Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1335844 original size:128 final size:127
Alignment explanation
Indices: 1335458--1335844 Score: 428
Period size: 128 Copynumber: 3.0 Consensus size: 127
1335448 AAAAAATGTT
* * * * * * *
1335458 GCAATAGGTCAAGATCTATAACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCGATATCTATAAC
1 GCAAAAGGTCGAGATCTATAGCAGCGTTTTTAGAACAAACGCTGCAAAAGGTCGAGATCTATAGC
* * * *
1335523 GGCGCTTTTGGAACAAAC-GC-TACAAAAGGTC-GATATCTATAACGGC-ATTTTGGAACAAACA
66 GGCG-TTTTGGAACAAACAACGT--AAAAGGTCAGAT-T-TATAGCGGCGTTTTTTGAACAAA-A
1335584 -CC
125 GCC
* * * *
1335586 ACAAATGGTCGAGATCTATAGTAGCGTTTTTGGAACAAACG-TCGCAAAAGGTCGAGATCTATAG
1 GCAAAAGGTCGAGATCTATAGCAGCGTTTTTAGAACAAACGCT-GCAAAAGGTCGAGATCTATAG
* * * * *
1335650 CGGCATTTTTGGAACAATCACCGTAAAAGGTCAGATCTATAGCGGCGTTTTTTGGAACAAACGCC
65 CGGC-GTTTTGGAACAAACAACGTAAAAGGTCAGATTTATAGCGGCGTTTTTT-GAACAAAAGCC
*
1335715 GCAAAAGGTCGAGATCTATAGCAGCATTTTTAGAACAAACGCTGCAAAAGGTC-AGATCTATAGC
1 GCAAAAGGTCGAGATCTATAGCAGCGTTTTTAGAACAAACGCTGCAAAAGGTCGAGATCTATAGC
*
1335779 GGCGTTCTTGAAACAAACAACGTAAAAGGTCAGATTTATAGCGGCGTTTTTTGATACAAAAGCC
66 GGCGTT-TTGGAACAAACAACGTAAAAGGTCAGATTTATAGCGGCGTTTTTTGA-ACAAAAGCC
1335843 GC
1 GC
1335845 TAATTTCCTT
Statistics
Matches: 218, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
127 12 0.06
128 145 0.67
129 59 0.27
130 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (127 bp):
GCAAAAGGTCGAGATCTATAGCAGCGTTTTTAGAACAAACGCTGCAAAAGGTCGAGATCTATAGC
GGCGTTTTGGAACAAACAACGTAAAAGGTCAGATTTATAGCGGCGTTTTTTGAACAAAAGCC
Found at i:1338762 original size:21 final size:21
Alignment explanation
Indices: 1338737--1338777 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1338727 ATTGAGCCTT
1338737 GAGGAGAAACGACGGTGATCG
1 GAGGAGAAACGACGGTGATCG
** *
1338758 GAGGAGCGACGATGGTGATC
1 GAGGAGAAACGACGGTGATC
1338778 AGGCGCTGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.44, T:0.12
Consensus pattern (21 bp):
GAGGAGAAACGACGGTGATCG
Found at i:1339259 original size:81 final size:82
Alignment explanation
Indices: 1339025--1339320 Score: 211
Period size: 81 Copynumber: 3.7 Consensus size: 82
1339015 ACATTTGTTG
* * * * * ** * *
1339025 AAAAATGCCACTATAGATGAACCCTATTACGACATTTTTATACAAATACCACT-AA-TAGT--CT
1 AAAAACGCCACTATAGATGAAACCTATTGCGGCATTTTTATAAAAACGCCGCTAAAGTAATACCT
* * *
1339086 TTTTAGGCGTTTGTTGA
66 TGTCAGGCGTTTATTGA
* * *
1339103 AAAAATGCCACTATAGTTGAAACCTATTGCGGCATTTTTATACAAACGCCGCTAAAGTAATACCT
1 AAAAACGCCACTATAGATGAAACCTATTGCGGCATTTTTATAAAAACGCCGCTAAAGTAATACCT
1339168 TGTCATGGCGTTTATTG-
66 TGTCA-GGCGTTTATTGA
* * *
1339185 AGAAACGCCACTATGGATG-AACCTATTGTGGC-TTTTGTATAAAAACGCCGCTAAAGTACA-AC
1 AAAAACGCCACTATAGATGAAACCTATTGCGGCATTTT-TATAAAAACGCCGCTAAAGTA-ATAC
* *
1339247 TCTAT-TGC-GGCGTTTTTTTA
64 -CT-TGT-CAGGCGTTTATTGA
* * * * * * *
1339267 AAAAA-ACCACTATAGAT-TACCCAATTACGACATTTTTATACAAACGCCGCTAAA
1 AAAAACGCCACTATAGATGAAACCTATTGCGGCATTTTTATAAAAACGCCGCTAAA
1339321 CTACAACTCT
Statistics
Matches: 177, Mismatches: 28, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
78 46 0.26
79 2 0.01
80 7 0.04
81 78 0.44
82 32 0.18
83 12 0.07
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (82 bp):
AAAAACGCCACTATAGATGAAACCTATTGCGGCATTTTTATAAAAACGCCGCTAAAGTAATACCT
TGTCAGGCGTTTATTGA
Found at i:1342854 original size:47 final size:48
Alignment explanation
Indices: 1342816--1343046 Score: 195
Period size: 47 Copynumber: 5.0 Consensus size: 48
1342806 TGCATGCATG
*
1342816 TATAATTTATTAATGCATGTAT-CATGTATGTGTGATATGTATGTATA
1 TATAATTTATTAATGCATGTATGCATGTATGTATGATATGTATGTATA
* * *
1342863 TATAATTTATTAAAGCACGCATGCATAG-ATGTATG-TATGTATG-ATA
1 TATAATTTATTAATGCATGTATGCAT-GTATGTATGATATGTATGTATA
* * *
1342909 TGTATATATCATTAAT--A-GTATGTATGTATGTATG--A--TATGTATA
1 TATA-AT-TTATTAATGCATGTATGCATGTATGTATGATATGTATGTATA
*
1342952 TATAATTTATTAATGCATGTAT-CATGTATGTATGATACATGTATATATA
1 TATAATTTATTAATGCATGTATGCATGTATGTATGAT--ATGTATGTATA
* * *
1343001 TAT-ATGT-TTAATCGAATGTATGATATGTATGTATG-TATGTATGTAT
1 TATAATTTATTAAT-GCATGTATG-CATGTATGTATGATATGTATGTAT
1343047 GTATGTATCA
Statistics
Matches: 149, Mismatches: 17, Indels: 36
0.74 0.08 0.18
Matches are distributed among these distances:
41 7 0.05
42 6 0.04
43 18 0.12
44 6 0.04
45 13 0.09
46 7 0.05
47 44 0.30
48 25 0.17
49 12 0.08
50 11 0.07
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (48 bp):
TATAATTTATTAATGCATGTATGCATGTATGTATGATATGTATGTATA
Found at i:1342898 original size:4 final size:4
Alignment explanation
Indices: 1342891--1343066 Score: 87
Period size: 4 Copynumber: 43.8 Consensus size: 4
1342881 GCATGCATAG
* *
1342891 ATGT ATGT ATGT ATGAT ATGT ATAT AT-C AT-T AATAGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATG-T ATGT ATGT ATGT ATGT -AT-GT ATGT ATGT ATGT
* * * * *
1342940 ATGAT ATGT ATAT AT-A ATTT AT-T AATGC ATGT AT-C ATGT ATGT ATG-
1 ATG-T ATGT ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT ATGT ATGT
** * * * * * *
1342986 ATAC ATGT ATAT ATAT ATAT GTTT AATCGA ATGT ATGAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT -AT-GT ATGT ATG-T ATGT ATGT ATGT
*
1343037 ATGT ATGT ATGT ATGT AT-C ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1343067 CATAATTTAT
Statistics
Matches: 136, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
3 11 0.08
4 107 0.79
5 17 0.12
6 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:1343872 original size:108 final size:109
Alignment explanation
Indices: 1343679--1343901 Score: 385
Period size: 108 Copynumber: 2.1 Consensus size: 109
1343669 CTTTTTTTGT
* *
1343679 AATTTACTCCAATATAAATCACATCATAAACTCCATTTCAAACCCTATAAATTATATCATAATCT
1 AATTTACTCCAATATAAATCACATCATAAACTCCATATCAAACCCTATAAATTACATCATAATCT
*
1343744 TCAAACCCTATAAACATTTGTTCACCAACTTTGTAAATGAATTC
66 TCAAACCCTATAAACATTTGTTCACCAACTTTGTAAATGAATGC
1343788 AATTTACTCCAATATAAATCACATCAT-AACTCCATATCAAACCCTATAAATTACATCATAATCT
1 AATTTACTCCAATATAAATCACATCATAAACTCCATATCAAACCCTATAAATTACATCATAATCT
* * *
1343852 TCAAACCCTGTAAACTTTTGTTGACCAACTTTGTAAATGAATGC
66 TCAAACCCTATAAACATTTGTTCACCAACTTTGTAAATGAATGC
1343896 AATTTA
1 AATTTA
1343902 GTCTATTTTT
Statistics
Matches: 108, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 81 0.75
109 27 0.25
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (109 bp):
AATTTACTCCAATATAAATCACATCATAAACTCCATATCAAACCCTATAAATTACATCATAATCT
TCAAACCCTATAAACATTTGTTCACCAACTTTGTAAATGAATGC
Found at i:1345202 original size:128 final size:128
Alignment explanation
Indices: 1344974--1345229 Score: 496
Period size: 128 Copynumber: 2.0 Consensus size: 128
1344964 TTCTTAATGC
1344974 CTTTCATCAGTACCCGCTTATCATGGTTCTTCATGGTGGCTGGCTTTTGATAGCAGGTAAAAAGC
1 CTTTCATCAGTACCCGCTTATCATGGTTCTTCATGGTGGCTGGCTTTTGATAGCAGGTAAAAAGC
1345039 AGATTTGATCCCAAAAAAAATGGGGGGGGGGGGGGGCACACCCAAATATGTTTTCTAAAGCTG
66 AGATTTGATCCCAAAAAAAATGGGGGGGGGGGGGGGCACACCCAAATATGTTTTCTAAAGCTG
1345102 CTTTCATCAGTACCCGCTTATCATGGTTCTTCATGGTGGCTGGCTTTTGATAGCAGGTAAAAAGC
1 CTTTCATCAGTACCCGCTTATCATGGTTCTTCATGGTGGCTGGCTTTTGATAGCAGGTAAAAAGC
1345167 AGATTTGATCCC-AAAAAAATGGGGGGGGGGGGGGGGCACACCCAAATATGTTTTCTAAAGCTG
66 AGATTTGATCCCAAAAAAAAT-GGGGGGGGGGGGGGGCACACCCAAATATGTTTTCTAAAGCTG
1345230 TTTGTGAGAT
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
127 8 0.06
128 119 0.94
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (128 bp):
CTTTCATCAGTACCCGCTTATCATGGTTCTTCATGGTGGCTGGCTTTTGATAGCAGGTAAAAAGC
AGATTTGATCCCAAAAAAAATGGGGGGGGGGGGGGGCACACCCAAATATGTTTTCTAAAGCTG
Found at i:1346526 original size:18 final size:18
Alignment explanation
Indices: 1346492--1346542 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1346482 TTAATAAATC
*
1346492 AAATATTAATGATTATAA
1 AAATATTAATCATTATAA
*
1346510 AAATATT-ATCATATATAT
1 AAATATTAATCAT-TATAA
* *
1346528 ATATATTAATTATTA
1 AAATATTAATCATTA
1346543 AACAGACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATATTAATCATTATAA
Found at i:1350593 original size:35 final size:35
Alignment explanation
Indices: 1350554--1350640 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 35
1350544 GTGTTAAAAG
*
1350554 TTTCAAAGTTTGGTAA-CCAACTTTGGAAAATGTTT
1 TTTCAAAGTTTGGTAATCCAACTTTGAAAAATG-TT
****
1350589 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGT-AATCCAACTTTGAAAAATGTT
1350625 TTTCAAAGTTTGGTAA
1 TTTCAAAGTTTGGTAA
1350641 AATTTTGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 16 0.36
36 18 0.40
37 11 0.24
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTCAAAGTTTGGTAATCCAACTTTGAAAAATGTT
Found at i:1355027 original size:34 final size:35
Alignment explanation
Indices: 1354984--1355064 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 35
1354974 ATTGTTAAAG
*
1354984 TTTCAAAGTTTGGCAA-CCAACTTTGGAAAATGTT
1 TTTCAAAGTTTGGCAATCCAACTTTGAAAAATGTT
* ****
1355018 TTTCAAAG-TTGGTAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGCAATCCAACTTTGAAAAATGTT
1355052 TTTCAAAGTTTGG
1 TTTCAAAGTTTGG
1355065 TAAATTTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
33 6 0.15
34 29 0.74
35 4 0.10
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.42
Consensus pattern (35 bp):
TTTCAAAGTTTGGCAATCCAACTTTGAAAAATGTT
Found at i:1362678 original size:2 final size:2
Alignment explanation
Indices: 1362671--1362697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1362661 TAACCAAATA
1362671 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1362698 CTCTTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1369862 original size:17 final size:17
Alignment explanation
Indices: 1369839--1369882 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1369829 AATAAAATAC
1369839 ATAAAAAATAA-TTTTA
1 ATAAAAAATAATTTTTA
* *
1369855 TTTAAAAATAATTTTTA
1 ATAAAAAATAATTTTTA
1369872 ATAAAAAATAA
1 ATAAAAAATAA
1369883 AATCTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAAATAATTTTTA
Found at i:1373173 original size:3 final size:3
Alignment explanation
Indices: 1373165--1373201 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1373155 AGAGCATTCT
* *
1373165 TTA TTA TTA TTA TTA TTA TTA ATA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1373202 GTCTGCAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1379716 original size:10 final size:10
