Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1271225 original size:57 final size:57
Alignment explanation
Indices: 1271115--1271226 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
1271105 AATATATATA
* * **
1271115 TATATATATATATATATATATACTTTATATATAAAGTATATGTATTATATATAAAAAC
1 TATATATATATATATATATATAC-TTATATATAAACTATATATACCATATATAAAAAC
* * *
1271173 TATATAGTTTATATATATATATA-TTATGTATAAACTATATATACCATGTATAAA
1 TATATA-TATATATATATATATACTTATATATAAACTATATATACCATATATAAA
1271227 CTAAAATACT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 25 0.54
58 6 0.13
59 15 0.33
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (57 bp):
TATATATATATATATATATATACTTATATATAAACTATATATACCATATATAAAAAC
Found at i:1271308 original size:24 final size:22
Alignment explanation
Indices: 1271280--1271346 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 22
1271270 CTACATAGTT
1271280 TATATAAATTATATAGTTTATTAA
1 TATATAAATTATATAGTTTA-T-A
* *
1271304 TATATAAACTATATAATTTATA
1 TATATAAATTATATAGTTTATA
*
1271326 TATATATATATATATAGTTTA
1 TATATAAAT-TATATAGTTTA
1271347 AGGTTTAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.22
23 11 0.30
24 18 0.49
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (22 bp):
TATATAAATTATATAGTTTATA
Found at i:1271327 original size:18 final size:18
Alignment explanation
Indices: 1271236--1271327 Score: 51
Period size: 18 Copynumber: 4.7 Consensus size: 18
1271226 ACTAAAATAC
*
1271236 TATAATTTATATGAACTA
1 TATAATTTATATAAACTA
* *
1271254 T-TGAACTATATAGAAACTA
1 TAT-AA-TTTATATAAACTA
* * *
1271273 CATAGTTTATATAAATTA
1 TATAATTTATATAAACTA
1271291 TATAGTTTATTAATATATAAACTA
1 TATA----ATT--TATATAAACTA
1271315 TATAATTTATATA
1 TATAATTTATATA
1271328 TATATATATA
Statistics
Matches: 54, Mismatches: 11, Indels: 18
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.02
18 22 0.41
19 11 0.20
20 4 0.07
22 2 0.04
24 14 0.26
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
TATAATTTATATAAACTA
Found at i:1271328 original size:20 final size:20
Alignment explanation
Indices: 1271111--1271329 Score: 66
Period size: 20 Copynumber: 10.8 Consensus size: 20
1271101 CACTAATATA
* *
1271111 TATATATATATATATATATA-
1 TATATA-ATTTATATATAAAC
* *
1271131 TATATACTTTATATATAAAG
1 TATATAATTTATATATAAAC
* *
1271151 TATATGTATTATATATAAAAAC
1 TATAT-AATT-TATATATAAAC
*
1271173 TATATAGTTTATATAT--A-
1 TATATAATTTATATATAAAC
*
1271190 TATAT-A-TTATGTATAAAC
1 TATATAATTTATATATAAAC
* * *
1271208 TATATATACCATGTATAAACTAAAA
1 --TATATA--ATTTATATA-TAAAC
*
1271233 TACTATAA-TT-TATATGAAC
1 TA-TATAATTTATATATAAAC
* *
1271252 TAT-TGAA-CTATATAGAAAC
1 TATAT-AATTTATATATAAAC
* *
1271271 TACATAGTTTATATA-AATTA-
1 TATATAATTTATATATAA--AC
* *
1271291 TATAGTTTATTAATATATAAAC
1 TATA--TAATTTATATATAAAC
1271313 TATATAATTTATATATA
1 TATATAATTTATATATA
1271330 TATATATATA
Statistics
Matches: 143, Mismatches: 32, Indels: 48
0.64 0.14 0.22
Matches are distributed among these distances:
15 7 0.05
17 7 0.05
18 5 0.03
19 27 0.19
20 46 0.32
21 7 0.05
22 27 0.19
23 5 0.03
24 8 0.06
25 4 0.03
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
TATATAATTTATATATAAAC
Found at i:1271530 original size:22 final size:20
Alignment explanation
Indices: 1271485--1271534 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
1271475 TTTACATATG
1271485 AACTATAT-TATAACTATTA
1 AACTATATATATAACTATTA
*
1271504 AACTATATATATAAATTATGTA
1 AACTATATATAT-AACTAT-TA
1271526 AACTATATA
1 AACTATATA
1271535 GTTTACATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.30
20 3 0.11
21 5 0.19
22 11 0.41
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (20 bp):
AACTATATATATAACTATTA
Found at i:1271654 original size:16 final size:15
Alignment explanation
Indices: 1271633--1271673 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
1271623 TATATACTAC
1271633 ATACTAGTTTATATTT
1 ATACTA-TTTATATTT
1271649 ATACTA--TAT-TTT
1 ATACTATTTATATTT
1271661 ATACTATTTATAT
1 ATACTATTTATAT
1271674 AAAATATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 9 0.41
13 3 0.14
14 3 0.14
15 1 0.05
16 6 0.27
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (15 bp):
ATACTATTTATATTT
Found at i:1271739 original size:18 final size:18
Alignment explanation
Indices: 1271718--1271752 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1271708 ATAGTTGATA
*
1271718 TTTATATATGAACTATAG
1 TTTACATATGAACTATAG
1271736 TTTACATATGAACTATA
1 TTTACATATGAACTATA
1271753 TATATAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:1271809 original size:24 final size:24
Alignment explanation
Indices: 1271763--1271810 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1271753 TATATAAAAC
*
1271763 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAACTATA
*
1271787 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
1271811 AAACTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:1271846 original size:25 final size:25
Alignment explanation
Indices: 1271807--1271856 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1271797 ATTAGTGAAC
1271807 TATAAAACTATTATATAATATACTA
1 TATAAAACTATTATATAATATACTA
**
1271832 TATATAAACTA-TATATTTTATACTA
1 TATA-AAACTATTATATAATATACTA
1271857 CATACTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (25 bp):
TATAAAACTATTATATAATATACTA
Found at i:1271921 original size:22 final size:19
Alignment explanation
Indices: 1271824--1271913 Score: 58
Period size: 19 Copynumber: 4.6 Consensus size: 19
1271814 CTATTATATA
*
1271824 ATATACTATATATAAACTAT
1 ATATA-TATATATAAATTAT
* *
1271844 ATAT-TTTATACTACA-TACT
1 ATATATATATA-TAAATTA-T
* * *
1271863 ATAGTTTATATTTATATTAT
1 ATA-TATATATATAAATTAT
1271883 ATATATATATATAAATTAT
1 ATATATATATATAAATTAT
*
1271902 GTATACTATATA
1 ATATA-TATATA
1271914 GTATAATTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
18 7 0.13
19 24 0.44
20 18 0.33
21 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATATATATATAAATTAT
Found at i:1271923 original size:47 final size:47
Alignment explanation
Indices: 1271862--1271989 Score: 118
Period size: 47 Copynumber: 2.7 Consensus size: 47
1271852 TACTACATAC
* * * * *
1271862 TATAGTTTATATTTATATTATATATATATATATAAATTATGTATACTA
1 TATAGTATA-ATTTATATTATATATATATATAAAAATCATATAAACTA
*
1271910 TATAGTATAATTTACA-TATGA-ACTATATATAAAAATCATATAAACTA
1 TATAGTATAATTTATATTAT-ATA-TATATATAAAAATCATATAAACTA
* * *
1271957 TATACTATAGTTGATATT-TATATACTATATAAA
1 TATAGTATAATTTATATTATATATA-TATATAAA
1271990 TAATTTTACT
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
46 7 0.11
47 49 0.75
48 9 0.14
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (47 bp):
TATAGTATAATTTATATTATATATATATATAAAAATCATATAAACTA
Found at i:1272069 original size:18 final size:17
Alignment explanation
Indices: 1272046--1272158 Score: 63
Period size: 18 Copynumber: 6.5 Consensus size: 17
1272036 TAGTTCATTA
1272046 TATATATAAACTATATGT
1 TATATATAAACTATA-GT
*
1272064 TATATATAAAAACTATACAT
1 TATATAT--AAACTATA-GT
**
1272084 TATATAGTTTA-T-TAG-
1 TATATA-TAAACTATAGT
* *
1272099 CATATATAAACTACA-T
1 TATATATAAACTATAGT
* *
1272115 AATATATAAACTATATGG
1 TATATATAAACTATA-GT
*
1272133 TATATATAAACTATACAT
1 TATATATAAACTATA-GT
1272151 TATATATA
1 TATATATA
1272159 TTTCATAGTA
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
14 2 0.03
15 6 0.08
16 14 0.20
17 2 0.03
18 30 0.42
19 1 0.01
20 15 0.21
21 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (17 bp):
TATATATAAACTATAGT
Found at i:1272086 original size:20 final size:20
Alignment explanation
Indices: 1272041--1272089 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1272031 TTATGTAGTT
*
1272041 CATTATATATATAAACTATA
1 CATTATATATAAAAACTATA
**
1272061 TGTTATATATAAAAACTATA
1 CATTATATATAAAAACTATA
1272081 CATTATATA
1 CATTATATA
1272090 GTTTATTAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (20 bp):
CATTATATATAAAAACTATA
Found at i:1272154 original size:16 final size:16
Alignment explanation
Indices: 1272068--1272156 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
1272058 ATATGTTATA
*
1272068 TATAAAAACTATACAT
1 TATATAAACTATACAT
***
1272084 TATATAGTTTATTAGCA-
1 TATATAAACTA-TA-CAT
* * *
1272101 TATATAAACTACATAA
1 TATATAAACTATACAT
**
1272117 TATATAAACTATATGGT
1 TATATAAACTATA-CAT
1272134 ATATATAAACTATACAT
1 -TATATAAACTATACAT
1272151 TATATA
1 TATATA
1272157 TATTTCATAG
Statistics
Matches: 53, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
15 1 0.02
16 26 0.49
17 11 0.21
18 15 0.28
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.38
Consensus pattern (16 bp):
TATATAAACTATACAT
Found at i:1272158 original size:69 final size:66
Alignment explanation
Indices: 1272045--1272189 Score: 186
Period size: 69 Copynumber: 2.1 Consensus size: 66
1272035 GTAGTTCATT
*
1272045 ATATATATAAACTATATGTTATATATAAAAACTATACATTATATAGTTT-ATTAGCATATATAAA
1 ATATATATAAACTATATGGTATATAT-AAAACTATACATTATATA-TTTCA-TAGCATATATAAA
*
1272109 CTAC
63 ATAC
*
1272113 ATAATATATAAACTATATGGTATATAT-AAACTATACATTATATATATTTCATAGTATATATAAA
1 AT-ATATATAAACTATATGGTATATATAAAACTATACA-T-TATATATTTCATAGCATATATAAA
*
1272177 ATAT
63 ATAC
1272181 ATATATATA
1 ATATATATA
1272190 GTTCATTAGA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
67 17 0.25
68 22 0.32
69 30 0.43
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (66 bp):
ATATATATAAACTATATGGTATATATAAAACTATACATTATATATTTCATAGCATATATAAAATA
C
Found at i:1272189 original size:31 final size:34
Alignment explanation
Indices: 1272066--1272206 Score: 109
Period size: 31 Copynumber: 4.3 Consensus size: 34
1272056 CTATATGTTA
* *
1272066 TATATAAAAACTATACA-T-TATATAGTTTATTAG
1 TATATATAAAC-ATACATTATATATAGTTCATTAG
* * ** *
1272099 CATATATAAAC-TACATAATATATA-AACTATATGG
1 TATATATAAACATACATTATATATAGTTC-AT-TAG
*
1272133 TATATATAAACTATACATTATATATATTTCA-TAG
