Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 2 of 135
Found at i:321817 original size:20 final size:21
Alignment explanation
Indices: 321786--321825 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
321776 CCCTAAACAA
321786 GAGGGAAAGGGGAAAGGGAAG
1 GAGGGAAAGGGGAAAGGGAAG
321807 GAGGG-AAGGGGAAAGGGAA
1 GAGGGAAAGGGGAAAGGGAA
321826 CAGAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.00
Consensus pattern (21 bp):
GAGGGAAAGGGGAAAGGGAAG
Found at i:321878 original size:16 final size:16
Alignment explanation
Indices: 321857--321918 Score: 70
Period size: 16 Copynumber: 3.5 Consensus size: 16
321847 AAATGATGAT
321857 TATTTTAATAATTTTA
1 TATTTTAATAATTTTA
321873 TATTTTAATTTAATTTTAAAA
1 TATTTTAA--TAATTTT---A
321894 TAATTTTAATAATTTTA
1 T-ATTTTAATAATTTTA
321911 TATTTTAA
1 TATTTTAA
321919 AAAAATAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
16 15 0.38
17 2 0.05
18 7 0.17
20 7 0.17
21 2 0.05
22 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTAATAATTTTA
Found at i:321940 original size:41 final size:38
Alignment explanation
Indices: 321858--321940 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 38
321848 AATGATGATT
**
321858 ATTTTAATAATTTTATATTTTAATTTAATTTTAAAATA
1 ATTTTAATAATTTTATATTTTAAAATAATTTTAAAATA
321896 ATTTTAATAATTTTATATTTTAAAAAAATAATTTTAAAATA
1 ATTTTAATAATTTTATATTTT---AAAATAATTTTAAAATA
321937 ATTT
1 ATTT
321941 GCTGACGTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 21 0.52
41 19 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (38 bp):
ATTTTAATAATTTTATATTTTAAAATAATTTTAAAATA
Found at i:322378 original size:20 final size:21
Alignment explanation
Indices: 322353--322405 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
322343 TAAATAATTT
322353 AAAAATCATAAATATTC-AAA
1 AAAAATCATAAATATTCAAAA
*
322373 AAAAAT-A-AAAAATTCAAAA
1 AAAAATCATAAATATTCAAAA
322392 AAAAATCATGAAAT
1 AAAAATCAT-AAAT
322406 GCATGTGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.26
19 10 0.37
20 7 0.26
22 3 0.11
ACGTcount: A:0.70, C:0.08, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAATCATAAATATTCAAAA
Found at i:322380 original size:17 final size:17
Alignment explanation
Indices: 322341--322395 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
322331 ATGTCACGTC
* *
322341 AATAAATAATTTAAAAAT
1 AATAAAT-ATTCAAAAAA
*
322359 CATAAATATTCAAAAAA
1 AATAAATATTCAAAAAA
*
322376 AATAAAAAATTCAAAAAA
1 AAT-AAATATTCAAAAAA
322394 AA
1 AA
322396 ATCATGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAATATTCAAAAAA
Found at i:322797 original size:74 final size:74
Alignment explanation
Indices: 322716--322863 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
322706 GGGTCTAGGT
* *
322716 GGGCTGAATTCGAGCTTAAATTTTTTTTGAAATCAAATATAGACCAAGGCAATGAGTACCTTTAA
1 GGGCTGAATTCGAGCTTAAATTTTTTTTGAAATCAAATATAGACCAAAGCAATGAATACCTTTAA
322781 ATTTAATTC
66 ATTTAATTC
*
322790 GGGCTGAATTCGAGCTTAAATTTTTTTTGAAATCGAATATAGACCAAAGCAATGAATACCTTTAA
1 GGGCTGAATTCGAGCTTAAATTTTTTTTGAAATCAAATATAGACCAAAGCAATGAATACCTTTAA
322855 ATTTAATTC
66 ATTTAATTC
322864 CTATGCACAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (74 bp):
GGGCTGAATTCGAGCTTAAATTTTTTTTGAAATCAAATATAGACCAAAGCAATGAATACCTTTAA
ATTTAATTC
Found at i:326606 original size:86 final size:86
Alignment explanation
Indices: 326461--326631 Score: 245
Period size: 86 Copynumber: 2.0 Consensus size: 86
326451 AGGGAATACC
* * * *
326461 TCTATTTATAGTTGAGTTCTACTAAAATTAATGATACTGATTGAGTTACATTGACGGTCAAAATT
1 TCTATTTATAGTTGAGCTCTACTAAAATCAACGATACTGATTCAGTTACATTGACGGTCAAAATT
326526 AGAA-TCTATCTACAATTGAGT
66 AGAATTC-ATCTACAATTGAGT
* * *
326547 TCTATTTATAGTTGAGCTCTCCTAAAATCAACGGTACTGATTCAGTTACATTGACGGTCAAGATT
1 TCTATTTATAGTTGAGCTCTACTAAAATCAACGATACTGATTCAGTTACATTGACGGTCAAAATT
* *
326612 AGAGTTCATCTATAATTGAG
66 AGAATTCATCTACAATTGAG
326632 AGTTCTAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
86 73 0.97
87 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (86 bp):
TCTATTTATAGTTGAGCTCTACTAAAATCAACGATACTGATTCAGTTACATTGACGGTCAAAATT
AGAATTCATCTACAATTGAGT
Found at i:327251 original size:43 final size:43
Alignment explanation
Indices: 327190--327275 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
327180 ATTAAGAAAT
*
327190 GTGACAATTATTTTAAGGGTAAATTATATAGATAGTGATCTAA
1 GTGACAATTATTTTAAGGGTAAATAATATAGATAGTGATCTAA
327233 GTGACAATTATTTTAAGGGTAAATAATATAGATAGTGATCTAA
1 GTGACAATTATTTTAAGGGTAAATAATATAGATAGTGATCTAA
327276 TTATAAAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (43 bp):
GTGACAATTATTTTAAGGGTAAATAATATAGATAGTGATCTAA
Found at i:329549 original size:22 final size:22
Alignment explanation
Indices: 329524--329569 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
329514 GGTTTCAATA
* *
329524 TTCAACTTGATATTTGAGTTTT
1 TTCAACTTGATACTTAAGTTTT
329546 TTCAACTTGATACTTAAGTTTT
1 TTCAACTTGATACTTAAGTTTT
329568 TT
1 TT
329570 TTTTTGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (22 bp):
TTCAACTTGATACTTAAGTTTT
Found at i:334185 original size:42 final size:45
Alignment explanation
Indices: 334138--334242 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
334128 CCCATTTCAA
* *
334138 ACTTATCATAGT-GAAATAGTTT-T-T-TGCGTGTTAGAAAGGTAT
1 ACTTATCATA-TCGAAATAATTTGTGTGTGCGTGTAAGAAAGGTAT
* * *
334180 ACTTATCATATCAAAATAATTTGTGTGTGTGTGTAAGAAATGTAT
1 ACTTATCATATCGAAATAATTTGTGTGTGCGTGTAAGAAAGGTAT
334225 ACTTATCATATCGAAATA
1 ACTTATCATATCGAAATA
334243 TAATTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 18 0.34
43 1 0.02
44 1 0.02
45 32 0.60
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (45 bp):
ACTTATCATATCGAAATAATTTGTGTGTGCGTGTAAGAAAGGTAT
Found at i:336071 original size:2 final size:2
Alignment explanation
Indices: 336064--336107 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
336054 ATCATTTAAA
336064 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
336106 AT
1 AT
336108 TAAAATTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:336308 original size:23 final size:23
Alignment explanation
Indices: 336264--336309 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
336254 AATTATATTA
* * * *
336264 AAAAAATATTAATTTGATTGAAT
1 AAAAAATAATAAATTAAATGAAT
336287 AAAAAATAATAAATTAAATGAAT
1 AAAAAATAATAAATTAAATGAAT
336310 TAATTAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAAAATAATAAATTAAATGAAT
Found at i:338413 original size:18 final size:19
Alignment explanation
Indices: 338378--338414 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
338368 TTAACTTTTA
*
338378 AAATTCAAGTATAATTATT
1 AAATTCAACTATAATTATT
338397 AAATTCAACTA-AATTATT
1 AAATTCAACTATAATTATT
338415 TTATTAAATT
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:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
AAATTCAACTATAATTATT
Found at i:340264 original size:22 final size:23
Alignment explanation
Indices: 340245--340293 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
340235 TCTTATTTTT
340245 AATTAAAA-AAATCATAATTTAA
1 AATTAAAAGAAATCATAATTTAA
*
340267 AATTAAAAGAAATTATAAATATTAA
1 AATTAAAAGAAATCAT-AAT-TTAA
340292 AA
1 AA
340294 CCCAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 6 0.26
24 3 0.13
25 6 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
AATTAAAAGAAATCATAATTTAA
Found at i:354451 original size:2 final size:2
Alignment explanation
Indices: 354444--354473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
354434 ATATTATTTC
354444 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
354474 GGTAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:361924 original size:8 final size:8
Alignment explanation
Indices: 361910--361953 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
361900 ATACATACAC
361910 ATATGTAT
1 ATATGTAT
*
361918 GTATGTAT
1 ATATGTAT
**
361926 GCATGTAT
1 ATATGTAT
*
361934 ACATGTAT
1 ATATGTAT
361942 ATATGTAT
1 ATATGTAT
361950 ATAT
1 ATAT
361954 ACGTGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (8 bp):
ATATGTAT
Found at i:361954 original size:20 final size:20
Alignment explanation
Indices: 361916--361955 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
361906 ACACATATGT
* *
361916 ATGTATGTATGCATGTATAC
1 ATGTATATATGCATATATAC
*
361936 ATGTATATATGTATATATAC
1 ATGTATATATGCATATATAC
361956 GTGTTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATATATGCATATATAC
Found at i:362003 original size:162 final size:157
Alignment explanation
Indices: 361680--362054 Score: 467
Period size: 162 Copynumber: 2.4 Consensus size: 157
361670 GCTGTTGCAT
* * * *
361680 TAACAAGAAGACTACAACAACAAGCTTCAAAGTTACAGTAATAAAGAAGCCAT-AGGAAACCTAG
1 TAACAAGAAGACTACAACAA-AAACTTCAAAGTTACAGTAATAAAGAAGCCATGATGAAACATAA
** * * *
361744 CAAACAAATGATACATATGTATGTTTGTATGCATGTATATATATATATATGTCTTTATAAGACAG
65 CAAACAAATGATACATATGTATGCATGTATACATGTATATATATATATACGTCTTTATAAAACAG
*
361809 CAAAATCCAAATATATGTATCATTGCAC
130 CAAAATCCAAATATATGTATCATTGAAC
361837 TAACAAGAAGACTACAACAAAAAACTTCAAAGTTACAGTAAT-AAGAAGCCATGATGAAACATGA
1 TAACAAGAAGACTACAAC-AAAAACTTCAAAGTTACAGTAATAAAGAAGCCATGATGAAACAT-A
* ** *
361901 TACATACACATATG-TATGTATGTATGCATGTATACATGTATATATGTATATATACGTGTTTATA
64 -ACA-A-ACAAATGATACATATGTATGCATGTATACATGTATATA--TATATATACGTCTTTATA
* **
361965 AAATAGCAAAATCCATCTATATGTATCATTGAAC
124 AAACAGCAAAATCCAAATATATGTATCATTGAAC
*
361999 TAACAAGAAGACTACAAC---AACTTCAAAGTTATAGT-ATAAAGAAGCCATGATGAAAC
1 TAACAAGAAGACTACAACAAAAACTTCAAAGTTACAGTAATAAAGAAGCCATGATGAAAC
362055 CTAGTAAACA
Statistics
Matches: 191, Mismatches: 18, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
156 10 0.05
157 47 0.25
158 37 0.19
159 2 0.01
160 26 0.14
161 6 0.03
162 63 0.33
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (157 bp):
TAACAAGAAGACTACAACAAAAACTTCAAAGTTACAGTAATAAAGAAGCCATGATGAAACATAAC
AAACAAATGATACATATGTATGCATGTATACATGTATATATATATATACGTCTTTATAAAACAGC
AAAATCCAAATATATGTATCATTGAAC
Found at i:362111 original size:17 final size:17
Alignment explanation
Indices: 362089--362121 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
362079 TACATACATG
362089 CATAATGTTATGTATGA
1 CATAATGTTATGTATGA
362106 CATAATGTTATGTATG
1 CATAATGTTATGTATG
362122 TATAAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (17 bp):
CATAATGTTATGTATGA
Found at i:364361 original size:31 final size:31
Alignment explanation
Indices: 364290--364361 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
364280 TAATGTGAAG
* *
364290 TTATATACATAAAATTTTAATTGTGATTTAA
1 TTATATATATAAAATTTTAATTGTAATTTAA
* * *
364321 ATGTATATATAAAATTTTAATTTTAATTTAA
1 TTATATATATAAAATTTTAATTGTAATTTAA
364352 TTATATATAT
1 TTATATATAT
364362 TTAAGTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (31 bp):