Alignment explanation
Indices: 1379701--1379727 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1379691 ATATATTGCA
1379701 GTTCTTTAGT
1 GTTCTTTAGT
1379711 GTTCTTTAGT
1 GTTCTTTAGT
1379721 GTTCTTT
1 GTTCTTT
1379728 TTTTCTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.11, G:0.19, T:0.63
Consensus pattern (10 bp):
GTTCTTTAGT
Found at i:1400421 original size:25 final size:24
Alignment explanation
Indices: 1400392--1400443 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
1400382 AAAAATTTCC
1400392 AAATAAAAGTCATAATTGTTTTT-AA
1 AAATAAAA-T-ATAATTGTTTTTCAA
* *
1400417 AAATAATATTTAATTGTTTTTCAA
1 AAATAAAATATAATTGTTTTTCAA
1400441 AAA
1 AAA
1400444 AATGGTTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.46
24 6 0.25
25 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (24 bp):
AAATAAAATATAATTGTTTTTCAA
Found at i:1410152 original size:22 final size:22
Alignment explanation
Indices: 1410127--1410218 Score: 82
Period size: 23 Copynumber: 4.1 Consensus size: 22
1410117 CACAGCTTGT
1410127 ATAATTTG-CACCGAAGTG-CCAC
1 ATAATTTGTC-CCGAAG-GACCAC
1410149 ATAA-TTGTCCCGAAGGACCAC
1 ATAATTTGTCCCGAAGGACCAC
* *
1410170 ATAATTTTGTCCCGAATGACCAT
1 ATAA-TTTGTCCCGAAGGACCAC
* **
1410193 ATAATTTTGTCTCGAATAACCAC
1 ATAA-TTTGTCCCGAAGGACCAC
1410216 ATA
1 ATA
1410219 GAACCCTCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
20 1 0.02
21 17 0.28
22 5 0.08
23 38 0.62
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (22 bp):
ATAATTTGTCCCGAAGGACCAC
Found at i:1410183 original size:23 final size:23
Alignment explanation
Indices: 1410137--1410218 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
1410127 ATAATTTGCA
1410137 CCGAAGTG-CCACATAA--TTGTC
1 CCGAAG-GACCACATAATTTTGTC
1410158 CCGAAGGACCACATAATTTTGTC
1 CCGAAGGACCACATAATTTTGTC
* *
1410181 CCGAATGACCATATAATTTTGTC
1 CCGAAGGACCACATAATTTTGTC
* **
1410204 TCGAATAACCACATA
1 CCGAAGGACCACATA
1410219 GAACCCTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 14 0.26
23 38 0.72
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (23 bp):
CCGAAGGACCACATAATTTTGTC
Found at i:1416929 original size:19 final size:19
Alignment explanation
Indices: 1416894--1416943 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1416884 ATTGCATTTT
1416894 ATGCATCGATG--CACACC
1 ATGCATCGATGCACACACC
1416911 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
1416930 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1416944 TTAGGCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.35
19 20 0.65
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (19 bp):
ATGCATCGATGCACACACC
Found at i:1416986 original size:80 final size:82
Alignment explanation
Indices: 1416829--1416989 Score: 245
Period size: 80 Copynumber: 2.0 Consensus size: 82
1416819 AATGCAATTT
* * * * * *
1416829 ATGCATCGATGCACTCTCCATGCATCGATTCACTCAGGTTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
1416894 ATGCATCGATGCACACC
66 ATGCATCGATGCACACC
*
1416911 ATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTT-ATCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
1416974 ATGCATCGATGCACAC
66 ATGCATCGATGCACAC
1416990 TTAGTGCACC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 36 0.50
81 2 0.03
82 34 0.47
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (82 bp):
ATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
ATGCATCGATGCACACC
Found at i:1417003 original size:82 final size:83
Alignment explanation
Indices: 1416814--1417006 Score: 250
Period size: 82 Copynumber: 2.3 Consensus size: 83
1416804 AAAAATTGAA
* * * * * *
1416814 CATCGAATGCA-ATTTATGCATCGATGCACTCTCCATGCATCGATTCACTCAGGTTTTAATGAAA
1 CATCG-ATGCACACTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAA
*
1416878 ACATCGATTGCATTTTATG
65 ACATCGAATGCATTTTATG
* *
1416897 CATCGATGCACAC-CATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTT-ATCAAAA
1 CATCGATGCACACTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAA
1416959 CATCGAATGCATTTTATG
66 CATCGAATGCATTTTATG
*
1416977 CATCGATGCACACTTAGTGCACCGATGCAC
1 CATCGATGCACACTTA-TGCATCGATGCAC
1417007 TAAGTGTTCC
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
80 36 0.38
81 3 0.03
82 51 0.53
83 6 0.06
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (83 bp):
CATCGATGCACACTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAAAA
CATCGAATGCATTTTATG
Found at i:1431522 original size:22 final size:22
Alignment explanation
Indices: 1431479--1431558 Score: 117
Period size: 22 Copynumber: 3.6 Consensus size: 22
1431469 ATCGAAGTGT
* *
1431479 CACATAA-TTGTCCCAAAGGAC
1 CACATAATTTGTCCTAAATGAC
1431500 CACATAATTTGTCCTAAATGAC
1 CACATAATTTGTCCTAAATGAC
*
1431522 CACATAATTTGTCCTAAATAAC
1 CACATAATTTGTCCTAAATGAC
1431544 CACATAATTTTGTCC
1 CACATAA-TTTGTCC
1431559 GGAAGGACCA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 7 0.13
22 40 0.74
23 7 0.13
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (22 bp):
CACATAATTTGTCCTAAATGAC
Found at i:1436706 original size:35 final size:35
Alignment explanation
Indices: 1436660--1436731 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1436650 CCAAAAAAGA
1436660 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
*
1436695 AGAGTTGGATTAGGACTCAAATATTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1436730 AG
1 AG
1436732 GGTTTTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:1437132 original size:17 final size:18
Alignment explanation
Indices: 1437106--1437145 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1437096 ATTATATGGA
1437106 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
1437122 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
1437140 TATTAT
1 TATTAT
1437146 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:1437409 original size:2 final size:2
Alignment explanation
Indices: 1437404--1437444 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1437394 CTTATAACTT
1437404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1437445 TATTTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1437516 original size:41 final size:42
Alignment explanation
Indices: 1437436--1437521 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
1437426 TATATATATA
* * *
1437436 TATATATATTATTTTTTAATATTTTCGTTTTTTATTCATTAT
1 TATATATATTATTTTTTAAAATCTTCGTTCTTTATTCATTAT
1437478 TATATATA-TATTTTTTAAAAATCTT-GTGTCTTTA-TCATTAT
1 TATATATATTATTTTTT-AAAATCTTCGT-TCTTTATTCATTAT
1437519 TAT
1 TAT
1437522 TATTAAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (42 bp):
TATATATATTATTTTTTAAAATCTTCGTTCTTTATTCATTAT
Found at i:1445981 original size:106 final size:106
Alignment explanation
Indices: 1445791--1446558 Score: 1022
Period size: 106 Copynumber: 7.4 Consensus size: 106
1445781 GATTTTAGCT
** * *
1445791 AGAGTCAATTTCAACTTCACAGTAAAGGATATTGGATTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* *
1445856 CGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * * *
1445897 AGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
** *
1445962 TAAAGGGACGGTTGGTTGTCAACAAATAATTTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* *
1446003 AGAGTTAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
1446068 CGAAGGGACAGCTAGTTGTCAACAAATAATCTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
1446109 AGAG-C-----CAA--T---AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
*
1446163 CGAAGGGACGGTTGGTTGTCAACAAATAATTTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* *
1446204 AGGGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC--CACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1446267 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * * **
1446308 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTTGAGATGACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
1446373 CGAATGGACGGCAGGTTGTCAATAAATAATTTCCCAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * * * * * *
1446414 AGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * * * * * *
1446479 CGAAGGGGCGGTTGGCTGCCAACAAACAATTTTCCAGTTCC
66 CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
* * *
1446520 AGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1446559 AGAACAATAC
Statistics
Matches: 577, Mismatches: 72, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
95 84 0.15
96 1 0.00
98 1 0.00
100 3 0.01
101 3 0.01
103 1 0.00
104 97 0.17
106 387 0.67
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (106 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTC
Found at i:1447135 original size:35 final size:35
Alignment explanation
Indices: 1447043--1447114 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1447033 CCAAAAAAGA
1447043 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1447078 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1447113 AG
1 AG
1447115 GGTTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:1447515 original size:17 final size:18
Alignment explanation
Indices: 1447489--1447528 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1447479 ATTATATGGA
1447489 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
1447505 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
1447523 TATTAT
1 TATTAT
1447529 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:1448091 original size:2 final size:2
Alignment explanation
Indices: 1448084--1448132 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1448074 TACTTTGATG
1448084 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1448126 TA TA TA T
1 TA TA TA T
1448133 TCCTTTTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1448205 original size:9 final size:9
Alignment explanation
Indices: 1448184--1448235 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
1448174 TTTTTTTTTC
1448184 TTTATCTTA-
1 TTTAT-TTAT
1448193 TTTATTTAT
1 TTTATTTAT
1448202 TTTATTTAT
1 TTTATTTAT
1448211 TTTATTT-T
1 TTTATTTAT
*
1448219 TTTCCTTTTAT
1 TTT--ATTTAT
1448230 TTTATT
1 TTTATT
1448236 CTCTTTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 23 0.62
10 3 0.08
11 4 0.11
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1448216 original size:5 final size:5
Alignment explanation
