1 TTCATCCCAAAAACCCTCATTTGATCTTCAAAAACACC-AAACCCAAACCATTTATGT-TTTTTT
5319969 TCGATCAAACACCCA
64 TC-ATCAAACACCCA
5319984 AAAATTCATC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
90 2 0.03
91 32 0.48
92 21 0.31
94 12 0.18
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (92 bp):
TTCATCCCAAAAACCCTCATTTGATCTTCAAAAACACCAAACCCAAACCATTTATGTTTTTTTTC
ATCAAACACCCATAATTTCAACCCTTT
Found at i:5320008 original size:94 final size:89
Alignment explanation
Indices: 5319832--5320080 Score: 238
Period size: 92 Copynumber: 2.8 Consensus size: 89
5319822 AAAAACCCTC
* * *
5319832 ATTTGATTTTCAAAAACACC-AAACCCAAACCATTTCATGTTTTTTTATCAAACACCCATAATTT
1 ATTTGATCTTCAAAAACACCAAAACCCAAACCATTTCATGTTTTTTTATCAAACACCCAAAAATT
* *
5319896 CAACCCTTTTTCATCCCAAA-AATCTT
66 CAACCCTTCTT-ATCCCAAACCA--TT
* * * **
5319922 CCTTTGATCTTCAGAAACACCAAAACCCAAACTATTTTGTGTTTTTTTCGATCAAACACCCAAAA
1 -ATTTGATCTTCAAAAACACCAAAACCCAAACCATTTCATGTTTTTTT--ATCAAACACCCAAAA
*
5319987 ATTCATCCCAGTTCTT-TCCCAAACCATT
63 ATTCAACCC--TTCTTATCCCAAACCATT
* * * * *
5320015 ATTTGATCTTCACAAACACCAAAACCTAAACCCA-TTCCT-TTTTTTGATCAAACACCCAAAAGT
1 ATTTGATCTTCAAAAACACCAAAACCCAAA-CCATTTCATGTTTTTTTATCAAACACCCAAAAAT
5320078 TCA
65 TCA
5320081 TTTATTATTC
Statistics
Matches: 132, Mismatches: 19, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
89 19 0.14
91 23 0.17
92 53 0.40
93 4 0.03
94 28 0.21
95 1 0.01
96 4 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (89 bp):
ATTTGATCTTCAAAAACACCAAAACCCAAACCATTTCATGTTTTTTTATCAAACACCCAAAAATT
CAACCCTTCTTATCCCAAACCATT
Found at i:5320321 original size:6 final size:6
Alignment explanation
Indices: 5320299--5320362 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
5320289 CCTTAACTTG
* * * * *
5320299 AACCCT AACCAA AACCCA AACCCG AGCCCA AACCCA AACCTGA AA-CCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACC-CA AACCCA
5320347 AACCCA AACCCA AACC
1 AACCCA AACCCA AACC
5320363 TGAACCCAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 3 0.06
6 41 0.87
7 3 0.06
ACGTcount: A:0.47, C:0.45, G:0.05, T:0.03
Consensus pattern (6 bp):
AACCCA
Found at i:5320363 original size:24 final size:24
Alignment explanation
Indices: 5320325--5320403 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
5320315 CAAACCCGAG
5320325 CCCAAACCCAAACCTGAAACCAAA
1 CCCAAACCCAAACCTGAAACCAAA
*
5320349 CCCAAACCCAAACCTG-AACCCAA
1 CCCAAACCCAAACCTGAAACCAAA
* ** * *
5320372 TCCAAACCTGAATCTGAATCCAAA
1 CCCAAACCCAAACCTGAAACCAAA
*
5320396 CCCGAACC
1 CCCAAACC
5320404 TGAATCCAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 18 0.40
24 27 0.60
ACGTcount: A:0.43, C:0.42, G:0.06, T:0.09
Consensus pattern (24 bp):
CCCAAACCCAAACCTGAAACCAAA
Found at i:5320371 original size:18 final size:18
Alignment explanation
Indices: 5320299--5320362 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
5320289 CCTTAACTTG
* *
5320299 AACCCTAACCAAAACCCA
1 AACCCGAACCCAAACCCA
*
5320317 AACCCGAGCCCAAACCCA
1 AACCCGAACCCAAACCCA
* *
5320335 AACCTGAAACCAAACCCA
1 AACCCGAACCCAAACCCA
*
5320353 AACCCAAACC
1 AACCCGAACC
5320363 TGAACCCAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.47, C:0.45, G:0.05, T:0.03
Consensus pattern (18 bp):
AACCCGAACCCAAACCCA
Found at i:5320385 original size:12 final size:12
Alignment explanation
Indices: 5320329--5320371 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5320319 CCCGAGCCCA
5320329 AACCCAAACCTG
1 AACCCAAACCTG
* **
5320341 AAACCAAACCCA
1 AACCCAAACCTG
5320353 AACCCAAACCTG
1 AACCCAAACCTG
5320365 AACCCAA
1 AACCCAA
5320372 TCCAAACCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.42, G:0.05, T:0.05
Consensus pattern (12 bp):
AACCCAAACCTG
Found at i:5320393 original size:18 final size:17
Alignment explanation
Indices: 5320356--5320414 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
5320346 AAACCCAAAC
**
5320356 CCAAACCTGAACCCAAT
1 CCAAACCTGAACTGAAT
5320373 CCAAACCTGAATCTGAAT
1 CCAAACCTGAA-CTGAAT
*
5320391 CCAAACCCGAACCTGAAT
1 CCAAACCTGAA-CTGAAT
5320409 CCAAAC
1 CCAAAC
5320415 TATTCGAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 11 0.30