1 TATATATAAAC-ATACATTATATATAGTTCATTAG
*
1272167 TATATATAAA-ATATA-TATATATAGTTCATTAG
1 TATATATAAACATACATTATATATAGTTCATTAG
1272199 -ATATATAA
1 TATATATAA
1272207 CCTATATAAG
Statistics
Matches: 86, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
31 24 0.28
32 7 0.08
33 17 0.20
34 24 0.28
36 13 0.15
37 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (34 bp):
TATATATAAACATACATTATATATAGTTCATTAG
Found at i:1274227 original size:92 final size:93
Alignment explanation
Indices: 1274069--1274466 Score: 727
Period size: 92 Copynumber: 4.3 Consensus size: 93
1274059 ATGAGGTTAA
*
1274069 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGG-TGCTGCCCATTCTTGCTAAACTG
1 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTC-TGCTAAACTG
1274133 TGTATTCTTTAACA-TGTGAAATAGTATT
65 TGTATTCTTTAACACTGTGAAATAGTATT
*
1274161 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAATGT
1 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
1274226 GTATTCTTTAACACTGTGAAATAGTATT
66 GTATTCTTTAACACTGTGAAATAGTATT
1274254 TGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
1 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
1274318 GTATTCTTTAACACTGTGAAA-AGTATT
66 GTATTCTTTAACACTGTGAAATAGTATT
1274345 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
1 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
1274410 GTATTCTTTAACACTGTGAAATAGTA-T
66 GTATTCTTTAACACTGTGAAATAGTATT
1274437 TGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
1 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
1274467 TGCAATCCAT
Statistics
Matches: 299, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
91 20 0.07
92 242 0.81
93 37 0.12
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (93 bp):
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATT
Found at i:1274553 original size:19 final size:19
Alignment explanation
Indices: 1274513--1274637 Score: 117
Period size: 19 Copynumber: 7.1 Consensus size: 19
1274503 ATAGTTACTT
* *
1274513 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1274533 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1274552 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1274571 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1274585 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1274604 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1274618 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1274637 T
1 T
1274638 GCGATTTTCA
Statistics
Matches: 86, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 42 0.49
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1274592 original size:33 final size:32
Alignment explanation
Indices: 1274549--1274637 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 32
1274539 CGCGAAACCA
**
1274549 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1274581 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1274614 AAGATCGCAACGCGAAACCAAAAT
1 AA-ATCGCAACGCGAAACCAAAAT
1274638 GCGATTTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1274691 original size:20 final size:19
Alignment explanation
Indices: 1274637--1274699 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
1274627 GAAACCAAAA
1274637 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTT-AGTTTCGCGT
*
1274656 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
1274675 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-AGTTTCGCGT
1274695 TGCGA
1 TGCGA
1274700 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 26 0.67
20 13 0.33
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:1276608 original size:14 final size:14
Alignment explanation
Indices: 1276589--1276620 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1276579 ATTGTTTAAT
1276589 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1276603 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1276617 TGAT
1 TGAT
1276621 CTGTGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1276746 original size:19 final size:19
Alignment explanation
Indices: 1276730--1276825 Score: 139
Period size: 19 Copynumber: 5.3 Consensus size: 19
1276720 AAAAATGACT
1276730 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1276749 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1276768 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1276782 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1276801 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1276821 ATCGC
1 ATCGC
1276826 GACGAGAGAT
Statistics
Matches: 69, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.57
20 14 0.20
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1276858 original size:52 final size:53
Alignment explanation
Indices: 1276730--1276844 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 53
1276720 AAAAATGACT
1276730 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
1276782 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCGACGAGAG-
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1276834 ATCGCAATGCG
1 ATCGCAATGCG
1276845 TTTATAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 40 0.66
53 21 0.34
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1276891 original size:52 final size:52
Alignment explanation
Indices: 1276851--1277060 Score: 404
Period size: 52 Copynumber: 4.0 Consensus size: 52
1276841 TGCGTTTATA
1276851 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1276903 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1276955 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1277006 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1277059 AT
1 AT
1277061 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
51 51 0.33
52 88 0.56
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1276893 original size:33 final size:33
Alignment explanation
Indices: 1276851--1277002 Score: 150
Period size: 33 Copynumber: 4.5 Consensus size: 33
1276841 TGCGTTTATA
1276851 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1276884 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
1276924 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1276955 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1276987 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1277003 TTCATTTCGC
Statistics
Matches: 96, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
31 9 0.09
32 25 0.26
33 31 0.32
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1276897 original size:19 final size:19
Alignment explanation
Indices: 1276873--1277088 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
1276863 GATTCTCTCG
1276873 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1276892 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1276911 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1276925 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1276944 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1276963 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1276977 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1276995 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1277014 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1277028 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1277048 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1277062 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1277081 TTGCGATT
1 TTGCGATT
1277089 CTCTCGTTGC
Statistics
Matches: 168, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
15 3 0.02
16 24 0.14
17 16 0.10
18 9 0.05
19 75 0.45
20 12 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1277110 original size:33 final size:33
Alignment explanation
Indices: 1276892--1277102 Score: 241
Period size: 33 Copynumber: 6.2 Consensus size: 33
1276882 TCATTTCGCA
1276892 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1276925 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1276961 CATTGCGATTCTCTCGTTGCG-ATTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCATTGCGATTCTCTCG
1276995 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1277028 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1277062 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1277095 TTGCGATT
1 TTGCGATT
1277103 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 16, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.04
31 5 0.03
32 12 0.08
33 65 0.44
34 31 0.21
35 4 0.03
36 6 0.04
38 9 0.06
39 5 0.03
40 6 0.04
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1280283 original size:20 final size:20
Alignment explanation
Indices: 1280255--1280484 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
1280245 AAATTTCAGT
* *
1280255 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1280275 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1280295 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1280315 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1280335 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1280355 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* * *
1280375 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* ** * *
1280395 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCTC
* *
1280415 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * *
1280435 GTTGCAATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
1280455 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
1280475 GTTGCGATTT
1 GTTGCGATTT
1280485 TAATATTCGC
Statistics
Matches: 181, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1280493 original size:20 final size:20
Alignment explanation
Indices: 1280471--1280568 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
1280461 ATTTATGTGT
*
