Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 21 of 29
Found at i:3205825 original size:39 final size:39
Alignment explanation
Indices: 3205701--3205825 Score: 101
Period size: 39 Copynumber: 3.2 Consensus size: 39
3205691 TGTTTATAAC
3205701 TTTATATTTATATTAATTTGTAATAGGATAATTTTTCTT
1 TTTATATTTATATTAATTTGTAATAGGATAATTTTTCTT
* * * * ** * * * ***
3205740 TTTATA-TGA-CTTAGTATAAAATATTGATTTGATTTATAAC
1 TTTATATTTATATTAATTTGTAATA-GGA--TAATTTTTCTT
3205780 TTTATATTTATATTAATTTGTAATAGGATAATTTTTCTT
1 TTTATATTTATATTAATTTGTAATAGGATAATTTTTCTT
3205819 TTTATAT
1 TTTATAT
3205826 GACTTAGTAT
Statistics
Matches: 57, Mismatches: 24, Indels: 10
0.63 0.26 0.11
Matches are distributed among these distances:
37 9 0.16
38 4 0.07
39 19 0.33
40 12 0.21
41 4 0.07
42 9 0.16
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (39 bp):
TTTATATTTATATTAATTTGTAATAGGATAATTTTTCTT
Found at i:3206210 original size:18 final size:17
Alignment explanation
Indices: 3206178--3206211 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3206168 TTAAATTATT
*
3206178 TAATTTATTATTTATAG
1 TAATTTATTAATTATAG
3206195 TAATTATATTAATTATA
1 TAATT-TATTAATTATA
3206212 ATATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TAATTTATTAATTATAG
Found at i:3207283 original size:26 final size:25
Alignment explanation
Indices: 3207254--3207316 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
3207244 AATTATATTT
*
3207254 TATTATTATAATTATAAATTAATAAA
1 TATTATTATAATCA-AAATTAATAAA
* **
3207280 TATTTTTATAATCAATTTTAATAAA
1 TATTATTATAATCAAAATTAATAAA
3207305 TATTAATTATAA
1 TATT-ATTATAA
3207317 ATAATGATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTATTATAATCAAAATTAATAAA
Found at i:3207327 original size:26 final size:25
Alignment explanation
Indices: 3207273--3207328 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
3207263 AATTATAAAT
* **
3207273 TAATAAATATTTTTATAATCAATTT
1 TAATAAATATTATTATAATCAATGA
3207298 TAATAAATATTAATTATAAAT-AATGA
1 TAATAAATATT-ATTAT-AATCAATGA
3207324 TAATA
1 TAATA
3207329 TAAAATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.42
26 12 0.46
27 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATAAATATTATTATAATCAATGA
Found at i:3222228 original size:2 final size:2
Alignment explanation
Indices: 3222215--3222258 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
3222205 GCTTACGAAA
* *
3222215 AT AT AC AT AT AT AT AT AT AT AT AT AT AT TT 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
3222257 AT
1 AT
3222259 CTTCTATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3225130 original size:2 final size:2
Alignment explanation
Indices: 3225119--3225147 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3225109 CACAAGCTTA
3225119 AT AT -T 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
3225148 CCAAAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3228603 original size:2 final size:2
Alignment explanation
Indices: 3228591--3228623 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3228581 ACATCTGATC
3228591 AT AT A- 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
3228624 GAAGTTCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3231770 original size:13 final size:13
Alignment explanation
Indices: 3231752--3231788 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3231742 TAAATGCATT
3231752 CGCAGGTCATGAG
1 CGCAGGTCATGAG
*
3231765 CGCAGGTCGTGAG
1 CGCAGGTCATGAG
*
3231778 CACAGGTCATG
1 CGCAGGTCATG
3231789 TTAGTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (13 bp):
CGCAGGTCATGAG
Found at i:3233125 original size:6 final size:6
Alignment explanation
Indices: 3233114--3233140 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3233104 ATGGTGAAGA
3233114 GTTAGG GTTAGG GTTAGG GTTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTT
3233141 CTGACATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (6 bp):
GTTAGG
Found at i:3233712 original size:2 final size:2
Alignment explanation
Indices: 3233705--3233750 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
3233695 TATTTTGGGC
*
3233705 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3233747 -A TA T
1 TA TA T
3233751 TAGTTGACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3252190 original size:2 final size:2
Alignment explanation
Indices: 3252183--3252207 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3252173 CATACATTTA
3252183 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 T
3252208 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3252212 original size:2 final size:2
Alignment explanation
Indices: 3252207--3252238 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
3252197 TCTCTCTCTC
3252207 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
3252239 CTCCATCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3252550 original size:28 final size:29
Alignment explanation
Indices: 3252514--3252568 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
3252504 TTAATTAACA
3252514 AATTTTATT-TAAATTTAAA-AATAAAAAT
1 AATTTTATTAT-AATTTAAATAATAAAAAT
*
3252542 AATTTTATTATATTTTAAATAATAAAA
1 AATTTTATTATAATTTAAATAATAAAA
3252569 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTTTATTATAATTTAAATAATAAAAAT
Found at i:3252746 original size:17 final size:17
Alignment explanation
Indices: 3252703--3252751 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 17
3252693 CTTAAATACG
*
3252703 AATAT-TATTAAAATTT
1 AATATCTATTTAAATTT
*
3252719 GATA-C-ATTTAAATTT
1 AATATCTATTTAAATTT
3252734 AATATCTATTTAAATTT
1 AATATCTATTTAAATTT
3252751 A
1 A
3252752 TTAAACTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AATATCTATTTAAATTT
Found at i:3253513 original size:2 final size:2
Alignment explanation
Indices: 3253506--3253537 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3253496 AACCGCAAGC
3253506 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
3253538 GTTTACGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3254438 original size:21 final size:20
Alignment explanation
Indices: 3254414--3254465 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
3254404 ATAATCAAAG
* *
3254414 TATATTTTATTTATTAAATTA
1 TATATTTTACTTA-AAAATTA
*
3254435 TATATATATACTTAAAAATTA
1 TATAT-TTTACTTAAAAATTA
3254456 TATAATTTTA
1 TAT-ATTTTA
3254466 ATGTAATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATTTTACTTAAAAATTA
Found at i:3254676 original size:2 final size:2
Alignment explanation
Indices: 3254669--3254701 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3254659 CTATCTCATA
