Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 45 of 49
Found at i:9234206 original size:42 final size:41
Alignment explanation
Indices: 9234159--9234281 Score: 140
Period size: 41 Copynumber: 3.0 Consensus size: 41
9234149 TCAAAGAATT
*
9234159 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGTGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
9234201 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
* * * * *
9234242 TGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAA
9234282 TTTGCGATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 58 0.78
42 16 0.22
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:9234233 original size:21 final size:21
Alignment explanation
Indices: 9234207--9234390 Score: 88
Period size: 21 Copynumber: 8.6 Consensus size: 21
9234197 GAAATGGAAA
9234207 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
9234228 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* *
9234248 ACCACAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
9234269 ATCGCAACGCGAATTTGCGA-T
1 ATCGCAACGCG-ATTTTCAACT
* *
9234290 GAT-GGAGATCGCGTTGCGATTTCAACT
1 -ATCGCA-A-CGCGAT----TTTCAACT
* *
9234317 ATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
9234338 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
9234358 AACGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
9234379 ATCGCAATGCGA
1 ATCGCAACGCGA
9234391 AATGCAACGT
Statistics
Matches: 114, Mismatches: 37, Indels: 24
0.65 0.21 0.14
Matches are distributed among these distances:
20 27 0.24
21 58 0.51
22 10 0.09
23 4 0.04
25 5 0.04
26 7 0.06
27 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:9234242 original size:41 final size:41
Alignment explanation
Indices: 9234184--9234281 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
9234174 ACAACTGTAG
* * *
9234184 ACTATCGCAACGTGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
9234225 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
9234266 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
9234282 TTTGCGATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
Found at i:9234823 original size:41 final size:40
Alignment explanation
Indices: 9234766--9234907 Score: 186
Period size: 41 Copynumber: 3.5 Consensus size: 40
9234756 CGCAACTCAG
9234766 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATT-CGAT
9234807 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTACGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATT-CGAT
* *
9234848 TTTCCAAATTCGCAAC-TGAAT-T-TCAAATTCGCAATT-GAA
1 TTTCCAAATTCGCAACGCGAATATGT-AAA-TCGC-ATTCGAT
9234887 TTT-CAAATTCGCAACGCGAAT
1 TTTCCAAATTCGCAACGCGAAT
9234908 TTAATTTCGC
Statistics
Matches: 93, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
38 13 0.14
39 13 0.14
40 8 0.09
41 59 0.63
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (40 bp):
TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTCGAT
Found at i:9234860 original size:21 final size:21
Alignment explanation
Indices: 9234795--9234861 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
9234785 AATATGTAAA
9234795 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
** * * **
9234816 TCGCAACGCGAATATGTAAA-
1 TCGCATTGCGATTTTCCAAAT
*
9234836 TCGCATTACGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
9234857 TCGCA
1 TCGCA
9234862 ACTGAATTTC
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:9234876 original size:19 final size:19
Alignment explanation
Indices: 9234852--9234920 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
9234842 TACGATTTTC
9234852 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACTGAATTT
*
9234871 CAAATTCGCAATTGAATTT
1 CAAATTCGCAACTGAATTT
*
9234890 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAAC-TGAATTT
*
9234910 -AATTTCGCAAC
1 CAAATTCGCAAC
9234921 AGGTTTTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 39 0.87
20 6 0.13
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (19 bp):
CAAATTCGCAACTGAATTT
Found at i:9234909 original size:20 final size:20
Alignment explanation
Indices: 9234711--9234920 Score: 150
Period size: 20 Copynumber: 10.6 Consensus size: 20
9234701 AAATGACCAA
*
9234711 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
*
9234730 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
9234750 CAATTTCGCAACTC-AGTTT
1 CAAATTCGCAACGCGAATTT
9234769 CCAAATTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** *
9234792 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
9234810 CCAAATTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
*** *
9234833 -AAA-TCGCATTACGATTTT
1 CAAATTCGCAACGCGAATTT
*
9234851 CCAAATTCGCAAC-TGAATTT
1 -CAAATTCGCAACGCGAATTT
**
9234871 CAAATTCGCAA-TTGAATTT
1 CAAATTCGCAACGCGAATTT
9234890 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
9234910 -AATTTCGCAAC
1 CAAATTCGCAAC
9234921 AGGTTTTAGT
Statistics
Matches: 150, Mismatches: 26, Indels: 30
0.73 0.13 0.15
Matches are distributed among these distances:
18 2 0.01
19 59 0.39
20 62 0.41
21 23 0.15
22 2 0.01
23 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:9237325 original size:19 final size:19
Alignment explanation
Indices: 9237280--9237327 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
9237270 TTGTTTACAT
* *
9237280 TTGTGTTGCAAAATTAATA
1 TTGTGTTTCGAAATTAATA
9237299 TTGTGTTTCGAAATTAATA
1 TTGTGTTTCGAAATTAATA
9237318 TTGTGTTTCG
1 TTGTGTTTCG
9237328 CGTAATAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (19 bp):
TTGTGTTTCGAAATTAATA
Found at i:9237434 original size:20 final size:20
Alignment explanation
Indices: 9237391--9237434 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9237381 CAAATTCGCT
* *
9237391 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTAACTA
9237411 TCGCGTTGCGAATTTAACTA
1 TCGCGTTGCGAATTTAACTA
9237431 TCGC
1 TCGC
9237435 AACGCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAACTA
Found at i:9240582 original size:16 final size:16
Alignment explanation
Indices: 9240561--9240594 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9240551 TCTTTATAAA
9240561 TTTTTAAAAGTTAATT
1 TTTTTAAAAGTTAATT
**
9240577 TTTTTAAATTTTAATT
1 TTTTTAAAAGTTAATT
9240593 TT
1 TT
9240595 AATCATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTAAAAGTTAATT
Found at i:9242068 original size:40 final size:40
Alignment explanation
Indices: 9242021--9242096 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
9242011 TGGAAATTTA
*
9242021 GGATTATTTTCATTTTGAATTCCTTTTTATTTTTAAGATC
1 GGATTATTTTCATTTTGAATTCCTTGTTATTTTTAAGATC
*
9242061 GGATTATTTTCATTTTGAATTTCTTGTTATTTTTAA
1 GGATTATTTTCATTTTGAATTCCTTGTTATTTTTAA
9242097 AACTTAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.59
Consensus pattern (40 bp):
GGATTATTTTCATTTTGAATTCCTTGTTATTTTTAAGATC
Found at i:9250183 original size:2 final size:2
Alignment explanation
Indices: 9250176--9250202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9250166 TTCCCCTGTT
9250176 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
9250203 GCCCTGAATT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9259935 original size:32 final size:32
Alignment explanation
Indices: 9259894--9259963 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
9259884 GTTGTGCACA
* * *
9259894 TCATCTTCAATCTCTTACACAACACACTTTTT
1 TCATCTTCAATATCTTACACAACAAACTTCTT
9259926 TCATCTTCAATATCTTACACAACAAACTTCTT
1 TCATCTTCAATATCTTACACAACAAACTTCTT
9259958 TCATCT
1 TCATCT
9259964 AACCAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (32 bp):
TCATCTTCAATATCTTACACAACAAACTTCTT
Found at i:9261091 original size:21 final size:21
Alignment explanation
Indices: 9261050--9261091 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
9261040 TTAGGGATTT
9261050 TTTATTTCAAATTAATTAAATA
1 TTTATTT-AAATTAATTAAATA
9261072 TTTATTT-AATTAATTTAAAT
1 TTTATTTAAATTAA-TTAAAT
9261092 TAAATATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 6 0.32
22 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATTTAAATTAATTAAATA
Found at i:9270063 original size:13 final size:14
Alignment explanation
Indices: 9270031--9270060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9270021 TTGATTAGAC
9270031 TAATATAACTCTTT
1 TAATATAACTCTTT
*
9270045 TAATATAACTTTTT
1 TAATATAACTCTTT
9270059 TA
1 TA
9270061 TATTTATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATAACTCTTT
Found at i:9272806 original size:14 final size:14
Alignment explanation
