Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 9 of 19
Found at i:3110339 original size:16 final size:18
Alignment explanation
Indices: 3110296--3110339 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
3110286 TTATTGCACT
3110296 AATTGATAAAATAATTATA
1 AATT-ATAAAATAATTATA
3110315 AATTATAAAA-AATTA-A
1 AATTATAAAATAATTATA
*
3110331 AATTTTAAA
1 AATTATAAA
3110340 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 6 0.25
19 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATTATAAAATAATTATA
Found at i:3110339 original size:23 final size:21
Alignment explanation
Indices: 3110308--3110352 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
3110298 TTGATAAAAT
3110308 AATTATAAATTATAAAAAATTAA
1 AATTATAAATT-T-AAAAATTAA
*
3110331 AATTTTAAATTTAAAAATTAA
1 AATTATAAATTTAAAAATTAA
3110352 A
1 A
3110353 TTAAAGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTATAAATTTAAAAATTAA
Found at i:3110424 original size:58 final size:57
Alignment explanation
Indices: 3110327--3110448 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 57
3110317 TTATAAAAAA
** * * * *
3110327 TTAAAATTTTAAATTTAAAAATTAAATTAAAGTCTTAATTATAAATTTTTTTATATT
1 TTAAAATTTTAAAAATAAAAATAAAATTAAAGTCTTAATTATAAAATTGTTAATATT
* *
3110384 TTAATATTTTAAAAATAAATAATAAAATTAATA-TTTTAATTATAAAATTGTTAATATT
1 TTAAAATTTTAAAAATAAA-AATAAAATTAA-AGTCTTAATTATAAAATTGTTAATATT
3110442 TTAAAAT
1 TTAAAAT
3110449 AAAATATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
57 16 0.30
58 37 0.69
59 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (57 bp):
TTAAAATTTTAAAAATAAAAATAAAATTAAAGTCTTAATTATAAAATTGTTAATATT
Found at i:3110453 original size:22 final size:23
Alignment explanation
Indices: 3110411--3110453 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3110401 AATAATAAAA
*
3110411 TTAATATTTTAATTATAAAATTG
1 TTAATATTTTAATAATAAAATTG
3110434 TTAATATTTTAA-AATAAAAT
1 TTAATATTTTAATAATAAAAT
3110454 ATAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAATATTTTAATAATAAAATTG
Found at i:3110497 original size:23 final size:21
Alignment explanation
Indices: 3110467--3110520 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
3110457 AATTATTAAG
3110467 ATTT-TTAAATTAAAATAAATA
1 ATTTATTAAATTAAAAT-AATA
* *
3110488 ATTATATTAACATTTAAATAATC
1 ATT-TATTAA-ATTAAAATAATA
3110511 ATTTATTAAA
1 ATTTATTAAA
3110521 ATAATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 4 0.14
22 7 0.25
23 10 0.36
24 7 0.25
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTATTAAATTAAAATAATA
Found at i:3112518 original size:18 final size:19
Alignment explanation
Indices: 3112495--3112531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3112485 AATAAAGATC
3112495 AATTTA-AATTTTTTTAAT
1 AATTTAGAATTTTTTTAAT
3112513 AATTTAGGAATTTTTTTAA
1 AATTTA-GAATTTTTTTAA
3112532 ACATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
AATTTAGAATTTTTTTAAT
Found at i:3116262 original size:46 final size:47
Alignment explanation
Indices: 3116198--3116317 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 47
3116188 TTCTAGAATT
*
3116198 TTTTTAATAAA-T-AAAAATTATTTTTAGGTTTCTT-AAATTTTTAGAA
1 TTTTTAA-AAATTAAAAAATTATTTTTAGGTTT-TTAAAATTTATAGAA
* * *
3116244 TTTTT-AAAATTAAAAAATTATTTTTATGTTTTTCAAAATTTATGGAT
1 TTTTTAAAAATTAAAAAATTATTTTTAGGTTTTT-AAAATTTATAGAA
*
3116291 TTTTTCAAAAATTTAAAAA-TATTTTTA
1 TTTTT-AAAAATTAAAAAATTATTTTTA
3116318 ATTTTTTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
44 3 0.05
45 4 0.06
46 23 0.37
47 14 0.22
48 8 0.13
49 11 0.17
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (47 bp):
TTTTTAAAAATTAAAAAATTATTTTTAGGTTTTTAAAATTTATAGAA
Found at i:3118501 original size:14 final size:14
Alignment explanation
Indices: 3118482--3118509 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3118472 TATTCTTGAA
3118482 GATTGAGCTTATCT
1 GATTGAGCTTATCT
3118496 GATTGAGCTTATCT
1 GATTGAGCTTATCT
3118510 AAAATGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
GATTGAGCTTATCT
Found at i:3127815 original size:3 final size:3
Alignment explanation
Indices: 3127807--3127831 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3127797 ACTTGAAATG
3127807 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
3127832 CTTTTACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3128625 original size:18 final size:17
Alignment explanation
Indices: 3128602--3128641 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3128592 TGAATTCTAA
*
3128602 TTTTATTTTAATTTAAAT
1 TTTTATTGT-ATTTAAAT
*
3128620 TTTTATTGTATTTTAAT
1 TTTTATTGTATTTAAAT
3128637 TTTTA
1 TTTTA
3128642 ATACTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTATTGTATTTAAAT
Found at i:3147853 original size:30 final size:30
Alignment explanation
Indices: 3147812--3147875 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
3147802 TGCGTTCAGT
*
3147812 TAAACTCTTATACTTTTATTTTAAGTAAAA
1 TAAACTCTTATACTTTTATTTTAAATAAAA
* * *
3147842 TAAACTTTTATATTTTTATTTTAAATCAAA
1 TAAACTCTTATACTTTTATTTTAAATAAAA
3147872 TAAA
1 TAAA
3147876 TCCTTAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (30 bp):
TAAACTCTTATACTTTTATTTTAAATAAAA
Found at i:3152385 original size:31 final size:31
Alignment explanation
Indices: 3152347--3152411 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
3152337 TGTAGGCACT
3152347 TAGCCTGCTTCCTAGCTTAAGTTAATATAGA
1 TAGCCTGCTTCCTAGCTTAAGTTAATATAGA
3152378 TAGCCTGCTTCCTAGCTTAAGTTAATATAGA
1 TAGCCTGCTTCCTAGCTTAAGTTAATATAGA
3152409 TAG
1 TAG
3152412 AATTTTACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
TAGCCTGCTTCCTAGCTTAAGTTAATATAGA
Found at i:3153657 original size:5 final size:5
Alignment explanation
Indices: 3153647--3153678 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3153637 GTGTATATTT
3153647 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA AT
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA AT
3153679 GTTTATGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (5 bp):
ATCAA
Found at i:3159832 original size:31 final size:30
Alignment explanation
Indices: 3159797--3159858 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
3159787 AAATGATTTT
3159797 GTTTAG-GCTTCAAATATCTCAATAATAAAGG
1 GTTTAGAGCTT-AAATATCTCAA-AATAAAGG
* * *
3159828 GTTTAGATCTTGAATATTTCAAAATAAAGG
1 GTTTAGAGCTTAAATATCTCAAAATAAAGG
3159858 G
1 G
3159859 GTACTTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.33
31 15 0.56
32 3 0.11
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (30 bp):
GTTTAGAGCTTAAATATCTCAAAATAAAGG
Found at i:3186027 original size:21 final size:20
Alignment explanation
Indices: 3185983--3186036 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3185973 ATTATTATTT
* * *
3185983 TATTGTTAAAATAATAAAAA
1 TATTGTTTATATATTAAAAA
*
3186003 TATTGTTTTTATATTAAAAA
1 TATTGTTTATATATTAAAAA
3186023 TTATTGTTTATATA
1 -TATTGTTTATATA
3186037 ATTGGGTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TATTGTTTATATATTAAAAA
Found at i:3186032 original size:19 final size:19
Alignment explanation
Indices: 3185997--3186035 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
3185987 GTTAAAATAA
3185997 TAAAAATATTGTTTTTATAT
1 TAAAAATATTG-TTTTATAT
3186017 TAAAAATTATTG-TTTATAT
1 TAAAAA-TATTGTTTTATAT
3186036 AATTGGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TAAAAATATTGTTTTATAT
Found at i:3186941 original size:16 final size:16
Alignment explanation
Indices: 3186916--3186946 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3186906 TAACTTATTC
*
3186916 AAAAATAAAAGAAAAT
1 AAAAAGAAAAGAAAAT
3186932 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
3186947 CTAGATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAT
Found at i:3191693 original size:39 final size:38
Alignment explanation
Indices: 3191650--3191728 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 38
3191640 TTAATAGGTC
3191650 AACAACATAAATAATTTCTAAACTTATCCATTTTATATT
1 AACAACATAAATAATTTCTAAA-TTATCCATTTTATATT
* * ** *
3191689 AACAATATAAATAATTTTTAAATTATTTATTTTATTTT
1 AACAACATAAATAATTTCTAAATTATCCATTTTATATT
3191727 AA
1 AA
3191729 ATATTATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
38 15 0.43
39 20 0.57
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (38 bp):
AACAACATAAATAATTTCTAAATTATCCATTTTATATT
Found at i:3191724 original size:5 final size:5
Alignment explanation
Indices: 3191714--3191766 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
3191704 TTTTAAATTA
* *
3191714 TTTAT TTTAT TTTAAAT ATTAT TTAAT TGTTAT TTTAT TTTATT TTTAT
1 TTTAT TTTAT TTT--AT TTTAT TTTAT T-TTAT TTTAT TTTA-T TTTAT
3191763 TTTA
1 TTTA
3191767 AAAATACGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 27 0.68
6 9 0.22
7 4 0.10
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:3191736 original size:21 final size:22
Alignment explanation
Indices: 3191702--3191750 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