3254669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3254702 AAGTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3255092 original size:2 final size:2
Alignment explanation
Indices: 3255087--3255129 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3255077 CTTTTTTGTG
*
3255087 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3255127 TA T
1 TA T
3255130 TTTTTGAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3255442 original size:21 final size:23
Alignment explanation
Indices: 3255418--3255469 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
3255408 ATATCATCGA
3255418 ATATAATTA-CAATATAT-AAAT
1 ATATAATTATCAATATATCAAAT
*
3255439 ATAT-ATAATCAATATATCAAAT
1 ATATAATTATCAATATATCAAAT
3255461 ATA-AATTAT
1 ATATAATTAT
3255470 ATTAAAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 11 0.42
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAATTATCAATATATCAAAT
Found at i:3257401 original size:22 final size:21
Alignment explanation
Indices: 3257346--3257404 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
3257336 TAAATAACAA
* *
3257346 ATTAAAAAAAGTAAGTTAAAT
1 ATTAAAAAAAATAAATTAAAT
* *
3257367 CTTAATAATAAATAAATTAAAT
1 ATTAA-AAAAAATAAATTAAAT
3257389 ATTAAAACAAAATAAA
1 ATTAAAA-AAAATAAA
3257405 AGTGCACCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (21 bp):
ATTAAAAAAAATAAATTAAAT
Found at i:3258150 original size:18 final size:18
Alignment explanation
Indices: 3258127--3258161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3258117 AGAAAATAGG
* *
3258127 AAAATACAAAATTAAATA
1 AAAATAAAAAATCAAATA
3258145 AAAATAAAAAATCAAAT
1 AAAATAAAAAATCAAAT
3258162 TTTGAGGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAAAATCAAATA
Found at i:3258193 original size:3 final size:3
Alignment explanation
Indices: 3258181--3258231 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
3258171 ATGACAAAGT
3258181 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3258228 ATA A
1 ATA A
3258232 ATGATAATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3259724 original size:19 final size:18
Alignment explanation
Indices: 3259688--3259752 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
3259678 TATCAACATA
3259688 ATAAATAT-TAAAATTTTAT
1 ATAAATATAT-AAA-TTTAT
*
3259707 ATAAATATATAATATTTAA
1 ATAAATATATAA-ATTTAT
* **
3259726 AAAAATATATAAAAATAT
1 ATAAATATATAAATTTAT
3259744 ATAAATATA
1 ATAAATATA
3259753 ATATGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 11 0.29
19 25 0.66
20 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATATATAAATTTAT
Found at i:3259944 original size:3 final size:3
Alignment explanation
Indices: 3259936--3259973 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3259926 TCTTAACCCT
3259936 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3259974 TTCAGCCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3262120 original size:2 final size:2
Alignment explanation
Indices: 3262115--3262157 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3262105 TTCTTTTTGG
3262115 AT AT AT AT 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 AT AT AT AT
3262157 A
1 A
3262158 AGGGAGCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3262772 original size:14 final size:14
Alignment explanation
Indices: 3262749--3262785 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3262739 TTATTGTGTT
*
3262749 TATATATATATATA
1 TATATGTATATATA
3262763 TATATGTATATATA
1 TATATGTATATATA
*
3262777 TGTATGTAT
1 TATATGTAT
3262786 GTGTGTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:3262778 original size:10 final size:10
Alignment explanation
Indices: 3262749--3262781 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3262739 TTATTGTGTT
*
3262749 TATATATATA
1 TATATATATG
3262759 TATATATATG
1 TATATATATG
3262769 TATATATATG
1 TATATATATG
3262779 TAT
1 TAT
3262782 GTATGTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:3263151 original size:11 final size:11
Alignment explanation
Indices: 3263135--3263172 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
3263125 TTTAATATAA
3263135 AAATATAATAT
1 AAATATAATAT
3263146 AAATATAAT-T
1 AAATATAATAT
*
3263156 AAAAAT-ATAT
1 AAATATAATAT
3263166 AAATATA
1 AAATATA
3263173 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.09
10 12 0.52
11 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3263179 original size:18 final size:18
Alignment explanation
Indices: 3263142--3263226 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
3263132 TAAAAATATA
3263142 ATATAAATATAATTAAAAAT
1 ATATAAATAT-ATT-AAAAT
3263162 ATATAAATATATTAAAAT
1 ATATAAATATATTAAAAT
*
3263180 -T-T--ATATAATAAAAT
1 ATATAAATATATTAAAAT
* * *
3263194 TTATTAATATATTACAATTTT
1 ATATAAATATATTA-AA--AT
3263215 ATATAAATATAT
1 ATATAAATATAT
3263227 AATATTTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 11 0.21
15 1 0.02
16 2 0.04
17 1 0.02
18 12 0.23
19 5 0.09
20 10 0.19
21 11 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAATATATTAAAAT
Found at i:3263184 original size:20 final size:19
Alignment explanation
Indices: 3263142--3263226 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
3263132 TAAAAATATA
*
3263142 ATATAAATATAATTAAAAAT
1 ATATAAATAT-ATTAAAATT
3263162 ATATAAATATATTAAAATT
1 ATATAAATATATTAAAATT
3263181 -TAT--ATA-A-TAAAATT
1 ATATAAATATATTAAAATT
* *
3263195 -TATTAATATATTACAATTTT
1 ATATAAATATATTA-AA-ATT
3263215 ATATAAATATAT
1 ATATAAATATAT
3263227 AATATTTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 6 0.11
17 1 0.02
18 5 0.09
19 10 0.18
20 12 0.22
21 10 0.18
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAAATATATTAAAATT
Found at i:3263185 original size:14 final size:14
Alignment explanation
Indices: 3263168--3263202 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3263158 AAATATATAA
*
3263168 ATATATTAAAATTT
1 ATATAATAAAATTT
3263182 ATATAATAAAATTT
1 ATATAATAAAATTT
3263196 AT-TAATA
1 ATATAATA
3263203 TATTACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:3263203 original size:32 final size:32
Alignment explanation
Indices: 3263148--3263256 Score: 104
Period size: 32 Copynumber: 3.5 Consensus size: 32
3263138 TATAATATAA
*
3263148 ATATAATTAAAAATATATAAATATATTAAAATTT
1 ATATAA-T-AAAATATATTAATATATTAAAATTT
* *
3263182 ATATAATAAAATTTATTAATATATTACAATTT
1 ATATAATAAAATATATTAATATATTAAAATTT
*
3263214 -TAT-AT-AAATATA-TAATAT-TTTAAATTT
1 ATATAATAAAATATATTAATATATTAAAATTT
*
3263241 A-ATTATAAAAATATAT
1 ATATAAT-AAAATATAT
3263257 CAACATAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
27 9 0.14
28 8 0.12
29 6 0.09
30 9 0.14
31 3 0.05
32 22 0.34
33 1 0.02
34 6 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATAATAAAATATATTAATATATTAAAATTT
