Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 67 of 187
Found at i:19609277 original size:16 final size:17
Alignment explanation
Indices: 19609250--19609284 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
19609240 TAATATAATG
19609250 TATTTGTATTTAAATTT
1 TATTTGTATTTAAATTT
19609267 TATTT-TATTTAAATTT
1 TATTTGTATTTAAATTT
19609283 TA
1 TA
19609285 ATCTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTTGTATTTAAATTT
Found at i:19609291 original size:16 final size:16
Alignment explanation
Indices: 19609256--19609292 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
19609246 AATGTATTTG
* *
19609256 TATTTAAATTTTATTT
1 TATTTAAATTTTAATC
19609272 TATTTAAATTTTAATC
1 TATTTAAATTTTAATC
19609288 TATTT
1 TATTT
19609293 TTTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTAAATTTTAATC
Found at i:19630629 original size:18 final size:19
Alignment explanation
Indices: 19630603--19630638 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19630593 AAGGGAAAAA
19630603 GTAAAAAAAAAAA-TAAAT
1 GTAAAAAAAAAAAGTAAAT
*
19630621 GTAATAAAAAAAAGTAAA
1 GTAAAAAAAAAAAGTAAA
19630639 AGGTGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (19 bp):
GTAAAAAAAAAAAGTAAAT
Found at i:19630631 original size:19 final size:18
Alignment explanation
Indices: 19630603--19630638 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19630593 AAGGGAAAAA
19630603 GTAAAAAAAAAAATAAAT
1 GTAAAAAAAAAAATAAAT
*
19630621 GTAATAAAAAAAAGTAAA
1 GTAA-AAAAAAAAATAAA
19630639 AGGTGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
GTAAAAAAAAAAATAAAT
Found at i:19630910 original size:6 final size:6
Alignment explanation
Indices: 19630899--19630943 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
19630889 CCACCGGCCT
* * *
19630899 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC CCACCG TCTCCC TCT
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCT
19630944 GGAAATCTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.02, C:0.64, G:0.02, T:0.31
Consensus pattern (6 bp):
TCTCCC
Found at i:19631153 original size:25 final size:24
Alignment explanation
Indices: 19631125--19631183 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
19631115 GTTTTTCTTA
19631125 AATATTTATATAATTATTTTTAATT
1 AATATTTATATAA-TATTTTTAATT
* *
19631150 AATATTAACATAATATTTTTAATT
1 AATATTTATATAATATTTTTAATT
19631174 ATATATTTAT
1 A-ATATTTAT
19631184 TTATAAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AATATTTATATAATATTTTTAATT
Found at i:19631209 original size:19 final size:19
Alignment explanation
Indices: 19631181--19631217 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19631171 ATTATATATT
*
19631181 TATTTATAAACTTTTTATA
1 TATTTATAAAATTTTTATA
*
19631200 TATTTTTAAAATTTTTAT
1 TATTTATAAAATTTTTAT
19631218 TTCAGTTTAG
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:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATAAAATTTTTATA
Found at i:19633923 original size:28 final size:28
Alignment explanation
Indices: 19633890--19633949 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
19633880 AATGTTAATC
* *
19633890 TTTCATAGTTTGCCACAAAGGCTTATTT
1 TTTCATAGTTCGCCACAAAGGCTTATTA
19633918 TTTCATAGTTCGCCACAAAGGCTTATTA
1 TTTCATAGTTCGCCACAAAGGCTTATTA
19633946 TTTC
1 TTTC
19633950 CTGACATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (28 bp):
TTTCATAGTTCGCCACAAAGGCTTATTA
Found at i:19635320 original size:22 final size:22
Alignment explanation
Indices: 19635280--19635321 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19635270 TTTCACCCGT
*
19635280 CAAGCTTCGGTGTCACGACAAC
1 CAAGCTTCGGTATCACGACAAC
* *
19635302 CAAGCTTTGGTATCGCGACA
1 CAAGCTTCGGTATCACGACA
19635322 TCTTCGGCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (22 bp):
CAAGCTTCGGTATCACGACAAC
Found at i:19637120 original size:46 final size:46
Alignment explanation
Indices: 19637050--19637234 Score: 289
Period size: 46 Copynumber: 4.0 Consensus size: 46
19637040 CATGGGAAAG
* * *
19637050 TGTGAAACGTAGGTATGGTATTTCAATGAAGAAAACCATACTGGGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
19637096 TGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
19637142 TGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
19637188 TGTGAAAAGTAGGTATGGTATTTCTGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
19637234 T
1 T
19637235 ATAGCAATGT
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 127 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:19638975 original size:38 final size:38
Alignment explanation
Indices: 19638924--19639016 Score: 134
Period size: 38 Copynumber: 2.4 Consensus size: 38
19638914 CTACTGAGTG
* *
19638924 CATGTTAAGCATGTGTACTACTACTATTAAA-CAGAATA
1 CATGTTAAGCATGTCTACGACTACTATTAAATCA-AATA
* *
19638962 CATGTTAAGCATGTCTACGGCTACTATTAAATTAAATA
1 CATGTTAAGCATGTCTACGACTACTATTAAATCAAATA
19639000 CATGTTAAGCATGTCTA
1 CATGTTAAGCATGTCTA
19639017 TTATTTCTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 49 0.98
39 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (38 bp):
CATGTTAAGCATGTCTACGACTACTATTAAATCAAATA
Found at i:19639238 original size:22 final size:23
Alignment explanation
Indices: 19639176--19639238 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
19639166 AAAAATAATA
*
19639176 GTGGTTCATCCCCAAATTTTTACTG
1 GTGGTTCATCCTCAAA--TTTACTG
* *
19639201 GTAGTTTAT-CTACAAA-TTACTG
1 GTGGTTCATCCT-CAAATTTACTG
19639223 GTGGTTCATCCTCAAA
1 GTGGTTCATCCTCAAA
19639239 ATGGAATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 17 0.55
23 2 0.06
24 1 0.03
25 11 0.35
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (23 bp):
GTGGTTCATCCTCAAATTTACTG
Found at i:19642099 original size:3 final size:3
Alignment explanation
Indices: 19642091--19642135 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19642081 AATATTATGG
19642091 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19642136 AACGCAAGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19652778 original size:49 final size:49
Alignment explanation
Indices: 19652723--19652821 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
19652713 ATATCACAAA
19652723 TGTGGCTCTAAAAACTAGTACATATAAAACCATAAGCTTGAAATAAACT
1 TGTGGCTCTAAAAACTAGTACATATAAAACCATAAGCTTGAAATAAACT
19652772 TGTGGCTCTAAAAACTAGTACATATAAAACCATAAGCTTGAAATAAACT
1 TGTGGCTCTAAAAACTAGTACATATAAAACCATAAGCTTGAAATAAACT
19652821 T
1 T
19652822 TTGAATTAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.27
Consensus pattern (49 bp):
TGTGGCTCTAAAAACTAGTACATATAAAACCATAAGCTTGAAATAAACT
Found at i:19653095 original size:12 final size:13
Alignment explanation
Indices: 19653062--19653099 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
19653052 TAGTAATTTT
19653062 ATATTATTTATGA
1 ATATTATTTATGA
*
19653075 AT-TTTTTTA-GA
1 ATATTATTTATGA
19653086 ATATTATTTATGA
1 ATATTATTTATGA
19653099 A
1 A
19653100 AATAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.19
12 12 0.57
13 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (13 bp):
ATATTATTTATGA
Found at i:19661396 original size:27 final size:27
Alignment explanation
Indices: 19661375--19661427 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
19661365 ATGCTGATTG
*
19661375 CCAGGCTGGTGTTCAAATTGCTGCTGA
1 CCAGACTGGTGTTCAAATTGCTGCTGA
*
19661402 CTAGACTGGTGTTCAAATTGCTGCTG
1 CCAGACTGGTGTTCAAATTGCTGCTG
19661428 GGTAGGCCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (27 bp):
CCAGACTGGTGTTCAAATTGCTGCTGA
Found at i:19661439 original size:27 final size:27
Alignment explanation
Indices: 19661390--19661622 Score: 241
Period size: 27 Copynumber: 8.6 Consensus size: 27
19661380 CTGGTGTTCA
** * * * *
19661390 AATTGCTGCTGACTAGACTGGTGTTCA
1 AATTGCTGCTGGGTAGGCCGGTGATCG
19661417 AATTGCTGCTGGGTAGGCCGGTGATCG
1 AATTGCTGCTGGGTAGGCCGGTGATCG
* *
19661444 AATTGCTGCTGGTTAGGCCGGTGCTCG
1 AATTGCTGCTGGGTAGGCCGGTGATCG
* * * *
19661471 AATGGCTGTTGGTTAGGCCGGTGTTCG
1 AATTGCTGCTGGGTAGGCCGGTGATCG
* * * * *
19661498 AATGGTTGTTGGTTAGGCCGGTGATCA
1 AATTGCTGCTGGGTAGGCCGGTGATCG
* *
19661525 AATTGCTGTTGGGTAGGCCGGTGTTCG
1 AATTGCTGCTGGGTAGGCCGGTGATCG
* *
19661552 AATGGCTGTTGGGTAGGCCGGTGATCG
1 AATTGCTGCTGGGTAGGCCGGTGATCG
** * *
19661579 AATTGCTGCTGGGCCGGCAGATGATCG
1 AATTGCTGCTGGGTAGGCCGGTGATCG
19661606 AATTGCTGCTGGGTAGG
1 AATTGCTGCTGGGTAGG
19661623 GCAATAGTCG
Statistics
Matches: 177, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 177 1.00
ACGTcount: A:0.15, C:0.17, G:0.38, T:0.30
Consensus pattern (27 bp):
AATTGCTGCTGGGTAGGCCGGTGATCG
Found at i:19661494 original size:81 final size:81
Alignment explanation
Indices: 19661409--19661622 Score: 293
Period size: 81 Copynumber: 2.6 Consensus size: 81
19661399 TGACTAGACT
* *
19661409 GGTGTTCAAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCTCGAAT
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
*
19661474 GGCTGTTGGTTAGGCC
66 GGCTGTTGGGTAGGCC
* * * * * * *
19661490 GGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCAAATTGCTGTTGGGTAGGCCGGTGTTCGAAT
