Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3721990 original size:21 final size:22
Alignment explanation
Indices: 3721955--3722003 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3721945 AATATACATA
*
3721955 TATTTT-AGTAATTTA-ATTTT
1 TATTTTAAGTAATTTATATATT
*
3721975 TATTTTAAGTATTTTATATATT
1 TATTTTAAGTAATTTATATATT
3721997 T-TTTTAA
1 TATTTTAA
3722004 TGTTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTTTAAGTAATTTATATATT
Found at i:3722419 original size:21 final size:21
Alignment explanation
Indices: 3722367--3722412 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
3722357 TGAAAAATAT
*
3722367 TTTTAAAATATTGAAATATGA
1 TTTTAGAATATTGAAATATGA
*
3722388 TTTTAGAATATT-AAATATTA
1 TTTTAGAATATTGAAATATGA
3722408 TTTTA
1 TTTTA
3722413 TTGATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTAGAATATTGAAATATGA
Found at i:3722526 original size:97 final size:101
Alignment explanation
Indices: 3722383--3722583 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 101
3722373 AATATTGAAA
3722383 TATGATTTTAGAATATTAAATATTATTTTATTGATATTTTAATTTGATTTTAATAAGTGAATATG
1 TATGATTTTAGAATATTAAATATTATTTTATTGATATTTTAATTTGATTTTAATAAGTGAATATG
3722448 TTGAATTTTTTAAAATTGGAATTTTAGTGACT-AAT
66 TTGAATTTTTTAAAATTGGAATTTTAGTGACTAAAT
3722483 TATGATTTTAGAATATT-AA-A-TATTTTATTGATATTTTAATTTGATTTTAATAAGTGAATATG
1 TATGATTTTAGAATATTAAATATTATTTTATTGATATTTTAATTTGATTTTAATAAGTGAATATG
*
3722545 TTGAATTTTTTAAAATTGGAATTTTAGTTACTAAAT
66 TTGAATTTTTTAAAATTGGAATTTTAGTGACTAAAT
3722581 TAT
1 TAT
3722584 AAAGTGATCA
Statistics
Matches: 99, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
97 73 0.74
98 7 0.07
99 2 0.02
100 17 0.17
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.51
Consensus pattern (101 bp):
TATGATTTTAGAATATTAAATATTATTTTATTGATATTTTAATTTGATTTTAATAAGTGAATATG
TTGAATTTTTTAAAATTGGAATTTTAGTGACTAAAT
Found at i:3724939 original size:268 final size:265
Alignment explanation
Indices: 3724365--3725057 Score: 790
Period size: 268 Copynumber: 2.6 Consensus size: 265
3724355 TGATTCATTC
* * *
3724365 CACTATTCTTTAGGGAAGATTGAATCGGAGATGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
1 CACTACTCTTCAGGGAAGATTGAATCGGAG-TGATTTGCTTCACAGCTCTTCAGGAAGACCAAAT
* * * *
3724430 CTGAAA-AAAAAGAATATGCTCCA-CTACTCTCTAGGGGAGGTCAGACTCAAGAAAACTTTGATC
65 CTGAAAGAAGAAGAATATGCT-CAGCTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATC
* * * ***
3724493 CACTTTGA-TGTTGTTCAGGGAAGATTGAATCGAACATGATTTGCTTTGTTCCTCTTCAGAGACC
129 CAC-TTCACTGCTCTTCAGGGAAGATTGAATCGAACATGATTTGCTTCACTCCTCTTCAGAGACC
* * * * *
3724557 AAATCTGAAAGATGAAGAATCTGCTCAACTACTCTTTAGAGGAGTTCAGACTCGAAAAAAATTTG
193 AAATATAAAAGAAGAAGAATCTGCTCAACTACTATTTAGAGGAGTTCAGACTCGAAAAAAACTTG
3724622 ATCCACTT
258 ATCCACTT
** * * * *
3724630 TGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACAACTCTTTAGGAAGACCAAAT
1 CACTACTCTTCAGGGAAGATTGAATCGGA-GTGATTTGCTTCACAGCTCTTCAGGAAGACCAAAT
* * ** * * *
3724695 CTGAAAGAAGAAGAATTTGGTTTGTTACTCTTTAGGGGAGATCAGACTTGAGAAAAATTTTGATC
65 CTGAAAGAAGAAGAATATGCTCAGCTACTCTTTAGGGGAGATCAGACTCGAG-AAAACTTTGATC
* * * * *
3724760 CACTTCACTACTCTTTAGGGAAGGTTGAATC-ATA-ATCGATTTGCTTCACTGCTCTTTAGGAAG
129 CACTTCACTGCTCTTCAGGGAAGATTGAATCGA-ACAT-GATTTGCTTCACTCCTCTTCA-G-AG
* * * *
3724823 ACCAAATATAAAAGAAGAAGAATCTGCTCCACTACTATTTAGA-GAGATT-AGACTCTAGAAAAC
190 ACCAAATATAAAAGAAGAAGAATCTGCTCAACTACTATTTAGAGGAG-TTCAGACTCGAAAAAAA
3724886 CTTGATCCACTT
254 CTTGATCCACTT
*
3724898 CACTACTCTTCAGGGAAGATTGAATCGGAGTCGACTTGCTTCA-ATGCTCTTCAGGAAGACCAAA
1 CACTACTCTTCAGGGAAGATTGAATCGGAGT-GATTTGCTTCACA-GCTCTTCAGGAAGACCAAA
* * * * *
3724962 TCTGAAAGACGAAGAATCTACTCAGCTACTATTTAGGGGAGATCAGACTCGAGAGAACTTTGATC
64 TCTGAAAGAAGAAGAATATGCTCAGCTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATC
* *
3725027 CACTTCACTGCTCTTCAGGAAATATTGAATC
129 CACTTCACTGCTCTTCAGGGAAGATTGAATC
3725058 AAATTTGATT
Statistics
Matches: 353, Mismatches: 63, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
265 60 0.17
266 41 0.12
267 88 0.25
268 122 0.35
269 42 0.12
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (265 bp):
CACTACTCTTCAGGGAAGATTGAATCGGAGTGATTTGCTTCACAGCTCTTCAGGAAGACCAAATC
TGAAAGAAGAAGAATATGCTCAGCTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCA
CTTCACTGCTCTTCAGGGAAGATTGAATCGAACATGATTTGCTTCACTCCTCTTCAGAGACCAAA
TATAAAAGAAGAAGAATCTGCTCAACTACTATTTAGAGGAGTTCAGACTCGAAAAAAACTTGATC
CACTT
Found at i:3724946 original size:133 final size:133
Alignment explanation
Indices: 3724365--3725057 Score: 718
Period size: 133 Copynumber: 5.2 Consensus size: 133
3724355 TGATTCATTC
* * * *
3724365 CACTATTCTTTAGGGAAGATTGAATCGGAGATGATTTGCTTCACTGCTCTTCAGGAAGACCAAAT
1 CACTACTCTTCAGGGAAGATTGAATCGAAG-TGATTTGCTTCAATGCTCTTCAGGAAGACCAAAT
* * * * *
3724430 CTGAAA-AAAAAGAATATGCTCCACTACTCTCTAGGGGAGGTCAGACTCAAGAAAACTTTGATCC
65 CTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
3724494 ACTTT
130 AC-TT
* ** * * *** *
3724499 GA-TGTTGTTCAGGGAAGATTGAATCGAACATGATTTGCTTTGTTCCTCTTCA-G-AGACCAAAT
1 CACTACTCTTCAGGGAAGATTGAATCGAA-GTGATTTGCTTCAATGCTCTTCAGGAAGACCAAAT
* * * * * *
3724561 CTGAAAGATGAAGAATCTGCTCAACTACTCTTTAGAGGAGTTCAGACTCGAAAAAAATTTGATCC
65 CTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCC
3724626 ACTT
130 ACTT
** * * *
3724630 TGCTGCTCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCACA-ACTCTTTAGGAAGACCAAA
1 CACTACTCTTCAGGGAAGATTGAATCGAA-GTGATTTGCTTCA-ATGCTCTTCAGGAAGACCAAA
* * **** * *
3724694 TCTGAAAGAAGAAGAATTTGGTTTGTTACTCTTTAGGGGAGATCAGACTTGAGAAAAATTTTGAT
64 TCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAG-AAAACTTTGAT
3724759 CCACTT
128 CCACTT
* * * * *
3724765 CACTACTCTTTAGGGAAGGTTGAATC-ATAATCGATTTGCTTCACTGCTCTTTAGGAAGACCAAA
1 CACTACTCTTCAGGGAAGATTGAATCGA-AGT-GATTTGCTTCAATGCTCTTCAGGAAGACCAAA
* * * * * * *
3724829 TATAAAAGAAGAAGAATCTGCTCCACTACTATTTA-GAGAGATTAGACTCTAGAAAACCTTGATC
64 TCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATC
3724893 CACTT
129 CACTT
* *
3724898 CACTACTCTTCAGGGAAGATTGAATCGGAGTCGACTTGCTTCAATGCTCTTCAGGAAGACCAAAT
1 CACTACTCTTCAGGGAAGATTGAATCGAAGT-GATTTGCTTCAATGCTCTTCAGGAAGACCAAAT
* * * *
3724963 CTGAAAGACGAAGAATCTACT-CAGCTACTATTTAGGGGAGATCAGACTCGAGAGAACTTTGATC
65 CTGAAAGAAGAAGAATCTGCTCCA-CTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATC
3725027 CACTT
129 CACTT
* * *
3725032 CACTGCTCTTCAGGAAATATTGAATC
1 CACTACTCTTCAGGGAAGATTGAATC
3725058 AAATTTGATT
Statistics
Matches: 461, Mismatches: 85, Indels: 26
0.81 0.15 0.05
Matches are distributed among these distances:
131 17 0.04
132 93 0.20
133 140 0.30
134 118 0.26
135 93 0.20
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (133 bp):
CACTACTCTTCAGGGAAGATTGAATCGAAGTGATTTGCTTCAATGCTCTTCAGGAAGACCAAATC
TGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCA
CTT
Found at i:3725814 original size:42 final size:42
Alignment explanation
Indices: 3725744--3725823 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
3725734 ATGAAAATAA
* * *
3725744 TGAATGATTGACTTCTCTTCACGAGAAAGTCAAGAATATCAT
1 TGAAAGATTAACTACTCTTCACGAGAAAGTCAAGAATATCAT
* *
3725786 TGAAAGATTAACTACTCTTCGCGAGAAAGTCAGGAATA
1 TGAAAGATTAACTACTCTTCACGAGAAAGTCAAGAATA
3725824 ACATCACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (42 bp):
TGAAAGATTAACTACTCTTCACGAGAAAGTCAAGAATATCAT
Found at i:3725966 original size:45 final size:44
Alignment explanation
Indices: 3725691--3726090 Score: 267
Period size: 45 Copynumber: 9.0 Consensus size: 44
3725681 AATAAAAAAG
* * *
3725691 GACAACAAC-AAAAGATCT-ACTTCTCTTCATGAGAAAGTTAAGAA
1 GACAAC-ACTAAAAGAT-TGACTCCTCTTCACGAGAAAGTCAAGAA
* * * * * *
3725735 TGAAAATAATGAATGATTGACTTCTCTTCACGAGAAAGTCAAG-A
1 -GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * * * * * * *
3725779 -ATATCATTGAAAGATTAACTACTCTTCGCGAGAAAGTCAGGAA
1 GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * * * * *
3725822 TAACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTTAAGAA
1 -GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * * * *
3725867 CAACAACACTAAAAGGTTGACTTCTCTTCACGAGAAATTCAAGTAG
1 -GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAG-AA
* * *
3725913 GACCACACTAAAAGATTGACTCCTATTCACGAGAGAGTCAAAGAA
1 GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTC-AAGAA
*
3725958 GATAACACTAAAAGATTGACTCCTCGTTCTA--A-AAACGTCAAGAA
1 GACAACACTAAAAGATTGACTCCTC-TTC-ACGAGAAA-GTCAAGAA
* * * * *
3726002 GGACAAGACTAAAACATTGACTCCTCTTCGCGAGAATGTCAAGAG
1 -GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
* * **
3726047 GATAACACTAAAAGTTTGACTCCTCTAT-ACGAGGGAGTCAAGAA
1 GACAACACTAAAAGATTGACTCCTCT-TCACGAGAAAGTCAAGAA
3726091 TAACAAAGGT
Statistics
Matches: 281, Mismatches: 59, Indels: 31
0.76 0.16 0.08
Matches are distributed among these distances:
42 32 0.11
43 1 0.00
44 46 0.16
45 192 0.68
46 9 0.03
47 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (44 bp):
GACAACACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
Found at i:3726125 original size:38 final size:38
Alignment explanation
Indices: 3726082--3726318 Score: 197
Period size: 38 Copynumber: 6.1 Consensus size: 38
3726072 TATACGAGGG
*
3726082 AGTCAAGAATAACAAAGGTCGACTTCTCTTCACAAGGA
1 AGTCAAGAATAACAAAGATCGACTTCTCTTCACAAGGA
* *
3726120 AGTCAAGAATAATAAAGATCGACTTCTCTTCGCAAGGA
1 AGTCAAGAATAACAAAGATCGACTTCTCTTCACAAGGA
* * * * * * *
3726158 AATCAATAATAATAAAGAACGATTTCTCTTCACGAGAA
1 AGTCAAGAATAACAAAGATCGACTTCTCTTCACAAGGA
* * * * * * *
3726196 AGCCAATAATAACATTGAAAGATTGACTCCTCTTCGCGAGGG
1 AGTCAAGAATAAC----AAAGATCGACTTCTCTTCACAAGGA
* * *
3726238 AGTCAGGAATAACAAAGATTGACCTCTCTTCACGAA-GA
1 AGTCAAGAATAACAAAGATCGACTTCTCTTCAC-AAGGA
* * * **
3726276 AGTCAAGAGTAACAAAGATTGACTTCTATTCATGAGGA
1 AGTCAAGAATAACAAAGATCGACTTCTCTTCACAAGGA
3726314 AGTCA
1 AGTCA
3726319 TGTTGAAAAA
Statistics
Matches: 159, Mismatches: 34, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
37 1 0.01
38 129 0.81
39 1 0.01
42 28 0.18
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Consensus pattern (38 bp):
AGTCAAGAATAACAAAGATCGACTTCTCTTCACAAGGA
Found at i:3726289 original size:80 final size:77
Alignment explanation
Indices: 3726025--3726299 Score: 227
Period size: 76 Copynumber: 3.5 Consensus size: 77
3726015 ACATTGACTC
* * *
3726025 CTCTTCGCGAGAATGTCAAGAGGATAACACTAAAAGTTTGACTCCTCTAT-ACGAGGGAGTCAAG
1 CTCTTCACGAGAA-GTCAAGA--ATAACA-T-AAAGATTGACTCCTCT-TCGCGAGGGAGTCAAG
* *
3726089 AATAACAAAGGTCGACTT
60 AATAACAAAGATCGACCT
* * * * * * *
3726107 CTCTTCACAAGGAAGTCAAGAAT-A-ATAAAGATCGACTTCTCTTCGCAAGGAAATCAATAATAA
1 CTCTTCACGA-GAAGTCAAGAATAACATAAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAA
* * **
3726170 TAAAGAACGATTT
65 CAAAGATCGACCT
* * *
3726183 CTCTTCACGAGAAAGCCAATAATAACATTGAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAAT
1 CTCTTCACGAG-AAGTCAAGAATAACA-T-AAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAAT
*
3726248 AACAAAGATTGACCT
63 AACAAAGATCGACCT
*
3726263 CTCTTCACGAAGAAGTCAAGAGTAAC--AAAGATTGACT
1 CTCTTCACG-AGAAGTCAAGAATAACATAAAGATTGACT
3726300 TCTATTCATG
Statistics