Found at i:3263230 original size:28 final size:27
Alignment explanation
Indices: 3263158--3263255 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 27
3263148 ATATAATTAA
3263158 AAATATATAAATATATTAAAATTTATATAAT
1 AAATATAT-AATATATT-AAATTT-TAT-AT
*
3263189 AAAATTTATTAATATATTACAATTTTATAT
1 -AAATATA-TAATATATTA-AATTTTATAT
* *
3263219 AAATATATAATATTTTAAATTTAATTAT
1 AAATATATAATATATTAAATTTTA-TAT
*
3263247 AAAAATATA
1 AAATATATA
3263256 TCAACATAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
27 6 0.10
28 20 0.34
29 6 0.10
30 2 0.03
31 4 0.07
32 19 0.33
33 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATATATAATATATTAAATTTTATAT
Found at i:3263704 original size:13 final size:14
Alignment explanation
Indices: 3263678--3263708 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3263668 AATAAAATAT
3263678 TTTAAATATTAAAA
1 TTTAAATATTAAAA
3263692 TTTAAAT-TTAAAA
1 TTTAAATATTAAAA
3263705 TTTA
1 TTTA
3263709 TTAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAATATTAAAA
Found at i:3265404 original size:17 final size:17
Alignment explanation
Indices: 3265310--3265405 Score: 67
Period size: 16 Copynumber: 5.6 Consensus size: 17
3265300 AGAATCGTAT
3265310 TAAAT-AAATCATACAAAA
1 TAAATAAAAT-ATA-AAAA
*
3265328 T-AATAAAATAGAAAAA
1 TAAATAAAATATAAAAA
3265344 T-AA-AAAATATAACAAA
1 TAAATAAAATATAA-AAA
* * *
3265360 TTAAATTAAATGTTAATAA
1 -TAAATAAAAT-ATAAAAA
*
3265379 TAAAT-AAATATTAAAA
1 TAAATAAAATATAAAAA
3265395 TAAATAAAATA
1 TAAATAAAATA
3265406 AAACTAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
15 8 0.13
16 19 0.30
17 15 0.24
18 12 0.19
19 6 0.10
20 3 0.05
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATAAAATATAAAAA
Found at i:3265957 original size:20 final size:21
Alignment explanation
Indices: 3265900--3265957 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
3265890 ACACAAAAAT
*
3265900 TTTAATAATTAAAATTAATTTAA
1 TTTAATAA-TAAAATTTA-TTAA
*
3265923 TTTAAT--TTAAA-TTATT-A
1 TTTAATAATAAAATTTATTAA
3265940 TTTAATAATAAAATTTAT
1 TTTAATAATAAAATTTAT
3265958 ATATATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
17 7 0.24
18 2 0.07
19 6 0.21
20 8 0.28
23 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAATAATAAAATTTATTAA
Found at i:3265982 original size:21 final size:22
Alignment explanation
Indices: 3265953--3265995 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3265943 AATAATAAAA
3265953 TTTATATA-TATAAATATAATTT
1 TTTATATATTAT-AATATAATTT
*
3265975 TTTA-ATATTATAATATTATTT
1 TTTATATATTATAATATAATTT
3265996 AAATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATATATTATAATATAATTT
Found at i:3266008 original size:19 final size:18
Alignment explanation
Indices: 3265930--3266008 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
3265920 TAATTTAATT
*
3265930 TAAATTATTATTTAATAA
1 TAAAATATTATTTAATAA
*
3265948 TAAAAT-TTATAT-AT-A
1 TAAAATATTATTTAATAA
* *
3265963 TAAATATAATTTTTTAATAT
1 TAAA-AT-ATTATTTAATAA
*
3265983 TATAATATTATTTAAATAA
1 TAAAATATTATTT-AATAA
3266002 TAAAATA
1 TAAAATA
3266009 AATTATCATA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
15 5 0.11
16 4 0.09
17 5 0.11
18 15 0.33
19 14 0.30
20 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAATATTATTTAATAA
Found at i:3266024 original size:54 final size:52
Alignment explanation
Indices: 3265923--3266027 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 52
3265913 ATTAATTTAA
**
3265923 TTTAATTTAAATTATTATTTAATAATAAAATTTATATATATAAATATAATTT
1 TTTAATTTAAATTATTATTTAATAATAAAATAAATATATATAAATATAATTT
*
3265975 TTTAATATTATAA-TATTATTTAAATAATAAAATAAATTATCATATATATATAA
1 TTTAAT-TTA-AATTATTATTT-AATAATAAAATAAA-TAT-ATATAAATATAA
3266028 ACTTGATTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
52 6 0.13
53 11 0.24
54 14 0.31
55 3 0.07
56 11 0.24
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (52 bp):
TTTAATTTAAATTATTATTTAATAATAAAATAAATATATATAAATATAATTT
Found at i:3267918 original size:21 final size:20
Alignment explanation
Indices: 3267879--3267920 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3267869 TAGGCCTAAT
* *
3267879 TAAAATTTAATTTTTAAATA
1 TAAAATTTAATATTAAAATA
3267899 TAAAATATTAATATTAAAATA
1 TAAAAT-TTAATATTAAAATA
3267920 T
1 T
3267921 CTTTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATTTAATATTAAAATA
Found at i:3268265 original size:35 final size:34
Alignment explanation
Indices: 3268200--3268266 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
3268190 AGGTTATTTA
* *
3268200 AATTAATTTTATTAATTTATTTTTAATAATTAAAT
1 AATTAATTTTATTAATATATATTT-ATAATTAAAT
3268235 AATTAATTATTATTTAATATATATTT-TAATTA
1 AATTAATT-TTA-TTAATATATATTTATAATTA
3268267 TTTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 14 0.50
36 3 0.11
37 11 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
AATTAATTTTATTAATATATATTTATAATTAAAT
Found at i:3268279 original size:22 final size:23
Alignment explanation
Indices: 3268237--3268287 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
3268227 AATTAAATAA
3268237 TTAATTATTATTTAATATATATT
1 TTAATTATTATTTAATATATATT
3268260 TTAATTATT-TATT-ATATATATT
1 TTAATTATTAT-TTAATATATATT
3268282 TTAATT
1 TTAATT
3268288 TAATATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTAATTATTATTTAATATATATT
Found at i:3269138 original size:2 final size:2
Alignment explanation
Indices: 3269133--3269168 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3269123 GTGTGTGTAC
3269133 AT 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 AT
3269169 GTATTTTTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3269426 original size:19 final size:19
Alignment explanation
Indices: 3269404--3269453 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
3269394 AAAAAAATTT
*
3269404 AAAATATGATAAAAATATA
1 AAAATATAATAAAAATATA
*
3269423 AAAATATAATATAAATATA
1 AAAATATAATAAAAATATA
*
3269442 TAAATA-AATAAA
1 AAAATATAATAAA
3269454 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATAATAAAAATATA
Found at i:3269435 original size:13 final size:13
Alignment explanation
Indices: 3269417--3269449 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3269407 ATATGATAAA
3269417 AATATAAAAATAT
1 AATATAAAAATAT
*
3269430 AATATAAATATAT
1 AATATAAAAATAT
3269443 AA-ATAAA
1 AATATAAA
3269450 TAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATAAAAATAT
Found at i:3269442 original size:8 final size:8
Alignment explanation
Indices: 3269405--3269479 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
3269395 AAAAAATTTA
3269405 AAATATGAT
1 AAATAT-AT
*
3269414 AAAAATAT
1 AAATATAT
3269422 AAA-A-AT
1 AAATATAT