Indices: 9272768--9272816 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
9272758 TACGTTTCTG
*
9272768 TTTATATGCAGAGA
1 TTTATTTGCAGAGA
*
9272782 TTT-TTACGCAGAGA
1 TTTATT-TGCAGAGA
*
9272796 TTTATTTGCAGGGA
1 TTTATTTGCAGAGA
9272810 TTTATTT
1 TTTATTT
9272817 ATATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 26 0.90
15 2 0.07
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (14 bp):
TTTATTTGCAGAGA
Found at i:9275574 original size:31 final size:31
Alignment explanation
Indices: 9275503--9275578 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
9275493 GGTATTTGGA
*
9275503 TCGGATTTTTTTAAAAAAAATCGGGATCGGG
1 TCGGATTTTTTTAAAAAAAATCGGGATCAGG
** * *
9275534 TCATATTTTTTTAAAAAAATTCGGGTTCAGG
1 TCGGATTTTTTTAAAAAAAATCGGGATCAGG
*
9275565 TCGGGTTTTTTTAA
1 TCGGATTTTTTTAA
9275579 GTTTGATATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (31 bp):
TCGGATTTTTTTAAAAAAAATCGGGATCAGG
Found at i:9275600 original size:33 final size:34
Alignment explanation
Indices: 9275552--9275621 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
9275542 TTTTAAAAAA
* *
9275552 ATTCGGGTTCAGGTCGGGTTTTTTTAAGTTTGAT
1 ATTCGGGTTCAGGTCGGATTTTTTTAAGTGTGAT
*
9275586 ATTCGGGTT-GGGTCGGATTTTTTTAAGTGTGAT
1 ATTCGGGTTCAGGTCGGATTTTTTTAAGTGTGAT
9275619 ATT
1 ATT
9275622 ACCATGCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 24 0.73
34 9 0.27
ACGTcount: A:0.16, C:0.07, G:0.30, T:0.47
Consensus pattern (34 bp):
ATTCGGGTTCAGGTCGGATTTTTTTAAGTGTGAT
Found at i:9277799 original size:21 final size:20
Alignment explanation
Indices: 9277713--9277869 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
9277703 AAATGACCAA
**
9277713 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
9277732 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
9277752 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
9277772 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
9277793 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
9277813 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
9277833 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
9277854 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
9277870 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:9277822 original size:41 final size:41
Alignment explanation
Indices: 9277713--9277869 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
9277703 AAATGACCAA
* **
9277713 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
9277752 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
9277793 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
9277834 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
9277870 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:9277879 original size:20 final size:20
Alignment explanation
Indices: 9277856--9278029 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
9277846 GCGAATATGA
9277856 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
9277876 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
9277896 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
9277916 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
9277936 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
9277956 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
9277976 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
9277996 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
9278017 AAATCGCAACGCG
1 AAATCGCAACGCG
9278030 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:9277900 original size:40 final size:39
Alignment explanation
Indices: 9277836--9278030 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
9277826 CGATTTTCCA
* ** *
9277836 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
9277876 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
9277916 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
9277956 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
9277996 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
9278031 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:9277921 original size:60 final size:60
Alignment explanation
Indices: 9277836--9278029 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
9277826 CGATTTTCCA
* ** * *
9277836 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
9277896 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
9277956 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
9278017 AAATCGCAACGCG
1 AAATCGCAACGCG
9278030 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:9278447 original size:33 final size:33
Alignment explanation
Indices: 9278408--9278478 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
9278398 TTCACTTAGA
9278408 TTTCATTTCGCGTTACTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACTATTCTCTCGTTGCGAT
*
9278441 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACTATTCTCTCGTTGCGAT
9278474 TTTCA
1 TTTCA
9278479 AGTTAGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.11, C:0.24, G:0.15, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACTATTCTCTCGTTGCGAT
Found at i:9278615 original size:19 final size:20
Alignment explanation
Indices: 9278558--9278632 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
9278548 TGCAGAAGAG
* *
9278558 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
9278579 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
9278599 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
9278618 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
9278633 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:9278635 original size:14 final size:14
Alignment explanation
Indices: 9278616--9278672 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
9278606 GCGAAATGAC
9278616 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
9278630 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
9278649 AATCGCAACGAGAG
1 AATCGCAACGAGAG
9278663 AATCGCAACG
1 AATCGCAACG
9278673 GGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:9278641 original size:33 final size:33
Alignment explanation
Indices: 9278570--9278688 Score: 148
Period size: 33 Copynumber: 3.4 Consensus size: 33
9278560 GCAACGAGAT
9278570 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
*
9278609 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
*
9278642 AAATGAAAATCGCAACGAGAGAATCGCAACGGG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
9278675 AAACCAAAATCGCA
1 AAATGAAAATCGCA
9278689 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
33 53 0.71
36 1 0.01
38 1 0.01
39 20 0.27
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:9278654 original size:19 final size:19
Alignment explanation
Indices: 9278570--9278658 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
9278560 GCAACGAGAT
*
9278570 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
***
9278589 AGAATGACTGTCGCAACGCG
1 A-AATGAAAATCGCAACGCG
*
9278609 AAATGACAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
9278626 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
9278642 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
9278659 AGAGAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 25 0.45
20 15 0.27
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:9278724 original size:14 final size:14
Alignment explanation
Indices: 9278705--9278794 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
9278695 TTTTATTTCG
9278705 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
9278719 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
9278738 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
9278752 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
9278771 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
9278785 CGTTGCGATT
1 CGTTGCGATT
9278795 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:9278741 original size:33 final size:33
Alignment explanation
Indices: 9278689--9278802 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
9278679 CAAAATCGCA
9278689 TTGCGATTTT-ATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
9278721 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
9278754 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
9278787 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
9278803 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
32 10 0.13
33 69 0.87
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:9278743 original size:19 final size:19
