Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 23 of 33
Found at i:3673627 original size:20 final size:22
Alignment explanation
Indices: 3673602--3673650 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
3673592 ATATTATTTA
3673602 ATTAAATTTA-AATTAAA-AAT
1 ATTAAATTTATAATTAAATAAT
*
3673622 ATTAAATTTATTATTAAATAAT
1 ATTAAATTTATAATTAAATAAT
3673644 -TTAAATT
1 ATTAAATT
3673651 GAACTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.38
21 13 0.50
22 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAAATTTATAATTAAATAAT
Found at i:3674277 original size:15 final size:15
Alignment explanation
Indices: 3674253--3674301 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
3674243 AAATATTTTT
*
3674253 ATATTATTAAATTTA
1 ATATTTTTAAATTTA
* *
3674268 ATATTTTTAATTTTT
1 ATATTTTTAAATTTA
3674283 ATATTTTTAAATTATA
1 ATATTTTTAAATT-TA
3674299 ATA
1 ATA
3674302 AAAATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTTTAAATTTA
Found at i:3674288 original size:8 final size:8
Alignment explanation
Indices: 3674245--3674291 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
3674235 AGTGAAAAAA
3674245 ATATTTTT
1 ATATTTTT
*
3674253 ATATTATT
1 ATATTTTT
* *
3674261 A-AATTTA
1 ATATTTTT
3674268 ATATTTTT
1 ATATTTTT
3674276 A-ATTTTT
1 ATATTTTT
3674283 ATATTTTT
1 ATATTTTT
3674291 A
1 A
3674292 AATTATAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
7 11 0.35
8 20 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATATTTTT
Found at i:3675025 original size:16 final size:16
Alignment explanation
Indices: 3674970--3675076 Score: 54
Period size: 17 Copynumber: 6.1 Consensus size: 16
3674960 ATATATTAAA
* *
3674970 ATTTAATATATTTTAA
1 ATTTTATATATTTTAT
3674986 ATTATGTATA-ATTTTAT
1 ATT-T-TATATATTTTAT
*
3675003 GTATTTATATATTTTAT
1 AT-TTTATATATTTTAT
*
3675020 ATTTTATTTTATTATAATTAT
1 ATTTTA---TA-TAT-TTTAT
* *
3675041 ATTTGAAATATTTTAT
1 ATTTTATATATTTTAT
*
3675057 ATTTATATAAATTTTTAT
1 ATTT-TATATA-TTTTAT
3675075 AT
1 AT
3675077 ATTAATAATT
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
16 19 0.28
17 23 0.33
18 13 0.19
19 2 0.03
20 3 0.04
21 9 0.13
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTATATATTTTAT
Found at i:3675175 original size:14 final size:15
Alignment explanation
Indices: 3675142--3675178 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3675132 AATTATATTT
3675142 TAATATTT-TATATA
1 TAATATTTATATATA
*
3675156 TCATATTTATATA-A
1 TAATATTTATATATA
3675170 TAATATTTA
1 TAATATTTA
3675179 AAATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATTTATATATA
Found at i:3675275 original size:19 final size:20
Alignment explanation
Indices: 3675241--3675285 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3675231 TATAATATTT
*
3675241 TAAATATAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
*
3675261 TAAATTTAA-TATAAATATA
1 TAAATTTAATTATAAAAATA
*
3675280 TTAATT
1 TAAATT
3675286 ATCAAACTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:3675514 original size:16 final size:16
Alignment explanation
Indices: 3675495--3675525 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3675485 TATTTTGTAA
3675495 AAATAAAATAAAATTG
1 AAATAAAATAAAATTG
*
3675511 AAATAGAATAAAATT
1 AAATAAAATAAAATT
3675526 ATTATAACAG
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:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATAAAATAAAATTG
Found at i:3678023 original size:14 final size:14
Alignment explanation
Indices: 3677999--3678038 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3677989 TTTATAATAA
3677999 AAAATAA-AATTAT
1 AAAATAATAATTAT
3678012 AAAATAATAATTAT
1 AAAATAATAATTAT
* *
3678026 AATATTATAATTA
1 AAAATAATAATTA
3678039 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATAATAATTAT
Found at i:3678232 original size:7 final size:7
Alignment explanation
Indices: 3678220--3678245 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3678210 ATAGCAAGCA
3678220 TCTAGCC
1 TCTAGCC
3678227 TCTAGCC
1 TCTAGCC
3678234 TCTAGCC
1 TCTAGCC
3678241 TCTAG
1 TCTAG
3678246 GATCCAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.31
Consensus pattern (7 bp):
TCTAGCC
Found at i:3678884 original size:17 final size:18
Alignment explanation
Indices: 3678845--3678885 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3678835 AACTGAATTA
*
3678845 AATTTAAATTTTAAATCT
1 AATTTAAATTATAAATCT
*
3678863 -TTTTAAATTAT-AATCT
1 AATTTAAATTATAAATCT
3678879 AATTTAA
1 AATTTAA
3678886 TTAAATTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAAATTATAAATCT
Found at i:3683586 original size:15 final size:15
Alignment explanation
Indices: 3683562--3683640 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
3683552 ACAACAAAAT
3683562 AATTAAAATATTATA
1 AATTAAAATATTATA
*
3683577 AATTATAATATTAT-
1 AATTAAAATATTATA
* *
3683591 -ATAAAAATATAAATA
1 AATTAAAATAT-TATA
* *
3683606 AAGT-AAATATTTTAA
1 AATTAAAATATTAT-A
* *
3683621 AATTTAAATAATATA
1 AATTAAAATATTATA
3683636 AATTA
1 AATTA
3683641 TTATTATATC
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
13 8 0.17
14 3 0.06
15 28 0.60
16 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (15 bp):
AATTAAAATATTATA
Found at i:3683679 original size:59 final size:58
Alignment explanation
Indices: 3683562--3683682 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 58
3683552 ACAACAAAAT
* *
3683562 AATTAAAATATTATAAATTATAATATTATATAAAAATATAAATAAAGTAAATATTTTAA
1 AATTAAAATAATATAAATTAT-ATATTATATAAAAATATAAATAAAATAAATATTTTAA
*
3683621 AATTTAAATAATATAAATTAT-TATTATATCAAAAAT-TAAATTAAATATAAA-ATATTTAA
1 AATTAAAATAATATAAATTATATATTATAT-AAAAATATAAA-TAAA-ATAAATAT-TTTAA
3683680 AAT
1 AAT
3683683 ATAATTATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
57 12 0.22
58 12 0.22
59 31 0.56
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (58 bp):
AATTAAAATAATATAAATTATATATTATATAAAAATATAAATAAAATAAATATTTTAA
Found at i:3684299 original size:77 final size:76
Alignment explanation
Indices: 3684157--3684356 Score: 357
Period size: 76 Copynumber: 2.6 Consensus size: 76
3684147 AGTATTTTAT
3684157 TAAATATAATAATTATCAATTTTATTTATTA-TTTTAATATATTAAATAAAAATATTACTACATA
1 TAAATATAATAATTATCAATTTTATTTATTATTTTTAATATATTAAATAAAAATATTACTACATA
3684221 TAATAAAATTA
66 TAATAAAATTA
*
3684232 TAAAATATAATAATTATCAATTTTATTTATTATTTTTAATATATTAAATAAAAATATTACTATAT
1 T-AAATATAATAATTATCAATTTTATTTATTATTTTTAATATATTAAATAAAAATATTACTACAT
3684297 ATAATAAAATTA
65 ATAATAAAATTA
* *
3684309 TAAATATAATGATTATCAATTTTATTTATAATTTTTAATATATTAAAT
1 TAAATATAATAATTATCAATTTTATTTATTATTTTTAATATATTAAAT
3684357 GAATATTATT
Statistics
Matches: 120, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
75 1 0.01
76 75 0.62
77 44 0.37
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (76 bp):
TAAATATAATAATTATCAATTTTATTTATTATTTTTAATATATTAAATAAAAATATTACTACATA
TAATAAAATTA
Found at i:3684316 original size:21 final size:21
Alignment explanation
Indices: 3684269--3684316 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3684259 TATTATTTTT
*
3684269 AATATATTAAATAAAAATATT
1 AATATATTAAATAAAAATATA
* *
3684290 ACTATA-TATAATAAAATTATA
1 AATATATTA-AATAAAAATATA
3684311 AATATA
1 AATATA
3684317 ATGATTATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATATTAAATAAAAATATA
Found at i:3684569 original size:17 final size:17
Alignment explanation
Indices: 3684547--3684592 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
3684537 GAAAGGAGAG
3684547 AAAGGAGAAAAAAAGAA
1 AAAGGAGAAAAAAAGAA
*
3684564 AAA-G-GAACAAAAGAA
1 AAAGGAGAAAAAAAGAA
3684579 AGAAGAGAGAAAAA
1 A-AAG-GAGAAAAA
3684593 TTTATTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 3 0.13
18 1 0.04
19 5 0.22
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGGAGAAAAAAAGAA
Found at i:3684673 original size:31 final size:29
Alignment explanation
Indices: 3684602--3684675 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
3684592 ATTTATTTGT
*
3684602 TTATATTTGTATTATTTTTTATTTAAAATA
1 TTATATTT-TATTATTTTTTATATAAAATA
*
3684632 TTATATTTTTATATATTTTTTATATATTAATAA
1 TTATA-TTTTAT-TATTTTTTATATA-AAAT-A
3684665 TT-TATTTTATT
1 TTATATTTTATT
3684676 TAATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 9 0.24
31 21 0.55
32 5 0.13
33 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATATTTTATTATTTTTTATATAAAATA
Found at i:3684714 original size:21 final size:21
