Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000880.1 Hibiscus syriacus cultivar Beakdansim tig00001713_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1459553
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:127494 original size:17 final size:15
Alignment explanation
Indices: 127471--127519 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
127461 CTTTTTTCCA
127471 ACTTTTTCAACCTTTT
1 ACTTTTTCAA-CTTTT
*
127487 TCTATTTTCAACTATTT
1 ACT-TTTTCAACT-TTT
127504 ACTTTTTCAAACTTTT
1 ACTTTTTC-AACTTTT
127520 GACATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.57
Consensus pattern (15 bp):
ACTTTTTCAACTTTT
Found at i:127512 original size:16 final size:16
Alignment explanation
Indices: 127471--127519 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
127461 CTTTTTTCCA
127471 ACTTTTTCAACCTTTT
1 ACTTTTTCAACCTTTT
*
127487 TCTATTTTCAA-CTATTT
1 ACT-TTTTCAACCT-TTT
*
127504 ACTTTTTCAAACTTTT
1 ACTTTTTCAACCTTTT
127520 GACATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.57
Consensus pattern (16 bp):
ACTTTTTCAACCTTTT
Found at i:127709 original size:13 final size:13
Alignment explanation
Indices: 127691--127715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127681 TTATAATTTT
127691 TTTCTTTTTTAAC
1 TTTCTTTTTTAAC
127704 TTTCTTTTTTAA
1 TTTCTTTTTTAA
127716 TTAGTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTTTTAAC
Found at i:128310 original size:13 final size:13
Alignment explanation
Indices: 128292--128323 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
128282 TTTACATTTG
*
128292 AACTATATGTATA
1 AACTATATATATA
128305 AACTATATATATA
1 AACTATATATATA
128318 AACTAT
1 AACTAT
128324 GTAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (13 bp):
AACTATATATATA
Found at i:128452 original size:18 final size:19
Alignment explanation
Indices: 128411--128486 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 19
128401 ATTAGTGAAC
*
128411 TATATAAACTAT-TTAT-A
1 TATATAAACTATAGTATAA
*
128428 TAGTATATACTATA-TATAA
1 TA-TATAAACTATAGTATAA
* *
128447 TATATAAAGTATAGTTTATA
1 TATATAAACTATAGTATA-A
* * *
128467 TTTATATACTATATTATAA
1 TATATAAACTATAGTATAA
128486 T
1 T
128487 TTACATATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
17 2 0.04
18 21 0.47
19 8 0.18
20 14 0.31
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (19 bp):
TATATAAACTATAGTATAA
Found at i:128523 original size:33 final size:33
Alignment explanation
Indices: 128481--128707 Score: 160
Period size: 33 Copynumber: 6.6 Consensus size: 33
128471 TATACTATAT
128481 TATAATTTACATATGAACTATTTATATAAACTA
1 TATAATTTACATATGAACTATTTATATAAACTA
* * *
128514 TATAATTTACATATGAGCTATATATATATACTA
1 TATAATTTACATATGAACTATTTATATAAACTA
*
128547 TAGTTGATATTTATATATGAACTATAGATTACATATAAACTA
1 TA--T-A-ATTTACATATGAACTAT---TT--ATATAAACTA
* * * *
128589 TAT-ATATATATAT--A-TATTACATATGAAC--
1 TATAATTTACATATGAACTATT-TATATAAACTA
* *
128617 TATAGTTCACATATGAACTATTTATATAAACTA
1 TATAATTTACATATGAACTATTTATATAAACTA
* * *
128650 TATAGTTTACATATGAACTATATATATATACTA
1 TATAATTTACATATGAACTATTTATATAAACTA
*
128683 TAGTTGATATTTATATATGAACTAT
1 TA--T-A-ATTTACATATGAACTAT
128708 AGTTTACATA
Statistics
Matches: 153, Mismatches: 21, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
28 3 0.02
29 6 0.04
30 7 0.05
31 9 0.06
32 4 0.03
33 64 0.42
34 3 0.02
35 3 0.02
36 2 0.01
37 39 0.25
40 2 0.01
42 11 0.07
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (33 bp):
TATAATTTACATATGAACTATTTATATAAACTA
Found at i:128579 original size:55 final size:52
Alignment explanation
Indices: 128499--128671 Score: 164
Period size: 48 Copynumber: 3.4 Consensus size: 52
128489 ACATATGAAC
* *
128499 TATTTATATA--AACTATATAATTTACATATGAGCTATATATATATACTATAGTTGA
1 TATTTATATATGAACTATA-GA-TTACATATGAACTATATATATATACTATA--T-A
*
128554 TATTTATATATGAACTATAGATTACATATAAAC--TATATATATA-TATATA
1 TATTTATATATGAACTATAGATTACATATGAACTATATATATATACTATATA
* * *
128603 TA-TTACATATGAACTATAG-TTCACATATGAACTATTTATATAAACTATATA
1 TATTTATATATGAACTATAGATT-ACATATGAACTATATATATATACTATATA
* *
128654 -GTTTACATATGAACTATA
1 TATTTATATATGAACTATA
128672 TATATATACT
Statistics
Matches: 103, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
47 2 0.02
48 25 0.24
49 3 0.03
50 9 0.09
51 22 0.21
52 4 0.04
53 10 0.10
55 20 0.19
56 1 0.01
57 7 0.07
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (52 bp):
TATTTATATATGAACTATAGATTACATATGAACTATATATATATACTATATA
Found at i:128635 original size:136 final size:137
Alignment explanation
Indices: 128489--128737 Score: 455
Period size: 136 Copynumber: 1.8 Consensus size: 137
128479 ATTATAATTT
*
128489 ACATATGAACTATTTATATAAACTATATAATTTACATATGAGCTATATATATATACTATAGTTGA
1 ACATATGAACTATTTATATAAACTATATAATTTACATATGAACTATATATATATACTATAGTTGA
128554 TATTTATATATGAACTATAGATTACATATAAACTATATA-TATATATATATATTACATATGAACT
66 TATTTATATATGAACTATAGATTACATATAAACTATATAGTATATATATATATTACATATGAACT
128618 ATAGTTC
131 ATAGTTC
*
128625 ACATATGAACTATTTATATAAACTATATAGTTTACATATGAACTATATATATATACTATAGTTGA
1 ACATATGAACTATTTATATAAACTATATAATTTACATATGAACTATATATATATACTATAGTTGA
* *
128690 TATTTATATATGAACTATAGTTTACATATAAACTATATAGTTTATATA
66 TATTTATATATGAACTATAGATTACATATAAACTATATAGTATATATA
128738 CTAACTATAG
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
136 101 0.94
137 7 0.06
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (137 bp):
ACATATGAACTATTTATATAAACTATATAATTTACATATGAACTATATATATATACTATAGTTGA
TATTTATATATGAACTATAGATTACATATAAACTATATAGTATATATATATATTACATATGAACT
ATAGTTC
Found at i:128668 original size:20 final size:20
Alignment explanation
Indices: 128640--128808 Score: 94
Period size: 18 Copynumber: 8.7 Consensus size: 20
128630 TGAACTATTT
*
128640 ATATAAACTATATAGTTTAC
1 ATATGAACTATATAGTTTAC
128660 ATATGAACTATATA-TATATAC
1 ATATGAACTATATAGT-T-TAC
* *
128681 -TAT--AGT-TGATA-TTTAT
1 ATATGAACTAT-ATAGTTTAC
128697 ATATGAAC--TATAGTTTAC
1 ATATGAACTATATAGTTTAC
* *
128715 ATATAAACTATATAGTTTAT
1 ATATGAACTATATAGTTTAC
128735 ATACT-AAC--TATAGTTTAC
1 ATA-TGAACTATATAGTTTAC
* *
128753 ATATAAACTATAGTTGATATTTAC
1 ATATGAACTATA--T-A-GTTTAC
* *
128777 GTATGAAC--TATAGCTTAC
1 ATATGAACTATATAGTTTAC
128795 ATATGAACTATATA
1 ATATGAACTATATA
128809 TATAAACTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
16 2 0.02
17 9 0.08
18 44 0.38
19 3 0.03
20 39 0.34
21 4 0.03
22 3 0.03
23 1 0.01
24 11 0.09
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (20 bp):
ATATGAACTATATAGTTTAC
Found at i:128744 original size:38 final size:38
Alignment explanation
Indices: 128640--128808 Score: 159
Period size: 38 Copynumber: 4.4 Consensus size: 38
128630 TGAACTATTT
* * *
128640 ATATAAACTATATAGTTTACATATGAACTATA-TATAT
1 ATATAAACTATATAGTTTATATATGAACTATAGTTTAC
* *
128677 ATACTATAGT-TGATA-TTTATATATGAACTATAGTTTAC
1 ATA-TAAACTAT-ATAGTTTATATATGAACTATAGTTTAC
128715 ATATAAACTATATAGTTTATATACT-AACTATAGTTTAC
1 ATATAAACTATATAGTTTATATA-TGAACTATAGTTTAC
* *
128753 ATATAAACTATAGTTGATATT-TACGTATGAACTATAGCTTAC
1 ATATAAACTATA-TAG-T-TTATA--TATGAACTATAGTTTAC
*
128795 ATATGAACTATATA
1 ATATAAACTATATA
128809 TATAAACTAT
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
37 27 0.25
38 47 0.43
39 3 0.03
40 3 0.03
41 4 0.04
42 25 0.23
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (38 bp):
ATATAAACTATATAGTTTATATATGAACTATAGTTTAC
Found at i:128766 original size:18 final size:18
Alignment explanation
Indices: 128556--128767 Score: 110
Period size: 18 Copynumber: 12.1 Consensus size: 18
128546 ATAGTTGATA
* *
128556 TTTATATATGAACTATAG
1 TTTACATATAAACTATAG
*
128574 ATTACATATAAACTATA-
1 TTTACATATAAACTATAG
* *
128591 --TATATATATA-TATA-
1 TTTACATATAAACTATAG
*
128605 -TTACATATGAACTATAG
1 TTTACATATAAACTATAG
* *
128622 TTCACATATGAAC--TA-
1 TTTACATATAAACTATAG
128637 TTT--ATATAAACTATATAG
1 TTTACATATAAAC--TATAG
*
128655 TTTACATATGAACTATA-
1 TTTACATATAAACTATAG
* * **
128672 TATATATACTATAGTTGATA-
1 TTTACATA-TA-AACT-ATAG
* *
128692 TTTATATATGAACTATAG
1 TTTACATATAAACTATAG
128710 TTTACATATAAACTATATAG
1 TTTACATATAAAC--TATAG
*
128730 TTTATATACT-AACTATAG
1 TTTACATA-TAAACTATAG
128748 TTTACATATAAACTATAG
1 TTTACATATAAACTATAG
128766 TT
1 TT
128768 GATATTTACG
Statistics
Matches: 150, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
13 7 0.05
14 4 0.03
15 17 0.11
16 6 0.04
17 12 0.08
18 68 0.45
19 3 0.02
20 32 0.21
21 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (18 bp):
TTTACATATAAACTATAG
Found at i:128782 original size:80 final size:75
Alignment explanation
Indices: 128640--128808 Score: 223
Period size: 80 Copynumber: 2.2 Consensus size: 75
128630 TGAACTATTT
* *
128640 ATATAAACTATATAGTTTACATATGAACTATATATATATACTATAGTTGATATTTATATATGAAC
1 ATATAAACTATATAGTTTACATATGAACTATATATATAAACTATAGTTGATATTTACATATGAAC
*
128705 TATAGTTTAC
66 TATAGCTTAC
* *
128715 ATATAAACTATATAGTTTATATACT-AACTATAGTTTACATATAAACTATAGTTGATATTTACGT
1 ATATAAACTATATAGTTTACATA-TGAACTATA---T--ATATAAACTATAGTTGATATTTACAT
128779 ATGAACTATAGCTTAC
60 ATGAACTATAGCTTAC
*
128795 ATATGAACTATATA
1 ATATAAACTATATA
128809 TATAAACTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
75 29 0.35
76 1 0.01
78 1 0.01
80 51 0.62
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.41
Consensus pattern (75 bp):
ATATAAACTATATAGTTTACATATGAACTATATATATAAACTATAGTTGATATTTACATATGAAC
TATAGCTTAC
Found at i:128888 original size:18 final size:18
Alignment explanation
Indices: 128862--128896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
128852 TAGTGAACTA
*
128862 TATAAACTATTTATATAG
1 TATAAACTATATATATAG
*
128880 TATATACTATATATATA
1 TATAAACTATATATATA
128897 AACTATAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAAACTATATATATAG
Found at i:128896 original size:20 final size:20
Alignment explanation
Indices: 128873--128979 Score: 76
Period size: 20 Copynumber: 5.3 Consensus size: 20
128863 ATAAACTATT
*
128873 TATATAGTATATACTATATA
1 TATATACTATATACTATATA
* * *