TTATATATATAAAATTTTAATTGTAATTTAA
Found at i:370660 original size:25 final size:23
Alignment explanation
Indices: 370618--370663 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
370608 CCAATTAGGG
370618 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
370641 AATTATCTTTTTAGAGTTTAATT
1 AATTAT-TGTTTAGA-TTTAATT
370664 AGATCCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:371863 original size:22 final size:22
Alignment explanation
Indices: 371835--371901 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
371825 TTTAAAATCA
371835 AGACTAAACTAACATAATGTAT
1 AGACTAAACTAACATAATGTAT
*
371857 AGACTAAACTAACACAATGTAT
1 AGACTAAACTAACATAATGTAT
*
371879 AGACTAAACTAATATAATGTAT
1 AGACTAAACTAACATAATGTAT
371901 A
1 A
371902 ACTGTTGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (22 bp):
AGACTAAACTAACATAATGTAT
Found at i:395685 original size:30 final size:30
Alignment explanation
Indices: 395651--395714 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
395641 CTTCAATTTT
* *
395651 TTTTTTAAAATATTCATT-ATACTCCTAAAA
1 TTTTTGAAAATATTAATTAATAC-CCTAAAA
*
395681 TTTTTGAAAATTTTAATTAAATACCCTAAAA
1 TTTTTGAAAATATTAATT-AATACCCTAAAA
395712 TTT
1 TTT
395715 AATGTCAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 15 0.52
31 10 0.34
32 4 0.14
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTTTGAAAATATTAATTAATACCCTAAAA
Found at i:398190 original size:28 final size:27
Alignment explanation
Indices: 398146--398205 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
398136 ATATAAATTT
*
398146 TAAATCTAAACTTTAAA-TCCTAAATAA
1 TAAATCTAAACTCTAAACTCC-AAATAA
398173 TAAACTCTAAACTCTAAACTCCAAATAA
1 TAAA-TCTAAACTCTAAACTCCAAATAA
*
398201 AAAAT
1 TAAAT
398206 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 21 0.72
29 3 0.10
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.28
Consensus pattern (27 bp):
TAAATCTAAACTCTAAACTCCAAATAA
Found at i:400874 original size:29 final size:27
Alignment explanation
Indices: 400842--400906 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
400832 ACCTTTAGTT
*
400842 ATTTAAAAACTTTAATTATAGCTCTCAAA
1 ATTTAAAAA-TTTAATTA-AGCTCCCAAA
*
400871 ATTTTTAAAAATTTAATTAAGTTCCCAAA
1 A--TTTAAAAATTTAATTAAGCTCCCAAA
*
400900 ACTTAAA
1 ATTTAAA
400907 TAGTAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 5 0.16
29 10 0.32
30 8 0.26
31 8 0.26
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.38
Consensus pattern (27 bp):
ATTTAAAAATTTAATTAAGCTCCCAAA
Found at i:402873 original size:24 final size:24
Alignment explanation
Indices: 402841--402887 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
402831 TTGAGAGAGG
* *
402841 TTAAAATATAATTTTATCATTTTA
1 TTAAAATATAATTTCATAATTTTA
*
402865 TTAACATATAATTTCATAATTTT
1 TTAAAATATAATTTCATAATTTT
402888 TAAAGGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAAATATAATTTCATAATTTTA
Found at i:403665 original size:15 final size:17
Alignment explanation
Indices: 403635--403667 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
403625 TCATGACATA
403635 ATATCATTGAGGAATGC
1 ATATCATTGAGGAATGC
403652 ATATCA-TG-GGAATGC
1 ATATCATTGAGGAATGC
403667 A
1 A
403668 GCAGGGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (17 bp):
ATATCATTGAGGAATGC
Found at i:404237 original size:31 final size:29
Alignment explanation
Indices: 404202--404268 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
404192 AAAGTACTGG
* *
404202 AACTAAAATTGACCAATTTAAAAAGTACAAA
1 AACTAAAATCGACCAAATT-AAAA-TACAAA
* *
404233 AACTAAAATCGATCAAATTAAAATATAAA
1 AACTAAAATCGACCAAATTAAAATACAAA
404262 AACTAAA
1 AACTAAA
404269 TTCATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.38
30 4 0.12
31 16 0.50
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.22
Consensus pattern (29 bp):
AACTAAAATCGACCAAATTAAAATACAAA
Found at i:405960 original size:59 final size:59
Alignment explanation
Indices: 405883--406010 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
405873 AAAATCCAAA
*
405883 ATAGTTGGTGACCAAAAAAGACAAAATT-GAATAGTT-GAGTGACAATTTTGTAACTTTTC
1 ATAGTTGGTGACCAAAAAA-ACAAAATTAGAATAATTGGA-TGACAATTTTGTAACTTTTC
* * **
405942 ATAGTTGAGTGACC-AAAAAAGAAAATTACTAATAATTGGATGATTATTTTGTAACTTTTC
1 ATAGTTG-GTGACCAAAAAAACAAAATTA-GAATAATTGGATGACAATTTTGTAACTTTTC
*
406002 ACAGTTGGT
1 ATAGTTGGT
406011 AGTCAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
58 7 0.12
59 14 0.24
60 36 0.61
61 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (59 bp):
ATAGTTGGTGACCAAAAAAACAAAATTAGAATAATTGGATGACAATTTTGTAACTTTTC
Found at i:417456 original size:48 final size:48
Alignment explanation
Indices: 417386--417482 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
417376 AGAAAAAAAG
417386 AAAATTACGGCATATAACTGAGAACATGCTATGTTGGAAAGTTTGTTA
1 AAAATTACGGCATATAACTGAGAACATGCTATGTTGGAAAGTTTGTTA
*
417434 AAAATTACGGCATATAACTGAGAACGTGCTATGTTGGAAAGTTTGTTA
1 AAAATTACGGCATATAACTGAGAACATGCTATGTTGGAAAGTTTGTTA
417482 A
1 A
417483 GTTATATTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (48 bp):
AAAATTACGGCATATAACTGAGAACATGCTATGTTGGAAAGTTTGTTA
Found at i:426695 original size:6 final size:6
Alignment explanation
Indices: 426675--426708 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
426665 ATTAAAAATT
*
426675 ATATAA A-AAAA ATATAA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
426709 TATTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
ATATAA
Found at i:445285 original size:22 final size:22
Alignment explanation
Indices: 445260--445326 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 22
445250 CAAATTTTAA
445260 ATTTATTTATAAGCTTCAAAAC
1 ATTTATTTATAAGCTTCAAAAC
* * **
445282 A-TT-TTAATCAAACTT-TTAA-
1 ATTTATTTAT-AAGCTTCAAAAC
445301 ATTTATTTATAAGCTTCAAAAC
1 ATTTATTTATAAGCTTCAAAAC
445323 ATTT
1 ATTT
445327 TAATCGAACG
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 13 0.41
22 5 0.16
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (22 bp):
ATTTATTTATAAGCTTCAAAAC
Found at i:445299 original size:41 final size:40
Alignment explanation
Indices: 445250--445331 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 40
445240 AATTATGGAG
445250 CAAATTTTAAATTTATTTATAAGCTTCAAAACATTTTAAT
1 CAAATTTTAAATTTATTTATAAGCTTCAAAACATTTTAAT
445290 CAAACTTTTAAATTTATTTATAAGCTTCAAAACATTTTAAT
1 CAAA-TTTTAAATTTATTTATAAGCTTCAAAACATTTTAAT
445331 C
1 C
445332 GAACGTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 4 0.10
41 37 0.90
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (40 bp):
CAAATTTTAAATTTATTTATAAGCTTCAAAACATTTTAAT
Found at i:445344 original size:41 final size:41
Alignment explanation
Indices: 445258--445344 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
445248 AGCAAATTTT
* *
445258 AAATTTATTTATAAGCTTCAAAACATTTTAATCAAACTTTT
1 AAATTTATTTATAAGCTTCAAAACATTTTAATCAAACGTTG
*
445299 AAATTTATTTATAAGCTTCAAAACATTTTAATCGAACGTTG
1 AAATTTATTTATAAGCTTCAAAACATTTTAATCAAACGTTG
445340 AAATT
1 AAATT
445345 AAAATATCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (41 bp):
AAATTTATTTATAAGCTTCAAAACATTTTAATCAAACGTTG
Found at i:445667 original size:31 final size:30
Alignment explanation
Indices: 445545--445676 Score: 106
Period size: 31 Copynumber: 4.3 Consensus size: 30
445535 TTAATTAGGT
* *
445545 CCCTTAAAATTTTCT-AAAATTTTTATTAAC
1 CCCTCAAAATTTT-TAAAAATTTTAATTAAC
* * *
445575 CCTCACAAAATTTTTAAAAATTTTGATTAAA
1 CC-CTCAAAATTTTTAAAAATTTTAATTAAC
* ** * * *
445606 CTCTCAATTTTTTTTAAAAAAATCTCATTAAAC
1 CCCTCAA-AATTTTT-AAAAATTTTAATT-AAC
445639 CCCTCAAAATTTTTAAAAATTTTAATTAAC
1 CCCTCAAAATTTTTAAAAATTTTAATTAAC
445669 CCC-CAAAA
1 CCCTCAAAA
445677 CTAACTATTA
Statistics
Matches: 79, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
29 5 0.06
30 13 0.16
31 38 0.48
32 15 0.19
33 8 0.10
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (30 bp):
CCCTCAAAATTTTTAAAAATTTTAATTAAC
Found at i:448042 original size:18 final size:18
Alignment explanation
Indices: 448002--448044 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
447992 TTTTCAGTTG
448002 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
448020 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
448038 TAATTAA
1 TAATTAA
448045 AAAATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:451667 original size:29 final size:29
Alignment explanation
Indices: 451612--451668 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
451602 TCAAATTAAA
* * *
451612 ATTTAATTTTTAATAGTTTATATTTTTAT
1 ATTTAATTTTTAATAATTTAAAATTTTAT
* *
451641 ATTTTATTTTTACTAATTTAAAATTTTA
1 ATTTAATTTTTAATAATTTAAAATTTTA
451669 AAATACTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
ATTTAATTTTTAATAATTTAAAATTTTAT
Found at i:452930 original size:15 final size:15
Alignment explanation
Indices: 452910--452939 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
452900 AAACCCACAT
452910 TCATTTAAACCAAAC
1 TCATTTAAACCAAAC
*
452925 TCATTTGAACCAAAC
1 TCATTTAAACCAAAC
452940 CAAATGAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.03, T:0.27
Consensus pattern (15 bp):
TCATTTAAACCAAAC
Found at i:453002 original size:20 final size:21
Alignment explanation
Indices: 452977--453021 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
452967 AGTCAAACCA
452977 TTGACCGGCGTTGATCGAC-G
1 TTGACCGGCGTTGATCGACTG
* *
452997 TTGACCGGTGTTGATTGACTG
1 TTGACCGGCGTTGATCGACTG
453018 TTGA
1 TTGA
453022 TCGTTGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGACCGGCGTTGATCGACTG
Found at i:453027 original size:7 final size:7
Alignment explanation
Indices: 453011--453076 Score: 73
Period size: 7 Copynumber: 9.7 Consensus size: 7
453001 CCGGTGTTGA
*
453011 TTGACTG
1 TTGACCG
*
453018 TTGATCG
1 TTGACCG
*
453025 TTGA-CT
1 TTGACCG
453031 TTGACCG
1 TTGACCG
453038 TTGACCG
1 TTGACCG
453045 TTGA-CG
1 TTGACCG
*
453051 TTAACCG
1 TTGACCG
453058 TTGACCG
1 TTGACCG
*
453065 TTGATCG
1 TTGACCG
453072 TTGAC
1 TTGAC
453077 TTTTTTCGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 10 0.20
7 39 0.80
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (7 bp):
TTGACCG
Found at i:453039 original size:13 final size:14
Alignment explanation
Indices: 453011--453068 Score: 66
Period size: 13 Copynumber: 4.3 Consensus size: 14
453001 CCGGTGTTGA
*
453011 TTGACTGTTGATCG
1 TTGACTGTTGACCG
453025 TTGACT-TTGACCG
1 TTGACTGTTGACCG
*
453038 TTGACCGTTGA-CG
1 TTGACTGTTGACCG
* *
453051 TTAACCGTTGACCG
1 TTGACTGTTGACCG
453065 TTGA
1 TTGA
453069 TCGTTGACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 23 0.61
14 15 0.39
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (14 bp):
TTGACTGTTGACCG
Found at i:453040 original size:20 final size:20
Alignment explanation