Matches: 153, Mismatches: 32, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
75 2 0.01
76 65 0.42
77 2 0.01
78 2 0.01
79 2 0.01
80 60 0.39
81 2 0.01
82 15 0.10
83 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (77 bp):
CTCTTCACGAGAAGTCAAGAATAACATAAAGATTGACTCCTCTTCGCGAGGGAGTCAAGAATAAC
AAAGATCGACCT
Found at i:3731665 original size:3 final size:3
Alignment explanation
Indices: 3731657--3731683 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3731647 ACCTGCAAAG
3731657 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3731684 TAAGGACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3732297 original size:135 final size:134
Alignment explanation
Indices: 3731882--3732583 Score: 797
Period size: 135 Copynumber: 5.3 Consensus size: 134
3731872 ATTCTATTGT
* * * *
3731882 TCTTCAGGGAAGATTGAATCAGA-GCGATTTGCTTCATTGCTCTTCAGGAAGACCAAATCTAAAA
1 TCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
* * * * * * **
3731946 AAAGAAGAATTTGCACCACTACACTCTACGGGAGATCAGACTCGAGAAAACTTTGATCCACTTTG
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
*
3732011 TTGC
131 CTGC
* * ** * ** * *
3732015 TATTCAGGGAAGATTGAATCGAACATGATTTGTTTCGTTGCTCTTCATGAAGAACAAATCT-AAA
1 TCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
* * * * * *
3732079 GATGAAAAATTTGCTCCACTACTCTTTAAGGGAGATCAGACT--A-AAAAATTTGATCCACTTCG
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
3732141 CTGC
131 CTGC
* *
3732145 TTTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTTAGGAAGACCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
** * *
3732210 GAAGAAGAATCTGCTCTGCTACTCTTTAGGGGAGATCATACTCGAGAAAAAATTTGATCCACTTC
66 GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAG-AAAACTTTGATCCACTTC
*
3732275 ACTAC
130 ACTGC
* * **
3732280 TCTTTAGAGAAGATTGAATCGGA-GTCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAA
1 TCTTCAGGGAAGATTGAATCAAATGT-GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAA
* * *
3732344 AGAAGAAGAATATGCTCCAATACGCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTC
65 AGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTC
*
3732409 ACTGG
130 ACTGC
* * * * * * * * *
3732414 TCTTCAGGGACGACTGAATCGGAAT-CGATTTGCTTTAATGCTATTCAGGAAATACCAAATCTTA
1 TCTTCAGGGAAGATTGAATC-AAATGTGATTTGCTTCACTGCTCTTCAGG-AAGACCAAATCTGA
* * * **
3732478 AAGACGGAGAATCTGCTCCTCTACTCTTTAGGGGAGATCAGGTTCGAGAAAACTTTGATCCACTT
64 AAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTT
3732543 CACTGC
129 CACTGC
*
3732549 TCTTCAGGGAAGATTGAATCAAATTTGATTTGCTT
1 TCTTCAGGGAAGATTGAATCAAATGTGATTTGCTT
3732584 ATCTTGTCTT
Statistics
Matches: 481, Mismatches: 77, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
130 71 0.15
131 39 0.08
133 59 0.12
134 92 0.19
135 220 0.46
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (134 bp):
TCTTCAGGGAAGATTGAATCAAATGTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
GAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCA
CTGC
Found at i:3733269 original size:45 final size:42
Alignment explanation
Indices: 3733213--3733339 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 42
3733203 GGCAACAGCA
* * *
3733213 AAAGATCGACTTCTCTTCGTGAGAAAGTCAAGAATGACAATATTG
1 AAAGATTGACTTCTCTTCGCGAGAAAGTCAAGAAT---AACATTG
* * * *
3733258 AACGATTGACTTTTCTTCACGAGAAAGTTAAGAATAACATTG
1 AAAGATTGACTTCTCTTCGCGAGAAAGTCAAGAATAACATTG
* * *
3733300 AAATATTGACTCCGCTTCGCGAGAAAGTCAAGAATAACAT
1 AAAGATTGACTTCTCTTCGCGAGAAAGTCAAGAATAACAT
3733340 CATAAAAGGT
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
42 39 0.57
45 29 0.43
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (42 bp):
AAAGATTGACTTCTCTTCGCGAGAAAGTCAAGAATAACATTG
Found at i:3733453 original size:45 final size:45
Alignment explanation
Indices: 3733359--3733619 Score: 238
Period size: 45 Copynumber: 5.8 Consensus size: 45
3733349 TTGACGTCAG
* * * * * * ** * *
3733359 TAAAAGGTTGAATTCTCTTTACGATAAACTCAAGAACAACACCAT
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACAC
* * * * *
3733404 TAAAAGGTTGACTTCTCTTCACGAGAAATTCAAGTAGGACCACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACAC
* *
3733449 TAAAAGATTGACTCCTCTTCACGAGAGAGTCAAGGAA-GATAACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGGACAACAC
* ** *
3733494 TAAACGATTGACTCCTCGTT-GTGAGAAAGTCAAGAAGGACAACAA
1 TAAAAGATTGACTCCTC-TTCACGAGAAAGTCAAGAAGGACAACAC
* * *
3733539 TAAAAGATTGACTCCTCTTCGCGAGAATGTCAAGAAGGATAACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACAC
* * **
3733584 TAAAAGATTGACTCCTCTACATGAGGGAGTCAAGAA
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
3733620 TAACAAAGGT
Statistics
Matches: 178, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
44 5 0.03
45 169 0.95
46 4 0.02
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (45 bp):
TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACAC
Found at i:3733527 original size:90 final size:90
Alignment explanation
Indices: 3733426--3733600 Score: 264
Period size: 90 Copynumber: 1.9 Consensus size: 90
3733416 TTCTCTTCAC
* * * *
3733426 GAGAAATTCAAGTAGGACCACACTAAAAGATTGACTCCTCTTCACGAGAGA-GTCAAGGAA-GAT
1 GAGAAAGTCAAGAAGGACAACAATAAAAGATTGACTCCTCTTCACGAGA-ATGTCAA-GAAGGAT
*
3733489 AACACTAAACGATTGACTCCTCGTTGT
64 AACACTAAAAGATTGACTCCTCGTTGT
*
3733516 GAGAAAGTCAAGAAGGACAACAATAAAAGATTGACTCCTCTTCGCGAGAATGTCAAGAAGGATAA
1 GAGAAAGTCAAGAAGGACAACAATAAAAGATTGACTCCTCTTCACGAGAATGTCAAGAAGGATAA
3733581 CACTAAAAGATTGACTCCTC
66 CACTAAAAGATTGACTCCTC
3733601 TACATGAGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
89 4 0.05
90 73 0.95
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (90 bp):
GAGAAAGTCAAGAAGGACAACAATAAAAGATTGACTCCTCTTCACGAGAATGTCAAGAAGGATAA
CACTAAAAGATTGACTCCTCGTTGT
Found at i:3733647 original size:38 final size:38
Alignment explanation
Indices: 3733586--3733736 Score: 169
Period size: 38 Copynumber: 4.0 Consensus size: 38
3733576 GATAACACTA
* * * *
3733586 AAAGATTGACTCCTC-TACATGAGGGAGTCAAGAATAAC
1 AAAGATCGACTTCTCTTA-ATGAGGAAGTCAAGAATAAT
*
3733624 AAAGGTCGACTTCTCTTAATGAGGAAGTCAAGAATAAT
1 AAAGATCGACTTCTCTTAATGAGGAAGTCAAGAATAAT
* ** *
3733662 AAAGATCGACTTCTATTCGTGAGGAAATCAAGAATAAT
1 AAAGATCGACTTCTCTTAATGAGGAAGTCAAGAATAAT
*** *
3733700 AAAGATCGACTTCTCTTCGCGATGAAGTCAAGAATAA
1 AAAGATCGACTTCTCTTAATGAGGAAGTCAAGAATAA
3733737 CATTAAAAGA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 96 0.98
39 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (38 bp):
AAAGATCGACTTCTCTTAATGAGGAAGTCAAGAATAAT
Found at i:3733759 original size:42 final size:42
Alignment explanation
Indices: 3733534--3733780 Score: 162
Period size: 38 Copynumber: 6.1 Consensus size: 42
3733524 CAAGAAGGAC
* * *
3733534 AACAATAAAAGATTGACTCCTCTTCGCGA-GAATGTCAAGAAGGAT
1 AACATTAAAAGATCGACTTCTCTTCGCGAGGAA-GTCAAG-A--AT
* * * * ** *
3733579 AACACTAAAAGATTGACTCCTCTACATGAGGGAGTCAAGAAT
1 AACATTAAAAGATCGACTTCTCTTCGCGAGGAAGTCAAGAAT
* ***
3733621 AAC----AAAGGTCGACTTCTCTTAATGAGGAAGTCAAGAAT
1 AACATTAAAAGATCGACTTCTCTTCGCGAGGAAGTCAAGAAT
* * *
3733659 -A-A-T-AAAGATCGACTTCTATTCGTGAGGAAATCAAGAAT
1 AACATTAAAAGATCGACTTCTCTTCGCGAGGAAGTCAAGAAT
*
3733697 -A-A-T-AAAGATCGACTTCTCTTCGCGATGAAGTCAAGAAT
1 AACATTAAAAGATCGACTTCTCTTCGCGAGGAAGTCAAGAAT
* * *
3733735 AACATTAAAAGATTGAC-TCATCTTCGCGAGGGAGTCAGGAAT
1 AACATTAAAAGATCGACTTC-TCTTCGCGAGGAAGTCAAGAAT
3733777 AACA
1 AACA
3733781 AAGATTGACC
Statistics
Matches: 170, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
37 1 0.01
38 93 0.55
39 1 0.01
40 1 0.01
41 3 0.02
42 37 0.22
44 1 0.01
45 31 0.18
46 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (42 bp):
AACATTAAAAGATCGACTTCTCTTCGCGAGGAAGTCAAGAAT
Found at i:3733795 original size:80 final size:78
Alignment explanation
Indices: 3733577--3733817 Score: 238
Period size: 80 Copynumber: 3.1 Consensus size: 78
3733567 GTCAAGAAGG
* * * * *
3733577 ATAACACTAAAAGATTGACTCCTCTACATGAGGGAGTCAAGAATAACAAAGGTCGACTTCTCTTA
1 ATAACA-TAAAAGATTGACT-CTCTTCGTGAGGGAGTCAAGAATAACAAAGATCGACCTCTCTTC
* *
3733642 ATGAGGAAGTCAAGA
64 ACGATGAAGTCAAGA
* * * * * * *
3733657 AT-A-AT-AAAGATCGACTTCTATTCGTGAGGAAATCAAGAATAATAAAGATCGACTTCTCTTCG
1 ATAACATAAAAGATTGAC-TCTCTTCGTGAGGGAGTCAAGAATAACAAAGATCGACCTCTCTTCA
3733719 CGATGAAGTCAAGA
65 CGATGAAGTCAAGA
* * *
3733733 ATAACATTAAAAGATTGACTCATCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACCTCTCTTC
1 ATAACA-TAAAAGATTGACTC-TCTTCGTGAGGGAGTCAAGAATAACAAAGATCGACCTCTCTTC
3733798 ACGAAT-AAGTCAAGA
64 ACG-ATGAAGTCAAGA
*
3733813 GTAAC
1 ATAAC
3733818 CAAGATTGAC
Statistics
Matches: 131, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
76 59 0.45
77 3 0.02
78 2 0.02
79 4 0.03
80 61 0.47
81 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (78 bp):
ATAACATAAAAGATTGACTCTCTTCGTGAGGGAGTCAAGAATAACAAAGATCGACCTCTCTTCAC
GATGAAGTCAAGA
Found at i:3733797 original size:38 final size:38
Alignment explanation
Indices: 3733606--3733845 Score: 212
Period size: 38 Copynumber: 6.2 Consensus size: 38
3733596 TCCTCTACAT
* * ***
3733606 GAGGGAGTCAAGAATAACAAAGGTCGACTTCTCTTAAT
1 GAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCGC
* * *
3733644 GAGGAAGTCAAGAATAATAAAGATCGACTTCTATTCGT
1 GAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCGC
* *
3733682 GAGGAAATCAAGAATAATAAAGATCGACTTCTCTTCGC
1 GAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCGC
* *
3733720 GATGAAGTCAAGAATAACATTAAAAGATTGAC-TCATCTTCGC
1 GAGGAAGTCAAGAATAAC----AAAGATCGACTTC-TCTTCGC
* * * * *
3733762 GAGGGAGTCAGGAATAACAAAGATTGACCTCTCTTCAC
1 GAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCGC
** * * * * *
3733800 GAATAAGTCAAGAGTAACCAAGATTGACTTATCTTCAC
1 GAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCGC
3733838 GAGGAAGT
1 GAGGAAGT
3733846 TAAATTGAAA
Statistics
Matches: 169, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
38 134 0.79
39 2 0.01
41 2 0.01
42 31 0.18
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (38 bp):
GAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCGC
Found at i:3733829 original size:156 final size:158
Alignment explanation
Indices: 3733541--3733829 Score: 368
Period size: 156 Copynumber: 1.8 Consensus size: 158
3733531 GACAACAATA
* * *
3733541 AAAGATTGACTCCTCTTCGCGAGAATGTCAAGAAGGATAACACTAAAAGATTGACTCCTCTACAT
1 AAAGATCGACTCCTCTTCGCGAGAATGTCAAGAA-GATAACACTAAAAGATTGACTCATCTACAC
* * * * *
3733606 GAGGGAGTCAAGAATAACAAAGGTCGACTTCTCTTAATGAGGAAGTCAAGAATAATAAAGATCGA
65 GAGGGAGTCAAGAATAACAAAGATCGACCTCTCTTAACGAAGAAGTCAAGAATAACAAAGATCGA
3733671 CTTCTATTCGTGAGGAAATCAAGAATAAT
130 CTTCTATTCGTGAGGAAATCAAGAATAAT
* * * *
3733700 AAAGATCGACTTCTCTTCGCGATGAA-GTCAAG-A-ATAACATTAAAAGATTGACTCATCTTCGC
1 AAAGATCGACTCCTCTTCGCGA-GAATGTCAAGAAGATAACACTAAAAGATTGACTCATCTACAC
* * * * * * *
3733762 GAGGGAGTCAGGAATAACAAAGATTGACCTCTCTTCACGAATAAGTCAAGAGTAACCAAGATTGA
65 GAGGGAGTCAAGAATAACAAAGATCGACCTCTCTTAACGAAGAAGTCAAGAATAACAAAGATCGA
3733827 CTT
130 CTT
3733830 ATCTTCACGA
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
156 80 0.73
158 1 0.01
159 26 0.24
