Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002727.1 Hibiscus syriacus cultivar Beakdansim tig00005624_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: 169216
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:425 original size:37 final size:38
Alignment explanation
Indices: 370--456 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 38
360 ATAATGTGTA
*
370 GCGGCGTTTTAGAAAAAAACGCCACTAAAT-ACTTATT
1 GCGGCGTTTGAGAAAAAAACGCCACTAAATAACTTATT
* * **
407 GCGGCGTTTGCGATAAAAACGCTGCTAAATCAACACTTATT
1 GCGGCGTTTGAGAAAAAAACGCCACTAAAT--A-ACTTATT
448 GCGGCGTTT
1 GCGGCGTTT
457 TTTAGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 25 0.61
41 16 0.39
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (38 bp):
GCGGCGTTTGAGAAAAAAACGCCACTAAATAACTTATT
Found at i:542 original size:43 final size:43
Alignment explanation
Indices: 400--628 Score: 209
Period size: 43 Copynumber: 5.4 Consensus size: 43
390 GCCACTAAAT
* * *
400 ACTTATTGCGGCGTTTGCGATAAAAACGCTGCTAAA--TCAAC
1 ACTTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAC
* * * * * *
441 ACTTATTGCGGCGTTTTTTAGAAAAACACCTCT-ATTCTC-AT
1 ACTTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAC
** *
482 ACTTATTATGGCATTTGTGAGAAAAACGCCGCTAAATCTCAAC
1 ACTTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAC
* * *
525 ACTTATTGCGACGTTTGTGATAAAAACGCAGCTAAATCTCAAC
1 ACTTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAC
* * * * *
568 ACCTACTGCGGCGTTTGTG-GTAAAAATGTCGTTAAA-CATCAAC
1 ACTTATTGCGGCGTTTGTGAG-AAAAACGCCGCTAAATC-TCAAC
*
611 ACGTATTGCGGCGTTTGT
1 ACTTATTGCGGCGTTTGT
629 TTAACAAACG
Statistics
Matches: 148, Mismatches: 34, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 53 0.36
42 8 0.05
43 86 0.58
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
ACTTATTGCGGCGTTTGTGAGAAAAACGCCGCTAAATCTCAAC
Found at i:550 original size:84 final size:82
Alignment explanation
Indices: 398--551 Score: 200
Period size: 82 Copynumber: 1.9 Consensus size: 82
388 ACGCCACTAA
* * * * * * *
398 ATACTTATTGCGGCGTTTGCGATAAAAACGCTGCTAAATCAACACTTATTGCGGCGTTTTTTAGA
1 ATACTTATTACGGCATTTGCGAGAAAAACGCCGCTAAATCAACACTTATTGCGACGTTTGTGAGA
463 AAAACACCTCTATTCTC
66 AAAACACCTCTATTCTC
* *
480 ATACTTATTATGGCATTTGTGAGAAAAACGCCGCTAAATCTCAACACTTATTGCGACGTTTGTGA
1 ATACTTATTACGGCATTTGCGAGAAAAACGCCGCTAAA--TCAACACTTATTGCGACGTTTGTGA
*
545 TAAAAAC
64 GAAAAAC
552 GCAGCTAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 32 0.53
84 28 0.47
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (82 bp):
ATACTTATTACGGCATTTGCGAGAAAAACGCCGCTAAATCAACACTTATTGCGACGTTTGTGAGA
AAAACACCTCTATTCTC
Found at i:644 original size:43 final size:43
Alignment explanation
Indices: 403--687 Score: 190
Period size: 43 Copynumber: 6.7 Consensus size: 43
393 ACTAAATACT
* * * *
403 TATTGCGGCGTTTGCGATAAAAACGCTGCTAAA--TCAACACT
1 TATTGCGGCGTTTGTGTTAAAAACGCCGCTAAATCTCAACACC
* * * * *
444 TATTGCGGCGTTT-T-TTAGAAAAACACCTCT-ATTCTC-ATACT
1 TATTGCGGCGTTTGTGTT--AAAAACGCCGCTAAATCTCAACACC
** * ** *
485 TATTATGGCATTTGTGAGAAAAACGCCGCTAAATCTCAACACT
1 TATTGCGGCGTTTGTGTTAAAAACGCCGCTAAATCTCAACACC
* * *
528 TATTGCGACGTTTGTGATAAAAACGCAGCTAAATCTCAACACC
1 TATTGCGGCGTTTGTGTTAAAAACGCCGCTAAATCTCAACACC
* * * * * *
571 TACTGCGGCGTTTGTGGTAAAAATGTCGTTAAA-CATCAACACG
1 TATTGCGGCGTTTGTGTTAAAAACGCCGCTAAATC-TCAACACC
* * * **
614 TATTGCGGCGTTTGT-TTAACAAACGCCGTTATATATCGTCACC
1 TATTGCGGCGTTTGTGTTAA-AAACGCCGCTAAATCTCAACACC
*
657 TATTGCGGCGTTTTTCGTTAACAAACGCCGC
1 TATTGCGGCGTTTGT-GTTAA-AAACGCCGC
688 GAACTTTAGC
Statistics
Matches: 189, Mismatches: 42, Indels: 22
0.75 0.17 0.09
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 46 0.24
42 12 0.06
43 116 0.61
45 13 0.07
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
TATTGCGGCGTTTGTGTTAAAAACGCCGCTAAATCTCAACACC
Found at i:1027 original size:60 final size:60
Alignment explanation
Indices: 949--1236 Score: 335
Period size: 60 Copynumber: 4.8 Consensus size: 60
939 ACGAGGATGA
* * * *
949 AGATGGAATAGCACTAGAGATGGAGTTATGTGGAGATGGATTAATAGAAGTGAAATGTTG
1 AGATGGAATAGCAGTAGAGATGGAATTATGTGGAGATGGATTGATAGAAGTGAAATGTGG
* * * * *
1009 AGATGGAATAGCAGTAGAGTTGGAATTATGTAGAGATGGATTGGTAGAAGTGGAGTGTGG
1 AGATGGAATAGCAGTAGAGATGGAATTATGTGGAGATGGATTGATAGAAGTGAAATGTGG
* * * * * *
1069 AGATGAAATAACAGTAGAGAT-GATATTTTGTGGAGATGGATTGATAGAGGTGGAGTGTGG
1 AGATGGAATAGCAGTAGAGATGGA-ATTATGTGGAGATGGATTGATAGAAGTGAAATGTGG
* * *
1129 AGATGGAATAGCAGTAGAGATGGAATTATGTGAAGATGGATTGGTAGGAGTGAAATGTGG
1 AGATGGAATAGCAGTAGAGATGGAATTATGTGGAGATGGATTGATAGAAGTGAAATGTGG
* * * * * * *
1189 AGAGGGAATAGTAGTAGGGATGGAGTTATGTGGAAATGAATTAATAGA
1 AGATGGAATAGCAGTAGAGATGGAATTATGTGGAGATGGATTGATAGA
1237 GGTTATAGGA
Statistics
Matches: 191, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
59 2 0.01
60 187 0.98
61 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.37, T:0.26
Consensus pattern (60 bp):
AGATGGAATAGCAGTAGAGATGGAATTATGTGGAGATGGATTGATAGAAGTGAAATGTGG
Found at i:1221 original size:120 final size:120
Alignment explanation
Indices: 953--1239 Score: 371
Period size: 120 Copynumber: 2.4 Consensus size: 120
943 GGATGAAGAT
* * *
953 GGAATAGCACTAGAGATGGAGTTATGTGGAGATGGATTAATAGAAGTGAAATGTTGAGATGGAAT
1 GGAATAGCAGTAGAGATGGAGTTATGTGGAGATGGATTAATAGAGGTGAAATGTGGAGATGGAAT
* * * *
1018 AGCAGTAGAGTTGGAATTATGTAGAGATGGATTGGTAGAAGTGGAGTGTGGAGAT
66 AGCAGTAGAGATGGAATTATGTAGAGATGGATTGGTAGAAGTGAAATGTGGAGAG
* * * * * * *
1073 GAAATAACAGTAGAGAT-GATATTTTGTGGAGATGGATTGATAGAGGTGGAGTGTGGAGATGGAA
1 GGAATAGCAGTAGAGATGGA-GTTATGTGGAGATGGATTAATAGAGGTGAAATGTGGAGATGGAA
*
1137 TAGCAGTAGAGATGGAATTATGT-GAAGATGGATTGGTAGGAGTGAAATGTGGAGAG
65 TAGCAGTAGAGATGGAATTATGTAG-AGATGGATTGGTAGAAGTGAAATGTGGAGAG
* * * *
1193 GGAATAGTAGTAGGGATGGAGTTATGTGGAAATGAATTAATAGAGGT
1 GGAATAGCAGTAGAGATGGAGTTATGTGGAGATGGATTAATAGAGGT
1240 TATAGGAGGG
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
119 3 0.02
120 135 0.96
121 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.37, T:0.26
Consensus pattern (120 bp):
GGAATAGCAGTAGAGATGGAGTTATGTGGAGATGGATTAATAGAGGTGAAATGTGGAGATGGAAT
AGCAGTAGAGATGGAATTATGTAGAGATGGATTGGTAGAAGTGAAATGTGGAGAG
Found at i:9182 original size:20 final size:20
Alignment explanation
Indices: 9157--9211 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
9147 AAGATAAAAT
* *
9157 AATAATAAAATAATTAATGC
1 AATAATAAAATAATAAAAGC
*
9177 AATAATCAAAAT-ATAAAAGT
1 AATAAT-AAAATAATAAAAGC
9197 AATAATAAAATAATA
1 AATAATAAAATAATA
9212 TTGCAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 5 0.17
20 20 0.67
21 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
AATAATAAAATAATAAAAGC
Found at i:10107 original size:11 final size:11
Alignment explanation
Indices: 10093--10129 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
10083 TCGGTGGTAA
10093 GTTTCTTCTCT
1 GTTTCTTCTCT
10104 GTTTCTTCTCT
1 GTTTCTTCTCT
* *
10115 CTTTCTTTTCT
1 GTTTCTTCTCT
10126 GTTT
1 GTTT
10130 GCTGTTATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (11 bp):
