Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 17
Found at i:2670362 original size:51 final size:51
Alignment explanation
Indices: 2670279--2670407 Score: 206
Period size: 51 Copynumber: 2.5 Consensus size: 51
2670269 ATTAATAAAC
* *
2670279 TTTT-TATTATTTTTATTATAAATTTAATATTATTTCATTTATTTAAATTA
1 TTTTATATTATTTTTATTATAAATCTAAAATTATTTCATTTATTTAAATTA
* * *
2670329 TTTTATATTATTTTTATTATAAATCTAAAATTATTTCCTTTATTTTAATTG
1 TTTTATATTATTTTTATTATAAATCTAAAATTATTTCATTTATTTAAATTA
2670380 TTTTATATTATTTTTATTATAAATCTAA
1 TTTTATATTATTTTTATTATAAATCTAA
2670408 TATTTTATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
50 4 0.05
51 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (51 bp):
TTTTATATTATTTTTATTATAAATCTAAAATTATTTCATTTATTTAAATTA
Found at i:2679945 original size:20 final size:20
Alignment explanation
Indices: 2679920--2679957 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2679910 CATTGAACAT
2679920 GGGGGTTTCAAAACCTATGA
1 GGGGGTTTCAAAACCTATGA
2679940 GGGGGTTTCAAAACCTAT
1 GGGGGTTTCAAAACCTAT
2679958 AGGCCAATTT
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:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
GGGGGTTTCAAAACCTATGA
Found at i:2680081 original size:23 final size:23
Alignment explanation
Indices: 2680055--2680112 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2680045 TTTTAAGACT
2680055 TTTTTAAAAATTAATTTTTT-TAA
1 TTTTTAAAAATT-ATTTTTTATAA
* *
2680078 TTTTTTAACATTATTTTTTATAA
1 TTTTTAAAAATTATTTTTTATAA
* *
2680101 ATTTGAAAAATT
1 TTTTTAAAAATT
2680113 CTTGAATTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTTAAAAATTATTTTTTATAA
Found at i:2682275 original size:22 final size:22
Alignment explanation
Indices: 2682245--2682320 Score: 134
Period size: 22 Copynumber: 3.4 Consensus size: 22
2682235 TGCCTTATTT
2682245 TTTTCGAAACCTCAAGGAGAGGG
1 TTTT-GAAACCTCAAGGAGAGGG
2682268 TTTTGAAACCTCAAGGAGAGGG
1 TTTTGAAACCTCAAGGAGAGGG
*
2682290 TTTTGAAACCTTAAGGAGAGGG
1 TTTTGAAACCTCAAGGAGAGGG
2682312 TTTTGAAAC
1 TTTTGAAAC
2682321 ATCTTCTCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 48 0.92
23 4 0.08
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (22 bp):
TTTTGAAACCTCAAGGAGAGGG
Found at i:2683451 original size:21 final size:21
Alignment explanation
Indices: 2683425--2683474 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2683415 CATAGTGTAC
*
2683425 CGATGCACTAGCCGTATGCAT
1 CGATGCACTAGCCCTATGCAT
*
2683446 CGATGCACTATCCCTATGCAT
1 CGATGCACTAGCCCTATGCAT
2683467 CGATGCAC
1 CGATGCAC
2683475 CAGACGCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (21 bp):
CGATGCACTAGCCCTATGCAT
Found at i:2683808 original size:16 final size:16
Alignment explanation
Indices: 2683787--2683824 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2683777 ACATCTTTCA
2683787 TTGTGAGTTTGCAAAT
1 TTGTGAGTTTGCAAAT
*
2683803 TTGTGAGTTTGCGAAT
1 TTGTGAGTTTGCAAAT
2683819 TTGTGA
1 TTGTGA
2683825 ATTTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (16 bp):
TTGTGAGTTTGCAAAT
Found at i:2691538 original size:15 final size:15
Alignment explanation
Indices: 2691518--2691547 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2691508 ATTTAACAAG
2691518 GGGGAGAAGTGTTAA
1 GGGGAGAAGTGTTAA
2691533 GGGGAGAAGTGTTAA
1 GGGGAGAAGTGTTAA
2691548 AGTAAGGGGG
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:0.00, G:0.47, T:0.20
Consensus pattern (15 bp):
GGGGAGAAGTGTTAA
Found at i:2697473 original size:21 final size:21
Alignment explanation
Indices: 2697449--2697516 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
2697439 TTAAAGCCCT
2697449 TTGAAGCATTAATTTTGCTCA
1 TTGAAGCATTAATTTTGCTCA
*
2697470 TTGAAGCATTAATTTCGCTCA
1 TTGAAGCATTAATTTTGCTCA
*
2697491 TTGAAACATTAATTTTGCTCA
1 TTGAAGCATTAATTTTGCTCA
2697512 TTGAA
1 TTGAA
2697517 TGCAAGGCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (21 bp):
TTGAAGCATTAATTTTGCTCA
Found at i:2701050 original size:14 final size:14
Alignment explanation
Indices: 2701025--2701062 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2701015 AGACAATATT
2701025 AATAAT-AATATAA
1 AATAATAAATATAA
*
2701038 TATAATAAATATAA
1 AATAATAAATATAA
2701052 AATAATAAATA
1 AATAATAAATA
2701063 ATACTATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAATAAATATAA
Found at i:2701222 original size:24 final size:27
Alignment explanation
Indices: 2701177--2701232 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
2701167 TTTCAAAAAT
2701177 TATACATTTTCAAAAACCATA-TAT-TA
1 TATACATTTTCAAAAA-CATATTATATA
**
2701203 TATACATTTTCTGAAA-ATATTATATA
1 TATACATTTTCAAAAACATATTATATA
2701229 TATA
1 TATA
2701233 TTAAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 3 0.12
26 20 0.77
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (27 bp):
TATACATTTTCAAAAACATATTATATA
Found at i:2710936 original size:20 final size:21
Alignment explanation
Indices: 2710911--2710950 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2710901 TCAATCTTCA
* *
2710911 CTTC-AATTCCTTTTTTTCTG
1 CTTCAAATTCATTCTTTTCTG
2710931 CTTCAAATTCATTCTTTTCT
1 CTTCAAATTCATTCTTTTCT
2710951 ATTTCCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.57
Consensus pattern (21 bp):
CTTCAAATTCATTCTTTTCTG
Found at i:2714649 original size:16 final size:16
Alignment explanation
Indices: 2714628--2714658 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2714618 ATATATTATA
2714628 TTTTAAAAATAATATG
1 TTTTAAAAATAATATG
*
2714644 TTTTAAAAATTATAT
1 TTTTAAAAATAATAT
2714659 ATTATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTTAAAAATAATATG
Found at i:2714698 original size:39 final size:40
Alignment explanation
Indices: 2714618--2714722 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
2714608 ACTATATAAC
* * * *
2714618 ATATATTATATTTTAAAAATAATATGTTTTAAAAATTATAT
1 ATATATTATATTTTTAAAA-ACTATGTTTCAAAAATCATAT
*
2714659 AT-TATATATATTTTTAAAAACTAT-TTTCAAAAGTCATAT
1 ATATAT-TATATTTTTAAAAACTATGTTTCAAAAATCATAT
*
2714698 ATATATTATATGTTTTCAAAACTAT
1 ATATATTATAT-TTTTAAAAACTAT
2714723 ATAATATATT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
39 19 0.35
40 22 0.40
41 14 0.25
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (40 bp):
ATATATTATATTTTTAAAAACTATGTTTCAAAAATCATAT
Found at i:2714730 original size:23 final size:21
Alignment explanation
Indices: 2714699--2714756 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
2714689 AAGTCATATA
* *
2714699 TATATTATATGTTTTCAAAAC
1 TATATAATATATTTTCAAAAC
2714720 TATATAATATATTTTCAAAA-
1 TATATAATATATTTTCAAAAC
2714740 -AT-T-ATATATTTTCAAAA
1 TATATAATATATTTTCAAAA
2714757 ACCATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 14 0.40
18 1 0.03
19 2 0.06
21 18 0.51
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATAATATATTTTCAAAAC
Found at i:2714748 original size:17 final size:17
Alignment explanation
Indices: 2714702--2714757 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
2714692 TCATATATAT
*
2714702 ATTATATGTTTTCAAAA
1 ATTATATATTTTCAAAA
2714719 CTATATAATATATTTTCAAAA
1 --AT-T-ATATATTTTCAAAA
2714740 ATTATATATTTTCAAAA
1 ATTATATATTTTCAAAA
2714757 A
1 A
2714758 CCATTTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 15 0.44
18 1 0.03
19 4 0.12
20 1 0.03
21 13 0.38
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTATATATTTTCAAAA
Found at i:2714766 original size:17 final size:17
Alignment explanation
Indices: 2714726--2714766 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2714716 AAACTATATA
**
2714726 ATATATTTTCAAAAATT
1 ATATATTTTCAAAAACC
2714743 ATATATTTTCAAAAACC
1 ATATATTTTCAAAAACC
*
2714760 ATTTATT
1 ATATATT
2714767 ACATACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTTTCAAAAACC
Found at i:2720101 original size:35 final size:35
Alignment explanation
Indices: 2720001--2720120 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 35
2719991 TTGATCAAGC
* *** * * *
2720001 TGGTAATTCCTTATATAAGTTCATTTCTGATGAAGC
1 TGGTAATTCCTTATATAGGTTCAACACCGAT-TAGT
2720037 TGGTAA-TCCTTTATATAGGTTCAACACCGATT-GAT
1 TGGTAATTCC-TTATATAGGTTCAACACCGATTAG-T
* **
2720072 TGGTAATTCCTTATATAGGTTTAGTACCGATTAGT
1 TGGTAATTCCTTATATAGGTTCAACACCGATTAGT
*
2720107 TGGTAATTTCTTAT
1 TGGTAATTCCTTAT
2720121 GGATCTAAGG
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
34 1 0.01
35 42 0.61
36 26 0.38
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (35 bp):
TGGTAATTCCTTATATAGGTTCAACACCGATTAGT
Found at i:2724398 original size:36 final size:36
Alignment explanation
Indices: 2724358--2724437 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
2724348 AAGTCTTTGT
*
2724358 AGGTTCAGCT-TTGATCAACCTAGTAATTCCTTATAA
1 AGGTTCAGCTCTT-ATCAACCTAGTAATCCCTTATAA
* * * *
2724394 AGGTTTAGCTCTTATCAAGCTGGTAATCCCTTATAC
1 AGGTTCAGCTCTTATCAACCTAGTAATCCCTTATAA
2724430 AGGTTCAG
1 AGGTTCAG
2724438 TACCGATCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (36 bp):
AGGTTCAGCTCTTATCAACCTAGTAATCCCTTATAA
Found at i:2724461 original size:35 final size:35
Alignment explanation
Indices: 2724380--2724497 Score: 114
Period size: 35 Copynumber: 3.3 Consensus size: 35
2724370 GATCAACCTA
* * **
2724380 GTAATTCCTTATAAAGGTTTAGCT-CTTATCAAGCTG
1 GTAATTCCTTATACAGGTTCA-CTACCGATC-AGCTG
* * *
2724416 GTAATCCCTTATACAGGTTCAGTACCGATC-GATTG
1 GTAATTCCTTATACAGGTTCACTACCGATCAG-CTG
*
2724451 GTAATTCCTTATATAGGTTCACTACCGATCAGCTG
1 GTAATTCCTTATACAGGTTCACTACCGATCAGCTG
*
2724486 GAAATTCCTTAT
1 GTAATTCCTTAT
2724498 GGATCCAAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
34 1 0.01
35 43 0.64
36 23 0.34
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (35 bp):
GTAATTCCTTATACAGGTTCACTACCGATCAGCTG