160 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (158 bp):
AAAGATCGACTCCTCTTCGCGAGAATGTCAAGAAGATAACACTAAAAGATTGACTCATCTACACG
AGGGAGTCAAGAATAACAAAGATCGACCTCTCTTAACGAAGAAGTCAAGAATAACAAAGATCGAC
TTCTATTCGTGAGGAAATCAAGAATAAT
Found at i:3735333 original size:35 final size:35
Alignment explanation
Indices: 3735287--3735353 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
3735277 CGTCAACTCC
*
3735287 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCAGCA
1 AGTAAGGCCCTGAGAACAAAGCCGAGGAGCCAGCA
3735322 AGTAAGGCCCTGAGAACAAAGCCGAGGAGCCA
1 AGTAAGGCCCTGAGAACAAAGCCGAGGAGCCA
3735354 CCAGTAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.27, G:0.31, T:0.06
Consensus pattern (35 bp):
AGTAAGGCCCTGAGAACAAAGCCGAGGAGCCAGCA
Found at i:3735444 original size:24 final size:24
Alignment explanation
Indices: 3735403--3735449 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3735393 TTCAGATGTC
*
3735403 AGAACATAATTCAAGTCAAGTATT
1 AGAACATAATCCAAGTCAAGTATT
* *
3735427 AGAACATAATCCAGGTCAGGTAT
1 AGAACATAATCCAAGTCAAGTAT
3735450 CAAATCAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (24 bp):
AGAACATAATCCAAGTCAAGTATT
Found at i:3739108 original size:24 final size:24
Alignment explanation
Indices: 3739058--3739116 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
3739048 TTCAAAAAAA
*
3739058 TTGAAAAATATCAATTAAAATAATT
1 TTGAAAAATATCAATCAAAAT-ATT
*
3739083 TTGAAAAATGATTAATCAAAAT-TT
1 TTGAAAAAT-ATCAATCAAAATATT
3739107 TTGAAAAATA
1 TTGAAAAATA
3739117 GTTCCCTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.03
24 11 0.35
25 9 0.29
26 10 0.32
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (24 bp):
TTGAAAAATATCAATCAAAATATT
Found at i:3740080 original size:21 final size:22
Alignment explanation
Indices: 3740046--3740092 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3740036 TGATTTATTT
*
3740046 TCTTTCTCATTTTTCTTTTTCC
1 TCTTTCTCATTTTTATTTTTCC
* *
3740068 TCTTTTTC-TTTTTATTTTTCT
1 TCTTTCTCATTTTTATTTTTCC
3740089 TCTT
1 TCTT
3740093 CTTTTCCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTTTCTCATTTTTATTTTTCC
Found at i:3744796 original size:28 final size:28
Alignment explanation
Indices: 3744734--3744806 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
3744724 TCTGAATCAT
*
3744734 AATAAAAT-AATAAACAAATACAAACAGTT
1 AATAAAATGAAT-AA-AAATACAAACAGTG
*
3744763 ACTAAAATGAATAAAAATA-AAACCAGTG
1 AATAAAATGAATAAAAATACAAA-CAGTG
*
3744791 AATAAATTTGAATAAA
1 AATAAA-ATGAATAAA
3744807 CTAGAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 3 0.08
28 14 0.38
29 17 0.46
30 3 0.08
ACGTcount: A:0.63, C:0.08, G:0.07, T:0.22
Consensus pattern (28 bp):
AATAAAATGAATAAAAATACAAACAGTG
Found at i:3746943 original size:40 final size:40
Alignment explanation
Indices: 3746898--3746976 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
3746888 TTGAGGGATA
* * * * *
3746898 TGATATATGGAATGTGAATTCAGAATGTGCATATGATATG
1 TGATATATGGAATATAAAGTCAAAATGTGCATACGATATG
3746938 TGATATATGGAATATAAAGTCAAAATGTGCATACGATAT
1 TGATATATGGAATATAAAGTCAAAATGTGCATACGATAT
3746977 TACACTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (40 bp):
TGATATATGGAATATAAAGTCAAAATGTGCATACGATATG
Found at i:3749493 original size:21 final size:20
Alignment explanation
Indices: 3749447--3749495 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3749437 AAAAAACTCA
3749447 TTAAAATAATATTTAATATT
1 TTAAAATAATATTTAATATT
** *
3749467 CAAAAATCATATTTCAATATT
1 TTAAAATAATATTT-AATATT
3749488 TTAAAATA
1 TTAAAATA
3749496 TTTTCCCTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAATAATATTTAATATT
Found at i:3768039 original size:44 final size:42
Alignment explanation
Indices: 3767957--3768039 Score: 94
Period size: 44 Copynumber: 1.9 Consensus size: 42
3767947 CTTAAACAAT
**
3767957 AACATGGGAAGTATAATTTCTACACAAGAAGTACCATCATAA
1 AACATGGGAAGTATAATTTCTACACAAGAACCACCATCATAA
* * * *
3767999 AACATGGTGTAAGTTTAATTTCTACCCAAGCACCATCATCA
1 AACATGG-G-AAGTATAATTTCTACACAAGAACCACCATCA
3768040 AACCTGTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
42 7 0.21
43 1 0.03
44 25 0.76
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (42 bp):
AACATGGGAAGTATAATTTCTACACAAGAACCACCATCATAA
Found at i:3769517 original size:23 final size:23
Alignment explanation
Indices: 3769475--3769518 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
3769465 TTTGTTTTCA
3769475 ATTTATAATATAAATTTATAAAT
1 ATTTATAATATAAATTTATAAAT
3769498 ATTTA-AAT-TAATATTATATAA
1 ATTTATAATATAA-ATT-TATAA
3769519 TCTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.16
22 6 0.32
23 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTATAATATAAATTTATAAAT
Found at i:3774402 original size:38 final size:39
Alignment explanation
Indices: 3774359--3774435 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
3774349 ACCGCTTTTG
3774359 AAACTTAAATGTATGTTTTTATTTTGCACTGCTA-AACA
1 AAACTTAAATGTATGTTTTTATTTTGCACTGCTAGAACA
3774397 AAACTTAAATGTATGTTTTTATTTTGCACTGCTAGAACA
1 AAACTTAAATGTATGTTTTTATTTTGCACTGCTAGAACA
3774436 CACTAAGCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 34 0.89
39 4 0.11
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (39 bp):
AAACTTAAATGTATGTTTTTATTTTGCACTGCTAGAACA
Found at i:3786490 original size:29 final size:30
Alignment explanation
Indices: 3786439--3786497 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
3786429 AAATCATATC
3786439 TATAAAAATTAATGATATCATCTTTTTATT
1 TATAAAAATTAATGATATCATCTTTTTATT
*
3786469 TATAAAAATTAAT-ATATTATCTTTTTATT
1 TATAAAAATTAATGATATCATCTTTTTATT
3786498 AATTGTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (30 bp):
TATAAAAATTAATGATATCATCTTTTTATT
Found at i:3787184 original size:38 final size:38
Alignment explanation
Indices: 3787133--3787207 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
3787123 TTTGTATCAC
3787133 ATCTTAGCAACATAAAAATGATTAAAATATACTTTAGT
1 ATCTTAGCAACATAAAAATGATTAAAATATACTTTAGT
*
3787171 ATCTTAGCGACATAAAAATGATTAAAATATACTTTAG
1 ATCTTAGCAACATAAAAATGATTAAAATATACTTTAG
3787208 AACCAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (38 bp):
ATCTTAGCAACATAAAAATGATTAAAATATACTTTAGT
Found at i:3787583 original size:16 final size:17
Alignment explanation
Indices: 3787556--3787591 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3787546 ATGATTTTAT
3787556 TTAAATAAATTACTTAA
1 TTAAATAAATTACTTAA
*
3787573 TTAAA-AAATTAGTTAA
1 TTAAATAAATTACTTAA
3787589 TTA
1 TTA
3787592 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATAAATTACTTAA
Found at i:3789521 original size:17 final size:17
Alignment explanation
Indices: 3789499--3789531 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3789489 CCCCCCAAAT
*
3789499 TTTTATTTTTTCTTTTC
1 TTTTATTTTTTATTTTC
3789516 TTTTATTTTTTATTTT
1 TTTTATTTTTTATTTT
3789532 TATTTTCCCA
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:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTATTTTTTATTTTC
Found at i:3789533 original size:30 final size:30
Alignment explanation
Indices: 3789497--3789567 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
3789487 TACCCCCCAA
* **
3789497 ATTTTTATTTTTTCTTTTCTTTTATTT-TTT
1 ATTTTTATTTTTCCACTTCTTTT-TTTATTT
*
3789527 ATTTTTATTTTCCCACTTCTTTTTTTATTT
1 ATTTTTATTTTTCCACTTCTTTTTTTATTT
3789557 A-TTTTATTTTT
1 ATTTTTATTTTT
3789568 ATTTCTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (30 bp):
ATTTTTATTTTTCCACTTCTTTTTTTATTT
Found at i:3789722 original size:63 final size:63
Alignment explanation
Indices: 3789604--3789727 Score: 148
Period size: 62 Copynumber: 2.0 Consensus size: 63
3789594 TTTATTATTT
* *
3789604 TATTTTCTGAAATTTAATATTTCTTCATTTATTTAATTTTTTTCTTTAACATTTTT-ATATAA
1 TATTTTCTAAAATTTAATATTTCTTCATTTATTTAATTTTTTTATTTAACATTTTTGATATAA
* *
3789666 TATTTTTTAAAATTTAATATTTCCTTC-TTTGATTT-ATTTTTTAATATTTAA-TTTTTTGATAT
1 TATTTTCTAAAATTTAATATTT-CTTCATTT-ATTTAATTTTTT--TATTTAACATTTTTGATAT
3789728 TTCTTTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
62 30 0.57
63 13 0.25
64 10 0.19
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.63
Consensus pattern (63 bp):
TATTTTCTAAAATTTAATATTTCTTCATTTATTTAATTTTTTTATTTAACATTTTTGATATAA
Found at i:3809616 original size:18 final size:18
Alignment explanation
Indices: 3809593--3809635 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3809583 CGTTAGATTA
* *
3809593 TTTATTTAATTTTTTTCT
1 TTTATTTAATTCTTATCT
3809611 TTTATTTAATTCTTATCT
1 TTTATTTAATTCTTATCT
3809629 TTTATTT
1 TTTATTT
3809636 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTCTTATCT
Found at i:3809878 original size:24 final size:25
Alignment explanation
Indices: 3809846--3809910 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
3809836 ATTTTCTCAC
*
3809846 TTCTTTTTTTATTTTATTTTA-ATT
1 TTCTATTTTTATTTTATTTTATATT
* * **
3809870 TTCTCTTTTAACATTATTTTATATT
1 TTCTATTTTTATTTTATTTTATATT
*
3809895 TTATTATTTTTATTTT
1 TT-CTATTTTTATTTT
3809911 CTGAAATTTA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
24 17 0.57
25 5 0.17
26 8 0.27
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (25 bp):
TTCTATTTTTATTTTATTTTATATT
Found at i:3811013 original size:41 final size:41
Alignment explanation
Indices: 3810957--3811649 Score: 483
Period size: 41 Copynumber: 17.0 Consensus size: 41
3810947 CGTTTTTTGA
* * * * *
3810957 ACAAACGCTGGTAAATACTCGTACGTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* *
3810998 ATAAACGCCGCTAAATACT-ATACTTTAGTGGCGTTTTTGT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* * * * * * * *
3811038 ACAAATGTCACTAAAGACTCGTACTTTAGTGGTGTTTTAAGC
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTA-T
* * * * * *
3811080 ACAAATGCCGCTAAATACACGTTCTTTAGTGTCATTTTTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* ** * *
3811121 ATAAACGCCGCTAAATA-TTGTACTTTAGTGGTGTTTGTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
** * * *
3811161 ACAAACTTCGCTAAAGACTCATACTTTAGTAGTGTTTTTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* * * * * *
3811202 ACAAACACCGCTGAAGACTCATACTTTAGTGGTGTTTTAAGC
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTA-T
* * *
3811244 ACACACACCGTTAAATACTCATACTTTAGTGAG-GTTTTTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTG-GCGTTTTTAT
* * * * * *
3811285 ATAAACACAGCTAAATA-TTATACTTTAGTGGCATTTGTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
** * * * * * *
3811325 ACAAAAACTGAC-AAAGACACGTACTTTAGTGGCATTTTAAGT
1 ACAAACGCCG-CTAAATACTCATACTTTAGTGGCGTTTTTA-T
* * **
3811367 ACAAACGTCGCTGAATACTCATACTTTAGTGGTTTTTTTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* * * * *
3811408 ATACACGTCGCTAAATACT-ATACTTTAGTGGCATTTGTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* * * *
3811448 ATC-GACG-C-C-AAAGACTCGTACTTTAGTGGTGTTTTTAT
1 A-CAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* *
3811486 ATAAACGCCGCTAAATACT-ATACTTTAGTGGCGTTTGTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
** * * * * *
3811526 ACAAACGGTGCCAAATACTCATACTTTAATGGTGTTTTAAGC
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTA-T
* *
