Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 38
Found at i:2762763 original size:15 final size:15
Alignment explanation
Indices: 2762743--2762800 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2762733 ATTTTATTGG
2762743 TATGTGGAAATGTTA
1 TATGTGGAAATGTTA
*
2762758 TATGT-GAATATGTTT
1 TATGTGGAA-ATGTTA
* *
2762773 TATATGGAAATGTTC
1 TATGTGGAAATGTTA
* *
2762788 CATGTGAAAATGT
1 TATGTGGAAATGT
2762801 GTAAAGTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 3 0.09
15 29 0.83
16 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.41
Consensus pattern (15 bp):
TATGTGGAAATGTTA
Found at i:2762996 original size:23 final size:22
Alignment explanation
Indices: 2762960--2763038 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 22
2762950 GAGTCGAGGG
*
2762960 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACG-TGTCCTTCGGGACAA
** *
2762983 TTCTACGTGCTCCTTCGAAAAAA
1 TTCTACGTG-TCCTTCGGGACAA
2763006 TTCTACGTAGTCCTTCGGGACAAA
1 TTCTACGT-GTCCTTCGGGAC-AA
2763030 TTCTACGTG
1 TTCTACGTG
2763039 GCAGTTTGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.02
23 34 0.74
24 11 0.24
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (22 bp):
TTCTACGTGTCCTTCGGGACAA
Found at i:2775516 original size:21 final size:20
Alignment explanation
Indices: 2775492--2775531 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2775482 TTAAATTTTA
2775492 AAATAAAAATATTACAAAATG
1 AAATAAAAATATTA-AAAATG
*
2775513 AAATATAAATATTAAAAAT
1 AAATAAAAATATTAAAAAT
2775532 TATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
AAATAAAAATATTAAAAATG
Found at i:2775577 original size:21 final size:19
Alignment explanation
Indices: 2775551--2775595 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
2775541 TTAAATATAT
*
2775551 ATTAAAAACACTAAAAATACA
1 ATTAAAAACA-TAAAAA-AAA
*
2775572 ATTAAAAATATAAAAAAAA
1 ATTAAAAACATAAAAAAAA
2775591 ATTAA
1 ATTAA
2775596 GAATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 6 0.27
21 9 0.41
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (19 bp):
ATTAAAAACATAAAAAAAA
Found at i:2776394 original size:12 final size:14
Alignment explanation
Indices: 2776368--2776394 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2776358 ATTGTTTTTT
2776368 TATTTTTTAATATA
1 TATTTTTTAATATA
2776382 TATTTTTTAATAT
1 TATTTTTTAATAT
2776395 TTTAGTAATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTTAATATA
Found at i:2776450 original size:30 final size:30
Alignment explanation
Indices: 2776421--2776481 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2776411 TTTTTATATT
2776421 TATTTATTGATTTTTAAATATTCAAATATTTA
1 TATTTA-T-ATTTTTAAATATTCAAATATTTA
2776453 TATTTATATTTTTAAATATTCAAATATTT
1 TATTTATATTTTTAAATATTCAAATATTT
2776482 TTATATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 22 0.76
31 1 0.03
32 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (30 bp):
TATTTATATTTTTAAATATTCAAATATTTA
Found at i:2776451 original size:18 final size:18
Alignment explanation
Indices: 2776430--2776484 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
2776420 TTATTTATTG
2776430 ATTTTTAAATATTCAAAT
1 ATTTTTAAATATTCAAAT
*
2776448 A--TTT--ATATT--TAT
1 ATTTTTAAATATTCAAAT
2776460 ATTTTTAAATATTCAAAT
1 ATTTTTAAATATTCAAAT
2776478 ATTTTTA
1 ATTTTTA
2776485 TATTTTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
12 3 0.10
14 8 0.28
16 8 0.28
18 10 0.34
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAAATATTCAAAT
Found at i:2782306 original size:4 final size:4
Alignment explanation
Indices: 2782297--2782329 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2782287 TTTCCAACAC
2782297 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
2782330 GTTTCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2796131 original size:2 final size:2
Alignment explanation
Indices: 2796119--2796153 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2796109 CTTATAATTT
*
2796119 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2796154 TTTATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2796270 original size:24 final size:23
Alignment explanation
Indices: 2796242--2796293 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
2796232 TTTCTTCCCC
2796242 TTTTA-TACCTATACTATTTATTTA
1 TTTTATTACCT-TACT-TTTATTTA
*
2796266 TTTTATTTTCCTTACTTTTATTTA
1 TTTTA-TTACCTTACTTTTATTTA
2796290 TTTT
1 TTTT
2796294 TATCATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 17 0.68
25 4 0.16
26 4 0.16
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTACCTTACTTTTATTTA
Found at i:2796338 original size:4 final size:4
Alignment explanation
Indices: 2796329--2796369 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
2796319 TTTCCAACAC
2796329 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
2796370 GTTTCATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2799925 original size:19 final size:20
Alignment explanation
Indices: 2799901--2799938 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2799891 GTCGTATCGT
*
2799901 AAAACAA-TATTATTTTTAA
1 AAAACAATTATGATTTTTAA
2799920 AAAACAATTATGATTTTTA
1 AAAACAATTATGATTTTTA
2799939 TTTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAACAATTATGATTTTTAA
Found at i:2803221 original size:133 final size:134
Alignment explanation
Indices: 2802892--2803246 Score: 396
Period size: 134 Copynumber: 2.7 Consensus size: 134
2802882 GGTCGTCTAA
* * * * * *
2802892 GGGTGACACGA-CTCCTACGTGATTAGGAGATCTGGTCAATGGATGACACGGCTCGTACGTGGTG
1 GGGTGACAC-ATCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATG
* * * * * * *
2802956 AAGA-GTTCTGGCCATCTTTAGGGAGGGTGATAACACGGTTCCTATGCGATATGGACGGCTGATT
65 AGGACG-ACAGGCCATCTTTAGGGAGGGTGATAACACGATTCCTACGCGATAAGGACGACTGATT
*
2803020 ATATAG
129 ATACAG
* * *
2803026 GGGTGACAC-TGCTCCTACGTGATGAGGAGGTCTGGTC-GGTGGATGACACGGTTTCTATGTGAT
1 GGGTGACACAT-CTCCTACGTGATGAGGAGGTCTGGTCAAG-GGATGACACGGTTCCTACGTGAT
* * * *
2803089 GAGGACGGCAGGCCATCTTTAGGGAGGGTGATAACATGATTCCTACGCGATAAGGGCGACTGGTT
64 GAGGACGACAGGCCATCTTTAGGGAGGGTGATAACACGATTCCTACGCGATAAGGACGACTGATT
2803154 AT-CAG
129 ATACAG
* * *
2803159 GGGTGACACATCTCTTACGTGATGAGGAGGTATGGTCAAGGGATGACACAGTTCCTACGTGATGA
1 GGGTGACACATCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATGA
* * *
2803224 GGACGACATGCCTTATTTAGGGA
66 GGACGACAGGCCATCTTTAGGGA
2803247 TAATAGTTTC
Statistics
Matches: 185, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
133 76 0.41
134 108 0.58
135 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (134 bp):
GGGTGACACATCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTGATGA
GGACGACAGGCCATCTTTAGGGAGGGTGATAACACGATTCCTACGCGATAAGGACGACTGATTAT
ACAG
Found at i:2803370 original size:31 final size:29
Alignment explanation
Indices: 2803314--2803390 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
2803304 AGAGACAAAA
2803314 TTTGTTTCAAG-GAAACGACTCAAAGATGGT
1 TTTGTTTCAAGAGAAACGACTCAAAGAT--T
* *
2803344 TTTGTTTCTAGAGAAACAGA-TTAAAGATT
1 TTTGTTTCAAGAGAAAC-GACTCAAAGATT
*
2803373 TTGTGTTTCCAGAGAAAC
1 TT-TGTTTCAAGAGAAAC
2803391 TGCCTCAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 3 0.07
30 24 0.59
31 12 0.29
32 2 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (29 bp):
TTTGTTTCAAGAGAAACGACTCAAAGATT
Found at i:2803515 original size:28 final size:28
Alignment explanation
Indices: 2803479--2803534 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2803469 CAAAACTTTG
* *
2803479 TTTCCAAAGAAACATACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
2803507 TTTCAAAAGAAACAGACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
2803535 CTTGTTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:2803630 original size:32 final size:32
Alignment explanation
Indices: 2803589--2803653 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2803579 TTCGTATAAA
* * *
2803589 GATGTTGAATCCCCAATGATGCCTCAACGTTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
*
2803621 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
2803653 G
1 G
2803654 TTATTTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAACATTC
Found at i:2804728 original size:14 final size:13
Alignment explanation
Indices: 2804658--2804764 Score: 73
Period size: 14 Copynumber: 8.4 Consensus size: 13
2804648 AGTAAATGAC
*
2804658 TCTTTGC-TCTTT
1 TCTTTGCTTTTTT
2804670 TCTTTG--TTTTT
1 TCTTTGCTTTTTT
*
2804681 TCTTTG-TTTTCT
1 TCTTTGCTTTTTT
*
2804693 T-TTT-CTTCTTT
1 TCTTTGCTTTTTT
* *
2804704 GCTTTTTCTTTTTAT
1 TC-TTTGCTTTTT-T
2804719 TCTTTGCTTTTTT
1 TCTTTGCTTTTTT
*
2804732 CTCTTTGTTTCTTTT
1 -TCTTTGCTT-TTTT
*
2804747 TCTTTACTTTTTT
1 TCTTTGCTTTTTT
2804760 TCTTT
1 TCTTT
2804765 TTGCTCTTTG
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
11 17 0.22
12 11 0.14
13 13 0.17
14 29 0.38
15 6 0.08
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.76
Consensus pattern (13 bp):
TCTTTGCTTTTTT