Found at i:2739698 original size:44 final size:44
Alignment explanation
Indices: 2739639--2739747 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
2739629 TGGCTCATTT
* * *
2739639 ATCACACAAGGAGTTGGATCAGCATCAACATTT-TGTTTGATTCC
1 ATCACATAAGGAGTTGGATCAGCATCAACATTTAT-CTCGATTCC
* * *
2739683 CTCACATAAGAAGTTGGATCAGTATCAACATTTATCTCGATTCC
1 ATCACATAAGGAGTTGGATCAGCATCAACATTTATCTCGATTCC
2739727 ATCACATAAGGAGTTGGATCA
1 ATCACATAAGGAGTTGGATCA
2739748 ATGATAACTC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 55 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCACATAAGGAGTTGGATCAGCATCAACATTTATCTCGATTCC
Found at i:2753598 original size:18 final size:18
Alignment explanation
Indices: 2753577--2753616 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2753567 CTTTCGAGAG
2753577 ATTGTCATTTTTCTAGAA
1 ATTGTCATTTTTCTAGAA
2753595 ATTGTCATTTTTCTAGAA
1 ATTGTCATTTTTCTAGAA
2753613 ATTG
1 ATTG
2753617 ATTCTTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (18 bp):
ATTGTCATTTTTCTAGAA
Found at i:2754453 original size:44 final size:44
Alignment explanation
Indices: 2754343--2754454 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
2754333 CATTCCGCTC
* * * **
2754343 GATTCCATCACATAAGTAGTTGAATAAGGATTATTACTTTGCTT
1 GATTCCATCACATAAGGAGTTGGATAAGCATTACAACTTTGCTT
* * *
2754387 GATTCTATCACATAAGGAGTTGGATCAGCATTACAATTTTGCTT
1 GATTCCATCACATAAGGAGTTGGATAAGCATTACAACTTTGCTT
*
2754431 GTTTCCATCACATAAGGAGTTGGA
1 GATTCCATCACATAAGGAGTTGGA
2754455 ACAACATTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (44 bp):
GATTCCATCACATAAGGAGTTGGATAAGCATTACAACTTTGCTT
Found at i:2761116 original size:15 final size:15
Alignment explanation
Indices: 2761091--2761130 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
2761081 ATTTAGAAAA
2761091 TGATGGCTACTCAGTT
1 TGAT-GCTACTCAGTT
2761107 TGATGCTACTCAGTT
1 TGATGCTACTCAGTT
*
2761122 TGATACTAC
1 TGATGCTAC
2761131 GATCAAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (15 bp):
TGATGCTACTCAGTT
Found at i:2766281 original size:397 final size:397
Alignment explanation
Indices: 2765548--2766339 Score: 1521
Period size: 397 Copynumber: 2.0 Consensus size: 397
2765538 TGATGGCTTA
2765548 TGGATTTGTATCATTGTATAAACTGTATCTTGGAGATACAGATTTGTAAAGTACAGCTCTGATCA
1 TGGATTTGTATCATTGTATAAACTGTATCTTGGAGATACAGATTTGTAAAGTACAGCTCTGATCA
*
2765613 AGCTGGAAAATTTTTATGGACCTAATGTGACTCTTAGGTAGGCTCTGCGGCCCTAAGATCATTCT
66 AGCTGGAAAATTTTTATGGACCTAATGTGACTCTTAGGTAGGCTCTGCAGCCCTAAGATCATTCT
*
2765678 CGGGTAGGCCCTACGGCCCTAAGATATGTTCTTAGGTAGGCCACATGGCCCCAAACTTTCTTGGG
131 CGGGTAGGCCCTACGGCCCTAAGATATGTTCTTAGGTAAGCCACATGGCCCCAAACTTTCTTGGG
2765743 TAGGCTCTCAGGCCCTAAGATATTCCCTTAGGTTAACTCTTTGTACGATGGTTTTGAAAATACGA
196 TAGGCTCTCAGGCCCTAAGATATTCCCTTAGGTTAACTCTTTGTACGATGGTTTTGAAAATACGA
*
2765808 GTTTAAAAAGCTCTACTACAGTATGGTTTATGGGATTTATTGAACTATCATTTGATTAGTGTACC
261 GTTTAAAAAGCTCTACTACAGTATGGTTTATGGGATTTACTGAACTATCATTTGATTAGTGTACC
2765873 TATTATGATTTTATCGTACTGATGGAACACACTAGACATCCTATTCGACCTCATGAAAACGTGAC
326 TATTATGATTTTATCGTACTGATGGAACACACTAGACATCCTATTCGACCTCATGAAAACGTGAC
2765938 TGTATCT
391 TGTATCT
2765945 TGGATTTGTATCATTGTATAAACTGTATCTTGGAGATACAGATTTGTAAAGTACAGCTCTGATCA
1 TGGATTTGTATCATTGTATAAACTGTATCTTGGAGATACAGATTTGTAAAGTACAGCTCTGATCA
2766010 AGCTGGAAAATTTTTATGGACCTAATGTGACTCTTAGGTAGGCTCTGCAGCCCTAAGATCATTCT
66 AGCTGGAAAATTTTTATGGACCTAATGTGACTCTTAGGTAGGCTCTGCAGCCCTAAGATCATTCT
* * *
2766075 CGGGTAGGCCTTACGGCCCTAAGATATGTTCTTAGGTAAGCCACGTGGCCCCGAACTTTCTTGGG
131 CGGGTAGGCCCTACGGCCCTAAGATATGTTCTTAGGTAAGCCACATGGCCCCAAACTTTCTTGGG
*
2766140 TAGGCTCTCAGGCCCTAAGATGTTCCCTTAGGTTAACTCTTTGTACGATGGTTTTGAAAATACGA
196 TAGGCTCTCAGGCCCTAAGATATTCCCTTAGGTTAACTCTTTGTACGATGGTTTTGAAAATACGA
2766205 GTTTAAAAAGCTCTACTACAGTATGGTTTATGGGATTTACTGAACTATCATTTGATTAGTGTACC
261 GTTTAAAAAGCTCTACTACAGTATGGTTTATGGGATTTACTGAACTATCATTTGATTAGTGTACC
2766270 TATTATGATTTTATCGTACTGATGGAACACACTAGACATCCTATTCGACCTCATGAAAACGTGAC
326 TATTATGATTTTATCGTACTGATGGAACACACTAGACATCCTATTCGACCTCATGAAAACGTGAC
2766335 TGTAT
391 TGTAT
2766340 GGAAGGTTTC
Statistics
Matches: 388, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
397 388 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (397 bp):
TGGATTTGTATCATTGTATAAACTGTATCTTGGAGATACAGATTTGTAAAGTACAGCTCTGATCA
AGCTGGAAAATTTTTATGGACCTAATGTGACTCTTAGGTAGGCTCTGCAGCCCTAAGATCATTCT
CGGGTAGGCCCTACGGCCCTAAGATATGTTCTTAGGTAAGCCACATGGCCCCAAACTTTCTTGGG
TAGGCTCTCAGGCCCTAAGATATTCCCTTAGGTTAACTCTTTGTACGATGGTTTTGAAAATACGA
GTTTAAAAAGCTCTACTACAGTATGGTTTATGGGATTTACTGAACTATCATTTGATTAGTGTACC
TATTATGATTTTATCGTACTGATGGAACACACTAGACATCCTATTCGACCTCATGAAAACGTGAC
TGTATCT
Found at i:2767975 original size:42 final size:43
Alignment explanation
Indices: 2767859--2767977 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 43
2767849 ATTATCATCT
* * * *
2767859 CCATCTCACTCCATTTA-CC--C-TACTTCATCTACTTATTCA
1 CCATCTCACTCCATTCATCCTTCATACTTCATCTTCTCATTAA
* * *
2767898 CTATCTCACTCCATTCATCCTTCA-ACTTAAACTTCTCATTAA
1 CCATCTCACTCCATTCATCCTTCATACTTCATCTTCTCATTAA
*
2767940 CCATCTCACTTCATTCATCCTT-ATACTTCATCTTCTCA
1 CCATCTCACTCCATTCATCCTTCATACTTCATCTTCTCA
2767978 CGCCATCCCC
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 15 0.23
40 2 0.03
41 1 0.02
42 46 0.72
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.39
Consensus pattern (43 bp):
CCATCTCACTCCATTCATCCTTCATACTTCATCTTCTCATTAA
Found at i:2776777 original size:36 final size:36
Alignment explanation
Indices: 2776713--2776801 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
2776703 TGTATGATAT
** * * *
2776713 AAATAAAAAGAGTATGGATTTGAAATGATCTGATTTCG
1 AAATAAAAA-AGTACAGTTTTGAAATGATATGAATT-G
* *
2776751 AAA-AGAAAAGTACAGTTTTGCAATGATATGAATTG
1 AAATAAAAAAGTACAGTTTTGAAATGATATGAATTG
2776786 AAATAAAAAAGTACAG
1 AAATAAAAAAGTACAG
2776802 ATCTAAAATG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
35 4 0.10
36 31 0.74
37 4 0.10
38 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (36 bp):
AAATAAAAAAGTACAGTTTTGAAATGATATGAATTG
Found at i:2788860 original size:6 final size:6
Alignment explanation
Indices: 2788849--2788873 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2788839 ATTAAATCCT
2788849 GAATTA GAATTA GAATTA GAATTA G
1 GAATTA GAATTA GAATTA GAATTA G
2788874 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (6 bp):
GAATTA
Found at i:2802940 original size:73 final size:74
Alignment explanation
Indices: 2802843--2803016 Score: 217
Period size: 73 Copynumber: 2.4 Consensus size: 74
2802833 GATCATATTC
* * * * * *
2802843 ATCAACTTGTTCAATATCTAAAAGTATCAATCATCATCGCATAAGTATCAATATTTTAAATTTCA
1 ATCAACTTTTTCAATATTTAAAAGTATCAATCATCACCACATAACTATCAATATATTAAATTTCA
*
2802908 ATCTT-TTT
66 ATCTTATCT
* * * * *
2802916 ATCAAGTTTTTCAATTTTTAAAAGTATCAATCATTACCACATAACTATCAATATATTAACTTTCG
1 ATCAACTTTTTCAATATTTAAAAGTATCAATCATCACCACATAACTATCAATATATTAAATTTCA
2802981 ATCTTATCT
66 ATCTTATCT
*
2802990 -TCAACTTTTTCAATATTAAAAAGTATC
1 ATCAACTTTTTCAATATTTAAAAGTATC
2803017 GATATTTAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 83 0.98
74 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (74 bp):
ATCAACTTTTTCAATATTTAAAAGTATCAATCATCACCACATAACTATCAATATATTAAATTTCA
ATCTTATCT
Found at i:2803296 original size:77 final size:77
Alignment explanation
Indices: 2803065--2803296 Score: 220
Period size: 77 Copynumber: 3.0 Consensus size: 77
2803055 GCTTAAACTA
* * * * *
2803065 TTTTATTAATAAAAATATTAACATTACAGATCGCAACCTATTTCTTAATGAACCATGACATTCTT
1 TTTTATTAATAAAAATATTAACATTACATATCACAACATATTTCTTAGTGAACTATGACATTCTT
**
2803130 AAGCACAA-CAT
66 GGGCACAACCAT
* * * *
2803141 ATTTATT-A-AAAAATAGTAACATTACATTGCAGATCACAACCTTATTTCTTAGTGAA-TCATTA
1 TTTTATTAATAAAAATATTAACATTACA-T----ATCACAA-CATATTTCTTAGTGAACT-ATGA
* *** *
2803203 CATTTTTGGATGCAACCTT
59 CATTCTTGGGCACAACCAT
*
2803222 TTTTATTAATAAAAATATTAACATTACATATCACAACATATTTCTTAGTGAACTATGACATGCTT
1 TTTTATTAATAAAAATATTAACATTACATATCACAACATATTTCTTAGTGAACTATGACATTCTT
2803287 GGGCACAACC
66 GGGCACAACC
2803297 GTAGTTCTTA
Statistics
Matches: 121, Mismatches: 24, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
74 17 0.14
75 1 0.01
76 6 0.05
77 30 0.25
78 8 0.07
79 6 0.05
80 26 0.21
81 8 0.07
82 2 0.02
83 17 0.14
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTACATATCACAACATATTTCTTAGTGAACTATGACATTCTT
GGGCACAACCAT
Found at i:2803563 original size:77 final size:77
Alignment explanation
Indices: 2803404--2803563 Score: 218
Period size: 77 Copynumber: 2.1 Consensus size: 77
2803394 TTAGGTGCAA
* *
2803404 CTATTTTATTACTAAAAATATTAAGATTCTAGATTACAACCTACTTTCTTAGTGACCATGACATT
1 CTATTTTATTACTAAAAATATTAACATTCTAGATCACAACCTACTTTCTTAGTGACCATGACATT
* *
2803469 TTTGGGCGCAAC
66 ATTGGGCGAAAC
*
2803481 CTATTTTATTACTAAAAATGTTAACATTAC-AGA-CACAACCTA-TTTCTTAGTGAACCATGACA
1 CTATTTTATTACTAAAAATATTAACATT-CTAGATCACAACCTACTTTCTTAGTG-ACCATGACA
*
2803543 TTATTGGGTGAAAC
64 TTATTGGGCGAAAC
2803557 CGTATTT
1 C-TATTT
2803564 CTTATATATA
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
75 10 0.14
76 29 0.39
77 34 0.46
78 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (77 bp):
CTATTTTATTACTAAAAATATTAACATTCTAGATCACAACCTACTTTCTTAGTGACCATGACATT
ATTGGGCGAAAC
Found at i:2806666 original size:29 final size:28
Alignment explanation
Indices: 2806627--2806707 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
2806617 AATTATTATA
*
2806627 TAAAAATATAAAATTATTAAAATAATATT
1 TAAAAATATAAAAATATTAAAATAAT-TT
* *
2806656 TAAAAGTATAAAAACATTAAAATAATTT
1 TAAAAATATAAAAATATTAAAATAATTT
* * *
2806684 TGAAATTCTAAAAATATTTAAAAT
1 TAAAAATATAAAAATA-TTAAAAT