GTTTCTTCTCT
Found at i:10581 original size:19 final size:18
Alignment explanation
Indices: 10548--10602 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 18
10538 AATATTTATT
10548 TAATAATATTAATAAAAA
1 TAATAATATTAATAAAAA
*
10566 TAATAATGTATAATAAAAA
1 TAATAATAT-TAATAAAAA
10585 TAATAA-A--AATAAAAA
1 TAATAATATTAATAAAAA
10600 TAA
1 TAA
10603 AAGCAAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 11 0.32
18 8 0.24
19 15 0.44
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
TAATAATATTAATAAAAA
Found at i:10587 original size:9 final size:9
Alignment explanation
Indices: 10557--10596 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
10547 TTAATAATAT
10557 TAATAAAAA
1 TAATAAAAA
**
10566 TAATAATGTA
1 TAATAA-AAA
10576 TAATAAAAA
1 TAATAAAAA
10585 TAATAAAAA
1 TAATAAAAA
10594 TAA
1 TAA
10597 AAATAAAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
TAATAAAAA
Found at i:10989 original size:74 final size:73
Alignment explanation
Indices: 10758--11191 Score: 672
Period size: 74 Copynumber: 5.9 Consensus size: 73
10748 GGTCTTATGA
* *
10758 ATGACCCTGAAGCTTTAAAATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
*
10823 TCTTATAG
66 TCTTACAG
* * * *
10831 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTACACTGTAAG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
10896 TCTTACAG
66 TCTTACAG
*
10904 AGGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTAG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAG
10969 GTCTTACAG
65 GTCTTACAG
* *
10978 ATGACCCTGAGGCTTTAAAATAAAAAAGCTCCTGAAGGCTTTTTTGAAAACATCATGCACTGTAG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAG
*
11043 GACTTACAG
65 GTCTTACAG
* * *
11052 ATGACCCTGAGTCTTTAAAATCAAAAAGCTCCTGAAGGC-TTTTGAAAACATCATGCACTATAGG
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
11116 TCTTACAG
66 TCTTACAG
* * *
11124 ATGACCCTAAGGCTTTAAAATCAAAAAGCTCCCAAAGGTTTTTTTTGAAAACATCATGCACTGTA
1 ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGG--CTTTTTGAAAACATCATGCACTGTA
11189 GGT
64 GGT
11192 GTTAAAGTTG
Statistics
Matches: 331, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
72 65 0.20
73 103 0.31
74 138 0.42
75 25 0.08
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (73 bp):
ATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
TCTTACAG
Found at i:11015 original size:147 final size:146
Alignment explanation
Indices: 10760--11188 Score: 671
Period size: 146 Copynumber: 2.9 Consensus size: 146
10750 TCTTATGAAT
*
10760 GACCCTGAAGCTTTAAAATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTC
1 GACCCTGAGGCTTTAAAATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTC
* * * *
10825 TTATAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTACAC
66 TTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAC
*
10890 TGTAAGTCTTACAGAG
131 TGTAAGACTTACAGAG
*
10906 GACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTTGAAAACATCATGCACTGTAGGT
1 GACCCTGAGGCTTTAAAATCAAAAAGCTCCTGAAGGC-TTTTTGAAAACATCATGCACTGTAGGT
* *
10971 CTTACAGATGACCCTGAGGCTTTAAAATAAAAAAGCTCCTGAAGGCTTTTTTGAAAACATCATGC
65 CTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGC
* *
11036 ACTGTAGGACTTACAGAT
129 ACTGTAAGACTTACAGAG
* *
11054 GACCCTGAGTCTTTAAAATCAAAAAGCTCCTGAAGGC-TTTTGAAAACATCATGCACTATAGGTC
1 GACCCTGAGGCTTTAAAATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTC
* * *
11118 TTACAGATGACCCTAAGGCTTTAAAATCAAAAAGCTCCCAAAGGTTTTTTTTGAAAACATCATGC
66 TTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGG--CTTTTTGAAAACATCATGC
11183 ACTGTA
129 ACTGTA
11189 GGTGTTAAAG
Statistics
Matches: 260, Mismatches: 19, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
146 101 0.39
147 93 0.36
148 66 0.25
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (146 bp):
GACCCTGAGGCTTTAAAATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTC
TTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCAC
TGTAAGACTTACAGAG
Found at i:11894 original size:22 final size:22
Alignment explanation
Indices: 11866--11944 Score: 140
Period size: 22 Copynumber: 3.6 Consensus size: 22
11856 AATAAAGTTT
11866 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
11888 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
11910 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAAAGAGAATCTA
11932 TCATCTTTGAAAA
1 TCATCTTTGAAAA
11945 ATATAGATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:21706 original size:13 final size:13
Alignment explanation
Indices: 21688--21715 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21678 AGGTACTCGA
21688 ATTGTCCTTGTTG
1 ATTGTCCTTGTTG
21701 ATTGTCCTTGTTG
1 ATTGTCCTTGTTG
21714 AT
1 AT
21716 GGCCCCTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.11, C:0.14, G:0.21, T:0.54
Consensus pattern (13 bp):
ATTGTCCTTGTTG
Found at i:22101 original size:19 final size:20
Alignment explanation
Indices: 22079--22120 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
22069 AAATAAATAA
*
22079 ATATTAATAAA-ACATTTAT
1 ATATTAAAAAATACATTTAT
*
22098 ATA-TAAAAAATAGATTTAT
1 ATATTAAAAAATACATTTAT
22117 ATAT
1 ATAT
22121 AATTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATTAAAAAATACATTTAT
Found at i:22107 original size:17 final size:19
Alignment explanation
Indices: 22061--22122 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 19
22051 TCTTTTCTTA
* **
22061 ATATA-AAAAAATAAATAA
1 ATATATAAAAAATACATTT
*
22079 ATAT-TAATAAA-ACATTT
1 ATATATAAAAAATACATTT
*
22096 ATATATAAAAAATAGATTT
1 ATATATAAAAAATACATTT
22115 ATATATAA
1 ATATATAA
22123 TTTATAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.20
18 15 0.43
19 13 0.37
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
ATATATAAAAAATACATTT
Found at i:22392 original size:18 final size:18
Alignment explanation
Indices: 22366--22403 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
22356 ATATTAAAAA
*
22366 TAAATAAATAT-TATTATT
1 TAAACAAATATATA-TATT
22384 TAAACAAATATATATATT
1 TAAACAAATATATATATT
22402 TA
1 TA
22404 TAAGACTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAACAAATATATATATT
Found at i:23208 original size:13 final size:13
Alignment explanation
Indices: 23190--23214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23180 TCGTCTGTCG
23190 TCGCCGACCACCA
1 TCGCCGACCACCA
23203 TCGCCGACCACC
1 TCGCCGACCACC
23215 GTGAATGGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.56, G:0.16, T:0.08
Consensus pattern (13 bp):
TCGCCGACCACCA
Found at i:23861 original size:3 final size:3
Alignment explanation
Indices: 23838--23911 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
23828 AATATTTATT
* *
23838 TAA TAA TAT TAA TAA -AA -AA TAA TAA TGTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
23882 TAA TAA TAA TAA TAA AAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23912 AAAAAAAACA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.07
3 55 0.90
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:25131 original size:30 final size:30
