Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 39
Found at i:2296066 original size:131 final size:131
Alignment explanation
Indices: 2295851--2296186 Score: 372
Period size: 131 Copynumber: 2.6 Consensus size: 131
2295841 AGTTGGAGTG
* * ** *
2295851 ATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTTGATTTTGCCA
1 ATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCT
* * * * * *
2295916 TTTTCTCTCGAATTAATATT-GATTCTT-AGGATGAAATAGTGATATCTCTTCATTTCGATTGAT
66 TTTTCACTCGAATCAATATTAAATT-TTAAGGAT-AAATAGTAATATCTCTTCATTTCAATTGAG
2295979 GCA
129 GCA
** *
2295982 ATAAATGTA-TGCTTTAAGGTATGAGATATCATTTATTCTCGATTGGAAATCATTAGATATTATC
1 ATAAATG-ACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
* * * * * *
2296046 TTTTTAACTCGAATCGATATTAAATTTTAAGGCTTAATAGTAATATCTCTTTATTTCAATTGGGG
65 TTTTTCACTCGAATCAATATTAAATTTTAAGGATAAATAGTAATATCTCTTCATTTCAATTGAGG
*
2296111 TA
130 CA
* * * * * * *
2296113 ATAAATGATTGTTTTAATGCACGAAAGGTCATTTATTCTAGATTGGAAATAATTAGATATTATCT
1 ATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCT
2296178 TTTTCACTC
66 TTTTCACTC
2296187 TTAAAATTAT
Statistics
Matches: 170, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
130 1 0.01
131 161 0.95
132 8 0.05
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (131 bp):
ATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCT
TTTTCACTCGAATCAATATTAAATTTTAAGGATAAATAGTAATATCTCTTCATTTCAATTGAGGC
A
Found at i:2297986 original size:22 final size:22
Alignment explanation
Indices: 2297959--2298008 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
2297949 GACTGATAAA
2297959 GATGATGTTTATTTATTATCCT
1 GATGATGTTTATTTATTATCCT
*
2297981 GATGATGTTTATTTATTATGCT
1 GATGATGTTTATTTATTATCCT
*
2298003 AATGAT
1 GATGAT
2298009 CATTCTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (22 bp):
GATGATGTTTATTTATTATCCT
Found at i:2305285 original size:33 final size:32
Alignment explanation
Indices: 2305247--2305317 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 32
2305237 TGGAATCAAT
*
2305247 ATCTTTTGCACTAGCAATTTCATGTTTTTTCCA
1 ATCTTTTGCACTAGCAATTTCATG-TTTTCCCA
* *
2305280 ATCTTTTGCATTAGCATTTTCATGTTTTCCCA
1 ATCTTTTGCACTAGCAATTTCATGTTTTCCCA
2305312 ATCTTT
1 ATCTTT
2305318 AAGTCTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 13 0.37
33 22 0.63
ACGTcount: A:0.20, C:0.21, G:0.08, T:0.51
Consensus pattern (32 bp):
ATCTTTTGCACTAGCAATTTCATGTTTTCCCA
Found at i:2316799 original size:90 final size:90
Alignment explanation
Indices: 2316636--2316813 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
2316626 TAATCCCGAA
* * * * *
2316636 TATTTAATTTCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAAACCCTAATATGAC
2316701 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
2316726 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACTCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAAACCCTAATATGAC
*
2316791 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
2316814 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:2323590 original size:90 final size:90
Alignment explanation
Indices: 2323427--2323604 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
2323417 TAATCCCGAA
* * * * *
2323427 TATTTAATTTCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAAACCCTAATATGAC
2323492 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
2323517 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACTCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAAACCCTAATATGAC
*
2323582 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
2323605 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAAATAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:2325025 original size:36 final size:36
Alignment explanation
Indices: 2324978--2325083 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
2324968 AAATGCTTAA
* *
2324978 GTGTACCGATACACCCTACAATGTATCCATACACTG
1 GTGTACCGATACACCCTGCAGTGTATCCATACACTG
*
2325014 GTGTACCGATACACCCTGCAGTGTATCCATACGCTG
1 GTGTACCGATACACCCTGCAGTGTATCCATACACTG
* * *
2325050 GTGTACTGATACACTCTGTAGTGTATCCATACAC