Indices: 453011--453076 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
453001 CCGGTGTTGA
* * *
453011 TTGACTGTTGATCGTTGACT
1 TTGACCGTTGACCGTTGACG
453031 TTGACCGTTGACCGTTGACG
1 TTGACCGTTGACCGTTGACG
*
453051 TTAACCGTTGACCGTTGATCG
1 TTGACCGTTGACCGTTGA-CG
453072 TTGAC
1 TTGAC
453077 TTTTTTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 34 0.85
21 6 0.15
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACG
Found at i:456730 original size:31 final size:31
Alignment explanation
Indices: 456594--456730 Score: 93
Period size: 31 Copynumber: 4.5 Consensus size: 31
456584 AAAAAAATTG
** * *
456594 AAAATTTTAATTAGGCCCCTTAAAATTTTCT-
1 AAAATTTTAATTAAACCTCTCAAAATTTT-TA
* *
456625 AAAATTTTCAA-TAAGCATCTCAAAATTTTTA
1 AAAATTTT-AATTAAACCTCTCAAAATTTTTA
** * **
456656 AATTTTTTTATTAAA-CTCTCAATTTTTTTA
1 AAAATTTTAATTAAACCTCTCAAAATTTTTA
* * *
456686 AAAGA-TCTCATTAAACCGCTCAAAATTTTTA
1 AAA-ATTTTAATTAAACCTCTCAAAATTTTTA
456717 AAAATTTTAATTAA
1 AAAATTTTAATTAA
456731 CCCCCAAAAC
Statistics
Matches: 80, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
30 25 0.31
31 53 0.66
32 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (31 bp):
AAAATTTTAATTAAACCTCTCAAAATTTTTA
Found at i:460109 original size:22 final size:22
Alignment explanation
Indices: 460084--460150 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 22
460074 CAAATTTTAA
460084 ATTTATTTATAAGCTTCAAAAC
1 ATTTATTTATAAGCTTCAAAAC
* **
460106 A-TT-TTAATCGAA-CTT-TTAA-
1 ATTTATTTAT--AAGCTTCAAAAC
460125 ATTTATTTATAAGCTTCAAAAC
1 ATTTATTTATAAGCTTCAAAAC
460147 ATTT
1 ATTT
460151 TAATCGAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 11 0.34
22 7 0.22
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (22 bp):
ATTTATTTATAAGCTTCAAAAC
Found at i:460123 original size:41 final size:41
Alignment explanation
Indices: 460078--460168 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
460068 ATGGAGCAAA
460078 TTTTAAATTTATTTATAAGCTTCAAAACATTTTAATCGAAC
1 TTTTAAATTTATTTATAAGCTTCAAAACATTTTAATCGAAC
460119 TTTTAAATTTATTTATAAGCTTCAAAACATTTTAATCGAAC
1 TTTTAAATTTATTTATAAGCTTCAAAACATTTTAATCGAAC
* *
460160 GTTGAAATT
1 TTTTAAATT
460169 AAAATATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (41 bp):
TTTTAAATTTATTTATAAGCTTCAAAACATTTTAATCGAAC
Found at i:460328 original size:30 final size:31
Alignment explanation
Indices: 460283--460365 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 31
460273 CCCAACCAGG
460283 AAAAAGTTAGAAAATTTTAA-TAAG-CTTCT
1 AAAAAGTTAGAAAATTTTAATTAAGCCTTCT
* *
460312 AAAAAGTTTTGAAAATTTTAATTAAGCCTTTT
1 AAAAAG-TTAGAAAATTTTAATTAAGCCTTCT
*
460344 AAAAAATTCA-AAAA-TTTAATTA
1 AAAAAGTT-AGAAAATTTTAATTA
460366 GGTCCCTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 6 0.13
30 21 0.46
31 10 0.22
32 9 0.20
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.37
Consensus pattern (31 bp):
AAAAAGTTAGAAAATTTTAATTAAGCCTTCT
Found at i:460491 original size:31 final size:30
Alignment explanation
Indices: 460369--460500 Score: 108
Period size: 31 Copynumber: 4.3 Consensus size: 30
460359 TTAATTAGGT
* *
460369 CCCTTAAAATTTTCT-AAAATTTTTATTAAC
1 CCCTCAAAATTTT-TAAAAATTTTAATTAAC
* * *
460399 CCTCACAAAATTTTTAAAAATTTTGATTAAA
1 CC-CTCAAAATTTTTAAAAATTTTAATTAAC
* * * *
460430 CTCTC-AAATTTTTAAAAAAAAATCTCATTAAAC
1 CCCTCAAAATTTTT---AAAAATTTTAATT-AAC
460463 CCCTCAAAATTTTTAAAAATTTTAATTAAC
1 CCCTCAAAATTTTTAAAAATTTTAATTAAC
460493 CCC-CAAAA
1 CCCTCAAAA
460501 CTAACTATTA
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
29 13 0.16
30 11 0.14
31 33 0.41
32 10 0.12
33 6 0.07
34 8 0.10
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (30 bp):
CCCTCAAAATTTTTAAAAATTTTAATTAAC
Found at i:466420 original size:17 final size:17
Alignment explanation
Indices: 466389--466432 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
466379 TTGATTCGAG
*
466389 TTAATTTCAAGTTCAAA
1 TTAATTTCGAGTTCAAA
* *
466406 TTAATTTCGATTTCATA
1 TTAATTTCGAGTTCAAA
466423 -TAATTTCGAG
1 TTAATTTCGAG
466433 CTCATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (17 bp):
TTAATTTCGAGTTCAAA
Found at i:484106 original size:7 final size:7
Alignment explanation
Indices: 484083--484128 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
484073 AATTGAAACA
484083 AAAACG-
1 AAAACGT
**
484089 AAAACCC
1 AAAACGT
484096 AAAACGT
1 AAAACGT
484103 AAAACGT
1 AAAACGT
484110 AAAACGT
1 AAAACGT
*
484117 TAAACGT
1 AAAACGT
484124 AAAAC
1 AAAAC
484129 AAAGAGGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (7 bp):
AAAACGT
Found at i:486026 original size:41 final size:41
Alignment explanation
Indices: 485951--486030 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
485941 TTTTATTGTA
* * *
485951 TTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAATATCG
1 TTTTCAATTTATTTGTTGTTTTAAGAATTATTTTAATATCG
* * *
485992 TTTTTAATTTATTTGTTGTTTTAATATTTATTTTAATAT
1 TTTTCAATTTATTTGTTGTTTTAAGAATTATTTTAATAT
486031 TTTTAAATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.64
Consensus pattern (41 bp):
TTTTCAATTTATTTGTTGTTTTAAGAATTATTTTAATATCG
Found at i:486043 original size:24 final size:24
Alignment explanation
Indices: 486016--486074 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
486006 GTTGTTTTAA
* *
486016 TATTTAT-TTTAATATTTTTAAAT
1 TATTTATATATAATATTTTAAAAT
*
486039 GTATTTGATATATCATATTTTAAAAT
1 -TATTT-ATATATAATATTTTAAAAT
486065 TATTTATATA
1 TATTTATATA
486075 ATAAAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 7 0.23
26 13 0.43
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (24 bp):
TATTTATATATAATATTTTAAAAT
Found at i:486051 original size:21 final size:21
Alignment explanation
Indices: 486010--486051 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
486000 TTATTTGTTG
* *
486010 TTTTAATATTTATTTTAATAT
1 TTTTAATATGTATTTGAATAT
486031 TTTTAA-ATGTATTTGATATAT
1 TTTTAATATGTATTTGA-ATAT
486052 CATATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTAATATGTATTTGAATAT
Found at i:486057 original size:26 final size:24
Alignment explanation
Indices: 486027--486074 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
486017 ATTTATTTTA
*
486027 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
486053 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
486075 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:490529 original size:43 final size:42
Alignment explanation
Indices: 490481--490563 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 42
490471 AAATACGTGT
490481 GTTCGAGTGCATTAAACGTATTATCCTCTTTATTCATGAGTGG
1 GTTCGAGTGCATTAAACGTATTATCCTC-TTATTCATGAGTGG
* * *
490524 GTTCGAGTGCATTAAATGTATTATTCTCTTATTTATGAGT
1 GTTCGAGTGCATTAAACGTATTATCCTCTTATTCATGAGT
490564 TGAGGAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 11 0.30
43 26 0.70
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (42 bp):
GTTCGAGTGCATTAAACGTATTATCCTCTTATTCATGAGTGG
Found at i:494568 original size:29 final size:30
Alignment explanation
Indices: 494494--494569 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
494484 TTTGGCTACT
* *
494494 TTAAAAGTTAGAGAAATTTTTTTTAAGCTCC
1 TTAAAAGTT-GATAAATTTTTTTTAAGCCCC
*
494525 TTAAAAGTTGGTAAATTTTTTTTGAA-CCCC
1 TTAAAAGTTGATAAATTTTTTTT-AAGCCCC
494555 TTAAAA-TTGATAAAT
1 TTAAAAGTTGATAAAT
494570 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 8 0.20
30 21 0.52
31 11 0.28
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (30 bp):
TTAAAAGTTGATAAATTTTTTTTAAGCCCC
Found at i:496485 original size:29 final size:29
Alignment explanation
Indices: 496452--496509 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
496442 TTACCCTTTT
* * *
496452 TTTAATAGTATAGAGATTAAATTGATCCA
1 TTTAAGAGTAGAGAGACTAAATTGATCCA
* *
496481 TTTAAGAGTAGAGGGACTAATTTGATCCA
1 TTTAAGAGTAGAGAGACTAAATTGATCCA
496510 ATCTCAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (29 bp):
TTTAAGAGTAGAGAGACTAAATTGATCCA
Found at i:500864 original size:5 final size:6
Alignment explanation
Indices: 500847--500871 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
500837 TCATGTTCAC
500847 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
500872 GATGAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:501442 original size:19 final size:20
Alignment explanation
Indices: 501402--501442 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
501392 AAATCGATTT
501402 AATCGACCCTTAGCGTGGTTC
1 AATCGACCCTTAGCG-GGTTC
501423 AATCGACCCTTAGC-GGTTC
1 AATCGACCCTTAGCGGGTTC
501442 A
1 A
501443 TGGGTCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
21 14 0.70
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (20 bp):
AATCGACCCTTAGCGGGTTC
Found at i:502536 original size:2 final size:2
Alignment explanation
Indices: 502529--502553 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
502519 CGATCCCTTT
502529 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
502554 TGTTTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:517238 original size:31 final size:31
Alignment explanation
Indices: 517200--517261 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
517190 TTACAATATG
* *
517200 ATCATTGAACTATTTGAAAGTTTTTATTTAA
1 ATCATTGAACTATTCGAAAGTTTTCATTTAA
*
517231 ATCATTGAATTATTCGAAAGTTTTCATTTAA
1 ATCATTGAACTATTCGAAAGTTTTCATTTAA
517262 GTCACTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (31 bp):
ATCATTGAACTATTCGAAAGTTTTCATTTAA
Found at i:528136 original size:19 final size:19
Alignment explanation
Indices: 528102--528154 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
528092 TGATTTTTGG
* *
528102 AAAATTAATTTTAATCAAGT
1 AAAATTAA-ATTAATCAAAT
528122 AAAATTAAATTAATCAAAT
1 AAAATTAAATTAATCAAAT
* *
528141 TAATTTAAATTAAT
1 AAAATTAAATTAAT
528155 ATGATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTAAATTAATCAAAT
Found at i:528283 original size:20 final size:18
Alignment explanation
Indices: 528259--528307 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
528249 AATAATATTT
528259 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
528277 GTGATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
528297 T-TTAATTTAAT
1 TATTAATTTAAT
528308 GTTATATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 4 0.15
20 14 0.52
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:533044 original size:19 final size:18
Alignment explanation
Indices: 533006--533040 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
532996 TCATTTGTTT
533006 TTATTAATTTACAATTTA
1 TTATTAATTTACAATTTA
533024 TTATTAAATTTA-AATTT
1 TTATT-AATTTACAATTT
533041 TATTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTAATTTACAATTTA
Found at i:533593 original size:27 final size:27
Alignment explanation