Indices: 1448172--1448235 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
1448162 ATTACTTTAC
*
1448172 TATTT T-TTT T-TCTT TATCT TA-TT TA-TT TATTT TA-TT TATTT TATTT
1 TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
**
1448218 T-TTT CCTTT TATTT TATT
1 TATTT TATTT TATTT TATT
1448236 CTCTTTATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
4 19 0.39
5 29 0.59
6 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:1448242 original size:14 final size:13
Alignment explanation
Indices: 1448175--1448250 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 13
1448165 ACTTTACTAT
*
1448175 TTTTTTTTCTTTA
1 TTTTATTTCTTTA
* *
1448188 TCTTATTTATTTA
1 TTTTATTTCTTTA
*
1448201 TTTTATTTATTTTA
1 TTTTATTT-CTTTA
1448215 TTTT-TTTCCTTTTA
1 TTTTATTT-C-TTTA
1448229 TTTTATTCTCTTTA
1 TTTTATT-TCTTTA
*
1448243 TCTTATTT
1 TTTTATTT
1448251 GTTTTCTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 21 0.41
14 26 0.51
15 3 0.06
16 1 0.02
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTCTTTA
Found at i:1448964 original size:20 final size:21
Alignment explanation
Indices: 1448926--1448965 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1448916 ATTGCAGGAA
* *
1448926 TTTATGGCCTCGATGAAAGAT
1 TTTATGGCCTCCATCAAAGAT
1448947 TTTATGGCCTCCA-CAAAGA
1 TTTATGGCCTCCATCAAAGA
1448966 CCTTGATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TTTATGGCCTCCATCAAAGAT
Found at i:1455667 original size:19 final size:19
Alignment explanation
Indices: 1455643--1455690 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1455633 TAAGAGGTGT
1455643 ATCGATGCACCCCGTATGC
1 ATCGATGCACCCCGTATGC
1455662 ATCGATGCACCCCGTATGC
1 ATCGATGCACCCCGTATGC
1455681 ATCGATGCAC
1 ATCGATGCAC
1455691 TCACTGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGATGCACCCCGTATGC
Found at i:1458059 original size:2 final size:2
Alignment explanation
Indices: 1458052--1458080 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1458042 AAATATTGAG
1458052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1458081 TAAAACATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1458510 original size:2 final size:2
Alignment explanation
Indices: 1458503--1458530 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1458493 TAAAGTTGTA
1458503 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
1458531 TACTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1459146 original size:15 final size:16
Alignment explanation
Indices: 1459092--1459139 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1459082 ATAAAAGAAA
*
1459092 GGATTTTCATTATTTGCT
1 GGATTTTC-TTA-TTGAT
1459110 GCGATTTTCTTATTGAT
1 G-GATTTTCTTATTGAT
*
1459127 GGATTTTTTTATT
1 GGATTTTCTTATT
1459140 TTGGATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 11 0.41
17 5 0.19
18 4 0.15
19 7 0.26
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (16 bp):
GGATTTTCTTATTGAT
Found at i:1459812 original size:3 final size:3
Alignment explanation
Indices: 1459804--1459858 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
1459794 TGTAAAATAC
* *
1459804 AAT AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AGT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1459850 AAT AA- AAT A
1 AAT AAT AAT A
1459859 TTAAAAAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1460335 original size:111 final size:111
Alignment explanation
Indices: 1460063--1460475 Score: 605
Period size: 111 Copynumber: 3.7 Consensus size: 111
1460053 CAAAGTAGAC
1460063 TTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATATGTTCCGCTTCCTCTGA
1 TTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATATGTTCCGCTTCCTCTGA
* *
1460128 GGGAATATGAGATATGGGAGAGTTGATCCATTGAATC-GGGCAGAT
66 GGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCGGGGCAGAT
* **
1460173 TTGTTCCGCTGTCACTCAGGGAATGTCAAATCTTGAAAGAGAGAGATATGTTCTTCTTCCTCTGA
1 TTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATATGTTCCGCTTCCTCTGA
* *
1460238 GGGAATATCAGATCTAGGTGAGTTGATCCATTGAATCGGGGCAGAT
66 GGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCGGGGCAGAT
* * * *
1460284 TTGTTTCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAAAAAGATATGTTCCGCTTCCTTTGA
1 TTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATATGTTCCGCTTCCTCTGA
* * *
1460349 GGAAATATCAGATCTGGGAGAGTTGATCCATTGAATCGAGGTAGAT
66 GGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCGGGGCAGAT
* * * * * *
1460395 TTGTTCCGCTGTCACTCAAGGAATATCAAATCTTGAAAAATAG-GAATTTGTTCCACTTCCTCTA
1 TTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAG-ATATGTTCCGCTTCCTCTG
* *
1460459 ATGGAATATCATATCTG
65 AGGGAATATCAGATCTG
1460476 AATTTGCTTC
Statistics
Matches: 270, Mismatches: 31, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
110 96 0.36
111 174 0.64
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (111 bp):
TTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATATGTTCCGCTTCCTCTGA
GGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCGGGGCAGAT
Found at i:1460529 original size:37 final size:37
Alignment explanation
Indices: 1460477--1460550 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
1460467 TCATATCTGA
* ** *
1460477 ATTTGCTTCATTACTCTTTTGTGAAGGCTTAAGATTG
1 ATTTGCTTCACTACTCTTCGGTGAAGACTTAAGATTG
*
1460514 ATTTGCTTCACTACTCTTCGGTGAAGACTTTAGATTG
1 ATTTGCTTCACTACTCTTCGGTGAAGACTTAAGATTG
1460551 CCCGGAGGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (37 bp):
ATTTGCTTCACTACTCTTCGGTGAAGACTTAAGATTG
Found at i:1460622 original size:23 final size:23
Alignment explanation
Indices: 1460596--1460664 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1460586 AAGATGACCC
1460596 GAAGGATTTAAGCATCATGCTTG
1 GAAGGATTTAAGCATCATGCTTG
* * *
1460619 GAA-GACTT-A-C-TGATGACCT-
1 GAAGGATTTAAGCATCATG-CTTG
*
1460638 GAAGGATTTAAGCATCATGCTCG
1 GAAGGATTTAAGCATCATGCTTG
1460661 GAAG
1 GAAG
1460665 ACTTACTGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 2 0.06
22 6 0.18
23 11 0.33
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (23 bp):
GAAGGATTTAAGCATCATGCTTG
Found at i:1460634 original size:42 final size:42
Alignment explanation
Indices: 1460551--1460731 Score: 254
Period size: 42 Copynumber: 4.3 Consensus size: 42
1460541 CTTTAGATTG
* * * * * **
1460551 CCCGGAGGACTTAATCATCATGCTCGAAAGGCTTAAAGATGA
1 CCCGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
*
1460593 CCCGAAGGATTTAAGCATCATGCTTGGAAGACTTACTGATGA
1 CCCGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
*
1460635 CCTGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
1 CCCGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
* *
1460677 CACGGAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
1 CCCGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
*
1460719 CCTGAAGGATTTA
1 CCCGAAGGATTTA
1460732 TAAATTTTGG
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 123 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (42 bp):
CCCGAAGGATTTAAGCATCATGCTCGGAAGACTTACTGATGA
Found at i:1463374 original size:10 final size:10
Alignment explanation
Indices: 1463374--1463426 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
1463364 TTCTTTTTTA
1463374 TTTATTCTTCT
1 TTTATTCTT-T
1463385 TTT-TTCTTCT
1 TTTATTCTT-T
1463395 TTT-TTC-TT
1 TTTATTCTTT
1463403 TTTATTCTTT
1 TTTATTCTTT
1463413 TTTATTCATTT
1 TTTATTC-TTT
1463424 TTT
1 TTT
1463427 CCCTTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 22 0.56
11 9 0.23
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTCTTT
Found at i:1463404 original size:16 final size:16
Alignment explanation
Indices: 1463385--1463415 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1463375 TTATTCTTCT
*
1463385 TTTTTCTTCTTTTTTC
1 TTTTTATTCTTTTTTC
1463401 TTTTTATTCTTTTTT
1 TTTTTATTCTTTTTT
1463416 ATTCATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTATTCTTTTTTC
Found at i:1463427 original size:27 final size:27
Alignment explanation
Indices: 1463361--1463427 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1463351 TCAATCTTCC
* *
1463361 TTATTCTTTTTTATTTATTCTTCTTTT
1 TTATTCTTTTTTCTTTATTATTCTTTT
*
1463388 TTCTTCTTTTTTCTTT-TTATTCTTTT
1 TTATTCTTTTTTCTTTATTATTCTTTT
1463414 TTATTCATTTTTTC
1 TTATTC-TTTTTTC
1463428 CCTTTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 14 0.40
27 21 0.60
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (27 bp):
TTATTCTTTTTTCTTTATTATTCTTTT
Found at i:1471752 original size:3 final size:3
Alignment explanation
Indices: 1471744--1471789 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
1471734 TGTAAATTAC
1471744 AAT AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1471789 A
1 A
1471790 TTAAAAAACG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1471794 original size:8 final size:8
Alignment explanation
Indices: 1471744--1471795 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
1471734 TGTAAATTAC
1471744 AATAAT-A
1 AATAATAA
*
1471751 ATTAATAA
1 AATAATAA
1471759 TAATAATAA
1 -AATAATAA
1471768 TAATAATAA
1 -AATAATAA
1471777 TAATAATAA
1 -AATAATAA
*
1471786 AATATTAA
1 AATAATAA
1471794 AA
1 AA
1471796 AACGAGACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
7 5 0.12
8 10 0.25
9 25 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATAA
Found at i:1482900 original size:143 final size:143
Alignment explanation
Indices: 1482642--1482924 Score: 530
Period size: 143 Copynumber: 2.0 Consensus size: 143
1482632 AAAACTTGAA
* *
1482642 CTCGACTATTCTTTGATTGGGAGGCACTGGTCTAGGAACCAGCTCTCTTATTCCACTGTTTCCTT
1 CTCGACTATTCTTTGATTGGGAGGCACTGGTCGAGGAACCAGCTCTCTTATTCCACTATTTCCTT
* *
1482707 TGCTCCACAAACCTTTCATTTTGAGCTCGCTCCAGGGCTTTGTCTCTATTCACTACCTATTGGAA
66 TGCTCCACAAACCTTTCATTTTGAGCTCGCTCCAAGGCTTTGGCTCTATTCACTACCTATTGGAA
1482772 TGAGGAGAGGAAC
131 TGAGGAGAGGAAC
1482785 CTCGACTATTCTTTGATTGGGAGGCACTGGTCGAGGAACCAGCTCTCTTATTCCACTATTTCCTT
1 CTCGACTATTCTTTGATTGGGAGGCACTGGTCGAGGAACCAGCTCTCTTATTCCACTATTTCCTT
1482850 TGCTCCACAAACCTTTCATTTTGAGCTCGCTCCAAGGCTTTGGCTCTATTCACTACCTATTGGAA
66 TGCTCCACAAACCTTTCATTTTGAGCTCGCTCCAAGGCTTTGGCTCTATTCACTACCTATTGGAA
1482915 TGAGGAGAGG
131 TGAGGAGAGG
1482925 TTGAGTGCCA
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 136 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (143 bp):