Alignment explanation
Indices: 25097--25173 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
25087 ATGGTCCAAA
25097 TGACCGGTTTGACCGGTTTTGGAGCAAAGT
1 TGACCGGTTTGACCGGTTTTGGAGCAAAGT
* * *
25127 TGACCGGTTTGACCGATTTTGGAGTAGAGT
1 TGACCGGTTTGACCGGTTTTGGAGCAAAGT
25157 TGACCGGTTTGACCGGT
1 TGACCGGTTTGACCGGT
25174 CACAACCTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (30 bp):
TGACCGGTTTGACCGGTTTTGGAGCAAAGT
Found at i:25208 original size:13 final size:13
Alignment explanation
Indices: 25181--25215 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
25171 GGTCACAACC
*
25181 TGACCCGA-ACGT
1 TGACCCGACCCGT
25193 TGACCCGACCCGT
1 TGACCCGACCCGT
25206 TGACCCGACC
1 TGACCCGACC
25216 AGACCCGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.14
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:25220 original size:18 final size:18
Alignment explanation
Indices: 25194--25264 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
25184 CCCGAACGTT
25194 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
* *
25212 GACCAGACCCGTTGCCCC
1 GACCCGACCCGTTGACCC
* *
25230 AACCCGACCCGTTGACCT
1 GACCCGACCCGTTGACCC
*
25248 GACCCGATCCGTTGACC
1 GACCCGACCCGTTGACC
25265 GACTCGTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.18, C:0.46, G:0.21, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:28247 original size:32 final size:31
Alignment explanation
Indices: 28174--28248 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
28164 CTAATGTGAC
* *
28174 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** * **
28205 TCTCGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
28237 TCTTAGGTAGGC
1 TCTTAGGTAGGC
28249 TCCATGGCCC
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
31 23 0.68
32 11 0.32
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:28276 original size:63 final size:63
Alignment explanation
Indices: 28174--28297 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
28164 CTAATGTGAC
** * * * **
28174 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATCATTCTCGGGTAGGCACTCAGGCCCTAAGATGTGT
* *
28237 TCTTAGGTAGGCTCCATGGCCCCGAAATC-TATCTTGGGTAGGCACTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATCAT-TCTCGGGTAGGCACTCAGGCCCTAAGATGT
28298 TCCCTTAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 1 0.02
63 50 0.98
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCCACGGCCCCGAAATCATTCTCGGGTAGGCACTCAGGCCCTAAGATGTGT
Found at i:29513 original size:43 final size:43
Alignment explanation
Indices: 29432--29527 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
29422 CTTGATAAAA
* * *
29432 TAAATAAATTTAAATATAATATTTTATAATTCCATTATATATT
1 TAAATAATTTTAAATATAATATTTAATAATTCCATTATAGATT
* * ** *
29475 TGAATAATTTTAAACTA-AATATTTAATATTTCTTTTATAGGTT
1 TAAATAATTTTAAA-TATAATATTTAATAATTCCATTATAGATT
29518 TAAATAATTT
1 TAAATAATTT
29528 AAAAGTTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
43 41 0.95
44 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (43 bp):
TAAATAATTTTAAATATAATATTTAATAATTCCATTATAGATT
Found at i:31309 original size:26 final size:26
Alignment explanation
Indices: 31272--31359 Score: 167
Period size: 26 Copynumber: 3.4 Consensus size: 26
31262 AGATATAAGT
*
31272 TTTTCTTTCTCCAAAATCCTCTTGTA
1 TTTTCTTCCTCCAAAATCCTCTTGTA
31298 TTTTCTTCCTCCAAAATCCTCTTGTA
1 TTTTCTTCCTCCAAAATCCTCTTGTA
31324 TTTTCTTCCTCCAAAATCCTCTTGTA
1 TTTTCTTCCTCCAAAATCCTCTTGTA
31350 TTTTCTTCCT
1 TTTTCTTCCT
31360 TCATATTAGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.17, C:0.30, G:0.03, T:0.50
Consensus pattern (26 bp):
TTTTCTTCCTCCAAAATCCTCTTGTA
Found at i:35691 original size:5 final size:5
Alignment explanation
Indices: 35683--35711 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35673 ACAAAAGGTA
35683 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
35712 ATATAGCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:36788 original size:113 final size:113
Alignment explanation
Indices: 36590--36815 Score: 425
Period size: 113 Copynumber: 2.0 Consensus size: 113
36580 TACATTGGTA
* *
36590 TTTATATTTCGATGGAAGCAGTCATTGGAAAACTGCTGAGACATTCGCACCTAAATCTATTTTCT
1 TTTATATTTCAATGGAAGCAGTCATTGGAAAACTGCTGAGACATTCGCACCTAAATCCATTTTCT
36655 CGACCCCGGTAAGCTTCCTTTTAGTCGTACAGAGATCCTTCAAAAACC
66 CGACCCCGGTAAGCTTCCTTTTAGTCGTACAGAGATCCTTCAAAAACC
*
36703 TTTATATTTCAATGGAAGCGGTCATTGGAAAACTGCTGAGACATTCGCACCTAAATCCATTTTCT
1 TTTATATTTCAATGGAAGCAGTCATTGGAAAACTGCTGAGACATTCGCACCTAAATCCATTTTCT
36768 CGACCCCGGTAAGCTTCCTTTTAGTCGTACAGAGATCCTTCAAAAACC
66 CGACCCCGGTAAGCTTCCTTTTAGTCGTACAGAGATCCTTCAAAAACC
36816 GACAATACCT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (113 bp):
TTTATATTTCAATGGAAGCAGTCATTGGAAAACTGCTGAGACATTCGCACCTAAATCCATTTTCT
CGACCCCGGTAAGCTTCCTTTTAGTCGTACAGAGATCCTTCAAAAACC
Found at i:38730 original size:18 final size:15
Alignment explanation
Indices: 38696--38743 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 15
38686 TTTAAATAGT
38696 AATAAAAAAAGATTA
1 AATAAAAAAAGATTA
38711 AATAAAATAAAGCAATTA
1 AATAAAA-AAAG--ATTA
38729 AAGTAAAAATAAGAT
1 AA-TAAAAA-AAGAT
38744 GATAGAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.25
16 4 0.14
17 2 0.07
18 7 0.25
19 8 0.29
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (15 bp):
AATAAAAAAAGATTA
Found at i:45264 original size:32 final size:31
Alignment explanation
Indices: 45223--45332 Score: 103
Period size: 32 Copynumber: 3.5 Consensus size: 31
45213 CTAAGGTGAC
* * *
45223 CTTGGGTAGGCTGTGAGGCCCCAAGGCATTTT
1 CTTGGGTAGGCTCTAAGGCCCCAAGGCA-CTT
* *
45255 CTTGGGTAGGCTTTAAGGCCCCAAGGTACTT
1 CTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* * * *
45286 CATTGGGTAGGCTCTTAGGCCCTAAGGTACTC
1 C-TTGGGTAGGCTCTAAGGCCCCAAGGCACTT
*
45318 CATTAGGTAGGCTCT
1 C-TTGGGTAGGCTCT
45333 CAAGCCTTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 3 0.04
32 65 0.96
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (31 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
Found at i:52528 original size:2 final size:2
Alignment explanation
Indices: 52523--52574 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
52513 ATATTCATCC
52523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52565 AT AT AT AT AT
1 AT AT AT AT AT
52575 GGATTAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56491 original size:20 final size:21
Alignment explanation
Indices: 56441--56492 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
56431 ATTATGACTA
56441 TCGCAATGCGATTTTACAATT
1 TCGCAATGCGATTTTACAATT
** *
56462 TCGCGTTGCGATTTTCCAA-T
1 TCGCAATGCGATTTTACAATT
56482 TCGCAATGCGA
1 TCGCAATGCGA
56493 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGCAATGCGATTTTACAATT
Found at i:56525 original size:21 final size:21
Alignment explanation
Indices: 56482--56575 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
56472 ATTTTCCAAT
** *
56482 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