1280471 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
1280491 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
1280512 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
1280533 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
1280554 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1280569 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:1280564 original size:42 final size:43
Alignment explanation
Indices: 1280471--1280569 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
1280461 ATTTATGTGT
* *
1280471 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
1280512 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
1280554 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1280570 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:1280738 original size:22 final size:22
Alignment explanation
Indices: 1280710--1280761 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1280700 CGATTTTCTC
*
1280710 TATATATAAAGTATAT-GTATTA
1 TATATATAAACTATATAGT-TTA
1280732 TATATATAAACTATATAGTTTA
1 TATATATAAACTATATAGTTTA
1280754 TATATATA
1 TATATATA
1280762 TATTATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (22 bp):
TATATATAAACTATATAGTTTA
Found at i:1280746 original size:11 final size:11
Alignment explanation
Indices: 1280709--1280797 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
1280699 GCGATTTTCT
1280709 CTATATATAAA
1 CTATATATAAA
* * *
1280720 GTATATGTATTA
1 CTATATATA-AA
1280732 -TATATATAAA
1 CTATATATAAA
**
1280742 CTATATAGTTTA
1 CTATATA-TAAA
*
1280754 -TATATATATA
1 CTATATATAAA
* *
1280764 TTATGTATAAA
1 CTATATATAAA
1280775 CTATATAT--A
1 CTATATATAAA
*
1280784 CTATGTATAAA
1 CTATATATAAA
1280795 CTA
1 CTA
1280798 AAATACTATA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
9 8 0.14
10 4 0.07
11 44 0.75
12 3 0.05
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (11 bp):
CTATATATAAA
Found at i:1280781 original size:20 final size:20
Alignment explanation
Indices: 1280756--1280806 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1280746 ATAGTTTATA
*
1280756 TATATATATTATGTATAAAC
1 TATATATACTATGTATAAAC
1280776 TATATATACTATGTATAAAC
1 TATATATACTATGTATAAAC
*
1280796 TA-AAATACTAT
1 TATATATACTAT
1280807 ATAATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (20 bp):
TATATATACTATGTATAAAC
Found at i:1281072 original size:22 final size:22
Alignment explanation
Indices: 1280983--1281072 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
1280973 TAACTTATTC
* *
1280983 TATATGTAAACTATATATACTA
1 TATATATAAACTATATAAACTA
* *
1281005 TATAGT-T-TAC-ATATGAACTA
1 TATA-TATAAACTATATAAACTA
*
1281025 TATGTATAAACTATATAAACTA
1 TATATATAAACTATATAAACTA
* *
1281047 TATATATAAATTATGTAAACTA
1 TATATATAAACTATATAAACTA
1281069 TATA
1 TATA
1281073 GTTTACATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 12 0.22
21 4 0.07
22 37 0.67
23 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (22 bp):
TATATATAAACTATATAAACTA
Found at i:1281152 original size:18 final size:18
Alignment explanation
Indices: 1281112--1281159 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1281102 TTAGTGAATT
*
1281112 GTATAAACTATTTATATA
1 GTATAAACTATATATATA
*
1281130 GTATATACTATATATAATA
1 GTATAAACTATATAT-ATA
*
1281149 -TATAAATTATA
1 GTATAAACTATA
1281160 GTTTATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (18 bp):
GTATAAACTATATATATA
Found at i:1281186 original size:20 final size:20
Alignment explanation
Indices: 1281163--1281216 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1281153 AATTATAGTT
1281163 TATATTTATATACTACATAC
1 TATATTTATATACTACATAC
* *
1281183 TATAGTTTATAT-TTATATAC
1 TATA-TTTATATACTACATAC
1281203 TATATTT-TATACTA
1 TATATTTATATACTA
1281217 TTTATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 14 0.48
21 7 0.24
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (20 bp):
TATATTTATATACTACATAC
Found at i:1281213 original size:27 final size:27
Alignment explanation
Indices: 1281154--1281213 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
1281144 TAATATATAA
1281154 ATTATAGTTTATATTTATATACTACAT
1 ATTATAGTTTATATTTATATACTACAT
* *
1281181 ACTATAGTTTATATTTATATACTATAT
1 ATTATAGTTTATATTTATATACTACAT
*
1281208 TTTATA
1 ATTATA
1281214 CTATTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTATAGTTTATATTTATATACTACAT
Found at i:1281215 original size:12 final size:13
Alignment explanation
Indices: 1281163--1281232 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
1281153 AATTATAGTT
1281163 TATATTTATATAC
1 TATATTTATATAC
* * *
1281176 TACATACTATAGT-T
1 TATAT-TTATA-TAC
1281190 TATATTTATATAC
1 TATATTTATATAC
1281203 TATATTT-TATAC
1 TATATTTATATAC
*
1281215 TAT-TTATATAAAC
1 TATATT-TATATAC
1281228 TATAT
1 TATAT
1281233 AGTTTACATA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
11 2 0.05
12 10 0.23
13 22 0.50
14 9 0.20
15 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:1281291 original size:18 final size:18
Alignment explanation
Indices: 1281270--1281304 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1281260 ATAGTTGATA
*
1281270 TTTATATATGAACTATAG
1 TTTACATATGAACTATAG
1281288 TTTACATATGAACTATA
1 TTTACATATGAACTATA
1281305 TATATAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:1281315 original size:31 final size:32
Alignment explanation
Indices: 1281272--1281343 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
1281262 AGTTGATATT
*
1281272 TATATATGAAC-TATAGTTTACATATGAACTA
1 TATATATAAACATATAGTTTACATATGAACTA
*
1281303 TATATATAAACTATATAGTTTACATATGACCTA
1 TATATATAAAC-ATATAGTTTACATATGAACTA
1281336 TATATATA
1 TATATATA
1281344 GTTTATTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 10 0.27
33 27 0.73
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (32 bp):
TATATATAAACATATAGTTTACATATGAACTA
Found at i:1281360 original size:24 final size:24
Alignment explanation
Indices: 1281314--1281363 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1281304 ATATATAAAC
*
1281314 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAACTATA
*
1281338 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
1281362 TA
1 TA
1281364 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:1281362 original size:86 final size:84
Alignment explanation
Indices: 1281210--1281401 Score: 207
Period size: 86 Copynumber: 2.3 Consensus size: 84
1281200 TACTATATTT
* *
1281210 TATACTATTTATATAAACTATATAGTTTACATATAAACAATATATATACTATAGTTGATATTTAT
1 TATACTATATATATAAACTATATAGTTTACATATAAACAATATATATACTATAGTTGATATCTAT
*
1281275 ATATGAACTATAGTT-TA-CATA
66 ATA--AACTAT--TTATATAATA
* * * *
1281296 TGA-ACTATATATATAAACTATATAGTTTACATATGACCTATATATATAGTTTATTAG-TGA-A-
1 T-ATACTATATATATAAACTATATAGTTTACATATAAACAATATATATA--CTA-TAGTTGATAT
1281357 CTATATAAACTATTTATATAATA
62 CTATATAAACTATTTATATAATA
1281380 TATACTATATATATAAACTATA
1 TATACTATATATATAAACTATA
1281402 GTTTATATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
82 2 0.02
83 3 0.03
84 29 0.32
86 48 0.52
87 2 0.02
88 5 0.05
89 3 0.03
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (84 bp):
TATACTATATATATAAACTATATAGTTTACATATAAACAATATATATACTATAGTTGATATCTAT
ATAAACTATTTATATAATA
Found at i:1281376 original size:2 final size:2
Alignment explanation
Indices: 1281371--1281604 Score: 65
Period size: 2 Copynumber: 112.5 Consensus size: 2
1281361 ATAAACTATT
* * *
1281371 TA TA TA -A TA TA TA CTA TA TA TA TA AA CTA TA GTT TA TA TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* * *
1281413 TT TA TA CTA CA TA CTA TA TT TA TA TA T- TA TA TA T- 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
* * * *
1281455 TA TA AA T- TA TG TA TA CTA TA TA GTA TA -A TT TA CA TA TGA -A
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA T-A TA
* * * *
1281495 CTA TA TA TA AA AA TCA TA TA AA CTA TA TA CTA TA GT- TGA TA TT
1 -TA TA TA TA TA TA T-A TA TA TA -TA TA TA -TA TA -TA T-A TA TA
* * *
1281538 TA TA TA CTA TA TA -A AA TA -A TT TA TA CTA TA GTA TA TA TA AA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
*
1281579 CTA TA TA -A TA TA TA TA AA CTA TA TA T
1 -TA TA TA TA TA TA TA TA TA -TA TA TA T
1281605 TATGTAGTTC
Statistics
Matches: 170, Mismatches: 33, Indels: 58
0.65 0.13 0.22
Matches are distributed among these distances:
1 10 0.06
2 131 0.77
3 29 0.17
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1281401 original size:20 final size:19
Alignment explanation
Indices: 1281358--1281732 Score: 97
Period size: 18 Copynumber: 20.3 Consensus size: 19
1281348 ATTAGTGAAC
*
1281358 TATATAAACTATTTATATA
1 TATATAAACTATATATATA
*
1281377 -ATATATACTATATATATA
1 TATATAAACTATATATATA
* *** * *
1281395 AACTATAGTTTATATTTATT
1 TA-TATAAACTATATATATA
*
1281415 TATACTACATACTATATTTATA
1 TATA-TA-A-ACTATATATATA
*
1281437 TAT-TATA-TAT-TATATA
1 TATATAAACTATATATATA
*
1281453 TATATAAA-T-TATGTATA
1 TATATAAACTATATATATA
* *
1281470 CTATAT--AGTATA-ATTTA
1 -TATATAAACTATATATATA
* * *
1281487 CATATGAACTATATATAAAAA
1 TATATAAACTATATAT--ATA
1281508 TCATATAAACTATATACTATA
1 T-ATATAAACTATATA-TATA
**
1281529 GT-TGAT-ATTTATATACTATA
1 -TAT-ATAAACTATATA-TATA
* **
1281549 TAAAATAATTTATACTATAGTA
1 T-ATATAAACTATA-TATA-TA
1281571 TATATAAACTATATA-ATA
1 TATATAAACTATATATATA
1281589 TATATAAACTATATAT-TA
1 TATATAAACTATATATATA
* * *
1281607 TGTAGT--TC-AT-TA-GTA
1 TATA-TAAACTATATATATA
*
1281622 TATATAAACTATATGT-TA
1 TATATAAACTATATATATA
*
1281640 TATATAAAACTATACAT-TA
1 TATAT-AAACTATATATATA
*
1281659 TATAGT----T-TAT-TAGCA
1 TATA-TAAACTATATATA-TA
*
1281674 TATATAAACTACATA-ATA
1 TATATAAACTATATATATA
**
1281692 TATATAAACTATAT-GGTA
1 TATATAAACTATATATATA
*
1281710 TATATAAACTATACAT-TA
1 TATATAAACTATATATATA
1281728 TATAT
1 TATAT
1281733 TTTCATTAGT
Statistics
Matches: 266, Mismatches: 46, Indels: 89
0.66 0.11 0.22
