Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 11 of 311
Found at i:3138737 original size:16 final size:17
Alignment explanation
Indices: 3138716--3138748 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3138706 ATGATGGTGC
3138716 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
3138732 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
3138749 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:3155035 original size:23 final size:23
Alignment explanation
Indices: 3155009--3155062 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3154999 TCATTCTTGC
*
3155009 TTAGTTTTA-TTTCTATTTGTAAT
1 TTAGTTTTATTTTC-AGTTGTAAT
*
3155032 TTAGGTTTATTTTCAGTTGTAAT
1 TTAGTTTTATTTTCAGTTGTAAT
3155055 TGTAGTTT
1 T-TAGTTT
3155063 AGTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (23 bp):
TTAGTTTTATTTTCAGTTGTAAT
Found at i:3156956 original size:46 final size:46
Alignment explanation
Indices: 3156904--3156997 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
3156894 GGATTAGGAT
* * *
3156904 TAGTTTAGTCTTGCCTCCCTTGGGTATGATCATCGGAGTACTTCCA
1 TAGTTTAGTCTCGCCTCCCCTGGGTACGATCATCGGAGTACTTCCA
*
3156950 TAGTTTAGTCTCGCCTCCCCTGGGTACGATCTTCGGAGTACTTCCA
1 TAGTTTAGTCTCGCCTCCCCTGGGTACGATCATCGGAGTACTTCCA
3156996 TA
1 TA
3156998 CTTCATTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (46 bp):
TAGTTTAGTCTCGCCTCCCCTGGGTACGATCATCGGAGTACTTCCA
Found at i:3158710 original size:50 final size:50
Alignment explanation
Indices: 3158635--3158734 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
3158625 GCGATCTGCC
* *
3158635 ATCTATTAGTCCATGACATCATCCACCATGTATGTTTAAAGTATGTAAAT
1 ATCTATTAGTCCAAGACATCATCCACCACGTATGTTTAAAGTATGTAAAT
3158685 ATCTATTAGTCCACAG-CATCATCCACCACGTATGTTTAAAGTATGTAAAT
1 ATCTATTAGTCCA-AGACATCATCCACCACGTATGTTTAAAGTATGTAAAT
3158735 GTTTTAAGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (50 bp):
ATCTATTAGTCCAAGACATCATCCACCACGTATGTTTAAAGTATGTAAAT
Found at i:3161362 original size:20 final size:20
Alignment explanation
Indices: 3161337--3161382 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3161327 TCTTTATTTA
* *
3161337 GCACTTCGATGTCTCTGATT
1 GCACTTCAATGCCTCTGATT
*
3161357 GCACTTCAATGCCTCTGTTT
1 GCACTTCAATGCCTCTGATT
3161377 GCACTT
1 GCACTT
3161383 AGGCGCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.39
Consensus pattern (20 bp):
GCACTTCAATGCCTCTGATT
Found at i:3164276 original size:19 final size:20
Alignment explanation
Indices: 3164233--3164290 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
3164223 ATTCTAACTA
*
3164233 ATATTAATTTGT-ATATTTT
1 ATATTAATTTTTAATATTTT
*
3164252 AAATTAATTTTTAATATTTT
1 ATATTAATTTTTAATATTTT
3164272 -TATT-ATTTTT-AT-TTTT
1 ATATTAATTTTTAATATTTT
3164288 ATA
1 ATA
3164291 ATCACATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 6 0.18
19 13 0.38
20 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATATTAATTTTTAATATTTT
Found at i:3164384 original size:2 final size:2
Alignment explanation
Indices: 3164372--3164401 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3164362 TTATATTTAC
3164372 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3164402 ACTGATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3175210 original size:24 final size:24
Alignment explanation
Indices: 3175174--3175222 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3175164 GAATCTAGAA
3175174 TGATAAAAAGAAAAATGAAAAACT
1 TGATAAAAAGAAAAATGAAAAACT
*
3175198 TGATAAAAGGAAAAATGAAAAACT
1 TGATAAAAAGAAAAATGAAAAACT
3175222 T
1 T
3175223 CTAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.63, C:0.04, G:0.14, T:0.18
Consensus pattern (24 bp):
TGATAAAAAGAAAAATGAAAAACT
Found at i:3177353 original size:11 final size:11
Alignment explanation
Indices: 3177339--3177364 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3177329 TAGAGGAGTT
3177339 CTTAAGGAATC
1 CTTAAGGAATC
3177350 CTTAAGGAATC
1 CTTAAGGAATC
3177361 CTTA
1 CTTA
3177365 CTTGAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (11 bp):
CTTAAGGAATC
Found at i:3178395 original size:22 final size:23
Alignment explanation
Indices: 3178370--3178415 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3178360 CAACCAAATC
3178370 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3178392 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3178415 A
1 A
3178416 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3178421 original size:23 final size:23
Alignment explanation
Indices: 3178377--3178421 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3178367 ATCAATTCAA
*
3178377 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
3178400 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
3178422 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:3179135 original size:59 final size:54
Alignment explanation
Indices: 3179005--3179137 Score: 153
Period size: 54 Copynumber: 2.4 Consensus size: 54
3178995 TTGCAGCGGG
* *
3179005 ATTACCAGTCCAGGCTAAATCCCCTGCAACATAAACTCATAGAGTATTGTCGGG
1 ATTACCAGTCCAGGCTAAATCCCCTGCAACATAAACTCATAGAGTATGGTCGGA
* *
3179059 ATTACCAGTCCAGGCTAAATCCCTTGCAACGATAATTACTC-TAATGAGCT-TGGATCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAAC-ATAA--ACTCAT-A-GAG-TATGG-TCGGA
3179118 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
3179138 TTAGACCCTA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
54 29 0.43
55 4 0.06
56 1 0.01
57 5 0.07
58 5 0.07
59 24 0.35
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (54 bp):
ATTACCAGTCCAGGCTAAATCCCCTGCAACATAAACTCATAGAGTATGGTCGGA
Found at i:3179257 original size:17 final size:17
Alignment explanation
Indices: 3179235--3179268 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3179225 CCGGGCTAGA
3179235 TCCTTTTTACCGTCAAT
1 TCCTTTTTACCGTCAAT
3179252 TCCTTTTTACCGTCAAT
1 TCCTTTTTACCGTCAAT
3179269 CGAATTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.47
Consensus pattern (17 bp):
TCCTTTTTACCGTCAAT
Found at i:3183136 original size:23 final size:25
Alignment explanation
Indices: 3183110--3183157 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
3183100 CTAAGGAAAA
* *
3183110 CAAATCAACAATC-GAA-ATTAACT
1 CAAATAAACAAACAGAAGATTAACT
3183133 CAAATAAACAAACAGAAGATTAACT
1 CAAATAAACAAACAGAAGATTAACT
3183158 GACGTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (25 bp):
CAAATAAACAAACAGAAGATTAACT
Found at i:3187121 original size:17 final size:16
Alignment explanation
Indices: 3187099--3187131 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3187089 TTTATAAGCA
3187099 TATATCATTCATTTCAT
1 TATATCATT-ATTTCAT
3187116 TATATCATTATTTCAT
1 TATATCATTATTTCAT
3187132 GCACCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATCATTATTTCAT
Found at i:3188219 original size:31 final size:31
Alignment explanation
Indices: 3188181--3188249 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
3188171 AGTGTTTGAA
3188181 GTATATGTCTAAGATAATAAAAATATAACTT
1 GTATATGTCTAAGATAATAAAAATATAACTT
3188212 GTATATGTCTAAGATAATAAAAATATAACTT
1 GTATATGTCTAAGATAATAAAAATATAACTT
3188243 GTA-ATGT
1 GTATATGT
3188250 GAAAATATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (31 bp):
GTATATGTCTAAGATAATAAAAATATAACTT
Found at i:3189274 original size:14 final size:15
Alignment explanation
Indices: 3189255--3189287 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3189245 AATGATGAGA
*
3189255 ATAATAGTAAT-AAT
1 ATAATAATAATAAAT
3189269 ATAATAATAATAAAT
1 ATAATAATAATAAAT
3189284 ATAA
1 ATAA
3189288 AAAAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:3189819 original size:11 final size:11
Alignment explanation
Indices: 3189803--3189832 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3189793 CAGAGGACCG
3189803 GTCACCGGTCC
1 GTCACCGGTCC
3189814 GTCACCGGTCC
1 GTCACCGGTCC
3189825 GTCACCGG
1 GTCACCGG
3189833 ACCACCGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.43, G:0.30, T:0.17
Consensus pattern (11 bp):
GTCACCGGTCC
Found at i:3189912 original size:17 final size:17
Alignment explanation
Indices: 3189898--3189935 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3189888 TTTCTTTTTC
3189898 TTTTTATTTTATTTTAT
1 TTTTTATTTTATTTTAT
3189915 TTTTTATATGTT-TTTTAT
1 TTTTTAT-T-TTATTTTAT
3189933 TTT
1 TTT
3189936 ATATATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 10 0.53
19 2 0.11
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTATTTTAT
Found at i:3190533 original size:24 final size:25
Alignment explanation
Indices: 3190502--3190549 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3190492 TATTTGGTTC
3190502 TTGGGTTAGTGGT-TA-TTGGGTTTT
1 TTGGGTTAG-GGTATATTTGGGTTTT
3190526 TTGGGTTAGGGTATATTTGGGTTT
1 TTGGGTTAGGGTATATTTGGGTTT
3190550 GATTGTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.50
25 8 0.36
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.52
Consensus pattern (25 bp):
TTGGGTTAGGGTATATTTGGGTTTT
Found at i:3190715 original size:46 final size:46