Alignment explanation
Indices: 9278684--9278780 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
9278674 GAAACCAAAA
*
9278684 TCGCATTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
9278702 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
9278716 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
9278735 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
9278749 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
9278768 TCGCGTTGCGATT
1 TCGCGTTGCGATT
9278781 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
14 20 0.32
16 7 0.11
17 3 0.05
18 10 0.16
19 22 0.35
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:9280368 original size:20 final size:19
Alignment explanation
Indices: 9280293--9280403 Score: 116
Period size: 19 Copynumber: 6.3 Consensus size: 19
9280283 GGTACTCTAC
9280293 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
9280312 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCATT
*
9280331 GCGA--TTC-TCTCG--TT
1 GCGATTTTCATTTCGCATT
9280345 GCGATTTTCATTTCCGCATT
1 GCGATTTTCATTT-CGCATT
9280365 GCGATTTTCA--T-G--TT
1 GCGATTTTCATTTCGCATT
* *
9280379 GGGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCATT
9280398 GCGATT
1 GCGATT
9280404 GTAATTTCCG
Statistics
Matches: 77, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
14 17 0.22
16 9 0.12
17 6 0.08
18 3 0.04
19 30 0.39
20 12 0.16
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATT
Found at i:9280368 original size:34 final size:33
Alignment explanation
Indices: 9280310--9280403 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
9280300 TCATTTCGCA
9280310 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
9280343 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
* *
9280377 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
9280404 GTAATTTCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:9282691 original size:26 final size:27
Alignment explanation
Indices: 9282658--9282722 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
9282648 CCGTGGCATT
9282658 TTCTTTTCTTC-GGGGACTTTTTCTTC
1 TTCTTTTCTTCGGGGGACTTTTTCTTC
9282684 TTCTTTTCTTCGGGGGACTTTTTCTTC
1 TTCTTTTCTTCGGGGGACTTTTTCTTC
9282711 TTCTTTTTCTTC
1 TTC-TTTTCTTC
9282723 TTCAGGATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 11 0.30
27 18 0.49
28 8 0.22
ACGTcount: A:0.03, C:0.23, G:0.14, T:0.60
Consensus pattern (27 bp):
TTCTTTTCTTCGGGGGACTTTTTCTTC
Found at i:9282718 original size:12 final size:12
Alignment explanation
Indices: 9282701--9282725 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9282691 CTTCGGGGGA
9282701 CTTTTTCTTCTT
1 CTTTTTCTTCTT
9282713 CTTTTTCTTCTT
1 CTTTTTCTTCTT
9282725 C
1 C
9282726 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:9283647 original size:20 final size:20
Alignment explanation
Indices: 9283619--9283828 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
9283609 AAATTTCAGT
* * *
9283619 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
9283639 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
9283659 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
9283679 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
9283699 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
9283719 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
9283739 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
9283759 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
9283779 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
9283799 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
9283819 GTTGCGATTT
1 GTTGCGATTT
9283829 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:9283845 original size:21 final size:20
Alignment explanation
Indices: 9283795--9283892 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
9283785 ATTTATGTGT
* * * *
9283795 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
9283815 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
9283836 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
9283856 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
9283877 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
9283893 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:9283887 original size:41 final size:41
Alignment explanation
Indices: 9283795--9283951 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
9283785 ATTTATGTGT
* * *
9283795 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
9283836 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
9283877 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
9283917 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
9283952 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:9286637 original size:18 final size:19
Alignment explanation
Indices: 9286608--9286643 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9286598 ATATAGTGTA
*
9286608 TATATATATAAATTATATT
1 TATATATATAAACTATATT
9286627 TATAT-TATAAACTATAT
1 TATATATATAAACTATAT
9286644 AATTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATATAAACTATATT
Found at i:9286648 original size:15 final size:14
Alignment explanation
Indices: 9286627--9286691 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 14
9286617 AAATTATATT
9286627 TATATTATAAACTA
1 TATATTATAAACTA
9286641 TATAATTATTATAAGCTA
1 TAT-ATTA-TA-AA-CTA
9286659 TATA-TATAAACTA
1 TATATTATAAACTA
* *
9286672 TGTTTATATAAACTA
1 TATAT-TATAAACTA
9286687 TATAT
1 TATAT
9286692 ACAACAACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 18 0.44
16 4 0.10
17 3 0.07
18 6 0.15
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:9287216 original size:12 final size:12
Alignment explanation
Indices: 9287201--9287257 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 12
9287191 ATGTAGAAAT
*
9287201 TTATGTATATAC
1 TTATATATATAC
9287213 TTATATATATA-
1 TTATATATATAC
9287224 -TATATATATA-
1 TTATATATATAC
9287234 -TATATATATA-
1 TTATATATATAC
9287244 -TATATATATA-
1 TTATATATATAC
9287254 TTAT
1 TTAT
9287258 TCAAAGTGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
10 30 0.70
11 3 0.07
12 10 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (12 bp):
TTATATATATAC
Found at i:9287219 original size:2 final size:2
Alignment explanation
Indices: 9287214--9287254 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9287204 TGTATATACT
9287214 TA TA TA TA TA 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 TA T
9287255 TATTCAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9287355 original size:19 final size:20
Alignment explanation
Indices: 9287327--9287383 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
9287317 TTTATTTTAT
9287327 TTGG-GAATTTAGAGGGAAA
1 TTGGAGAATTTAGAGGGAAA
9287346 TT-GAGAATTTAGAGGGAAA
1 TTGGAGAATTTAGAGGGAAA
* *
9287365 TTGGAAAATGTAGAGGGAA
1 TTGGAGAATTTAGAGGGAA
9287384 TAGAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.03
19 19 0.56
20 14 0.41
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (20 bp):
TTGGAGAATTTAGAGGGAAA
Found at i:9287380 original size:20 final size:19
Alignment explanation
Indices: 9287336--9287383 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
9287326 TTTGGGAATT
* *
9287336 TAGAGGGAAATTGAGAATT
1 TAGAGGGAAATTGAAAATG
9287355 TAGAGGGAAATTGGAAAATG
1 TAGAGGGAAATT-GAAAATG
9287375 TAGAGGGAA
1 TAGAGGGAA
9287384 TAGAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (19 bp):
TAGAGGGAAATTGAAAATG
Found at i:9287617 original size:24 final size:23
Alignment explanation
Indices: 9287591--9287652 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
9287581 ACTTTTAATT
9287591 ATATATAAACATATATATGTAT-
1 ATATATAAACATATATATGTATA
* *
9287613 GTATATAAAC-TCTATATGTATAA
1 ATATATAAACATATATATGTAT-A
9287636 ACTATATAAA-ATATATA
1 A-TATATAAACATATATA
9287653 GTTTATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 10 0.31
22 9 0.28
24 13 0.41
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (23 bp):
ATATATAAACATATATATGTATA
Found at i:9287630 original size:21 final size:22
Alignment explanation
Indices: 9287592--9287633 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9287582 CTTTTAATTA
9287592 TATATAAACATATATATGTATG
1 TATATAAACATATATATGTATG
*
9287614 TATATAAAC-TCTATATGTAT
1 TATATAAACATATATATGTAT
9287634 AAACTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (22 bp):
TATATAAACATATATATGTATG
Found at i:9287641 original size:22 final size:22