3191692 AATATAAATA
*
3191702 ATTTTTAAATTATTT-ATT-TT
1 ATTTTAAAATTATTTAATTGTT
3191722 ATTTTAAATATTATTTAATTGTT
1 ATTTTAAA-ATTATTTAATTGTT
3191745 ATTTTA
1 ATTTTA
3191751 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 3 0.12
23 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTAAAATTATTTAATTGTT
Found at i:3191751 original size:16 final size:16
Alignment explanation
Indices: 3191732--3191766 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3191722 ATTTTAAATA
3191732 TTATTTAATTGTTATT
1 TTATTTAATTGTTATT
* *
3191748 TTATTTTATTTTTATT
1 TTATTTAATTGTTATT
3191764 TTA
1 TTA
3191767 AAAATACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTATTTAATTGTTATT
Found at i:3191758 original size:21 final size:20
Alignment explanation
Indices: 3191704--3191750 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
3191694 TATAAATAAT
3191704 TTTTAA-ATTATTTATTTTA
1 TTTTAATATTATTTATTTTA
3191723 TTTTAAATATTATTTAATTGTTA
1 TTTT-AATATTATTT-ATT-TTA
3191746 TTTTA
1 TTTTA
3191751 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.17
20 2 0.08
21 7 0.29
22 4 0.17
23 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTAATATTATTTATTTTA
Found at i:3191760 original size:11 final size:10
Alignment explanation
Indices: 3191714--3191766 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
3191704 TTTTAAATTA
3191714 TTTATTTTAT
1 TTTATTTTAT
*
3191724 TTTAAATATTAT
1 TTT--ATTTTAT
*
3191736 TTAATTGTTAT
1 TTTATT-TTAT
3191747 TTTATTTTATT
1 TTTATTTTA-T
3191758 TTTATTTTA
1 TTTATTTTA
3191767 AAAATACGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 8 0.23
11 19 0.54
12 8 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:3193343 original size:251 final size:248
Alignment explanation
Indices: 3192683--3193434 Score: 817
Period size: 251 Copynumber: 3.0 Consensus size: 248
3192673 TTCATCTACT
* * *
3192683 AATTTTCACTATAATTCTTTATATTCTTACTATTATTCGTACATAGATTAAAATTTGTAAGCCAC
1 AATTTTCACTATAATTCTTT-TATCCTTACTATTATTCATACATAGATTAAAATTTGTAAGCTAC
* * * * *
3192748 AAAACACTTTAGATTCGAGAATAACAATTTAAATGTTTAATTTCTTCAAAAATTTTATTTATTTA
65 -AAACACTTTAAATTCGAGAATAACAATTTAAATATTTAATTTCTTTAAAAATTATATTTATTTG
* * * * *
3192813 ATATAATTAACTTATTATATTATATCTCACACATTTTTGTTAATATTTTAAAATGTTTGTCTTAC
129 ATATAATTAACTTATTACATTAAATCTCACACATTTATGTCAATATTTTAAAAT-CTTGTCTTAC
** * * ** * **
3192878 CTTTAT-AATTTTTATATTAATTCTTATAATTTTACGTCAAGACTTTTCAACTATT
193 AATTATAAATTTTTATATTAATTCTTATCACTTTACGTCAAGGTTTTTCAATTACC
* * * * * *
3192933 AATTTTAATTATAATTTTTTTATCCTTACTATTATTCATATATAGATTAAGATTTGTAAACCGTA
1 AATTTTCACTATAATTCTTTTATCCTTACTATTATTCATACATAGATTAAAATTTGT-AAGC-TA
* * * * * * * *
3192998 -AAGCACTTTAAACTCTAGAATAACAATTTAGATATTTAATTTCTCTGAAAATTATGTTTATTGG
64 CAAACACTTTAAATTCGAGAATAACAATTTAAATATTTAATTTCTTTAAAAATTATATTTATTTG
* * *
3193062 ATTTATGATTAACGTATTACATTAAATCTCACACATTTATGTCAATATTTTAACAATACTTGTTT
129 A--TATAATTAACTTATTACATTAAATCTCACACATTTATGTCAATATTTTAA-AAT-CTTGTCT
* * * *
3193127 TACAATTATAAAGTTTTATGTTAATTCTTACCACTTTATGTCAAGGTTTTTCAATTACC
190 TACAATTATAAATTTTTATATTAATTCTTATCACTTTACGTCAAGGTTTTTCAATTACC
* * * *
3193186 AATTTTCACCATAATTCATTTTATCCTTATTATTATTCACACATAAATTAAAATTTGTAAGCTAC
1 AATTTTCACTATAATTC-TTTTATCCTTACTATTATTCATACATAGATTAAAATTTGTAAGCTAC
* * * *
3193251 AAACACTTTAAATTAGAGAACAAAAATTTAAATATTTAATTTTTTTAAAAATTATATTTATTTGA
65 AAACACTTTAAATTCGAGAATAACAATTTAAATATTTAATTTCTTTAAAAATTATATTTATTTGA
* * * * * *
3193316 CATAATTAACTTGTTACATTAAATCTCACACGTTTATGTCAATATTTTCATAATCTT-TGTTGCA
130 TATAATTAACTTATTACATTAAATCTCACACATTTATGTCAATATTTT-AAAATCTTGTCTTACA
* * * *
3193380 TCTGTATAATTTTTTATATTAATTCTTATCACTTTAGGTCAAGGTTTTTAAATTA
194 -AT-TATAAATTTTTATATTAATTCTTATCACTTTACGTCAAGGTTTTTCAATTA
3193435 TAGTGAAATT
Statistics
Matches: 410, Mismatches: 81, Indels: 21
0.80 0.16 0.04
Matches are distributed among these distances:
249 90 0.22
250 24 0.06
251 136 0.33
252 18 0.04
253 107 0.26
254 35 0.09
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (248 bp):
AATTTTCACTATAATTCTTTTATCCTTACTATTATTCATACATAGATTAAAATTTGTAAGCTACA
AACACTTTAAATTCGAGAATAACAATTTAAATATTTAATTTCTTTAAAAATTATATTTATTTGAT
ATAATTAACTTATTACATTAAATCTCACACATTTATGTCAATATTTTAAAATCTTGTCTTACAAT
TATAAATTTTTATATTAATTCTTATCACTTTACGTCAAGGTTTTTCAATTACC
Found at i:3195439 original size:252 final size:251
Alignment explanation
Indices: 3194385--3195927 Score: 1314
Period size: 254 Copynumber: 6.2 Consensus size: 251
3194375 TGATTAGAAG
* *
3194385 AAGTATTGTTAAAATATTTGTA--TAAATGTATGAGATTTAACATAACAAGTTAATCATATGTCA
1 AAGTATTGTCAAAATA-TTG-ACGTAAATGTGTGAGATTTAACATAACAAGTTAATCATATGTCA
* * * * ** *
3194448 AATAAACATACTTTTTAAAAAAATTAAATATTTAAATTATTATTTTTGAGTTTAAAGTGTTTTAC
64 AATAAACATAATTTTTAGAAAAATTAAACATTTAAATTGTTA-TTTCAAGTTTAAAGTATTTTAC
** * *
3194513 GGCTTACAAATTTTAATCTATGTGA-GAATAATAGTAAGAATATAAAGAATTATGGTAAAAATTA
128 GGCTTA-AAATTTTAATCTAT-ACATGAATAATAGTAAGAATAAAAAGAATTATGGTGAAAATTA
* * * * * *
3194577 ATAGTTGAAAAACCTTGACGTAGAACTATAAGAATTAATGTAAAACATTATAAAGCGGGAAC
191 ATAATTGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTATAAAG-TGAAAC
* * * * ** * *
3194639 AAATGTTATCAAAATATTTATATAAATATGTGAGATTTAACATAACAAGTTAATCATATGGCAAA
1 AAGTATTGTCAAAATATTGACGTAAATGTGTGAGATTTAACATAACAAGTTAATCATATGTCAAA
* * * * * ** *
3194704 TAAATATAATTTTTGGGAAAATCAAACATTTGAATTGTTATTCTTGAGTTTAACGTATTTTACGG
66 TAAACATAATTTTTAGAAAAATTAAACATTTAAATTGTTATT-TCAAGTTTAAAGTATTTTACGG
* * * * * *
3194769 TTTATAAATTTTAATCTATACATGAATAACAATAAGGATAAAAAAGAATTATAGTGAAAATTAGT
130 CTTA-AAATTTTAATCTATACATGAATAATAGTAAGAAT-AAAAAGAATTATGGTGAAAATTAAT
* *** * * * * *
3194834 AGTTGAAATGTCTTGATGCAAAGCCGTAAGAATTAACATAAAACA-TA-AAA-T-----
193 AATTGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTATAAAGTGAAAC
* * * * * * * * *
3194885 -ATTA-T-T-AAAATATTGACGTAAATATATGAGATTGAACGTAATAAGTCAAT--TATATAAAA
1 AAGTATTGTCAAAATATTGACGTAAATGTGTGAGATTTAACATAACAAGTTAATCATATGTCAAA
* * * * *
3194944 TAAATATAATTTTTAGAAAAATTAGACACTTAAATTGTTAGTTT-GAGTTTAAAGTGTTTTACGG
66 TAAACATAATTTTTAGAAAAATTAAACATTTAAATTGTTA-TTTCAAGTTTAAAGTATTTTACGG
* * ** *
3195008 CTTAAAAAATTTAATTTATACATGAATAATAGTAAGAATAAAAAGAATTATAATGTAAATTAATA
130 CTT-AAAATTTTAATCTATACATGAATAATAGTAAGAATAAAAAGAATTATGGTGAAAATTAATA
* * * * * *
3195073 ATTAAAAAATCTTGATGTAAAACTGTAAAAATTAATGTAAAACATTATAAAGGTGAACC
194 ATTGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTATAAA-GTGAAAC
* * * * * * * *
3195132 AAGCACTATAAAAATATTAACATAAATGTGTGAGATTTAATATAACAAG-TAATCATACGTCAAA
1 AAGTATTGTCAAAATATTGACGTAAATGTGTGAGATTTAACATAACAAGTTAATCATATGTCAAA
* * * *
3195196 TAAACATAATTTTCAGAAAAATTAAACATTTGAATTGTTATTTACAAGTTCAAAATATTTTACGG
66 TAAACATAATTTTTAGAAAAATTAAACATTTAAATTGTTATTT-CAAGTTTAAAGTATTTTACGG
* * * *
3195261 CTTACAATTTTAATATATACGTGAATAATGGTAA-AGATAAAAAGAATTATGGTGAAAATTAATA
130 CTTAAAATTTTAATCTATACATGAATAATAGTAAGA-ATAAAAAGAATTATGGTGAAAATTAATA
* * *
3195325 ATT-CAAAGCCTTGACGTAAAACTATAAGAATTAACGTAAAACATTATAAATGTGAAAC
194 ATTGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTATAAA-GTGAAAC
* * * *
3195383 AAATATTGTCAAAATATTGACGTAAATGTGTGAAATTTAACACAACAAGTTAATCATAAGTCAAA
1 AAGTATTGTCAAAATATTGACGTAAATGTGTGAGATTTAACATAACAAGTTAATCATATGTCAAA
* * * **
3195448 TAAACACAATTTTT-GAAGAAATTAAATATTTAAATTGTTATTTACAAATTTAAAGTGCTTTACG
66 TAAACATAATTTTTAGAA-AAATTAAACATTTAAATTGTTATTT-CAAGTTTAAAGTATTTTACG
* * * * * *
3195512 ACTTAAAAATTTTAATTTATACATAAATAGTAGTAAGAATAAAAAGAATTATGGTAAAAATTAGT
129 GCTT-AAAATTTTAATCTATACATGAATAATAGTAAGAATAAAAAGAATTATGGTGAAAATTAAT
* * ** * * *
3195577 AGTTGAAAAACCTTAATATAAAGCTGTAAGAATTAATGTAAAACTTTATAAAAGT-AGAAC
193 AATTGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTAT-AAAGTGA-AAC
* * * *
3195637 AAGTATTGTCAAAATCTCGA-GATAAATGTGTGGGATTTAA-AGTAATAAGTTAAT--TATGTCA
1 AAGTATTGTCAAAATATTGACG-TAAATGTGTGAGATTTAACA-TAACAAGTTAATCATATGTCA
*
3195698 AATAAATA-AATTTTT-GAAAAAATTAAACATTTAAATTGTTATTCTCAAGTTTAAAGTGA-TTT
64 AATAAACATAATTTTTAG-AAAAATTAAACATTTAAATTGTTATT-TCAAGTTTAAAGT-ATTTT
* * *** * * * *
3195760 ACAGCTTACAAATTTTAAT-TTTGTGTGAATAATAGTAAGGATAAAAACAATTATGGCGTAAATT
126 ACGGCTTA-AAATTTTAATCTATACATGAATAATAGTAAGAATAAAAAGAATTATGGTGAAAATT
* * * * * * * * * *
3195824 AA-AATTTTAAAAATCTTAACATAAAATTGTAAGAATTAACATAAAAAATTATAAAACTGGAAT
190 AATAA-TTGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTAT-AAAGTGAAAC
* * * *
3195887 AAGTATTGTAAAAATATTAATGTAAATATGTGAGATTTAAC
1 AAGTATTGTCAAAATATTGACGTAAATGTGTGAGATTTAAC
3195928 GTAATAAGCC
Statistics
Matches: 1041, Mismatches: 206, Indels: 87
0.78 0.15 0.07
Matches are distributed among these distances:
238 57 0.05
239 51 0.05
240 45 0.04
241 2 0.00
242 37 0.04
243 1 0.00
244 1 0.00
245 2 0.00
248 2 0.00
249 2 0.00
250 117 0.11
251 184 0.18
252 180 0.17
253 83 0.08
254 219 0.21
255 58 0.06
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (251 bp):
