Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008192.1 Hibiscus syriacus cultivar Beakdansim tig00110809_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: 1702141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:311073 original size:59 final size:60
Alignment explanation
Indices: 310981--311144 Score: 142
Period size: 59 Copynumber: 2.7 Consensus size: 60
310971 TTAGATAGAA
* * * * * *
310981 AAAT-AAATAAATAAAAATGAAAAGACAAATAAAAATAAAAAATAATAGTAGTGATA-TAAAA-
1 AAATCAAAGAAAT-AAAATGAAAA-A-AATTAAAAATAAAAAAAAATAATAGT-AAACAAAAAC
*
311042 AAATCAAAGGAA-AAAA-GAAATAAAGATT-AAAATAAAATAAAAATAATAGTAAACAAAAAC
1 AAATCAAAGAAATAAAATGAAA-AAA-ATTAAAAATAAAA-AAAAATAATAGTAAACAAAAAC
311102 AAATCAAAGAAATAAAATGAAAAAAATTAGATAAATAAAAAAA
1 AAATCAAAGAAATAAAATGAAAAAAATTA-A-AAATAAAAAAA
311145 TATTTTAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
58 12 0.14
59 21 0.25
60 19 0.23
61 11 0.13
62 13 0.15
63 8 0.10
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (60 bp):
AAATCAAAGAAATAAAATGAAAAAAATTAAAAATAAAAAAAAATAATAGTAAACAAAAAC
Found at i:312588 original size:39 final size:38
Alignment explanation
Indices: 312545--312676 Score: 108
Period size: 39 Copynumber: 3.4 Consensus size: 38
312535 TTTTCAAAAC
* *
312545 TATATAATTTATA-TTTTCAAAAATTGCTTTAAAAACTTA
1 TATATAATATATATTTTTCAAAAA-CGCTTTAAAAA-TTA
* *
312584 TATATTATATATATTTTTCAAAAACGTTTTAAAAATTA
1 TATATAATATATATTTTTCAAAAACGCTTTAAAAATTA
* * * *
312622 TATA-ATATATATAAGTTTTT-TAAAATGTTTTAAAAACTA
1 TATATA-ATATAT-A-TTTTTCAAAAACGCTTTAAAAATTA
312661 TATAATATATATATAT
1 TAT-ATA-ATATATAT
312677 ATATATATAT
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
38 13 0.16
39 41 0.52
40 17 0.22
41 8 0.10
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATAATATATATTTTTCAAAAACGCTTTAAAAATTA
Found at i:312632 original size:38 final size:38
Alignment explanation
Indices: 312514--312876 Score: 214
Period size: 35 Copynumber: 9.1 Consensus size: 38
312504 AAACCATATA
* * * * *
312514 ATATATATGTTTAAAAAATAATTTTCAAAACTATATAAT
1 ATATATATTTTTCAAAAAT-GTTTTAAAAATTATATAAT
* *
312553 -T-TATA-TTTTCAAAAATTGCTTTAAAAACTTATATATT
1 ATATATATTTTTCAAAAA-TGTTTTAAAAA-TTATATAAT
*
312590 ATATATATTTTTCAAAAACGTTTTAAAAATTATATAAT
1 ATATATATTTTTCAAAAATGTTTTAAAAATTATATAAT
*
312628 ATATATAAGTTTTT-TAAAATGTTTTAAAAACTATATAATATAT
1 ATATAT-A-TTTTTCAAAAATGTTTTAAAAA-T-TAT-ATA-AT
*
312671 ATATATATATATATAT-ATATATATATGTTTTCAAAATGTTTTAAAAACTATATAAT
1 ATATATAT-T-T-T-TCA-A-A-A-ATGTTTT-AAAA----------ATTATATAAT
*
312727 ATATATATGTTTTC-AAAATGTTTTAAAAACTATATAAT
1 ATATATAT-TTTTCAAAAATGTTTTAAAAATTATATAAT
*
312765 ATAT-T-TTTTTC-AAAATGTTTTCAAAATTATATAAT
1 ATATATATTTTTCAAAAATGTTTTAAAAATTATATAAT
* *
312800 ATATAT-GTTTTCAAAAATGTTTTAAAAACTATAT-AT
1 ATATATATTTTTCAAAAATGTTTTAAAAATTATATAAT
* *
312836 CATATAGA--TTTC-AAAATGTTTTCAAAATTATATAAT
1 -ATATATATTTTTCAAAAATGTTTTAAAAATTATATAAT
312872 ATATA
1 ATATA
312877 CATATATAAA
Statistics
Matches: 265, Mismatches: 23, Indels: 76
0.73 0.06 0.21
Matches are distributed among these distances:
35 55 0.21
36 30 0.11
37 37 0.14
38 30 0.11
39 28 0.11
40 16 0.06
41 4 0.02
42 5 0.02
43 9 0.03
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
48 5 0.02
49 14 0.05
50 5 0.02
51 1 0.00
52 1 0.00
53 1 0.00
54 1 0.00
55 1 0.00
56 11 0.04
57 3 0.01
58 3 0.01
60 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (38 bp):
ATATATATTTTTCAAAAATGTTTTAAAAATTATATAAT
Found at i:312670 original size:2 final size:2
Alignment explanation
Indices: 312659--312696 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
312649 TTTTAAAAAC
312659 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
312697 GTTTTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:312710 original size:60 final size:60
Alignment explanation
Indices: 312620--312734 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
312610 TTTTAAAAAT
*
312620 TATATAATATATATAAGTTTTTTAAAATGTTTTAAAAACTATATAATATATATATATATA
1 TATATAATATATATAAGTTTTTCAAAATGTTTTAAAAACTATATAATATATATATATATA
*
312680 TATATATATATATATATG-TTTTCAAAATGTTTTAAAAACTATATAATATATATAT
1 TATATA-ATATATATAAGTTTTTCAAAATGTTTTAAAAACTATATAATATATATAT
312735 GTTTTCAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 42 0.81
61 10 0.19
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (60 bp):
TATATAATATATATAAGTTTTTCAAAATGTTTTAAAAACTATATAATATATATATATATA
Found at i:312714 original size:99 final size:97
Alignment explanation
Indices: 312582--312768 Score: 304
Period size: 98 Copynumber: 1.9 Consensus size: 97
312572 TTTAAAAACT
* *
312582 TATATATTATATATATTTTTCAAAAACGTTTTAAAAATTATATAATATATATAAGTTTTTTAAAA
1 TATATATTATATATATTTTTCAAAAACGTTTTAAAAACTATATAATATATATAAG-TTTTCAAAA
312647 TGTTTTAAAAACTATATAATATATATATATATA
65 TGTTTTAAAAACTATATAATATATATATATATA
* *
312680 TATATATATATATATATGTTTTC-AAAATGTTTTAAAAACTATATAATATATATATGTTTTCAAA
1 TATATAT-TATATATAT-TTTTCAAAAACGTTTTAAAAACTATATAATATATATAAGTTTTCAAA
312744 ATGTTTTAAAAACTATATAATATAT
64 ATGTTTTAAAAACTATATAATATAT
312769 TTTTTTCAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
98 39 0.47
99 39 0.47
100 5 0.06
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (97 bp):
TATATATTATATATATTTTTCAAAAACGTTTTAAAAACTATATAATATATATAAGTTTTCAAAAT
GTTTTAAAAACTATATAATATATATATATATA
Found at i:312767 original size:72 final size:73
Alignment explanation
Indices: 312684--312876 Score: 286
Period size: 72 Copynumber: 2.6 Consensus size: 73
312674 TATATATATA
* *
312684 TATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATATATGTTTTC-AAAATGT
1 TATATA-ATATATGTTTTCAAAATGTTTTCAAAATTATATAATATATATATGTTTTCAAAAATGT
312748 TTTAAAAAC
65 TTTAAAAAC
*
312757 TATATAATATATTTTTTTCAAAATGTTTTCAAAATTATAT-A-ATATATATGTTTTCAAAAATGT
1 TATATAATATA-TGTTTTCAAAATGTTTTCAAAATTATATAATATATATATGTTTTCAAAAATGT
312820 TTTAAAAAC
65 TTTAAAAAC
*
312829 TATAT-ATCATATAGATTTCAAAATGTTTTCAAAATTATATAATATATA
1 TATATAAT-ATAT-GTTTTCAAAATGTTTTCAAAATTATATAATATATA
312877 CATATATAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
71 17 0.16
72 55 0.50
73 32 0.29
74 5 0.05
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (73 bp):
TATATAATATATGTTTTCAAAATGTTTTCAAAATTATATAATATATATATGTTTTCAAAAATGTT
TTAAAAAC
Found at i:312776 original size:35 final size:36
Alignment explanation
Indices: 312682--312876 Score: 270
Period size: 35 Copynumber: 5.4 Consensus size: 36
312672 TATATATATA
312682 TATATATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATA-ATATATATGTTTTCAAAATGTTTTAAAAAC
312719 TATATAATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATAT-A-ATATATATGTTTTCAAAATGTTTTAAAAAC
* * *
312757 TATATAATATAT-TTTTTTCAAAATGTTTTCAAAAT
1 TATATAATATATATGTTTTCAAAATGTTTTAAAAAC
312792 TATATAATATATATGTTTTCAAAAATGTTTTAAAAAC
1 TATATAATATATATGTTTTC-AAAATGTTTTAAAAAC
* * *
312829 TATAT-ATCATATA-GATTTCAAAATGTTTTCAAAAT
1 TATATAAT-ATATATGTTTTCAAAATGTTTTAAAAAC
312864 TATATAATATATA
1 TATATAATATATA
312877 CATATATAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 12
0.87 0.05 0.07
Matches are distributed among these distances:
35 56 0.39
36 21 0.15
37 30 0.21
38 37 0.26
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATAATATATATGTTTTCAAAATGTTTTAAAAAC
Found at i:318151 original size:4 final size:4
Alignment explanation
Indices: 318142--318173 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
318132 ATTATATGGT
*
318142 ATGC ATGC ATGC ATGC ATGC ATGC ATTC ATGC
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC
318174 TGCCAGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (4 bp):
ATGC
Found at i:319202 original size:15 final size:15
Alignment explanation
Indices: 319184--319322 Score: 72
Period size: 15 Copynumber: 9.0 Consensus size: 15
319174 AATATAAGTT
319184 TATATATAAAC--TA
1 TATATATAAACTATA
319197 TATATATAAACTATA
1 TATATATAAACTATA
*
319212 TTTATATTATAAATTATA
1 --TATA-TATAAACTATA
*
319230 TA-ATTATTATAAGT-TA
1 TATA-TA-TA-AACTATA
* *
319246 TATATATAAATTATG
1 TATATATAAACTATA
* *
319261 TTTATATGAACTATA
1 TATATATAAACTATA
*
319276 TATATATATATA-AACTA
1 TATATATA-A-ACTA-TA
*
319293 TATATGTAAACTATA
1 TATATATAAACTATA
**
319308 TAGGTATAAACTATA
1 TATATATAAACTATA
319323 AAAAGTATAT
Statistics
Matches: 97, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
13 11 0.11
14 3 0.03
15 41 0.42
16 14 0.14
17 18 0.19
18 10 0.10
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:319224 original size:18 final size:19
Alignment explanation
Indices: 319195--319295 Score: 64
Period size: 19 Copynumber: 5.9 Consensus size: 19
319185 ATATATAAAC
319195 TATATATATAAACTATATT
1 TATATATATAAACTATATT
*
319214 TATAT-TATAAA-T-TATA
1 TATATATATAAACTATATT
* *
319230 TA-AT-TAT-TA-TA-AGT
1 TATATATATAAACTATATT
*
319244 TATATATATAAA-T-TATG