2806708 TTCATGTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 14 0.32
29 30 0.68
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (28 bp):
TAAAAATATAAAAATATTAAAATAATTT
Found at i:2809378 original size:32 final size:29
Alignment explanation
Indices: 2809319--2809378 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
2809309 ATAATATATA
*
2809319 TTATAAAATTATTTATTAAAAAAATAAAC
1 TTATAAAATTAATTATTAAAAAAATAAAC
*
2809348 TTATAGAAATATAATTAGTTAAAAACATAAA
1 TTATA-AAAT-TAATTA-TTAAAAAAATAAA
2809379 ATCACCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 5 0.19
32 12 0.46
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (29 bp):
TTATAAAATTAATTATTAAAAAAATAAAC
Found at i:2810952 original size:15 final size:15
Alignment explanation
Indices: 2810925--2810958 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2810915 TATTTTTTCT
2810925 AAAT-ATTTAAAAAA
1 AAATAATTTAAAAAA
*
2810939 AAATAATTTTAAAAA
1 AAATAATTTAAAAAA
2810954 AAATA
1 AAATA
2810959 TAAATACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATTTAAAAAA
Found at i:2817336 original size:33 final size:33
Alignment explanation
Indices: 2817282--2817418 Score: 145
Period size: 33 Copynumber: 4.1 Consensus size: 33
2817272 AATCCAAAAA
**
2817282 AAAAGAAA-AAGATGAGGCAAGATC-CAAGAAAG
1 AAAAGAAAGAAGATGAAACAAGATCTC-AGAAAG
2817314 AAGAA-AAAGAAGATGAAACAAGATCTCAGAAAG
1 AA-AAGAAAGAAGATGAAACAAGATCTCAGAAAG
*
2817347 AAAAGGAAGAAGATGAAACAAGATCTCAGAAAG
1 AAAAGAAAGAAGATGAAACAAGATCTCAGAAAG
* * ** *
2817380 AAAAGGAAGAAGTTGACGCAAGATCCCAGAGGAAG
1 AAAAGAAAGAAGATGAAACAAGATCTCAGA--AAG
2817415 AAAA
1 AAAA
2817419 AGGATGAGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
32 7 0.08
33 77 0.84
34 1 0.01
35 7 0.08
ACGTcount: A:0.57, C:0.10, G:0.25, T:0.08
Consensus pattern (33 bp):
AAAAGAAAGAAGATGAAACAAGATCTCAGAAAG
Found at i:2820327 original size:22 final size:22
Alignment explanation
Indices: 2820294--2820358 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
2820284 GTTTGAAAAC
*
2820294 TATCTTTCTATTATTTAGGAAT
1 TATCTTTCTATTAATTAGGAAT
*
2820316 TATCTCTT-TATTAATTAGGATTT
1 TATCT-TTCTATTAATTAGGA-AT
*
2820339 TAGT-TTTCTAATAATTAGGA
1 TA-TCTTTCTATTAATTAGGA
2820359 TTTAAGTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 18 0.50
23 17 0.47
24 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (22 bp):
TATCTTTCTATTAATTAGGAAT
Found at i:2820410 original size:18 final size:18
Alignment explanation
Indices: 2820387--2820430 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
2820377 TTAGGATTAT
*
2820387 CTTTAGGTGTTTTATTTC
1 CTTTAGGTATTTTATTTC
2820405 CTTTAGGTATTTTATTTC
1 CTTTAGGTATTTTATTTC
2820423 CTTTAGGT
1 CTTTAGGT
2820431 TATCTTAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (18 bp):
CTTTAGGTATTTTATTTC
Found at i:2829613 original size:2 final size:2
Alignment explanation
Indices: 2829606--2829632 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2829596 CATACGATAA
2829606 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2829633 AACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2829641 original size:2 final size:2
Alignment explanation
Indices: 2829636--2829667 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2829626 ACACACAAAC
2829636 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
2829668 CAGAAAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2831981 original size:21 final size:21
Alignment explanation
Indices: 2831956--2831996 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2831946 GTGTACCTAA
2831956 AAAATATAAAGAAA-AATAAAT
1 AAAATA-AAAGAAATAATAAAT
*
2831977 AAAATAAAATAAATAATAAA
1 AAAATAAAAGAAATAATAAA
2831997 ATGGGTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATAAAAGAAATAATAAAT
Found at i:2850377 original size:52 final size:52
Alignment explanation
Indices: 2850315--2850420 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
2850305 GGGAGAAGTG
* *
2850315 TTAAGTGTTAAAAGTTTTAAAGGGGAGAAGTTTTATAGTAAGGGGGATTAAT
1 TTAAGTGTTAAAAGTTTTAAAGGGGAGAAGTGTTATAGTAAGGGGGAGTAAT
2850367 TTAAGTGTTAAAAGTTTTAAAGGGGAGAAGTGTTATAGTAAGGGGGAGTAAT
1 TTAAGTGTTAAAAGTTTTAAAGGGGAGAAGTGTTATAGTAAGGGGGAGTAAT
2850419 TT
1 TT
2850421 CAAAATTGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (52 bp):
TTAAGTGTTAAAAGTTTTAAAGGGGAGAAGTGTTATAGTAAGGGGGAGTAAT
Found at i:2850854 original size:45 final size:46
Alignment explanation
Indices: 2850805--2850892 Score: 160
Period size: 45 Copynumber: 1.9 Consensus size: 46
2850795 GAACATCGAA
*
2850805 TGCATTTGATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
2850850 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
2850893 CAGGCTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:2851899 original size:61 final size:61
Alignment explanation
Indices: 2851812--2851929 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 61
2851802 TGCACTAAAC
* *
2851812 TTACGCTCTACTGCTAATCCAGATATGACACATAAGGTCGTGCCCACCACCTACACTAGGT
1 TTACACTCTACTGCCAATCCAGATATGACACATAAGGTCGTGCCCACCACCTACACTAGGT
* * * *
2851873 TTACACTCTAGTGCCAATCCAGATATGACACATAAGGTTGTGCCCTCCACCTGCACT
1 TTACACTCTACTGCCAATCCAGATATGACACATAAGGTCGTGCCCACCACCTACACT
2851930 TAGTTTCCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (61 bp):
TTACACTCTACTGCCAATCCAGATATGACACATAAGGTCGTGCCCACCACCTACACTAGGT
Found at i:2868817 original size:2 final size:2
Alignment explanation
Indices: 2868812--2868854 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2868802 TATATATATA
2868812 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2868854 T
1 T
2868855 TGTATTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2869290 original size:42 final size:43
Alignment explanation
Indices: 2869215--2869301 Score: 158
Period size: 42 Copynumber: 2.0 Consensus size: 43
2869205 ATAAATATTG
2869215 AACATATAAATCCATAAAAAAAGCTCATAACAAAAACATGTTC
1 AACATATAAATCCATAAAAAAAGCTCATAACAAAAACATGTTC
*
2869258 AACATATAAATCCAT-AAAAAATCTCATAACAAAAACATGTTC
1 AACATATAAATCCATAAAAAAAGCTCATAACAAAAACATGTTC
2869300 AA
1 AA
2869302 TAAGCAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.56, C:0.18, G:0.03, T:0.22
Consensus pattern (43 bp):
AACATATAAATCCATAAAAAAAGCTCATAACAAAAACATGTTC
Found at i:2876136 original size:8 final size:8
Alignment explanation
Indices: 2876098--2876154 Score: 66
Period size: 8 Copynumber: 7.5 Consensus size: 8
2876088 GATATGTTAA
2876098 AATAAAAT
1 AATAAAAT
* *
2876106 AATTATAT
1 AATAAAAT
2876114 -ATAAAA-
1 AATAAAAT
*
2876120 AAGAAAAT
1 AATAAAAT
2876128 AATAAAAT
1 AATAAAAT
2876136 AATAAAAT
1 AATAAAAT
2876144 AAT-AAAT
1 AATAAAAT
2876151 AATA
1 AATA
2876155 GTAATAAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
7 16 0.40
8 24 0.60
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:2876161 original size:16 final size:16
Alignment explanation
Indices: 2876098--2876154 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 16
2876088 GATATGTTAA
* *
2876098 AATAAAATAATTATAT
1 AATAAAATAATAAAAT
*
2876114 -ATAAAA-AAGAAAAT
1 AATAAAATAATAAAAT
2876128 AATAAAATAATAAAAT
1 AATAAAATAATAAAAT
2876144 AAT-AAATAATA
1 AATAAAATAATA
2876155 GTAATAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.14
15 20 0.57
16 10 0.29
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AATAAAATAATAAAAT
Found at i:2876218 original size:18 final size:18
Alignment explanation
Indices: 2876195--2876237 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2876185 GTTGTTTTTA
**
2876195 AAATAAAAGATTAGAATT
1 AAATAAAAGAAAAGAATT
*
2876213 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
2876231 AAATAAA
1 AAATAAA
2876238 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:2880891 original size:5 final size:5
Alignment explanation
Indices: 2880881--2880977 Score: 70
Period size: 5 Copynumber: 18.8 Consensus size: 5
2880871 TGTTCAAAGA
* * ****
2880881 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAGT TTGGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
* * *
2880931 AAAAAT AAAAT AAAAAT AAAAC GAAAT AAAAT GAAAT AAAAAT AAAA
1 -AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
2880978 ATATAACAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
4 4 0.06
5 53 0.75
6 14 0.20
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2880896 original size:10 final size:10
Alignment explanation
Indices: 2880881--2880977 Score: 70
Period size: 11 Copynumber: 9.4 Consensus size: 10
2880871 TGTTCAAAGA
2880881 AAAATAAAAT
1 AAAATAAAAT
2880891 AAAATAAAAT
1 AAAATAAAAT
2880901 AAAAT-AAAT
1 AAAATAAAAT
*
2880910 AGAATGAAAAT
1 AAAAT-AAAAT
* ****
2880921 AAAGTTTGGT
1 AAAATAAAAT
2880931 AAAAATAAAAT
1 -AAAATAAAAT
*
2880942 AAAAATAAAAC
1 -AAAATAAAAT
*
2880953 GAAATAAAAT
1 AAAATAAAAT
*
2880963 GAAATAAAAAT
1 AAAAT-AAAAT
2880974 AAAA
1 AAAA
2880978 ATATAACAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
9 8 0.12
10 29 0.43
11 30 0.45
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:2880901 original size:15 final size:15
Alignment explanation
Indices: 2880881--2880977 Score: 70
Period size: 16 Copynumber: 6.3 Consensus size: 15
2880871 TGTTCAAAGA
2880881 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
2880896 AAAATAAAAT-AAAT
1 AAAATAAAATAAAAT
* *
2880910 AGAATGAAAATAAAGT
1 AAAAT-AAAATAAAAT
****
2880926 TTGGTAAAAATAAAAT
1 AAAAT-AAAATAAAAT
**
2880942 AAAAATAAAACGAAAT
1 -AAAATAAAATAAAAT
*
2880958 AAAATGAAATAAAAAT
1 AAAATAAAAT-AAAAT
2880974 AAAA
1 AAAA
2880978 ATATAACAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
14 8 0.13
15 23 0.38
16 29 0.48
17 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:2880972 original size:21 final size:21