128893 TATAAACTATAGT-TTATATT
1 TATATACTATA-TACTATATA
* *
128913 TATATACTACATACTATAGTT
1 TATATACTATATACTATA-TA
*
128934 TATAT-TTATATACTATATA
1 TATATACTATATACTATATA
* *
128953 TTATATA-TGTAAACTATATA
1 -TATATACTATATACTATATA
128973 TACTATA
1 TA-TATA
128980 TAGCATAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.06
20 57 0.83
21 8 0.12
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (20 bp):
TATATACTATATACTATATA
Found at i:128957 original size:27 final size:27
Alignment explanation
Indices: 128862--128957 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 27
128852 TAGTGAACTA
* * * *
128862 TATAAACTATTTA-TATAGTATATA-C
1 TATATACTATATACTATAGTTTATATT
*
128887 TATATA-TATAAACTATAGTTTATATT
1 TATATACTATATACTATAGTTTATATT
*
128913 TATATACTACATACTATAGTTTATATT
1 TATATACTATATACTATAGTTTATATT
*
128940 TATATACTATATATTATA
1 TATATACTATATACTATA
128958 TATGTAAACT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.07
25 15 0.25
26 6 0.10
27 34 0.58
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (27 bp):
TATATACTATATACTATAGTTTATATT
Found at i:129012 original size:16 final size:16
Alignment explanation
Indices: 128973--129005 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
128963 AAACTATATA
128973 TACTATATAGCATAAT
1 TACTATATAGCATAAT
128989 TACTATATAGCATAAT
1 TACTATATAGCATAAT
129005 T
1 T
129006 TACATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (16 bp):
TACTATATAGCATAAT
Found at i:129104 original size:9 final size:9
Alignment explanation
Indices: 129092--129124 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
129082 TACTATAGTA
129092 TATATAAAC
1 TATATAAAC
129101 TATATAATA-
1 TATATAA-AC
129110 TATATAAAC
1 TATATAAAC
129119 TATATA
1 TATATA
129125 TTATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAC
Found at i:129111 original size:18 final size:18
Alignment explanation
Indices: 129085--129430 Score: 185
Period size: 18 Copynumber: 19.2 Consensus size: 18
129075 TAATTTATAC
129085 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
129103 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
***
129121 TATA-T-TATATATTTTA
1 TATAGTATATATAAACTA
129137 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
129154 TATGGTATATATAAAACTA
1 TATAGTATATAT-AAACTA
* ***
129173 TACA-T-TATATAGTTTA
1 TATAGTATATATAAACTA
129189 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
* * *
129206 TATAATATATAAAAATTA
1 TATAGTATATATAAACTA
* *
129224 TATGGTATATATAAACTC
1 TATAGTATATATAAACTA
*
129242 TATAGTATATGTAAACTA
1 TATAGTATATATAAACTA
* ** *
129260 TATATTATATAGTTCATTA
1 TATAGTATATA-TAAACTA
* *
129279 GTATA-TATAGCCTATATAGTA
1 -TATAGTATA---TATAAACTA
* *
129300 TATGGTATATACAAACTA
1 TATAGTATATATAAACTA
* ** *
129318 TATATTATATAGTGCATTA
1 TATAGTATATA-TAAACTA
* *
129337 GTATA-TATAACCTATATAGTA
1 -TATAGTAT-A--TATAAACTA
* *
129358 TATGGTATATACAAACTA
1 TATAGTATATATAAACTA
**
129376 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
*
129392 T-TAGTATAAATAAACTA
1 TATAGTATATATAAACTA
*
129409 TATAGTATATATAAAATA
1 TATAGTATATATAAACTA
129427 TATA
1 TATA
129431 TTGAAAAGTT
Statistics
Matches: 242, Mismatches: 62, Indels: 48
0.69 0.18 0.14
Matches are distributed among these distances:
15 7 0.03
16 22 0.09
17 31 0.13
18 125 0.52
19 22 0.09
20 16 0.07
21 15 0.06
22 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:129193 original size:52 final size:52
Alignment explanation
Indices: 129087--129225 Score: 219
Period size: 52 Copynumber: 2.7 Consensus size: 52
129077 ATTTATACTA
* *
129087 TAGTATATATAAACTATATAATATATAT-AAACTATATATTATATATTTTAT
1 TAGTATATATAAACTATATAATATATATAAAACTATACATTATATAGTTTAT
**
129138 TAGTATATATAAACTATATGGTATATATAAAACTATACATTATATAGTTTAT
1 TAGTATATATAAACTATATAATATATATAAAACTATACATTATATAGTTTAT
*
129190 TAGTATATATAAACTATATAATATATA-AAAATTATA
1 TAGTATATATAAACTATATAATATATATAAAACTATA
129226 TGGTATATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 34 0.43
52 46 0.57
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (52 bp):
TAGTATATATAAACTATATAATATATATAAAACTATACATTATATAGTTTAT
Found at i:129271 original size:87 final size:87
Alignment explanation
Indices: 129108--129302 Score: 252
Period size: 87 Copynumber: 2.3 Consensus size: 87
129098 AACTATATAA
* ** *
129108 TATATATAAACTATAT-AT-TATATATTTTATTAGTATATATAAACTATATGGTATATATAAAAC
1 TATATATAAACTATATAATATATAAAAATTATTAGTATATATAAACTATATAGTATATATAAAAC
*
129171 TATACATTATATAGTTTATTAG
66 TATACATTATATAGTTCATTAG
* * *
129193 TATATATAAACTATATAATATATAAAAATTATATGGTATATATAAACTCTATAGTATATGT-AAA
1 TATATATAAACTATATAATATATAAAAATTAT-TAGTATATATAAACTATATAGTATATATAAAA
*
129257 CTATATATTATATAGTTCATTAG
65 CTATACATTATATAGTTCATTAG
** *
129280 TATATATAGCCTATATAGTATAT
1 TATATATAAACTATATAATATAT
129303 GGTATATACA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
85 16 0.17
86 2 0.02
87 53 0.56
88 24 0.25
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (87 bp):
TATATATAAACTATATAATATATAAAAATTATTAGTATATATAAACTATATAGTATATATAAAAC
TATACATTATATAGTTCATTAG
Found at i:129317 original size:58 final size:58
Alignment explanation
Indices: 129254--129463 Score: 310
Period size: 58 Copynumber: 3.7 Consensus size: 58
129244 TAGTATATGT
*
129254 AAACTATATATTATATAGTTCATTAGTATATATAGCCTATATAGTATATGGTATATAC
1 AAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATAC
*
129312 AAACTATATATTATATAGTGCATTAGTATATATAACCTATATAGTATATGGTATATAC
1 AAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATAC
* *
129370 AAACTATATATTATATAGTTCATTAGTATAAATAAACTATATAG--TA---TATATA-
1 AAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATAC
*
129422 AAA-TATATATTGA-AAAGTTCATTAGTATATATAACCTATATA
1 AAACTATATATT-ATATAGTTCATTAGTATATATAACCTATATA
129464 TTAATTTATT
Statistics
Matches: 143, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
51 34 0.24
52 4 0.03
53 6 0.04
56 2 0.01
58 97 0.68
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (58 bp):
AAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGTATATAC
Found at i:129378 original size:109 final size:108
Alignment explanation
Indices: 129228--129463 Score: 239
Period size: 109 Copynumber: 2.2 Consensus size: 108
129218 AAATTATATG
* * * * * *
129228 GTATATATAAACTCTATAGTATATGTAAACTATATATTATATAGTTCAT-TAGTAT-ATATAGCC
1 GTATATATAACCTATATAGTATATGTAAACTACAAACTATATA-TT-ATATAGT-TCAT-TAGCA
* * * * *
129291 T-ATATAGTATATGGTATATACAAACTATATATT-ATATAGTGCATTA
62 TAATAAACTATATAGTATATACAAAATATATATTGA-AAAGTGCATTA
* *
129337 GTATATATAACCTATATAGTATATGGTATA-TACAAACTATATATTATATAGTTCATTAGTATAA
1 GTATATATAACCTATATAGTATAT-GTAAACTACAAACTATATATTATATAGTTCATTAGCAT-A
* *
129401 ATAAACTATATAGTATATATAAAATATATATTGAAAAGTTCATTA
64 ATAAACTATATAGTATATACAAAATATATATTGAAAAGTGCATTA
129446 GTATATATAACCTATATA
1 GTATATATAACCTATATA
129464 TTAATTTATT
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
107 7 0.07
108 8 0.08
109 86 0.81
110 5 0.05
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (108 bp):
GTATATATAACCTATATAGTATATGTAAACTACAAACTATATATTATATAGTTCATTAGCATAAT
AAACTATATAGTATATACAAAATATATATTGAAAAGTGCATTA
Found at i:129411 original size:51 final size:51
Alignment explanation
Indices: 129356--129463 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
129346 ACCTATATAG
* * *
129356 TATATGGTATATACAAACTATATATT-ATATAGTTCATTAGTATAAATAAAC
1 TATATAGTATATACAAAATATATATTGA-AAAGTTCATTAGTATAAATAAAC
* * *
129407 TATATAGTATATATAAAATATATATTGAAAAGTTCATTAGTATATATAACC
1 TATATAGTATATACAAAATATATATTGAAAAGTTCATTAGTATAAATAAAC
129458 TATATA
1 TATATA
129464 TTAATTTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 49 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (51 bp):
TATATAGTATATACAAAATATATATTGAAAAGTTCATTAGTATAAATAAAC
Found at i:130060 original size:113 final size:113
Alignment explanation
Indices: 129867--130216 Score: 330
Period size: 123 Copynumber: 3.1 Consensus size: 113
129857 AAATCATCCG
* * * * * *
129867 TGTTTTTCATTTGTTCATCCCAATTCTTCCCCAAAACCCTCCTTTGATCATC-AAAA-AC---AC
1 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACAAAAC
* *
129927 A-AAA--TTTTC-T-TTTTTTCGATCAAACACCCAAATATTCATCCA-
66 ACAAACCATTTCATGGTTTTTCGATCAAACACCCAAATATTCATCCAT
*
129969 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCCT-CATTTGATCTTCAAAAACACCAAA
1 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATAC-TTTGATCTTCAAAAACA-CAAA
* *
130033 ACACAAACCATTTCATGGTTTTTCGATCAAACACCAAAATTTTCATCGGTGTTCATCT
64 ACACAAACCATTTCATGGTTTTTCGATCAAACACCCAAATATTCATC------CA--T
**
130091 GTGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACTGAA
1 -TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACAAAA
* * * * *
130156 CCCAAACCATTTCGTGTTTTTTTGATCAAACA-CCAACAAATTCATCCAT
65 CACAAACCATTTCATGGTTTTTCGATCAAACACCCAA-ATATTCATCCAT
*
130205 TGTTCATCATTT
1 TGTTCTTCATTT
130217 TCTTCCCCAA
Statistics
Matches: 205, Mismatches: 19, Indels: 37
0.79 0.07 0.14
Matches are distributed among these distances:
101 1 0.00
102 46 0.22
103 4 0.02
104 1 0.00
105 1 0.00
108 3 0.01
109 3 0.01
111 4 0.02
112 1 0.00
113 38 0.19
114 1 0.00
116 2 0.01
119 2 0.01
121 3 0.01
122 38 0.19
123 56 0.27
124 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (113 bp):
TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACAAAAC
ACAAACCATTTCATGGTTTTTCGATCAAACACCCAAATATTCATCCAT
Found at i:130104 original size:123 final size:122
Alignment explanation
Indices: 129969--130191 Score: 358
Period size: 123 Copynumber: 1.8 Consensus size: 122
129959 TATTCATCCA
*
129969 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCCT-CATTTGATCTTCAAAAACACCAAA
1 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATAC-TTTGATCTTCAAAAACA-CAAA
130033 ACACAAACCATTTCATGGTTTTTCGATCAAACACCAAAATTTTCATCGGTGTTCATCTG
64 ACACAAACCATTTCATGGTTTTTCGATCAAACACCAAAATTTTCATCGGTGTTCATCTG
**
130092 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACTGAAC
1 TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACAAAAC
* * * *
130157 CCAAACCATTTCGTGTTTTTTTGATCAAACACCAA
66 ACAAACCATTTCATGGTTTTTCGATCAAACACCAA
130192 CAAATTCATC
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
122 35 0.38
123 56 0.61
124 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (122 bp):
TGTTCTTCATTTGTTCATCCTAGTTCTTCCCCAAAACCATACTTTGATCTTCAAAAACACAAAAC
ACAAACCATTTCATGGTTTTTCGATCAAACACCAAAATTTTCATCGGTGTTCATCTG
Found at i:130380 original size:6 final size:6
Alignment explanation
Indices: 130356--130578 Score: 55
Period size: 6 Copynumber: 37.5 Consensus size: 6
130346 AGTGAACCAT
* * * * * * **
130356 AACCCT AACCTA AAACCA AACCCA AACCCA AATCC- AGCCCT AACTTA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * ** *
130403 AACCTA AA-CTA AA-CTA AACCCCA AACCCA AACCCA AA-TTA AACCTA
1 AACCCA AACCCA AACCCA AA-CCCA AACCCA AACCCA AACCCA AACCCA
* * ** * *
130449 AA--TA GAACCTA AACCCTA AACCCA AACTTA AACCCTA AACCTA AACCTA
1 AACCCA -AACCCA AACCC-A AACCCA AACCCA AACCC-A AACCCA AACCCA
* * * * ** * * *
130498 AATCTA AACCTA AACCTGA AA-CCA AAATCG AACCTA AACCCA AACCTA
1 AACCCA AACCCA AACC-CA AACCCA AACCCA AACCCA AACCCA AACCCA
* * **
130546 AACTCA AACCCT AACCCA AACCTG AACCCA AAC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AAC
130579 TATTCAAAAC
Statistics
Matches: 162, Mismatches: 44, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
4 2 0.01
5 21 0.13
6 119 0.73
7 20 0.12
ACGTcount: A:0.48, C:0.36, G:0.02, T:0.13
Consensus pattern (6 bp):
AACCCA
Found at i:130482 original size:12 final size:12
Alignment explanation
Indices: 130402--130578 Score: 105
Period size: 12 Copynumber: 14.3 Consensus size: 12
130392 GCCCTAACTT
*
130402 AAACCTAAA-CT
1 AAACCTAAACCC
130413 AAA-CTAAACCCC
1 AAACCTAAA-CCC
*
130425 AAACCCAAACCC
1 AAACCTAAACCC
* *
130437 AAA-TTAAACCT
1 AAACCTAAACCC
*
130448 AAA--TAGAACCT
1 AAACCTA-AACCC
130459 AAACCCTAAACCC
1 AAA-CCTAAACCC
*
130472 AAACTTAAACCC
1 AAACCTAAACCC
*
130484 TAAACCTAAACCT
1 -AAACCTAAACCC
* *
130497 AAATCTAAACCT
1 AAACCTAAACCC
130509 AAACCTGAAACCAAAATC
1 AAACCT-AAACC-----C
*
130527 GAACCTAAACCC
1 AAACCTAAACCC
*
130539 AAACCTAAACTC
1 AAACCTAAACCC
130551 AAACCCT-AACCC
1 AAA-CCTAAACCC
*
130563 AAACCTGAACCC
1 AAACCTAAACCC
130575 AAAC
1 AAAC
130579 TATTCAAAAC
Statistics
Matches: 134, Mismatches: 16, Indels: 31
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.05
11 22 0.16
12 64 0.48
13 29 0.22
14 2 0.01
17 5 0.04
18 5 0.04
ACGTcount: A:0.50, C:0.34, G:0.02, T:0.14
Consensus pattern (12 bp):
AAACCTAAACCC
Found at i:130506 original size:18 final size:18
Alignment explanation
Indices: 130401--130578 Score: 111
Period size: 18 Copynumber: 9.9 Consensus size: 18
130391 AGCCCTAACT
130401 TAAACCTAAA-CTAAA-C
1 TAAACCTAAACCTAAACC
* *
130417 TAAACCCCAAACCCAAACC
1 TAAA-CCTAAACCTAAACC
* *
130436 CAAA-TTAAACCTAAA--
1 TAAACCTAAACCTAAACC
130451 TAGAACCTAAACCCTAAACC
1 TA-AACCTAAA-CCTAAACC
* *
130471 CAAACTTAAACCCTAAACC
1 TAAACCTAAA-CCTAAACC
*
130490 TAAACCTAAATCTAAACC
1 TAAACCTAAACCTAAACC
* *
130508 TAAACCTGAAACCAAAATC
1 TAAACCT-AAACCTAAACC
* *
130527 -GAACCTAAACCCAAACC
1 TAAACCTAAACCTAAACC
130544 TAAA-CTCAAACCCT-AACC
1 TAAACCT-AAA-CCTAAACC
* * *
130562 CAAACCTGAACCCAAAC
1 TAAACCTAAACCTAAAC
130579 TATTCAAAAC
Statistics
Matches: 124, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
15 1 0.01
16 6 0.05
17 30 0.24
18 46 0.37
19 40 0.32
20 1 0.01
ACGTcount: A:0.49, C:0.34, G:0.02, T:0.14
Consensus pattern (18 bp):
TAAACCTAAACCTAAACC
Found at i:130804 original size:2 final size:2
Alignment explanation
Indices: 130797--130821 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
130787 TATATGCTTG
130797 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
130822 AGGTTTATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:130858 original size:31 final size:31
Alignment explanation
Indices: 130823--131246 Score: 634
Period size: 31 Copynumber: 13.7 Consensus size: 31
130813 ATATATATAA
* *
130823 GGTTTATTATTGTTGATGTAAATGATATACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
*
130854 GGTTTATTGTTGTTGATGTAAATGATGTATT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
*
130885 GGTTTATTGTTGTTAATGTAAATGATGTACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
* *
130916 GGTTTATTTTTGTTGATGTAAATGATGTACC
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
*
130947 AGTTTATTGTTGTTGATGTAAATGATGTACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
* *
130978 GGTTTATTGCTGTTGATGTAAATGATGTACC
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
*
131009 GGTTTATTGCTGTTGATGTAAATGATGTACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
* * *
131040 GGTTTATTGCTATTGATGTAAATGATATACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
131071 GGTTTATTGTTGTTGATGTAAATGATGTACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
* *
131102 GGTTTATTGCTATTGATGTAAATGATGTACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
* *
131133 GGTTTATTGTTGTTGCTGTAAATGATATACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
** * *
131164 ATTTTATTGTTGTTGATGTAAATGATATATT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
*
131195 GGTTTATTGTTGTTGATGTAAATGATATACT
1 GGTTTATTGTTGTTGATGTAAATGATGTACT
*
131226 GGTTTATTGTTG-TAATGTAAA
1 GGTTTATTGTTGTTGATGTAAA
131247 CTAAACATGG
Statistics
Matches: 359, Mismatches: 34, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
30 8 0.02
31 351 0.98
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (31 bp):
GGTTTATTGTTGTTGATGTAAATGATGTACT
Found at i:133383 original size:13 final size:13
Alignment explanation
Indices: 133365--133394 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
133355 CCCTGAATTC
133365 ATTCGAATTAGAG
1 ATTCGAATTAGAG
*
133378 ATTCGAATTGGAG
1 ATTCGAATTAGAG
133391 ATTC
1 ATTC
133395 TATCTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (13 bp):
ATTCGAATTAGAG
Found at i:133571 original size:20 final size:20
Alignment explanation
Indices: 133542--133592 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
133532 TGCTTTATTA
* * *
133542 TGTTTTATATTGTTTGCTTC
1 TGTTTGATATTGCTTGCATC
133562 TGTTTGATATTGCTTGCATC
1 TGTTTGATATTGCTTGCATC
**
133582 TACTTGATATT
1 TGTTTGATATT
133593 TGTAAGGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.57
Consensus pattern (20 bp):
TGTTTGATATTGCTTGCATC
Found at i:133734 original size:23 final size:23
Alignment explanation
Indices: 133685--133741 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
133675 CTTAATGCAG
*
133685 GATGCTTGCTGAATCGATGCAAC
1 GATGCTTGCTGAATCGATACAAC
* * **
133708 GATGCTTGCTGAATTGGTACATT
1 GATGCTTGCTGAATCGATACAAC
133731 GATGCTTGCTG
1 GATGCTTGCTG
133742 GTTGTTGCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (23 bp):
GATGCTTGCTGAATCGATACAAC
Found at i:134540 original size:24 final size:23
Alignment explanation
Indices: 134479--134540 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
134469 TTTCAAAAAG
* * *
134479 TAATCATATTAATTTAATTATCA
1 TAATTATATTAATTTAAATAACA
* *
134502 TAAGTTTTATAAATTTAAAATAACA
1 TAA-TTATATTAATTT-AAATAACA
134527 TAATTATATTAATT
1 TAATTATATTAATT
134541 GTAACTTCAC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 3 0.10
24 18 0.60
25 9 0.30
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATTATATTAATTTAAATAACA
Found at i:135289 original size:30 final size:29
Alignment explanation
Indices: 135240--135302 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
135230 TCTGTGACTA
135240 GTGGTCTGATTGAACAAATTAAATAGTTAG
1 GTGGTCTGATTGAACAAATTAAA-AGTTAG
* * *
135270 GTGGTTTGATTG-ACAAAATTGAAAGTTCG
1 GTGGTCTGATTGAAC-AAATTAAAAGTTAG
135299 GTGG
1 GTGG
135303 AAAACGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (29 bp):
GTGGTCTGATTGAACAAATTAAAAGTTAG
Found at i:136531 original size:18 final size:18
Alignment explanation
Indices: 136508--136542 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
136498 TTTACCCGTT
136508 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
136526 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
136543 GGTATTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:136542 original size:13 final size:13
Alignment explanation
Indices: 136501--136531 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
136491 CGACCCGTTT
136501 ACCCGTTGACCCG
1 ACCCGTTGACCCG
136514 ACCCGTTGACCCG
1 ACCCGTTGACCCG
136527 ACCCG
1 ACCCG
136532 ACCCGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:136602 original size:29 final size:29
Alignment explanation
Indices: 136548--136682 Score: 132
Period size: 29 Copynumber: 4.8 Consensus size: 29
136538 TGACCGGTAT
*** *
136548 TATTCTGGGAATTAATTTGGGTTTGGTGT
1 TATTCTGGGAATTAATTTGAAATTGGTGC
136577 TATTCTGGGAATTAATTTGAAATTGGTGC
1 TATTCTGGGAATTAATTTGAAATTGGTGC
* * * ** *
136606 TATTTTGGTAATT--TTTCAAA-AAGTGA
1 TATTCTGGGAATTAATTTGAAATTGGTGC
*
136632 TATTCTGGGAATTAATTCGAAATTGGTGC
1 TATTCTGGGAATTAATTTGAAATTGGTGC
* *
136661 TATTTTGGGAATTAATTCGAAA
1 TATTCTGGGAATTAATTTGAAA
136683 AGGGTAATAT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
26 14 0.16
27 6 0.07
28 5 0.06
29 60 0.71
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (29 bp):
TATTCTGGGAATTAATTTGAAATTGGTGC
Found at i:136693 original size:29 final size:29
Alignment explanation
Indices: 136631--136703 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
136621 TCAAAAAGTG
* ** *
136631 ATATTCTGGGAATTAATTCGAAATTGGTG
1 ATATTTTGGGAATTAATTCGAAAAGGGTA
*
136660 CTATTTTGGGAATTAATTCGAAAAGGGTA
1 ATATTTTGGGAATTAATTCGAAAAGGGTA
*
136689 ATATTTTGGTAATTA
1 ATATTTTGGGAATTA
136704 TTTTAAAAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (29 bp):
ATATTTTGGGAATTAATTCGAAAAGGGTA
Found at i:136694 original size:84 final size:85
Alignment explanation
Indices: 136548--136720 Score: 213
Period size: 84 Copynumber: 2.0 Consensus size: 85
136538 TGACCGGTAT
* *** * * ** **
