Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 39 of 172
Found at i:12312771 original size:42 final size:42
Alignment explanation
Indices: 12312724--12312832 Score: 130
Period size: 43 Copynumber: 2.6 Consensus size: 42
12312714 CTAAGATTAT
12312724 GTGTAAGACCATATCTGGGATATGGCATCGATACGAA-ACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATA-GAAGACTTC
* * * * *
12312766 GTGTAAGACCATAGCTGGGCTATTCGCATCGATATAAGATTTC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATAGAAGACTTC
* *
12312809 ATGTAAGACCATATCTAGGATATG
1 GTGTAAGACCATATCTGGGATATG
12312833 ACATTGGTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
42 23 0.42
43 32 0.58
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATAGAAGACTTC
Found at i:12317963 original size:29 final size:29
Alignment explanation
Indices: 12317872--12317951 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
12317862 CGATATCCAT
* * * *
12317872 CACCAATACATAGTACCTGCAAAATAAAA
1 CACCAGTACAAAGTACCTGCTAAAGAAAA
* ** *
12317901 CACTAACACAAAGTGCCTGCTAAAGAAAA
1 CACCAGTACAAAGTACCTGCTAAAGAAAA
12317930 CACCAGTACAAAGTACCTGCTA
1 CACCAGTACAAAGTACCTGCTA
12317952 TTGAAATCAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.16
Consensus pattern (29 bp):
CACCAGTACAAAGTACCTGCTAAAGAAAA
Found at i:12320071 original size:18 final size:18
Alignment explanation
Indices: 12320045--12320107 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
12320035 TACTAAAACG
*
12320045 AAAAACAATTGAGTGAAT
1 AAAAGCAATTGAGTGAAT
*
12320063 AAAAGCAATGTGAG-GATT
1 AAAAGCAAT-TGAGTGAAT
* *
12320081 AAAAGCAAAGTGAGTGGCAT
1 AAAAGC-AATTGAGT-GAAT
12320101 AAAAGCA
1 AAAAGCA
12320108 TGATTAGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 21 0.58
19 7 0.19
20 8 0.22
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.17
Consensus pattern (18 bp):
AAAAGCAATTGAGTGAAT
Found at i:12325767 original size:40 final size:40
Alignment explanation
Indices: 12325723--12325828 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 40
12325713 CGACGACAAA
*
12325723 TCAACTATGTTTGGCACTTAGTGTGC-ATTTCGAGATAGCT
1 TCAACTATATTTGGCACTTAGTGTGCGATTTCGA-ATAGCT
* *
12325763 TCAACTATATATATAGCACTTAGTGTGCGATTTGGAATAGCT
1 TCAACTATAT-T-TGGCACTTAGTGTGCGATTTCGAATAGCT
* *
12325805 TCAGCTATATGTGGCACTTAGTGT
1 TCAACTATATTTGGCACTTAGTGT
12325829 TGGCTGATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
40 21 0.37
41 1 0.02
42 29 0.51
43 6 0.11
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (40 bp):
TCAACTATATTTGGCACTTAGTGTGCGATTTCGAATAGCT
Found at i:12342329 original size:40 final size:39
Alignment explanation
Indices: 12342258--12342468 Score: 282
Period size: 40 Copynumber: 5.3 Consensus size: 39
12342248 CCTTCGAGGT
* *
12342258 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGAAC
1 TTAGCCCGGTTATAG-TAACTCGCACAAATGCCTTCGG-AC
*
12342297 TTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTC-GGAC
* *
12342337 TTAGCCCGGTTATAGTAACTCACACAATTGCCTTCGGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTC-GGAC
* *
12342377 TTGGCCCGGTTATAGTAACTCACACAAATGCCTTCAGGAC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTC-GGAC
* *
12342417 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGC
1 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGAC
12342456 TTAGCCCGGTTAT
1 TTAGCCCGGTTAT
12342469 CAATCCGAAT
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 20 0.13
40 135 0.86
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (39 bp):
TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGAC
Found at i:12344558 original size:55 final size:54
Alignment explanation
Indices: 12344463--12344612 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
12344453 CTACTTTGTT
* ** * *
12344463 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
12344517 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
12344572 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
12344613 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:12344575 original size:27 final size:27
Alignment explanation
Indices: 12344435--12344612 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
12344425 TAAATTGTAC
12344435 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
12344462 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
12344488 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
12344516 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
12344544 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
12344571 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
12344598 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12344613 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:12344576 original size:82 final size:81
Alignment explanation
Indices: 12344436--12344591 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
12344426 AAATTGTACA
* * * *
12344436 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
12344501 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
12344517 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
12344580 TGTGCGAGTTGA
63 TGTGCGAATTGA
12344592 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:12347940 original size:53 final size:53
Alignment explanation
Indices: 12347861--12347970 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
12347851 TGCAAAGAAT
*
12347861 GAAA-GGCCTAAATGTGATCAATGTGGAAGATGACATTTTGGTGAATGTTGGG
1 GAAAGGGCCTAAATGTGATCAATGTGGAAGACGACATTTTGGTGAATGTTGGG
* *
12347913 GAAAGGGCCTGAATGTGATCAATGTGGAAGACGACATTTTGGTGAATGTTGTG
1 GAAAGGGCCTAAATGTGATCAATGTGGAAGACGACATTTTGGTGAATGTTGGG
12347966 GAAAG
1 GAAAG
12347971 AGTAATAATC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 4 0.07
53 50 0.93
ACGTcount: A:0.31, C:0.08, G:0.34, T:0.27
Consensus pattern (53 bp):
GAAAGGGCCTAAATGTGATCAATGTGGAAGACGACATTTTGGTGAATGTTGGG
Found at i:12368856 original size:34 final size:34
Alignment explanation
Indices: 12368818--12368882 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
12368808 AGTAACAGTC
12368818 CAGTAACAAT-TAGGGCCTTAGCCCAATACAGTAT
1 CAGTAACAATGT-GGGCCTTAGCCCAATACAGTAT
** * *
12368852 CAGTAGTAGTGTGGGCCTTAGCCCATTACAG
1 CAGTAACAATGTGGGCCTTAGCCCAATACAG
12368883 CAATAGTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 25 0.96
35 1 0.04
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (34 bp):
CAGTAACAATGTGGGCCTTAGCCCAATACAGTAT
Found at i:12390070 original size:12 final size:12
Alignment explanation
Indices: 12390053--12390093 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
12390043 GTGAAATGTG
12390053 ATAAATTGATGA
1 ATAAATTGATGA
*
12390065 ATAAATTCAT--
1 ATAAATTGATGA
12390075 ATAAATTGATGA
1 ATAAATTGATGA
12390087 ATAAATT
1 ATAAATT
12390094 CATTTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (12 bp):
ATAAATTGATGA
Found at i:12390081 original size:22 final size:22
Alignment explanation
Indices: 12390053--12390096 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12390043 GTGAAATGTG
12390053 ATAAATTGATGAATAAATTCAT
1 ATAAATTGATGAATAAATTCAT
12390075 ATAAATTGATGAATAAATTCAT
1 ATAAATTGATGAATAAATTCAT
12390097 TTATATAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
ATAAATTGATGAATAAATTCAT
Found at i:12400511 original size:25 final size:24
Alignment explanation
Indices: 12400465--12400546 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
12400455 GGCTATATAA
*
12400465 CGGGAAGCTCAT-AAGAGCCATAAT
1 CGGGAAGCTCATAAAGAACCAT-AT
*
12400489 CGGGAAGTTCATAAAGAACCATAT
1 CGGGAAGCTCATAAAGAACCATAT
* * *
12400513 CGGAAAGCTCACAAAAAACCATAT
1 CGGGAAGCTCATAAAGAACCATAT
*
12400537 CAGGAAGCTC
1 CGGGAAGCTC
12400547 CAGAAAACCA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 41 0.84
25 8 0.16
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (24 bp):
CGGGAAGCTCATAAAGAACCATAT
Found at i:12400553 original size:25 final size:24
Alignment explanation
Indices: 12400482--12400556 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
12400472 CTCATAAGAG
* * * *
12400482 CCATAATCGGGAAGTTCATAAAGAA
1 CCAT-ATCGGAAAGCTCACAAAAAA
12400507 CCATATCGGAAAGCTCACAAAAAA
1 CCATATCGGAAAGCTCACAAAAAA
*
12400531 CCATATCAGG-AAGCTC-CAGAAAA
1 CCATATC-GGAAAGCTCACAAAAAA
12400554 CCA
1 CCA
12400557 ATAACGGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 9 0.20
24 29 0.66
25 6 0.14
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (24 bp):
CCATATCGGAAAGCTCACAAAAAA
Found at i:12400566 original size:24 final size:24
Alignment explanation
Indices: 12400482--12400567 Score: 59
Period size: 24 Copynumber: 3.5 Consensus size: 24
12400472 CTCATAAGAG
* * * *
12400482 CCATAATCGGGAAGTTCATAAAGAA
1 CCATAA-CAGGAAGCTCACAAAAAA
*
12400507 CCATATC-GGAAAGCTCACAAAAAA
1 CCATAACAGG-AAGCTCACAAAAAA
* *
12400531 CCATATCAGGAAGCTC-CAGAAAA
1 CCATAACAGGAAGCTCACAAAAAA
*
12400554 CCAATAACGGGAAG
1 CC-ATAACAGGAAG
12400568 TTCAAGCTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.20
24 34 0.67
25 7 0.14
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (24 bp):
CCATAACAGGAAGCTCACAAAAAA
Found at i:12404609 original size:48 final size:48
Alignment explanation
Indices: 12404482--12405094 Score: 446
Period size: 48 Copynumber: 12.8 Consensus size: 48
12404472 TATGTGCGCT
* * * * **
12404482 AGTGTAAGACCATGTCTGGGAAATGGCGTTGGCGACAAATAAT-AGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-A-ATATTGTGAGAGCC
* * * * *
12404531 AGCGTAAGACCATGTTTGGAACATGACATCGGCAATATTGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATATTGTGAGAGCC
* * * *