Alignment explanation
Indices: 3190665--3191012 Score: 376
Period size: 46 Copynumber: 7.6 Consensus size: 46
3190655 CCATAGTGTT
* * *
3190665 TTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATGGTATC
* ** * * ** * *
3190711 TTTCAACCCTGGTCTTGTTCATTTCATGTTACATTACTATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * **
3190757 TTTCAACCTTGGTCTTATTCA-TTCCCATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * * * * * *
3190802 TTTCAACTATGGTCTTATTCTTTTCATGTCACGTTGTCATGCTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * *
3190848 TTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * *
3190894 TTTCAACCATAGTCTTACACATTTCATATCATGTTGCCATGGTGTC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* *
3190940 TTTCAACCATGGTCTTACACATTTCATATCATGTTGTCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* *
3190986 TTTCAACCATGGTCTTACACTTTTCAT
1 TTTCAACCATGGTCTTACTCATTTCAT
3191013 TTCAGAAAGA
Statistics
Matches: 254, Mismatches: 46, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
45 38 0.15
46 216 0.85
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.43
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
Found at i:3209107 original size:29 final size:27
Alignment explanation
Indices: 3209044--3209107 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 27
3209034 TTTCATGTGT
* * *
3209044 ATAATTGCATTAAATTAAAATTTATGT
1 ATAATTGCATTAAATCAAAATTAATGA
3209071 ATCAAATTGCACATTAAATCAAAATTAATGA
1 AT--AATTG--CATTAAATCAAAATTAATGA
3209102 ATAATT
1 ATAATT
3209108 TTGGGATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.07
29 9 0.30
31 19 0.63
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (27 bp):
ATAATTGCATTAAATCAAAATTAATGA
Found at i:3210685 original size:68 final size:68
Alignment explanation
Indices: 3210613--3210788 Score: 175
Period size: 68 Copynumber: 2.6 Consensus size: 68
3210603 CATCATGTGT
** * * *
3210613 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-CC
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATTCAAGGGAAGGA-CACC
3210675 ATGTAG
63 ATGTAG
* * *
3210681 ACAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGATATAAATGTAGCTAGGTCACATGTGTGATT-CAAGGGAAGGACACC
3210746 ATGTAG
63 ATGTAG
*
3210752 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
3210789 GTCGTACTAA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 33 0.36
69 7 0.08
70 6 0.07
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATTCAAGGGAAGGACACCATG
TAG
Found at i:3219940 original size:23 final size:20
Alignment explanation
Indices: 3219914--3219961 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
3219904 ACATTAATAA
*
3219914 TTTATCCAACCTAATATTTATTT
1 TTTAT-CAACC-AATATAT-TTT
*
3219937 TTTATTAACCAATATATTTT
1 TTTATCAACCAATATATTTT
3219957 TTTAT
1 TTTAT
3219962 TAAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 6 0.26
22 4 0.17
23 5 0.22
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATCAACCAATATATTTT
Found at i:3220374 original size:15 final size:15
Alignment explanation
Indices: 3220354--3220384 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3220344 TAGGCTTAAA
3220354 TAATTATAACATTAT
1 TAATTATAACATTAT
*
3220369 TAATTATAATATTAT
1 TAATTATAACATTAT
3220384 T
1 T
3220385 CAGCCATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATAACATTAT
Found at i:3220657 original size:6 final size:6
Alignment explanation
Indices: 3220641--3220692 Score: 86
Period size: 6 Copynumber: 8.5 Consensus size: 6
3220631 ACAAAGACAT
*
3220641 ATGATCC ATGACC ATGACC ATAACC ATGACC ATGACC ATGACC ATGACC
1 ATGA-CC ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC ATGACC
3220690 ATG
1 ATG
3220693 TTTACTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
6 39 0.91
7 4 0.09
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (6 bp):
ATGACC
Found at i:3223697 original size:89 final size:90
Alignment explanation
Indices: 3223510--3223739 Score: 345
Period size: 89 Copynumber: 2.6 Consensus size: 90
3223500 TATGTAGCAT
* * *
3223510 CACCAAGGTGGTCATGCCAAAGAGAATGGCTCTACCAAAATAAAAAATAAAAACTTTATTTTTAT
1 CACCAAAGTGGTCATGCCAAAGAGAATGGCTCCACCAAAATAAAAAA-AAAAACTTAATTTTTAT
** *
3223575 GGTGGTCACATTATTTTCAATGGCAC
65 GGTGGTCACACCATTCTCAATGGCAC
* *
3223601 CATCAAAGTGGTCATGCCAAAGAGAATGGCTCCATCAAAATAAAAAAAAAAA-TTAATTTTTATG
1 CACCAAAGTGGTCATGCCAAAGAGAATGGCTCCACCAAAATAAAAAAAAAAACTTAATTTTTATG
3223665 GTGGTCACACCATTCTCAATGGCAC
66 GTGGTCACACCATTCTCAATGGCAC
* * *
3223690 CACCAAAGTGGCCACGCCAAAGAGAATGACTCCACCAAAATAAAAAAAAA
1 CACCAAAGTGGTCATGCCAAAGAGAATGGCTCCACCAAAATAAAAAAAAA
3223740 TTATTAAAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
89 78 0.62
90 5 0.04
91 43 0.34
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (90 bp):
CACCAAAGTGGTCATGCCAAAGAGAATGGCTCCACCAAAATAAAAAAAAAAACTTAATTTTTATG
GTGGTCACACCATTCTCAATGGCAC
Found at i:3226105 original size:13 final size:14
Alignment explanation
Indices: 3226084--3226117 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3226074 AAAATACAAA
3226084 AATAATT-AAAAAT
1 AATAATTAAAAAAT
*
3226097 AATATTTAAAAAAT
1 AATAATTAAAAAAT
3226111 AATAATT
1 AATAATT
3226118 TTTATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATTAAAAAAT
Found at i:3226116 original size:17 final size:17
Alignment explanation
Indices: 3226094--3226128 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3226084 AATAATTAAA
3226094 AATAATATTTAAAAAAT
1 AATAATATTTAAAAAAT
* *
3226111 AATAATTTTTATAAAAT
1 AATAATATTTAAAAAAT
3226128 A
1 A
3226129 TTTTTTCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATATTTAAAAAAT
Found at i:3227334 original size:22 final size:23
Alignment explanation
Indices: 3227306--3227349 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3227296 CTAAAAATAT
* *
3227306 AAAAATTTAATTTA-ATTTTTAA
1 AAAAATTAAAATTATATTTTTAA
3227328 AAAAATTAAAATTATATTTTTA
1 AAAAATTAAAATTATATTTTTA
3227350 TATATAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAATTAAAATTATATTTTTAA
Found at i:3227340 original size:23 final size:22
Alignment explanation
Indices: 3227306--3227349 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3227296 CTAAAAATAT
* *
3227306 AAAAATTTAATTTA-ATTTTTA
1 AAAAAATTAAATTATATTTTTA
3227327 AAAAAATTAAAATTATATTTTTA
1 AAAAAATT-AAATTATATTTTTA
3227350 TATATAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAAATTAAATTATATTTTTA
Found at i:3228211 original size:39 final size:39
Alignment explanation
Indices: 3228137--3228212 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
3228127 CCTCTATCTA
* *
3228137 TTTTACCCATTTTCTTATATTTTCTTCTCATCAAACAAT
1 TTTTACCCATTTTCTTATATTTTCATCTCACCAAACAAT
*
3228176 TTTTACCAGATTTTCTTAT-TTTCTCATC-CACCAAACA
1 TTTTACC-CATTTTCTTATATTT-TCATCTCACCAAACA
3228213 CCCCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 18 0.56
40 14 0.44
ACGTcount: A:0.26, C:0.25, G:0.01, T:0.47
Consensus pattern (39 bp):
TTTTACCCATTTTCTTATATTTTCATCTCACCAAACAAT
Found at i:3237469 original size:15 final size:16
Alignment explanation
Indices: 3237446--3237489 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
3237436 AATATAAAAA
*
3237446 TATTATATATATTAAAT
1 TATTATAAAT-TTAAAT
3237463 TATTATAAATTTAAAT
1 TATTATAAATTTAAAT
3237479 T-TTATACAATT
1 TATTATA-AATT
3237490 AACAAAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 11 0.44
17 9 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATAAATTTAAAT
Found at i:3240717 original size:23 final size:25
Alignment explanation
Indices: 3240691--3240757 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
3240681 AAAACAAATT
*
3240691 AAAATTAATTT-ATTTT-AATGATC
1 AAAATAAATTTAATTTTAAATGATC
3240714 AAAATAAATTTAAATTTTAAATGATC
1 AAAATAAATTT-AATTTTAAATGATC
*
3240740 AAAA-ATATTTAATATTTA
1 AAAATAAATTTAAT-TTTA
3240758 TTTATTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.26
24 3 0.08
25 14 0.37
26 11 0.29
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (25 bp):
AAAATAAATTTAATTTTAAATGATC
Found at i:3240749 original size:25 final size:26
Alignment explanation
Indices: 3240701--3240756 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
3240691 AAAATTAATT
3240701 TATTTTAATGATCAAAATAAATTTAA
1 TATTTTAATGATCAAAATAAATTTAA
*
3240727 -ATTTTAAATGATCAAAA-ATATTTAA
1 TATTTT-AATGATCAAAATAAATTTAA
3240752 TATTT
1 TATTT
3240757 ATTTATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
TATTTTAATGATCAAAATAAATTTAA
Found at i:3240980 original size:15 final size:16
Alignment explanation
Indices: 3240953--3240984 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3240943 AATATATATT
3240953 TATATTAATAAAATTA
1 TATATTAATAAAATTA
3240969 TATATT-ATAAAATTA
1 TATATTAATAAAATTA
3240984 T
1 T
3240985 TTTCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATTAATAAAATTA
Found at i:3242329 original size:16 final size:18
Alignment explanation
Indices: 3242297--3242329 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3242287 GACACCATCC