Alignment explanation
Indices: 3684688--3684735 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3684678 ATATATATTT
3684688 TTATATGTACGTATATTTATA
1 TTATATGTACGTATATTTATA
** *
3684709 TTATATGTATTTATTTTTATA
1 TTATATGTACGTATATTTATA
3684730 TTATAT
1 TTATAT
3684736 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATATGTACGTATATTTATA
Found at i:3685312 original size:489 final size:499
Alignment explanation
Indices: 3684545--3685445 Score: 1276
Period size: 489 Copynumber: 1.8 Consensus size: 499
3684535 AGGAAAGGAG
** *
3684545 AGAAAGGAGAAAAAAAGAAAAAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTT
1 AGAAAGGAGAAAAAAAGAAAAAGGAACAAAAGAAAGAAGAGAGAAAAATTTAAGTGTTCATATTT
*
3684610 GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTAT
66 GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTAT
* * * * *
3684675 TTAATATATATTTTTATATGTACGTATATTTATATTATATGTATTTATTTTTATATTATATTTTT
131 TTAATATATATTTTTATATGTACATATATTCATATTATATGCATTTATTTTCATAGTATATTTTT
* *
3684740 AAATATTTTTTATAAATATCGCGTTTATATTATTTTTTTATATTTAAAATAAAATAAATTTATAT
196 AAATATTTTTTATAAACATCGCGTTTATATTAGTTTTTTATATTTAAAATAAAATAAATTTATAT
* * * * * *
3684805 AAATTTTTACATGTTAATTATTTATTTATCTATATTTTAACATATTCGTGTATACATACTATATT
261 AAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATT
*
3684870 TATATTATTTTTCATGTTATATTTTAATTTTTTATCTATATGTTAAATGTGTATTATATCTCAAT
326 TATATTATTTTTCATGTTATATTTTAA-TTTTT-T-TATATGTTAAATGTATATTATATCTCAAT
3684935 TCATGTTATATTTT-ATATAGCTAATCACTATGATTCATATAAAATCAACTACACAAACTAATAT
388 TCATGTTATATTTTGA-ATAGCTAATCACTATGATTCATATAAAATCAACTACACAAACTAATAT
3684999 GGTGCTAACATGTGACTTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
452 GGTGCTAACATGTGACTTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
* * *
3685047 AGAAAGGAGAAGAAAAGAAAGAGGAA-AGAAAGAAA-AAGA-A-AAAATTTTAAGTGTTCATA-T
1 AGAAAGGAGAAAAAAAGAAAAAGGAACA-AAAGAAAGAAGAGAGAAAAATTTAAGTGTTCATATT
*
3685107 T-TA-TGTTTTTTATTTAAAATATTATATTTTTATAT-TTTTTTACATATTAATAATTTATTTTA
65 TGTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTA
* * * * * *
3685169 TTTTATGTATA-TTTTATATGTACATGTATTCGTGTTATGTGCATATTATTTTCAT-GT-TATTT
130 TTTAATATATATTTTTATATGTACATATATTCATATTATATGCAT-TTATTTTCATAGTATATTT
* * *
3685231 TTAAATATTTTTTATAAACATCGTG-TT-TA-T-GTTTTTTATGTTTAAAATAAAATAAATTTTT
194 TTAAATATTTTTTATAAACATCGCGTTTATATTAGTTTTTTATATTTAAAATAAAATAAATTTAT
* * * * *
3685292 ATAAATTTTTACACGTTAATTATTCATATATCTATATTTTGACATATTCATGCATTCGTACCGTG
259 ATAAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATA
* * *
3685357 TTTATATTATTTTTCATGTTGTGTTTTAATTTTTTTATATGTTAAATTTATATTATATCTCAATT
324 TTTATATTATTTTTCATGTTATATTTTAATTTTTTTATATGTTAAATGTATATTATATCTCAATT
*
3685422 TATGTTATATTTTGAATAGCTAAT
389 CATGTTATATTTTGAATAGCTAAT
3685446 TACCGTGATT
Statistics
Matches: 356, Mismatches: 40, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
486 49 0.14
487 2 0.01
488 5 0.01
489 109 0.31
490 1 0.00
491 2 0.01
492 2 0.01
493 28 0.08
494 27 0.08
495 44 0.12
496 31 0.09
497 2 0.01
498 2 0.01
499 15 0.04
500 1 0.00
501 5 0.01
502 31 0.09
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (499 bp):
AGAAAGGAGAAAAAAAGAAAAAGGAACAAAAGAAAGAAGAGAGAAAAATTTAAGTGTTCATATTT
GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTAT
TTAATATATATTTTTATATGTACATATATTCATATTATATGCATTTATTTTCATAGTATATTTTT
AAATATTTTTTATAAACATCGCGTTTATATTAGTTTTTTATATTTAAAATAAAATAAATTTATAT
AAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATT
TATATTATTTTTCATGTTATATTTTAATTTTTTTATATGTTAAATGTATATTATATCTCAATTCA
TGTTATATTTTGAATAGCTAATCACTATGATTCATATAAAATCAACTACACAAACTAATATGGTG
CTAACATGTGACTTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
Found at i:3686187 original size:20 final size:17
Alignment explanation
Indices: 3686156--3686221 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
3686146 ATTTATTTGA
3686156 ATAATT-TATTTATCAAATT
1 ATAATTATATTTA--AAA-T
3686175 ATAATTATATTTAAAAT
1 ATAATTATATTTAAAAT
* *
3686192 ATTATAATATTTAAAAT
1 ATAATTATATTTAAAAT
*
3686209 ATTATTATATTTA
1 ATAATTATATTTA
3686222 TATATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 28 0.65
18 3 0.07
19 6 0.14
20 6 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATTATATTTAAAAT
Found at i:3686203 original size:17 final size:17
Alignment explanation
Indices: 3686181--3686221 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3686171 AATTATAATT
3686181 ATATTTAAAATATTATA
1 ATATTTAAAATATTATA
*
3686198 ATATTTAAAATATTATT
1 ATATTTAAAATATTATA
3686215 ATATTTA
1 ATATTTA
3686222 TATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTTAAAATATTATA
Found at i:3686265 original size:60 final size:58
Alignment explanation
Indices: 3686178--3686307 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
3686168 TCAAATTATA
* *
3686178 ATTATA-TTTAA--AATATTATAATATTTAAAATATTATTATATT-TATATATATTTTT
1 ATTATATTTTAATTAATATTATAAAATTTAAAATATT-TAATATTATATATATATTTTT
* * *
3686233 A-TATATTTATAATTAATATTATATAAATTTTAAAGTATTTAATATTATATTTTTATTTTT
1 ATTATATTT-TAATTAATATTATA-AAA-TTTAAAATATTTAATATTATATATATATTTTT
3686293 ATTATATTTTAATTA
1 ATTATATTTTAATTA
3686308 TTTTTATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
54 4 0.06
55 3 0.05
56 3 0.05
58 9 0.15
59 8 0.13
60 28 0.45
61 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (58 bp):
ATTATATTTTAATTAATATTATAAAATTTAAAATATTTAATATTATATATATATTTTT
Found at i:3686308 original size:20 final size:20
Alignment explanation
Indices: 3686210--3686318 Score: 84
Period size: 20 Copynumber: 5.4 Consensus size: 20
3686200 ATTTAAAATA
3686210 TTATTATA-TTTATATATATTT
1 TTATTATATTTTA-AT-TATTT
* *
3686231 TTA-TATATTTATAATTAATA
1 TTATTATATTT-TAATTATTT
* *
3686251 TTATATAAATTTTAAAGTATTT
1 TTAT-TATATTTT-AATTATTT
*
3686273 AATATTATA-TTT--TTATTT
1 -TTATTATATTTTAATTATTT
3686291 TTATTATATTTTAATTATTT
1 TTATTATATTTTAATTATTT
3686311 TTATTATA
1 TTATTATA
3686319 ATGATAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 19
0.70 0.10 0.19
Matches are distributed among these distances:
17 7 0.10
18 8 0.12
20 24 0.35
21 11 0.16
22 16 0.23
23 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
TTATTATATTTTAATTATTT
Found at i:3686422 original size:4 final size:4
Alignment explanation
Indices: 3686415--3686452 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
3686405 TATGTAGTGG
*
3686415 GAAA GAAA GAAA GAAA -AAA AAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
3686453 AAAAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3686440 original size:11 final size:11
Alignment explanation
Indices: 3686424--3686458 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3686414 GGAAAGAAAG
3686424 AAAGAAAAAAA
1 AAAGAAAAAAA
*
3686435 AAAGAAAGAAA
1 AAAGAAAAAAA
*
3686446 GAAGAAAAAAA
1 AAAGAAAAAAA
3686457 AA
1 AA
3686459 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:3686440 original size:19 final size:20
Alignment explanation
Indices: 3686416--3686457 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
3686406 ATGTAGTGGG
3686416 AAAGAAAGAAAGAA-AAAAA
1 AAAGAAAGAAAGAAGAAAAA
3686435 AAAGAAAGAAAGAAGAAAAA
1 AAAGAAAGAAAGAAGAAAAA
3686455 AAA
1 AAA
3686458 ATTATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAGAAGAAAAA
Found at i:3686445 original size:23 final size:22
Alignment explanation
Indices: 3686415--3686458 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3686405 TATGTAGTGG
3686415 GAAAGAAAGAAAGAAAAAAAAAA
1 GAAAGAAAG-AAGAAAAAAAAAA
3686438 GAAAGAAAGAAGAAAAAAAAA
1 GAAAGAAAGAAGAAAAAAAAA
3686459 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAGAAAAAAAAAA
Found at i:3686535 original size:26 final size:24
Alignment explanation
Indices: 3686485--3686554 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 24
3686475 ATGTTTGTAT
3686485 TTATATTTTTTTATTTTTAAAATA
1 TTATATTTTTTTATTTTTAAAATA
* *
3686509 TTATATTTTTGTATATTTTTGACATA
1 TTATATTTTT-T-TATTTTTAAAATA
3686535 TTAATAATTTATTTTATTTT
1 TT-AT-ATTT-TTTTATTTT
3686555 ATGTATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 13 0.33
27 8 0.21
28 5 0.13
29 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (24 bp):
TTATATTTTTTTATTTTTAAAATA
Found at i:3686664 original size:17 final size:17
Alignment explanation
Indices: 3686629--3686666 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3686619 TATTATTTAA