Found at i:2804780 original size:21 final size:18
Alignment explanation
Indices: 2804667--2804806 Score: 86
Period size: 20 Copynumber: 7.2 Consensus size: 18
2804657 CTCTTTGCTC
2804667 TTTTCTTTGTTTTTTCTT-T
1 TTTTCTTT-TTTTTT-TTCT
*
2804686 GTTTTCTTTTTCTTCTTTGCT
1 -TTTTCTTTTT-TT-TTTTCT
*
2804707 TTTTCTTTTTATTCTTTGCT
1 TTTTCTTTTT-TT-TTTTCT
* * *
2804727 TTTT-TCTCTTTGTTTCT
1 TTTTCTTTTTTTTTTTCT
*
2804744 TTTTCTTTACTTTTTTTCT
1 TTTTCTTT-TTTTTTTTCT
2804763 TTTTGCTCTTTGTTTTTTTCCT
1 TTTT-CT-TTT-TTTTTTT-CT
*
2804785 TTCTTCTTTTTTTTTTTGT
1 TT-TTCTTTTTTTTTTTCT
2804804 TTT
1 TTT
2804807 GATTGGATCT
Statistics
Matches: 100, Mismatches: 10, Indels: 22
0.76 0.08 0.17
Matches are distributed among these distances:
17 8 0.08
18 5 0.05
19 21 0.21
20 43 0.43
21 15 0.15
22 6 0.06
23 2 0.02
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTTCT
Found at i:2809862 original size:17 final size:17
Alignment explanation
Indices: 2809840--2809874 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2809830 TTCAAGCTCC
2809840 ATTCAAACTCGAACTCG
1 ATTCAAACTCGAACTCG
*
2809857 ATTCAAGCTCGAACTCG
1 ATTCAAACTCGAACTCG
2809874 A
1 A
2809875 ATTTGAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (17 bp):
ATTCAAACTCGAACTCG
Found at i:2810872 original size:12 final size:12
Alignment explanation
Indices: 2810855--2810879 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2810845 TTATTTAAAG
2810855 ATAAACAAACTC
1 ATAAACAAACTC
2810867 ATAAACAAACTC
1 ATAAACAAACTC
2810879 A
1 A
2810880 CCAGAGGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAACAAACTC
Found at i:2811373 original size:3 final size:3
Alignment explanation
Indices: 2811367--2811391 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2811357 CAACAACAAC
2811367 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2811392 GGAAAACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2814847 original size:35 final size:34
Alignment explanation
Indices: 2814762--2814848 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2814752 ATTTGGTATT
*
2814762 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2814796 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2814834 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2814849 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2815076 original size:12 final size:12
Alignment explanation
Indices: 2815058--2815107 Score: 82
Period size: 12 Copynumber: 4.2 Consensus size: 12
2815048 ACTCCTTGCT
2815058 GTCATCGTCGTC
1 GTCATCGTCGTC
*
2815070 ATCATCGTCGTC
1 GTCATCGTCGTC
*
2815082 GTCGTCGTCGTC
1 GTCATCGTCGTC
2815094 GTCATCGTCGTC
1 GTCATCGTCGTC
2815106 GT
1 GT
2815108 TCTGAGCAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.08, C:0.32, G:0.26, T:0.34
Consensus pattern (12 bp):
GTCATCGTCGTC
Found at i:2815080 original size:3 final size:3
Alignment explanation
Indices: 2815062--2815107 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
2815052 CTTGCTGTCA
* * *
2815062 TCG TCG TCA TCA TCG TCG TCG TCG TCG TCG TCG TCA TCG TCG TCG T
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG T
2815108 TCTGAGCAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.07, C:0.33, G:0.26, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:2817065 original size:18 final size:17
Alignment explanation
Indices: 2817033--2817078 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
2817023 GAATTATATT
2817033 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
2817050 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
2817068 ATTAAATATAT
1 AGTAAA-ATAT
2817079 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:2817378 original size:51 final size:51
Alignment explanation
Indices: 2817301--2817430 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
2817291 CCCTTACGTG
* * **
2817301 GCGTATAGCGCGGAT-CAGGGGTCGCGCTATA-CCCACGTGTAATCCATGTCA
1 GCGTATAGCGCGG-TGCAGGGGGCGCGCTATACCCCACGTG-AAGCCAAATCA
**
2817352 GCGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGAAGCCAAATCA
* *
2817403 GCATATAGCGCGGGGCAGGGGGCGCGCT
1 GCGTATAGCGCGGTGCAGGGGGCGCGCT
2817431 TTACTGCTAC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 1 0.01
51 60 0.87
52 8 0.12
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.16
Consensus pattern (51 bp):
GCGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGAAGCCAAATCA
Found at i:2818193 original size:13 final size:13
Alignment explanation
Indices: 2818118--2818197 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
2818108 TCAATCATTA
*
2818118 TTTAGGGTTTAGGG
1 TTTAAGGTTTA-GG
*
2818132 TTTAAAGTTTAGG
1 TTTAAGGTTTAGG
* *
2818145 TTT-GGGTTCAGGG
1 TTTAAGGTTTA-GG
* *
2818158 TTTAAGATTTGATG
1 TTTAAGGTTT-AGG
*
2818172 TTAAAGGTTTAGG
1 TTTAAGGTTTAGG
*
2818185 TTTAGGGTTTAGG
1 TTTAAGGTTTAGG
2818198 GTTTTAGGGG
Statistics
Matches: 49, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
12 4 0.08
13 23 0.47
14 21 0.43
15 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.34, T:0.44
Consensus pattern (13 bp):
TTTAAGGTTTAGG
Found at i:2818205 original size:8 final size:7
Alignment explanation
Indices: 2818118--2818206 Score: 60
Period size: 7 Copynumber: 13.0 Consensus size: 7
2818108 TCAATCATTA
2818118 TTTAGGG
1 TTTAGGG
2818125 TTTAGGG
1 TTTAGGG
**
2818132 TTTAAAG
1 TTTAGGG
2818139 TTTA-GG
1 TTTAGGG
2818145 TTT-GGG
1 TTTAGGG
*
2818151 TTCAGGG
1 TTTAGGG
* *
2818158 TTTAAGA
1 TTTAGGG
*
2818165 TTT-GATG
1 TTTAG-GG
* *
2818172 TTAAAGG
1 TTTAGGG
2818179 TTTA-GG
1 TTTAGGG
2818185 TTTAGGG
1 TTTAGGG
2818192 TTTAGGG
1 TTTAGGG
2818199 TTTTAGGG
1 -TTTAGGG
2818207 GGCTTTTATT
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
6 14 0.23
7 41 0.66
8 7 0.11
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:2819331 original size:23 final size:23
Alignment explanation
Indices: 2819297--2819365 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2819287 CACCACAGCT
* *
2819297 CGTATAAATGCACCGAAGTGCTA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2819320 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2819343 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2819366 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2821201 original size:24 final size:20
Alignment explanation
Indices: 2821144--2821181 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2821134 TTCCCCTTGA
2821144 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2821164 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2821182 TTAACATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2823169 original size:2 final size:2
Alignment explanation
Indices: 2823158--2823191 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2823148 TTAACTAAAG
2823158 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2823192 TATTGTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2826035 original size:39 final size:39
Alignment explanation
Indices: 2825976--2826053 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
2825966 AGTTTTAATG
*
2825976 AAAATTATTGATTTACTAGTTTATGAACCATGACAACAT
1 AAAAGTATTGATTTACTAGTTTATGAACCATGACAACAT
2826015 AAAAGTATTGATTTACTAGTTTATGAACCATGACAACAT
1 AAAAGTATTGATTTACTAGTTTATGAACCATGACAACAT
2826054 GGTATGTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
AAAAGTATTGATTTACTAGTTTATGAACCATGACAACAT
Found at i:2830357 original size:18 final size:18
Alignment explanation
Indices: 2830331--2830365 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2830321 TGTTAAAAAG
* *
2830331 TATTGATAATATATTTTT
1 TATTAATAAAATATTTTT
2830349 TATTAATAAAATATTTT
1 TATTAATAAAATATTTT
2830366 ATATAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTAATAAAATATTTTT
Found at i:2831805 original size:3 final size:3
Alignment explanation
Indices: 2831797--2831821 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2831787 TTTTGCCATG
2831797 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
2831822 GCATGTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:2835763 original size:60 final size:61
Alignment explanation
Indices: 2835665--2835825 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 61
2835655 TGGAAGATCT
* * * * *
2835665 AAAAGTTTAGGGACCAATTTAAAATGAGATTCATAGTTTGGA-GAAGAAATTCAAATGTTC
1 AAAAGTTTAAGGACTAATTCAAAATGAGAGTCATAGTTTGGAGGAAGAAATTCAAATATTC
* * * * * * *
2835725 AAAATTTTAAGGACTAATTCAGAATGAGAGTCTTAGTTT-GAGGATGGAATTGAAATATTT
1 AAAAGTTTAAGGACTAATTCAAAATGAGAGTCATAGTTTGGAGGAAGAAATTCAAATATTC
* *
2835785 GAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTGG
1 AAAAGTTTAAGGACTAATTCAAAATGAGAGTCATAGTTTGG
2835826 GGACATATGA
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 2 0.02
60 79 0.96
61 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (61 bp):
AAAAGTTTAAGGACTAATTCAAAATGAGAGTCATAGTTTGGAGGAAGAAATTCAAATATTC
Found at i:2838539 original size:4 final size:4
Alignment explanation