56502 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
56523 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
56544 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
56565 TCGCAACGCGA
1 TCGCAATGCGA
56576 TACTGACTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
20 12 0.17
21 57 0.83
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:56589 original size:20 final size:20
Alignment explanation
Indices: 56564--56678 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
56554 AATTTGGAAA
56564 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
56584 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
56605 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
56625 TTCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
56645 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
56665 TTCACAACGAGATA
1 ATCGCAACGCGATA
56679 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 62 0.77
21 15 0.19
22 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:56606 original size:41 final size:41
Alignment explanation
Indices: 56561--56698 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
56551 GCGAATTTGG
*
56561 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
56602 AAAATCGCAACGCGATACTGACTTTCGCAATGCGATACTTAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** * *
56644 --TTTCGCAACGCGATACTGACTTTCACAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
56683 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
56699 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.37
41 46 0.56
42 3 0.04
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:56891 original size:21 final size:21
Alignment explanation
Indices: 56865--56907 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
56855 CACTCTCTCA
56865 CCCATCTCCGACGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
56886 CCCATCTCCGACGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
56907 C
1 C
56908 TATCTCCATC
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:0.23, C:0.44, G:0.14, T:0.19
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCCGT
Found at i:57219 original size:20 final size:20
Alignment explanation
Indices: 57170--57228 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
57160 TTTATTCTCT
* **
57170 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
57190 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
57210 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
57229 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:57419 original size:25 final size:24
Alignment explanation
Indices: 57365--57419 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
57355 TGTTTATTAT
* *
57365 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
57389 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
57415 TGTTT
1 TGTTT
57420 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:58040 original size:14 final size:14
Alignment explanation
Indices: 58006--58044 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
57996 TTGATTGTTT
58006 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
58020 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
58034 TGTTGATTTGT
1 AATTGATTTGT
58045 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:58208 original size:19 final size:19
Alignment explanation
Indices: 58184--58236 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
58174 GCAACGAGAG
58184 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58203 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58222 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
58237 ATCGCAATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:58236 original size:14 final size:14
Alignment explanation
Indices: 58219--58248 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
58209 AATGCGAAAT
58219 GAAAATCGCAATGC
1 GAAAATCGCAATGC
58233 GAAAATCGCAATGC
1 GAAAATCGCAATGC
58247 GA
1 GA
58249 TTTTCATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (14 bp):
GAAAATCGCAATGC
Found at i:58292 original size:20 final size:20
Alignment explanation
Indices: 58267--58342 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
58257 TCGCATTACG
*
58267 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
58287 ATTTTCGCGTTGAGATAGCT
1 ATTTTCGCGTTGCGATAGCC
*
58307 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
58327 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
58343 TTTCCCGTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:58346 original size:14 final size:14
Alignment explanation
Indices: 58327--58356 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58317 TGCGATAGTC
*
58327 ATTTTCGCGTTGCG
1 ATTTTCCCGTTGCG
58341 ATTTTCCCGTTGCG
1 ATTTTCCCGTTGCG
58355 AT
1 AT
58357 AGTCAAATGA
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:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
ATTTTCCCGTTGCG
Found at i:58352 original size:34 final size:34
Alignment explanation
Indices: 58255--58361 Score: 106
Period size: 34 Copynumber: 3.0 Consensus size: 34
58245 GCGATTTTCA
* * * *
58255 TTTCGCATTACGATTTTCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCCCGTTGCGATAGTCAT
* *
58289 TTTCGCGTTGAGATAGCTATTTTCGCGTTGCGATAGTCAT
1 TTTCGCG-T----T-GCGATTTTCCCGTTGCGATAGTCAT
58329 TTTCGCGTTGCGATTTTCCCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCCCGTTGCGATAGTCA
58362 AATGAATGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
34 28 0.47
35 2 0.03
39 2 0.03
40 28 0.47
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCCCGTTGCGATAGTCAT
Found at i:58588 original size:20 final size:20
Alignment explanation
Indices: 58565--58653 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
58555 ATTGCGATTT
*
58565 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
58585 TCAGAATCACGTTGTGAAAG
1 TCAGAATCGCGTTGCGAAAG
58605 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
58625 TCAGTATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
58645 TCAGTATCG
1 TCAGAATCG
58654 TTGTTTTCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:59431 original size:38 final size:37
Alignment explanation
Indices: 59389--59466 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
59379 AAATATTCAG
* *
59389 GTCAGGTCAAAGTCGATTGGAAGATATATATTTTTCGA
1 GTCAGGTCAAA-TCGATTGAAAGATATATAATTTTCGA
* *
59427 GTCAGTTTAAATCGATTGAAAGATATATAATTTTCGA
1 GTCAGGTCAAATCGATTGAAAGATATATAATTTTCGA
59464 GTC
1 GTC
59467 GAATCGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 27 0.75
38 9 0.25
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (37 bp):
GTCAGGTCAAATCGATTGAAAGATATATAATTTTCGA
Found at i:63600 original size:182 final size:180
Alignment explanation
Indices: 63284--63940 Score: 940
Period size: 182 Copynumber: 3.6 Consensus size: 180
63274 CAAATGAAAT
* * *
63284 ATGTATCGCTCCATAGCAATATTACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACAAAAC
1 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-CGGTCTCAAAATGACAAAAC
* *
63349 CGGTAAAACACTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACA-TTTTCTG
65 CGGTAAAA-ACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTT-GG
* * * *
63413 AATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTATCAACAC-TTTATGAAA
128 AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGATACTTTTA-AAAA
*
63466 ATGTATCGATCCATAACAATATAACAGTTAAAAATATGACAAAATCGGTCTCAAAATGACAAAAC
1 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-CGGTCTCAAAATGACAAAAC
* * *
63531 AGGTAAATAATTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGA
65 CGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGGA
63596 ATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
129 ATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
* *
63648 ATGTATCGATCCATAATAATATAACAGGTAAAAATATGACAAAACATGTCTCAAAAATGACAAAA
1 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC-GGTCTC-AAAATGACAAAA
*
63713 CCGGTAAAAAGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGG
64 CCGGTAAAAA-CTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGG
* * * *
63778 AATTTAAAAGAGAATAAATTATAGCGTCTATAAAGTGTCGATACTTTTAAAAA
128 AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
* * * * *
63831 ATGTATCGATCCATAATAATATAACATGCAAAAATATGATAAAAACAGTCTCAAAATGACAAAAC
1 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAAACGGTCTCAAAATGACAAAAC
* * * *
63896 CGGTAAAGCACTACCGGATATGTTGAGAGTGTAGATACTTTAATA
65 CGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATAATTTAATA
63941 AGTACGCGTA
Statistics
Matches: 434, Mismatches: 33, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
181 1 0.00
182 256 0.59
183 172 0.40
184 5 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (180 bp):
ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACGGTCTCAAAATGACAAAACC
GGTAAAAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTGGAAT
TTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
Found at i:63937 original size:365 final size:364
Alignment explanation
Indices: 63284--63940 Score: 989
Period size: 365 Copynumber: 1.8 Consensus size: 364
63274 CAAATGAAAT
* * * *
63284 ATGTATCGCTCCATAGCAATATTACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACAAAAC
1 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTCAAAATGACAAAAC
* *
63349 CGGTAAAACACTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACATTTTCTGA
66 CGGTAAAACAATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACATTTTCGGA
* *
63414 ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTATCAACACTTTATGAAAATGTATCGATCCA
131 ATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTATCAACACTTTATAAAAATGTATCGATCCA
* * * * *
63479 TAACAATATAACAGTTAAAAATATGACAAAATCGGTCTCAAAATGACAAAACAGGTAAATAATTA
196 TAACAATATAACAGTCAAAAATATGACAAAAACAGTCTCAAAATGACAAAACAGGTAAAGAACTA
*
63544 CCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
261 CCGGATATGTTGAAAGTGTAGATACTTTAATATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
63609 GAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
326 GAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
* *
63648 ATGTATCGATCCATAATAATATAACAGGTAAAAATATGACAAAACATGTCTCAAAAATGACAAAA
1 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTC-AAAATGACAAAA
*
63713 CCGGTAAAA-AGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTT-
65 CCGGTAAAACA-ATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACA-TTTTC
* * * * * *
63776 GGAATTTAAAAGAGAATAAATTATAGCGTCTATAAAGTGTCGATACTTT-TAAAAAATGTATCGA
128 GGAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTATCAACACTTTAT-AAAAATGTATCGA
* * *
63840 TCCATAATAATATAACA-TGCAAAAATATGATAAAAACAGTCTCAAAATGACAAAACCGGTAAAG
192 TCCATAACAATATAACAGT-CAAAAATATGACAAAAACAGTCTCAAAATGACAAAACAGGTAAAG
* *
63904 CACTACCGGATATGTTGAGAGTGTAGATACTTTAATA
256 AACTACCGGATATGTTGAAAGTGTAGATACTTTAATA
63941 AGTACGCGTA
Statistics
Matches: 260, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
364 49 0.19
365 207 0.80
366 4 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (364 bp):
ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTCAAAATGACAAAAC
CGGTAAAACAATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACATTTTCGGA
ATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTATCAACACTTTATAAAAATGTATCGATCCA
TAACAATATAACAGTCAAAAATATGACAAAAACAGTCTCAAAATGACAAAACAGGTAAAGAACTA
CCGGATATGTTGAAAGTGTAGATACTTTAATATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
GAAGTTATAGCGCCTATAAAGTATCGATACTTTTAAAAA
Found at i:65059 original size:23 final size:23
Alignment explanation
Indices: 65003--65059 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
64993 TTTATGAGAA
*
65003 AATATGTCAATATAAGCGTTACCT
1 AATATGT-TATATAAGCGTTACCT
* **
65027 ATTACATTATATAAGCGTTACCT
1 AATATGTTATATAAGCGTTACCT
65050 AATATGTTAT
1 AATATGTTAT
65060 TGTACTTGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (23 bp):
AATATGTTATATAAGCGTTACCT
Found at i:65112 original size:87 final size:86
Alignment explanation
Indices: 65012--65178 Score: 289
Period size: 87 Copynumber: 1.9 Consensus size: 86
65002 AAATATGTCA
*
65012 ATATAAGCGTTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
65077 CCGGTTAAATGCATATTTTGTT
66 CCGATTAAATG-ATATTTTGTT
*
65099 ATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
65164 TCGATTAAATGATAT
66 CCGATTAAATGATAT
65179 AACATAACCG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 4 0.05
87 72 0.95
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (86 bp):
ATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGATTAAATGATATTTTGTT
Found at i:65146 original size:23 final size:23
Alignment explanation
Indices: 65095--65146 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
65085 ATGCATATTT
* *
65095 TGTTATATAAGCGTTACCTATTA
1 TGTTATATAAGCGCTACCTAATA
**
65118 CATTATATAAGCGCTACCTAATA
1 TGTTATATAAGCGCTACCTAATA
65141 TGTTAT
1 TGTTAT
65147 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (23 bp):
TGTTATATAAGCGCTACCTAATA
Found at i:77274 original size:3 final size:3
Alignment explanation
Indices: 77257--77316 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
77247 GTAAAAAATG
* *
77257 ATA ATA AAA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTAA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
77304 ATA TTA ATA ATA A
1 ATA ATA ATA ATA A
77317 CCCGAACAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 45 0.92
4 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:79176 original size:24 final size:24
Alignment explanation
Indices: 79120--79180 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
79110 TCCAGAAGCT
*
79120 GAGTCAACTCAGATCGAGTTAACC
1 GAGTCAACTCAGATCGAATTAACC
*
79144 GAGTCAACTCAGATCGAATTGAATC
1 GAGTCAACTCAGATCGAATT-AACC
*
79169 -AGTTAACTCAGA
1 GAGTCAACTCAGA
79181 CCAGGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (24 bp):
GAGTCAACTCAGATCGAATTAACC
Found at i:81340 original size:28 final size:28