1 TATATATATAAACTATATT
* *
319261 T-T-TATATGAACTATATA
1 TATATATATAAACTATATT
319278 TATATATATAAACTATAT
1 TATATATATAAACTATAT
319296 ATGTAAACTA
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
14 5 0.08
15 14 0.22
16 10 0.16
17 9 0.14
18 7 0.11
19 18 0.29
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (19 bp):
TATATATATAAACTATATT
Found at i:319259 original size:13 final size:13
Alignment explanation
Indices: 319158--319259 Score: 65
Period size: 13 Copynumber: 8.2 Consensus size: 13
319148 AAAAAACATA
*
319158 ATATATATATA-T
1 ATATATATAAATT
*
319170 ATATAATATAAGTT
1 ATAT-ATATAAATT
*
319184 -TATATATAAACT
1 ATATATATAAATT
*
319196 ATATATATAAACT
1 ATATATATAAATT
*
319209 ATAT-T-TATATT
1 ATATATATAAATT
*
319220 ATAAATTATATAA-T
1 ATATA-TATA-AATT
*
319234 -TAT-TATAAGTT
1 ATATATATAAATT
319245 ATATATATAAATT
1 ATATATATAAATT
319258 AT
1 AT
319260 GTTTATATGA
Statistics
Matches: 69, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
10 1 0.01
11 12 0.17
12 15 0.22
13 36 0.52
14 4 0.06
15 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (13 bp):
ATATATATAAATT
Found at i:319279 original size:13 final size:13
Alignment explanation
Indices: 319278--319322 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
319268 GAACTATATA
319278 TATATATATAAAC
1 TATATATATAAAC
*
319291 TATATATGTAAAC
1 TATATATATAAAC
319304 TATATAGGTATAAAC
1 TATATA--TATAAAC
319319 TATA
1 TATA
319323 AAAAGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 18 0.64
15 10 0.36
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:319309 original size:2 final size:2
Alignment explanation
Indices: 319158--319297 Score: 59
Period size: 2 Copynumber: 72.0 Consensus size: 2
319148 AAAAAACATA
* *
319158 AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
* * *
319200 AT AT AA ACT AT AT TT AT AT -T AT AA AT -T AT AT A- AT -T AT -T
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
319238 AT A- AGT -T AT AT AT AT AA AT -T AT GT TT AT AT GA- ACT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT
*
319277 AT AT AT AT AT AA ACT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT
319298 GTAAACTATA
Statistics
Matches: 103, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
1 11 0.11
2 87 0.84
3 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:319490 original size:17 final size:18
Alignment explanation
Indices: 319468--319502 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
319458 GAGGGAAATT
319468 TTGAGAATATAG-GGAAA
1 TTGAGAATATAGAGGAAA
*
319485 TTGAGAATTTAGAGGAAA
1 TTGAGAATATAGAGGAAA
319503 ATTGGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.26
Consensus pattern (18 bp):
TTGAGAATATAGAGGAAA
Found at i:319504 original size:19 final size:18
Alignment explanation
Indices: 319451--319551 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 18
319441 TTTTATTTGG
319451 GAATTTAGAGGGAAATTTTGA
1 GAATTTAGA-GGAAA--TTGA
*
319472 GAATATAG-GGAAATTGA
1 GAATTTAGAGGAAATTGA
*
319489 GAATTTAGAGGAAAATTGG
1 GAATTTAGAGG-AAATTGA
* *
319508 GAAATTTAGAGGGAATAGA
1 G-AATTTAGAGGAAATTGA
* *
319527 AAATTTTGGAGGGAAATTGA
1 GAA-TTTAGA-GGAAATTGA
319547 GAATT
1 GAATT
319552 GAGATTTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
17 11 0.17
18 4 0.06
19 23 0.36
20 19 0.30
21 7 0.11
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (18 bp):
GAATTTAGAGGAAATTGA
Found at i:320030 original size:15 final size:15
Alignment explanation
Indices: 320005--320056 Score: 79
Period size: 15 Copynumber: 3.4 Consensus size: 15
319995 ATAAATCATG
320005 TATAGTATATATAAAC
1 TATA-TATATATAAAC
320021 TATATATATATAACAC
1 TATATATATATAA-AC
320037 -ATATATATATAAAC
1 TATATATATATAAAC
320051 TATATA
1 TATATA
320057 AAGTAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.06
15 26 0.76
16 6 0.18
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:320127 original size:21 final size:21
Alignment explanation
Indices: 320089--320128 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
320079 ATAGAAACCC
* **
320089 TAAACCCTAAACTTTAAACTA
1 TAAACACTAAACCATAAACTA
320110 TAAACACTAAACCATAAAC
1 TAAACACTAAACCATAAAC
320129 CCTAATGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACACTAAACCATAAACTA
Found at i:320218 original size:21 final size:21
Alignment explanation
Indices: 320194--320244 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
320184 TAGTTTATAG
*
320194 AAACCCTAAATCA-TAAACTAT
1 AAACCCTAAAT-ATTAAACCAT
* *
320215 AAACCATAAATATTAAACCCT
1 AAACCCTAAATATTAAACCAT
320236 AAACCCTAA
1 AAACCCTAA
320245 TATAAATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAATATTAAACCAT
Found at i:320240 original size:111 final size:112
Alignment explanation
Indices: 320045--320263 Score: 350
Period size: 111 Copynumber: 2.0 Consensus size: 112
320035 ACATATATAT
* * * *
320045 ATAAACTATATAAAGTAATAAATTATATAGGTTTATAGAAACCCTAAACCCTAAACTTTAAACTA
1 ATAAACTATATAAAGTAATAAAATATATAGGTTTATAGAAACCCTAAACCATAAACTATAAACCA
*
320110 TAAACACTAAACCATAAACCCTAATGTAAATAGACTAGCACTAATGC
66 TAAACACTAAACCATAAACCCTAATATAAATAGACTAGCACTAATGC
*
320157 ATAAACTATATAAAGTAATAAAATATATA-GTTTATAGAAACCCTAAATCATAAACTATAAACCA
1 ATAAACTATATAAAGTAATAAAATATATAGGTTTATAGAAACCCTAAACCATAAACTATAAACCA
* * *
320221 TAAATATTAAACCCTAAACCCTAATATAAATAGACTAGCACTA
66 TAAACACTAAACCATAAACCCTAATATAAATAGACTAGCACTA
320264 TGTTAGTGTT
Statistics
Matches: 98, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 70 0.71
112 28 0.29
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27
Consensus pattern (112 bp):
ATAAACTATATAAAGTAATAAAATATATAGGTTTATAGAAACCCTAAACCATAAACTATAAACCA
TAAACACTAAACCATAAACCCTAATATAAATAGACTAGCACTAATGC
Found at i:320585 original size:14 final size:14
Alignment explanation
Indices: 320566--320609 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
320556 AATGGACTAG
*
320566 CACTAAACCATAAA
1 CACTAAACCCTAAA
320580 CACTAAACCCTAAA
1 CACTAAACCCTAAA
* *
320594 CCCTACACCCTAAA
1 CACTAAACCCTAAA
320608 CA
1 CA
320610 ATTACAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.14
Consensus pattern (14 bp):
CACTAAACCCTAAA
Found at i:321318 original size:17 final size:17
Alignment explanation
Indices: 321258--321318 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
321248 CTATAAAAAG
*
321258 TATATA-GTTTATAAAC
1 TATATATGTATATAAAC
* *
321274 TATA-ATTTATATTAA-
1 TATATATGTATATAAAC
*
321289 TATAGTATATATATAAAC
1 TATA-TATGTATATAAAC
321307 TATATATGTATA
1 TATATATGTATA
321319 AATTATATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.14
16 10 0.29
17 16 0.46
18 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (17 bp):
TATATATGTATATAAAC
Found at i:321496 original size:7 final size:7
Alignment explanation
Indices: 321475--321548 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
321465 TAATTTATGA
321475 AAACTCT
1 AAACTCT
321482 AAAC-CT
1 AAACTCT
321488 AAACTCT
1 AAACTCT
*
321495 AAACCCT
1 AAACTCT
321502 AAA-TCAT
1 AAACTC-T
*
321509 AAACACT
1 AAACTCT
321516 AAAACT-T
1 -AAACTCT
321523 AAA-TCTT
1 AAACTC-T
*
321530 AAACCCT
1 AAACTCT
*
321537 AAACACT
1 AAACTCT
321544 AAACT
1 AAACT
321549 ACATAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
5 1 0.02
6 10 0.19
7 36 0.68
8 6 0.11
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACTCT
Found at i:321504 original size:14 final size:14
Alignment explanation
Indices: 321475--321548 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
321465 TAATTTATGA
321475 AAACTCTAAA-CCT
1 AAACTCTAAACCCT
321488 AAACTCTAAACCCT
1 AAACTCTAAACCCT
*
321502 AAA-TCATAAACACT
1 AAACTC-TAAACCCT
* *
321516 AAAACT-TAAATCTT
1 -AAACTCTAAACCCT
* *
321530 AAACCCTAAACACT
1 AAACTCTAAACCCT
321544 AAACT
1 AAACT
321549 ACATAAATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
13 16 0.34
14 27 0.57
15 3 0.06
16 1 0.02
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACTCTAAACCCT
Found at i:321517 original size:21 final size:21
Alignment explanation
Indices: 321487--321555 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
321477 ACTCTAAACC
*
321487 TAAACTCTAAACCCTAAATCA
1 TAAACACTAAACCCTAAATCA
* * *
321508 TAAACACTAAAACTTAAATCT
1 TAAACACTAAACCCTAAATCA
* *
321529 TAAACCCTAAACACTAAACTACA
1 TAAACACTAAACCCTAAA-T-CA
321552 TAAA
1 TAAA
321556 TTAATAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 31 0.84
22 1 0.03
23 5 0.14
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACACTAAACCCTAAATCA
Found at i:321589 original size:7 final size:7
Alignment explanation
Indices: 321579--321636 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
321569 TAGTGTATAA
321579 AAACCCT
1 AAACCCT
*
321586 AAACCTT
1 AAACCCT
* *
321593 AAATCAT
1 AAACCCT
321600 AAACCCT
1 AAACCCT
**
321607 AAACTTT
1 AAACCCT
*
321614 AAACCAT