Alignment explanation
Indices: 9287593--9287667 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
9287583 TTTTAATTAT
**
9287593 ATATAAACATATATATGTATGT
1 ATATAAACATATATATGTATAA
*
9287615 ATATAAAC-TCTATATGTATAA
1 ATATAAACATATATATGTATAA
* *
9287636 ACTATATAAAATATATAGTTTATAA
1 A-TATA-AACATATATA-TGTATAA
9287661 ATTATAA
1 A-TATAA
9287668 TTTATATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 11 0.26
22 12 0.29
23 2 0.05
24 6 0.14
25 11 0.26
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
ATATAAACATATATATGTATAA
Found at i:9287841 original size:7 final size:7
Alignment explanation
Indices: 9287831--9287868 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
9287821 CTAAACCACC
*
9287831 AACCTTT
1 AACCCTT
9287838 AACCCTT
1 AACCCTT
9287845 AACCCTT
1 AACCCTT
9287852 AACCCTT
1 AACCCTT
9287859 AACCC-T
1 AACCCTT
9287865 AACC
1 AACC
9287869 TCTAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (7 bp):
AACCCTT
Found at i:9287841 original size:21 final size:21
Alignment explanation
Indices: 9287817--9287866 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9287807 CTAAATTGAG
*
9287817 AACCCTAAACCAC-CAACCTTT
1 AACCCTAAACC-CTCAACCCTT
* *
9287838 AACCCTTAACCCTTAACCCTT
1 AACCCTAAACCCTCAACCCTT
9287859 AACCCTAA
1 AACCCTAA
9287867 CCTCTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTAAACCCTCAACCCTT
Found at i:9287934 original size:16 final size:15
Alignment explanation
Indices: 9287919--9287961 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
9287909 ACCATGTATA
9287919 ATATATATAAACTAT
1 ATATATATAAACTAT
*
9287934 ATATATATATACCTAT
1 ATATATATA-AACTAT
9287950 ATATATATAAAC
1 ATATATATAAAC
9287962 ATTATAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATATAAACTAT
Found at i:9288072 original size:21 final size:21
Alignment explanation
Indices: 9288042--9288099 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
9288032 TAGTTTATAG
* **
9288042 AAATCCTAAACCCTAAAATTT
1 AAATCATAAACCCTAAAACCT
* *
9288063 AAATCATAAACACTAAACCCT
1 AAATCATAAACCCTAAAACCT
9288084 AAATCATAAACCCTAA
1 AAATCATAAACCCTAA
9288100 TATAAATGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATCATAAACCCTAAAACCT
Found at i:9288373 original size:23 final size:25
Alignment explanation
Indices: 9288317--9288373 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 25
9288307 TTAATCATGT
*
9288317 TTTATATAATTTACATTTAAATAAT
1 TTTATATAATTTACATTTAAATAAA
*
9288342 TTTAT-TAATTT-TA-TTAAATAAA
1 TTTATATAATTTACATTTAAATAAA
9288364 TTTATATAAT
1 TTTATATAAT
9288374 ATGTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 13 0.45
23 5 0.17
24 6 0.21
25 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATATAATTTACATTTAAATAAA
Found at i:9289024 original size:2 final size:2
Alignment explanation
Indices: 9288964--9289015 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
9288954 ATAAACCATG
*
9288964 TA TA -A TA TA TA TA CA CTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
9289006 TA TA TA TA TA
1 TA TA TA TA TA
9289016 AACTATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9289024 original size:9 final size:9
Alignment explanation
Indices: 9288964--9289041 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 9
9288954 ATAAACCATG
*
9288964 TATAATATA
1 TATAAAATA
* *
9288973 TATACACTA
1 TATAAAATA
*
9288982 TATATATATA
1 TATA-AAATA
*
9288992 TATATATATA
1 TATA-AAATA
*
9289002 TATATATATA
1 TATA-AAATA
*
9289012 TATAAACTA
1 TATAAAATA
*
9289021 TATAAAGTA
1 TATAAAATA
9289030 -ATAAAATA
1 TATAAAATA
9289038 TATA
1 TATA
9289042 GTTTATAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
8 7 0.12
9 24 0.42
10 26 0.46
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (9 bp):
TATAAAATA
Found at i:9289087 original size:14 final size:14
Alignment explanation
Indices: 9289070--9289128 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
9289060 CCCTAAATCA
*
9289070 TAAACCTTAAACCT
1 TAAACCTTAAACCC
**
9289084 TAAAATTTAAACCC
1 TAAACCTTAAACCC
* *
9289098 TAAACCCTAAACTC
1 TAAACCTTAAACCC
9289112 TAAA-CTATAAACCC
1 TAAACCT-TAAACCC
9289126 TAA
1 TAA
9289129 TGTAAATGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 1 0.03
14 34 0.97
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:9289114 original size:7 final size:7
Alignment explanation
Indices: 9289050--9289128 Score: 50
Period size: 7 Copynumber: 11.3 Consensus size: 7
9289040 TAGTTTATAG
*
9289050 AAACCTT
1 AAACCCT
*
9289057 AACCCCT
1 AAACCCT
* *
9289064 AAATCAT
1 AAACCCT
*
9289071 AAACCTT
1 AAACCCT
*
9289078 AAACCTT
1 AAACCCT
***
9289085 AAAATTT
1 AAACCCT
9289092 AAACCCT
1 AAACCCT
9289099 AAACCCT
1 AAACCCT
*
9289106 AAACTCT
1 AAACCCT
**
9289113 AAACTAT
1 AAACCCT
9289120 AAACCCT
1 AAACCCT
9289127 AA
1 AA
9289129 TGTAAATGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (7 bp):
AAACCCT
Found at i:9289115 original size:21 final size:20
Alignment explanation
Indices: 9289050--9289128 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 20
9289040 TAGTTTATAG
*
9289050 AAACCTTAACCCCTAAATCAT
1 AAACCTTAAACCCTAAATC-T
* *
9289071 AAACCTTAAACCTTAAAATTT
1 AAACCTTAAACCCT-AAATCT
*
9289092 AAACCCTAAACCCTAAACTCT
1 AAACCTTAAACCCTAAA-TCT
9289113 AAA-CTATAAACCCTAA
1 AAACCT-TAAACCCTAA
9289129 TGTAAATGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 4 0.08
21 40 0.83
22 4 0.08
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACCTTAAACCCTAAATCT
Found at i:9289523 original size:2 final size:2
Alignment explanation
Indices: 9289518--9289544 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9289508 AACTATATAT
9289518 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
9289545 TATATATATA
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:9289665 original size:49 final size:49
Alignment explanation
Indices: 9289562--9289666 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 49
9289552 ATATATATAT
* **
9289562 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGC
1 ATAAACTATATAAAGTAAATAACTTATATAGTTTATAGAAACACTAACC
*
9289611 ATAAACTATATAAAGT-AATAAAC-TATATAGTTTATAGAAACCCTTAACC
1 ATAAACTATATAAAGTAAAT-AACTTATATAGTTTATAGAAACAC-TAACC
*
9289660 CTAAACT
1 ATAAACT
9289667 TTAAACCCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 22 0.45
49 27 0.55
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAACTTATATAGTTTATAGAAACACTAACC
Found at i:9289678 original size:7 final size:7
Alignment explanation
Indices: 9289648--9289691 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
9289638 TAGTTTATAG
9289648 AAACCCT
1 AAACCCT
*
9289655 TAACCCT
1 AAACCCT
**
9289662 AAACTTT
1 AAACCCT
9289669 AAACCCT
1 AAACCCT
*
9289676 AAACACT
1 AAACCCT
9289683 AAACCCT
1 AAACCCT
9289690 AA
1 AA
9289692 TATAAATGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:9289965 original size:23 final size:25
Alignment explanation
Indices: 9289909--9289965 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 25
9289899 TTAATCATGT
*
9289909 TTTATATAATTTACATTTAAATAAT
1 TTTATATAATTTACATTTAAATAAA
*
9289934 TTTAT-TAATTT-TA-TTAAATAAA
1 TTTATATAATTTACATTTAAATAAA
9289956 TTTATATAAT
1 TTTATATAAT
9289966 ATGTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 13 0.45
23 5 0.17
24 6 0.21
25 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATATAATTTACATTTAAATAAA
Found at i:9290663 original size:14 final size:14
Alignment explanation
Indices: 9290646--9290704 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
9290636 CCCTAAATCA
*
9290646 TAAACCTTAAACCT
1 TAAACCTTAAACCC
**
9290660 TAAAATTTAAACCC
1 TAAACCTTAAACCC
* *
9290674 TAAACCCTAAACTC
1 TAAACCTTAAACCC
9290688 TAAA-CTATAAACCC
1 TAAACCT-TAAACCC
9290702 TAA
1 TAA
9290705 TGTAAATGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 1 0.03
14 34 0.97
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:9290690 original size:7 final size:7
Alignment explanation
Indices: 9290626--9290704 Score: 50
Period size: 7 Copynumber: 11.3 Consensus size: 7
9290616 TAGTTTATAG
*
9290626 AAACCTT
1 AAACCCT
*
9290633 AACCCCT
1 AAACCCT
* *
9290640 AAATCAT
1 AAACCCT
*
9290647 AAACCTT
1 AAACCCT
*
9290654 AAACCTT
1 AAACCCT
***
9290661 AAAATTT
1 AAACCCT
9290668 AAACCCT
1 AAACCCT
9290675 AAACCCT
1 AAACCCT
*
9290682 AAACTCT
1 AAACCCT
**
9290689 AAACTAT
1 AAACCCT
9290696 AAACCCT
1 AAACCCT
9290703 AA
1 AA
9290705 TGTAAATGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (7 bp):
AAACCCT
Found at i:9290691 original size:21 final size:20
