Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 80 of 93
Found at i:12198718 original size:24 final size:24
Alignment explanation
Indices: 12198683--12198768 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 24
12198673 TTTTTTTATT
12198683 TTATT-AAA-TTTATATATAATTA
1 TTATTAAAATTTTATATATAATTA
*
12198705 TTATTAAAATTTTAAAT-TAAATTA
1 TTATTAAAATTTTATATAT-AATTA
* * * *
12198729 TTTTTATATTTTTATA-ATATTTTAAA
1 TTATTAAAATTTTATATATA-ATT--A
12198755 TTATTAAAATTTTA
1 TTATTAAAATTTTA
12198769 AAACATAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
22 5 0.10
23 5 0.10
24 26 0.54
26 12 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTAAAATTTTATATATAATTA
Found at i:12198723 original size:16 final size:16
Alignment explanation
Indices: 12198704--12198770 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
12198694 ATATATAATT
12198704 ATTATTAAAATTTTAA
1 ATTATTAAAATTTTAA
* *
12198720 ATTA--AATTATTTTTAT
1 ATTATTAA--AATTTTAA
*
12198736 ATTTTTATAATATTTTAA
1 ATTATTA-AA-ATTTTAA
12198754 ATTATTAAAATTTTAA
1 ATTATTAAAATTTTAA
12198770 A
1 A
12198771 ACATAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
14 2 0.05
16 21 0.54
17 3 0.08
18 12 0.31
19 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATTAAAATTTTAA
Found at i:12200213 original size:51 final size:51
Alignment explanation
Indices: 12200153--12200255 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
12200143 CTCTAGGGTG
** * *
12200153 GAGCTGATCTGCTGATTGAGCCCTTCATAGCTCCTGCTCTGCGGCATTTCT
1 GAGCTGATCTGCTGACCGAGCCCATCAGAGCTCCTGCTCTGCGGCATTTCT
*
12200204 GAGCTGATCTGCTGACCGAGTCCATCAGAGCTCCTGCTCTGCGGCATTTCT
1 GAGCTGATCTGCTGACCGAGCCCATCAGAGCTCCTGCTCTGCGGCATTTCT
12200255 G
1 G
12200256 TATCCGTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGCTGATCTGCTGACCGAGCCCATCAGAGCTCCTGCTCTGCGGCATTTCT
Found at i:12209935 original size:5 final size:5
Alignment explanation
Indices: 12209925--12209952 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12209915 AAATAAAGAA
12209925 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
12209953 AGCATAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:12210208 original size:14 final size:15
Alignment explanation
Indices: 12210157--12210232 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 15
12210147 AACATAAACC
12210157 AAAAAT-AAATTTTT
1 AAAAATAAAATTTTT
12210171 AAAAAATCATAAAATTTTT
1 --AAAA--ATAAAATTTTT
* *
12210190 GAAAATAAAATTTTAA
1 AAAAATAAAATTTT-T
12210206 AAAAATTTAAAATTTTT
1 AAAAA--TAAAATTTTT
12210223 CAAAAATAAA
1 -AAAAATAAA
12210233 TATAAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
15 10 0.20
16 12 0.24
17 3 0.06
18 16 0.33
19 8 0.16
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (15 bp):
AAAAATAAAATTTTT
Found at i:12210209 original size:34 final size:34
Alignment explanation
Indices: 12210156--12210232 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
12210146 AAACATAAAC
*
12210156 CAAAAAT-AAATTTTTAAAAAATCATAAAATTTTT
1 CAAAAATAAAATTTTAAAAAAAT-ATAAAATTTTT
* *
12210190 -GAAAATAAAATTTTAAAAAAATTTAAAATTTTT
1 CAAAAATAAAATTTTAAAAAAATATAAAATTTTT
12210223 CAAAAATAAA
1 CAAAAATAAA
12210233 TATAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 15 0.41
34 22 0.59
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (34 bp):
CAAAAATAAAATTTTAAAAAAATATAAAATTTTT
Found at i:12210250 original size:22 final size:21
Alignment explanation
Indices: 12210200--12210251 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
12210190 GAAAATAAAA
*
12210200 TTTTAAAAAAATTTAAAATTT
1 TTTTAAAAAAATATAAAATTT
**
12210221 TTCAAAAATAAATATAAAATTT
1 TTTTAAAA-AAATATAAAATTT
12210243 TTTTAAAAA
1 TTTTAAAAA
12210252 CTTTCGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTAAAAAAATATAAAATTT
Found at i:12214351 original size:14 final size:14
Alignment explanation
Indices: 12214327--12214363 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
12214317 TTTATTAGAA
12214327 TTAATAAATATATAT
1 TTAA-AAATATATAT
12214342 TTAAAAATATATAT
1 TTAAAAATATATAT
12214356 TTATAAAA
1 TTA-AAAA
12214364 AAAACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:12214525 original size:17 final size:18
Alignment explanation
Indices: 12214497--12214535 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
12214487 AAACACCTAT
12214497 TAAATAAAAATACAAAAA
1 TAAATAAAAATACAAAAA
*
12214515 TAAAT-AAAATATAAAAA
1 TAAATAAAAATACAAAAA
12214532 TAAA
1 TAAA
12214536 AATGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAATAAAAATACAAAAA
Found at i:12214528 original size:7 final size:6
Alignment explanation
Indices: 12214498--12214546 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
12214488 AACACCTATT
*
12214498 AAATAA AAATACA AAA-AT AAATAA AATATAA AAATAA AAATGAA AAATA
1 AAATAA AAATA-A AAATAA AAATAA AA-ATAA AAATAA AAAT-AA AAATA
12214547 TTTTACATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 18 0.49
7 16 0.43
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:12216384 original size:23 final size:23
Alignment explanation
Indices: 12216357--12216435 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
12216347 ATTAAATTAA
*
12216357 ATTAAATGAAT-TAATTTATAAAT
1 ATTAAATAAATAT-ATTTATAAAT
12216380 ATTAAATAAATATATTTATAAAT
1 ATTAAATAAATATATTTATAAAT
* * *
12216403 A-TATATTAACATATTTATAAAT
1 ATTAAATAAATATATTTATAAAT
*
12216425 AATAAATAAAT
1 ATTAAATAAAT
12216436 TATAACCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 19 0.40
23 27 0.57
24 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATTAAATAAATATATTTATAAAT
Found at i:12216419 original size:22 final size:23
Alignment explanation
Indices: 12216370--12216434 Score: 87
Period size: 22 Copynumber: 2.9 Consensus size: 23
12216360 AAATGAATTA
*
12216370 ATTTATAAATATTAAATAAATAT
1 ATTTATAAATATTAAATAAACAT
* *
12216393 ATTTATAAATA-TATATTAACAT
1 ATTTATAAATATTAAATAAACAT
*
12216415 ATTTATAAATAATAAATAAA
1 ATTTATAAATATTAAATAAA
12216435 TTATAACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTATAAATATTAAATAAACAT
Found at i:12220639 original size:13 final size:14
Alignment explanation
Indices: 12220621--12220654 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
12220611 AATTGGATAA
12220621 TAAATTTTAA-ATT
1 TAAATTTTAATATT
12220634 TAAATTTTAATATT
1 TAAATTTTAATATT
12220648 TATAATT
1 TA-AATT
12220655 ATATAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 5 0.26
15 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:12221037 original size:21 final size:20
Alignment explanation
Indices: 12220989--12221029 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
12220979 TTTAATTTTT
12220989 AAAATTTTATATTTAAATTA
1 AAAATTTTATATTTAAATTA
12221009 AAAATTTT-TATTTATAATTA
1 AAAATTTTATATTTA-AATTA
12221029 A
1 A
12221030 TTAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTTTATATTTAAATTA
Found at i:12224521 original size:2 final size:2
Alignment explanation
Indices: 12224514--12224549 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12224504 CACTTTTCAA
12224514 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12224550 TTAAATCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12224967 original size:16 final size:16
Alignment explanation
Indices: 12224946--12224978 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12224936 AAGGTAATTA
12224946 TTTTGTCTTTTT-TTTT
1 TTTTGT-TTTTTCTTTT
12224962 TTTTGTTTTTTCTTTT
1 TTTTGTTTTTTCTTTT
12224978 T
1 T
12224979 CTTCAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTGTTTTTTCTTTT
Found at i:12226687 original size:282 final size:281
Alignment explanation
Indices: 12226183--12226749 Score: 933
Period size: 282 Copynumber: 2.0 Consensus size: 281
12226173 TATAAGGATA
* * *
12226183 AATCTTATATAAATATATAAAAGTCAAAGTTTTTGACAAAAGTGAAAAAAATTCTATGTGAACAG
1 AATCTTATATAAATATATAAAAGTCAAAGCTTTTGACAAAAATGAAAAAAATCCTATGTGAACAG
* * *
12226248 CTTAAAATATTGACATGTGGATGATTTTAAAAATCAATACGTGACATCTAATAAATGTATTTTAT
66 CTTAAAATATTGACATATGGATGATTTTAAAAATCAATAC-TAACATCTAATAAATATATTTTAT
*
12226313 TTTATTTAATACATTTTAATTTAAAAATAATGCAAAAAATTAAATTGATTATATTTATGTTTTTA
130 TTTATTTAATACATTTTAATTTAAAAATAATGCAAAAAACTAAATTGATTATATTTATGTTTTTA
*
12226378 TTATTAACCTTAAACCATTCTCAATTCAATTGATATTAGAAGTATTAAAATTTTAAAAATTTCTT
195 TTATTAACCTTAAACCATTCTCAATTCAATTGATATTAAAAGTATTAAAATTTTAAAAATTTCTT
*
12226443 AATTTGACAAATTAAATCAATC
260 AATTTGACAAATCAAATCAATC
*
12226465 AATCTTATATAAATATATAAAAGTCAAAGCTTTTGACAAAAATGAAAAAAATCCTATGTGAACGG
1 AATCTTATATAAATATATAAAAGTCAAAGCTTTTGACAAAAATGAAAAAAATCCTATGTGAACAG
* * *
12226530 CTTAAAATGTTGACATATGGAT-ACTTTTAAAAATCGTCATA-TAACATCTAATAAATATGTTTT
66 CTTAAAATATTGACATATGGATGA-TTTTAAAAATC--AATACTAACATCTAATAAATATATTTT
*
12226593 GTTTTATTTAATACATTTTTAATTTAAAAATAATGCAAAAAACTAAATTGATTATATTTATGTTT
128 ATTTTATTTAATACA-TTTTAATTTAAAAATAATGCAAAAAACTAAATTGATTATATTTATGTTT
*
12226658 TTATTATTAACCTT-AATCATTCTCAATTCAATTGATATTAAAAGTATTAAAATTTTAAAAATTT
192 TTATTATTAACCTTAAACCATTCTCAATTCAATTGATATTAAAAGTATTAAAATTTTAAAAATTT
12226722 CTTAATTTGACAAATCAAATCAATC
257 CTTAATTTGACAAATCAAATCAATC
12226747 AAT
1 AAT
12226750 ATAGAATTAA
Statistics
Matches: 266, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
281 1 0.00
282 200 0.75
283 62 0.23
284 3 0.01
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.40
Consensus pattern (281 bp):
AATCTTATATAAATATATAAAAGTCAAAGCTTTTGACAAAAATGAAAAAAATCCTATGTGAACAG
CTTAAAATATTGACATATGGATGATTTTAAAAATCAATACTAACATCTAATAAATATATTTTATT
TTATTTAATACATTTTAATTTAAAAATAATGCAAAAAACTAAATTGATTATATTTATGTTTTTAT
TATTAACCTTAAACCATTCTCAATTCAATTGATATTAAAAGTATTAAAATTTTAAAAATTTCTTA
ATTTGACAAATCAAATCAATC
Found at i:12227111 original size:270 final size:270
Alignment explanation
Indices: 12226622--12227168 Score: 785
Period size: 270 Copynumber: 2.0 Consensus size: 270
12226612 TAATTTAAAA