Matches are distributed among these distances:
13 1 0.00
14 4 0.02
15 13 0.05
16 17 0.06
17 19 0.07
18 96 0.36
19 26 0.10
20 35 0.13
21 23 0.09
22 31 0.12
23 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (19 bp):
TATATAAACTATATATATA
Found at i:1281442 original size:7 final size:7
Alignment explanation
Indices: 1281370--1281464 Score: 54
Period size: 7 Copynumber: 13.6 Consensus size: 7
1281360 TATAAACTAT
1281370 TTATATA
1 TTATATA
*
1281377 ATATATA
1 TTATATA
*
1281384 CTATATA
1 TTATATA
*
1281391 -TATAAA
1 TTATATA
*
1281397 CTATAGT-
1 TTATA-TA
1281404 TTATAT-
1 TTATATA
1281410 TTATTTATA
1 TTA--TATA
* *
1281419 CTACATA
1 TTATATA
*
1281426 CTATAT-
1 TTATATA
1281432 TTATATA
1 TTATATA
1281439 TTATATA
1 TTATATA
1281446 TTATATA
1 TTATATA
*
1281453 TATATAAA
1 T-TATATA
1281461 TTAT
1 TTAT
1281465 GTATACTATA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
6 14 0.20
7 46 0.65
8 9 0.13
9 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (7 bp):
TTATATA
Found at i:1281474 original size:22 final size:22
Alignment explanation
Indices: 1281423--1281604 Score: 99
Period size: 22 Copynumber: 8.1 Consensus size: 22
1281413 TTTATACTAC
* *
1281423 ATACTATATTTATATATTATAT
1 ATACTATATATATAAATTATAT
*
1281445 ATTA-TATATATATAAATTATGT
1 A-TACTATATATATAAATTATAT
* *
1281467 ATACTATATAGTATAATTTACAT
1 ATACTATATA-TATAAATTATAT
* *
1281490 ATGAACTATATATAAAAATCATAT
1 AT--ACTATATATATAAATTATAT
* *
1281514 AAACTATATACTAT-AGTTGATAT
1 ATACTATATA-TATAAATT-ATAT
* * *
1281537 TTA-TATACTATATAAAATAATTT
1 ATACTATA-TATAT-AAATTATAT
1281560 ATACTATAGTATATATAA--ACTAT
1 ATACTATA-TATATA-AATTA-TAT
*
1281583 ATA--ATATATATAAACTATAT
1 ATACTATATATATAAATTATAT
1281603 AT
1 AT
1281605 TATGTAGTTC
Statistics
Matches: 123, Mismatches: 22, Indels: 32
0.69 0.12 0.18
Matches are distributed among these distances:
19 2 0.02
20 11 0.09
21 6 0.05
22 41 0.33
23 33 0.27
24 22 0.18
25 8 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (22 bp):
ATACTATATATATAAATTATAT
Found at i:1281583 original size:9 final size:9
Alignment explanation
Indices: 1281571--1281603 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1281561 TACTATAGTA
1281571 TATATAAAC
1 TATATAAAC
1281580 TATATAATA-
1 TATATAA-AC
1281589 TATATAAAC
1 TATATAAAC
1281598 TATATA
1 TATATA
1281604 TTATGTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAC
Found at i:1281677 original size:52 final size:51
Alignment explanation
Indices: 1281570--1281953 Score: 221
Period size: 51 Copynumber: 7.3 Consensus size: 51
1281560 ATACTATAGT
* * *
1281570 ATATATAAACTATATAATATATATAAACTATATATTATGTAGTTCATTAGT
1 ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCATTAGC
** *
1281621 ATATATAAACTATATGTTATATATAAAACTATACATTATATAGTTTATTAGC
1 ATATATAAACTATATAATATATAT-AAACTATACATTATATAGTTCATTAGC
* *** **
1281673 ATATATAAACTACATAATATATATAAACTATATGGTATATA-TAAACTATA-C
1 ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCA-T-TAGC
* * * * *
1281724 AT-TATATA-T-TTTCATTAGTATATAAA-T-TATATTATATAGTTCATTAGT
1 ATATATAAACTATAT-AATA-TATATAAACTATACATTATATAGTTCATTAGC
* * * **
1281772 ATATATAACCTATATAATATATGGTATATACAAACTATATATTATATAGATCATTAAT
1 ATATATAAACTATAT-A-ATA---TATAT--AAACTATACATTATATAGTTCATTAGC
* * *
1281830 ATATATAACCTATATAGTATATGGTATATACAAACTATATA-T-TATAGTTCATTAGT
1 ATATATAAACTATATA--ATA---TATAT--AAACTATACATTATATAGTTCATTAGC
* ** * * *
1281886 ATATATAAATTATATAGCATATATAAACTATATATTGA-AAAGTTCATTAGT
1 ATATATAAACTATATAATATATATAAACTATACATT-ATATAGTTCATTAGC
*
1281937 ATATTATAACCTATATA
1 ATA-TATAAACTATATA
1281954 TTAATTTATT
Statistics
Matches: 272, Mismatches: 39, Indels: 43
0.77 0.11 0.12
Matches are distributed among these distances:
47 2 0.01
48 13 0.05
49 21 0.08
50 17 0.06
51 63 0.23
52 59 0.22
54 7 0.03
56 29 0.11
57 3 0.01
58 58 0.21
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (51 bp):
ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCATTAGC
Found at i:1281770 original size:29 final size:32
Alignment explanation
Indices: 1281710--1281785 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 32
1281700 CTATATGGTA
*
1281710 TATATAAACTATACATTATATATTTTCATTAG
1 TATATAAACTATACATTATATATGTTCATTAG
*
1281742 TATATAAA-T-TATATTATATA-GTTCATTAG
1 TATATAAACTATACATTATATATGTTCATTAG
1281771 TATATATAACCTATA
1 TATATA-AA-CTATA
1281786 TAATATATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 14 0.37
30 12 0.32
31 1 0.03
32 9 0.24
33 2 0.05
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATAAACTATACATTATATATGTTCATTAG
Found at i:1281775 original size:70 final size:69
Alignment explanation
Indices: 1281620--1281749 Score: 210
Period size: 70 Copynumber: 1.9 Consensus size: 69
1281610 AGTTCATTAG
*
1281620 TATATATAAACTATATGTTATATATAAAACTATACATTATATAGTTTATTAGCATATATAAACTA
1 TATATATAAACTATATGGTATATATAAAACTATACATTATATAGTTTATTAG-ATATATAAACTA
1281685 CATAA
65 CATAA
*
1281690 TATATATAAACTATATGGTATATAT-AAACTATACATTATATATTTTCATTAG-TATATAAA
1 TATATATAAACTATATGGTATATATAAAACTATACATTATATAGTTT-ATTAGATATATAAA
1281750 TTATATTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
68 8 0.14
69 20 0.35
70 29 0.51
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (69 bp):
TATATATAAACTATATGGTATATATAAAACTATACATTATATAGTTTATTAGATATATAAACTAC
ATAA
Found at i:1281876 original size:56 final size:58
Alignment explanation
Indices: 1281751--1281953 Score: 264
Period size: 58 Copynumber: 3.6 Consensus size: 58
1281741 GTATATAAAT
*
1281751 TATATTATATAGTTCATTAGTATATATAACCTATATAATATATGGTATATACAAACTA
1 TATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATACAAACTA
* *
1281809 TATATTATATAGATCATTAATATATATAACCTATATAGTATATGGTATATACAAACTA
1 TATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATACAAACTA
* *
1281867 TATA-T-TATAGTTCATTAGTATATATAA---AT-TA-TATA--GCATATATAAACTA
1 TATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATACAAACTA
*
1281916 TATATTGA-AAAGTTCATTAGTATATTATAACCTATATA
1 TATATT-ATATAGTTCATTAGTATA-TATAACCTATATA
1281954 TTAATTTATT
Statistics
Matches: 129, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
49 16 0.12
50 1 0.01
51 19 0.15
52 7 0.05
53 2 0.02
55 2 0.02
56 22 0.17
57 1 0.01
58 59 0.46
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (58 bp):
TATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATACAAACTA
Found at i:1282139 original size:60 final size:59
Alignment explanation
Indices: 1282029--1282140 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
1282019 AACAAATTTT
1282029 AAATATGAAGCTTAAATTAATAAACTATAATATAAATTTGGACTAAATTGAAAAAGTTG
1 AAATATGAAGCTTAAATTAATAAACTATAATATAAATTTGGACTAAATTGAAAAAGTTG
* * * *
1282088 AAATATGAAGCTTAAATTAGTATATTGCATCAT-TAAATTTGGACTAAATTGAA
1 AAATATGAAGCTTAAATTAATAAACT--ATAATATAAATTTGGACTAAATTGAA
1282141 CAAATTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
59 23 0.49
60 20 0.43
61 4 0.09
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (59 bp):
AAATATGAAGCTTAAATTAATAAACTATAATATAAATTTGGACTAAATTGAAAAAGTTG
Found at i:1282556 original size:113 final size:112
Alignment explanation
Indices: 1282354--1282695 Score: 435
Period size: 113 Copynumber: 3.0 Consensus size: 112
1282344 AAATAAACCA
* * * * *
1282354 TGTTTTTCATTTATTCATCCAAGTTCTTCCCC-AAACCCTCATTTGATCTTCAAAAATACCAAAA
1 TGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
*
1282418 C-CAAAACATTTTCGTGTTTTTTCGATCAAACACCCAAATATTCATCCG
66 CACAAACCA-TTTC-TGTTTTTTCGATCAAACACCCAAATATTCATCCG
1282466 TGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
1 TGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
*
1282531 CACAAACCATTTCATGTTTTTTCGATCAAACACCCAAATTTTCATCGGTGTTCATCTG
66 CACAAACCATTTC-TGTTTTTTCGATCAAACACCCAAA---T-A------TTCATCCG
*
1282589 TGTTCTTCATTTGTTCATCCCAGTTCTT-CCCAAAACCCTCATTTGATCTT-AAAAACA-CTGAA
1 TGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
*
1282651 CACAATCCATTTCTGTTTTTTCGATCAAACACCCACAA-ATTCATC
66 CACAAACCATTTCTGTTTTTTCGATCAAACACCCA-AATATTCATC
1282696 TATTGTTCAT
Statistics
Matches: 207, Mismatches: 10, Indels: 29
0.84 0.04 0.12
Matches are distributed among these distances:
109 6 0.03
112 29 0.14
113 59 0.29
114 6 0.03
115 1 0.00
116 1 0.00
117 1 0.00
119 22 0.11
120 18 0.09
121 7 0.03
122 22 0.11
123 35 0.17
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (112 bp):
TGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAA
CACAAACCATTTCTGTTTTTTCGATCAAACACCCAAATATTCATCCG
Found at i:1282712 original size:120 final size:123
Alignment explanation
Indices: 1282458--1282716 Score: 411
Period size: 120 Copynumber: 2.1 Consensus size: 123
1282448 CACCCAAATA
1282458 TTCATCCGTGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAA
1 TTCATCCGTGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAA
* *
1282523 CACCTAAACACAAACCATTTCATGTTTTTTCGATCAAACACCCAAATTTTCATCGGTG
66 CACCTAAACACAAACCATTTCATGTTTTTTCGATCAAACACCCAAATATTCATCAGTG
*
1282581 TTCATCTGTGTTCTTCATTTGTTCATCCCAGTTCTT-CCCAAAACCCTCATTTGATCTT-AAAAA
1 TTCATCCGTGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAA
* * *
1282644 CA-CTGAACACAATCCATTTC-TGTTTTTTCGATCAAACACCCACAA-ATTCATCTATTG
66 CACCTAAACACAAACCATTTCATGTTTTTTCGATCAAACACCCA-AATATTCATC-AGTG
1282701 TTCATCCGTGTTCTTC
1 TTCATCCGTGTTCTTC
1282717 CCCAAATCCT
Statistics
Matches: 127, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
119 28 0.22
120 35 0.28
121 7 0.06
122 22 0.17
123 35 0.28
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.37
Consensus pattern (123 bp):
TTCATCCGTGTTCTTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAA
CACCTAAACACAAACCATTTCATGTTTTTTCGATCAAACACCCAAATATTCATCAGTG
Found at i:1283214 original size:31 final size:31
Alignment explanation
Indices: 1283176--1283583 Score: 582
Period size: 31 Copynumber: 13.5 Consensus size: 31