Indices: 2838532--2838574 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
2838522 ATAAATGAAA
* *
2838532 ATAC ATAC ATAC ATGC AAAC ATAC ATAC ATA- ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2838575 GTAAGTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.51, C:0.23, G:0.02, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:2840097 original size:3 final size:3
Alignment explanation
Indices: 2840089--2840118 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2840079 AAATAAGTTT
2840089 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2840119 ACAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2841431 original size:89 final size:89
Alignment explanation
Indices: 2841271--2841433 Score: 283
Period size: 89 Copynumber: 1.8 Consensus size: 89
2841261 ATTTAATTTT
*
2841271 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAATAGGGTACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAATAGGGTACTTA
2841336 GATATAAAATGATTATTAAATTCC
66 GATATAAAATGATTATTAAATTCC
*
2841360 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAATAGGGT-ACTT
*
2841424 AGCTATAAAA
65 AGATATAAAA
2841434 GGGTGTGTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
88 17 0.24
89 53 0.76
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAATAGGGTACTTA
GATATAAAATGATTATTAAATTCC
Found at i:2843587 original size:23 final size:22
Alignment explanation
Indices: 2843561--2843623 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 22
2843551 CCAAAAGGTG
2843561 AAAAAGTTTGATGAAGAAGTTTT
1 AAAAAGTTTGATGAAGAA-TTTT
*
2843584 AAAATGCTTT-ATGAAAGAATTTT
1 AAAAAG-TTTGATG-AAGAATTTT
2843607 AAATAATGTTTGATGAA
1 AAA-AA-GTTTGATGAA
2843624 AAAATTATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
23 15 0.45
24 14 0.42
25 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (22 bp):
AAAAAGTTTGATGAAGAATTTT
Found at i:2843622 original size:25 final size:24
Alignment explanation
Indices: 2843561--2843648 Score: 85
Period size: 25 Copynumber: 3.7 Consensus size: 24
2843551 CCAAAAGGTG
2843561 AAAAA-GTTTGATG-AAGAAGTTTT
1 AAAAATGTTTGATGAAAGAA-TTTT
2843584 -AAAATGCTTT-ATGAAAGAATTTT
1 AAAAATG-TTTGATGAAAGAATTTT
* *
2843607 AAATAATGTTTGATGAAAAAATTATG
1 AAA-AATGTTTGATGAAAGAATT-TT
*
2843633 AAAAATGTTTAATGAA
1 AAAAATGTTTGATGAA
2843649 GTTTTTAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
22 4 0.07
23 8 0.15
24 13 0.24
25 26 0.47
26 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.35
Consensus pattern (24 bp):
AAAAATGTTTGATGAAAGAATTTT
Found at i:2850313 original size:321 final size:321
Alignment explanation
Indices: 2849724--2850369 Score: 1195
Period size: 321 Copynumber: 2.0 Consensus size: 321
2849714 TCATGCAGGA
*
2849724 ACAACTATTATTATCATATCATACACATCATATCAAATCGTCTCACTCATATGCTTTTCATATAA
1 ACAACTATTATTATCATATCATACACATCATATCAAATCATCTCACTCATATGCTTTTCATATAA
2849789 CAATTACATACATATCATCATTTATGTTTTTATATGGCTCCTATACTATTATACTTCATATCTCT
66 CAATTACATACATATCATCATTTATGTTTTTATATGGCTCCTATACTATTATACTTCATATCTCT
*
2849854 TATTTCTTATTCATATGATCTCTTATATTCATATTCTATAACTTATAACAAATTCTTATATCATC
131 TATTTCTTATTCATATGATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATC
2849919 ATATATAAGTCATTTATACTCACTCACATATACATCAACATATATTCATGTAACAGATACAATAA
196 ATATATAAGTCATTTATACTCACTCACATATACATCAACATATATTCATGTAACAGATACAATAA
* * * *
2849984 CCCATATCACACATATATCATATCATGTAATTCATATATATGTATCACATGCATTGATTTC
261 CCCATATCACACATACATCATATCATGCAATTCATATACATGTATCACATACATTGATTTC
2850045 ACAACTATTATTATCATATCATACACATCATATCAAATCATCTCACTCATATGCTTTTCATATAA
1 ACAACTATTATTATCATATCATACACATCATATCAAATCATCTCACTCATATGCTTTTCATATAA
*
2850110 CAATTACATACATATCATCATTTATGTTTTTATCCT-GCTCCTATACTATTATACTTCATATCTC
66 CAATTACATACATATCATCATTTATGTTTTTAT-ATGGCTCCTATACTATTATACTTCATATCTC
*
2850174 TTATTTCTTATTCATATGATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATGTCAT
130 TTATTTCTTATTCATATGATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCAT
2850239 CATATATAAGTCATTTATACTCACTCACATATACATCAACATATATTCATGTAACAGATACAATA
195 CATATATAAGTCATTTATACTCACTCACATATACATCAACATATATTCATGTAACAGATACAATA
*
2850304 ACTCATATCACACATACATCATATCATGCAATTCATATACATGTATCACATACATTGATTTC
260 ACCCATATCACACATACATCATATCATGCAATTCATATACATGTATCACATACATTGATTTC
2850366 ACAA
1 ACAA
2850370 TTATCTCTTT
Statistics
Matches: 315, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
321 314 1.00
322 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.40
Consensus pattern (321 bp):
ACAACTATTATTATCATATCATACACATCATATCAAATCATCTCACTCATATGCTTTTCATATAA
CAATTACATACATATCATCATTTATGTTTTTATATGGCTCCTATACTATTATACTTCATATCTCT
TATTTCTTATTCATATGATCTCTTACATTCATATTCTATAACTTATAACAAATTCTTATATCATC
ATATATAAGTCATTTATACTCACTCACATATACATCAACATATATTCATGTAACAGATACAATAA
CCCATATCACACATACATCATATCATGCAATTCATATACATGTATCACATACATTGATTTC
Found at i:2850518 original size:18 final size:18
Alignment explanation
Indices: 2850495--2850582 Score: 95
Period size: 18 Copynumber: 4.4 Consensus size: 18
2850485 TTTGTCAAAT
2850495 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
2850513 ATGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
2850531 AGGACCACATATCACATATGTCCCGA
1 AGG---AC----CAC-TATGTCCCGA
2850557 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
2850575 AGGACCAC
1 AGGACCAC
2850583 ATAGACCCTC
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
18 37 0.62
19 3 0.05
21 2 0.03
23 2 0.03
25 3 0.05
26 13 0.22
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:2853236 original size:23 final size:23
Alignment explanation
Indices: 2853210--2853253 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2853200 GAGTAGAGGG
*
2853210 TCTACGTGGTCCTTCGGGACAAT
1 TCTACGTGGTCATTCGGGACAAT
2853233 TCTACGTGGTCATTCGGGACA
1 TCTACGTGGTCATTCGGGACA
2853254 TATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TCTACGTGGTCATTCGGGACAAT
Found at i:2853351 original size:22 final size:24
Alignment explanation
Indices: 2853315--2853369 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
2853305 CATTGGTATA
* *
2853315 TCTATATGATTCTTAAGGA-AT-T
1 TCTATATGGTCCTTAAGGACATAT
*
2853337 TCTATATGGTCCTTAGGGACATAT
1 TCTATATGGTCCTTAAGGACATAT
*
2853361 TATATATGG
1 TCTATATGG
2853370 CACTACGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (24 bp):
TCTATATGGTCCTTAAGGACATAT
Found at i:2853455 original size:24 final size:23
Alignment explanation
Indices: 2853367--2853452 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
2853357 ATATTATATA
* *
2853367 TGGCACTACGTTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
2853390 TGGCACTTCGGTGCATTTGTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
2853413 CGGTC-CTTCGG-GACAAATTCTATG
1 TGG-CACTTCGGTG-C-AATTCTACG
2853437 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
2853453 ATTTATACGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.63
24 16 0.33
25 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2859235 original size:15 final size:15
Alignment explanation
Indices: 2859215--2859247 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2859205 GCTTAATTGG
2859215 ATTGAAACCATATTT
1 ATTGAAACCATATTT
*
2859230 ATTGAAATCATATTT
1 ATTGAAACCATATTT
2859245 ATT
1 ATT
2859248 TCATTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTGAAACCATATTT
Found at i:2866158 original size:27 final size:27
Alignment explanation
Indices: 2866125--2866186 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
2866115 CGACCCGTTG
2866125 ACTGTTGATTGTTGAACGGCGTTGACC
1 ACTGTTGATTGTTGAACGGCGTTGACC
2866152 ACTGTTGATTGTTGAACGGCGTTGACC
1 ACTGTTGATTGTTGAACGGCGTTGACC
2866179 ACTGTTGA
1 ACTGTTGA
2866187 CCAAAACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (27 bp):
ACTGTTGATTGTTGAACGGCGTTGACC
Found at i:2866868 original size:36 final size:36
Alignment explanation
Indices: 2866821--2866893 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2866811 AGTTTTGGAA
2866821 TTAAGTGATAAAAGAATCAGCCATCGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATCGATATGTAGAT
* *
2866857 TTAAGTGATAAAAGAATCAGCCATGGATGTGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATCGATATGTAGAT
2866893 T
1 T
2866894 ATAATTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGCCATCGATATGTAGAT
Found at i:2868680 original size:24 final size:24
Alignment explanation
Indices: 2868653--2868740 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
2868643 ATTTCCGACT
*
2868653 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATACATGATC
* *
2868677 TGAATTCTGTTTTGATTTC-TGATC
1 TGAATTCTGTTCTGA-TACATGATC
* * * *
2868701 TGGATTCTGTTCTGATATATGTTT
1 TGAATTCTGTTCTGATACATGATC
*
2868725 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
2868741 TTCTGATATC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 1 0.02
24 48 0.94
25 2 0.04
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATACATGATC
Found at i:2868696 original size:12 final size:12
Alignment explanation