1 AAACCCT
321621 AAACCCT
1 AAACCCT
*
321628 AAATCCT
1 AAACCCT
321635 AA
1 AA
321637 TATAAATGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:321604 original size:21 final size:21
Alignment explanation
Indices: 321579--321630 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
321569 TAGTGTATAA
*
321579 AAACCCTAAACCTTAAATCAT
1 AAACCCTAAACCTTAAACCAT
*
321600 AAACCCTAAACTTTAAACCAT
1 AAACCCTAAACCTTAAACCAT
321621 AAACCCTAAA
1 AAACCCTAAA
321631 TCCTAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCCTAAACCTTAAACCAT
Found at i:322125 original size:148 final size:148
Alignment explanation
Indices: 321857--322145 Score: 569
Period size: 148 Copynumber: 2.0 Consensus size: 148
321847 ATATGACATG
*
321857 TACTATTTATGAACCATATAATATGCAATGTGACATATTAATTATTTAACACCTAATTAATCATG
1 TACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAATTAATCATG
321922 TTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATTTAATATGTATG
66 TTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATTTAATATGTATG
321987 TATAAACCATACATGTAC
131 TATAAACCATACATGTAC
322005 TACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAATTAATCATG
1 TACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAATTAATCATG
322070 TTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATTTAATATGTATG
66 TTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATTTAATATGTATG
322135 TATAAACCATA
131 TATAAACCATA
322146 TATAGTATAT
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 140 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (148 bp):
TACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAATTAATCATG
TTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATTTAATATGTATG
TATAAACCATACATGTAC
Found at i:322171 original size:15 final size:15
Alignment explanation
Indices: 322146--322211 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
322136 ATAAACCATA
322146 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
322162 TATATATATATAACC
1 TATATATATATAAAC
*
322177 TATATATATATATA-
1 TATATATATATAAAC
* *
322191 TATAAACTATATAAAG
1 TATATA-TATATAAAC
322207 TATAT
1 TATAT
322212 TACTTATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
14 5 0.12
15 29 0.69
16 8 0.19
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:322188 original size:21 final size:21
Alignment explanation
Indices: 322162--322203 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
322152 ATATATAAAC
*
322162 TATATATATATAACCTATATA
1 TATATATATATAAACTATATA
322183 TATATATATATAAACTATATA
1 TATATATATATAAACTATATA
322204 AAGTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATATATATAAACTATATA
Found at i:322203 original size:2 final size:2
Alignment explanation
Indices: 322143--322194 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
322133 TGTATAAACC
* * *
322143 AT AT AT AGT AT AT AT AA ACT AT AT AT AT AT A- AC CT AT AT AT AT
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
322186 AT AT AT AT A
1 AT AT AT AT A
322195 AACTATATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:322286 original size:7 final size:7
Alignment explanation
Indices: 322276--322344 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
322266 ATAGAAATCT
*
322276 TAAACCC
1 TAAACCA
*
322283 TAAATCA
1 TAAACCA
*
322290 TAAACCT
1 TAAACCA
322297 TAAACCA
1 TAAACCA
**
322304 TAAACTT
1 TAAACCA
322311 TAAACCA
1 TAAACCA
322318 TAAA-CA
1 TAAACCA
*
322324 CTAAA-TA
1 -TAAACCA
322331 CTAAACCA
1 -TAAACCA
322339 TAAACC
1 TAAACC
322345 CTAATATAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
6 2 0.04
7 46 0.94
8 1 0.02
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:322293 original size:14 final size:14
Alignment explanation
Indices: 322270--322342 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 14
322260 TAGTTTATAG
*
322270 AAATCTTAAACCCT
1 AAATCATAAACCCT
*
322284 AAATCATAAACCTT
1 AAATCATAAACCCT
* **
322298 AAACCATAAACTTT
1 AAATCATAAACCCT
* *
322312 AAACCATAAACACT
1 AAATCATAAACCCT
*
322326 AAAT-ACTAAACCAT
1 AAATCA-TAAACCCT
322340 AAA
1 AAA
322343 CCCTAATATA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
13 1 0.02
14 48 0.98
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCATAAACCCT
Found at i:322300 original size:21 final size:21
Alignment explanation
Indices: 322276--322348 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
322266 ATAGAAATCT
*
322276 TAAACCCTAAATCATAAACCT
1 TAAACCCTAAATCATAAACCA
* *
322297 TAAACCATAAA-CTTTAAACCA
1 TAAACCCTAAATC-ATAAACCA
*
322318 TAAACACTAAAT-ACTAAACCA
1 TAAACCCTAAATCA-TAAACCA
322339 TAAACCCTAA
1 TAAACCCTAA
322349 TATAAATAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAATCATAAACCA
Found at i:322348 original size:14 final size:14
Alignment explanation
Indices: 322276--322328 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
322266 ATAGAAATCT
*
322276 TAAACCCTAAATCA
1 TAAACCCTAAACCA
*
322290 TAAACCTTAAACCA
1 TAAACCCTAAACCA
**
322304 TAAACTTTAAACCA
1 TAAACCCTAAACCA
*
322318 TAAACACTAAA
1 TAAACCCTAAA
322329 TACTAAACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:322840 original size:16 final size:16
Alignment explanation
Indices: 322819--322857 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
322809 CGGATCATTT
322819 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
322835 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
322851 ACAGGTC
1 ACAGGTC
322858 GGGTAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:322957 original size:31 final size:32
Alignment explanation
Indices: 322882--322958 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
322872 ATTTACCAGG
322882 TCAATCTCGGGTTCGGGTTCATATCAATCGGAT
1 TCAAT-TCGGGTTCGGGTTCATATCAATCGGAT
* * **
322915 GCAGTTCGGGTTCGGGTATCATAT-TTTC-GAT
1 TCAATTCGGGTTCGGGT-TCATATCAATCGGAT
322946 TCAATTCGGGTTC
1 TCAATTCGGGTTC
322959 AGGTCGTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 14 0.38
32 14 0.38
33 9 0.24
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (32 bp):
TCAATTCGGGTTCGGGTTCATATCAATCGGAT
Found at i:328391 original size:47 final size:47
Alignment explanation
Indices: 328322--328411 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
328312 CCAGATGCTC
* *
328322 CACGATATTTCAAGGAAATCTCCAAAAATG-TGTTTTAACAGTTGCCT
1 CACGATAGTTAAAGGAAATCTCCAAAAA-GATGTTTTAACAGTTGCCT
328369 CACGATAGTTAAAGGAAATCTCCAAAAAGATGTTTTAACAGTT
1 CACGATAGTTAAAGGAAATCTCCAAAAAGATGTTTTAACAGTT
328412 CTTGACTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (47 bp):
CACGATAGTTAAAGGAAATCTCCAAAAAGATGTTTTAACAGTTGCCT
Found at i:332367 original size:21 final size:21
Alignment explanation
Indices: 332334--332386 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
332324 ATTCTAACTA
332334 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
332355 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
332376 TCGCAATGCGA
1 TCGCATTGCGA
332387 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:332401 original size:20 final size:20
Alignment explanation
Indices: 332376--332549 Score: 285
Period size: 20 Copynumber: 8.7 Consensus size: 20
332366 TTTTCCTAAT
332376 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
332396 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATACG-TAAA
*
332417 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
332437 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
332457 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
332477 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
332497 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
332517 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
332537 TCGCAACGCGAAT
1 TCGCAATGCGAAT
332550 CTGACTATCG
Statistics
Matches: 142, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
20 126 0.89
21 16 0.11
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:332800 original size:20 final size:20
Alignment explanation
Indices: 332775--332891 Score: 73
Period size: 20 Copynumber: 6.5 Consensus size: 20
332765 AGAATAGTTT
332775 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
332795 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
332811 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
332828 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
332844 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
332862 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
332882 ACTATCGCAA
1 ACTATCGCAA
332892 CGAGAGAATC
Statistics
Matches: 78, Mismatches: 5, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 14 0.18
16 10 0.13
17 8 0.10
18 5 0.06
19 7 0.09
20 34 0.44
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:332821 original size:34 final size:34
Alignment explanation