1283166 ATAGATATAG
*
1283176 ACTGGTTTATTGTTGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
1283207 ATTGGTTTATTGTTGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1283238 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
1283269 ACTGGTTTATTGATGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
1283300 ATTGGTTTATTGTTGTTGATGTAGATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* * *
1283331 ACTGGTTTATTGATGATGATGTAGATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
1283362 ATTGGTTTATTGTTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
1283393 ACTGGTTTATTGATGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* * *
1283424 ACTGGTTTATTGCTGTAGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
1283455 ACTGGTTTATTGCTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
1283486 ACTGGTTTA------TTGCTGT---TGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1283508 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
1283539 ACTGGTTTATTGATGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1283570 ACTGGTTTATTGTT
1 ACTGGTTTATTGTT
1283584 ATAATGTAAA
Statistics
Matches: 342, Mismatches: 26, Indels: 18
0.89 0.07 0.05
Matches are distributed among these distances:
22 15 0.04
25 6 0.02
28 6 0.02
31 315 0.92
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.48
Consensus pattern (31 bp):
ACTGGTTTATTGTTGTTGATGTAAATGATGT
Found at i:1283508 original size:22 final size:22
Alignment explanation
Indices: 1283480--1283530 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1283470 TTGATGTAAA
1283480 TGATGTACTGGTTTATTGCTGT
1 TGATGTACTGGTTTATTGCTGT
*
1283502 TGATGTACTGGTTTATTGTTGT
1 TGATGTACTGGTTTATTGCTGT
1283524 TGATGTA
1 TGATGTA
1283531 AATGATGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.06, G:0.27, T:0.51
Consensus pattern (22 bp):
TGATGTACTGGTTTATTGCTGT
Found at i:1283622 original size:146 final size:146
Alignment explanation
Indices: 1283356--1283635 Score: 408
Period size: 146 Copynumber: 1.9 Consensus size: 146
1283346 ATGATGTAGA
*
1283356 TGATGTATTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
* * * * *
1283421 TATACTGGTTTATTGCTGTAGATGTAAATGATATACTGGTTTATTGCTGTTGATGTAAATGATGT
66 TATACTGGTTTATTGCTATAGATGTAAATCATATACTGGTTTATTGCAGTGGATGTAAATGATAT
1283486 ACTGGTTTATTGCTGT
131 ACTGGTTTATTGCTGT
1283502 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
* *
1283567 TATACTGGTTTATTGTTATA-ATGTAAA-CA-A-ACCATGGTTTTTTTGCAAAG-GGATGTAAAT
66 TATACTGGTTTATTGCTATAGATGTAAATCATATA-C-TGG-TTTATTGC--AGTGGATGTAAAT
1283627 GATATACTG
126 GATATACTG
1283636 TCTGAAGCAA
Statistics
Matches: 121, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
142 1 0.01
143 2 0.02
144 4 0.03
145 14 0.12
146 99 0.82
147 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (146 bp):
TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
TATACTGGTTTATTGCTATAGATGTAAATCATATACTGGTTTATTGCAGTGGATGTAAATGATAT
ACTGGTTTATTGCTGT
Found at i:1286839 original size:51 final size:51
Alignment explanation
Indices: 1286784--1286880 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
1286774 ATATAAAACT
*
1286784 AAATTTTAAAAAGTAATCATATTAATTTAATTATCAAAATAATTTATGATA
1 AAATTTCAAAAAGTAATCATATTAATTTAATTATCAAAATAATTTATGATA
*
1286835 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAGTAATCATATTAATTTAATTATCAAAATAATTTA
1286881 ATTATTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (51 bp):
AAATTTCAAAAAGTAATCATATTAATTTAATTATCAAAATAATTTATGATA
Found at i:1286872 original size:17 final size:17
Alignment explanation
Indices: 1286850--1286890 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1286840 TCAAAAAGTA
*
1286850 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
1286867 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
*
1286884 ATTATAA
1 ATCATAA
1286891 GTTTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:1288337 original size:29 final size:29
Alignment explanation
Indices: 1288297--1288352 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1288287 TGATGATTAT
* *
1288297 AAAATAATAATAAAAATATCAAACTGAAA
1 AAAATAACAATAAAAATACCAAACTGAAA
* *
1288326 AAAATAACAATATATATACCAAACTGA
1 AAAATAACAATAAAAATACCAAACTGA
1288353 GAATTCGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (29 bp):
AAAATAACAATAAAAATACCAAACTGAAA
Found at i:1295941 original size:3 final size:3
Alignment explanation
Indices: 1295935--1295983 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1295925 TACAACAAAT
1295935 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1295983 T
1 T
1295984 TTAAACATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1296814 original size:4 final size:4
Alignment explanation
Indices: 1296797--1296884 Score: 131
Period size: 4 Copynumber: 22.0 Consensus size: 4
1296787 ATCATTTACA
* *
1296797 ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
1296845 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATCT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1296885 TTTTTTCATA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 79 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:1296820 original size:10 final size:10
Alignment explanation
Indices: 1296797--1296884 Score: 131
Period size: 10 Copynumber: 8.8 Consensus size: 10
1296787 ATCATTTACA
* *
1296797 ATATACATAC
1 ATATATATAT
1296807 ATATATATAT
1 ATATATATAT
1296817 ATATATATAT
1 ATATATATAT
1296827 ATATATATAT
1 ATATATATAT
1296837 ATATATATAT
1 ATATATATAT
1296847 ATATATATAT
1 ATATATATAT
1296857 ATATATATAT
1 ATATATATAT
* *
1296867 ATATGTATGT
1 ATATATATAT
*
1296877 ATCTATAT
1 ATATATAT
1296885 TTTTTTCATA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 72 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:1296824 original size:14 final size:14
Alignment explanation
Indices: 1296797--1296884 Score: 131
Period size: 14 Copynumber: 6.3 Consensus size: 14
1296787 ATCATTTACA
* *
1296797 ATATACATACATAT
1 ATATATATATATAT
1296811 ATATATATATATAT
1 ATATATATATATAT
1296825 ATATATATATATAT
1 ATATATATATATAT
1296839 ATATATATATATAT
1 ATATATATATATAT
1296853 ATATATATATATAT
1 ATATATATATATAT
* * *
1296867 ATATGTATGTATCT
1 ATATATATATATAT
1296881 ATAT
1 ATAT
1296885 TTTTTTCATA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 69 1.00
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:1300387 original size:21 final size:20
Alignment explanation
Indices: 1300301--1300458 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1300291 AAATGACCAA
**
1300301 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1300320 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1300340 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1300360 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1300381 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1300402 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1300422 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1300443 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1300459 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1300487 original size:20 final size:20
Alignment explanation
Indices: 1300425--1300618 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
1300415 CGATTTTCCA
* ** *
1300425 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1300445 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1300465 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1300485 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1300505 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1300525 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1300545 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*** * *
1300565 AAATCGCAA-ATATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1300585 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1300606 AAATCGCAACGCG
1 AAATCGCAACGCG
1300619 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1300509 original size:60 final size:60
Alignment explanation
Indices: 1300425--1300618 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
1300415 CGATTTTCCA
* ** * *
1300425 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1300485 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* ****
1300545 ATATCGCAACGCGTATCCGTAAATCGCAAATATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1300606 AAATCGCAACGCG
1 AAATCGCAACGCG
1300619 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 79 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1301041 original size:33 final size:33
Alignment explanation
Indices: 1301002--1301072 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1300992 TTCACTTAGA
*
1301002 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1301035 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1301068 TTTCA
1 TTTCA
1301073 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1301196 original size:20 final size:20
Alignment explanation
Indices: 1301152--1301261 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1301142 TGCAGAAGAG
*
1301152 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1301173 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1301193 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1301214 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1301228 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1301247 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1301262 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1301209 original size:41 final size:38
Alignment explanation
Indices: 1301145--1301261 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
1301135 TTCAATTTGC
* *