Indices: 2868681--2868745 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
2868671 ATGACCTGAA
2868681 TTCTGTTTTGAT
1 TTCTGTTTTGAT
* *
2868693 TTCTGATCTGGA-
1 TTCTG-TTTTGAT
*
2868705 TTCTGTTCTGAT
1 TTCTGTTTTGAT
* * *
2868717 ATATGTTTTGAA
1 TTCTGTTTTGAT
2868729 TTCTGTTTTGAT
1 TTCTGTTTTGAT
2868741 TTCTG
1 TTCTG
2868746 ATATCTCTGA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 3 0.08
12 32 0.82
13 4 0.10
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (12 bp):
TTCTGTTTTGAT
Found at i:2868708 original size:48 final size:48
Alignment explanation
Indices: 2868656--2868747 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
2868646 TCCGACTTGA
2868656 ATTCTGTTCTGATACATGACCTGAATTCTGTTTTGATTTCTGATCTGG
1 ATTCTGTTCTGATACATGACCTGAATTCTGTTTTGATTTCTGATCTGG
* ***
2868704 ATTCTGTTCTGATATATGTTTTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATACATGACCTGAATTCTGTTTTGATTTCTGAT
2868748 ATCTCTGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (48 bp):
ATTCTGTTCTGATACATGACCTGAATTCTGTTTTGATTTCTGATCTGG
Found at i:2871176 original size:60 final size:60
Alignment explanation
Indices: 2871112--2871238 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
2871102 TAGAAAGGGT
* * *
2871112 GTCATA-ATTTAGAGATGAAATTAGAATGCTT-AAATGTTTAAGGA-CTAATTTAGAATAAGA
1 GTCATAGA-TTAGAGATGAAATTAGAAT-ATTCAAAAGTTTAAGGACCT-ATTTAAAATAAGA
* * *
2871172 GTCATAGATTCGGGATGAAATTGGAATATTCAAAAGTTTAAGGACCTATTTAAAATAAGA
1 GTCATAGATTAGAGATGAAATTAGAATATTCAAAAGTTTAAGGACCTATTTAAAATAAGA
*
2871232 GTTATAG
1 GTCATAG
2871239 TTGGGGACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.04
60 52 0.91
61 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (60 bp):
GTCATAGATTAGAGATGAAATTAGAATATTCAAAAGTTTAAGGACCTATTTAAAATAAGA
Found at i:2882115 original size:105 final size:105
Alignment explanation
Indices: 2881933--2882965 Score: 1605
Period size: 105 Copynumber: 9.9 Consensus size: 105
2881923 AGATAACACG
* * * * **
2881933 AGTTCAACTTCACGACGAAGGGACGGCTGGTTGTTAACAACAATTTTCCAATTTTGGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
* * * *
2881998 TTAACTTTACAGCGAAGGATATTGGACTCCAGACGACACA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
2882038 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAATAACTTCCCAATTTCGGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
2882103 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
2882143 AGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
2882208 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
2882248 AGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
2882313 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
2882353 AGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
* * *
2882418 TCGACTTCACGGCGAAGGATATTGGATTCCAGACAACGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
2882458 AGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTTCGGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
*
2882523 TCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
2882563 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
*
2882628 TCAACTTCACAGCGAA-GAGTATTGGACTCCAGACAATGCA
66 TCAACTTCACAGCGAAGGA-TATTGGACTCCAGACAACGCA
2882668 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
*
2882733 TCAACTTCCCAGCGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* * * * *
2882773 AGTTCAACTTCACGACGAAGGGACCGATGGTTATCAAC-A-AAGTT-TC-A-TTCAGAGTCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
* * * * *
2882833 TCAACTTCACAGTGAAGGATATTAGACTCGAGACAGCACA
66 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* * ** * * *
2882873 AGCTCAACTTCAC-AGCGAATGGG-CGGCTGACTGTCAACAAACAATTTCCCAATTCCAGAACCA
1 AGTTCAACTTCACGA-CGAA-GGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
2882936 ATTTCAACTTCACAGCGGAGGATATTGGAC
63 ATTTCAACTTCACAGCGAAGGATATTGGAC
2882966 GCGGAATAAT
Statistics
Matches: 860, Mismatches: 58, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
99 1 0.00
100 72 0.08
101 4 0.00
102 2 0.00
103 8 0.01
104 4 0.00
105 733 0.85
106 36 0.04
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (105 bp):
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
Found at i:2884602 original size:2 final size:2
Alignment explanation
Indices: 2884597--2884638 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2884587 CTACAAACTA
2884597 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
2884639 TACTTTTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2884860 original size:9 final size:9
Alignment explanation
Indices: 2884846--2884890 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
2884836 ATTAGTGTTA
2884846 TTATTTT-T
1 TTATTTTAT
2884854 TTCATTTTAT
1 TT-ATTTTAT
2884864 TTATTTTAT
1 TTATTTTAT
*
2884873 ATATTTTAT
1 TTATTTTAT
*
2884882 TCATTTTAT
1 TTATTTTAT
2884891 ATTTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 2 0.06
9 27 0.84
10 3 0.09
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTTTAT
Found at i:2884869 original size:18 final size:18
Alignment explanation
Indices: 2884857--2884892 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2884847 TATTTTTTTC
2884857 ATTTTATTTATTTTATAT
1 ATTTTATTTATTTTATAT
*
2884875 ATTTTATTCATTTTATAT
1 ATTTTATTTATTTTATAT
2884893 TTACTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATTTATTTTATAT
Found at i:2885650 original size:20 final size:21
Alignment explanation
Indices: 2885625--2885672 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2885615 AAATTTTCAA
2885625 ACAAATTAGGAGTT-TAACAG
1 ACAAATTAGGAGTTCTAACAG
* *
2885645 ACAAATTAGTAGTTCTATCAG
1 ACAAATTAGGAGTTCTAACAG
2885666 ATCAAAT
1 A-CAAAT
2885673 CTTTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 6 0.25
22 5 0.21
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (21 bp):
ACAAATTAGGAGTTCTAACAG
Found at i:2885822 original size:25 final size:25
Alignment explanation
Indices: 2885794--2885847 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
2885784 GATGAGAAAG
2885794 ATTCCCAATAGGGGAGTAATAAAAT
1 ATTCCCAATAGGGGAGTAATAAAAT
*
2885819 ATTCCCAGTAGGGGAGTAATAAAAT
1 ATTCCCAATAGGGGAGTAATAAAAT
2885844 ATTC
1 ATTC
2885848 TCAACAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (25 bp):
ATTCCCAATAGGGGAGTAATAAAAT
Found at i:2886020 original size:14 final size:14
Alignment explanation
Indices: 2886001--2886030 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2885991 GCTATAGACT
2886001 TTTGTTTTCACAAA
1 TTTGTTTTCACAAA
2886015 TTTGTTTTCACAAA
1 TTTGTTTTCACAAA
2886029 TT
1 TT
2886031 ATCATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTGTTTTCACAAA
Found at i:2886392 original size:29 final size:29
Alignment explanation
Indices: 2886350--2886420 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
2886340 TCAAACACAA
2886350 TAATGTAACATTCCCAGTAATGTGTAAGG
1 TAATGTAACATTCCCAGTAATGTGTAAGG
*
2886379 TAATGTAACATTCCCAGTAATTTGTAAGG
1 TAATGTAACATTCCCAGTAATGTGTAAGG
*
2886408 TAATATAACATTC
1 TAATGTAACATTC
2886421 AATGAACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (29 bp):
TAATGTAACATTCCCAGTAATGTGTAAGG
Found at i:2887014 original size:17 final size:17
Alignment explanation
Indices: 2886989--2887024 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2886979 ATTCAACGAT
*
2886989 CAGTCAACAACGATCAA
1 CAGTCAACAACAATCAA
*
2887006 CAGTTAACAACAATCAA
1 CAGTCAACAACAATCAA
2887023 CA
1 CA
2887025 ATTTTGGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.08, T:0.14
Consensus pattern (17 bp):
CAGTCAACAACAATCAA
Found at i:2890101 original size:39 final size:39
Alignment explanation
Indices: 2890058--2890133 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
2890048 AGGTTTATCC
* *
2890058 TGTGTACA-AAGAAAATGAGCCTTCAGTAAGGACTTACCT
1 TGTGT-CAGAAGAAAAGGAGCCTACAGTAAGGACTTACCT
* * *
2890097 TGTGTCAGAAGCATAGGAGCCTACAGTAAGGTCTTAC
1 TGTGTCAGAAGAAAAGGAGCCTACAGTAAGGACTTAC
2890134 AAGTCATAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (39 bp):
TGTGTCAGAAGAAAAGGAGCCTACAGTAAGGACTTACCT
Found at i:2893558 original size:14 final size:14
Alignment explanation
Indices: 2893539--2893685 Score: 81
Period size: 14 Copynumber: 10.2 Consensus size: 14
2893529 ATGTGATAAG
2893539 GTTTAGGGTTTAGA
1 GTTTAGGGTTTAGA
*
2893553 GTTTAGAGTTTAGA
1 GTTTAGGGTTTAGA
2893567 GTTTATGTGATATGATTTA-A
1 GTTTA-G-G----G-TTTAGA
*
2893587 GGTTTAGGGTTTATA
1 -GTTTAGGGTTTAGA
*
2893602 GTTTAGAGTTTAGA
1 GTTTAGGGTTTAGA
* *
2893616 GTTTA-TGTAATAG-
1 GTTTAGGGT-TTAGA
*
2893629 GATTTAAGGTTTAGA
1 G-TTTAGGGTTTAGA
* *
2893644 GTTTAGTGTTTACA
1 GTTTAGGGTTTAGA
*
2893658 GTTTAAGG--TAG-
1 GTTTAGGGTTTAGA
2893669 GTTTAGGGTTTAGA
1 GTTTAGGGTTTAGA
2893683 GTT
1 GTT
2893686 CAAAATTTAG
Statistics
Matches: 102, Mismatches: 15, Indels: 32
0.68 0.10 0.21
Matches are distributed among these distances:
11 7 0.07
12 2 0.02
13 6 0.06
14 68 0.67
15 6 0.06
19 1 0.01
20 3 0.03
21 9 0.09