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
19661555 GGCTGTTGGGTAGGCC
66 GGCTGTTGGGTAGGCC
* ** * *
19661571 GGTGATCGAATTGCTGCTGGGCCGGCAGATGATCGAATTGCTGCTGGGTAGG
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGGTAGG
19661623 GCAATAGTCG
Statistics
Matches: 112, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 112 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.29
Consensus pattern (81 bp):
GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
GGCTGTTGGGTAGGCC
Found at i:19661633 original size:27 final size:27
Alignment explanation
Indices: 19661573--19661640 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
19661563 GGTAGGCCGG
*
19661573 TGATCGAATTGCTGCTGGGCCGGCAGA
1 TGATCGAATTGCTGCTGGGACGGCAGA
*
19661600 TGATCGAATTGCTGCTGGGTAGGGCA-A
1 TGATCGAATTGCTGCTGGG-ACGGCAGA
19661627 T-AGTCGAATTGCTG
1 TGA-TCGAATTGCTG
19661641 GGGGTTATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.03
27 32 0.86
28 4 0.11
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.26
Consensus pattern (27 bp):
TGATCGAATTGCTGCTGGGACGGCAGA
Found at i:19666270 original size:33 final size:32
Alignment explanation
Indices: 19666154--19666276 Score: 131
Period size: 33 Copynumber: 3.8 Consensus size: 32
19666144 GCAGTAGTCA
* * * *
19666154 CACCCTCCCCATCAGCTTTTACCTTTTCAACAT
1 CACCCTCCCTAGCAGCTTCTACC-CTTCAACAT
* *
19666187 CACCCTCCCTAACAACTTCTATCCCTTCAACAT
1 CACCCTCCCTAGCAGCTTCTA-CCCTTCAACAT
*
19666220 CACCCT-CTTCAGCAGCTTCTACACCTTCAACAT
1 CACCCTCCCT-AGCAGCTTCTAC-CCTTCAACAT
*
19666253 CACCCTCCCTAGTAGCTTCTACCC
1 CACCCTCCCTAGCAGCTTCTACCC
19666277 CCTCCCTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
32 5 0.07
33 67 0.88
34 4 0.05
ACGTcount: A:0.23, C:0.45, G:0.04, T:0.28
Consensus pattern (32 bp):
CACCCTCCCTAGCAGCTTCTACCCTTCAACAT
Found at i:19666279 original size:21 final size:21
Alignment explanation
Indices: 19666255--19666297 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19666245 TTCAACATCA
19666255 CCCTCCCTAGTAGCTTCTACC
1 CCCTCCCTAGTAGCTTCTACC
19666276 CCCTCCCTAGTAGCTTCTACC
1 CCCTCCCTAGTAGCTTCTACC
19666297 C
1 C
19666298 TTTCAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.49, G:0.09, T:0.28
Consensus pattern (21 bp):
CCCTCCCTAGTAGCTTCTACC
Found at i:19666292 original size:54 final size:54
Alignment explanation
Indices: 19666232--19666363 Score: 151
Period size: 54 Copynumber: 2.4 Consensus size: 54
19666222 CCCTCTTCAG
* * *
19666232 CAGCTTCTACACC-TTCAACATCACCCTCCCTAGTAGCTTCTACCCCCTCCCTAGT
1 CAGCTTCTAC-CCATTCAACATCACCCTCACTAGCAGCTTCTACCCCCTCCCCA-T
* * * * *
19666287 -AGCTTCTACCCTTTCAACAACACCCTCATTAGCAGTTTGTACCCCCTCCCCAT
1 CAGCTTCTACCCATTCAACATCACCCTCACTAGCAGCTTCTACCCCCTCCCCAT
*
19666340 CAGTTTCTACCCATTCAACATCAC
1 CAGCTTCTACCCATTCAACATCAC
19666364 ACTCTCCATC
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
53 3 0.05
54 62 0.95
ACGTcount: A:0.23, C:0.42, G:0.07, T:0.28
Consensus pattern (54 bp):
CAGCTTCTACCCATTCAACATCACCCTCACTAGCAGCTTCTACCCCCTCCCCAT
Found at i:19672599 original size:22 final size:22
Alignment explanation
Indices: 19672532--19672604 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
19672522 ATGAACCTTG
*
19672532 TTGTAGAATACTGCAAACTATA
1 TTGTAGAATACTGCAAACTGTA
* ** *
19672554 TCTGAAGAAATGTTACGAAA-TGTA
1 T-TGTAG-AATACTGC-AAACTGTA
19672578 TTGTAGAATACTGCAAACTGTA
1 TTGTAGAATACTGCAAACTGTA
19672600 TTGTA
1 TTGTA
19672605 ATCCATAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
21 3 0.08
22 15 0.39
23 8 0.21
24 9 0.24
25 3 0.08
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (22 bp):
TTGTAGAATACTGCAAACTGTA
Found at i:19672938 original size:134 final size:134
Alignment explanation
Indices: 19672692--19673361 Score: 696
Period size: 134 Copynumber: 5.0 Consensus size: 134
19672682 TAAGTAAAAG
* * * * * *
19672692 GTCGTGATCGTAAATCAGCGAACTGATTAAGTGGAGTCGCGATTGTAAATCAACGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCAATCGTAAATCGACGAACTCTTTAT
* * * * * * *
19672757 AAAGTGATCATGATCGTAAATCAATGAATTGAAGATGTGATCGTAAATTAGCGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATTGTAAATCAACGAGCTTTAAAAAT
*
19672822 GATA
131 GACA
* * * * * * *
19672826 GTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTCGCTACCGTAAATTGATGAACTCTTTTT
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCAATCGTAAATCGACGAACTCTTTAT
** * * * *
19672891 GAAGTGTTTGTGATCGTAAATCAATAAACTAAAGTTGTAATTATAAATCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATTGTAAATCAACGAGCTTTAAAAAT
19672956 GACA
131 GACA
* * * * *
19672960 GTCGTGATCGTAAATCAGCTAACTATTTAAGTGGAGTCGCAATCGTAAATCGATGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCAATCGTAAATCGACGAACTCTTTAT
* * * * * * *
19673025 GAAGTGATCATGATCGTAAGTCGATGAACTGAAGCTATGATCGTAAGTCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATTGTAAATCAACGAGCTTTAAAAAT
19673090 GACA
131 GACA
* ** * * * * * *
19673094 GTTGTGATTATAAATCGGTGAA-TCGTTTAAGTGGAGTAGCAATCGTAAATTGGCAAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACT-GTTTAAGTGGAGTCGCAATCGTAAATCGACGAACTCTTTA
* * * * ** * * *
19673158 TGAAGTGTTCATAATCGTAAATCAATAAACTAAAATCATAATAGTAAATCATCGAGCTTTAAAAA
65 TGAAGTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATTGTAAATCAACGAGCTTTAAAAA
19673223 TGACA
130 TGACA
* * ** *
19673228 ATCATGATCGTAAATCAGCGAACTGTTTAAGTGGAGT-GTTGATCGTAAATCGAAGAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCG-CAATCGTAAATCGACGAACTCTTTA
* * * * * *
19673292 TGAAGTGTTTACGATCGTAAATTAATGAACTGAAGTCGTGATTGTAAATCGACAAGCTTTAAAAA
65 TGAAGTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATTGTAAATCAACGAGCTTTAAAAA
19673357 TGACA
130 TGACA
19673362 ATCAGGATTG
Statistics
Matches: 431, Mismatches: 102, Indels: 6
0.80 0.19 0.01
Matches are distributed among these distances:
133 2 0.00
134 428 0.99
135 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (134 bp):
GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCAATCGTAAATCGACGAACTCTTTAT
GAAGTGTTCATGATCGTAAATCAATGAACTGAAGTTGTGATTGTAAATCAACGAGCTTTAAAAAT
GACA
Found at i:19673177 original size:268 final size:267
Alignment explanation
Indices: 19672692--19673361 Score: 828
Period size: 268 Copynumber: 2.5 Consensus size: 267
19672682 TAAGTAAAAG
*
19672692 GTCGTGATCGTAAATCAGCGAACTGA-TTAAGTGGAGTCGCGATTGTAAATC-AACGAACTGTTT
1 GTCGTGATCGTAAATCAGCGAACT-ATTTAAGTGGAGTCGCGATCGTAAATCGAA-GAACTGTTT
* * * *
19672755 AAAAAGTGATCATGATCGTAAATCAATGAATTGAAGATGTGATCGTAAATTAGCGAGCTTTAAAA
64 AAGAAGTGATCATGATCGTAAATCAATGAACTGAAG-TGTGATCGTAAATCAACGAGCTTTAAAA
* * * **
19672820 ATGATAGTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTCGCTACCGTAAATTGATGAACT
128 ATGACAGTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTAGCAACCGTAAATTGACAAACT
* ** * * **
19672885 CTTTTTGAAGTGTTTGTGATCGTAAATCAATAAACTAAAGTTGTAATTA-TAAATCAACGAGCTT
193 CTTTATGAAGTGTTCATAATCGTAAATCAATAAACTAAAATCATAA-TAGTAAATCAACGAGCTT
19672949 TAAAAATGACA
257 TAAAAATGACA
* * *
19672960 GTCGTGATCGTAAATCAGCTAACTATTTAAGTGGAGTCGCAATCGTAAATCGATGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTATTTAAGTGGAGTCGCGATCGTAAATCGAAGAACTGTTTAA
* * * *
19673025 GAAGTGATCATGATCGTAAGTCGATGAACTGAAGCTATGATCGTAAGTCAACGAGCTTTAAAAAT
66 GAAGTGATCATGATCGTAAATCAATGAACTGAAG-TGTGATCGTAAATCAACGAGCTTTAAAAAT
* * * * * * *
19673090 GACAGTTGTGATTATAAATCGGTGAA-TCGTTTAAGTGGAGTAGCAATCGTAAATTGGCAAACTC
130 GACAGTCGTGATCATAAATCAGCGAACT-GTTTAAGTGAAGTAGCAACCGTAAATTGACAAACTC
*
19673154 TTTATGAAGTGTTCATAATCGTAAATCAATAAACTAAAATCATAATAGTAAATCATCGAGCTTTA
194 TTTATGAAGTGTTCATAATCGTAAATCAATAAACTAAAATCATAATAGTAAATCAACGAGCTTTA
19673219 AAAATGACA
259 AAAATGACA
* * * * *
19673228 ATCATGATCGTAAATCAGCGAACTGTTTAAGTGGAGT-GTTGATCGTAAATCGAAGAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACTATTTAAGTGGAGTCG-CGATCGTAAATCGAAGAACTGTTTA
* * * * * * * *
19673292 TGAAGTGTTTACGATCGTAAATTAATGAACTGAAGTCGTGATTGTAAATCGACAAGCTTTAAAAA
65 AGAAGTGATCATGATCGTAAATCAATGAACTGAAGT-GTGATCGTAAATCAACGAGCTTTAAAAA
19673357 TGACA
129 TGACA
19673362 ATCAGGATTG
Statistics
Matches: 343, Mismatches: 53, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
267 6 0.02
268 336 0.98
269 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (267 bp):
GTCGTGATCGTAAATCAGCGAACTATTTAAGTGGAGTCGCGATCGTAAATCGAAGAACTGTTTAA
GAAGTGATCATGATCGTAAATCAATGAACTGAAGTGTGATCGTAAATCAACGAGCTTTAAAAATG
ACAGTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTAGCAACCGTAAATTGACAAACTCTT
TATGAAGTGTTCATAATCGTAAATCAATAAACTAAAATCATAATAGTAAATCAACGAGCTTTAAA
AATGACA
Found at i:19700194 original size:23 final size:23
Alignment explanation
Indices: 19700124--19700209 Score: 110
Period size: 21 Copynumber: 4.0 Consensus size: 23
19700114 CCTGATCAAT
19700124 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
19700145 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
19700165 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
19700188 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