12404579 AGTGTAAGACCACGTCTGGGACATGGCATCGGCATTGATATGT--GCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAT-AT-TGTGAGAGCC
* * * * * *
12404627 AGTGTAAGACCATGCCCGGGACATGGCATCGGCCACATTATAAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATATTGTGAGAGCC
* * * * *
12404675 AGTGTAAGACCATGTCTAGGACATGGCATCGAC-AT-TGAGATGATAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATAT-TG-TGAGAGCC
** * * *
12404723 AGTGTAAGACCATGTCTGGGACATGGCATCAACATTGATATGT--GCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAT-AT-TGTGAGAGCC
** * * * *
12404771 AGTGTAAGACCATGTCCAGGACATGGCATTGGCCACATTTTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATATTGTGAGAGCC
* * * *
12404819 AGTGTAAGACCATGTCTGGGTCATGGCATCGGC-AT-TGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATAT-TG-TGAGAGCC
* * *
12404867 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGT--GCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAT-AT-TGTGAGAGCC
** * *
12404915 AGTGTAAGACCATGTCCCGGACATGGCATCGGCCATATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATATTGTGAGAGCC
* * * * *
12404963 AGTGTAAGACCATGTCTGGGACATGGCATTGAC-AT-TGAGACGAGAGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATAT-TG-TGAGAGCC
* ** *
12405011 AGTGTAAGACCATGTCTGGGACATGGCATTGGCCTTGACATGT--GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAT-A-TTGTGAGAGCC
* *
12405059 AGTGTAAGACCATGTCTAGGACATGGCATCAGCAAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAT
12405095 TGACCCTCTT
Statistics
Matches: 441, Mismatches: 98, Indels: 51
0.75 0.17 0.09
Matches are distributed among these distances:
46 9 0.02
47 14 0.03
48 378 0.86
49 31 0.07
50 4 0.01
51 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATATTGTGAGAGCC
Found at i:12404678 original size:96 final size:96
Alignment explanation
Indices: 12404534--12405097 Score: 542
Period size: 96 Copynumber: 5.9 Consensus size: 96
12404524 TAGAGCCAGC
* * * * * * * * * *
12404534 GTAAGACCATGTTTGGAACATGACATCGGCAATATTGTGAGAGTCAGTGTAAGACCACGTCTGGG
1 GTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTAAGACCATGTCTAGG
*
12404599 ACATGGCATCGGCATTGATATGTGCGCTAGT
66 ACATGGCATCGGCATTGATATGTGAGCTAGT
* *
12404630 GTAAGACCATGCCCGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTAAGACCATGTCTAGG
1 GTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTAAGACCATGTCTAGG
* *
12404695 ACATGGCATCGACATTGAGATGAT-AGCTAGT
66 ACATGGCATCGGCATTGATATG-TGAGCTAGT
* * * *
12404726 GTAAGACCATGTCTGGGACATGGCAT---CAACATTGATATGTGCGCTAGTGTAAGACCATGTCC
1 GTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATAAGAGC-C-AGTGTAAGACCATGTCT
* * *
12404788 AGGACATGGCATTGGCCACATT--T-TGAGAGCCAGT
63 AGGACATGGCATCGG---CATTGATATGTGAGCTAGT
* * *
12404822 GTAAGACCATGTCTGGGTCATGGCATCGG---CATTGAGACGAGAGCTAGTGTAAGACCATGTCT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATA--AGAGCCAGTGTAAGACCATGTCT
* *
12404884 GGGACATGGCATCGGCATTGATATGTGCGCTAGT
63 AGGACATGGCATCGGCATTGATATGTGAGCTAGT
** * * *
12404918 GTAAGACCATGTCCCGGACATGGCATCGGCCATATTATGAGAGCCAGTGTAAGACCATGTCTGGG
1 GTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTAAGACCATGTCTAGG
* * * * * *
12404983 ACATGGCATTGACATTGAGACGAGAGCAAGT
66 ACATGGCATCGGCATTGATATGTGAGCTAGT
* *
12405014 GTAAGACCATGTCTGGGACATGGCATTGGCCTTGACA-TGT--GAGCCAGTGTAAGACCATGTCT
1 GTAAGACCATGTCTGGGACATGGCATCGGCC---ACATTATAAGAGCCAGTGTAAGACCATGTCT
*
12405076 AGGACATGGCATCAGCAATTGA
63 AGGACATGGCATCGGC-ATTGA
12405098 CCCTCTTGTA
Statistics
Matches: 385, Mismatches: 60, Indels: 45
0.79 0.12 0.09
Matches are distributed among these distances:
93 10 0.03
94 6 0.02
95 2 0.01
96 346 0.90
97 6 0.02
98 6 0.02
99 9 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (96 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTAAGACCATGTCTAGG
ACATGGCATCGGCATTGATATGTGAGCTAGT
Found at i:12404727 original size:144 final size:144
Alignment explanation
Indices: 12404469--12405088 Score: 825
Period size: 144 Copynumber: 4.3 Consensus size: 144
12404459 GACATTTGGG
** * * * * *
12404469 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGAAATGGCGTTGGCGACA-AATAATAGAGCCAG
1 TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATCGGCCACATTAT-A-AGAGCCAG
* * * * * * * *
12404533 CGTAAGACCATGTTTGGAACATGACATCGGCAATAT-TG-TGAGAG-TCAGTGTAAGACCACGTC
64 TGTAAGACCATGTCTGGGACATGGCATCGAC-AT-TGAGACGAGAGCT-AGTGTAAGACCATGTC
12404595 TGGGACATGGCATCGGCAT
126 TGGGACATGGCATCGGCAT
* *
12404614 TGATATGTGCGCTAGTGTAAGACCATGCCCGGGACATGGCATCGGCCACATTATAAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATCGGCCACATTATAAGAGCCAGTG
* * *
12404679 TAAGACCATGTCTAGGACATGGCATCGACATTGAGATGATAGCTAGTGTAAGACCATGTCTGGGA
66 TAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
**
12404744 CATGGCATCAACAT
131 CATGGCATCGGCAT
* * *
12404758 TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATTGGCCACATTTTGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATCGGCCACATTATAAGAGCCAGTG
* *
12404823 TAAGACCATGTCTGGGTCATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
66 TAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
12404888 CATGGCATCGGCAT
131 CATGGCATCGGCAT
* * *
12404902 TGATATGTGCGCTAGTGTAAGACCATGTCCCGGACATGGCATCGGCCATATTATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATCGGCCACATTATAAGAGCCAGTG
* *
12404967 TAAGACCATGTCTGGGACATGGCATTGACATTGAGACGAGAGCAAGTGTAAGACCATGTCTGGGA
66 TAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
* *
12405032 CATGGCATTGGCCT
131 CATGGCATCGGCAT
* * * *
12405046 TGACATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC
1 TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATC
12405089 AGCAATTGAC
Statistics
Matches: 426, Mismatches: 45, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
142 1 0.00
143 3 0.01
144 374 0.88
145 46 0.11
146 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (144 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCCAGGACATGGCATCGGCCACATTATAAGAGCCAGTG
TAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAGACCATGTCTGGGA
CATGGCATCGGCAT
Found at i:12408558 original size:21 final size:21
Alignment explanation
Indices: 12408514--12408558 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12408504 TTGCAAATTA
*
12408514 ATTTGCATTTTGGGCCTTGTT
1 ATTTGCATTTTGGGCCTTGGT
*
12408535 ATTTGGATTTTGGG-CTTGGGT
1 ATTTGCATTTTGGGCCTT-GGT
12408556 ATT
1 ATT
12408559 ATTATGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.11, C:0.09, G:0.29, T:0.51
Consensus pattern (21 bp):
ATTTGCATTTTGGGCCTTGGT
Found at i:12408598 original size:14 final size:14
Alignment explanation
Indices: 12408579--12408625 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
12408569 TTGGACTTTA
12408579 ATTTTGGTTTTTGT
1 ATTTTGGTTTTTGT
12408593 ATTTTGGTTTATTTTGT
1 ATTTTGG--T-TTTTGT
*
12408610 TTTTTGGTTTTTGT
1 ATTTTGGTTTTTGT
12408624 AT
1 AT
12408626 GGGACTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 14 0.50
15 1 0.04
16 1 0.04
17 12 0.43
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (14 bp):
ATTTTGGTTTTTGT
Found at i:12408609 original size:17 final size:17
Alignment explanation
Indices: 12408587--12408619 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12408577 TAATTTTGGT
12408587 TTTTGTATTTTGGTTTA
1 TTTTGTATTTTGGTTTA
*
12408604 TTTTGTTTTTTGGTTT
1 TTTTGTATTTTGGTTT
12408620 TTGTATGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76
Consensus pattern (17 bp):
TTTTGTATTTTGGTTTA
Found at i:12409348 original size:21 final size:21
Alignment explanation
Indices: 12409324--12409382 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
12409314 GTTCAGAAAA
*
12409324 CACACGGGTGTGTTGCCCTTC
1 CACACGGGCGTGTTGCCCTTC
* *
12409345 CACACGGACCTGTTGCCCTTC
1 CACACGGGCGTGTTGCCCTTC
*
12409366 CACATGGGCGTG-TGCCC
1 CACACGGGCGTGTTGCCC
12409383 CTGTCTGCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.24
Consensus pattern (21 bp):
CACACGGGCGTGTTGCCCTTC
Found at i:12417449 original size:50 final size:50
Alignment explanation
Indices: 12417338--12417471 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
12417328 CTGGTACGCA
* * * * *
12417338 TAGTAACCTGCACTTAGTACTACACATACAACC-AATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATACGATACACG
* * * *
12417387 TAGTAGCTTGCACTTAGTACTACACACGTGACCTAACTATATGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATACGATACACG
*
12417437 TAGTAGCCTGCACTTAATACTACACATGCGACCTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTA
12417472 GCTACATATA
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 27 0.38
50 44 0.62
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATACGATACACG
Found at i:12419078 original size:35 final size:35
Alignment explanation
Indices: 12419039--12419106 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
12419029 ATTTTCACAC
*
12419039 AATCATGCAATCATATCATAGACCTCAAAATAAAA
1 AATCATGCAACCATATCATAGACCTCAAAATAAAA
12419074 AATCATGCAACCATATCATAGACCTCAAAATAA
1 AATCATGCAACCATATCATAGACCTCAAAATAA
12419107 TCATAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (35 bp):
AATCATGCAACCATATCATAGACCTCAAAATAAAA
Found at i:12420603 original size:57 final size:57
Alignment explanation
Indices: 12420515--12420629 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
12420505 TCATACATGT
12420515 GTCTCTCATACTCATTTTACCTTGTCTATTATAGTACCACTTATACATTTATACCAA
1 GTCTCTCATACTCATTTTACCTTGTCTATTATAGTACCACTTATACATTTATACCAA
*
12420572 GTCTCTCATACTTATTTTACCTTGTCTATTATAGTACCACTTATACATTTATACCAA
1 GTCTCTCATACTCATTTTACCTTGTCTATTATAGTACCACTTATACATTTATACCAA
12420629 G