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:2893607 original size:49 final size:49
Alignment explanation
Indices: 2893535--2893662 Score: 195
Period size: 49 Copynumber: 2.6 Consensus size: 49
2893525 AATTATGTGA
* * *
2893535 TAAGGTTTAGGGTTTAGAGTTTAGAGTTTAGAGTTTATGTGATATGATT
1 TAAGGTTTAGGGTTTATAGTTTAGAGTTTAGAGTTTATGTAATAGGATT
2893584 TAAGGTTTAGGGTTTATAGTTTAGAGTTTAGAGTTTATGTAATAGGATT
1 TAAGGTTTAGGGTTTATAGTTTAGAGTTTAGAGTTTATGTAATAGGATT
* *
2893633 TAAGGTTTAGAGTTTAGT-GTTTACAGTTTA
1 TAAGGTTTAGGGTTTA-TAGTTTAGAGTTTA
2893663 AGGTAGGTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
49 72 0.99
50 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (49 bp):
TAAGGTTTAGGGTTTATAGTTTAGAGTTTAGAGTTTATGTAATAGGATT
Found at i:2893785 original size:21 final size:21
Alignment explanation
Indices: 2893699--2893788 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
2893689 AATTTAGAGT
2893699 TTTAGAGTTTATGTGATATGA
1 TTTAGAGTTTATGTGATATGA
* ** *
2893720 TTTA-AGGTTTATATTTTAGGA
1 TTTAGA-GTTTATGTGATATGA
*
2893741 TTTAGAGTTTA---G--A-GT
1 TTTAGAGTTTATGTGATATGA
2893756 TTTAGAGTTTATGTGATATGA
1 TTTAGAGTTTATGTGATATGA
*
2893777 TTTAAAGTTTAT
1 TTTAGAGTTTAT
2893789 ATGTTTAGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
15 12 0.23
16 1 0.02
18 1 0.02
20 2 0.04
21 36 0.68
22 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (21 bp):
TTTAGAGTTTATGTGATATGA
Found at i:2895741 original size:11 final size:11
Alignment explanation
Indices: 2895725--2895790 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
2895715 TAACCTATCC
2895725 TCGAGCTT-AA
1 TCGAGCTTGAA
2895735 GTCGAGCTTGAA
1 -TCGAGCTTGAA
2895747 TCGAGCTTGAA
1 TCGAGCTTGAA
**
2895758 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
2895770 TCGAGCTTCAA
1 TCGAGCTTGAA
*
2895781 TTGAGCTTGA
1 TCGAGCTTGA
2895791 GTCTTGAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
11 36 0.77
12 11 0.23
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:2896553 original size:18 final size:18
Alignment explanation
Indices: 2896530--2896567 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2896520 AAAGATAAGG
2896530 AATATTATAATCTT-AATT
1 AATATTA-AATCTTGAATT
*
2896548 AATATTAAATTTTGAATT
1 AATATTAAATCTTGAATT
2896566 AA
1 AA
2896568 ATTTTAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATTAAATCTTGAATT
Found at i:2897243 original size:22 final size:25
Alignment explanation
Indices: 2897208--2897265 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
2897198 AAATAGGCCT
*
2897208 ATTATATAAGATTATTT-AATA-AA
1 ATTATATAAAATTATTTAAATATAA
2897231 ATT-TATAAAATTATTTAAATATAA
1 ATTATATAAAATTATTTAAATATAA
2897255 ATTATATAAAA
1 ATTATATAAAA
2897266 CATGATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 12 0.39
23 7 0.23
24 5 0.16
25 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTATATAAAATTATTTAAATATAA
Found at i:2897344 original size:23 final size:24
Alignment explanation
Indices: 2897304--2897357 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
2897294 CAATGATTAA
*
2897304 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAACTAATATAGTTTAATTT
2897328 ATGTAAACT-ATATAGTTTAATTT
1 ATGTAAACTAATATAGTTTAATTT
2897351 ATGTAAA
1 ATGTAAA
2897358 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
ATGTAAACTAATATAGTTTAATTT
Found at i:2898169 original size:13 final size:13
Alignment explanation
Indices: 2898127--2898195 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
2898117 TAATAATTGT
2898127 ATGTTATTAATTC
1 ATGTTATTAATTC
*
2898140 ATGTGA-T-ATTGC
1 ATGTTATTAATT-C
2898152 ATGTTATTAATTC
1 ATGTTATTAATTC
**
2898165 ATG-T-TGCATTGC
1 ATGTTATTAATT-C
2898177 ATGTTATTAATTC
1 ATGTTATTAATTC
2898190 ATGTTA
1 ATGTTA
2898196 CATTAGGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
11 7 0.16
12 12 0.27
13 18 0.41
14 7 0.16
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (13 bp):
ATGTTATTAATTC
Found at i:2898207 original size:25 final size:25
Alignment explanation
Indices: 2898122--2898199 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
2898112 TTAAATAATA
* * *
2898122 ATTGTATGTTATTAATTCATGTGAT
1 ATTGCATGTTATTAATTCATGTTAC
*
2898147 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTTAC
2898172 ATTGCATGTTATTAATTCATGTTAC
1 ATTGCATGTTATTAATTCATGTTAC
2898197 ATT
1 ATT
2898200 AGGTGTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTAC
Found at i:2898893 original size:6 final size:6
Alignment explanation
Indices: 2898882--2898952 Score: 52
Period size: 6 Copynumber: 13.0 Consensus size: 6
2898872 GCTAATAAAA
2898882 TAATAT TAATA- TAA-AT TATATAT T-ATAAT TAATAT TAATA- T-A-AT
1 TAATAT TAATAT TAATAT TA-ATAT TAAT-AT TAATAT TAATAT TAATAT
*
2898926 TAATAT TAA-CT T-ATAT TAATA- TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT
2898953 AGTTTATAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 22
0.68 0.03 0.29
Matches are distributed among these distances:
3 1 0.02
4 4 0.08
5 18 0.35
6 24 0.46
7 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATAT
Found at i:2898894 original size:29 final size:29
Alignment explanation
Indices: 2898861--2898950 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
2898851 TTTCATCCCT
*
2898861 ATATAATTTATGCTAATA-AAATAATATTA
1 ATATAATTTAT-ATAATATAAATAATATTA
* * *
2898890 ATATAAATTATATATTATAATTAATATTA
1 ATATAATTTATATAATATAAATAATATTA
* *
2898919 ATATAA-TTA-AT-AT-TAACTTATATTA
1 ATATAATTTATATAATATAAATAATATTA
2898944 ATATAAT
1 ATATAAT
2898951 ATAGTTTATA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
25 16 0.31
26 1 0.02
27 2 0.04
28 7 0.13
29 26 0.50
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATAATTTATATAATATAAATAATATTA
Found at i:2898904 original size:11 final size:11
Alignment explanation
Indices: 2898881--2898952 Score: 64
Period size: 11 Copynumber: 6.6 Consensus size: 11
2898871 TGCTAATAAA
2898881 ATAATATTAAT
1 ATAATATTAAT
2898892 ATAA-ATTATAT
1 ATAATATTA-AT
*
2898903 ATTATAATTAAT
1 ATAAT-ATTAAT
2898915 ATTAATA-TAAT
1 A-TAATATTAAT
2898926 -TAATATTAACT
1 ATAATATTAA-T
2898937 -T-ATATTAAT
1 ATAATATTAAT
2898946 ATAATAT
1 ATAATAT
2898953 AGTTTATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
9 6 0.12
10 15 0.29
11 19 0.37
12 4 0.08
13 7 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:2898909 original size:25 final size:28
Alignment explanation
Indices: 2898882--2898949 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 28
2898872 GCTAATAAAA
*
2898882 TAATATTAATATAAATTATATATTATAAT
1 TAATATTAATATAAATTA-ATATTATAAC
2898911 TAATATTAATAT-AATTAATA-T-TAAC
1 TAATATTAATATAAATTAATATTATAAC
*
2898936 TTATATTAATATAA
1 TAATATTAATATAA
2898950 TATAGTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 14 0.39
26 2 0.06
27 3 0.08
28 5 0.14
29 12 0.33
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATATTAATATAAATTAATATTATAAC
Found at i:2898950 original size:25 final size:28
Alignment explanation
Indices: 2898882--2899014 Score: 103
Period size: 29 Copynumber: 4.5 Consensus size: 28
2898872 GCTAATAAAA
2898882 TAATATTAATATAAATTATATATTATAAT
1 TAATATTAATAT-AATTATATATTATAAT
*
2898911 TAATATTAATATAATTA-ATATTA-ACT
1 TAATATTAATATAATTATATATTATAAT
*
2898937 T-ATATTAATATAATATAGTTTATAATTTGTAAT
1 TAATATTAATATAAT-TA---TAT-A-TTATAAT
* *
2898970 TAATATTACTATAA-AATATAGTCTATAAAAT
1 TAATATTAATATAATTATATA-T-TAT--AAT
2899001 TAATATTAATATAA
1 TAATATTAATATAA
2899015 ACTATATTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
25 13 0.15
26 5 0.06
27 6 0.07
28 7 0.08
29 17 0.20
30 2 0.02
31 17 0.20
32 3 0.04
33 3 0.04
34 11 0.13
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
TAATATTAATATAATTATATATTATAAT
Found at i:2899029 original size:31 final size:31
Alignment explanation
Indices: 2898967--2899109 Score: 86
Period size: 31 Copynumber: 4.8 Consensus size: 31
2898957 TATAATTTGT
* * *
2898967 AATTAATATTACTATAAAATATAGTCT-ATAA
1 AATTAATATTAATATAAACTATA-TTTAATAA
2898998 AATTAATATTAATATAAACTATATTTAAT-A
1 AATTAATATTAATATAAACTATATTTAATAA
* * * *
2899028 AATT-ATA-TAGTAT--AGTTTA-TAAACTATA
1 AATTAATATTAATATAAACTATATTTAA-TA-A
* * * * *
2899056 TACT-ATATTAATATAAATTATATTTAAGAT
1 AATTAATATTAATATAAACTATATTTAATAA
*
2899086 AATTAACATTAATATAAACTATAT
1 AATTAATATTAATATAAACTATAT
2899110 AGTACATTAA
Statistics
Matches: 84, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
25 3 0.04
26 5 0.06
28 11 0.13
29 8 0.10
30 9 0.11
31 45 0.54
32 3 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
AATTAATATTAATATAAACTATATTTAATAA
Found at i:2899034 original size:14 final size:15
Alignment explanation
Indices: 2898874--2899109 Score: 90
Period size: 15 Copynumber: 16.0 Consensus size: 15
2898864 TAATTTATGC
*
2898874 TAATA-AAATAATAT
1 TAATATAAATTATAT
2898888 TAATATAAATTATA-
1 TAATATAAATTATAT
*
2898902 TATTAT-AATTAATAT
1 TAATATAAATT-ATAT
2898917 TAATAT-AATTA-A-
1 TAATATAAATTATAT
*
2898929 T-AT-TAACTTATAT