19700210 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.16
21 23 0.42
23 23 0.42
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:19700206 original size:44 final size:41
Alignment explanation
Indices: 19700124--19700210 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 41
19700114 CCTGATCAAT
* *
19700124 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
19700165 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
19700209 AT
1 AT
19700211 CGGCAAAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 11 0.28
42 10 0.25
43 1 0.03
44 18 0.45
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:19700585 original size:16 final size:17
Alignment explanation
Indices: 19700564--19700595 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19700554 TAATAATAGT
19700564 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
19700580 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
19700596 GCTTGTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:19701243 original size:18 final size:17
Alignment explanation
Indices: 19701208--19701255 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
19701198 TAAACCCTAG
19701208 TTTTCGTTTCTTTCTCT
1 TTTTCGTTTCTTTCTCT
19701225 TTTTCTGTTT-TTT-T-T
1 TTTTC-GTTTCTTTCTCT
19701240 TCTTTC-TTTCTTTCTC
1 T-TTTCGTTTCTTTCTC
19701256 ACCTGTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
14 3 0.12
15 5 0.19
16 6 0.23
17 8 0.31
18 4 0.15
ACGTcount: A:0.00, C:0.21, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTCGTTTCTTTCTCT
Found at i:19704287 original size:16 final size:17
Alignment explanation
Indices: 19704260--19704294 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19704250 TAGAATTGGG
*
19704260 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
19704277 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
19704293 TT
1 TT
19704295 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:19705261 original size:39 final size:39
Alignment explanation
Indices: 19705207--19705289 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
19705197 AGGAGATACG
19705207 ATTGTGTAATCTTAGAGTTCTAATTGTATACAGCTTCTA
1 ATTGTGTAATCTTAGAGTTCTAATTGTATACAGCTTCTA
* *
19705246 ATTGTGTAATCTTAGAGTTCTAATTGTATACATCTTTTA
1 ATTGTGTAATCTTAGAGTTCTAATTGTATACAGCTTCTA
19705285 ATTGT
1 ATTGT
19705290 AGCCATTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (39 bp):
ATTGTGTAATCTTAGAGTTCTAATTGTATACAGCTTCTA
Found at i:19711389 original size:24 final size:23
Alignment explanation
Indices: 19711362--19711420 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
19711352 TCTACTACAA
* *
19711362 GTAGGAGGAGTTGTGTTACTCTTT
1 GTAGGAGCA-TTGTCTTACTCTTT
*
19711386 GTAGGGAGCATTGTCTTACTGTTT
1 GTA-GGAGCATTGTCTTACTCTTT
19711410 GTAGAGAGCAT
1 GTAG-GAGCAT
19711421 CAAAAATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 24 0.80
25 5 0.17
ACGTcount: A:0.20, C:0.10, G:0.32, T:0.37
Consensus pattern (23 bp):
GTAGGAGCATTGTCTTACTCTTT
Found at i:19717074 original size:2 final size:2
Alignment explanation
Indices: 19717067--19717096 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19717057 ATTTGCTCTT
19717067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19717097 GATTTGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19717918 original size:22 final size:23
Alignment explanation
Indices: 19717872--19717950 Score: 124
Period size: 23 Copynumber: 3.5 Consensus size: 23
19717862 ATATATATAA
19717872 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
19717895 AAAATATATATTTGATT-AAAAT
1 AAAATATATATTTGATTAAAAAT
* *
19717917 AAATTATATATCTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
*
19717940 AAAAAATATAT
1 AAAATATATAT
19717951 ATTTAATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.39
23 31 0.61
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATATATATTTGATTAAAAAT
Found at i:19720742 original size:18 final size:20
Alignment explanation
Indices: 19720718--19720760 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
19720708 TTTATTTGTT
*
19720718 TTATTATAATAATATAATATA
1 TTATTAT-ATAATAAAATATA
19720739 TTATTATATAATAAAATATA
1 TTATTATATAATAAAATATA
19720759 TT
1 TT
19720761 TACTCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTATATAATAAAATATA
Found at i:19727053 original size:27 final size:26
Alignment explanation
Indices: 19727037--19727232 Score: 214
Period size: 27 Copynumber: 7.3 Consensus size: 26
19727027 TATAACAGTT
19727037 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCG-TC
** * *
19727064 ATTTTACCCTATCAGGGCATTTTGGTC
1 ATTTTACCCTATGGGGGTA-TTTCGTC
19727091 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTC-GTC
* *
19727118 ATTTTACCTTATGGAGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCG-TC
*
19727145 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTA-TTTCGTC
* **
19727172 ATTTTACCTTAT-GGAATATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTC-GTC
* *
19727198 ATTTTACCCTATAGGGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTC-GTC
19727225 ATTTTACC
1 ATTTTACC
19727233 TTAATTTAGG
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.02
26 22 0.15
27 109 0.77
28 8 0.06
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTATGGGGGTATTTCGTC
Found at i:19727095 original size:54 final size:53
Alignment explanation
Indices: 19727037--19727232 Score: 243
Period size: 54 Copynumber: 3.7 Consensus size: 53
19727027 TATAACAGTT
* *
19727037 ATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATCAGGGCATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-AGGGAATTTTGGTC
* * * * *
19727091 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTATGGAGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAG-GGAATTTTGGTC
* *
19727145 ATTTTACCCTATGGGGGTATTTTGGTCATTTTA-CCT-TATGGAATATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGAAT-TTT-GGTC
* *
19727198 ATTTTACCCTATAGGGGTATTTCGGTTATTTTACC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
19727233 TTAATTTAGG
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
51 4 0.03
52 3 0.02
53 36 0.30
54 79 0.65
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (53 bp):
ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGAATTTTGGTC
Found at i:19727142 original size:81 final size:79
Alignment explanation
Indices: 19727037--19727232 Score: 275
Period size: 81 Copynumber: 2.4 Consensus size: 79
19727027 TATAACAGTT
19727037 ATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATCAGGGCATTTTGGTCATTTTACCCTA
1 ATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTATCAGGGCATTTTGGTCATTTTACCCTA
**
19727102 TGGGGGTATTTCGGTC
65 T-GGAATATTTCGGTC
* ** * *
19727118 ATTTTACCTTATGGAGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTA
1 ATTTTACCCTATGG-GGTATTTCGATCATTTTACCCTATCAGGGCATTTTGGTCATTTTACCCTA
19727183 TGGAATATTTCGGTC
65 TGGAATATTTCGGTC
* *
19727198 ATTTTACCCTATAGGGGTATTTCGGTTATTTTACC
1 ATTTTACCCTAT-GGGGTATTTCGATCATTTTACC
19727233 TTAATTTAGG
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
80 43 0.42
81 60 0.58
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (79 bp):
ATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATCAGGGCATTTTGGTCATTTTACCCTAT
GGAATATTTCGGTC
Found at i:19733456 original size:40 final size:40
Alignment explanation
Indices: 19733401--19733642 Score: 102
Period size: 37 Copynumber: 6.3 Consensus size: 40
19733391 ACCAGTTTGG
19733401 CACCCAGTG-CGTCATCGAATAATTCAAAGTAATAAATTGA
1 CACCCAGTGTC-TCATCGAATAATTCAAAGTAATAAATTGA
* * * *
19733441 CACCCAGTGTCTCATCGACTAAATCGAAG---TAAATTGG
1 CACCCAGTGTCTCATCGAATAATTCAAAGTAATAAATTGA
* * * * ** * *
19733478 CACCCAATGCCTCATTG-A-AA--CACACCAGT---TTGG
1 CACCCAGTGTCTCATCGAATAATTCAAAGTAATAAATTGA
* *
19733511 CATCCAGTG-CGTCATCAAATAATTCAAAGTAATAAATTGA
1 CACCCAGTGTC-TCATCGAATAATTCAAAGTAATAAATTGA
* ** ** *
19733551 CACCCAGTGTCTCATTGGCTAAACCGAAG---TAAATT-A
1 CACCCAGTGTCTCATCGAATAATTCAAAGTAATAAATTGA
* * * * * *
19733587 GCACCCAGTGCCTTATTGAATTAATCCGAAGTAACAAATTGA
1 -CACCCAGTGTCTCATCGAA-TAATTCAAAGTAATAAATTGA
19733629 CACCCAGTGTCTCA
1 CACCCAGTGTCTCA
19733643 CCGACTCGAA
Statistics
Matches: 147, Mismatches: 36, Indels: 37
0.67 0.16 0.17
Matches are distributed among these distances:
32 1 0.01
33 17 0.12
34 1 0.01
35 4 0.03
36 2 0.01
37 47 0.32
38 9 0.06
40 46 0.31
41 19 0.13
42 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (40 bp):
CACCCAGTGTCTCATCGAATAATTCAAAGTAATAAATTGA
Found at i:19733483 original size:37 final size:37
Alignment explanation
Indices: 19733397--19733492 Score: 95
Period size: 40 Copynumber: 2.5 Consensus size: 37
19733387 ACACACCAGT
*
19733397 TTGGCACCCAGTGCGTCATCGAATAATTCAAAGTAATAAA
1 TTGGCACCCAGTGC-TCATCGAATAAATCAAAG--ATAAA
* * *
19733437 TTGACACCCAGTGTCTCATCGACTAAATCGAAG-TAAA
1 TTGGCACCCAGTG-CTCATCGAATAAATCAAAGATAAA
*
19733474 TTGGCACCCAATGCCTCAT
1 TTGGCACCCAGTG-CTCAT
19733493 TGAAACACAC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 20 0.42