Alignment explanation
Indices: 2880933--2880971 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2880923 AGTTTGGTAA
2880933 AAATAAAATAAAAATAAAACG
1 AAATAAAATAAAAATAAAACG
*
2880954 AAATAAAAT-GAAATAAAA
1 AAATAAAATAAAAATAAAA
2880972 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAATAAAATAAAAATAAAACG
Found at i:2888114 original size:19 final size:20
Alignment explanation
Indices: 2888063--2888115 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2888053 AACATCAAGG
*
2888063 AAAGTTTTGAAACTTTTGTT
1 AAAGTTTTGAAACTATTGTT
*
2888083 AAAATTTTGAAACTATTG-T
1 AAAGTTTTGAAACTATTGTT
* *
2888102 GAAGTTTTTAAACT
1 AAAGTTTTGAAACT
2888116 CCAAAGTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (20 bp):
AAAGTTTTGAAACTATTGTT
Found at i:2889205 original size:33 final size:33
Alignment explanation
Indices: 2889168--2889230 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2889158 AATATCCAAG
2889168 AAAGAAGAA-AAAGAAGATAAAGCAAGATCCCAT
1 AAAGAA-AAGAAAGAAGATAAAGCAAGATCCCAT
* * *
2889201 AAAGAAAAGAAAGAAGTTGACGCAAGATCC
1 AAAGAAAAGAAAGAAGATAAAGCAAGATCC
2889231 TAGATGAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.08
33 24 0.92
ACGTcount: A:0.57, C:0.13, G:0.21, T:0.10
Consensus pattern (33 bp):
AAAGAAAAGAAAGAAGATAAAGCAAGATCCCAT
Found at i:2891242 original size:47 final size:47
Alignment explanation
Indices: 2891173--2891635 Score: 586
Period size: 47 Copynumber: 9.7 Consensus size: 47
2891163 GTATGTTTTA
* *
2891173 TCATAACTAAAAATGCATGAAATGATGCATTAAGGCATGAAAGAATG
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* **
2891220 TCATAACTAAAAATTCATGAAATAATGCATTAAGGCATGAAAGGATGAAAGG
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT-----G
2891272 ATGCCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 -T--CATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
2891322 TCATAACTAAAAAGGCATGATAGGATGCATTAAAGCATGAAAGGATG
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
2891369 TCATAACTAAAAATGCATAAAAGGATGCATTAAGGCATGAAAGGAT-
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
2891415 TCCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATG
1 T-CATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
2891463 CCATAACTAAAAATGCATGAAATGATGCAATAAGGCATGAATGAATG
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
2891510 TCATAATTAAAAATGCATGAAATGATGCGTTAAGGCATGAAAGGATG
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
2891557 CCACAATTAAAAATGCATGAAAGGATGCATTAATGCATGAAAGGATG
1 TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
** * * **
2891604 TCGCAATTATAAATGCATGAACTGATGCATTA
1 TCATAACTAAAAATGCATGAAAGGATGCATTA
2891636 TAAGATGAAA
Statistics
Matches: 369, Mismatches: 37, Indels: 20
0.87 0.09 0.05
Matches are distributed among these distances:
46 1 0.00
47 322 0.87
49 1 0.00
50 1 0.00
52 1 0.00
53 1 0.00
55 42 0.11
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (47 bp):
TCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:2891574 original size:27 final size:24
Alignment explanation
Indices: 2891544--2891624 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 24
2891534 ATGCGTTAAG
2891544 GCATGAAAGGATGCCACAATTAAAAAT
1 GCATGAAAGGATG-C-CAATT-AAAAT
2891571 GCATGAAAGGATG-C-ATT--AAT
1 GCATGAAAGGATGCCAATTAAAAT
2891591 GCATGAAAGGATGTCGCAATTATAAAT
1 GCATGAAAGGATG-C-CAATTA-AAAT
2891618 GCATGAA
1 GCATGAA
2891625 CTGATGCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
20 16 0.34
23 4 0.09
24 4 0.09
27 23 0.49
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (24 bp):
GCATGAAAGGATGCCAATTAAAAT
Found at i:2898802 original size:47 final size:47
Alignment explanation
Indices: 2898435--2898781 Score: 577
Period size: 47 Copynumber: 7.4 Consensus size: 47
2898425 ATGCATTAAG
*
2898435 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
* **
2898482 GCATGAAAAGATGCATTAACACATGAAAGGATGTCATAACTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
* * *
2898529 GCATGAAAGGATGCATTAAGGCATGAAAGGGTGACATAGCTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
2898576 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
2898623 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
*
2898670 GCATGAAAGGATGCATTAAGCCATGAAAGGATGTCATAACTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
* * * *
2898717 GCACGAAAGGATGCATTAAGCCATGAAAGGATGTCATAATTATAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
*
2898764 GCATGAACGGATGCATTA
1 GCATGAAAGGATGCATTA
2898782 TGAGATGAAA
Statistics
Matches: 281, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 281 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAAAT
Found at i:2900852 original size:29 final size:29
Alignment explanation
Indices: 2900814--2900875 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
2900804 ATCAAAAGGA
2900814 AGATTAATACAAAATAAGACATACATAAG
1 AGATTAATACAAAATAAGACATACATAAG
2900843 AGATTAATACAAAATAAGACATACATAAG
1 AGATTAATACAAAATAAGACATACATAAG
2900872 AGAT
1 AGAT
2900876 GATATTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.21
Consensus pattern (29 bp):
AGATTAATACAAAATAAGACATACATAAG
Found at i:2901282 original size:2 final size:2
Alignment explanation
Indices: 2901271--2901305 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2901261 AAAATTAAGA
2901271 AT AT -T 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
2901306 GCAAAACTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2913343 original size:139 final size:139
Alignment explanation
Indices: 2912938--2913452 Score: 571
Period size: 139 Copynumber: 3.8 Consensus size: 139
2912928 ACGTTGATCT
* *
2912938 AACTCCATATGCGATGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
1 AACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
* * * * * * *
2913003 TCGTTTGGATGAGTTTTTCTCATTATGAACTTTCCA-T-G--A---TAATCCCTCAAGCGAGGCG
66 TC-ATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTG
**
2913061 TCACTGATTC
130 TTGCTGATTC
* * * *
2913071 GAA----ATA-CCG-TGAATTGAG-TGATAGGTTGAACAAGCTCTTCCCATTATGAACTTTTTCT
1 -AACTCCATATGCGATGAATCGAGCT-A-AGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT
* * * * *
2913129 CTCTTATCGAATGAGTTATTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGTGAGG
63 CCCTCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGG
*
2913194 TGTTGTTGATTC
128 TGTTGCTGATTC
* *
2913206 AACTCCATATGTGATGAATCGAGCTAAGGTTGAACAATTTCTTCTCATTATGAACTTTTTCTCCC
1 AACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
* *
2913271 TCATCGGATGAGTTCTTCTCATTATGAACTCTCTACTGGAAATGTTGATCCCTCAAGTGAGGTGT
66 TCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGT
2913336 TGCTGATTC
131 TGCTGATTC
* * * * *
2913345 AACTCCATATGTGATAAATCGAGCTAAGGCTGAACAA----TTCTCATTATGAAATTATTCTCCC
1 AACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
* * *
2913406 TCATCGGATGAGTTATTCTTATTATGAACTATCCATTGGAAATGTTG
66 TCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTG
2913453 CTTGGTTTAC
Statistics
Matches: 322, Mismatches: 43, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
127 1 0.00
128 37 0.11
129 38 0.12
130 4 0.01
132 1 0.00
134 4 0.01
135 86 0.27
138 3 0.01
139 138 0.43
140 9 0.03
141 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (139 bp):
AACTCCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
TCATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCAAGTGAGGTGT
TGCTGATTC
Found at i:2913446 original size:274 final size:265
Alignment explanation
Indices: 2912930--2913452 Score: 601
Period size: 274 Copynumber: 1.9 Consensus size: 265
2912920 AAGTGATGAC
2912930 GTTGATCTAACTCCATATGCGATGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTT
1 GTTGATCTAACTCCATATGCGATGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTT
* * * *
2912995 CTTCTCCCTCGTTTGGATGAGTTTTTCTCATTATGAACTTTCCATGATAATCCCTCAAGCGAGGC
66 CTTCTCCCTCGATCGGATGAGTTCTTCTCATTATGAACTTTCAATGATAATCCCTCAAGCGAGGC
* * * *
2913060 GTCACTGATTCGAAATACCGTGAATTGAGTGATAGGTTGAACAAGCTCTTCCCATTATGAACTTT
131 GTCACTGATTCGAAATACCGTGAATCGAGTGATAGGCTGAACAA---CTTCCCATTATGAAATTA
* * *
2913125 TTCTCTCTTATCGAATGAGTTATTCTCATTATGAACTCTCCATTGGAAATGTTGATCCCTCGAGT
193 TTCTCCCTCATCGAATGAGTTATTCTCATTATGAACTATCCATTGGAAATGTTGATCCCTCGAGT
2913190 GAGGTGTT
258 GAGGTGTT
* * *
2913198 GTTGAT-TCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAATTTCTTCTCATTATGAACT
1 GTTGATCT-AACTCCATATGCGATGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACT
* * *
2913262 TTTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTCTCTACTGGAAATGTTGATCCCTCA
65 TCTTCTCCCTCGATCGGATGAGTTCTTCTCATTATGAACT-T-T-C----AATGATAATCCCTCA
* * ** * *
2913326 AGTGAGGTGTTGCTGATTC-AACTCCATA-TGTGATAAATCGAGCT-A-AGGCTGAACAA-TTCT
123 AGCGAGGCGTCACTGATTCGAA----ATACCGTG---AATCGAG-TGATAGGCTGAACAACTTCC
* *
2913386 CATTATGAAATTATTCTCCCTCATCGGATGAGTTATTCTTATTATGAACTATCCATTGGAAATGT
180 CATTATGAAATTATTCTCCCTCATCGAATGAGTTATTCTCATTATGAACTATCCATTGGAAATGT
2913451 TG
245 TG
2913453 CTTGGTTTAC
Statistics
Matches: 214, Mismatches: 25, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
267 26 0.12
268 70 0.33
269 1 0.00
270 1 0.00
273 2 0.01
274 90 0.42
276 3 0.01
277 3 0.01
278 10 0.05
279 7 0.03
280 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (265 bp):
GTTGATCTAACTCCATATGCGATGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTT
CTTCTCCCTCGATCGGATGAGTTCTTCTCATTATGAACTTTCAATGATAATCCCTCAAGCGAGGC
GTCACTGATTCGAAATACCGTGAATCGAGTGATAGGCTGAACAACTTCCCATTATGAAATTATTC
TCCCTCATCGAATGAGTTATTCTCATTATGAACTATCCATTGGAAATGTTGATCCCTCGAGTGAG
GTGTT
Found at i:2914097 original size:41 final size:40