AAGTATTGTCAAAATATTGACGTAAATGTGTGAGATTTAACATAACAAGTTAATCATATGTCAAA
TAAACATAATTTTTAGAAAAATTAAACATTTAAATTGTTATTTCAAGTTTAAAGTATTTTACGGC
TTAAAATTTTAATCTATACATGAATAATAGTAAGAATAAAAAGAATTATGGTGAAAATTAATAAT
TGAAAAACCTTGACGTAAAACTGTAAGAATTAACGTAAAACATTATAAAGTGAAAC
Found at i:3195848 original size:22 final size:20
Alignment explanation
Indices: 3195823--3195869 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
3195813 TGGCGTAAAT
*
3195823 TAAAATTTTAAAAATCTTAACA
1 TAAAATTGTAAAAA--TTAACA
*
3195845 TAAAATTGTAAGAATTAACA
1 TAAAATTGTAAAAATTAACA
3195865 TAAAA
1 TAAAA
3195870 AATTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (20 bp):
TAAAATTGTAAAAATTAACA
Found at i:3196085 original size:5 final size:6
Alignment explanation
Indices: 3196067--3196095 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3196057 TTTATAAATG
3196067 AATAAA AATAAA AATAAA AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAA
3196096 TTATAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:3205070 original size:17 final size:17
Alignment explanation
Indices: 3205043--3205079 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3205033 ACATTAAATA
3205043 TTATATTTTGTATGTGAT
1 TTATATTTTGTAT-TGAT
3205061 TTAT-TTTTGTATTGAT
1 TTATATTTTGTATTGAT
3205077 TTA
1 TTA
3205080 CAGAAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.65
Consensus pattern (17 bp):
TTATATTTTGTATTGAT
Found at i:3220984 original size:41 final size:41
Alignment explanation
Indices: 3220939--3221029 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
3220929 CAAGCAGGCG
3220939 CGAAACGAACCCAAGCCAACAAGCAAATGCTGCCTCCGTTT
1 CGAAACGAACCCAAGCCAACAAGCAAATGCTGCCTCCGTTT
*
3220980 CGAAACGAACCCAAGCCAACACGCAAATGCTGCCTCCGTTT
1 CGAAACGAACCCAAGCCAACAAGCAAATGCTGCCTCCGTTT
3221021 CGAAACGAA
1 CGAAACGAA
3221030 ACCCTTCAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.35, C:0.34, G:0.18, T:0.13
Consensus pattern (41 bp):
CGAAACGAACCCAAGCCAACAAGCAAATGCTGCCTCCGTTT
Found at i:3224340 original size:18 final size:18
Alignment explanation
Indices: 3224317--3224360 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3224307 ATTTTTATTG
3224317 TATTTA-ATTAAGTTTTTT
1 TATTTATATTAA-TTTTTT
*
3224335 TATTTATATTTATTTTTT
1 TATTTATATTAATTTTTT
3224353 TAATTTAT
1 T-ATTTAT
3224361 CCAATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTTATATTAATTTTTT
Found at i:3224353 original size:19 final size:19
Alignment explanation
Indices: 3224306--3224360 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
3224296 TGATTTTTTA
3224306 TATTTTTATTGTATTTA-ATT
1 TATTTTT-TT-TATTTATATT
* *
3224326 AAGTTTTTTTATTTATATT
1 TATTTTTTTTATTTATATT
*
3224345 TATTTTTTTAATTTAT
1 TATTTTTTTTATTTAT
3224361 CCAATTGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 18 0.62
20 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TATTTTTTTTATTTATATT
Found at i:3225776 original size:5 final size:5
Alignment explanation
Indices: 3225766--3225822 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
3225756 AATTTTTAAA
* *
3225766 TTATT TTATT TTATT TTAAATA TTATT TAATT GTTATT TTATT TTATTT
1 TTATT TTATT TTATT TT--ATT TTATT TTATT -TTATT TTATT TTA-TT
3225815 TTATT TTA
1 TTATT TTA
3225823 AAATATACGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 31 0.70
6 9 0.20
7 4 0.09
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:3225816 original size:11 final size:10
Alignment explanation
Indices: 3225766--3225822 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 10
3225756 AATTTTTAAA
3225766 TTATTTTATT
1 TTATTTTATT
*
3225776 TTATTTTAAATA
1 TTATTTT--ATT
*
3225788 TTATTTAATT
1 TTATTTTATT
3225798 GTTATTTTATT
1 -TTATTTTATT
3225809 TTATTTTTATT
1 TTA-TTTTATT
3225820 TTA
1 TTA
3225823 AAATATACGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 12 0.31
11 19 0.49
12 8 0.21
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTATTTTATT
Found at i:3225843 original size:40 final size:38
Alignment explanation
Indices: 3225766--3225845 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
3225756 AATTTTTAAA
*** *
3225766 TTATTTTATTTTATTTTAAATATTATTTAATTGTTATT
1 TTATTTTATTTTATTTTAAATATTACGAAATTATTATT
3225804 TTATTTTATTTTTATTTTAAA-ATATACGAATATTATTATT
1 TTATTTTA-TTTTATTTTAAATAT-TACGAA-ATTATTATT
3225844 TT
1 TT
3225846 TAATATTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 10 0.29
39 15 0.43
40 10 0.29
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (38 bp):
TTATTTTATTTTATTTTAAATATTACGAAATTATTATT
Found at i:3240110 original size:150 final size:149
Alignment explanation
Indices: 3239876--3240147 Score: 418
Period size: 150 Copynumber: 1.8 Consensus size: 149
3239866 ATACTAGCAC
* *
3239876 GACGTTGATGTTGATGGTGAAAAAAGTCACATGATCATATTATTATACCAAATTAACAAGTTATA
1 GACGTTGATGTTGATAGTGAAAAAAGTCACATGATCATATTATTATACCAAATTAACAAGTCATA
* *
3239941 TTATAATCAATTATCATCAATTATGATATGTTAAATTATCACATAATCTATCACTTATCATTTTA
66 TTATAATCAATTATCATCAATTATGATATGTCAAATTATCACATAATC-ATCAATTATCATTTTA
3240006 TATTCACATGACATTGATAT
130 TATTCACATGACATTGATAT
* * * * * * *
3240026 GACGTTGATGTTGATAGTGAAAAAATTCATATTATCATGTTATTATGCCAAATTAGCATGTCATA
1 GACGTTGATGTTGATAGTGAAAAAAGTCACATGATCATATTATTATACCAAATTAACAAGTCATA
* *
3240091 TTATAATCTATTATCATCAATTATGATATGTCAAATTATCACATCATCATCAATTAT
66 TTATAATCAATTATCATCAATTATGATATGTCAAATTATCACATAATCATCAATTAT
3240148 TATATATTAA
Statistics
Matches: 109, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
149 8 0.07
150 101 0.93
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (149 bp):
GACGTTGATGTTGATAGTGAAAAAAGTCACATGATCATATTATTATACCAAATTAACAAGTCATA
TTATAATCAATTATCATCAATTATGATATGTCAAATTATCACATAATCATCAATTATCATTTTAT
ATTCACATGACATTGATAT
Found at i:3240708 original size:30 final size:31
Alignment explanation
Indices: 3240633--3240709 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
3240623 TTCAAGAAAA
*
3240633 TTCAAATAAA-CTTTTTATTCTTTTATTGTG
1 TTCAAATAAATCTTTATATTCTTTTATTGTG
* *
3240663 TTCAATTAAATCTTTATA-T-TTTTATTTTAG
1 TTCAAATAAATCTTTATATTCTTTTATTGT-G
3240693 TTCAAATAAATCTTTAT
1 TTCAAATAAATCTTTAT
3240710 GATTAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 8 0.20
30 27 0.66
31 6 0.15
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (31 bp):
TTCAAATAAATCTTTATATTCTTTTATTGTG
Found at i:3243905 original size:22 final size:22
Alignment explanation
Indices: 3243880--3243926 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3243870 ATCACCGTGA
3243880 CTAAACTTCCAGCAAACAGCAC
1 CTAAACTTCCAGCAAACAGCAC
* * *
3243902 CTAAACTTCTAGCAGATAGCAC
1 CTAAACTTCCAGCAAACAGCAC
3243924 CTA
1 CTA
3243927 TTTATTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (22 bp):
CTAAACTTCCAGCAAACAGCAC
Found at i:3259425 original size:33 final size:33
Alignment explanation
Indices: 3259379--3259457 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
3259369 TCTCATGTGC
* *
3259379 TAATAAAAGCATCCTACAAATATGCATCAT-ATA
1 TAATAAAAACATCCTACAAATATGCATC-TGACA
*
3259412 TAATAAAAACATCCTACAAATATTCATCTGACA
1 TAATAAAAACATCCTACAAATATGCATCTGACA
*
3259445 TGATAAAAACATC
1 TAATAAAAACATC
3259458 TAAGGTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 1 0.02
33 40 0.98
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (33 bp):
TAATAAAAACATCCTACAAATATGCATCTGACA
Found at i:3262227 original size:54 final size:55
Alignment explanation
Indices: 3262155--3262263 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 55
3262145 CAAATTCAAC
*
3262155 AAGGTAAAAAAAAGGTGTAACCAATAAATTGTTATCTAATGCAAATAGAATTATG
1 AAGGTAAAAAAAACGTGTAACCAATAAATTGTTATCTAATGCAAATAGAATTATG
* *
3262210 AAGGT-AAAAAAACGTGTAACCAATAAATTTTTATCTAATGCGAATAGAATTATG
1 AAGGTAAAAAAAACGTGTAACCAATAAATTGTTATCTAATGCAAATAGAATTATG
3262264 CTAACAGTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 46 0.90
55 5 0.10
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (55 bp):
AAGGTAAAAAAAACGTGTAACCAATAAATTGTTATCTAATGCAAATAGAATTATG
Found at i:3266932 original size:31 final size:32
Alignment explanation
Indices: 3266879--3266938 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3266869 TAATTTAATC
*
3266879 TTTATTTTTTTATTATATTCAAATAAACTTTT
1 TTTATTTTTTTATTATAGTCAAATAAACTTTT
3266911 TTTATTTTTATT-TTA-AGTCAAATAAACT
1 TTTATTTTT-TTATTATAGTCAAATAAACT
3266939 CTTAACATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.46
32 12 0.46
33 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATTTTTTTATTATAGTCAAATAAACTTTT
Found at i:3267445 original size:36 final size:37
Alignment explanation
Indices: 3267385--3267455 Score: 119
Period size: 36 Copynumber: 1.9 Consensus size: 37
3267375 AATTCAATAC
3267385 CATCAAATTTCTCTTACAAATTCTAAGG-AAGAGAAAA
1 CATCAAATTTCTCTTACAAATTCT-AGGAAAGAGAAAA
3267422 CATCAAATTTCT-TTACAAATTCTAGGAAAGAGAA
1 CATCAAATTTCTCTTACAAATTCTAGGAAAGAGAA
3267456 GAGAAAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 3 0.09