40 27 0.56
41 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (37 bp):
TTGGCACCCAGTGCTCATCGAATAAATCAAAGATAAA
Found at i:19733579 original size:110 final size:110
Alignment explanation
Indices: 19733385--19733606 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 110
19733375 GATCCAACCA
*
19733385 AAACACACCAGTTTGGCACCCAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
1 AAACACACCAGTTTGGCACCCAGTGCGTCATCAAATAATTCAAAGTAATAAATTGACACCCAGTG
* *
19733450 TCTCATCGACTAAATCGAAGTAAATTGGCACCCAATGCCTCATTG
66 TCTCATCGACTAAACCGAAGTAAATTAGCACCCAATGCCTCATTG
*
19733495 AAACACACCAGTTTGGCATCCAGTGCGTCATCAAATAATTCAAAGTAATAAATTGACACCCAGTG
1 AAACACACCAGTTTGGCACCCAGTGCGTCATCAAATAATTCAAAGTAATAAATTGACACCCAGTG
* * * *
19733560 TCTCATTGGCTAAACCGAAGTAAATTAGCACCCAGTGCCTTATTG
66 TCTCATCGACTAAACCGAAGTAAATTAGCACCCAATGCCTCATTG
19733605 AA
1 AA
19733607 TTAATCCGAA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 104 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (110 bp):
AAACACACCAGTTTGGCACCCAGTGCGTCATCAAATAATTCAAAGTAATAAATTGACACCCAGTG
TCTCATCGACTAAACCGAAGTAAATTAGCACCCAATGCCTCATTG
Found at i:19734601 original size:17 final size:16
Alignment explanation
Indices: 19734560--19734602 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
19734550 TTTCGTTTGG
19734560 CTTTCTCTGTT-TCTTT
1 CTTTCTCT-TTCTCTTT
19734576 CTTTCTCTTTCTCTTT
1 CTTTCTCTTTCTCTTT
*
19734592 CCTTTTTCTTT
1 -CTTTCTCTTT
19734603 TTAGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (16 bp):
CTTTCTCTTTCTCTTT
Found at i:19742080 original size:49 final size:49
Alignment explanation
Indices: 19742023--19742120 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
19742013 GCCTAAGACG
*
19742023 GTCCAAATTATGTGTATTAATTCATAATATATTTAATTTTAATTTTAAT
1 GTCCAAATTATGTGTATTAATTCATAATATAATTAATTTTAATTTTAAT
19742072 GTCCAAATTATGTGTATTAATTCATAATATAATTAATTTTAATTTTAAT
1 GTCCAAATTATGTGTATTAATTCATAATATAATTAATTTTAATTTTAAT
19742121 CCAATCGAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (49 bp):
GTCCAAATTATGTGTATTAATTCATAATATAATTAATTTTAATTTTAAT
Found at i:19743135 original size:126 final size:126
Alignment explanation
Indices: 19742910--19743148 Score: 424
Period size: 126 Copynumber: 1.9 Consensus size: 126
19742900 ACGATAAATT
* *
19742910 GACATTTACTTGTTACTTTATTACTTGTTGCGATTGTGTACACTTGCACATTTCCATCGTTCTAA
1 GACATTTACTTGTCACTTTATTACTTGTTGCGATTGTGTACACTTGCACATTTCCATCATTCTAA
* *
19742975 GTTTTTGGCGTCGTTACCGGGGACTATTTTAAAAAGTCATTATTTGTGGTTACAATAACTC
66 GTATTTGGCGTCGTTACCGAGGACTATTTTAAAAAGTCATTATTTGTGGTTACAATAACTC
19743036 GACATTTACTTGTCACTTTATTACTTGTTGCGATTGTGTACACTTGCACATTTCCATCATTCTAA
1 GACATTTACTTGTCACTTTATTACTTGTTGCGATTGTGTACACTTGCACATTTCCATCATTCTAA
* *
19743101 GTATTTGGCGTCGTTGCCGAGGACTATTTTAAAAAGTCATTGTTTGTG
66 GTATTTGGCGTCGTTACCGAGGACTATTTTAAAAAGTCATTATTTGTG
19743149 AATTTGTTAG
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 107 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (126 bp):
GACATTTACTTGTCACTTTATTACTTGTTGCGATTGTGTACACTTGCACATTTCCATCATTCTAA
GTATTTGGCGTCGTTACCGAGGACTATTTTAAAAAGTCATTATTTGTGGTTACAATAACTC
Found at i:19743760 original size:15 final size:15
Alignment explanation
Indices: 19743740--19743773 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
19743730 AGCAGAAAGA
19743740 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
19743755 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
19743770 TTCC
1 TTCC
19743774 CGCCTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (15 bp):
TTCCTCATGAAGTAT
Found at i:19752667 original size:9 final size:9
Alignment explanation
Indices: 19752653--19752746 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
19752643 GTAGTGATTC
*
19752653 AATTTGGTT
1 AATTCGGTT
*
19752662 AATTTGGTT
1 AATTCGGTT
*
19752671 AATTCGGGT
1 AATTCGGTT
*
19752680 AATTTGGTT
1 AATTCGGTT
*
19752689 AATTCGGGT
1 AATTCGGTT
*
19752698 AATTCGGGT
1 AATTCGGTT
*
19752707 AATTCGGGT
1 AATTCGGTT
19752716 AATTCGGTT
1 AATTCGGTT
19752725 AATTCGGTT
1 AATTCGGTT
19752734 AATTCGGTT
1 AATTCGGTT
19752743 AATT
1 AATT
19752747 TTTAACCAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 78 1.00
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:19753754 original size:20 final size:22
Alignment explanation
Indices: 19753708--19753754 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
19753698 AAATGACCAA
19753708 GAAAGAAAAAGAAGGAAAAAAG
1 GAAAGAAAAAGAAGGAAAAAAG
19753730 G--AGAAAAAGAA-G-AAAAAG
1 GAAAGAAAAAGAAGGAAAAAAG
19753748 GAAAGAA
1 GAAAGAA
19753755 GGGCTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 14 0.61
22 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAAGAAGGAAAAAAG
Found at i:19758771 original size:18 final size:19
Alignment explanation
Indices: 19758725--19758784 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
19758715 AAAAAATTAG
*
19758725 TTTTTA-ACTTTCTTTACATA
1 TTTTTATACTTTTTTTA-A-A
19758745 TTCTTTATA-TTTTTTTAAA
1 TT-TTTATACTTTTTTTAAA
*
19758764 TTTTTATACTTTTTTTTAA
1 TTTTTATACTTTTTTTAAA
19758783 TT
1 TT
19758785 CAACTTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 6 0.17
19 14 0.40
20 3 0.09
21 11 0.31
22 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATACTTTTTTTAAA
Found at i:19758818 original size:19 final size:19
Alignment explanation
Indices: 19758789--19758836 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
19758779 TTAATTCAAC
19758789 TTTTGGAATTTTTATAAA-TA
1 TTTT-GAATTTTTA-AAATTA
19758809 TTTTGAA-TTTTAAAATTTA
1 TTTTGAATTTTTAAAA-TTA
19758828 TTTTGAATT
1 TTTTGAATT
19758837 ATTTTGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 5 0.20
19 12 0.48
20 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:19760511 original size:19 final size:20
Alignment explanation
Indices: 19760466--19760548 Score: 89
Period size: 20 Copynumber: 4.1 Consensus size: 20
19760456 ATTTTAAATT
*
19760466 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAA-AT-TATTTTG-AA
*
19760489 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
19760508 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
* *
19760527 TTTTTGAAAATTATTTTAAA
1 TTTTTAAAAATTATTTTGAA
19760547 TT
1 TT
19760549 ATTTTTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
18 8 0.15
19 11 0.21
20 25 0.47
22 1 0.02
23 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:19764042 original size:27 final size:27
Alignment explanation
Indices: 19763987--19764107 Score: 138
Period size: 27 Copynumber: 4.5 Consensus size: 27
19763977 AGGGGAATAA
* *
19763987 CGATCATTTTACCCTTC--GGGATATTT
1 CGATAATTTTACCCATCAAGGG-TATTT
* ** *
19764013 CGATAATTTTACTCATTTAGAGTATTT
1 CGATAATTTTACCCATCAAGGGTATTT
19764040 CGATAATTTTACCCATCAAGGGTATTT
1 CGATAATTTTACCCATCAAGGGTATTT
* *
19764067 CAATAATTTTACCCATCGAGGGTATTT
1 CGATAATTTTACCCATCAAGGGTATTT
*
19764094 CGATCATTTTACCC
1 CGATAATTTTACCC
19764108 TAAAGGGGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.16
27 65 0.81
28 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (27 bp):
CGATAATTTTACCCATCAAGGGTATTT
Found at i:19764073 original size:54 final size:53
Alignment explanation
Indices: 19763987--19764107 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 53
19763977 AGGGGAATAA
* * * **
19763987 CGATCATTTTACCCTTCGGGATATTTCGATAATTTTACTCATTTAGAGTATTT
1 CGATCATTTTACCCATCGGGATATTTCAATAATTTTACCCATCGAGAGTATTT
* *
19764040 CGATAATTTTACCCATCAAGGG-TATTTCAATAATTTTACCCATCGAGGGTATTT
1 CGATCATTTTACCCATC--GGGATATTTCAATAATTTTACCCATCGAGAGTATTT
19764094 CGATCATTTTACCC
1 CGATCATTTTACCC
19764108 TAAAGGGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 15 0.26
54 40 0.69
55 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (53 bp):
CGATCATTTTACCCATCGGGATATTTCAATAATTTTACCCATCGAGAGTATTT
Found at i:19768759 original size:28 final size:27
Alignment explanation
Indices: 19768691--19768760 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
19768681 GGTTTGGCTA
*
19768691 TTTGGTCACTTTCGCCCTCTATTTTTT
1 TTTGGTCACTTTGGCCCTCTATTTTTT
*
19768718 TTTGGAGCACTTTGGCCC-CTAATGTTTTT
1 TTTGG-TCACTTTGGCCCTCT-AT-TTTTT
*
19768747 TTTGGTCAATTTGG
1 TTTGGTCACTTTGG
19768761 TCTATTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.19
28 19 0.53
29 10 0.28
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (27 bp):
TTTGGTCACTTTGGCCCTCTATTTTTT
Found at i:19769199 original size:29 final size:30
Alignment explanation
Indices: 19769145--19769214 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
19769135 GGTTTTTGAG
**
19769145 TTTGGGGATTTAGGATTTTGGGTTGTCGAA
1 TTTGGGGATTTAGGATTTAAGGTTGTCGAA
*
19769175 TTTGGGGATTT-TGATTTAAGGTTGTCGAA
1 TTTGGGGATTTAGGATTTAAGGTTGTCGAA
19769204 TTTGGGGATTT
1 TTTGGGGATTT
19769215 GGGCTAGGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.17, C:0.03, G:0.34, T:0.46
Consensus pattern (30 bp):
TTTGGGGATTTAGGATTTAAGGTTGTCGAA
Found at i:19769226 original size:29 final size:28
Alignment explanation