3686629 AATATTATAAATTTATGT
1 AATATTATAAA-TTATGT
3686647 AATATTTATAAA-TATGT
1 AATA-TTATAAATTATGT
3686664 AAT
1 AAT
3686667 TATATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATTATAAATTATGT
Found at i:3690079 original size:2 final size:2
Alignment explanation
Indices: 3690074--3690115 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3690064 TAAAACACAC
3690074 TA TA TA 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 TA TA TA
3690116 GGATGATTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3691149 original size:14 final size:15
Alignment explanation
Indices: 3691113--3691151 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3691103 CATGTACAAC
3691113 TTTAAATATTATTAT
1 TTTAAATATTATTAT
3691128 TTTAAATATATATT-T
1 TTTAAATAT-TATTAT
3691143 TTT-AATATT
1 TTTAAATATT
3691152 TTAATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 5 0.22
15 13 0.57
16 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAAATATTATTAT
Found at i:3691536 original size:18 final size:19
Alignment explanation
Indices: 3691513--3691549 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3691503 AACTTTTAGC
3691513 TAAAATA-ATTTTATTATT
1 TAAAATATATTTTATTATT
*
3691531 TAAAATATATTTTTTTATT
1 TAAAATATATTTTATTATT
3691550 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAAATATATTTTATTATT
Found at i:3693104 original size:18 final size:19
Alignment explanation
Indices: 3693069--3693118 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
3693059 ATGAATTTAT
* *
3693069 TTAT-ATTATTTTTTATG-
1 TTATAATTATATTTAATGA
3693086 TTATAATTATATTTAATGTA
1 TTATAATTATATTTAATG-A
3693106 TTATATATTATAT
1 TTATA-ATTATAT
3693119 AAATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 11 0.41
20 5 0.19
21 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTATAATTATATTTAATGA
Found at i:3693127 original size:20 final size:20
Alignment explanation
Indices: 3693086--3693175 Score: 53
Period size: 21 Copynumber: 4.5 Consensus size: 20
3693076 ATTTTTTATG
* *
3693086 TTATA-ATTATATTTAATGTA
1 TTATATATTATA-TAAATTTA
3693106 TTATATATTATATAAATTTA
1 TTATATATTATATAAATTTA
*
3693126 TTTATTATGTTA-AT-AATTTA
1 -TTA-TATATTATATAAATTTA
* * *
3693146 TTTTATATAAATTTAACA-TTA
1 TTATATAT-TATATAA-ATTTA
3693167 TTATATATT
1 TTATATATT
3693176 CGTATCATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
18 4 0.07
19 3 0.06
20 18 0.33
21 22 0.41
22 7 0.13
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATATATTATATAAATTTA
Found at i:3693131 original size:17 final size:17
Alignment explanation
Indices: 3693106--3693160 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3693096 ATTTAATGTA
*
3693106 TTATATATTATATAAAT
1 TTATTTATTATATAAAT
*
3693123 TTATTTATTATGTTAATAAT
1 TTATTTATTAT-AT-A-AAT
3693143 TTA-TT-TTATATAAAT
1 TTATTTATTATATAAAT
3693158 TTA
1 TTA
3693161 ACATTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 11 0.34
18 5 0.16
19 3 0.09
20 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATTTATTATATAAAT
Found at i:3693212 original size:27 final size:27
Alignment explanation
Indices: 3693182--3693235 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3693172 TATTCGTATC
3693182 ATATTTATA-TTATTTTTTTATAATATT
1 ATATTT-TAGTTATTTTTTTATAATATT
*
3693209 ATATTTTAGTTATTTTTTTATTATATT
1 ATATTTTAGTTATTTTTTTATAATATT
3693236 TAAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
ATATTTTAGTTATTTTTTTATAATATT
Found at i:3695933 original size:37 final size:37
Alignment explanation
Indices: 3695891--3695965 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
3695881 AAAATATTAA
*
3695891 ATTAAAATATGTATATATA-T-AATAAATAATTAAAAAT
1 ATTAAAAAATGTATATATATTAAATAAA-AA-TAAAAAT
* *
3695928 ATTAAAAAATTTATTTATATTAAATAAAAATAAAAAT
1 ATTAAAAAATGTATATATATTAAATAAAAATAAAAAT
3695965 A
1 A
3695966 ATATTTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 3 0.09
39 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (37 bp):
ATTAAAAAATGTATATATATTAAATAAAAATAAAAAT
Found at i:3696398 original size:2 final size:2
Alignment explanation
Indices: 3696391--3696417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3696381 ACCATGTATG
3696391 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 T
3696418 TTTGAATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3699643 original size:2 final size:2
Alignment explanation
Indices: 3699636--3699680 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3699626 TACCTACTCG
3699636 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
3699678 AT A
1 AT A
3699681 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3699685 original size:2 final size:2
Alignment explanation
Indices: 3699680--3699724 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3699670 ATATATATAT
3699680 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
3699722 AG A
1 AG A
3699725 TCTTCTATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3702113 original size:38 final size:38
Alignment explanation
Indices: 3702071--3702149 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
3702061 AAAGCTAATC
*
3702071 AACTACCTACAGATCCTTAACAATTTATCAAAACAAGT
1 AACTACCTACAGACCCTTAACAATTTATCAAAACAAGT
* *
3702109 AACTACCTGCAGACCCTTAACAATTTATCAAAACATGT
1 AACTACCTACAGACCCTTAACAATTTATCAAAACAAGT
3702147 AAC
1 AAC
3702150 AAATAAGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.25
Consensus pattern (38 bp):
AACTACCTACAGACCCTTAACAATTTATCAAAACAAGT
Found at i:3703331 original size:12 final size:12
Alignment explanation
Indices: 3703314--3703339 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3703304 TGCAAGATTG
3703314 CAACAAACCAAA
1 CAACAAACCAAA
3703326 CAACAAACCAAA
1 CAACAAACCAAA
3703338 CA
1 CA
3703340 GAAAGTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (12 bp):
CAACAAACCAAA
Found at i:3704009 original size:3 final size:3
Alignment explanation
Indices: 3704001--3704030 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3703991 AAGGGTAACT
3704001 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3704031 AGGCCTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3708207 original size:2 final size:2
Alignment explanation
Indices: 3708202--3708242 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3708192 TCATTTTTAA
3708202 AG AG AG AG AG 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 AG AG AG AG AG A
3708243 TAGATTTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3713652 original size:26 final size:25
Alignment explanation
Indices: 3713576--3713652 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 25
3713566 AATAAATTTT
3713576 TTAAAAATTATT-TTTTATAAATATGA
1 TTAAAAATTATTATTTTATAAATA--A
*
3713602 TAAAAAATTATTA-TTTA-AAATAA
1 TTAAAAATTATTATTTTATAAATAA
3713625 TTAAAAATTATTATTTTATATAATAA
1 TTAAAAATTATTATTTTATA-AATAA
3713651 TT
1 TT
3713653 TTTTATACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
23 13 0.29
24 4 0.09
25 6 0.13
26 22 0.49
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (25 bp):
TTAAAAATTATTATTTTATAAATAA
Found at i:3713721 original size:28 final size:29
Alignment explanation
Indices: 3713680--3713735 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 29
3713670 TATCATTATT
3713680 TTTAATAAAAATTTTA-AAAAATATATAG
1 TTTAATAAAAATTTTACAAAAATATATAG
3713708 TTTAA-AAAATATTTTATCAAAAATATAT
1 TTTAATAAAA-ATTTTA-CAAAAATATAT
3713736 TTATAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
30 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TTTAATAAAAATTTTACAAAAATATATAG
Found at i:3713738 original size:15 final size:13
Alignment explanation
Indices: 3713676--3713743 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 13
3713666 TTATTATCAT
3713676 TATTTT-TAATAAA
1 TATTTTATAA-AAA
* *
3713689 AATTTTAAAAAATA
1 TATTTTATAAAA-A
3713703 TATAGTTTA-AAAAA
1 TAT--TTTATAAAAA
3713717 TATTTTATCAAAAA
1 TATTTTAT-AAAAA
3713731 TATATTTATAAAA
1 TAT-TTTATAAAA
3713744 TTAAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 21 0.47
15 9 0.20
16 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (13 bp):
TATTTTATAAAAA
Found at i:3714262 original size:18 final size:19
Alignment explanation
Indices: 3714227--3714277 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
3714217 ATATTTAAGA
3714227 TATTATATATTTATATAAATT
1 TATTATATA-TTATAT-AATT
3714248 T-TTATATATTA-ATAATT