CTCGACTATTCTTTGATTGGGAGGCACTGGTCGAGGAACCAGCTCTCTTATTCCACTATTTCCTT
TGCTCCACAAACCTTTCATTTTGAGCTCGCTCCAAGGCTTTGGCTCTATTCACTACCTATTGGAA
TGAGGAGAGGAAC
Found at i:1484389 original size:23 final size:22
Alignment explanation
Indices: 1484327--1484399 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
1484317 CACCAAAGTG
* *
1484327 CCACATAA-TTGTCCCGAAGGA
1 CCACATAATTTGTTCCGAATGA
1484348 CCACATAATTTG-TCTCGAATGA
1 CCACATAATTTGTTC-CGAATGA
1484370 CCACATAATTTTGTTCCGAATGA
1 CCACATAA-TTTGTTCCGAATGA
*
1484393 GCACATA
1 CCACATA
1484400 GAACCCCCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.20
22 17 0.38
23 17 0.38
24 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (22 bp):
CCACATAATTTGTTCCGAATGA
Found at i:1487239 original size:25 final size:25
Alignment explanation
Indices: 1487199--1487254 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
1487189 AAGGGGCAAT
1487199 ATTTTCTCAAAATC-TTTAATTAAAC
1 ATTTTCTCAAAATCTTTTAATT-AAC
*
1487224 ATTTT-TCAAAACTCTTTTAATTGAC
1 ATTTTCTCAAAA-TCTTTTAATTAAC
1487249 ATTTTC
1 ATTTTC
1487255 AGAATTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 6 0.22
25 14 0.52
26 7 0.26
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTTTCTCAAAATCTTTTAATTAAC
Found at i:1487577 original size:37 final size:37
Alignment explanation
Indices: 1487539--1487608 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1487529 TAAAGATAAT
*
1487539 TTTTC-TAAAAAATAAATTTTGTCTCGCTTGAGACAA
1 TTTTCTTAAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
1487575 TTTTCTTTAAAAACAAGTTTTGTCTCTCTTGAGA
1 TTTTCTTAAAAAACAAATTTTGTCTCGCTTGAGA
1487609 GAGTTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 5 0.17
37 24 0.83
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTTCTTAAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:1487931 original size:131 final size:131
Alignment explanation
Indices: 1487694--1488191 Score: 549
Period size: 131 Copynumber: 3.8 Consensus size: 131
1487684 TGAAACCATT
*
1487694 ATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACTGTGTCATCCACC-GACCAGACCTCC
1 ATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCC-CCTGACCAGACCTCC
* ** * *
1487758 TCATCACGTAGGAGTTGTGTTACCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCATGATA
65 TCATCACGTAGGAGTCGCATCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCATGATA
1487823 TC
130 TC
* *
1487825 ATCCCTAAAGATGG-CATGTCATCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCTCC
1 ATCCCTAAAGATGGCCA-GTCATCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
* * * *
1487889 TCATCACATAGGAGTCGCATCACCCTTAGATAACCAGTCATCCTCATCACGTAGGAACTATGAAA
65 TCATCACGTAGGAGTCGCATCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCATGATA
1487954 TC
130 TC
** ** *
1487956 ATCCCTAAAGATGATTCA-TTGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCATACCTCC
1 ATCCCTAAAGATG-GCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
* * * *** *
1488020 TCATGACGTAAGAG-C-CATGTCACCCCTAGATAACCAGTCGT-CTCCATCGTATAGGAACCGTG
65 TCATCACGTAGGAGTCGCA--TCACCCCTAGATAACCAGTCATCCT-CATCACGTAGGAACCATG
*
1488082 TTATCACC
127 --AT-ATC
* * * * *
1488090 ATTCCCTAAAGATGGCCAGTCGTCCTCGTCGCGTAGGAACCGTGTCATCCACTGACCAGATCTCC
1 A-TCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
* ** * *
1488155 TCATCACGTAGGATTCATATCACCCTTAGACAACCAG
65 TCATCACGTAGGAGTCGCATCACCCCTAGATAACCAG
1488192 AACTCTTCAT
Statistics
Matches: 310, Mismatches: 43, Indels: 24
0.82 0.11 0.06
Matches are distributed among these distances:
129 2 0.01
130 7 0.02
131 212 0.68
133 3 0.01
134 5 0.02
135 79 0.25
136 1 0.00
137 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCT
CATCACGTAGGAGTCGCATCACCCCTAGATAACCAGTCATCCTCATCACGTAGGAACCATGATAT
C
Found at i:1488206 original size:266 final size:262
Alignment explanation
Indices: 1487715--1488207 Score: 643
Period size: 266 Copynumber: 1.9 Consensus size: 262
1487705 TGGCCAGTCA
* * *** *
1487715 TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGTTGTGTTA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAAGAGCCATGTCA
* *
1487780 CCCCTAGATAACCAGCCATCCTCATCACGTAGGAACCATGATATCATCCCTAAAGATGGCATGTC
66 CCCCTAGATAACCAGCCATCCTCATCACATAGGAACCATGATACCATCCCTAAAGATGGCATGTC
* *
1487845 ATCCTCATCACGTAGGAACAGTGTCATCCCCTGACCAGATCTCCTCATCACATAGGAGTCGCATC
131 ATCCTCATCACGTAGGAACAGTGTCATCCACTGACCAGATCTCCTCATCACATAGGAGTCACATC
* *
1487910 ACCCTTAGATAACCAGTCATCCTCATCACGTAGGAACTATGAAATCATCCCTAAAGATGATTCAT
196 ACCCTTAGACAACCAGACATCCTCATCACGTAGGAACTATGAAATCATCCCTAAAGATGATTCAT
1487975 TG
261 TG
* *
1487977 TCCTCATCACGTAGGAACCGTGTCATCC-CCTGACCATACCTCCTCATGACGTAAGAGCCATGTC
1 TCCTCATCACGTAGGAACCGTGTCATCCACC-GACCAGACCTCCTCATCACGTAAGAGCCATGTC
* * ** *
1488041 ACCCCTAGATAACCAGTCGT-CTCCATCGTATAGGAACCGTGTTATCACCATTCCCTAAAGATGG
65 ACCCCTAGATAACCAGCCATCCT-CATCACATAGGAACCATG--AT-ACCA-TCCCTAAAGATGG
* * * * * *
1488105 CCA-GTCGTCCTCGTCGCGTAGGAACCGTGTCATCCACTGACCAGATCTCCTCATCACGTAGGAT
125 -CATGTCATCCTCATCACGTAGGAACAGTGTCATCCACTGACCAGATCTCCTCATCACATAGGAG
* *
1488169 TCATATCACCCTTAGACAACCAGA-ACTCTTCATCACGTA
189 TCACATCACCCTTAGACAACCAGACA-TCCTCATCACGTA
1488208 TGAGCAGTGT
Statistics
Matches: 196, Mismatches: 27, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
261 4 0.02
262 85 0.43
264 2 0.01
265 4 0.02
266 99 0.51
267 2 0.01
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (262 bp):
TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAAGAGCCATGTCA
CCCCTAGATAACCAGCCATCCTCATCACATAGGAACCATGATACCATCCCTAAAGATGGCATGTC
ATCCTCATCACGTAGGAACAGTGTCATCCACTGACCAGATCTCCTCATCACATAGGAGTCACATC
ACCCTTAGACAACCAGACATCCTCATCACGTAGGAACTATGAAATCATCCCTAAAGATGATTCAT
TG
Found at i:1493830 original size:4 final size:4
Alignment explanation
Indices: 1493823--1493852 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1493813 TTTGGTCCTT
1493823 TTTA TTTA TTTA TTTA TTTA TTT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1493853 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTA
Found at i:1493915 original size:20 final size:22
Alignment explanation
Indices: 1493874--1493918 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1493864 ACTAACTTTC
*
1493874 ATTTATCTTTGTTATCTATTAT
1 ATTTATCTTTATTATCTATTAT
1493896 ATTTAT-TTTATTAT-TATTAT
1 ATTTATCTTTATTATCTATTAT
1493916 ATT
1 ATT
1493919 AATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTATCTTTATTATCTATTAT
Found at i:1494041 original size:6 final size:6
Alignment explanation
Indices: 1494030--1494055 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1494020 AATCGGGTTC
1494030 TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT
1494056 TCACGAATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:1494426 original size:84 final size:84
Alignment explanation
Indices: 1494296--1494726 Score: 499
Period size: 84 Copynumber: 5.1 Consensus size: 84
1494286 AAACTCGTCG
* * *
1494296 GGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
1 GGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCT
*
1494361 GAGCGTAGTCAAACTCGAA
66 GAGCGTAGTCGAACTCGAA
* * * * * * *
1494380 GGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCAAATGATGTACCTTGGAGCT
1 GGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCT
* *
1494445 GAGTGTAATCGAACTCGAA
66 GAGCGTAGTCGAACTCGAA
* * *
1494464 GGATTTTTTGGTTGGCAGATAACCCTTCTCGACATAAGTTATGCTGCAAATGATGTGCCGTT-GA
1 GG--TCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGA
*
1494528 GCTGAGCGTAGTCGAACTCAAA
63 GCTGAGCGTAGTCGAACTCGAA
* * * * * *
1494550 GGTC-TTGTGTTGGCAGACAACCCTTCTAGAGTTAAGTTGTGTTGTAAATGATATGCCTTGGAGC
1 GGTCTTTG-GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
1494614 TGAGCGTAGTCGAACTCGAA
65 TGAGCGTAGTCGAACTCGAA
* * * * * *
1494634 GGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGC
1 GGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGC
* * **
1494698 TGAGTGTAATCGAACTCGGG
65 TGAGCGTAGTCGAACTCGAA
1494718 GGTCTTTGG
1 GGTCTTTGG
1494727 CAGATAGCCT
Statistics
Matches: 294, Mismatches: 46, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
83 42 0.14
84 178 0.61
85 3 0.01
86 69 0.23
87 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (84 bp):
GGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCT
GAGCGTAGTCGAACTCGAA
Found at i:1494601 original size:170 final size:167
Alignment explanation
Indices: 1494296--1494714 Score: 518
Period size: 170 Copynumber: 2.5 Consensus size: 167
1494286 AAACTCGTCG
* *
1494296 GGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
1 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCT
* * * * * * *
1494361 GAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGTTATGTTGCA
65 GAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAAACAACCCTTCTAGACTTAAGTTATGTTGCA
* *
1494426 AATGATGTACCTTGGAGCTGAGTGTAATCGAACTCGAA
130 AATGATATACCTTGGAGCTGAGCGTAATCGAACTCGAA
* *
1494464 GGATTTTTTGGTTGGCAGATAACCCTTCTCGACATAAGTTATGCTGCAAATGATGTGCCGTTGAG
1 GG--TCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAG
* * *
1494529 CTGAGCGTAGTCGAACTCAAAGGTC-TTGTGTTGGCAGACAACCCTTCTAGAGTTAAGTTGTGTT
63 CTGAGCGTAGTCGAACTCAAAGGTCTTTG-GTTGGCAAACAACCCTTCTAGACTTAAGTTATGTT
* * *
1494593 GTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
127 GCAAATGATATACCTTGGAGCTGAGCGTAATCGAACTCGAA
* * * * * *
1494634 GGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGC
1 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGC
* *
1494698 TGAGTGTAATCGAACTC
64 TGAGCGTAGTCGAACTC
1494715 GGGGGTCTTT
Statistics
Matches: 216, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
167 41 0.19
168 28 0.13
169 3 0.01
170 142 0.66
171 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (167 bp):
GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTG
AGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAAACAACCCTTCTAGACTTAAGTTATGTTGCAA
ATGATATACCTTGGAGCTGAGCGTAATCGAACTCGAA
Found at i:1494987 original size:106 final size:106
Alignment explanation
Indices: 1494853--1496086 Score: 1963
Period size: 106 Copynumber: 11.6 Consensus size: 106
1494843 GCATTGCTCC
* * * * *
1494853 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAATTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1494918 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