18 26 0.70
ACGTcount: A:0.41, C:0.37, G:0.08, T:0.14
Consensus pattern (17 bp):
CCAAACCTGAACTGAAT
Found at i:5323301 original size:2 final size:2
Alignment explanation
Indices: 5323296--5323363 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
5323286 TATATAAGGG
5323296 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
* * * * *
5323338 AT TT AT GT CT AT AT AA AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5323364 TTATTATACG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5325179 original size:20 final size:20
Alignment explanation
Indices: 5325154--5325217 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
5325144 GACGTTTTGG
*
5325154 TGTTTGATTCTATTTTATAT
1 TGTTTGATTCTATTTGATAT
* * *
5325174 TGTTTGTTTCTGTTTGCTAT
1 TGTTTGATTCTATTTGATAT
* *
5325194 TGTTTGCTTCTACTTGATAGT
1 TGTTTGATTCTATTTGATA-T
5325215 TGT
1 TGT
5325218 AAGGGTTTGG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.61
Consensus pattern (20 bp):
TGTTTGATTCTATTTGATAT
Found at i:5325338 original size:23 final size:23
Alignment explanation
Indices: 5325308--5325364 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
5325298 CTTAAAGCAG
* *
5325308 GATGCTTGTTGAATTGATGCAAC
1 GATGCTTGTCGAATTGATACAAC
* *
5325331 GATGCTTGCCGAATTGATACAAT
1 GATGCTTGTCGAATTGATACAAC
5325354 GATGCTTGTCG
1 GATGCTTGTCG
5325365 GTTGATGCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (23 bp):
GATGCTTGTCGAATTGATACAAC
Found at i:5326146 original size:16 final size:16
Alignment explanation
Indices: 5326112--5326146 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5326102 TGAATCAATT
*
5326112 ACAAGTCAGGTTCATA
1 ACAAGTCAGGTTCAAA
*
5326128 ACAAGTCAGGTTGAAA
1 ACAAGTCAGGTTCAAA
5326144 ACA
1 ACA
5326147 TGTAGGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (16 bp):
ACAAGTCAGGTTCAAA
Found at i:5328966 original size:17 final size:17
Alignment explanation
Indices: 5328941--5328979 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5328931 ACGATTTCAA
*
5328941 AAAAAATATTTTTTAAT
1 AAAATATATTTTTTAAT
*
5328958 AAAATATATTTTTTATT
1 AAAATATATTTTTTAAT
5328975 AAAAT
1 AAAAT
5328980 TTACGCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATATATTTTTTAAT
Found at i:5337635 original size:20 final size:20
Alignment explanation
Indices: 5337610--5337648 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5337600 CAGGAGATCG
5337610 TTATTAT-TATTATTTTATTA
1 TTATTATAT-TTATTTTATTA
5337630 TTATTATATTTATTTTATT
1 TTATTATATTTATTTTATT
5337649 TTTTGTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTATATTTATTTTATTA
Found at i:5344191 original size:25 final size:25
Alignment explanation
Indices: 5344163--5344218 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
5344153 AACTACGTGC
5344163 CTATGTGAATAAATGTGATAATGAA
1 CTATGTGAATAAATGTGATAATGAA
5344188 CTATGTGAATAAATGTGATAATGAA
1 CTATGTGAATAAATGTGATAATGAA
5344213 CTATGT
1 CTATGT
5344219 AATCCTTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (25 bp):
CTATGTGAATAAATGTGATAATGAA
Found at i:5344195 original size:15 final size:15
Alignment explanation
Indices: 5344175--5344218 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5344165 ATGTGAATAA
5344175 ATGTGATAATGAACT
1 ATGTGATAATGAACT
5344190 ATGTG--AAT-AA--
1 ATGTGATAATGAACT
5344200 ATGTGATAATGAACT
1 ATGTGATAATGAACT
5344215 ATGT
1 ATGT
5344219 AATCCTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 5 0.21
12 5 0.21
13 5 0.21
15 9 0.38
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (15 bp):
ATGTGATAATGAACT
Found at i:5345924 original size:6 final size:6
Alignment explanation
Indices: 5345892--5345955 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
5345882 ATAAATAAAT
* *
5345892 AAAGAA AATGAA AATGAA AAGAGGAA AAAGAAA AAAGAAA AAAGAA AAA-AGA
1 AAAGAA AAAGAA AAAGAA AA-A-GAA AAAG-AA AAAG-AA AAAGAA AAAGA-A
5345944 AAA-AA AAAGAA A
1 AAAGAA AAAGAA A
5345956 GAAAATAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
5 5 0.10
6 27 0.53
7 14 0.27
8 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:5345928 original size:7 final size:7