1 TATTATATATTATATAATT
*
3714265 TATAATATATTAT
1 TATTATATATTAT
3714278 TTTTAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 11 0.41
19 3 0.11
20 7 0.26
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATATATTATATAATT
Found at i:3714623 original size:13 final size:13
Alignment explanation
Indices: 3714593--3714630 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3714583 AATTGAATTA
3714593 ATTTATATAAATAT
1 ATTTA-ATAAATAT
3714607 ATTTAA-AAATAAT
1 ATTTAATAAAT-AT
3714620 ATTTAATAAAT
1 ATTTAATAAAT
3714631 TTAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 9 0.41
14 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTAATAAATAT
Found at i:3714680 original size:14 final size:14
Alignment explanation
Indices: 3714616--3714677 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 14
3714606 TATTTAAAAA
3714616 TAATATTTAATAAATT
1 TAAT-TTTAAT-AATT
* *
3714632 TAAATTTTATTATTT
1 T-AATTTTAATAATT
3714647 ATAATTTTTAATAATT
1 -TAA-TTTTAATAATT
3714663 TAATTTTAATTAATT
1 TAATTTTAA-TAATT
3714678 AATGGAACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
14 6 0.16
15 13 0.34
16 16 0.42
17 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATTTTAATAATT
Found at i:3714903 original size:16 final size:14
Alignment explanation
Indices: 3714853--3714908 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
3714843 AATTTAATTC
* *
3714853 AATTA-ATTTATAT
1 AATTATATTTAAAA
3714866 AATTATATTTAAAA
1 AATTATATTTAAAA
*
3714880 AATAATATTTAATAA
1 AATTATATTTAA-AA
3714895 AATT-TATATTAAAA
1 AATTATAT-TTAAAA
3714909 TCTTATTACC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 5 0.14
14 22 0.61
15 9 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTATATTTAAAA
Found at i:3718895 original size:306 final size:307
Alignment explanation
Indices: 3718283--3718900 Score: 1105
Period size: 306 Copynumber: 2.0 Consensus size: 307
3718273 ATTCAACCTG
*
3718283 ATATTGTTGAAGCTTGTTTAAGACCATATATCGACTTCTCAAGTTGACAAACTTTATGTTCGTAT
1 ATATTGTTAAAGCTTGTTTAAGACCATATATCGACTTCTCAAGTTGACAAACTTTATGTTCGTAT
*
3718348 CCCTCTACAACAAAACCCTTAAGTAGTTTTATGTAGATTTCTTCATTCAAATCACCATTGAAGAA
66 CCCTCTACAACAAAACCCTTAAGTAGTTTTATGTAGATTTCTTCATTCAAAACACCATTGAAGAA
3718413 AGCAGTGTTAACATCCATTAGATGGAATTCCAAGTCCAAATTTTCAATAACAGCTAGAATCAACC
131 AGCAGTGTTAACATCCATTAGATGGAATTCCAAGTCCAAATTTTCAATAACAGCTAGAATCAACC
3718478 TAATAGAGTTGAATCTCCTAGCAGGTGAAAAACTATCTTTGTAATTAATACCTTCTACTCATGTA
196 TAATAGAGTTGAATCTCCTAGCAGGTGAAAAACTATCTTTGTAATTAATACCTTCTACTCATGTA
*
3718543 TATTTCTTGGCAACCAAACATCTTTGTATCTCTCTATAGTACCATCC
261 TATCTCTTGGCAACCAAACATCTTTGTATCTCTCTATAGTACCATCC
* *
3718590 ATATTGTTAAAGCTTGTTTAAGACCATATATCGACTTCTTAAGTTGACAAACTTTATGTTCTTAT
1 ATATTGTTAAAGCTTGTTTAAGACCATATATCGACTTCTCAAGTTGACAAACTTTATGTTCGTAT
3718655 CCCTCTACAACAAAACCCTTAAGTAGTTTTATGTAGATTTCTTCATTCAAAACACCATTGAAGAA
66 CCCTCTACAACAAAACCCTTAAGTAGTTTTATGTAGATTTCTTCATTCAAAACACCATTGAAGAA
* * *
3718720 AGCAGTTTTCACATCCA-TAGATGGAATTCCAAGTCCAAATTTTCAATAACAGCTAGAATCAACT
131 AGCAGTGTTAACATCCATTAGATGGAATTCCAAGTCCAAATTTTCAATAACAGCTAGAATCAACC
* * *
3718784 TGATAGAGTTGAATCTCCTAGCAGGTGAAAAACTATCTTTGTAATTAATACCTTTTACTCGTGTA
196 TAATAGAGTTGAATCTCCTAGCAGGTGAAAAACTATCTTTGTAATTAATACCTTCTACTCATGTA
*
3718849 T-TCCTCTTGGCAACCAAACATCTTTGTATCTCTCTATATTACCATCC
261 TAT-CTCTTGGCAACCAAACATCTTTGTATCTCTCTATAGTACCATCC
3718896 ATATT
1 ATATT
3718901 TCTCTTAATT
Statistics
Matches: 298, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
305 1 0.00
306 156 0.52
307 141 0.47
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (307 bp):
ATATTGTTAAAGCTTGTTTAAGACCATATATCGACTTCTCAAGTTGACAAACTTTATGTTCGTAT
CCCTCTACAACAAAACCCTTAAGTAGTTTTATGTAGATTTCTTCATTCAAAACACCATTGAAGAA
AGCAGTGTTAACATCCATTAGATGGAATTCCAAGTCCAAATTTTCAATAACAGCTAGAATCAACC
TAATAGAGTTGAATCTCCTAGCAGGTGAAAAACTATCTTTGTAATTAATACCTTCTACTCATGTA
TATCTCTTGGCAACCAAACATCTTTGTATCTCTCTATAGTACCATCC
Found at i:3720913 original size:21 final size:21
Alignment explanation
Indices: 3720889--3720938 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3720879 TTTCTTGAAA
*
3720889 GTTCTCCATTCTTGGAGTTTT
1 GTTCTCCATTCTTAGAGTTTT
* *
3720910 GTTCTTCACTCTTAGAGTTTT
1 GTTCTCCATTCTTAGAGTTTT
*
3720931 -TTTTCCAT
1 GTTCTCCAT
3720939 GAACATTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.12, C:0.20, G:0.14, T:0.54
Consensus pattern (21 bp):
GTTCTCCATTCTTAGAGTTTT
Found at i:3725873 original size:6 final size:6
Alignment explanation
Indices: 3725841--3725870 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3725831 TCTTTCGTCA
*
3725841 AAGGAG AAGGAG AAGGAG AAGGAG GAGGAG
1 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG
3725871 GAGTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:3735185 original size:10 final size:10
Alignment explanation
Indices: 3735170--3735198 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3735160 CACAAACCTC
3735170 CCAAATCCCA
1 CCAAATCCCA
3735180 CCAAATCCCA
1 CCAAATCCCA
3735190 CCAAA-CCCA
1 CCAAATCCCA
3735199 AATCTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.41, C:0.52, G:0.00, T:0.07
Consensus pattern (10 bp):
CCAAATCCCA
Found at i:3743302 original size:3 final size:3
Alignment explanation
Indices: 3743288--3743319 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3743278 TCGCCAAAAG
*
3743288 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
3743320 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3744656 original size:18 final size:18
Alignment explanation
Indices: 3744625--3744668 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3744615 ACAACATAAA
3744625 AAATAATTAAAATCAATAT
1 AAAT-ATTAAAATCAATAT
* *
3744644 AAATATTATAATCTATAT
1 AAATATTAAAATCAATAT
3744662 ATAATAT
1 A-AATAT
3744669 AAGTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATTAAAATCAATAT
Found at i:3747653 original size:23 final size:23
Alignment explanation
Indices: 3747627--3747750 Score: 69
Period size: 24 Copynumber: 5.9 Consensus size: 23
3747617 ATACGTAGTG
3747627 TATTTA-TAATATATAAATT-TA
1 TATTTATTAATATATAAATTATA
* *
3747648 TA--TATTATTA-ATAAATTAAA
1 TATTTATTAATATATAAATTATA
*
3747668 T-TTTATTAA-AAATAAAATTATA
1 TATTTATTAATATAT-AAATTATA
3747690 TATTTATTAATAT-T--ATT-TA
1 TATTTATTAATATATAAATTATA
* *
3747709 -ATTTATTAATA-ATATATTGTA
1 TATTTATTAATATATAAATTATA
*
3747730 TTAATTTGTTAA-ATATAAATT
1 -T-ATTTATTAATATATAAATT
3747751 TTTTAATTAA
Statistics
Matches: 80, Mismatches: 7, Indels: 29
0.69 0.06 0.25
Matches are distributed among these distances:
18 12 0.15
19 11 0.14
20 13 0.16
21 11 0.14
22 8 0.10
23 10 0.12
24 15 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTATTAATATATAAATTATA
Found at i:3747685 original size:17 final size:18
Alignment explanation
Indices: 3747652--3747686 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3747642 AATTTATATA
*
3747652 TTATTAATAAATTAAATT
1 TTATTAATAAATAAAATT
3747670 TTATTAA-AAATAAAATT
1 TTATTAATAAATAAAATT
3747687 ATATATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTAATAAATAAAATT
Found at i:3747688 original size:15 final size:18
Alignment explanation
Indices: 3747639--3747688 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3747629 TTTATAATAT
*
3747639 ATAAATTTATATATTATTA
1 ATAAA-TTAAATATTATTA
*
3747658 ATAAATTAAATTTTATTA
1 ATAAATTAAATATTATTA
3747676 A-AAA-TAAA-ATTAT
1 ATAAATTAAATATTAT
3747689 ATATTTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 3 0.11
18 12 0.43
19 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATTAAATATTATTA
Found at i:3748449 original size:24 final size:25
Alignment explanation
Indices: 3748417--3748465 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3748407 ATTAATATTT
3748417 TATATTATATAAATTTATT-TTTTA
1 TATATTATATAAATTTATTATTTTA
* *
3748441 TATATTATATATATTTTTTATTTTA
1 TATATTATATAAATTTATTATTTTA
3748466 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATATTATATAAATTTATTATTTTA
Found at i:3748852 original size:27 final size:27
Alignment explanation
Indices: 3748817--3748869 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3748807 AGATTTAATT
*
3748817 TAATTTAATT-TTAAAATAATTAAAATG
1 TAATATAATTATTAAAA-AATTAAAATG
*
3748844 TAATATAATTATTAAAAATTTAAAAT
1 TAATATAATTATTAAAAAATTAAAAT
3748870 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
TAATATAATTATTAAAAAATTAAAATG