Alignment explanation
Indices: 2914031--2914144 Score: 113
Period size: 42 Copynumber: 2.8 Consensus size: 40
2914021 ACATGCCGCC
* * **
2914031 CGAAAGTCTTATGGATGTCCCGAAGGACTTATCATCT-TGCT
1 CGAAAGACTTAT-GATGACCCGAAGGACTTAGAAT-TGTGCT
* *
2914072 CGAAAGACTTATAGATGACCTGAAGGATTTAAGAATTGTGCT
1 CGAAAGACTTAT-GATGACCCGAAGGACTT-AGAATTGTGCT
*
2914114 CGAAAGACTTACTGATGGCCCGAAGGACTTA
1 CGAAAGACTTA-TGATGACCCGAAGGACTTA
2914145 AGCTGATTCG
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 27 0.45
42 32 0.53
43 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (40 bp):
CGAAAGACTTATGATGACCCGAAGGACTTAGAATTGTGCT
Found at i:2914665 original size:55 final size:55
Alignment explanation
Indices: 2914565--2914902 Score: 397
Period size: 55 Copynumber: 6.2 Consensus size: 55
2914555 AAAAATTGGA
*
2914565 CTTAGTTTATTTCAAAA--TCATTTGAAAAT-ATCAAGAAAC-TCATGAAAATCAAG
1 CTTAGTTTCTTT-AAAAGCTCATTTGAAAATCATCAAGAAACTTC-TGAAAATCAAG
* * * * * *
2914618 CTTAATTTCTTTGAAAGTTCATTTAAAAATCATTAAGAAACTTATGAAAAATC-AG
1 CTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTCTG-AAAATCAAG
* *
2914673 ACTTAGTTTCTTTAAAA-CTTATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGAG
1 -CTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTCTGAAAATCA-AG
*
2914729 -TTAGTTTCTTTAAAAACTCATTTGAAAATCATCAAGAAACTTCTTGAAAATC-AG
1 CTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTC-TGAAAATCAAG
* * *
2914783 ACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCTGAAAAACAGAG
1 -CTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTCTGAAAATCA-AG
** *
2914840 -TTAGTTTCTTTAAAAGCTCATTTGAAAATTGTCAAGAAACTTCTGAAAATCAAA
1 CTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTCTGAAAATCAAG
2914894 CTTAGTTTC
1 CTTAGTTTC
2914903 CAAAAAAACA
Statistics
Matches: 244, Mismatches: 26, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
52 3 0.01
53 10 0.04
54 35 0.14
55 123 0.50
56 71 0.29
57 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (55 bp):
CTTAGTTTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTCTGAAAATCAAG
Found at i:2914750 original size:110 final size:110
Alignment explanation
Indices: 2914563--2914902 Score: 447
Period size: 110 Copynumber: 3.1 Consensus size: 110
2914553 CCAAAAATTG
* *
2914563 GACTTAGTTTATTTCAAAA-TCATTTGAAAAT-ATCAAGAAAC-TCATGAAAATCA-AGCTTAAT
1 GACTTAGTTTCTTTCAAAACTCATTTGAAAATCATCAAGAAACTTC-TGAAAATCAGAG-TTAGT
* * * *
2914624 TTCTTTGAAAGTTCATTTAAAAATCATTAAGAAACTTATGAAAAATCA
64 TTCTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTATG-AAAATCA
* *
2914672 GACTTAGTTTCTTT-AAAACTTATTTGAAAATCGTCAAGAAACTTCTGAAAATCAGAGTTAGTTT
1 GACTTAGTTTCTTTCAAAACTCATTTGAAAATCATCAAGAAACTTCTGAAAATCAGAGTTAGTTT
* *
2914736 CTTTAAAAACTCATTTGAAAATCATCAAGAAACTTCTTGAAAATCA
66 CTTTAAAAGCTCATTTGAAAATCATCAAGAAACTT-ATGAAAATCA
* * * *
2914782 GACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCTGAAAAACAGAGTTAGTTT
1 GACTTAGTTTCTTTCAAAACTCATTTGAAAATCATCAAGAAACTTCTGAAAATCAGAGTTAGTTT
** *
2914847 CTTTAAAAGCTCATTTGAAAATTGTCAAGAAACTTCTGAAAATCA
66 CTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTATGAAAATCA
*
2914892 AACTTAGTTTC
1 GACTTAGTTTC
2914903 CAAAAAAACA
Statistics
Matches: 205, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
108 4 0.02
109 24 0.12
110 94 0.46
111 83 0.40
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (110 bp):
GACTTAGTTTCTTTCAAAACTCATTTGAAAATCATCAAGAAACTTCTGAAAATCAGAGTTAGTTT
CTTTAAAAGCTCATTTGAAAATCATCAAGAAACTTATGAAAATCA
Found at i:2914795 original size:166 final size:163
Alignment explanation
Indices: 2914564--2914902 Score: 511
Period size: 166 Copynumber: 2.1 Consensus size: 163
2914554 CAAAAATTGG
* *
2914564 ACTTAGTTTATTTCAAAATCATTTGAAAATATCAAGAAACTCATGAAAATCAAGCTTAATTTCTT
1 ACTTAGTTTCTTTAAAAATCATTTGAAAATATCAAGAAACTCATGAAAATCAAGCTTAATTTCTT
* * *
2914629 TGAAAGTTCATTTAAAAATCATTAAGAAACTTATGAAAAATCAGACTTAGTTTCTTTAAAA-CTT
66 TGAAAGCTCATTTAAAAATCATCAAGAAACTTATGAAAAA-CAGACTTAGTTTCTTTAAAAGCTC
*
2914693 ATTTGAAAATCGTCAAGAAACTTCTGAAAATCAG
130 ATTTGAAAATCGTCAAGAAACTTCTGAAAATCAA
* * *
2914727 AGTTAGTTTCTTTAAAAACTCATTTGAAAATCATCAAGAAACTTCTTGAAAATC-AGACTTAGTT
1 ACTTAGTTTCTTTAAAAA-TCATTTGAAAAT-ATCAAGAAAC-TCATGAAAATCAAG-CTTAATT
* *
2914791 TCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCTGAAAAACAGAGTTAGTTTCTTTAAAAG
62 TCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTATGAAAAACAGACTTAGTTTCTTTAAAAG
*
2914856 CTCATTTGAAAATTGTCAAGAAACTTCTGAAAATCAA
127 CTCATTTGAAAATCGTCAAGAAACTTCTGAAAATCAA
2914893 ACTTAGTTTC
1 ACTTAGTTTC
2914903 CAAAAAAACA
Statistics
Matches: 158, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
163 15 0.09
164 12 0.08
165 31 0.20
166 100 0.63
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (163 bp):
ACTTAGTTTCTTTAAAAATCATTTGAAAATATCAAGAAACTCATGAAAATCAAGCTTAATTTCTT
TGAAAGCTCATTTAAAAATCATCAAGAAACTTATGAAAAACAGACTTAGTTTCTTTAAAAGCTCA
TTTGAAAATCGTCAAGAAACTTCTGAAAATCAA
Found at i:2916775 original size:9 final size:9
Alignment explanation
Indices: 2916761--2916854 Score: 75
Period size: 9 Copynumber: 10.4 Consensus size: 9
2916751 TGGATCTGTA
2916761 TTTTTTTCT
1 TTTTTTTCT
2916770 TTTTTTT-T
1 TTTTTTTCT
* *
2916778 CATTTTCTCT
1 -TTTTTTTCT
*
2916788 TTTTCTTCT
1 TTTTTTTCT
* *
2916797 GTTTTCTCT
1 TTTTTTTCT
2916806 TTCTTTTTCT
1 TT-TTTTTCT
*
2916816 CTTTTTT-T
1 TTTTTTTCT
* *
2916824 TCTCTTTCT
1 TTTTTTTCT
2916833 TTTTTTTCT
1 TTTTTTTCT
*
2916842 TTTTTCTCT
1 TTTTTTTCT
2916851 TTTT
1 TTTT
2916855 ACTTTCTATT
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
8 6 0.09
9 50 0.78
10 8 0.12
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:2916788 original size:18 final size:19
Alignment explanation
Indices: 2916762--2916865 Score: 68
Period size: 18 Copynumber: 5.2 Consensus size: 19
2916752 GGATCTGTAT
*
2916762 TTTTTTCTTTTTTTTTC-A
1 TTTTCTCTTTTTTTTTCTA
* *
2916780 TTTTCTC-TTTTTCTTCTG
1 TTTTCTCTTTTTTTTTCTA
*
2916798 TTTTCTCTTTCTTTTTCTCTTTT
1 TTTTCTCTTT-TTTTT-TC--TA
*
2916821 TTTTCTCTTTCTTTTTTTTCTT
1 TTTTCTC--T-TTTTTTTTCTA
*
2916843 TTTTCTCTTTTTACTTTCTA
1 TTTTCTCTTTTT-TTTTCTA
2916863 TTT
1 TTT
2916866 GTGTGTGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
17 8 0.12
18 13 0.19
19 6 0.09
20 13 0.19
21 2 0.03
22 9 0.13
23 8 0.12
24 2 0.03
25 6 0.09
26 2 0.03
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (19 bp):
TTTTCTCTTTTTTTTTCTA
Found at i:2916790 original size:24 final size:23
Alignment explanation
Indices: 2916763--2916853 Score: 89
Period size: 24 Copynumber: 3.9 Consensus size: 23
2916753 GATCTGTATT
2916763 TTTTTCTTTTTTTTTCATTTTCTC
1 TTTTTCTTTTTTTTTC-TTTTCTC
* * *
2916787 TTTTTCTTCTGTTTTCTCTT-TC
1 TTTTTCTTTTTTTTTCTTTTCTC
2916809 TTTTTCTCTTTTTTTTCTCTTTCT-
1 TTTTTCT-TTTTTTTTCT-TTTCTC
2916833 TTTTT-TTCTTTTTTCTCTTTT
1 TTTTTCTT-TTTTTT-TCTTTT
2916854 TACTTTCTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 10 0.18
23 21 0.38
24 24 0.43
25 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (23 bp):
TTTTTCTTTTTTTTTCTTTTCTC
Found at i:2916813 original size:22 final size:22
Alignment explanation
Indices: 2916763--2916852 Score: 108
Period size: 22 Copynumber: 4.0 Consensus size: 22
2916753 GATCTGTATT
* *
2916763 TTTTTCTTTTTTTTTCATTTTCTC
1 TTTTTCTTCTTTTTTC-TCTT-TC
*
2916787 TTTTTCTTCTGTTTTCTCTTTC
1 TTTTTCTTCTTTTTTCTCTTTC
*
2916809 TTTTTCTCTTTTTTTTCTCTTTC
1 TTTTTCT-TCTTTTTTCTCTTTC
*
2916832 TTTTTTTTCTTTTTTCTCTTT
1 TTTTTCTTCTTTTTTCTCTTT
2916853 TTACTTTCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
22 22 0.38
23 22 0.38
24 14 0.24
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTCTCTTTC
Found at i:2916816 original size:30 final size:28
Alignment explanation
Indices: 2916780--2916852 Score: 55
Period size: 28 Copynumber: 2.6 Consensus size: 28
2916770 TTTTTTTTCA
* * *
2916780 TTTTCTCTTTTTCT-TCTGTTTTCTCTT
1 TTTTTTCTTTTTCTCTTTCTTTTCTCTT
*
2916807 TCTTTTTCTCTTTT-T-TTTCTCTT-TCTT
1 T-TTTTTCT-TTTTCTCTTTCTTTTCTCTT
2916834 TTTTTTCTTTTTTCTCTTT
1 TTTTTTC-TTTTTCTCTTT
2916853 TTACTTTCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
26 10 0.27
27 8 0.22
28 15 0.41
29 4 0.11
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (28 bp):
TTTTTTCTTTTTCTCTTTCTTTTCTCTT
Found at i:2916836 original size:45 final size:46
Alignment explanation
Indices: 2916763--2916852 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
2916753 GATCTGTATT
*
2916763 TTTTTCTTTTTTTTTCATTTTCTCTTTTTCTTCTGTTTTCTCTTTC
1 TTTTTCTTTTTTTTTCATCTTCTCTTTTTCTTCTGTTTTCTCTTTC
* *
2916809 TTTTTCTCTTTTTTTTC-TCTT-TCTTTTTTTTCTTTTTTCTCTTT
1 TTTTTCT-TTTTTTTTCATCTTCTCTTTTTCTTCTGTTTTCTCTTT
2916853 TTACTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 21 0.52
46 10 0.25
47 9 0.22
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (46 bp):
TTTTTCTTTTTTTTTCATCTTCTCTTTTTCTTCTGTTTTCTCTTTC
Found at i:2917132 original size:2 final size:2
Alignment explanation
Indices: 2917125--2917160 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2917115 GGACAACAAG
*
2917125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2917161 TTTTGAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2922659 original size:42 final size:41
Alignment explanation
Indices: 2922536--2922659 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 41
2922526 GAAAACATTG
* **
2922536 TGTCACTAGTCTTAGTTGT-ATTTGTGACTATAATTGTTTT
1 TGTCACTAGTCTTAGTTGTGATTTGTGACAATAATAATTTT
* *
2922576 TGCCACTAGTCTTAGTTAGTGATTTGTGACAATAATGATTTT
1 TGTCACTAGTCTTAGTT-GTGATTTGTGACAATAATAATTTT
* * * *
2922618 TGTCATTAGTATTAGTTGTTGATTTGTGACGAGAATAATTTT
1 TGTCACTAGTCTTAGTTG-TGATTTGTGACAATAATAATTTT