12226622 ATAATGCAAAAAACTAAATTGATTATATTTATGTTTTTATTATTAACCTTAATCATTCTCAATTC
1 ATAATGCAAAAAACTAAATTGATTATATTTATGTTTTTATTATTAACCTTAATCATTCTCAATTC
*
12226687 AATTGATATTAAAAGTATTAAAATTTTAAAAATTTCTTAATTTGACAAATCAAATCAATCAATAT
66 AATTCATATTAAAAGTATTAAAATTTTAAAAATTTCTTAATTTGACAAATCAAATCAATCAATAT
12226752 AGAATTAATAAATTAATAAATACTAAAATTACAATTATAAAATAGCTAATTCTCTAATCAATTAT
131 AGAATTAATAAATTAATAAATACTAAAATTACAATTATAAAATAGCTAATTCTCTAATCAATTAT
* * *
12226817 TTGATACATTTATATTTAATTAAATATAATATCC-AGTAATTTATGTATTTCATATGTAAATATA
196 TTGATACATTTATATCTAATTAAATATAATATCCTAGTAATTGATGTATTTCATACGTAAATATA
12226881 TAAAGCAAAT
261 TAAAGCAAAT
* * **
12226891 ATAATTCAAAAAA-TAAAATTGATTATATTTATGTTTTTATTATTGATTTTAAATCACTT-TCAA
1 ATAATGCAAAAAACT-AAATTGATTATATTTATGTTTTTATTATTAACCTT-AATCA-TTCTCAA
* * * *
12226954 TTTAATTCATATTAAAAGTATTAAAATTTTAAAAATTTCTTATTTTGATAAATTAAATCAATCAA
63 TTCAATTCATATTAAAAGTATTAAAATTTTAAAAATTTCTTAATTTGACAAATCAAATCAATCAA
* * * * * * * *
12227019 TATATAATTAATAAATTAATAAATACTACAATTATAATTATAAAATAGTTGATTTTGTAATTAAT
128 TATAGAATTAATAAATTAATAAATACTAAAATTACAATTATAAAATAGCTAATTCTCTAATCAAT
* ** * *
12227084 TATTTGATACATTTATATCTGATTAAATATGGTATCCATTTGAGTAATTGATGTATTTTATGCGT
193 TATTTGATACATTTATATCTAATTAAATATAATATCC---T-AGTAATTGATGTATTTCATACGT
12227149 AAATATATAAAGCAAAT
254 AAATATATAAAGCAAAT
12227166 ATA
1 ATA
12227169 TCAAATTAAT
Statistics
Matches: 245, Mismatches: 25, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
268 1 0.00
269 44 0.18
270 159 0.65
271 2 0.01
275 39 0.16
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (270 bp):
ATAATGCAAAAAACTAAATTGATTATATTTATGTTTTTATTATTAACCTTAATCATTCTCAATTC
AATTCATATTAAAAGTATTAAAATTTTAAAAATTTCTTAATTTGACAAATCAAATCAATCAATAT
AGAATTAATAAATTAATAAATACTAAAATTACAATTATAAAATAGCTAATTCTCTAATCAATTAT
TTGATACATTTATATCTAATTAAATATAATATCCTAGTAATTGATGTATTTCATACGTAAATATA
TAAAGCAAAT
Found at i:12227940 original size:31 final size:32
Alignment explanation
Indices: 12227867--12227944 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
12227857 TTCATTAAAA
* *
12227867 ATGATTTCATTTGGTAAAATATTAATACACTT
1 ATGATTTCATTTGATAAAATATTAATACACGT
* *
12227899 TTGATTTCATTTGATAAAATATTAATGCACGT
1 ATGATTTCATTTGATAAAATATTAATACACGT
12227931 AT-ATTTCATTTGAT
1 ATGATTTCATTTGAT
12227945 TTCATTTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 12 0.29
32 29 0.71
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (32 bp):
ATGATTTCATTTGATAAAATATTAATACACGT
Found at i:12236636 original size:21 final size:21
Alignment explanation
Indices: 12236612--12236857 Score: 89
Period size: 21 Copynumber: 10.9 Consensus size: 21
12236602 TCCTGAATCT
*
12236612 TTAAATTAGAATCTTTGAGTC
1 TTAAATGAGAATCTTTGAGTC
*
12236633 TTAAATGAGAATCTTTAAGACGTT
1 TTAAATGAGAATCTTT--GA-GTC
*
12236657 TTCAAATGAGAATGTTTGAGTC
1 TT-AAATGAGAATCTTTGAGTC
* * *
12236679 TTAAATAAGAATATTTAAGAAATCC
1 TTAAATGAGAATCTTT--G-AGT-C
* * * *
12236704 TCAAGTGAGAATTTTTAAGTC
1 TTAAATGAGAATCTTTGAGTC
* *
12236725 TGAAATGAGAATCTTTAAGAAATC
1 TTAAATGAGAATCTTT--G-AGTC
* * * *
12236749 TTAAATGAAAATTTTTAAAAAATC
1 TTAAATGAGAATCTTT---GAGTC
* * *
12236773 TCCAAATAAGAATATTTGAGT-
1 T-TAAATGAGAATCTTTGAGTC
*
12236794 TTCAAATGAGAATCTTTGAGTT
1 TT-AAATGAGAATCTTTGAGTC
* ** * *
12236816 TTAAAATGAAAAAATTTTAGTTT
1 TT-AAATGAGAATCTTTGAG-TC
*
12236839 TTAAATGAGAATATTTGAG
1 TTAAATGAGAATCTTTGAG
12236858 ATAAGAAACC
Statistics
Matches: 170, Mismatches: 39, Indels: 31
0.71 0.16 0.13
Matches are distributed among these distances:
21 58 0.34
22 37 0.22
23 9 0.05
24 27 0.16
25 39 0.23
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
TTAAATGAGAATCTTTGAGTC
Found at i:12236675 original size:46 final size:46
Alignment explanation
Indices: 12236614--12236756 Score: 162
Period size: 46 Copynumber: 3.1 Consensus size: 46
12236604 CTGAATCTTT
* ** **
12236614 AAATTAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGACGTTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCCTC
* * *
12236660 AAATGAGAATGTTTGAGTCTTAAATAAGAATATTTAAGAAATCCTC
1 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCCTC
* * * * *
12236706 AAGTGAGAATTTTTAAGTCTGAAATGAGAATCTTTAAGAAAT-CTT
1 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCCTC
12236751 AAATGA
1 AAATGA
12236757 AAATTTTTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 7 0.09
46 74 0.91
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (46 bp):
AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCCTC
Found at i:12236765 original size:24 final size:24
Alignment explanation
Indices: 12236677--12236773 Score: 76
Period size: 24 Copynumber: 4.1 Consensus size: 24
12236667 AATGTTTGAG
*
12236677 TCTTAAAT-AAGAATATTTAAGAAA
1 TCTTAAATGAA-AATTTTTAAGAAA
* * *
12236701 TCCTCAAGTGAGAATTTTTAAG---
1 T-CTTAAATGAAAATTTTTAAGAAA
* * *
12236723 TCTGAAATGAGAATCTTTAAGAAA
1 TCTTAAATGAAAATTTTTAAGAAA
*
12236747 TCTTAAATGAAAATTTTTAAAAAA
1 TCTTAAATGAAAATTTTTAAGAAA
12236771 TCT
1 TCT
12236774 CCAAATAAGA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
21 17 0.30
22 1 0.02
24 24 0.42
25 14 0.25
26 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (24 bp):
TCTTAAATGAAAATTTTTAAGAAA
Found at i:12236766 original size:70 final size:70
Alignment explanation
Indices: 12236677--12236810 Score: 164
Period size: 70 Copynumber: 1.9 Consensus size: 70
12236667 AATGTTTGAG
* * * * *
12236677 TCTTAAATAAGAATATTTAAGAAATC-CTCAAGTGAGAATTTTTAAGTCTGAAATGAGAATCTTT
1 TCTTAAATAAGAATATTTAAAAAATCTC-CAAATAAGAATATTTAAGTCTCAAATGAGAATCTTT
12236741 AAGAAA
65 AAGAAA
* * *
12236747 TCTTAAATGAA-AATTTTTAAAAAATCTCCAAATAAGAATATTTGAGTTTCAAATGAGAATCTTT
1 TCTTAAAT-AAGAATATTTAAAAAATCTCCAAATAAGAATATTTAAGTCTCAAATGAGAATCTTT
12236811 GAGTTTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 51 0.94
71 3 0.06
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (70 bp):
TCTTAAATAAGAATATTTAAAAAATCTCCAAATAAGAATATTTAAGTCTCAAATGAGAATCTTTA
AGAAA
Found at i:12236854 original size:22 final size:22
Alignment explanation
Indices: 12236776--12236857 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
12236766 AAAAATCTCC
* *
12236776 AAATAAGAATATTTGAG-TTTC
1 AAATGAGAATATTTGAGTTTTA
*
12236797 AAATGAGAATCTTTGAGTTTTA
1 AAATGAGAATATTTGAGTTTTA
* * * *
12236819 AAATGAAAAAATTTTAGTTTTT
1 AAATGAGAATATTTGAGTTTTA
12236841 AAATGAGAATATTTGAG
1 AAATGAGAATATTTGAG
12236858 ATAAGAAACC
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 15 0.31
22 34 0.69
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (22 bp):
AAATGAGAATATTTGAGTTTTA
Found at i:12237573 original size:38 final size:40
Alignment explanation
Indices: 12237495--12237587 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 40
12237485 TATGATTGTC
* *
12237495 GAAGAGCTTTTATTTTTTAAAGTCGTTGAGCATCTATTTA
1 GAAGAGCTTTTATTTTTCAAAGTCATTGAGCATCTATTTA
* * * *
12237535 GAAGAGC-TTT-TTTTTCAAAGTTATTGATCTTCTGTTTA
1 GAAGAGCTTTTATTTTTCAAAGTCATTGAGCATCTATTTA
* *
12237573 GAGGAGCCTTTATTT
1 GAAGAGCTTTTATTT
12237588 ATTTTCATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 28 0.64
39 6 0.14
40 10 0.23
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (40 bp):
GAAGAGCTTTTATTTTTCAAAGTCATTGAGCATCTATTTA
Found at i:12240850 original size:30 final size:30
Alignment explanation
Indices: 12240819--12240922 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
12240809 GTTTTATATT
12240819 AAGAGCTTATTT-AGATATAAATAAAAAATTA
1 AAGA-CTTATTTGA-ATATAAATAAAAAATTA
* * *
12240850 AAGATTTATTTGAATATAAATTAAAAGTTA
1 AAGACTTATTTGAATATAAATAAAAAATTA
* * * * * *
12240880 ATGATTTATTTAAATACAAATTAAAATTTA
1 AAGACTTATTTGAATATAAATAAAAAATTA
* *
12240910 AAAACTTCTTTGA
1 AAGACTTATTTGA
12240923 GTGTAATAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 55 0.92
31 5 0.08
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (30 bp):
AAGACTTATTTGAATATAAATAAAAAATTA
Found at i:12240911 original size:60 final size:58
Alignment explanation
Indices: 12240825--12240972 Score: 138
Period size: 60 Copynumber: 2.5 Consensus size: 58
12240815 TATTAAGAGC
* * * * * * *
12240825 TTATTTAGATATAAATAAAAAATTAAAGATTTATTTGAATATAAATTAAAAGT-TAATGAT
1 TTATTTAAATA-AAATTAAAATTTAAAAACTTATTTGAATAT-AA-TAAAAATATAATAAT
* * *
12240885 TTATTTAAATACAAATTAAAATTTAAAAACTTCTTTGAGTGTAATAAAAATATAATAAT
1 TTATTTAAATA-AAATTAAAATTTAAAAACTTATTTGAATATAATAAAAATATAATAAT
12240944 TTATTTAAATAAAATACTAAAA-TTAAAAA
1 TTATTTAAATAAAAT--TAAAATTTAAAAA
12240973 TATATATTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 10 0.14
59 26 0.35
60 38 0.51
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (58 bp):
TTATTTAAATAAAATTAAAATTTAAAAACTTATTTGAATATAATAAAAATATAATAAT
Found at i:12243879 original size:32 final size:31
Alignment explanation
Indices: 12243822--12243881 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
12243812 ATTATATCTC
*
12243822 TTTAATAAATAAAATTAAAAGTAATAAGGCT
1 TTTAATAAATAAAAATAAAAGTAATAAGGCT
*
12243853 TTTAA-AAATAAAAAATAAATATTAATAAG
1 TTTAATAAAT-AAAAATAAA-AGTAATAAG
12243882 TTTATTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.16
31 13 0.52
32 8 0.32
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (31 bp):
TTTAATAAATAAAAATAAAAGTAATAAGGCT
Found at i:12248288 original size:20 final size:19
Alignment explanation
Indices: 12248245--12248288 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12248235 ATCTTTATTT
12248245 TATAAAAATTTAAAATATA
1 TATAAAAATTTAAAATATA
*
12248264 GATAAAAATTAATAAAA-ATA
1 TATAAAAATT--TAAAATATA
12248284 TATAA
1 TATAA
12248289 TTTGGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TATAAAAATTTAAAATATA
Found at i:12250858 original size:24 final size:25
Alignment explanation
Indices: 12250810--12250859 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12250800 TTTTGACATT
* *
12250810 AAAAATTATAAAACTTTCATTTTAA
1 AAAAATTATAAAACTTTAATATTAA