3811568 ACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
* * ** * *
3811609 ATAAACGCCGATAAATA-TTGTACTTTAGTGGTGTTTGTAT
1 ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
3811649 A
1 A
3811650 AGACTCGTAC
Statistics
Matches: 508, Mismatches: 126, Indels: 37
0.76 0.19 0.06
Matches are distributed among these distances:
37 6 0.01
38 22 0.04
39 3 0.01
40 165 0.32
41 187 0.37
42 124 0.24
43 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (41 bp):
ACAAACGCCGCTAAATACTCATACTTTAGTGGCGTTTTTAT
Found at i:3811107 original size:42 final size:41
Alignment explanation
Indices: 3810968--3811110 Score: 112
Period size: 42 Copynumber: 3.5 Consensus size: 41
3810958 CAAACGCTGG
* * * * * *
3810968 TAAATACTCGTACGTTAGTGGCATTTTTA-TATAAACGCCGC
1 TAAATACACGTACTTTAGTGGC-GTTTTAGCACAAATGCCGC
* * * *
3811009 TAAATACTA--TACTTTAGTGGCGTTTTTGTACAAATGTCAC
1 TAAATAC-ACGTACTTTAGTGGCGTTTTAGCACAAATGCCGC
* * *
3811049 TAAAGACTCGTACTTTAGTGGTGTTTTAAGCACAAATGCCGC
1 TAAATACACGTACTTTAGTGGCGTTTT-AGCACAAATGCCGC
*
3811091 TAAATACACGTTCTTTAGTG
1 TAAATACACGTACTTTAGTG
3811111 TCATTTTTAT
Statistics
Matches: 79, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 4 0.05
40 25 0.32
41 23 0.29
42 27 0.34
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (41 bp):
TAAATACACGTACTTTAGTGGCGTTTTAGCACAAATGCCGC
Found at i:3811117 original size:123 final size:123
Alignment explanation
Indices: 3810968--3811649 Score: 534
Period size: 123 Copynumber: 5.6 Consensus size: 123
3810958 CAAACGCTGG
* * *
3810968 TAAATACTCGTACGTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCGTT
1 TAAAGACTCGTACTTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGTGTT
* * *
3811033 TTTGTACAAATGTCACTAAAGACTCGTACTTTAGTGGTGTTTTAAGCACAAATGCCGC
66 TTTATACAAATGTCACTAAATACTCATACTTTAGTGGTGTTTTAAGCACAAATGCCGC
* * * * * *
3811091 TAAATACACGTTCTTTAGTGTCATTTTTATATAAACGCCGCTAAATATTGTACTTTAGTGGTGTT
1 TAAAGACTCGTACTTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGTGTT
* * * * * * **
3811156 TGTATACAAACT-TCGCTAAAGACTCATACTTTAGTAGTGTTTTTA-TACAAACACCGC
66 TTTATACAAA-TGTCACTAAATACTCATACTTTAGTGGTGTTTTAAGCACAAATGCCGC
* * ** * * * * * *
3811213 TGAAGACTCATACTTTAGTGGTGTTTTAAGCACACACACCGTTAAATACTCATACTTTAGTGAG-
1 TAAAGACTCGTACTTTAGTGGCATTTTTA-TATAAACGCCGCTAAATACT-ATACTTTAGTG-GT
* ** * ** * *
3811277 GTTTTTATATAAA-CACAGCTAAATA-TTATACTTTAGTGGCATTTGTATA-CAAAAACTG--AC
63 GTTTTTATACAAATGTCA-CTAAATACTCATACTTTAGTGGTGTTT-TA-AGCACAAA-TGCCGC
* * * * * *
3811337 -AAAGACACGTACTTTAGTGGCATTTTAAGTACAAACGTCGCTGAATACTCATACTTTAGTGGTT
1 TAAAGACTCGTACTTTAGTGGCATTTTTA-TATAAACGCCGCTAAATACT-ATACTTTAGTGGTG
* * * * ** * * *
3811401 TTTTTATATACACGTCGCTAAATACT-ATACTTTAGTGG-CATTT--G--TATATCGACGC
64 TTTTTATACAAATGTCACTAAATACTCATACTTTAGTGGTGTTTTAAGCACAAAT-GCCGC
* ** *
3811456 CAAAGACTCGTACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCGTT
1 TAAAGACTCGTACTTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGTGTT
* * * *
3811521 TGTATACAAACGGTGC-C-AAATACTCATACTTTAATGGTGTTTTAAGCACAAACGCCGC
66 TTTATACAAA-TGT-CACTAAATACTCATACTTTAGTGGTGTTTTAAGCACAAATGCCGC
* * * *
3811579 TAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGATAAATATTGTACTTTAGTGGTGTT
1 TAAAGACTCGTACTTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGTGTT
*
3811644 TGTATA
66 TTTATA
3811650 AGACTCGTAC
Statistics
Matches: 438, Mismatches: 96, Indels: 50
0.75 0.16 0.09
Matches are distributed among these distances:
116 1 0.00
117 3 0.01
118 28 0.06
119 32 0.07
120 28 0.06
121 1 0.00
122 33 0.08
123 272 0.62
124 34 0.08
125 6 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (123 bp):
TAAAGACTCGTACTTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGTGTT
TTTATACAAATGTCACTAAATACTCATACTTTAGTGGTGTTTTAAGCACAAATGCCGC
Found at i:3811288 original size:164 final size:162
Alignment explanation
Indices: 3811006--3811649 Score: 669
Period size: 164 Copynumber: 4.0 Consensus size: 162
3810996 ATATAAACGC
* * * * *
3811006 CGCTAAATACTATACTTTAGTGGCGTTTTTGTACAAATGTCACTAAAGACTCGTACTTTAGTGGT
1 CGCTAAAGACTATACTTTAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCATACTTTAGTGGT
* * * * *
3811071 GTTTTAAGCACAAATGCCGCTAAATACACGTTCTTTAGTGTCATTTTTATATAAACGCCGCTAAA
66 GTTTTAAGCACAAACGCCGCTAAATACTCATACTTTAGTGGCATTTTTATATAAACGCCGCTAAA
3811136 TATTGTACTTTAGTGGTGTTTGTATACAAACTT
131 TATTGTACTTTAGTGGTGTTTGTATACAAAC-T
* * ** *
3811169 CGCTAAAGACTCATACTTTAGTAGTGTTTTTATACAAACACCGCTGAAGACTCATACTTTAGTGG
1 CGCTAAAGACT-ATACTTTAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCATACTTTAGTGG
* * * * * *
3811234 TGTTTTAAGCACACACACCGTTAAATACTCATACTTTAGTGAG-GTTTTTATATAAACACAGCTA
65 TGTTTTAAGCACAAACGCCGCTAAATACTCATACTTTAGTG-GCATTTTTATATAAACGCCGCTA
* **
3811298 AATATTATACTTTAGTGGCATTTGTATACAAAAACT
129 AATATTGTACTTTAGTGGTGTTTGTATAC--AAACT
* * * *
3811334 -GAC-AAAGAC-ACGTACTTTAGTGGCATTTTAAGTACAAACGTCGCTGAATACTCATACTTTAG
1 CG-CTAAAGACTA--TACTTTAGTGGCGTTTTTA-TACAAACGTCGCTAAAGACTCATACTTTAG
* * * * * * * *
3811396 TGGTTTTTTTA-TATACACGTCGCTAAATACT-ATACTTTAGTGGCATTTGTATAT---CGACGC
62 TGGTGTTTTAAGCACAAACGCCGCTAAATACTCATACTTTAGTGGCATTTTTATATAAACGCCGC
* * * * * *
3811456 CAAAGACTCGTACTTTAGTGGTGTTTTTATATAAACGC
127 TAAATA-TTGTACTTTAGTGGTGTTTGTATACAAAC-T
* * * * *
3811494 CGCTAAATACTATACTTTAGTGGCGTTTGTATACAAACGGT-GCCAAATACTCATACTTTAATGG
1 CGCTAAAGACTATACTTTAGTGGCGTTTTTATACAAAC-GTCGCTAAAGACTCATACTTTAGTGG
* *
3811558 TGTTTTAAGCACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTATATAAACGCCGATAA
65 TGTTTTAAGCACAAACGCCGCTAAATACTCATACTTTAGTGGCATTTTTATATAAACGCCGCTAA
3811623 ATATTGTACTTTAGTGGTGTTTGTATA
130 ATATTGTACTTTAGTGGTGTTTGTATA
3811650 AGACTCGTAC
Statistics
Matches: 388, Mismatches: 73, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
159 37 0.10
160 42 0.11
161 46 0.12
162 3 0.01
163 51 0.13
164 167 0.43
165 38 0.10
166 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (162 bp):
CGCTAAAGACTATACTTTAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCATACTTTAGTGGT
GTTTTAAGCACAAACGCCGCTAAATACTCATACTTTAGTGGCATTTTTATATAAACGCCGCTAAA
TATTGTACTTTAGTGGTGTTTGTATACAAACT
Found at i:3811483 original size:78 final size:80
Alignment explanation
Indices: 3810973--3811615 Score: 326
Period size: 83 Copynumber: 7.9 Consensus size: 80
3810963 GCTGGTAAAT
* * ** * * *
3810973 ACTCGTACGTTAGTGGCATTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCGTTTTTGT
1 ACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCATTTGTAT
* *
3811038 A-CAAATGTCACTAAAG
66 ATCAAACGGC-C-AAAG
* * * * * * * *
3811054 ACTCGTACTTTAGTGGTGTTTTAAGCACAAATGCCGCTAAATAC-ACGTTCTTTAGTGTCATTTT
1 ACTCATACTTTAGTGGTGTTTTTA-TATAAACGCCGCTAAATACTA--TACTTTAGTGGCATTTG
* *
3811118 TATAT-AAACGCCGCTAAAT
63 TATATCAAACG--GCCAAAG
** * * ** * * ** *
3811137 A-TTGTACTTTAGTGGTGTTTGTATACAAACTTCGCTAAAGACTCATACTTTAGTAGTGTTTTTA
1 ACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACT-ATACTTTAGTGGCATTTGTA
* **
3811201 TA-CAAACACCGCTGAAG
65 TATC-AA-ACGGCCAAAG
* * * * * * * *
3811218 ACTCATACTTTAGTGGTGTTTTAAGCACACACACCGTTAAATACTCATACTTTAGTGAG-GTTTT
1 ACTCATACTTTAGTGGTGTTTTTA-TATAAACGCCGCTAAATACT-ATACTTTAGTG-GCATTTG
* * * *
3811282 TATATAAACACAGCTAAAT
63 TATATCAA-ACGGCCAAAG
* ** * * ** * *
3811301 A-TTATACTTTAGTGGCATTTGTATACAAAAACTGAC-AAAGAC-ACGTACTTTAGTGGCATTT-
1 ACTCATACTTTAGTGGTGTTTTTATATAAACGCCG-CTAAATACTA--TACTTTAGTGGCATTTG
** *
3811362 TA-AGTACAAACGTCGCTGAAT
63 TATA-T-CAAACG--GCCAAAG
* * *
3811383 ACTCATACTTTAGTGGTTTTTTTATATACACGTCGCTAAATACTATACTTTAGTGGCATTTGTAT
1 ACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCATTTGTAT
*
3811448 ATC-GAC-GCCAAAG
66 ATCAAACGGCCAAAG
* *
3811461 ACTCGTACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCGTTTGTAT
1 ACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCATTTGTAT
*
3811526 A-CAAACGGTGCCAAAT
66 ATCAAAC-G-GCCAAAG
* * * * * *
3811542 ACTCATACTTTAATGGTGTTTTAAGCACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTT
1 ACTCATACTTTAGTGGTGTTTTTA-TATAAACGCCGCTAAATACT-ATACTTTAGTGGCATTTGT
3811607 ATAT-AAACG
64 ATATCAAACG
3811616 CCGATAAATA
Statistics
Matches: 436, Mismatches: 91, Indels: 69
0.73 0.15 0.12
Matches are distributed among these distances:
77 1 0.00
78 67 0.15
79 2 0.00
80 6 0.01
81 113 0.26
82 116 0.27
83 127 0.29
84 3 0.01
85 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (80 bp):
ACTCATACTTTAGTGGTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCATTTGTAT
ATCAAACGGCCAAAG
Found at i:3811502 original size:201 final size:201
Alignment explanation
Indices: 3811260--3811649 Score: 512
Period size: 201 Copynumber: 1.9 Consensus size: 201
3811250 ACCGTTAAAT
*
3811260 ACTCATACTTTAGTGAGGTTTTTATATAAACACAGCTAAATATTATACTTTAGTGGCATTTGTAT
1 ACTCATACTTTAGTGAGGTTTTTATATAAACACAGCTAAATACTATACTTTAGTGGCATTTGTAT
* * * * *
3811325 ACAAAAACTGACAAAGACACGTACTTTAGTGGCATTTTAAGTACAAACGTCGCTGAATACTCATA
66 ACAAAAACTGACAAAGACACATACTTTAATGGCATTTTAAGCACAAACGCCGCTAAATACTCATA
** * * *
3811390 CTTTAGTGGTTTTTTTATATACACGTCGCTAAATACTATACTTTAGTGGCATTTGTATATCGACG
131 CTTTAGTGGCATTTTTATATAAACGCCGATAAATACTATACTTTAGTGGCATTTGTATATCGACG
3811455 CCAAAG
196 CCAAAG
* * * *
3811461 ACTCGTACTTTAGTG-GTGTTTTTATATAAACGCCGCTAAATACTATACTTTAGTGGCGTTTGTA
1 ACTCATACTTTAGTGAG-GTTTTTATATAAACACAGCTAAATACTATACTTTAGTGGCATTTGTA
*** * * * ** *
3811525 TACAAACGGTGCCAAATACTCATACTTTAATGGTGTTTTAAGCACAAACGCCGCTAAATACTCGT
65 TACAAAAACTGACAAAGACACATACTTTAATGGCATTTTAAGCACAAACGCCGCTAAATACTCAT
* * **
3811590 ACTTTAGTGGCATTTTTATATAAACGCCGATAAATATTGTACTTTAGTGGTGTTTGTATA
130 ACTTTAGTGGCATTTTTATATAAACGCCGATAAATACTATACTTTAGTGGCATTTGTATA
3811650 AGACTCGTAC
Statistics
Matches: 160, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
200 1 0.01
201 159 0.99
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (201 bp):
ACTCATACTTTAGTGAGGTTTTTATATAAACACAGCTAAATACTATACTTTAGTGGCATTTGTAT
ACAAAAACTGACAAAGACACATACTTTAATGGCATTTTAAGCACAAACGCCGCTAAATACTCATA
CTTTAGTGGCATTTTTATATAAACGCCGATAAATACTATACTTTAGTGGCATTTGTATATCGACG
CCAAAG
Found at i:3814152 original size:21 final size:21
Alignment explanation
Indices: 3814128--3814176 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3814118 GTAAACTTTG
*
3814128 ATTTATTATTATGGATTTCAA
1 ATTTATTATTATGGATGTCAA
* *
3814149 ATTTCTTGTTATGGATGTCAA
1 ATTTATTATTATGGATGTCAA
*
3814170 GTTTATT
1 ATTTATT
3814177 GGATAATGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (21 bp):
ATTTATTATTATGGATGTCAA
Found at i:3814490 original size:44 final size:44
Alignment explanation
Indices: 3814396--3814480 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
3814386 TTTTACATTC
* *
3814396 ACAAATGTCACTATATGACATAATATTTAGCGGTGTTTTTGAGA
1 ACAAATGTCACTATATGACAGAACATTTAGCGGTGTTTTTGAGA
* *
3814440 ACAAATGTCATTATATGTCAGAACATTTAGC-GTCGTTTTTG
1 ACAAATGTCACTATATGACAGAACATTTAGCGGT-GTTTTTG
3814481 GGGGAAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (44 bp):
ACAAATGTCACTATATGACAGAACATTTAGCGGTGTTTTTGAGA
Found at i:3817841 original size:105 final size:104
Alignment explanation
Indices: 3817686--3817892 Score: 290