36 18 0.55
37 12 0.36
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (37 bp):
CATCAAATTTCTCTTACAAATTCTAGGAAAGAGAAAA
Found at i:3277358 original size:18 final size:19
Alignment explanation
Indices: 3277317--3277352 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
3277307 GATTATTCTA
3277317 AATAATTATATAATTTTAT
1 AATAATTATATAATTTTAT
3277336 AATAA-TATAT-ATTTTAT
1 AATAATTATATAATTTTAT
3277353 CGATAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATAATTATATAATTTTAT
Found at i:3280283 original size:2 final size:2
Alignment explanation
Indices: 3280276--3280306 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3280266 TTTTTATAAA
3280276 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3280307 ATAAGCTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3284334 original size:33 final size:35
Alignment explanation
Indices: 3284287--3284353 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 35
3284277 ATCCTTTCTC
3284287 TTCTCTTTCCTAGAATTTGT-AGA-AATTTGATGT
1 TTCTCTTTCCTAGAATTTGTAAGAGAATTTGATGT
3284320 TTCTC-TTCCTTAGAATTTGTAAGAGAATTTGATG
1 TTCTCTTTCC-TAGAATTTGTAAGAGAATTTGATG
3284354 GTATTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 4 0.13
33 15 0.48
34 3 0.10
35 9 0.29
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (35 bp):
TTCTCTTTCCTAGAATTTGTAAGAGAATTTGATGT
Found at i:3284661 original size:16 final size:17
Alignment explanation
Indices: 3284627--3284661 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3284617 ATTTTTAATA
3284627 AATAATTTTTCAAATGTC
1 AATAATTTTTC-AATGTC
3284645 AATAATTTTTC-ATGTC
1 AATAATTTTTCAATGTC
3284661 A
1 A
3284662 TCATTTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (17 bp):
AATAATTTTTCAATGTC
Found at i:3284820 original size:30 final size:32
Alignment explanation
Indices: 3284784--3284844 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
3284774 AATTAATGTT
* *
3284784 AAAGTTTATTTGACT-TAA-AATAAAATAAAA
1 AAAGTTTATTTGAATATAATAAAAAAATAAAA
3284814 AAAGTTTATTTGAATATAATAAAAAAATAAA
1 AAAGTTTATTTGAATATAATAAAAAAATAAA
3284845 GATTAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 14 0.52
31 3 0.11
32 10 0.37
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (32 bp):
AAAGTTTATTTGAATATAATAAAAAAATAAAA
Found at i:3285357 original size:30 final size:28
Alignment explanation
Indices: 3285308--3285380 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 28
3285298 CCCATCCTCA
* *
3285308 CCGATTCCCCGC-CCCCCCTCCCATGAGT
1 CCGATTCCCC-CTGCCCCCTCCCACGAGT
3285336 CCCGATTCTCCCCTGCCCCCTCCCACGAGT
1 -CCGATTC-CCCCTGCCCCCTCCCACGAGT
3285366 CCGATTCCCCCTGCC
1 CCGATTCCCCCTGCC
3285381 GGCCTGTGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 8 0.20
29 15 0.38
30 17 0.43
ACGTcount: A:0.10, C:0.58, G:0.14, T:0.19
Consensus pattern (28 bp):
CCGATTCCCCCTGCCCCCTCCCACGAGT
Found at i:3289377 original size:57 final size:57
Alignment explanation
Indices: 3289310--3289426 Score: 189
Period size: 57 Copynumber: 2.1 Consensus size: 57
3289300 ATCTAATTCA
*
3289310 TATTCATGGGATCATCAAAGATATGCACAGCCTTCATATGCCCCATCAAACCAAGAC
1 TATTCATGGGATCATCAAAGATATGCACAGCCGTCATATGCCCCATCAAACCAAGAC
* * * *
3289367 TATTCATGGGATCATCAAAGATATGCACGGCCGTCATATGCTCCATCAAGCCGAGAC
1 TATTCATGGGATCATCAAAGATATGCACAGCCGTCATATGCCCCATCAAACCAAGAC
3289424 TAT
1 TAT
3289427 GTTCCTCAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (57 bp):
TATTCATGGGATCATCAAAGATATGCACAGCCGTCATATGCCCCATCAAACCAAGAC
Found at i:3291442 original size:3 final size:3
Alignment explanation
Indices: 3291434--3291470 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3291424 GTCCTATTAA
3291434 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3291471 TATTGTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3296326 original size:19 final size:20
Alignment explanation
Indices: 3296290--3296329 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3296280 CATGTTTTCA
* *
3296290 TATTGAATTTTTTTATTTTT
1 TATTGAATTTATTAATTTTT
3296310 TATT-AATTTATTAATTTTT
1 TATTGAATTTATTAATTTTT
3296329 T
1 T
3296330 TTATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTGAATTTATTAATTTTT
Found at i:3297374 original size:26 final size:24
Alignment explanation
Indices: 3297315--3297376 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 24
3297305 CCCCTTCATT
*
3297315 TTCTCTCTCTAAAGCCACTCTCTC
1 TTCTCTCTCTAAAGCCACTCTCCC
3297339 TGTCTTCTCTCT-AAGACCGACTCTCCC
1 T-TC-TCTCTCTAAAG-CC-ACTCTCCC
3297366 TTCTCCTCTCT
1 TTCT-CTCTCT
3297377 CCCGTAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 17 0.53
27 8 0.25
ACGTcount: A:0.13, C:0.42, G:0.06, T:0.39
Consensus pattern (24 bp):
TTCTCTCTCTAAAGCCACTCTCCC
Found at i:3312933 original size:2 final size:2
Alignment explanation
Indices: 3312926--3312976 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3312916 AAAGAAACAT
3312926 AG AG 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 AG AG
3312968 AG AG AG AG A
1 AG AG AG AG A
3312977 AACCCACTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3313758 original size:86 final size:87
Alignment explanation
Indices: 3313609--3313768 Score: 198
Period size: 87 Copynumber: 1.9 Consensus size: 87
3313599 TAATGATTCC
* * * **
3313609 TTATTAAACTAAACTTTCTTTAATTAACAATCTTTTATTGAATTAGACATTAACTATTTTTTTAT
1 TTATTAAACTAAACTTTCCTTAATTAACAATCTTTTATTAAATTAAACATTAACTATACTTTTAT
*
3313674 -TTTTTATTAACATTGAAATAT
66 CTATTTATTAACATTGAAATAT
* * * * *
3313695 TTATTAAAGTAAACTTTCCTTAATTGATCAATTTTTTATTAAATTAAATATTAGCTA-ACTTTTA
1 TTATTAAACTAAACTTTCCTTAATT-AACAATCTTTTATTAAATTAAACATTAACTATACTTTTA
3313759 TCTATTTATT
65 TCTATTTATT
3313769 TTCTTATTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
86 29 0.48
87 32 0.52
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (87 bp):
TTATTAAACTAAACTTTCCTTAATTAACAATCTTTTATTAAATTAAACATTAACTATACTTTTAT
CTATTTATTAACATTGAAATAT
Found at i:3331333 original size:156 final size:155
Alignment explanation
Indices: 3331130--3331832 Score: 961
Period size: 156 Copynumber: 4.5 Consensus size: 155
3331120 TTTAGAACTC
* * * *
3331130 TTTTTCTTGTTTTTTTTTTCAATTATTTTAATGATTTAAAATATATATTTACATTGCTAATGAAG
1 TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAG
* * * *
3331195 TTTTTAGTA-GGAATTTAGAACTTTCTTTCTTGGTTTT-TTGTATTTCTTTAGTCATGAAGCTTT
66 CTTTTAGGATGG-ATTTAGAACTTTCTTTCTT-GTTTTCTTGTATTTCTTTAATTATGAAGCTTT
* *
3331258 AAGGATGGATTTAGAATTCTTTTTCTTT
129 TAGGATGGATTTAGAACTCTTTTTC-TT
* *
3331286 TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGGTTTAGAATATATATTTGCATTGCTAATGAAG
1 TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAG
* * *
3331351 CTTTTAGGATGGATTCAGAATTTTTCTTTCTTGTTTTCTTGTATTTCTTTAGTTATGAAGCTTTT
66 CTTTTAGGATGGATTTAGAA-CTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTT
*
3331416 AGGA-AGATTTAGAACTCTTTTTCTT
130 AGGATGGATTTAGAACTCTTTTTCTT
* * * ** *
3331441 GTATTCTTGTATTTTCTTTCCATTTTTTTAATGATTTAGAATATATATTTATGTTGCTCATGAAG
1 TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAG
* *
3331506 CTTTTAGGATAGATTTAGAACTTTCTTTCTTGTTTTCTTGTATTTATTTAATTATGAAGCTTTTA
66 CTTTTAGGATGGATTTAGAACTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTA
3331571 GGATGGATTTAGAACTCTTTTTCTT
131 GGATGGATTTAGAACTCTTTTTCTT
* * * *
3331596 GTTTTCTTCTATTTTCTTTCAA-TTTTTTAATGATTTAGAATATGTATTTATATTGCTAATGAAG
1 TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAG
* * *
3331660 CTTTTAGGATGGATGTAGAACTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATAAAG-TTTTT
66 CTTTTAGGATGGATTTAGAACTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTA
* *
3331724 GGATGGATTTAAAACTCTTTTTTTTTGT
131 GGATGGATTTAGAACTC--TTTTTCT-T
* * *
3331752 TTTTTTTTGTTTTTTCTTTCAATTTTTTT-ATGATTTAGAATATATATTTGA-GTTGCTAATGAA
1 TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTT-ACATTGCTAATGAA
3331815 GCTTTTAGGATGGATTTA
65 GCTTTTAGGATGGATTTA
3331833 AAATTAACGA
Statistics
Matches: 490, Mismatches: 48, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
153 20 0.04
154 139 0.28
155 122 0.25
156 161 0.33
157 48 0.10
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.55
Consensus pattern (155 bp):
TTTTTCTTGTATTTTCTTTCAATTTTTTTAATGATTTAGAATATATATTTACATTGCTAATGAAG
CTTTTAGGATGGATTTAGAACTTTCTTTCTTGTTTTCTTGTATTTCTTTAATTATGAAGCTTTTA
GGATGGATTTAGAACTCTTTTTCTT
Found at i:3331450 original size:58 final size:61
Alignment explanation
Indices: 3331345--3331459 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 61
3331335 TGCATTGCTA
* * * *
3331345 ATGAAGCTTTTAGGATGGATTCAGAATTTTTCTTTCTTGTTTTCTTGTA-TTTCTTTAGTT
1 ATGAAGCTTTTAGGATAGATTCAGAACTCTTCTTTCTTGTATTCTTGTATTTTCTTTAGTT
*
3331405 ATGAAGCTTTTAGGA-AGATTTAGAACTCTT-TTTCTTGTATTCTTGTATTTTCTTT
1 ATGAAGCTTTTAGGATAGATTCAGAACTCTTCTTTCTTGTATTCTTGTATTTTCTTT
3331460 CCATTTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 16 0.33
59 18 0.37
60 15 0.31