*
3269428 ATA-ATAT
1 AAATATAT
3269435 AAATATAT
1 AAATATAT
*
3269443 AAATAAAT
1 AAATATAT
*
3269451 AAAT-TTT
1 AAATATAT
*
3269458 AAAATAAAT
1 -AAATATAT
*
3269467 AAATAAAT
1 AAATATAT
3269475 AAATA
1 AAATA
3269480 AATGTGCGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
6 5 0.09
7 6 0.11
8 37 0.69
9 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (8 bp):
AAATATAT
Found at i:3269450 original size:4 final size:4
Alignment explanation
Indices: 3269428--3269482 Score: 58
Period size: 4 Copynumber: 13.5 Consensus size: 4
3269418 ATATAAAAAT
* * *
3269428 ATAA TATAA ATAT ATAA ATAA ATAA AT-T TTAAA ATAA ATAA ATAA ATAA
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA
3269477 ATAA AT
1 ATAA AT
3269483 GTGCGCATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
3 1 0.02
4 36 0.86
5 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (4 bp):
ATAA
Found at i:3269548 original size:16 final size:17
Alignment explanation
Indices: 3269527--3269563 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
3269517 TCTCTGCTTT
3269527 TTTTCGTTTG-CTTT-TG
1 TTTTCG-TTGCCTTTCTG
3269543 TTTTCGTTGCCTTTCTG
1 TTTTCGTTGCCTTTCTG
3269560 TTTT
1 TTTT
3269564 GTCTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 10 0.53
17 6 0.32
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (17 bp):
TTTTCGTTGCCTTTCTG
Found at i:3272892 original size:18 final size:17
Alignment explanation
Indices: 3272865--3272923 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
3272855 TAATATAAAA
*
3272865 TTTTAATATATTAATAAT
1 TTTTATTATATT-ATAAT
3272883 TTTTATTATA-TA-AA-
1 TTTTATTATATTATAAT
*
3272897 TTTTATCATATTTATATAT
1 TTTTATTATA-TTATA-AT
3272916 TTTTATTA
1 TTTTATTA
3272924 AATTTATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.27
15 2 0.06
16 3 0.09
17 2 0.06
18 10 0.30
19 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTATATTATAAT
Found at i:3272900 original size:32 final size:34
Alignment explanation
Indices: 3272852--3272923 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 34
3272842 AAGTGTTATA
3272852 TATTAATATAAAATTTTAAT-ATATTAATA-ATTTT
1 TATT-ATATAAAATTTT-ATCATATTAATATATTTT
*
3272886 TATTATAT-AAATTTTATCATATTTATATATTTT
1 TATTATATAAAATTTTATCATATTAATATATTTT
3272919 TATTA
1 TATTA
3272924 AATTTATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
31 2 0.06
32 15 0.43
33 14 0.40
34 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TATTATATAAAATTTTATCATATTAATATATTTT
Found at i:3272944 original size:13 final size:13
Alignment explanation
Indices: 3272908--3272949 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3272898 TTTATCATAT
3272908 TTATATATTTT-TA
1 TTATA-ATTTTATA
3272921 TTA-AA-TTTATA
1 TTATAATTTTATA
3272932 TTATAATTTTATA
1 TTATAATTTTATA
3272945 TTATA
1 TTATA
3272950 TTTAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 6 0.23
12 3 0.12
13 14 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATAATTTTATA
Found at i:3272946 original size:24 final size:24
Alignment explanation
Indices: 3272908--3272953 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3272898 TTTATCATAT
3272908 TTATATATTTTTATTAAATTTATA
1 TTATATATTTTTATTAAATTTATA
*
3272932 TTATA-ATTTTATATTATATTTA
1 TTATATATTTT-TATTAAATTTA
3272954 AATATTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATATTTTTATTAAATTTATA
Found at i:3272950 original size:18 final size:18
Alignment explanation
Indices: 3272850--3272951 Score: 58
Period size: 17 Copynumber: 5.6 Consensus size: 18
3272840 TAAAGTGTTA
*
3272850 TATATTA-ATATAAAATTT
1 TATATTATAT-TATAATTT
3272868 TA-A-TATATTAATAATTT
1 TATATTATATT-ATAATTT
3272885 T-TATTATA-TA-AATTT
1 TATATTATATTATAATTT
3272900 TATCA-TAT-TTATATATTTT
1 TAT-ATTATATTATA-A-TTT
3272919 TATTAAATTTATATTATAATTT
1 TA-T--A-TTATATTATAATTT
3272941 TATATTATATT
1 TATATTATATT
3272952 TAAATATTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 30
0.68 0.02 0.30
Matches are distributed among these distances:
15 6 0.09
16 10 0.15
17 14 0.21
18 14 0.21
19 6 0.09
20 1 0.01
21 2 0.03
22 5 0.07
23 4 0.06
24 5 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTATATTATAATTT
Found at i:3272955 original size:30 final size:30
Alignment explanation
Indices: 3272871--3272956 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
3272861 AAAATTTTAA
3272871 TATATTAATAATTTT-TATTATA--TAAATT
1 TATATT-ATAATTTTATATTATATTTAAATT
* *
3272899 T-TATCAT-ATTTATATATT-TTTATTAAATT
1 TATATTATAATTT-TATATTATAT-TTAAATT
3272928 TATATTATAATTTTATATTATATTTAAAT
1 TATATTATAATTTTATATTATATTTAAAT
3272957 ATTTTTGGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
25 4 0.09
26 4 0.09
27 7 0.15
28 1 0.02
29 7 0.15
30 17 0.37
31 6 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TATATTATAATTTTATATTATATTTAAATT
Found at i:3275751 original size:18 final size:18
Alignment explanation
Indices: 3275728--3275764 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3275718 ATTTTGAATT
3275728 TTAATTTT-TTTAATATAA
1 TTAATTTTATTTAAT-TAA
3275746 TTAATTTTATTTAATTAA
1 TTAATTTTATTTAATTAA
3275764 T
1 T
3275765 ATTAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATTTTATTTAATTAA
Found at i:3276423 original size:11 final size:12
Alignment explanation
Indices: 3276387--3276432 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
3276377 TATTTATATC
3276387 ATATTATATATTT
1 ATATTAT-TATTT
3276400 AATATT-TTATTT
1 -ATATTATTATTT
3276412 ATATTATT-TTT
1 ATATTATTATTT
*
3276423 ATATAATTAT
1 ATATTATTAT
3276433 ATTTAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 15 0.52
12 8 0.28
13 1 0.03
14 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATATTATTATTT
Found at i:3276435 original size:30 final size:30
Alignment explanation
Indices: 3276376--3276436 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
3276366 TTTAAAATAC
*
3276376 TTATTTATATCATATTATATATTTAATATT
1 TTATTTATATCATATTATATAATTAATATT
* *
3276406 TTATTTATATTATTTTTATATAATT-ATATT
1 TTATTTATATCA-TATTATATAATTAATATT
3276436 T
1 T
3276437 AAAATCGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATTTATATCATATTATATAATTAATATT
Found at i:3280589 original size:2 final size:2
Alignment explanation
Indices: 3280582--3280619 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3280572 AAACATACAC
3280582 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3280620 CTTACACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3282225 original size:2 final size:2
Alignment explanation
Indices: 3282218--3282243 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3282208 CTAAATACAA
3282218 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