Period size: 105 Copynumber: 2.0 Consensus size: 104
3817676 TTGTCAATAG
* *
3817686 TATCAAACATTTTGTCACTAAAAAACACTTACTGTGACAACATTGGTGGTCACAAAATATACTTT
1 TATCAAACATTTGGTCACTAAAAAACACTTACTGTGACAACATTGATGGTCACAAAATATACTTT
* * * *
3817751 CAGTGTCAAATAA-ATTTATCACAATTTCTATTGATAATGA
66 CAGTGT-AAA-AAGAATCATCACAATTTATATTAATAATGA
* * * *
3817791 TATCAAACATTTGGTCACTAAAAAATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTT
1 TATCAAACATTTGGTCACTAAAAAACACTTACTGTGACAACATTGATGGTCACAAAATATACTTT
*
3817856 TAGTGTAAAAAGAATCATCACAATTTATATTAATAAT
66 CAGTGTAAAAAGAATCATCACAATTTATATTAATAAT
3817893 TGTGTCAAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
103 2 0.02
104 24 0.27
105 64 0.71
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (104 bp):
TATCAAACATTTGGTCACTAAAAAACACTTACTGTGACAACATTGATGGTCACAAAATATACTTT
CAGTGTAAAAAGAATCATCACAATTTATATTAATAATGA
Found at i:3817919 original size:105 final size:105
Alignment explanation
Indices: 3817699--3817921 Score: 263
Period size: 105 Copynumber: 2.1 Consensus size: 105
3817689 CAAACATTTT
* *
3817699 GTCACTAAAAAACACTTACTGTGACAACATTGGTGGTCACAAAATATACTTTCAGTGTCAAATAA
1 GTCACAAAAAAACACTTACTGTGACAACATTGATGGTCACAAAATATACTTTCAGTGTCAAATAA
* * * * **
3817764 ATTTATCACAATTTCTATTGATAATGATATCAAACATTTG
66 AATCATCACAATTTATATTAATAATGATATCAAACAAATG
* * * * * *
3817804 GTCACTAAAAAATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTTTAGTGT-AAA-AA
1 GTCACAAAAAAACACTTACTGTGACAACATTGATGGTCACAAAATATACTTTCAGTGTCAAATAA
* *
3817867 GAATCATCACAATTTATATTAATAATTG-TGTCAAATAAATG
66 -AATCATCACAATTTATATTAATAA-TGATATCAAACAAATG
3817908 GTCACAAAAAAACA
1 GTCACAAAAAAACA
3817922 ATTGTGACAA
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
103 2 0.02
104 44 0.44
105 54 0.54
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (105 bp):
GTCACAAAAAAACACTTACTGTGACAACATTGATGGTCACAAAATATACTTTCAGTGTCAAATAA
AATCATCACAATTTATATTAATAATGATATCAAACAAATG
Found at i:3819636 original size:26 final size:26
Alignment explanation
Indices: 3819600--3819716 Score: 180
Period size: 26 Copynumber: 4.5 Consensus size: 26
3819590 ATTAACACCA
* ** *
3819600 TTTGCACTTGCATCCCGCATTTCATC
1 TTTGCATTTGCATCCCATATTGCATC
3819626 TTTGCATTTGCATCCCATATTGCATC
1 TTTGCATTTGCATCCCATATTGCATC
*
3819652 TTTGCATTTGTATCCCATATTGCATC
1 TTTGCATTTGCATCCCATATTGCATC
*
3819678 TTTGCATTTGTATCCCATATTGCATC
1 TTTGCATTTGCATCCCATATTGCATC
3819704 TTTGCATTTGCAT
1 TTTGCATTTGCAT
3819717 TTATGTGTAT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 85 1.00
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.44
Consensus pattern (26 bp):
TTTGCATTTGCATCCCATATTGCATC
Found at i:3821172 original size:2 final size:2
Alignment explanation
Indices: 3821165--3821205 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3821155 TCAGTATGTT
3821165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3821206 TTTAGTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3821274 original size:16 final size:15
Alignment explanation
Indices: 3821218--3821276 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
3821208 TAGTAATTTA
* *
3821218 ATTTTTATTTTTAGT
1 ATTTTTATATTTAAT
3821233 ATTTTTATATTTAAT
1 ATTTTTATATTTAAT
3821248 -TTTTTGAATATTTGAAT
1 ATTTTT--ATATTT-AAT
3821265 ATTTTTATATTT
1 ATTTTTATATTT
3821277 TAAATTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.13
15 13 0.34
16 12 0.32
17 3 0.08
18 5 0.13
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Found at i:3822383 original size:2 final size:2
Alignment explanation
Indices: 3822378--3822463 Score: 122
Period size: 2 Copynumber: 43.5 Consensus size: 2
3822368 TTAAAACAAC
*
3822378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3822420 -A TA TA TA TA TA TA TA TA TA TA -A TG TA TA AA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
3822461 TA T
1 TA T
3822464 TTGTATAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
1 2 0.03
2 71 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3822537 original size:21 final size:21
Alignment explanation
Indices: 3822513--3822561 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3822503 ATTGAACTAT
*
3822513 ATATAACTACATAGTTTATTA
1 ATATAAATACATAGTTTATTA
*
3822534 ATATAAATATATAGTTTATTA
1 ATATAAATACATAGTTTATTA
3822555 ATATAAA
1 ATATAAA
3822562 CTATATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
ATATAAATACATAGTTTATTA
Found at i:3822571 original size:11 final size:11
Alignment explanation
Indices: 3822555--3822579 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3822545 TAGTTTATTA
3822555 ATATAAACTAT
1 ATATAAACTAT
3822566 ATATAAACTAT
1 ATATAAACTAT
3822577 ATA
1 ATA
3822580 ATTTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAACTAT
Found at i:3822711 original size:15 final size:17
Alignment explanation
Indices: 3822691--3822729 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3822681 ATATAAACAA
3822691 TATATACTAACT-TATAC
1 TATAT-CTAACTATATAC
*
3822708 TATATGTAACTATATAC
1 TATATCTAACTATATAC
3822725 TATAT
1 TATAT
3822730 AGTTTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (17 bp):
TATATCTAACTATATAC
Found at i:3822723 original size:17 final size:16
Alignment explanation
Indices: 3822698--3822729 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3822688 CAATATATAC
3822698 TAACTTATACTATATG
1 TAACTTATACTATATG
3822714 TAACTATATACTATAT
1 TAACT-TATACTATAT
3822730 AGTTTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (16 bp):
TAACTTATACTATATG
Found at i:3822796 original size:28 final size:28
Alignment explanation
Indices: 3822709--3822803 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
3822699 AACTTATACT
*
3822709 ATATGTAACTATATA-CTATATAGTTTAC
1 ATATG-AACTATATATATATATAGTTTAC
** *
3822737 ATATGAACTATGGATACTTTATAGTTTAC
1 ATATGAACTATATATA-TATATAGTTTAC
3822766 ATATGAACTATATATATATATAGTTTAC
1 ATATGAACTATATATATATATAGTTTAC
3822794 ATATGAACTA
1 ATATGAACTA
3822804 CATGTATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.12
28 26 0.45
29 25 0.43
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (28 bp):
ATATGAACTATATATATATATAGTTTAC
Found at i:3822857 original size:22 final size:22
Alignment explanation
Indices: 3822831--3822878 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3822821 CTATGTAAAC
3822831 TATATAGTTTACGTA-TGAACTA
1 TATATAGTTTA-GTAGTGAACTA
*
3822853 TATATAGTTTATTAGTGAACTA
1 TATATAGTTTAGTAGTGAACTA
3822875 TATA
1 TATA
3822879 AATTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (22 bp):
TATATAGTTTAGTAGTGAACTA
Found at i:3822884 original size:20 final size:22
Alignment explanation
Indices: 3822846--3822885 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3822836 AGTTTACGTA
*
3822846 TGAACTATATATAGTTTATTAG
1 TGAACTATATATAGATTATTAG
3822868 TGAACTATATA-A-ATTATT
1 TGAACTATATATAGATTATT
3822886 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 1 0.06
22 11 0.65
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (22 bp):
TGAACTATATATAGATTATTAG
Found at i:3822891 original size:2 final size:2
Alignment explanation
Indices: 3822873--3823011 Score: 63
Period size: 2 Copynumber: 67.0 Consensus size: 2
3822863 ATTAGTGAAC
* * *
3822873 TA TA TA AA T- TA TT TA TA TA TA TA TA -A CTA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * **
3822914 TA TA TA TA TA TA AA CTA TA GTT TA TA TT TA TA T- TA CG TA CTA
1 TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* *
3822956 TA GT- TGA TA TT TA TA TA CTA TA T- TA TA TA TA TA AA CTA TA TA
1 TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
3822998 TA CTA TA TA GTA TA
1 TA -TA TA TA -TA TA
3823012 ATTTACATAT
Statistics
Matches: 102, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
1 5 0.05
2 83 0.81
3 14 0.14
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3822912 original size:106 final size:106
Alignment explanation
Indices: 3822723--3822931 Score: 230
Period size: 106 Copynumber: 2.0 Consensus size: 106
3822713 GTAACTATAT
* ** *
3822723 ACTATATAGTTTACATATGAACTATGGATACTTTATAGTTTACATATGAACTATATATATATATA
1 ACTATATAGTTTACATATGAACTATAGATACTTTATAGTGAACATATAAACTATATATATATATA
* *
3822788 GTTTACATATGAACTACATGTATA-A-ACTATAAACTATGTAA
66 G-TAACATATGAACTACATATATATATA-TATAAACTATGTAA
* * * * *
3822829 ACTATATAGTTTACGTATGAACTATATATAGTTTATTAGTGAACTATATAAATTATTTATATATA
1 ACTATATAGTTTACATATGAACTATAGATACTTTA-TAGTGAAC-ATATAAACTATATATATATA
3822894 TA-TAACTATAT-ATA-TACATATATATATATATAAACTAT
64 TAGTAAC-ATATGA-ACTACATATATATATATATAAACTAT
3822932 AGTTTATATT
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
106 44 0.51
107 22 0.26
108 20 0.23
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (106 bp):
ACTATATAGTTTACATATGAACTATAGATACTTTATAGTGAACATATAAACTATATATATATATA
GTAACATATGAACTACATATATATATATATAAACTATGTAA
Found at i:3823056 original size:27 final size:27
Alignment explanation
Indices: 3823026--3823082 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3823016 ACATATGAAC
3823026 TATATAAA-AACTATAAATTATAGTTTA
1 TATATAAACAA-TATAAATTATAGTTTA
* *
3823053 TATATAAACTATATAAATTATATTTTA
1 TATATAAACAATATAAATTATAGTTTA
3823080 TAT
1 TAT
3823083 TGAACTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (27 bp):
TATATAAACAATATAAATTATAGTTTA
Found at i:3823063 original size:36 final size:36
Alignment explanation
Indices: 3822981--3823069 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
3822971 TACTATATTA
* *
3822981 TATATATAAACTATAT--ATACTATATAGTATAATT
1 TATATATAAACTATATAAAAACTATAAAGTATAATT
* * * *
3823015 TACATATGAACTATATAAAAACTATAAATTATAGTT
1 TATATATAAACTATATAAAAACTATAAAGTATAATT
3823051 TATATATAAACTATATAAA
1 TATATATAAACTATATAAA
3823070 TTATATTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
34 14 0.31
36 31 0.69
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (36 bp):
TATATATAAACTATATAAAAACTATAAAGTATAATT
Found at i:3823117 original size:22 final size:22
Alignment explanation
Indices: 3823092--3823133 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3823082 TTGAACTATA
3823092 GTTTACATA-TGAACTATATATG
1 GTTTA-ATAGTGAACTATATATG
*
3823114 GTTTATTAGTGAACTATATA
1 GTTTAATAGTGAACTATATA
3823134 AACTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (22 bp):
GTTTAATAGTGAACTATATATG
Found at i:3823294 original size:27 final size:25
Alignment explanation
Indices: 3823264--3823347 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 25
3823254 ATATGAACTA
3823264 TATATAAAAACTATATAAACTATAGTT
1 TATATAAAAACTATAT--ACTATAGTT
*
3823291 TATATATAAACTATATACTATAGTT
1 TATATAAAAACTATATACTATAGTT
* * * *
3823316 GATATTTATATAGTATATACTATAGTT
1 --TATATAAAAACTATATACTATAGTT
*
3823343 GATAT
1 TATAT
3823348 TTATATACTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 12 0.24
27 37 0.76
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (25 bp):
TATATAAAAACTATATACTATAGTT
Found at i:3823348 original size:27 final size:27
Alignment explanation
Indices: 3823277--3823393 Score: 130
Period size: 27 Copynumber: 4.4 Consensus size: 27
3823267 ATAAAAACTA
* * *