*
12250835 AAAAATTTTAAAA-TTTAATATTAA
1 AAAAATTATAAAACTTTAATATTAA
12250859 A
1 A
12250860 TATATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATTATAAAACTTTAATATTAA
Found at i:12252501 original size:29 final size:27
Alignment explanation
Indices: 12252461--12252514 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
12252451 AATATAAATA
12252461 TGACATATTGATTATATACGT-TATACG
1 TGACATATTGATTA-ATACGTGTATACG
12252488 TGACATAATATGATTAATACGTGTATA
1 TGACAT-AT-TGATTAATACGTGTATA
12252515 ATTAATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.25
28 8 0.33
29 10 0.42
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (27 bp):
TGACATATTGATTAATACGTGTATACG
Found at i:12252570 original size:19 final size:20
Alignment explanation
Indices: 12252527--12252576 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
12252517 TAATCTATTT
* *
12252527 AAATATGATATAAATAAATAT
1 AAATA-GATACAAATAAATAC
*
12252548 AAATA-ATACAAATATATAC
1 AAATAGATACAAATAAATAC
12252567 AAATAGATAC
1 AAATAGATAC
12252577 GACTAACACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 16 0.64
20 4 0.16
21 5 0.20
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (20 bp):
AAATAGATACAAATAAATAC
Found at i:12253204 original size:14 final size:15
Alignment explanation
Indices: 12253185--12253214 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12253175 AAAATAAACA
12253185 TAAAATATAT-TTTT
1 TAAAATATATATTTT
12253199 TAAAATATATATTTT
1 TAAAATATATATTTT
12253214 T
1 T
12253215 TGTATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAATATATATTTT
Found at i:12254367 original size:18 final size:18
Alignment explanation
Indices: 12254346--12254383 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12254336 TTTTAAAATT
*
12254346 TTAAATTAATTTAATATA
1 TTAAATCAATTTAATATA
*
12254364 TTAAATCAATTTGATATA
1 TTAAATCAATTTAATATA
12254382 TT
1 TT
12254384 TAATGCTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAAATCAATTTAATATA
Found at i:12261675 original size:17 final size:17
Alignment explanation
Indices: 12261653--12261686 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12261643 TGTCACAATT
12261653 ATGTTCACTTAATTTTA
1 ATGTTCACTTAATTTTA
12261670 ATGTTCACTTAATTTTA
1 ATGTTCACTTAATTTTA
12261687 CATTTAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
ATGTTCACTTAATTTTA
Found at i:12262446 original size:100 final size:100
Alignment explanation
Indices: 12262276--12262475 Score: 337
Period size: 100 Copynumber: 2.0 Consensus size: 100
12262266 TCTTGACATA
* ** *
12262276 GAAAAATGAATCATCTCCTTGAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCTA
1 GAAAAATGAATCATCTCATCAAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCAA
12262341 GGCCTAGAGGTAGTGGATACTAAGTGTATAATAAT
66 GGCCTAGAGGTAGTGGATACTAAGTGTATAATAAT
* *
12262376 GAAAAATGAATCATCTCATCAAAGATTTTGTGATGAAATTTGAGTCGCTTTTCACTTTTCAGCAA
1 GAAAAATGAATCATCTCATCAAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCAA
*
12262441 GGCCTAGAGGTAGTGGATACTATGTGTATAATAAT
66 GGCCTAGAGGTAGTGGATACTAAGTGTATAATAAT
12262476 CATCTACACT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (100 bp):
GAAAAATGAATCATCTCATCAAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCAA
GGCCTAGAGGTAGTGGATACTAAGTGTATAATAAT
Found at i:12265044 original size:28 final size:29
Alignment explanation
Indices: 12264984--12265044 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
12264974 TGTATTCATG
* * *
12264984 TTATTTTTTATATTTTAATAAAACTATAT
1 TTATTTTTTATAATTTAATAAAACTAAAA
12265013 TTATTTTTTGATAATTT-ATAAAA-TAAAA
1 TTATTTTTT-ATAATTTAATAAAACTAAAA
12265041 TTAT
1 TTAT
12265045 ATTAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 15 0.54
30 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TTATTTTTTATAATTTAATAAAACTAAAA
Found at i:12266400 original size:112 final size:112
Alignment explanation
Indices: 12266202--12266426 Score: 387
Period size: 112 Copynumber: 2.0 Consensus size: 112
12266192 ATCCTAAATC
* *
12266202 TAAGATTTGAAGTCCTAAATTAAACCAAATTTCATTCATTTGAAATTAAAAAGTATAAAATCAAA
1 TAAGATTTGAAGTCCCAAATCAAACCAAATTTCATTCATTTGAAATTAAAAAGTATAAAATCAAA
* *
12266267 GACAAATCATTTGTTCTTTTTACTTTTTTGTTTGATTTGGTGTTTAT
66 GACAAATCATTTGTTCATTTTACCTTTTTGTTTGATTTGGTGTTTAT
*
12266314 TAAGATTTGAAGTCCCAAATCAAGCCAAATTTCATTCATTTGAAATTAAAAAGTATAAAATCAAA
1 TAAGATTTGAAGTCCCAAATCAAACCAAATTTCATTCATTTGAAATTAAAAAGTATAAAATCAAA
* *
12266379 GATAAATCGTTTGTTCATTTTACCTTTTTGTTTGATTTGGTGTTTAT
66 GACAAATCATTTGTTCATTTTACCTTTTTGTTTGATTTGGTGTTTAT
12266426 T
1 T
12266427 TCATATGTTT
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (112 bp):
TAAGATTTGAAGTCCCAAATCAAACCAAATTTCATTCATTTGAAATTAAAAAGTATAAAATCAAA
GACAAATCATTTGTTCATTTTACCTTTTTGTTTGATTTGGTGTTTAT
Found at i:12266517 original size:34 final size:34
Alignment explanation
Indices: 12266474--12266544 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
12266464 GGTTTTGAGA
* * * *
12266474 TTTTCAAAATAGATTTCTAAAAGTTTTTAAATAT
1 TTTTAAAAATAGATATCTAAAAGATTTTAAAAAT
**
12266508 TTTTAAAAATTTATATCTAAAAGATTTTAAAAAT
1 TTTTAAAAATAGATATCTAAAAGATTTTAAAAAT
12266542 TTT
1 TTT
12266545 CGAAAATCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (34 bp):
TTTTAAAAATAGATATCTAAAAGATTTTAAAAAT
Found at i:12272932 original size:19 final size:20
Alignment explanation
Indices: 12272893--12272973 Score: 58
Period size: 19 Copynumber: 4.1 Consensus size: 20
12272883 TAATCTATTT
* *
12272893 AAATACGATATAAATAAATAC
1 AAATA-GATACAAATATATAC
12272914 AAATA-ATACAAATATATAC
1 AAATAGATACAAATATATAC
* * * *
12272933 GAATAGATACGACTA-ACAC
1 AAATAGATACAAATATATAC
* **
12272952 AAATATATATGAATATATAC
1 AAATAGATACAAATATATAC
12272972 AA
1 AA
12272974 TTAACATAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
19 30 0.64
20 12 0.26
21 5 0.11
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (20 bp):
AAATAGATACAAATATATAC
Found at i:12272990 original size:29 final size:29
Alignment explanation
Indices: 12272900--12272990 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
12272890 TTTAAATACG
* *
12272900 ATATAAATAAATACAAATAATACAAATAT
1 ATATGAATAAATACAAATAACACAAATAT
* * * *
12272929 ATACGAATAGATACGACTAACACAAATAT
1 ATATGAATAAATACAAATAACACAAATAT
* * *
12272958 ATATGAATATATACAATTAACATAAATAT
1 ATATGAATAAATACAAATAACACAAATAT
12272987 ATAT
1 ATAT
12272991 AAGAATACAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (29 bp):
ATATGAATAAATACAAATAACACAAATAT
Found at i:12292083 original size:69 final size:68
Alignment explanation
Indices: 12291930--12292526 Score: 636
Period size: 69 Copynumber: 8.8 Consensus size: 68
12291920 ATTTTAGGAT
* * *
12291930 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTT-AAAAATCCTTTTTTGAAATCTTTA
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTT-TTCAAAAAT-ATTTTTTGAAATTTTTA
***
12291994 T-TTT
64 TCAAA
12291998 TTTTATTCTT-AAGGAAAATTGATA-TTGTCAACTTTTTTTCAAAAATATTTTTTGAAATTTTTA
1 TTTTATT-TTCAAGGAAAATTGATACTT-TCAACTTTTTTTCAAAAATATTTTTTGAAATTTTTA
12292061 TCAAAA
64 TC-AAA
* *
12292067 TTTTATTTTCAAGGAAAATTGATACTTTTAA-TTTTTCCTCAAAAATATTTTTTGAAATTTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTT-TTCAAAAATATTTTTTGAAATTTTTAT
12292131 CAAAA
65 C-AAA
* * * *
12292136 TTTTATTTTAAAAGAAAATTGATACTTTCAACTTTTCCTT-AAAAATATTTTTTGAAAATTTT-T
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTT-TTTCAAAAATATTTTTTGAAATTTTTAT
12292199 ---A
65 CAAA
** * *
12292200 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAATATGTTTTGAAATTTTTATC
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAATTTTTATC
12292265 AAA
66 AAA
* * * *
12292268 TTTTATTTTTAAGGAAAACTGATACTTTCAACTTTTTTTGAAAAATGTTTTTTGAAATTATTT-T
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAATT-TTTAT
12292332 ---A
65 CAAA
* * *
12292333 TTTTATTTTTAA-AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTCG-AATTTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTT-GAAATTTTTAT
12292396 CAAAA
65 C-AAA
* * * *
12292401 TTTTATTTTCAAGAAAAATTGATATTTTCAACTTTTCCTT-AAAAATGTTTTTTGAAATTTTTAT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTT-TTTCAAAAATATTTTTTGAAATTTTTAT
12292465 CAAAA
65 C-AAA
* * *
12292470 ATTTATTTTAAAGAAAAATTAATTGATACTTTCAA-TTTTTTCTCAAAAATATTTTTT
1 TTTTATTTTCAAG--GAA--AATTGATACTTTCAACTTTTTT-TCAAAAATATTTTTT
12292527 ATTTTAATAG
Statistics
Matches: 459, Mismatches: 39, Indels: 57
0.83 0.07 0.10
Matches are distributed among these distances:
63 5 0.01
64 95 0.21
65 15 0.03
67 20 0.04
68 111 0.24
69 168 0.37
70 10 0.02
71 4 0.01
72 5 0.01
73 26 0.06
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (68 bp):
TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAATTTTTATC
AAA
Found at i:12292350 original size:132 final size:133
Alignment explanation
Indices: 12291930--12292526 Score: 679
Period size: 133 Copynumber: 4.4 Consensus size: 133
12291920 ATTTTAGGAT
* * * *
12291930 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATCCTTTTTTGAAATCTTTAT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAATTTTTAT
*** * *
12291995 --TTTTTTTATTCTTAAGGAAAATTGATA-TTGTCAACTTTT-TTTCAAAAATATTTTTTGAAAT
65 CAAAATTTTATTTTTAAGGAAAATTGATACTT-TCAACTTTTCCTT-AAAAATATTTTTTGAAAT
12292056 TTTTATCAAAA
128 TTTT-T----A
* * *
12292067 TTTTATTTTCAAGGAAAATTGATACTTTTAATTTTTCCTCAAAAATATTTTTTGAAATTTTTATC
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATC
* * *
12292132 AAAATTTTATTTTAAAAGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAAATTT
66 AAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAATTTT
12292197 TTA
131 TTA
* * *
12292200 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAATATGTTTTGAAATTTTTATC
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATC
* * *
12292265 -AAATTTTATTTTTAAGGAAAACTGATACTTTCAACTTTT-TTTGAAAAATGTTTTTTGAAATTA