Indices: 19769164--19769243 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
19769154 TTAGGATTTT
**
19769164 GGGTTGTCGAATTTGGGGATTTTGATTTA
1 GGGTTGTCGAATTTGGGGA-TTTGAGCTA
* *
19769193 AGGTTGTCGAATTTGGGGATTTGGGCTA
1 GGGTTGTCGAATTTGGGGATTTGAGCTA
* *
19769221 GGGGT-TCTAATTTTGGGGATTTG
1 GGGTTGTCGAA-TTTGGGGATTTG
19769244 TTTAGGGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.09
28 21 0.49
29 18 0.42
ACGTcount: A:0.16, C:0.05, G:0.38, T:0.41
Consensus pattern (28 bp):
GGGTTGTCGAATTTGGGGATTTGAGCTA
Found at i:19769292 original size:30 final size:29
Alignment explanation
Indices: 19769244--19769300 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
19769234 TGGGGATTTG
* ** *
19769244 TTTAGGGTTTTTTGATTTTAGGGATTTTCA
1 TTTAAGGTTTTTAAATTTT-GGAATTTTCA
19769274 TTTAAGGTTTTTAAATTTTGGAATTTT
1 TTTAAGGTTTTTAAATTTTGGAATTTT
19769301 TGTTTATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (29 bp):
TTTAAGGTTTTTAAATTTTGGAATTTTCA
Found at i:19769321 original size:29 final size:29
Alignment explanation
Indices: 19769252--19769321 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
19769242 TGTTTAGGGT
* *
19769252 TTTTTGATTTTAGGGATTTTCATTTAAGG
1 TTTTTGATTTTTGGAATTTTCATTTAAGG
* * ** **
19769281 TTTTTAAATTTTGGAATTTTTGTTTATTG
1 TTTTTGATTTTTGGAATTTTCATTTAAGG
19769310 TTTTTGATTTTT
1 TTTTTGATTTTT
19769322 AAGACATTGG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.19, C:0.01, G:0.16, T:0.64
Consensus pattern (29 bp):
TTTTTGATTTTTGGAATTTTCATTTAAGG
Found at i:19778183 original size:159 final size:159
Alignment explanation
Indices: 19777885--19778199 Score: 404
Period size: 159 Copynumber: 2.0 Consensus size: 159
19777875 GGTGAGGGTC
* * *
19777885 ACAATAGAAGATCATGCATTCAAACTAACACAACTGGATCACAGATATATCATTAACACTTTTTC
1 ACAACAGAAGATCATGCAATCAAACTAACACAACTGGATCACAGATATATCATAAACACTTTTTC
* * * * *
19777950 ACTATGAAGATCTTAAATATTTAAGTCTAATTTGGGGTTTTACAATTTTTTTCTCAGTCTGGTAC
66 ACTATCAAGATCTTAAATATTTAAATCTAATTTAGGGTTGTACAATTTTTTTCTCAGTCTAGTAC
19778015 GAGTACAAGAACTAAAAGCCAAAAAAAGA
131 GAGTACAAGAACTAAAAGCCAAAAAAAGA
* * *
19778044 ACAACAGAAGATCATGCAATC-AACTTACCACAACTGGATCACAGGTATATCGTAAACACTTTTT
1 ACAACAGAAGATCATGCAATCAAAC-TAACACAACTGGATCACAGATATATCATAAACACTTTTT
* * * *
19778108 TACTGTCAAG-T-TTCAAAATATTTAAATCTAATTTAGGGTTGT-GATTTTTTTGTCTCAGTCTA
65 CACTATCAAGATCTT--AAATATTTAAATCTAATTTAGGGTTGTACAATTTTTT-TCTCAGTCTA
* * *
19778170 GTATGAGTGCAAGAACTAGAAGCCAAAAAA
127 GTACGAGTACAAGAACTAAAAGCCAAAAAA
19778200 GGATGGTATA
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
157 2 0.01
158 11 0.08
159 121 0.90
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (159 bp):
ACAACAGAAGATCATGCAATCAAACTAACACAACTGGATCACAGATATATCATAAACACTTTTTC
ACTATCAAGATCTTAAATATTTAAATCTAATTTAGGGTTGTACAATTTTTTTCTCAGTCTAGTAC
GAGTACAAGAACTAAAAGCCAAAAAAAGA
Found at i:19780025 original size:2 final size:2
Alignment explanation
Indices: 19780020--19780057 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19780010 TCACTATAGA
19780020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19780058 TAGATTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19781379 original size:29 final size:30
Alignment explanation
Indices: 19781336--19781393 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
19781326 TTGGCCTTAT
*
19781336 TTGATTCTTTTTAATAATACATGAACTAAA
1 TTGATTCTATTTAATAATACATGAACTAAA
* *
19781366 TTGA-TCTATTTAATAATAGATGGACTAA
1 TTGATTCTATTTAATAATACATGAACTAA
19781394 TTTAATACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (30 bp):
TTGATTCTATTTAATAATACATGAACTAAA
Found at i:19782026 original size:11 final size:11
Alignment explanation
Indices: 19782010--19782035 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19782000 TTATACTACT
19782010 AATATGAGATA
1 AATATGAGATA
19782021 AATATGAGATA
1 AATATGAGATA
19782032 AATA
1 AATA
19782036 AATACAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (11 bp):
AATATGAGATA
Found at i:19782135 original size:25 final size:24
Alignment explanation
Indices: 19782090--19782137 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
19782080 CGAAATTAAA
* *
19782090 TTATAATTTTAATAGCCTAAATCT
1 TTATAATTTTAAAAGACTAAATCT
*
19782114 TTATAATTTTTAAAAGATTAAATC
1 TTATAA-TTTTAAAAGACTAAATC
19782138 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (24 bp):
TTATAATTTTAAAAGACTAAATCT
Found at i:19787671 original size:19 final size:21
Alignment explanation
Indices: 19787633--19787671 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19787623 TCTTTTTTAA
*
19787633 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
19787654 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
19787672 AAAGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:19787812 original size:22 final size:23
Alignment explanation
Indices: 19787785--19787829 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19787775 GGGTATCTAC
19787785 AAATTAAATC-TCTAAGATTACA
1 AAATTAAATCTTCTAAGATTACA
*
19787807 AAATTATATCTTCTAAGATTACA
1 AAATTAAATCTTCTAAGATTACA
19787830 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (23 bp):
AAATTAAATCTTCTAAGATTACA
Found at i:19787837 original size:22 final size:23
Alignment explanation
Indices: 19787795--19787839 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19787785 AAATTAAATC
*
19787795 TCTAAGATTACAAAATTATATCT
1 TCTAAGATTACAAAATCATATCT
*
19787818 TCTAAGATTAC-ATATCATATCT
1 TCTAAGATTACAAAATCATATCT
19787840 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:19787842 original size:19 final size:19
Alignment explanation
Indices: 19787818--19787873 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
19787808 AATTATATCT
19787818 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
19787837 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
19787858 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
19787874 CTCGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
21 18 0.56
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:19787855 original size:21 final size:21
Alignment explanation
Indices: 19787829--19787872 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19787819 CTAAGATTAC
19787829 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
19787850 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
19787871 AT
1 AT
19787873 CCTCGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:19794416 original size:18 final size:18
Alignment explanation
Indices: 19794393--19794428 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19794383 ATAATGGTCT
19794393 AGCAATTTTGATTTGACC
1 AGCAATTTTGATTTGACC
19794411 AGCAATTTTGATTTGACC
1 AGCAATTTTGATTTGACC
19794429 CTATATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
AGCAATTTTGATTTGACC
Found at i:19799223 original size:28 final size:28
Alignment explanation
Indices: 19799183--19799240 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
19799173 TTATTTAGGG
* * *
19799183 TTATTTTGATTTCGATTTCGATTCTGAT
1 TTATTTCGATTTCAATTTAGATTCTGAT
*
19799211 TTATTTCGATTTCAATTTAGATTTTGAT
1 TTATTTCGATTTCAATTTAGATTCTGAT
19799239 TT
1 TT
19799241 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (28 bp):
TTATTTCGATTTCAATTTAGATTCTGAT
Found at i:19799276 original size:6 final size:6
Alignment explanation
Indices: 19799266--19799318 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
19799256 CACTGGTTCT
* * * *
19799266 GATTTT GATTTC AATTTC GATTTT GATTTC GATTTC GATTTC GATTTA
1 GATTTC GATTTC GATTTC GATTTC GATTTC GATTTC GATTTC GATTTC
19799314 GATTT
1 GATTT
19799319 TGGTTTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (6 bp):
GATTTC
Found at i:19799582 original size:20 final size:22
Alignment explanation
Indices: 19799542--19799582 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
19799532 TTACCTTCTA
19799542 TATTGTACTAGTTATTATCTGT
1 TATTGTACTAGTTATTATCTGT
*
19799564 TATTGT-CTA-TTATTGTCTG
1 TATTGTACTAGTTATTATCTG
19799583 CCATGTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (22 bp):
TATTGTACTAGTTATTATCTGT
Found at i:19799699 original size:57 final size:58
Alignment explanation
Indices: 19799573--19799701 Score: 181
Period size: 62 Copynumber: 2.2 Consensus size: 58
19799563 TTATTGTCTA
19799573 TTATTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTACTTTTGTATTGG
1 TTATTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTA----TGTATTGG
* *
19799635 TTGTTGTCTGCCATGTGCATGACAGAAATGGTTTGTGTTTGTATTAAA-TA-GTATTGG
1 TTATTGTCTGCCATGTGCATGACAAAAATGG-TTGTGTTTGTATTAAATTATGTATTGG
19799692 TTATTGTCTG
1 TTATTGTCTG
19799702 ACAGAAATGG
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
57 16 0.25
62 31 0.49
63 16 0.25
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.45
Consensus pattern (58 bp):
TTATTGTCTGCCATGTGCATGACAAAAATGGTTGTGTTTGTATTAAATTATGTATTGG
Found at i:19802273 original size:21 final size:21
Alignment explanation
Indices: 19802247--19802298 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