Indices: 533555--533611 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
533545 GAACTGTATT
533555 GAATCAGAAGAAAATTTTATGATTTTA
1 GAATCAGAAGAAAATTTTATGATTTTA
*
533582 GAATGAGAAGAAAATTTTATGATTTTA
1 GAATCAGAAGAAAATTTTATGATTTTA
533609 GAA
1 GAA
533612 ATAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.35
Consensus pattern (27 bp):
GAATCAGAAGAAAATTTTATGATTTTA
Found at i:533767 original size:19 final size:19
Alignment explanation
Indices: 533739--533781 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
533729 ATAATTAATT
*
533739 TTAATTAAATAAAATT-AAA
1 TTAATCAAAT-AAATTAAAA
*
533758 TTAATCAAATTAATTAAAA
1 TTAATCAAATAAATTAAAA
533777 TTAAT
1 TTAAT
533782 ATGATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATCAAATAAATTAAAA
Found at i:539022 original size:2 final size:2
Alignment explanation
Indices: 539017--539047 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
539007 GATAGTGCAT
539017 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
539048 TACATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:546618 original size:13 final size:13
Alignment explanation
Indices: 546600--546628 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
546590 GGATGTAATA
546600 ACAAGACACAGAT
1 ACAAGACACAGAT
546613 ACAAGACACAGAT
1 ACAAGACACAGAT
546626 ACA
1 ACA
546629 TACATAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.14, T:0.07
Consensus pattern (13 bp):
ACAAGACACAGAT
Found at i:550236 original size:29 final size:30
Alignment explanation
Indices: 550204--550269 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
550194 GTACATTTGG
**
550204 AATTTAGTCCTAT-T-ATTTTTATTTTTAAA
1 AATTTAGTCC-ATCTGATTTTTAAATTTAAA
* *
550233 AATTTAATCCATCTGTTTTTTAAATTTAAA
1 AATTTAGTCCATCTGATTTTTAAATTTAAA
550263 AATTTAG
1 AATTTAG
550270 ATCTAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.07
29 10 0.33
30 18 0.60
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.53
Consensus pattern (30 bp):
AATTTAGTCCATCTGATTTTTAAATTTAAA
Found at i:550862 original size:22 final size:22
Alignment explanation
Indices: 550837--550917 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 22
550827 AAAAATTATA
550837 TTATTGTTTTGGTTCTGGTTTT
1 TTATTGTTTTGGTTCTGGTTTT
550859 TTATTGTTTTGGTTGCT-GTTTT
1 TTATTGTTTTGGTT-CTGGTTTT
* * *
550881 TTACTGTTTTAGTGT-TGTTGTTT
1 TTATTGTTTTGGT-TCTGGT-TTT
550904 TTATTGTTTTGGTT
1 TTATTGTTTTGGTT
550918 TTTTTTACTG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.02
22 32 0.64
23 17 0.34
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (22 bp):
TTATTGTTTTGGTTCTGGTTTT
Found at i:550944 original size:38 final size:44
Alignment explanation
Indices: 550856--550940 Score: 131
Period size: 41 Copynumber: 2.0 Consensus size: 44
550846 TGGTTCTGGT
550856 TTTTTATTGTTTTGGTTGCTGTTTTTTACTGTTTTAGTGTTGTTG
1 TTTTTATTGTTTTGGTT-CTGTTTTTTACTGTTTTAGTGTTGTTG
*
550901 TTTTTATTGTTTTGG-T-T-TTTTTTACTGTTTTGGTGTTGTT
1 TTTTTATTGTTTTGGTTCTGTTTTTTACTGTTTTAGTGTTGTT
550941 TTTACTGTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 22 0.56
42 1 0.03
44 1 0.03
45 15 0.38
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69
Consensus pattern (44 bp):
TTTTTATTGTTTTGGTTCTGTTTTTTACTGTTTTAGTGTTGTTG
Found at i:550954 original size:23 final size:22
Alignment explanation
Indices: 550878--550954 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 22
550868 TGGTTGCTGT
* *
550878 TTTTTACTGTTTTAGTGTTGTTG
1 TTTTTACTGTTTT-TTGGTGTTG
*
550901 TTTTTA-T-TGTTTTGGT-TT-
1 TTTTTACTGTTTTTTGGTGTTG
550919 TTTTTACTG--TTTTGGTGTTG
1 TTTTTACTGTTTTTTGGTGTTG
550939 TTTTTACTGTTATTTT
1 TTTTTACTGTT-TTTT
550955 TGCTACTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
18 13 0.30
19 5 0.11
20 12 0.27
21 3 0.07
22 1 0.02
23 10 0.23
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (22 bp):
TTTTTACTGTTTTTTGGTGTTG
Found at i:550966 original size:11 final size:12
Alignment explanation
Indices: 550949--551003 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
550939 TTTTTACTGT
550949 TATTTTTGCTAC
1 TATTTTTGCTAC
*
550961 TATTTTTGCTAT
1 TATTTTTGCTAC
* **
550973 TATTTTTGTTGT
1 TATTTTTGCTAC
* *
550985 TATTTTTGTTGC
1 TATTTTTGCTAC
550997 TATTTTT
1 TATTTTT
551004 TATTTTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.69
Consensus pattern (12 bp):
TATTTTTGCTAC
Found at i:550988 original size:24 final size:24
Alignment explanation
Indices: 550928--550992 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
550918 TTTTTTACTG
* * * *
550928 TTTTGGTGTTGTTTTTACTGTTAT
1 TTTTGCTGTTATTTTTGCTATTAT
**
550952 TTTTGCTACTATTTTTGCTATTAT
1 TTTTGCTGTTATTTTTGCTATTAT
*
550976 TTTTGTTGTTATTTTTG
1 TTTTGCTGTTATTTTTG
550993 TTGCTATTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.68
Consensus pattern (24 bp):
TTTTGCTGTTATTTTTGCTATTAT
Found at i:551018 original size:36 final size:35
Alignment explanation
Indices: 550946--551018 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 35
550936 TTGTTTTTAC
550946 TGTTATTTTTGCTACTATTTTTGCTATTATTTTTGT
1 TGTTATTTTTGCTACTATTTTT-CTATTATTTTTGT
* *
550982 TGTTATTTTTGTTGCTATTTTT-TATT-TTTTTGT
1 TGTTATTTTTGCTACTATTTTTCTATTATTTTTGT
551015 TGTT
1 TGTT
551019 TTGGTTGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
33 11 0.31
34 4 0.11
36 20 0.57
ACGTcount: A:0.11, C:0.05, G:0.12, T:0.71
Consensus pattern (35 bp):
TGTTATTTTTGCTACTATTTTTCTATTATTTTTGT
Found at i:551031 original size:30 final size:31
Alignment explanation
Indices: 550972--551032 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
550962 ATTTTTGCTA
*
550972 TTATTTTTGTTGTTATTTTTGTTGCTATTTT
1 TTATTTTTGTTGTTATTTTGGTTGCTATTTT
* *
551003 TTATTTTT-TTGTTGTTTTGGTTGTTATTTT
1 TTATTTTTGTTGTTATTTTGGTTGCTATTTT
551033 GGTTGTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.08, C:0.02, G:0.15, T:0.75
Consensus pattern (31 bp):
TTATTTTTGTTGTTATTTTGGTTGCTATTTT
Found at i:551101 original size:21 final size:21
Alignment explanation
Indices: 551059--551101 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
551049 TTTTTATGCG
* * * *
551059 TTTTTATTATTGTTTTATTAT
1 TTTTTAATATTATTTGAATAT
551080 TTTTTAATATTATTTGAATAT
1 TTTTTAATATTATTTGAATAT
551101 T
1 T
551102 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTAATATTATTTGAATAT
Found at i:555998 original size:22 final size:21
Alignment explanation
Indices: 555968--556011 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
555958 ACAAAATAAA
*
555968 TTTAGTTTTG-ATTGTGAATTTG
1 TTTAATTTTGCATT-TG-ATTTG
555990 TTTAATTTTGCATTTGATTTG
1 TTTAATTTTGCATTTGATTTG
556011 T
1 T
556012 CAAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 11 0.55
23 3 0.15
ACGTcount: A:0.18, C:0.02, G:0.18, T:0.61
Consensus pattern (21 bp):
TTTAATTTTGCATTTGATTTG
Found at i:583291 original size:14 final size:14
Alignment explanation
Indices: 583272--583301 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
583262 ACCATTTTTA
583272 TTAAGTGAGATATT
1 TTAAGTGAGATATT
583286 TTAAGTGAGATATT
1 TTAAGTGAGATATT
583300 TT
1 TT
583302 TGGAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (14 bp):
TTAAGTGAGATATT
Found at i:583375 original size:103 final size:103
Alignment explanation
Indices: 583190--583377 Score: 288
Period size: 103 Copynumber: 1.8 Consensus size: 103
583180 ATTTGGTGGA
* *
583190 AGATATTTTTGGAGGCAAAGTTTTGGGCCAAAGTGTAAAGTTGGAAGGTCTAGGGACTAAAAGTG
1 AGATATTTTTGGAGGCAAAGTTTTGGGCCAAAGTGTAAAGTTGAAAGGTCTAGGGACTAAAAGAG
* * * **
583255 CAATTTTACCATTTTTATTAAGTGAGATATTTTAAGTG
66 CAAATTGACAAAATTTATTAAGTGAGATATTTTAAGTG
583293 AGATATTTTTGGAGGCAAAGTTTTGGGCCAAAGTGTAAAGTTGAAAGGTCTAGGGACTAAAAGAG
1 AGATATTTTTGGAGGCAAAGTTTTGGGCCAAAGTGTAAAGTTGAAAGGTCTAGGGACTAAAAGAG
*
583358 TAAATTGA-AAGAATTTATTA
66 CAAATTGACAA-AATTTATTA
583378 TATAAATTGG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
102 1 0.01
103 75 0.99
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (103 bp):
AGATATTTTTGGAGGCAAAGTTTTGGGCCAAAGTGTAAAGTTGAAAGGTCTAGGGACTAAAAGAG
CAAATTGACAAAATTTATTAAGTGAGATATTTTAAGTG
Found at i:583938 original size:71 final size:68
Alignment explanation
Indices: 583845--583995 Score: 198
Period size: 71 Copynumber: 2.1 Consensus size: 68
583835 ACGTCTCGTG
* *
583845 CTCTCTATTATTAGCACTGTGTGTGCTCTCTGATT-AGCACTT-TGTGTACTCTCTGATTAGTAC
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTG-TTCAGCACTTATGTG--CTCTATG-TTAGTAC
583908 TTTGTGTA
62 TTTG-GTA
583916 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTATGTTAGTACT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTATGTTAGTACT
583981 TTGGTA
63 TTGGTA
583987 CTCTCTGTT
1 CTCTCTGTT
583996 TGTTCCGTAT
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
70 2 0.03
71 43 0.59
72 11 0.15
73 6 0.08
74 7 0.10
75 4 0.05
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (68 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTATGTTAGTACTTTG
GTA
Found at i:583947 original size:48 final size:46
Alignment explanation
Indices: 583854--583947 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 46
583844 GCTCTCTATT
* *
583854 ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTACTCTCTG
1 ATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTACTCTCTG
* * *
583900 ATTAGTACTTTGTGTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTACTCTCTG--ATTAGCACTGTGTGTACTCTCTG
583948 TTGCCCAGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
46 20 0.49
48 21 0.51
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (46 bp):
ATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGTGTACTCTCTG
Found at i:583949 original size:25 final size:24
Alignment explanation
Indices: 583821--583948 Score: 138
Period size: 23 Copynumber: 5.4 Consensus size: 24
583811 ACACTAGCGC
*
583821 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTGT-GT
*
583844 GCTCTCTATTATTAGCACTGTGTGT
1 GCTCTCT-GTATTAGCACTGTGTGT
*
583869 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
* * *
583892 ACTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
*
583915 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
583940 GCTCTCTGT
1 GCTCTCTGT
583949 TGCCCAGCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
23 50 0.55
24 2 0.02
25 36 0.40
26 3 0.03
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:586486 original size:210 final size:209
Alignment explanation
Indices: 586163--587306 Score: 1329
Period size: 210 Copynumber: 5.4 Consensus size: 209
586153 AAGAGACTCA
* * ** * ** * * * *
586163 AAATCTGGAATGGAATTTAAGTTACCACAATGGGATAGCTTTAACTCTTTCAGACAAGTGGCA-A
1 AAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGG-AGG
** * * *
586227 TAGACGGCCAATCTTCTATCTTGCTTAATTTTTGACACT--GGAAAATGTGAAGCTTTTCAAGAG