2922660 ATCACTATTG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
40 16 0.23
41 3 0.04
42 52 0.73
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.48
Consensus pattern (41 bp):
TGTCACTAGTCTTAGTTGTGATTTGTGACAATAATAATTTT
Found at i:2924499 original size:21 final size:22
Alignment explanation
Indices: 2924454--2924514 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
2924444 AATGCTCGGA
2924454 GGGAACCGATTTTCCCCCAAGG
1 GGGAACCGATTTTCCCCCAAGG
2924476 GGGAACCGATTTTCCCCCAAGG
1 GGGAACCGATTTTCCCCCAAGG
*
2924498 GGGTACCGA-TTTCCCCC
1 GGGAACCGATTTTCCCCC
2924515 TGTTTAACAG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 8 0.21
22 30 0.79
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTTTCCCCCAAGG
Found at i:2931847 original size:18 final size:18
Alignment explanation
Indices: 2931812--2931850 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2931802 AGAGCAGCAC
*
2931812 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
2931830 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
2931848 GAG
1 GAG
2931851 TATCAAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:2934224 original size:105 final size:104
Alignment explanation
Indices: 2934037--2934255 Score: 260
Period size: 105 Copynumber: 2.1 Consensus size: 104
2934027 GTGACGAAGT
* * * * * * * **
2934037 TATTGTTAATAGTATTGAAGATTTGGTCACTAAAATACACTTATTGTGACGACATTGGTGGTAAC
1 TATTGATAATAATATCGAACATTTGATCACTAAAAAACACTTAGTGTGACGACATTAATGGTAAC
* ** *
2934102 AAAATATATTTTCAGTGTCAACTAAATTTATCACAAATTC
66 AAAATATATTTTCAGTGTCAA-AAAAAATATCACAAATTA
* *
2934142 TATTGATAATAATATCGAACATTTGATCACTAAAAAATACTTAGTGTGAC-ACTATTAATGGTCA
1 TATTGATAATAATATCGAACATTTGATCACTAAAAAACACTTAGTGTGACGAC-ATTAATGGTAA
* *
2934206 CAAAATATATTTTTAGTGTCAAAAAAAATATCACAATTTA
65 CAAAATATATTTTCAGTGTCAAAAAAAATATCACAAATTA
2934246 TATTGATAAT
1 TATTGATAAT
2934256 TGTGTGAGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
104 25 0.26
105 71 0.74
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (104 bp):
TATTGATAATAATATCGAACATTTGATCACTAAAAAACACTTAGTGTGACGACATTAATGGTAAC
AAAATATATTTTCAGTGTCAAAAAAAATATCACAAATTA
Found at i:2934668 original size:24 final size:19
Alignment explanation
Indices: 2934610--2934666 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
2934600 AGAGCAAAAC
2934610 CTCTAATAGAATGTGATGT
1 CTCTAATAGAATGTGATGT
2934629 CTCTAATAGAATGTGATGT
1 CTCTAATAGAATGTGATGT
2934648 CTCTAATAGAATGTGATGT
1 CTCTAATAGAATGTGATGT
2934667 GAGCGATCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
CTCTAATAGAATGTGATGT
Found at i:2939127 original size:12 final size:13
Alignment explanation
Indices: 2939105--2939151 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
2939095 GTTTTTAATT
*
2939105 TATATATTAAAAA
1 TATATAATAAAAA
2939118 TAT-TAATAAAAA
1 TATATAATAAAAA
* *
2939130 TATATAATTTATAA
1 TATATAA-TAAAAA
2939144 TATATAAT
1 TATATAAT
2939152 TTAAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 11 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATATAATAAAAA
Found at i:2939145 original size:14 final size:14
Alignment explanation
Indices: 2939128--2939154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2939118 TATTAATAAA
2939128 AATATATAATTTAT
1 AATATATAATTTAT
2939142 AATATATAATTTA
1 AATATATAATTTA
2939155 AAAAATTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATATAATTTAT
Found at i:2946353 original size:3 final size:3
Alignment explanation
Indices: 2946341--2946404 Score: 89
Period size: 3 Copynumber: 21.7 Consensus size: 3
2946331 CAAAATGATG
2946341 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
2946385 TAA -AA TTAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TA
2946405 TTAAAATTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.11
3 46 0.82
4 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2946778 original size:40 final size:39
Alignment explanation
Indices: 2946703--2946780 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
2946693 TGGTTATCTA
*
2946703 GGGGTGACACGACTCCTACGCGATAAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGCGATAAGGAGATCTGGTCG
* * *
2946742 GGGGATGACACGGCTCATACGTGATGAA-GAGTTCTGGTC
1 GGGG-TGACACGACTCATACGCGAT-AAGGAGATCTGGTC
2946781 ATCTTTAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.82
41 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGCGATAAGGAGATCTGGTCG
Found at i:2946841 original size:133 final size:134
Alignment explanation
Indices: 2946613--2946886 Score: 435
Period size: 133 Copynumber: 2.1 Consensus size: 134
2946603 CGTCTAAGGG
*
2946613 TGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCTTA
1 TGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
* * * *
2946678 CGCGATGAGTAAGGCTGGTTATCTAGGGGTGACAC-GACTCCTACGCGATAAGGAGATCTGGTCG
66 CGCGATGAGGAAGGCTGGTTATCTAGGGGTGACACAG-CTCCTACACGATAAGAAGATCTGGTCA
2946742 GGGGA
130 GGGGA
*
2946747 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAA-GGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
* * * *
2946811 CGCGATGAGGACGGCTGGTTATCTAGGGGTGACACAGCTCCTACACGATGAGAAGGTCTGTTCAG
66 CGCGATGAGGAAGGCTGGTTATCTAGGGGTGACACAGCTCCTACACGATAAGAAGATCTGGTCAG
2946876 GGGA
131 GGGA
2946880 TGACACG
1 TGACACG
2946887 ATTCCTATGT
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
133 84 0.65
134 45 0.35
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (134 bp):
TGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
CGCGATGAGGAAGGCTGGTTATCTAGGGGTGACACAGCTCCTACACGATAAGAAGATCTGGTCAG
GGGA
Found at i:2946917 original size:133 final size:134
Alignment explanation
Indices: 2946613--2946921 Score: 381
Period size: 133 Copynumber: 2.3 Consensus size: 134
2946603 CGTCTAAGGG
* * * * * *
2946613 TGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCTTA
1 TGACACGACTCATACGTGATGAAGAGTGCTAGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
* * * *
2946678 CGCGATGAGTAAGGCTGGTTATCTAGGGGTGACACGACTCCTACGCGATAAGGAGATCTGGTCGG
66 CGCGATGAGGAAGGCTGGTTATCTAGGGGTGACACGACTCCTACACGATAAGAAGATCTGGTCAG
2946743 GGGA
131 GGGA
* * * *
2946747 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAA-GGTGATAACTCGGTTCCTA
1 TGACACGACTCATACGTGATGAAGAGTGCTAGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
* * * *
2946811 CGCGATGAGGACGGCTGGTTATCTAGGGGTGACAC-AGCTCCTACACGATGAGAAGGTCTGTTCA
66 CGCGATGAGGAAGGCTGGTTATCTAGGGGTGACACGA-CTCCTACACGATAAGAAGATCTGGTCA
2946875 GGGGA
130 GGGGA
* * * *
2946880 TGACACGATTCCTATGTGATGAGGA-TGGCTAGCCATCTTTAG
1 TGACACGACTCATACGTGATGAAGAGT-GCTAGCCATCTTTAG
2946922 TGATTATGGT
Statistics
Matches: 155, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
132 2 0.01
133 109 0.70
134 44 0.28
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (134 bp):
TGACACGACTCATACGTGATGAAGAGTGCTAGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
CGCGATGAGGAAGGCTGGTTATCTAGGGGTGACACGACTCCTACACGATAAGAAGATCTGGTCAG
GGGA
Found at i:2946970 original size:28 final size:28
Alignment explanation
Indices: 2946930--2947039 Score: 105
Period size: 28 Copynumber: 3.8 Consensus size: 28
2946920 AGTGATTATG
** *
2946930 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
2946958 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
* * *
2946986 ATTTCAAGAA-AAACAAACTCAAAGGTGATGT
1 GTTTCAA-AAGAAACAGACTCAAA---GATTT
* *
2947017 GTTTCAAAAGAAACTGTCTCAAA
1 GTTTCAAAAGAAACAGACTCAAA
2947040 ATAGACAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
28 43 0.64
29 2 0.03
30 2 0.03
31 20 0.30
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:2947205 original size:66 final size:64
Alignment explanation
Indices: 2947017--2947210 Score: 176
Period size: 66 Copynumber: 3.0 Consensus size: 64
2947007 AAGGTGATGT
* * *
2947017 GTTTCAAAAGAAACTGTCTCAAAAT-AGACAAAATTCGTTTAAAGGGAAATGA-CTCAAAAGATG
1 GTTT-AAAGGAAACTATCTC-AAATGAGACAAAATTCGTTTAAAGGGAAACGATCTC-AAAGATG
2947080 AC
63 AC
* ** * * * *
2947082 GTTTAAAGGAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGG
1 GTTTAAAGGAAACTATCTCAAATGAGACAAAATTCG-TTTAAAGGGAAACGATCTCAAAGAT-GA
*
2947147 T
64 C
** * * *
2947148 GTTTCATGGGAAAGTATCTCAAATGAGACAAAATTCGTTTCAAGGGAAACGATCTCAATGATG
1 GTTT-AAAGGAAACTATCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATG
2947211 TTTGTTTTAT
Statistics
Matches: 105, Mismatches: 19, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
63 2 0.02
64 25 0.24
65 23 0.22
66 30 0.29
67 25 0.24
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (64 bp):
GTTTAAAGGAAACTATCTCAAATGAGACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGAC
Found at i:2947371 original size:64 final size:62
Alignment explanation
Indices: 2947248--2947384 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 62
2947238 CAAAGATGGT
* *
2947248 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCCCGAGAGAAACA
1 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCAC-A-AGAGACA
* * * * *
2947312 AAATTTTGTTTCCAAAGAAACATATTCAATGATTTTT-TCAAA-ATACATTGTCATAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGA-A-ACTGTCACAAGAGACA
*
2947374 AAACTTTGTTT
1 AAATTTTGTTT
2947385 TTCAGAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 17 0.27
63 7 0.11
64 39 0.62
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (62 bp):
AAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCACAAGAGACA
Found at i:2947632 original size:31 final size:31
Alignment explanation
Indices: 2947564--2947624 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2947554 AAGGGAAATG
2947564 ACTCAAAGATGGTTTTATTTCAAGAGAAACAA
1 ACTCAAAGAT-GTTTTATTTCAAGAGAAACAA
*
2947596 ACTCAAAGAT-TTTGTATTTCTAGAGAAAC