1 TAATATAAATTATAT
*
2898942 TAATAT-AATATAGTTT
1 TAATATAAAT-TA-TAT
* *
2898958 ATAATTTGTAATTAATAT
1 -TAATAT-AAATT-ATAT
* *
2898976 TACTATAAAATATAGT
1 TAATATAAATTATA-T
2898992 CT-ATA-AAATTAATAT
1 -TAATATAAATT-ATAT
*
2899007 TAATATAAACTATAT
1 TAATATAAATTATAT
*
2899022 TTA-ATAAATTATA-
1 TAATATAAATTATAT
* *
2899035 TAGTAT-AGTT-TAT
1 TAATATAAATTATAT
* * *
2899048 AAACTATATACTATAT
1 TAA-TATAAATTATAT
2899064 TAATATAAATTATATT
1 TAATATAAATTATA-T
* *
2899080 TAAGAT-AATTAACAT
1 TAATATAAATT-ATAT
*
2899095 TAATATAAACTATAT
1 TAATATAAATTATAT
2899110 AGTACATTAA
Statistics
Matches: 162, Mismatches: 33, Indels: 53
0.65 0.13 0.21
Matches are distributed among these distances:
10 1 0.01
11 6 0.04
12 4 0.02
13 11 0.07
14 33 0.20
15 59 0.36
16 31 0.19
17 10 0.06
18 3 0.02
19 4 0.02
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
TAATATAAATTATAT
Found at i:2899036 original size:88 final size:91
Alignment explanation
Indices: 2898882--2899149 Score: 256
Period size: 88 Copynumber: 3.0 Consensus size: 91
2898872 GCTAATAAAA
* * *
2898882 TAATATTAATATAAATTATATAT-TATAATTAATATTAATAT-AATTA-ATATTAACTTATATTA
1 TAATATTAATATAAATTATATATATAAAATTAATATTAATATAAACTATATATTAAC-TAAATTA
** * *
2898944 ATATAATATAGTTTATAATTTGTA-AT
65 ATATAATATAGTTTATAAACTATATAC
* * *
2898970 TAATATTACTATAAAATATAGTCTATAAAATTAATATTAATATAAACTATAT-TTAA-TAAATT-
1 TAATATTAATATAAATTATA-TATATAAAATTAATATTAATATAAACTATATATTAACTAAATTA
*
2899032 ATATAGTATAGTTTATAAACTATATAC
65 ATATAATATAGTTTATAAACTATATAC
* * *
2899059 T-ATATTAATATAAATTATATTTA-AGATAATTAACATTAATATAAACTATATAGT-AC---ATT
1 TAATATTAATATAAATTATATATATA-A-AATTAATATTAATATAAACTATATATTAACTAAATT
*
2899118 AATATAAACTATAGTTTATAAATTATATAC
64 AATAT-AA-TATAGTTTATAAACTATATAC
2899148 TA
1 TA
2899150 TAGGTTATAA
Statistics
Matches: 149, Mismatches: 18, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
86 4 0.03
87 8 0.05
88 79 0.53
89 31 0.21
90 17 0.11
91 8 0.05
92 2 0.01
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (91 bp):
TAATATTAATATAAATTATATATATAAAATTAATATTAATATAAACTATATATTAACTAAATTAA
TATAATATAGTTTATAAACTATATAC
Found at i:2899041 original size:21 final size:21
Alignment explanation
Indices: 2899010--2899078 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
2899000 TTAATATTAA
*
2899010 TATAAACTATATTTAATAAAT
1 TATATACTATATTTAATAAAT
* *
2899031 TATATAGTATAGTTT-ATAAAC
1 TATATACTATA-TTTAATAAAT
*
2899052 TATATACTATATTAATATAAAT
1 TATATACTATATTTA-ATAAAT
2899074 TATAT
1 TATAT
2899079 TTAAGATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.05
21 24 0.62
22 13 0.33
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (21 bp):
TATATACTATATTTAATAAAT
Found at i:2899116 original size:22 final size:22
Alignment explanation
Indices: 2899091--2899193 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
2899081 AAGATAATTA
2899091 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
2899113 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
2899133 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
2899155 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
2899177 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
2899194 TGTTTACAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
20 10 0.15
21 22 0.34
22 28 0.43
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:2899149 original size:21 final size:21
Alignment explanation
Indices: 2899120--2899172 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2899110 AGTACATTAA
* *
2899120 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
2899141 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
2899162 TATAAACTATA
1 TATAAACTATA
2899173 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:2899242 original size:20 final size:20
Alignment explanation
Indices: 2899212--2899314 Score: 78
Period size: 20 Copynumber: 5.2 Consensus size: 20
2899202 AACTATACGT
2899212 TACATAT-ATAGTTTATATA
1 TACATATAATAGTTTATATA
2899231 -ACATATAAATAGATTGTATATA
1 TACATAT-AATAG-TT-TATATA
*
2899253 TACATATACTATAG-GT-TATA
1 TACATATA--ATAGTTTATATA
2899273 T--ATAT-ATAGTTTATATA
1 TACATATAATAGTTTATATA
*
2899290 TAC-TATACATAGTTTATACA
1 TACATATA-ATAGTTTATATA
2899310 TACAT
1 TACAT
2899315 CTACTATAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 26
0.70 0.03 0.27
Matches are distributed among these distances:
15 4 0.06
16 1 0.01
17 5 0.07
18 13 0.19
20 23 0.34
21 4 0.06
22 7 0.10
23 6 0.09
24 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (20 bp):
TACATATAATAGTTTATATA
Found at i:2899264 original size:57 final size:55
Alignment explanation
Indices: 2899203--2899340 Score: 170
Period size: 59 Copynumber: 2.4 Consensus size: 55
2899193 TTGTTTACAA
* *
2899203 ACTATACGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATATAC-TATAAATAG-TT-TATACATACATAT
* * * *
2899260 ACTATAGGTTATATATATATAGTTTATATATACTATACATAGTTTATACATACATCT
1 ACTATAAG-T-TACATATATAGTTTATATATACTATAAATAGTTTATACATACATAT
2899317 ACTATAAGTTACATATATAGTTTA
1 ACTATAAGTTACATATATAGTTTA
2899341 CATGTATACA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
55 14 0.20
56 1 0.01
57 25 0.35
58 3 0.04
59 26 0.37
60 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (55 bp):
ACTATAAGTTACATATATAGTTTATATATACTATAAATAGTTTATACATACATAT
Found at i:2899266 original size:24 final size:21
Alignment explanation
Indices: 2899215--2899276 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
2899205 TATACGTTAC
2899215 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATACAT
*
2899235 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATATACAT
*
2899258 ATACTATAGGTTATATATA
1 ATA-TATAGTTTATATATA
2899277 TATAGTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 7 0.20
21 2 0.06
22 14 0.40
23 8 0.23
24 4 0.11
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (21 bp):
ATATATAGTTTATATATACAT
Found at i:2899277 original size:24 final size:22
Alignment explanation
Indices: 2899215--2899278 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
2899205 TATACGTTAC
2899215 ATATATA-GTTTATATA-ACAT
1 ATATATAGGTTTATATATACAT
* *
2899235 ATAAATAGATTGTATATATACAT
1 ATATATAGGTT-TATATATACAT
2899258 ATACTATAGGTTATATATATA
1 ATA-TATAGGTT-TATATATA
2899279 TAGTTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.17
21 2 0.06
22 6 0.17
23 7 0.20
24 14 0.40
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (22 bp):
ATATATAGGTTTATATATACAT
Found at i:2899280 original size:15 final size:16
Alignment explanation
Indices: 2899256--2899296 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
2899246 GTATATATAC
2899256 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
2899272 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
2899287 ATATACTATA
1 ATATACTATA
2899297 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:2899337 original size:35 final size:36
Alignment explanation
Indices: 2899298--2899371 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
2899288 TATACTATAC
*
2899298 ATAGTTT-ATACATACATCTACTATAAG-TTACATAT
1 ATAGTTTAATACATACATATACTAT-AGCTTACATAT
**
2899333 ATAGTTTACATGTATACATATACTATAGCTTACATAT
1 ATAGTTTA-ATACATACATATACTATAGCTTACATAT
2899370 AT
1 AT
2899372 TAACTATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 7 0.21
36 2 0.06
37 24 0.73
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAGCTTACATAT
Found at i:2899349 original size:57 final size:58
Alignment explanation
Indices: 2899203--2899360 Score: 180
Period size: 57 Copynumber: 2.7 Consensus size: 58
2899193 TTGTTTACAA
* * *
2899203 ACTATACGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATATACATATACATAGATTGTATACATACATAT
* * *
2899260 ACTATAGGTTATATATATATAGTTTATATATAC-TATACATAG-TT-TATACATACATCT
1 ACTATAAG-T-TACATATATAGTTTATATATACATATACATAGATTGTATACATACATAT
*
2899317 ACTATAAGTTACATATATAGTTTACATGTATACATATACTATAG
1 ACTATAAGTTACATATATAGTTT--ATATATACATATAC-ATAG
2899361 CTTACATATA
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
55 13 0.15
56 1 0.01
57 32 0.37
58 8 0.09
59 30 0.35
60 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (58 bp):
ACTATAAGTTACATATATAGTTTATATATACATATACATAGATTGTATACATACATAT
Found at i:2899470 original size:2 final size:2
Alignment explanation
Indices: 2899463--2899496 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2899453 ATCAACTGTC
2899463 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
2899497 GTTTATGGTT
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):
TA
Found at i:2899513 original size:7 final size:7
Alignment explanation
Indices: 2899497--2899570 Score: 76
Period size: 7 Copynumber: 10.6 Consensus size: 7
2899487 TATATATATA
*
2899497 GTTTATG
1 GTTTAGG
2899504 GTTTAGG
1 GTTTAGG
*
2899511 GTTTAGT
1 GTTTAGG
*
2899518 GTTTATG
1 GTTTAGG
* **
2899525 CTTTAAA
1 GTTTAGG
2899532 GTTTAGG
1 GTTTAGG
*
2899539 GTTTATG
1 GTTTAGG
*
2899546 CTTTAGG
1 GTTTAGG