3242297 CCAACCTAAACCCAATAT
1 CCAACCTAAACCCAATAT
3242315 CCAACC-AAA-CCAATA
1 CCAACCTAAACCCAATA
3242330 CAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.12
Consensus pattern (18 bp):
CCAACCTAAACCCAATAT
Found at i:3246235 original size:40 final size:40
Alignment explanation
Indices: 3246180--3246260 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3246170 GCTCCGTTAA
3246180 TGGTTCAAAGGCAATTTGCTTCACGACAGTTCATACTCAC
1 TGGTTCAAAGGCAATTTGCTTCACGACAGTTCATACTCAC
3246220 TGGTTCAAAGGCAATTTGCTTCACGACAGTTCATACTCAC
1 TGGTTCAAAGGCAATTTGCTTCACGACAGTTCATACTCAC
3246260 T
1 T
3246261 ACCGGAGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (40 bp):
TGGTTCAAAGGCAATTTGCTTCACGACAGTTCATACTCAC
Found at i:3247629 original size:38 final size:38
Alignment explanation
Indices: 3247578--3247653 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3247568 CAAAAGATCT
3247578 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
1 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
3247616 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
1 GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
3247654 AAGAAAAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (38 bp):
GATGGCCAAAATGATGGAGATGATGACAGCTTTGGTCA
Found at i:3253392 original size:39 final size:39
Alignment explanation
Indices: 3253346--3253422 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
3253336 TGCATCTTCA
3253346 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
3253385 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATA
1 AATGAGCATATATGAAGTCCCTACACATTGTTTCAATA
3253423 TTGAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (39 bp):
AATGAGCATATATGAAGTCCCTACACATTGTTTCAATAC
Found at i:3255828 original size:77 final size:78
Alignment explanation
Indices: 3255559--3255868 Score: 412
Period size: 77 Copynumber: 4.0 Consensus size: 78
3255549 TTATTACTAT
* *
3255559 TTTTTTAAAAAAAATGAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
1 TTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
3255624 TCTTTAGTTCCTA
66 TCTTTAGTTCCTA
** *** * * *
3255637 TTTTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAAATCACGCACTAAGGTA
1 TTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
*
3255702 T-TTTCAATT--TA
66 TCTTT-AGTTCCTA
** *
3255713 TGATTCAAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
1 TTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
3255778 TCTTTAGTTCCTA
66 TCTTTAGTTCCTA
* * *
3255791 TTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTTGAGGTA
1 TTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
* *
3255855 TTTTTAGTTTCTA
66 TCTTTAGTTCCTA
3255868 T
1 T
3255869 CAACTTATAT
Statistics
Matches: 199, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
76 62 0.31
77 72 0.36
78 65 0.33
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (78 bp):
TTTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
TCTTTAGTTCCTA
Found at i:3255921 original size:64 final size:64
Alignment explanation
Indices: 3255803--3255922 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 64
3255793 TTTCAAAAAA
* *** *
3255803 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGTTGAGGTATTTTTAGTTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTTTAGTTTCT
*
3255867 ATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTT
3255923 CAATTTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (64 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGATATTTTTAGTTTCT
Found at i:3256272 original size:26 final size:26
Alignment explanation
Indices: 3256236--3256297 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
3256226 CTACAAAAGA
*
3256236 TCTCCTTGAAGTTTCAATGGATCTCT
1 TCTCCTTGAAGTTTCAATAGATCTCT
*
3256262 TCTCCTTGAAGTTTCAGTAGATCTCT
1 TCTCCTTGAAGTTTCAATAGATCTCT
*
3256288 TCTCCCTGAA
1 TCTCCTTGAA
3256298 ATGGCATTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (26 bp):
TCTCCTTGAAGTTTCAATAGATCTCT
Found at i:3256385 original size:44 final size:45
Alignment explanation
Indices: 3256330--3256440 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 45
3256320 CCACAACAAG
* * * *
3256330 ATCTCCTTGAAGTTTCAGCGGAGAACATTGAAG-TCA-CAAGTCTT
1 ATCTCCCTGAAGTTCCAGCGGAGAACACTGAAGAT-AGCAAATCTT
* * * **
3256374 ATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATAGCAAATCTT
1 ATCTCCCTGAAGTTCCAGCGGAGAACACTGAAGATAGCAAATCTT
*
3256419 ATTTCCCTGAAGTTCCAGCGGA
1 ATCTCCCTGAAGTTCCAGCGGA
3256441 TTAGATCGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
44 27 0.50
45 27 0.50
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (45 bp):
ATCTCCCTGAAGTTCCAGCGGAGAACACTGAAGATAGCAAATCTT
Found at i:3257196 original size:13 final size:14
Alignment explanation
Indices: 3257178--3257209 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3257168 ACCTAAGGTG
3257178 ATTTTATTA-TTTT
1 ATTTTATTATTTTT
3257191 ATTTTATTATTTTT
1 ATTTTATTATTTTT
3257205 ATTTT
1 ATTTT
3257210 TTTCGAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTTATTATTTTT
Found at i:3257861 original size:3 final size:3
Alignment explanation
Indices: 3257853--3258046 Score: 52
Period size: 3 Copynumber: 64.7 Consensus size: 3
3257843 CTTTATTAAA
* * * * *
3257853 TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAA CAC TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3257898 TAT TAT ATAT TAG TAT ATAT TTT TAT TAT CTAT GTA- TAT GTA- TAT
1 TAT TAT -TAT TAT TAT -TAT TAT TAT TAT -TAT -TAT TAT -TAT TAT
* * * * *
3257943 ATAT T-T ATAT ATAG TAT TAT TTT TAAT TAC T-T TAT T-T TAA TAT TTT
1 -TAT TAT -TAT -TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
** * *
3257989 TAT TA- TAT TA- TAT T-T GCT T-T T-T GTAT T-T CAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
3258029 TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT -TAT TA
3258047 GTGTATTTTT
Statistics
Matches: 140, Mismatches: 30, Indels: 42
0.66 0.14 0.20
Matches are distributed among these distances:
2 18 0.13
3 96 0.69
4 26 0.19
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3257914 original size:10 final size:10
Alignment explanation
Indices: 3257886--3258088 Score: 63
Period size: 10 Copynumber: 20.3 Consensus size: 10
3257876 ATATTAACAC
3257886 TATTATTAT-
1 TATTATTATA
3257895 TATTATTATA
1 TATTATTATA
*
3257905 TATTAGTATA
1 TATTATTATA
*
3257915 TATTTTTAT-
1 TATTATTATA
3257924 TATCTATGTATA
1 TAT-TAT-TATA
*
3257936 T-GTA-TATA
1 TATTATTATA
3257944 TATT-TATATA
1 TATTAT-TATA
*
3257954 TAGTATTAT-
1 TATTATTATA
* *
3257963 TTTTAATTACTT
1 TATT-ATTA-TA
3257975 TATT-TTA-A
1 TATTATTATA
*
3257983 TATTTTTATTA
1 TATTATTA-TA
*
3257994 TATTA-TATT
1 TATTATTATA
* * *
3258003 TGCTTTTTGTA
1 T-ATTATTATA
*
3258014 T-TTCAATAT-
1 TATT-ATTATA
3258023 TATTATTAT-
1 TATTATTATA
3258032 TATTATTATA
1 TATTATTATA
*
3258042 TATTAGTGTATT
1 TATTA-T-TATA
*
3258054 TTTTATTATA
1 TATTATTATA
*
3258064 TATGTA-TATG
1 TAT-TATTATA
3258074 TATATATTTATA
1 TAT-TA-TTATA
3258086 TAT
1 TAT
3258089 AGTATTATTT
Statistics
Matches: 142, Mismatches: 28, Indels: 45
0.66 0.13 0.21
Matches are distributed among these distances:
8 9 0.06
9 36 0.25
10 63 0.44
11 17 0.12
12 17 0.12
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (10 bp):
TATTATTATA
Found at i:3257935 original size:29 final size:29
Alignment explanation
Indices: 3257886--3257962 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
3257876 ATATTAACAC
*
3257886 TATTATTATTATTATTATATAT-TAGTATA
1 TATTTTTATTATTATTATATATGTA-TATA
*
3257915 TATTTTTATTATCTA-TGTATATGTATATA
1 TATTTTTATTAT-TATTATATATGTATATA
* *
3257944 TATTTATATATAGTATTAT
1 TATTTTTAT-TATTATTAT
3257963 TTTTAATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 31 0.79
30 8 0.21
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.58
Consensus pattern (29 bp):
TATTTTTATTATTATTATATATGTATATA
Found at i:3258094 original size:134 final size:135
Alignment explanation
Indices: 3257886--3258305 Score: 667
Period size: 134 Copynumber: 3.1 Consensus size: 135
3257876 ATATTAACAC
*
3257886 TATTATTATTATTATTATATATTAGTATATATTTTTATTATCTATGTATATGTATATATATTTAT
1 TATTATTATTATTATTATATATTAGTGTATATTTTTATTATCTATGTATATG-ATATATATTTAT
3257951 ATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
65 ATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATT
3258016 TCAATAT
130 TC-ATAT
*
3258023 TATTATTATTATTATTATATATTAGTGTAT-TTTTTATTATATATGTATATG-TATATATTTATA
1 TATTATTATTATTATTATATATTAGTGTATATTTTTATTATCTATGTATATGATATATATTTATA
*
3258086 TATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTGTTGTATTT
66 TATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATTT
3258151 C--A-
131 CATAT
*
3258153 -A-TATTATTATTATTAT-TATTAGTGTATATTTTTATTATCTATGTATATGTATATATATTTAA
1 TATTATTATTATTATTATATATTAGTGTATATTTTTATTATCTATGTATATG-ATATATATTTAT
*
3258215 ATATAGTATTATTTTTAATTACTTTATTTTAATATTATTATTATATTATATTTGCTTTTTTGTAT