1 ACTCAAAGATGTTT-TATTTCAAGAGAAAC
2947625 TGCCTCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 10 0.37
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATGTTTTATTTCAAGAGAAACAA
Found at i:2948270 original size:3 final size:3
Alignment explanation
Indices: 2948258--2948321 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
2948248 CAAAATGATG
*
2948258 TAA T-A TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA -AA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
2948302 TAA -AA TTAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TA
2948322 TTAAAATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 6 0.11
3 44 0.81
4 4 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2949217 original size:21 final size:22
Alignment explanation
Indices: 2949178--2949219 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2949168 GAGGAGACAT
2949178 AAAACCCTACGGTGATGGCATC
1 AAAACCCTACGGTGATGGCATC
* *
2949200 AAAA-CCTACTGTGGTGGCAT
1 AAAACCCTACGGTGATGGCAT
2949220 ATGAAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (22 bp):
AAAACCCTACGGTGATGGCATC
Found at i:2953168 original size:31 final size:29
Alignment explanation
Indices: 2953121--2953183 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 29
2953111 TTAAAATTAA
2953121 CTTTAAAAAAATAAAAAAT-GAGAAATGGC
1 CTTTAAAAAAATAAAAAATAG-GAAATGGC
2953150 CTTTAAAAAAATAAAAAAAATAGGAAATGGC
1 CTTTAAAAAAAT--AAAAAATAGGAAATGGC
2953181 CTT
1 CTT
2953184 AGTGTGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 12 0.39
31 18 0.58
32 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.22
Consensus pattern (29 bp):
CTTTAAAAAAATAAAAAATAGGAAATGGC
Found at i:2953648 original size:51 final size:51
Alignment explanation
Indices: 2953587--2953689 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 51
2953577 AATGATGAAC
*
2953587 AAAAAAAATCTTTTTTAGTTTTTTT-GTAGCAACGGTAGAATAACGCTTAT
1 AAAAAAAATCTTTTTTAGTTTTTTTGGCAGCAACGGTAGAATAACGCTTAT
*
2953637 AAAAAATAATCTTTTTTAGTTTTTTTGGCAGTAACGGTAGAATAACGCTTAT
1 AAAAAA-AATCTTTTTTAGTTTTTTTGGCAGCAACGGTAGAATAACGCTTAT
2953689 A
1 A
2953690 GCGTTTCGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 6 0.12
51 19 0.39
52 24 0.49
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.40
Consensus pattern (51 bp):
AAAAAAAATCTTTTTTAGTTTTTTTGGCAGCAACGGTAGAATAACGCTTAT
Found at i:2957854 original size:10 final size:10
Alignment explanation
Indices: 2957839--2957864 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2957829 TTCAAATTGC
2957839 ATTATATGTG
1 ATTATATGTG
2957849 ATTATATGTG
1 ATTATATGTG
2957859 ATTATA
1 ATTATA
2957865 ATAAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (10 bp):
ATTATATGTG
Found at i:2958647 original size:27 final size:27
Alignment explanation
Indices: 2958606--2958658 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2958596 TGGTGGCGGC
* *
2958606 GGCGGCGGCGGCATCGGGTAAGGGAAT
1 GGCGGCAGCGACATCGGGTAAGGGAAT
* *
2958633 GGCGGCAGCGACATCTGGTAATGGAA
1 GGCGGCAGCGACATCGGGTAAGGGAA
2958659 AGGTGGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.45, T:0.13
Consensus pattern (27 bp):
GGCGGCAGCGACATCGGGTAAGGGAAT
Found at i:2959314 original size:19 final size:19
Alignment explanation
Indices: 2959290--2959327 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2959280 AAATCGATTT
2959290 TTAAATATTAAAATTCATA
1 TTAAATATTAAAATTCATA
2959309 TTAAATATTAAAATTCATA
1 TTAAATATTAAAATTCATA
2959328 CCTGTATGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATATTAAAATTCATA
Found at i:2960412 original size:9 final size:9
Alignment explanation
Indices: 2960377--2960433 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
2960367 TTTATAGCTA
*
2960377 TAAAAAAAT
1 TAAATAAAT
*
2960386 TAAAT-AAG
1 TAAATAAAT
*
2960394 TAAA-ATAT
1 TAAATAAAT
2960402 TAAATAAAT
1 TAAATAAAT
*
2960411 TAAAT-ACT
1 TAAATAAAT
2960419 TAAATAAAT
1 TAAATAAAT
2960428 TAAATA
1 TAAATA
2960434 CAAAATATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 18 0.47
9 20 0.53
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAATAAAT
Found at i:2960414 original size:17 final size:17
Alignment explanation
Indices: 2960379--2960431 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
2960369 TATAGCTATA
* *
2960379 AAAAAATTAAAT-AAGT
1 AAAATATTAAATAAATT
2960395 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
2960412 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
2960429 AAA
1 AAA
2960432 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.50
17 14 0.44
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:2960422 original size:25 final size:26
Alignment explanation
Indices: 2960377--2960433 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
2960367 TTTATAGCTA
* *
2960377 TAAAAAAATTAAATAAGTAAA-ATAT
1 TAAATAAATTAAATAAGTAAATAAAT
**
2960402 TAAATAAATTAAATACTTAAATAAAT
1 TAAATAAATTAAATAAGTAAATAAAT
2960428 TAAATA
1 TAAATA
2960434 CAAAATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
TAAATAAATTAAATAAGTAAATAAAT
Found at i:2960432 original size:17 final size:17
Alignment explanation
Indices: 2960385--2960434 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
2960375 TATAAAAAAA
* *
2960385 TTAAATAAGTAAAATA-
1 TTAAATAAATTAAATAC
2960401 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2960418 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2960435 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:2964790 original size:23 final size:23
Alignment explanation
Indices: 2964763--2964817 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
2964753 ATATAAGATA
2964763 AGTTATATGCTAAAGATCTATAG
1 AGTTATATGCTAAAGATCTATAG
*
2964786 AGTTATAAGCTAAAGATCTATAG
1 AGTTATATGCTAAAGATCTATAG
2964809 AGTTATATG
1 AGTTATATG
2964818 AAAATGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (23 bp):
AGTTATATGCTAAAGATCTATAG
Found at i:2971218 original size:12 final size:12
Alignment explanation
Indices: 2971203--2971235 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2971193 TTAATCATAT
2971203 GAATAATGATAA
1 GAATAATGATAA
*
2971215 GAATAATAATAA
1 GAATAATGATAA
2971227 GAATAATGA
1 GAATAATGA
2971236 AATGATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (12 bp):
GAATAATGATAA
Found at i:2974695 original size:81 final size:81
Alignment explanation
Indices: 2974596--2974750 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 81
2974586 AACTTAATTC
* * * * * *
2974596 ATTCCATTTACAAACGTTATA-ATTCAAACTATTGATCTTACTTAAGAGATTTGATGAGACCCTA
1 ATTCCATTCACAAACGTTA-AGATTCAAACTACTGACCTTACTTAAGAAATCTGATGAGACCCCA
2974660 CTAGACCAACTGACTTT
65 CTAGACCAACTGACTTT
* *
2974677 ATTCCATTCACAAGCGTTAAGATTTAAACTACTGACCTTACTTAAGAAATCTGATGAGACCCCAC
1 ATTCCATTCACAAACGTTAAGATTCAAACTACTGACCTTACTTAAGAAATCTGATGAGACCCCAC
2974742 TAGACCAAC
66 TAGACCAAC
2974751 CGATTGTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
80 1 0.02
81 64 0.98
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (81 bp):
ATTCCATTCACAAACGTTAAGATTCAAACTACTGACCTTACTTAAGAAATCTGATGAGACCCCAC
TAGACCAACTGACTTT
Found at i:2976195 original size:20 final size:20
Alignment explanation
Indices: 2976172--2976234 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
2976162 ATCTAAATTC
2976172 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
2976192 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
2976215 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
2976235 AATAACAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:2976390 original size:24 final size:27
Alignment explanation
Indices: 2976329--2976382 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
2976319 CCAATATATA
*
2976329 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
2976356 GAAGCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
2976383 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:2982718 original size:37 final size:35
Alignment explanation
Indices: 2982574--2982901 Score: 345
Period size: 35 Copynumber: 9.0 Consensus size: 35
2982564 AATTTCAATT
*
2982574 ATAGTTTTTGAAAATATATAATATATAGTTTTTGAAA
1 ATAG-TTTTGAAAACATATAATATATAGTTTTT-AAA
* * *
2982611 ACTTATTTTTAAAAACGTATAATATATAGTTTTTTAAA
1 A--TAGTTTTGAAAACATATAATATATAG-TTTTTAAA
2982649 ATAGTTTTGAAAACATATAATATATAGTTTTTAAA
1 ATAGTTTTGAAAACATATAATATATAGTTTTTAAA
* * *
2982684 ATGGCTTTGAAAACATATAGTATATAGTTTTTTTAAA
1 ATAGTTTTGAAAACATATAATATATAG--TTTTTAAA
* *
2982721 ATAGTTTTGAAAACGTATAACATATAGTTTTTAAA
1 ATAGTTTTGAAAACATATAATATATAGTTTTTAAA
* * **
2982756 ATAGTTTTGAAAACGTATAATATACAGTTTAAAAAAA
1 ATAGTTTTGAAAACATATAATATATAGTTT--TTAAA
* *
2982793 ACAGTTTTGAAAACATAT-ATAATATAGTTTTTGAA
1 ATAGTTTTGAAAACATATAAT-ATATAGTTTTTAAA
*
2982828 AT-GATTTTGAAAACATATAGTATATAGATTTTTAAA
1 ATAG-TTTTGAAAACATATAATATATAG-TTTTTAAA
* * *
2982864 ATAATTTTAAAAACGTATAATATATATAGTTTTTAAA
1 ATAGTTTTGAAAACATAT-A-ATATATAGTTTTTAAA
2982901 A
1 A
2982902 ACAATTTTTA
Statistics
Matches: 245, Mismatches: 32, Indels: 28
0.80 0.10 0.09
Matches are distributed among these distances:
34 1 0.00
35 91 0.37
36 47 0.19
37 68 0.28
38 31 0.13
39 7 0.03
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (35 bp):
ATAGTTTTGAAAACATATAATATATAGTTTTTAAA
Found at i:2982731 original size:72 final size:71
Alignment explanation
Indices: 2982574--2982901 Score: 363
Period size: 72 Copynumber: 4.5 Consensus size: 71
2982564 AATTTCAATT
* * * *
2982574 ATAGTTTTTGAAAATATATAATATATAGTTTTTGAAAACTTATTTTTAAAAACGTATAATATATA
1 ATAG-TTTTGAAAACATATAATATATAGTTTTT-AAAA--TAGTTTTGAAAACATATAATATATA
2982639 GTTTTTTAAA
62 GTTTTTTAAA
* * *