Indices: 332778--332871 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
332768 ATAGTTTACT
* * *
332778 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
**
332812 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
*
332845 ATCGCAACGCGAAAATGACTATCGCAA
1 ATCGCAATGCGAAAATGACTATCGCAA
332872 TGCGAATTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACAACAAA
Found at i:333514 original size:21 final size:21
Alignment explanation
Indices: 333423--333527 Score: 88
Period size: 21 Copynumber: 5.0 Consensus size: 21
333413 GACTCACATG
*
333423 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
333445 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
**
333465 TCATCCCTCAAG-GGTCCCCTC
1 TCATCGTTCAAGAGG-CCCCTC
* * * *
333486 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
333507 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
333528 CCAACATTCT
Statistics
Matches: 63, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
20 5 0.08
21 55 0.87
22 3 0.05
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:333527 original size:42 final size:42
Alignment explanation
Indices: 333421--333530 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
333411 CCGACTCACA
* *
333421 TGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGTCCCT-CCC-ACCGTTCAAGAGGCCAC
* **
333463 TATCATCCCTCAAG-GGTCCCCTCCCACCGTTCAAGAGGCCAC
1 TGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCAC
*
333505 TGTCATCGTTGAAGAGGTCCCTCCCA
1 TGTCATCGTTCAAGAGGTCCCTCCCA
333531 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
41 2 0.04
42 44 0.80
43 6 0.11
44 3 0.05
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCAC
Found at i:334931 original size:14 final size:14
Alignment explanation
Indices: 334912--334947 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
334902 ATTGCTTAAT
334912 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
334926 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
334940 TGATTTGT
1 TGATTTGT
334948 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:335149 original size:20 final size:20
Alignment explanation
Indices: 335124--335217 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
335114 GCGATTCTCT
335124 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
335144 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
335164 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
335184 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
335204 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
335218 AATGAATGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 67 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:338687 original size:20 final size:20
Alignment explanation
Indices: 338662--338708 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
338652 AAATTCAGTA
*
338662 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
338682 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
338702 TTGCGAT
1 TTGCGAT
338709 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:338718 original size:20 final size:20
Alignment explanation
Indices: 338695--338788 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
338685 CGATAGTCAG
*
338695 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
338715 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
338735 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
338756 ATTCACGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
338776 ATTTGCATTGCGA
1 ATTCGCATTGCGA
338789 ATTAGGAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:338826 original size:61 final size:60
Alignment explanation
Indices: 338683--338829 Score: 179
Period size: 61 Copynumber: 2.4 Consensus size: 60
338673 AGAATCTCGT
* * * *
338683 TGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCAT
1 TGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACGAAATCGCAA
** * * *
338743 TGCGATTTTCCA-AATTCACGTTGCGATTTACGTATTTGCATTGCGAATTAGGAAAATCGCAA
1 TGCGATAGT-CAGAA-TCGCGTTGCGATTTACGTATTCGCATTGCGAATTACG-AAATCGCAA
338805 TGCGATAGTCAGAATCGCGTTGCGA
1 TGCGATAGTCAGAATCGCGTTGCGA
338830 ATCTGGAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
60 8 0.11
61 47 0.66
62 16 0.23
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (60 bp):
TGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTACGAAATCGCAA
Found at i:343139 original size:20 final size:20
Alignment explanation
Indices: 343114--343170 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
343104 TAATGTCATG
*
343114 AGGGTATCGATACCCCCAGT
1 AGGGTATCGATACCCCCAAT
343134 AGGGTATCGATACCCCCAAT
1 AGGGTATCGATACCCCCAAT
343154 AGGGTATCGATACCCCC
1 AGGGTATCGATACCCCC
343171 TAAAGGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (20 bp):
AGGGTATCGATACCCCCAAT
Found at i:344728 original size:24 final size:24
Alignment explanation
Indices: 344701--344768 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
344691 TATGTGGCCA
344701 TTCGGGACAAATTCTACGCGATC-C
1 TTCGGGACAAATTCTACGCGA-CAC
344725 TTCGGGACAAATTTCTACGCGACAC
1 TTCGGGACAAA-TTCTACGCGACAC
344750 TTCGGTG-CAAAATTCTACG
1 TTCGG-GAC-AAATTCTACG
344769 TGAAACTACG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
24 12 0.30
25 24 0.60
26 4 0.10
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (24 bp):
TTCGGGACAAATTCTACGCGACAC
Found at i:344780 original size:25 final size:25
Alignment explanation
Indices: 344709--344784 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
344699 CATTCGGGAC
** *
344709 AAATTCTACGCGATCCTTCGG-GACA
1 AAATTCTACGCGAAACTACGGTG-CA
* * *
344734 AATTTCTACGCGACACTTCGGTGCA
1 AAATTCTACGCGAAACTACGGTGCA
*
344759 AAATTCTACGTGAAACTACGGTGCA
1 AAATTCTACGCGAAACTACGGTGCA
344784 A
1 A
344785 TTTATATGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 42 0.98
26 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (25 bp):
AAATTCTACGCGAAACTACGGTGCA
Found at i:348572 original size:31 final size:30
Alignment explanation
Indices: 348526--348612 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
348516 AAATATATAA
348526 TTTT-TAAAATTATATTTTAATCCCTAAAC
1 TTTTATAAAATTATATTTTAATCCCTAAAC
*
348555 TTTTATAAAATTTATATTTTAGTCGCC-AAAC
1 TTTTATAAAA-TTATATTTTAATC-CCTAAAC
* *
348586 TTTTA-AAAATTACATTTTAATCACTAA
1 TTTTATAAAATTATATTTTAATCCCTAA
348613 CCGAAATTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.02
29 17 0.34
30 9 0.18
31 21 0.42
32 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTTATAAAATTATATTTTAATCCCTAAAC
Found at i:352883 original size:2 final size:2
Alignment explanation
Indices: 352876--352917 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
352866 TTACATCATA
352876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
352917 A
1 A
352918 CCACAGCGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354141 original size:3 final size:3
Alignment explanation
Indices: 354133--354175 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
354123 TTTATTTTAT
* * *
354133 TAA TAA TAA TAA TTA TTA TTA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
354176 GGAGCCTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:354157 original size:21 final size:21
Alignment explanation
Indices: 354124--354166 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
354114 TCTGTTGTCT
354124 TTATTTTATTAATAATAATAA
1 TTATTTTATTAATAATAATAA
354145 TTATTATTA-TAATAATAATAA
1 TTATT-TTATTAATAATAATAA
354166 T
1 T
354167 AATAATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTTTATTAATAATAATAA
Found at i:354160 original size:24 final size:24
Alignment explanation
Indices: 354124--354169 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
354114 TCTGTTGTCT
* *
354124 TTATTTTATTAATAATAATAATTA
1 TTATTATAATAATAATAATAATTA
354148 TTATTATAATAATAATAATAAT
1 TTATTATAATAATAATAATAAT
354170 AATAATGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATTATAATAATAATAATAATTA
Found at i:354975 original size:22 final size:24
Alignment explanation
Indices: 354931--354978 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
354921 GTTAATGACA
354931 TTTTTTGTGATATTGATTATAAATT
1 TTTTTTGTGATATT-ATTATAAATT
*
354956 TTTTTTGTG-TATT-TTTTAAATT
1 TTTTTTGTGATATTATTATAAATT
354978 T
1 T
354979 AATTAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
24 4 0.18
25 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (24 bp):
TTTTTTGTGATATTATTATAAATT
Found at i:356451 original size:15 final size:16
Alignment explanation
Indices: 356426--356455 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
356416 TCTAAGTAAT
356426 AATTATAAAAAAAATC
1 AATTATAAAAAAAATC
356442 AATT-TAAAAAAAAT
1 AATTATAAAAAAAAT
356456 AAAAGATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AATTATAAAAAAAATC