Alignment explanation
Indices: 81307--81363 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
81297 AGATATGAAA
81307 TTGGAATATGTTACCCGCTCTATGAACC
1 TTGGAATATGTTACCCGCTCTATGAACC
81335 TTGGAATATGTTACCCGCTCTATGAACC
1 TTGGAATATGTTACCCGCTCTATGAACC
81363 T
1 T
81364 AACATTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (28 bp):
TTGGAATATGTTACCCGCTCTATGAACC
Found at i:99192 original size:19 final size:20
Alignment explanation
Indices: 99170--99210 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
99160 TTTAAATAGT
*
99170 AATAAAAACGATT-AAATAA
1 AATAAAAACAATTAAAATAA
*
99189 AATAAAAGCAATTAAAATAA
1 AATAAAAACAATTAAAATAA
99209 AA
1 AA
99211 ATAAGAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.20
Consensus pattern (20 bp):
AATAAAAACAATTAAAATAA
Found at i:106485 original size:20 final size:20
Alignment explanation
Indices: 106457--106506 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
106447 TTAAAATCAA
*
106457 TATCAATACCAC-CCTACGAG
1 TATCGATACCACACCTAC-AG
106477 TATCGATACCACACCTACAG
1 TATCGATACCACACCTACAG
*
106497 TATGGATACC
1 TATCGATACC
106507 CATTGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (20 bp):
TATCGATACCACACCTACAG
Found at i:110205 original size:20 final size:19
Alignment explanation
Indices: 110177--110226 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
110167 TTTTTCTAGA
* *
110177 TTTAATTTTTCACAATCACT
1 TTTACTTTTTCAAAAT-ACT
*
110197 TTTACTTTTTTGAAAATACT
1 TTTAC-TTTTTCAAAATACT
110217 TTTACTTTTT
1 TTTACTTTTT
110227 TACATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 12 0.46
21 9 0.35
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTACTTTTTCAAAATACT
Found at i:120571 original size:24 final size:24
Alignment explanation
Indices: 120544--120593 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
120534 ATCTATGTTT
*
120544 CACTTCGGTGCATATTCTACGTGG
1 CACTTCGGTGCAAATTCTACGTGG
120568 CACTTCGGTGCAAATTCTACGTGG
1 CACTTCGGTGCAAATTCTACGTGG
120592 CA
1 CA
120594 GTTTCAACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (24 bp):
CACTTCGGTGCAAATTCTACGTGG
Found at i:121533 original size:15 final size:15
Alignment explanation
Indices: 121513--121542 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
121503 AGTATTGTTT
121513 CAGGACGTTGGATGC
1 CAGGACGTTGGATGC
121528 CAGGACGTTGGATGC
1 CAGGACGTTGGATGC
121543 GATTCTGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (15 bp):
CAGGACGTTGGATGC
Found at i:129949 original size:24 final size:24
Alignment explanation
Indices: 129901--129973 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 24
129891 TGTCATATAA
* * **
129901 AATTTGTCGCGAAGGACCATGTAG
1 AATTTATCCCGAAGGACCACATAG
129925 AATTTATCCCGAAGGACCACATAG
1 AATTTATCCCGAAGGACCACATAG
* * *
129949 -ATTTATCCTGAATGACCGCATAG
1 AATTTATCCCGAAGGACCACATAG
129972 AA
1 AA
129974 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
AATTTATCCCGAAGGACCACATAG
Found at i:129956 original size:23 final size:23
Alignment explanation
Indices: 129910--129972 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
129900 AAATTTGTCG
**
129910 CGAAGGACCATGTAGAATTTATCC
1 CGAAGGACCACATAG-ATTTATCC
129934 CGAAGGACCACATAGATTTATCC
1 CGAAGGACCACATAGATTTATCC
* * *
129957 TGAATGACCGCATAGA
1 CGAAGGACCACATAGA
129973 ACCCTCGACT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (23 bp):
CGAAGGACCACATAGATTTATCC
Found at i:130021 original size:21 final size:21
Alignment explanation
Indices: 129997--130045 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
129987 GCATGCCAAC
129997 TATACCTCTAATTCTCATACA
1 TATACCTCTAATTCTCATACA
130018 TATACCTCTAATTCTCATACA
1 TATACCTCTAATTCTCATACA
130039 TATACCT
1 TATACCT
130046 TAAGATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.39
Consensus pattern (21 bp):
TATACCTCTAATTCTCATACA
Found at i:135876 original size:37 final size:36
Alignment explanation
Indices: 135801--135876 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
135791 TTTTTATATT
*
135801 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
135837 TTTATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
135874 TTT
1 TTT
135877 TTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 25 0.74
37 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:136058 original size:20 final size:20
Alignment explanation
Indices: 136022--136059 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
136012 ATCCTATTCC
**
136022 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
136042 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
136060 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:136425 original size:30 final size:30
Alignment explanation
Indices: 136389--136453 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
136379 TTAACTTATC
*
136389 ATATATTATATTCTTAAATTAAATCATTAA
1 ATATATTATAGTCTTAAATTAAATCATTAA
** *
136419 ATATATTATAGTCTTACCTTAAATTATTAA
1 ATATATTATAGTCTTAAATTAAATCATTAA
136449 ATATA
1 ATATA
136454 ATTTATCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (30 bp):
ATATATTATAGTCTTAAATTAAATCATTAA
Found at i:136489 original size:30 final size:31
Alignment explanation
Indices: 136437--136520 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 31
136427 TAGTCTTACC
*
136437 TTAAATTATTAAATATA-A-TTTATCCTTA-TT
1 TTAAATTA--AAATATATATTTTATCATTATTT
*
136467 TTAACA-TAAAATATATATTTTATTATTATTT
1 TTAA-ATTAAAATATATATTTTATCATTATTT
*
136498 TTAAATTAAAATTTATATTTTAT
1 TTAAATTAAAATATATATTTTAT
136521 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 7 0.15
29 1 0.02
30 15 0.33
31 23 0.50
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (31 bp):
TTAAATTAAAATATATATTTTATCATTATTT
Found at i:136528 original size:25 final size:25
Alignment explanation
Indices: 136474--136534 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
136464 ATTTTAACAT
* * *
136474 AAAATATATATTTTATTATTATTTT
1 AAAATAAAAATTTTATTATTATTTA
* *
136499 TAAATTAAAATTTATATT-TTATTTA
1 AAAATAAAAATTT-TATTATTATTTA
136524 AAAATAAAAAT
1 AAAATAAAAAT
136535 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAATAAAAATTTTATTATTATTTA
Found at i:136532 original size:5 final size:6
Alignment explanation
Indices: 136522--136547 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
136512 ATATTTTATT
136522 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
136548 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:136687 original size:31 final size:30
Alignment explanation
Indices: 136580--136697 Score: 113
Period size: 31 Copynumber: 4.0 Consensus size: 30
136570 TTAAAATATT
* *
136580 ATAAGAATAAAATATAAATATTTAAGTTAA
1 ATAAGAATAAAATATATATTTTTAAGTTAA
* *
136610 GGTAAGAAT-AAAT-TAT-TTTTTAA-TTTA
1 -ATAAGAATAAAATATATATTTTTAAGTTAA
*
136637 ATAA-ATATTAAA-ATATATTTTTAAGTTAA
1 ATAAGA-ATAAAATATATATTTTTAAGTTAA
136666 ATTAAGAATAAAATATATATTTTTAATGTTAA
1 A-TAAGAATAAAATATATATTTTTAA-GTTAA
136698 GATGTTAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