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.54
Consensus pattern (61 bp):
ATGAAGCTTTTAGGATAGATTCAGAACTCTTCTTTCTTGTATTCTTGTATTTTCTTTAGTT
Found at i:3331757 original size:11 final size:10
Alignment explanation
Indices: 3331741--3331766 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3331731 TTTAAAACTC
3331741 TTTTTTTTTG
1 TTTTTTTTTG
3331751 TTTTTTTTTG
1 TTTTTTTTTG
3331761 TTTTTT
1 TTTTTT
3331767 CTTTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3332548 original size:15 final size:15
Alignment explanation
Indices: 3332528--3332575 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
3332518 AAATCATGCT
*
3332528 ATAAATGTGCATTTA
1 ATAAATGTGCATTCA
*
3332543 ATAAA--T-CATGCA
1 ATAAATGTGCATTCA
3332555 ATAAATGTGCATTCA
1 ATAAATGTGCATTCA
3332570 ATAAAT
1 ATAAAT
3332576 CATGTCATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
14 1 0.04
15 16 0.59
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
ATAAATGTGCATTCA
Found at i:3332558 original size:27 final size:27
Alignment explanation
Indices: 3332518--3332579 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
3332508 CATAAACATA
* *
3332518 AAATCATGCTATAAATGTGCATTTAAT
1 AAATCATGCAATAAATGTGCATTCAAT
3332545 AAATCATGCAATAAATGTGCATTCAAT
1 AAATCATGCAATAAATGTGCATTCAAT
3332572 AAATCATG
1 AAATCATG
3332580 TCATAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (27 bp):
AAATCATGCAATAAATGTGCATTCAAT
Found at i:3333827 original size:9 final size:10
Alignment explanation
Indices: 3333803--3333827 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3333793 CCTGGCTTTG
3333803 ATTTTTAATT
1 ATTTTTAATT
3333813 ATTTTTAATT
1 ATTTTTAATT
3333823 ATTTT
1 ATTTT
3333828 GTTTCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTAATT
Found at i:3336528 original size:746 final size:717
Alignment explanation
Indices: 3335303--3336757 Score: 1824
Period size: 746 Copynumber: 2.0 Consensus size: 717
3335293 TTTATTCATA
*
3335303 CCTTTTTTCTCTTTTTTGTACGTTTCCTCAAGGGCAGTTTAAATTTCTTTTCTTGAAGTCTTATT
1 CCTTTTTTCTCTTTTTTGTACATTTCCTCAAGGGCAGTTTAAATTTCTTTTCTTGAAGTCTTATT
* * * * *
3335368 TTTAAAGAGATTATATAATCGATCAGTGAAATTGAGATTGCATCCACAACATATAAACTCGTCTC
66 TCTAAAGAAATCATACAATCGATCAGTGAAATTGAGAATGCATCCACAACATATAAACTCGTCTC
* * * * *
3335433 ATTTCCATTTTTCTCCATGTTAACATCAGTCGTGGTTGCGACAATTGTGGATGTAGCAATGGTTC
131 ATTTCCATTTTTCTCCA-GTTAACATCAATCGTGGTTGCAACAATTGTGGAGGCAGCAATGCTTC
** * * *
3335498 CAGATGGTGTTAATTGTGTTCCTTCTACTAATGTGATCTCTTTTAGAATTGATGGTTGATCCGTC
195 CAGACAGTGTTAATTGTGTTCCTTCAACTAATGTAATCTCTTTTAGAATTGATGGTTGATCCATC
* * * *
3335563 TAAAGAATATAATAAATCTTCAATATGATTAATAGGAATACCATTTTGTCCCTCCATTTAGTGAA
260 TAAAGAACATAATAAAGCTTCAATATGATTAATAGAAATACCATTTTGTCCCTCCATCTAGTGAA
* * * *
3335628 GTTCATTCCGTCAAATCTATCGAGTTTGATCACTTTTTTATCTTGGAAGTGAACTTTCACATTTG
325 GTTCATTCCATCAAATATATCGAGTTTGATCACTTCTTGATCTTGGAAGTGAACTTTCACATTTG
* * *
3335693 GAGATTTAAGAAATACCTTAAGACTTTCCTTAAGGTATTTTTTCACTCTTCTTGATTTTAAATCT
390 AAGATTTAAGAAATACCCTAAGACTTTCCTTAAGATATTTTTTCACTCTTCTTGATTTTAAATCT
* ** *
3335758 AACCTAGTCTCCATAATGAAACAATGTCGAAAAGGTTTAAGAAA-TACCTTAAGATTGTTAGAAA
455 AACCCAGTCTCCATAACAAAACAATGTCGAAAAGGTTTAA-AAAGTACCTTAAGATTGTTAAAAA
*
3335822 TTTTTTAGAAGAAGAAAAAGAATATGACTTTAAGGGCGTGAACGAAAACACTTTCCTTAACTCAT
519 TTTTTT---AGAAGAAAAAGAATATGACTTTAAGGACGTGAA-GAAAACACTTTCCTTAA--CAT
* * *
3335887 TTTTTCAACCTCTAAGATAT-AATAAAGTCTTTGACACATTTATCAGAATAGTGAAAATGGTAGC
578 TTTTT-----T-T-A-ATATCAA-AAA-----T-ACAC--TTATCAAAATAATGAAAATAGTAGC
*
3335951 ATAATGACGTTGTCTATATAATAAATGAACATATATATCTTTCGATGTAAA-AAGTTGTTTCCTT
626 ATAATGACGTTGTCTATATAAT-AACGAACATATATATCTTTCGATGTAAAGAA-TTGTTTCCTT
3336015 TCATATTATAATTATTCAAACAATTGTTT
689 TCATATTATAATTATTCAAACAATTGTTT
* * * * *
3336044 CCTTTTTTCTCTTTTTTTTTGGTACATTTCCTCAAGTGCATTTTAAATTTTTTTTGTTGAAGTTT
1 CCTTTTTTCTC---TTTTTT-GTACATTTCCTCAAGGGCAGTTTAAATTTCTTTTCTTGAAGTCT
* **
3336109 TATTTCTGAAGAAATCATACAATCGATCAGTGAGAGAATTGAGAATGCATCCACGGCATATAAAC
62 TATTTCTAAAGAAATCATACAATCGATCAGT--GA-AATTGAGAATGCATCCACAACATATAAAC
** * * *
3336174 TCGTCTTGTTTCTATTTTTC-CACA-TTAACATCAATCGTGGTTGCAATAGTTGTGGAGGCAGCA
124 TCGTCTCATTTCCATTTTTCTC-CAGTTAACATCAATCGTGGTTGCAACAATTGTGGAGGCAGCA
* * * * *
3336237 ATGCTTCCAGACAGTGTTATTTGTGTTTCTTCAATTGATGTAATCTCTTTTGGAATTGATGGTTG
188 ATGCTTCCAGACAGTGTTAATTGTGTTCCTTCAACTAATGTAATCTCTTTTAGAATTGATGGTTG
* * *
3336302 ATCCATCTGAAGAACATAATAAAGCTTCAATGTGGTTAATAGAAATACCATTTTGTCCCTCCATC
253 ATCCATCTAAAGAACATAATAAAGCTTCAATATGATTAATAGAAATACCATTTTGTCCCTCCATC
* * * *
3336367 TAGTGAAGTTTATTCCATCAAATATATTGAGTTTGATCACTTCTTGATTTTGGAGGTGAAGC-TT
318 TAGTGAAGTTCATTCCATCAAATATATCGAGTTTGATCACTTCTTGATCTTGGAAGTGAA-CTTT
* * * **
3336431 CGCATTTGAAGGTTTAAGCAATACCCTAAGACTTTTTTTAAGATATTTTTTCACTCTTCTTGATT
382 CACATTTGAAGATTTAAGAAATACCCTAAGACTTTCCTTAAGATATTTTTTCACTCTTCTTGATT
* * * *
3336496 TTGAATCTAGCCCAGTCTCCATCACAAAACAATTTCGAAAAGGTTTAAAAAGTACCTTAAGATTG
447 TTAAATCTAACCCAGTCTCCATAACAAAACAATGTCGAAAAGGTTTAAAAAGTACCTTAAGATTG
* * * * *
3336561 TTAAAAATTTTTTAGAAGAAAAAGAATATGATTTTAATGACGTGAATAAAACCCTTTCCTTAAGA
512 TTAAAAATTTTTTAGAAGAAAAAGAATATGACTTTAAGGACGTGAAGAAAACACTTTCCTTAACA
* * * *
3336626 TTTTTTTTAATCTCCAAAATACACTTATCAAAATAATGAAAATAGTAGCATAATGATGTTGTTTA
577 TTTTTTTTAATATCAAAAATACACTTATCAAAATAATGAAAATAGTAGCATAATGACGTTGTCTA
*
3336691 TATAATAACGAACATATATGTCTTTCGATGTAAAGAATTGTTTCCTTTCATATTATAATTATTCA
642 TATAATAACGAACATATATATCTTTCGATGTAAAGAATTGTTTCCTTTCATATTATAATTATTCA
3336756 AA
707 AA
3336758 TTATGATAAC
Statistics
Matches: 622, Mismatches: 80, Indels: 42
0.84 0.11 0.06
Matches are distributed among these distances:
723 56 0.09
724 44 0.07
726 4 0.01
727 1 0.00
732 6 0.01
733 2 0.00
734 1 0.00
735 1 0.00
740 7 0.01
741 11 0.02
742 15 0.02
743 30 0.05
744 6 0.01
745 67 0.11
746 322 0.52
747 4 0.01
748 45 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (717 bp):
CCTTTTTTCTCTTTTTTGTACATTTCCTCAAGGGCAGTTTAAATTTCTTTTCTTGAAGTCTTATT
TCTAAAGAAATCATACAATCGATCAGTGAAATTGAGAATGCATCCACAACATATAAACTCGTCTC
ATTTCCATTTTTCTCCAGTTAACATCAATCGTGGTTGCAACAATTGTGGAGGCAGCAATGCTTCC
AGACAGTGTTAATTGTGTTCCTTCAACTAATGTAATCTCTTTTAGAATTGATGGTTGATCCATCT
AAAGAACATAATAAAGCTTCAATATGATTAATAGAAATACCATTTTGTCCCTCCATCTAGTGAAG
TTCATTCCATCAAATATATCGAGTTTGATCACTTCTTGATCTTGGAAGTGAACTTTCACATTTGA
AGATTTAAGAAATACCCTAAGACTTTCCTTAAGATATTTTTTCACTCTTCTTGATTTTAAATCTA
ACCCAGTCTCCATAACAAAACAATGTCGAAAAGGTTTAAAAAGTACCTTAAGATTGTTAAAAATT
TTTTAGAAGAAAAAGAATATGACTTTAAGGACGTGAAGAAAACACTTTCCTTAACATTTTTTTTA
ATATCAAAAATACACTTATCAAAATAATGAAAATAGTAGCATAATGACGTTGTCTATATAATAAC
GAACATATATATCTTTCGATGTAAAGAATTGTTTCCTTTCATATTATAATTATTCAAACAATTGT
TT
Found at i:3346788 original size:15 final size:15
Alignment explanation
Indices: 3346770--3346798 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3346760 TTATTAAATT
3346770 TATTTTTTAAAAAAA
1 TATTTTTTAAAAAAA
3346785 TATTTTTTAAAAAA
1 TATTTTTTAAAAAA
3346799 GTTTTCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTTTTAAAAAAA
Found at i:3356680 original size:10 final size:10
Alignment explanation
Indices: 3356665--3356694 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3356655 GACTATTACG
3356665 TATATACATA
1 TATATACATA
3356675 TATATACATA
1 TATATACATA
*
3356685 TATACACATA
1 TATATACATA
3356695 CAAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (10 bp):
TATATACATA
Found at i:3357118 original size:21 final size:21
Alignment explanation
Indices: 3357094--3357134 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3357084 ATTTATCTTT
*
3357094 TTTTTTGTTATGTGAATTTTA
1 TTTTTTATTATGTGAATTTTA
* *
3357115 TTTTTTATTATTTTAATTTT
1 TTTTTTATTATGTGAATTTT
3357135 TAAAAATTAA
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:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTTTTATTATGTGAATTTTA
Found at i:3360642 original size:2 final size:2
Alignment explanation
Indices: 3360635--3360667 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3360625 NNNNNNNNNN
3360635 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
3360668 CAACAAGTGC
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:3367246 original size:26 final size:27
Alignment explanation
Indices: 3367205--3367258 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
3367195 TTAAATAATT
*
3367205 TTTTTATTTTTATTATGTTT-AATCAAA
1 TTTTTATATTTATTAT-TTTGAATCAAA
3367232 TTTTTATATTT-TTATTTTGAATCAAA
1 TTTTTATATTTATTATTTTGAATCAAA
3367258 T
1 T
3367259 AAGCTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 3 0.12
26 12 0.48
27 10 0.40
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTTATATTTATTATTTTGAATCAAA
Found at i:3373947 original size:26 final size:25
Alignment explanation
Indices: 3373914--3373977 Score: 67
Period size: 29 Copynumber: 2.4 Consensus size: 25
3373904 AAATATTTAT
3373914 TTGATTTAAAATAAAA-ATATAAAAA
1 TTGATTTAAAATAAAAGA-ATAAAAA