136548 TATTCTGGGAATTAATTTGGGTTTGGTGTTATTCTGGGAATTAATTTGAAATTGGTGCTATTTTG
1 TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTAATATTTTG
136613 GTAATT-TTTCAAAAAGTGA
66 GTAATTATTTCAAAAAGTGA
*
136632 TATTCTGGGAATTAATTCGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTAATATTTTG
1 TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTAATATTTTG
* * *
136697 GTAATTATTTTAAAAGGTGC
66 GTAATTATTTCAAAAAGTGA
136717 TATT
1 TATT
136721 TGTGTATAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 60 0.81
85 14 0.19
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (85 bp):
TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTAATATTTTG
GTAATTATTTCAAAAAGTGA
Found at i:136776 original size:10 final size:12
Alignment explanation
Indices: 136752--136783 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
136742 TATTGACCTC
136752 CTTTGACCAGAA
1 CTTTGACCAGAA
136764 CTTTGACC-G-A
1 CTTTGACCAGAA
136774 CTTTGACCAG
1 CTTTGACCAG
136784 CTATTAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (12 bp):
CTTTGACCAGAA
Found at i:143929 original size:29 final size:29
Alignment explanation
Indices: 143868--143942 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
143858 CCGTTGACCT
* ***
143868 GTGCTATTCTGGGAATTAATTCAGTTTTA
1 GTGCTATTATGGGAATTAATTCAGAAATA
143897 GTGCTATTATGGGAATTAATTC-GAAATA
1 GTGCTATTATGGGAATTAATTCAGAAATA
* *
143925 GGTGCTATTTTGGTAATT
1 -GTGCTATTATGGGAATT
143943 TTTTCAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 3 0.08
29 36 0.92
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.43
Consensus pattern (29 bp):
GTGCTATTATGGGAATTAATTCAGAAATA
Found at i:143998 original size:29 final size:29
Alignment explanation
Indices: 143925--143992 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 29
143915 ATTCGAAATA
143925 GGTGCTATTTTGGTAATTTTTTCAAAAAG
1 GGTGCTATTTTGGTAATTTTTTCAAAAAG
143954 GGTGCTATTTTGGTAATTATTTT-AAAAAG
1 GGTGCTATTTTGGTAATT-TTTTCAAAAAG
143983 GGTGCTATTT
1 GGTGCTATTT
143993 GTGTAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTTTTTCAAAAAG
Found at i:150842 original size:72 final size:72
Alignment explanation
Indices: 150721--150869 Score: 271
Period size: 72 Copynumber: 2.1 Consensus size: 72
150711 CGGAGAGATT
*
150721 GTTGTGTGAAAGATCTAGGCTTTCTACAACTCTCAAGTTTCCCATCGATGAAGGTATTTGACCGA
1 GTTGTGTGAAAGATCTAGGCTTTCTACAACTCTCAAGTTTCCCAACGATGAAGGTATTTGACCGA
150786 TCAGAAG
66 TCAGAAG
*
150793 GTTGTGTGAAAGATCTAGGCTTTCTACACCTCTCAAGTTTCCCAACGATGAAGGTATTTGACCGA
1 GTTGTGTGAAAGATCTAGGCTTTCTACAACTCTCAAGTTTCCCAACGATGAAGGTATTTGACCGA
*
150858 TGAGAAG
66 TCAGAAG
150865 GTTGT
1 GTTGT
150870 TCGACATGTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (72 bp):
GTTGTGTGAAAGATCTAGGCTTTCTACAACTCTCAAGTTTCCCAACGATGAAGGTATTTGACCGA
TCAGAAG
Found at i:155471 original size:45 final size:44
Alignment explanation
Indices: 155402--155499 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
155392 ATTTCAACGA
* *
155402 TATCGATACTGTCCAAGGAGTATCGATACTACTTTGTATAGTAG
1 TATCGATACTGTCCAAGGAGTATCGATACTACTGTGTAAAGTAG
*
155446 TATCGATA-TCGTCCCAATGAGTATCGATACTACTGTGTAAAGTAG
1 TATCGATACT-GT-CCAAGGAGTATCGATACTACTGTGTAAAGTAG
*
155491 TATCTATAC
1 TATCGATAC
155500 CGATCATGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 1 0.02
44 10 0.21
45 36 0.77
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (44 bp):
TATCGATACTGTCCAAGGAGTATCGATACTACTGTGTAAAGTAG
Found at i:157779 original size:2 final size:2
Alignment explanation
Indices: 157772--157796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
157762 AAAACAAAAG
157772 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
157797 TAAAACAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:157827 original size:19 final size:21
Alignment explanation
Indices: 157796--157834 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
157786 TATATATATA
157796 TTAAAACAAAATT-AATTTTT
1 TTAAAACAAAATTAAATTTTT
157816 TTAAAA-AAAATTAAATTTT
1 TTAAAACAAAATTAAATTTT
157835 GATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAACAAAATTAAATTTTT
Found at i:157845 original size:20 final size:21
Alignment explanation
Indices: 157822--157867 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
157812 TTTTTTAAAA
**
157822 AAAATTAAATTTTGATTTT-T
1 AAAATTAAATGATGATTTTGT
*
157842 AAAA-AAAATGATGATTTTGT
1 AAAATTAAATGATGATTTTGT
157862 AAAATT
1 AAAATT
157868 GGTTGTAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
AAAATTAAATGATGATTTTGT
Found at i:158359 original size:20 final size:21
Alignment explanation
Indices: 158320--158369 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
158310 GTATGAACAA
*
158320 TATCGATACTCATTCTAGTAG
1 TATCGATACTCATGCTAGTAG
158341 TATCGATACT-ATGCTAGTAG
1 TATCGATACTCATGCTAGTAG
*
158361 TATTGATAC
1 TATCGATAC
158370 CTAACAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (21 bp):
TATCGATACTCATGCTAGTAG
Found at i:161531 original size:129 final size:128
Alignment explanation
Indices: 161391--161624 Score: 310
Period size: 129 Copynumber: 1.8 Consensus size: 128
161381 TGACCGTTGG
* * *
161391 ATCCTTAGTGCATCGGTGCACTAAG-A-GTGCAACGATGCATTAAGTGCATTCGATGTTTCAAAA
1 ATCCTCAGTGCATCGGTGCA-T-AGTATGTGCAACGATGCATGAAATGCATTCGATG-TTCAAAA
161454 TAGCCAAAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAA
63 TAGCCAAAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAA
161519 A
128 A
* * ** *
161520 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAT
1 ATCCTCAGTGCATCGGTGCATAGTATGTGCAACGATGCATGAAATGCATTCGATGTTCAAAATAG
* ** * *
161585 TCATGGTGCATCGATGCATGGTTGGTGCATCGGTGCATCA
66 CCAAAGTGCATCGATGCATGGCTGGTGCATCGATGCATCA
161625 CTCTAAAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
127 1 0.01
128 44 0.49
129 45 0.50
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (128 bp):
ATCCTCAGTGCATCGGTGCATAGTATGTGCAACGATGCATGAAATGCATTCGATGTTCAAAATAG
CCAAAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA
Found at i:161550 original size:65 final size:64
Alignment explanation
Indices: 161391--161576 Score: 198
Period size: 65 Copynumber: 2.9 Consensus size: 64
161381 TGACCGTTGG
* * * * *
161391 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCAACGATGCATTAAGTGCATTCGATG-TTTCAAAA
1 ATCCTAAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
161454 T
64 T
* * * * *
161455 AGCCAAAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA
1 ATCCTAAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
161520 -
64 T
* *
161520 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTT
1 ATCCTAAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
161577 CAATTTATTC
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 42 0.42
65 53 0.53
66 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
ATCCTAAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:169850 original size:65 final size:65
Alignment explanation
Indices: 169717--169876 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
169707 TGCACTAAGA
* * * *
169717 GTGCATTGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAATGCATCGATGCATGGCTG
* * *
169781 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAATGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAATGCATCGATGCATGGCT
*
169844 AT
65 -G
* * *
169846 GTGCATCGATGTATAAAATGCATTCGTTGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
169877 CAATTTAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 28 0.34
65 51 0.62
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAATGCATCGATGCATGGCTG
Found at i:169912 original size:20 final size:20
Alignment explanation
Indices: 169889--169944 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
169879 ATTTAATTCA
169889 TGGTGCATCAATGCATGGAT
1 TGGTGCATCAATGCATGGAT
*
169909 TGGTGCATCGATGCATGGAT
1 TGGTGCATCAATGCATGGAT
*
169929 TGGTGCATCAGTGCAT
1 TGGTGCATCAATGCAT
169945 CACTCTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (20 bp):
TGGTGCATCAATGCATGGAT
Found at i:170772 original size:24 final size:24
Alignment explanation
Indices: 170740--170791 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
170730 AACTAGGAAA
170740 AAATTAGTCATGTTGAGTGAATCT
1 AAATTAGTCATGTTGAGTGAATCT
*
170764 AAATTAGTCATTTTGAGTGAATCT
1 AAATTAGTCATGTTGAGTGAATCT
170788 AAAT
1 AAAT
170792 GCACCATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (24 bp):
AAATTAGTCATGTTGAGTGAATCT
Found at i:173306 original size:35 final size:35
Alignment explanation
Indices: 173267--173338 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
173257 TGAATGGATG
* * *
173267 TTGGCTTGATTTGCTCAAACAATAAGTTTAATGCT
1 TTGGCTAGATTTGCTAAAACAATAAGTTTAAGGCT
*
173302 TTGGCTAGATTTGTTAAAACAATAAGTTTAAGGCT
1 TTGGCTAGATTTGCTAAAACAATAAGTTTAAGGCT
173337 TT
1 TT
173339 CTCTCTTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
TTGGCTAGATTTGCTAAAACAATAAGTTTAAGGCT
Found at i:174501 original size:17 final size:17
Alignment explanation
Indices: 174472--174504 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
174462 GTATTTATTT
174472 ATATAAAATATAATATA
1 ATATAAAATATAATATA
174489 ATATGAAAA-ATAATAT
1 ATAT-AAAATATAATAT
174505 TGTGATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:174606 original size:17 final size:17
Alignment explanation
Indices: 174575--174617 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
174565 CTCAAAATTA
*
174575 AATATTATTTTAAATAAT
1 AATATT-TTTAAAATAAT
*
174593 TATATTTTTAAAATAAT
1 AATATTTTTAAAATAAT
174610 AATATTTT
1 AATATTTT
174618 CACCTCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTTTTAAAATAAT
Found at i:182546 original size:81 final size:81
Alignment explanation
Indices: 182411--182573 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
182401 GATTTAAGTT
182411 AAAACATACCTTGTTAGATTGAATCAAATATCTTTAGTCAAAAGACGAAAATTGTTTGTCAAGAG
1 AAAACATACCTTGTTAGATTGAATCAAATATCTTTAGTCAAAAGACGAAAATTGTTTGTCAAGAG
182476 TAGAACAAGTTGAGAA
66 TAGAACAAGTTGAGAA