1301145 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1301183 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1301224 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1301257 AGAAT
1 AGAAT
1301262 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1301231 original size:14 final size:14
Alignment explanation
Indices: 1301212--1301268 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1301202 GAGAAATGAA
1301212 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1301226 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1301245 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1301259 AATCGCAACG
1 AATCGCAACG
1301269 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1301244 original size:33 final size:33
Alignment explanation
Indices: 1301204--1301284 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1301194 CGCAACGAGA
1301204 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1301237 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1301270 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1301285 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1301325 original size:33 final size:33
Alignment explanation
Indices: 1301283--1301399 Score: 198
Period size: 33 Copynumber: 3.5 Consensus size: 33
1301273 ACCAAAATCG
*
1301283 CATTGCGATTTTAATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1301316 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1301349 CGTTGCGATTGTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
1301382 CGTTGCGATTTTCATTTC
1 CATTGCGATTTTCATTTC
1301400 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1301342 original size:19 final size:19
Alignment explanation
Indices: 1301280--1301377 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
1301270 GAAACCAAAA
* *
1301280 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1301299 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1301313 TCTCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1301332 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1301346 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1301365 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1301378 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 19 0.32
16 5 0.08
17 5 0.08
19 31 0.52
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1301354 original size:14 final size:14
Alignment explanation
Indices: 1301302--1301391 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1301292 TTTAATTTCG
1301302 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1301316 CATTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1301335 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1301349 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1301368 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1301382 CGTTGCGATT
1 CGTTGCGATT
1301392 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 19 0.32
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1303256 original size:93 final size:93
Alignment explanation
Indices: 1303097--1303565 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
1303087 TAGATTGCTT
*
1303097 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1303162 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1303190 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1303255 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1303283 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1303348 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1303376 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1303441 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1303469 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1303534 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1303561 AGTAA
1 AGTAA
1303566 TGCAATCCAA
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 369 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1303658 original size:19 final size:19
Alignment explanation
Indices: 1303618--1303746 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1303608 TAGTTTACTT
* *
1303618 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1303638 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1303657 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1303676 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1303690 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1303709 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1303723 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1303742 TCGCA
1 TCGCA
1303747 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1303697 original size:33 final size:32
Alignment explanation
Indices: 1303654--1303746 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1303644 CGCGAAACCA
**
1303654 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1303686 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1303719 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1303747 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1303744 original size:52 final size:52
Alignment explanation
Indices: 1303618--1303746 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1303608 TAGTTTACTT
**
1303618 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1303670 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1303723 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1303747 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1303764 original size:19 final size:18
Alignment explanation
Indices: 1303742--1303860 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
1303732 GAAACCAAAA
*
1303742 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
1303761 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
1303777 T--CGTTGCGATTTTCTTT
1 TCGCGTTGCGATTTTC-TT
* *
1303794 TCGCATTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
1303810 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
1303827 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
1303846 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1303861 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.48
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:1303783 original size:14 final size:14
Alignment explanation
Indices: 1303764--1303820 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1303754 TTTCATTTCG
1303764 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1303778 CGTTGCGATTTTCTTTT
1 CGTTGCGA--TTC-TTT
*
1303795 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1303811 CGTTGCGATT
1 CGTTGCGATT
1303821 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1303789 original size:33 final size:33
Alignment explanation
Indices: 1303747--1303839 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1303737 CAAAATCGCA
*
1303747 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
1303780 TTGCGATTTTCTTTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1303813 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1303840 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1303868 original size:20 final size:19
Alignment explanation
Indices: 1303811--1303876 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
1303801 GCGATTCTGT
1303811 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1303830 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
1303849 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1303869 TGTTGCGA
1 CGTTGCGA
1303877 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:1305817 original size:14 final size:14
Alignment explanation
Indices: 1305798--1305833 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1305788 ATTGTTTAAT
1305798 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1305812 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1305826 TGATTTGT
1 TGATTTGT
1305834 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1306008 original size:20 final size:19
Alignment explanation
Indices: 1305940--1306018 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
1305930 AAAAATGACT
1305940 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1305959 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1305973 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1305992 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1306012 ATCGCAA
1 ATCGCAA
1306019 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1306080 original size:33 final size:32
Alignment explanation
Indices: 1306043--1306290 Score: 164
Period size: 33 Copynumber: 7.5 Consensus size: 32
1306033 TGCGTTTATA
* *
1306043 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-
1 ATTTCGCATTGCGATT-T-TCATTGCGCA-TTGCG
*
1306076 ATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTTTCATTGCGCATTGCG
* * *
1306108 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT-TCGCATTGCGATTTTCATTGCGCATTGCG
* * * *
1306141 ATTCTCTCGTTGCGATTCTCTCGTTGCG-ATTTTC-
1 ATT-TCGCATTGCGATT-T-TCATTGCGCA-TTGCG
*
1306175 ATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTTTCATTGCGCATTGCG
* * * *
1306207 ATTCTCTCGTTGAGATTTTCATTTCCGCATTGCG
1 ATT-TCGCATTGCGATTTTCA-TTGCGCATTGCG
* * *
1306241 ATTT-TCATGTTGGGATTTTCATTTCGCATTGCG
1 ATTTCGCA--TTGCGATTTTCATTGCGCATTGCG
* *
1306274 ATTCTCTCGTTGCGATT
1 ATT-TCGCATTGCGATT
1306291 GTAATTTCCG
Statistics
Matches: 179, Mismatches: 22, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
31 18 0.10
32 12 0.07
33 107 0.60
34 31 0.17
35 11 0.06
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (32 bp):
ATTTCGCATTGCGATTTTCATTGCGCATTGCG
Found at i:1306089 original size:19 final size:19
Alignment explanation
Indices: 1306065--1306276 Score: 186
Period size: 19 Copynumber: 12.4 Consensus size: 19
1306055 GATTCTCTCG