3373939 CTTGATTTAGTATAATAAAAGAATAAAAA
1 -TTGATTTA--A-AATAAAAGAATAAAAA
*
3373968 TTTATTTAAA
1 TTGATTTAAA
3373978 TTTTTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
25 1 0.03
26 9 0.27
28 8 0.24
29 14 0.42
30 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (25 bp):
TTGATTTAAAATAAAAGAATAAAAA
Found at i:3376661 original size:22 final size:19
Alignment explanation
Indices: 3376640--3376678 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3376630 GCCGTAATTA
3376640 ATTTATATATATATATGTATT
1 ATTTAT-TATATATA-GTATT
*
3376661 ATTTATTATTTATAGTAT
1 ATTTATTATATATAGTAT
3376679 ATATAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTTATTATATATAGTATT
Found at i:3381244 original size:1 final size:1
Alignment explanation
Indices: 3381240--3381282 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
3381230 GAGGCCCGGC
3381240 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3381283 TGATGAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3395356 original size:9 final size:9
Alignment explanation
Indices: 3395342--3395371 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3395332 TTAACTAGTC
3395342 AAAGTAAGA
1 AAAGTAAGA
3395351 AAAGTAAGA
1 AAAGTAAGA
3395360 AAAGTAAGA
1 AAAGTAAGA
3395369 AAA
1 AAA
3395372 TGCAAGGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (9 bp):
AAAGTAAGA
Found at i:3400822 original size:3 final size:3
Alignment explanation
Indices: 3400814--3400845 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3400804 ACTGTTTTGT
3400814 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3400846 TTGCTGCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3412099 original size:19 final size:19
Alignment explanation
Indices: 3412077--3412146 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
3412067 ATATTGAATG
3412077 TTATTATATTTGATAAATA
1 TTATTATATTTGATAAATA
* * *
3412096 TTATGATATTT-ATAATTTT
1 TTATTATATTTGATAA-ATA
3412115 TTATTATAAATTTGAATAAA-A
1 TTATTAT--ATTTG-ATAAATA
*
3412136 TAATTATATTT
1 TTATTATATTT
3412147 TAAATTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
18 4 0.10
19 21 0.54
21 10 0.26
23 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TTATTATATTTGATAAATA
Found at i:3425770 original size:2 final size:2
Alignment explanation
Indices: 3425765--3425794 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3425755 TTTTTCGATA
*
3425765 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3425795 GTCTGTACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3438400 original size:25 final size:28
Alignment explanation
Indices: 3438347--3438400 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
3438337 TCTGATTTAT
3438347 AATTATAATTAATGTTTTGAAATATATA
1 AATTATAATTAATGTTTTGAAATATATA
* *
3438375 AATTATTATT-AT-TTTTTAAATA-ATA
1 AATTATAATTAATGTTTTGAAATATATA
3438400 A
1 A
3438401 GGTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 9 0.38
27 2 0.08
28 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
AATTATAATTAATGTTTTGAAATATATA
Found at i:3446866 original size:21 final size:22
Alignment explanation
Indices: 3446829--3446894 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
3446819 ATGTTGCCTC
3446829 TTTATACT-TTTTTTTCCCTATT
1 TTTAT-CTCTTTTTTTCCCTATT
* *
3446851 TTTCTC-CTTTTCTTCCCT-TT
1 TTTATCTCTTTTTTTCCCTATT
3446871 TTTATCTCTTTTTTTCCCCTATT
1 TTTATCTCTTTTTTT-CCCTATT
3446894 T
1 T
3446895 CCTTTCCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 7 0.19
21 18 0.50
22 8 0.22
23 3 0.08
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATCTCTTTTTTTCCCTATT
Found at i:3446872 original size:11 final size:10
Alignment explanation
Indices: 3446837--3446888 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
3446827 TCTTTATACT
3446837 TTTTTTTCCC
1 TTTTTTTCCC
*
3446847 TATTTTTCTCC
1 TTTTTTTC-CC
*
3446858 TTTTCTTCCC
1 TTTTTTTCCC
*
3446868 TTTTTTATCTC
1 TTTTTT-TCCC
3446879 TTTTTTTCCC
1 TTTTTTTCCC
3446889 CTATTTCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 17 0.50
11 17 0.50
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTCCC
Found at i:3449064 original size:93 final size:93
Alignment explanation
Indices: 3448889--3449158 Score: 249
Period size: 93 Copynumber: 2.9 Consensus size: 93
3448879 CATTGAAGGG
* * * * * * * *
3448889 TAGTTCTCATCAACAGCGTAGGAGGGTTTCTAGAAGCCAGCTAACCAAGTTTATTGAGAGGGAAG
1 TAGTTCTCATCAGCAGCTTAGGAGGATTCCGAGAAGCAAGCAAACCAAGATTATTGAGAGGGAAG
* *
3448954 ATGCAGTTTCGTCTGATTCTCCAGATGA
66 ATGCAGTTTCGTATGATTCACCAGATGA
* * *
3448982 TAGTTCTCTTCAGCAGCTTAGGAGGATTCCGAGAAGTAAGCAAACCAAGATTCTTGAGAGGGAAG
1 TAGTTCTCATCAGCAGCTTAGGAGGATTCCGAGAAGCAAGCAAACCAAGATTATTGAGAGGGAAG
**
3449047 ATGCAGTTTCAG-ATGATTCACTGGATGA
66 ATGCAGTTTC-GTATGATTCACCAGATGA
* * * * * * ***
3449075 TACTTCTCAGCAGCAGCTTAGAAAGACTCCTAGAAGC-AGACAAGGGAA-ATTTATTGAGAGGGA
1 TAGTTCTCATCAGCAGCTTAGGAGGATTCCGAGAAGCAAG-CAAACCAAGA-TTATTGAGAGGGA
* **
3449138 GGATGCAGTTTTATATGATTC
64 AGATGCAGTTTCGTATGATTC
3449159 GTTGGATGAG
Statistics
Matches: 143, Mismatches: 30, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
92 3 0.02
93 139 0.97
94 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (93 bp):
TAGTTCTCATCAGCAGCTTAGGAGGATTCCGAGAAGCAAGCAAACCAAGATTATTGAGAGGGAAG
ATGCAGTTTCGTATGATTCACCAGATGA
Found at i:3451678 original size:11 final size:11
Alignment explanation
Indices: 3451649--3451683 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3451639 TTCTCTCACC
3451649 TTATTATTATTA
1 TTATTATT-TTA
3451661 TTATTATTTTA
1 TTATTATTTTA
*
3451672 TTTTTATTTTA
1 TTATTATTTTA
3451683 T
1 T
3451684 CATCTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:3454157 original size:7 final size:7
Alignment explanation
Indices: 3454141--3454174 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
3454131 CAAGTTGTAA
3454141 TCATCCC
1 TCATCCC
*
3454148 TCATCTC
1 TCATCCC
3454155 TCATCCC
1 TCATCCC
3454162 -CATCCC
1 TCATCCC
3454168 TCATCCC
1 TCATCCC
3454175 ACCACATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.29
Consensus pattern (7 bp):
TCATCCC
Found at i:3454170 original size:13 final size:14
Alignment explanation
Indices: 3454141--3454174 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3454131 CAAGTTGTAA
*
3454141 TCATCCCTCATCTC
1 TCATCCCTCATCCC
3454155 TCATCCC-CATCCC
1 TCATCCCTCATCCC
3454168 TCATCCC
1 TCATCCC
3454175 ACCACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.29
Consensus pattern (14 bp):
TCATCCCTCATCCC
Found at i:3455478 original size:2 final size:2
Alignment explanation
Indices: 3455471--3455501 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3455461 GGGATGGCAT
3455471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3455502 CACATACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3462144 original size:30 final size:28
Alignment explanation
Indices: 3462105--3462165 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
3462095 CTGTTGGGGC
* *
3462105 AATTTCAAAAGATGAAAATAC-ATCAATTA
1 AATTTCAAAACAAG-AAATACAATC-ATTA
3462134 AATTTGCAAAACAAGAAATACAATCATTA
1 AATTT-CAAAACAAGAAATACAATCATTA
3462163 AAT
1 AAT
3462166 ATATGATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (28 bp):
AATTTCAAAACAAGAAATACAATCATTA
Found at i:3474580 original size:18 final size:18
Alignment explanation
Indices: 3474557--3474595 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3474547 GGCTGAATCT
*
3474557 TATATCCATAGTGATTCA
1 TATATCCATAGAGATTCA
3474575 TATATCCATAGAGATTCA
1 TATATCCATAGAGATTCA
3474593 TAT
1 TAT
3474596 CTCTAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (18 bp):
TATATCCATAGAGATTCA
Found at i:3488015 original size:34 final size:33
Alignment explanation
Indices: 3487977--3488047 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
3487967 ACACCAGATA
3487977 TTACATACT-AAAACCAAAGCTTTAACATCAAATG
1 TTACAT-CTCAAAACC-AAGCTTTAACATCAAATG
* * *
3488011 TTACATGTCAAAGCCAAGCTTTAACATCAAATT
1 TTACATCTCAAAACCAAGCTTTAACATCAAATG
3488044 TTAC
1 TTAC
3488048 GCTCCAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (33 bp):
TTACATCTCAAAACCAAGCTTTAACATCAAATG
Found at i:3489090 original size:97 final size:97
Alignment explanation
Indices: 3488945--3489138 Score: 318
Period size: 97 Copynumber: 2.0 Consensus size: 97
3488935 AACTAAAGAA
* *
3488945 AGAAAATTTAAGAACTTATATGAAAGGCTTTTAGTTTCTATATGGACACAACAACATTATAAGTA
1 AGAAAATTTAAGAACTTAGATGAAAGGCTTTTAGTTTCTATATAGACACAACAACATTATAAGTA
*
3489010 TAAAAATAATAAAAAACTCAAATAATAAAAGC
66 TAAAAATAATAAAAAACCCAAATAATAAAAGC
* *
3489042 AGAAAATTTAAGAAC-TAGGATGAAAGGCTTTTAGTTTCTGTTTAGACACAACAACATTATAAGT
1 AGAAAATTTAAGAACTTA-GATGAAAGGCTTTTAGTTTCTATATAGACACAACAACATTATAAGT
*
3489106 ATAAAAATAATAAAGAACCCAAATAATAAAAGC
65 ATAAAAATAATAAAAAACCCAAATAATAAAAGC
3489139 TTGAATAAAC
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
96 2 0.02
97 88 0.98
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.27