25 1 0.01
26 5 0.07
27 9 0.13
28 13 0.18
29 6 0.08
30 12 0.17
31 20 0.28
32 5 0.07
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (30 bp):
ATAAGAATAAAATATATATTTTTAAGTTAA
Found at i:136720 original size:18 final size:18
Alignment explanation
Indices: 136687--136733 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
136677 AATATATATT
*
136687 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
136706 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
136724 TTTAAGTTAA
1 TTTAATTTAA
136734 AAATTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:137439 original size:25 final size:26
Alignment explanation
Indices: 137403--137456 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
137393 CGCGAGCAAC
* *
137403 TAAAAAATATAATTTATTAA-AAAAT
1 TAAAAAAAATAAATTATTAATAAAAT
*
137428 TAAAAAAAATAAATTATTAATAATAT
1 TAAAAAAAATAAATTATTAATAAAAT
137454 TAA
1 TAA
137457 TATTTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAAAAAATAAATTATTAATAAAAT
Found at i:144183 original size:58 final size:57
Alignment explanation
Indices: 143994--144207 Score: 155
Period size: 58 Copynumber: 3.7 Consensus size: 57
143984 AAACAAAATA
* ** * * **** *
143994 ATACAAGATTCTATGAAAATAAATTTAACAATTTATTTCCTTCTACAAAATGGAATT
1 ATACAAGATTCTAAGAAAATAAATTTAATGATTTATTTACTTTTACAATCCAGAATC
* * * * *
144051 GTTCAAGATTTCTAAGAAAATAAATTTGATGTTTTATTTTCTTTTACAATCCAGAATC
1 ATACAAGA-TTCTAAGAAAATAAATTTAATGATTTATTTACTTTTACAATCCAGAATC
* * *
144109 ATATAAGATTCATAAGAAAAAAAATTTAATGATTTATTTACTTTT-CAAAGT-TAGAATC
1 ATACAAGATTC-TAAGAAAATAAATTTAATGATTTATTTACTTTTAC-AA-TCCAGAATC
* *
144167 A-ACGCAAGATTCTAAGATGAAATAAATTCAATAATTTATTT
1 ATA--CAAGATTCTAAGA--AAATAAATTTAATGATTTATTT
144208 CTCTTTTCCA
Statistics
Matches: 123, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
57 11 0.09
58 85 0.69
59 8 0.07
60 19 0.15
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (57 bp):
ATACAAGATTCTAAGAAAATAAATTTAATGATTTATTTACTTTTACAATCCAGAATC
Found at i:145077 original size:157 final size:157
Alignment explanation
Indices: 144756--145427 Score: 757
Period size: 157 Copynumber: 4.3 Consensus size: 157
144746 GGTATATGAG
* * * *
144756 CATGTGGTTCAAATTTGGTAAAAACATACTTAAAAT-AAGGATGAATTAAAGAAATAAGGAATTT
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
* * * * *
144820 ATGAAAAAA-TGAGGGACTAAATTGAAAAATAG-AAATTTCATTATAAAAAAGA-G-TTTGAAAA
66 AT-AAAAAATTTAAGGACTAAATTGAAAAATAGAAAATTT-GTTATCAAAAAGATGAATTGAAAA
* * *
144881 TACATATGTATTATACGAAGGTTTAGGAA
129 TACATATGTATTCTACGATGATTTAGGAA
*
144910 CATGTAGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
* *
144975 AT-AAAAATTTGAAGGAGTAAATTGGAAAATAGAAAATTTGTTATCAAAAA-ATGGAATTGAAAA
66 ATAAAAAATTT-AAGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAT-GAATTGAAAA
* *
145038 TACATATGTATTCTACGATGTTTTAGGAG
129 TACATATGTATTCTACGATGATTTAGGAA
* * *
145067 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
* *
145132 ATAAAAAAAGTTAAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGAGGAATTGAA
66 AT-AAAAAATTTAA-GGACTAAATTGAAAAATAGAAAATTTGTTATC-AAAA-AGATGAATTGAA
* * * * *
145197 AGTACATATATATTCTACAATGATTTACGAT
127 AATACATATGTATTCTACGATGATTTAGGAA
* *
145228 CATGTGGTTCAAATTTGGTAAAAA-AAGAATTAAAATAAAGGATGAATTGAAAAAATAA-AGAAA
1 CATGTGGTTCAAATTTGGTAAAAACAA-ACTTAAAATAAAGGATGAATTGAAGAAATAAGA-AAA
* * * * *
145291 TTATAAGAAATTTAGGGAGTAAA-T-----A-A-AAAATTTGTTATCAAAAAGATTAATTGAAAG
64 TTATAAAAAATTTAAGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGATGAATTGAAAA
* *
145348 TACATATATATTCTACGATGATTTAAGAA
129 TACATATGTATTCTACGATGATTTAGGAA
* * ** * *
145377 TATGTAGTTCAAATTTAATAAAAACGAACTTAAAATAAAAGATGAATTGAA
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAA
145428 TGAATAATGA
Statistics
Matches: 451, Mismatches: 51, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
149 80 0.18
150 5 0.01
151 13 0.03
152 1 0.00
153 6 0.01
154 36 0.08
155 54 0.12
156 7 0.02
157 95 0.21
158 3 0.01
159 44 0.10
160 13 0.03
161 93 0.21
162 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (157 bp):
CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
ATAAAAAATTTAAGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGATGAATTGAAAATA
CATATGTATTCTACGATGATTTAGGAA
Found at i:145263 original size:161 final size:158
Alignment explanation
Indices: 144756--145440 Score: 739
Period size: 161 Copynumber: 4.4 Consensus size: 158
144746 GGTATATGAG
* * * *
144756 CATGTGGTTCAAATTTGGTAAAAACATACTTAAAAT-AAGGATGAATTAAAGAAATAAGGAATTT
1 CATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
* * *
144820 ATGAAAAAA-TGAGGGACTAAATTGAAAAATAG-AAATTTCATTAT-AAAAAAGA-G-TTTGAAA
66 AT-AAAAAATTAAGGGACTAAATTGAAAAATAGAAAATTT-GTTATCAAAAAAGAGGAATTGAAA
* * * *
144880 ATACATATGTATTATACGAA-GGTTTAGGAA
129 ATACATATATATTCTAC-AATGATTTAGGAT
* *
144910 CATGTAGTTCAAATTTGGTAAAAACAA-ACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAAT
1 CATGTGGTTCAAATTTGGTAAAAA-AAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAAT
* * * *
144974 TATAAAAATTTGAA-GGAGTAAATTGGAAAATAGAAAATTTGTTATCAAAAAA-TGGAATTGAAA
65 TATAAAAAATT-AAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAAGAGGAATTGAAA
* * * *
145037 ATACATATGTATTCTACGATGTTTTAGGAG
129 ATACATATATATTCTACAATGATTTAGGAT
* *
145067 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
1 CATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
145132 ATAAAAAAAGTTAAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGAGGAATTGAA
66 AT-AAAAAA-TTAAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAA-AGAGGAATTGAA
* *
145197 AGTACATATATATTCTACAATGATTTACGAT
128 AATACATATATATTCTACAATGATTTAGGAT
* * *
145228 CATGTGGTTCAAATTTGGTAAAAAAAGAATTAAAATAAAGGATGAATTGAAAAAATAAAGAAATT
1 CATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
* * * ** *
145293 ATAAGAAATTTAGGGAGTAAA-T-----A-A-AAAATTTGTTATC-AAAAAGATTAATTGAAAGT
66 ATAAAAAATTAAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAAGAGGAATTGAAAAT
* *
145349 ACATATATATTCTACGATGATTTAAGAAT
131 ACATATATATTCTACAATGATTT-AGGAT
* ** * * *
145378 -ATGTAGTTCAAATTTAAT-AAAAACGAACTTAAAATAAAAGATGAATTGAATG-AATAATGAAA
1 CATGTGGTTCAAATTTGGTAAAAAAAG-ACTTAAAATAAAGGATGAATTGAA-GAAATAAGGAAA
145440 T
64 T
145441 AAGGGACCAA
Statistics
Matches: 462, Mismatches: 51, Indels: 41
0.83 0.09 0.07
Matches are distributed among these distances:
148 6 0.01
149 82 0.18
150 7 0.02
151 13 0.03
152 1 0.00
153 1 0.00
154 37 0.08
155 50 0.11
156 16 0.03
157 91 0.20
158 8 0.02
159 48 0.10
160 6 0.01
161 96 0.21
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (158 bp):
CATGTGGTTCAAATTTGGTAAAAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
ATAAAAAATTAAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAAGAGGAATTGAAAAT
ACATATATATTCTACAATGATTTAGGAT
Found at i:145410 original size:310 final size:308
Alignment explanation
Indices: 144756--145440 Score: 856
Period size: 310 Copynumber: 2.2 Consensus size: 308
144746 GGTATATGAG
* * * *