Found at i:356696 original size:16 final size:17
Alignment explanation
Indices: 356661--356703 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
356651 TTATGAGGTA
356661 AAAAATAATATTATTGT
1 AAAAATAATATTATTGT
356678 AAAAAT-ATAATTATT-T
1 AAAAATAAT-ATTATTGT
356694 -AAAATAATAT
1 AAAAATAATAT
356704 CTTTACCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAAATAATATTATTGT
Found at i:356748 original size:18 final size:17
Alignment explanation
Indices: 356725--356758 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
356715 CGATATCATA
*
356725 ATATTATTTGTTCATATT
1 ATATTATAT-TTCATATT
356743 ATATTATATTTCATAT
1 ATATTATATTTCATAT
356759 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
ATATTATATTTCATATT
Found at i:357434 original size:6 final size:6
Alignment explanation
Indices: 357423--357473 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
357413 CTAACATCTC
* * *
357423 TATTAG TATTAG TATTAG TATTGG TATTAG TATTAG TATTGG TATTGG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
357471 TAT
1 TAT
357474 AGTGTTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:357449 original size:18 final size:18
Alignment explanation
Indices: 357423--357473 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
357413 CTAACATCTC
*
357423 TATTAGTATTAGTATTAG
1 TATTGGTATTAGTATTAG
357441 TATTGGTATTAGTATTAG
1 TATTGGTATTAGTATTAG
*
357459 TATTGGTATTGGTAT
1 TATTGGTATTAGTAT
357474 AGTGTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (18 bp):
TATTGGTATTAGTATTAG
Found at i:358428 original size:69 final size:70
Alignment explanation
Indices: 358317--358458 Score: 277
Period size: 69 Copynumber: 2.0 Consensus size: 70
358307 AAAAACTCAT
358317 TATACCGATGTTTTTACCGAAATATCACCCATAACATCAATAATTACCTTTCATACACTCTCA-C
1 TATACCGATGTTTTTACCGAAATATCACCCATAACATCAATAATTACCTTTCATACACTCTCAGC
358381 CTTAA
66 CTTAA
358386 TATACCGATGTTTTTACCGAAATATCACCCATAACATCAATAATTACCTTTCATACACTCTCAGC
1 TATACCGATGTTTTTACCGAAATATCACCCATAACATCAATAATTACCTTTCATACACTCTCAGC
358451 CTTAA
66 CTTAA
358456 TAT
1 TAT
358459 TATCGATATG
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 63 0.88
70 9 0.12
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (70 bp):
TATACCGATGTTTTTACCGAAATATCACCCATAACATCAATAATTACCTTTCATACACTCTCAGC
CTTAA
Found at i:362341 original size:14 final size:15
Alignment explanation
Indices: 362322--362354 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
362312 TAATTATATC
362322 TAAATAA-AAACATA
1 TAAATAACAAACATA
*
362336 TAAATAACCAACATA
1 TAAATAACAAACATA
362351 TAAA
1 TAAA
362355 AAGCTGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAATAACAAACATA
Found at i:362486 original size:16 final size:17
Alignment explanation
Indices: 362467--362501 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
362457 TTTAATAAAA
362467 AAAACTTA-TTTAAACT
1 AAAACTTATTTTAAACT
362483 AAAACTTATTTTAAACT
1 AAAACTTATTTTAAACT
362500 AA
1 AA
362502 TACACGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAACTTATTTTAAACT
Found at i:363762 original size:53 final size:53
Alignment explanation
Indices: 363660--363968 Score: 389
Period size: 53 Copynumber: 5.9 Consensus size: 53
363650 TCTTCAAATG
* * ***
363660 ACGGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCA
* ** * *
363714 ACGGGTTCGCTCCCTATTGCTTCAATGAGTAGAACTCGAATAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCA
363767 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCA
*
363820 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCA
* * * *
363873 AC-AG-TC-CTCCCTCTTGCTTCAAGGAGTAAAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCA
* * *
363923 AC-AG-TC-CTCCCTCTTGCTTCAGGGAGTAAAACTTGAACAATCTTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
363969 AGTGTGATTC
Statistics
Matches: 233, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
50 86 0.37
51 2 0.01
52 1 0.00
53 119 0.51
54 18 0.08
55 7 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCA
Found at i:364408 original size:42 final size:42
Alignment explanation
Indices: 364362--364588 Score: 192
Period size: 42 Copynumber: 5.5 Consensus size: 42
364352 CAGAGGACTT
364362 ATCATC-TCGCTCGAAAGACTTACAAATGACCCGAAGGATTTC
1 ATCATCAT-GCTCGAAAGACTTACAAATGACCCGAAGGATTTC
* *
364404 ATCATCGTGCTCGAAAGACTTAC---TGA--TG-A--ATTTGC
1 ATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTT-C
* * * * * *
364439 TTCA-CTACT-CTTCGGTGAAGGCTTA-AAATGGCCCGGAGGACTT-
1 ATCATC-A-TGC-TC-G-AAAGACTTACAAATGACCCGAAGGATTTC
*
364482 ATCACCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTC
** *
364524 ATCATCATGCTCGAAAGACTTACTGATGACCCGAAGAATTTC
1 ATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTC
364566 ATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTAC
364589 TGATGGCACT
Statistics
Matches: 148, Mismatches: 18, Indels: 38
0.73 0.09 0.19
Matches are distributed among these distances:
34 5 0.03
35 5 0.03
36 4 0.03
37 2 0.01
38 7 0.05
39 3 0.02
40 9 0.06
41 16 0.11
42 86 0.58
43 7 0.05
44 1 0.01
45 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACAAATGACCCGAAGGATTTC
Found at i:364528 original size:120 final size:120
Alignment explanation
Indices: 364325--364552 Score: 395
Period size: 120 Copynumber: 1.9 Consensus size: 120
364315 TTGCTCCAAC
* *
364325 ACTCTTCTGAGAAGGCTTAAAATGGCCCAGAGGACTTATCATCTCGCTCGAAAGACTTACAAATG
1 ACTCTTCGGAGAAGGCTTAAAATGGCCCAGAGGACTTATCACCTCGCTCGAAAGACTTACAAATG
*
364390 ACCCGAAGGATTTCATCATCGTGCTCGAAAGACTTACTGATGAATTTGCTTCACT
66 ACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
* *
364445 ACTCTTCGGTGAAGGCTTAAAATGGCCCGGAGGACTTATCACCAT-GCTCGAAAGACTTACAAAT
1 ACTCTTCGGAGAAGGCTTAAAATGGCCCAGAGGACTTATCACC-TCGCTCGAAAGACTTACAAAT
364509 GACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGA
65 GACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGA
364553 CCCGAAGAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
120 101 0.99
121 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (120 bp):
ACTCTTCGGAGAAGGCTTAAAATGGCCCAGAGGACTTATCACCTCGCTCGAAAGACTTACAAATG
ACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
Found at i:364861 original size:42 final size:41
Alignment explanation
Indices: 364779--364862 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 41
364769 TTACGGATTG
* * *
364779 CCCGAAGGACTTATCATCCTGCTCTAAAGGCTTACAGATGA
1 CCCGAAGGACTTAGCATCATGCTCTAAAGACTTACAGATGA
* *
364820 CCCGAAGGATTTAAGCATCATGCT-TGAAAGACTTACTGATGA
1 CCCGAAGGACTT-AGCATCATGCTCT-AAAGACTTACAGATGA
364862 C
1 C
364863 ACTAAGGTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 12 0.33
42 24 0.67
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (41 bp):
CCCGAAGGACTTAGCATCATGCTCTAAAGACTTACAGATGA
Found at i:370231 original size:21 final size:21
Alignment explanation
Indices: 370205--370249 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
370195 GATTTCTGGG
* *
370205 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
370226 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
370247 CAA
1 CAA
370250 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:370856 original size:18 final size:18
Alignment explanation
Indices: 370833--370867 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
370823 CTAGGAGATT
370833 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
370851 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
370868 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:371933 original size:149 final size:149
Alignment explanation
Indices: 371754--372068 Score: 528
Period size: 149 Copynumber: 2.1 Consensus size: 149
371744 GAGTCGAGGG
* *
371754 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCT-GATGAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGA-AAGACACA
371818 TA-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCAT
65 TACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCAT
*
371882 TATATGGCACTACGGTGCAAT
129 TATATGGCACTACAGTGCAAT
*
371903 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
371968 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCATTA
372033 TATGGCACTACAGTGCAAT
131 TATGGCACTACAGTGCAAT
372052 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
372069 TGCAATTATA
Statistics
Matches: 157, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
148 1 0.01
149 153 0.97
150 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCATTA
TATGGCACTACAGTGCAAT
Found at i:372071 original size:23 final size:23
Alignment explanation
Indices: 372036--372080 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
372026 ATCATTATAT
*
372036 GGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTATACGC
* *
372059 GGCACTTCGGTGCAATTATACG
1 GGCACTACAGTGCAATTATACG