1 GTGTACCGATACACCCTGCAGTGTATCCATACAC
2325084 CCTGGCTGCA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (36 bp):
GTGTACCGATACACCCTGCAGTGTATCCATACACTG
Found at i:2325045 original size:20 final size:18
Alignment explanation
Indices: 2324977--2325087 Score: 54
Period size: 20 Copynumber: 6.0 Consensus size: 18
2324967 AAAATGCTTA
*
2324977 AGTGTACCGATACACCCTAC
1 AGTGTACC-ATACACCCT-G
*
2324997 AATGTATCCATACA--CTG
1 AGTGTA-CCATACACCCTG
2325014 -GTGTACCGATACACCCTG
1 AGTGTACC-ATACACCCTG
*
2325032 CAGTGTATCCAT--ACGCTG
1 -AGTGTA-CCATACACCCTG
* *
2325050 -GTGTACTGATACACTCTG
1 AGTGTAC-CATACACCCTG
2325068 TAGTGTATCCATACACCCTG
1 -AGTGTA-CCATACACCCTG
2325088 GCTGCAATGG
Statistics
Matches: 70, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
15 3 0.04
16 16 0.23
18 15 0.21
20 31 0.44
21 5 0.07
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (18 bp):
AGTGTACCATACACCCTG
Found at i:2325518 original size:34 final size:34
Alignment explanation
Indices: 2325449--2325520 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
2325439 TTTTGTAAAG
* * *
2325449 GGGAAAGGTTCTAGCTAAACCTGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTAAACCCGTGAAAAAACTA
* * *
2325483 GGGAAAGGTTCTAGTTTATCCCGTGAAAAAACTA
1 GGGAAAGGTTCTAGCTAAACCCGTGAAAAAACTA
2325517 GGGA
1 GGGA
2325521 GTTGTAAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTAAACCCGTGAAAAAACTA
Found at i:2339942 original size:27 final size:26
Alignment explanation
Indices: 2339881--2339942 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2339871 AAATGATATA
*
2339881 TTTTATATATAATAATTTCTTTTAAAT
1 TTTTAT-TATAATAATATCTTTTAAAT
* * *
2339908 TTAT-TTATAATATATATCTTTTTATT
1 TTTTATTATAATA-ATATCTTTTAAAT
2339934 TTTTATTAT
1 TTTTATTAT
2339943 TCAATGGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 7 0.25
26 14 0.50
27 7 0.25
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTATTATAATAATATCTTTTAAAT
Found at i:2340015 original size:14 final size:14
Alignment explanation
Indices: 2339971--2340018 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2339961 AATATATCAT
2339971 TTAAATTATTTTAG
1 TTAAATTATTTTAG
* *
2339985 TTTAA--ATTTTAA
1 TTAAATTATTTTAG
*
2339997 ATAAATTATTTTAG
1 TTAAATTATTTTAG
2340011 TTAAATTA
1 TTAAATTA
2340019 GAATAATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 9 0.35
14 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (14 bp):
TTAAATTATTTTAG
Found at i:2344155 original size:18 final size:18
Alignment explanation
Indices: 2344129--2344163 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2344119 ATGCTCAAAT
2344129 GGTACCGATACCCCCATA
1 GGTACCGATACCCCCATA
*
2344147 GGTATCGATACCCCCAT
1 GGTACCGATACCCCCAT
2344164 GCAATGGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (18 bp):
GGTACCGATACCCCCATA
Found at i:2344172 original size:22 final size:19
Alignment explanation
Indices: 2344126--2344182 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 19
2344116 AGAATGCTCA
2344126 AATGGTACCGATACCCCCAT
1 AATGGTA-CGATACCCCCAT
2344146 -A-GGTATCGATACCCCCAT
1 AATGGTA-CGATACCCCCAT
2344164 GCAATGGTACTGATACCCC
1 --AATGGTAC-GATACCCC
2344183 TCAGGTGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 16 0.52
19 1 0.03
21 2 0.06
22 12 0.39
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (19 bp):
AATGGTACGATACCCCCAT
Found at i:2349952 original size:44 final size:43
Alignment explanation
Indices: 2349898--2350045 Score: 160
Period size: 44 Copynumber: 3.4 Consensus size: 43
2349888 ATTTTTGTGC
***
2349898 ATAGAGTATCGATACCCCTAAAAAT-GGTATCGATACCCCCTTTGA
1 ATAG-GTATCGATACCCCTTTGAATAGGTATCGATACCCCC--TGA
2349943 ATAGGTATCGATACCCCCTTTGAATAGGTATCGATA-CCCCTGCA
1 ATAGGTATCGATA-CCCCTTTGAATAGGTATCGATACCCCCTG-A
* *
2349987 ATAGGTATCGATACCATCTTTGAATGGGTATCGATACCCCCCTG-
1 ATAGGTATCGATACC-CCTTTGAATAGGTATCGATA-CCCCCTGA
2350031 AT-GGTATCGATACCC
1 ATAGGTATCGATACCC
2350046 TCCACGGGAT
Statistics
Matches: 91, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
43 16 0.18
44 43 0.47
45 16 0.18
46 16 0.18
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (43 bp):