66 AAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTT-AAAAATATTTTTTGAAATT-
12292328 TTTTA
129 TTTTA
* *
12292333 TTTTATTTTTAA-AAAAATTGATACTTTCAACTTTTCTTCAAAAATATTTTTTCG-AATTTTTAT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAATTTTTAT
* * * *
12292396 CAAAATTTTATTTTCAAGAAAAATTGATATTTTCAACTTTTCCTTAAAAATGTTTTTTGAAATTT
65 CAAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAATTT
12292461 TTATCAAAA
130 TT-T----A
* * * *
12292470 ATTTATTTTAAAGAAAAATTAATTGATACTTTCAATTTTTTCTCAAAAATATTTTTT
1 TTTTATTTTCAAG--AAA--AATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
12292527 ATTTTAATAG
Statistics
Matches: 401, Mismatches: 40, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
131 2 0.00
132 102 0.25
133 134 0.33
134 2 0.00
136 16 0.04
137 53 0.13
138 51 0.13
139 4 0.01
140 3 0.01
142 34 0.08
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (133 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATC
AAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAATTTT
TTA
Found at i:12292611 original size:15 final size:15
Alignment explanation
Indices: 12292593--12292635 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
12292583 AATTTTAATT
* *
12292593 TAATTAATAATTAAA
1 TAATAAATAAATAAA
12292608 TAATAAATAAATAAA
1 TAATAAATAAATAAA
12292623 TAGATAAAATAAA
1 TA-AT-AAATAAA
12292636 GTCTTGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.62
16 2 0.08
17 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
TAATAAATAAATAAA
Found at i:12294044 original size:79 final size:79
Alignment explanation
Indices: 12293937--12294116 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 79
12293927 GCATATGTCG
* ** * * *
12293937 AAATCCAAAAATAGAATGACCTAGATTGAATCGAAATCTGAAACAAATAATTTAAACTAAG-AAG
1 AAATCC-AAAACAGAAAAACCTAGATTGAACCGAAACCTGAAACAAATAACTTAAACTAAGAAAG
12294001 AATTTGACAAAAGTCA
65 -ATTTGACAAAAGTCA
* * *
12294017 AAATCCAAAACAGAAAAACCTAGATTGAACCGAAACCTGAAACGAATGACTTAGACTAAGAAAGA
1 AAATCCAAAACAGAAAAACCTAGATTGAACCGAAACCTGAAACAAATAACTTAAACTAAGAAAGA
12294082 TTTGACAAAAGTCA
66 TTTGACAAAAGTCA
*
12294096 AAATCCAAAACTGAAAAACCT
1 AAATCCAAAACAGAAAAACCT
12294117 GGACTAAATA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
79 80 0.90
80 9 0.10
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (79 bp):
AAATCCAAAACAGAAAAACCTAGATTGAACCGAAACCTGAAACAAATAACTTAAACTAAGAAAGA
TTTGACAAAAGTCA
Found at i:12294137 original size:79 final size:79
Alignment explanation
Indices: 12293969--12294152 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 79
12293959 AGATTGAATC
* * * *
12293969 GAAATCTGAAACAAATAATTTAAACTAAGAAGAATTTGACAAAAGTCAAAATCCAAAACAGAAAA
1 GAAACCTGAAACGAATAACTTAGACTAAGAAGAATTTGACAAAAGTCAAAATCCAAAACAGAAAA
* * *
12294034 ACCTAGATTGAACC
66 ACCTAGACTAAACA
* *
12294048 GAAACCTGAAACGAATGACTTAGACTAAGAA-AGATTTGACAAAAGTCAAAATCCAAAACTGAAA
1 GAAACCTGAAACGAATAACTTAGACTAAGAAGA-ATTTGACAAAAGTCAAAATCCAAAACAGAAA
* *
12294112 AACCTGGACTAAATA
65 AACCTAGACTAAACA
*** * *
12294127 GAAGTTTGAAATGAATAACTTGGACT
1 GAAACCTGAAACGAATAACTTAGACT
12294153 TAGTCGAAGA
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 86 0.99
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (79 bp):
GAAACCTGAAACGAATAACTTAGACTAAGAAGAATTTGACAAAAGTCAAAATCCAAAACAGAAAA
ACCTAGACTAAACA
Found at i:12294413 original size:86 final size:86
Alignment explanation
Indices: 12294113--12294413 Score: 334
Period size: 86 Copynumber: 3.5 Consensus size: 86
12294103 AAACTGAAAA
* * * * * *
12294113 ACCTGGACTAAATAGAAGTTTGAAATGAATAACTTGGACTTAGTCGAAGAATGATCTGGCATAGG
1 ACCTGGATTAAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCGAAGAAAGATCTGGCATATG
*
12294178 TCAAAATTTGAAAATAGAATG
66 TCAAAATTTAAAAATAGAATG
* * * * * * * * *
12294199 ACTTGGATTGAACCGAAGTCTGAAATAAATAACTTGGACTAGGCCAAAGAAGGATCTGACATATG
1 ACCTGGATTAAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCGAAGAAAGATCTGGCATATG
*
12294264 TCAAAATTTAAAAACAGAATG
66 TCAAAATTTAAAAATAGAATG
* * * * *
12294285 ACCTAGATTAAATCGAAGTTTAAAATGAATAACTTAGG-CTAAGTCGAAGAAAGATATGGTATAT
1 ACCTGGATTAAATCGAAGTCTGAAATGAATAACTT-GGACTAAGTCGAAGAAAGATCTGGCATAT
* * *
12294349 GCCGAAATTTAAAAATAGGATG
65 GTCAAAATTTAAAAATAGAATG
* * *
12294371 ACCTGGATTGAATTGAAGTCTGAAATGAATGACTTGGACTAAG
1 ACCTGGATTAAATCGAAGTCTGAAATGAATAACTTGGACTAAG
12294414 AATGATTTGA
Statistics
Matches: 173, Mismatches: 40, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
85 2 0.01
86 169 0.98
87 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (86 bp):
ACCTGGATTAAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCGAAGAAAGATCTGGCATATG
TCAAAATTTAAAAATAGAATG
Found at i:12294491 original size:79 final size:79
Alignment explanation
Indices: 12294390--12294571 Score: 242
Period size: 79 Copynumber: 2.3 Consensus size: 79
12294380 GAATTGAAGT
* * * *
12294390 CTGAAATGAATGACTTGGACTAAGAATGATTTGACAAAAGTTAAAATCCAAAA-TAGAAAGA-TC
1 CTGAAATGAATAACTTAGACTAAGAAGGATTTGACAAAAGTCAAAATCCAAAACT-GAAAGACTC
*
12294453 AGGATTGAACCAAAGC
65 A-GACTGAACCAAAGC
* *
12294469 CTGAAATGAATAACTTAAACTAAGAAGGATTTGACAAAAGTCAAAATCCAAAACTGAAAGACTTA
1 CTGAAATGAATAACTTAGACTAAGAAGGATTTGACAAAAGTCAAAATCCAAAACTGAAAGACTCA
*
12294534 GACTGAACCGAAGC
66 GACTGAACCAAAGC
* *
12294548 TTAAAATGAATAACTTAGACTAAG
1 CTGAAATGAATAACTTAGACTAAG
12294572 TTATAATACG
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 87 0.97
80 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (79 bp):
CTGAAATGAATAACTTAGACTAAGAAGGATTTGACAAAAGTCAAAATCCAAAACTGAAAGACTCA
GACTGAACCAAAGC
Found at i:12295475 original size:58 final size:58
Alignment explanation
Indices: 12295366--12295477 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
12295356 TTTTTGAAAT
* * * *
12295366 TCAAACTGCCCGTTACGGGTTTTCAATTTGAGCTTTTTTTTTATTTTTTTTTTTTAAC
1 TCAAACTACCCGTTACAGGTTTTCAATTTGAGCTTTTTTTTTATCTCTTTTTTTTAAC
12295424 TCAAACTACCC-TTCACAGGTTTTCAATTTGAGCTCTTTTTTTT-TCTCTTTTTTT
1 TCAAACTACCCGTT-ACAGGTTTTCAATTTGAGCT-TTTTTTTTATCTCTTTTTTT
12295478 GTTTTTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 2 0.04
58 38 0.79
59 8 0.17
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (58 bp):
TCAAACTACCCGTTACAGGTTTTCAATTTGAGCTTTTTTTTTATCTCTTTTTTTTAAC
Found at i:12295567 original size:77 final size:76
Alignment explanation
Indices: 12295398--12295621 Score: 287
Period size: 77 Copynumber: 3.0 Consensus size: 76
12295388 TCAATTTGAG
* * * * *
12295398 CTTTTTTT-TTATTTTTTTTTTTT-AACTCAAACTACCCTTCACAGGTTTTCAATTTGAG--CTC
1 CTTTTTTTGTT-TTTTTTTTTTTTGAACTCAAATTGCCCTTTACAAGTTTTCAATTTGAGCCCTT
12295459 TTT-TTTTTTCT
65 TTTCTTTTTTCT
* * *
12295470 CTTTTTTTGTTTTTTATTTTTTTGAACTAAAATTGCCTTTTACAAGTTTTCAATTTGAGCCCTTT
1 CTTTTTTTGTTTTTTTTTTTTTTGAACTCAAATTGCCCTTTACAAGTTTTCAATTTGAGCCCTTT
12295535 TTCTTTTTTCT
66 TTCTTTTTTCT
* * *
12295546 CTTTTTTTGTTTTTATTTTTTTTTGAACTCAAATCGCCCTTTACAAGTTTTCAATTTAAGCCATT
1 CTTTTTTTGTTTTT-TTTTTTTTTGAACTCAAATTGCCCTTTACAAGTTTTCAATTTGAGCC-CT
12295611 TTTTCTTTTTT
64 TTTTCTTTTTT
12295622 TTTTTTAATT
Statistics
Matches: 131, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
72 19 0.15
73 31 0.24
75 5 0.04
76 22 0.17
77 42 0.32
78 12 0.09
ACGTcount: A:0.17, C:0.16, G:0.07, T:0.60
Consensus pattern (76 bp):
CTTTTTTTGTTTTTTTTTTTTTTGAACTCAAATTGCCCTTTACAAGTTTTCAATTTGAGCCCTTT
TTCTTTTTTCT
Found at i:12295586 original size:150 final size:142
Alignment explanation
Indices: 12295398--12295673 Score: 322
Period size: 144 Copynumber: 1.9 Consensus size: 142
12295388 TCAATTTGAG
* * *
12295398 CTTTTTTTTTATTTTTTTTTTTTAACTCAAACTACCCTTCACAGGTTTTCAATTTGAGCTCTTTT
1 CTTTTTTTTTATTTTTTTTTTTTAACTCAAACTACCCTTCACAAGTTTTCAATTTAAGC-C---A
* ***
12295463 TTTTTCTCTTTTTTTGTTTTTTATTTTTTTGAACTAAAATTGCCTTTTACAAGTTTTCAATTTGA
62 TTTTT-TCTTTTTTT-TTTTTAATTTTTTTGAACTAAAACCACCTTTTACAAGTTTTCAATTTGA
12295528 GCCCTTTTTCTTTTTTCT
125 GCCCTTTTTCTTTTTTCT
* *
12295546 CTTTTTTTGTT-TTTATTTTTTTTTGAACTCAAA-TCGCCCTTTACAAGTTTTCAATTTAAGCCA
1 CTTTTTTT-TTATTT-TTTTTTTTT-AACTCAAACT-ACCCTTCACAAGTTTTCAATTTAAGCCA
* * ***
12295609 TTTTTTCTTTTTTTTTTTTAATTTTTTTTAACTCAAACCACCTTTTATGGGTTTTCAATTTGAGC
62 TTTTTTCTTTTTTTTTTTTAATTTTTTTGAACTAAAACCACCTTTTACAAGTTTTCAATTTGAGC
12295674 TTTTTTTTGT
Statistics
Matches: 110, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
144 42 0.38
145 9 0.08
146 5 0.05
148 11 0.10
149 13 0.12
150 30 0.27
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.58
Consensus pattern (142 bp):
CTTTTTTTTTATTTTTTTTTTTTAACTCAAACTACCCTTCACAAGTTTTCAATTTAAGCCATTTT
TTCTTTTTTTTTTTTAATTTTTTTGAACTAAAACCACCTTTTACAAGTTTTCAATTTGAGCCCTT
TTTCTTTTTTCT
Found at i:12295680 original size:67 final size:69
Alignment explanation
Indices: 12295537--12295681 Score: 177
Period size: 67 Copynumber: 2.1 Consensus size: 69
12295527 AGCCCTTTTT
* * * *
12295537 CTTTTTTCTCTTTTTTTGTTTTTATTTTTTTTTGAACTCAAATCGCCCTTTACAAGTTTTCAATT
1 CTTTTTTTTCTTTTTTTGTTTTTAATTTTTTTTGAACTCAAACCACCCTTTACAAGTTTTCAATT
12295602 TAAG
66 TAAG
** * ***
12295606 CCATTTTTTCTTTTTTT-TTTTTAATTTTTTTT-AACTCAAACCACCTTTTATGGGTTTTCAATT
1 CTTTTTTTTCTTTTTTTGTTTTTAATTTTTTTTGAACTCAAACCACCCTTTACAAGTTTTCAATT
*
12295669 TGAG
66 TAAG
12295673 CTTTTTTTT
1 CTTTTTTTT
12295682 GTTGAGAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
67 35 0.56
68 14 0.22
69 14 0.22
ACGTcount: A:0.18, C:0.15, G:0.07, T:0.60
Consensus pattern (69 bp):
CTTTTTTTTCTTTTTTTGTTTTTAATTTTTTTTGAACTCAAACCACCCTTTACAAGTTTTCAATT
TAAG
Found at i:12301534 original size:89 final size:89
Alignment explanation
Indices: 12301383--12301553 Score: 315
Period size: 89 Copynumber: 1.9 Consensus size: 89
12301373 CCATAATGAT
* * *
12301383 AATCACAATGAGCATTTGGGTTATACCATTTAGGGAAAGGTTGTTTCACAGGATCTACAGGGACA
1 AATCACAATGAGCATTTGGGTCATACCATTTAGAGAAAGGTGGTTTCACAGGATCTACAGGGACA
12301448 CAAGCTACTAAATTTTTCTCCACG
66 CAAGCTACTAAATTTTTCTCCACG