Found at i:3749454 original size:19 final size:18
Alignment explanation
Indices: 3749432--3749501 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 18
3749422 AATTATTTTA
3749432 AAATATTATATATTTATAT
1 AAAT-TTATATATTTATAT
3749451 AAATTTA-ATATATTA-AT
1 AAATTTATATAT-TTATAT
*
3749468 -AATTTATAT-TATATA-
1 AAATTTATATATTTATAT
3749483 AAATTTAATATATTTATAT
1 AAATTT-ATATATTTATAT
3749502 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
15 2 0.05
16 13 0.31
17 12 0.29
18 11 0.26
19 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTTATATATTTATAT
Found at i:3749464 original size:26 final size:27
Alignment explanation
Indices: 3749428--3749503 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 27
3749418 TTATAATTAT
*
3749428 TTTAAAATATTATATATTTATAT-AAA
1 TTTAATATATTATATATTTATATAAAA
3749454 TTTAATATATTAATAATTTATATTATATAAAA
1 TTTAATATATT-AT-A--TAT-TTATATAAAA
3749486 TTTAATATATT-TATATTT
1 TTTAATATATTATATATTT
3749504 TTTATTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
26 12 0.28
27 5 0.12
28 1 0.02
29 1 0.02
30 4 0.09
31 6 0.14
32 14 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAATATATTATATATTTATATAAAA
Found at i:3749476 original size:32 final size:33
Alignment explanation
Indices: 3749440--3749510 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
3749430 TAAAATATTA
3749440 TATATTTATAT-AAATTTAATATATTAATAATT
1 TATATTTATATAAAATTTAATATATTAATAATT
* *
3749472 TATA-TTATATAAAATTTAATATATTTATATTT
1 TATATTTATATAAAATTTAATATATTAATAATT
*
3749504 TTTATTT
1 TATATTT
3749511 TTATTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 6 0.18
32 26 0.76
33 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATTTATATAAAATTTAATATATTAATAATT
Found at i:3749502 original size:6 final size:6
Alignment explanation
Indices: 3749491--3749558 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
3749481 TAAAATTTAA
* * * *
3749491 TATATT TATATTT TTTATT TTTATT TATATT TTTA-T TATTTT TATATT
1 TATATT TATA-TT TATATT TATATT TATATT TATATT TATATT TATATT
* *
3749539 ATATAAT AATA-T TATATT TA
1 -TATATT TATATT TATATT TA
3749559 AAGAGTATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 7 0.14
6 32 0.65
7 10 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:3749515 original size:19 final size:20
Alignment explanation
Indices: 3749493--3749542 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
3749483 AAATTTAATA
3749493 TATTTATATTTT-TTATTTT
1 TATTTATATTTTATTATTTT
3749512 TATTTATATTTTTATTATTTT
1 TATTTATA-TTTTATTATTTT
3749533 TATATTATAT
1 TAT-TTATAT
3749543 AATAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.29
20 4 0.14
21 11 0.39
22 5 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTATATTTTATTATTTT
Found at i:3751924 original size:20 final size:20
Alignment explanation
Indices: 3751899--3751971 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
3751889 TATAATTGAT
3751899 AATATTTTAATATTATATTA
1 AATATTTTAATATTATATTA
* * *
3751919 AATATTATATTATTAAATTA
1 AATATTTTAATATTATATTA
*
3751939 ATTATTTATAATATT-TATTA
1 AATATTT-TAATATTATATTA
**
3751959 TTTA-TTTAATATT
1 AATATTTTAATATT
3751972 TAAAATTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.16
19 2 0.05
20 29 0.66
21 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTTAATATTATATTA
Found at i:3751958 original size:16 final size:17
Alignment explanation
Indices: 3751921--3751973 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
3751911 TTATATTAAA
3751921 TATTATATTATTAA-ATT
1 TATTAT-TTATTAATATT
*
3751938 AATTATTTA-TAATATT
1 TATTATTTATTAATATT
3751954 TATTATTTATTTAATATT
1 TATTATTTA-TTAATATT
3751972 TA
1 TA
3751974 AAATTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 3 0.10
16 14 0.45
17 5 0.16
18 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATTTATTAATATT
Found at i:3751959 original size:12 final size:13
Alignment explanation
Indices: 3751900--3751959 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 13
3751890 ATAATTGATA
*
3751900 ATATTTTAATATT
1 ATATTATAATATT
3751913 ATATTA-AATATT
1 ATATTATAATATT
3751925 ATATTATTAA-ATT
1 ATATTA-TAATATT
3751938 AATTATTTATAATATT
1 -A-TA-TTATAATATT
3751954 -TATTAT
1 ATATTAT
3751960 TTATTTAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
12 16 0.40
13 10 0.25
14 3 0.08
15 5 0.12
16 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTATAATATT
Found at i:3751984 original size:18 final size:18
Alignment explanation
Indices: 3751938--3751986 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3751928 TTATTAAATT
*
3751938 AATTATTTATAATATTTAT
1 AATTATTT-TAATATTTAA
*
3751957 TATT-TATTTAATATTTAA
1 AATTAT-TTTAATATTTAA
3751975 AATTATTTTAAT
1 AATTATTTTAAT
3751987 CAAATCACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTATTTTAATATTTAA
Found at i:3753106 original size:15 final size:17
Alignment explanation
Indices: 3753080--3753128 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
3753070 TTAAAATATG
3753080 ATAA-ATTAAAATTTAT
1 ATAATATTAAAATTTAT
3753096 ATAATA-T-AAA-TTAT
1 ATAATATTAAAATTTAT
*
3753110 A-ATTATTAAAATTTAT
1 ATAATATTAAAATTTAT
3753126 ATA
1 ATA
3753129 TAAAATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.11
14 6 0.22
15 6 0.22
16 10 0.37
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATATTAAAATTTAT
Found at i:3753147 original size:14 final size:13
Alignment explanation
Indices: 3753071--3753172 Score: 55
Period size: 15 Copynumber: 7.2 Consensus size: 13
3753061 AAAAATAATT
3753071 TAAAATATGATAAA
1 TAAAATAT-ATAAA
*
3753085 TTAAAATTTATATAA
1 -TAAAATATATA-AA
3753100 TATAAAT-TATAATTA
1 TA-AAATATATAA--A
* *
3753115 TTAAAATTTATATA
1 -TAAAATATATAAA
3753129 TAAAATATCATAAA
1 TAAAATAT-ATAAA
3753143 TAAAAT-TATGAAA
1 TAAAATATAT-AAA
*
3753156 TAGTAAATATACAAA
1 TA--AAATATATAAA
3753171 TA
1 TA
3753173 GCGATATGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
12 2 0.03
13 14 0.20
14 20 0.28
15 27 0.38
16 8 0.11
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (13 bp):
TAAAATATATAAA
Found at i:3754535 original size:25 final size:24
Alignment explanation
Indices: 3754506--3754566 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
3754496 GTTAATAATA
*
3754506 TATATTATATAAATTTATATTATAT
1 TATATTTTATAAATTTATA-TATAT
* *
3754531 TATATTTTAATTATTTTATATATAT
1 TATATTTT-ATAAATTTATATATAT
3754556 TAT-TTTTATAA
1 TATATTTTATAA
3754567 TCATATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 3 0.10
24 4 0.13
25 15 0.48
26 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATATTTTATAAATTTATATATAT
Found at i:3754543 original size:16 final size:17
Alignment explanation
Indices: 3754506--3754583 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 17
3754496 GTTAATAATA
*
3754506 TATATTATA-TA-AATT
1 TATATTATATTATATTT
3754521 TATATTATATTATATTT
1 TATATTATATTATATTT
*
3754538 TA-ATTATTTTATATATAT
1 TATATTATATTATAT-T-T
* *
3754556 TATTTTTATAATCATATTT
1 TA-TATTAT-ATTATATTT
*
3754575 AATATTATA
1 TATATTATA
3754584 AATTTACTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
15 9 0.18
16 13 0.27
17 7 0.14
18 8 0.16
19 2 0.04
20 5 0.10
21 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTATATTATATTT
Found at i:3766438 original size:16 final size:14
Alignment explanation
Indices: 3766404--3766512 Score: 66
Period size: 14 Copynumber: 7.7 Consensus size: 14
3766394 GAAAAAAAGA
3766404 ATATTTATATATTT
1 ATATTTATATATTT
3766418 ATATTTATATTAATTT
1 ATATTTATA-T-ATTT
* *
3766434 TTATTTA-AAATATT
1 ATATTTATATAT-TT
* **
3766448 ATATTTTTATATAAA
1 ATATTTATATAT-TT
*
3766463 ATATATTA-ATACTT
1 ATAT-TTATATATTT
3766477 -T-TTTATATATTT
1 ATATTTATATATTT
3766489 ATA-TTATATATATT
1 ATATTTATATAT-TT
*
3766503 ATTTTTATAT
1 ATATTTATAT
3766513 TATGTTTTAA
Statistics
Matches: 72, Mismatches: 13, Indels: 19
0.69 0.12 0.18
Matches are distributed among these distances:
11 3 0.04
12 6 0.08
13 12 0.17
14 20 0.28
15 19 0.26
16 12 0.17
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATTTATATATTT
Found at i:3766439 original size:22 final size:21
Alignment explanation
Indices: 3766413--3766494 Score: 53
Period size: 22 Copynumber: 3.8 Consensus size: 21
3766403 AATATTTATA
3766413 TATTTATATTTATATTAATTTT
1 TATTTA-ATTTATATTAATTTT
*
3766435 TATTTAA--AATATTATATTTT
1 TATTTAATTTATATTA-ATTTT
* **
3766455 TATATAAAATATATTAATACTTT
1 TATTTAATTTATATTAAT--TTT
3766478 T-TTATATATTTATATTA