*
1494959 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* ** *
1495024 CAAGTTGTCCCTTCATCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
1495065 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1495130 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
1495171 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1495236 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * *
1495277 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1495342 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
*
1495383 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1495448 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * *
1495489 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1495554 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
** *
1495595 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1495660 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* *
1495701 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
1495766 CCAGCGGTCCCTTCGTCGTGACGTTGAACATGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * *
1495807 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTG-GAAAGTTATTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTGTTGACA
* *
1495871 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * *
1495913 GAGTCCACTATCCTTCGTTGTGAAGTTGAAATTGGCTCTAGAAGTGGA-AAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAGTTGTTTGTTGACA
1495977 ACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-TAGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACAT-GCGTTGTCTG
* * * * * *
1496019 GAGTCCAATTTTCTTCGCTGCGAAGTTGAAATAGACTCCGAATGAAATTG-GAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-C---TGAAATTGAG-AAGTTGTTTGTT
1496083 GACA
61 GACA
1496087 GACAACTTTT
Statistics
Matches: 1053, Mismatches: 65, Indels: 16
0.93 0.06 0.01
Matches are distributed among these distances:
105 2 0.00
106 1025 0.97
107 6 0.01
109 5 0.00
110 15 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
Found at i:1500438 original size:34 final size:34
Alignment explanation
Indices: 1500395--1500463 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1500385 AGTTTGACGG
1500395 TTGTATTGGGATGAATATGCAAACTTATATAAAT
1 TTGTATTGGGATGAATATGCAAACTTATATAAAT
1500429 TTGTATTGGGATGAATATGCAAACTTATATAAAT
1 TTGTATTGGGATGAATATGCAAACTTATATAAAT
1500463 T
1 T
1500464 AAGCGTTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (34 bp):
TTGTATTGGGATGAATATGCAAACTTATATAAAT
Found at i:1506290 original size:83 final size:82
Alignment explanation
Indices: 1506151--1506317 Score: 316
Period size: 83 Copynumber: 2.0 Consensus size: 82
1506141 ATCCTACAAC
1506151 AATATTATATATATATATATATATATAAAATATAACCTTCTCCCGAATGAAGAAAACTCGGACTA
1 AATATTATATATATATATATATATATAAAATATAACCTTCTCCCGAATGAAGAAAACTCGGACTA
1506216 AAAAACCAGTGAAATCT
66 AAAAACCAGTGAAATCT
*
1506233 AATATATATATATATATATATATGTATAAAATATAACCTTCTCCCGAATGAAGAAAACTCGGACT
1 AATAT-TATATATATATATATATATATAAAATATAACCTTCTCCCGAATGAAGAAAACTCGGACT
1506298 AAAAAACCAGTGAAATCT
65 AAAAAACCAGTGAAATCT
1506316 AA
1 AA
1506318 CATGAACATT
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 5 0.06
83 78 0.94
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (82 bp):
AATATTATATATATATATATATATATAAAATATAACCTTCTCCCGAATGAAGAAAACTCGGACTA
AAAAACCAGTGAAATCT
Found at i:1511593 original size:40 final size:40
Alignment explanation
Indices: 1511540--1511919 Score: 370
Period size: 40 Copynumber: 9.3 Consensus size: 40
1511530 GCAACGTTTA
* * *
1511540 ATAAACACTGCAATAGTCATGTACTTTAGTGGCGTTTTTT
1 ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTTT
** * *
1511580 ATAAACGCCGCAATAACCATGCACTTTATTGGCTTTTTTGT
1 ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTT-T
* *
1511621 AATAAACGCTGCAATAGTCATGCACTTTAGTGACGTTTTTT
1 -ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTTT
1511662 ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTTGT
1 ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTT-T
** * * *
1511703 AATAAGTGTCGCAATAGTCATGC-CTTTAGCGGTGTTTTTT
1 -ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTTT
** ** *
1511743 ATAAACATCGCAATAGTCATGCACTTTAACGGTGTTTTTAT
1 ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTT-T
* * * * * *
1511784 AGTAAACGTCGCAATAATCATGCGCCTTA-TCGACGTTTTTG
1 A-TAAACGCCGCAATAGTCATGCACTTTAGT-GGCGTTTTTT
* * *
1511825 ATAAACGCCGCAATAATCATGCACTTTA-TCGGCCTTTTTC
1 ATAAACGCCGCAATAGTCATGCACTTTAGT-GGCGTTTTTT
* * *
1511865 ATAAACGTCGCAATAATCATGCACTTTAGTGGCGTTTTGTA
1 ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTT-TT
*
1511906 ATAAATGCCGCAAT
1 ATAAACGCCGCAAT
1511920 TGTACAATCC
Statistics
Matches: 287, Mismatches: 43, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
39 19 0.07
40 152 0.53
41 34 0.12
42 82 0.29
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (40 bp):
ATAAACGCCGCAATAGTCATGCACTTTAGTGGCGTTTTTT
Found at i:1511633 original size:82 final size:82
Alignment explanation
Indices: 1511549--1511919 Score: 414
Period size: 82 Copynumber: 4.5 Consensus size: 82
1511539 AATAAACACT
* * *
1511549 GCAATAGTCATGTACTTTAGTGGCGTTTTTTATAAACGCCGCAATAACCATGCACTTTATTGGCT
1 GCAATAGTCATGCACTTTAGTGGCGTTTTTTATAAACGCCGCAATAATCATGCACTTTATCGGCT
1511614 TTTTTGTAATAAACG-C
66 TTTTTGTAATAAACGTC
* *
1511630 TGCAATAGTCATGCACTTTAGTGACGTTTTTTATAAACGCCGCAATAGTCATGCACTTTAGT-GG
1 -GCAATAGTCATGCACTTTAGTGGCGTTTTTTATAAACGCCGCAATAATCATGCACTTTA-TCGG
* **
1511694 CGTTTTTGTAATAAGTGTC
64 CTTTTTTGTAATAAACGTC
* * ** * *
1511713 GCAATAGTCATGC-CTTTAGCGGTGTTTTTTATAAACATCGCAATAGTCATGCACTTTAACGG-T
1 GCAATAGTCATGCACTTTAGTGGCGTTTTTTATAAACGCCGCAATAATCATGCACTTTATCGGCT
* *
1511776 GTTTTTATAGTAAACGTC
66 -TTTTTGTAATAAACGTC
* * * * *
1511794 GCAATAATCATGCGCCTTA-TCGACGTTTTTGATAAACGCCGCAATAATCATGCACTTTATCGGC
1 GCAATAGTCATGCACTTTAGT-GGCGTTTTTTATAAACGCCGCAATAATCATGCACTTTATCGGC
* *
1511858 -CTTTT-TCATAAACGTC
65 TTTTTTGTAATAAACGTC
* * *
1511874 GCAATAATCATGCACTTTAGTGGCGTTTTGTAATAAATGCCGCAAT
1 GCAATAGTCATGCACTTTAGTGGCGTTTT-TTATAAACGCCGCAAT
1511920 TGTACAATCC
Statistics
Matches: 244, Mismatches: 36, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
80 33 0.14
81 86 0.35
82 123 0.50
83 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (82 bp):
GCAATAGTCATGCACTTTAGTGGCGTTTTTTATAAACGCCGCAATAATCATGCACTTTATCGGCT
TTTTTGTAATAAACGTC
Found at i:1511757 original size:163 final size:164
Alignment explanation
Indices: 1511549--1511902 Score: 416
Period size: 163 Copynumber: 2.2 Consensus size: 164
1511539 AATAAACACT
* * **
1511549 GCAATAGTCATGTACTTTAGTGGCGTTTTTTATAAACGCCGCAATAACCATGCACTTTATTGGCT
1 GCAATAGTCATGTACTTTAGCGGCGTTTTTTATAAACACCGCAATAACCATGCACTTTAACGG-T
* * * *
1511614 -TTTTTGTAATAAACG-CTGCAATAGTCATGCACTTTAGT-GACGTTTTTTATAAACGCCGCAAT
65 GTTTTTATAATAAACGTC-GCAATAATCATGCACCTTA-TCGACGTTTTTGATAAACGCCGCAAT
*
1511676 AGTCATGCACTTTAGTGGCGTTTTTGTAATAAGTGTC
128 AATCATGCACTTTAGTGGCGTTTTTGTAATAAGTGTC
* * * **
1511713 GCAATAGTCATG-CCTTTAGCGGTGTTTTTTATAAACATCGCAATAGTCATGCACTTTAACGGTG
1 GCAATAGTCATGTACTTTAGCGGCGTTTTTTATAAACACCGCAATAACCATGCACTTTAACGGTG
* *
1511777 TTTTTATAGTAAACGTCGCAATAATCATGCGCCTTATCGACGTTTTTGATAAACGCCGCAATAAT
66 TTTTTATAATAAACGTCGCAATAATCATGCACCTTATCGACGTTTTTGATAAACGCCGCAATAAT
* * **
1511842 CATGCACTTTA-TCGGC-CTTTT-TCATAAACGTC
131 CATGCACTTTAGT-GGCGTTTTTGTAATAAGTGTC
* * *
1511874 GCAATAATCATGCACTTTAGTGGCGTTTT
1 GCAATAGTCATGTACTTTAGCGGCGTTTT
1511903 GTAATAAATG
Statistics
Matches: 161, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
161 19 0.12
162 20 0.12
163 109 0.68
164 13 0.08
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (164 bp):
GCAATAGTCATGTACTTTAGCGGCGTTTTTTATAAACACCGCAATAACCATGCACTTTAACGGTG
TTTTTATAATAAACGTCGCAATAATCATGCACCTTATCGACGTTTTTGATAAACGCCGCAATAAT
CATGCACTTTAGTGGCGTTTTTGTAATAAGTGTC
Found at i:1523839 original size:26 final size:28
Alignment explanation
Indices: 1523801--1523854 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
1523791 TAATAATCTG
*
1523801 TTATCACTCCTAAAATTTTATAGATTTA
1 TTATCACTCCTAAAATTTTATAAATTTA
1523829 TTAT-ACT-CTAAAATTTTATAAATTTA
1 TTATCACTCCTAAAATTTTATAAATTTA
1523855 CTCTCAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 18 0.72
27 3 0.12
28 4 0.16
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (28 bp):
TTATCACTCCTAAAATTTTATAAATTTA
Found at i:1524493 original size:2 final size:2
Alignment explanation
Indices: 1524486--1524516 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1524476 TAAATATTTT
1524486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1524517 CAAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1525935 original size:20 final size:20
Alignment explanation
Indices: 1525903--1525943 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1525893 TAGTTTTAAA
*
1525903 TATAACTTTAAAAATATATT
1 TATAACTTTAAAAATAAATT
1525923 TATAA-TTTCAAAAATAAATT
1 TATAACTTT-AAAAATAAATT
1525943 T
1 T
1525944 TAAAAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAACTTTAAAAATAAATT
Found at i:1530210 original size:31 final size:31
Alignment explanation
Indices: 1530175--1530291 Score: 137
Period size: 31 Copynumber: 3.8 Consensus size: 31
1530165 TAAATTTCCG
* * * * *
1530175 TAAGTTTAAAGATCATTTTGTAATAGTTTGA
1 TAAGTTTAATGACCATTTTGTAACAATTAGA
**
1530206 TAAGTGCAATGACCATTTTGTAACAATTAGA
1 TAAGTTTAATGACCATTTTGTAACAATTAGA
1530237 TAAGTTTAATGACCATTTTGTAACAATTCA-A
1 TAAGTTTAATGACCATTTTGTAACAATT-AGA
* *
1530268 AAAGTTTAATGATCATTTTGTAAC
1 TAAGTTTAATGACCATTTTGTAAC
1530292 TTTCAAAACT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 73 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (31 bp):
TAAGTTTAATGACCATTTTGTAACAATTAGA
Found at i:1532279 original size:43 final size:43
Alignment explanation
Indices: 1532231--1532317 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1532221 AAATTATGCG
1532231 AATGAAATGCATACACTGTGATTATGTATAAGATAGTAAGCTT
1 AATGAAATGCATACACTGTGATTATGTATAAGATAGTAAGCTT
** *
1532274 AATGAAATGCATATGCTGTGATTATGTATAAGATTGTAAGCTT
1 AATGAAATGCATACACTGTGATTATGTATAAGATAGTAAGCTT
1532317 A
1 A
1532318 CTTACTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (43 bp):