12301472 AATCACAATGAGCATTTGGGTCATACCATTTAGAGAAAGGTGGTTTCACAGGATCTACAGGGACA
1 AATCACAATGAGCATTTGGGTCATACCATTTAGAGAAAGGTGGTTTCACAGGATCTACAGGGACA
12301537 CAAGCTACTAAATTTTT
66 CAAGCTACTAAATTTTT
12301554 TTTCATGAGC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (89 bp):
AATCACAATGAGCATTTGGGTCATACCATTTAGAGAAAGGTGGTTTCACAGGATCTACAGGGACA
CAAGCTACTAAATTTTTCTCCACG
Found at i:12303062 original size:15 final size:15
Alignment explanation
Indices: 12303042--12303072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12303032 TGTTAAATAT
*
12303042 AATGAATGAGAATGC
1 AATGAATGAAAATGC
12303057 AATGAATGAAAATGC
1 AATGAATGAAAATGC
12303072 A
1 A
12303073 TGGATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (15 bp):
AATGAATGAAAATGC
Found at i:12306410 original size:69 final size:67
Alignment explanation
Indices: 12306168--12306768 Score: 678
Period size: 69 Copynumber: 8.8 Consensus size: 67
12306158 CATTTTAGGG
* * *
12306168 TTTTAATTTTCAAGAAAAATTGATACTTTTC-ACTTTTCCTTAAAAATCTTTTTTTGAAATCTTT
1 TTTT-ATTTTCAAGAAAAATTGATAC-TTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAATTTTT
**
12306232 AT-TT
63 ATAAA
* * *
12306236 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTTCCAAAATCTT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTT--GAAATTTT
**
12306301 TAT-TT
62 TATAAA
* * *
12306306 TTTTATTTTCATGAAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTGTTTTTGAAATTTTT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA--T-TTTTTGAAATTTTT
*
12306371 AT-AT
63 ATAAA
* * *
12306375 TTTTATTTTTAA-AGAAAATTGATACTTTTAACTTTTGCTCAAAAATATTTTTTGAAATTTTTAT
1 TTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTAT
12306439 CAAAA
65 --AAA
* * *
12306444 TTTTAGTTTCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATC
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTAT-
12306509 AAAA
65 -AAA
* * *
12306513 TTTTATTTTCAAGAAAAATTGATACTTTCAAGTTTTCCT-AAAAACTGTTTTTTG--ATTTTTTT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTGAAATTTTTAT
***
12306575 TTC
65 AAA
* *
12306578 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATGTTTTGAAATTTTTATC
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTAT-
12306643 AAAA
65 -AAA
12306647 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATC
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTAT-
12306712 AAAA
65 -AAA
* * * *
12306716 TTTTATTTTAAAGAAAAATTGATACTTTTAATTTTTTCTCAAAAATATTTTTT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
12306769 ATTTTAAGAG
Statistics
Matches: 471, Mismatches: 45, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
65 44 0.09
66 25 0.05
67 50 0.11
68 16 0.03
69 274 0.58
70 57 0.12
71 5 0.01
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.50
Consensus pattern (67 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATA
AA
Found at i:12306613 original size:203 final size:202
Alignment explanation
Indices: 12306168--12306773 Score: 755
Period size: 203 Copynumber: 3.0 Consensus size: 202
12306158 CATTTTAGGG
* * * *
12306168 TTTTAATTTTCAAGAAAAATTGATACTTTTC-ACTTTTCCTTAAAAATCTTTTTTTGAAATCTTT
1 TTTTTATTTTCAAGAAAAATTGATAC-TTTCAACTTTTCCTCAAAAAT-ATTTTTTGAAATTTTT
** * *
12306232 AT---TTTTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTTCCA
64 ATCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTT--G
* ** * *
12306294 AAATCTTTAT---TTTTTTATTTTCATGAAAAATTAATACTTTCAACTTTTTCTCAAAAATATTT
125 AAATTTTTATCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA--T
12306356 GTTTTTGAAATTTTTATA
188 -TTTTTG--ATTTTTATA
* * *
12306374 TTTTTATTTTTAA-AGAAAATTGATACTTTTAACTTTTGCTCAAAAATATTTTTTGAAATTTTTA
1 TTTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTA
* * *
12306438 TCAAAATTTTAGTTTCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTGAAATT
65 TCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATT
* * *
12306503 TTTATCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAAGTTTTCCT-AAAAACTGTTTTTTG
130 TTTATCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAA-TATTTTTTG
* *
12306567 ATTTTTTTT
194 ATTTTTATA
* *
12306576 TCTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATGTTTTGAAATTTTTA
1 T-TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTA
12306641 TCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATT
65 TCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATT
* * *
12306706 TTTATCAAAATTTTATTTTAAAGAAAAATTGATACTTTTAATTTTTTCTCAAAAATATTTTTT-A
130 TTTATCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGA
12306770 TTTT
195 TTTT
12306774 AAGAGAATCA
Statistics
Matches: 352, Mismatches: 36, Indels: 28
0.85 0.09 0.07
Matches are distributed among these distances:
202 13 0.04
203 171 0.49
204 21 0.06
205 21 0.06
206 47 0.13
207 36 0.10
208 43 0.12
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.50
Consensus pattern (202 bp):
TTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTAT
CAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTT
TTATCAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAT
TTTTATA
Found at i:12306620 original size:272 final size:268
Alignment explanation
Indices: 12306175--12306768 Score: 811
Period size: 272 Copynumber: 2.2 Consensus size: 268
12306165 GGGTTTTAAT
* * * **
12306175 TTTCAAGAAAAATTGATACTTTTCACTTTTCCTTAAAAATCTTTTTTTGAAATCTTTATTTTTTT
1 TTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAAT-ATTTTTTGAAATCTTTATAATTTT
*
12306240 ATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTTCCAAAATCTTTATT
65 ATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT-AAAAATACTTTTTTT---AAATCTTTATT
*
12306305 TTTTTATTTTCATGAAAAATTAATACTTTCAACTTTTTCTCAAAAATATTTGTTTTTGAAATTTT
126 TTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTTCTCAAAAATA--TG-TTTTGAAATTTT
* * *
12306370 TAT-ATTTTTATTTTTAAAG-AAAATTGATACTTTTAACTTTTGCTCAAAAATATTTTTTGAAAT
188 TATAAATTTTA-TTTTAAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAT
12306433 TTTTATCAAAATTTTAG
252 TTTTATCAAAATTTTAG
* *
12306450 TTTCAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATCAAAATT
1 TTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTGAAATCTTTAT---AATT
* * * *
12306515 TTATTTTCAAGAAAAATTGATACTTTCAAGTTTTCCT-AAAA-ACTGTTTTTT-GATTTTTTTTT
63 TTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATACT-TTTTTTAAATCTTTATTT
*
12306577 CTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATGTTTTGAAATTTTTAT
127 -TTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTTCTCAAAAATATGTTTTGAAATTTTTAT
*
12306642 CAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTT
191 --AAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTT
*
12306707 TTATCAAAATTTTAT
254 TTATCAAAATTTTAG
* * *
12306722 TTTAAAGAAAAATTGATACTTTTAATTTTTTCTCAAAAATATTTTTT
1 TTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTT
12306769 ATTTTAAGAG
Statistics
Matches: 287, Mismatches: 23, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
269 15 0.05
270 2 0.01
271 15 0.05
272 152 0.53
274 19 0.07
275 47 0.16
277 37 0.13
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (268 bp):
TTTCAAGAAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTGAAATCTTTATAATTTTA
TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATACTTTTTTTAAATCTTTATTTTTTT
ATTTTCAAGAAAAATTAATACTTTCAACTTTTTCTCAAAAATATGTTTTGAAATTTTTATAAATT
TTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATCAA
AATTTTAG
Found at i:12308425 original size:51 final size:51
Alignment explanation
Indices: 12308321--12308425 Score: 158
Period size: 52 Copynumber: 2.1 Consensus size: 51
12308311 GAGAACCCTT
* **
12308321 AATTAAGAAGGAAAAAATAGTAGTAGAAATATTCACATACATGTACTCTCA
1 AATTAAGAAGGAAAAAATAGTAGTAGAAATATTCACATACACGTACTAGCA
*
12308372 AATTAAGAAGGAAAAAAATAGTAGTAGAAATATTCATATACACGTA-TAGCA
1 AATTAAGAAGG-AAAAAATAGTAGTAGAAATATTCACATACACGTACTAGCA
12308423 AAT
1 AAT
12308426 GTTTTCACAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 17 0.35
52 32 0.65
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (51 bp):
AATTAAGAAGGAAAAAATAGTAGTAGAAATATTCACATACACGTACTAGCA
Found at i:12318283 original size:28 final size:28
Alignment explanation
Indices: 12318247--12318488 Score: 88
Period size: 28 Copynumber: 8.2 Consensus size: 28
12318237 AAGTTTCAGA
12318247 GTTTGGGATTTAGGGTTTTGATTTTAAG
1 GTTTGGGATTTAGGGTTTTGATTTTAAG
** * * * *
12318275 GTTTGGGATTTGAATGTTTAAGGTCTCAAG
1 GTTTGGGATTT-AGGGTTT-TGATTTTAAG
*
12318305 TGTTTGGGGTTTTGATTTTAGGATTTTGATTTT-AG
1 -GTTT--GG----GA-TTTAGGGTTTTGATTTTAAG
*
12318340 GATTTGGGGTTT-GGGATTTTGATTTT-AG
1 G-TTTGGGATTTAGGG-TTTTGATTTTAAG
* *
12318368 AGTTT-CGATTGTAAGGTTTTGATTTTAAG
1 -GTTTGGGATT-TAGGGTTTTGATTTTAAG
* *
12318397 ATTTAGGG-TTTAGGATTTT-AGTTTT-AG
1 GTTT-GGGATTTAGGGTTTTGA-TTTTAAG
* * *
12318424 GTTTGAAAGATTTAGGGTTTTGACTTTAGG
1 GTTTG--GGATTTAGGGTTTTGATTTTAAG
* *
12318454 GTTTGAGG-TTT-GAGGTTTTGACTTTAGG
1 GTTTG-GGATTTAG-GGTTTTGATTTTAAG
12318482 GTTTGGG
1 GTTTGGG
12318489 GTTTCGATTT
Statistics
Matches: 161, Mismatches: 28, Indels: 51
0.67 0.12 0.21
Matches are distributed among these distances:
26 1 0.01
27 14 0.09
28 78 0.48
29 28 0.17
30 14 0.09
31 4 0.02
33 4 0.02
34 1 0.01
35 5 0.03
36 3 0.02
37 6 0.04
38 3 0.02
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (28 bp):
GTTTGGGATTTAGGGTTTTGATTTTAAG
Found at i:12318333 original size:14 final size:14
Alignment explanation
Indices: 12318314--12318424 Score: 84
Period size: 14 Copynumber: 7.9 Consensus size: 14
12318304 GTGTTTGGGG
12318314 TTTTGATTTTAGGA
1 TTTTGATTTTAGGA
12318328 TTTTGATTTTAGGA
1 TTTTGATTTTAGGA
* ** *
12318342 TTTGGGGTTTGGGA
1 TTTTGATTTTAGGA
12318356 TTTTGATTTTA-GA
1 TTTTGATTTTAGGA
* *
12318369 GTTTCGATTGTAAGG-
1 -TTTTGATT-TTAGGA
*
12318384 TTTTGATTTTAAGA
1 TTTTGATTTTAGGA
* **
12318398 TTTAGGGTTTAGGA
1 TTTTGATTTTAGGA
12318412 TTTT-AGTTTTAGG