1 TATT-TA-ATTTATATTA
3766495 TATATATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
19 6 0.13
20 11 0.23
21 3 0.06
22 13 0.28
23 6 0.13
24 8 0.17
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTAATTTATATTAATTTT
Found at i:3766448 original size:19 final size:20
Alignment explanation
Indices: 3766424--3766466 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3766414 ATTTATATTT
*
3766424 ATATTA-ATTTTTATTTAAA
1 ATATTATATTTTTATATAAA
3766443 ATATTATATTTTTATATAAA
1 ATATTATATTTTTATATAAA
3766463 ATAT
1 ATAT
3766467 ATTAATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTATATTTTTATATAAA
Found at i:3766549 original size:39 final size:40
Alignment explanation
Indices: 3766477--3766560 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 40
3766467 ATTAATACTT
* * * *
3766477 TTTTATATATTTATATTATATATATTATTTTTATATTATG
1 TTTTAAATATTTATATTATAAATATCATGTTTATATTATG
* *
3766517 TTTTAAATATTT-TTTTATAAATATCATGTTTATATTATT
1 TTTTAAATATTTATATTATAAATATCATGTTTATATTATG
3766556 TTTTA
1 TTTTA
3766561 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (40 bp):
TTTTAAATATTTATATTATAAATATCATGTTTATATTATG
Found at i:3766745 original size:12 final size:12
Alignment explanation
Indices: 3766722--3766768 Score: 62
Period size: 11 Copynumber: 4.1 Consensus size: 12
3766712 TATTCACGTC
3766722 ATATTA-TTTTT
1 ATATTATTTTTT
3766733 ATATTATTTTTT
1 ATATTATTTTTT
3766745 A-ATTATTTTTT
1 ATATTATTTTTT
* *
3766756 ATGTTATATTTT
1 ATATTATTTTTT
3766768 A
1 A
3766769 AATTTTTCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:3766754 original size:23 final size:22
Alignment explanation
Indices: 3766724--3766769 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
3766714 TTCACGTCAT
*
3766724 ATTATTTTTATATTATTTTTTA
1 ATTATTTTTATATTATATTTTA
*
3766746 ATTATTTTTTATGTTATATTTTA
1 ATTA-TTTTTATATTATATTTTA
3766769 A
1 A
3766770 ATTTTTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTATTTTTATATTATATTTTA
Found at i:3767009 original size:16 final size:17
Alignment explanation
Indices: 3766978--3767011 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3766968 TTAATTTAAT
*
3766978 TAAAATAATTACAAATA
1 TAAAATAATTAAAAATA
3766995 TAAAA-AATTAAAAATA
1 TAAAATAATTAAAAATA
3767011 T
1 T
3767012 TGTTAACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATAATTAAAAATA
Found at i:3767706 original size:15 final size:16
Alignment explanation
Indices: 3767686--3767716 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3767676 ATTTTTAAAT
3767686 TAATTTTA-TTAATTA
1 TAATTTTATTTAATTA
3767701 TAATTTTATTTAATTA
1 TAATTTTATTTAATTA
3767717 AAAATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTTTATTTAATTA
Found at i:3767850 original size:18 final size:19
Alignment explanation
Indices: 3767822--3767868 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
3767812 CGTGTCACTT
*
3767822 TTTTGTTTTTGGCTTTCAA-
1 TTTT-TTTTTGGCTTTAAAC
3767841 TTTTTTTTTGGCTTTAAAC
1 TTTTTTTTTGGCTTTAAAC
3767860 TTTTTTTTT
1 TTTTTTTTT
3767869 AAGTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTTTTTTTGGCTTTAAAC
Found at i:3767947 original size:24 final size:24
Alignment explanation
Indices: 3767920--3767968 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
3767910 ATATTTGTAT
3767920 TTATAATTTTT-TATATTTAAAATA
1 TTAT-ATTTTTATATATTTAAAATA
*
3767944 TTATATTTTTATATTTTTAAAATA
1 TTATATTTTTATATATTTAAAATA
3767968 T
1 T
3767969 ATTAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATATTTTTATATATTTAAAATA
Found at i:3768296 original size:22 final size:21
Alignment explanation
Indices: 3768271--3768323 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
3768261 ATTCGTATCG
3768271 TGTTTATGTTATTTTTTTATTA
1 TGTTTATGTTA-TTTTTTATTA
*
3768293 TGTTT-TAATTATTTTTTATTA
1 TGTTTAT-GTTATTTTTTATTA
3768314 T-TGTTATGTT
1 TGT-TTATGTT
3768324 CATATAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 1 0.04
21 16 0.62
22 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (21 bp):
TGTTTATGTTATTTTTTATTA
Found at i:3768992 original size:13 final size:13
Alignment explanation
Indices: 3768974--3769060 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 13
3768964 TTGTCTTATA
3768974 TTTTATATAAATT
1 TTTTATATAAATT
*
3768987 TTTTATATGATTAAAT
1 TTTTATAT-A--AATT
* *
3769003 TTTAACTTTAAATT
1 TTTTA-TATAAATT
3769017 TATTTAT-TAAATAT
1 T-TTTATATAAAT-T
*
3769031 TTTTAAATAAATT
1 TTTTATATAAATT
*
3769044 TTATTAAATATAATT
1 TT-TTATATA-AATT
3769059 TT
1 TT
3769061 ATTTAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
13 20 0.34
14 20 0.34
15 9 0.15
16 8 0.14
17 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (13 bp):
TTTTATATAAATT
Found at i:3769060 original size:15 final size:15
Alignment explanation
Indices: 3769033--3769085 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
3769023 TTAAATATTT
3769033 TTAAATA-AATTTTA
1 TTAAATATAATTTTA
3769047 TTAAATATAATTTTA
1 TTAAATATAATTTTA
* *
3769062 TTTAATTAAAAATTTTA
1 -TTAAAT-ATAATTTTA
3769079 -TAAATAT
1 TTAAATAT
3769086 TAAAACTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 5 0.16
17 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATATAATTTTA
Found at i:3769066 original size:16 final size:15
Alignment explanation
Indices: 3769011--3769071 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 15
3769001 ATTTTAACTT
*
3769011 TAAA-TTTATTT-AT
1 TAAATTTTATTTAAA
*
3769024 TAAATATT-TTTAAA
1 TAAATTTTATTTAAA
3769038 TAAATTTTA-TTAAA
1 TAAATTTTATTTAAA
*
3769052 TATAATTTTATTTAAT
1 TA-AATTTTATTTAAA
3769068 TAAA
1 TAAA
3769072 AATTTTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 7 0.18
14 17 0.44
15 9 0.23
16 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATTTTATTTAAA
Found at i:3770900 original size:29 final size:29
Alignment explanation
Indices: 3770850--3770924 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
3770840 AATTTTTAAG
*
3770850 TATATTTTAATTTTATAAAAATTTATATAAAA
1 TATA-TTTATTTTTATAAAAA-TTATA-AAAA
3770882 T-TATTTATTTTTAT-AAAATTATAAAAA
1 TATATTTATTTTTATAAAAATTATAAAAA
*
3770909 TAATATATATTTTTAT
1 T-ATATTTATTTTTAT
3770925 TTTAAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 5 0.13
28 5 0.13
29 16 0.41
30 10 0.26
31 2 0.05
32 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TATATTTATTTTTATAAAAATTATAAAAA
Found at i:3770958 original size:34 final size:34
Alignment explanation
Indices: 3770862--3770958 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 34
3770852 TATTTTAATT
*
3770862 TTATAAAAATTTATATAAAATTATTTATTTTTATAAAA
1 TTATAAAAA-TAATAT-AAA-TATTTA-TTTTATAAAA
* *
3770900 TTATAAAAATAATATATATTTTTATTTTA-AAAA
1 TTATAAAAATAATATAAATATTTATTTTATAAAA
*
3770933 CTT-TAATAATAATTATAAATATTTAT
1 -TTATAAAAATAA-TATAAATATTTAT
3770959 AAAATTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
33 12 0.24
34 18 0.35
35 5 0.10
36 2 0.04
37 5 0.10
38 9 0.18
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (34 bp):
TTATAAAAATAATATAAATATTTATTTTATAAAA
Found at i:3770992 original size:37 final size:36
Alignment explanation
Indices: 3770934--3771031 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 36
3770924 TTTTAAAAAC
3770934 TTTAATA-ATAATTATAAATATTTATAAAATTTTTATA
1 TTTAATATATAATTATAAATATTT-TAAAATTTTT-TA
* * *
3770971 TTTAATATATGATT-TATATATTTTATAATTTTTTA
1 TTTAATATATAATTATAAATATTTTAAAATTTTTTA
*
3771006 -TTAATTATATAAAT-TAAA-ATTTTAAA
1 TTTAA-TATATAATTATAAATATTTTAAA
3771032 TATGAATGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
34 11 0.21
35 12 0.23
36 9 0.17
37 15 0.29
38 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
TTTAATATATAATTATAAATATTTTAAAATTTTTTA
Found at i:3771085 original size:17 final size:16
Alignment explanation
Indices: 3771046--3771087 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
3771036 AATGTAATAA
3771046 ATATATTAAATATATT
1 ATATATTAAATATATT
3771062 ATCATATT-AATAAGTATT
1 AT-ATATTAAAT-A-TATT
3771080 ATATATTA
1 ATATATTA
3771088 TTTTTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATTAAATATATT
Found at i:3780037 original size:89 final size:90
Alignment explanation
Indices: 3779886--3780055 Score: 254
Period size: 89 Copynumber: 1.9 Consensus size: 90
3779876 TTGGATATTA
* *
3779886 ATGTTATATAATGAAGGATTGAATGCATTGGAATGTGAACACTTACTGGAAAGTTGTTATTTCA-
1 ATGTTATATAAAGAAGGAATGAATGCATTGGAATGTGAACACTTACTGGAAAGTTGTTATTTCAT