AATGAAATGCATACACTGTGATTATGTATAAGATAGTAAGCTT
Found at i:1533340 original size:15 final size:14
Alignment explanation
Indices: 1533290--1533340 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 14
1533280 AGGTAATACA
1533290 AATTTAATT-TATAT
1 AATTT-ATTATATAT
*
1533304 AATTTA-GATATAT
1 AATTTATTATATAT
1533317 AATTT-TTATATATT
1 AATTTATTATATA-T
1533331 AATTTATTAT
1 AATTTATTAT
1533341 CTTTGTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 16 0.52
14 11 0.35
15 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
AATTTATTATATAT
Found at i:1534201 original size:36 final size:36
Alignment explanation
Indices: 1534161--1534232 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1534151 TGGGTTATAT
1534161 TTATAATATTAATTAT-AA-TTTTTTAATAATTTTAAA
1 TTATAATA-TAATTATAAATTTTTTTAAT-ATTTTAAA
* *
1534197 TTATAATATATTTTTAAATTTTTTTAATATTTTAAA
1 TTATAATATAATTATAAATTTTTTTAATATTTTAAA
1534233 AGTAATACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 5 0.16
36 18 0.56
37 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (36 bp):
TTATAATATAATTATAAATTTTTTTAATATTTTAAA
Found at i:1534229 original size:18 final size:18
Alignment explanation
Indices: 1534179--1534232 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1534169 TTAATTATAA
1534179 TTTTTTAATAATTTTAAAT
1 TTTTTTAAT-ATTTTAAAT
* **
1534198 TATAAT-ATATTTTTAAAT
1 TTTTTTAATA-TTTTAAAT
1534216 TTTTTTAATATTTTAAA
1 TTTTTTAATATTTTAAA
1534233 AGTAATACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
17 1 0.04
18 20 0.74
19 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTTAATATTTTAAAT
Found at i:1534643 original size:21 final size:21
Alignment explanation
Indices: 1534629--1534683 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1534619 TTATATTTTT
1534629 AAATTAAATAATTATAAATTA
1 AAATTAAATAATTATAAATTA
* *
1534650 AAATTAAAT-ATAATAAATATT
1 AAATTAAATAATTATAAAT-TA
*
1534671 AAATTATATAATT
1 AAATTAAATAATT
1534684 TATTTAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
21 18 0.64
22 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTAAATAATTATAAATTA
Found at i:1535379 original size:30 final size:30
Alignment explanation
Indices: 1535333--1535399 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
1535323 TTTGGTCAAA
1535333 TTTATGGGTCAAAATGATAATTTATCTAAAG
1 TTTA-GGGTCAAAATGATAATTTATCTAAAG
*
1535364 TTTAGGGTTAAAATGATAATTTATCTAAAG
1 TTTAGGGTCAAAATGATAATTTATCTAAAG
1535394 TTTAGG
1 TTTAGG
1535400 ATTACATTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.40
Consensus pattern (30 bp):
TTTAGGGTCAAAATGATAATTTATCTAAAG
Found at i:1536531 original size:37 final size:36
Alignment explanation
Indices: 1536456--1536531 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1536446 TTTTTATATT
*
1536456 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAAATATTATCAA
* *
1536492 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATATAAATATTAT-CAA
1536529 TTT
1 TTT
1536532 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAATTATATAAATATTATCAA
Found at i:1536685 original size:16 final size:18
Alignment explanation
Indices: 1536664--1536708 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1536654 AACATTTTCA
1536664 GTAATCTTATT-CT-CTG
1 GTAATCTTATTCCTACTG
1536680 GTAATCTTTTATTCCTACTG
1 GTAATC--TTATTCCTACTG
1536700 GTAATCTTA
1 GTAATCTTA
1536709 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
18 8 0.32
19 2 0.08
20 9 0.36
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (18 bp):
GTAATCTTATTCCTACTG
Found at i:1536713 original size:20 final size:20
Alignment explanation
Indices: 1536677--1536714 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536667 ATCTTATTCT
**
1536677 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
1536697 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1536715 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:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:1536959 original size:20 final size:20
Alignment explanation
Indices: 1536922--1536959 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536912 AAATTTTATT
*
1536922 AAAAATATTTTTTATTTTTA
1 AAAAATATTATTTATTTTTA
1536942 AAAAATATATATTT-TTTT
1 AAAAATAT-TATTTATTTT
1536960 CAATTAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAAAATATTATTTATTTTTA
Found at i:1538046 original size:217 final size:216
Alignment explanation
Indices: 1537666--1538363 Score: 1083
Period size: 217 Copynumber: 3.3 Consensus size: 216
1537656 ATTTAAGAAT
* *
1537666 TAAATTGAACAAATATGAAATTGCAAATAAAAATTTAAATCAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-ACACACATTGATGAG
* *
1537731 GGATCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAAATACTAAATTATA
65 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAAGTACTAAATTATA
* * * *
1537796 CCCATTT-AAAAGTTATGGGCCAATTAAAAAAATAGAATTAAGTAAAAAGTATGGATCAATTTCA
130 CCCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCA
1537860 TATGCAAATAAAATTTGGAGGAC
194 TATGCAAATAAAATTTGGAGGAC
* *
1537883 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAATAGCACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACA-CACACATTGATGAG
*
1537948 GGATCAAATCGAAATAATTTTAAATTGTGATATTGAAATTAATACAAAAAAAGTACTAAATTATA
65 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAAGTACTAAATTATA
* *
1538013 CCCATTTAAAAAGTTATGGGCCAATTTAAAAATAAAAATAAGTAATAAGTATGGGTCAATTCCAT
130 CCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAT
1538078 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
* * * * *
1538100 TAAATTGAACAAATATAAAATTACATATAAAAAATTAAATAAACTAAACA-ACACA---A-AAGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACACACACATTGATGAGG
* * *
1538160 GATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATAC--AAAATGTACTAAATTATAC
66 GATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAAGTACTAAATTATAC
*
1538223 TCATTTAAAAAGTTATGGGCCAA-TTAATAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAT
131 CCATTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGTATGGGTCAATTTCAT
*
1538287 ATGCAAATAAAATGTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
1538309 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACA-ACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACACACACA
1538364 AAAGGGATAA
Statistics
Matches: 447, Mismatches: 31, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
208 4 0.01
209 146 0.33
211 44 0.10
212 1 0.00
215 5 0.01
216 1 0.00
217 228 0.51
218 18 0.04
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACACACACATTGATGAGG
GATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
TGCAAATAAAATTTGGAGGAC
Found at i:1538451 original size:2 final size:2
Alignment explanation
Indices: 1538446--1538559 Score: 76
Period size: 2 Copynumber: 57.5 Consensus size: 2
1538436 AAAACTACTA
* *
1538446 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
* * * * *
1538489 AT AT AA AGT AT AT GT AT -T AT AT TT AT AA AT -T AT AT AGT TT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
1538531 AT AT AT AT AT -T AT GT AT AA AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1538560 CCGTGAATAA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
1 5 0.06
2 76 0.89
3 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1538545 original size:42 final size:42
Alignment explanation
Indices: 1538446--1538547 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 42
1538436 AAAACTACTA
*
1538446 ATATATATATATATATA-TATATAATATAAACTATATAGTTT
1 ATATATATATATATGTATTATATAATATAAACTATATAGTTT
* * *
1538487 ATATATAAAGTATATGTATTATAT-TTATAAATTATATAGTTT
1 ATATATATA-TATATGTATTATATAATATAAACTATATAGTTT
1538529 ATATATATATATTATGTAT
1 ATATATATATA-TATGTAT
1538548 AAATTATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 10 0.19
42 38 0.72
43 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (42 bp):
ATATATATATATATGTATTATATAATATAAACTATATAGTTT
Found at i:1538641 original size:11 final size:11
Alignment explanation
Indices: 1538627--1538664 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1538617 CCTACATAGT
1538627 TTATATATAAA
1 TTATATATAAA
*
1538638 TTATATATGAA
1 TTATATATAAA
1538649 TTATATATAAA
1 TTATATATAAA
*
1538660 CTATA
1 TTATA
1538665 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:1538745 original size:22 final size:24
Alignment explanation
Indices: 1538708--1538775 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 24
1538698 TTATAAATAA
*
1538708 TATATATTGTATAAATTATATAGTT
1 TATATA-TATATAAATTATATAGTT
1538733 TAT-TA-ATATAAATTATATAGTT
1 TATATATATATAAATTATATAGTT
*
1538755 TATATATATATAGATATATAT
1 TATATATATATAAAT-TATAT
1538776 GTAGTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 19 0.50
23 2 0.05
24 9 0.24
25 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (24 bp):
TATATATATATAAATTATATAGTT
Found at i:1538849 original size:7 final size:7
Alignment explanation
Indices: 1538837--1538873 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1538827 AACTTATGGT
1538837 TTTAGGG
1 TTTAGGG
1538844 TTTAGGG
1 TTTAGGG
1538851 TTTA--G
1 TTTAGGG
1538856 TTTAGGG
1 TTTAGGG
*
1538863 TTTAAGG
1 TTTAGGG
1538870 TTTA
1 TTTA
1538874 TATTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
5 5 0.19
7 22 0.81
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:1538861 original size:19 final size:19
Alignment explanation
Indices: 1538837--1538873 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1538827 AACTTATGGT
*
1538837 TTTAGGGTTTAGGGTTTAG
1 TTTAGGGTTTAAGGTTTAG
1538856 TTTAGGGTTTAAGGTTTA
1 TTTAGGGTTTAAGGTTTA
1538874 TATTTATATT
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:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (19 bp):
TTTAGGGTTTAAGGTTTAG
Found at i:1538921 original size:20 final size:20
Alignment explanation
Indices: 1538896--1538964 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
1538886 TATAAACTAC
1538896 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
1538916 ATACTATATTTTATACTATGTAT
1 ATACTATAATTTATA-T-T-TAT
* *
1538939 ATAAACTATAGTTTATATTTAC
1 AT--ACTATAATTTATATTTAT
1538961 ATAC
1 ATAC
1538965 CATATATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
20 16 0.39
21 1 0.02
22 5 0.12