1 TTTTGA-TTTTAGG
12318425 TTTGAAAGAT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
13 5 0.07
14 64 0.89
15 2 0.03
16 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.27, T:0.52
Consensus pattern (14 bp):
TTTTGATTTTAGGA
Found at i:12318399 original size:22 final size:22
Alignment explanation
Indices: 12318374--12318416 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12318364 TTAGAGTTTC
*
12318374 GATTGTAAGGTTT-TGATTTTAA
1 GATT-TAAGGTTTAGGATTTTAA
*
12318396 GATTTAGGGTTTAGGATTTTA
1 GATTTAAGGTTTAGGATTTTA
12318417 GTTTTAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
GATTTAAGGTTTAGGATTTTAA
Found at i:12318453 original size:14 final size:14
Alignment explanation
Indices: 12318434--12318485 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
12318424 GTTTGAAAGA
12318434 TTTAGGGTTTTGAC
1 TTTAGGGTTTTGAC
*
12318448 TTTAGGG-TTTGAGG
1 TTTAGGGTTTTGA-C
12318462 TTT-GAGGTTTTGAC
1 TTTAG-GGTTTTGAC
12318476 TTTAGGGTTT
1 TTTAGGGTTT
12318486 GGGGTTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 6 0.19
14 20 0.62
15 6 0.19
ACGTcount: A:0.13, C:0.04, G:0.33, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTTGAC
Found at i:12318491 original size:28 final size:28
Alignment explanation
Indices: 12318439--12318674 Score: 126
Period size: 28 Copynumber: 8.2 Consensus size: 28
12318429 AAAGATTTAG
12318439 GGTTTTGACTTTAGGGTTTGAGGTTTGA
1 GGTTTTGACTTTAGGGTTTGAGGTTTGA
*
12318467 GGTTTTGACTTTAGGGTTTGGGGTTTCGA
1 GGTTTTGACTTTAGGGTTTGAGGTTT-GA
12318496 --TTTTAAGA-TTTAGGGTTTAGGAGGATTT-A
1 GGTTTT--GACTTTAGGGTTT--GAGG-TTTGA
* *
12318525 GGATTTT-AGTTTTAGGGTTTTGAGGTTTTA
1 GG-TTTTGA-CTTTAGGG-TTTGAGGTTTGA
* * *
12318555 GGGTTT-AGTTTTAGGGTTTGAAGGTTTTAA
1 GGTTTTGA-CTTTAGGGTTTG-AGG-TTTGA
* * * * * *
12318585 GGTTTCGATTTTAGGGTCTAAAGTTTGG
1 GGTTTTGACTTTAGGGTTTGAGGTTTGA
* * * *
12318613 GGTTTCGATTTTAGGGTTTGAAAGTTTAA
1 GGTTTTGACTTTAGGGTTTG-AGGTTTGA
* * * *
12318642 GG-TTTAATTTTAGGGTTTGAGATATGA
1 GGTTTTGACTTTAGGGTTTGAGGTTTGA
12318669 GGTTTT
1 GGTTTT
12318675 AAGGTTTAGA
Statistics
Matches: 169, Mismatches: 21, Indels: 36
0.75 0.09 0.16
Matches are distributed among these distances:
27 10 0.06
28 78 0.46
29 35 0.21
30 28 0.17
31 11 0.07
32 7 0.04
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.47
Consensus pattern (28 bp):
GGTTTTGACTTTAGGGTTTGAGGTTTGA
Found at i:12318500 original size:21 final size:21
Alignment explanation
Indices: 12318460--12318500 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12318450 TAGGGTTTGA
*
12318460 GGTTTGAGGTTTTGACTTTAG
1 GGTTTGAGGTTTCGACTTTAG
* *
12318481 GGTTTGGGGTTTCGATTTTA
1 GGTTTGAGGTTTCGACTTTA
12318501 AGATTTAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.05, G:0.34, T:0.49
Consensus pattern (21 bp):
GGTTTGAGGTTTCGACTTTAG
Found at i:12318544 original size:8 final size:8
Alignment explanation
Indices: 12318521--12318589 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
12318511 TTTAGGAGGA
*
12318521 TTTAGGAT
1 TTTAGGGT
12318529 TTTA--GT
1 TTTAGGGT
12318535 TTTAGGGT
1 TTTAGGGT
12318543 TTT-GAGGT
1 TTTAG-GGT
12318551 TTTAGGG-
1 TTTAGGGT
12318558 TTTA--GT
1 TTTAGGGT
12318564 TTTAGGGT
1 TTTAGGGT
* *
12318572 TTGAAGGT
1 TTTAGGGT
*
12318580 TTTAAGGT
1 TTTAGGGT
12318588 TT
1 TT
12318590 CGATTTTAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 1 0.02
6 9 0.18
7 5 0.10
8 34 0.68
9 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.52
Consensus pattern (8 bp):
TTTAGGGT
Found at i:12318567 original size:29 final size:29
Alignment explanation
Indices: 12318504--12318601 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
12318494 GATTTTAAGA
* * *
12318504 TTTAGGGTTTAGGAGGATTTAGGATTTTAGT
1 TTTAGGGTTT-TGAGGTTTTAGG-GTTTAGT
12318535 TTTAGGGTTTTGAGGTTTTAGGGTTTAGT
1 TTTAGGGTTTTGAGGTTTTAGGGTTTAGT
* *
12318564 TTTAGGG-TTTGAAGGTTTTAAGGTTTCGAT
1 TTTAGGGTTTTG-AGGTTTTAGGGTTTAG-T
12318594 TTTAGGGT
1 TTTAGGGT
12318602 CTAAAGTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
28 4 0.07
29 27 0.46
30 18 0.31
31 10 0.17
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (29 bp):
TTTAGGGTTTTGAGGTTTTAGGGTTTAGT
Found at i:12318610 original size:29 final size:29
Alignment explanation
Indices: 12318563--12318661 Score: 130
Period size: 28 Copynumber: 3.4 Consensus size: 29
12318553 TAGGGTTTAG
*
12318563 TTTTAGGGTTTGAAGGTTTTAAGGTTTCGA
1 TTTTAGGGTTTGAAAG-TTTAAGGTTTCGA
* **
12318593 TTTTAGGGTCT-AAAGTTTGGGGTTTCGA
1 TTTTAGGGTTTGAAAGTTTAAGGTTTCGA
*
12318621 TTTTAGGGTTTGAAAGTTTAAGGTTT-AA
1 TTTTAGGGTTTGAAAGTTTAAGGTTTCGA
12318649 TTTTAGGGTTTGA
1 TTTTAGGGTTTGA
12318662 GATATGAGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 35 0.58
29 15 0.25
30 10 0.17
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.46
Consensus pattern (29 bp):
TTTTAGGGTTTGAAAGTTTAAGGTTTCGA
Found at i:12318994 original size:3 final size:3
Alignment explanation
Indices: 12318988--12319018 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
12318978 AATAATAATA
12318988 ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
12319019 TAACACTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:12319088 original size:15 final size:15
Alignment explanation
Indices: 12319068--12319118 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12319058 AAGTTTTGAA
12319068 ATCATTTTTATTATT
1 ATCATTTTTATTATT
* *
12319083 ATCATTGTTATTGTT
1 ATCATTTTTATTATT
* *
12319098 ATTATTATTAATTATT
1 ATCATT-TTTATTATT
12319114 ATCAT
1 ATCAT
12319119 AAAACAACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (15 bp):
ATCATTTTTATTATT
Found at i:12320888 original size:15 final size:16
Alignment explanation
Indices: 12320868--12320897 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12320858 AAATAAACAT
12320868 AAAATATAT-TTTTTA
1 AAAATATATATTTTTA
12320883 AAAATATATATTTTT
1 AAAATATATATTTTT
12320898 TATTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATATTTTTA
Found at i:12321836 original size:20 final size:20
Alignment explanation
Indices: 12321797--12321836 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12321787 TGATATACTC
* *
12321797 TGATCAATTTTAAAAAAAAA
1 TGATAAATTTAAAAAAAAAA
12321817 TGATAAATTTAAAAAAAAAA
1 TGATAAATTTAAAAAAAAAA
12321837 AAAAACCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TGATAAATTTAAAAAAAAAA
Found at i:12329907 original size:2 final size:2
Alignment explanation
Indices: 12329868--12329897 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12329858 GTGTATCATA
12329868 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12329898 CAGTTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12330119 original size:98 final size:99
Alignment explanation
Indices: 12329953--12330150 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 99
12329943 TCTTGACATA
* *
12329953 GAAAAATGAATCATCTCCTTGATGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCTA
1 GAAAAATGAATCATCTCATTGAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCTA
12330018 GGCCTAGAGGTAGTGGACAC-TGTGTATAATAAT
66 GGCCTAGAGGTAGTGGACACATGTGTATAATAAT
* *
12330051 GAAAAATGAATCATCTCATTGAAGATTTTGTGACGAAATTTGTGTCGCTTTTCACTTTTCAGCTA
1 GAAAAATGAATCATCTCATTGAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCTA
*
12330116 GGCCTAGAGGTAGTGGATACTATGTGTATAATAAT
66 GGCCTAGAGGTAGTGGACAC-ATGTGTATAATAAT
12330151 CATCTACACT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 80 0.86
100 13 0.14
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (99 bp):
GAAAAATGAATCATCTCATTGAAGATTTTGTGACGAAATTTGAGTCACTTTTCACTTTTCAGCTA
GGCCTAGAGGTAGTGGACACATGTGTATAATAAT
Found at i:12334098 original size:34 final size:34
Alignment explanation
Indices: 12334060--12334145 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
12334050 ATGAATTTTT
*
12334060 GAAAGTTTTTAAATATTTTCAAAAATTTATAT-CC
1 GAAAGTTTTTAAATATTTTCAAAAATCTAT-TGCC
* * *
12334094 GAAAGATTTTAAGA-GTTTTCAAAAATCTATTGTC
1 GAAAGTTTTTAA-ATATTTTCAAAAATCTATTGCC
*
12334128 GAAAGTTTTTTAATATTT
1 GAAAGTTTTTAAATATTT
12334146 CTGAAAATAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
33 2 0.05
34 39 0.93
35 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (34 bp):
GAAAGTTTTTAAATATTTTCAAAAATCTATTGCC
Found at i:12348921 original size:16 final size:15
Alignment explanation
Indices: 12348900--12348932 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
12348890 ATTCTCAAAA
12348900 TTTTTATTTTTTCTAT
1 TTTTTATTTTTT-TAT
12348916 TTTTTATTTTTTTAT
1 TTTTTATTTTTTTAT
12348931 TT
1 TT
12348933 GTTTTCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTATTTTTTTAT
Found at i:12348937 original size:9 final size:8
Alignment explanation
Indices: 12348900--12348937 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
12348890 ATTCTCAAAA
12348900 TTTTTATT
1 TTTTTATT
12348908 TTTTCTA-T
1 TTTT-TATT
12348916 TTTTTATT
1 TTTTTATT
12348924 TTTTTATT
1 TTTTTATT
12348932 TGTTTT
1 T-TTTT
12348938 CTAAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 2 0.07
8 19 0.70
9 6 0.22
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.84
Consensus pattern (8 bp):
TTTTTATT
Found at i:12350161 original size:42 final size:41
Alignment explanation
Indices: 12350007--12350163 Score: 170
Period size: 41 Copynumber: 3.8 Consensus size: 41
12349997 GAAGCTCAAC
*
12350007 AACTTTGAAAAATAAAATGCTCCTTTAAACAGAGGCACCAT
1 AACTTTGAAAAATAAAATGCTCCTCTAAACAGAGGCACCAT
* * * * * *
12350048 AACTTTAAAAAATAAATTGCTCATTTAAACAGAGGCACTAC
1 AACTTTGAAAAATAAAATGCTCCTCTAAACAGAGGCACCAT
* * * * *
12350089 AAGTTTGAAAAATAAATTACTCCTCCAAACAAAGGCACCAT
1 AACTTTGAAAAATAAAATGCTCCTCTAAACAGAGGCACCAT
** *
12350130 AACTTTGAGGCAACAAAATGCTCCTCTAAACAGA
1 AACTTTGA-AAAATAAAATGCTCCTCTAAACAGA
12350164 TGTGTCATAA
Statistics
Matches: 93, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 75 0.81