65 TAGACAACCCATCTCCTATCTTGCTTAATTTTTGACA-TAAGG-AAATGAGAAGCTTTTCAAGAG
*
586290 ATGAACAT-TGTCTTCTTATTGGAACAATTTCCAGTTCGTCGCAGTTTGATATTTCTAAAATTTG
128 ATGAACATCT-TCCTCTTATTGGAACAATTTCCAGTTCG-CGCAGTTTGATATTTCTAAAATTTG
*
586354 AAGAGAGGAAAACCCTTCC
191 AAGAGAGGAAAATCCTTCC
* * *
586373 AAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTCAAGGTAAGTGGAGGT
1 AAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGGT
* *
586438 AGACAATCCATCTCCTATCTTGCTTAATTTTTGACATAAGGAAATGTGAAGCTTTTCAAGAGATG
66 AGACAACCCATCTCCTATCTTGCTTAATTTTTGACATAAGGAAATGAGAAGCTTTTCAAGAGATG
* * * * * * * *
586503 AGCA-CTGTCCTCCTATCGGAACAATTTCCAGATT-GTGACAGATTGATATATCCAAAATTCGAA
131 AACATCT-TCCTCTTATTGGAACAATTTCCAG-TTCGCG-CAGTTTGATATTTCTAAAATTTGAA
586566 GAGAGGAAAATCCTTCC
193 GAGAGGAAAATCCTTCC
* *
586583 AAATCAGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTTAAGATAAGTGGAGGT
1 AAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGGT
* * * **
586648 AGACAACCCGTCTCCTATCTTGCTTAAGTTTTCACACGAGGAAATGAGAAGCTTTTCAAGAGATG
66 AGACAACCCATCTCCTATCTTGCTTAATTTTTGACATAAGGAAATGAGAAGCTTTTCAAGAGATG
* * * *
586713 AACATCTTCCTCTTATTGGAACAATTTCCAGTTTGCGACAGATTGATATATCTAAAATTCGAAGA
131 AACATCTTCCTCTTATTGGAACAATTTCCAGTTCGCG-CAGTTTGATATTTCTAAAATTTGAAGA
586778 GAGGAAAATCCTTCC
195 GAGGAAAATCCTTCC
* * ** * *
586793 AAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTCAGACAAGTGGAGGT
1 AAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGGT
** * * ** * *
586858 AGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACCAA-GAAATGAAAAGCTTTTCAAGAGAT
66 AGACAACCCATCTCCTATCTTGCTTAATTTTTGACA-TAAGGAAATGAGAAGCTTTTCAAGAGAT
* * *
586922 GAACATCTTCCTCTTATTGGAACAATTTCCAGTTTGCTGCACTTTGATATTTCT-AGATTTCGAA
130 GAACATCTTCCTCTTATTGGAACAATTTCCAGTTCGC-GCAGTTTGATATTTCTAAAATTT-GAA
* *
586986 GAAAGGAAAATCCATCC
193 GAGAGGAAAATCCTTCC
* ** *
587003 ATAA-CTGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGGAGG
1 A-AATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGG
* * * * *
587067 TAGACAAACCGTCTCCTATCTTGCTTAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGAT
65 TAGACAACCCATCTCCTATCTTGCTTAATTTTTGACATAAGGAAATGAGAAGCTTTTCAAGAGAT
* * *
587132 AAACATCTTCCTCTTATTGGAACAATTTCCAGTTCGCTGCACTTTGATATTTCT-AGATTTCGAA
130 GAACATCTTCCTCTTATTGGAACAATTTCCAGTTCGC-GCAGTTTGATATTTCTAAAATTT-GAA
* *
587196 GAAAGGAAAATCCATCC
193 GAGAGGAAAATCCTTCC
* *** *
587213 ATAA-CTGGAATGGAACTTAAATTAGCACAACCACTTAGCTTTAGTTCTTTAAGATAAGTGGAGG
1 A-AATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGG
* *
587277 TAGACAACCCGTCTCCAATCTTGCTTAATT
65 TAGACAACCCATCTCCTATCTTGCTTAATT
587307 CCTTACACTC
Statistics
Matches: 824, Mismatches: 97, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
209 10 0.01
210 803 0.97
211 11 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (209 bp):
AAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGGT
AGACAACCCATCTCCTATCTTGCTTAATTTTTGACATAAGGAAATGAGAAGCTTTTCAAGAGATG
AACATCTTCCTCTTATTGGAACAATTTCCAGTTCGCGCAGTTTGATATTTCTAAAATTTGAAGAG
AGGAAAATCCTTCC
Found at i:587406 original size:210 final size:209
Alignment explanation
Indices: 586242--587426 Score: 1019
Period size: 210 Copynumber: 5.6 Consensus size: 209
586232 GGCCAATCTT
* * * * * *
586242 CTATCTTGCTTAATTTTTGACA-CTGGAAAATGTGAAGCTTTTCAAGAGATGAACAT-TGTCTTC
1 CTATCTTGCTTAAGTTTT-ACACCAGG-AAATGAGAAGATTTTCAAGAGAAGAACATCT-TCCTC
* * * * * * * * *
586305 TTATTGGAACAATTTCCAGTTCG-TCGCAGTTTGATATTTCTAAAATTT-GAAGAGAGGAAAACC
63 TTATTGGAACAATTTCCAGTTTGCT-GCAATATGAAACTTAT-AGATTTCGAAGAAAGGAAAATC
* * * * ** * **
586368 CTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTCAAGGTAAGTG
126 CATCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTG
* *
586433 GAGGTAGACAATCCATCTC
191 GAGGTAGACAACCCGTCTC
* ** * * * * *
586452 CTATCTTGCTTAATTTTTGACATAAGGAAATGTGAAGCTTTTCAAGAGATGAGCA-CTGTCCTCC
1 CTATCTTGCTTAAGTTTT-ACACCAGGAAATGAGAAGATTTTCAAGAGAAGAACATCT-TCCTCT
* * * * * *
586516 TATCGGAACAATTTCCAGATTG-TGACAGAT-TGATA--TATCCAAAATTCGAAGAGAGGAAAAT
64 TATTGGAACAATTTCCAGTTTGCTG-CA-ATATGAAACTTAT--AGATTTCGAAGAAAGGAAAAT
* * * ** *
586577 CCTTCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTTAAGATAAGT
125 CCATCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGT
586642 GGAGGTAGACAACCCGTCTC
190 GGAGGTAGACAACCCGTCTC
* * *
586662 CTATCTTGCTTAAGTTTTCACACGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTT
1 CTATCTTGCTTAAGTTTT-ACACCAGGAAATGAGAAGATTTTCAAGAGAAGAACATCTTCCTCTT
* * * * *
586727 ATTGGAACAATTTCCAGTTTGC-GACAGAT-TGATA-TATCTAAAATTCGAAGAGAGGAAAATCC
65 ATTGGAACAATTTCCAGTTTGCTG-CA-ATATGAAACT-TATAGATTTCGAAGAAAGGAAAATCC
* *
586789 TTCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTCAGACAAGTGG
127 ATCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGG
** ** *
586854 AGGTAGACCGCCAATCTT
192 AGGTAGACAACCCGTCTC
* * * * *
586872 CTATCTTGCTTAA-TTTAGGACACCAAGAAATGAAAAGCTTTTCAAGAGATGAACATCTTCCTCT
1 CTATCTTGCTTAAGTTT--TACACCAGGAAATGAGAAGATTTTCAAGAGAAGAACATCTTCCTCT
* * * * *
586936 TATTGGAACAATTTCCAGTTTGCTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCAT
64 TATTGGAACAATTTCCAGTTTGCTGCAATATGAAACTTATAGATTTCGAAGAAAGGAAAATCCAT
*
587001 CCATAA-CTGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGGA
129 CCA-AATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGGA
*
587065 GGTAGACAAACCGTCTC
193 GGTAGACAACCCGTCTC
** *
587082 CTATCTTGCTTAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGATA-AACATCTTCCTCT
1 CTATCTTGCTTAAGTTTT-ACACCAGGAAATGAGAAGATTTTCAAGAGA-AGAACATCTTCCTCT
* * * * * *
587146 TATTGGAACAATTTCCAGTTCGCTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCAT
64 TATTGGAACAATTTCCAGTTTGCTGCAATATGAAACTTATAGATTTCGAAGAAAGGAAAATCCAT
* * *** * ** * *
587211 CCATAA-CTGGAATGGAACTTAAATTAGCACAACCACTTAGCTTTAGTTCTTTAAGATAAGTGGA
129 CCA-AATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGGA
587275 GGTAGACAACCCGTCTC
193 GGTAGACAACCCGTCTC
* * *
587292 CAATCTTGCTTAA-TTCCTTACACTCA-GAAACGCA-AA-ATTCTTCAAGAGAAGAACATATTCC
1 CTATCTTGCTTAAGTT--TTACAC-CAGGAAATG-AGAAGATT-TTCAAGAGAAGAACATCTTCC
* * * * * * **
587353 TGC-TATTGGAACAATATCCAATTTGCAGCAATCAT-AAACATATACACTTCGAAGAGCGGAAAA
61 T-CTTATTGGAACAATTTCCAGTTTGCTGCAAT-ATGAAACTTATAGATTTCGAAGAAAGGAAAA
* *
587416 CCCATTCAAAT
124 TCCATCCAAAT
587427 TTGGAATTGA
Statistics
Matches: 852, Mismatches: 95, Indels: 56
0.85 0.09 0.06
Matches are distributed among these distances:
208 2 0.00
209 17 0.02
210 813 0.95
211 18 0.02
212 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (209 bp):
CTATCTTGCTTAAGTTTTACACCAGGAAATGAGAAGATTTTCAAGAGAAGAACATCTTCCTCTTA
TTGGAACAATTTCCAGTTTGCTGCAATATGAAACTTATAGATTTCGAAGAAAGGAAAATCCATCC
AAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGGAGGT
AGACAACCCGTCTC
Found at i:587406 original size:420 final size:412
Alignment explanation
Indices: 586242--587426 Score: 1305
Period size: 420 Copynumber: 2.8 Consensus size: 412
586232 GGCCAATCTT
* * * * *
586242 CTATCTTGCTTAATTTTTGACACTG-GAAAATGTGAAGCTTTTCAAGAGATGAACAT-TGTCTTC
1 CTATCTTGCTTAAGTTTTCACA-TGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCT-TCCTC
*
586305 TTATTGGAACAATTTCCAGTTCG-TCGCAGTTTGATATTTCTAAAATTT-GAAGAGAGGAAAACC
64 TTATTGGAACAATTTCCAGTTCGCT-GCAGTTTGATATTTCT-AAATTTCGAAGAGAGGAAAATC
* * *
586368 CTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTCAAGGTAAGTG
127 CTTCCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTG
* * * **
586433 GAGGTAGACAATCCATCTCCTATCTTGCTTAATTTTTGACA-TAAGGAAATGTGAAGCTTTTCAA
192 GAGGTAGACAACCCATCTCCTATCTTGCTTAATTATT-ACACTCA-GAAA--TGAAAATTTTCAA
* * * **
586497 GAGATGAGCACTGTCCTCCTATCGGAACAATTTCCAGATTGTGACAG-ATTGATATATCCA-A-A
253 GAGATGAACA-TTTCCT-CTATTGGAACAATTTCCA-ATT-TG-CAGCA---ATATAAACATATA
* * * **
586559 ATTCGAAGAGAGGAAAATCCTTCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTTAACTT
310 ATTCGAAGAAAGGAAAATCCATCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAACAC
* *
586624 TAATTCTTTAAGATAAGTGGAGGTAGACAACCCGTCTC
375 TAATTCTTTAAGACAAGTGGAGGTAGACAAACCGTCTC
*
586662 CTATCTTGCTTAAGTTTTCACACGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTT
1 CTATCTTGCTTAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTT
* * * *
586727 ATTGGAACAATTTCCAGTTTGC-GACAGATTGATATATCTAAAATTCGAAGAGAGGAAAATCCTT
66 ATTGGAACAATTTCCAGTTCGCTG-CAGTTTGATATTTCTAAATTTCGAAGAGAGGAAAATCCTT
* * ** * *
586791 CCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATTCTTTCAGACAAGTGGAG
130 CCAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAG
** * * **
586856 GTAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACAC-CAAGAAATGAAAAGCTTTTCAAGAG
195 GTAGACAACCCATCTCCTATCTTGCTTAA-TTATTACACTC-AGAAATGAAAA--TTTTCAAGAG
* * * * * ** *
586920 ATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTTGCTGCACTTTGATATTTCTAGATTTCGA
256 ATGAACAT-TTCCTC-TATTGGAACAATTTCCAATTTGCAGCAATAT-AAACATATA-A-TTCGA
* *
586985 AGAAAGGAAAATCCATCCATAA-CTGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAATT
316 AGAAAGGAAAATCCATCCA-AATCAGGAATGGAACTTAAATTAGGACAATTGCTCAACACTAATT
587049 CTTTAAGACAAGTGGAGGTAGACAAACCGTCTC
380 CTTTAAGACAAGTGGAGGTAGACAAACCGTCTC
*
587082 CTATCTTGCTTAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGATAAACATCTTCCTCTT
1 CTATCTTGCTTAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTT
* * * *
587147 ATTGGAACAATTTCCAGTTCGCTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATC
66 ATTGGAACAATTTCCAGTTCGCTGCAGTTTGATATTTCTAAATTTCGAAGAGAGGAAAATCCTTC
* *** *
587212 CATAA-CTGGAATGGAACTTAAATTAGCACAACCACTTAGCTTTAGTTCTTTAAGATAAGTGGAG
131 CA-AATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAG
* * * *
587276 GTAGACAACCCGTCTCCAATCTTGCTTAATTCCTTACACTCAGAAACGCAAAATTCTTCAAGAGA
195 GTAGACAACCCATCTCCTATCTTGCTTAATT-ATTACACTCAGAAATG-AAAATT-TTCAAGAGA
* *
587341 AGAACATATTCCTGCTATTGGAACAATATCCAATTTGCAGCAATCATAAACATATACACTTCGAA
257 TGAACAT-TTCCT-CTATTGGAACAATTTCCAATTTGCAGCAAT-ATAAACATATA-A-TTCGAA
** * *
587406 GAGCGGAAAACCCATTCAAAT
317 GAAAGGAAAATCCATCCAAAT
587427 TTGGAATTGA
Statistics
Matches: 638, Mismatches: 99, Indels: 56
0.80 0.12 0.07
Matches are distributed among these distances:
415 2 0.00
416 2 0.00
417 2 0.00
418 8 0.01
419 18 0.03
420 590 0.92
421 16 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (412 bp):
CTATCTTGCTTAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTT
ATTGGAACAATTTCCAGTTCGCTGCAGTTTGATATTTCTAAATTTCGAAGAGAGGAAAATCCTTC
CAAATCTGGAATGGAACTTAAATTAGGACAATTGCTTAGCTTTAATTCTTTAAGATAAGTGGAGG
TAGACAACCCATCTCCTATCTTGCTTAATTATTACACTCAGAAATGAAAATTTTCAAGAGATGAA
CATTTCCTCTATTGGAACAATTTCCAATTTGCAGCAATATAAACATATAATTCGAAGAAAGGAAA
ATCCATCCAAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAACACTAATTCTTTAAGACAA
GTGGAGGTAGACAAACCGTCTC