23 6 0.15
24 1 0.02
25 12 0.29
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:1538932 original size:12 final size:13
Alignment explanation
Indices: 1538907--1538956 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1538897 TACTATAATT
1538907 TATATTTATATAC
1 TATATTTATATAC
1538920 TATATTT-TATAC
1 TATATTTATATAC
* * *
1538932 TATGTATATAAAC
1 TATATTTATATAC
1538945 TATAGTTTATAT
1 TATA-TTTATAT
1538957 TTACATACCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 10 0.34
13 14 0.48
14 5 0.17
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:1538954 original size:45 final size:45
Alignment explanation
Indices: 1538898--1538994 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 45
1538888 TAAACTACAT
* * * *
1538898 ACTATAATTTATATTTATATACTATAT-TTTATACTATGTATATAA
1 ACTATAATTTATATTTACATACCATATATATA-ACTATATATATAA
*
1538943 ACTATAGTTTATATTTACATACCATATATATGAACTATATATATAA
1 ACTATAATTTATATTTACATACCATATATAT-AACTATATATATAA
1538989 ACTATA
1 ACTATA
1538995 TAGGTTACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 24 0.53
46 20 0.44
47 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (45 bp):
ACTATAATTTATATTTACATACCATATATATAACTATATATATAA
Found at i:1538982 original size:13 final size:13
Alignment explanation
Indices: 1538966--1538996 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1538956 TTTACATACC
*
1538966 ATATATATGAACT
1 ATATATATAAACT
1538979 ATATATATAAACT
1 ATATATATAAACT
1538992 ATATA
1 ATATA
1538997 GGTTACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:1539007 original size:33 final size:33
Alignment explanation
Indices: 1538970--1539200 Score: 142
Period size: 33 Copynumber: 6.8 Consensus size: 33
1538960 CATACCATAT
*
1538970 ATATGAACTATATATATAAACTATATAGGTTAC
1 ATATGAACTATATATATAAACTATATAGTTTAC
* *
1539003 ATATGAACTATATATATACTAAAGT-TAATA-TTTAT
1 ATATGAAC--TATATATA-TAAACTAT-ATAGTTTAC
*
1539038 ATATGAACTATAGTTTACATATAAACTATATAGTTTAT
1 ATATGAACTATA---T--ATATAAACTATATAGTTTAC
*
1539076 ATACT-AACTATAGTTTACATATAAACTATAGTTGATATTTAC
1 ATA-TGAACTATA---T--ATATAAACTATA--T-A-GTTTAC
*
1539118 ATATGAAC------TATCAAC--TATAGTTTAC
1 ATATGAACTATATATATAAACTATATAGTTTAC
1539143 ATATGAACTATATATATAAACTATATAGTTTAC
1 ATATGAACTATATATATAAACTATATAGTTTAC
* *
1539176 ATATGACCTATATATATATACTATA
1 ATATGAACTATATATATAAACTATA
1539201 GTTTATATTT
Statistics
Matches: 162, Mismatches: 11, Indels: 50
0.73 0.05 0.22
Matches are distributed among these distances:
25 13 0.08
26 1 0.01
27 1 0.01
29 2 0.01
31 12 0.07
33 45 0.28
35 20 0.12
36 9 0.06
37 8 0.05
38 37 0.23
39 1 0.01
40 1 0.01
41 2 0.01
42 10 0.06
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (33 bp):
ATATGAACTATATATATAAACTATATAGTTTAC
Found at i:1539054 original size:18 final size:18
Alignment explanation
Indices: 1539033--1539113 Score: 92
Period size: 18 Copynumber: 4.4 Consensus size: 18
1539023 AAAGTTAATA
*
1539033 TTTATATATGAACTATAG
1 TTTATATATAAACTATAG
*
1539051 TTTACATATAAACTATATAG
1 TTTATATATAAAC--TATAG
1539071 TTTATATACT-AACTATAG
1 TTTATATA-TAAACTATAG
*
1539089 TTTACATATAAACTATAG
1 TTTATATATAAACTATAG
*
1539107 TTGATAT
1 TTTATAT
1539114 TTACATATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.02
18 36 0.68
20 15 0.28
21 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (18 bp):
TTTATATATAAACTATAG
Found at i:1539085 original size:38 final size:38
Alignment explanation
Indices: 1538983--1539105 Score: 141
Period size: 38 Copynumber: 3.3 Consensus size: 38
1538973 TGAACTATAT
* * *
1538983 ATATAAACTATATAGGTTACATATGAACTATA---TAT
1 ATATAAACTATATAGTTTATATATGAACTATAGTTTAC
*
1539018 ATACTAAAGT-TAATA-TTTATATATGAACTATAGTTTAC
1 ATA-TAAACTAT-ATAGTTTATATATGAACTATAGTTTAC
1539056 ATATAAACTATATAGTTTATATACT-AACTATAGTTTAC
1 ATATAAACTATATAGTTTATATA-TGAACTATAGTTTAC
1539094 ATATAAACTATA
1 ATATAAACTATA
1539106 GTTGATATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
35 19 0.25
36 8 0.11
37 8 0.11
38 39 0.52
39 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.40
Consensus pattern (38 bp):
ATATAAACTATATAGTTTATATATGAACTATAGTTTAC
Found at i:1539145 original size:25 final size:24
Alignment explanation
Indices: 1539080--1539154 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1539070 GTTTATATAC
*
1539080 TAACTATAGTTTACATATAAACTA
1 TAACTATAGTTTACATATGAACTA
**
1539104 TAGTTGATA-TTTACATATGAACTA
1 TAACT-ATAGTTTACATATGAACTA
1539128 TCAACTATAGTTTACATATGAACTA
1 T-AACTATAGTTTACATATGAACTA
1539153 TA
1 TA
1539155 TATATAAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 22 0.51
25 21 0.49
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (24 bp):
TAACTATAGTTTACATATGAACTA
Found at i:1539225 original size:19 final size:21
Alignment explanation
Indices: 1539184--1539242 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
1539174 ACATATGACC
1539184 TATATATAT-ATACTATAGT-T
1 TATATATATAATACTATA-TAT
1539204 TATAT-T-TAATACTATATAT
1 TATATATATAATACTATATAT
1539223 TATATATATAA-ACTATATAT
1 TATATATATAATACTATATAT
1539243 ACTATATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.06
19 15 0.43
20 15 0.43
21 3 0.09
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
TATATATATAATACTATATAT
Found at i:1539366 original size:18 final size:18
Alignment explanation
Indices: 1539343--1539480 Score: 85
Period size: 18 Copynumber: 7.9 Consensus size: 18
1539333 TATATTATAG
1539343 TATATATAAACTATATGA
1 TATATATAAACTATATGA
* *
1539361 TATATATAAATTATATGG
1 TATATATAAACTATATGA
*
1539379 TATATATAAACTATA-CA
1 TATATATAAACTATATGA
* * *
1539396 T-TATATATA-TTTCATTA
1 TATATATAAACTAT-ATGA
**
1539413 GTATATATAAACTATATCT
1 -TATATATAAACTATATGA
**
1539432 TATATAGTTCA-T-TA-G-
1 TATATA-TAAACTATATGA
1539447 TATATATAAACTATAT-A
1 TATATATAAACTATATGA
*
1539464 GTATATGTAAACTATAT
1 -TATATATAAACTATAT
1539481 TAGTGTACTA
Statistics
Matches: 91, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
14 2 0.02
15 9 0.10
16 10 0.11
17 4 0.04
18 53 0.58
19 11 0.12
20 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATATAAACTATATGA
Found at i:1539436 original size:33 final size:34
Alignment explanation
Indices: 1539340--1539462 Score: 144
Period size: 33 Copynumber: 3.6 Consensus size: 34
1539330 ATTTATATTA
*
1539340 TAGTATATATAAACTATATGATATATATAAATT-AT
1 TAGTATATATAAACTATAT-CTATATAT-AATTCAT
* *
1539375 ATGGTATATATAAACTATA-CATTATATATATTTCAT
1 -TAGTATATATAAACTATATC--TATATATAATTCAT
*
1539411 TAGTATATATAAACTATATCT-TATATAGTTCAT
1 TAGTATATATAAACTATATCTATATATAATTCAT
1539444 TAGTATATATAAACTATAT
1 TAGTATATATAAACTATAT
1539463 AGTATATGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
33 30 0.38
34 1 0.01
35 20 0.26
36 27 0.35
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (34 bp):
TAGTATATATAAACTATATCTATATATAATTCAT
Found at i:1539516 original size:21 final size:21
Alignment explanation
Indices: 1539491--1539543 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1539481 TAGTGTACTA
* *
1539491 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
1539512 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
1539533 TATAGTTTATA
1 TATAGTTTATA
1539544 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:1539618 original size:21 final size:20
Alignment explanation
Indices: 1539592--1539643 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
1539582 ATTATAAACT
*
1539592 ATATTATATTAA-TATAAGTTA
1 ATATTATACTAATTAT-A-TTA
1539613 ATATTAATACTAATTATATTA
1 ATATT-ATACTAATTATATTA
1539634 ATATTA-ACTA
1 ATATTATACTA
1539644 TAATATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 1 0.04
21 13 0.46
22 7 0.25
23 3 0.11
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (20 bp):
ATATTATACTAATTATATTA
Found at i:1539632 original size:31 final size:33
Alignment explanation
Indices: 1539561--1539676 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 33
1539551 ACTATATAAT
1539561 TTATATTAATATTAATTATAAATTATAAACTATA
1 TTATATTAATA-TAATTATAAATTATAAACTATA
* *
1539595 TTATATTAATATAAGTTA-ATATTA-ATACTA-A
1 TTATATTAATATAA-TTATAAATTATAAACTATA
*
1539626 TTATATTAATATTAACTAT-AA-TAT--A-TA-A
1 TTATATTAATA-TAATTATAAATTATAAACTATA
*
1539654 TTATTTTAATATTAATTATAAAT
1 TTATATTAATA-TAATTATAAAT
1539677 CATTTATTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
28 20 0.29
29 3 0.04
30 2 0.03
31 15 0.21
32 8 0.11
33 8 0.11
34 14 0.20
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (33 bp):
TTATATTAATATAATTATAAATTATAAACTATA
Found at i:1539645 original size:15 final size:15
Alignment explanation
Indices: 1539561--1539673 Score: 97
Period size: 15 Copynumber: 7.3 Consensus size: 15
1539551 ACTATATAAT
1539561 TTATATTAATATTAA
1 TTATATTAATATTAA
* *
1539576 TTATAAATTATAAACTATA
1 TTAT--ATTA-ATATTA-A
1539595 TTATATTAATA-TAA
1 TTATATTAATATTAA
*
1539609 GTTAATATTAATACTAA
1 -TT-ATATTAATATTAA
1539626 TTATATTAATATTAA
1 TTATATTAATATTAA
* *
1539641 CTATAAT-ATA-TAA
1 TTATATTAATATTAA
*
1539654 TTATTTTAATATTAA
1 TTATATTAATATTAA
1539669 TTATA
1 TTATA
1539674 AATCATTTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.09
14 7 0.09
15 32 0.41
16 13 0.16
17 11 0.14
18 4 0.05
19 5 0.06
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (15 bp):
TTATATTAATATTAA
Found at i:1543272 original size:16 final size:16
Alignment explanation
Indices: 1543253--1543291 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1543243 TGAGTCAATT
*
1543253 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
1543269 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
1543285 ACAGGTC
1 ACAGGTC
1543292 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:1545005 original size:73 final size:73
Alignment explanation
Indices: 1544921--1545069 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
1544911 ATATTCGAAT
1544921 AATTATATCGAATATACTTAGAAAATCATTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGT
1 AATTATATCGAATATACTTAGAAAATCATTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGT
1544986 TATATCGA
66 TATATCGA
1544994 AATTATATCGAATATACTTAGAAAATCATTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGT
1 AATTATATCGAATATACTTAGAAAATCATTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGT
1545059 TATATCGA
66 TATATCGA
1545067 AAT
1 AAT