2899553 GTTTAGG
1 GTTTAGG
2899560 GTTTAGG
1 GTTTAGG
2899567 GTTT
1 GTTT
2899571 CTATAAACTA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.16, C:0.03, G:0.31, T:0.50
Consensus pattern (7 bp):
GTTTAGG
Found at i:2899521 original size:21 final size:21
Alignment explanation
Indices: 2899497--2899564 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
2899487 TATATATATA
* *
2899497 GTTTATGGTTTAGGGTTTAGT
1 GTTTATGCTTTAGGGTTTAGG
**
2899518 GTTTATGCTTTAAAGTTTAGG
1 GTTTATGCTTTAGGGTTTAGG
2899539 GTTTATGCTTTAGGGTTTAGG
1 GTTTATGCTTTAGGGTTTAGG
2899560 GTTTA
1 GTTTA
2899565 GGGTTTCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (21 bp):
GTTTATGCTTTAGGGTTTAGG
Found at i:2899681 original size:15 final size:15
Alignment explanation
Indices: 2899652--2899703 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
2899642 TAATTTACTT
2899652 TATATAGTTT-T-TA
1 TATATAGTTTATATA
2899665 TATATAGGTTATATATA
1 TATATA-GTT-TATATA
2899682 TATATAGTTTATATA
1 TATATAGTTTATATA
2899697 TACTATA
1 TA-TATA
2899704 CATAGTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.18
14 3 0.09
15 9 0.26
16 8 0.24
17 8 0.24
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:2899685 original size:17 final size:17
Alignment explanation
Indices: 2899663--2899703 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2899653 ATATAGTTTT
2899663 TATATATAGGTTATATA
1 TATATATAGGTTATATA
*
2899680 TATATATAGTTTATATA
1 TATATATAGGTTATATA
2899697 TACTATA
1 TA-TATA
2899704 CATAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (17 bp):
TATATATAGGTTATATA
Found at i:2899708 original size:20 final size:20
Alignment explanation
Indices: 2899674--2899719 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2899664 ATATATAGGT
*
2899674 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
2899693 TATATACTATACATAGTTTA
1 TATATACTATACATAGTTTA
*
2899713 TACATAC
1 TATATAC
2899720 ATGTACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:2899783 original size:21 final size:20
Alignment explanation
Indices: 2899758--2899802 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2899748 GGGGTTATGA
2899758 TTTAGGATTCAAGGTTAAGGG
1 TTTAGGATTC-AGGTTAAGGG
* * *
2899779 TTTAGGGTTCATGTTTAGGG
1 TTTAGGATTCAGGTTAAGGG
2899799 TTTA
1 TTTA
2899803 TGGTTAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.42
Consensus pattern (20 bp):
TTTAGGATTCAGGTTAAGGG
Found at i:2900224 original size:19 final size:19
Alignment explanation
Indices: 2900187--2900243 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2900177 TTTTCTATTC
*
2900187 CCTCTAAATTTCTCAATTTT
1 CCTCTAAA-TTCCCAATTTT
2900207 CCTCTAAATTCCCAA-TTT
1 CCTCTAAATTCCCAATTTT
*
2900225 CTCTTTAAATTCCCAATTT
1 C-CTCTAAATTCCCAATTT
2900244 CCTTATATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.12
19 19 0.58
20 10 0.30
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (19 bp):
CCTCTAAATTCCCAATTTT
Found at i:2900283 original size:19 final size:19
Alignment explanation
Indices: 2900189--2900286 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
2900179 TTCTATTCCC
* *
2900189 TCTAAATTTCTCAATTTTCC
1 TCTAAA-TTCCCAATTTTCA
2900209 TCTAAATTCCCAATTTCTC-
1 TCTAAATTCCCAATTT-TCA
* *
2900228 TTTAAATTCCCAATTTCCTTATA
1 TCTAAATTCCCAA-TT--TT-CA
2900251 TTCTCAAAACTTCCCAATTTTCA
1 -TCT--AAA-TTCCCAATTTTCA
2900274 TCTAAATTCCCAA
1 TCTAAATTCCCAA
2900287 ATAAAATAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
19 28 0.44
20 13 0.21
21 1 0.02
22 4 0.06
23 1 0.02
24 4 0.06
26 5 0.08
27 7 0.11
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (19 bp):
TCTAAATTCCCAATTTTCA
Found at i:2900394 original size:13 final size:13
Alignment explanation
Indices: 2900378--2900602 Score: 101
Period size: 13 Copynumber: 17.3 Consensus size: 13
2900368 ACTATATTAA
2900378 TATAAATATAGTT
1 TATAAATATAGTT
2900391 TATACATATATAGTT
1 TATA-A-ATATAGTT
* *
2900406 TACATATATAGTT
1 TATAAATATAGTT
* *
2900419 TTTATATATAGTT
1 TATAAATATAGTT
* *
2900432 CATATAAACATAATT
1 --TATAAATATAGTT
* *
2900447 TATATATATAGCT
1 TATAAATATAGTT
2900460 TAT-AATA-A--T
1 TATAAATATAGTT
* *
2900469 TATATAATTTA-TAA
1 TATA-AATATAGT-T
2900483 TATAAATATAGTT
1 TATAAATATAGTT
* *
2900496 TATATATATTGTT
1 TATAAATATAGTT
* *
2900509 TTTATATATAGTT
1 TATAAATATAGTT
* *
2900522 CATATAAACATAATT
1 --TATAAATATAGTT
* *
2900537 TATATATATAGCT
1 TATAAATATAGTT
2900550 TAT-AATA-A--T
1 TATAAATATAGTT
* *
2900559 TATATAATTTA-TAA
1 TATA-AATATAGT-T
2900573 TATAAATATAGTT
1 TATAAATATAGTT
*
2900586 TAGAAATATAGTT
1 TATAAATATAGTT
2900599 TATA
1 TATA
2900603 TATAAACTTA
Statistics
Matches: 158, Mismatches: 36, Indels: 36
0.69 0.16 0.16
Matches are distributed among these distances:
9 8 0.05
11 8 0.05
12 8 0.05
13 94 0.59
14 11 0.07
15 29 0.18
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAAATATAGTT
Found at i:2900491 original size:18 final size:17
Alignment explanation
Indices: 2900470--2900503 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2900460 TATAATAATT
2900470 ATATAATTTATAATATAA
1 ATATAATTTAT-ATATAA
*
2900488 ATATAGTTTATATATA
1 ATATAATTTATATATA
2900504 TTGTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATAATTTATATATAA
Found at i:2900496 original size:90 final size:90
Alignment explanation
Indices: 2900398--2900606 Score: 373
Period size: 90 Copynumber: 2.3 Consensus size: 90
2900388 GTTTATACAT
2900398 ATATAGTTTACATATATAGTTTTTATATATAGTTCATATAAACATAATTTATATATATAGCTTAT
1 ATATAGTTTACATATATAGTTTTTATATATAGTTCATATAAACATAATTTATATATATAGCTTAT
2900463 AATAATTATATAATTTATAATATAA
66 AATAATTATATAATTTATAATATAA
* *
2900488 ATATAGTTTATATATATTGTTTTTATATATAGTTCATATAAACATAATTTATATATATAGCTTAT
1 ATATAGTTTACATATATAGTTTTTATATATAGTTCATATAAACATAATTTATATATATAGCTTAT
2900553 AATAATTATATAATTTATAATATAA
66 AATAATTATATAATTTATAATATAA
* * *
2900578 ATATAGTTTAGAAATATAGTTTATATATA
1 ATATAGTTTACATATATAGTTTTTATATA
2900607 AACTTATATT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 113 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (90 bp):
ATATAGTTTACATATATAGTTTTTATATATAGTTCATATAAACATAATTTATATATATAGCTTAT
AATAATTATATAATTTATAATATAA
Found at i:2900625 original size:49 final size:48
Alignment explanation
Indices: 2900433--2900627 Score: 145
Period size: 49 Copynumber: 4.1 Consensus size: 48
2900423 TATATAGTTC
* *
2900433 ATATAAACATAATTTATATATATAGCTTATAATAATTATATAATTTATA
1 ATATAAACATAATTTAGAAATATAGCTTATAATAATTATAT-ATTTATA
* * * * * * * *
2900482 ATATAAATATAGTTTATATATATTG-TT-T--TTA-TATATA-GT-TC
1 ATATAAACATAATTTAGAAATATAGCTTATAATAATTATATATTTATA
* *
2900523 ATATAAACATAATTTATATATATAGCTTATAATAATTATATAATTTATA
1 ATATAAACATAATTTAGAAATATAGCTTATAATAATTATAT-ATTTATA
* * *
2900572 ATATAAATATAGTTTAGAAATATAGTTTATATATAAACTTATAT-TTTATA
1 ATATAAACATAATTTAGAAATATAGCTTATA-AT-AA-TTATATATTTATA
2900622 TATATA
1 -ATATA
2900628 TTATTTTTCC
Statistics
Matches: 117, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
41 23 0.20
42 3 0.03
43 2 0.02
44 5 0.04
45 4 0.03
46 5 0.04
47 2 0.02
48 3 0.03
49 49 0.42
50 8 0.07
51 7 0.06
52 6 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (48 bp):
ATATAAACATAATTTAGAAATATAGCTTATAATAATTATATATTTATA
Found at i:2901916 original size:39 final size:39
Alignment explanation
Indices: 2901825--2901919 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
2901815 TAATGATAAT
* **
2901825 GTGAAATAATTTAAGAAATTAAGAATTTAGAATGTTATT
1 GTGAAATAATTTAAGAAATTAAGAATTTAGAATATTAGA
* * *
2901864 CTTACAA-AATTTAAGAAATTAGGAATTTAGAATATTAGA
1 GTGA-AATAATTTAAGAAATTAAGAATTTAGAATATTAGA
*
2901903 GTGAAATACTTTAAGAA
1 GTGAAATAATTTAAGAA
2901920 TCACGAACAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
38 2 0.04
39 41 0.91
40 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (39 bp):
GTGAAATAATTTAAGAAATTAAGAATTTAGAATATTAGA
Found at i:2901951 original size:3 final size:3
Alignment explanation
Indices: 2901939--2902007 Score: 115
Period size: 3 Copynumber: 23.3 Consensus size: 3
2901929 AAAAACGAAT
2901939 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2901986 ATA ATA ATA ATA TATA A-A ATA A
1 ATA ATA ATA ATA -ATA ATA ATA A
2902008 ATCGGATATT
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.06
3 56 0.89
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2905126 original size:2 final size:2
Alignment explanation
Indices: 2905119--2905151 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2905109 TCAATCTACA
2905119 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 A
2905152 ATTTACGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2905246 original size:13 final size:13
Alignment explanation
Indices: 2905230--2905275 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
2905220 AGCAATGTAA
2905230 GTCATAAATGCGT
1 GTCATAAATGCGT
* *
2905243 GTCATAAATGAGC
1 GTCATAAATGCGT
2905256 GTCATAAATGCGT
1 GTCATAAATGCGT
*
2905269 GTAATAA
1 GTCATAA