2982649 ATAGTTTTGAAAACATATAATATATAGTTTTTAAAATGGCTTTGAAAACATATAGTATATAGTTT
1 ATAGTTTTGAAAACATATAATATATAGTTTTTAAAATAGTTTTGAAAACATATAATATATAG-TT
2982714 TTTTAAA
65 TTTTAAA
* * * *
2982721 ATAGTTTTGAAAACGTATAACATATAGTTTTTAAAATAGTTTTGAAAACGTATAATATACAGTTT
1 ATAGTTTTGAAAACATATAATATATAGTTTTTAAAATAGTTTTGAAAACATATAATATATAGTTT
***
2982786 AAAAAAA
66 -TTTAAA
* * * *
2982793 ACAGTTTTGAAAACATAT-ATAATATAGTTTTTGAAAT-GATTTTGAAAACATATAGTATATAGA
1 ATAGTTTTGAAAACATATAAT-ATATAGTTTTTAAAATAG-TTTTGAAAACATATAATATATAGT
2982856 TTTTTAAA
64 TTTTTAAA
* * *
2982864 ATAATTTTAAAAACGTATAATATATATAGTTTTTAAAA
1 ATAGTTTTGAAAACATAT-A-ATATATAGTTTTTAAAA
2982902 ACAATTTTTA
Statistics
Matches: 213, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
71 42 0.20
72 120 0.56
73 18 0.08
74 29 0.14
75 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (71 bp):
ATAGTTTTGAAAACATATAATATATAGTTTTTAAAATAGTTTTGAAAACATATAATATATAGTTT
TTTAAA
Found at i:2982924 original size:39 final size:38
Alignment explanation
Indices: 2982790--2982926 Score: 97
Period size: 35 Copynumber: 3.7 Consensus size: 38
2982780 CAGTTTAAAA
* * *
2982790 AAAACAGTTTTGAAAACATAT-ATA-ATATAG-TTTTT
1 AAAACAATTTTAAAAAAATATAATATATATAGATTTTT
* ** * * *
2982825 GAAATGATTTTGAAAACATAT-A-GTATATAGATTTTT
1 AAAACAATTTTAAAAAAATATAATATATATAGATTTTT
* **
2982861 AAAATAATTTTAAAAACGTATAATATATATAG-TTTTT
1 AAAACAATTTTAAAAAAATATAATATATATAGATTTTT
*
2982898 AAAAACAATTTTTAAAAAAATGTAATATA
1 -AAAACAA-TTTTAAAAAAATATAATATA
2982927 ATATTATATA
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
35 24 0.29
36 22 0.27
37 6 0.07
38 13 0.16
39 17 0.21
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (38 bp):
AAAACAATTTTAAAAAAATATAATATATATAGATTTTT
Found at i:2982976 original size:13 final size:13
Alignment explanation
Indices: 2982944--2982991 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
2982934 ATAGTTATTA
*
2982944 TTATTATTATTAATT
1 TTATT-TTATTTA-T
2982959 TTATTTTATTTAT
1 TTATTTTATTTAT
*
2982972 TTATTTCATTTAT
1 TTATTTTATTTAT
2982985 TTATTTT
1 TTATTTT
2982992 TTTCATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 19 0.63
14 6 0.20
15 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:2982983 original size:17 final size:17
Alignment explanation
Indices: 2982963--2982999 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2982953 TTAATTTTAT
2982963 TTTATTTATTTATTTCA
1 TTTATTTATTTATTTCA
*
2982980 TTTATTTATTTTTTTCA
1 TTTATTTATTTATTTCA
2982997 TTT
1 TTT
2983000 CAGGTTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTATTTCA
Found at i:2990873 original size:17 final size:17
Alignment explanation
Indices: 2990853--2990904 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2990843 TAAACATTTT
2990853 TTTCTTTCTTCATTTCA
1 TTTCTTTCTTCATTTCA
* *
2990870 TTTCTTTCGT-ATTTAA
1 TTTCTTTCTTCATTTCA
*
2990886 TTTTATTTCTTCATTTCA
1 -TTTCTTTCTTCATTTCA
2990904 T
1 T
2990905 GTAGGATACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 5 0.18
17 18 0.64
18 5 0.18
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTCTTTCTTCATTTCA
Found at i:2993679 original size:20 final size:20
Alignment explanation
Indices: 2993641--2993679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2993631 CACATACATT
**
2993641 TTTACATAAAAACTTAATAA
1 TTTACATAAAAACAAAATAA
*
2993661 TTTACATAAATACAAAATA
1 TTTACATAAAAACAAAATA
2993680 TGTAAGAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTACATAAAAACAAAATAA
Found at i:2996592 original size:23 final size:23
Alignment explanation
Indices: 2996527--2996614 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
2996517 TAGCTCGTAA
2996527 TTTGCACCGAAGTGCCACATA--
1 TTTGCACCGAAGTGCCACATAGG
*
2996548 ATTGTC-CCGAAG-GACCACATAGG
1 TTTG-CACCGAAGTG-CCACATAGG
*
2996571 TTTGCACCGAAGTGCCATATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
2996594 TTTGTACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
2996615 TTTCTCCCGA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.02
21 16 0.29
22 2 0.04
23 36 0.64
24 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:3003991 original size:51 final size:51
Alignment explanation
Indices: 3003929--3004025 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
3003919 GAGATACGTA
* *
3003929 AAGAACCCGATTTAGGTGAGACCCAAACCCAAGTAGAGATCTGTGACGGTG
1 AAGAACACGATTTAGGTGAGACCCAAACCCAAGAAGAGATCTGTGACGGTG
* *
3003980 AAGAACACGATTTAGGTGAGACTCAAACCTAAGAAGAGATCTGTGA
1 AAGAACACGATTTAGGTGAGACCCAAACCCAAGAAGAGATCTGTGA
3004026 ATAACCTGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (51 bp):
AAGAACACGATTTAGGTGAGACCCAAACCCAAGAAGAGATCTGTGACGGTG
Found at i:3007320 original size:2 final size:2
Alignment explanation
Indices: 3007313--3007338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3007303 TTTACTTTTA
3007313 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
3007339 TAATAGTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3007547 original size:26 final size:26
Alignment explanation
Indices: 3007518--3007570 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3007508 GACTTAAAAC
*
3007518 AATTATAGCAGATGTAAGAAAAATGA
1 AATTATAGCAGATCTAAGAAAAATGA
3007544 AATTATAGCAGATCTAAGAAAAATGA
1 AATTATAGCAGATCTAAGAAAAATGA
3007570 A
1 A
3007571 CTTCGTACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.23
Consensus pattern (26 bp):
AATTATAGCAGATCTAAGAAAAATGA
Found at i:3011176 original size:21 final size:20
Alignment explanation
Indices: 3011134--3011208 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 20
3011124 GCCATTTTTG
*
3011134 GTATCGATACCATAGGGTCA
1 GTATCGATACCATAAGGTCA
3011154 GTATCGATACCATAAGAGTCA
1 GTATCGATACCATAAG-GTCA
* *
3011175 GTATCGATACTATCAAGGCCA
1 GTATCGATACCAT-AAGGTCA
*
3011196 GTATCGGTACCAT
1 GTATCGATACCAT
3011209 TATCCTAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.31
21 30 0.62
22 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATAAGGTCA
Found at i:3013254 original size:3 final size:3
Alignment explanation
Indices: 3013246--3013275 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3013236 TTATCCTAAA
3013246 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
3013276 ATAGATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3013311 original size:2 final size:2
Alignment explanation
Indices: 3013304--3013339 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3013294 TCTTTTAAAC
3013304 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3013340 TTCAAAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3013384 original size:25 final size:25
Alignment explanation
Indices: 3013356--3013574 Score: 80
Period size: 27 Copynumber: 9.2 Consensus size: 25
3013346 ACCACGTTAA
3013356 ATATTTTCAAAACCATATATTTATT
1 ATATTTTCAAAACCATATATTTATT
* *
3013381 ATATGTTTTTAAAA-C-TATA-TTA-A
1 ATA--TTTTCAAAACCATATATTTATT
3013404 ATATTTTCAAAACCATATA--TATT
1 ATATTTTCAAAACCATATATTTATT
* *
3013427 ATATGGTTTCAAATCC--ATATGTA-T
1 ATAT--TTTCAAAACCATATATTTATT
* * *
3013451 ATA-TAT--ATA-TATATA-TTA-T
1 ATATTTTCAAAACCATATATTTATT
* ** *
3013470 ATGTTTTCAAATTCATATATATATT
1 ATATTTTCAAAACCATATATTTATT
*
3013495 ATATGTTCTCAAAACCATATATATATT
1 ATAT-TT-TCAAAACCATATATTTATT
* *
3013522 ATTTGTTCTCAAAA--TTATA-TTA-T
1 ATAT-TT-TCAAAACCATATATTTATT
* *
3013545 ATATTTTTAAAACCATATATATATAT
1 ATATTTTCAAAACCATATATTTAT-T
3013571 ATAT
1 ATAT
3013575 ATATATATAT
Statistics
Matches: 144, Mismatches: 26, Indels: 47
0.66 0.12 0.22
Matches are distributed among these distances:
19 6 0.04
20 5 0.03
21 15 0.10
22 6 0.04
23 27 0.19
24 13 0.09
25 26 0.18
26 8 0.06
27 38 0.26
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (25 bp):
ATATTTTCAAAACCATATATTTATT
Found at i:3013395 original size:48 final size:48
Alignment explanation
Indices: 3013320--3013439 Score: 138
Period size: 48 Copynumber: 2.5 Consensus size: 48
3013310 TATTATATAT
* *
3013320 ATATATATATATATATATATTTCAAAACCACGTTAAATATTTTCAAAACC
1 ATATAT-TAT-TATATGTATTTCAAAACCACATTAAATATTTTCAAAACC
* * *
3013370 ATATATTTATTATATGT-TTTTAAAACTATATTAAATATTTTCAAAACC
1 ATATA-TTATTATATGTATTTCAAAACCACATTAAATATTTTCAAAACC
*
3013418 ATATA-TATTATATG-GTTTCAAA
1 ATATATTATTATATGTATTTCAAA
3013440 TCCATATGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
46 15 0.24
48 32 0.52
49 6 0.10
50 8 0.13
51 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (48 bp):
ATATATTATTATATGTATTTCAAAACCACATTAAATATTTTCAAAACC
Found at i:3013410 original size:21 final size:21
Alignment explanation
Indices: 3013334--3013421 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 21
3013324 ATATATATAT
**
3013334 ATATATTTCAAAACCACGTTAA
1 ATAT-TTTCAAAACCATATTAA
3013356 ATATTTTCAAAACCATATATTTATTA
1 ATATTTTCAAAACC--ATA-TTA--A
* * *
3013382 TATGTTTTTAAAACTATATTAA
1 -ATATTTTCAAAACCATATTAA
3013404 ATATTTTCAAAACCATAT
1 ATATTTTCAAAACCATAT
3013422 ATATTATATG
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
21 25 0.48
22 5 0.10
23 1 0.02
24 6 0.12
25 3 0.06
26 1 0.02
27 11 0.21
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATTTTCAAAACCATATTAA
Found at i:3013463 original size:41 final size:40
Alignment explanation
Indices: 3013418--3013498 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
3013408 TTTCAAAACC
*
3013418 ATATATATTATATGGTTTCAAATCCATATGTATATATATAT
1 ATATATATTATATGGTTTCAAATCCATATATATAT-TATAT
* *
3013459 ATATATATTATATGTTTTCAAATTCATATATATATTATAT
1 ATATATATTATATGGTTTCAAATCCATATATATATTATAT
3013499 GTTCTCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 5 0.14
41 32 0.86
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (40 bp):
ATATATATTATATGGTTTCAAATCCATATATATATTATAT
Done.