3823277 TATAAACTATAGTT--TATATATAAAC
1 TATATACTATAGTTGATATTTATATAC
*
3823302 TATATACTATAGTTGATATTTATATAG
1 TATATACTATAGTTGATATTTATATAC
3823329 TATATACTATAGTTGATATTTATATAC
1 TATATACTATAGTTGATATTTATATAC
* * * * *
3823356 TATATAATATAATTTATACTTATATAA
1 TATATACTATAGTTGATATTTATATAC
*
3823383 TTTATACTATA
1 TATATACTATA
3823394 TAAATTCAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
25 13 0.17
27 65 0.83
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (27 bp):
TATATACTATAGTTGATATTTATATAC
Found at i:3823382 original size:15 final size:14
Alignment explanation
Indices: 3823362--3823396 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
3823352 ATACTATATA
3823362 ATATAATTTATACTT
1 ATATAATTTATAC-T
3823377 ATATAATTTATACT
1 ATATAATTTATACT
3823391 ATATAA
1 ATATAA
3823397 ATTCAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATAATTTATACT
Found at i:3823481 original size:18 final size:16
Alignment explanation
Indices: 3823460--3823701 Score: 59
Period size: 18 Copynumber: 14.9 Consensus size: 16
3823450 ATAAACTATT
3823460 TATATAGTATATACTACC
1 TATATAGTATATA-TA-C
3823478 TATATAGTTTATATATAC
1 TATATAG--TATATATAC
*
3823496 TATATAGTTTACATATGAAC
1 TATATAG--TATATAT--AC
* *
3823516 TATATA-TA-AAAAAC
1 TATATAGTATATATAC
*
3823530 TATATA-TATA-A-AG
1 TATATAGTATATATAC
* *
3823543 TATATGGTATATACAAAC
1 TATATAGTATAT--ATAC
*
3823561 TATATA-T-TATATAG
1 TATATAGTATATATAC
3823575 T-TATTAGTATATATAAAC
1 TATA-TAGTATATAT--AC
* *
3823593 TATATATTATATAGTTC
1 TATATAGTATATA-TAC
*
3823610 -AT-TCGTATATATAAAC
1 TATATAGTATATAT--AC
3823626 TATATAGTATATATAAAC
1 TATATAGTATATAT--AC
*
3823644 TATACA-T-TATAGT-C
1 TATATAGTATATA-TAC
*
3823658 -AT-TAGTATATAAAC
1 TATATAGTATATATAC
*
3823672 TATATA-T-TATATAG
1 TATATAGTATATATAC
*
3823686 TTTATCAGTATATATA
1 TATAT-AGTATATATA
3823702 AACTATATAT
Statistics
Matches: 172, Mismatches: 22, Indels: 61
0.67 0.09 0.24
Matches are distributed among these distances:
12 1 0.01
13 11 0.06
14 36 0.21
15 13 0.08
16 20 0.12
17 15 0.09
18 57 0.33
19 5 0.03
20 14 0.08
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (16 bp):
TATATAGTATATATAC
Found at i:3823511 original size:20 final size:18
Alignment explanation
Indices: 3823477--3823521 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
3823467 TATATACTAC
3823477 CTATATAGTTTATAT-ATA
1 CTATATAGTTTATATGA-A
3823495 CTATATAGTTTACATATGAA
1 CTATATAGTTT--ATATGAA
3823515 CTATATA
1 CTATATA
3823522 TAAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.46
20 12 0.50
21 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (18 bp):
CTATATAGTTTATATGAA
Found at i:3823585 original size:32 final size:32
Alignment explanation
Indices: 3823526--3823638 Score: 149
Period size: 32 Copynumber: 3.5 Consensus size: 32
3823516 TATATATAAA
* * *
3823526 AAACTATATA-TATAAAG-TATATGGTATATAC
1 AAACTATATATTATATAGTTAT-TAGTATATAT
3823557 AAACTATATATTATATAGTTATTAGTATATAT
1 AAACTATATATTATATAGTTATTAGTATATAT
*
3823589 AAACTATATATTATATAGTTCATTCGTATATAT
1 AAACTATATATTATATAGTT-ATTAGTATATAT
*
3823622 AAACTATATAGTATATA
1 AAACTATATATTATATA
3823639 TAAACTATAC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
31 10 0.14
32 34 0.46
33 30 0.41
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (32 bp):
AAACTATATATTATATAGTTATTAGTATATAT
Found at i:3823703 original size:79 final size:82
Alignment explanation
Indices: 3823532--3823710 Score: 258
Period size: 79 Copynumber: 2.2 Consensus size: 82
3823522 TAAAAAACTA
* * * *
3823532 TATATATAAAGTATATGGTATATACAAACTATATATTATATAGTTATTAGTATATATAAACTATA
1 TATATATAAACTATATAGTATATACAAACTATACATTATATAGTCATTAG-ATATATAAACTATA
3823597 TATTATATAGTTCATTCG
65 TATTATATAGTTCATTCG
*
3823615 TATATATAAACTATATAGTATATATAAACTATACA-T-TATAGTCATTAG-TATATAAACTATAT
1 TATATATAAACTATATAGTATATACAAACTATACATTATATAGTCATTAGATATATAAACTATAT
*
3823677 ATTATATAGTTTA-TCAG
66 ATTATATAGTTCATTC-G
3823694 TATATATAAACTATATA
1 TATATATAAACTATATA
3823711 TTAATTTATT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
78 2 0.02
79 44 0.49
81 11 0.12
82 1 0.01
83 31 0.35
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (82 bp):
TATATATAAACTATATAGTATATACAAACTATACATTATATAGTCATTAGATATATAAACTATAT
ATTATATAGTTCATTCG
Found at i:3823849 original size:61 final size:60
Alignment explanation
Indices: 3823783--3823909 Score: 200
Period size: 61 Copynumber: 2.1 Consensus size: 60
3823773 ATGAACAAAT
*
3823783 TTTAAATATGAAGCTTAAATTAATAAATTGTAACATTAAATTTGGACTAAATTAAAGAAAA
1 TTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACTAAATTAAA-AAAA
* * * *
3823844 TTTAAATATGAAGCTTAAATTAATATATTGCATCATTAAATTTGGACTAAATTGAACAAA
1 TTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACTAAATTAAAAAAA
3823904 TTTAAA
1 TTTAAA
3823910 ACTGGGAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
60 9 0.15
61 52 0.85
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (60 bp):
TTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACTAAATTAAAAAAA
Found at i:3824323 original size:103 final size:104
Alignment explanation
Indices: 3824136--3824432 Score: 315
Period size: 103 Copynumber: 2.9 Consensus size: 104
3824126 TTTATAAGTT
* *
3824136 TTCATCT-GTGTTCATCCCAAAAAACCCTCATTTGATCTTCACAAACACCAAAA-CCTAACCATT
1 TTCATCTCGTGTTCATCCC-AAAAACCCTTATTTGATCTTCACAAACACCAAAACCCAAACCATT
** * *
3824199 TTGTGTTTTTTTCGATCAAACACCCATAAT-TTCAAC-CTTTG
65 TCATG-TTTTTT-GATCAAACACCCAAAATATTCAACAC-GTG
* *
3824240 TTTATC-CGTGTTCATCCCAAAAACCCTTATTTGATCTTCAAAAACACCAAAACCCAAACCATTT
1 TTCATCTCGTGTTCATCCCAAAAACCCTTATTTGATCTTCACAAACACCAAAACCCAAACCATTT
*
3824304 CATGTTTTTTAGATCAAACA-CCAAAATATTCATCACGTG
66 CATGTTTTTT-GATCAAACACCCAAAATATTCAACACGTG
** * * * *
3824343 TTCATCTC-AATTCTTCCC-CAAACCATTATTTGATCTTCACAAACACCAAAACCTAAACTCATT
1 TTCATCTCGTGTTCATCCCAAAAACCCTTATTTGATCTTCACAAACACCAAAACCCAAAC-CATT
* *
3824406 CCTAT-TTTTTTTATCAAACACCCAAAA
65 TC-ATGTTTTTTGATCAAACACCCAAAA
3824433 GTTCATCTAT
Statistics
Matches: 165, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
102 50 0.30
103 83 0.50
104 32 0.19
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (104 bp):
TTCATCTCGTGTTCATCCCAAAAACCCTTATTTGATCTTCACAAACACCAAAACCCAAACCATTT
CATGTTTTTTGATCAAACACCCAAAATATTCAACACGTG
Found at i:3824672 original size:6 final size:6
Alignment explanation
Indices: 3824657--3824831 Score: 134
Period size: 6 Copynumber: 29.2 Consensus size: 6
3824647 TCTAACCCTG
* * ** *
3824657 AACCCG AACCAA AACCCA AACCCA AACCTG AACCCA AACCCA AATCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * * * * *
3824705 AGCTCA AACCTA AACCCA AACCCA AACTCG AACTCA AACCCG AACCTA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * *
3824753 AAACCA AACCCA AACCCA AACCCG AACTCG AACCCA AACCCA AACTCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * * *
3824801 AAACCT AACCCG AATCCA GACCCG AACCCA A
1 AACCCA AACCCA AACCCA AACCCA AACCCA A
3824832 TCCAATCCAA
Statistics
Matches: 127, Mismatches: 42, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 127 1.00
ACGTcount: A:0.46, C:0.42, G:0.06, T:0.06
Consensus pattern (6 bp):
AACCCA
Found at i:3824687 original size:30 final size:30
Alignment explanation
Indices: 3824653--3824831 Score: 162
Period size: 30 Copynumber: 6.0 Consensus size: 30
3824643 ATTCTCTAAC
* *
3824653 CCTGAACCCGAACCAAAACCCAAACCCAAA
1 CCTGAACCCAAACCCAAACCCAAACCCAAA
* * *
3824683 CCTGAACCCAAACCCAAATCCAAGCTCAAA
1 CCTGAACCCAAACCCAAACCCAAACCCAAA
* * * *
3824713 CCTAAACCCAAACCCAAACTCGAACTCAAA
1 CCTGAACCCAAACCCAAACCCAAACCCAAA
* * *
3824743 CCCGAACCTAAAACCAAACCCAAACCCAAA
1 CCTGAACCCAAACCCAAACCCAAACCCAAA
* * * *
3824773 CCCGAACTCGAACCCAAACCCAAACTCAAAA
1 CCTGAACCCAAACCCAAACCCAAAC-CCAAA
* * * *
3824804 CCT-AACCCGAATCCAGACCCGAACCCAA
1 CCTGAACCCAAACCCAAACCCAAACCCAA
3824832 TCCAATCCAA
Statistics
Matches: 120, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
29 3 0.03
30 111 0.93
31 6 0.05
ACGTcount: A:0.45, C:0.42, G:0.06, T:0.07
Consensus pattern (30 bp):
CCTGAACCCAAACCCAAACCCAAACCCAAA
Found at i:3824804 original size:48 final size:48
Alignment explanation
Indices: 3824663--3824811 Score: 178
Period size: 48 Copynumber: 3.1 Consensus size: 48
3824653 CCTGAACCCG
* * *
3824663 AACCAAAACCCAAACCCAAAC-CTGAACCCAAACCCAAA-TCCAAGCTCA
1 AACCCAAACCCAAACCCAAACTC-GAACCCAAACCCAAACTCAAAAC-CA
* * *
3824711 AACCTAAACCCAAACCCAAACTCGAACTCAAACCCGAAC-CTAAAACCA
1 AACCCAAACCCAAACCCAAACTCGAACCCAAACCCAAACTC-AAAACCA
* *
3824759 AACCCAAACCCAAACCCGAACTCGAACCCAAACCCAAACTCAAAACCT
1 AACCCAAACCCAAACCCAAACTCGAACCCAAACCCAAACTCAAAACCA
3824807 AACCC
1 AACCC
3824812 GAATCCAGAC
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
48 82 0.94
49 5 0.06
ACGTcount: A:0.47, C:0.42, G:0.04, T:0.07
Consensus pattern (48 bp):
AACCCAAACCCAAACCCAAACTCGAACCCAAACCCAAACTCAAAACCA
Found at i:3827484 original size:20 final size:20
Alignment explanation
Indices: 3827452--3827512 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3827442 AAATATTTGG
* *
3827452 TGCTTGATTCTGTTTTATAT
1 TGCTTGCTTCTGTTTGATAT
*
3827472 TGTTTGCTTCTGTTTGATAT
1 TGCTTGCTTCTGTTTGATAT
**
3827492 TGCTTGCTTCTACTTGATAT
1 TGCTTGCTTCTGTTTGATAT
3827512 T
1 T
3827513 TGTAAGGGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.57
Consensus pattern (20 bp):
TGCTTGCTTCTGTTTGATAT
Found at i:3827636 original size:23 final size:23
Alignment explanation
Indices: 3827606--3827659 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
3827596 CTTAATGCAG
*
3827606 GATGCTTGCTGAATTGATGC-GAT
1 GATGCTTGCTGAATTGATACAG-T
3827629 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATACAGT
3827652 GATGCTTG
1 GATGCTTG
3827660 TCGGTTGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATACAGT
Found at i:3828355 original size:27 final size:26
Alignment explanation
Indices: 3828314--3828364 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
3828304 TAATCATATT
*
3828314 AATTTAAATATCATAAGTT-TATTATA
1 AATTTAAATAACATAA-TTATATTATA
3828340 AATTTAAAATAACATAATTATATTA
1 AATTT-AAATAACATAATTATATTA
3828365 ATTGTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
AATTTAAATAACATAATTATATTATA
Found at i:3828479 original size:16 final size:16
Alignment explanation
Indices: 3828445--3828488 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3828435 TGAGTCAATT
* *
3828445 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTACAAA
*
3828461 ACAGGTCAGGTAGAAA
1 ACAGGTCAGGTACAAA
*
3828477 ACAGGTCGGGTA
1 ACAGGTCAGGTA
3828489 ATACCAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTACAAA
Found at i:3832583 original size:17 final size:18
Alignment explanation
Indices: 3832561--3832595 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3832551 TTATCTGTAA
3832561 TAATTTATAT-ATTATTT
1 TAATTTATATAATTATTT
*
3832578 TAATTTATTTAATTATTT
1 TAATTTATATAATTATTT
3832596 CTATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATTTATATAATTATTT
Found at i:3834505 original size:37 final size:37
Alignment explanation
Indices: 3834459--3834674 Score: 321
Period size: 37 Copynumber: 5.9 Consensus size: 37