ATAGGTATCGATACCCCTTTGAATAGGTATCGATACCCCCTGA
Found at i:2349953 original size:23 final size:23
Alignment explanation
Indices: 2349898--2350045 Score: 159
Period size: 23 Copynumber: 6.7 Consensus size: 23
2349888 ATTTTTGTGC
***
2349898 ATAGAGTATCGATA-CCCCTAAAA
1 ATAG-GTATCGATACCCCCTTTGA
2349921 AT-GGTATCGATACCCCCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
2349943 ATAGGTATCGATACCCCCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
2349966 ATAGGTATCGATA-CCCC--TGCA
1 ATAGGTATCGATACCCCCTTTG-A
**
2349987 ATAGGTATCGATACCATCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
* *
2350010 ATGGGTATCGATACCCCC-CTG-
1 ATAGGTATCGATACCCCCTTTGA
2350031 AT-GGTATCGATACCC
1 ATAGGTATCGATACCC
2350046 TCCACGGGAT
Statistics
Matches: 110, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
20 15 0.14
21 25 0.23
22 17 0.15
23 51 0.46
24 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (23 bp):
ATAGGTATCGATACCCCCTTTGA
Found at i:2350011 original size:67 final size:65
Alignment explanation
Indices: 2349898--2350045 Score: 192
Period size: 67 Copynumber: 2.2 Consensus size: 65
2349888 ATTTTTGTGC
* *
2349898 ATAGAGTATCGATACCCCTAAAAATGGTATCGATACCCCCTTTGAATAGGTATCGATACCCCCTT
1 ATAG-GTATCGATACCCCTAAAAATGGTATCGATACCACCTTTGAATAGGTATCGATACCCCC-C
2349963 TG
64 TG
** * *
2349965 AATAGGTATCGATACCCCT-GCAATAGGTATCGATACCATCTTTGAATGGGTATCGATACCCCCC
1 -ATAGGTATCGATACCCCTAAAAAT-GGTATCGATACCACCTTTGAATAGGTATCGATACCCCCC
2350029 TG
64 TG
2350031 AT-GGTATCGATACCC
1 ATAGGTATCGATACCC
2350046 TCCACGGGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
64 13 0.18
65 2 0.03
66 5 0.07
67 49 0.67
68 4 0.05
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (65 bp):
ATAGGTATCGATACCCCTAAAAATGGTATCGATACCACCTTTGAATAGGTATCGATACCCCCCTG
Found at i:2381087 original size:31 final size:33
Alignment explanation
Indices: 2381022--2381101 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
2381012 TTAATAATTC
* *
2381022 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
2381056 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
2381087 TATAAAATATAATAA
1 TA-AAAAAATAATAA
2381102 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:2387863 original size:24 final size:24
Alignment explanation
Indices: 2387836--2387889 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2387826 GTATTCGAAA
2387836 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2387860 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2387884 TTTGAT
1 TTTGAT
2387890 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2390462 original size:33 final size:33
Alignment explanation
Indices: 2390425--2390605 Score: 209
Period size: 33 Copynumber: 5.3 Consensus size: 33
2390415 GGAAATTACT
2390425 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * * *
2390458 ATCGCAACGTGAAAATCGCAACGCGAATATGAAT
1 ATCGCAACGAGAGAATCGCAATGCGAA-ATGAAA
* * *
2390492 ATCGCAACGCGAAAATGACTATCGCAATGCAAAATAAAA
1 ATCGCAA--CG-AGA-GA--ATCGCAATGCGAAATGAAA
2390531 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * *
2390564 ATCGCAACGAGGGAATCGCAAAGAGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
2390597 ATCGCAACG
1 ATCGCAACG
2390606 CGAATTTAGT
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
33 80 0.65
34 12 0.10
35 2 0.02
36 4 0.03
37 3 0.02
38 1 0.01
39 11 0.09
40 11 0.09
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:2390472 original size:14 final size:14
Alignment explanation
Indices: 2390453--2390480 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2390443 CAATGCGAAA
2390453 TGAAAATCGCAACG
1 TGAAAATCGCAACG
2390467 TGAAAATCGCAACG
1 TGAAAATCGCAACG
2390481 CGAATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:2390490 original size:20 final size:20
Alignment explanation
Indices: 2390467--2390539 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
2390457 AATCGCAACG
*
2390467 TGAAAATCGCAACGCGAATA
1 TGAAAATCGCAACGCGAAAA
*
2390487 TGAATATCGCAACGCGAAAA
1 TGAAAATCGCAACGCGAAAA
** *
2390507 TGACTATCGCAATGC-AAAA
1 TGAAAATCGCAACGCGAAAA
*