Alignment explanation
Indices: 9290626--9290704 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 20
9290616 TAGTTTATAG
*
9290626 AAACCTTAACCCCTAAATCAT
1 AAACCTTAAACCCTAAATC-T
* *
9290647 AAACCTTAAACCTTAAAATTT
1 AAACCTTAAACCCT-AAATCT
*
9290668 AAACCCTAAACCCTAAACTCT
1 AAACCTTAAACCCTAAA-TCT
9290689 AAA-CTATAAACCCTAA
1 AAACCT-TAAACCCTAA
9290705 TGTAAATGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 4 0.08
21 40 0.83
22 4 0.08
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACCTTAAACCCTAAATCT
Found at i:9290731 original size:2 final size:2
Alignment explanation
Indices: 9290724--9290749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9290714 ACTAACACTA
9290724 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
9290750 TTGTAATAAA
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:9291229 original size:48 final size:49
Alignment explanation
Indices: 9291135--9291229 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
9291125 TATATATATA
* *
9291135 TATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
1 TATACATAAACTATATAAAGTAAATAACTTATATAGTTTATAGAAACAC
9291184 TATACATAAACTATATAAAGT-AATAAAC-TATATAGTTTATAGAAAC
1 TATACATAAACTATATAAAGTAAAT-AACTTATATAGTTTATAGAAAC
9291230 CCTAAACCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 21 0.49
49 22 0.51
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (49 bp):
TATACATAAACTATATAAAGTAAATAACTTATATAGTTTATAGAAACAC
Found at i:9291236 original size:7 final size:7
Alignment explanation
Indices: 9291226--9291269 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
9291216 TAGTTTATAG
9291226 AAACCCT
1 AAACCCT
9291233 AAACCCT
1 AAACCCT
**
9291240 AAACTTT
1 AAACCCT
9291247 AAACCCT
1 AAACCCT
* *
9291254 GAACACT
1 AAACCCT
9291261 AAACCCT
1 AAACCCT
9291268 AA
1 AA
9291270 TGTAAATGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:9291244 original size:49 final size:49
Alignment explanation
Indices: 9291140--9291236 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 49
9291130 ATATATATAT
* *
9291140 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATAC
1 ATAAACTATATAAAGTAAATAACTTATATAGTTTATAGAAACACTAAAC
*
9291189 ATAAACTATATAAAGT-AATAAAC-TATATAGTTTATAGAAACCCTAAAC
1 ATAAACTATATAAAGTAAAT-AACTTATATAGTTTATAGAAACACTAAAC
9291237 CCTAAACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 26 0.59
49 18 0.41
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAACTTATATAGTTTATAGAAACACTAAAC
Found at i:9291600 original size:13 final size:15
Alignment explanation
Indices: 9291569--9291602 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
9291559 ATGTATAGTA
9291569 TATATATATATAACT
1 TATATATATATAACT
9291584 TATATATATA-AAC-
1 TATATATATATAACT
9291597 TATATA
1 TATATA
9291603 AAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 3 0.16
15 10 0.53
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATATATAACT
Found at i:9291728 original size:21 final size:21
Alignment explanation
Indices: 9291704--9291743 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9291694 CCCTAATCCC
*
9291704 TAAACTTTAAACCATAAATAT
1 TAAACATTAAACCATAAATAT
*
9291725 TAAACATTAAACCCTAAAT
1 TAAACATTAAACCATAAAT
9291744 CACAAACCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACATTAAACCATAAATAT
Found at i:9291750 original size:21 final size:21
Alignment explanation
Indices: 9291690--9291750 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
9291680 CCATAAACCC
* *
9291690 TAAACCCT-AATCCCTAAACTT
1 TAAACCCTAAATCAC-AAACAT
* *
9291711 TAAACCATAAAT-ATTAAACAT
1 TAAACCCTAAATCA-CAAACAT
9291732 TAAACCCTAAATCACAAAC
1 TAAACCCTAAATCACAAAC
9291751 CCTAATATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAATCACAAACAT
Found at i:9292272 original size:14 final size:14
Alignment explanation
Indices: 9292255--9292294 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
9292245 CCCTAAATCA
*
9292255 TAAACTCTAAACTT
1 TAAACCCTAAACTT
*
9292269 TAAACCCTAAATTT
1 TAAACCCTAAACTT
9292283 TAAACCCTAAAC
1 TAAACCCTAAAC
9292295 CCTAATGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAACCCTAAACTT
Found at i:9292279 original size:21 final size:21
Alignment explanation
Indices: 9292236--9292299 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
9292226 AGTTTATAAA
* * *
9292236 AAAC-CTAACCCCTAAATCAT
1 AAACTCTAAACCCTAAACCCT
**
9292256 AAACTCTAAACTTTAAACCCT
1 AAACTCTAAACCCTAAACCCT
* *
9292277 AAATTTTAAACCCTAAACCCT
1 AAACTCTAAACCCTAAACCCT
9292298 AA
1 AA
9292300 TGTAAATGGA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACTCTAAACCCTAAACCCT
Found at i:9300848 original size:20 final size:20
Alignment explanation
Indices: 9300823--9300860 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9300813 TTTTGGTGCA
9300823 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
*
9300843 GAGGGAATCGATTCCCCC
1 GAGGGAATCGATACCCCC
9300861 TTTGAAGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:9300877 original size:23 final size:23
Alignment explanation
Indices: 9300845--9300905 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
9300835 ACCCCCATGA
*
9300845 GGGAATCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
9300868 GGGAACCGATTCCCCTTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
9300891 GGGAACCGATTCCCC
1 GGGAACCGATTCCCC
9300906 GCTGGGGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:9304232 original size:20 final size:20
Alignment explanation
Indices: 9304207--9304251 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
9304197 TAAATCGTTG
9304207 TGCAATTAGTTTCAATTTTC
1 TGCAATTAGTTTCAATTTTC
9304227 TGCAATTAGTTTCAATTTTC
1 TGCAATTAGTTTCAATTTTC
9304247 TGCAA
1 TGCAA
9304252 AAGCTTCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (20 bp):
TGCAATTAGTTTCAATTTTC
Found at i:9304544 original size:14 final size:14
Alignment explanation
Indices: 9304522--9304578 Score: 105
Period size: 14 Copynumber: 4.1 Consensus size: 14
9304512 TCGATTATAT
*
9304522 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
9304536 GTTCATTTATGTTC
1 GTTCATTTATGTTC
9304550 GTTCATTTATGTTC
1 GTTCATTTATGTTC
9304564 GTTCATTTATGTTC
1 GTTCATTTATGTTC
9304578 G
1 G
9304579 AACAGAGGGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:9304856 original size:10 final size:10
Alignment explanation
Indices: 9304843--9304900 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
9304833 GTGTTTTTGT
9304843 TGTTCGTTTA
1 TGTTCGTTTA
9304853 TGTTCGTTTA
1 TGTTCGTTTA
9304863 --TT-GTGTT-
1 TGTTCGT-TTA
* **
9304870 CGTTCGTTCG
1 TGTTCGTTTA
9304880 TGTTCGTTTA
1 TGTTCGTTTA
9304890 TGTTCGTTTA
1 TGTTCGTTTA
9304900 T
1 T
9304901 TATTTAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 3 0.08
10 30 0.77
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:9304874 original size:27 final size:26
Alignment explanation
Indices: 9304840--9304890 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
9304830 TGTGTGTTTT
*
9304840 TGTTGTTCGTTTATGTTCGTTTATTG
1 TGTTGTTCGTTCATGTTCGTTTATTG
*
9304866 TGTTCGTTCGTTCGTGTTCGTTTAT
1 TGTT-GTTCGTTCATGTTCGTTTAT
9304891 GTTCGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.59
Consensus pattern (26 bp):
TGTTGTTCGTTCATGTTCGTTTATTG
Found at i:9306058 original size:31 final size:31
Alignment explanation
Indices: 9306023--9306081 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
9306013 GGTAGATAGG
* *
9306023 TTAAAATTGAATTGG-TCGATAATGTTAGGGA
1 TTAAAATTGAA-CGGATCGATAACGTTAGGGA
*
9306054 TTAAATTTGAACGGATCGATAACGTTAG
1 TTAAAATTGAACGGATCGATAACGTTAG
9306082 AAATTACGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (31 bp):
TTAAAATTGAACGGATCGATAACGTTAGGGA
Found at i:9311792 original size:19 final size:20
Alignment explanation
Indices: 9311743--9311795 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
9311733 TTAGCCCAAG
*
9311743 AGTATCAATAC-TCCTACAAA
1 AGTATCAATACTTTCTAC-AA
* *
9311763 AGTTTCGATACTTTCTAC-A
1 AGTATCAATACTTTCTACAA
9311782 AGTATCAATACTTT
1 AGTATCAATACTTT
9311796 TAAAAATTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.48
20 9 0.33
21 5 0.19
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (20 bp):
AGTATCAATACTTTCTACAA
Found at i:9317312 original size:12 final size:12
Alignment explanation
Indices: 9317295--9317320 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9317285 AAATTTAGTT
9317295 TAATTAATATTA
1 TAATTAATATTA
9317307 TAATTAATATTA
1 TAATTAATATTA
9317319 TA
1 TA