2905276 CTGTGCGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:2905283 original size:26 final size:26
Alignment explanation
Indices: 2905230--2905287 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
2905220 AGCAATGTAA
*
2905230 GTCATAAATGCGTGTCATAAATGAGC
1 GTCATAAATGCGTGTAATAAATGAGC
* *
2905256 GTCATAAATGCGTGTAATAACTGTGC
1 GTCATAAATGCGTGTAATAAATGAGC
2905282 GTCATA
1 GTCATA
2905288 GATTTATGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (26 bp):
GTCATAAATGCGTGTAATAAATGAGC
Found at i:2918097 original size:2 final size:2
Alignment explanation
Indices: 2918090--2918114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2918080 TCAATCTACA
2918090 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
2918115 ATTTCTGAAA
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:2918494 original size:85 final size:85
Alignment explanation
Indices: 2918171--2918482 Score: 473
Period size: 85 Copynumber: 3.7 Consensus size: 85
2918161 AATGGCGTGT
* * *
2918171 GCTTCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
**
2918236 CA-AACAGATTTATGACGGGG
66 CATATTA-ATTTATGACGGGG
* *
2918256 GCTTCAATGACGCACAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
*
2918321 CATCTTAATTTATGACGGGG
66 CATATTAATTTATGACGGGG
* * *
2918341 GCTTTAATGACGCGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACATACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
*
2918406 CATATTAATTTATGACGGAG
66 CATATTAATTTATGACGGGG
* * *
2918426 GCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTTATAGATTTATGACACACAA
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAA
2918483 TTGCGCGTCA
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
85 204 1.00
86 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGT
CATATTAATTTATGACGGGG
Found at i:2920556 original size:23 final size:23
Alignment explanation
Indices: 2920526--2920666 Score: 191
Period size: 23 Copynumber: 6.3 Consensus size: 23
2920516 CCGAGGGTTT
2920526 TATGTGGTCCTTCGGGACAAATC
1 TATGTGGTCCTTCGGGACAAATC
2920549 TATGTGGTCCTTCGGGACAAATC
1 TATGTGGTCCTTCGGGACAAATC
* *
2920572 TATATGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAATC
* *
2920595 TATGTGGTCATTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAATC
*
2920618 TATGTTGTCCTTCGGGACAAA--
1 TATGTGGTCCTTCGGGACAAATC
*
2920639 TATGTGG-CACTTCGGTACAAAT-
1 TATGTGGTC-CTTCGGGACAAATC
2920661 TATGTG
1 TATGTG
2920667 AGCAGTGGTG
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
20 1 0.01
21 17 0.16
22 6 0.06
23 84 0.78
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAATC
Found at i:2921837 original size:57 final size:60
Alignment explanation
Indices: 2921758--2921901 Score: 168
Period size: 57 Copynumber: 2.4 Consensus size: 60
2921748 ATAAAAATTA
* * * * *
2921758 AAAATATTTTGATAATAATATTAATTATTATTTCAAATT-T-AATATTTTTAT-AATGTAT
1 AAAATA-TTTCATGATAATATTAATTATTATTTAAAATTCTAAATAATTTTATAAATATAT
2921816 AAAATATTTCATGATAATATTAATTATTATTTAAAATTCTAAAATAATTTTATAAATATAT
1 AAAATATTTCATGATAATATTAATTATTATTTAAAATTCT-AAATAATTTTATAAATATAT
* *
2921877 ACAATTATTCTCATGATAATTTTAA
1 A-AAATATT-TCATGATAATATTAA
2921902 AATATCTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
57 29 0.40
58 7 0.10
60 10 0.14
61 7 0.10
62 6 0.08
63 14 0.19
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (60 bp):
AAAATATTTCATGATAATATTAATTATTATTTAAAATTCTAAATAATTTTATAAATATAT
Found at i:2929350 original size:28 final size:28
Alignment explanation
Indices: 2929310--2929400 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 28
2929300 AATTGAATCT
* *
2929310 TTTAGATATATATTTTGACAAAAAATAC
1 TTTAGATAAATATTTTGACAAAAAATAA
* **
2929338 TTTAGATACATATTTTGACTAAATTGATAA
1 TTTAGATAAATATTTTGAC-AAA-AAATAA
2929368 TTTA-AGTAAATATTTTGATCAAAAAATAA
1 TTTAGA-TAAATATTTTGA-CAAAAAATAA
2929397 TTTA
1 TTTA
2929401 AGTGTTTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
28 18 0.35
29 12 0.23
30 21 0.40
31 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (28 bp):
TTTAGATAAATATTTTGACAAAAAATAA
Found at i:2930082 original size:2 final size:2
Alignment explanation
Indices: 2930071--2930135 Score: 73
Period size: 2 Copynumber: 33.0 Consensus size: 2
2930061 TTTCGAGCTT
* *
2930071 TA TA TA -A TA TA TG TA TA TCA CA TA TGA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA
2930113 TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
2930136 ATTATAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
1 3 0.06
2 49 0.91
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2939403 original size:24 final size:26
Alignment explanation
Indices: 2939358--2939409 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
2939348 CGTTCGTGAA
*
2939358 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
2939384 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
2939408 CG
1 CG
2939410 AACAGATGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:2942823 original size:2 final size:2
Alignment explanation
Indices: 2942818--2942846 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2942808 CGTGTGTGTC
2942818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2942847 GCTTTACTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2943617 original size:41 final size:42
Alignment explanation
Indices: 2943558--2943690 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 42
2943548 GTGTTTTTCG
* * *
2943558 TTCACAAACTCCGTTAAAGGTTATG-TTTTTAGCGGCGTTTT
1 TTCACAAACACCGTTAAAGGTTATGATATTTAGCGGCATTTT
* * * * *
2943599 TTCACAAACACAGCTAAAGGTAACGATATTTAGCGGTATTTT
1 TTCACAAACACCGTTAAAGGTTATGATATTTAGCGGCATTTT
* * * *
2943641 TTTACAAACGCCGTTAAAGGTTATGATATTTAACGGTATTTT
1 TTCACAAACACCGTTAAAGGTTATGATATTTAGCGGCATTTT
2943683 TTC-CAAAC
1 TTCACAAAC
2943691 GCCGCTATTT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 25 0.33
42 50 0.67
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (42 bp):
TTCACAAACACCGTTAAAGGTTATGATATTTAGCGGCATTTT
Found at i:2944058 original size:21 final size:21
Alignment explanation
Indices: 2944034--2944092 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
2944024 ATTATCCAAT
* *
2944034 AAACTTGACATCCATAAGAAC
1 AAACTTGAAATCCATAACAAC
*
2944055 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
2944076 AGACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
2944093 TAAATCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:2956116 original size:41 final size:40
Alignment explanation
Indices: 2956059--2956173 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 40
2956049 CACGCGAATC
* *
2956059 TACTAGTCTTTAGCGGCGTTTGTCTAAAAACG-ATATTAAAG
1 TACTAGT-TTTAGCGGCATTTGTCTAAAAACGCA-ACTAAAG
* *
2956100 TACTAGGTTTTAGCGGCATTTGTCAAAAAATGCAACTAAAG
1 TACTA-GTTTTAGCGGCATTTGTCTAAAAACGCAACTAAAG
*
2956141 TACTAAGTTTTAGCGGTATTTGTCTAAAAACGC
1 TACT-AGTTTTAGCGGCATTTGTCTAAAAACGC
2956174 CATGATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 60 0.94
42 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (40 bp):
TACTAGTTTTAGCGGCATTTGTCTAAAAACGCAACTAAAG
Found at i:2960353 original size:194 final size:194
Alignment explanation
Indices: 2960018--2960408 Score: 773
Period size: 194 Copynumber: 2.0 Consensus size: 194
2960008 CGAGGAGTGT
2960018 CAGACTTCAGGGAGTAAGAAGGGCTGACGCAAATTTTGAGTAAATGCCAATGAAATCAGAGAGGA
1 CAGACTTCAGGGAGTAAGAAGGGCTGACGCAAATTTTGAGTAAATGCCAATGAAATCAGAGAGGA
2960083 AGGTATATCTCAACACTACTCTAGTGTTCTTTTGAGTTTGATTTGTTGTTTTAAGTGAGTATAGG
66 AGGTATATCTCAACACTACTCTAGTGTTCTTTTGAGTTTGATTTGTTGTTTTAAGTGAGTATAGG
*
2960148 TCGATCAAGACCTAACTTTTAACGCGGAGGAAACAAAGTTTGGAGGGGATCTAAGACTTTGCCG
131 TCGAGCAAGACCTAACTTTTAACGCGGAGGAAACAAAGTTTGGAGGGGATCTAAGACTTTGCCG
2960212 CAGACTTCAGGGAGTAAGAAGGGCTGACGCAAATTTTGAGTAAATGCCAATGAAATCAGAGAGGA
1 CAGACTTCAGGGAGTAAGAAGGGCTGACGCAAATTTTGAGTAAATGCCAATGAAATCAGAGAGGA
2960277 AGGTATATCTCAACACTACTCTAGTGTTCTTTTGAGTTTGATTTGTTGTTTTAAGTGAGTATAGG
66 AGGTATATCTCAACACTACTCTAGTGTTCTTTTGAGTTTGATTTGTTGTTTTAAGTGAGTATAGG
2960342 TCGAGCAAGACCTAACTTTTAACGCGGAGGAAACAAAGTTTGGAGGGGATCTAAGACTTTGCCG
131 TCGAGCAAGACCTAACTTTTAACGCGGAGGAAACAAAGTTTGGAGGGGATCTAAGACTTTGCCG
2960406 CAG
1 CAG
2960409 GACCAGGAGG
Statistics
Matches: 196, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 196 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (194 bp):
CAGACTTCAGGGAGTAAGAAGGGCTGACGCAAATTTTGAGTAAATGCCAATGAAATCAGAGAGGA
AGGTATATCTCAACACTACTCTAGTGTTCTTTTGAGTTTGATTTGTTGTTTTAAGTGAGTATAGG
TCGAGCAAGACCTAACTTTTAACGCGGAGGAAACAAAGTTTGGAGGGGATCTAAGACTTTGCCG
Found at i:2966894 original size:31 final size:31
Alignment explanation
Indices: 2966851--2966909 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2966841 TCTGTTTTCG
2966851 CCCCCTAAAATTTTATAAGTTCAAGTTCGTC
1 CCCCCTAAAATTTTATAAGTTCAAGTTCGTC
* *
2966882 CCCCCTAGAATTTTATAAGTTCTAGTTC
1 CCCCCTAAAATTTTATAAGTTCAAGTTC
2966910 ACCCCCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (31 bp):
CCCCCTAAAATTTTATAAGTTCAAGTTCGTC
Done.