3282244 GCATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3283395 original size:50 final size:48
Alignment explanation
Indices: 3283341--3283501 Score: 178
Period size: 49 Copynumber: 3.2 Consensus size: 48
3283331 AGTTGCTTAG
* * *
3283341 AGTCAATAATTATAGCCACCTCTCTCTATTGTCAAAAGTTAGTGAAGAAT
1 AGTCAACAATTACAGCCACCTCTCTCGATTGTC-AAAGTT-GTGAAGAAT
* * * *
3283391 AGTCAACAATTACGGTCATCTCTCTCGATTATCAAAGTTGATGAAGAAT
1 AGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAGTTG-TGAAGAAT
* * *
3283440 AGTTAACAATTACAGCCGCCTCTCTCGATTGTCAAAGATTGGTGAAAAAT
1 AGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAG-TT-GTGAAGAAT
*
3283490 AGTCAATAATTA
1 AGTCAACAATTA
3283502 TGACCACCTC
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 45 0.49
50 45 0.49
51 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (48 bp):
AGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAGTTGTGAAGAAT
Found at i:3283448 original size:49 final size:49
Alignment explanation
Indices: 3283341--3283501 Score: 180
Period size: 50 Copynumber: 3.2 Consensus size: 49
3283331 AGTTGCTTAG
* * *
3283341 AGTCAATAATTATAGCCACCTCTCTCTATTGTCAAAAGTT-AGTGAAGAAT
1 AGTCAACAATTACAGCCACCTCTCTCGATTGTC-AAAGTTGA-TGAAGAAT
* * * *
3283391 AGTCAACAATTACGGTCATCTCTCTCGATTATCAAAGTTGATGAAGAAT
1 AGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAGTTGATGAAGAAT
* * * *
3283440 AGTTAACAATTACAGCCGCCTCTCTCGATTGTCAAAGATTGGTGAAAAAT
1 AGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAG-TTGATGAAGAAT
*
3283490 AGTCAATAATTA
1 AGTCAACAATTA
3283502 TGACCACCTC
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 45 0.49
50 47 0.51
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (49 bp):
AGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAGTTGATGAAGAAT
Found at i:3287936 original size:50 final size:50
Alignment explanation
Indices: 3287875--3288046 Score: 211
Period size: 50 Copynumber: 3.5 Consensus size: 50
3287865 AGTTGCTTAA
* * * *
3287875 AGTCAATAATTACGGTCACCTCTTTCTATTGTCAAAAATTGGTGAAGAAT
1 AGTCAATAATTACGATCACCTCTCTCAATTGTCAAAGATTGGTGAAGAAT
* * * * *
3287925 AGTCAACAATTACGATCATCTCTCTCGATTATC-AAGGTTGGTGAAGAAT
1 AGTCAATAATTACGATCACCTCTCTCAATTGTCAAAGATTGGTGAAGAAT
* **
3287974 AGTCAATAATTAGGATCACCTCTCTCAATTGTCAAAGATTAATGAAGAAT
1 AGTCAATAATTACGATCACCTCTCTCAATTGTCAAAGATTGGTGAAGAAT
* *
3288024 TGTCAATAAATACGATCACCTCT
1 AGTCAATAATTACGATCACCTCT
3288047 TTTGTACCCA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 42 0.41
50 60 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (50 bp):
AGTCAATAATTACGATCACCTCTCTCAATTGTCAAAGATTGGTGAAGAAT
Found at i:3288187 original size:6 final size:6
Alignment explanation
Indices: 3288178--3288211 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3288168 AATTTTAATT
3288178 TCATTA TCATTA TCATTA TCATTA TCATTA TCAT
1 TCATTA TCATTA TCATTA TCATTA TCATTA TCAT
3288212 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATTA
Found at i:3293736 original size:18 final size:20
Alignment explanation
Indices: 3293701--3293737 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3293691 ATTTTAGTTT
*
3293701 TCAATATATATATCTAATTA
1 TCAATATATATATATAATTA
3293721 TCAATATA-A-ATATAATT
1 TCAATATATATATATAATT
3293738 TTATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 1 0.06
20 8 0.50
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (20 bp):
TCAATATATATATATAATTA
Found at i:3293840 original size:20 final size:20
Alignment explanation
Indices: 3293815--3293857 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3293805 TTAATCAAAT
* * *
3293815 ATTATTTTTATTTTTATTTA
1 ATTATTATTATTATTATTAA
3293835 ATTATTATTATTATTATTAA
1 ATTATTATTATTATTATTAA
3293855 ATT
1 ATT
3293858 TAAACATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATTATTATTATTATTAA
Found at i:3293896 original size:21 final size:21
Alignment explanation
Indices: 3293870--3293931 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3293860 AACATATATT
3293870 TTATTATTAATTTTAATTTTA
1 TTATTATTAATTTTAATTTTA
* *
3293891 TTATTA-TAATAATTAAATTTA
1 TTATTATTAAT-TTTAATTTTA
*
3293912 TTATTATT-TTTTTAATTTTA
1 TTATTATTAATTTTAATTTTA
3293932 CCGTTTATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 12 0.35
21 21 0.62
22 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATTAATTTTAATTTTA
Found at i:3293927 original size:27 final size:27
Alignment explanation
Indices: 3293836--3293919 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
3293826 TTTTATTTAA
* * **
3293836 TTATTATTATTATTATTAAATTTAAAC
1 TTATTATTATAATAATTAAATTTAATT
* * * *
3293863 ATA-TATT-TTATTATTAATTTTAATT
1 TTATTATTATAATAATTAAATTTAATT
3293888 TTATTATTATAATAATTAAATTT-ATT
1 TTATTATTATAATAATTAAATTTAATT
3293914 ATTATT
1 -TTATT
3293920 TTTTTAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 17 0.37
26 11 0.24
27 18 0.39
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTATTATAATAATTAAATTTAATT
Found at i:3298054 original size:13 final size:13
Alignment explanation
Indices: 3298033--3298084 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
3298023 AAATTTGAAT
*
3298033 ATTTGAATATTTA
1 ATTTAAATATTTA
3298046 ATTTAAATAATTTA
1 ATTTAAAT-ATTTA
*
3298060 ATTTATAA-ATTTT
1 ATTTA-AATATTTA
3298073 ATTTAAAT-TTTA
1 ATTTAAATATTTA
3298085 TTTTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.15
13 16 0.48
14 10 0.30
15 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
ATTTAAATATTTA
Found at i:3298060 original size:14 final size:14
Alignment explanation
Indices: 3298041--3298080 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
3298031 ATATTTGAAT
3298041 ATTTAATTTAAATA
1 ATTTAATTTAAATA
*
3298055 ATTTAATTTATA-A
1 ATTTAATTTAAATA
*
3298068 ATTTTATTTAAAT
1 ATTTAATTTAAAT
3298081 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTAATTTAAATA
Found at i:3298188 original size:18 final size:18
Alignment explanation
Indices: 3298152--3298191 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3298142 GAATTTGAAT
**
3298152 TTAAATATAAAGGTAAAA
1 TTAAATATAAAAATAAAA
*
3298170 TTAAATATAAAAATTAAA
1 TTAAATATAAAAATAAAA
3298188 TTAA
1 TTAA
3298192 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATATAAAAATAAAA
Found at i:3300884 original size:2 final size:2
Alignment explanation
Indices: 3300877--3300902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3300867 AAAACTCAAC
3300877 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3300903 GCATATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3301127 original size:19 final size:20
Alignment explanation