1545070 ATCAAAATGC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (73 bp):
AATTATATCGAATATACTTAGAAAATCATTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGT
TATATCGA
Found at i:1555768 original size:16 final size:16
Alignment explanation
Indices: 1555747--1555788 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
1555737 TAGCCGCAGC
1555747 TAGTATTGTAGTGTCG
1 TAGTATTGTAGTGTCG
1555763 TAGTATTGTAGTGTCG
1 TAGTATTGTAGTGTCG
1555779 TAGTATTGTA
1 TAGTATTGTA
1555789 ATATTGAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (16 bp):
TAGTATTGTAGTGTCG
Found at i:1559954 original size:21 final size:21
Alignment explanation
Indices: 1559928--1559979 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1559918 ACTGACAATG
1559928 GAATTTGATGGTGAGATCGTT
1 GAATTTGATGGTGAGATCGTT
1559949 GAATTTGATGGTGAGATCGTT
1 GAATTTGATGGTGAGATCGTT
1559970 GAATTTGATG
1 GAATTTGATG
1559980 TTTATAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.04, G:0.33, T:0.38
Consensus pattern (21 bp):
GAATTTGATGGTGAGATCGTT
Found at i:1560490 original size:14 final size:14
Alignment explanation
Indices: 1560471--1560521 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1560461 GAGGCAAACC
1560471 ATTTCATTTTATTT
1 ATTTCATTTTATTT
**
1560485 ATTTCATTCCATTT
1 ATTTCATTTTATTT
*
1560499 ATTTTATTTTTATTT
1 ATTTCA-TTTTATTT
1560514 -TTT-ATTTT
1 ATTTCATTTT
1560522 TCTCTGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 4 0.13
13 1 0.03
14 20 0.65
15 6 0.19
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTCATTTTATTT
Found at i:1562229 original size:28 final size:29
Alignment explanation
Indices: 1562191--1562251 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
1562181 TTTAAATAGG
1562191 TTTTTAGTATTTTA-ATTAAGTTTTAGGAA
1 TTTTTAGTATTTTATATT-AGTTTTAGGAA
* *
1562220 TTTTTA-TATTTTATATTTGTTTTAGGTA
1 TTTTTAGTATTTTATATTAGTTTTAGGAA
1562248 TTTT
1 TTTT
1562252 AGTTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (29 bp):
TTTTTAGTATTTTATATTAGTTTTAGGAA
Found at i:1562938 original size:4 final size:4
Alignment explanation
Indices: 1562929--1562978 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
1562919 CTCAATCTCT
* * *
1562929 TTTA TTTA TTTA TTTA TTTA TTTCT TTTA TTTA ATT- CTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA
1562976 TTT
1 TTT
1562979 TAAAAGCAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 5 0.13
4 30 0.79
5 3 0.08
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1562959 original size:13 final size:13
Alignment explanation
Indices: 1562926--1562978 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
1562916 TATCTCAATC
1562926 TCTTTTATTTATT
1 TCTTTTATTTATT
*
1562939 T-ATTTATTTATT
1 TCTTTTATTTATT
*
1562951 TCTTTTATTTAAT
1 TCTTTTATTTATT
*
1562964 TCTTATTTTTTATT
1 TCTT-TTATTTATT
1562978 T
1 T
1562979 TAAAAGCAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
12 11 0.33
13 14 0.42
14 8 0.24
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (13 bp):
TCTTTTATTTATT
Found at i:1566040 original size:36 final size:38
Alignment explanation
Indices: 1565973--1566075 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 38
1565963 AAATAGATAG
* *
1565973 ATGACCCGAAGGATTTACAAATTACCTGAAGG-TT-AA
1 ATGACCCGAAGGCTTTACAAATGACCTGAAGGCTTAAA
*
1566009 ATGACCCAAAGGCTTTACAAATGA-CTCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAAATGACCT-GAAGGC-TTA-AA
*
1566049 ATGACCCCGAATGCTTTACAAATGACC
1 ATGA-CCCGAAGGCTTTACAAATGACC
1566076 CAATGGCTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
35 2 0.04
36 26 0.47
38 2 0.04
40 6 0.11
41 18 0.33
42 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (38 bp):
ATGACCCGAAGGCTTTACAAATGACCTGAAGGCTTAAA
Found at i:1566064 original size:21 final size:20
Alignment explanation
Indices: 1565973--1566091 Score: 131
Period size: 20 Copynumber: 6.1 Consensus size: 20
1565963 AAATAGATAG
*
1565973 ATGACCCGAAGGATTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
1565993 ATTACCTGAAGG--TT--AA
1 ATGACCCGAAGGCTTTACAA
*
1566009 ATGACCCAAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
1566029 ATGACTCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
1566049 ATGACCCCGAATGCTTTACAA
1 ATGA-CCCGAAGGCTTTACAA
1566070 ATGACCC-AATGGCTTTACAA
1 ATGACCCGAA-GGCTTTACAA
1566090 AT
1 AT
1566092 TCATGAGAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
16 11 0.13
18 4 0.05
19 2 0.02
20 48 0.58
21 18 0.22
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:1566069 original size:41 final size:40
Alignment explanation
Indices: 1566007--1566091 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 40
1565997 CCTGAAGGTT
*
1566007 AAATGACCCAAAGGCTTTACAAATGACTCGAA-GGCTTTAC
1 AAATGACCCAAAGGCTTTACAAATGAC-CCAATGGCTTTAC
* *
1566047 AAATGACCCCGAATGCTTTACAAATGACCCAATGGCTTTAC
1 AAATGA-CCCAAAGGCTTTACAAATGACCCAATGGCTTTAC
1566088 AAAT
1 AAAT
1566092 TCATGAGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 9 0.22
41 31 0.77
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (40 bp):
AAATGACCCAAAGGCTTTACAAATGACCCAATGGCTTTAC
Found at i:1570678 original size:20 final size:20
Alignment explanation
Indices: 1570650--1570827 Score: 213
Period size: 20 Copynumber: 9.1 Consensus size: 20
1570640 AAACTGATAG
*
1570650 ATGACCCGAAGGATTTACAA
1 ATGACCCGAAGGCTTTACAA
*
1570670 ATTACCCGAAGGC--T--AA
1 ATGACCCGAAGGCTTTACAA
* *
1570686 ATGACCCAAACGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
1570706 ATGACCC-AGAGGCTTTACAA
1 ATGACCCGA-AGGCTTTACAA
*
1570726 ATGATCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
1570746 ATGACCCGAAGGCTTTATAA
1 ATGACCCGAAGGCTTTACAA
*
1570766 ATGACCCGAAGGCATTACAA
1 ATGACCCGAAGGCTTTACAA
* *
1570786 ATGACACGGAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
1570806 ATGACTCGGAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
1570826 AT
1 AT
1570828 TCATGAGAAA
Statistics
Matches: 137, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
16 12 0.09
18 2 0.01
19 1 0.01
20 121 0.88
21 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:1574255 original size:96 final size:96
Alignment explanation
Indices: 1574130--1574309 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 96
1574120 TAGTATATTC
* * * **
1574130 CATGATCCATAAATCAGTAACAATCATATTTT-CTAGTGAAAGCAGGAAACCAGATAACACATTT
1 CATGATCCATAAATCAGTAACAATAATATTTTGCTA-TGAAAACAGGAAACCAGAGAACACATAC
1574194 CAGGTAACCATAGTTCATAAACCAATAGATTT
65 CAGGTAACCATAGTTCATAAACCAATAGATTT
* * *
1574226 CATGATCCATAAATCA-TGAACTATAATATTTTGCTATGAAAACAGGTAACCAGAGAACATATAC
1 CATGATCCATAAATCAGT-AACAATAATATTTTGCTATGAAAACAGGAAACCAGAGAACACATAC
* *
1574290 CATGTAGCCATAGTTCATAA
65 CAGGTAACCATAGTTCATAA
1574310 GCCAGTAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
95 1 0.01
96 68 0.94
97 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (96 bp):
CATGATCCATAAATCAGTAACAATAATATTTTGCTATGAAAACAGGAAACCAGAGAACACATACC
AGGTAACCATAGTTCATAAACCAATAGATTT
Found at i:1576259 original size:17 final size:17
Alignment explanation
Indices: 1576233--1576265 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1576223 CAGTAAATAA
1576233 AAAATATGACTTTTTGG
1 AAAATATGACTTTTTGG
*
1576250 AAAATTTGACTTTTTG
1 AAAATATGACTTTTTG
1576266 AGGCAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (17 bp):
AAAATATGACTTTTTGG
Found at i:1579336 original size:96 final size:96
Alignment explanation
Indices: 1579172--1579358 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
1579162 TAGTAACCGG
* *
1579172 TAGATTCCATGATCCATAAATCAGGAACAATCATATTTTTTAGTGAAAACATGAAACCATATAAC
1 TAGATTCCATGATCCATAAATCAGGAACAATCATATTTTTTAGTGAAAACATGAAACCAGAGAAC
* *
1579237 ATATTTCAGGTAATCATAGTTCATAAACCAA
66 ATATATCAGGTAACCATAGTTCATAAACCAA
* * * *
1579268 TAGATTCCATGATTCATAAATCAGGAACTATTATATTTTCTT-GTGAAAACATGTAACCAGAGAA
1 TAGATTCCATGATCCATAAATCAGGAACAATCATATTTT-TTAGTGAAAACATGAAACCAGAGAA
* *
1579332 CATATATCATGTAGCCATAGTTCATAA
65 CATATATCAGGTAACCATAGTTCATAA
1579359 GCCAGTAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 78 0.98
97 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (96 bp):
TAGATTCCATGATCCATAAATCAGGAACAATCATATTTTTTAGTGAAAACATGAAACCAGAGAAC
ATATATCAGGTAACCATAGTTCATAAACCAA
Found at i:1583012 original size:15 final size:16
Alignment explanation
Indices: 1582992--1583022 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1582982 TCATATAGTG
1582992 AAAGTTTT-GTAACTA
1 AAAGTTTTAGTAACTA
1583007 AAAGTTTTAGTAACTA
1 AAAGTTTTAGTAACTA
1583023 TGACAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
AAAGTTTTAGTAACTA
Found at i:1584081 original size:2 final size:2
Alignment explanation
Indices: 1584076--1584101 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1584066 AAATTGAACA
1584076 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
1584102 TGAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1584312 original size:18 final size:18
Alignment explanation
Indices: 1584289--1584330 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1584279 TATAACTATT
1584289 TTTTTAAAAGGAAATTGA
1 TTTTTAAAAGGAAATTGA
* *
1584307 TTTTTAAAGGGAAATTGG
1 TTTTTAAAAGGAAATTGA
1584325 TTTTTA
1 TTTTTA
1584331 GAGAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (18 bp):
TTTTTAAAAGGAAATTGA
Found at i:1584315 original size:17 final size:17
Alignment explanation
Indices: 1584289--1584346 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
1584279 TATAACTATT
1584289 TTTTTAAAAGGAAATTGA
1 TTTTT-AAAGGAAATTGA
*
1584307 TTTTTAAAGGGAAATTGG
1 TTTTTAAA-GGAAATTGA
* *
1584325 TTTTTAGA-GAAATTTA
1 TTTTTAAAGGAAATTGA
1584341 TTTTTA
1 TTTTTA
1584347 TTTATTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.34
17 3 0.09
18 20 0.57
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (17 bp):
TTTTTAAAGGAAATTGA
Found at i:1590001 original size:14 final size:15
Alignment explanation
Indices: 1589979--1590015 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1589969 TTTCTCTCCT
1589979 TTTTCTTCTTTTTTA
1 TTTTCTTCTTTTTTA
1589994 TTTT-TTCTTTTTT-
1 TTTTCTTCTTTTTTA
1590007 TCTTTCTTC
1 T-TTTCTTC
1590016 GGGAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 12 0.60
15 7 0.35
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTCTTTTTTA
Done.