1 G
12420630 GTCATCATCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (57 bp):
GTCTCTCATACTCATTTTACCTTGTCTATTATAGTACCACTTATACATTTATACCAA
Found at i:12422027 original size:50 final size:50
Alignment explanation
Indices: 12421893--12422042 Score: 221
Period size: 50 Copynumber: 3.0 Consensus size: 50
12421883 TATCTAGCCA
* * *
12421893 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-
1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCT
* * * * *
12421942 AATTATCCGTTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCT
12421992 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCT
1 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCT
12422042 A
1 A
12422043 GCTACATATA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 42 0.48
50 46 0.52
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (50 bp):
AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCT
Found at i:12423645 original size:35 final size:35
Alignment explanation
Indices: 12423599--12423666 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
12423589 AAATTTTCAC
12423599 ACAATCATGCAATCATATCATAGACCTCAAAATAA
1 ACAATCATGCAATCATATCATAGACCTCAAAATAA
12423634 ACAATCATGCAATCATATCATAGACCTCAAAAT
1 ACAATCATGCAATCATATCATAGACCTCAAAAT
12423667 TGTAACACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (35 bp):
ACAATCATGCAATCATATCATAGACCTCAAAATAA
Found at i:12425273 original size:28 final size:28
Alignment explanation
Indices: 12425210--12425332 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
12425200 ATATTAAGTC
*
12425210 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
12425237 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
12425265 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
12425293 CGTACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
12425322 CGCACACTTAG
1 CGCACACTTAG
12425333 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 50 0.57
29 15 0.17
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:12425280 original size:55 final size:57
Alignment explanation
Indices: 12425209--12425332 Score: 180
Period size: 55 Copynumber: 2.2 Consensus size: 57
12425199 TATATTAAGT
* *
12425209 CCGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAATTCAAAC
* * * *
12425264 TCGCACACTTAGTGCTATATAATCAAACTCGTACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAATTCAAAC
12425321 CCGCACACTTAG
1 CCGCACACTTAG
12425333 CGCCAATCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 22 0.37
56 22 0.37
57 16 0.27
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAATTCAAAC
Found at i:12427931 original size:15 final size:16
Alignment explanation
Indices: 12427895--12427924 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12427885 ACATATCATT
12427895 TATTTCATTATATCAA
1 TATTTCATTATATCAA
12427911 TATTTCA-TATATCA
1 TATTTCATTATATCA
12427925 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:12428941 original size:60 final size:60
Alignment explanation
Indices: 12428873--12428991 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
12428863 GAACACTTCG
12428873 GAATATAATTCAGATACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAACTAA
1 GAATATAATTCAGATACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAACTAA
*
12428933 GAATATAATTCGGATACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAACTA
1 GAATATAATTCAGATACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAACTA
12428992 TCTGGTACGC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (60 bp):
GAATATAATTCAGATACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAACTAA
Found at i:12429058 original size:48 final size:50
Alignment explanation
Indices: 12429003--12429135 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
12428993 CTGGTACGCA
* * *
12429003 TAGTAGCCTGCACTTAGTACTACATATGTGACC-AA-TTTCCGTTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCCGATACACG
* * *
12429051 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCCGATACACG
*
12429101 TAGTAGCCTGCACTTAGTACTACACATGCGACCTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTA
12429136 GCTACATATA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
48 31 0.41
49 2 0.03
50 42 0.56
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACTATCCGATACACG
Found at i:12430914 original size:48 final size:48
Alignment explanation
Indices: 12430856--12431177 Score: 283
Period size: 48 Copynumber: 6.7 Consensus size: 48
12430846 TATGTGCACT
* *
12430856 AGTGTAAGACCATGTCTGGGACATGGCGTCGTCCATGATATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
* * * * * * * *
12430904 AGTGTAAGACCATGTTTGGAACATGGCATTGGCAACGCTGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
* * * * * * *
12430952 AATGTAAAACCATGTTTGGGACATGGCATTGG-CATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAGAGCC
* * * *
12431000 AGTTGTTAGACCATGTCCGGAACATGGCATCGGCCA-CATTATGAGAGCC
1 AG-TGTAAGACCATGTCTGGGACATGGCATCGGCCATGA-TATGAGAGCC
* * * *
12431049 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAGAGCC
* * * * * *
12431097 AGTGTAAGACCATCTCTGGGCCATGACATTGGCC-TCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-GATATGAGAGCC
*
12431145 AGTGTAAGACCATGTCTGGGACATGACATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
12431178 AATTTACCCT
Statistics
Matches: 214, Mismatches: 52, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
47 4 0.02
48 173 0.81
49 35 0.16
50 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
Found at i:12431055 original size:97 final size:96
Alignment explanation
Indices: 12430856--12431178 Score: 317
Period size: 96 Copynumber: 3.4 Consensus size: 96
12430846 TATGTGCACT
* * *
12430856 AGTGTAAGACCATGTCTGGGACATGGCGTCGTCCA-TGATATGAGAGCCAGTGTAAGACCATGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCG-GCATTGATATGAGAGCCAGTGTAAGACCATGTC
* * * * *
12430920 TGGAACATGGCATTGGCAACGCTGTGAGAGTC
65 CGGAACATGGCATCGGCAACACTATGAGAGCC
* * * * * * * *
12430952 AATGTAAAACCATGTTTGGGACATGGCATTGGCATTGATATGTGCGCTAGTTGTTAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCCAG-TGTAAGACCATGTC
* *
12431017 CGGAACATGGCATCGGCCACATTATGAGAGCC
65 CGGAACATGGCATCGGCAACACTATGAGAGCC
* * * * * *
12431049 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGAGCTAGTGTAAGACCATCTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCCAGTGTAAGACCATGTCC
** * * ** *
12431114 GGGCCATGACATTGGCCTCGAC-ATGTGAGCC
66 GGAACATGGCATCGGCAAC-ACTATGAGAGCC
*
12431145 AGTGTAAGACCATGTCTGGGACATGACATCGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
12431179 ATTTACCCTC
Statistics
Matches: 185, Mismatches: 39, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
95 2 0.01
96 104 0.56
97 79 0.43
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCCAGTGTAAGACCATGTCC
GGAACATGGCATCGGCAACACTATGAGAGCC
Found at i:12431127 original size:145 final size:144
Alignment explanation
Indices: 12430843--12431177 Score: 370
Period size: 145 Copynumber: 2.3 Consensus size: 144
12430833 GACATTTGGG
* * * *
12430843 TGATATGTGCACTAGTGTAAGACCATGTCTGGGACATGGCGTCGTCCATGATATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATCATATGAGAGCCAGTG
* ** * * * *
12430908 TAAGACCATGTTTGGAACATGGCATTGGCAACGCTGTGAGAGTCAATGTAAAACCATGTTTGGGA
66 TAAGACCATGTCTGGAACATGGCATCAGCAACGCAGCGAGAGTCAATGTAAAACCATCTCTGGGA
*
12430973 CATGGCATTGGCAT
131 CATGACATTGGCAT
* * *
12430987 TGATATGTGCGCTAGTTGTTAGACCATGTCCGGAACATGGCATCGGCCA-CATTATGAGAGCCAG
1 TGATATGTGCGCTAG-TGTAAGACCATGTCTGGGACATGGCATCGGCCATCA-TATGAGAGCCAG
* ** * *
12431051 TGTAAGACCATGTCTGGGACATGGCATCAGCATTG-AGACGAGAG-CTAGTGTAAGACCATCTCT
64 TGTAAGACCATGTCTGGAACATGGCATCAGCAACGCAG-CGAGAGTC-AATGTAAAACCATCTCT
* *
12431114 GGGCCATGACATTGGCCT
127 GGGACATGACATTGGCAT
* * * * *
12431132 CGACATGTGAGCCAGTGTAAGACCATGTCTGGGACATGACATCGGC
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
12431178 AATTTACCCT
Statistics
Matches: 157, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
144 44 0.28
145 113 0.72
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (144 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATCATATGAGAGCCAGTG
TAAGACCATGTCTGGAACATGGCATCAGCAACGCAGCGAGAGTCAATGTAAAACCATCTCTGGGA
CATGACATTGGCAT
Found at i:12432226 original size:20 final size:21
Alignment explanation
Indices: 12432201--12432239 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12432191 TCCTTAAAAT
12432201 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
*
12432221 AGGGCAACATGCCCGTGTG
1 AGGGCAACACGCCCGTGTG
12432240 ACCAACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.21, C:0.28, G:0.38, T:0.13
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:12433450 original size:47 final size:45
Alignment explanation
Indices: 12433398--12433640 Score: 227
Period size: 46 Copynumber: 5.2 Consensus size: 45
12433388 CCCAAATAGG
*
12433398 GTCTTACATTGGCTCACATCTCAAGCTGATGCCATGTCCCAGACAT
1 GTCTTACACTGGCTCACATCTCAAGCTGATG-CATGTCCCAGACAT
* * * *
12433444 GCTCTTACGCTGACT-ATCATCTCATAGCCGATGCATGTCCTAGACAT
1 G-TCTTACACTGGCTCA-CATCTCA-AGCTGATGCATGTCCCAGACAT
* * * * *
12433491 GTCTTACACTAGCTTACGTCTCGAGGCCGATGCATGTCCCAGACAT
1 GTCTTACACTGGCTCACATCTC-AAGCTGATGCATGTCCCAGACAT
* * *
12433537 GTCTTACACTAGCTCTCGTCTCAATGCTGATGCCATGTCCCAGACAT
1 GTCTTACACTGGCTCACATCTCAA-GCTGATG-CATGTCCCAGACAT
* * * ***
12433584 GGACTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAGACAT
1 -GTCTTACACTGGCTCACAT-CTCAAGCTGATGCATGTCCCAGACAT
12433631 GTCTTACACT
1 GTCTTACACT
12433641 AGCCAAAAAT
Statistics