Indices: 3301089--3301127 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3301079 ACAGAATATA
* *
3301089 TTTTTTAAAATATATTAAAT
1 TTTTTTAAAATAAATAAAAT
3301109 TTTTTTAAAA-AAATAAAAT
1 TTTTTTAAAATAAATAAAAT
3301128 ATATTCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTTAAAATAAATAAAAT
Found at i:3306493 original size:29 final size:29
Alignment explanation
Indices: 3306461--3306522 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
3306451 AGTGAGGGGA
*
3306461 ATGTTCCCGGCCAGT-GAACAAGATTTATC
1 ATGTTCCCGGCCAGTCG-ACAAGATTTAGC
3306490 ATGTTCCCGGCCAGTCGACAAGATTTAGC
1 ATGTTCCCGGCCAGTCGACAAGATTTAGC
3306519 ATGT
1 ATGT
3306523 AACTAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (29 bp):
ATGTTCCCGGCCAGTCGACAAGATTTAGC
Found at i:3310458 original size:15 final size:15
Alignment explanation
Indices: 3310417--3310459 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3310407 GATTTATATT
*
3310417 TAAATTTTAAATTTA
1 TAAATTTTAAATTCA
* *
3310432 TGATTTTTAAATTCA
1 TAAATTTTAAATTCA
*
3310447 TAAATTTAAAATT
1 TAAATTTTAAATT
3310460 TTTTATTAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TAAATTTTAAATTCA
Found at i:3321647 original size:3 final size:3
Alignment explanation
Indices: 3321641--3321671 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3321631 AAACATCATC
3321641 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3321672 ATGCAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3322374 original size:2 final size:2
Alignment explanation
Indices: 3322367--3322394 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3322357 ATATAAACTA
3322367 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
3322395 GTTAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3325305 original size:13 final size:14
Alignment explanation
Indices: 3325281--3325310 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3325271 AATTTAATAT
3325281 ATTTTAAAAATTAA
1 ATTTTAAAAATTAA
3325295 ATTTT-AAAATTAA
1 ATTTTAAAAATTAA
3325308 ATT
1 ATT
3325311 ATTCTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTTAAAAATTAA
Found at i:3325364 original size:21 final size:23
Alignment explanation
Indices: 3325338--3325380 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3325328 AAATTAGTTC
3325338 ATTATTT-AT-ATTAAAAATTAT
1 ATTATTTAATGATTAAAAATTAT
3325359 ATTATTTAATGATTAAAAATTA
1 ATTATTTAATGATTAAAAATTA
3325381 ATCGTGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTATTTAATGATTAAAAATTAT
Found at i:3325893 original size:17 final size:17
Alignment explanation
Indices: 3325871--3325973 Score: 73
Period size: 17 Copynumber: 6.5 Consensus size: 17
3325861 AAAAATTAAA
3325871 AAATATATATATAATAT
1 AAATATATATATAATAT
*
3325888 AAATATATAATATATTA-
1 AAATATAT-ATATAATAT
*
3325905 AAATTTATATA-AATAT
1 AAATATATATATAATAT
*
3325921 AAA-ATAT-TTTAAATAT
1 AAATATATATAT-AATAT
* *
3325937 AATTATA-ATA-AAAAT
1 AAATATATATATAATAT
3325952 AAA-A-ATAT-T-ATAT
1 AAATATATATATAATAT
3325965 AAATATATA
1 AAATATATA
3325974 AGTTATTGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
13 7 0.11
14 5 0.08
15 15 0.23
16 13 0.20
17 19 0.29
18 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATATATAATAT
Found at i:3325919 original size:27 final size:27
Alignment explanation
Indices: 3325884--3325974 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 27
3325874 TATATATATA
3325884 ATATAAATATATAATATATTAAAATTT
1 ATATAAATATATAATATATTAAAATTT
* * *
3325911 ATATAAATATAAAATAT-TTTAAATAT
1 ATATAAATATATAATATATTAAAATTT
* * *
3325937 A-AT-TATA-ATAA-AAATAAAAATATT
1 ATATAAATATATAATATATTAAAAT-TT
3325961 ATATAAATATATAA
1 ATATAAATATATAA
3325975 GTTATTGAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
22 1 0.02
23 8 0.16
24 5 0.10
25 4 0.08
26 11 0.22
27 20 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATAAATATATAATATATTAAAATTT
Found at i:3325922 original size:6 final size:6
Alignment explanation
Indices: 3325871--3325971 Score: 50
Period size: 6 Copynumber: 17.2 Consensus size: 6
3325861 AAAAATTAAA
* * **
3325871 AAATAT ATATAT -AATAT AAATAT ATAATAT ATTAAAAT TTATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT A-AATAT A--AATAT AAATAT AAATAT
* * * * * *
3325921 AAA-AT -ATTTT AAATAT AATTAT -AATAA AAATAA AAATAT -TATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
3325965 AAATAT A
1 AAATAT A
3325972 TAAGTTATTG
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
4 1 0.01
5 14 0.20
6 44 0.63
7 6 0.09
8 5 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATAT
Found at i:3327978 original size:15 final size:15
Alignment explanation
Indices: 3327958--3327987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3327948 TTAAAATTTT
*
3327958 ATATAATTATTATAA
1 ATATAATAATTATAA
3327973 ATATAATAATTATAA
1 ATATAATAATTATAA
3327988 TTATTATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAATAATTATAA
Found at i:3334204 original size:2 final size:2
Alignment explanation
Indices: 3334193--3334223 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3334183 CCAAAAAATA
*
3334193 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3334224 CACATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3342021 original size:2 final size:2
Alignment explanation
Indices: 3342014--3342046 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3342004 AAATGTCAAA
3342014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3342047 GTATGAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3342691 original size:2 final size:2
Alignment explanation
Indices: 3342684--3342713 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3342674 ACCTACTTTC
3342684 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
3342714 GTGCCAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3348175 original size:21 final size:20
Alignment explanation
Indices: 3348145--3348185 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3348135 ATTTACGAGT
*
3348145 TTTATAAAATAAATATTTTTA
1 TTTATAAAAT-AATAATTTTA
*
3348166 TTTATTAAATAATAATTTTA
1 TTTATAAAATAATAATTTTA
3348186 GATTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATAAAATAATAATTTTA
Found at i:3350899 original size:17 final size:17
Alignment explanation
Indices: 3350881--3350946 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
3350871 AAATCGATAT
3350881 TTTAAATT-AATTAAAA
1 TTTAAATTAAATTAAAA
3350897 TTTAAATTAAATTAATTAA
1 TTTAAATTAAATTAA--AA
* * *
3350916 ATTAAATTTAATT-AAT
1 TTTAAATTAAATTAAAA
*
3350932 TTTTAATTAAATTAA
1 TTTAAATTAAATTAA
3350947 TTTTAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 19 0.47
17 7 0.17
18 1 0.03
19 13 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATTAAATTAAAA
Found at i:3350906 original size:5 final size:5
Alignment explanation
Indices: 3350882--3350956 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
3350872 AATCGATATT
* *
3350882 TTAAA TT-AA TTAAAA TTTAAA TTAAA TT-AA TTAAA TTAAA TTTAA TTAATT
1 TTAAA TTAAA TT-AAA -TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA-A
* * *
3350933 TTTAA TTAAA TTAAT TTTAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAA
3350957 CTTTTACTCG
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
4 8 0.15
5 37 0.67
6 8 0.15
7 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (5 bp):
TTAAA
Found at i:3350921 original size:35 final size:35
Alignment explanation
Indices: 3350882--3350948 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3350872 AATCGATATT
3350882 TTAAA-TTAATTAAAATTTAAATTAAATTAATTAAA
1 TTAAATTTAATT-AAATTTAAATTAAATTAATTAAA
* *
3350917 TTAAATTTAATTAATTTTTAATTAAATTAATT
1 TTAAATTTAATTAAATTTAAATTAAATTAATT
3350949 TTAATTAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TTAAATTTAATTAAATTTAAATTAAATTAATTAAA
Found at i:3350926 original size:15 final size:15
Alignment explanation
Indices: 3350898--3350956 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
3350888 TAATTAAAAT
3350898 TTAAATTAAA-TTAA
1 TTAAATTAAATTTAA
3350912 TTAAATTAAATTTAA
1 TTAAATTAAATTTAA
3350927 TT-AATT---TTTAA
1 TTAAATTAAATTTAA
*
3350938 TTAAATTAATTTTAA
1 TTAAATTAAATTTAA
3350953 TTAA
1 TTAA
3350957 CTTTTACTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.17
12 4 0.10
14 14 0.35
15 15 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATTAAATTTAA
Found at i:3350937 original size:26 final size:26
Alignment explanation
Indices: 3350879--3350962 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
3350869 TTAAATCGAT
*
3350879 ATTTTAAATT-AATTAAAATTTAAATTA
1 ATTTTTAATTAAATT-AAATTT-AATTA
*
3350906 A--ATTAATTAAATTAAATTTAATTA
1 ATTTTTAATTAAATTAAATTTAATTA
*
3350930 ATTTTTAATTAAATTAATTTTAATTA
1 ATTTTTAATTAAATTAAATTTAATTA
*
3350956 ACTTTTA
1 ATTTTTA
3350963 CTCGTCCCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
24 6 0.12
25 11 0.22
26 31 0.63
27 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTTTAATTAAATTAAATTTAATTA
Found at i:3360389 original size:2 final size:2
Alignment explanation
Indices: 3360382--3360410 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3360372 TAGCATTAGG
3360382 TC 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 TC T
3360411 TTCTGAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3362236 original size:2 final size:2
Alignment explanation
Indices: 3362229--3362261 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3362219 TTAATTCCCA
3362229 TC TC TC 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 TC TC TC T
3362262 ATTTCTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3372524 original size:6 final size:6
Alignment explanation
Indices: 3372515--3372539 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3372505 ACATAAATAT
3372515 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
3372540 GCCAATATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:3374272 original size:23 final size:22
Alignment explanation
Indices: 3374231--3374273 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
3374221 GATAAAAAAT
3374231 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAATATTTATA
3374253 TATTTTTAATAATTAA-ATTTA
1 TATTTTT-AT-ATTAATATTTA
3374274 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:3374812 original size:2 final size:2
Alignment explanation
Indices: 3374805--3374844 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3374795 TTTCTCCCAC
3374805 AT AT AT 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 AT AT AT
3374845 CCAGCATCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3378057 original size:20 final size:20
Alignment explanation
Indices: 3378005--3378057 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
3377995 AAATAAGTAA
**
3378005 AAAAATATCAATCATAATTT
1 AAAAATATCAAAAATAATTT
**
3378025 AAAAATAAAAAAAATTAA-TT
1 AAAAATATCAAAAA-TAATTT
3378045 AAAAATATCAAAA
1 AAAAATATCAAAA
3378058 TTCAATCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATATCAAAAATAATTT
Found at i:3379811 original size:21 final size:21
Alignment explanation
Indices: 3379768--3379820 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3379758 TTTAAAAAAT
*
3379768 TTTAATTAAATTTAATAGGTA
1 TTTAATTAAATTTAATAAGTA
*
3379789 TTTAATT-AATTTATATAATTA
1 TTTAATTAAATTTA-ATAAGTA
*
3379810 -TTAATAAAATT
1 TTTAATTAAATT
3379821 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTAATTAAATTTAATAAGTA
Found at i:3381737 original size:2 final size:2
Alignment explanation
Indices: 3381730--3381762 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3381720 GCCAAGTAAG
3381730 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 T
3381763 TAAACCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3382333 original size:2 final size:2
Alignment explanation
Indices: 3382320--3382352 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3382310 TCCAAACCTA
*
3382320 AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3382353 CTTCCCTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3382693 original size:2 final size:2
Alignment explanation
Indices: 3382686--3382723 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3382676 CCATTATTTC
3382686 AT AT 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 AT AT
3382724 TTCTTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3383243 original size:83 final size:83
Alignment explanation
Indices: 3383104--3383273 Score: 304
Period size: 83 Copynumber: 2.0 Consensus size: 83
3383094 TTAGAAGTTG
*
3383104 TCAACTCAATCTTGATTCATTACCATAAAATTTCAGATCTATTACTAAGCAACATCCTATATGGA
1 TCAACTCAATCTTGATTCATTACCATAAAATTTCAGATCTATTACAAAGCAACATCCTATATGGA
3383169 CTTTCGGAGAACCAAATC
66 CTTTCGGAGAACCAAATC
* *
3383187 TCAACTCGATCTTGATTCATTACGATAAAATTTCAGATCTATTACAAAGCAACATCCTATATGGA
1 TCAACTCAATCTTGATTCATTACCATAAAATTTCAGATCTATTACAAAGCAACATCCTATATGGA
*
3383252 CTTTCGGGGAACCAAATC
66 CTTTCGGAGAACCAAATC
3383270 TCAA
1 TCAA
3383274 AAGTCAATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (83 bp):
TCAACTCAATCTTGATTCATTACCATAAAATTTCAGATCTATTACAAAGCAACATCCTATATGGA
CTTTCGGAGAACCAAATC
Found at i:3386829 original size:22 final size:22
Alignment explanation
Indices: 3386804--3386846 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3386794 TAATATTACT
*
3386804 AATTAATTACATAAATATATTA
1 AATTAATTACAAAAATATATTA
* *
3386826 AATTTATTATAAAAATATATT
1 AATTAATTACAAAAATATATT