Alignment explanation
Indices: 5345902--5345965 Score: 76
Period size: 7 Copynumber: 9.1 Consensus size: 7
5345892 AAAGAAAATG
*
5345902 AAAATGA
1 AAAAAGA
* *
5345909 AAAGAGG
1 AAAAAGA
5345916 AAAAAGA
1 AAAAAGA
5345923 AAAAAGA
1 AAAAAGA
5345930 AAAAAGA
1 AAAAAGA
5345937 AAAAAGA
1 AAAAAGA
5345944 AAAAA-A
1 AAAAAGA
5345950 AAGAAAGA
1 AA-AAAGA
*
5345958 AAATAGA
1 AAAAAGA
5345965 A
1 A
5345966 CAAGTATTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
6 3 0.06
7 43 0.88
8 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:5348058 original size:3 final size:3
Alignment explanation
Indices: 5348052--5348132 Score: 89
Period size: 3 Copynumber: 27.7 Consensus size: 3
5348042 TTTATTATCG
* *
5348052 TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA TAA TTA -TA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5348095 TTA TTA TTA TTA TT- TATA TTA TTA ATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
5348133 TACATTACAG
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 7 0.11
3 55 0.83
4 4 0.06
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5348069 original size:24 final size:23
Alignment explanation
Indices: 5348037--5348133 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 23
5348027 TTTCATCCAT
* *
5348037 TTTTTTTTATTATCGTTATTATTA
1 TTTTATTTATTAT-ATTATTATTA
*
5348061 TTTTATTTA-T-TACTATTATTA
1 TTTTATTTATTATATTATTATTA
*
5348082 TTTTA-TAATTATATTATTATTA
1 TTTTATTTATTATATTATTATTA
5348104 TTATTTATATTATTAATATTATTATTA
1 -T-TTTAT-TTATT-ATATTATTATTA
5348131 TTT
1 TTT
5348134 ACATTACAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.03
21 14 0.23
22 11 0.18
23 2 0.03
24 12 0.20
25 2 0.03
26 5 0.08
27 12 0.20
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (23 bp):
TTTTATTTATTATATTATTATTA
Found at i:5349553 original size:4 final size:4
Alignment explanation
Indices: 5349546--5349577 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
5349536 AAATAAATAA
5349546 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
5349578 GTATCCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:5353722 original size:15 final size:15
Alignment explanation
Indices: 5353704--5353735 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5353694 GATCAATACC
5353704 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
5353719 TTTTGCATACATTCA
1 TTTTGCATACATGCA
5353734 TT
1 TT
5353736 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:5361069 original size:14 final size:13
Alignment explanation
Indices: 5361050--5361110 Score: 72
Period size: 15 Copynumber: 4.5 Consensus size: 13
5361040 ATTATGCTTG
5361050 AAGAAAAAATGAAA
1 AAGAAAAAATG-AA
5361064 AAGAAAAAAATGAA
1 AAG-AAAAAATGAA
5361078 AAGAAAAAAAATG-A
1 AAG--AAAAAATGAA
5361092 AA-AAAAAATGAA
1 AAGAAAAAATGAA
5361104 AAGAAAA
1 AAGAAAA
5361111 TGAGGGTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.19
12 3 0.07
13 4 0.09
14 11 0.26
15 17 0.40
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (13 bp):
AAGAAAAAATGAA
Found at i:5361095 original size:11 final size:11
Alignment explanation
Indices: 5361048--5361113 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 11
5361038 ATATTATGCT
*
5361048 TGAAGAAAAAA
1 TGAAAAAAAAA
5361059 TGAAAAAGAAAA
1 TGAAAAA-AAAA
**
5361071 --AAATGAAAA
1 TGAAAAAAAAA
5361080 -G-AAAAAAAA
1 TGAAAAAAAAA
5361089 TGAAAAAAAAA
1 TGAAAAAAAAA
*
5361100 TGAAAAGAAAA
1 TGAAAAAAAAA
5361111 TGA
1 TGA
5361114 GGGTCAAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 10 0.22
10 4 0.09
11 27 0.60
12 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:5361110 original size:15 final size:14
Alignment explanation
Indices: 5361053--5361099 Score: 76
Period size: 15 Copynumber: 3.2 Consensus size: 14
5361043 ATGCTTGAAG
5361053 AAAAAATGAAAAAGA
1 AAAAAATGAAAAA-A
5361068 AAAAAATGAAAAGAA
1 AAAAAATGAAAA-AA
5361083 AAAAAATGAAAAAA
1 AAAAAATGAAAAAA
5361097 AAA
1 AAA
5361100 TGAAAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.16
15 25 0.81
16 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAATGAAAAAA
Found at i:5363692 original size:112 final size:112
Alignment explanation
Indices: 5363487--5363814 Score: 452
Period size: 112 Copynumber: 2.9 Consensus size: 112
5363477 GCAAAGATTC
* * **
5363487 GAATCCATCATTCGATGGATCAAC-TATTCCAG-AAGTTCATAATGAGAAGAACTCATCAAAAAA
1 GAATTCATCATTCGATGGATCAACAT-TTCCGGAAAGTTCATAATGAGAAGAACTCATCTGAAAA
* *
5363550 AGGAAAAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTTTGCT-T
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCT
* *
5363597 GAATTCATCATTCGATGGATCAACATTTCCGGAAGAGTTCATAATGAGAAGAATTTATCTGAAAA
1 GAATTCATCATTCGATGGATCAACATTTCCGGAA-AGTTCATAATGAGAAGAACTCATCTGAAAA
5363662 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCT
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCT
* **
5363710 -AATTCATCACTT-GATGGATCAGCATCGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
1 GAATTCATCA-TTCGATGGATCAACATTTCC-GG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* *
5363773 GAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
63 AAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTT
5363815 AATTTGATTC
Statistics
Matches: 196, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
110 28 0.14
111 2 0.01
112 129 0.66
113 35 0.18
114 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
GAATTCATCATTCGATGGATCAACATTTCCGGAAAGTTCATAATGAGAAGAACTCATCTGAAAAA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCT
Found at i:5364181 original size:3 final size:3
Alignment explanation
Indices: 5364167--5364229 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
5364157 TCCATTTGTT
* *
5364167 TTA TTA TCA TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
5364211 TAA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
5364230 TACATTACAG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5364273 original size:29 final size:26
Alignment explanation
Indices: 5364240--5364307 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 26
5364230 TACATTACAG
5364240 ACCCAGACCGGCCCAGTTACAAGAAACCA
1 ACCCAGACCGGCCCAGTTACAAG-AA--A
*
5364269 ACCCAGACCGACCCAGTTACAAGAAA
1 ACCCAGACCGGCCCAGTTACAAGAAA
5364295 ACCCAGACCGGCC
1 ACCCAGACCGGCC
5364308 TAATAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 13 0.35
28 2 0.05
29 22 0.59
ACGTcount: A:0.37, C:0.40, G:0.18, T:0.06
Consensus pattern (26 bp):
ACCCAGACCGGCCCAGTTACAAGAAA
Found at i:5371072 original size:24 final size:23
Alignment explanation
Indices: 5371026--5371087 Score: 99
Period size: 24 Copynumber: 2.7 Consensus size: 23
5371016 CTATGCGGTA
5371026 GGGT-TCGATACCCCCTTTGAAT
1 GGGTATCGATACCCCCTTTGAAT
5371048 GGGTATCGATACCCCTCTTTGAAT
1 GGGTATCGATACCCC-CTTTGAAT
*
5371072 GGGTACCGATACCCCC
1 GGGTATCGATACCCCC
5371088 CTGAGAGTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 4 0.11
23 11 0.30
24 22 0.59
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (23 bp):
GGGTATCGATACCCCCTTTGAAT
Found at i:5371788 original size:15 final size:15
Alignment explanation
Indices: 5371768--5371797 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5371758 CTAAAGCATT
5371768 TGGCTTAGATAATGA
1 TGGCTTAGATAATGA
5371783 TGGCTTAGATAATGA
1 TGGCTTAGATAATGA
5371798 AAAGAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
TGGCTTAGATAATGA
Found at i:5376645 original size:45 final size:45
Alignment explanation
Indices: 5376591--5376737 Score: 276
Period size: 45 Copynumber: 3.3 Consensus size: 45
5376581 TGATTTGATC
5376591 TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTAGATCTAAGT
1 TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTAGATCTAAGT
*
5376636 TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTATATCTAAGT
1 TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTAGATCTAAGT
5376681 TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTAGATCTAAGT
1 TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTAGATCTAAGT
*
5376726 TTCCCTAAAGAA
1 TTCCTTAAAGAA
5376738 GCGAAACAGC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 99 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (45 bp):
TTCCTTAAAGAACAGTGGAATGAATCAATGTTTTTAGATCTAAGT
Done.