9317321 TGTACAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTAATATTA
Found at i:9317985 original size:2 final size:2
Alignment explanation
Indices: 9317978--9318011 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9317968 TCTAAAATTC
9317978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9318012 TTCAGGTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9320132 original size:42 final size:42
Alignment explanation
Indices: 9320075--9320179 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
9320065 GGTCTCAAAC
* * *
9320075 CCATCACCCACCCACTACCCGTGACGGGTACCACTTTCTAAAT
1 CCAT-ACCCGCCCACTACCCATGACAGGTACCACTTTCTAAAT
* *
9320118 CCATACTCGCCCACTACCCATGACATGTACCACTTTCTAAAT
1 CCATACCCGCCCACTACCCATGACAGGTACCACTTTCTAAAT
9320160 CCATACCCGCCCACTACCCA
1 CCATACCCGCCCACTACCCA
9320180 CTAAAGTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
42 52 0.93
43 4 0.07
ACGTcount: A:0.27, C:0.44, G:0.09, T:0.21
Consensus pattern (42 bp):
CCATACCCGCCCACTACCCATGACAGGTACCACTTTCTAAAT
Found at i:9326788 original size:19 final size:19
Alignment explanation
Indices: 9326764--9326804 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
9326754 GCTGGAAACT
9326764 GGTTTTGACCGGTTTAACC
1 GGTTTTGACCGGTTTAACC
*
9326783 GGTTTTGACCGGTTTGACC
1 GGTTTTGACCGGTTTAACC
9326802 GGT
1 GGT
9326805 CACGACCCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.37
Consensus pattern (19 bp):
GGTTTTGACCGGTTTAACC
Found at i:9326793 original size:10 final size:10
Alignment explanation
Indices: 9326764--9326804 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
9326754 GCTGGAAACT
9326764 GGTTTTGACC
1 GGTTTTGACC
*
9326774 GG-TTTAACC
1 GGTTTTGACC
9326783 GGTTTTGACC
1 GGTTTTGACC
9326793 GG-TTTGACC
1 GGTTTTGACC
9326802 GGT
1 GGT
9326805 CACGACCCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 17 0.63
10 10 0.37
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:9326811 original size:19 final size:19
Alignment explanation
Indices: 9326770--9326817 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
9326760 AACTGGTTTT
***
9326770 GACCGGTTTAACCGGTTTT
1 GACCGGTTTAACCGGTCAC
*
9326789 GACCGGTTTGACCGGTCAC
1 GACCGGTTTAACCGGTCAC
*
9326808 GACCCGTTTA
1 GACCGGTTTA
9326818 CCCGTTTACC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (19 bp):
GACCGGTTTAACCGGTCAC
Found at i:9326844 original size:18 final size:18
Alignment explanation
Indices: 9326821--9326868 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
9326811 CCGTTTACCC
*
9326821 GTTTACCCGACCCGACTA
1 GTTTACCCGACCCGACCA
*
9326839 GTTTACCCGACCCGACCC
1 GTTTACCCGACCCGACCA
9326857 GTTTACCCGACC
1 GTTTACCCGACC
9326869 GTTGACCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.21
Consensus pattern (18 bp):
GTTTACCCGACCCGACCA
Found at i:9326864 original size:13 final size:13
Alignment explanation
Indices: 9326847--9326888 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
9326837 TAGTTTACCC
9326847 GACCCGACCCGTT
1 GACCCGACCCGTT
*
9326860 TACCCGA-CCGTT
1 GACCCGACCCGTT
9326872 GACCCGACCCGTT
1 GACCCGACCCGTT
9326885 GACC
1 GACC
9326889 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:9326890 original size:7 final size:7
Alignment explanation
Indices: 9326880--9326910 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
9326870 TTGACCCGAC
9326880 CCGTTGA
1 CCGTTGA
9326887 CCGTTGA
1 CCGTTGA
9326894 CCGTTGA
1 CCGTTGA
9326901 CCGTTGA
1 CCGTTGA
9326908 CCG
1 CCG
9326911 GTGTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:9326971 original size:29 final size:29
Alignment explanation
Indices: 9326910--9326976 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
9326900 ACCGTTGACC
* *** *
9326910 GGTGTTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
9326939 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
9326968 GGTGCTATT
1 GGTGCTATT
9326977 TTAGTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:9327033 original size:29 final size:29
Alignment explanation
Indices: 9326910--9327034 Score: 83
Period size: 29 Copynumber: 4.3 Consensus size: 29
9326900 ACCGTTGACC
* * ****
9326910 GGTGTTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
*
9326939 GGTGCTATTCTGGGAATTAATTCG-AAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
* * * *
9326967 GGGTGCTATTTTAGTAATT-TTTCGAAAAA
1 -GGTGCTATTTTGGGAATTAATTCGAAAAT
*****
9326996 AAAAATATTTTGGGAATTAATTCGAAAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
9327025 GGTGCTATTT
1 GGTGCTATTT
9327035 GTGTAAAATG
Statistics
Matches: 70, Mismatches: 23, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
28 16 0.23
29 54 0.77
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAT
Found at i:9333832 original size:9 final size:9
Alignment explanation
Indices: 9333814--9333877 Score: 83
Period size: 9 Copynumber: 6.8 Consensus size: 9
9333804 GAAAAATGGT
9333814 TTTGACCGG
1 TTTGACCGG
*
9333823 TTTAACCGG
1 TTTGACCGG
9333832 TTTTGACCGG
1 -TTTGACCGG
*
9333842 TTTAACCGG
1 TTTGACCGG
9333851 TTTTTGACCGG
1 --TTTGACCGG
9333862 TTTGACCGG
1 TTTGACCGG
9333871 TTTGACC
1 TTTGACC
9333878 TCACGACCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
9 32 0.67
10 8 0.17
11 8 0.17
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (9 bp):
TTTGACCGG
Found at i:9333835 original size:19 final size:19
Alignment explanation
Indices: 9333811--9333877 Score: 109
Period size: 19 Copynumber: 3.5 Consensus size: 19
9333801 CTGGAAAAAT
9333811 GGTTTTGACCGGTTTAACC
1 GGTTTTGACCGGTTTAACC
9333830 GGTTTTGACCGGTTTAACC
1 GGTTTTGACCGGTTTAACC
*
9333849 GGTTTTTGACCGGTTTGACC
1 GG-TTTTGACCGGTTTAACC
9333869 GG-TTTGACC
1 GGTTTTGACC
9333878 TCACGACCGT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 7 0.15
19 21 0.46
20 18 0.39
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.37
Consensus pattern (19 bp):
GGTTTTGACCGGTTTAACC
Found at i:9333857 original size:20 final size:20
Alignment explanation
Indices: 9333813--9333873 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
9333803 GGAAAAATGG
9333813 TTTTGACCGGTTTAACCGG-
1 TTTTGACCGGTTTAACCGGT
9333832 TTTTGACCGGTTTAACCGGT
1 TTTTGACCGGTTTAACCGGT
*
9333852 TTTTGACCGGTTTGACCGGT
1 TTTTGACCGGTTTAACCGGT
9333872 TT
1 TT
9333874 GACCTCACGA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 19 0.47
20 21 0.52
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (20 bp):
TTTTGACCGGTTTAACCGGT
Found at i:9333917 original size:18 final size:18
Alignment explanation
Indices: 9333894--9333940 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
9333884 CCGTTTACCC
9333894 GTTTACCCGACCCGACCA
1 GTTTACCCGACCCGACCA
*
9333912 GTTTACCCGACCCGACCC
1 GTTTACCCGACCCGACCA
9333930 GTTTA-CCGACC
1 GTTTACCCGACC
9333941 GTTGACCGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.19, C:0.45, G:0.17, T:0.19
Consensus pattern (18 bp):
GTTTACCCGACCCGACCA
Found at i:9333960 original size:7 final size:7
Alignment explanation
Indices: 9333950--9333988 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
9333940 CGTTGACCGC
9333950 CCGTTGA
1 CCGTTGA
9333957 CCGTTGA
1 CCGTTGA
9333964 CCGTTGA
1 CCGTTGA
9333971 CCGTTGA
1 CCGTTGA
9333978 CCGTTGA
1 CCGTTGA
9333985 CCGT
1 CCGT
9333989 GTATTCTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.31, G:0.28, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:9334010 original size:28 final size:28
Alignment explanation
Indices: 9333979--9334035 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
9333969 GACCGTTGAC
9333979 CGTTGACCGTG-TATTCTGGGAATTAATT
1 CGTT-ACCGTGCTATTCTGGGAATTAATT
***
9334007 CGTTTTGGTGCTATTCTGGGAATTAATT
1 CGTTACCGTGCTATTCTGGGAATTAATT
9334035 C
1 C
9334036 AATGGGTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (28 bp):
CGTTACCGTGCTATTCTGGGAATTAATT
Found at i:9335772 original size:64 final size:65
Alignment explanation
Indices: 9335704--9335826 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
9335694 TTGGAATACT
* *
9335704 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCAATG-TTTGAAAAATAGCC
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAAATAGCC
***** *
9335768 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAA
9335827 TATTCAGAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 42 0.84
65 8 0.16
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAAATAGCC
Found at i:9335827 original size:64 final size:66
Alignment explanation
Indices: 9335722--9335883 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 66