1306065 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306084 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1306103 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1306117 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1306136 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1306150 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1306164 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306183 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1306202 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1306216 TTGAGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1306236 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1306250 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306269 TTGCGATT
1 TTGCGATT
1306277 CTCTCGTTGC
Statistics
Matches: 162, Mismatches: 10, Indels: 42
0.76 0.05 0.20
Matches are distributed among these distances:
14 42 0.26
16 23 0.14
17 20 0.12
18 3 0.02
19 63 0.39
20 11 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1306100 original size:52 final size:52
Alignment explanation
Indices: 1306043--1306248 Score: 350
Period size: 52 Copynumber: 4.0 Consensus size: 52
1306033 TGCGTTTATA
1306043 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1306095 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1306145 -TCTCG--TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1306194 ATTTCGCATTGCGATTCTCTCGTTGAGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1306247 AT
1 AT
1306249 GTTGGGATTT
Statistics
Matches: 145, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
47 39 0.27
49 7 0.05
50 7 0.05
52 75 0.52
53 17 0.12
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1306122 original size:14 final size:14
Alignment explanation
Indices: 1306103--1306171 Score: 84
Period size: 14 Copynumber: 4.6 Consensus size: 14
1306093 TCATTTCGCA
1306103 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1306117 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1306134 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1306150 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
1306164 TTGCGATT
1 TTGCGATT
1306172 TTCATTTCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
14 28 0.58
16 7 0.15
17 7 0.15
19 6 0.12
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1306167 original size:99 final size:100
Alignment explanation
Indices: 1306051--1306243 Score: 370
Period size: 99 Copynumber: 1.9 Consensus size: 100
1306041 TAATTTCGCA
1306051 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
1306116 GTTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
66 GTTGAGATTTTCATTTCCGCATTGCGATTCTCTCG
1306150 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1306215 GTTGAGATTTTCATTTCCGCATTGCGATT
66 GTTGAGATTTTCATTTCCGCATTGCGATT
1306244 TTCATGTTGG
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
99 80 0.87
100 12 0.13
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (100 bp):
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
GTTGAGATTTTCATTTCCGCATTGCGATTCTCTCG
Found at i:1306298 original size:33 final size:33
Alignment explanation
Indices: 1306084--1306290 Score: 269
Period size: 33 Copynumber: 6.2 Consensus size: 33
1306074 TCATTTCGCA
1306084 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1306117 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* * * * *
1306150 TTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1306183 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
1306216 TTGAGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1306250 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1306283 TTGCGATT
1 TTGCGATT
1306291 GTAATTTCCG
Statistics
Matches: 150, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 91 0.61
34 34 0.23
35 10 0.07
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1308797 original size:24 final size:24
Alignment explanation
Indices: 1308763--1308809 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1308753 CTGAAACATC
1308763 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1308787 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1308810 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1309520 original size:20 final size:20
Alignment explanation
Indices: 1309492--1309721 Score: 230
Period size: 20 Copynumber: 11.5 Consensus size: 20
1309482 AAATTTCAGT
* * *
1309492 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1309512 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1309532 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1309552 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1309572 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1309592 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1309612 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1309632 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1309652 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1309672 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
1309692 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
1309712 GTTGCGATTT
1 GTTGCGATTT
1309722 TGGAAAATCA
Statistics
Matches: 183, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.02
20 175 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1309781 original size:42 final size:43
Alignment explanation
Indices: 1309688--1309786 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
1309678 ATTTATGTGT
* *
1309688 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
* ** *
1309729 TCACAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
1309771 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1309787 GAAACTGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
41 9 0.20
42 32 0.71
43 4 0.09
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:1309954 original size:17 final size:18
Alignment explanation
Indices: 1309929--1309977 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1309919 ATTTTCTCTT
*
1309929 TAAAAAAAAT-AATTGAA
1 TAAACAAAATAAATTGAA
*
1309946 TAAACAAAATAGAATTGTA
1 TAAACAAAATA-AATTGAA
1309965 TAAAC-AAATAAAT
1 TAAACAAAATAAAT
1309978 GACTAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 12 0.43
18 5 0.18
19 11 0.39
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (18 bp):
TAAACAAAATAAATTGAA
Found at i:1310619 original size:2 final size:2
Alignment explanation
Indices: 1310612--1310639 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1310602 TCATAAATTA
1310612 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
1310640 GTATGAGGAA
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:1328903 original size:76 final size:76
Alignment explanation
Indices: 1328777--1328928 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
1328767 TTAAAGTAGG
1328777 GCTCTCATATTGGCCATTAATGTAATCTAATCGTAGTAGTTGATTGTAGGGGGACTCCAACTGTA
1 GCTCTCATATTGGCCATTAATGTAATCTAATCGTAGTAGTTGATTGTAGGGGGACTCCAACTGTA
1328842 ACATCCTCAAT
66 ACATCCTCAAT
*
1328853 GCTCTCATATTGGCCATTAATGTAATCTAATCTTAGTAGTTGATTGTAGGGGGACTCCAACTGTA
1 GCTCTCATATTGGCCATTAATGTAATCTAATCGTAGTAGTTGATTGTAGGGGGACTCCAACTGTA
1328918 ACATCCTCAAT
66 ACATCCTCAAT
1328929 ACCGGGTTAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (76 bp):
GCTCTCATATTGGCCATTAATGTAATCTAATCGTAGTAGTTGATTGTAGGGGGACTCCAACTGTA
ACATCCTCAAT
Found at i:1329689 original size:20 final size:20
Alignment explanation
Indices: 1329664--1329717 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1329654 GAATGTAATA
1329664 AGGGTATCGATACCTTAGGG
1 AGGGTATCGATACCTTAGGG
1329684 AGGGTATCGATACCTTAGGG
1 AGGGTATCGATACCTTAGGG
*
1329704 AAGGTATCGATACC
1 AGGGTATCGATACC
1329718 CCCTAAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (20 bp):
AGGGTATCGATACCTTAGGG
Found at i:1330892 original size:22 final size:22
Alignment explanation
Indices: 1330834--1330894 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1330824 GGGTCTACGC
*
1330834 GGTCATTCGGGAA-ATATACAGA
1 GGTCATTC-GGAACAAATACAGA
* * * *
1330856 GGTCCTACGGGACAAATACATA
1 GGTCATTCGGAACAAATACAGA
1330878 GGTCATTCGGAACAAAT
1 GGTCATTCGGAACAAAT
1330895 TTCACATGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (22 bp):
GGTCATTCGGAACAAATACAGA
Found at i:1331553 original size:22 final size:21
Alignment explanation
Indices: 1331525--1331584 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1331515 TTTTAGCATT
1331525 TGGTACTGTTCACTACTATTCA
1 TGGTACTGTTCA-TACTATTCA
* *
1331547 TGGTACTATTCATTACTGTTCA
1 TGGTACTGTTCA-TACTATTCA
**
1331569 CAGTACTGTTCATACT
1 TGGTACTGTTCATACT
1331585 GTATAGTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (21 bp):
TGGTACTGTTCATACTATTCA
Found at i:1334819 original size:64 final size:64
Alignment explanation
Indices: 1334751--1334907 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
1334741 TTGAAGGTGT
**
1334751 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAAATAAAACATCGAATGCA-ATTAGTG
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAAAAATAAAACATCGAATGCATATTA-TG
1334814 C
64 C
* * * *
1334815 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAAAAATAAAACATCGAATGCATATTATGC
* *
1334879 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
1334908 ACCTTCATCA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAAAAATAAAACATCGAATGCATATTATGC
Found at i:1335452 original size:15 final size:15
Alignment explanation
Indices: 1335434--1335467 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1335424 GAGGGTATAA
1335434 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
1335449 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
1335464 TAGT
1 TAGT
1335468 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:1339411 original size:123 final size:123
Alignment explanation