19802237 CAAGTGGTTG
* *
19802247 CCCCAACTCAGCAA-CAGGCTA
1 CCCCAACTCAGCAAGAAAG-TA
*
19802268 CCCCAAATCAGCAAGAAAGTA
1 CCCCAACTCAGCAAGAAAGTA
19802289 CCCCAACTCA
1 CCCCAACTCA
19802299 ACAGGCTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (21 bp):
CCCCAACTCAGCAAGAAAGTA
Found at i:19802787 original size:22 final size:23
Alignment explanation
Indices: 19802736--19802780 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19802726 CTTTTCTTCT
*
19802736 AACATATGAGAATTGAAAAAATA
1 AACATGTGAGAATTGAAAAAATA
*
19802759 AACATGTGAGAATT-AAGAAATA
1 AACATGTGAGAATTGAAAAAATA
19802781 CAAATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (23 bp):
AACATGTGAGAATTGAAAAAATA
Found at i:19803850 original size:29 final size:30
Alignment explanation
Indices: 19803808--19803864 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
19803798 AATGAAAATT
19803808 TAAATACTTCAATTT-TAGTATAGAAATTTA
1 TAAATACTTCAATTTATAGTATA-AAATTTA
* *
19803838 TAAATA-TTGAATTTATATTATAAAATT
1 TAAATACTTCAATTTATAGTATAAAATT
19803865 GTTTAGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (30 bp):
TAAATACTTCAATTTATAGTATAAAATTTA
Found at i:19816385 original size:17 final size:18
Alignment explanation
Indices: 19816345--19816386 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
19816335 AATTACTGCT
*
19816345 TTCTTGTTGTTTTTATTA
1 TTCTTGTTGATTTTATTA
*
19816363 TT-TTGTTGATTTT-TTC
1 TTCTTGTTGATTTTATTA
19816379 TTCTTGTT
1 TTCTTGTT
19816387 TTTTCACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 15 0.71
18 2 0.10
ACGTcount: A:0.07, C:0.07, G:0.12, T:0.74
Consensus pattern (18 bp):
TTCTTGTTGATTTTATTA
Found at i:19817024 original size:21 final size:21
Alignment explanation
Indices: 19816971--19817027 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19816961 ACCGTTGTTT
*
19816971 CTAATCTCACCGCTAAAATAT
1 CTAATCTCACCGCTAAAATAA
* * *
19816992 CCAACCTCACCGCTATAATAA
1 CTAATCTCACCGCTAAAATAA
*
19817013 CTAATCTTACCGCTA
1 CTAATCTCACCGCTA
19817028 CTGCTATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.26
Consensus pattern (21 bp):
CTAATCTCACCGCTAAAATAA
Found at i:19820194 original size:19 final size:18
Alignment explanation
Indices: 19820172--19820232 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
19820162 TGAAAAATAT
19820172 ATTAAAAATACAAAATGAA
1 ATTAAAAATA-AAAATGAA
* *
19820191 ATTAAAATTTAGAAATGAA
1 ATTAAAA-ATAAAAATGAA
*
19820210 TATTAAAAACAAAAAT-AA
1 -ATTAAAAATAAAAATGAA
19820228 ATTAA
1 ATTAA
19820233 CAAAAAGGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 2 0.06
19 19 0.54
20 9 0.26
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (18 bp):
ATTAAAAATAAAAATGAA
Found at i:19823596 original size:50 final size:50
Alignment explanation
Indices: 19823482--19823786 Score: 385
Period size: 50 Copynumber: 5.8 Consensus size: 50
19823472 AATAATAACA
* * **
19823482 TGCCAAAGCCATGTCCAAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
19823533 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
19823583 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
19823633 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
19823688 ATGCCAATGACATGTCCTAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
*
19823744 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
19823787 TTACTCCAAT
Statistics
Matches: 231, Mismatches: 17, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
50 100 0.43
51 32 0.14
53 5 0.02
55 2 0.01
56 92 0.40
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:19831342 original size:50 final size:50
Alignment explanation
Indices: 19831227--19831475 Score: 347
Period size: 50 Copynumber: 4.8 Consensus size: 50
19831217 GATAATAACA
* * **
19831227 TGCCAAAGCCATGTCCAAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
19831278 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
19831328 TGCCAACT-CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
19831378 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
19831433 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
19831476 TTACCCAAAT
Statistics
Matches: 178, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
50 97 0.54
51 33 0.19
53 5 0.03
55 2 0.01
56 41 0.23
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:19833230 original size:15 final size:15
Alignment explanation
Indices: 19833210--19833241 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19833200 CATTTCACTA
*
19833210 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
19833225 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
19833240 TT
1 TT
19833242 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:19834711 original size:19 final size:20
Alignment explanation
Indices: 19834669--19834711 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
19834659 TCATGCTTTC
*
19834669 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
19834689 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
19834707 TATTC
1 TATTC
19834712 CACAATTACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:19834937 original size:23 final size:23
Alignment explanation
Indices: 19834913--19835058 Score: 175
Period size: 23 Copynumber: 6.3 Consensus size: 23
19834903 TACACACGAG
* * *
19834913 GTGCCTGAAATATGACACACAAG
1 GTGCCTGAAATACGACACATAAA
* * *
19834936 GTGTCTAAAATTCGACACATAAA
1 GTGCCTGAAATACGACACATAAA
* *
19834959 GTGTCTGATATACGACACATAAA
1 GTGCCTGAAATACGACACATAAA
*
19834982 GTGCCTAAAATACGACACATAAA
1 GTGCCTGAAATACGACACATAAA
* *
19835005 GTGCCTGATATGCGACACATAAA
1 GTGCCTGAAATACGACACATAAA
* *
19835028 GTGCTTGAAATACGACAGATAAA
1 GTGCCTGAAATACGACACATAAA
19835051 GTGCCTGA
1 GTGCCTGA
19835059 GCGGCATAGC
Statistics
Matches: 103, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 103 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (23 bp):
GTGCCTGAAATACGACACATAAA
Found at i:19834993 original size:69 final size:68
Alignment explanation
Indices: 19834884--19835056 Score: 181
Period size: 69 Copynumber: 2.5 Consensus size: 68
19834874 TCAGTATGTA
* ** * * * * *
19834884 ACACAT-AAGTGTCTGAA-ACTACACACGAGGTGCCTGAAATATGACACACAAGGTGTCTAAAAT
1 ACACATAAAGTGTCTGAATACGACACATAAAGTGCCTAAAATACGACACACAAAGTGCCTAAAAT
*
19834947 TCG
66 GCG
* * *
19834950 ACACATAAAGTGTCTGATATACGACACATAAAGTGCCTAAAATACGACACATAAAGTGCCTGATA
1 ACACATAAAGTGTCTGA-ATACGACACATAAAGTGCCTAAAATACGACACACAAAGTGCCTAAAA
19835015 TGCG
65 TGCG
*
19835019 ACACATAAAGTG-CTTGAAATACGACAGATAAAGTGCCT
1 ACACATAAAGTGTC-TG-AATACGACACATAAAGTGCCT
19835057 GAGCGGCATA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
66 6 0.07
67 10 0.11
68 2 0.02
69 70 0.79
70 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (68 bp):
ACACATAAAGTGTCTGAATACGACACATAAAGTGCCTAAAATACGACACACAAAGTGCCTAAAAT
GCG
Found at i:19838529 original size:21 final size:20
Alignment explanation
Indices: 19838480--19838519 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19838470 ATGGATGAGC
*
19838480 ATGTATGAATTATGAAGTTT
1 ATGTAAGAATTATGAAGTTT
19838500 ATGTAAGAATTATGAAGTTT
1 ATGTAAGAATTATGAAGTTT
19838520 TATGGTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (20 bp):
ATGTAAGAATTATGAAGTTT
Found at i:19838816 original size:21 final size:21
Alignment explanation
Indices: 19838786--19838825 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19838776 TTTTCCAAAG
* *
19838786 ATGTGTATTGGATTGAATTAA
1 ATGTGAATTGGATTAAATTAA
*
19838807 ATGTGAATTGTATTAAATT
1 ATGTGAATTGGATTAAATT
19838826 GAGCTAAATT
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:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTAA
Found at i:19839277 original size:25 final size:25
Alignment explanation
Indices: 19839232--19839355 Score: 108
Period size: 25 Copynumber: 5.0 Consensus size: 25
19839222 TAACTCGTAT
* *
19839232 GAGCTTCCCGATA-ATTGGCTCGCAA
1 GAGCTTCCCGTTACA-TCGCTCGCAA
** *
19839257 GAGCTTCCCGTTACATCGCTCATAT
1 GAGCTTCCCGTTACATCGCTCGCAA
** *
19839282 GAGCTTCCCGTTACATCGCTCATAT
1 GAGCTTCCCGTTACATCGCTCGCAA
* * *
19839307 GAGCTTCCCGTTATATGGCTCGAAA
1 GAGCTTCCCGTTACATCGCTCGCAA
*
19839332 GAGCTTTCCGATTACAT-GCTCGCA
1 GAGCTTCCCG-TTACATCGCTCGCA
19839356 TGGGCATACC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
25 78 0.93
26 6 0.07
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (25 bp):
GAGCTTCCCGTTACATCGCTCGCAA
Found at i:19839336 original size:50 final size:50
Alignment explanation
Indices: 19839257--19839352 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
19839247 TGGCTCGCAA
*
19839257 GAGCTTCCCGTTACATCGCTCATATGAGCTTCCCG-TTACATCGCTCATAT
1 GAGCTTCCCGTTACATCGCTCATAAGAGCTTCCCGATTACAT-GCTCATAT
* * *
19839307 GAGCTTCCCGTTATATGGCTCGA-AAGAGCTTTCCGATTACATGCTC
1 GAGCTTCCCGTTACATCGCTC-ATAAGAGCTTCCCGATTACATGCTC
19839353 GCATGGGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 33 0.82
51 7 0.17
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (50 bp):
GAGCTTCCCGTTACATCGCTCATAAGAGCTTCCCGATTACATGCTCATAT
Found at i:19847292 original size:16 final size:17