182492 AAAACATACCTTGTTAGATTGAATCAAATATCTTTAGTCAAAAGACGAAAATTGTTTGTCAAGAG
1 AAAACATACCTTGTTAGATTGAATCAAATATCTTTAGTCAAAAGACGAAAATTGTTTGTCAAGAG
182557 TAGAACAAGTTGAGAA
66 TAGAACAAGTTGAGAA
182573 A
1 A
182574 GAGGAAACTA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (81 bp):
AAAACATACCTTGTTAGATTGAATCAAATATCTTTAGTCAAAAGACGAAAATTGTTTGTCAAGAG
TAGAACAAGTTGAGAA
Found at i:193742 original size:115 final size:115
Alignment explanation
Indices: 193603--193836 Score: 416
Period size: 115 Copynumber: 2.0 Consensus size: 115
193593 TTTTTTTTGC
* * *
193603 TTTT-TAGTTCATATGCTAGGGAAGTTGAAAAACGTTTGGTTAATGTCAATTGCGGCAGCGCTTT
1 TTTTGTAGTTCATATACTAGGGAAGTTGAAAAAAGTTAGGTTAATGTCAATTGCGGCAGCGCTTT
*
193667 GGAGTTCTGGTTAGCTTGTAATGATTGGGAGTTCAATGATAAACAATTAT
66 GGAGTTCTGGTTAGCTTGTAATGATTGGGAGTTCAATGATAAACAAGTAT
*
193717 TTTTGTAGTTCATGTACTAGGGAAGTTGAAAAAAGTTAGGTTAATGTCAATTGCGGCAGCGCTTT
1 TTTTGTAGTTCATATACTAGGGAAGTTGAAAAAAGTTAGGTTAATGTCAATTGCGGCAGCGCTTT
193782 GGAGTTCTGGTTAGCTTGTAATGATTGGGAGTTCAATGATAAACAAGTAT
66 GGAGTTCTGGTTAGCTTGTAATGATTGGGAGTTCAATGATAAACAAGTAT
193832 TTTTG
1 TTTTG
193837 AACTACTTGG
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
114 4 0.04
115 110 0.96
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (115 bp):
TTTTGTAGTTCATATACTAGGGAAGTTGAAAAAAGTTAGGTTAATGTCAATTGCGGCAGCGCTTT
GGAGTTCTGGTTAGCTTGTAATGATTGGGAGTTCAATGATAAACAAGTAT
Found at i:196550 original size:95 final size:96
Alignment explanation
Indices: 196381--196582 Score: 229
Period size: 95 Copynumber: 2.1 Consensus size: 96
196371 ACCGAAGAGG
*
196381 TAGTATCGATACCATGATAAGGAGTATCGATACCAAGAAACATCGAATCAATTTTGGTATCGATA
1 TAGTATCGATACCATGATAAGGAGTATCGATACCAAGAAACATCGAACCAATTTTGGTATCGATA
*
196446 TCGATAGGGGGTATCAGA-ACCATAG-A-AGAA
66 CCGATAGGGGGTATC-GATACCATAGTATAG-A
* * * * ** *
196476 TAGTATCGATACCAT-ATTAAGG-GTGTCGATATCAGGCAACATCGAACCTGTTTTTGGTATTGA
1 TAGTATCGATACCATGA-TAAGGAGTATCGATACCAAGAAACATCGAACC-AATTTTGGTATCGA
196539 TACCCGA-AGGGGGTATCGATACCATAGTATAGA
64 TA-CCGATAGGGGGTATCGATACCATAGTATAGA
196572 -AGTATCGATAC
1 TAGTATCGATAC
196583 TAGGGTAGTA
Statistics
Matches: 92, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
94 24 0.26
95 61 0.66
96 5 0.05
97 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (96 bp):
TAGTATCGATACCATGATAAGGAGTATCGATACCAAGAAACATCGAACCAATTTTGGTATCGATA
CCGATAGGGGGTATCGATACCATAGTATAGA
Found at i:197081 original size:59 final size:59
Alignment explanation
Indices: 196905--197084 Score: 288
Period size: 59 Copynumber: 3.1 Consensus size: 59
196895 ATGTATAGTG
* * * *
196905 ATTTCCAGATAGAGCACTTCGTGTGCTAAAATGATAAGAAAATCATACTAAGTGTATGT
1 ATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
*
196964 ATTTCCAGATAGGACACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
* * *
197023 ATTTCCAGATAGGGCAGTTTGTGTGCTAAAATAATAAGGAAATCATACTAATTGTATGA
1 ATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
197082 ATT
1 ATT
197085 ACCTATTGAA
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 112 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (59 bp):
ATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
Found at i:201387 original size:45 final size:45
Alignment explanation
Indices: 201337--201426 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
201327 ACCAAGACAA
*
201337 CTCATTTCGTTCCAGTTCGAGTAGACTACTCAATGAATAAGTATG
1 CTCATTTCATTCCAGTTCGAGTAGACTACTCAATGAATAAGTATG
*
201382 CTCATTTCATTCCAGTTTGAGTAGACTACTCAATGAATAAGTATG
1 CTCATTTCATTCCAGTTCGAGTAGACTACTCAATGAATAAGTATG
201427 TTGAGATGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (45 bp):
CTCATTTCATTCCAGTTCGAGTAGACTACTCAATGAATAAGTATG
Found at i:205122 original size:21 final size:22
Alignment explanation
Indices: 205081--205121 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
205071 ATTTTTTTCT
*
205081 TTTTCACATTTTTGTTGTTTTA
1 TTTTCACATTTTTATTGTTTTA
205103 TTTTC-CATTTTTA-TGTTTT
1 TTTTCACATTTTTATTGTTTT
205122 TTTCTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTCACATTTTTATTGTTTTA
Found at i:205124 original size:23 final size:23
Alignment explanation
Indices: 205067--205125 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
205057 TCGAAATGCA
*
205067 TTTGATTTTTTTCTTTTTCACATT
1 TTTG-TTTTTTTCATTTTCACATT
*
205091 TTTGTTGTTTT-ATTTTC-CATTT
1 TTTGTTTTTTTCATTTTCACA-TT
205113 TTATGTTTTTTTC
1 TT-TGTTTTTTTC
205126 TCTTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.07
22 9 0.31
23 14 0.48
24 4 0.14
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (23 bp):
TTTGTTTTTTTCATTTTCACATT
Found at i:210972 original size:20 final size:21
Alignment explanation
Indices: 210947--210987 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
210937 ATTTTATTAT
**
210947 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
210967 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
210988 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:211716 original size:16 final size:15
Alignment explanation
Indices: 211695--211730 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
211685 CCTCGGTAAG
*
211695 TCTTTCTCTTCCTTTT
1 TCTTTCTCTT-CTGTT
211711 TCTTTCTCTTCTGTT
1 TCTTTCTCTTCTGTT
211726 TCTTT
1 TCTTT
211731 GCTACTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TCTTTCTCTTCTGTT
Found at i:212293 original size:3 final size:3
Alignment explanation
Indices: 212285--212355 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
212275 TAATATATTT
*
212285 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
212333 TAA TAA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
212356 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:213060 original size:113 final size:113
Alignment explanation
Indices: 212491--213338 Score: 1184
Period size: 113 Copynumber: 7.5 Consensus size: 113
212481 ATTGAATAAA
* * ** *
212491 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATGATCCATC
* * * * *
212555 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* * * *
212604 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCC
* * * * *
212668 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* *
212720 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGGTAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* ** *
212785 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* * *
212834 TTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACCTTTTCTTGGAAAAGATAATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC-TGGAAAAGATGATCCATC
* * *
212899 AAGTGATGAATTCATGTAACAGGTTGAACAAATTCTTCTCATTATGAAT
65 AAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
*
212948 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* * *
213013 AGTGATAAATTCAGGTAACAGGTTGAACAAATTCTTCTCATTATGAAT
66 AGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
*
213061 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
*
213126 AGTGATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAAT
66 AGTGAT-GAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
* * * *
213174 TTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAACCTTCTCTTGAAATG-TCAGTCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGA-TCCATC
*
213238 AAGTGATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAAT
65 AAGTGAT-GAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
*
213287 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTTGAAA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
213339 TGTCAATCCA
Statistics
Matches: 684, Mismatches: 41, Indels: 20
0.92 0.06 0.03
Matches are distributed among these distances:
112 5 0.01
113 367 0.54
114 186 0.27
115 19 0.03
116 85 0.12
117 20 0.03
118 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
AGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
Found at i:214145 original size:83 final size:84
Alignment explanation
Indices: 214006--214232 Score: 386
Period size: 83 Copynumber: 2.7 Consensus size: 84
213996 GTAGTTCTTA
*
214006 CCAAACCAGATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
214071 ATTCAATGATTGGTTCTG-
66 ATTCAATGATTGGTTCTGT
* * * * *
214089 CCAAACCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
214154 ATTCAATGATTGGTTCTGT
66 ATTCAATGATTGGTTCTGT
214173 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTT
214233 TCAGTTAATG
Statistics
Matches: 133, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
83 131 0.98
84 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
ATTCAATGATTGGTTCTGT
Found at i:215041 original size:16 final size:19
Alignment explanation
Indices: 214996--215035 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
214986 CATATAAAAG
*
214996 AATAAATTGAATTTCCAAT
1 AATAAATTGAATCTCCAAT
*
215015 AATAAATTGAATCTCAAAT
1 AATAAATTGAATCTCCAAT
215034 AA
1 AA
215036 ATTGAACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
AATAAATTGAATCTCCAAT
Found at i:215050 original size:16 final size:16
Alignment explanation
Indices: 214996--215041 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
214986 CATATAAAAG
*
214996 AATAAATTGAATTTCCAA
1 AATAAATTGAATCT-C-A
215014 TAATAAATTGAATCTCA
1 -AATAAATTGAATCTCA
215031 AATAAATTGAA
1 AATAAATTGAA
215042 CTTGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 1 0.04
19 13 0.50
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (16 bp):
AATAAATTGAATCTCA
Found at i:215397 original size:11 final size:11
Alignment explanation
Indices: 215369--215400 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
215359 TTGACCCCTC
215369 TTTTTTCTCTTT
1 TTTTTTCT-TTT
215381 TTTTTTCTTTT
1 TTTTTTCTTTT
215392 TTTTTTCTT
1 TTTTTTCTT
215401 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:226001 original size:13 final size:15
Alignment explanation
Indices: 225979--226015 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
225969 TTTGACAGAA
225979 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
225991 AAATAAAATACTTGC