372081 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGC
Found at i:375245 original size:21 final size:21
Alignment explanation
Indices: 375219--375263 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
375209 GATTTCTGGG
*
375219 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
375240 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
375261 CAA
1 CAA
375264 ACGAACAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:375866 original size:18 final size:18
Alignment explanation
Indices: 375843--375877 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
375833 CTAGGAGATT
375843 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
375861 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
375878 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:376952 original size:146 final size:146
Alignment explanation
Indices: 376760--377069 Score: 527
Period size: 148 Copynumber: 2.1 Consensus size: 146
376750 GAGTCGAGGG
* *
376760 TCTACGCGGTCCTTCGGGATATATATATTCTTTGGAACATGTGTGAAGTCT-GATGAGACACATA
1 TCTACGCGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTCTGGA-AAGACACATA
376824 -TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
65 CTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
376888 TGGCACTACGGTGCAAT
130 TGGCACTACGGTGCAAT
*
376905 TCTACGCGGTCCTTCGGGACATATGTATATCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
1 TCTACGCGGTCCTTCGGGACATATATAT-TCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
*
376970 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
65 C-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
377035 ATGGCACTACGGTGCAAT
129 ATGGCACTACGGTGCAAT
377053 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
377070 TGCAATTATA
Statistics
Matches: 156, Mismatches: 4, Indels: 7
0.93 0.02 0.04
Matches are distributed among these distances:
145 26 0.17
146 32 0.21
147 3 0.02
148 95 0.61
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATAC
TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
GGCACTACGGTGCAAT
Found at i:377070 original size:23 final size:23
Alignment explanation
Indices: 377037--377081 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
377027 ATCATTATAT
*
377037 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
377060 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
377082 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:392415 original size:17 final size:17
Alignment explanation
Indices: 392395--392435 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
392385 CCCTTCCCCT
392395 CCCTCCCGTCCTCCTAC
1 CCCTCCCGTCCTCCTAC
392412 CCCTCCCGTCCTCCTAC
1 CCCTCCCGTCCTCCTAC
392429 CCCTCCC
1 CCCTCCC
392436 TTCCCCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.05, C:0.68, G:0.05, T:0.22
Consensus pattern (17 bp):
CCCTCCCGTCCTCCTAC
Found at i:392416 original size:21 final size:21
Alignment explanation
Indices: 392390--392436 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 21
392380 CTCACCCCTT
392390 CCCCTCCCTCCCGTCCTCCTA
1 CCCCTCCCTCCCGTCCTCCTA
392411 ---C-CCCTCCCGTCCTCCTA
1 CCCCTCCCTCCCGTCCTCCTA
392428 CCCCTCCCT
1 CCCCTCCCT
392437 TCCCCTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
17 16 0.73
18 1 0.05
20 1 0.05
21 4 0.18
ACGTcount: A:0.04, C:0.68, G:0.04, T:0.23
Consensus pattern (21 bp):
CCCCTCCCTCCCGTCCTCCTA
Found at i:393413 original size:25 final size:25
Alignment explanation
Indices: 393379--393434 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
393369 CAATAGAGAC
393379 GTGGGGGAGGGAGGCTGGGTGTGGA
1 GTGGGGGAGGGAGGCTGGGTGTGGA
393404 GTGGGGGAGGGAGGCTGGGTGTGGA
1 GTGGGGGAGGGAGGCTGGGTGTGGA
393429 GTGGGG
1 GTGGGG
393435 AATTGCAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.11, C:0.04, G:0.70, T:0.16
Consensus pattern (25 bp):
GTGGGGGAGGGAGGCTGGGTGTGGA
Found at i:407105 original size:42 final size:42
Alignment explanation
Indices: 407053--407134 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
407043 TTCGAATTTG
* * *
407053 TAAATTCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATGTT
**
407095 TAAATCCTTCGGGTCATTTGTAAGCCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATG
407135 ATAAGACCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGCCTTTCGAGCAAGATGTT
Found at i:407643 original size:41 final size:41
Alignment explanation
Indices: 407555--407645 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
407545 TGAAGTAAGT
* * *
407555 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAAGTTAAAT
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATAAAGATAAAA
* ** *
407596 CATTCGGGTTATCTGTAAGTCTTTCGAGCA-AAATGATAAAA
1 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATAAA-GATAAAA
407637 CCTTCGGGC
1 CCTTCGGGC
407646 ATGATGTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
40 2 0.05
41 38 0.95
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (41 bp):
CCTTCGGGCCATCAGTAAGTCTTTCGAGCATAAAGATAAAA
Found at i:407856 original size:42 final size:42
Alignment explanation
Indices: 407797--407879 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
407787 ATCTTGATTT
* *
407797 TTAAATCCTTCGGGTCATC-AGTAAGTCTTTCGAGCATGATGC
1 TTAAATCCTTCGGGTCATCTA-TAAGCCTTTCGAGCAAGATGC
*
407839 TTAAATCCTTCGGGTCATCTATATGCCTTTCGAGCAAGATG
1 TTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATG
407880 ATAAGTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
TTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGC
Found at i:414799 original size:3 final size:3
Alignment explanation
Indices: 414793--414861 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
414783 TTGTCTAGTT
414793 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
414839 TTA TTA TTA -TA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
414862 AATAATAATA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
2 6 0.10
3 56 0.90
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:414828 original size:14 final size:14
Alignment explanation
Indices: 414793--414861 Score: 104
Period size: 14 Copynumber: 4.9 Consensus size: 14
414783 TTGTCTAGTT
414793 TTATTATTATTATTA
1 TTATTATTATTA-TA
414808 TTATTATTATTAT-
1 TTATTATTATTATA
414821 TATATTATTATTATA
1 T-TATTATTATTATA
414836 TTATTATTATTATA
1 TTATTATTATTATA
*
414850 GTATTATTATTA
1 TTATTATTATTA
414862 AATAATAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
13 1 0.02
14 37 0.73
15 13 0.25
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:415122 original size:16 final size:17
Alignment explanation
Indices: 415101--415133 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
415091 ATCTAGAGGA
415101 AACCCTAGGGTT-TCAT
1 AACCCTAGGGTTATCAT
415117 AACCCTAGGGTTATCAT
1 AACCCTAGGGTTATCAT
415134 CTTGTCGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (17 bp):
AACCCTAGGGTTATCAT
Found at i:420075 original size:40 final size:40
Alignment explanation
Indices: 420031--420172 Score: 284
Period size: 40 Copynumber: 3.5 Consensus size: 40
420021 TCATTTATTT
420031 ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
1 ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
420071 ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
1 ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
420111 ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
1 ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
420151 ATTAAATGAACGAACATGAACA
1 ATTAAATGAACGAACATGAACA
420173 GAGGGCTCGT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (40 bp):
ATTAAATGAACGAACATGAACAATATTTTGTGTTTGTTTA
Found at i:420199 original size:14 final size:14
Alignment explanation
Indices: 420180--420241 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
420170 ACAGAGGGCT
420180 CGTTCGTTCATTTA
1 CGTTCGTTCATTTA
*
420194 CGTTCGTT-A-ATA
1 CGTTCGTTCATTTA
*
420206 TGTTCGTTCATTTA
1 CGTTCGTTCATTTA
* * *
420220 TGTTCGTTCGTTTG
1 CGTTCGTTCATTTA
420234 CGTTCGTT
1 CGTTCGTT
420242 TATGGATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 9 0.22
13 2 0.05
14 29 0.73
ACGTcount: A:0.11, C:0.18, G:0.19, T:0.52
Consensus pattern (14 bp):
CGTTCGTTCATTTA
Found at i:422180 original size:24 final size:24
Alignment explanation
Indices: 422153--422200 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
422143 GGACCTGTTT
422153 CTTCCAACAGTAGAAGAGGTTCGA
1 CTTCCAACAGTAGAAGAGGTTCGA
*
422177 CTTCCAGCAGTAGAAGAGGTTCGA
1 CTTCCAACAGTAGAAGAGGTTCGA
422201 TTGGAGGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (24 bp):
CTTCCAACAGTAGAAGAGGTTCGA
Found at i:431469 original size:21 final size:21
Alignment explanation
Indices: 431444--431494 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
431434 AGTAAAAAAA
431444 CCGGATCGGTTTTTATCCGAT