65 ATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGC-TTTTTGTAT
3258280 TTCATTAT
129 TTCA-TAT
** *
3258288 TATTGCTAATATTATTAT
1 TATTATTATTATTATTAT
3258306 CATTATCATC
Statistics
Matches: 263, Mismatches: 10, Indels: 20
0.90 0.03 0.07
Matches are distributed among these distances:
127 11 0.04
128 35 0.13
129 1 0.00
130 64 0.24
131 12 0.05
134 78 0.30
136 21 0.08
137 41 0.16
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (135 bp):
TATTATTATTATTATTATATATTAGTGTATATTTTTATTATCTATGTATATGATATATATTTATA
TATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATTT
CATAT
Found at i:3258187 original size:19 final size:19
Alignment explanation
Indices: 3258160--3258200 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3258150 TCAATATTAT
3258160 TATTATTATTAT-TAGTGTA
1 TATTATTATTATCTA-TGTA
*
3258179 TATTTTTATTATCTATGTA
1 TATTATTATTATCTATGTA
3258198 TAT
1 TAT
3258201 GTATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (19 bp):
TATTATTATTATCTATGTA
Found at i:3258187 original size:25 final size:25
Alignment explanation
Indices: 3258153--3258211 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
3258143 TTGTATTTCA
3258153 ATATTATTATTAT-TAT-TATTAGTGT
1 ATATTATTATTATCTATGTA-TA-TGT
*
3258178 ATATTTTTATTATCTATGTATATGT
1 ATATTATTATTATCTATGTATATGT
3258203 ATATATATT
1 ATAT-TATT
3258212 TAAATATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 19 0.66
26 8 0.28
27 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (25 bp):
ATATTATTATTATCTATGTATATGT
Found at i:3258231 original size:18 final size:20
Alignment explanation
Indices: 3258196--3258232 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
3258186 ATTATCTATG
3258196 TATATGTATATATATTTAAA
1 TATATGTATATATATTTAAA
*
3258216 TATA-GTAT-TATTTTTAA
1 TATATGTATATATATTTAA
3258233 TTACTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATATGTATATATATTTAAA
Found at i:3258434 original size:264 final size:262
Alignment explanation
Indices: 3257890--3258436 Score: 637
Period size: 264 Copynumber: 2.1 Consensus size: 262
3257880 TAACACTATT
*
3257890 ATTATTATTATTATATATTAGTATATATTTTTATTATCTATGTATATGTATATATATTTATATAT
1 ATTATTATTATTAT-TATTAGTATATATTTTTATTATCTATGTATATGTATATATATTTAAATAT
*
3257955 AGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTGTATTTCAA
65 AGTATTATTTTTAATTACTTTATTTTAATATTATTATTATATTATATTTGCTTTTTGTATTTCAA
* * * * * * *
3258020 TATTATTATTATTATTATTATATATTAGTGTATTTTTTATTATATATGTATATGTATATATTTAT
130 TATTATTACTAATATTATTATATATCAGTGCATTATTAAATATATATGTATATGTATATATTTAT
* * ** * * *
3258085 ATATAGTATTATTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTGTTGTATT
195 ATACAGTATTATTTTTAACTAC-TTATTACAATA-TTATATTATATTATATTTGATTATTGTATT
* *
3258150 TCAAT
258 ACAAC
*
3258155 ATTATTATTATTATTATTAGTGTATATTTTTATTATCTATGTATATGTATATATATTTAAATATA
1 ATTATTATTATTATTATTAGTATATATTTTTATTATCTATGTATATGTATATATATTTAAATATA
*
3258220 GTATTATTTTTAATTACTTTATTTTAATATTATTATTATATTATATTTGCTTTTTTGTATTTCAT
66 GTATTATTTTTAATTACTTTATTTTAATATTATTATTATATTATATTTGC-TTTTTGTATTTCAA
* * *
3258285 TATTATTGCTAATATTATTATCATTATCA-T-CATTATTAACATATATATGTATACATGTGTATT
130 TATTATTACTAATATTATTAT-A-TATCAGTGCATTATTAA-ATATATATGTAT--ATGTATATA
* * *
3258348 TTTCATGTACA-TATTAGTATTTTCCACTA-TTATTACAA-A-TATATTAT-TTCT-TTT-ATTA
190 TTT-ATATACAGTATTA-T-TTTT-AACTACTTATTACAATATTATATTATATTATATTTGATTA
*
3258406 TAT-TATTAGAAC
251 T-TGTATTACAAC
*
3258418 ATTATTTTTCATTATTATT
1 ATTATTATT-ATTATTATT
3258437 TTCTTTATAG
Statistics
Matches: 242, Mismatches: 28, Indels: 25
0.82 0.09 0.08
Matches are distributed among these distances:
263 17 0.07
264 111 0.46
265 54 0.22
266 20 0.08
267 4 0.02
268 16 0.07
269 13 0.05
270 4 0.02
271 3 0.01
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (262 bp):
ATTATTATTATTATTATTAGTATATATTTTTATTATCTATGTATATGTATATATATTTAAATATA
GTATTATTTTTAATTACTTTATTTTAATATTATTATTATATTATATTTGCTTTTTGTATTTCAAT
ATTATTACTAATATTATTATATATCAGTGCATTATTAAATATATATGTATATGTATATATTTATA
TACAGTATTATTTTTAACTACTTATTACAATATTATATTATATTATATTTGATTATTGTATTACA
AC
Found at i:3259397 original size:16 final size:16
Alignment explanation
Indices: 3259378--3259422 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3259368 AGAGAGCAGG
* *
3259378 GGAAAGAAAGAAGGAA
1 GGAAAAAAAGAAAGAA
3259394 GGAAAAAAAGAAAGAA
1 GGAAAAAAAGAAAGAA
*
3259410 GGAAAAAGAGAAA
1 GGAAAAAAAGAAA
3259423 AATTGGGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GGAAAAAAAGAAAGAA
Found at i:3261422 original size:46 final size:46
Alignment explanation
Indices: 3261370--3261598 Score: 352
Period size: 46 Copynumber: 5.0 Consensus size: 46
3261360 AGTGTGCTCT
3261370 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3261416 CTGATATGAAATGTGTAGGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3261462 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
***
3261508 CTGATATGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
3261554 GTGACATGAAAAGAATAAG-CCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3261599 ATGACAGAAA
Statistics
Matches: 170, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 26 0.15
46 144 0.85
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3266365 original size:28 final size:28
Alignment explanation
Indices: 3266312--3266395 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
3266302 CACTTTGTGC
3266312 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
3266341 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
3266369 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
3266396 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:3266407 original size:23 final size:24
Alignment explanation
Indices: 3266316--3266409 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
3266306 TTGTGCTATT
3266316 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
3266343 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
3266373 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
3266396 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
3266410 TTGGACATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:3266423 original size:23 final size:23
Alignment explanation
Indices: 3266370--3266429 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
3266360 GGATTATATG
*
3266370 ATACTGGTGTGTTTTGGAGGATT
1 ATACTGGTGTGTTTTGGAGGATC
*
3266393 ATACTGGTGTGTTTTGGTTGGA-C
1 ATACTGGTGTGTTTTGG-AGGATC
*
3266416 ATATTGGTGTGTTT
1 ATACTGGTGTGTTT
3266430 GGATGGAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.15, C:0.05, G:0.33, T:0.47
Consensus pattern (23 bp):
ATACTGGTGTGTTTTGGAGGATC
Found at i:3266648 original size:21 final size:21
Alignment explanation
Indices: 3266624--3266680 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3266614 TGTCATATTT
3266624 CAGGCACTTTGTGTGTCGCAG
1 CAGGCACTTTGTGTGTCGCAG
* * ***
3266645 CAGGCACCTCGTGTGTCGTTT
1 CAGGCACTTTGTGTGTCGCAG
3266666 CAGGCACTTATGTGT
1 CAGGCACTT-TGTGT
3266681 CGTATTCTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.32
Consensus pattern (21 bp):
CAGGCACTTTGTGTGTCGCAG
Found at i:3270056 original size:15 final size:16
Alignment explanation
Indices: 3270011--3270061 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 16
3270001 AAATATTGAA
*
3270011 TAAAAATTAATAA-A-
1 TAAAAATTTATAATAT
3270025 TAAAAATTTATAATAT
1 TAAAAATTTATAATAT
*
3270041 TAAATATTTA-AATAT
1 TAAAAATTTATAATAT
3270056 TAAAAA
1 TAAAAA
3270062 AAACTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.38
15 11 0.34
16 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATTTATAATAT
Found at i:3279079 original size:20 final size:20
Alignment explanation
Indices: 3279028--3279079 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
3279018 ATCTATATTG
**
3279028 AAGTATCGATACTTTTCCTA
1 AAGTATCGATACTTTGACTA
* *
3279048 TAGTATCAATACTTTGACTA
1 AAGTATCGATACTTTGACTA
*
3279068 AAGTATTGATAC
1 AAGTATCGATAC
3279080 CTTCCTTAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
AAGTATCGATACTTTGACTA
Found at i:3283582 original size:118 final size:118
Alignment explanation
Indices: 3283353--3283570 Score: 364
Period size: 118 Copynumber: 1.8 Consensus size: 118
3283343 TATTTCCAGT
3283353 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
3283418 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATAATCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATAATCATAACCTCGGC
**** * *
3283471 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGATGCGAAGTAGAATGACAACCCAAGTAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
3283536 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGC
3283571 TGTACTCATA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 92 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATAATCATAACCTCGGC
Found at i:3284541 original size:15 final size:16
Alignment explanation
Indices: 3284505--3284556 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
3284495 TAAATGAAAT
*
3284505 AAAATAAAATAAAATAA