1 AAATAAAATACTTGC
226006 AAATAAAATA
1 AAATAAAATA
226016 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:226043 original size:9 final size:9
Alignment explanation
Indices: 226012--226062 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
226002 TTGCAAATAA
226012 AATAAAACAT
1 AATAAAA-AT
*
226022 -ATAAATAT
1 AATAAAAAT
*
226030 TATAAAAAT
1 AATAAAAAT
226039 AATAAAAA-
1 AATAAAAAT
226047 AATAAAAA-
1 AATAAAAAT
226055 AATAAAAA
1 AATAAAAA
226063 AATTTGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 18 0.49
9 19 0.51
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (9 bp):
AATAAAAAT
Found at i:226063 original size:9 final size:8
Alignment explanation
Indices: 226031--226065 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
226021 TATAAATATT
226031 ATAAAAATA
1 ATAAAAA-A
226040 ATAAAAAA
1 ATAAAAAA
226048 ATAAAAAA
1 ATAAAAAA
226056 ATAAAAAA
1 ATAAAAAA
226064 AT
1 AT
226066 TTGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:226779 original size:20 final size:21
Alignment explanation
Indices: 226756--226796 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
226746 TATTATATAT
**
226756 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
226776 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
226797 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:227640 original size:16 final size:15
Alignment explanation
Indices: 227619--227654 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
227609 CCTCGGTAAG
*
227619 TCTTTCTCTTCCTTTT
1 TCTTTCTCTT-CTGTT
227635 TCTTTCTCTTCTGTT
1 TCTTTCTCTTCTGTT
227650 TCTTT
1 TCTTT
227655 GCTACTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TCTTTCTCTTCTGTT
Found at i:228209 original size:11 final size:11
Alignment explanation
Indices: 228186--228217 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
228176 TGTAATTAAT
228186 TATTTATATATA
1 TATTTA-ATATA
228198 TATTTAATATA
1 TATTTAATATA
228209 TATTTAATA
1 TATTTAATA
228218 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:228221 original size:3 final size:3
Alignment explanation
Indices: 228213--228295 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
228203 AATATATATT
228213 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
228261 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
228296 TGGATAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:232076 original size:22 final size:20
Alignment explanation
Indices: 232035--232088 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
232025 CCGGTAGAGC
* *
232035 GTATCGGTACCATATAAAGG
1 GTATCGATACCATAGAAAGG
*
232055 TAGTATCGATACCATAGCAAGG
1 --GTATCGATACCATAGAAAGG
232077 GTATCGATACCA
1 GTATCGATACCA
232089 GGCAACATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 12 0.41
22 17 0.59
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (20 bp):
GTATCGATACCATAGAAAGG
Found at i:232134 original size:95 final size:96
Alignment explanation
Indices: 231956--232143 Score: 247
Period size: 95 Copynumber: 2.0 Consensus size: 96
231946 GATACTGAAG
*
231956 AGGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATC
1 AGGTAGTATCGATACCATGACAAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATC
* * *
232021 GATACCGGTAGAGCGTATCGGTACCATATAA
66 GATACCGGAAGAGAGTATCGATACCATATAA
* * *
232052 AGGTAGTATCGATACCAT-AGCAA-GGGTATCGATACCAGGCAACATCGAA-CTTATTTTTGGTA
1 AGGTAGTATCGATACCATGA-CAAGGGGTATCGATACCAAGAAACATCGAATC-TAATTTTGGTA
* * *
232114 TTGATACCTGAAGGGAGTATCGATACCATA
64 TCGATACCGGAAGAGAGTATCGATACCATA
232144 GTATAGAAGT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
94 1 0.01
95 59 0.74
96 20 0.25
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (96 bp):
AGGTAGTATCGATACCATGACAAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATC
GATACCGGAAGAGAGTATCGATACCATATAA
Found at i:232582 original size:59 final size:59
Alignment explanation
Indices: 232517--233039 Score: 750
Period size: 59 Copynumber: 8.9 Consensus size: 59
232507 TGATTTCTAT
* * *
232517 ATAGGGCATTTCCTGTGCTAAAATGATAAGGAAATCATACTTAGTGTATGAATTTCTAG
1 ATAGGGCATTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
*
232576 ATAGGGCACTTT-GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATAAATTTCCAG
1 ATAGGGCA-TTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
* *
232635 ATAGGGAACTTT-GTGTGCTAAAAT-ATAAGGAAATCATACTAAGTGTATGAATTTCTAG
1 ATAGGGCA-TTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
* * * *
232693 ATAGGGCACTCCGTGTTCTAAAATGATAAGGAAATCATACCAAGTGTATGAATTTCCAG
1 ATAGGGCATTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
* * * *
232752 ATAGGGCACTTCGTGTGCTAAAATGATAAGGAACTCATACTAGGTGTTTGAATTTCCAG
1 ATAGGGCATTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
* * * * * *
232811 ATAGGGAACTTCGTGTGCTAAAATTATAAAGAACTAATACTAAGTGTATGAATTTCCAG
1 ATAGGGCATTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
232870 ATAGGGCACTTT-GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
1 ATAGGGCA-TTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
* * *
232929 ATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCACACTATGTGTATGAATTTCCAG
1 ATAGGGCATTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
* *
232988 ATAGGGCACTTT-GTGTGCTAAAATGATAAGTAAATCATACTAATTGTATGAA
1 ATAGGGCA-TTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAA
233040 ATACCTATTG
Statistics
Matches: 419, Mismatches: 39, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
57 1 0.00
58 52 0.12
59 359 0.86
60 7 0.02
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (59 bp):
ATAGGGCATTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAG
Found at i:240773 original size:17 final size:17
Alignment explanation
Indices: 240732--240776 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
240722 TCCTATTTGA
240732 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
240749 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
240766 TTAAATATTTA
1 TTAAATATTTA
240777 TTTGTACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:242545 original size:46 final size:46
Alignment explanation
Indices: 242469--242594 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 46
242459 CTATAAAGTC
* * *
242469 TCAACATTCCCAATGATTTCCAAACTTCTAAACAGCAGCTTGAGGA
1 TCAACATTCCCCATGCTTTCCAACCTTCTAAACAGCAGCTTGAGGA
* * * * *
242515 TCAATATTCCCCATGCTTTTCAACCTTCTAAATAGTAGTTTGAGGA
1 TCAACATTCCCCATGCTTTCCAACCTTCTAAACAGCAGCTTGAGGA
* *
242561 CCAACATTCCCCATGCTCTCCAACCTTCTAAACA
1 TCAACATTCCCCATGCTTTCCAACCTTCTAAACA
242595 ACTGAGAGAC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (46 bp):
TCAACATTCCCCATGCTTTCCAACCTTCTAAACAGCAGCTTGAGGA
Found at i:254234 original size:42 final size:42
Alignment explanation
Indices: 254148--254242 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
254138 GGATAGCCCA
* * * *
254148 AAGGACTT-ATCATCTTGCTCAAAAGACTTATAGGTGACCTG
1 AAGGACTTAAGCATCATGCTCAAAAGACTTATAGATGACCCG
* *
254189 AAGGATTTAAGCATCATGCTCAAAAGACTTACT-GATGGCCCG
1 AAGGACTTAAGCATCATGCTCAAAAGACTTA-TAGATGACCCG
254231 AAGGACTTAAGC
1 AAGGACTTAAGC
254243 TGATTCAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 7 0.16
42 37 0.82
43 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
AAGGACTTAAGCATCATGCTCAAAAGACTTATAGATGACCCG
Found at i:254369 original size:61 final size:60
Alignment explanation
Indices: 254250--254401 Score: 180
Period size: 61 Copynumber: 2.5 Consensus size: 60
254240 AGCTGATTCA
**
254250 AAGTGTTGTGAATCGAGCCATGGGAAATGTTAACCCCCTCTGGAGGGGCATTACTGATTTG
1 AAGTGTTGTGAATCGAG-CAAAGGAAATGTTAACCCCCTCTGGAGGGGCATTACTGATTTG
* * * **
254311 AAGTGTTGTGAATCGAGCAAAGGAAATTTTAA-CCCCTCTGGTGGTGCATTTTGTTGATTTG
1 AAGTGTTGTGAATCGAGCAAAGGAAATGTTAACCCCCTCTGGAGGGGCA--TTACTGATTTG
* * *
254372 AAATGTCGTGAATCGAGCAAAGAAAATGTT
1 AAGTGTTGTGAATCGAGCAAAGGAAATGTT
254402 GAAAACATCC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 14 0.18
60 12 0.15
61 52 0.67
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (60 bp):
AAGTGTTGTGAATCGAGCAAAGGAAATGTTAACCCCCTCTGGAGGGGCATTACTGATTTG
Found at i:254658 original size:52 final size:52
Alignment explanation
Indices: 254589--254785 Score: 241
Period size: 52 Copynumber: 3.7 Consensus size: 52
254579 TTTTAGTTAT
*
254589 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTCAAAAA
* * * * * *
254641 CATCAATAAATCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATCAT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAG--T-TTCTAAAAACTCATT-CAAA--AA
* * * *
254699 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTTATTCGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTCAAAAA
254751 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
254786 TTTAGAAATT
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
52 62 0.51
54 3 0.02
55 25 0.21
56 4 0.03
58 27 0.22
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.29
Consensus pattern (52 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTCAAAAA
Found at i:254725 original size:110 final size:110
Alignment explanation
Indices: 254587--254795 Score: 337
Period size: 110 Copynumber: 1.9 Consensus size: 110
254577 CGTTTTAGTT
* * * *
254587 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAACATCAATAAAT
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAACTCATTCAAAAACATCAAGAAAC
254652 CCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
66 CCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * *
254697 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTTATTCGAAAACATCAAGAAAC
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAACTCATTCAAAAACATCAAGAAAC
* *
254762 CCCTAAAAATTAGGCTTAGTTTCTTTTAGAAATT
66 CCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATT
254796 ATTTTGAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 90 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (110 bp):
ATCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTAAAAACTCATTCAAAAACATCAAGAAAC
CCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
Found at i:256728 original size:4 final size:4
Alignment explanation
Indices: 256719--256766 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
256709 TTGGATCTAT
*
256719 TTTC TTTC -TTC TTTC TTTC GTTTC TTT- TTTT TTTC TTT- TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC
256764 TTT
1 TTT
256767 TTATGTGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
3 12 0.31
4 23 0.59
5 4 0.10
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:256744 original size:20 final size:20
Alignment explanation
Indices: 256719--256756 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
256709 TTGGATCTAT
256719 TTTCTTTCTTCTTTCTTTCG
1 TTTCTTTCTTCTTTCTTTCG
* *
256739 TTTCTTTTTTTTTTCTTT
1 TTTCTTTCTTCTTTCTTT
256757 TTTTTTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTCTTTCTTCTTTCTTTCG
Found at i:256768 original size:11 final size:11
Alignment explanation
Indices: 256739--256768 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
256729 CTTTCTTTCG
256739 TTTCTTTTTTT
1 TTTCTTTTTTT
256750 TTTC-TTTTTT
1 TTTCTTTTTTT
256760 TTTCTTTTT
1 TTTCTTTTT
256769 ATGTGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:257045 original size:2 final size:2
Alignment explanation
Indices: 257038--257091 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
257028 GGGACAACAA
257038 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
257080 AT AT AT AT AT AT
1 AT AT AT AT AT AT
257092 GCAAGGATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258468 original size:21 final size:21
Alignment explanation
Indices: 258442--258506 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
258432 GAATGACCAC
258442 TATGTCCCGAAGGACCACTGA
1 TATGTCCCGAAGGACCACTGA
258463 TATGTCCCGAAGGACCACTGA
1 TATGTCCCGAAGGACCACTGA
258484 TATGTCCCGAAGGACCACTGA
1 TATGTCCCGAAGGACCACTGA
258505 TA
1 TA
258507 ATCCCTTGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (21 bp):
TATGTCCCGAAGGACCACTGA
Found at i:259978 original size:24 final size:20
Alignment explanation
Indices: 259922--259979 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
259912 TTTCCTTTGA
*
259922 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
259942 AGTTCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
259965 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
259980 CTAATTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:261420 original size:18 final size:18
Alignment explanation
Indices: 261394--261479 Score: 118
Period size: 18 Copynumber: 4.7 Consensus size: 18
261384 TGAATATTTT
*
261394 TCCCTAAGGACCACTATG
1 TCCCGAAGGACCACTATG
261412 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
261430 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACT-A-TG
* *
261450 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
*
261468 TCTCGAAGGACC
1 TCCCGAAGGACC
261480 CCTGATAGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
18 43 0.72
19 2 0.03
20 15 0.25
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:261463 original size:38 final size:38
Alignment explanation
Indices: 261394--261491 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
261384 TGAATATTTT
* *
261394 TCCCTAAGGACCACT-A-TGTCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTGATTGTCCCGAAGAACCACTATG
*
261430 TCCCGAAGGACCACTGATTGTTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTGATTGTCCCGAAGAACCACTATG
* * *
261468 TCTCGAAGGACCCCTGATAGTCCC
1 TCCCGAAGGACCACTGATTGTCCC
261492 TCAACTCTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 14 0.26
37 1 0.02
38 38 0.72
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (38 bp):
TCCCGAAGGACCACTGATTGTCCCGAAGAACCACTATG
Found at i:268234 original size:18 final size:18
Alignment explanation
Indices: 268211--268283 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
268201 ACTGAATATT
268211 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
268229 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
268248 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
268267 TGTCCCAAAGGACCACT
1 TGTCCCGAAGGACCACT
268284 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:268258 original size:38 final size:38
Alignment explanation
Indices: 268210--268286 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
268200 CACTGAATAT
* *
268210 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
*
268248 TTGTTCCGAAGAACCACTATGTCCCAAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
268286 T
1 T
268287 AATCCCTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
Found at i:273625 original size:22 final size:24
Alignment explanation
Indices: 273579--273625 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
273569 AAGACCAGAC
*
273579 AAAAGGAAATCAATGTTAGTAGAA
1 AAAAGGAAATCAATGTCAGTAGAA
*
273603 AAAAGG-AATCAA-GTCAGTTGAA
1 AAAAGGAAATCAATGTCAGTAGAA
273625 A
1 A
273626 TAATTAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (24 bp):
AAAAGGAAATCAATGTCAGTAGAA
Found at i:273643 original size:16 final size:16
Alignment explanation
Indices: 273622--273658 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
273612 CAAGTCAGTT
273622 GAAATAATTAGTCAAA
1 GAAATAATTAGTCAAA
273638 GAAATAATTAGTCAAA
1 GAAATAATTAGTCAAA
273654 GAAAT
1 GAAAT
273659 GTATCTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (16 bp):
GAAATAATTAGTCAAA
Found at i:274545 original size:17 final size:17
Alignment explanation
Indices: 274482--274546 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
274472 AACTTAATTT
274482 AAAA-AAAATAAAACAA
1 AAAATAAAATAAAACAA
*
274498 TAAAT-AAATAAAAACAGA
1 AAAATAAAAT-AAAACA-A
*
274516 AAAA-ACAACATAAAATAA
1 AAAATA-AA-ATAAAACAA
274534 AAAATAAAATAAA
1 AAAATAAAATAAA
274547 CCTAAATATC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
16 7 0.18
17 11 0.28
18 11 0.28
19 8 0.21
20 2 0.05
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (17 bp):
AAAATAAAATAAAACAA
Found at i:284413 original size:22 final size:24
Alignment explanation
Indices: 284367--284413 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
284357 AAGACCAGAC
*
284367 AAAAGGAAATCAATGTTAGTAGAA
1 AAAAGGAAATCAATGTCAGTAGAA
*
284391 AAAAGG-AATCAA-GTCAGTTGAA
1 AAAAGGAAATCAATGTCAGTAGAA
284413 A
1 A
284414 TAATTAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (24 bp):
AAAAGGAAATCAATGTCAGTAGAA
Found at i:285280 original size:17 final size:17
Alignment explanation
Indices: 285253--285320 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
285243 AACTTAATTT
285253 AAAAAATAAAAAA-AAA
1 AAAAAATAAAAAACAAA
*
285269 AAAAAATGAAAAACAAA
1 AAAAAATAAAAAACAAA
* * *
285286 AAAACAGAAAAAACAAC
1 AAAAAATAAAAAACAAA
* *
285303 ATAAAATAAAAAATAAA
1 AAAAAATAAAAAACAAA
285320 A
1 A
285321 TAAACCTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 12 0.29
17 29 0.71
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.07
Consensus pattern (17 bp):
AAAAAATAAAAAACAAA
Found at i:285321 original size:12 final size:12
Alignment explanation
Indices: 285252--285324 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
285242 AAACTTAATT
285252 TAAAAAATAAAA
1 TAAAAAATAAAA
*
285264 -AAAAAAAAAAA
1 TAAAAAATAAAA
* *
285275 TGAAAAACAAAA
1 TAAAAAATAAAA
*
285287 -AAACAGA-AAAA
1 TAAA-AAATAAAA
* *
285298 -ACAACATAAAA
1 TAAAAAATAAAA
285309 TAAAAAATAAAA
1 TAAAAAATAAAA
285321 TAAA
1 TAAA
285325 CCTAAATGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 2 0.04
11 22 0.46
12 24 0.50
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:285934 original size:8 final size:8
Alignment explanation
Indices: 285921--285945 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
285911 TTCAAGAAAC
285921 AAAAACAA
1 AAAAACAA
285929 AAAAACAA
1 AAAAACAA
285937 AAAAACAA
1 AAAAACAA
285945 A
1 A
285946 GAAAGACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:287349 original size:16 final size:18
Alignment explanation
Indices: 287328--287366 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
287318 ATCTTAATTA
287328 TTAAA-TTATTTT-TCTT
1 TTAAATTTATTTTATCTT
*
287344 TTAAATTTTTTTTATCTT
1 TTAAATTTATTTTATCTT
287362 TTAAA
1 TTAAA
287367 CTAATACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAAATTTATTTTATCTT
Found at i:296110 original size:131 final size:131
Alignment explanation
Indices: 295964--296284 Score: 452
Period size: 134 Copynumber: 2.4 Consensus size: 131
295954 TAAATGAACA
* *
295964 AATAAGTAAATAAATAAACAATGGTTAGAATGAAATAAAATAAGAGTCAGTAGTTAGCAGAG-TC
1 AATAAATAAATAAATAAACAATGGTTAGAATGAAATAAAATAAAAGTCAGTAGTTAGCAGAGAT-
* * *
296028 CGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGCCAAATCGAATATTGGAA
65 CAAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGCCAAATCGAATAATAGAA
296093 AC
130 AC
* * * *
296095 AATAAATACATAAATAAATAACAATGATTA-AAGTGCAATAAAATAAAAGTTAGTAGTTAGCAGA
1 AATAAATAAATAAAT--A-AACAATGGTTAGAA-TGAAATAAAATAAAAGTCAGTAGTTAGCAGA
*
296159 GATCAAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGCTAAATCGAATAATA
62 GATCAAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGCCAAATCGAATAATA
296224 GAAAC
127 GAAAC
*
296229 AATAAATAAATTAAA-AAACAATGGTTAGAAT-ATAATAAAATAAAAATCAGTAGTTA
1 AATAAATAAA-TAAATAAACAATGGTTAGAATGA-AATAAAATAAAAGTCAGTAGTTA
296285 ATATGCAGTA
Statistics
Matches: 167, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
131 45 0.27
132 3 0.02
133 3 0.02
134 111 0.66
135 5 0.03
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.21
Consensus pattern (131 bp):
AATAAATAAATAAATAAACAATGGTTAGAATGAAATAAAATAAAAGTCAGTAGTTAGCAGAGATC
AAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCACAAGGCCAAATCGAATAATAGAAA
C
Found at i:296284 original size:29 final size:28
Alignment explanation
Indices: 296229--296284 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
296219 TAATAGAAAC
* *