Consensus pattern (97 bp):
AGAAAATTTAAGAACTTAGATGAAAGGCTTTTAGTTTCTATATAGACACAACAACATTATAAGTA
TAAAAATAATAAAAAACCCAAATAATAAAAGC
Found at i:3489937 original size:14 final size:14
Alignment explanation
Indices: 3489918--3489947 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3489908 GGAAGTGTGT
3489918 CAAAGCCAAAAGTG
1 CAAAGCCAAAAGTG
3489932 CAAAGCCAAAAGTG
1 CAAAGCCAAAAGTG
3489946 CA
1 CA
3489948 CACAACGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.20, T:0.07
Consensus pattern (14 bp):
CAAAGCCAAAAGTG
Found at i:3492536 original size:17 final size:17
Alignment explanation
Indices: 3492496--3492537 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3492486 TCCGAAATTA
*
3492496 ATTAT-TTTTATTTTTT
1 ATTATATTTAATTTTTT
3492512 ATTATATTTAATTTATTT
1 ATTATATTTAATTT-TTT
3492530 ATT-TATTT
1 ATTATATTT
3492538 TTAAACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTATATTTAATTTTTT
Found at i:3509660 original size:2 final size:2
Alignment explanation
Indices: 3509653--3509678 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3509643 TCCCCCATCC
3509653 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
3509679 NNNNNNNNNN
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3523544 original size:41 final size:41
Alignment explanation
Indices: 3523487--3523565 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
3523477 GATCTGGGTG
*
3523487 CTTCAGAGCCACTGGTTGTTTAATGAGAAAAACAGTAAGTT
1 CTTCAGAGCCACTGGTTCTTTAATGAGAAAAACAGTAAGTT
*
3523528 CTTCAGAGCCACTGGTTCTTTAATGAGACAAACAGTAA
1 CTTCAGAGCCACTGGTTCTTTAATGAGAAAAACAGTAA
3523566 TCTCATTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (41 bp):
CTTCAGAGCCACTGGTTCTTTAATGAGAAAAACAGTAAGTT
Found at i:3542278 original size:2 final size:2
Alignment explanation
Indices: 3542271--3542312 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3542261 TTATACATAC
*
3542271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC A- 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
3542312 A
1 A
3542313 AAGATTAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3546346 original size:8 final size:8
Alignment explanation
Indices: 3546328--3546357 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3546318 ATACAAAAAG
3546328 TTTATTTTT
1 TTTA-TTTT
3546337 TTTATTTT
1 TTTATTTT
3546345 TTTATTTT
1 TTTATTTT
3546353 TTTAT
1 TTTAT
3546358 ATATTGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTATTTT
Found at i:3547843 original size:50 final size:50
Alignment explanation
Indices: 3547721--3547895 Score: 226
Period size: 50 Copynumber: 3.5 Consensus size: 50
3547711 AAAGAATTAA
* *
3547721 TAAAAAAATTTACAAAGTTTGAAAATATCTTGACAAATAAAAAAGTCAAAA
1 TAAAAAAATTTACAAAGTTTGAAAGTATCTTGACAAA-AAAAAAGTCAAAG
* ** *
3547772 TAAAAGAGCTCACAAAGTTTGAAAGTATCTTGACAAAAAAAAAGTCAAAG
1 TAAAAAAATTTACAAAGTTTGAAAGTATCTTGACAAAAAAAAAGTCAAAG
* * * *
3547822 TAAAAAAATTTTCAAAATTTGAAAGTATCTTGTCAATCAAAAAA-TCAAAG
1 TAAAAAAATTTACAAAGTTTGAAAGTATCTTGACAA-AAAAAAAGTCAAAG
*
3547872 TAAAAAAGTTTACAAAGTTTGAAA
1 TAAAAAAATTTACAAAGTTTGAAA
3547896 ATGTCCAATG
Statistics
Matches: 106, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
50 68 0.64
51 38 0.36
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (50 bp):
TAAAAAAATTTACAAAGTTTGAAAGTATCTTGACAAAAAAAAAGTCAAAG
Found at i:3557523 original size:27 final size:27
Alignment explanation
Indices: 3557496--3557667 Score: 123
Period size: 27 Copynumber: 6.2 Consensus size: 27
3557486 ACATAGTATG
*
3557496 TAACAACTAAATTTTTAACATGACATG
1 TAACAACTAAATTTTTAACATGACATA
*
3557523 TAACAACTATATAAATTTTTAACATGACGTA
1 TAACAAC----TAAATTTTTAACATGACATA
* * * * *
3557554 TAATAACTAAATCTTCAACATGACGTG
1 TAACAACTAAATTTTTAACATGACATA
* * * * *
3557581 TAAAAATTATATTTTTCAACATAATATA
1 TAACAACTAAATTTTT-AACATGACATA
* * *
3557609 TAACAACTAAA-TTTTAATATGGCTTA
1 TAACAACTAAATTTTTAACATGACATA
* *
3557635 TAACAAC-AACATTTTCAACATGGCATA
1 TAACAACTAA-ATTTTTAACATGACATA
3557662 TAACAA
1 TAACAA
3557668 TTATTTACAA
Statistics
Matches: 112, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
25 2 0.02
26 14 0.12
27 57 0.51
28 15 0.13
31 24 0.21
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (27 bp):
TAACAACTAAATTTTTAACATGACATA
Found at i:3557562 original size:31 final size:31
Alignment explanation
Indices: 3557503--3557562 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3557493 ATGTAACAAC
*
3557503 TAAATTTTTAACATGACATGTAACAACTATA
1 TAAATTTTTAACATGACATATAACAACTATA
* *
3557534 TAAATTTTTAACATGACGTATAATAACTA
1 TAAATTTTTAACATGACATATAACAACTA
3557563 AATCTTCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTTTTAACATGACATATAACAACTATA
Found at i:3557734 original size:27 final size:28
Alignment explanation
Indices: 3557671--3557735 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
3557661 ATAACAATTA
*
3557671 TTTACAACATGGTGTGTAATAACTAAAT
1 TTTACAACATGGCGTGTAATAACTAAAT
* * *
3557699 TTTAAAACATGGCGTGTAA-CACTACAT
1 TTTACAACATGGCGTGTAATAACTAAAT
*
3557726 TTTTCAACAT
1 TTTACAACAT
3557736 AGCATTTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 14 0.45
28 17 0.55
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (28 bp):
TTTACAACATGGCGTGTAATAACTAAAT
Found at i:3567590 original size:14 final size:15
Alignment explanation
Indices: 3567571--3567599 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3567561 TCCCTTCCCT
3567571 TGTGACT-CTGTTGC
1 TGTGACTGCTGTTGC
3567585 TGTGACTGCTGTTGC
1 TGTGACTGCTGTTGC
3567600 CTCTTCATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.21, G:0.31, T:0.41
Consensus pattern (15 bp):
TGTGACTGCTGTTGC
Found at i:3571254 original size:4 final size:4
Alignment explanation
Indices: 3571245--3571275 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3571235 AGCTTATCTT
3571245 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
3571276 TTTGGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:3573515 original size:2 final size:2
Alignment explanation
Indices: 3573508--3573534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3573498 CATTAATTTC
3573508 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 A
3573535 ATAAAATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3573598 original size:28 final size:30
Alignment explanation
Indices: 3573524--3573597 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
3573514 ATATATATAT
3573524 ATATATA-TATAATAAAATAATACATATCA
1 ATATATACTATAATAAAATAATACATATCA
* *
3573553 ATATATACTAT-ATAAAATTA-ACATATTA
1 ATATATACTATAATAAAATAATACATATCA
3573581 AT-TATACTTATAATAAA
1 ATATATAC-TATAATAAA
3573598 TAAGTAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
28 12 0.30
29 20 0.50
30 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (30 bp):
ATATATACTATAATAAAATAATACATATCA
Found at i:3582327 original size:27 final size:26
Alignment explanation
Indices: 3582272--3582328 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
3582262 TATTTATTTT
* *
3582272 ATTT-TTTAAATATTAATCATTTATA
1 ATTTATTTAAATATTAATAATTGATA
*
3582297 ATTTATTTAAAATATTAATAATTGATC
1 ATTTATTT-AAATATTAATAATTGATA
3582324 ATTTA
1 ATTTA
3582329 ATTGTTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 3 0.11
27 20 0.74
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGATA
Found at i:3582526 original size:52 final size:51
Alignment explanation
Indices: 3582463--3582744 Score: 171
Period size: 52 Copynumber: 5.7 Consensus size: 51
3582453 TAATTGATCA
3582463 TTTAAATATTAATATTTTATTTATAATTT-ATATATTATTATGATTACTT-ATT
1 TTTAAATATTAATATTTTATTTATAATTTAATA-ATTATTATGA-TA-TTAATT
* * *
3582515 TTTAAATATTAATA----ATTCATAATTTAATAATTATATTAATGATAATTGATAA
1 TTTAAATATTAATATTTTATTTATAATTTAATAA-T-TATT-ATGAT-ATTAAT-T
* *
3582567 TTTAAATATTAATATTTTA-TTATAACTTAATCATTA--AT-AT-TTAA--
1 TTTAAATATTAATATTTTATTTATAATTTAATAATTATTATGATATTAATT
*
3582611 ---AAATATTAATATTTTATTTATAATTTAA-ATATTATTATGATTATTAACT
1 TTTAAATATTAATATTTTATTTATAATTTAATA-ATTATTATGA-TATTAATT
* *
3582660 TTTAAATATTAATAATTTATAATT-T-ATTTAA-AA-TATTA--ATAATTGATT
1 TTTAAATATTAAT-ATTT-TATTTATAATTTAATAATTATTATGAT-ATTAATT
* * *
3582708 ATATAAATATTAATATGTTATTTAT-ATTTAATTATTA
1 -TTTAAATATTAATATTTTATTTATAATTTAATAATTA
3582745 ATATTTGAGG
Statistics
Matches: 185, Mismatches: 15, Indels: 62
0.71 0.06 0.24
Matches are distributed among these distances:
41 16 0.09
42 14 0.08
44 2 0.01
45 1 0.01
46 1 0.01
47 12 0.06
48 27 0.15
49 19 0.10
50 16 0.09
51 8 0.04
52 45 0.24
53 7 0.04
54 5 0.03
55 11 0.06
56 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (51 bp):
TTTAAATATTAATATTTTATTTATAATTTAATAATTATTATGATATTAATT
Found at i:3582615 original size:145 final size:142
Alignment explanation
Indices: 3582466--3582750 Score: 405
Period size: 145 Copynumber: 2.0 Consensus size: 142
3582456 TTGATCATTT
* *
3582466 AAATATTAATATTTTATTTATAATTTATATATTATTATGATTACTT-ATTTTTAAATATTAATAA