144756 CATGTGGTTCAAATTTGGTAAAAACATACTTAAAAT-AAGGATGAATTAAAGAAATAAGGAATTT
1 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
* * *
144820 ATGAAAAAATGAGGGACTAAATTGAAAAATAGAAATTTCATTATAAAAAAGAGTTTGAAAATACA
66 ATAAAAAAATAAGGGACTAAATTGAAAAATAGAAATTTCATTATAAAAAAGAGATTGAAAATACA
* * * *
144885 TATGTATTATACGAAGGTTTAGGAACATGTAGTTCAAATTTGGTAAAAACAAACTTAAAATAAAG
131 TATATATTATACGAAGATTTACGAACATGTAGTTCAAATTTGGTAAAAACAAAATTAAAATAAAG
*
144950 GATGAATTGAAGAAATAAGAAAATTATAAAAATTTGAAGGAGTAAATTGGAAAATAGAAAATTTG
196 GATGAATTGAAAAAATAAGAAAATTATAAAAATTTGAAGGAGTAAATT----AATAGAAAATTTG
* * * *
145015 TTATCAAAAAATGGAATTGAAAATACATATGTATTCTACGATGTTTTAGGAG
257 TTATCAAAAAATGGAATTGAAAATACATATATATTCTACGATGATTTAAGAA
145067 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
1 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
*
145132 ATAAAAAAAGTTAAGGGACTAAATTGAAAAATAGAAAATTT-GTTATCAAAAAGAGAGGAATTGA
66 ATAAAAAAA--TAAGGGACTAAATTGAAAAATAG-AAATTTCATTAT-AAAAA-AGA-G-ATTGA
* * * *
145196 AAGTACATATATATTCTAC-AATGATTTACGATCATGTGGTTCAAATTTGGTAAAAA-AAGAATT
124 AAATACATATATATTATACGAA-GATTTACGAACATGTAGTTCAAATTTGGTAAAAACAA-AATT
*
145259 AAAATAAAGGATGAATTGAAAAAATAA-AGAAATTATAAGAAATTT-AGGGAGTAAA-T-A-A-A
187 AAAATAAAGGATGAATTGAAAAAATAAGA-AAATTATAA-AAATTTGAAGGAGTAAATTAATAGA
* *
145318 AAATTTGTTATCAAAAAGAT-TAATTGAAAGTACATATATATTCTACGATGATTTAAGAA
250 AAATTTGTTATCAAAAA-ATGGAATTGAAAATACATATATATTCTACGATGATTTAAGAA
* * * * *
145377 TATGTAGTTCAAATTTAATAAAAAC-GAACTTAAAATAAAAGATGAATTGAATG-AATAATGAAA
1 CATGTGGTTCAAATTTGATAAAAACAG-ACTTAAAATAAAGGATGAATTGAA-GAAATAAGGAAA
145440 T
64 T
145441 AAGGGACCAA
Statistics
Matches: 330, Mismatches: 29, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
309 1 0.00
310 106 0.32
311 38 0.12
312 35 0.11
314 26 0.08
315 11 0.03
316 3 0.01
317 7 0.02
318 97 0.29
319 6 0.02
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (308 bp):
CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATT
ATAAAAAAATAAGGGACTAAATTGAAAAATAGAAATTTCATTATAAAAAAGAGATTGAAAATACA
TATATATTATACGAAGATTTACGAACATGTAGTTCAAATTTGGTAAAAACAAAATTAAAATAAAG
GATGAATTGAAAAAATAAGAAAATTATAAAAATTTGAAGGAGTAAATTAATAGAAAATTTGTTAT
CAAAAAATGGAATTGAAAATACATATATATTCTACGATGATTTAAGAA
Found at i:152201 original size:19 final size:19
Alignment explanation
Indices: 152177--152213 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
152167 ATCATAAAAT
*
152177 TTATAATTACAATTTGAAC
1 TTATAATCACAATTTGAAC
152196 TTATAATCACAATTTGAA
1 TTATAATCACAATTTGAA
152214 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATAATCACAATTTGAAC
Found at i:152268 original size:16 final size:18
Alignment explanation
Indices: 152236--152282 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
152226 TTTCTATTTT
152236 ATAAAAATAAA-AGAT-A
1 ATAAAAATAAATAGATAA
152252 ATAAAAATAAATA-ATAA
1 ATAAAAATAAATAGATAA
152269 ATAGAAAATCAAAT
1 ATA-AAAAT-AAAT
152283 CAAGTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 13 0.48
17 5 0.19
18 5 0.19
19 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (18 bp):
ATAAAAATAAATAGATAA
Found at i:152335 original size:117 final size:116
Alignment explanation
Indices: 152095--152314 Score: 316
Period size: 117 Copynumber: 1.8 Consensus size: 116
152085 ACCGAAAACA
152095 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAATAATAAATAGAAAAATCAAA
1 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAATAATAAATAGAAAAATCAAA
* *
152160 TCAAATAATCATAAAATTTATAATTACAATTTGAACTTATAATCACAATTTG
66 TCAAATAATCATAAAATTTATAATTAAAATATGAACTTATAATCACAA-TTG
* *
152212 AAATTTATTTTAAATTTCTATTTTATAAAAATAAAAGATAATAAAAATAAATAATAAATAG-AAA
1 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAG---AT---AATAAATAATAAATAGAAAA
*
152276 ATCAAATCAAGTAATCATAAAATTTATAATTATAAATAT
60 ATCAAATCAAATAATCATAAAATTTATAATTA-AAATAT
152315 ATTTTAAATA
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
117 35 0.38
120 2 0.02
122 34 0.37
123 20 0.22
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (116 bp):
AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAATAATAAATAGAAAAATCAAA
TCAAATAATCATAAAATTTATAATTAAAATATGAACTTATAATCACAATTG
Found at i:153148 original size:3 final size:3
Alignment explanation
Indices: 153140--153194 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
153130 TATTATATTA
153140 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
153188 AAT AAT A
1 AAT AAT A
153195 TAAAATGTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:153713 original size:16 final size:19
Alignment explanation
Indices: 153693--153734 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 19
153683 AATAACGTAA
153693 ATAAAATATA-TTAT-ATT
1 ATAAAATATATTTATAATT
153710 -TAAAATATATTTATAATT
1 ATAAAATATATTTATAATT
153728 ATAAAAT
1 ATAAAAT
153735 GGTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 3 0.14
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATATATTTATAATT
Found at i:153833 original size:14 final size:12
Alignment explanation
Indices: 153803--153827 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
153793 TATACAATTG
153803 AAATTTTAAAAT
1 AAATTTTAAAAT
153815 AAATTTTAAAAT
1 AAATTTTAAAAT
153827 A
1 A
153828 TAAATTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTTAAAAT
Found at i:160957 original size:39 final size:39
Alignment explanation
Indices: 160883--160957 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
160873 TTTTAGGGAC
* *
160883 CAAAGATGAAATTCTCATATGCACAATTTGGCCACCTAT
1 CAAAGATGAAATTCTCATATGCACAAGTTGACCACCTAT
* * *
160922 CAAAGATG-AATTTTCAATGTGTACAAGTTGACCACC
1 CAAAGATGAAATTCTC-ATATGCACAAGTTGACCACC
160958 AACCAACTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 6 0.20
39 24 0.80
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (39 bp):
CAAAGATGAAATTCTCATATGCACAAGTTGACCACCTAT
Found at i:160982 original size:17 final size:17
Alignment explanation
Indices: 160960--160993 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
160950 TGACCACCAA
*
160960 CCAACTTGTCAACTTTG
1 CCAACTTGTCAAATTTG
160977 CCAACTTGTCAAATTTG
1 CCAACTTGTCAAATTTG
160994 ACAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (17 bp):
CCAACTTGTCAAATTTG
Found at i:164305 original size:19 final size:19
Alignment explanation
Indices: 164281--164318 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
164271 TTATATGTGT
164281 GACACGTGTCAGGTAACAA
1 GACACGTGTCAGGTAACAA
*
164300 GACACGTGTTAGGTAACAA
1 GACACGTGTCAGGTAACAA
164319 CCAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (19 bp):
GACACGTGTCAGGTAACAA
Found at i:169092 original size:15 final size:17
Alignment explanation
Indices: 169061--169094 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
169051 GGTATCGCAG
169061 AACGAATTTTGTCTTAA
1 AACGAATTTTGTCTTAA
169078 AACG-ATTTT-TCTTAA
1 AACGAATTTTGTCTTAA
169093 AA
1 AA
169095 TTGTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 5 0.29
17 4 0.24
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (17 bp):
AACGAATTTTGTCTTAA
Done.