1 CCGGATCGGTTTTTATCCGAT
*
431465 CCGGATCGATTTTTATCCGAT
1 CCGGATCGGTTTTTATCCGAT
*
431486 CCGAATCGG
1 CCGGATCGG
431495 ATTTAAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (21 bp):
CCGGATCGGTTTTTATCCGAT
Found at i:440946 original size:54 final size:54
Alignment explanation
Indices: 440864--440971 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
440854 AGCTTAAGCT
440864 ATGGCACTAGATCATCGAAAGAAACCTATGAAATTACTTATATCATATTTCAAA
1 ATGGCACTAGATCATCGAAAGAAACCTATGAAATTACTTATATCATATTTCAAA
*
440918 ATGGCACTAGATCATTGAAAGAAACCTATGAAATTACTTATATCATATTTCAAA
1 ATGGCACTAGATCATCGAAAGAAACCTATGAAATTACTTATATCATATTTCAAA
440972 CAAAAAAATC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.31
Consensus pattern (54 bp):
ATGGCACTAGATCATCGAAAGAAACCTATGAAATTACTTATATCATATTTCAAA
Found at i:442531 original size:20 final size:20
Alignment explanation
Indices: 442437--442805 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
442427 GATTTTCCAT
* ** *
442437 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
442457 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
442477 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
442497 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
442517 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
442537 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
442557 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
442577 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
442597 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
442617 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
442637 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
442657 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
442677 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
442697 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
442717 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
442737 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
442757 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
442777 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
442797 AATCACAAC
1 AATCGCAAC
442806 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:443527 original size:24 final size:24
Alignment explanation
Indices: 443488--443534 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
443478 AAATTTGGTC
443488 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
443512 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
443535 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:443726 original size:12 final size:12
Alignment explanation
Indices: 443709--443733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
443699 ATATAATCCT
443709 GAAGAAGAAAAA
1 GAAGAAGAAAAA
443721 GAAGAAGAAAAA
1 GAAGAAGAAAAA
443733 G
1 G
443734 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:446039 original size:19 final size:19
Alignment explanation
Indices: 446017--446309 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
446007 CGGAAAATAC
*
446017 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
446036 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
446050 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
446070 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
446084 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446103 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
446122 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
446136 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
446155 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446174 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446193 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446212 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446231 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446250 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
446264 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446283 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
446302 AATCGCAA
1 AATCGCAA
446310 CGAGATAATC
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 165 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:446132 original size:52 final size:55
Alignment explanation
Indices: 446045--446331 Score: 356
Period size: 52 Copynumber: 5.4 Consensus size: 55
446035 AAATCCCAAC
*
446045 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
446098 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
446150 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
446207 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
446262 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
446312 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
446332 TATAAACGCA
Statistics
Matches: 222, Mismatches: 2, Indels: 21
0.91 0.01 0.09
Matches are distributed among these distances:
50 2 0.01
52 127 0.57
53 16 0.07
54 6 0.03
55 7 0.03
57 64 0.29
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:446228 original size:128 final size:128
Alignment explanation
Indices: 446017--446331 Score: 462
Period size: 128 Copynumber: 2.6 Consensus size: 128
446007 CGGAAAATAC
* *
446017 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
446077 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
446136 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
446201 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
446264 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
446324 TGCGAAAT
66 TGCGAAAT
446332 TATAAACGCA
Statistics
Matches: 179, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
119 24 0.13
121 1 0.01
123 34 0.19
124 17 0.09
125 2 0.01
126 2 0.01
127 1 0.01
128 98 0.55
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (128 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:446447 original size:19 final size:19
Alignment explanation
Indices: 446338--446439 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
446328 AAATTATAAA
446338 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
446357 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
446377 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
446393 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
446410 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
446429 CGCATTGCGAT
1 CGCATTGCGAT
446440 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:446565 original size:14 final size:14
Alignment explanation
Indices: 446546--446582 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
446536 CATCAATTAC
446546 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
446560 ACAAATCATCTTTT
1 ACAAATCAACTTTT
446574 ACAAATCAA
1 ACAAATCAA
446583 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:448559 original size:14 final size:14
Alignment explanation
Indices: 448540--448596 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
448530 GCGAAATGAA
*
448540 AATCGCAACGACAG
1 AATCGCAACGAAAG
448554 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
448571 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
448587 AATCGCAACG
1 AATCGCAACG
448597 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:448567 original size:33 final size:33
Alignment explanation
Indices: 448521--448613 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
448511 GCGAAACCAA
*
448521 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
448554 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
448587 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
448614 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:448578 original size:19 final size:19
Alignment explanation
Indices: 448484--448618 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
448474 TAGTTTACTT
* *
448484 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
448504 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
448523 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
448542 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
448556 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
448575 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
448589 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
448608 TCGCAATGCGA
1 TCGCAACGCGA
448619 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:448636 original size:19 final size:19
Alignment explanation
Indices: 448614--448742 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
448604 AAAATCGCAA
448614 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
448633 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
448647 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
448666 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