Found at i:587408 original size:630 final size:630
Alignment explanation
Indices: 586208--587378 Score: 1573
Period size: 630 Copynumber: 1.9 Consensus size: 630
586198 TAGCTTTAAC
* ** **
586208 TCTTTCAGACAAGTGGCAATAGACGGCCAATCTTCTATCTTGCTTAATTTTTGACACTGGAAAAT
1 TCTTTCAGACAAGTGGCAATAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACAAGAAAAT
** * *
586273 GTGAAGCTTTTCAAGAGATGAACATTGTCTTCTTATTGGAACAATTTCCAGTTCGTCGCAGTTTG
66 GAAAAGCTTTTCAAGAGATGAACATTGTCCTCTTATTGGAACAATTTCCAGTTCGTCGCACTTTG
* *
586338 ATATTTCTAAAATTTGAAGAGAGGAAAACCCTTCCAAATCTGGAATGGAACTTAAATTAGGACAA
131 ATATTTCTAAAATTTGAAGAAAGGAAAACCCATCCAAATCTGGAATGGAACTTAAATTAGGACAA
* ** ** * *
586403 TTGCTTAACTTTAATTCTTCAAGGTAAGTGGAGGTAGACAATCCATCTCCTATCTTGCTTAATTT
196 TTGCTCAACACTAATTCTTCAAGACAAGTGGAGGTAGACAAACCATCTCCTATCTTGCTTAAGTT
* * * *
586468 TTGACATAAGGAAATGTGAAGCTTTTCAAGAGATGAGCACTGTCCTCCTATCGGAACAATTTCCA
261 TTCACATAAGGAAATGAGAAGCTTTTCAAGAGATAAACACTGTCCTCCTATCGGAACAATTTCCA
* * *
586533 GATTGTGACAGATTGATATATCCAAAATTCGAAGAGAGGAAAATCCTTCCAAATCAGGAATGGAA
326 GATTGTGACACATTGATATATCCAAAATTCGAAGAAAGGAAAATCCATCCAAATCAGGAATGGAA
* ***
586598 CTTAAATTAGGACAATTGCTTAACTTTAATTCTTTAAGATAAGTGGAGGTAGACAACCCGTCTCC
391 CTTAAATTAGCACAACCACTTAACTTTAATTCTTTAAGATAAGTGGAGGTAGACAACCCGTCTCC
* * * * * *
586663 TATCTTGCTTAAGTTTTCACACGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTTA
456 AATCTTGCTTAAGTTTTCACACCAGGAAACGAGAAGATTTTCAAGAGAAGAACATATTCCTCTTA
* * * *
586728 TTGGAACAATTTCCAGTTTGCGACAGATTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCC
521 TTGGAACAATATCCAATTTGCGACAGATTCATATAACTAAAATTCGAAGAGAGGAAAATCCTTCC
586793 AAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAAT
586 AAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAAT
*
586838 TCTTTCAGACAAGTGG-AGGTAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACCAAG-AA
1 TCTTTCAGACAAGTGGCA-ATAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACA-CAAGAAA
*
586901 ATGAAAAGCTTTTCAAGAGATGAACATCT-TCCTCTTATTGGAACAATTTCCAGTTTG-CTGCAC
64 ATGAAAAGCTTTTCAAGAGATGAACAT-TGTCCTCTTATTGGAACAATTTCCAGTTCGTC-GCAC
* *
586964 TTTGATATTTCT-AGATTTCGAAGAAAGGAAAATCCATCCATAA-CTGGAATGGAACTTAAATTA
127 TTTGATATTTCTAAAATTT-GAAGAAAGGAAAACCCATCCA-AATCTGGAATGGAACTTAAATTA
* * *
587027 GGACAATTGCTCAGCACTAATTCTTTAAGACAAGTGGAGGTAGACAAACCGTCTCCTATCTTGCT
190 GGACAATTGCTCAACACTAATTCTTCAAGACAAGTGGAGGTAGACAAACCATCTCCTATCTTGCT
* * *
587092 TAAGTTTTCACATGAGGAAATGAGAAGCTTTTCAAGAGATAAACATCT-TCCTCTTATTGGAACA
255 TAAGTTTTCACATAAGGAAATGAGAAGCTTTTCAAGAGATAAACA-CTGTCCTCCTATCGGAACA
* * * * *
587156 ATTTCCAG-TTCGCTG-CACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAA-C
319 ATTTCCAGATT-G-TGACACATTGATATATCCAAAATTCGAAGAAAGGAAAATCCATCCA-AATC
* * *
587218 TGGAATGGAACTTAAATTAGCACAACCACTTAGCTTTAGTTCTTTAAGATAAGTGGAGGTAGACA
381 AGGAATGGAACTTAAATTAGCACAACCACTTAACTTTAATTCTTTAAGATAAGTGGAGGTAGACA
587283 ACCCGTCTCCAATCTTGCTTAA-TTCCTT-ACACTCA-GAAACGCA-AA-ATTCTTCAAGAGAAG
446 ACCCGTCTCCAATCTTGCTTAAGTT--TTCACAC-CAGGAAACG-AGAAGATT-TTCAAGAGAAG
587343 AACATATTCCTGC-TATTGGAACAATATCCAATTTGC
506 AACATATTCCT-CTTATTGGAACAATATCCAATTTGC
587379 AGCAATCATA
Statistics
Matches: 470, Mismatches: 55, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
629 13 0.03
630 441 0.94
631 16 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (630 bp):
TCTTTCAGACAAGTGGCAATAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACAAGAAAAT
GAAAAGCTTTTCAAGAGATGAACATTGTCCTCTTATTGGAACAATTTCCAGTTCGTCGCACTTTG
ATATTTCTAAAATTTGAAGAAAGGAAAACCCATCCAAATCTGGAATGGAACTTAAATTAGGACAA
TTGCTCAACACTAATTCTTCAAGACAAGTGGAGGTAGACAAACCATCTCCTATCTTGCTTAAGTT
TTCACATAAGGAAATGAGAAGCTTTTCAAGAGATAAACACTGTCCTCCTATCGGAACAATTTCCA
GATTGTGACACATTGATATATCCAAAATTCGAAGAAAGGAAAATCCATCCAAATCAGGAATGGAA
CTTAAATTAGCACAACCACTTAACTTTAATTCTTTAAGATAAGTGGAGGTAGACAACCCGTCTCC
AATCTTGCTTAAGTTTTCACACCAGGAAACGAGAAGATTTTCAAGAGAAGAACATATTCCTCTTA
TTGGAACAATATCCAATTTGCGACAGATTCATATAACTAAAATTCGAAGAGAGGAAAATCCTTCC
AAATCAGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAAT
Found at i:591484 original size:16 final size:16
Alignment explanation
Indices: 591465--591507 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
591455 CTAAAATTTT
591465 AAAAATAAAAAAGT-AC
1 AAAAATAAAAAA-TAAC
591481 AAAAATTAAAAAATAAC
1 AAAAA-TAAAAAATAAC
*
591498 AAAATTAAAA
1 AAAAATAAAA
591508 TTTATGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAAATAAC
Found at i:591490 original size:17 final size:15
Alignment explanation
Indices: 591465--591507 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
591455 CTAAAATTTT
591465 AAAAA-TAAAAAAGTA
1 AAAAATTAAAAAA-TA
591480 CAAAAATTAAAAAATA
1 -AAAAATTAAAAAATA
591496 ACAAAATTAAAA
1 A-AAAATTAAAA
591508 TTTATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 17 0.68
17 7 0.28
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAAATTAAAAAATA
Found at i:595856 original size:31 final size:30
Alignment explanation
Indices: 595821--595893 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
595811 TTCAAAATAA
* *
595821 TCATTAAATTTTTCAAAAGTTTTTGTTTAAT
1 TCATTAAATTTTT-AAAAGTTTTTATTTAAG
* * *
595852 TCATTTAACTATTTAACAGTTTTTATTTAAG
1 TCA-TTAAATTTTTAAAAGTTTTTATTTAAG
*
595883 TCACTAAATTT
1 TCATTAAATTT
595894 AGTATTTTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
30 5 0.15
31 20 0.61
32 8 0.24
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (30 bp):
TCATTAAATTTTTAAAAGTTTTTATTTAAG
Found at i:598580 original size:23 final size:23
Alignment explanation
Indices: 598554--598638 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
598544 GCGCTTTCTG
598554 TTTAGCACTTTGTGTGCTCTCCA
1 TTTAGCACTTTGTGTGCTCTCCA
* * *
598577 TTTAGCACATCT-CGTGCTCTCCG
1 TTTAGCAC-TTTGTGTGCTCTCCA
* * * *
598600 TTTAGCGCTTCGTGGGCTCTCTGA
1 TTTAGCACTTTGTGTGCTCTC-CA
*
598624 -TTAGCACTTTCTGTG
1 TTTAGCACTTTGTGTG
598639 TTCAGTACTT
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
22 1 0.02
23 42 0.93
24 2 0.04
ACGTcount: A:0.12, C:0.27, G:0.21, T:0.40
Consensus pattern (23 bp):
TTTAGCACTTTGTGTGCTCTCCA
Found at i:600436 original size:15 final size:16
Alignment explanation
Indices: 600418--600448 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
600408 CTTCAATTGA
600418 ATATTTTT-AATTTTT
1 ATATTTTTCAATTTTT
600433 ATATTTTTCAATTTTT
1 ATATTTTTCAATTTTT
600449 TTAAAAAATT
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:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
ATATTTTTCAATTTTT
Found at i:604732 original size:8 final size:8
Alignment explanation
Indices: 604719--604744 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
604709 GTTCTTTAGC
604719 AAATTTTA
1 AAATTTTA
604727 AAATTTTA
1 AAATTTTA
604735 AAATTTTA
1 AAATTTTA
604743 AA
1 AA
604745 TTAATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:620266 original size:15 final size:15
Alignment explanation
Indices: 620246--620275 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
620236 TTTTCCCTTC
620246 TAACATTATATAATA
1 TAACATTATATAATA
620261 TAACATTATATAATA
1 TAACATTATATAATA
620276 GCTCCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
TAACATTATATAATA
Found at i:622250 original size:39 final size:39
Alignment explanation
Indices: 622207--622285 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
622197 ATAAAAAGTT
*
622207 TCAAATTGGGTACAGATAAATTCTAACCATATGACAAAA
1 TCAAATTGGGTACAGATAAATTCTAACCATAAGACAAAA
* *
622246 TCAAATTGGGTACCGATAAATTCTAACCATAAGATAAAA
1 TCAAATTGGGTACAGATAAATTCTAACCATAAGACAAAA
622285 T
1 T
622286 AGTACCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (39 bp):
TCAAATTGGGTACAGATAAATTCTAACCATAAGACAAAA
Found at i:643766 original size:513 final size:513
Alignment explanation
Indices: 642818--644895 Score: 3870
Period size: 513 Copynumber: 4.0 Consensus size: 513
642808 TTCTGATGGG
* *
642818 ATTTGAGCACGATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAACTCCCAGTCGATGACT
1 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCCAGTCGATGACT
*
642883 GTGAAGAGGTCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
66 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
* *
642948 TGGAGAATATACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATGATTCGGATCTTAT
131 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
643013 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATCT-GCCTTCCTC
196 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGAT-TGGCCTTCCTC
* * * *
643077 CGGCGTCTCGGCTGCTGCAGAAATCCAGTACTGCTCTTCTGAGTTTCCAGTGATGGAAATATTTT
260 CGGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTT
643142 TGACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTG
325 TGACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTG
* * * * *
643207 CATTTGACCCTTTCCACCTCAAATTTTGTGTATGGACTGAAAGCCAAAGTTTCCAAAAATTTGAG
390 CATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAG
*
643272 ATACCCATGACAATCGTAACTTTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
455 ATACCCATGACAATCGTAACTCTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
* *
643331 ATTTGAGCACCATAAACCTTGGTGACGCAAATGGCTTAATCGCAAGCAATTCCCAGTCGATGACT
1 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCCAGTCGATGACT
643396 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
66 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
643461 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
131 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
643526 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
196 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
*
643591 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTTTGAGTTTCCAGTGATGGAAACATTTTT
261 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTTT
643656 GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
326 GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
643721 ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGA
391 ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGA
*
643786 TACCCATGACAATTGTAACTCTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
456 TACCCATGACAATCGTAACTCTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
*
643844 ATTTGAGCACCATAAGCCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCCAGTCGATGACT
1 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCCAGTCGATGACT
643909 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
66 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
643974 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
131 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
644039 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
196 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