42 18 0.19
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (41 bp):
AACTTTGAAAAATAAAATGCTCCTCTAAACAGAGGCACCAT
Found at i:12350340 original size:23 final size:22
Alignment explanation
Indices: 12350309--12350359 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
12350299 TTCAGTTTCA
*
12350309 CAAGAATTCAAATTTGCAAGATTT
1 CAAG-ATTCAAATTTGCAA-ATTG
*
12350333 CAAGATTCACATTTGCAAATTG
1 CAAGATTCAAATTTGCAAATTG
12350355 CAAGA
1 CAAGA
12350360 CTCGCATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 13 0.52
24 4 0.16
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (22 bp):
CAAGATTCAAATTTGCAAATTG
Found at i:12351910 original size:17 final size:16
Alignment explanation
Indices: 12351885--12351959 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
12351875 TTTTCCATCA
*
12351885 TTTCA-TTTTTTTCTT
1 TTTCATTTTTTTTTTT
12351900 TTTCATTTTTTTTCTTT
1 TTTCATTTTTTTT-TTT
* * *
12351917 CTT-GTTTTCTTTTTT
1 TTTCATTTTTTTTTTT
12351932 TTTCATTTTTTTATTTT
1 TTTCATTTTTTT-TTTT
12351949 TTTCATCTTTT
1 TTTCAT-TTTT
12351960 CTCATCTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.21
16 20 0.42
17 14 0.29
18 4 0.08
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.80
Consensus pattern (16 bp):
TTTCATTTTTTTTTTT
Found at i:12351913 original size:10 final size:10
Alignment explanation
Indices: 12351898--12351964 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
12351888 CATTTTTTTC
12351898 TTTTTCATTT
1 TTTTTCATTT
*
12351908 TTTTTCTTTCT
1 TTTTTCATT-T
*
12351919 TGTTTTCTTTT
1 T-TTTTCATTT
12351930 TTTTTCA-TT
1 TTTTTCATTT
12351939 TTTTT-A-TT
1 TTTTTCATTT
*
12351947 TTTTTCATCT
1 TTTTTCATTT
*
12351957 TTTCTCAT
1 TTTTTCAT
12351965 CTATTAGTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.16
9 8 0.16
10 21 0.43
11 4 0.08
12 8 0.16
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.78
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:12352339 original size:24 final size:24
Alignment explanation
Indices: 12352305--12352352 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12352295 TTATTTGTAG
* *
12352305 CATTTTTCTTTTCTCTCTTTCTTT
1 CATTTTACTTTTCTCTCTCTCTTT
*
12352329 CATTTTACTTTTCTTTCTCTCTTT
1 CATTTTACTTTTCTCTCTCTCTTT
12352353 AAAACCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (24 bp):
CATTTTACTTTTCTCTCTCTCTTT
Found at i:12356563 original size:22 final size:22
Alignment explanation
Indices: 12356537--12356580 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12356527 TGTTCCCAAA
12356537 ATTTTTATTTTT-TCTATTTTTT
1 ATTTTT-TTTTTCTCTATTTTTT
*
12356559 ATTTTTTTTTTCTCTTTTTTTT
1 ATTTTTTTTTTCTCTATTTTTT
12356581 GAATTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (22 bp):
ATTTTTTTTTTCTCTATTTTTT
Found at i:12356569 original size:20 final size:21
Alignment explanation
Indices: 12356539--12356578 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12356529 TTCCCAAAAT
12356539 TTTTATTTTTTCTATTTTTTA
1 TTTTATTTTTTCTATTTTTTA
*
12356560 TTTT-TTTTTTCTCTTTTTT
1 TTTTATTTTTTCTATTTTTT
12356579 TTGAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTATTTTTTCTATTTTTTA
Found at i:12356927 original size:2 final size:2
Alignment explanation
Indices: 12356922--12356948 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12356912 CCTTTTTTTT
12356922 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
12356949 TTTAACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12357106 original size:21 final size:21
Alignment explanation
Indices: 12357082--12357127 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12357072 AACTTCTCAG
12357082 AAAAAAATTGCC-AAAAATTTC
1 AAAAAAATT-CCTAAAAATTTC
*
12357103 AAAAAAATTCCTAAAAATTTT
1 AAAAAAATTCCTAAAAATTTC
12357124 AAAA
1 AAAA
12357128 TTGCTTATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAAATTCCTAAAAATTTC
Found at i:12358146 original size:17 final size:17
Alignment explanation
Indices: 12358097--12358146 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
12358087 TGAAAATTTT
12358097 CAATTTTTTTTTATGTT-
1 CAATTTTTTTTT-TGTTA
** *
12358114 C-ATTTTGGTTTGGTTA
1 CAATTTTTTTTTTGTTA
12358130 CAATTTTTTTTTTGTTA
1 CAATTTTTTTTTTGTTA
12358147 ACACCGCTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 3 0.12
16 9 0.36
17 13 0.52
ACGTcount: A:0.16, C:0.06, G:0.12, T:0.66
Consensus pattern (17 bp):
CAATTTTTTTTTTGTTA
Found at i:12360413 original size:16 final size:16
Alignment explanation
Indices: 12360392--12360423 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12360382 CTCTTCATAA
12360392 ATATTCTCCCCATATC
1 ATATTCTCCCCATATC
12360408 ATATTCTCCCCATATC
1 ATATTCTCCCCATATC
12360424 CTCCTTCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATTCTCCCCATATC
Found at i:12361646 original size:28 final size:29
Alignment explanation
Indices: 12361608--12361668 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
12361598 TAAATTAAAG
*
12361608 TAAAATATTTTATATG-G-TACTTAAATTT
1 TAAAATATTTTA-ATGTGATACTTAAATTA
*
12361636 TAAAATTTTTTAATGTGATACTTAAATTA
1 TAAAATATTTTAATGTGATACTTAAATTA
12361665 TAAA
1 TAAA
12361669 TTTGTTAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 3 0.10
28 12 0.41
29 14 0.48
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (29 bp):
TAAAATATTTTAATGTGATACTTAAATTA
Found at i:12361668 original size:29 final size:27
Alignment explanation
Indices: 12361608--12361676 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
12361598 TAAATTAAAG
* *
12361608 TAAAATATTTTATATGGTACTTAAATTT
1 TAAAATTTTTTA-ATGGTACTTAAATTA
12361636 TAAAATTTTTTAATGTGATACTTAAATTA
1 TAAAATTTTTTAATG-G-TACTTAAATTA
*
12361665 T-AAATTTGTTAA
1 TAAAATTTTTTAA
12361677 CTAATTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 22 0.61
29 11 0.31
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (27 bp):
TAAAATTTTTTAATGGTACTTAAATTA
Found at i:12362106 original size:2 final size:2
Alignment explanation
Indices: 12362099--12362141 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
12362089 AGTTTTATTA
*
12362099 AT AT AT AT AT AT AT AT AT AT AT CT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12362140 AT
1 AT
12362142 TTTTATCCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12365039 original size:1 final size:1
Alignment explanation
Indices: 12365033--12365057 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12365023 AATCCCTCTC
12365033 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12365058 GAGGAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12368516 original size:7 final size:7
Alignment explanation
Indices: 12368506--12368536 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12368496 AAAGAAAAGA
*
12368506 AAGACGC
1 AAGAAGC
12368513 AAGAAGC
1 AAGAAGC
12368520 AAGAAGC
1 AAGAAGC
12368527 AAGAAGC
1 AAGAAGC
12368534 AAG
1 AAG
12368537 CAGTAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.55, C:0.16, G:0.29, T:0.00
Consensus pattern (7 bp):
AAGAAGC
Found at i:12372039 original size:8 final size:8
Alignment explanation
Indices: 12372013--12372062 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
12372003 TTTTAAATTA
*
12372013 ATATTTTT
1 ATATTTAT
12372021 AT-TTATAT
1 ATATT-TAT
12372029 ATATTTAT
1 ATATTTAT
*
12372037 ATAATTAT
1 ATATTTAT
*
12372045 ATATTTAA
1 ATATTTAT
12372053 ATATTTAT
1 ATATTTAT
12372061 AT
1 AT
12372063 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 2 0.06
8 31 0.89
9 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATTTAT
Found at i:12372061 original size:14 final size:16
Alignment explanation
Indices: 12372026--12372067 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
12372016 TTTTTATTTA
*
12372026 TATATATTTATATAAT
1 TATATATTTAAATAAT
12372042 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
12372057 T-TATATTTAAA
1 TATATATTTAAA
12372068 AAAATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:12372081 original size:22 final size:22
Alignment explanation
Indices: 12372050--12372104 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
12372040 ATTATATATT
12372050 TAAATA-TTTATATTTAAAAAA
1 TAAATATTTTATATTTAAAAAA
12372071 -ATAATATTTTATATTTAAAAAA
1 TA-AATATTTTATATTTAAAAAA
12372093 TAAATATTTTAT
1 TAAATATTTTAT
12372105 TAATTTCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 4 0.13
22 25 0.81
23 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATATTTTATATTTAAAAAA
Found at i:12373310 original size:54 final size:54
Alignment explanation
Indices: 12373228--12373340 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
12373218 GGTTGCTTGC
12373228 TTATAGTATTTGTCAGCTGTTGCTTCTCTTAAAATCGACCCATCAAATACATGA
1 TTATAGTATTTGTCAGCTGTTGCTTCTCTTAAAATCGACCCATCAAATACATGA
* *
12373282 TTATAGTATTTGTCAGCTGTTGCTTCTCTTAAAATTGATCCATCAAATACATGA
1 TTATAGTATTTGTCAGCTGTTGCTTCTCTTAAAATCGACCCATCAAATACATGA
12373336 TTATA
1 TTATA
12373341 ACTATCTGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (54 bp):
TTATAGTATTTGTCAGCTGTTGCTTCTCTTAAAATCGACCCATCAAATACATGA
Found at i:12380007 original size:12 final size:11
Alignment explanation
Indices: 12379976--12380006 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12379966 ACCGAAAAAT
12379976 AAAAATTTTCC
1 AAAAATTTTCC
12379987 AAAAATTTTCC
1 AAAAATTTTCC
12379998 AAAAATTTT
1 AAAAATTTT
12380007 TTTCAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATTTTCC
Found at i:12380299 original size:12 final size:12
Alignment explanation
Indices: 12380282--12380309 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12380272 TTTATCAATT
12380282 TTATTTTTTTTA
1 TTATTTTTTTTA
12380294 TTATTTTTTTTA
1 TTATTTTTTTTA
12380306 TTAT
1 TTAT
12380310 CACTATTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTTTA
Found at i:12380366 original size:12 final size:12
Alignment explanation