1 AAAAT-AAATAAAAGAA
*
3284522 TAAAT-AATAAAAGAA
1 AAAATAAATAAAAGAA
3284537 AAAATAAATAAAAAGAA
1 AAAATAAAT-AAAAGAA
3284554 AAA
1 AAA
3284557 GAAAGATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.43
16 3 0.10
17 14 0.47
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (16 bp):
AAAATAAATAAAAGAA
Found at i:3288334 original size:27 final size:27
Alignment explanation
Indices: 3288304--3288361 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3288294 AGATAATTAA
3288304 AATAA-AATCCTAAATATGAATAATCCT
1 AATAATAAT-CTAAATATGAATAATCCT
* * * *
3288331 AATAATTATCTTAATATTAATTATCCT
1 AATAATAATCTAAATATGAATAATCCT
3288358 AATA
1 AATA
3288362 GAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (27 bp):
AATAATAATCTAAATATGAATAATCCT
Found at i:3290197 original size:46 final size:47
Alignment explanation
Indices: 3290131--3290255 Score: 162
Period size: 47 Copynumber: 2.7 Consensus size: 47
3290121 TCACATATCA
* * ** * *
3290131 CACACCGAAGCCATAGCCCAGCCATGGTCTTACAC-GGATCACAGAT
1 CACACCGATGCCATATCCCAGATATGGTCTTACACAGAAGCACAGAT
* *
3290177 CACACTGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATAT
1 CACACCGATGCCATATCCCAGATATGGTCTTACACAGAAGCACAGAT
*
3290224 CACACCAATGCCATATCCCAGATATGGTCTTA
1 CACACCGATGCCATATCCCAGATATGGTCTTA
3290256 TGCCATATCC
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 30 0.44
47 38 0.56
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (47 bp):
CACACCGATGCCATATCCCAGATATGGTCTTACACAGAAGCACAGAT
Found at i:3290258 original size:24 final size:24
Alignment explanation
Indices: 3290231--3290279 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3290221 TATCACACCA
3290231 ATGCCATATCCCAGATATGGTCTT
1 ATGCCATATCCCAGATATGGTCTT
3290255 ATGCCATATCCCAGATATGGTCTT
1 ATGCCATATCCCAGATATGGTCTT
3290279 A
1 A
3290280 CACAGAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (24 bp):
ATGCCATATCCCAGATATGGTCTT
Found at i:3290268 original size:71 final size:71
Alignment explanation
Indices: 3290184--3290327 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
3290174 GATCACACTG
3290184 ATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATAT
1 ATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATAT
3290249 GGTCTT
66 GGTCTT
*
3290255 ATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCGATGCCATATCCCAGATAT
1 ATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATAT
3290320 GGTCTT
66 GGTCTT
3290326 AT
1 AT
3290328 ACGGAAGCTC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (71 bp):
ATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATAT
GGTCTT
Found at i:3290324 original size:47 final size:47
Alignment explanation
Indices: 3290255--3290449 Score: 277
Period size: 47 Copynumber: 4.1 Consensus size: 47
3290245 ATATGGTCTT
* * *
3290255 ATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCG
1 ATGCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTG
*
3290302 ATGCCATATCCCAGATATGGTCTTATACGGAAGCTCATATCACACTG
1 ATGCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTG
* *
3290349 ATGTCATATCCCAGATATGGTCTTATACGGAAGCTCATATCACACTG
1 ATGCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTG
* *
3290396 ATGCCATAGCCCA-ACTATGGTCTTATACGGAAATCACATATCACA-TG
1 ATGCCATATCCCAGA-TATGGTCTTATACGG-AAGCACATATCACACTG
*
3290443 TTGCCAT
1 ATGCCAT
3290450 GGTCTAACCA
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
46 1 0.01
47 123 0.90
48 12 0.09
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (47 bp):
ATGCCATATCCCAGATATGGTCTTATACGGAAGCACATATCACACTG
Found at i:3290357 original size:118 final size:117
Alignment explanation
Indices: 3290140--3290374 Score: 344
Period size: 118 Copynumber: 2.0 Consensus size: 117
3290130 ACACACCGAA
* * * *
3290140 GCCATAGCCCAGCCATGGTCTTACACGGATCACAGATCACACTGATGCCATATCCCAGATATGGT
1 GCCATAGCCCAGACATGGTCTTACACGAAGCACAGATCACACCGATGCCATATCCCAGATATGGT
3290205 CTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATATGGTCTTAT
66 CTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATATGGTCTTAT
* * *
3290257 GCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACACCGATGCCATATCCCAGATATGG
1 GCCATAGCCCAGACATGGTCTTACAC-GAAGCACAGATCACACCGATGCCATATCCCAGATATGG
* * * ** *
3290322 TCTTATACGGAAGCTCATATCACACTGATGTCATATCCCAGATATGGTCTTAT
65 TCTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATATGGTCTTAT
3290375 ACGGAAGCTC
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
117 23 0.22
118 81 0.78
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (117 bp):
GCCATAGCCCAGACATGGTCTTACACGAAGCACAGATCACACCGATGCCATATCCCAGATATGGT
CTTACACAGAAGCACATATCACACCAATGCCATATCCCAGATATGGTCTTAT
Found at i:3301326 original size:11 final size:11
Alignment explanation
Indices: 3301310--3301334 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3301300 TTACAATTGT
3301310 TTTTGTAATTA
1 TTTTGTAATTA
3301321 TTTTGTAATTA
1 TTTTGTAATTA
3301332 TTT
1 TTT
3301335 CTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGTAATTA
Found at i:3312975 original size:26 final size:26
Alignment explanation
Indices: 3312901--3312980 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
3312891 TATATATTTT
*
3312901 TATTT-TTATTAAATTATATTTGATAA
1 TATTTATTATTAAATTATATTT-AAAA
* *
3312927 TAATTA-TATTAAAATATGA-TTAAAA
1 TATTTATTATTAAATTAT-ATTTAAAA
*
3312952 TATTTATTATTGAATTATATTTAATAA
1 TATTTATTATTAAATTATATTTAA-AA
3312979 TA
1 TA
3312981 ACCTTATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
25 9 0.21
26 29 0.67
27 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTTATTATTAAATTATATTTAAAA
Found at i:3318281 original size:91 final size:91
Alignment explanation
Indices: 3318126--3318311 Score: 345
Period size: 91 Copynumber: 2.0 Consensus size: 91
3318116 TTACATAGTT
**
3318126 AAATAATTTATATTTTTTAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
1 AAATAATTTATATTTTAAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
3318191 CTATGAAAGTACCAAAAATTAAAATC
66 CTATGAAAGTACCAAAAATTAAAATC
*
3318217 AAATAATTTATATTTTAAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAGATAATTT
1 AAATAATTTATATTTTAAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
3318282 CTATGAAAGTACCAAAAATTAAAATC
66 CTATGAAAGTACCAAAAATTAAAATC
3318308 AAAT
1 AAAT
3318312 CATGACATGT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (91 bp):
AAATAATTTATATTTTAAAAAAAATATTAATTACTATAATAATATTAGTATGATAAAAATAATTT
CTATGAAAGTACCAAAAATTAAAATC
Found at i:3319610 original size:24 final size:23
Alignment explanation
Indices: 3319581--3319628 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
3319571 TATAATACGT
3319581 AAATAAAGTAAAAATAATATTAAA
1 AAATAAAGTAAAAATAATA-TAAA
3319605 AAATAAAGTAAAAATAATATAAA
1 AAATAAAGTAAAAATAATATAAA
3319628 A
1 A
3319629 TTTATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AAATAAAGTAAAAATAATATAAA
Found at i:3319627 original size:11 final size:12
Alignment explanation
Indices: 3319581--3319628 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
3319571 TATAATACGT
3319581 AAATAA-AGTAA
1 AAATAATAGTAA
*
3319592 AAATAATATTAAA
1 AAATAATAGT-AA
3319605 AAATAA-AGTAA
1 AAATAATAGTAA
3319616 AAATAATA-TAA
1 AAATAATAGTAA
3319627 AA
1 AA
3319629 TTTATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 19 0.59
12 5 0.16
13 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
AAATAATAGTAA
Found at i:3322187 original size:35 final size:35
Alignment explanation
Indices: 3322141--3322477 Score: 433
Period size: 35 Copynumber: 9.6 Consensus size: 35
3322131 CATGGCAAAG
* * *
3322141 TGTGAAACGTAGGTATAGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* * * *
3322176 TGTGAAACGTAGGCATGGAATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
3322211 TGTGAAACGTAGGCATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
*
3322246 TGTGAAACGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* *
3322281 TGTGAAACGTAGGTATGATATCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* ** *
3322316 TGTGAAACGTAGGTATGGTATTAACTGTACCGAGA
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
* * *
3322351 TGTGAAACGTAGGTATGGTATTAACCGTACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
*
3322386 TGTGAAACGTAGGTATGGTATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
** **
3322421 TAAGAAACGTAGGTATGACATT-TCCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAT-CCATACCGAGT
*
3322456 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
3322478 TCAATGAGGA
Statistics
Matches: 271, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
34 1 0.00
35 270 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTATCCATACCGAGT
Found at i:3322607 original size:31 final size:31
Alignment explanation
Indices: 3322572--3322664 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
3322562 AATAAGTAAT
*
3322572 TTGATCAGTGAGAAGTGGTACCTCTGGCTAC
1 TTGATCAGTGAGAAGTGGTACCTCCGGCTAC
*
3322603 TTGATCAGTGAGAAGTGGTAGCTCCGGCTAC
1 TTGATCAGTGAGAAGTGGTACCTCCGGCTAC