3386847 TTGAGCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTAATTACAAAAATATATTA
Found at i:3387419 original size:15 final size:15
Alignment explanation
Indices: 3387401--3387437 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3387391 GGTATTCCCC
3387401 TTATTTTTATTTTTT
1 TTATTTTTATTTTTT
3387416 TTATTTTTATTTTTT
1 TTATTTTTATTTTTT
*
3387431 TCATTTT
1 TTATTTT
3387438 CTGCTCATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTTTATTTTTT
Found at i:3399161 original size:16 final size:17
Alignment explanation
Indices: 3399140--3399173 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3399130 AAACAAGAGG
3399140 AGTTTCCCTAC-ATATA
1 AGTTTCCCTACAATATA
3399156 AGTTTCCCTACAATATA
1 AGTTTCCCTACAATATA
3399173 A
1 A
3399174 CTTATACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (17 bp):
AGTTTCCCTACAATATA
Found at i:3401286 original size:5 final size:5
Alignment explanation
Indices: 3401270--3401302 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3401260 CTGAGTGAGA
*
3401270 GTCTC GTATC GTCTC GTCTC GTCTC GTCTC GTC
1 GTCTC GTCTC GTCTC GTCTC GTCTC GTCTC GTC
3401303 ATTTCGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.36, G:0.21, T:0.39
Consensus pattern (5 bp):
GTCTC
Found at i:3401627 original size:2 final size:2
Alignment explanation
Indices: 3401620--3401655 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3401610 ATTTCTCCTG
3401620 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3401656 ATTATGAAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3401954 original size:2 final size:2
Alignment explanation
Indices: 3401947--3401975 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3401937 TCATATGTTA
3401947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3401976 CGGAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3407633 original size:18 final size:18
Alignment explanation
Indices: 3407607--3407641 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3407597 TTGCTTTAGC
*
3407607 AATTCATATTTCGAGTCT
1 AATTCATATTTAGAGTCT
*
3407625 AATTGATATTTAGAGTC
1 AATTCATATTTAGAGTC
3407642 AAGTGTCCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (18 bp):
AATTCATATTTAGAGTCT
Found at i:3409748 original size:2 final size:2
Alignment explanation
Indices: 3409741--3409786 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3409731 TTCTTTTGTT
*
3409741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
3409783 TA TA
1 TA TA
3409787 CATTTCTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3410038 original size:3 final size:3
Alignment explanation
Indices: 3410030--3410060 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3410020 TATTAGTATA
3410030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3410061 TATGTATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3419041 original size:22 final size:21
Alignment explanation
Indices: 3419016--3419071 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3419006 GCTTCCATCA
* *
3419016 TCAATTCATTATAAAATTCCGT
1 TCAACTCATT-TAAAATTCAGT
*
3419038 TCAACTCCTTTAAAATTCAGT
1 TCAACTCATTTAAAATTCAGT
*
3419059 TCAACTCCTTTAA
1 TCAACTCATTTAA
3419072 GAAAAGAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (21 bp):
TCAACTCATTTAAAATTCAGT
Found at i:3419051 original size:21 final size:21
Alignment explanation
Indices: 3419027--3419071 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3419017 CAATTCATTA
*
3419027 TAAAATTCCGTTCAACTCCTT
1 TAAAATTCAGTTCAACTCCTT
3419048 TAAAATTCAGTTCAACTCCTT
1 TAAAATTCAGTTCAACTCCTT
3419069 TAA
1 TAA
3419072 GAAAAGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAATTCAGTTCAACTCCTT
Found at i:3419800 original size:27 final size:27
Alignment explanation
Indices: 3419759--3419814 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3419749 TGGCCTTTTC
**
3419759 CTTTAGCCTTGGAATGGAATTCAAATT
1 CTTTAGCCTTGGAATCAAATTCAAATT
*
3419786 CTTTAGCCTTTGAATCAAATTCAAATT
1 CTTTAGCCTTGGAATCAAATTCAAATT
3419813 CT
1 CT
3419815 CTAAGTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (27 bp):
CTTTAGCCTTGGAATCAAATTCAAATT
Found at i:3419860 original size:6 final size:6
Alignment explanation
Indices: 3419851--3419884 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3419841 TGCAGGAGTG
3419851 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA GGTG
1 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA GGTG
3419885 TGGCTCGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.53, T:0.18
Consensus pattern (6 bp):
GGTGAA
Found at i:3420576 original size:2 final size:2
Alignment explanation
Indices: 3420571--3420603 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3420561 AAAGTAAAAT
3420571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3420604 GCTTAGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3422300 original size:13 final size:13
Alignment explanation
Indices: 3422284--3422320 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3422274 TAAATTAATG
3422284 ATTTAATTAAAAT
1 ATTTAATTAAAAT
3422297 ATTTAATTAAAAT
1 ATTTAATTAAAAT
3422310 -TTT-ATTAAAAT
1 ATTTAATTAAAAT
3422321 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
13 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAATTAAAAT
Found at i:3422360 original size:15 final size:17
Alignment explanation
Indices: 3422340--3422372 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3422330 AAAATTATTT
3422340 AATTTAA-TTT-TTTTG
1 AATTTAAGTTTATTTTG
3422355 AATTTAAGTTTATTTTG
1 AATTTAAGTTTATTTTG
3422372 A
1 A
3422373 TAAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
AATTTAAGTTTATTTTG
Found at i:3422639 original size:18 final size:18
Alignment explanation
Indices: 3422616--3422652 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3422606 TTTAAGATTC
3422616 AAAGAAAGAGAGATTGAA
1 AAAGAAAGAGAGATTGAA
*
3422634 AAAGAAAGAGGGATTGAA
1 AAAGAAAGAGAGATTGAA
3422652 A
1 A
3422653 CTCTGCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (18 bp):
AAAGAAAGAGAGATTGAA
Found at i:3423397 original size:14 final size:15
Alignment explanation
Indices: 3423366--3423438 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 15
3423356 ATATATATAT
*
3423366 ATTATTTTATTTTTA
1 ATTATTTTATTATTA
3423381 ATTATTTTA-TATTA
1 ATTATTTTATTATTA
*
3423395 ATTATTTAGATTATTTCA
1 ATTATTT-TATTA-TT-A
* *
3423413 ATTATATTATAATTTAA
1 ATTATTTTATTA-TT-A
3423430 ATTATTTTA
1 ATTATTTTA
3423439 AGTTTTAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 11 0.23
15 10 0.21
16 2 0.04
17 17 0.36
18 7 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (15 bp):
ATTATTTTATTATTA
Done.