9335712 CGGTGCACCA
* *
9335722 AGTGTGCATCGATGCATGAAATGCATTCAATG-TTTGAAAAATAGCCTGA-TGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
9335785 G
66 G
** * **
9335786 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
9335850 G
66 G
* * *
9335851 AGAGTGCATCGGTGCATGGAATGC-TTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
9335884 CAATTAATTC
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 46 0.55
65 37 0.45
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
G
Found at i:9335856 original size:19 final size:19
Alignment explanation
Indices: 9335832--9335870 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9335822 GAAAATATTC
9335832 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
9335851 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
9335870 A
1 A
9335871 ATGCTTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:9337301 original size:19 final size:21
Alignment explanation
Indices: 9337264--9337306 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
9337254 TAACTTTTTC
*
9337264 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
9337284 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
9337304 TTT
1 TTT
9337307 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:9340509 original size:24 final size:24
Alignment explanation
Indices: 9340482--9340531 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9340472 TGGTGGTTGA
*
9340482 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
9340506 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
9340530 TT
1 TT
9340532 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:9346192 original size:429 final size:429
Alignment explanation
Indices: 9345380--9346671 Score: 2178
Period size: 429 Copynumber: 3.0 Consensus size: 429
9345370 GTTGATTATG
* *
9345380 ATGAAA-TTTTTTCT-TCTGTGGTCAGGTACACTTCAATCCGAGCAGTACTTGCATTGGTGGCTA
1 ATGAAATTTTTTTCTCT-TGTGGTCAGGCACACTTCAATCCGAGCAGTACTTGTATTGGTGGCTA
* * *
9345443 GTTGGGATTTGCATTTAGAGCAGATAGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAG
65 GTTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAA
* * * *
9345508 CATATCTACATGCAGCAGTCTGAAGGTTTCACTCAACCTGAAAACGAGCATTTAGTTTGCAGATT
130 CAGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATT
*
9345573 GAAGAAATCTTTGTACGGGTTGAAACAGTCTCCGAGACAGTGGTATAAACGATTTGACTCCTATA
195 GAAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATA
* *
9345638 TGATCGCGATTGGCTACAATCGATGTGAG-ATTGATTGTTGTGTCTATGTTAAGAGCCTTGATGA
260 TGATCACGATTGGCTACAACCGATGTGAGTA-TGATTGTTGTGTCTATGTTAAGAGCCTTGATGA
* * *
9345702 TGGTTCTTTTATTTTCCTGTTACTGTATGTTAATGATATGTTGATTACTGTGAAGAACATGGATG
324 TGGTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATG
*
9345767 ATGTTATCGATTTGAAAACCTTATTGAGTCAGGAATTTGAT
389 ATGTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
* * *
9345808 ATGAATTTTTTTTCTCTTGTGGTCAAGCACACTTCAATCTGAGCAGTACTTGTATTGGTGGCTAG
1 ATGAAATTTTTTTCTCTTGTGGTCAGGCACACTTCAATCCGAGCAGTACTTGTATTGGTGGCTAG
* *
9345873 TTGAGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGATC
66 TTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAAC
*
9345938 AGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAATGAGCATTTAGTTTGCAGATTG
131 AGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATTG
*
9346003 AAGAAATCTTTGTACGGGTTGAAACAGTCTCCTAGACAGTGGTATAAACGATTTGACTCCTATAT
196 AAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATAT
* *
9346068 GATCACAATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGTCTTGATGATG
261 GATCACGATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGATG
* * *
9346133 GTTCTTTTATTTTTCTGTTACTATATGTTGATGATATGTTGATTACTACGAATAACATGGATGAT
326 GTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGAT
9346198 GTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
391 GTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
* *
9346237 ATGAAATTTTTTTCTCCTGTGGTCAGGCACACTTCAATCCGAGCAGAACTT-TCATTGGTGGCTA
1 ATGAAATTTTTTTCTCTTGTGGTCAGGCACACTTCAATCCGAGCAGTACTTGT-ATTGGTGGCTA
* * **
9346301 GTTGGGATTTGTATTTAGAGTAGATGGATGTTAAAACTGCTTTTTCCCATGGTGATTTAGAGGAA
65 GTTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAA
* * *
9346366 CAGATCTACATGCGACAGCCTGAAGGTTGCACTCAACCTGGAAACGAGCATTTAGTTTACAGATT
130 CAGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATT
9346431 GAAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATA
195 GAAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATA
*
9346496 TGATCACGATTGGCTAAAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGAT
260 TGATCACGATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGAT
*
9346561 GGTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTCGATTACTGCGAAGAACATGGATGA
325 GGTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGA
9346626 TGTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
390 TGTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
9346666 ATGAAA
1 ATGAAA
9346672 GATTTAGGTG
Statistics
Matches: 811, Mismatches: 49, Indels: 7
0.94 0.06 0.01
Matches are distributed among these distances:
428 6 0.01
429 803 0.99
430 2 0.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (429 bp):
ATGAAATTTTTTTCTCTTGTGGTCAGGCACACTTCAATCCGAGCAGTACTTGTATTGGTGGCTAG
TTGGGATTTGCATTTAGAGAAGATGGATGTTAAAACTGCTTTTTTGCATGGTGATTTAGAGGAAC
AGATCTACATGCGGCAGCCTGAAGGTTTCACTCAACCTGGAAACGAGCATTTAGTTTGCAGATTG
AAGAAATCTTTGTACGGGTTGAAACAGTCTCCAAGACAGTGGTATAAACGATTTGACTCCTATAT
GATCACGATTGGCTACAACCGATGTGAGTATGATTGTTGTGTCTATGTTAAGAGCCTTGATGATG
GTTCTTTTATTTTTCTGTTACTGTATGTTGATGATATGTTGATTACTGCGAAGAACATGGATGAT
GTTATCGGTTTGAAAACCTTATTGAGTCAGGAATTTGAT
Found at i:9358973 original size:146 final size:146
Alignment explanation
Indices: 9358747--9359010 Score: 332
Period size: 146 Copynumber: 1.8 Consensus size: 146
9358737 TTTTTATAAT
* * * ** *
9358747 AAAATATTAACATTTCATATCACAACTTATTTTCTTAATGAACCATAACATTTTTTGGCGTAACC
1 AAAATATTAACATTCCATATCACAACCTATTTTCTTAATGAACCATAACATTCTTAAGCGCAACC
* * *
9358812 CATCTTATCAAAAAAATGTTAATATTTCAAATCGCAACTTATTTATTAGTGAACCATGATATTCT
66 CATCTTATCAAAAAAATATTAACATTTCAAATCACAACTTATTTATTAGTGAACCATGATATTCT
9358877 CATGTTATTAATAAAA
131 CATGTTATTAATAAAA
* * * * * *
9358893 AAAATATTAACATTCCTTATCGCAACCTA-TTTCTTAGTGAACCATGACATTCTTAAGTGCAACT
1 AAAATATTAACATTCCATATCACAACCTATTTTCTTAATGAACCATAACATTCTTAAGCGCAACC
* * * * *
9358957 CATTTTATTAATAAAAATATTAACATTTTATATCACAACTTATTTCTTAGTGAA
66 CATCTTATCAA-AAAAATATTAACATTTCAAATCACAACTTATTTATTAGTGAA
9359011 TCATCACATT
Statistics
Matches: 97, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
145 36 0.37
146 61 0.63
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (146 bp):
AAAATATTAACATTCCATATCACAACCTATTTTCTTAATGAACCATAACATTCTTAAGCGCAACC
CATCTTATCAAAAAAATATTAACATTTCAAATCACAACTTATTTATTAGTGAACCATGATATTCT
CATGTTATTAATAAAA
Found at i:9358996 original size:40 final size:40
Alignment explanation
Indices: 9358952--9359074 Score: 94
Period size: 40 Copynumber: 3.1 Consensus size: 40
9358942 TTCTTAAGTG
9358952 CAACTCATTTTATTAATAAAAATATTAACATTTTATATCA
1 CAACTCATTTTATTAATAAAAATATTAACATTTTATATCA
* * * * * * *
9358992 CAACTTA-TTTCTTAGT--GAATCA-TCACATTTTTTTTGGCA
1 CAACTCATTTTATTAATAAAAAT-ATTAACATTTTATAT--CA
* *
9359031 CAAC-CTATTTTATTAATAAAAATATTAACATTTGACATCA
1 CAACTC-ATTTTATTAATAAAAATATTAACATTTTATATCA
9359071 CAAC
1 CAAC
9359075 CTATTTCTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 16
0.65 0.18 0.18
Matches are distributed among these distances:
37 13 0.22
38 1 0.02
39 14 0.24
40 19 0.32
41 1 0.02
42 11 0.19
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (40 bp):
CAACTCATTTTATTAATAAAAATATTAACATTTTATATCA
Found at i:9359005 original size:77 final size:78
Alignment explanation
Indices: 9358892--9359103 Score: 252
Period size: 79 Copynumber: 2.7 Consensus size: 78
9358882 TATTAATAAA
* *
9358892 AAAAATATTAACATTCCT-TATCGCAACCTATTTCTTAGTGAACCATGACATTCTTAAGT-G-CA
1 AAAAATATTAACATT-TTATATCACAACCTATTTCTTAGTGAACCATGACATT-TTAAGTGGACA
9358954 A-CTCATTTTATTAAT
64 ACCT-ATTTTATTAAT
* * * ***
9358969 AAAAATATTAACATTTTATATCACAACTTATTTCTTAGTGAATCATCACATTTTTTTTGGCACAA
1 AAAAATATTAACATTTTATATCACAACCTATTTCTTAGTGAACCATGACATTTTAAGTGG-ACAA
9359034 CCTATTTTATTAAT
65 CCTATTTTATTAAT
* * *
9359048 AAAAATATTAACATTTGACATCACAACCTATTTCTTAGTAAACCATGACAATTTTA
1 AAAAATATTAACATTTTATATCACAACCTATTTCTTAGTGAACCATGAC-ATTTTA
9359104 GGTACAACTG
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
76 4 0.04
77 46 0.40