* * * *
3322634 CTGATCAGTGAGTAGTGGTAGCTTCGGCTAC
1 TTGATCAGTGAGAAGTGGTACCTCCGGCTAC
3322665 AAGTGACAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (31 bp):
TTGATCAGTGAGAAGTGGTACCTCCGGCTAC
Found at i:3325693 original size:24 final size:25
Alignment explanation
Indices: 3325673--3325736 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
3325663 AGAGAGCCAT
3325673 TAACGGGAAGCTCATA-CGAGCTAA
1 TAACGGGAAGCTCATAGCGAGCTAA
* * *
3325697 TATCGGGAAGTTCA-AGTGAGCTAA
1 TAACGGGAAGCTCATAGCGAGCTAA
3325721 TAACGGGAAGCTCATA
1 TAACGGGAAGCTCATA
3325737 AAATATCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (25 bp):
TAACGGGAAGCTCATAGCGAGCTAA
Found at i:3326233 original size:21 final size:21
Alignment explanation
Indices: 3326207--3326247 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3326197 GAATTTAACA
*
3326207 TCAATTTAATACAAATCATAG
1 TCAATTCAATACAAATCATAG
* *
3326228 TCAATTCAATCCAATTCATA
1 TCAATTCAATACAAATCATA
3326248 TCCTAGACAA
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:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (21 bp):
TCAATTCAATACAAATCATAG
Found at i:3337224 original size:39 final size:43
Alignment explanation
Indices: 3337119--3337228 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 43
3337109 GGATTATAGG
3337119 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * *
3337164 TGTAATGGAATAGAGGCGTAATAG-TAATCTTA-TGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATC-AACTGTTTGGTTA
3337204 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
3337229 TAATGGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
39 20 0.34
40 2 0.03
43 1 0.02
44 11 0.19
45 24 0.41
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:3337511 original size:16 final size:16
Alignment explanation
Indices: 3337467--3337513 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
3337457 TACTATAAAA
*
3337467 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
3337483 TATTATT-AAATATAT
1 TATAATTAAAATATAT
3337498 TATAATTAAAATATAT
1 TATAATTAAAATATAT
3337514 AATTTAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:3337633 original size:18 final size:17
Alignment explanation
Indices: 3337612--3337646 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3337602 TTATTATTAA
*
3337612 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3337630 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3337647 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3337663 original size:16 final size:15
Alignment explanation
Indices: 3337638--3337667 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3337628 ATATATAATT
3337638 TAATAAAATTCTTAA
1 TAATAAAATTCTTAA
3337653 TAATCAAAATTCTTA
1 TAAT-AAAATTCTTA
3337668 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAAATTCTTAA
Found at i:3338006 original size:59 final size:58
Alignment explanation
Indices: 3337568--3337996 Score: 198
Period size: 59 Copynumber: 7.2 Consensus size: 58
3337558 CTCAAATCAT
* * * *
3337568 AATATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGA-ATAATTAATATTAAAAATATTTTAATTAA
* * * * * ** * ** * ** * *
3337627 AATATATAAT-TTAATAAAATTCTTAATAATCAA-AATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATACT-ATAAAA-T-ATAAT-TTGAATAATTAATAT-TAAAAATATTTTAATTAA
3337688 AATATATGATACTATAAAATATAATTTGAATTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAA-TAATTAATATTAAAAATATTTTAATTAA
* * * * * ** * *
3337747 AATATAT-A-A-T-T-TAATAAAATTCTTAATAATCAACATTCTTATATGAATTTACTAAAATCA
1 AATATATGATACTATAAAATATAATT-TGAATAATTAATATT-AAAAAT--ATTT--T--AATTA
*
3337807 T
58 A
3337808 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAA-TAATTAATATTAAAAATATTTTAATTAA
* * * * * ** * *
3337867 AATATAT-A-A-T-T-TAATAAAATTCTTAATAATCAACATTCTTATATGAATTTACTAAAATCA
1 AATATATGATACTATAAAATATAATT-TGAATAATTAATATT-AAAAAT--ATTT--T--AATTA
*
3337927 T
58 A
3337928 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAA-TAATTAATATTAAAAATATTTTAATTAA
3337987 AATATATGAT
1 AATATATGAT
3337997 TTAATAAAAT
Statistics
Matches: 265, Mismatches: 69, Indels: 72
0.65 0.17 0.18
Matches are distributed among these distances:
54 34 0.13
55 14 0.05
56 2 0.01
57 10 0.04
58 6 0.02
59 63 0.24
60 16 0.06
61 55 0.21
62 5 0.02
63 10 0.04
64 2 0.01
65 14 0.05
66 34 0.13
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTGAATAATTAATATTAAAAATATTTTAATTAA
Found at i:3338016 original size:120 final size:120
Alignment explanation
Indices: 3337360--3338007 Score: 1054
Period size: 120 Copynumber: 5.4 Consensus size: 120
3337350 ATATTTAAAC
* * *
3337360 ATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATA
1 ATAATTAA-TATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACA
*
3337424 -TCTTA-ATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT-AA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * * * * *
3337477 CATAATTATTATTAAATATATTATAATTAAAATATATAATTTAGTAAAATTCTTAAAAATTAATA
1 -ATAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACA
* *
3337542 TTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT-AA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * *
3337597 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAAA
1 -ATAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACA
3337662 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
65 TTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
3337718 TTAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACAT
1 ATAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACAT
3337783 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
*
3337838 GTAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACAT
1 ATAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACAT
3337903 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* *
3337958 GTAATTAATATTAAAAATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATT
3338008 TAAAATAATT
Statistics
Matches: 508, Mismatches: 18, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
118 57 0.11
119 7 0.01
120 442 0.87
121 2 0.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (120 bp):
ATAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAACAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:3338058 original size:47 final size:46
Alignment explanation
Indices: 3337989--3338156 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
3337979 TTAATTAAAA
*
3337989 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * *
3338036 TATATGAATTTGTATAATTTAAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
3338081 TA-AT-AATAATATATAATTTCATAA-AATTCGTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
3338127 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
3338157 ATATTAAATA
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 9 0.09
46 8 0.08
47 46 0.48
48 7 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:3338065 original size:101 final size:92
Alignment explanation
Indices: 3338004--3338180 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 92
3337994 GATTTAATAA
* *
3338004 AATTT-AAAATAATT-ATAACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTAT
1 AATTTCAAAA-AATTCATAA-TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAA
3338067 TATTAAATATAATTTAA-TAATAATATAT
64 TATTAAATATAATTTAATTAATAATATAT
* * * *
3338095 AATTTCATAAAATTCGTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
3338160 TTAAATATAATTTAA-TAATAA
66 TTAAATATAATTTAATTAATAA
3338181 AATGTTCTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
91 73 0.94
92 5 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (92 bp):
AATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
TTAAATATAATTTAATTAATAATATAT
Found at i:3338176 original size:17 final size:15
Alignment explanation
Indices: 3338145--3338183 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3338135 TTTATACAAT
3338145 TTAAAATAATTAATA
1 TTAAAATAATTAATA
3338160 TTAAATATAATTTAATA
1 TTAAA-ATAA-TTAATA
*
3338177 ATAAAAT
1 TTAAAAT
3338184 GTTCTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:3354367 original size:6 final size:6
Alignment explanation
Indices: 3354356--3354382 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3354346 TGTCTCATTT
3354356 ATGATA ATGATA ATGATA ATGATA ATG
1 ATGATA ATGATA ATGATA ATGATA ATG
3354383 GCAATGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (6 bp):
ATGATA
Found at i:3354388 original size:18 final size:18
Alignment explanation
Indices: 3354356--3354390 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3354346 TGTCTCATTT
*
3354356 ATGATAATGATAATGATA
1 ATGATAATGACAATGATA
*
3354374 ATGATAATGGCAATGAT
1 ATGATAATGACAATGAT
3354391 GTGGATGATG
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:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (18 bp):
ATGATAATGACAATGATA
Found at i:3355436 original size:20 final size:19
Alignment explanation