1 AAATATTAATATTTTATTTATAATTTAAATATTATTATGATTA-TTAACTTTTAAATATTAATAA
* * *
3582530 TTCATAATTTA-ATAATTATATTAATGATAATTGATAATTTAAATATTAATATTTTA-TTATAAC
65 TTCATAATTTATATAA-AATATT-A--ATAATTGATAATATAAATATTAATATGTTATTTAT-AC
3582593 TTAATCATTAATATTTAA
125 TTAATCATTAATATTTAA
3582611 AAATATTAATATTTTATTTATAATTTAAATATTATTATGATTATTAACTTTTAAATATTAATAAT
1 AAATATTAATATTTTATTTATAATTTAAATATTATTATGATTATTAACTTTTAAATATTAATAAT
* * * * *
3582676 TTATAATTTATTTAAAATATTAATAATTGATTATATAAATATTAATATGTTATTTATATTTAATT
66 TCATAATTTATATAAAATATTAATAATTGATAATATAAATATTAATATGTTATTTATACTTAATC
3582741 ATTAATATTT
131 ATTAATATTT
3582751 GAGGATTGTA
Statistics
Matches: 127, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
142 43 0.34
143 4 0.03
144 3 0.02
145 74 0.58
146 3 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (142 bp):
AAATATTAATATTTTATTTATAATTTAAATATTATTATGATTATTAACTTTTAAATATTAATAAT
TCATAATTTATATAAAATATTAATAATTGATAATATAAATATTAATATGTTATTTATACTTAATC
ATTAATATTTAA
Found at i:3582718 original size:22 final size:20
Alignment explanation
Indices: 3582678--3582722 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
3582668 TTAATAATTT
*
3582678 ATAATTTATTTAAAATATTA
1 ATAATTGATTTAAAATATTA
3582698 ATAATTGATTATATAAATATTA
1 ATAATTGATT-TA-AAATATTA
3582720 ATA
1 ATA
3582723 TGTTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAATTGATTTAAAATATTA
Found at i:3593591 original size:22 final size:22
Alignment explanation
Indices: 3593566--3593609 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3593556 TTTGAAATGG
3593566 AAGAAAACCAAACTTAAAATAT
1 AAGAAAACCAAACTTAAAATAT
*
3593588 AAGAAAACCAAACTTGAAATAT
1 AAGAAAACCAAACTTAAAATAT
3593610 CTTAAAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.14, G:0.07, T:0.18
Consensus pattern (22 bp):
AAGAAAACCAAACTTAAAATAT
Found at i:3613149 original size:18 final size:18
Alignment explanation
Indices: 3613104--3613139 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3613094 TCGCAGCGCG
3613104 AGCAAGAAGAGAGACGAGA
1 AGCAA-AAGAGAGACGAGA
3613123 AGCAAAAGAGAGA-GAGA
1 AGCAAAAGAGAGACGAGA
3613140 GAGAGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.56, C:0.08, G:0.36, T:0.00
Consensus pattern (18 bp):
AGCAAAAGAGAGACGAGA
Found at i:3615082 original size:2 final size:2
Alignment explanation
Indices: 3615077--3615127 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3615067 GTCACACTGA
3615077 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
3615119 AT AT AT AT A
1 AT AT AT AT A
3615128 ACAGCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3622155 original size:22 final size:24
Alignment explanation
Indices: 3622117--3622170 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
3622107 ATTAAACATC
3622117 AATAATTTACTATTAAATTA-TTA
1 AATAATTTACTATTAAATTAGTTA
3622140 AATAATTTA-TATTAAATTAGTTA
1 AATAATTTACTATTAAATTAGTTA
*
3622163 TATAATTT
1 AATAATTT
3622171 TTTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
AATAATTTACTATTAAATTAGTTA
Found at i:3625018 original size:2 final size:2
Alignment explanation
Indices: 3625011--3625036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3625001 ATTGGTGGTG
3625011 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3625037 TGTACTCGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3625520 original size:4 final size:4
Alignment explanation
Indices: 3625511--3625561 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
3625501 TGTTTCTTAT
* *
3625511 ATAC ATAC ATAT ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3625559 ATA
1 ATA
3625562 TATAAGAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:3625532 original size:16 final size:16
Alignment explanation
Indices: 3625511--3625561 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
3625501 TGTTTCTTAT
3625511 ATACATACATATATAC
1 ATACATACATATATAC
3625527 ATACATACATATATAC
1 ATACATACATATATAC
*
3625543 ATACATACATACATAC
1 ATACATACATATATAC
3625559 ATA
1 ATA
3625562 TATAAGAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (16 bp):
ATACATACATATATAC
Found at i:3629572 original size:2 final size:2
Alignment explanation
Indices: 3629560--3629589 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3629550 TATTTGAGTG
*
3629560 TA TA TA AA 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
3629590 ATGCTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3632413 original size:29 final size:29
Alignment explanation
Indices: 3632372--3632457 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 29
3632362 TCTCGTATAT
*
3632372 CTATTCACATACATCTTCTCCTCTTGTAC
1 CTATTCACATACAACTTCTCCTCTTGTAC
** * *
3632401 CTATTCATGTACAACTTCTTCTTTTGTAC
1 CTATTCACATACAACTTCTCCTCTTGTAC
* * * * * *
3632430 TTGTTCTCATATAACTTATTCTCTTGTA
1 CTATTCACATACAACTTCTCCTCTTGTA
3632458 TAGCTTTTTC
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.21, C:0.26, G:0.06, T:0.48
Consensus pattern (29 bp):
CTATTCACATACAACTTCTCCTCTTGTAC
Found at i:3634449 original size:24 final size:24
Alignment explanation
Indices: 3634404--3634449 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3634394 TAATATTAAT
* *
3634404 ATTATTTGATAAAATGTTATCAAA
1 ATTATTTCATAAAATGTGATCAAA
3634428 ATTATCTTCATAAAA-GTGATCA
1 ATTAT-TTCATAAAATGTGATCA
3634450 GGTGATCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (24 bp):
ATTATTTCATAAAATGTGATCAAA
Found at i:3645999 original size:21 final size:21
Alignment explanation
Indices: 3645974--3646021 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3645964 ACAATGTTTT
3645974 ATTTTTATTCAT-AATTTTTAA
1 ATTTTTATTCATCAA-TTTTAA
* *
3645995 ATTTTAATTCTTCAATTTTAA
1 ATTTTTATTCATCAATTTTAA
3646016 ATTTTT
1 ATTTTT
3646022 TAAAAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATTCATCAATTTTAA
Found at i:3653134 original size:17 final size:17
Alignment explanation
Indices: 3653096--3653134 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3653086 TCTATCATGT
*
3653096 ATTTAAATATTTATATT
1 ATTTAAATATTTATATA
* *
3653113 TTTTAAATATTTTTATA
1 ATTTAAATATTTATATA
3653130 ATTTA
1 ATTTA
3653135 GTCCTTTAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTAAATATTTATATA
Found at i:3654767 original size:8 final size:8
Alignment explanation
Indices: 3654750--3654787 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
3654740 TATTTTTCAC
3654750 AAAATTAT
1 AAAATTAT
*
3654758 AAAGTTAT
1 AAAATTAT
3654766 AAAATT-T
1 AAAATTAT
3654773 AAAATTAT
1 AAAATTAT
3654781 ATAAATT
1 A-AAATT
3654788 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 7 0.27
8 14 0.54
9 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
AAAATTAT
Found at i:3654840 original size:26 final size:28
Alignment explanation
Indices: 3654787--3654842 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
3654777 TTATATAAAT
* *
3654787 TTTAATTTTTTAAATATATTTTCGAAAA
1 TTTAATTTTATAAATATATTTTCAAAAA
*
3654815 TTTAATTTTATATA-ATATTTT-AAAAA
1 TTTAATTTTATAAATATATTTTCAAAAA
3654841 TT
1 TT
3654843 ATATCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 7 0.28
28 12 0.48
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAATTTTATAAATATATTTTCAAAAA
Found at i:3681601 original size:36 final size:36
Alignment explanation
Indices: 3681561--3681634 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
3681551 TCGTTTTTCC
*
3681561 TTCTCTATCGTACACCCTCTTTTCCCATGCATTGGA
1 TTCTCTATCGTACACCCTCTTTTCCCATGCATCGGA
3681597 TTCTCTATCGTACACCCTCTTTTCCCATGCATCGGA
1 TTCTCTATCGTACACCCTCTTTTCCCATGCATCGGA
3681633 TT
1 TT
3681635 GCCTGTCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.16, C:0.34, G:0.11, T:0.39
Consensus pattern (36 bp):
TTCTCTATCGTACACCCTCTTTTCCCATGCATCGGA
Found at i:3699249 original size:3 final size:3
Alignment explanation
Indices: 3699241--3699265 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3699231 TCATCTTTAC
3699241 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
3699266 GGCTGTTCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3699767 original size:41 final size:41
Alignment explanation
Indices: 3699710--3699790 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
3699700 GTGCAAGGTA
*
3699710 TTGCATCCCTTACTTCTATCAAAGATCCTCTTACAGTGAAC
1 TTGCACCCCTTACTTCTATCAAAGATCCTCTTACAGTGAAC
3699751 TTGCACCCCTTACTTCTATCAAAGATCCTCTTACAGTGAA
1 TTGCACCCCTTACTTCTATCAAAGATCCTCTTACAGTGAA
3699791 AGACCAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (41 bp):
TTGCACCCCTTACTTCTATCAAAGATCCTCTTACAGTGAAC
Found at i:3705326 original size:15 final size:16
Alignment explanation
Indices: 3705290--3705323 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3705280 ATGTTATTAT
3705290 AATTA-TTTATTTTTA
1 AATTATTTTATTTTTA
3705305 AATTATTTTATTTTTA
1 AATTATTTTATTTTTA
3705321 AAT
1 AAT
3705324 ATTAATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATTTTATTTTTA
Done.