Indices: 12380339--12380372 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12380329 AAACCTAAAG
12380339 ATAAATCAAAACA
1 ATAAAT-AAAACA
*
12380352 ATAAATAAAATA
1 ATAAATAAAACA
12380364 ATAAATAAA
1 ATAAATAAA
12380373 TAAAACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAAATAAAACA
Found at i:12380398 original size:24 final size:24
Alignment explanation
Indices: 12380339--12380415 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 24
12380329 AAACCTAAAG
*
12380339 ATAAATCAAAACAATAAATAAAATAATAA
1 ATAAAT-AAAAC--TAAACAAAA-AAT-A
12380368 ATAAATAAAACTAAACAAAAAATA
1 ATAAATAAAACTAAACAAAAAATA
12380392 ATAAATAATGAA--AAACAAAAAATA
1 ATAAATAA--AACTAAACAAAAAATA
12380416 TACTTAGACC
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
24 21 0.47
25 3 0.07
26 10 0.22
28 5 0.11
29 6 0.13
ACGTcount: A:0.74, C:0.06, G:0.01, T:0.18
Consensus pattern (24 bp):
ATAAATAAAACTAAACAAAAAATA
Found at i:12384687 original size:2 final size:2
Alignment explanation
Indices: 12384680--12384711 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12384670 TAATGTTAAC
*
12384680 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12384712 GCTGTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12393988 original size:24 final size:25
Alignment explanation
Indices: 12393961--12394007 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
12393951 AATAATTTTT
*
12393961 AATAAATGTATT-AAATCTAATATC
1 AATAAATGTATTCAAATCAAATATC
* *
12393985 AATAGATTTATTCAAATCAAATA
1 AATAAATGTATTCAAATCAAATA
12394008 AAAAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (25 bp):
AATAAATGTATTCAAATCAAATATC
Found at i:12401341 original size:82 final size:82
Alignment explanation
Indices: 12401247--12401398 Score: 243
Period size: 82 Copynumber: 1.9 Consensus size: 82
12401237 ATTTTGCAAT
** * * *
12401247 CAGATTAATTAGATAACATGTCACATAAGATTTCACTTT-AATTATAAAATTAAAAAATTTCAAT
1 CAGATTAATTAGATAACATAACACATAAAATTTCA-TTTCAATTATAAAAATAAAAAATTCCAAT
12401311 ATAAAAAATAACTATGAC
65 ATAAAAAATAACTATGAC
12401329 CAGATTAATTAGATAACATAACACATAAAATTTCATTTCAATTATAAAAATAAAAAATTCCAATA
1 CAGATTAATTAGATAACATAACACATAAAATTTCATTTCAATTATAAAAATAAAAAATTCCAATA
12401394 TAAAA
66 TAAAA
12401399 GGGAACTCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 3 0.05
82 61 0.95
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (82 bp):
CAGATTAATTAGATAACATAACACATAAAATTTCATTTCAATTATAAAAATAAAAAATTCCAATA
TAAAAAATAACTATGAC
Found at i:12415837 original size:19 final size:19
Alignment explanation
Indices: 12415796--12415837 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12415786 AAAGTTACTC
*
12415796 AAAAAATACTTTTAAGATG
1 AAAAAATACTTTTAAGATA
*
12415815 AAAAAATATTTTTATA-ATA
1 AAAAAATACTTTTA-AGATA
12415834 AAAA
1 AAAA
12415838 TATCACTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAAAATACTTTTAAGATA
Found at i:12416111 original size:2 final size:2
Alignment explanation
Indices: 12416104--12416137 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12416094 CTCTTTTGTA
12416104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12416138 TAATGTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12417823 original size:16 final size:16
Alignment explanation
Indices: 12417798--12417829 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12417788 CGATAAACGA
12417798 ATGATAATGATGATTT
1 ATGATAATGATGATTT
*
12417814 ATGATGATGATGATTT
1 ATGATAATGATGATTT
12417830 TCAATGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:12418310 original size:16 final size:17
Alignment explanation
Indices: 12418279--12418311 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12418269 AAATATATAG
*
12418279 ATTTTATTTGATAAATT
1 ATTTTATTTGAAAAATT
12418296 ATTTTA-TTGAAAAATT
1 ATTTTATTTGAAAAATT
12418312 TTAGAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTATTTGAAAAATT
Found at i:12418997 original size:5 final size:5
Alignment explanation
Indices: 12418987--12419011 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12418977 TAAAACATAA
12418987 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
12419012 GATTCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:12426978 original size:17 final size:16
Alignment explanation
Indices: 12426932--12426979 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
12426922 CAAAAATATT
*
12426932 AAAAACAAAAAAATGA
1 AAAAAGAAAAAAATGA
12426948 AAAAAGAATAAAAATAGA
1 AAAAAGAA-AAAAAT-GA
12426966 AAAATA-AAAAAAAT
1 AAAA-AGAAAAAAAT
12426980 TAAGGCCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 8 0.29
19 1 0.04
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAAGAAAAAAATGA
Found at i:12427224 original size:21 final size:22
Alignment explanation
Indices: 12427168--12427226 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
12427158 ATTAAGCTGA
*
12427168 AATATA-ATTTTATTAATATAAT
1 AATATATATTTT-TAAATATAAT
**
12427190 -ATATATATAATTAAATA-AAT
1 AATATATATTTTTAAATATAAT
12427210 AATATATATTTTTAAAT
1 AATATATATTTTTAAAT
12427227 GGTCTAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATATATTTTTAAATATAAT
Found at i:12427397 original size:16 final size:16
Alignment explanation
Indices: 12427373--12427426 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
12427363 ATATTATTTT
*
12427373 GATATATTTATTAATG
1 GATAAATTTATTAATG
12427389 GATAAATTT-TGT--TG
1 GATAAATTTAT-TAATG
*
12427403 TA-AAATTTATTAATG
1 GATAAATTTATTAATG
12427418 GATAAATTT
1 GATAAATTT
12427427 TGTTATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 7 0.23
14 4 0.13
15 4 0.13
16 15 0.50
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (16 bp):
GATAAATTTATTAATG
Found at i:12427412 original size:29 final size:29
Alignment explanation
Indices: 12427378--12427442 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
12427368 ATTTTGATAT
*
12427378 ATTTATTAATGGATAAATTTTGTTGTAAA
1 ATTTATTAATGGATAAATTTTGTTATAAA
12427407 ATTTATTAATGGATAAATTTTGTTATAAA
1 ATTTATTAATGGATAAATTTTGTTATAAA
12427436 ATTTATT
1 ATTTATT
12427443 TAATTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (29 bp):
ATTTATTAATGGATAAATTTTGTTATAAA
Found at i:12428303 original size:15 final size:15
Alignment explanation
Indices: 12428283--12428369 Score: 61
Period size: 15 Copynumber: 5.7 Consensus size: 15
12428273 AATATTTCTA
12428283 GGTTTAAAGTTTTTG
1 GGTTTAAAGTTTTTG
*
12428298 GGTTTAAAATTTTTG
1 GGTTTAAAGTTTTTG
* * *
12428313 GATTTCAAA-TTTCTA
1 GGTTT-AAAGTTTTTG
*
12428328 GATTTAAAGATTTTTG
1 GGTTTAAAG-TTTTTG
*
12428344 GG-TTAGAAGTTTCTG
1 GGTTTA-AAGTTTTTG
* *
12428359 AGTTCAAAGTT
1 GGTTTAAAGTT
12428370 CTAGGATTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.05
15 41 0.72
16 13 0.23
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.47
Consensus pattern (15 bp):
GGTTTAAAGTTTTTG
Found at i:12428365 original size:45 final size:45
Alignment explanation
Indices: 12428276--12428373 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
12428266 GGTATGAAAT
* * *
12428276 ATTTCTAGGTTTAAAGTTTTTGGGTTTAAAATTTTTGGATTTCAA
1 ATTTCTAGATTTAAAGTTTTTGGGTTTAAAATTTCTGGAGTTCAA
*
12428321 ATTTCTAGATTTAAAGATTTTTGGG-TTAGAAGTTTCT-GAGTTCAA
1 ATTTCTAGATTTAAAG-TTTTTGGGTTTA-AAATTTCTGGAGTTCAA
*
12428366 AGTTCTAG
1 ATTTCTAG
12428374 GATTGAGAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 32 0.70
46 14 0.30
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (45 bp):
ATTTCTAGATTTAAAGTTTTTGGGTTTAAAATTTCTGGAGTTCAA
Found at i:12428796 original size:13 final size:12
Alignment explanation
Indices: 12428772--12428810 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12428762 TGATCATAGG
12428772 TTTTTTTCTTTT
1 TTTTTTTCTTTT
*
12428784 TCTTTTTCTTTT
1 TTTTTTTCTTTT
*
12428796 TTTATTTTATTTT
1 TTT-TTTTCTTTT
12428809 TT
1 TT
12428811 AATTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:12430065 original size:26 final size:26
Alignment explanation
Indices: 12430010--12430066 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
12430000 AAATAAAAAT
* *
12430010 AAAAATAAAAGAAGAAAAAACATAAT
1 AAAAATAAAAAAAGAAAAAACATAAG
*
12430036 AAAAATAAAAAAATGAAAAAGCA-AAG
1 AAAAATAAAAAAA-GAAAAAACATAAG
12430062 AAAAA
1 AAAAA
12430067 AAAGTTGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (26 bp):
AAAAATAAAAAAAGAAAAAACATAAG
Found at i:12430224 original size:19 final size:19
Alignment explanation
Indices: 12430200--12430237 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12430190 CTCCACATTA
12430200 AAAAAATAAAAAATATTTT
1 AAAAAATAAAAAATATTTT
* *
12430219 AAAAAATTACAAATATTTT
1 AAAAAATAAAAAATATTTT
12430238 CATGTCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATAAAAAATATTTT
Found at i:12431237 original size:2 final size:2
Alignment explanation
Indices: 12431225--12431267 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
12431215 ATTTTTACAA
* *
12431225 AT AT TT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12431267 A
1 A
12431268 AACACATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12437123 original size:16 final size:16
Alignment explanation
Indices: 12437102--12437134 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12437092 ATCACCCACC
12437102 AGCAATGTCTTATTGT
1 AGCAATGTCTTATTGT
12437118 AGCAATGTCTTATTGT
1 AGCAATGTCTTATTGT
12437134 A
1 A
12437135 CTTATTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (16 bp):
AGCAATGTCTTATTGT
Found at i:12451173 original size:23 final size:24
Alignment explanation
Indices: 12451147--12451198 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
12451137 TTTTTTGTTT
12451147 TTTTTAGAATATCTCAAAA-T-TTA
1 TTTTTAGAATATCT-AAAATTCTTA
**
12451170 TTTTTTTAATATCTAAAATTCTTA
1 TTTTTAGAATATCTAAAATTCTTA
12451194 TTTTT
1 TTTTT
12451199 TTATATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 13 0.52
24 8 0.32
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTTAGAATATCTAAAATTCTTA
Done.