79 57 0.50
80 7 0.06
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.39
Consensus pattern (78 bp):
AAAAATATTAACATTTTATATCACAACCTATTTCTTAGTGAACCATGACATTTTAAGTGGACAAC
CTATTTTATTAAT
Found at i:9362798 original size:19 final size:19
Alignment explanation
Indices: 9362763--9362799 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9362753 CATATGGATG
*
9362763 AAAATTGATTTTAGGGGAA
1 AAAATTGATTTGAGGGGAA
*
9362782 AAAATTGATTTGGGGGGA
1 AAAATTGATTTGAGGGGA
9362800 GGGGTTCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (19 bp):
AAAATTGATTTGAGGGGAA
Found at i:9366211 original size:15 final size:15
Alignment explanation
Indices: 9366187--9366217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9366177 GCTAAGTCTG
9366187 CAAATGTTTCGAGTT
1 CAAATGTTTCGAGTT
*
9366202 CAAATTTTTCGAGTT
1 CAAATGTTTCGAGTT
9366217 C
1 C
9366218 GAGTCAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (15 bp):
CAAATGTTTCGAGTT
Found at i:9367109 original size:2 final size:2
Alignment explanation
Indices: 9367097--9367165 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
9367087 TTTATTTTAA
*
9367097 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9367139 AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9367166 GTGCGCGCGC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9372703 original size:2 final size:2
Alignment explanation
Indices: 9372696--9372722 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9372686 TTTTAGTATT
9372696 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 T
9372723 TGTGATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9376006 original size:23 final size:22
Alignment explanation
Indices: 9375980--9376049 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
9375970 AAAAAAAAAT
*
9375980 AGAGAAAAACGTATTACAAAGAC
1 AGAGATAAACGT-TTACAAAGAC
* *
9376003 AGAGATAAACGTTTCATAAAGAT
1 AGAGATAAACGTTT-ACAAAGAC
* *
9376026 AGAGATAAACATGTCACAAAGAC
1 AGAGATAAACGT-TTACAAAGAC
9376049 A
1 A
9376050 TAATTATTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 2 0.05
23 35 0.92
24 1 0.03
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (22 bp):
AGAGATAAACGTTTACAAAGAC
Found at i:9376680 original size:13 final size:13
Alignment explanation
Indices: 9376662--9376687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9376652 AATTATATTT
9376662 AAATTGTATTTTA
1 AAATTGTATTTTA
9376675 AAATTGTATTTTA
1 AAATTGTATTTTA
9376688 TTTAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AAATTGTATTTTA
Found at i:9378788 original size:17 final size:17
Alignment explanation
Indices: 9378766--9378817 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
9378756 ACTAGACAAA
*
9378766 TTTATTATTTTAAAGAG
1 TTTATTAATTTAAAGAG
**
9378783 TTTATTAATTTACCGAG
1 TTTATTAATTTAAAGAG
9378800 --TATTAATTTAAAGAG
1 TTTATTAATTTAAAGAG
9378815 TTT
1 TTT
9378818 CTGCTATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTAAAGAG
Found at i:9378815 original size:15 final size:15
Alignment explanation
Indices: 9378768--9378815 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9378758 TAGACAAATT
*
9378768 TATTATTTTAAAGAG
1 TATTAATTTAAAGAG
**
9378783 TTTATTAATTTACCGAG
1 --TATTAATTTAAAGAG
9378800 TATTAATTTAAAGAG
1 TATTAATTTAAAGAG
9378815 T
1 T
9378816 TTCTGCTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 14 0.54
17 12 0.46
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (15 bp):
TATTAATTTAAAGAG
Found at i:9381105 original size:3 final size:3
Alignment explanation
Indices: 9381097--9381180 Score: 66
Period size: 3 Copynumber: 28.0 Consensus size: 3
9381087 GGCCTGTTTG
*
9381097 TAA TAA TAA TAA TAA TAA TATA TAA TAA -AA TAAA TAA -AA TAG T-A
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA
* * * * *
9381141 TAA AAA TTAA TAA TAA TAT TAC TAA TAA TAT TAA AAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9381181 AAAACAAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
2 5 0.08
3 51 0.80
4 8 0.12
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9381860 original size:112 final size:116
Alignment explanation
Indices: 9381546--9382100 Score: 520
Period size: 112 Copynumber: 4.8 Consensus size: 116
9381536 GAATTAAGGC
*
9381546 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
9381610 TGAACACTTCTGGAAATGTTGA-TCTATCTCCTTATGTGATAGAGTCATGAAA
66 TGAACACTTCTGGAAATGTTGATTCTA-CT-CTGATGTGATAGAGTCAAGAAA
* * * * *
9381662 AAGGTTGAACAAGTTCTTCTTATTATGAACTTATTCTTCC-TCTTCAGATAAGTTCTTTTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
** * *
9381726 TGAACTTTCTCTAGAACA-GTTGATTC-A-T-TGA-GTGAT-GAATTCAAGCAAA
66 TGAACACT-TCTGGAA-ATGTTGATTCTACTCTGATGTGATAG-AGTCAAG-AAA
9381775 AA-GTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
** * * *
9381839 TGAACACTTCTGGAAATGTTGATGCTGATGCTGATCTATCTTCTTCTGTGATAGATTCATG-CA
66 TGAACACTTCTGGAAA---TG-T--TGA---T--TCTA-C-TCTGATGTGATAGAGTCAAGAAA
* *
9381902 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
9381966 TGAAC-TTTCTTGAAAAAT-TTGATTC-A-TCT-A-GTGAT-GAATTCGAGCAA
66 TGAACACTTC-TG-GAAATGTTGATTCTACTCTGATGTGATAG-AGTCAAGAAA
*
9382013 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
9382078 TTAACTTCTT-TGGAAATGTTGAT
66 TGAAC-ACTTCTGGAAATGTTGAT
9382101 CCATTGAGTA
Statistics
Matches: 370, Mismatches: 34, Indels: 74
0.77 0.07 0.15
Matches are distributed among these distances:
109 1 0.00
110 10 0.03
111 47 0.13
112 87 0.24
113 35 0.09
114 2 0.01
115 3 0.01
116 65 0.18
117 15 0.04
118 7 0.02
121 4 0.01
123 3 0.01
124 1 0.00
125 1 0.00
126 3 0.01
127 34 0.09
128 40 0.11
129 11 0.03
130 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (116 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACACTTCTGGAAATGTTGATTCTACTCTGATGTGATAGAGTCAAGAAA
Found at i:9382063 original size:239 final size:241
Alignment explanation
Indices: 9381629--9382100 Score: 756
Period size: 239 Copynumber: 2.0 Consensus size: 241
9381619 CTGGAAATGT
*
9381629 TGATCTATCTCCTTATGTGATAGAGTCATGAAAAAGGTTGAACAAGTTCTTCTTATTATGAACTT
1 TGATCTATCTCCTTATGTGATAGAGTCATGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* *
9381694 ATTCTTCCTCTTCAGATAAGTTCTTTTCATTATGAACTTTCTCTAGAACAGTTGATTCATTGAGT
66 ATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATTCATTGAGT
9381759 GATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
131 GATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
9381824 GAGTTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGATGCTGATGC
196 GAGTTCTTCTCATTATGAACTACTT-TGGAAATGTTGATGCTGATGC
* * * *
9381870 TGATCTATCTTCTTCTGTGATAGATTCATG-CAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
1 TGATCTATCTCCTTATGTGATAGAGTCATGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* *
9381934 CTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCT-T-GAAAAATTTGATTCATCT-A
66 ATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAG-AAAAGTTGATTCAT-TGA
* * *
9381996 GTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
129 GTGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
9382061 ATGAGTTCTTCTCATTATTAACTTCTTTGGAAATGTTGAT
194 ATGAGTTCTTCTCATTATGAACTACTTTGGAAATGTTGAT
9382101 CCATTGAGTA
Statistics
Matches: 214, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
238 1 0.00
239 110 0.51
240 76 0.36
241 27 0.13
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (241 bp):
TGATCTATCTCCTTATGTGATAGAGTCATGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
ATTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATTCATTGAGT
GATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTACTTTGGAAATGTTGATGCTGATGC
Found at i:9382501 original size:22 final size:22
Alignment explanation
Indices: 9382476--9382530 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
9382466 AGTAAAGCTT
*
9382476 TCATCTTTGAAAACAGAATTTA
1 TCATCTTTGAAAACAGAATCTA
* *
9382498 TCATCTTTGTAAAGAGAATCTA
1 TCATCTTTGAAAACAGAATCTA
*
9382520 TCATTTTTGAA
1 TCATCTTTGAA
9382531 GAGAAACTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (22 bp):
TCATCTTTGAAAACAGAATCTA
Found at i:9384741 original size:23 final size:23
Alignment explanation
Indices: 9384715--9384781 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
9384705 TTATTATATA
9384715 GCACTTCGGTGCATTTCTACGCG
1 GCACTTCGGTGCATTTCTACGCG
* **
9384738 GCACTAT-GGTGCAATTCTACATG
1 GCACT-TCGGTGCATTTCTACGCG
*
9384761 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
9384782 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Done.