Matches: 165, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
45 1 0.01
46 72 0.44
47 61 0.37
48 30 0.18
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (45 bp):
GTCTTACACTGGCTCACATCTCAAGCTGATGCATGTCCCAGACAT
Found at i:12435208 original size:21 final size:21
Alignment explanation
Indices: 12435151--12435210 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
12435141 GTTAAGAAAA
*
12435151 CACAAGGGTGTGTTGACCTTC
1 CACAAGGGTGTGTTGCCCTTC
* *
12435172 CACACGAGTGTGTTGCCCTTC
1 CACAAGGGTGTGTTGCCCTTC
* *
12435193 CACATGGGCGTGTTGCCC
1 CACAAGGGTGTGTTGCCC
12435211 CTGTTTGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (21 bp):
CACAAGGGTGTGTTGCCCTTC
Found at i:12436224 original size:70 final size:70
Alignment explanation
Indices: 12436150--12436289 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
12436140 ATTTAATCTA
*
12436150 ATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTAAGTTTTTTCATAGTTGAT
1 ATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTAAGTTTTATCATAGTTGAT
12436215 CTCTC
66 CTCTC
12436220 ATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTAAGTTTTATCATAGTTGAT
1 ATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTAAGTTTTATCATAGTTGAT
12436285 CTCTC
66 CTCTC
12436290 TAAACCCTCC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.49
Consensus pattern (70 bp):
ATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGATTAAGTTTTATCATAGTTGAT
CTCTC
Found at i:12440092 original size:30 final size:29
Alignment explanation
Indices: 12440027--12440093 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
12440017 AATGAAATTT
*
12440027 TAATTTT-TAATTTTAAATAATTAAATCA
1 TAATTTTATAATTTTAAAAAATTAAATCA
12440055 -AATTTTTATAATTTTAAAAAAATTAAAAT-A
1 TAA-TTTTATAATTTT-AAAAAATT-AAATCA
12440085 TAATTTTAT
1 TAATTTTAT
12440094 TTTTACTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 2 0.06
28 4 0.12
29 7 0.21
30 14 0.42
31 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TAATTTTATAATTTTAAAAAATTAAATCA
Found at i:12440508 original size:6 final size:6
Alignment explanation
Indices: 12440497--12440523 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12440487 TAAATTATAA
12440497 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
12440524 TACATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12443678 original size:21 final size:21
Alignment explanation
Indices: 12443652--12443692 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12443642 ATCTACTCAA
* *
12443652 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTATGGAGTAC
12443673 ACTCCACCTGCTATGGAGTA
1 ACTCCACCTGCTATGGAGTA
12443693 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTATGGAGTAC
Found at i:12448045 original size:21 final size:21
Alignment explanation
Indices: 12448019--12448072 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
12448009 TCTAGACATG
*
12448019 ATTATTAAAAAATCATAAATT
1 ATTATTAAAAAATCATAAAAT
* *
12448040 ATTATTTAAAAATTATAAAAT
1 ATTATTAAAAAATCATAAAAT
12448061 ATT-TTAAAAAAT
1 ATTATTAAAAAAT
12448073 AATTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTATTAAAAAATCATAAAAT
Found at i:12448079 original size:21 final size:21
Alignment explanation
Indices: 12448019--12448080 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
12448009 TCTAGACATG
* *
12448019 ATTATTAAAAAATCATAAATT
1 ATTATTAAAAAATAATAAAAT
* *
12448040 ATTATTTAAAAATTATAAAAT
1 ATTATTAAAAAATAATAAAAT
12448061 ATT-TTAAAAAATAATTAAAA
1 ATTATTAAAAAATAA-TAAAA
12448081 AATCATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTATTAAAAAATAATAAAAT
Found at i:12448099 original size:31 final size:30
Alignment explanation
Indices: 12448042--12448113 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
12448032 CATAAATTAT
* *
12448042 TATTTAAAAATTATAAAATATTTTAAAAAA
1 TATTAAAAAATCATAAAATATTTTAAAAAA
* *
12448072 TAATTAAAAAATCAT-AAATGTTATTAAATAA
1 T-ATTAAAAAATCATAAAATATT-TTAAAAAA
*
12448103 TTTTAAAAAAT
1 TATTAAAAAAT
12448114 AAAATAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTAAAAAATCATAAAATATTTTAAAAAA
Found at i:12448597 original size:16 final size:16
Alignment explanation
Indices: 12448568--12448611 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
12448558 CTTTTGAAAT
*
12448568 TTTTAATAAT-TTTTA
1 TTTTAAAAATATTTTA
12448583 TTTTAAAAATATTTTA
1 TTTTAAAAATATTTTA
12448599 TGATTTAAAAATA
1 T--TTTAAAAATA
12448612 ACCACGTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 9 0.36
16 6 0.24
18 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAAAAATATTTTA
Found at i:12450245 original size:27 final size:27
Alignment explanation
Indices: 12450197--12450248 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12450187 TTCCTGAAAA
* *
12450197 TAGAGCCCAGACTCTAAGCAAGTCAGT
1 TAGAGCCCACACTCTAAACAAGTCAGT
*
12450224 TAGAGCCCACACTTTAAACAAGTCA
1 TAGAGCCCACACTCTAAACAAGTCA
12450249 AGGTTTGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (27 bp):
TAGAGCCCACACTCTAAACAAGTCAGT
Found at i:12451089 original size:22 final size:20
Alignment explanation
Indices: 12451047--12451089 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
12451037 TCCATTGTTG
*
12451047 AGAAATTGATGAATTAGGCT
1 AGAAATTGATGAATTAAGCT
12451067 AGAAATTGATAGAAATTAAGCT
1 AGAAATTGAT-G-AATTAAGCT
12451089 A
1 A
12451090 AGATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (20 bp):
AGAAATTGATGAATTAAGCT
Found at i:12454144 original size:11 final size:12
Alignment explanation
Indices: 12454128--12454160 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12454118 TGACCCAAGA
12454128 TGAATTAATTT-
1 TGAATTAATTTG
*
12454139 TGAATTCATTTG
1 TGAATTAATTTG
12454151 TGAATTAATT
1 TGAATTAATT
12454161 CACTTGTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (12 bp):
TGAATTAATTTG
Found at i:12454801 original size:12 final size:12
Alignment explanation
Indices: 12454779--12454850 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
12454769 AATAGTTATT
12454779 ATATT-AATTTA
1 ATATTAAATTTA
12454790 ATATTAAATTTA
1 ATATTAAATTTA
*
12454802 AT-CTAATATTT-
1 ATATTAA-ATTTA
* *
12454813 ATCTTGATAATTATT
1 ATATT-A-AATT-TA
12454828 ATATT-AATTTA
1 ATATTAAATTTA
12454839 ATATTAAATTTA
1 ATATTAAATTTA
12454851 TTAAGTTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
11 16 0.33
12 23 0.47
13 4 0.08
14 2 0.04
15 4 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (12 bp):
ATATTAAATTTA
Found at i:12454990 original size:26 final size:26
Alignment explanation
Indices: 12454938--12454988 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
12454928 TGAATTCAAG
12454938 AGAAAATTCTCTAAAGAAATTATTTT
1 AGAAAATTCTCTAAAGAAATTATTTT
* * *
12454964 AGAAGATT-TCTAAAGATATTTTTTT
1 AGAAAATTCTCTAAAGAAATTATTTT
12454989 TATTTATGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAAATTATTTT
Found at i:12463643 original size:15 final size:15
Alignment explanation
Indices: 12463623--12463667 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
12463613 TAAATACCAT
12463623 GTATACATACACACA
1 GTATACATACACACA
12463638 GTATACATACATC-CA
1 GTATACATACA-CACA
12463653 GTATACATACACACA
1 GTATACATACACACA
12463668 AGTGAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.44, C:0.27, G:0.07, T:0.22
Consensus pattern (15 bp):
GTATACATACACACA
Found at i:12475458 original size:18 final size:18
Alignment explanation
Indices: 12475435--12475469 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12475425 AAGTTGCTAG
12475435 AATTAAATAAATTAATTT
1 AATTAAATAAATTAATTT
*
12475453 AATTAAATAAGTTAATT
1 AATTAAATAAATTAATT
12475470 AGTTTTCAGC
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:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAAATAAATTAATTT
Found at i:12479107 original size:46 final size:46
Alignment explanation
Indices: 12478941--12479103 Score: 161
Period size: 46 Copynumber: 3.5 Consensus size: 46
12478931 AACCCGCCCC
* * * *
12478941 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
* * * * *
12478987 TAAATGAATTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCATCCA
* * *
12479035 TCA-CGAACTCGGACTCAACTCAATGAGCTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
12479080 TAAGTGAACTCGGACTCAACTCAA
1 TAAGTGAACTCGGACTCAACTCAA
12479104 TGAGTTCGAA
Statistics
Matches: 92, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
43 6 0.07
44 2 0.02
45 2 0.02
46 48 0.52
47 26 0.28
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCA
Found at i:12481188 original size:31 final size:31
Alignment explanation
Indices: 12481150--12481211 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
12481140 GTGTCATGAC
12481150 ATACCCCTGAAGATATCCCAAGAGGAGTATA
1 ATACCCCTGAAGATATCCCAAGAGGAGTATA
12481181 ATACCCCTGAAGATATCCCAAGAGGAGTATA
1 ATACCCCTGAAGATATCCCAAGAGGAGTATA
12481212 TTGACTCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
ATACCCCTGAAGATATCCCAAGAGGAGTATA
Found at i:12483944 original size:29 final size:29
Alignment explanation
Indices: 12483910--12483968 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12483900 GGATATTACT
12483910 TTGGTTACCTTTTGGGACCAATTATATTA
1 TTGGTTACCTTTTGGGACCAATTATATTA
12483939 TTGGTTACCTTTTGGGACCAATTATATTA
1 TTGGTTACCTTTTGGGACCAATTATATTA
12483968 T
1 T
12483969 GTATTTCACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (29 bp):
TTGGTTACCTTTTGGGACCAATTATATTA
Found at i:12485609 original size:12 final size:13
Alignment explanation
Indices: 12485578--12485615 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
12485568 TAGTAATGTC
12485578 GTATAAAAATTTT
1 GTATAAAAATTTT