Indices: 3355411--3355448 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3355401 TAGAAAGATG
3355411 AATAATAACTCTTGTAAAAA
1 AATAATAACTCTT-TAAAAA
*
3355431 AATAATACCTCTTTAAAA
1 AATAATAACTCTTTAAAA
3355449 TAAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAATAACTCTTTAAAAA
Found at i:3355792 original size:89 final size:87
Alignment explanation
Indices: 3355606--3355887 Score: 267
Period size: 89 Copynumber: 3.1 Consensus size: 87
3355596 TTAAGGGTGT
*
3355606 AAAAGGCCCTAAAACTTTTTCAAAAAAAAAATCAATTAAGCCCTTGTTTTTTTTTTTGCACTCAA
1 AAAAGGCCCTCAAACTTTTTC---AAAAAAATCAATTAAGCCC-TG---TTTTTTTTGCACTCAA
* * * *
3355671 TTGGGTACTTGAACTTTTAAAATGCATAA
59 TTGGATAATTGAACTGTCAAAATGCATAA
* * * *
3355700 AAAAGGCCCTCAAACTTTTTCAAATAAAGCAATTAAGCCCCTAGTTTTTTTTGTACTTAATTGGA
1 AAAAGGCCCTCAAACTTTTTCAAAAAAATCAATTAAG-CCCT-GTTTTTTTTGCACTCAATTGGA
* * *
3355765 TAATTGAACTGTCCAGATGCATCA
64 TAATTGAACTGTCAAAATGCATAA
* * *
3355789 AAAAGGCCCTCGAACTTTTTCAAAAAAATTAATTAAGTCACTGTTTTTTTTTTTGCACTCAATTG
1 AAAAGGCCCTCAAACTTTTTCAAAAAAATCAATTAAG-CCCTG---TTTTTTTTGCACTCAATTG
* * * * *
3355854 AATACTTGAACTGCCAAAATGTATCA
62 GATAATTGAACTGTCAAAATGCATAA
3355880 AAAAGGCC
1 AAAAGGCC
3355888 AAGGGTGAAT
Statistics
Matches: 157, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
88 1 0.01
89 72 0.46
91 60 0.38
92 4 0.03
94 20 0.13
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (87 bp):
AAAAGGCCCTCAAACTTTTTCAAAAAAATCAATTAAGCCCTGTTTTTTTTGCACTCAATTGGATA
ATTGAACTGTCAAAATGCATAA
Found at i:3358538 original size:19 final size:19
Alignment explanation
Indices: 3358514--3358568 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
3358504 GTACGATAAT
3358514 TTTTATAATTTTTTACAAA
1 TTTTATAATTTTTTACAAA
**
3358533 TTTTAT-ATTTCTTTACATT
1 TTTTATAATTT-TTTACAAA
3358552 TTTTATAATTTTCTTAC
1 TTTTATAATTTT-TTAC
3358569 GGCTTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.13
19 19 0.61
20 8 0.26
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAA
Found at i:3360688 original size:86 final size:86
Alignment explanation
Indices: 3360413--3360727 Score: 356
Period size: 86 Copynumber: 3.6 Consensus size: 86
3360403 GCTCCTAGCT
* * *
3360413 TTTTTTATGCATTTTGGCAGTTCAAGTAC-CTAATT-AGT-ACTAAAAAAGAGCAGAGGCTTAAT
1 TTTTTTATACATTTTGACAGTTCAAGTACTC-AATTGAGTGA--AAAAAA-A--AGA-GATTAAT
* * *
3360475 TG-CTTTTTTTGAAAAAGTTTGAGG-GA
59 TGTTTTTTTTTGAAAAATTTTGAGGTCA
** * *
3360501 CTTTTAAATACATTTTGACAGTTCAAATACCCAATTGAGTGAAAAAAAAAGGAGATTAATTGTTT
1 -TTTTTTATACATTTTGACAGTTCAAGTACTCAATTGAGTGAAAAAAAAA-GAGATTAATTGTTT
*
3360566 TTTTTTGAAAAATTTTGAGGTCC
64 TTTTTTGAAAAATTTTGAGGTCA
* *
3360589 TTTTTTATGCATTTTGAAAGTTCAAGTACTCAATTGAGTG-AAAAAAAAGAGATTAATTGTTTTT
1 TTTTTTATACATTTTGACAGTTCAAGTACTCAATTGAGTGAAAAAAAAAGAGATTAATTG-TTTT
3360653 TTTTTGAAAAATTTTGAGGTCA
65 TTTTTGAAAAATTTTGAGGTCA
*
3360675 TTTTTTATACATTTTGACAGTTCAAGT-GTACAATTGAGTGAAAAAAAAAGAGA
1 TTTTTTATACATTTTGACAGTTCAAGTACT-CAATTGAGTGAAAAAAAAAGAGA
3360728 GCAAGGCTTA
Statistics
Matches: 197, Mismatches: 20, Indels: 20
0.83 0.08 0.08
Matches are distributed among these distances:
85 12 0.06
86 77 0.39
87 68 0.35
88 1 0.01
89 34 0.17
90 4 0.02
91 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (86 bp):
TTTTTTATACATTTTGACAGTTCAAGTACTCAATTGAGTGAAAAAAAAAGAGATTAATTGTTTTT
TTTTGAAAAATTTTGAGGTCA
Found at i:3361320 original size:38 final size:39
Alignment explanation
Indices: 3361253--3361358 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
3361243 TGTGATGCCA
* * *
3361253 AAATCTTTAACGGATGCCAAAATCTCTAA-CAAATA-TCG
1 AAATCTCTAACAGATACCAAAATCTCTAACCAAATACT-G
*
3361291 AAATTTCTAACAGATACCAAAATCTCTAACCAAATACTG
1 AAATCTCTAACAGATACCAAAATCTCTAACCAAATACTG
* * **
3361330 AAGTCTGTAATTGATACCAAAATCTCTAA
1 AAATCTCTAACAGATACCAAAATCTCTAA
3361359 TGGATACCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 25 0.44
39 31 0.54
40 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (39 bp):
AAATCTCTAACAGATACCAAAATCTCTAACCAAATACTG
Found at i:3361359 original size:19 final size:19
Alignment explanation
Indices: 3361250--3361399 Score: 93
Period size: 19 Copynumber: 7.8 Consensus size: 19
3361240 TAATGTGATG
* * *
3361250 CCAAAATCTTTAACGGATG
1 CCAAAATCTCTAACAGATA
*
3361269 CCAAAATCTCTAACAAATA
1 CCAAAATCTCTAACAGATA
* * *
3361288 TCGAAATTTCTAACAGATA
1 CCAAAATCTCTAACAGATA
*
3361307 CCAAAATCTCTAACCAAATA
1 CCAAAATCTCTAA-CAGATA
** * * **
3361327 CTGAAGTCTGTAATTGATA
1 CCAAAATCTCTAACAGATA
**
3361346 CCAAAATCTCTAATGGATA
1 CCAAAATCTCTAACAGATA
* ** *
3361365 CCAAAATTTGAAACCAAATA
1 CCAAAATCTCTAA-CAGATA
*
3361385 CCACAATCTCTAACA
1 CCAAAATCTCTAACA
3361400 AAAATCTCTA
Statistics
Matches: 95, Mismatches: 34, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
19 69 0.73
20 26 0.27
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (19 bp):
CCAAAATCTCTAACAGATA
Found at i:3365103 original size:26 final size:26
Alignment explanation
Indices: 3365067--3365175 Score: 191
Period size: 26 Copynumber: 4.2 Consensus size: 26
3365057 ATGAAATGCC
*
3365067 TATCATGGAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAACCCAT
3365093 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
* *
3365119 TATCATGGAATATTTACCTAATCCAT
1 TATCATGGAACATTTACCTAACCCAT
3365145 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
3365171 TATCA
1 TATCA
3365176 ATTTGTACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:3367320 original size:17 final size:17
Alignment explanation
Indices: 3367300--3367344 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
3367290 TATGAATTAA
3367300 ATATTATTATTATAATT
1 ATATTATTATTATAATT
*
3367317 ATATTATTATTGTAATT
1 ATATTATTATTATAATT
3367334 -TATTATTATTA
1 ATATTATTATTA
3367345 ATTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATATTATTATTATAATT
Found at i:3367400 original size:16 final size:16
Alignment explanation
Indices: 3367379--3367411 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3367369 AAATAAAGTA
*
3367379 AAAGAATAAAAGAAAC
1 AAAGAAGAAAAGAAAC
3367395 AAAGAAGAAAAGAAAC
1 AAAGAAGAAAAGAAAC
3367411 A
1 A
3367412 GAGACTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAC
Found at i:3367450 original size:14 final size:15
Alignment explanation
Indices: 3367431--3367460 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3367421 CGAAATAGGG
3367431 GAAAGAAAAA-GAAA
1 GAAAGAAAAATGAAA
3367445 GAAAGAAAAATGAAA
1 GAAAGAAAAATGAAA
3367460 G
1 G
3367461 GAAAAACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
GAAAGAAAAATGAAA
Found at i:3370535 original size:9 final size:9
Alignment explanation
Indices: 3370506--3370542 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3370496 TGAGTTTTCG
3370506 AATTCGAAT
1 AATTCGAAT
*
3370515 AACTCGAAT
1 AATTCGAAT
3370524 AATTCGAAT
1 AATTCGAAT
*
3370533 AATTAGAAT
1 AATTCGAAT
3370542 A
1 A
3370543 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3371088 original size:17 final size:17
Alignment explanation
Indices: 3371068--3371114 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3371058 CACATTTTAT
3371068 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
3371085 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
3371103 A-TATTTATATTA
1 ATTATTTATATTA
3371115 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:3371463 original size:5 final size:5
Alignment explanation
Indices: 3371453--3371478 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3371443 GAACAAATAT
3371453 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
3371479 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:3373242 original size:30 final size:30
Alignment explanation
Indices: 3373208--3373272 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3373198 TAATTAAAGT
* *
3373208 AAAATTATATTTTAA-CTTTCAAACATTATA
1 AAAATT-TAATTTAATCTTTCAAAAATTATA
* *
3373238 AAAATTTAATTTAATTTTTTAAAAATTATA
1 AAAATTTAATTTAATCTTTCAAAAATTATA
3373268 AAAAT
1 AAAAT
3373273 ATAGAACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (30 bp):
AAAATTTAATTTAATCTTTCAAAAATTATA
Found at i:3381882 original size:16 final size:16
Alignment explanation
Indices: 3381861--3381914 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
3381851 AACAAATTCC
*
3381861 AAAAAATAAAAAAGCA
1 AAAAAATAAAAAAACA
*
3381877 AAAAAATAAAAAAAATA
1 AAAAAAT-AAAAAAACA
3381894 AAAAAATAAAAAAACA
1 AAAAAATAAAAAAACA
3381910 AAAAA
1 AAAAA
3381915 TAGAATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 20 0.59
17 14 0.41
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.07
Consensus pattern (16 bp):
AAAAAATAAAAAAACA
Found at i:3381887 original size:8 final size:8
Alignment explanation
Indices: 3381861--3381914 Score: 72
Period size: 8 Copynumber: 6.6 Consensus size: 8
3381851 AACAAATTCC
3381861 AAAAAATA
1 AAAAAATA
**
3381869 AAAAAGCA
1 AAAAAATA
3381877 AAAAAATAA
1 AAAAAAT-A
3381886 AAAAAATA
1 AAAAAATA
3381894 AAAAAATA
1 AAAAAATA
*
3381902 AAAAAACA
1 AAAAAATA
3381910 AAAAA
1 AAAAA