296229 AATAAATAAATTAAAAAACAATGGTTAG
1 AATAAATAAAATAAAAAACAATAGTTAG
* *
296257 AATATAATAAAATAAAAATCAGTAGTTA
1 AATA-AATAAAATAAAAAACAATAGTTA
296285 ATATGCAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.27
Consensus pattern (28 bp):
AATAAATAAAATAAAAAACAATAGTTAG
Found at i:297492 original size:91 final size:91
Alignment explanation
Indices: 297368--297989 Score: 969
Period size: 91 Copynumber: 6.8 Consensus size: 91
297358 GATGGAATCA
* * *
297368 CCAAGGTTGAACAAGTTCTTCTCATTGTAAACTTCTTCTCCCTC-TTCGGATAAGTTCTTCTCAT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTT-GGATGAGTTCTTCTCAT
*
297432 TATGAACTCTCCATTGGAAATGTTGAT
65 TATGAACTCTCCACTGGAAATGTTGAT
* * * * *
297459 CCAATGTCGAACAAGTTCTTCTCAATATGAACTTCCTCTCCCTCGTTGAATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
* *
297524 ATGAACTCTCTATTGGAAATGTTGAT
66 ATGAACTCTCCACTGGAAATGTTGAT
* * *
297550 CCCAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
*
297615 ATGAACTCTCCACTGGAAACGTTGATT
66 ATGAACTCTCCACTGGAAATGTTGA-T
* *
297642 CC-AGGTTGAATAAGTTCTTCTCATTATTAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
*
297706 ATGAACTCTCCACTGGAAATGTTGAG
66 ATGAACTCTCCACTGGAAATGTTGAT
* * *
297732 CCAAGGTTGAACAAGTTCTTATGATTATGAACTTCTTCTCGCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
297797 ATGAACTCTCCACTGGAAATGTTGAT
66 ATGAACTCTCCACTGGAAATGTTGAT
*
297823 CCAAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
* *
297888 GTGAACTCTCCACTGGAAATGTTGAG
66 ATGAACTCTCCACTGGAAATGTTGAT
* * *
297914 CCAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGAAGAGTTCTTCTTATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
297979 ATGAACTCTCC
66 ATGAACTCTCC
297990 CCCTCAAGCG
Statistics
Matches: 485, Mismatches: 43, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
90 2 0.00
91 478 0.99
92 5 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (91 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATT
ATGAACTCTCCACTGGAAATGTTGAT
Found at i:299209 original size:21 final size:21
Alignment explanation
Indices: 299163--299214 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
299153 AAGGTATATT
* *
299163 TTATTATATTTAATATTTTTA
1 TTATTTTATTTAATATTTGTA
*
299184 GTATTTTATTTAAT-TATTGTA
1 TTATTTTATTTAATAT-TTGTA
299205 TTA-TTTATTT
1 TTATTTTATTT
299215 TTTATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATTTTATTTAATATTTGTA
Found at i:299225 original size:8 final size:8
Alignment explanation
Indices: 299159--299228 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
299149 TTATAAGGTA
299159 TATTTTAT
1 TATTTTAT
*
299167 TATATTTAA
1 TAT-TTTAT
299176 TA-TTT-T
1 TATTTTAT
*
299182 TAGTATT-T
1 TA-TTTTAT
*
299190 TATTTAAT
1 TATTTTAT
*
299198 TATTGTAT
1 TATTTTAT
299206 TA-TTTAT
1 TATTTTAT
299213 T-TTTTAT
1 TATTTTAT
299220 TATTTTAT
1 TATTTTAT
299228 T
1 T
299229 TAAATAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
6 2 0.04
7 16 0.33
8 24 0.50
9 6 0.12
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (8 bp):
TATTTTAT
Found at i:301030 original size:42 final size:41
Alignment explanation
Indices: 300917--301030 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
300907 GTCCGAAGGT
* **
300917 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCACGCTCGAAAGA
* * * *
300958 CTTATAGATGACCCAAAGGATTTAAGCATCACGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCACGCTCGAAAGA
301000 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
301031 AGAAACCCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
41 20 0.34
42 38 0.64
43 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCACGCTCGAAAGA
Found at i:301218 original size:55 final size:58
Alignment explanation
Indices: 301067--301218 Score: 142
Period size: 60 Copynumber: 2.7 Consensus size: 58
301057 TTCTTAGTTG
* * * *
301067 TCAAGGAAA-CCCTAAAAATTAGGCTTAACTTCCTTTTAAAAAATTCATTGAAAATCATCA
1 TCAA-GAAACCCCTAAAAATTAGGCTT-AGTTTCTTTTTAAAAACTCATTGAAAA-CATCA
* * *
301127 TCAAGAAACCCCTGAAAATCAGACTTAGTTTC----TAAAAACTCATTTG-AAA-A-CA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTTAAAAACTCA-TTGAAAACATCA
301179 TCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTTAAAA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTTAAAA
301219 TTTGCTTTGA
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
51 16 0.21
52 15 0.19
53 1 0.01
55 16 0.21
56 3 0.04
59 8 0.10
60 18 0.23
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (58 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTTAAAAACTCATTGAAAACATCA
Found at i:302536 original size:28 final size:29
Alignment explanation
Indices: 302495--302549 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
302485 TTAGGATGAC
302495 TTTGGGAAGGTAATGTGTTTCAGGTTAAT
1 TTTGGGAAGGTAATGTGTTTCAGGTTAAT
302524 TTTGGG-AGGTAATGTGTTTCAGGTTA
1 TTTGGGAAGGTAATGTGTTTCAGGTTA
302550 GCTCCTTGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.42
Consensus pattern (29 bp):
TTTGGGAAGGTAATGTGTTTCAGGTTAAT
Found at i:303212 original size:9 final size:9
Alignment explanation
Indices: 303185--303379 Score: 83
Period size: 9 Copynumber: 20.8 Consensus size: 9
303175 GATCTGTCTA
303185 TTTTCTTCTT
1 TTTTCTT-TT
**
303195 TTTGGTTTT
1 TTTTCTTTT
303204 TTTTCTTTT
1 TTTTCTTTT
303213 TTTCCTCTTTT
1 TTT--TCTTTT
*
303224 TCTTCTATTT
1 TTTTCT-TTT
*
303234 TTTCCTTTT
1 TTTTCTTTT
303243 TTTCTCTTTT
1 TTT-TCTTTT
*
303253 TCTTCTATTT
1 TTTTCT-TTT
*
303263 TTTCCTTTCT
1 TTTTCTTT-T
*
303273 TTTCTCTCTCT
1 TTT-TCT-TTT
* *
303284 TTCTCTATT
1 TTTTCTTTT
* **
303293 CTTT-TTCC
1 TTTTCTTTT
*
303301 TTTTC-CTT
1 TTTTCTTTT
**
303309 TTTTCGCTT
1 TTTTCTTTT
303318 TTTTCTTTT
1 TTTTCTTTT
303327 TTTTC--TT
1 TTTTCTTTT
303334 TTTTCTTTT
1 TTTTCTTTT
* *
303343 TTGATATTTT
1 TT-TTCTTTT
*
303353 TTATCTTTT
1 TTTTCTTTT
*
303362 TTTGCTATATT
1 TTTTCT-T-TT
303373 TTTTCTT
1 TTTTCTT
303380 CTTTCTCTCT
Statistics
Matches: 137, Mismatches: 33, Indels: 30
0.69 0.17 0.15
Matches are distributed among these distances:
7 7 0.05
8 9 0.07
9 58 0.42
10 42 0.31
11 20 0.15
12 1 0.01
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:303234 original size:21 final size:20
Alignment explanation
Indices: 303200--303301 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 20
303190 TTCTTTTTGG
*
303200 TTTTTTTTCTTTTTTTCCTC
1 TTTTTCTTCTTTTTTTCCTC
*
303220 TTTTTCTTCTATTTTTTCCTT
1 TTTTTCTTCT-TTTTTTCCTC
*
303241 TTTTTC-TCTTTTTCTT-CTA
1 TTTTTCTTCTTTTT-TTCCTC
*
303260 TTTTT-TCCTTTCTTTTCTCTC
1 TTTTTCTTCTTT-TTTTC-CTC
* *
303281 TCTTTCTCTATTCTTTTTCCT
1 TTTTTCT-TCTT-TTTTTCCT
303302 TTTCCTTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
19 17 0.26
20 16 0.25
21 21 0.32
22 3 0.05
23 7 0.11
24 1 0.02
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCTTCTTTTTTTCCTC
Found at i:303298 original size:34 final size:29
Alignment explanation
Indices: 303201--303304 Score: 138
Period size: 29 Copynumber: 3.4 Consensus size: 29
303191 TCTTTTTGGT
*
303201 TTTTTTTCTTTTTTTCCTCTTTTTCTTCTA
1 TTTTTTCCTTTTTTT-CTCTTTTTCTTCTA
303231 TTTTTTCCTTTTTTTCTCTTTTTCTTCTA
1 TTTTTTCCTTTTTTTCTCTTTTTCTTCTA
303260 TTTTTTCCTTTCTTTTCTCTCTCTTTC-TCTA
1 TTTTTTCCTTT-TTTTCTCT-T-TTTCTTCTA
303291 TTCTTTTTCCTTTT
1 -T-TTTTTCCTTTT
303305 CCTTTTTTCG
Statistics
Matches: 68, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
29 25 0.37
30 22 0.32
31 5 0.07
32 6 0.09
33 10 0.15
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTTTCCTTTTTTTCTCTTTTTCTTCTA
Found at i:303379 original size:20 final size:19
Alignment explanation
Indices: 303316--303379 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
303306 CTTTTTTCGC
*
303316 TTTTTTCTTTTTTT--T-C
1 TTTTTTCTTTTTTTGATAT
303332 TTTTTTC-TTTTTTGATAT
1 TTTTTTCTTTTTTTGATAT
*
303350 TTTTTATCTTTTTTTGCTAT
1 TTTTT-TCTTTTTTTGATAT
303370 ATTTTTTCTT
1 -TTTTTTCTT
303380 CTTTCTCTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 6 0.15
16 7 0.17
17 1 0.03
18 5 0.12
19 2 0.05
20 14 0.35
21 5 0.12
ACGTcount: A:0.08, C:0.09, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTTTTTTGATAT
Found at i:307451 original size:16 final size:16
Alignment explanation
Indices: 307414--307452 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
307404 TAGTAATTAA
*
307414 CGGTTAGAAAGGTTAG
1 CGGTTAGAAAAGTTAG
**
307430 TTGTTAGAAAAGTTAG
1 CGGTTAGAAAAGTTAG
307446 CGGTTAG
1 CGGTTAG
307453 CAGAGTCTGA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (16 bp):
CGGTTAGAAAAGTTAG
Found at i:307591 original size:138 final size:139
Alignment explanation
Indices: 307448--307823 Score: 492
Period size: 141 Copynumber: 2.7 Consensus size: 139
307438 AAAGTTAGCG
* * *
307448 GTTAGCAGAG-TCTGAATCATAATAATGTGGATCATACCTCGGATCGAGTCACCACAAGGTCGAA
1 GTTAGCAGAGTTC-GAACCATAATAATG-GGATCATACC-CGGATCGGGTCACCACAAGGCCGAA
* ** * *
307512 TCAAATATTAGAAGTAATAAATAAACAAATAAATAAAT-A-AA-AATGGTTAGAA-TGCAATAAA
63 TCGAATATTAGAAACAATAAATAAATAAATAAATAAATAATAACAATGATTA-AAGTGCAATAAA
307573 ATAAAAGTCAGTA
127 ATAAAAGTCAGTA
* * *
307586 GTTAGCAGAGTTCGAACCATAATAATAGGAATCACAACCCAGATCGGGTCACCACAAGGCCGAAT
1 GTTAGCAGAGTTCGAACCATAATAAT-GGGATCA-TACCCGGATCGGGTCACCACAAGGCCGAAT
* * *
307651 CGAATATTATAAACAATAAATACATAAATAAATAAATAATAACAATTATTAAAGTGCAATAAAAT
64 CGAATATTAGAAACAATAAATAAATAAATAAATAAATAATAACAATGATTAAAGTGCAATAAAAT
*
307716 AAAAGTTAGTA
129 AAAAGTCAGTA
*
307727 GTTAGCAGAGTTCGAACCATAATAATGCGGATCATACCCTGGATCGGGTTACCACAAGGCCGAAT
1 GTTAGCAGAGTTCGAACCATAATAATG-GGATCATACCC-GGATCGGGTCACCACAAGGCCGAAT
*
307792 CGAATAATAGAAACAATAAATAAATAAATAAA
64 CGAATATTAGAAACAATAAATAAATAAATAAA
307824 CAATGGTTAT
Statistics
Matches: 207, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
138 81 0.39
139 7 0.03
140 9 0.04
141 110 0.53
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.23
Consensus pattern (139 bp):
GTTAGCAGAGTTCGAACCATAATAATGGGATCATACCCGGATCGGGTCACCACAAGGCCGAATCG
AATATTAGAAACAATAAATAAATAAATAAATAAATAATAACAATGATTAAAGTGCAATAAAATAA
AAGTCAGTA
Done.