12485591 GTATAAAAATTTT
1 GTATAAAAATTTT
12485604 GT-TAAAAATTTT
1 GTATAAAAATTTT
12485616 AATGTTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (13 bp):
GTATAAAAATTTT
Found at i:12490983 original size:24 final size:23
Alignment explanation
Indices: 12490952--12490997 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
12490942 GGGGAGATTT
12490952 TTATTTATTCAATATTAATATAA
1 TTATTTATTCAATATTAATATAA
*
12490975 TTATATTATTTAATATTAATATA
1 TTAT-TTATTCAATATTAATATA
12490998 TAATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATTTATTCAATATTAATATAA
Found at i:12490989 original size:18 final size:18
Alignment explanation
Indices: 12490966--12491005 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12490956 TTATTCAATA
*
12490966 TTAATA-TAATTATATTAT
1 TTAATATTAA-TATATAAT
12490984 TTAATATTAATATATAAT
1 TTAATATTAATATATAAT
12491002 TTAA
1 TTAA
12491006 ATTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATATTAATATATAAT
Found at i:12491022 original size:31 final size:31
Alignment explanation
Indices: 12490952--12491022 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
12490942 GGGGAGATTT
*
12490952 TTATTTATTCAATATTAATATAATTATATTA
1 TTATATATTCAATATTAATATAATTATATTA
*
12490983 TT-TAATATT-AATATATAATTTAAATT-TATTA
1 TTAT-ATATTCAATAT-TAATAT-AATTATATTA
12491014 TTATATATT
1 TTATATATT
12491023 TTTTGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
30 6 0.18
31 23 0.68
32 5 0.15
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
TTATATATTCAATATTAATATAATTATATTA
Found at i:12491050 original size:52 final size:52
Alignment explanation
Indices: 12490981--12491149 Score: 165
Period size: 52 Copynumber: 3.2 Consensus size: 52
12490971 ATAATTATAT
* *
12490981 TATTTAA-TATTAATATATAATTTAAATTTATTATTATATATTTTTTGAAAA
1 TATTTAATTATTTATATATATTTTAAATTTATTATTATATATTTTTTGAAAA
* *
12491032 TATTTAATTATTTTTATATATTTTAAA-TT-TTA-CATATTATTTTTTGTCAACAA
1 TATTTAATTATTTATATATATTTTAAATTTATTATTATA-TATTTTTTG--AA-AA
*
12491085 TAATTT--TTATTTATATATATTTTTAAATTTTATTATTATATA-ATTTTGAAAA
1 T-ATTTAATTATTTATATATA-TTTTAAA-TTTATTATTATATATTTTTTGAAAA
12491137 TA-TTAATGTATTT
1 TATTTAAT-TATTT
12491150 TTAAATTTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
49 3 0.03
50 14 0.14
51 10 0.10
52 34 0.35
53 17 0.18
54 4 0.04
55 7 0.07
56 5 0.05
57 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (52 bp):
TATTTAATTATTTATATATATTTTAAATTTATTATTATATATTTTTTGAAAA
Found at i:12491875 original size:12 final size:12
Alignment explanation
Indices: 12491858--12491895 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12491848 TATAGTTTAA
12491858 TATTTTTAATAT
1 TATTTTTAATAT
* *
12491870 TATTTTCAAAAT
1 TATTTTTAATAT
12491882 TA-TTTTAATAT
1 TATTTTTAATAT
12491893 TAT
1 TAT
12491896 GGGGTGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTTTAATAT
Found at i:12492180 original size:125 final size:121
Alignment explanation
Indices: 12491971--12492205 Score: 312
Period size: 125 Copynumber: 1.9 Consensus size: 121
12491961 GCCCCAAAAT
* * * * *
12491971 ACGATGACGAACTGGGTGAGAGCATCCCGTACTAGTAGCATGGTACACATTTCTAATTATAATTA
1 ACGATGACGAACTGGGTGAGAGCATCCCCTAATAATAGCATAGTACACATTTCGAA-TATAATTA
*
12492036 ATGAAAGAGTGAAGATTGGTCAAAATTCAAGTTTCTTCTTCCCTCGCATAAAATTAA
65 ATGAAAGAGTGAAGATTGGTCAAAATTCAAGTTTCTTCTTACCTCGCATAAAATTAA
* *
12492093 ACGATGACGAAGTGGGTGAGAGCATCCCATCCTAATAATAGCATAGTACACATTTCGAGA-CTAA
1 ACGATGACGAACTGGGTGAGAGCAT-CC--CCTAATAATAGCATAGTACACATTTCGA-ATATAA
*
12492157 TTAATGAAAAGAGTGAA-ATTTGGTCAAATTTCAAGTTTCTTCTTACCTC
62 TTAATG-AAAGAGTGAAGA-TTGGTCAAAATTCAAGTTTCTTCTTACCTC
12492206 ACAAGAGATT
Statistics
Matches: 98, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
122 24 0.24
123 2 0.02
124 10 0.10
125 61 0.62
126 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (121 bp):
ACGATGACGAACTGGGTGAGAGCATCCCCTAATAATAGCATAGTACACATTTCGAATATAATTAA
TGAAAGAGTGAAGATTGGTCAAAATTCAAGTTTCTTCTTACCTCGCATAAAATTAA
Found at i:12492544 original size:22 final size:20
Alignment explanation
Indices: 12492492--12492544 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
12492482 TAGGATATTG
*
12492492 TTTTAATAAAATATTTAAAT
1 TTTTAAAAAAATATTTAAAT
*
12492512 TTTAAATAAAAAATATTTATAAT
1 TTT-TA-AAAAAATATTTA-AAT
12492535 ATTTTAAAAA
1 -TTTTAAAAA
12492545 TTAATAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.12
21 1 0.04
22 15 0.58
23 4 0.15
24 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTAAAAAAATATTTAAAT
Found at i:12495768 original size:26 final size:27
Alignment explanation
Indices: 12495723--12495774 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
12495713 ATTTTTTGGG
*
12495723 TAGTACAATAAAGTATTATTTAATTAA
1 TAGTACAAAAAAGTATTATTTAATTAA
12495750 TAGT-CAAAAAAGTATTATTTAATTA
1 TAGTACAAAAAAGTATTATTTAATTA
12495775 TTTATCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (27 bp):
TAGTACAAAAAAGTATTATTTAATTAA
Found at i:12497067 original size:17 final size:18
Alignment explanation
Indices: 12497039--12497072 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12497029 AAATATGATT
12497039 TTTATCATAATTTAAAAC
1 TTTATCATAATTTAAAAC
12497057 TTTAT-ATAATTTAAAA
1 TTTATCATAATTTAAAA
12497073 TGAAATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTATCATAATTTAAAAC
Found at i:12502802 original size:46 final size:48
Alignment explanation
Indices: 12502664--12502929 Score: 243
Period size: 47 Copynumber: 5.7 Consensus size: 48
12502654 AGGGTAAGGT
* * *
12502664 GCCGATGCCATGTCCTAGACATGGTCTTACACTTGG-TCATATCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACAC-TGGCTTACATCTCGAA
* * *
12502711 GTCGATGCCATGTCCCAGACATGGTCTTACACTGAC-TACCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTA-CATCTCGAA
* * *
12502759 GTCGATG-CATGTCCCAGACAT-ATCTTACACTGGCTTACATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAA
* * * *
12502805 GCCAATG-CATGTCCCAGACAT-GTCTTGCACTAGCCCT-CATCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-GGCTTACATCTCGAA
* **
12502850 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CAT-TATGTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACATCT-CGAA
12502899 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
12502930 AGCTCACACA
Statistics
Matches: 184, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 70 0.38
47 85 0.46
48 28 0.15
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAA
Found at i:12502918 original size:94 final size:95
Alignment explanation
Indices: 12502663--12502932 Score: 278
Period size: 94 Copynumber: 2.9 Consensus size: 95
12502653 TAGGGTAAGG
*
12502663 TGCCGATGCCATGTCCTAGACATGGTCTTACACTTGG-TCAT-ATCTCAAGT---CGATGCCATG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACAC-TGGCTC-TCATCT-AAGTGGCCGATG-CATG
*
12502723 TCCCAGACATGGTCTTACACT-G-ACTACCATCTCG
62 TCCCAGACAT-GTCTTACACTAGCACTA-CATCTCA
* * * * *
12502757 TAGTCGATG-CATGTCCCAGACAT-ATCTTACACTGGCT-TACATCT-CGAGGCCAATGCATGTC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATCTAAGTGGCCGATGCATGTC
* *
12502818 CCAGACATGTCTTGCACTAGCCCT-CATCTCAA
64 CCAGACATGTCTTACACTAGCACTACATCTC-A
*
12502850 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-TATGTGGCCGATGCATGTCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTAAGTGGCCGATGCATGTCCC
12502914 AGACATGTCTTACACTAGC
66 AGACATGTCTTACACTAGC
12502933 TCACACACGA
Statistics
Matches: 147, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
91 2 0.01
92 24 0.16
93 44 0.30
94 70 0.48
95 7 0.05
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (95 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTAAGTGGCCGATGCATGTCCC
AGACATGTCTTACACTAGCACTACATCTCA
Found at i:12504798 original size:17 final size:17
Alignment explanation
Indices: 12504776--12504809 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12504766 TCGACAATTT
12504776 CGCCCATACAAAACTTC
1 CGCCCATACAAAACTTC
12504793 CGCCCATACAAAACTTC
1 CGCCCATACAAAACTTC
12504810 ATAAAGTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.18
Consensus pattern (17 bp):
CGCCCATACAAAACTTC
Found at i:12507030 original size:80 final size:79
Alignment explanation
Indices: 12506862--12507087 Score: 285
Period size: 80 Copynumber: 2.8 Consensus size: 79
12506852 TCCGATAGCN
* ** *
12506862 ACAAATGCCTTTGGGA-CTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCG
1 ACAAATGCC-TTCGGATCTTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCG
12506926 GAATTAGTATCTCGC
65 GAATTAGTATCTCGC
* * *
12506941 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCG
*
12507006 GATTTAGTATCTCGC
65 GAATTAGTATCTCGC
* * * * *
12507021 ACAAATGCCTTCGGATCTTAGTCTGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCC
12507085 GGA
64 GGA
12507088 CATCATTCGA
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
78 5 0.04
79 43 0.34
80 71 0.56
81 8 0.06
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (79 bp):
ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
AATTAGTATCTCGC
Found at i:12507074 original size:40 final size:40
Alignment explanation
Indices: 12506862--12507048 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
12506852 TCCGATAGCN
* ** *
12506862 ACAAATGCCTTTGGGA-CTTAACCCGGATTTAGTAACTCGC
1 ACAAATGCC-TTCGGATCTTAGTCCGGATTTAGTATCTCGC
* * * *
12506902 ACCAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGC
1 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGC
12506941 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGC
1 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGC
12506981 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGC
1 ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGC
*
12507021 ACAAATGCCTTCGGATCTTAGTCTGGAT
1 ACAAATGCCTTCGGATCTTAGTCCGGAT
12507049 ATGGTCACTT
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
39 38 0.28
40 97 0.72
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (40 bp):
ACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGC
Found at i:12508360 original size:23 final size:24
Alignment explanation
Indices: 12508327--12508371 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
12508317 AGGATGGACA
*
12508327 CATTTTTTTTCT-TTTGTTTTCAT
1 CATTTTCTTTCTCTTTGTTTTCAT
*
12508350 CATTTTCTTTCTCTTTTTTTTC
1 CATTTTCTTTCTCTTTGTTTTC
12508372 CATTTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (24 bp):
CATTTTCTTTCTCTTTGTTTTCAT
Found at i:12514314 original size:60 final size:61
Alignment explanation
Indices: 12514241--12514361 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 61
12514231 TAAAAGGGCT
12514241 GGGCAAAACGGTGCGTTTTGCCGGCCTATATAAACTAATTAT-TTTTTTTATTTCATTTCC
1 GGGCAAAACGGTGCGTTTTGCCGGCCTATATAAACTAATTATGTTTTTTTATTTCATTTCC
12514301 GGGCAAAACGGTGCGTTTTGCCGGCCTATATAAACTAATTATGTTTTTTTATTTCATTTCC
1 GGGCAAAACGGTGCGTTTTGCCGGCCTATATAAACTAATTATGTTTTTTTATTTCATTTCC
12514362 TTTCTCCTCT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 42 0.70
61 18 0.30
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (61 bp):
GGGCAAAACGGTGCGTTTTGCCGGCCTATATAAACTAATTATGTTTTTTTATTTCATTTCC
Found at i:12514480 original size:9 final size:9
Alignment explanation
Indices: 12514468--12514492 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12514458 TTCTTCTTTT
12514468 TTTTTTATA
1 TTTTTTATA
12514477 TTTTTTATA
1 TTTTTTATA
12514486 TTTTTTA
1 TTTTTTA
12514493 GTGAGTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATA
Found at i:12516998 original size:32 final size:32
Alignment explanation
Indices: 12516961--12517025 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
12516951 GTTGTAGAGT
12516961 TTCTTACTTGACTGCGAGATTCTACAACATTG
1 TTCTTACTTGACTGCGAGATTCTACAACATTG
* *
12516993 TTCTTACTTGACTGTGAGATTCTACGACATTG
1 TTCTTACTTGACTGCGAGATTCTACAACATTG
12517025 T
1 T
12517026 CTTGATCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (32 bp):
TTCTTACTTGACTGCGAGATTCTACAACATTG
Found at i:12518139 original size:20 final size:21
Alignment explanation
Indices: 12518109--12518147 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12518099 GACTACCCTG
*
12518109 GTGGCCACATGGGCGTGTGTC
1 GTGGCCACATGGCCGTGTGTC
12518130 GTGG-CACATGGCCGTGTG
1 GTGGCCACATGGCCGTGTG
12518148 GATTTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.10, C:0.23, G:0.44, T:0.23
Consensus pattern (21 bp):
GTGGCCACATGGCCGTGTGTC
Found at i:12519175 original size:92 final size:93
Alignment explanation
Indices: 12519007--12519188 Score: 258
Period size: 92 Copynumber: 2.0 Consensus size: 93
12518997 GATGACATCA
* ** * * *
12519007 TATCGGTATAGCAGATTATTGCATTGCACTGTACCACATGTATGTTAGCTACGCTACGTACCATT
1 TATCGGTATAGCAAATTACCGCATTGCACCGTACCACATGTACGTTAGCTACGCTACGTACCACT
*
12519072 AACTGAACTGGCAGTT-TTACTGCAACC
66 AACTGAACTGGCAGTTCGTACTGCAACC
* *
12519099 TATCGGTATAGCAAATTACCGCATTGCACCGTACCGCATGTACGTTAGCTACGCTACGTACTACT
1 TATCGGTATAGCAAATTACCGCATTGCACCGTACCACATGTACGTTAGCTACGCTACGTACCACT
* *
12519164 AGCTGATCTGGCAGTTCGTACTGCA
66 AACTGAACTGGCAGTTCGTACTGCA
12519189 TGGCTGTACT
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
92 71 0.91
93 7 0.09
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (93 bp):
TATCGGTATAGCAAATTACCGCATTGCACCGTACCACATGTACGTTAGCTACGCTACGTACCACT
AACTGAACTGGCAGTTCGTACTGCAACC
Found at i:12519622 original size:18 final size:18
Alignment explanation
Indices: 12519580--12519624 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12519570 TGAGAATTAC
*
12519580 TGATACCGTGACTGAATG
1 TGATACTGTGACTGAATG
*
12519598 TGATACTGTGACTGGATG
1 TGATACTGTGACTGAATG
*
12519616 TGTTACTGT
1 TGATACTGT
12519625 TTGACTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (18 bp):
TGATACTGTGACTGAATG
Found at i:12522721 original size:31 final size:31
Alignment explanation
Indices: 12522667--12522726 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
12522657 GAGTTATTTG
*
12522667 AATTTAAGTTATTCTGATCAACTCGAATAAA
1 AATTTAAGTTATTCTGATCAACTCAAATAAA
* *
12522698 AATTTAAGTTTTTC-GATTTAACTCAAATA
1 AATTTAAGTTATTCTGA-TCAACTCAAATA
12522727 TGAATTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTTAAGTTATTCTGATCAACTCAAATAAA
Found at i:12525382 original size:48 final size:48
Alignment explanation
Indices: 12525317--12525541 Score: 176
Period size: 48 Copynumber: 4.7 Consensus size: 48
12525307 CTAAGTGCCA
* * *
12525317 ATATCATGG-CTAGAAGCCAAATCAATGAAGTTCGCATACAAAGTGTCG
1 ATATCATGGCCCA-AAGCCAAATCAATGAAGCTCGCATCCAAAGTGTCG
*
12525365 ATATCATGGCCCAAAGCCAAATCAATGTAA-CTCGCA-CTCGAAGTGTCG
1 ATATCATGGCCCAAAGCCAAATCAATG-AAGCTCGCATC-CAAAGTGTCG
* * * * * * *
12525413 ATATAATGACCCAAAGCTAAATAAATGTAA-CTTGCA-CCAGAAGTGCCA
1 ATATCATGGCCCAAAGCCAAATCAATG-AAGCTCGCATCCA-AAGTGTCG
*** * * *
12525461 ATATCATGGCATGAAGCCAAACCAAT-ATAGCTCGCACCCGAAGTG-CTG
1 ATATCATGGCCCAAAGCCAAATCAATGA-AGCTCGCATCCAAAGTGTC-G
*
12525509 ATATCATGGCCCGAAGCCAAATCAATGAAGCTC
1 ATATCATGGCCCAAAGCCAAATCAATGAAGCTC
12525542 TTAATGACAT
Statistics
Matches: 142, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
46 1 0.01
47 3 0.02
48 131 0.92
49 7 0.05
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (48 bp):
ATATCATGGCCCAAAGCCAAATCAATGAAGCTCGCATCCAAAGTGTCG
Found at i:12528165 original size:20 final size:20
Alignment explanation
Indices: 12528132--12528169 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12528122 AATAATTGTG
*
12528132 CATGTTATGCTTAAATGTTT
1 CATGTGATGCTTAAATGTTT
*
12528152 CATGTGATGGTTAAATGT
1 CATGTGATGCTTAAATGT
12528170 GGTATATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (20 bp):
CATGTGATGCTTAAATGTTT
Found at i:12531450 original size:131 final size:132
Alignment explanation
Indices: 12531215--12531481 Score: 419
Period size: 131 Copynumber: 2.0 Consensus size: 132
12531205 GAAAGAGTTA
* * * * *
12531215 AAAGCACAGTTGCAAGAACTAACGGATAAGGGTTTTGCAAGACCAAGCTTTTTGCCTTGGGGTGC
1 AAAGCACAATTGAAAGAACTAACGGATAAGGGTTTTCCAAGACCAAGCTTTTCGCCCTGGGGTGC
*
12531280 TCCCGTATTATTTGTAAAGAAGAAAGATGATTCGATGAGATTATGTATAGATTACCGCCAACTCA
66 TCCCGTATTATTTGTAAAGAAGAAAAATGATTCGATGAGATTATGTATAGATTACCGCCAACTCA
*
12531345 AT
131 AC
*
12531347 AAAGCACAATTGAAAGAACTGACGGATAAGGG-TTTCCAAGACCAAGCTTTTCGCCCTGGGGTGC
1 AAAGCACAATTGAAAGAACTAACGGATAAGGGTTTTCCAAGACCAAGCTTTTCGCCCTGGGGTGC
* * * *
12531411 TTCCGTATTATTTGTGAAGAAGAAAAATGGTTCGATGAGATTATGTATAGATTACTGCCAACTCA
66 TCCCGTATTATTTGTAAAGAAGAAAAATGATTCGATGAGATTATGTATAGATTACCGCCAACTCA
12531476 AC
131 AC
12531478 AAAG
1 AAAG
12531482 TAACTATTAA
Statistics
Matches: 123, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
131 94 0.76
132 29 0.24
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (132 bp):
AAAGCACAATTGAAAGAACTAACGGATAAGGGTTTTCCAAGACCAAGCTTTTCGCCCTGGGGTGC
TCCCGTATTATTTGTAAAGAAGAAAAATGATTCGATGAGATTATGTATAGATTACCGCCAACTCA
AC
Found at i:12533487 original size:25 final size:23
Alignment explanation
Indices: 12533458--12533522 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
12533448 AATAAAAAAC
*
12533458 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
12533483 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
12533504 -TAAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAACAAATA
12533523 AAAAATAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 10 0.27
20 7 0.19
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:12533515 original size:19 final size:19
Alignment explanation
Indices: 12533486--12533527 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
12533476 AAATACATTT
12533486 AAAACATAAAAACAAATATA
1 AAAACATAAAAACAAATA-A
12533506 AAAACA-AAAAACAAATAA
1 AAAACATAAAAACAAATAA
12533524 AAAA
1 AAAA
12533528 TAAGACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAACATAAAAACAAATAA
Found at i:12537664 original size:27 final size:26
Alignment explanation
Indices: 12537633--12537810 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
12537623 TAAATTGTAC
12537633 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
12537660 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
12537686 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
12537714 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
12537742 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
12537769 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
12537796 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12537811 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:12537749 original size:82 final size:81
Alignment explanation
Indices: 12537634--12537789 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
12537624 AAATTGTACA
* *
12537634 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12537698 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
12537715 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12537780 TGCGAGTTGA
65 TGCGAATTGA
12537790 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12537801 original size:82 final size:81
Alignment explanation
Indices: 12537630--12537810 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
12537620 GATTAAATTG
* *
12537630 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12537695 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