3381915 TAGAATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
8 32 0.80
9 8 0.20
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.07
Consensus pattern (8 bp):
AAAAAATA
Found at i:3381895 original size:25 final size:25
Alignment explanation
Indices: 3381861--3381914 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
3381851 AACAAATTCC
* *
3381861 AAAAAATAAAAAAGCAAAAAAATAA
1 AAAAAATAAAAAAACAAAAAAACAA
*
3381886 AAAAAATAAAAAAATAAAAAAACAA
1 AAAAAATAAAAAAACAAAAAAACAA
3381911 AAAA
1 AAAA
3381915 TAGAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.07
Consensus pattern (25 bp):
AAAAAATAAAAAAACAAAAAAACAA
Found at i:3383333 original size:60 final size:59
Alignment explanation
Indices: 3383232--3383373 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 59
3383222 ATATATACAT
* * *
3383232 ATATTC-TTAATATTATATATTGTATGTATTTTCTTATTATATGTGTATGTATAGTATGTAC
1 ATATTCTTTAATATTAT-TA-TGTATGTATTTTCTTAATATATGTATATATATAGTA-GTAC
*
3383293 ATATTCTTTAATATTATTATGTAT-TAATTTT-TTAAATATATGTATATATATATTAGTAC
1 ATATTCTTTAATATTATTATGTATGT-ATTTTCTT-AATATATGTATATATATAGTAGTAC
* *
3383352 TTATAT-TTT-GTATTATTATGTA
1 ATAT-TCTTTAATATTATTATGTA
3383374 AACGTCTTTC
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
58 12 0.17
59 13 0.18
60 28 0.39
61 8 0.11
62 10 0.14
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (59 bp):
ATATTCTTTAATATTATTATGTATGTATTTTCTTAATATATGTATATATATAGTAGTAC
Found at i:3384213 original size:2 final size:2
Alignment explanation
Indices: 3384208--3384233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3384198 TGTGTGATTG
3384208 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
3384234 GAGTGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3393026 original size:22 final size:21
Alignment explanation
Indices: 3392998--3393051 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
3392988 GCACTAATGG
3392998 ACAGAGAGCA-GTAAGGTGCTA
1 ACAGAGAGCACG-AAGGTGCTA
*
3393019 TACAGAGAGCACGAATGTGCTA
1 -ACAGAGAGCACGAAGGTGCTA
*
3393041 ACGGAGAGCAC
1 ACAGAGAGCAC
3393052 TAACGTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
22 18 0.62
23 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.31, T:0.13
Consensus pattern (21 bp):
ACAGAGAGCACGAAGGTGCTA
Found at i:3401207 original size:21 final size:22
Alignment explanation
Indices: 3401171--3401217 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
3401161 GGACTTACTA
*
3401171 CCATATATAGTAGCAAGTGTATT
1 CCATATATAGTAGCAA-TGTAAT
3401194 CCATATAT-GT-GCAATGTAAT
1 CCATATATAGTAGCAATGTAAT
3401214 CCAT
1 CCAT
3401218 GCTAATAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
22 2 0.09
23 8 0.35
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (22 bp):
CCATATATAGTAGCAATGTAAT
Found at i:3411223 original size:19 final size:19
Alignment explanation
Indices: 3411186--3411223 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3411176 GTAAAGTATT
*
3411186 TAATTTATAGCGTAAATAA
1 TAATTTATAGCATAAATAA
3411205 TAATTTA-AGCATAATATAA
1 TAATTTATAGCATAA-ATAA
3411224 GGAACAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (19 bp):
TAATTTATAGCATAAATAA
Found at i:3412280 original size:17 final size:18
Alignment explanation
Indices: 3412246--3412298 Score: 81
Period size: 17 Copynumber: 2.9 Consensus size: 18
3412236 AATCATATCT
3412246 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
3412264 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
3412281 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
3412299 TGAAGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:3412890 original size:45 final size:45
Alignment explanation
Indices: 3412835--3413031 Score: 252
Period size: 45 Copynumber: 4.4 Consensus size: 45
3412825 GGAAGGTGAT
* * *
3412835 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACACCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
3412880 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * *
3412925 ATCTGCT-TCTTCAATCTACTCACCGTCTAATACAGATATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
3412969 ATCTATTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
3413014 ATCTGTCATCTTGGATCT
1 ATCTGTTATCTTCGATCT
3413032 ACTTCGATGT
Statistics
Matches: 129, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
44 37 0.29
45 92 0.71
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.31
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:3412969 original size:89 final size:90
Alignment explanation
Indices: 3412835--3413018 Score: 262
Period size: 89 Copynumber: 2.1 Consensus size: 90
3412825 GGAAGGTGAT
** * * * *
3412835 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACACCAAATCTGTTATCTTCGATCTGC
1 ATCTGCTATCTTCAATCTACTCACCGTCTAATACAGAGACACCAAATCTATTATCTCCGATCTGC
3412900 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
* ** *
3412925 ATCTGCT-TCTTCAATCTACTCACCGTCTAATACAGATATGCCAAATCTATTATCTCCGATTTGC
1 ATCTGCTATCTTCAATCTACTCACCGTCTAATACAGAGACACCAAATCTATTATCTCCGATCTGC
*
3412989 TCCCCGTCTAATACAGAGATGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
3413014 ATCTG
1 ATCTG
3413019 TCATCTTGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 76 0.92
90 7 0.08
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTACTCACCGTCTAATACAGAGACACCAAATCTATTATCTCCGATCTGC
TCCCCGTCTAATACAGAGACGCCAA
Found at i:3413177 original size:78 final size:78
Alignment explanation
Indices: 3413048--3413342 Score: 434
Period size: 78 Copynumber: 3.8 Consensus size: 78
3413038 ATGTAAACAC
* * * * *
3413048 ATGAAGGTTAGATCTGCTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATACTAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATCT
3413113 TGGATCTGCTTCA
66 TGGATCTGCTTCA
*
3413126 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATC
3413190 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * *
3413204 ATGAAGGTCAGATTTACTGTGTCTTCGATCTG-TTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTT-CCCGTCTAATACAGAGATGCCAAATCATC
3413268 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* **
3413282 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGC-TCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTC-CCGTCTAATACAGAGATGCCAAATC
3413343 TGTTTCTTCG
Statistics
Matches: 196, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
77 5 0.03
78 190 0.97
79 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:3414065 original size:12 final size:12
Alignment explanation
Indices: 3414048--3414079 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3414038 CACTTACGTG
3414048 AATTCTTCGAAC
1 AATTCTTCGAAC
3414060 AATTCTTCGAAC
1 AATTCTTCGAAC
3414072 AATTCTTC
1 AATTCTTC
3414080 TATTTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (12 bp):
AATTCTTCGAAC
Found at i:3422240 original size:23 final size:21
Alignment explanation
Indices: 3422210--3422253 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3422200 AAATTAAATC
3422210 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC--AATCATATCT
*
3422233 TCTAAGATTGCAATCATATCT
1 TCTAAGATTACAATCATATCT
3422254 AAGGTTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (21 bp):
TCTAAGATTACAATCATATCT
Found at i:3422285 original size:19 final size:19
Alignment explanation
Indices: 3422233--3422304 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
3422223 AATCATATCT
3422233 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
3422251 TCTAAGGTTG--TATCATA
1 TCTAAGATTGCATATCATA
3422268 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
3422287 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
3422305 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
17 15 0.31
18 9 0.18
19 25 0.51
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3422311 original size:36 final size:35
Alignment explanation
Indices: 3422236--3422312 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
3422226 CATATCTTCT
* *
3422236 AAGATTGCAATCATATCTAAGGTTGTATCATATCT
1 AAGATTGCAATCATATCTAAGATTGTATCATATCG
3422271 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTGCA-ATCATATCTAAGATTG--TATCATATCG
3422307 AAGATT
1 AAGATT
3422313 ATATTTCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 9 0.24
36 21 0.57
37 1 0.03
38 6 0.16
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (35 bp):
AAGATTGCAATCATATCTAAGATTGTATCATATCG
Found at i:3422312 original size:17 final size:19
Alignment explanation
Indices: 3422236--3422312 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
3422226 CATATCTTCT
*
3422236 AAGATTGCA-ATCATATCT
1 AAGATTGCATATCATATCG
* *
3422254 AAGGTTG--TATCATATCT
1 AAGATTGCATATCATATCG
*
3422271 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
3422290 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
3422307 AAGATT
1 AAGATT
3422313 ATATTTCCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
17 21 0.40
18 7 0.13
19 25 0.47
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Done.