Indices: 1339192--1339437 Score: 456
Period size: 123 Copynumber: 2.0 Consensus size: 123
1339182 GGTGGAATTT
* *
1339192 CTCAAGGATTATGATGTTGTGATTGATTTCCACCCCGGAAAGGCAAATGTGGTAGCTGATGCCTT
1 CTCAAGGATTATGATGTTGTGATTGATTTCCACCCCGAAAAGGCAAATGTGGTAGCTAATGCCTT
*
1339257 GAGTAGAAAGACGTTTATAGCTTTGCGAGCTCTTGATGCTAGATTATCGTTAAGAGAA
66 GAGTAGAAAGACGTTTACAGCTTTGCGAGCTCTTGATGCTAGATTATCGTTAAGAGAA
*
1339315 CTCAAGGATTATGATGTTGTGATTGATTTCCATCCCGAAAAGGCAAATGTGGTAGCTAATGCCTT
1 CTCAAGGATTATGATGTTGTGATTGATTTCCACCCCGAAAAGGCAAATGTGGTAGCTAATGCCTT
1339380 GAGTAGAAAGACGTTTACAGCTTTGCGAGCTCTTGATGCTAGATTATCGTTAAGAGAA
66 GAGTAGAAAGACGTTTACAGCTTTGCGAGCTCTTGATGCTAGATTATCGTTAAGAGAA
1339438 AATGGTGCAA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (123 bp):
CTCAAGGATTATGATGTTGTGATTGATTTCCACCCCGAAAAGGCAAATGTGGTAGCTAATGCCTT
GAGTAGAAAGACGTTTACAGCTTTGCGAGCTCTTGATGCTAGATTATCGTTAAGAGAA
Found at i:1341376 original size:64 final size:60
Alignment explanation
Indices: 1341308--1341461 Score: 150
Period size: 64 Copynumber: 2.5 Consensus size: 60
1341298 TTGAAGGTGT
* ** *
1341308 ATCGATGCACATGTAGTGCATCGATGCA-CTCTTTTAAAAATAAAACATAGAATTCAATTAGTGC
1 ATCGATGCACAAGTAGTGCATCGATGCATC-CCATTAAAAATAAAACATAGAATGC-ATT--T-C
* * * * *
1341372 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTT
1 ATCGATGCACAA-GTAGTGCATCGATGCATCCCATTAAAAATAAAACATAGAATGCATTTC
1341432 ATGCGATGCACAAGTAGTGCATCGATGCAT
1 AT-CGATGCACAAGTAGTGCATCGATGCAT
1341462 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
60 4 0.05
61 23 0.31
63 3 0.04
64 42 0.56
65 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (60 bp):
ATCGATGCACAAGTAGTGCATCGATGCATCCCATTAAAAATAAAACATAGAATGCATTTC
Found at i:1346647 original size:8 final size:8
Alignment explanation
Indices: 1346634--1346659 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1346624 ACTAAAATAA
1346634 AAATTTTG
1 AAATTTTG
1346642 AAATTTTG
1 AAATTTTG
1346650 AAATTTTG
1 AAATTTTG
1346658 AA
1 AA
1346660 GTCTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (8 bp):
AAATTTTG
Found at i:1352484 original size:28 final size:28
Alignment explanation
Indices: 1352400--1352474 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
1352390 TGTCACGCTG
*
1352400 GAAAGAGCGTTTC-AGGTGACGCGCATTT
1 GAAAGAGCGTTTCAAGG-AACGCGCATTT
1352428 GAAAGAGCGTTTCAAGGAACGCGCATTT
1 GAAAGAGCGTTTCAAGGAACGCGCATTT
1352456 GAAAGAGCGTTTCAAGGAA
1 GAAAGAGCGTTTCAAGGAA
1352475 TGCGTCTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 42 0.93
29 3 0.07
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (28 bp):
GAAAGAGCGTTTCAAGGAACGCGCATTT
Found at i:1353505 original size:30 final size:28
Alignment explanation
Indices: 1353450--1353506 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1353440 TAGTAAGTAA
1353450 TATATTGGTCAAAGGGTATTATTTAGAG
1 TATATTGGTCAAAGGGTATTATTTAGAG
*
1353478 TATATTAGGTTCATAGGGTGATT-TTTAGA
1 TATATT-GG-TCAAAGGGT-ATTATTTAGA
1353507 TCAAATCGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 2 0.08
30 14 0.56
31 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.42
Consensus pattern (28 bp):
TATATTGGTCAAAGGGTATTATTTAGAG
Found at i:1355155 original size:20 final size:20
Alignment explanation
Indices: 1355111--1355155 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1355101 AAAGACTTTG
*
1355111 TAACTAACCATTAACAACCT
1 TAACTAAACATTAACAACCT
* *
1355131 CAACTAAACATTAACAGCCT
1 TAACTAAACATTAACAACCT
1355151 TAACT
1 TAACT
1355156 GCTAACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (20 bp):
TAACTAAACATTAACAACCT
Found at i:1355373 original size:36 final size:35
Alignment explanation
Indices: 1355326--1355435 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 35
1355316 AGATGAACAA
1355326 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCACT-
1 TTGAATCGAAAGTG-CGATGCTTCCTTTCGTTC-CTC
* * *
1355362 TTGAATTGAAAGTGCCGATGATTCCTTTCGTTCTTC
1 TTGAATCGAAAGTG-CGATGCTTCCTTTCGTTCCTC
* *
1355398 TTGAATCGAAAGTGCTGATGCTTCCTTTCATTCTTC
1 TTGAATCGAAAGTGC-GATGCTTCCTTTCGTTCCTC
1355434 TT
1 TT
1355436 CCTCACCTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 2 0.03
36 63 0.97
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (35 bp):
TTGAATCGAAAGTGCGATGCTTCCTTTCGTTCCTC
Found at i:1356813 original size:20 final size:20
Alignment explanation
Indices: 1356769--1356813 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1356759 AAAGACTTTG
*
1356769 TAACTAACCATTAACAACCT
1 TAACTAAACATTAACAACCT
* *
1356789 CAACTAAACATTAACAGCCT
1 TAACTAAACATTAACAACCT
1356809 TAACT
1 TAACT
1356814 GCTAACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (20 bp):
TAACTAAACATTAACAACCT
Found at i:1357032 original size:36 final size:36
Alignment explanation
Indices: 1356985--1357094 Score: 168
Period size: 36 Copynumber: 3.1 Consensus size: 36
1356975 AGATGAACAA
1356985 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT-
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-CTC
* *
1357021 TTGAATTGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCCTC
* *
1357057 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCCTC
1357093 TT
1 TT
1357095 CCTCACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 1 0.01
36 68 0.99
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCCTC
Found at i:1358472 original size:20 final size:20
Alignment explanation
Indices: 1358428--1358472 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1358418 AAAGACTTTG
*
1358428 TAACTAACCATTAACAACCT
1 TAACTAAACATTAACAACCT
* *
1358448 CAACTAAACATTAACAGCCT
1 TAACTAAACATTAACAACCT
1358468 TAACT
1 TAACT
1358473 GCTAACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (20 bp):
TAACTAAACATTAACAACCT
Found at i:1365765 original size:76 final size:75
Alignment explanation
Indices: 1365638--1365802 Score: 224
Period size: 76 Copynumber: 2.2 Consensus size: 75
1365628 TTAAACTCAA
* *
1365638 ATTTAGGATAATATTTTAAACATTATATTTTGTCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
1365703 TTTTAAGTAAG
65 TTTTAAGTAAG
* * * *
1365714 TTTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
* *
1365778 TTTTAATTAGG
65 TTTTAAGTAAG
*
1365789 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1365803 ATTATTTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 36 0.46
76 42 0.54
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAAGTAAG
Found at i:1366566 original size:21 final size:20
Alignment explanation
Indices: 1366526--1366578 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1366516 AAATCCTCCT
*
1366526 TTTATATTTATTACTATTACTA
1 TTTAT-TTTA-TATTATTACTA
*
1366548 TTTATTATTATATTATTACTT
1 TTTATT-TTATATTATTACTA
1366569 TTTATTTTAT
1 TTTATTTTAT
1366579 TTTAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.14
21 16 0.57
22 8 0.29
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTTTATATTATTACTA
Found at i:1366573 original size:18 final size:17
Alignment explanation
Indices: 1366532--1366579 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1366522 TCCTTTTATA
1366532 TTTATTACTATTACTATT
1 TTTATTA-TATTACTATT
*
1366550 TATTATTATATTATTACTT
1 T-TTATTATATTACTA-TT
*
1366569 TTTATTTTATT
1 TTTATTATATT
1366580 TTAATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTATATTACTATT
Found at i:1372450 original size:16 final size:17
Alignment explanation
Indices: 1372421--1372453 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1372411 TCAAACAATG
1372421 CAGTGCAGGAAAAAAAA
1 CAGTGCAGGAAAAAAAA
1372438 CAGTGCA-GAAAAAAAA
1 CAGTGCAGGAAAAAAAA
1372454 ATAGATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.12, G:0.21, T:0.06
Consensus pattern (17 bp):
CAGTGCAGGAAAAAAAA
Found at i:1372454 original size:17 final size:17
Alignment explanation
Indices: 1372421--1372454 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1372411 TCAAACAATG
*
1372421 CAGTGCAGGAAAAAAAA
1 CAGTGCAGAAAAAAAAA
1372438 CAGTGCAGAAAAAAAAA
1 CAGTGCAGAAAAAAAAA
1372455 TAGATTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.21, T:0.06
Consensus pattern (17 bp):
CAGTGCAGAAAAAAAAA
Found at i:1374206 original size:76 final size:75
Alignment explanation
Indices: 1374079--1374243 Score: 215
Period size: 76 Copynumber: 2.2 Consensus size: 75
1374069 TTAAACTCAA
* *
1374079 ATTTAGGATAATATTTTAAACATTATATTTTGTCTTTGTATTTTAGTTTAAAGAGGTTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAAGAGG-TTTTAGTA
1374144 TTTTAATTAAG
65 TTTTAATTAAG
* * * * * *
1374155 TTTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATATGTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAAGAGGTTTTAGTA
*
1374219 TTTTAATTAGG
65 TTTTAATTAAG
*
1374230 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1374244 ATTATTTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
75 37 0.48
76 40 0.52
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAAGAGGTTTTAGTAT
TTTAATTAAG
Found at i:1374918 original size:21 final size:22
Alignment explanation
Indices: 1374887--1374928 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1374877 AATCTCTTTA
1374887 ATTTGTTTATTTAATTATTATG
1 ATTTGTTTATTTAATTATTATG
*
1374909 ATTT-TTTATTTAATTCTTAT
1 ATTTGTTTATTTAATTATTAT
1374929 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTTGTTTATTTAATTATTATG
Found at i:1375016 original size:22 final size:22
Alignment explanation
Indices: 1374965--1375026 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
1374955 AAATCCCACT
1374965 TTTATATTTATTACTATTA-A-TA
1 TTTAT-TTTATTA-TATTATATTA
1374987 TTTA--TTATTATATTATATTA
1 TTTATTTTATTATATTATATTA
* *
1375007 TTTATTTTATTTTAATATAT
1 TTTATTTTATTATATTATAT
1375027 CTTTTTAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 6 0.18
22 16 0.47
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTTTATTATATTATATTA
Done.