448680 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
448699 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
448718 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
448738 TGCGA
1 TGCGA
448743 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:448656 original size:33 final size:33
Alignment explanation
Indices: 448614--448705 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
448604 AAAATCGCAA
448614 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
448647 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
448680 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
448706 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:449077 original size:93 final size:93
Alignment explanation
Indices: 448786--449257 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
448776 TTGAATGGAT
448786 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
448851 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
448879 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
448943 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
448971 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
449036 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
449064 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
449128 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
449156 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
449221 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
449249 AAATTTACT
1 AAATTTACT
449258 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:449098 original size:185 final size:185
Alignment explanation
Indices: 448786--449257 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
448776 TTGAATGGAT
448786 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
448851 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
448916 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
448971 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
449036 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
449101 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
449156 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
449221 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
449258 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:450983 original size:14 final size:14
Alignment explanation
Indices: 450964--451053 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
450954 TTGAAATGAA
450964 AATCGCAACGAGAG
1 AATCGCAACGAGAG
450978 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
450995 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
451011 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
451030 AATCGCAACGAGAG
1 AATCGCAACGAGAG
451044 AATCGCAACG
1 AATCGCAACG
451054 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:451001 original size:33 final size:33
Alignment explanation
Indices: 450956--451070 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
450946 TCTTTTGGTT
450956 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
450989 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
451022 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
451055 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
451071 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:451002 original size:19 final size:18
Alignment explanation
Indices: 450963--451075 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
450953 GTTGAAATGA
450963 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
450978 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
450995 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
451011 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
451028 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
451044 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
451061 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
451076 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:451106 original size:14 final size:14
Alignment explanation
Indices: 451087--451141 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
451077 TTTGGTTTCG
451087 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
451101 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
451120 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
451134 CGTTGCGA
1 CGTTGCGA
451142 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:451119 original size:33 final size:33
Alignment explanation
Indices: 451071--451141 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
451061 AAAATCGCAA
**
451071 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
451104 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
451137 TGCGA
1 TGCGA
451142 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:451149 original size:33 final size:33
Alignment explanation
Indices: 451082--451163 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
451072 GCGATTTTGG
***
451082 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
451115 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
451148 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
451164 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:451168 original size:20 final size:20
Alignment explanation
Indices: 451094--451182 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
451084 TCGCGTTGCG
451094 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
451114 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
451127 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
451147 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
451167 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
451183 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:451304 original size:33 final size:33
Alignment explanation
Indices: 451262--451332 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
451252 AATACTAACT
*
451262 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
451295 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
451328 TGAAA
1 TGAAA
451333 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:451566 original size:22 final size:22
Alignment explanation
Indices: 451514--451568 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
451504 TGGTTGTGAG
**
451514 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
451536 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
451558 GGATTTCTTCG
1 GGATTTCTTCG
451569 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:451739 original size:20 final size:20
Alignment explanation
Indices: 451714--451906 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
451704 CTTTAAATAT
451714 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
451734 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
451756 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
451775 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
451795 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
451815 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
451835 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
451855 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
451875 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
451895 CGCGTTGCGATT
1 CGCGTTGCGATT
451907 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:451901 original size:60 final size:60
Alignment explanation
Indices: 451714--451906 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
451704 CTTTAAATAT
**
451714 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
451775 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
451835 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
451895 CGCGTTGCGATT
1 CGCGTTGCGATT
451907 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:451987 original size:20 final size:20
Alignment explanation
Indices: 451962--452013 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
451952 AAGAATCGCG
*
451962 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
451982 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
452002 TTGCGATTCTGG
1 TTGCGATTCTGG
452014 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:461129 original size:21 final size:21
Alignment explanation
Indices: 461105--461165 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
461095 AAACATCTAC
461105 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
**
461126 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
461141 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
461162 CAAA
1 CAAA
461166 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 12 0.40
17 1 0.03
19 1 0.03
21 16 0.53
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Done.