12537711 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12537775 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12537793 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12537811 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:12537821 original size:27 final size:27
Alignment explanation
Indices: 12537715--12537821 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
12537705 TGACCATGCG
* * * *
12537715 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
12537743 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
12537770 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
12537797 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
12537822 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:12545788 original size:27 final size:26
Alignment explanation
Indices: 12545757--12545935 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 26
12545747 TAAATTGTAC
12545757 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
12545784 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
12545810 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
12545838 GGCACTAAGTGTGCGAGATTCGACTATGT
1 AGCACTAAGTGTGC--GATT-GACTATGT
* *
12545867 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
12545894 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
12545921 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12545936 GGCTCAATAT
Statistics
Matches: 128, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
27 101 0.79
28 7 0.05
29 20 0.16
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:12545818 original size:54 final size:54
Alignment explanation
Indices: 12545757--12545935 Score: 193
Period size: 54 Copynumber: 3.3 Consensus size: 54
12545747 TAAATTGTAC
* *
12545757 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAATTGAATATGAT
* ** *
12545812 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATTCGACTATG-T
1 AGCACTAAGTGTGCG-ATTGACTATGTAGCACTAAGTGTGCGA-ATT-GAATATGAT
* * * *
12545867 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCGAATTGAATATGAT
*
12545921 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12545936 GGCTCAATAT
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
54 55 0.52
55 9 0.09
56 41 0.39
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAATTGAATATGAT
Found at i:12545926 original size:83 final size:82
Alignment explanation
Indices: 12545754--12545936 Score: 226
Period size: 83 Copynumber: 2.2 Consensus size: 82
12545744 GATTAAATTG
* *
12545754 TACAGCACTAAGTGTGC-GATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTA
1 TACAGCACTAAGTGTGCGGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
12545818 AGTGTGCGAATTGACCA
66 AGTGTGCGAATTGACCA
* * ** *
12545835 TGCGGCACTAAGTGTGCGAGATTCGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCG-GATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
12545899 TAAGTGTGCGAGTTGATTA
64 TAAGTGTGCGAATTGACCA
* *
12545918 TATAGCACTGAGTGTGCGG
1 TACAGCACTAAGTGTGCGG
12545937 GCTCAATATA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 15 0.18
82 2 0.02
83 68 0.80
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (82 bp):
TACAGCACTAAGTGTGCGGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
AGTGTGCGAATTGACCA
Found at i:12545946 original size:27 final size:27
Alignment explanation
Indices: 12545839--12545946 Score: 72
Period size: 27 Copynumber: 3.9 Consensus size: 27
12545829 TGACCATGCG
* * *
12545839 GCACTAAGTGTGCGAGATTCGACTATGTA
1 GCACTAAGTGTGCGAG-CTC-AATATATA
** * * **
12545868 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
12545895 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
12545922 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
12545947 CATTCGTGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
27 50 0.75
28 2 0.03
29 15 0.22
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:12550124 original size:41 final size:40
Alignment explanation
Indices: 12550057--12550140 Score: 91
Period size: 41 Copynumber: 2.1 Consensus size: 40
12550047 ATATTGATTA
12550057 TGAATATATGTGTATTGAGAAAAATATGATTATT-ATAAAAT
1 TGAATATATGTGTATTGAGAAAAATAT-A-TATTCATAAAAT
* * * *
12550098 TGAATATATGTTTATATGTG-ATAATATATATTCATGAAAT
1 TGAATATATGTGTAT-TGAGAAAAATATATATTCATAAAAT
12550138 TGA
1 TGA
12550141 GACATTGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
39 4 0.11
40 10 0.27
41 20 0.54
42 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.42
Consensus pattern (40 bp):
TGAATATATGTGTATTGAGAAAAATATATATTCATAAAAT
Found at i:12576193 original size:6 final size:6
Alignment explanation
Indices: 12576182--12576208 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12576172 GTAATATTAT
12576182 TATAAA TATAAA TATAAA TATAAA TAT
1 TATAAA TATAAA TATAAA TATAAA TAT
12576209 TATTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TATAAA
Found at i:12577061 original size:26 final size:26
Alignment explanation
Indices: 12577032--12577085 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12577022 TTTTAAGAAA
* *
12577032 TATTTATTACTTA-ATTTTTTTTATTT
1 TATTTATTAATTACATTTTTATT-TTT
*
12577058 TATTTTTTAATTACATTTTTATTTTT
1 TATTTATTAATTACATTTTTATTTTT
12577084 TA
1 TA
12577086 ACTAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (26 bp):
TATTTATTAATTACATTTTTATTTTT
Found at i:12581132 original size:29 final size:29
Alignment explanation
Indices: 12581099--12581162 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
12581089 AAATAAGTTG
* *
12581099 ATCTTTATCCAACCAATTTCAAATATTTA
1 ATCTTTATCCAACCAACTTCAAATATTCA
* *
12581128 ATCTTTATCCAGCCAACTTCAAATCTTCA
1 ATCTTTATCCAACCAACTTCAAATATTCA
12581157 ATCTTT
1 ATCTTT
12581163 CAATCTACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.41
Consensus pattern (29 bp):
ATCTTTATCCAACCAACTTCAAATATTCA
Found at i:12584632 original size:16 final size:17
Alignment explanation
Indices: 12584613--12584645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12584603 TTTAATATAA
12584613 TTAAT-ATTTTGAAAAT
1 TTAATGATTTTGAAAAT
*
12584629 TTAATGATTTTGCAAAT
1 TTAATGATTTTGAAAAT
12584646 GAAGTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
TTAATGATTTTGAAAAT
Found at i:12589821 original size:23 final size:23
Alignment explanation
Indices: 12589784--12589828 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12589774 AGTTGGGTTC
* * *
12589784 AAACTTGATCGAGTATTATTATT
1 AAACTTAATCAAGTACTATTATT
12589807 AAACTTAATCAAGTACTATTAT
1 AAACTTAATCAAGTACTATTAT
12589829 CCAAGATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (23 bp):
AAACTTAATCAAGTACTATTATT
Found at i:12603956 original size:12 final size:12
Alignment explanation
Indices: 12603941--12603970 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12603931 ATTAACACTT
*
12603941 CACTAAACTAAC
1 CACTAAACCAAC
12603953 CACTAAACCAAC
1 CACTAAACCAAC
12603965 CACTAA
1 CACTAA
12603971 CTCCATCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (12 bp):
CACTAAACCAAC
Found at i:12604139 original size:24 final size:26
Alignment explanation
Indices: 12604088--12604140 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
12604078 TTTTTGGAGA
*
12604088 AAAAAGGAGAGAGTCTCGAATACAAG
1 AAAAAGGAGAGACTCTCGAATACAAG
*
12604114 AAAAA-GAGAGACTTTCG-ATACAAG
1 AAAAAGGAGAGACTCTCGAATACAAG
12604138 AAA
1 AAA
12604141 TACACGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 10 0.40
26 5 0.20
ACGTcount: A:0.53, C:0.11, G:0.23, T:0.13
Consensus pattern (26 bp):
AAAAAGGAGAGACTCTCGAATACAAG
Found at i:12604436 original size:3 final size:3
Alignment explanation
Indices: 12604428--12604589 Score: 59
Period size: 3 Copynumber: 52.0 Consensus size: 3
12604418 GTGTTATTTT
* * *
12604428 TTA TTA TTA TTAA TGTA TCA TTG TTA TTT TCTA TT- TTA TTA TTA CTT-
1 TTA TTA TTA TT-A T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA
* * *
12604475 TTA TTA CTA TTG TT- TCTA TTA TTA TTA TT- TTCA TTA CTTCCG TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT-A TTA -TT--A TTA
* * * * *
12604520 TTA TTA TCA TTA TTT TCTA TTA TCA TTA ATA TGTCG TT- TGT- TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-T-A TTA T-TA TTA TTA
12604567 TTA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
12604590 ACACTATTAT
Statistics
Matches: 120, Mismatches: 20, Indels: 38
0.67 0.11 0.21
Matches are distributed among these distances:
2 11 0.09
3 88 0.73
4 17 0.14
5 4 0.03
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12604525 original size:30 final size:30
Alignment explanation
Indices: 12604459--12604541 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
12604449 TGTTATTTTC
*
12604459 TATT-TTATTATTACTTTT-ATTACTATTGT
1 TATTATTATTATTA-TTTTCATTACTATCGT
12604488 T-TCTATTATTATTATTTTCATTACT-TCCGT
1 TAT-TATTATTATTATTTTCATTACTAT-CGT
*
12604518 TATTATTATCATTATTTTCTATTA
1 TATTATTATTATTATTTTC-ATTA
12604542 TCATTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
28 1 0.02
29 7 0.15
30 33 0.72
31 5 0.11
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (30 bp):
TATTATTATTATTATTTTCATTACTATCGT
Found at i:12605014 original size:125 final size:127
Alignment explanation
Indices: 12604832--12605093 Score: 309
Period size: 125 Copynumber: 2.1 Consensus size: 127
12604822 ATTTTTCAAG
** * *
12604832 TAAAGGCAATATTCGATACTTGGAAATTCAAGAAATCGTGTCCTAACGTACTAGGTTTC-AGTTT
1 TAAAGGCAATATTCGATACTTAAAAATTCAAGAAATCGTGCCCTAACATACTAGGTTTCGA-TTT
* * * *
12604896 TTCGTTTGATCTAAGTAACCGATTATCC-TTTTAAAA-TAAAATACATGAGTTTTAAAT-AACA
65 TCCGTTTGATCTAAATAACCAAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATGAA-A
* * * * *
12604957 TAAAGGCAATATTCCG-TATTTAAAAATTCGAGTAGTCGTGCCCTAACATACTGGGTTTCGATTT
1 TAAAGGCAATATT-CGATACTTAAAAATTCAAGAAATCGTGCCCTAACATACTAGGTTTCGATTT
* * *
12605021 TCCGTTTGATCTAAATATCCAAATATCCTTTTTAAAATTTAAATACATGTGTTTTAAATGAAA
65 TCCGTTTGATCTAAATAACCAAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATGAAA
12605084 TAGAAGGCAA
1 TA-AAGGCAA
12605094 GCTCATAATC
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
125 73 0.63
126 11 0.10
127 22 0.19
128 9 0.08
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (127 bp):
TAAAGGCAATATTCGATACTTAAAAATTCAAGAAATCGTGCCCTAACATACTAGGTTTCGATTTT
CCGTTTGATCTAAATAACCAAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATGAAA
Found at i:12612914 original size:16 final size:16
Alignment explanation
Indices: 12612893--12612926 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12612883 GTTTGATATC
12612893 TCCATTCTGTATGTAT
1 TCCATTCTGTATGTAT
12612909 TCCATTCTGTATGTAT
1 TCCATTCTGTATGTAT
12612925 TC
1 TC
12612927 ATCCCTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.50
Consensus pattern (16 bp):
TCCATTCTGTATGTAT
Found at i:12613370 original size:60 final size:60
Alignment explanation
Indices: 12613280--12613393 Score: 219
Period size: 60 Copynumber: 1.9 Consensus size: 60
12613270 CATGACACAT
12613280 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGATGGCAC
1 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGATGGCAC
*
12613340 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGGATTCATAGCGA
1 ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGA
12613394 GAAGCATGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (60 bp):
ATATAGGTAATGAAAAAGGAAATTACCATCATGGCCTAGATGAATTCATAGCGATGGCAC
Found at i:12630746 original size:46 final size:44
Alignment explanation
Indices: 12630686--12630800 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
12630676 ACAGGACAGA
* *
12630686 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
12630732 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
12630776 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
12630801 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:12630781 original size:44 final size:45
Alignment explanation
Indices: 12630686--12630819 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
12630676 ACAGGACAGA
* *
12630686 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
12630732 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
12630776 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
12630820 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:12632723 original size:39 final size:39
Alignment explanation
Indices: 12632680--12632766 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
12632670 TCGGCAATTA
*
12632680 GCCTGCTAGGTATAAACCTGAACTTATCATCGGCACAAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
* *
12632719 GCCTGCTAGGTATAAACCTGAATTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
12632758 GCCTGCTAG
1 GCCTGCTAG
12632767 ACATTAAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACAAG
Found at i:12636353 original size:43 final size:42
Alignment explanation
Indices: 12636306--12636399 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 42
12636296 CCCAGCGAGG
*
12636306 GTCTTACACGAAAT-CATATAACGATGCCAATGTCCCAGACATA
1 GTCTTACACGAAATCCA-AT-ACAATGCCAATGTCCCAGACATA
* * *
12636349 GTCTTACACGTAATCGCAATACAATTCCAATGTCCCAGACATG
1 GTCTTACACGAAATC-CAATACAATGCCAATGTCCCAGACATA
12636392 GTCTTACA
1 GTCTTACA
12636400 TGTAATCACA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 41 0.91
44 2 0.04
45 2 0.04
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (42 bp):
GTCTTACACGAAATCCAATACAATGCCAATGTCCCAGACATA
Found at i:12641599 original size:21 final size:21
Alignment explanation
Indices: 12641575--12641621 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
12641565 AGTTAGGGTT
12641575 TGAAATCAACAGAACAATGTA
1 TGAAATCAACAGAACAATGTA
*
12641596 TGAAATCAACATAACAATGTA
1 TGAAATCAACAGAACAATGTA
12641617 TGAAA
1 TGAAA
12641622 AGTAAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (21 bp):
TGAAATCAACAGAACAATGTA
Found at i:12643165 original size:6 final size:6
Alignment explanation
Indices: 12643156--12643185 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12643146 TGACGAGATT
*
12643156 CCCTTC CCCTTC CCCTTC CTCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
12643186 TCTTCTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCTTC
Found at i:12643188 original size:11 final size:12
Alignment explanation
Indices: 12643156--12643190 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12643146 TGACGAGATT
*
12643156 CCCTTCCCCTTC
1 CCCTTCCTCTTC
12643168 CCCTTCCTCTTC
1 CCCTTCCTCTTC
12643180 CCCTT-CTCTTC
1 CCCTTCCTCTTC
12643191 TTTCCCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (12 bp):
CCCTTCCTCTTC
Found at i:12652776 original size:18 final size:17
Alignment explanation
Indices: 12652735--12652780 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
12652725 TCAACAATCG
*
12652735 CTAAATAAAATTAGAAA
1 CTAAAAAAAATTAGAAA
12652752 CTAAAAAAAATATA-AAA
1 CTAAAAAAAAT-TAGAAA
12652769 CTTAAAAAAAAT
1 C-TAAAAAAAAT
12652781 CTAACAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (17 bp):
CTAAAAAAAATTAGAAA
Found at i:12652792 original size:19 final size:18
Alignment explanation
Indices: 12652753--12652792 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12652743 AATTAGAAAC
*
12652753 TAAAAAAAATATAAAACT
1 TAAAAAAAATATAAAAAT
*
12652771 TAAAAAAAATCTAACAAAT
1 TAAAAAAAATATAA-AAAT
12652790 TAA
1 TAA
12652793 TAAACACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAAAAAATATAAAAAT
Found at i:12653743 original size:15 final size:15
Alignment explanation
Indices: 12653723--12653752 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12653713 TTCACTGTTA
*
12653723 TGTCTTTAGTATTTT
1 TGTCTTTAATATTTT
12653738 TGTCTTTAATATTTT
1 TGTCTTTAATATTTT
12653753 GCATGCGTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (15 bp):
TGTCTTTAATATTTT
Found at i:12654933 original size:25 final size:26
Alignment explanation
Indices: 12654883--12654935 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12654873 AACTGTAGAG
12654883 AGAAAATTATCTAAAGAAATTATTTT
1 AGAAAATTATCTAAAGAAATTATTTT
* *
12654909 AGAAAATT-TCTAGAGATAATTTTTTT
1 AGAAAATTATCTAAAGA-AATTATTTT
12654935 A
1 A
12654936 TATACAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (26 bp):
AGAAAATTATCTAAAGAAATTATTTT
Found at i:12663189 original size:21 final size:21
Alignment explanation
Indices: 12663165--12663207 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12663155 CCTCATTGGC
*
12663165 AAGGTTTTAGTTCTCATGGTT
1 AAGGCTTTAGTTCTCATGGTT
* *
12663186 AAGGCTTTCGTTCTCGTGGTT
1 AAGGCTTTAGTTCTCATGGTT
12663207 A
1 A
12663208 TGTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (21 bp):
AAGGCTTTAGTTCTCATGGTT
Found at i:12666010 original size:83 final size:84
Alignment explanation
Indices: 12665858--12666040 Score: 269
Period size: 83 Copynumber: 2.2 Consensus size: 84
12665848 TCTTTGCTTG
* * *
12665858 GAAACAAAACAATATCGAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
1 GAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
12665923 TTAATTCTATTCTAATTTA
66 TTAATTCTATTCTAATTTA
* * ** * *
12665942 GAAACAAAATAAAATCAAATAAAGTCTTGTTAAATGG-GGGAATAAATTCCGAAATAGATTTTAT
1 GAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
*
12666006 TTAATTCTATTCTAATTTT
66 TTAATTCTATTCTAATTTA
12666025 GAAACAAAATAAAATC
1 GAAACAAAATAAAATC
12666041 CTGTTAAACG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 57 0.64
84 32 0.36
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (84 bp):
GAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGCAAATAAATCCCAAAATAGATTTTAT
TTAATTCTATTCTAATTTA
Found at i:12666223 original size:61 final size:62
Alignment explanation
Indices: 12666157--12666281 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 62
12666147 TCTTGAAACG
*
12666157 GATTTTATTTTACTCG-TTTTTTGAAATAAAACAAAATTTGAAATAAAATCGTTGAACGGCA
1 GATTTTATTTTACTCGTTTTTTTGAAATAAAACAAAATTTGAAATAAAATCGTTAAACGGCA
* *
12666218 GATTTTATTTTACTCGTTTTTTTTGAAATAAAACAAAATTTGTAATAAAATTGTTAAACGGCA
1 GATTTTATTTTACTCG-TTTTTTTGAAATAAAACAAAATTTGAAATAAAATCGTTAAACGGCA
12666281 G
1 G
12666282 GAATCAATCC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 16 0.27
63 43 0.73
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (62 bp):
GATTTTATTTTACTCGTTTTTTTGAAATAAAACAAAATTTGAAATAAAATCGTTAAACGGCA
Found at i:12666393 original size:89 final size:86
Alignment explanation
Indices: 12666237--12666396 Score: 196
Period size: 89 Copynumber: 1.8 Consensus size: 86
12666227 TTACTCGTTT
* * * * *
12666237 TTTTTGAAATAAAACAAAATTTGTAATAAAATTGTTAAACGGCAGGAATCAATCCTGAAATGAAT
1 TTTTGGAAATAAAACAAAATTAGTAATAAAATTGTTAAACGGCAGGAATAAATCCCGAAACGAAT
12666302 TTTATTTACCTTTAATTTCCC
66 TTTATTTACCTTTAATTTCCC
* **
12666323 TTTTGGAAATAAAATCAAAATAATAG-AATAAAATTCGTTGAACGGTGGGAATAAATCCCGAAAC
1 TTTTGGAAATAAAA-CAAAAT--TAGTAATAAAATT-GTTAAACGGCAGGAATAAATCCCGAAAC
*
12666387 GGATTTTATT
62 GAATTTTATT
12666397 AATTTTGGAC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
86 13 0.21
87 6 0.10
88 9 0.15
89 33 0.54
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (86 bp):
TTTTGGAAATAAAACAAAATTAGTAATAAAATTGTTAAACGGCAGGAATAAATCCCGAAACGAAT
TTTATTTACCTTTAATTTCCC
Done.