3834449 TTCAAAACTA
* * * *
3834459 TTTTAAAAAATGTTTTCGAAATTATATATTATATATG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
3834496 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
3834533 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
* *
3834570 TTTTTAAAAATGTTTCCAAAACTATATATTATATACG
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
**
3834607 TTTTCAAAAATGTTTT-AAAACTATATATTATATATA
1 TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
**
3834643 TTTAAAAAAATGTTTTCAAAA-T-TATATTATAT
1 TTTTCAAAAATGTTTTCAAAACTATATATTATAT
3834675 TATCATTATA
Statistics
Matches: 166, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
35 10 0.06
36 33 0.20
37 123 0.74
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTCAAAACTATATATTATATACG
Found at i:3834510 original size:12 final size:12
Alignment explanation
Indices: 3834493--3834553 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
3834483 TATATTATAT
3834493 ATGTTTTCAAAA
1 ATGTTTTCAAAA
3834505 ATGTTTTCAAAA
1 ATGTTTTCAAAA
* * * *
3834517 CTATATATT-ATAT
1 --ATGTTTTCAAAA
*
3834530 ACGTTTTCAAAA
1 ATGTTTTCAAAA
3834542 ATGTTTTCAAAA
1 ATGTTTTCAAAA
3834554 CTATATATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
11 4 0.11
12 25 0.69
13 2 0.06
14 5 0.14
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:3835476 original size:18 final size:19
Alignment explanation
Indices: 3835452--3835497 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3835442 AAAACCAAAC
3835452 AAAGTAATGCAACATTCC-
1 AAAGTAATGCAACATTCCT
* **
3835470 CAAGTAATGTTACATTCCT
1 AAAGTAATGCAACATTCCT
3835489 AAAGTAATG
1 AAAGTAATG
3835498 TTACATTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (19 bp):
AAAGTAATGCAACATTCCT
Found at i:3835495 original size:19 final size:18
Alignment explanation
Indices: 3835451--3835516 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 18
3835441 AAAAACCAAA
**
3835451 CAAAGTAATGCAACATTC
1 CAAAGTAATGTTACATTC
*
3835469 CCAAGTAATGTTACATTC
1 CAAAGTAATGTTACATTC
3835487 CTAAAGTAATGTTACATTC
1 C-AAAGTAATGTTACATTC
3835506 C-AA-TAATGTTA
1 CAAAGTAATGTTA
3835517 TTCCCAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.19
17 2 0.05
18 16 0.37
19 17 0.40
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (18 bp):
CAAAGTAATGTTACATTC
Found at i:3835967 original size:23 final size:23
Alignment explanation
Indices: 3835904--3835971 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3835894 TTAATATTTC
* *
3835904 TAATAATAT-ATATATTTTTATTA
1 TAATAATATAACATA-TTATATTA
*
3835927 TAATAAAATAATCA-ATTATATTA
1 TAATAATATAA-CATATTATATTA
*
3835950 TAATAATATAAGATATTATATT
1 TAATAATATAACATATTATATT
3835972 TATATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 33 0.89
24 2 0.05
25 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
TAATAATATAACATATTATATTA
Found at i:3835974 original size:29 final size:29
Alignment explanation
Indices: 3835905--3835997 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
3835895 TAATATTTCT
*
3835905 AATAATATATATATT-T-TTATTATAATA-A
1 AATAAT-TATAT-TTATATTATAATAATATA
*
3835933 AATAATCA-A-TTATATTATAATAATATA
1 AATAATTATATTTATATTATAATAATATA
*
3835960 AGAT-ATTATATTTATATTTTAATAATATA
1 A-ATAATTATATTTATATTATAATAATATA
3835989 AATAATTAT
1 AATAATTAT
3835998 TAATAAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 11 0.20
27 6 0.11
28 11 0.20
29 23 0.43
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
AATAATTATATTTATATTATAATAATATA
Found at i:3836090 original size:27 final size:27
Alignment explanation
Indices: 3836031--3836090 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
3836021 TTCATAGAAT
*
3836031 TAATATTATTAAATTATTAAAAATGAA
1 TAATATTATTAAATTATTAAAAATAAA
* * *
3836058 TAATATTATTATA-TATTAATATTAATA
1 TAATATTATTAAATTATTAAAAATAA-A
3836085 TAATAT
1 TAATAT
3836091 CTAATAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TAATATTATTAAATTATTAAAAATAAA
Found at i:3836271 original size:16 final size:16
Alignment explanation
Indices: 3836226--3836277 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
3836216 ATATTTTTAT
*
3836226 TTTTATTAATAAAAT-
1 TTTTAATAATAAAATA
*
3836241 TATTAA-AAT--AATA
1 TTTTAATAATAAAATA
3836254 TTTTAATAATAAAATA
1 TTTTAATAATAAAATA
3836270 TTTTAATA
1 TTTTAATA
3836278 TTTTAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.10
13 5 0.17
14 6 0.20
15 4 0.13
16 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAATAATAAAATA
Found at i:3836785 original size:4 final size:4
Alignment explanation
Indices: 3836776--3836814 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
3836766 AAAACATCAA
* *
3836776 AAAT AAAT AAAT AAAA AAGAA AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA
3836815 TCAAGAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:3836957 original size:35 final size:37
Alignment explanation
Indices: 3836890--3836999 Score: 104
Period size: 35 Copynumber: 3.0 Consensus size: 37
3836880 ATTTTAGAAA
3836890 AAAAAAGAAAAAAGAAAAAAT-AAATAATAAAAATATTAAG
1 AAAAAA-AAAAAA-AAAAAATGAAAT-A-AAAAATATTAAG
* * * *
3836930 -AGAGAAAAATAAAAAAA-GGAATAAAAAA-A-TAAG
1 AAAAAAAAAAAAAAAAAATGAAATAAAAAATATTAAG
3836963 AAAAAAAAAAAAAAAAAAATGAAATAAAAAATATTAA
1 -AAAAAAAAAAAAAAAAAATGAAATAAAAAATATTAA
3837000 TTTTAAGATA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
33 4 0.07
34 1 0.02
35 19 0.34
36 11 0.20
37 10 0.18
38 8 0.14
39 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (37 bp):
AAAAAAAAAAAAAAAAAATGAAATAAAAAATATTAAG
Found at i:3836959 original size:20 final size:19
Alignment explanation
Indices: 3836934--3836993 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
3836924 ATTAAGAGAG
3836934 AAAAATAAAAAAAGGAATAA
1 AAAAATAAAAAAA-GAATAA
*
3836954 AAAAATAAGAAAA-AA-AA
1 AAAAATAAAAAAAGAATAA
*
3836971 AAAAA-AAAAAATGAAATAA
1 AAAAATAAAAAAAG-AATAA
3836990 AAAA
1 AAAA
3836994 TATTAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 4 0.12
19 6 0.18
20 12 0.35
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.08
Consensus pattern (19 bp):
AAAAATAAAAAAAGAATAA
Found at i:3836967 original size:12 final size:11
Alignment explanation
Indices: 3836887--3836995 Score: 62
Period size: 12 Copynumber: 9.7 Consensus size: 11
3836877 TAAATTTTAG
*
3836887 AAAAAA-AAAG
1 AAAAAATAAAA
*
3836897 AAAAAAGAAAA
1 AAAAAATAAAA
*
3836908 AATAAATAATAA
1 AAAAAATAA-AA
* *
3836920 AAATATTAAGAGA
1 AAAAAATAA-A-A
*
3836933 GAAAAATAAAA
1 AAAAAATAAAA
*
3836944 AAAGGAATAAAA
1 AAA-AAATAAAA
* *
3836956 AAATAA-GAAA
1 AAAAAATAAAA
3836966 AAAAAA-AAAA
1 AAAAAATAAAA
*
3836976 AAAAAATGAAAT
1 AAAAAAT-AAAA
3836988 AAAAAATA
1 AAAAAATA
3836996 TTAATTTTAA
Statistics
Matches: 76, Mismatches: 17, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
10 23 0.30
11 16 0.21
12 30 0.39
13 7 0.09
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:3838585 original size:37 final size:37
Alignment explanation
Indices: 3838428--3838743 Score: 338
Period size: 37 Copynumber: 8.8 Consensus size: 37
3838418 TTTCCAAAAT
*
3838428 AAAACTATATA--ATATAT-TTTTTAAAATAG-TTT-A
1 AAAACTATATATTATATATATTTTCAAAAT-GTTTTCA
* **
3838461 AAAACTATATATTATACAT-TTTAAAAAATGTTTTC-
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
3838496 AAAA-T-TATA-TATCATATAGTTTCAAAAATG-TTT-A
1 AAAACTATATATTAT-ATATATTTTC-AAAATGTTTTCA
* * *
3838530 AAAA-AATATATTAAATATATTTTTAAAATGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
3838566 AAAACTATATATTATATATATATTTTCAAAACGTTTTCA
1 AAAACTATATA-T-TATATATATTTTCAAAATGTTTTCA
*
3838605 AAAACTATATATTATATATATTTTCAAAAAGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
* * *
3838642 AAAATTGTATAATATATATATTTTCAAAATGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
* *
3838679 AAAACTTTATATTATATAT-TTTTCAAAAAGTTTTCA
1 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
*
3838715 AAAACTATATA-TATATACATTTTCAAAAT
1 AAAACTATATATTATATATATTTTCAAAAT
3838744 TATTTTCTAA
Statistics
Matches: 240, Mismatches: 27, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
32 3 0.01
33 18 0.08
34 17 0.07
35 47 0.20
36 42 0.17
37 78 0.32
38 2 0.01
39 33 0.14
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATGTTTTCA
Found at i:3846126 original size:18 final size:20
Alignment explanation
Indices: 3846086--3846129 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3846076 TTTGGTTAAT
* *
3846086 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGAG
3846106 GGAATAAAAGATTA-CA-AG
1 GGAATAAAAGATTACCAGAG
3846124 GGAATA
1 GGAATA
3846130 TGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.20
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGAG
Found at i:3847571 original size:32 final size:33
Alignment explanation
Indices: 3847525--3847587 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
3847515 TATAAGAAAG
* * *
3847525 AAATATGATTAATAATGGAAT-AAGAAATGGAT
1 AAATAAGATAAATAATGAAATAAAGAAATGGAT
3847557 AAATAAGATAAATAATGAAATGAAAGAAATG
1 AAATAAGATAAATAATGAAAT-AAAGAAATG
3847588 AATAGAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 18 0.69
34 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (33 bp):
AAATAAGATAAATAATGAAATAAAGAAATGGAT
Found at i:3851127 original size:21 final size:21
Alignment explanation
Indices: 3851096--3851162 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
3851086 TTTCAGAGAC
*
3851096 ACTTACAAAGGTACTTTATCT
1 ACTTACAAAGGTACTTCATCT
* *
3851117 ATTTACTAAGGTACTTCATCT
1 ACTTACAAAGGTACTTCATCT
* * *
3851138 ACTTACCAAGGTAATCCATCT
1 ACTTACAAAGGTACTTCATCT
3851159 ACTT
1 ACTT
3851163 CTAATTCTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.37
Consensus pattern (21 bp):
ACTTACAAAGGTACTTCATCT
Found at i:3854435 original size:17 final size:17
Alignment explanation
Indices: 3854413--3854447 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3854403 CGTTGGTGCT
3854413 GGAACCCTTGACCTCTA
1 GGAACCCTTGACCTCTA
3854430 GGAACCCTTGACCTCTA
1 GGAACCCTTGACCTCTA
3854447 G
1 G
3854448 AATAACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (17 bp):
GGAACCCTTGACCTCTA
Found at i:3855002 original size:21 final size:21
Alignment explanation
Indices: 3854976--3855018 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3854966 AAATATAATT
3854976 TGGATAACTGTATACAAATCA
1 TGGATAACTGTATACAAATCA
*
3854997 TGGATAATTGTATACAAATCA
1 TGGATAACTGTATACAAATCA
3855018 T
1 T
3855019 AACAGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
TGGATAACTGTATACAAATCA
Found at i:3856867 original size:13 final size:13
Alignment explanation
Indices: 3856857--3856913 Score: 87
Period size: 13 Copynumber: 4.4 Consensus size: 13
3856847 TCTATGACGG
3856857 GCATTTATGACAC
1 GCATTTATGACAC
3856870 GCATTTATGACAC
1 GCATTTATGACAC
*
3856883 ACATTTATGACAC
1 GCATTTATGACAC
* *
3856896 GCATTTATAACGC
1 GCATTTATGACAC
3856909 GCATT
1 GCATT
3856914 GAGTGTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (13 bp):
GCATTTATGACAC
Found at i:3856879 original size:26 final size:26
Alignment explanation
Indices: 3856849--3856913 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