Alignment explanation
Indices: 19847259--19847292 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19847249 TTAACTTGTG
*
19847259 TATTTAATCAATTTTAA
1 TATTTAATCAATTATAA
19847276 TATTTAAT-AATTATAA
1 TATTTAATCAATTATAA
19847292 T
1 T
19847293 TAAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTAATCAATTATAA
Found at i:19847725 original size:5 final size:5
Alignment explanation
Indices: 19847715--19847741 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19847705 CTCAATCCTT
19847715 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
19847742 CTCTATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:19848942 original size:23 final size:23
Alignment explanation
Indices: 19848916--19848961 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19848906 ATGAGAATTT
**
19848916 TTAAAATTTTTAAATCAAAATAA
1 TTAAAATTTAAAAATCAAAATAA
*
19848939 TTAAAATTTAAAAATTAAAATAA
1 TTAAAATTTAAAAATCAAAATAA
19848962 ATAATCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAATTTAAAAATCAAAATAA
Found at i:19851822 original size:21 final size:21
Alignment explanation
Indices: 19851776--19851823 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
19851766 TGTTATGGAC
* *
19851776 TTTTGATTTTTGGTTTTATTT
1 TTTTTATTTATGGTTTTATTT
* *
19851797 ATTTTATTTATGGTTTGTTTTT
1 TTTTTATTTATGGTTT-TATTT
19851819 TTTTT
1 TTTTT
19851824 GTTTGGGCCC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.77
Consensus pattern (21 bp):
TTTTTATTTATGGTTTTATTT
Found at i:19852035 original size:44 final size:43
Alignment explanation
Indices: 19851985--19852263 Score: 184
Period size: 44 Copynumber: 6.3 Consensus size: 43
19851975 TCATTCTAAC
* *
19851985 CCACTGCAACTTTAG-AGGTACAGGATTTGTCA-CTTTAATCTATT
1 CCACTGCAACTTTAGAAGAT-CA-GATTTGT-AGCTTTAATCTACT
* * *
19852029 CCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTTA-GAAGATCAGATTTGTAGCTTTAATCTACT
* * * * * * *
19852073 CCACTGCAACTTTAGGGAGATGAGACTCGAATCTTCAATCTACT
1 CCACTGCAACTTTA-GAAGATCAGATTTGTAGCTTTAATCTACT
* * * * *
19852117 CCACTGCAACTTCAAGAAGATGAGACTTGTAACTTTAATCTGCT
1 CCACTGCAACTT-TAGAAGATCAGATTTGTAGCTTTAATCTACT
* * * * * ** * *
19852161 CCATTGCAACTTTAGGGAGATAAGACTTGTAACTTCCATTTGCT
1 CCACTGCAACTTTA-GAAGATCAGATTTGTAGCTTTAATCTACT
* * * * *
19852205 CCACTGCAACTTCAGGAAGATGAGAATCGTAGCTTTAATCTGCT
1 CCACTGCAACTTTA-GAAGATCAGATTTGTAGCTTTAATCTACT
*
19852249 CCATTGCAACTTTAG
1 CCACTGCAACTTTAG
19852264 GGAGATAAGA
Statistics
Matches: 190, Mismatches: 40, Indels: 11
0.79 0.17 0.05
Matches are distributed among these distances:
43 3 0.02
44 181 0.95
45 3 0.02
46 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (43 bp):
CCACTGCAACTTTAGAAGATCAGATTTGTAGCTTTAATCTACT
Found at i:19852136 original size:88 final size:89
Alignment explanation
Indices: 19852021--19852288 Score: 378
Period size: 88 Copynumber: 3.0 Consensus size: 89
19852011 TTGTCACTTT
* * * *
19852021 AATCTATTCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATGAGAATTGTAGCTTTAATCTGCTCCATTGCAACTTT
*
19852086 AGGGAGATGAGACTCG-AATCTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * *
19852109 AATCTACTCCACTGCAACTTCAAGAAGATGAGACTTGTAACTTTAATCTGCTCCATTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATGAGAATTGTAGCTTTAATCTGCTCCATTGCAACTTT
* *
19852174 AGGGAGATAAGACTTGTAA-CTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * *
19852197 CATTTGCTCCACTGCAACTTCAGGAAGATGAGAATCGTAGCTTTAATCTGCTCCATTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATGAGAATTGTAGCTTTAATCTGCTCCATTGCAACTTT
* *
19852262 AGGGAGATAAGATTCGCTATCTTC
66 AGGGAGATAAGACTCGCAATCTTC
19852286 AAT
1 AAT
19852289 TTGCTCTACT
Statistics
Matches: 158, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
88 150 0.95
89 8 0.05
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (89 bp):
AATCTACTCCACTGCAACTTCAGGAAGATGAGAATTGTAGCTTTAATCTGCTCCATTGCAACTTT
AGGGAGATAAGACTCGCAATCTTC
Found at i:19852226 original size:132 final size:132
Alignment explanation
Indices: 19852011--19852260 Score: 320
Period size: 132 Copynumber: 1.9 Consensus size: 132
19852001 GGTACAGGAT
* * * * * *
19852011 TTGTCACTTTAATCTATTCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCTCCA
1 TTGTAACTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAATCTGCTCCA
* * * *
19852076 CTGCAACTTTAGGGAGATGAGACTCGAATCTTCAATCTACTCCACTGCAACTTCAAGAAGATGAG
66 CTGCAACTTCAGGAAGATGAGAATCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATGAG
19852141 AC
131 AC
* * * * * *
19852143 TTGTAACTTTAATCTGCTCCATTGCAACTTTAGGGAGATAAGACTTGTAACTTCCATTTGCTCCA
1 TTGTAACTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAATCTGCTCCA
* * * *
19852208 CTGCAACTTCAGGAAGATGAGAATCGTAGCTTTAATCTGCTCCATTGCAACTT
66 CTGCAACTTCAGGAAGATGAGAATCGAAGCTTCAATCTACTCCACTGCAACTT
19852261 TAGGGAGATA
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
132 98 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (132 bp):
TTGTAACTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAACTTCAATCTGCTCCA
CTGCAACTTCAGGAAGATGAGAATCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATGAG
AC
Found at i:19852311 original size:45 final size:44
Alignment explanation
Indices: 19852028--19852320 Score: 250
Period size: 44 Copynumber: 6.6 Consensus size: 44
19852018 TTTAATCTAT
* * * * * *
19852028 TCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTAACTTCAATTTGC
* * * * *
19852072 TCCACTGCAACTTTAGGGAGATGAGACTCG-AATCTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTAA-CTTCAATTTGC
* * * * *
19852116 TCCACTGCAACTTCAAGAAGATGAGACTT-GTAACTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCGTAACTTCAATTTGC
* * *
19852160 TCCATTGCAACTTTAGGGAGATAAGACTT-GTAACTTCCATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCGTAACTTCAATTTGC
* * * * * *
19852204 TCCACTGCAACTTCAGGAAGATGAGAATCGTAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTAACTTCAATTTGC
* * *
19852248 TCCATTGCAACTTTAGGGAGATAAGATTCGCTATCTTCAATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TAACTTCAATTTGC
* * *
19852293 TCTACTACAAATTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
19852321 TGCCACGATG
Statistics
Matches: 200, Mismatches: 44, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
43 2 0.01
44 161 0.81
45 37 0.19
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCGTAACTTCAATTTGC
Found at i:19860127 original size:19 final size:21
Alignment explanation
Indices: 19860105--19860151 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
19860095 TTGTGAAACT
*
19860105 TAATGCAT-ATG-ATGAAATA
1 TAATGCATGATGAATGAAAAA
19860124 TAATGC-TGATGAATGAAAAA
1 TAATGCATGATGAATGAAAAA
19860144 TGAATGCA
1 T-AATGCA
19860152 AAGAGAGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 8 0.35
21 5 0.22
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (21 bp):
TAATGCATGATGAATGAAAAA
Found at i:19863788 original size:13 final size:13
Alignment explanation
Indices: 19863755--19863795 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
19863745 AAAATAAATT
19863755 AAATT-AAATTAA
1 AAATTAAAATTAA
19863767 GAAATTTAAAATTAA
1 -AAA-TTAAAATTAA
19863782 AAATTAAAA-TAA
1 AAATTAAAATTAA
19863794 AA
1 AA
19863796 TAAAAGAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 5 0.19
15 7 0.27
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAATTAAAATTAA
Found at i:19865282 original size:21 final size:21
Alignment explanation
Indices: 19865236--19865282 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
19865226 TGTTATGGAC
*
19865236 TTTTGATTTTTGGTTTTATTT
1 TTTTTATTTTTGGTTTTATTT
*
19865257 ATTTTATTTTTGGTTTGT-TTT
1 TTTTTATTTTTGGTTT-TATTT
19865278 TTTTT
1 TTTTT
19865283 CGGGCCTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.79
Consensus pattern (21 bp):
TTTTTATTTTTGGTTTTATTT
Found at i:19865787 original size:39 final size:41
Alignment explanation
Indices: 19865701--19865806 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 41
19865691 ATTTTCCCCT
* * * *
19865701 AAATTGCGTCCACGTCAGCGCGATGTCAGGGGACGTGTCAGC
1 AAATCGCGTCCACGTCAGCGCGAT-TCAGCGGACGTGGCAAC
**
19865743 AAATCGCGTCCACGTCAGCGCGATT-A-CTTACGTGGCAAC
1 AAATCGCGTCCACGTCAGCGCGATTCAGCGGACGTGGCAAC
*
19865782 AAATCGCGTCCACGTAAGCGCGATT
1 AAATCGCGTCCACGTCAGCGCGATT
19865807 TGCTGACGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
39 32 0.56
40 1 0.02
41 1 0.02
42 23 0.40
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (41 bp):
AAATCGCGTCCACGTCAGCGCGATTCAGCGGACGTGGCAAC
Found at i:19865827 original size:40 final size:39
Alignment explanation
Indices: 19865743--19865828 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
19865733 ACGTGTCAGC
* * *
19865743 AAATCGCGTCCACGTCAGCGCGATTACTTACGTGGCAAC
1 AAATCGCGTCCACGTAAGCGCGATTACTGACGTGGCAAA
*
19865782 AAATCGCGTCCACGTAAGCGCGATTTGCTGACGTGG-AAGA
1 AAATCGCGTCCACGTAAGCGCGA-TTACTGACGTGGCAA-A
19865822 AAATCGC
1 AAATCGC
19865829 ACTTACGTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 24 0.59
40 17 0.41