644104 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTTT
261 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTTT
644169 GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
326 GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
* *
644234 ATTTGGCCCTCTCCACCTCAAATTTTGTGTGTGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGG
391 ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGA
644299 TACCCATGACAATCGTAACTCTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
456 TACCCATGACAATCGTAACTCTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
* *
644357 ATTTGAGCGCCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCGAGTCGATGACT
1 ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCCAGTCGATGACT
644422 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
66 GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
644487 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
131 TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
644552 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
196 TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
*
644617 GGCTTGTTGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTTT
261 GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTTT
644682 GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
326 GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
644747 ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGA
391 ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGA
* *
644812 TACCCATGACAATCGTAACTCTCATCATGCATATAGCTCAAATATTTGTTCCTCGCCTCAC
456 TACCCATGACAATCGTAA--CTC-TCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
644873 ATTTGAGCACCATAAACCTTGGC
1 ATTTGAGCACCATAAACCTTGGC
644896 CATGCAATTG
Statistics
Matches: 1526, Mismatches: 35, Indels: 5
0.97 0.02 0.00
Matches are distributed among these distances:
512 1 0.00
513 1465 0.96
515 3 0.00
516 57 0.04
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (513 bp):
ATTTGAGCACCATAAACCTTGGCGACGCAAATGGCTTATTCGCAAGCAATTCCCAGTCGATGACT
GTGAAGAGATCACAGGAATTACCATCGAAAACATTGTAGTTTGCCAGCACACAGTTATTAAACGT
TGGAGAATCTACCCACCATAAGCATAAATAGCAACCTGATTGCACATGCATAATTCGGATCTTAT
TTGTTGCAGTGTCCACTGGGATAAGCTTGAACAACGTGCACGACTCCTCGGATTGGCCTTCCTCC
GGCTTGTCGGCTGCTGCAGAAATCCAATACTGCTCTTCTGAGTTTCCAGTGATGGAAACATTTTT
GACTCGTTTGCAGTATTTGTTGTTGTGGCAGCTCTTTATGTGCACCAACCCATCTTCCCCACTGC
ATTTGGCCCTCTCCACCTCAAATTTTGTGTATGGACTGCAAGCCAAAGTTTCCGAAAATCTGAGA
TACCCATGACAATCGTAACTCTCGTGCATATAGCTCAAATATTTGTTCCTCGCCTCGC
Found at i:648108 original size:59 final size:59
Alignment explanation
Indices: 648038--648242 Score: 191
Period size: 59 Copynumber: 3.5 Consensus size: 59
648028 TAGACACTTG
* * * * * *
648038 GGGGCAAAATGGTGACTTTTGGAAGGTTCGGGGTCAAAAATGGAATTATTGGACA-TCTA
1 GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTATTGAACATTC-A
* * * * * * *
648097 GGGGTAAAATGGTAATTTTTGGAAATTTTGAGATAAAAAATGGAGTTTTTGAACATTCG
1 GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTATTGAACATTCA
* * * *
648156 GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAAGGGAATTTTTTGAA-GTTCG
1 GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAA-TTATTGAACATTCA
* *
648215 GGGGTGAAA-GTATAATTTTTGGAAAGTT
1 GGGGTAAAATG-GTAATTTTTGGAAAGTT
648243 TAGGGGTCAA
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.01
59 110 0.91
60 10 0.08
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTATTGAACATTCA
Found at i:648205 original size:30 final size:29
Alignment explanation
Indices: 648054--648217 Score: 93
Period size: 29 Copynumber: 5.6 Consensus size: 29
648044 AAATGGTGAC
* *
648054 TTTTGGAAGGTTCGGGGTCAAAAATGGAAT
1 TTTTGGAAAGTTCGGGGT-AAAAAGGGAAT
* * * * *
648084 TATTGGACA-TCTAGGGGTAAAATGGTAAT
1 TTTTGGAAAGT-TCGGGGTAAAAAGGGAAT
* * * * * *
648113 TTTTGGAAATTTTGAGATAAAAAATGGAGT
1 TTTTGGAAAGTTCGGGGT-AAAAAGGGAAT
* *
648143 TTTT-GAACA-TTCGGGGGTAAAATGGTAAT
1 TTTTGGAA-AGTTC-GGGGTAAAAAGGGAAT
*
648172 TTTTGGAAAGTTCGAGGTCAAAAAGGGAAT
1 TTTTGGAAAGTTCGGGGT-AAAAAGGGAAT
*
648202 TTTTTG-AAGTTCGGGG
1 TTTTGGAAAGTTCGGGG
648218 GTGAAAGTAT
Statistics
Matches: 98, Mismatches: 28, Indels: 17
0.69 0.20 0.12
Matches are distributed among these distances:
29 50 0.51
30 48 0.49
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
TTTTGGAAAGTTCGGGGTAAAAAGGGAAT
Found at i:650075 original size:17 final size:17
Alignment explanation
Indices: 650052--650144 Score: 125
Period size: 17 Copynumber: 5.4 Consensus size: 17
650042 GCTTTTATTT
*
650052 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
*
650069 TTTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
* *
650087 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
650104 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
650121 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
650138 ATTTAAA
1 ATTTAAA
650145 AAATAAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
16 3 0.05
17 47 0.71
18 16 0.24
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:650079 original size:6 final size:6
Alignment explanation
Indices: 650052--650144 Score: 72
Period size: 6 Copynumber: 16.2 Consensus size: 6
650042 GCTTTTATTT
* ** *
650052 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
650099 A-TTAA ATTTAA ATTTAA A-ATAA ATTT-A ATCTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
650144 A
1 A
650145 AAATAAATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
4 1 0.01
5 18 0.26
6 45 0.66
7 4 0.06
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:650145 original size:11 final size:12
Alignment explanation
Indices: 650072--650126 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 12
650062 AGAATAATTT
*
650072 TAAATTTAAAAA
1 TAAATTTAAACA
*
650084 TAAATTTAAACT
1 TAAATTTAAACA
**
650096 TAAA-TTAAATT
1 TAAATTTAAACA
650107 TAAATTTAAA-A
1 TAAATTTAAACA
650118 TAAATTTAA
1 TAAATTTAA
650127 TCTTAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 19 0.50
12 19 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATTTAAACA
Found at i:650152 original size:52 final size:52
Alignment explanation
Indices: 650052--650153 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
650042 GCTTTTATTT
* * **
650052 ATTTAAATTTAGAATAATTTTAAATTTAAAAATAAATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAATAAATTAA
650104 ATTTAAATTTAAAATAAATTT-AATCTT-AAAATAAATTTAAAAAATAAATT
1 ATTTAAATTTAAAATAAATTTAAAT-TTAAAAATAAATTT-AAAAATAAATT
650154 TAGTTTGGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 14 0.32
52 30 0.68
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (52 bp):
ATTTAAATTTAAAATAAATTTAAATTTAAAAATAAATTTAAAAATAAATTAA
Found at i:655897 original size:25 final size:27
Alignment explanation
Indices: 655863--655919 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
655853 TCCGGAAAAC
655863 AAATACTATTAG-TATCAAATAATAA-
1 AAATACTATTAGATATCAAATAATAAT
* *
655888 AAATATTATTAGATATCAAATGATAAT
1 AAATACTATTAGATATCAAATAATAAT
655915 AAATA
1 AAATA
655920 ATTAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 11 0.39
26 12 0.43
27 5 0.18
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (27 bp):
AAATACTATTAGATATCAAATAATAAT
Found at i:660160 original size:13 final size:13
Alignment explanation
Indices: 660142--660171 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
660132 TAATTACACT
660142 AATATATTTAAAA
1 AATATATTTAAAA
660155 AATATATTTAAAA
1 AATATATTTAAAA
660168 AATA
1 AATA
660172 AATTATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATATTTAAAA
Found at i:662738 original size:31 final size:31
Alignment explanation
Indices: 662703--662810 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
662693 TTAATATAAT
* *
662703 ATTTGGTACCTGAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* * *
662734 ATTTGGTACATAAACTTTG----TTTTGACCCA
1 ATTTGGTACCTAAAC-TTGACACTTTT-TCCTA
* * *
662763 ATTTGGTACTTGAACTTGACACTTTCTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
662794 ATTTGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
662811 TTTTTGGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
28 7 0.12
29 15 0.25
31 31 0.53
32 6 0.10
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:662777 original size:60 final size:59
Alignment explanation
Indices: 662703--662890 Score: 236
Period size: 60 Copynumber: 3.2 Consensus size: 59
662693 TTAATATAAT
* *
662703 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACATAAACTTTGTTTT-GACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTT-TTTTAGA-CCA
* * *
662763 ATTTGGTACTTGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTGGACCA
1 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTAGACCA
* * * * *
662822 ATTTGGTACTTGAATTTGGCA-TTTTTTTCTAATTTGGTACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACACTTTTTCT-TAATTTGGTACCTAAACTTTTTTTAGA-CCA
662882 ATTTGGTAC
1 ATTTGGTAC
662891 CTAAATTTAT
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
58 4 0.04
59 51 0.45
60 58 0.51
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTAGACCA
Found at i:662778 original size:29 final size:29
Alignment explanation
Indices: 662733--662832 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 29
662723 ACTTTTTCTT
*
662733 AATTTGGTACATAAACTTTGTTTTGACCC
1 AATTTGGTACTTAAACTTTGTTTTGACCC
* * ** *
662762 AATTTGGTACTTGAAC-TTGACACTTTCTCCT
1 AATTTGGTACTTAAACTTTG---TTTTGACCC
*
662793 AATTTGGTACCTAAACTTT-TTTTGGA-CC
1 AATTTGGTACTTAAACTTTGTTTT-GACCC
662821 AATTTGGTACTT
1 AATTTGGTACTT
662833 GAATTTGGCA
Statistics
Matches: 53, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
28 18 0.34
29 14 0.26
31 19 0.36
32 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (29 bp):
AATTTGGTACTTAAACTTTGTTTTGACCC
Found at i:662854 original size:59 final size:58
Alignment explanation
Indices: 662703--662890 Score: 225
Period size: 59 Copynumber: 3.2 Consensus size: 58
662693 TTAATATAAT
* * *
662703 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACATAAACTTTGTTTTGACCCA
1 ATTTGGTACTTGAACTTGACATTTTTTC-TAATTTGGTACCTAAACTTT-TTTTGACCCA
* *
662763 ATTTGGTACTTGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTGGA-CCA
1 ATTTGGTACTTGAACTTGACA-TTTTTTCTAATTTGGTACCTAAACTTTTTTT-GACCCA
* * * **
662822 ATTTGGTACTTGAATTTGGCATTTTTTTCTAATTTGGTACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACA-TTTTTTCTAATTTGGTACCTAAACTTTTTTT-GACCCA
662882 ATTTGGTAC
1 ATTTGGTAC
662891 CTAAATTTAT
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
59 56 0.50
60 52 0.46
61 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (58 bp):
ATTTGGTACTTGAACTTGACATTTTTTCTAATTTGGTACCTAAACTTTTTTTGACCCA
Found at i:663122 original size:31 final size:31