3856839 GTCATAAATC
*
3856849 TATGACGGGCATTTATGACACGCATT
1 TATGACGCGCATTTATGACACGCATT
* *
3856875 TATGACACACATTTATGACACGCATT
1 TATGACGCGCATTTATGACACGCATT
*
3856901 TATAACGCGCATT
1 TATGACGCGCATT
3856914 GAGTGTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (26 bp):
TATGACGCGCATTTATGACACGCATT
Found at i:3860514 original size:5 final size:5
Alignment explanation
Indices: 3860504--3860529 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3860494 TCCAAAGCTT
3860504 GGGGA GGGGA GGGGA GGGGA GGGGA G
1 GGGGA GGGGA GGGGA GGGGA GGGGA G
3860530 AGAAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (5 bp):
GGGGA
Found at i:3862363 original size:20 final size:20
Alignment explanation
Indices: 3862340--3862381 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3862330 ATAACCAAGC
*
3862340 TATACAA-CATGCATCCAATA
1 TATACAAGCATG-ATACAATA
*
3862360 TATATAAGCATGATACAATA
1 TATACAAGCATGATACAATA
3862380 TA
1 TA
3862382 GTCATGAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (20 bp):
TATACAAGCATGATACAATA
Found at i:3863102 original size:92 final size:92
Alignment explanation
Indices: 3862991--3863171 Score: 227
Period size: 92 Copynumber: 2.0 Consensus size: 92
3862981 TTTTTCGCCG
** * * *
3862991 AGGGATCAATCCTTTTGAAAAGGGATTGATCCTATGCACAACATAAAGTTTGGGATCGATCCTTT
1 AGGGATCAATCCTTTTGAAAAGGGATAAATCCTATGCACAACAGAAACTTTGGGATCGATCCCTT
*
3863056 TGGTCGAGGGATCAATCCTTTTTCCTT
66 TGGTCGAGGGATCAATCATTTTTCCTT
* * * * *** *
3863083 AGGGATCGATTCTTTTGAAAAGGGATAAATCTTTTGCTGGACAGGAACTTTGGGATCGATCCCTT
1 AGGGATCAATCCTTTTGAAAAGGGATAAATCCTATGCACAACAGAAACTTTGGGATCGATCCCTT
*
3863148 TGGTCGAGGGATCGATCATTTTTC
66 TGGTCGAGGGATCAATCATTTTTC
3863172 TGGGAATGAC
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (92 bp):
AGGGATCAATCCTTTTGAAAAGGGATAAATCCTATGCACAACAGAAACTTTGGGATCGATCCCTT
TGGTCGAGGGATCAATCATTTTTCCTT
Found at i:3867412 original size:20 final size:20
Alignment explanation
Indices: 3867384--3867424 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3867374 CTGATTTTCA
*
3867384 TACTTTTCATTTTAA-TCACT
1 TACTGTTCA-TTTAATTCACT
3867404 TACTGTTCATTTAATTCACT
1 TACTGTTCATTTAATTCACT
3867424 T
1 T
3867425 GTATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (20 bp):
TACTGTTCATTTAATTCACT
Found at i:3867540 original size:19 final size:19
Alignment explanation
Indices: 3867516--3867556 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3867506 TTATCTATTA
*
3867516 ACTTTTCTAACTTTTAACT
1 ACTTTTCTAACTTCTAACT
*
3867535 ACTTTTTTAACTTCTAACT
1 ACTTTTCTAACTTCTAACT
3867554 ACT
1 ACT
3867557 AACCACTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (19 bp):
ACTTTTCTAACTTCTAACT
Found at i:3871093 original size:20 final size:20
Alignment explanation
Indices: 3871065--3871116 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3871055 GGATGACTGT
3871065 TGTGAGAAGTCACAACAACA
1 TGTGAGAAGTCACAACAACA
* *
3871085 TGTGTGAAGTCACAACAATA
1 TGTGAGAAGTCACAACAACA
3871105 TGTGAGAAGTCA
1 TGTGAGAAGTCA
3871117 GCTAAGCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (20 bp):
TGTGAGAAGTCACAACAACA
Found at i:3872076 original size:24 final size:24
Alignment explanation
Indices: 3872016--3872078 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
3872006 GATCAGCTGT
* *
3872016 AGCTGGGCATGGTTCCCTATAGGC
1 AGCTGGGCATGGTCCCCTACAGGC
* * *
3872040 AGTTTGGCATGGTCCCCTCCAGGC
1 AGCTGGGCATGGTCCCCTACAGGC
*
3872064 AGCTGGGCGTGGTCC
1 AGCTGGGCATGGTCC
3872079 TGACAGGATC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.35, T:0.24
Consensus pattern (24 bp):
AGCTGGGCATGGTCCCCTACAGGC
Found at i:3874964 original size:21 final size:20
Alignment explanation
Indices: 3874919--3874973 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
3874909 TAAGGAGGGA
*
3874919 ATAAGAAGAAAATATGAAAG
1 ATAAGAAGAAAATATCAAAG
*
3874939 CTAAGTAAGAAAATA-CAAATG
1 ATAAG-AAGAAAATATCAAA-G
*
3874960 ATAAGAACAAAATA
1 ATAAGAAGAAAATA
3874974 AAAAGGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.64, C:0.05, G:0.15, T:0.16
Consensus pattern (20 bp):
ATAAGAAGAAAATATCAAAG
Found at i:3875774 original size:28 final size:28
Alignment explanation
Indices: 3875734--3875788 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3875724 CATGCTTTCC
3875734 CATATACCATCTTGAAAGGTGACATTCT
1 CATATACCATCTTGAAAGGTGACATTCT
3875762 CATATACCATCTTGAAAGGTGACATTC
1 CATATACCATCTTGAAAGGTGACATTC
3875789 CCAAAGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (28 bp):
CATATACCATCTTGAAAGGTGACATTCT
Found at i:3883716 original size:19 final size:19
Alignment explanation
Indices: 3883692--3883757 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
3883682 TCTTTTTGAA
3883692 CTTCTTTTTCT-TTTCTTTT
1 CTTCTTTTTCTATTT-TTTT
*
3883711 CTTC-TTTTCTGATTTTTCT
1 CTTCTTTTTCT-ATTTTTTT
3883730 CTTCTTTTT-TATTTTTTCT
1 CTTCTTTTTCTATTTTTT-T
3883749 CTTCTTTTT
1 CTTCTTTTT
3883758 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 12 0.29
19 22 0.54
20 7 0.17
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
CTTCTTTTTCTATTTTTTT
Found at i:3886501 original size:21 final size:21
Alignment explanation
Indices: 3886458--3886499 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3886448 TGTCACAATC
*
3886458 TAGGATTTAAGTCAACCAAAA
1 TAGGATTTAAGTCAAACAAAA
*
3886479 TAGGATTTAAGTGATAACAAA
1 TAGGATTTAAGTCA-AACAAA
3886500 TAACACGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.26
Consensus pattern (21 bp):
TAGGATTTAAGTCAAACAAAA
Found at i:3887008 original size:19 final size:18
Alignment explanation
Indices: 3886984--3887030 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3886974 GTATAGTTTG
3886984 TAATGGTATGTACAAATGA
1 TAATGGTATGTA-AAATGA
*
3887003 TAATGGTGTGGTAAAATGA
1 TAATGGTAT-GTAAAATGA
3887022 -AATGG-ATGT
1 TAATGGTATGT
3887031 TGGTGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 5 0.20
19 14 0.56
20 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.32
Consensus pattern (18 bp):
TAATGGTATGTAAAATGA
Found at i:3889059 original size:80 final size:79
Alignment explanation
Indices: 3888903--3889063 Score: 263
Period size: 80 Copynumber: 2.0 Consensus size: 79
3888893 GTTAATATTT
* *
3888903 TTTAACATTTATGGTAAAGCGCTACCTAAAACATTATTTTTTCTACCAGAAATGTTAATATTGGG
1 TTTAACATTTATGATAAAGCGCTACCTAAAACATTATTTTTTCTACCAGAAATGTTAATATTGGA
3888968 TGCTACCTAAAATG
66 TGCTACCTAAAATG
3888982 TTTAACATTT-TCGATAAAGCGCTACCTAAAACATTATTTTTTTCTACC-GAAAATGTTAATATT
1 TTTAACATTTAT-GATAAAGCGCTACCTAAAACATTA-TTTTTTCTACCAG-AAATGTTAATATT
3889045 GGATGCTACCTAAAATG
63 GGATGCTACCTAAAATG
3889062 TT
1 TT
3889064 ATTTTTCTAC
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
78 1 0.01
79 34 0.44
80 42 0.55
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (79 bp):
TTTAACATTTATGATAAAGCGCTACCTAAAACATTATTTTTTCTACCAGAAATGTTAATATTGGA
TGCTACCTAAAATG
Found at i:3893360 original size:16 final size:16
Alignment explanation
Indices: 3893341--3893388 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
3893331 AAAGTAACCT
3893341 GAACCGAAACCAACTC
1 GAACCGAAACCAACTC
** *
3893357 GAACCGAAATTAACCC
1 GAACCGAAACCAACTC
* *
3893373 GAACCAAAAGCAACTC
1 GAACCGAAACCAACTC
3893389 ATATTGAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.33, G:0.12, T:0.08
Consensus pattern (16 bp):
GAACCGAAACCAACTC
Found at i:3894780 original size:81 final size:81
Alignment explanation
Indices: 3894644--3895040 Score: 481
Period size: 81 Copynumber: 4.9 Consensus size: 81
3894634 ATTTCTTTCT
* * ** * * * * * *
3894644 TCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTTGCATATTTGACACTTTTCTGTCAATTGC
1 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
*
3894709 ACAGCTAGTCCATT-A
66 ACAGCTAGGCCATTCA
* * *
3894724 TTCTTTTACTCAACAGTGTTTAATTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATG
1 -TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATG
*
3894789 CATAGCTAGGCCATTCA
65 CACAGCTAGGCCATTCA
** ** * * *
3894806 TCTTTTACTCAACGGTATTTAGCCGTAAATCAAACTGTCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
* *
3894871 ACAACTATGCCATTCA
66 ACAGCTAGGCCATTCA
* * * * *
3894887 TATTTTACTCAACGGTATTTAGTTGTTCATCTAATTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
* *
3894952 ACAACTAGGCTATTCA
66 ACAGCTAGGCCATTCA
* *
3894968 TCTTTTACTCAACGATATTCAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
3895033 ACAGCTAG
66 ACAGCTAG
3895041 CCTCAAAGGC
Statistics
Matches: 269, Mismatches: 46, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
81 268 1.00
82 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
ACAGCTAGGCCATTCA
Found at i:3895083 original size:67 final size:67
Alignment explanation
Indices: 3894993--3895158 Score: 253
Period size: 68 Copynumber: 2.4 Consensus size: 67
3894983 TATTCAATCG
* *
3894993 TTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTA-GCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACAC-TTTCTGCCAAATGAACAACTAGGCCTCAAAGGCACTTAG
*
3895057 CCT
65 CAT
* *
3895060 TTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGAACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGAACAACTAGGCCTCAAAGGCACTTAG
3895125 CAT
65 CAT
3895128 TTCATCTAACTGGCATAATTGACACCTTTCT
1 TTCATCTAACTGGCATAATTGACA-CTTTCT
3895159 CACATTTCTG
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
67 41 0.45
68 50 0.55
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACTTTCTGCCAAATGAACAACTAGGCCTCAAAGGCACTTAGC
AT
Found at i:3895430 original size:34 final size:34
Alignment explanation
Indices: 3895392--3895465 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
3895382 TTTCACATAT
*
3895392 ATTTCTCATAC-AGAACTTCATACACTTAGTATGA
1 ATTTCTCATACGA-AAATTCATACACTTAGTATGA
*
3895426 ATTTCTTATACGAAAATTCATACACTTAGTATGA
1 ATTTCTCATACGAAAATTCATACACTTAGTATGA
3895460 ATTTCT
1 ATTTCT
3895466 TAGTTTTGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (34 bp):
ATTTCTCATACGAAAATTCATACACTTAGTATGA
Found at i:3895920 original size:19 final size:19
Alignment explanation
Indices: 3895896--3895936 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3895886 GTATCGATAT
*
3895896 TACTATACTATGGTACCGA
1 TACTATACAATGGTACCGA
* *
3895915 TACTATGCAATGGTATCGA
1 TACTATACAATGGTACCGA
3895934 TAC
1 TAC
3895937 CATTTTTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (19 bp):
TACTATACAATGGTACCGA
Found at i:3896000 original size:20 final size:19
Alignment explanation
Indices: 3895961--3896011 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
3895951 ATTTTGAAAT
**
3895961 GGTATCGATACCTTCCTTC
1 GGTATCGATACCAGCCTTC
3895980 GGTATCGATACTCAGCCTTC
1 GGTATCGATAC-CAGCCTTC
3896000 GGTATCGATACC
1 GGTATCGATACC
3896012 GATTGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (19 bp):
GGTATCGATACCAGCCTTC
Found at i:3897553 original size:2 final size:2
Alignment explanation
Indices: 3897546--3897576 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3897536 CCAGAAAAGC
3897546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3897577 TTCTGACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.