3779950 TTTTCTCATTTCACTTCTTAATAAT
66 TTTTCTCATTTCACTTCTTAATAAT
* * * *
3779975 ATGTTATATAAAGAAGGAATGGATGCGTTGGAATGTTAAGACTTACTGGAAA-TGTGTTATTTCA
1 ATGTTATATAAAGAAGGAATGAATGCATTGGAATGTGAACACTTACTGGAAAGT-TGTTATTTCA
*
3780039 TTTTTTTCATTTCACTT
65 TTTTTCTCATTTCACTT
3780056 TATCTATTCT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
88 1 0.01
89 56 0.78
90 15 0.21
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.42
Consensus pattern (90 bp):
ATGTTATATAAAGAAGGAATGAATGCATTGGAATGTGAACACTTACTGGAAAGTTGTTATTTCAT
TTTTCTCATTTCACTTCTTAATAAT
Found at i:3780878 original size:21 final size:21
Alignment explanation
Indices: 3780853--3780901 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3780843 CGAGAGTGAT
*
3780853 GATG-AGGAGGAACATGAAGAA
1 GATGAAGGA-GAACAAGAAGAA
*
3780874 GATGAAGGAGAACAAGAGGAA
1 GATGAAGGAGAACAAGAAGAA
*
3780895 GAAGAAG
1 GATGAAG
3780902 AAGTGAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.04, G:0.39, T:0.06
Consensus pattern (21 bp):
GATGAAGGAGAACAAGAAGAA
Found at i:3784732 original size:3 final size:3
Alignment explanation
Indices: 3784724--3784765 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3784714 CGACGTGTGG
3784724 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
3784766 GTAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3789795 original size:2 final size:2
Alignment explanation
Indices: 3789782--3789823 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3789772 GGGAAAAAGC
*
3789782 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3789823 A
1 A
3789824 GCTAGAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3792348 original size:12 final size:12
Alignment explanation
Indices: 3792331--3792369 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
3792321 TGATTAGTAA
3792331 ATTT-AAATTATT
1 ATTTAAAATT-TT
3792343 ATTTAAAATTTT
1 ATTTAAAATTTT
3792355 -TTTAAAATTTT
1 ATTTAAAATTTT
3792366 ATTT
1 ATTT
3792370 TTATATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.44
12 9 0.36
13 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTAAAATTTT
Found at i:3792403 original size:20 final size:20
Alignment explanation
Indices: 3792367--3792404 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3792357 TAAAATTTTA
*
3792367 TTTTTATATTGATATTTATT
1 TTTTTATATTGAAATTTATT
3792387 TTTTTATAATT-AAATTTA
1 TTTTTAT-ATTGAAATTTA
3792405 AATAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTTATATTGAAATTTATT
Found at i:3795356 original size:2 final size:2
Alignment explanation
Indices: 3795349--3795393 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3795339 GCACACCCGC
3795349 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
3795391 AT A
1 AT A
3795394 AAGAAATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3803943 original size:20 final size:21
Alignment explanation
Indices: 3803918--3803973 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
3803908 TTGTATCATA
3803918 TTAATTTTTTATATT-ATGTT
1 TTAATTTTTTATATTCATGTT
3803938 TTAATTATTTT-TATGTCATGTT
1 TTAATT-TTTTATAT-TCATGTT
*
3803960 TTTA-TTTTTATATT
1 TTAATTTTTTATATT
3803974 TAAAGTAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 14 0.45
21 9 0.29
22 8 0.26
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
TTAATTTTTTATATTCATGTT
Found at i:3803951 original size:22 final size:22
Alignment explanation
Indices: 3803897--3803973 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 22
3803887 TATATATCTA
* *
3803897 TATTTTTATATT-TGTATCATAT
1 TATTTTTATATTATGTTTTA-AT
3803919 TAATTTTTTATATTATGTTTTAAT
1 T-A-TTTTTATATTATGTTTTAAT
* *
3803943 TATTTTTATGTCATG-TTT--T
1 TATTTTTATATTATGTTTTAAT
3803962 TATTTTTATATT
1 TATTTTTATATT
3803974 TAAAGTAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 11 0.24
21 3 0.07
22 12 0.26
23 2 0.04
24 13 0.28
25 5 0.11
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (22 bp):
TATTTTTATATTATGTTTTAAT
Found at i:3804458 original size:20 final size:20
Alignment explanation
Indices: 3804435--3804484 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3804425 CAAAAGATGC
3804435 AAAAAAAAAAGAAAAAAGAA
1 AAAAAAAAAAGAAAAAAGAA
* * *
3804455 AAAAATAAAAGAAGAGAGAA
1 AAAAAAAAAAGAAAAAAGAA
3804475 ATAAAAAAAA
1 A-AAAAAAAA
3804485 TTTAATGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAGAAAAAAGAA
Found at i:3804469 original size:16 final size:15
Alignment explanation
Indices: 3804438--3804482 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3804428 AAGATGCAAA
*
3804438 AAAAAAAGAAAAAAG
1 AAAAAAATAAAAAAG
3804453 AAAAAAATAAAAGAAG
1 AAAAAAATAAAA-AAG
* *
3804469 AGAGAAATAAAAAA
1 AAAAAAATAAAAAA
3804483 AATTTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (15 bp):
AAAAAAATAAAAAAG
Found at i:3804597 original size:22 final size:21
Alignment explanation
Indices: 3804571--3804636 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
3804561 TATTTTATGT
3804571 TTTTATATTCATGTTATATTTA
1 TTTTATATTCATGTT-TATTTA
*
3804593 TTTTATATT-ATGTTTTAATTA
1 TTTTATATTCATG-TTTATTTA
*
3804614 TTTTATA-TCATATTT-TTTA
1 TTTTATATTCATGTTTATTTA
3804633 TTTT
1 TTTT
3804637 TTGTTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 7 0.18
20 4 0.10
21 17 0.44
22 11 0.28
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTATATTCATGTTTATTTA
Found at i:3804614 original size:21 final size:22
Alignment explanation
Indices: 3804571--3804621 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
3804561 TATTTTATGT
*
3804571 TTTTATATTCATGTTATATTTA
1 TTTTATATTCATGTTATAATTA
*
3804593 TTTTATATT-ATGTTTTAATTA
1 TTTTATATTCATGTTATAATTA
3804614 TTTTATAT
1 TTTTATAT
3804622 CATATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTATATTCATGTTATAATTA
Found at i:3804629 original size:21 final size:20
Alignment explanation
Indices: 3804550--3804636 Score: 72
Period size: 21 Copynumber: 4.3 Consensus size: 20
3804540 ATTTGTATAA
*
3804550 TATTTTACAT-ATATTTTAT
1 TATTTTATATCATATTTTAT
* *
3804569 GT-TTTTATATTCATGTTATATT
1 -TATTTTATA-TCATATTTTA-T
* *
3804591 TATTTTATATTATGTTTTAAT
1 TATTTTATATCATATTTT-AT
3804612 TATTTTATATCATATTTT-T
1 TATTTTATATCATATTTTAT
3804631 TATTTT
1 TATTTT
3804637 TTGTTTATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
19 13 0.24
20 2 0.04
21 31 0.56
22 9 0.16
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTTTATATCATATTTTAT
Found at i:3804638 original size:21 final size:21
Alignment explanation
Indices: 3804557--3804638 Score: 55
Period size: 22 Copynumber: 3.8 Consensus size: 21
3804547 TAATATTTTA
*
3804557 CATATATTTTATGTTTTTATATT
1 CATATTTTTTAT-TTTTTATA-T
*
3804580 CATGTTATATTTA--TTTTATAT
1 CATATT-T-TTTATTTTTTATAT
*
3804601 --TATGTTTTAATTATTTTATAT
1 CATAT-TTTTTATT-TTTTATAT
3804622 CATATTTTTTATTTTTT
1 CATATTTTTTATTTTTT
3804639 GTTTATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 1 0.02
21 13 0.28
22 14 0.30
23 7 0.15
24 1 0.02
25 4 0.09
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
CATATTTTTTATTTTTTATAT
Found at i:3804812 original size:670 final size:665
Alignment explanation
Indices: 3803763--3805019 Score: 1597
Period size: 670 Copynumber: 1.9 Consensus size: 665
3803753 AGATGGAAAG
* * * *
3803763 AAAAAAAAAAGAAAAAAAAGAAAATGAGAGAAGGAAATAAAAGAAAATTTAATTTGTTTATGTTT
1 AAAAAAAAAAGAAAAAAAAAAAAATAAAAGAAGGAAATAAAAGAAAATTTAATGTGTTTATGTTT
* * * *
3803828 GTAATCATGTTATTTTTTTATTGTTTAAAGTATCGTAGAGTTATATAATATTTTACACATATATA
66 ATAATCATGTTATTTTTTTATTATTTAAAGTATCATAAAGTTATATAATATTTTA-ACATATATA
* *
3803893 TCTATATTTTTATATTTGTATCATATTAATTTTTTATATTATGTTTTAATTATTTTTATGTCATG
130 TCTATATTTTTATATTTGTATCATATT-ATATTTTATATTATGTTTTAATTATTTTTATATCATG
* *
3803958 TTTTTATTTTTATATTTAAAGTAGTATAAATTTATATAAATTTTTAAATATTAATTATTTATTTA
194 TTTTTATTTTTATATTTAAAGTAGTATAAATTTATATAAATTTTTAAACAATAATTATTTATTTA
* * * * * * *
3804023 TATAAATTTTGATATGTTAGTTTAATTATATGATATATTTAAAATGATAGATCCTCACATTAATA
259 TAT-AATATTGACATATTAGTGTAATTAAATGATATATTTAAAATGATAAATCCTCAAATTAATA
*
3804088 CATGATCGATTTAAAATTCATACCCTATTCTAAATGCAAATTTAAATAAATAAATATTATTTAAT
323 CATGATCAATTTAAAATTCATACCCTATTCTAAATGCAAATTTAAATAAATAAATATTATTTAAT
* * *
3804153 AAATTTTAATTTTTATT-AA-A-AA-T-ACAA-A-A-AAATTAAAAAT-ATCATTATTTATTTTA
388 AAA-ATTAATTTTTATTAAATATAATTAAAAATATATAAATTAAAAATAAT-ATTAATTATTTTA
* * *
3804209 TTTCTAAATGATGTGTTTAAAGTAATAAATTTTGATGTTA-ACTCACAAAATAATTAAATTTTAT