Alignment explanation
Indices: 663079--663146 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
663069 GGACCTCAAA
*
663079 AAGTTTAAGTACCAACTTAAAAAAAAGTATC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTATC
* ** *
663110 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTATC
663141 AAGTTT
1 AAGTTT
663147 GAGCATCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTATC
Found at i:663204 original size:90 final size:90
Alignment explanation
Indices: 663024--663194 Score: 225
Period size: 90 Copynumber: 1.9 Consensus size: 90
663014 ATTAAAAAAA
* ** *
663024 TTAGGTAACAAATTAGGAAAAACAGTCAAGTTCAAGTACCAAATTGGACCTCAAAAAGTTTAAGT
1 TTAGGTAACAAATTAGGAAAAACAGTCAAGTTCAAGCACCAAATTGGACCAAAAAAAATTTAAGT
*
663089 ACCAACTTAAAAAAAAGTATCAAGT
66 ACCAAATTAAAAAAAAGTATCAAGT
* ** ** * *
663114 TTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTGAGCATCAAATTGGACCAAAAAAACATTTAGG
1 TTAGGTAACAAATTAGGAAAAACAGTCAAGTTCAAGCACCAAATTGGACCAAAAAAA-ATTTAAG
663179 TACCAAATTAAAAAAA
65 TACCAAATTAAAAAAA
663195 TTGTCAAGTT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
90 48 0.71
91 20 0.29
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (90 bp):
TTAGGTAACAAATTAGGAAAAACAGTCAAGTTCAAGCACCAAATTGGACCAAAAAAAATTTAAGT
ACCAAATTAAAAAAAAGTATCAAGT
Found at i:663216 original size:90 final size:90
Alignment explanation
Indices: 663032--663216 Score: 210
Period size: 90 Copynumber: 2.1 Consensus size: 90
663022 AATTAGGTAA
* ** * *
663032 CAAATTAGGAAAAACAGTCAAGTTCAAGTACCAAATTGGACCTCAAAAAGTTTAAGTACCAACTT
1 CAAATTAGGAAAAACAGTCAAGTTCAAGCACCAAATTGGACCAAAAAAAATTTAAGTACCAAATT
* *
663097 AAAAAAAAGTATCAAGTTTAGGTAC
66 AAAAAAAAGTATCAAGTTCAAGTAC
** ** * *
663122 CAAATTAGGAAAAAGTGTCAAGTTTGAGCATCAAATTGGACCAAAAAAACATTTAGGTACCAAAT
1 CAAATTAGGAAAAACAGTCAAGTTCAAGCACCAAATTGGACCAAAAAAA-ATTTAAGTACCAAAT
* * *
663187 T-AAAAAAATTGTCAAGTTCAAGTAT
65 TAAAAAAAAGTATCAAGTTCAAGTAC
663212 CAAAT
1 CAAAT
663217 ATTATATTAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
90 65 0.83
91 13 0.17
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (90 bp):
CAAATTAGGAAAAACAGTCAAGTTCAAGCACCAAATTGGACCAAAAAAAATTTAAGTACCAAATT
AAAAAAAAGTATCAAGTTCAAGTAC
Found at i:676181 original size:29 final size:30
Alignment explanation
Indices: 676126--676576 Score: 161
Period size: 29 Copynumber: 15.4 Consensus size: 30
676116 ACCCCGAGGA
** *
676126 AAAATGGTAATTTCGGTGAAA-TCGGGGTCG
1 AAAATGGTAATTTTAGTAAAATTCGGGGT-G
*
676156 AAAATGG-AATTTTAG-AAAATTTGGGG-G
1 AAAATGGTAATTTTAGTAAAATTCGGGGTG
** * *
676183 TAAAATGGTAATTTCGGTGAAA-TCGGGGTTA
1 -AAAATGGTAATTTTAGTAAAATTCGGGG-TG
676214 AAAATGG-AATTTT-G-AAAAGTTCGAGGGT-
1 AAAATGGTAATTTTAGTAAAA-TTCG-GGGTG
* *
676242 AAAATGGTAATTTTTGGTAAAA-TCGGGGTTA
1 AAAATGGTAA-TTTTAGTAAAATTCGGGG-TG
* *
676273 AAAATGG-AATTTTAGAAAAATTTGGGG-G
1 AAAATGGTAATTTTAGTAAAATTCGGGGTG
* * * *
676301 TAAAATGGTAATTTTGGTGAAATT-AGGGTT
1 -AAAATGGTAATTTTAGTAAAATTCGGGGTG
* *
676331 AAAATGG-AATTTT-GGAAAGTTCGAGGGT-
1 AAAATGGTAATTTTAGTAAAATTCG-GGGTG
* * * *
676359 AAAATGGTAATTTTTGGTGAAA-TCGGAGTTA
1 AAAATGGTAA-TTTTAGTAAAATTCGG-GGTG
* * *
676390 AAAATGG-AATTTT-GGAAAGTTTGGGG-G
1 AAAATGGTAATTTTAGTAAAATTCGGGGTG
* * * *
676417 TAAAATGGTAATTTTTGGTGAAA-TCGAGGTTA
1 -AAAATGGTAA-TTTTAGTAAAATTCG-GGGTG
* * *
676449 AAAATGG-AATTTT-GGAAAGTTCGGGGTA
1 AAAATGGTAATTTTAGTAAAATTCGGGGTG
* * *
676477 AAAATGG-AATTTT-GGAGAGTTCGGGG-G
1 AAAATGGTAATTTTAGTAAAATTCGGGGTG
* * *
676504 TAAAATGGTAATTTTTGGTGAAA-TCGGGGTTA
1 -AAAATGGTAA-TTTTAGTAAAATTCGGGG-TG
* * *
676536 AAAATAG-AATTTT-GGAAAGTTCGAGGGT-
1 AAAATGGTAATTTTAGTAAAATTCG-GGGTG
676564 AAAATGGTAATTT
1 AAAATGGTAATTT
676577 CTGGTGAAAT
Statistics
Matches: 322, Mismatches: 56, Indels: 87
0.69 0.12 0.19
Matches are distributed among these distances:
27 9 0.03
28 90 0.28
29 100 0.31
30 81 0.25
31 38 0.12
32 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTAGTAAAATTCGGGGTG
Found at i:676284 original size:59 final size:59
Alignment explanation
Indices: 676126--676489 Score: 490
Period size: 59 Copynumber: 6.2 Consensus size: 59
676116 ACCCCGAGGA
* ** *
676126 AAAATGGTAA-TTTCGGTGAAATCGGGGTCGAAAATGGAATTTTAGAAAA-TTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAAGTTCGGGGGT
* *
676184 AAAATGGTAA-TTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGGT
* * *
676242 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAAAATTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GAAAAGTTCGGGGGT
** * *
676302 AAAATGGTAA-TTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGGT
* * *
676359 AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGGT
* *
676418 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC-GGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGGT
676476 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
676490 GGAGAGTTCG
Statistics
Matches: 276, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
57 26 0.09
58 98 0.36
59 130 0.47
60 22 0.08
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGGGGGT
Found at i:676287 original size:117 final size:117
Alignment explanation
Indices: 676126--676489 Score: 565
Period size: 117 Copynumber: 3.1 Consensus size: 117
676116 ACCCCGAGGA
* **
676126 AAAATGGTAA-TTTCGGTGAAATCGGGGTCGAAAATGGAATTTTAGAAAATTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAATTTGGGGGTAAAATG
* *
676190 GTAATTTCGGTGAAATCGGGGTTAAAAATGGAATTTTGAAAAGTTCGAGGGT
66 GTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
*
676242 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAAAATTTGGGGGTAAAAT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAAATTTGGGGGTAAAAT
**
676307 GGTAATTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGT
65 GGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * *
676359 AAAATGGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAATTTGGGGGTAAAATG
*
676424 GTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGT
66 GTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
676476 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
676490 GGAGAGTTCG
Statistics
Matches: 228, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
116 32 0.14
117 127 0.56
118 69 0.30
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAATTTGGGGGTAAAATG
GTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:676548 original size:59 final size:59
Alignment explanation
Indices: 676469--676597 Score: 206
Period size: 59 Copynumber: 2.2 Consensus size: 59
676459 TTTGGAAAGT
* * * *
676469 TCGGGG-TAAAAATGGAATTTTGGAGAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 TCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTCTGGTGAAA
676527 TCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTCTGGTGAAA
1 TCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTCTGGTGAAA
*
676586 TCGAGGTTAAAA
1 TCGGGGTTAAAA
676598 TGTAATTTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 6 0.09
59 59 0.91
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.30
Consensus pattern (59 bp):
TCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTCTGGTGAAA
Found at i:676582 original size:146 final size:145
Alignment explanation
Indices: 676301--676605 Score: 470
Period size: 146 Copynumber: 2.1 Consensus size: 145
676291 AATTTGGGGG
* *
676301 TAAAATGGTAATTTTGGTGAAA-TT-AGGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAT
1 TAAAATGG-AATTTT-G-GAAAGTTCGGGGTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAT
* * *
676364 GGTAATTTTTGGTGAAATCGGAGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAAT
63 GGTAATTTTTGGTGAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAAT
*
676429 TTTTGGTGAAATCGAGGT
128 TTCTGGTGAAATCGAGGT
* *
676447 TAAAAATGGAATTTTGGAAAGTTCGGGGTAAAAATGGAATTTTGGAGAGTTCGGGGGTAAAATGG
1 T-AAAATGGAATTTTGGAAAGTTCGGGGTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGG
*
676512 TAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTT
65 TAATTTTTGGTGAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTT
676577 CTGGTGAAATCGAGGT
130 CTGGTGAAATCGAGGT
*
676593 TAAAATGTAATTT
1 TAAAATGGAATTT
676606 CCTAAAATTT
Statistics
Matches: 146, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
144 4 0.03
145 14 0.10
146 121 0.83
147 7 0.05
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (145 bp):
TAAAATGGAATTTTGGAAAGTTCGGGGTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGT
AATTTTTGGTGAAATCGGAGTTAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTC
TGGTGAAATCGAGGT
Found at i:677692 original size:3 final size:3
Alignment explanation
Indices: 677686--677738 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
677676 TTATTTAAAC
*
677686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
677734 TAT TA
1 TAT TA
677739 ATGGCTGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:678556 original size:12 final size:13
Alignment explanation
Indices: 678533--678588 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 13
678523 ACTTTGGATT
678533 TTTTTAATTTAAA
1 TTTTTAATTTAAA
678546 TTTTTAA-TTAAA
1 TTTTTAATTTAAA
*
678558 TTTAAATTTATTTCAAA
1 TTT---TTAATTT-AAA
678575 TATTTTAATTTAAA
1 T-TTTTAATTTAAA
678589 ATGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 8 0.23
13 7 0.20
14 3 0.09
15 9 0.26
16 2 0.06
17 4 0.11
18 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAATTTAAA
Found at i:680635 original size:39 final size:39
Alignment explanation
Indices: 680581--680659 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
680571 GTGTTTTTTT
*
680581 TTATCATTTGGATCACATAATAATGAAATATTATTGCAA
1 TTATCATTTGGATCACACAATAATGAAATATTATTGCAA
*
680620 TTATCATTTGGATCACACAATGATGAAATATTATTGCAA
1 TTATCATTTGGATCACACAATAATGAAATATTATTGCAA
680659 T
1 T
680660 ATTAAACGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (39 bp):
TTATCATTTGGATCACACAATAATGAAATATTATTGCAA
Found at i:686803 original size:31 final size:31
Alignment explanation
Indices: 686768--686826 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
686758 AACCAGTTAC
*
686768 TTAAATAAAAACTTTCAAATAGTTCAATGAT
1 TTAAATAAAAACTTTCAAATAATTCAATGAT
* * *
686799 TTAAATGAAAATTTTCTAATAATTCAAT
1 TTAAATAAAAACTTTCAAATAATTCAAT
686827 CACCATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAATTCAATGAT
Found at i:690003 original size:31 final size:32
Alignment explanation
Indices: 689949--690008 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
689939 AACATTTTCC
**
689949 TTTAATTAAGTTAAAAATTTCAATTAATTAAA
1 TTTAATTAAGTTAAAAAAATCAATTAATTAAA
*
689981 TTTATTTAA-TTAAAAAAATCAATTAATT
1 TTTAATTAAGTTAAAAAAATCAATTAATT
690009 TACTTGGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (32 bp):
TTTAATTAAGTTAAAAAAATCAATTAATTAAA
Done.