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.20
Consensus pattern (39 bp):
AAATCGCGTCCACGTAAGCGCGATTACTGACGTGGCAAA
Found at i:19865894 original size:49 final size:49
Alignment explanation
Indices: 19865822--19865916 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
19865812 ACGTGGAAGA
19865822 AAATCGCACTTACGTGGACGTGATTTGCGTCGTACGTGAACAGTACAGC
1 AAATCGCACTTACGTGGACGTGATTTGCGTCGTACGTGAACAGTACAGC
*
19865871 AAATCGCGCTTACGTGGACGTGATTTGCGTCGTACGTGAACAGTAC
1 AAATCGCACTTACGTGGACGTGATTTGCGTCGTACGTGAACAGTAC
19865917 CCAGCAGTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (49 bp):
AAATCGCACTTACGTGGACGTGATTTGCGTCGTACGTGAACAGTACAGC
Found at i:19871594 original size:21 final size:22
Alignment explanation
Indices: 19871570--19871621 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19871560 CTCGTATATA
* *
19871570 GGTCAAAATGGGTT-AAATACT
1 GGTCAAAATGGATTAAAATACG
*
19871591 GGTCAAAATGGATTAAAATAGG
1 GGTCAAAATGGATTAAAATACG
19871613 GGTCAAAAT
1 GGTCAAAAT
19871622 ATGAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCAAAATGGATTAAAATACG
Found at i:19872049 original size:23 final size:20
Alignment explanation
Indices: 19872023--19872063 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
19872013 ACAATTAGTA
19872023 GAGAAGGTAAAAGAGAAAGAAAG
1 GAGAAGG-AAAA-A-AAAGAAAG
19872046 GAGAAGGAAAAAAAAGAA
1 GAGAAGGAAAAAAAAGAA
19872064 GAAGAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 4 0.22
23 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (20 bp):
GAGAAGGAAAAAAAAGAAAG
Found at i:19873037 original size:13 final size:13
Alignment explanation
Indices: 19873019--19873059 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
19873009 TTATCGACTT
19873019 ACATACATGCAAA
1 ACATACATGCAAA
*
19873032 ACATACATACAGAA
1 ACATACATGCA-AA
*
19873046 ATATACATGCAAA
1 ACATACATGCAAA
19873059 A
1 A
19873060 ATTAGATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.56, C:0.20, G:0.07, T:0.17
Consensus pattern (13 bp):
ACATACATGCAAA
Found at i:19873168 original size:44 final size:44
Alignment explanation
Indices: 19873058--19873169 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
19873048 ATACATGCAA
* * *
19873058 AAATTAGATTCATTGGAAGAAATTTGGAACAAACTTCGTAATTT
1 AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
* * * * * *
19873102 AAATGATATGCACTGCACCAAACTTGGAACAAACTTTGTAATTT
1 AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
19873146 AAATTAGATGCATTGGAACAAACT
1 AAATTAGATGCATTGGAACAAACT
19873170 CGGTAAAATA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (44 bp):
AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
Found at i:19874760 original size:27 final size:27
Alignment explanation
Indices: 19874720--19874772 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
19874710 TCGTACAACA
19874720 GCTCAATTGCCATCTGTTTAGCTATCT
1 GCTCAATTGCCATCTGTTTAGCTATCT
*
19874747 GCTCAATTGTCATCTGTTTAGCTATC
1 GCTCAATTGCCATCTGTTTAGCTATC
19874773 CATGATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.42
Consensus pattern (27 bp):
GCTCAATTGCCATCTGTTTAGCTATCT
Found at i:19884668 original size:17 final size:16
Alignment explanation
Indices: 19884627--19884668 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
19884617 AATTCAATTT
*
19884627 TAATATAAATATTCAA
1 TAATATAAAAATTCAA
19884643 T-ATACTAAACAATTCAA
1 TAATA-TAAA-AATTCAA
19884660 TAATATAAA
1 TAATATAAA
19884669 TAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 11 0.50
18 3 0.14
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATATAAAAATTCAA
Found at i:19884723 original size:36 final size:36
Alignment explanation
Indices: 19884653--19884725 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
19884643 TATACTAAAC
* **
19884653 AATTCAATAATATAAATAATATAATATGTGAAATTT
1 AATTCAATAATATAAATAATAGAATAAATGAAATTT
*
19884689 AATTTAATAATATAAATAATAGATATAAAT-AAATTT
1 AATTCAATAATATAAATAATAGA-ATAAATGAAATTT
19884725 A
1 A
19884726 TTACTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (36 bp):
AATTCAATAATATAAATAATAGAATAAATGAAATTT
Found at i:19884834 original size:15 final size:16
Alignment explanation
Indices: 19884804--19884837 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
19884794 TTAGGGGGAA
19884804 AATAAAAAGTTTTGAGG
1 AATAAAAAG-TTTGAGG
19884821 AATAAAAA-TTTGAGG
1 AATAAAAAGTTTGAGG
19884836 AA
1 AA
19884838 AAGTAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (16 bp):
AATAAAAAGTTTGAGG
Found at i:19894860 original size:2 final size:2
Alignment explanation
Indices: 19894855--19894913 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
19894845 TCAACAGGTT
19894855 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19894897 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
19894914 TTTCCCCAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19898979 original size:8 final size:8
Alignment explanation
Indices: 19898966--19899026 Score: 60
Period size: 7 Copynumber: 8.1 Consensus size: 8
19898956 TATGCTTGAG
19898966 TTATTATA
1 TTATTATA
*
19898974 TTATTAAA
1 TTATTATA
*
19898982 TTAATATA
1 TTATTATA
19898990 TTA-TATCA
1 TTATTAT-A
19898998 TTA-TATA
1 TTATTATA
19899005 TT-TTATA
1 TTATTATA
19899012 TT-TTATA
1 TTATTATA
19899019 TT-TTATA
1 TTATTATA
19899026 T
1 T
19899027 AATCATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
7 25 0.52
8 23 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATTATA
Found at i:19900273 original size:14 final size:14
Alignment explanation
Indices: 19900254--19900288 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19900244 AAAAAACAAG
19900254 TTATTTTCCAAAAA
1 TTATTTTCCAAAAA
*
19900268 TTATTTTTCAAAAA
1 TTATTTTCCAAAAA
*
19900282 TCATTTT
1 TTATTTT
19900289 TAGTGAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATTTTCCAAAAA
Found at i:19902176 original size:36 final size:36
Alignment explanation
Indices: 19902129--19902236 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
19902119 ACAGAGTTGT
19902129 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
*
19902165 TAACAAATCATCAAAATGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
19902201 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
19902237 ATGCTCATAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (36 bp):
TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
Found at i:19909433 original size:26 final size:26
Alignment explanation
Indices: 19909404--19909457 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
19909394 ATAACATAAG
*
19909404 TTATCTTCACCCTTTGAAAAGTTATC
1 TTATCTTCACCATTTGAAAAGTTATC
19909430 TTATCTTCACCATTTGAAAAGTTATC
1 TTATCTTCACCATTTGAAAAGTTATC
19909456 TT
1 TT
19909458 GAGAACTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.44
Consensus pattern (26 bp):
TTATCTTCACCATTTGAAAAGTTATC
Found at i:19910487 original size:26 final size:25
Alignment explanation
Indices: 19910441--19910491 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
19910431 ACAAACAAAT
* *
19910441 AATCAACCTAGTTATTATAATATAAG
1 AATCAACATAGTTAATATAAT-TAAG
19910467 AATCAACATCAGTTAAT-TAATTAAG
1 AATCAACAT-AGTTAATATAATTAAG
19910492 CCTAGTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
AATCAACATAGTTAATATAATTAAG
Found at i:19912231 original size:2 final size:2
Alignment explanation
Indices: 19912224--19912253 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19912214 ATCTATATGT
19912224 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19912254 TCACATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19915015 original size:24 final size:25
Alignment explanation
Indices: 19914962--19915017 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
19914952 TATTTTAATA
*
19914962 TATAAAATATAAATTTTAAATATTT
1 TATAAAATATAAATATTAAATATTT
*
19914987 T-TAAACA-ATAAATATT-AATTTTT
1 TATAAA-ATATAAATATTAAATATTT
19915010 TATAAAAT
1 TATAAAAT
19915018 TTAATTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
23 8 0.31
24 16 0.62
25 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAAAATATAAATATTAAATATTT
Found at i:19915049 original size:20 final size:21
Alignment explanation
Indices: 19915021--19915071 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
19915011 ATAAAATTTA
19915021 ATTAGAATATATAAACTAT-ATT
1 ATTA-AATATATAAA-TATAATT
*
19915043 -TTAAATATTTAAATATAATT
1 ATTAAATATATAAATATAATT
19915063 ATTAAATAT
1 ATTAAATAT
19915072 TTATAATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAAATATATAAATATAATT
Found at i:19915088 original size:21 final size:21
Alignment explanation
Indices: 19915021--19915074 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
19915011 ATAAAATTTA
*
19915021 ATTAGAATATATAAACTAT-ATT
1 ATTA-AATATTTAAA-TATAATT
19915043 -TTAAATATTTAAATATAATT
1 ATTAAATATTTAAATATAATT
19915063 ATTAAATATTTA
1 ATTAAATATTTA
19915075 TAATTAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 12 0.41
21 14 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTAAATATTTAAATATAATT
Done.