451 TTT-TAAATGATATATTTAAAATAATAAA---T-AT-TTACA-TCAC-----AATTAAATTTTAT
** *
3804273 TTTCAATTTTAAATGTAAAATTTAAATATATAATTATTATTTAATAAAATTTATTTTATAATTAA
504 TTTCAATTTTAAATACAAAATTTAAATACATAATTATTATTTAATAAAATTTATTTTATAATTAA
3804338 ATTTTCATTAATAATATCAAATTAACTATATAAATAAATCTAGTGTTGACTCCTATTTTTGAGTT
569 ATTTTCATTAATAATATCAAATTAACTATATAAATAAATCTAGTGTTGACTCCTATTTTTGAGTT
3804403 TTTTTTCAACAATAACGGAGAGCAAAAGATGC
634 TTTTTTCAACAATAACGGAGAGCAAAAGATGC
3804435 AAAAAAAAAAGAAAAAAGAAAAAAATAAAAGAAGAGAGAAATAAAA-AAAATTTAATGTGTTTAT
1 AAAAAAAAAAGAAAAAA-AAAAAAATAAAAG-A-AG-GAAATAAAAGAAAATTTAATGTGTTTAT
* * * * *
3804499 GTTTATATTTATGTTA-TTTTTTATTATTTAAAGTATTATAAATTTGTATAATATTTT-ACATAT
62 GTTTATAATCATGTTATTTTTTTATTATTTAAAGTATCATAAAGTTATATAATATTTTAACATAT
* *
3804562 AT-TTTATGTTTTTATATTCATGT-T-ATATT-TATTTTATATTATGTTTTAATTA-TTTTATAT
127 ATATCTATATTTTTATATT--TGTATCATATTATATTTTATATTATGTTTTAATTATTTTTATAT
* *
3804622 CATATTTTTTATTTTTTGTTTATATATTAAAGTAGTATAAATTTA-ATAAATTTTTACACAAT-A
190 CAT-GTTTTTA----TT-TTTATAT-TTAAAGTAGTATAAATTTATATAAATTTTTAAACAATAA
* * *
3804685 TTA-TTATTTATGT-ATATTGACATATTCGTGTAATTAAATGATATATTTAAAATGATAAATTCG
248 TTATTTATTTATATAATATTGACATATTAGTGTAATTAAATGATATATTTAAAATGATAAA-TCC
* ** * * * *
3804748 T-AAATTGATGTATGATCAATTTAAAATTTATACCTTATTTTAAATGTAAATTTAAATAAATAAA
312 TCAAATTAATACATGATCAATTTAAAATTCATACCCTATTCTAAATGCAAATTTAAATAAATAAA
3804812 TATTATTTAATAAAATTAATTTTTATTAAATATAATTAAAAATATATAAATTAAAAATAATATTA
377 TATTATTTAATAAAATTAATTTTTATTAAATATAATTAAAAATATATAAATTAAAAATAATATTA
* *
3804877 ATTATTTTATTTTAAATGATATATTTAAAATAATGAATATTTACATTACAATTAAATTTTATTTT
442 ATTATTTTATTTTAAATGATATATTTAAAATAATAAATATTTACATCACAATTAAATTTTATTTT
*
3804942 TAATTTTAAATACAAAATTTAAATACATAATTATTATTTAATAAAATTTATTTTATAATTAAATT
507 CAATTTTAAATACAAAATTTAAATACATAATTATTATTTAATAAAATTTATTTTATAATTAAATT
* *
3805007 TTTATTATTAATA
572 TTCATTAATAATA
3805020 ATTAAAATTT
Statistics
Matches: 508, Mismatches: 53, Indels: 54
0.83 0.09 0.09
Matches are distributed among these distances:
666 88 0.17
668 10 0.02
669 40 0.08
670 109 0.21
671 29 0.06
672 40 0.08
673 21 0.04
674 60 0.12
675 52 0.10
676 31 0.06
677 26 0.05
678 2 0.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (665 bp):
AAAAAAAAAAGAAAAAAAAAAAAATAAAAGAAGGAAATAAAAGAAAATTTAATGTGTTTATGTTT
ATAATCATGTTATTTTTTTATTATTTAAAGTATCATAAAGTTATATAATATTTTAACATATATAT
CTATATTTTTATATTTGTATCATATTATATTTTATATTATGTTTTAATTATTTTTATATCATGTT
TTTATTTTTATATTTAAAGTAGTATAAATTTATATAAATTTTTAAACAATAATTATTTATTTATA
TAATATTGACATATTAGTGTAATTAAATGATATATTTAAAATGATAAATCCTCAAATTAATACAT
GATCAATTTAAAATTCATACCCTATTCTAAATGCAAATTTAAATAAATAAATATTATTTAATAAA
ATTAATTTTTATTAAATATAATTAAAAATATATAAATTAAAAATAATATTAATTATTTTATTTTA
AATGATATATTTAAAATAATAAATATTTACATCACAATTAAATTTTATTTTCAATTTTAAATACA
AAATTTAAATACATAATTATTATTTAATAAAATTTATTTTATAATTAAATTTTCATTAATAATAT
CAAATTAACTATATAAATAAATCTAGTGTTGACTCCTATTTTTGAGTTTTTTTTCAACAATAACG
GAGAGCAAAAGATGC
Found at i:3804874 original size:16 final size:15
Alignment explanation
Indices: 3804840--3804880 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3804830 ATTTTTATTA
3804840 AATATAATTAAAAAT
1 AATATAATTAAAAAT
3804855 -ATATAAATTAAAAAT
1 AATAT-AATTAAAAAT
3804870 AATATTAATTA
1 AATA-TAATTA
3804881 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
16 8 0.35
17 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAATTAAAAAT
Found at i:3805000 original size:17 final size:20
Alignment explanation
Indices: 3804972--3805031 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 20
3804962 AAATACATAA
3804972 TTATTATT--TAA-TAAAAT
1 TTATTATTAATAATTAAAAT
*
3804989 TTATT-TT-ATAATTAAATTT
1 TTATTATTAATAATTAAA-AT
3805008 TTATTATTAATAATTAAAAT
1 TTATTATTAATAATTAAAAT
3805028 TTAT
1 TTAT
3805032 AAAATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.06
17 8 0.22
18 4 0.11
19 6 0.17
20 7 0.19
21 9 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTATTAATAATTAAAAT
Found at i:3805862 original size:2 final size:2
Alignment explanation
Indices: 3805855--3805888 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3805845 TAATTATAAT
3805855 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
3805889 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3807240 original size:28 final size:29
Alignment explanation
Indices: 3807200--3807265 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
3807190 TTATAATTAT
*
3807200 AATTTAATAATAAAA-AT-ATTTTTATTTA
1 AATTTTATAATAAAATATAATTTTT-TTTA
*
3807228 AATTTTATTATAAAATATAATTTTTTTTA
1 AATTTTATAATAAAATATAATTTTTTTTA
3807257 ATATTTTAT
1 A-ATTTTAT
3807266 GATTTTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 13 0.39
29 7 0.21
30 13 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTTATAATAAAATATAATTTTTTTTA
Found at i:3812643 original size:25 final size:25
Alignment explanation
Indices: 3812598--3812707 Score: 63
Period size: 23 Copynumber: 4.6 Consensus size: 25
3812588 AAAATTTATT
* *
3812598 TTATTTTT-CATTATATTTTTAAATA
1 TTATTTTTATATTA-ATATTTAAATA
3812623 TTATTTTTATATTAATATTT--ATA
1 TTATTTTTATATTAATATTTAAATA
* **
3812646 TT-TTTTTATAATTAAAAAATAAA-A
1 TTATTTTTAT-ATTAATATTTAAATA
* * * *
3812670 ATATTTTTAT-TT-TTATTAAAAAA
1 TTATTTTTATATTAATATTTAAATA
*
3812693 TTATTTTTATTTTAA
1 TTATTTTTATATTAA
3812708 ATAATACTTC
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.17
23 24 0.38
24 4 0.06
25 21 0.33
26 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATTTTTATATTAATATTTAAATA
Found at i:3813967 original size:20 final size:20
Alignment explanation
Indices: 3813934--3813977 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3813924 ATATATATAT
*
3813934 ATATATATATATTTGATAAA
1 ATATATATAAATTTGATAAA
* **
3813954 ATATATTTAAATTTTTTAAA
1 ATATATATAAATTTGATAAA
3813974 ATAT
1 ATAT
3813978 TTTTTATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATATATAAATTTGATAAA
Found at i:3814060 original size:13 final size:13
Alignment explanation
Indices: 3814042--3814066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3814032 AGATATACTG
3814042 AAAATAAATATTA
1 AAAATAAATATTA
3814055 AAAATAAATATT
1 AAAATAAATATT
3814067 TTAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAAATATTA
Found at i:3814087 original size:18 final size:18
Alignment explanation
Indices: 3814054--3814088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3814044 AATAAATATT
* *
3814054 AAAAATAAATATTTTAAA
1 AAAAATAAAAAGTTTAAA
3814072 AAAAATAAAAAGTTTAA
1 AAAAATAAAAAGTTTAA
3814089 GCAATTTTAT
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:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAATAAAAAGTTTAAA
Found at i:3817800 original size:2 final size:2
Alignment explanation
Indices: 3817793--3817819 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3817783 TTTTCTTTGG
3817793 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
3817820 AGAGCTGCCC
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:3826542 original size:63 final size:63
Alignment explanation
Indices: 3826468--3826592 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
3826458 ACTTTGGCTA
* *
3826468 AAACAGTATCTCATATTGGTATGCCCTCTCCTACTCAGGACTGCTGGTATTATCCCTTACCTC
1 AAACACTATCTCATATTGGTATGCCCTCTCCTACTCAGGACTGCTGGTATTATCCCTCACCTC
* *
3826531 AAACACTATCTCATATTGGTGTGCCCTCTCCTACTCAGGATTGCTGGTATTATCCCTCACCT
1 AAACACTATCTCATATTGGTATGCCCTCTCCTACTCAGGACTGCTGGTATTATCCCTCACCT
3826593 ACCAAAAGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (63 bp):
AAACACTATCTCATATTGGTATGCCCTCTCCTACTCAGGACTGCTGGTATTATCCCTCACCTC
Found at i:3829704 original size:35 final size:35
Alignment explanation
Indices: 3829644--3829712 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
3829634 TTGTTCAGAA
* **
3829644 CCTTGTGAATACCTTACTGTAAAGGTCATGGAAAC
1 CCTTGTGAATAACTTACTACAAAGGTCATGGAAAC
* *
3829679 CCTTGTGAATAACTTACTACCAAGGTCCTGGAAA
1 CCTTGTGAATAACTTACTACAAAGGTCATGGAAA
3829713 TGCCTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (35 bp):
CCTTGTGAATAACTTACTACAAAGGTCATGGAAAC
Found at i:3831673 original size:1 final size:1
Alignment explanation
Indices: 3831667--3831691 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3831657 TCCCTTGAGG
3831667 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3831692 CTAGTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.