2390526 TAAAAATCGCAACG
1 TGAAAATCGCAACG
2390540 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 14 0.31
20 31 0.69
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:2390640 original size:19 final size:19
Alignment explanation
Indices: 2390605--2390681 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
2390595 AAATCGCAAC
*
2390605 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
2390624 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
2390643 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
2390657 GCGATTTTCA-TTTCGCATT
1 GCGATTTT-AGTTTCGCGTT
2390676 GCGATT
1 GCGATT
2390682 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:2390662 original size:33 final size:33
Alignment explanation
Indices: 2390620--2390709 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
2390610 TTTAGTTTCG
* * *
2390620 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
2390653 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2390686 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
2390710 TGATAGTCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2390839 original size:14 final size:14
Alignment explanation
Indices: 2390820--2390856 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2390810 CATCAATTAA
2390820 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2390834 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2390848 ACAAATCAA
1 ACAAATCAA
2390857 TTAACAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2392135 original size:21 final size:21
Alignment explanation
Indices: 2392069--2392135 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2392059 GTGAATCGGG
*
2392069 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2392089 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2392111 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2392132 CTCT
1 CTCT
2392136 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2392154 original size:42 final size:41
Alignment explanation
Indices: 2392069--2392191 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2392059 GTGAATCGGG
* * * *
2392069 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2392111 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2392153 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2392192 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2392700 original size:94 final size:94
Alignment explanation
Indices: 2392539--2392795 Score: 462
Period size: 93 Copynumber: 2.7 Consensus size: 94
2392529 TGAAGTAATG
* *
2392539 CAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGTAACCGAACAAAT
1 CAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
*
2392604 TTACTTTCAACCAAAAGACAAAACAAAGA
66 TTACTTTCAACCAAAAGACAAAAAAAAGA
2392633 CAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
1 CAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
2392698 TTAC-TTCAACCAAAAGACAAAAAAAAGA
66 TTACTTTCAACCAAAAGACAAAAAAAAGA
* *
2392726 CAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAAAT
1 CAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
2392791 TTACT
66 TTACT
2392796 AAGCAATCTA
Statistics
Matches: 157, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
93 90 0.57
94 67 0.43
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (94 bp):
CAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
TTACTTTCAACCAAAAGACAAAAAAAAGA
Found at i:2394513 original size:20 final size:20
Alignment explanation
Indices: 2394483--2394544 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
2394473 TTTTGGTTGA
2394483 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
**
2394503 AATGACTATCGCAACGCA-A-
1 AATGAAAATCGCAACG-AGAG
2394522 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2394542 AAT
1 AAT
2394545 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.03
19 15 0.43
20 18 0.51
21 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2394547 original size:33 final size:37
Alignment explanation
Indices: 2394482--2394568 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 37
2394472 CTTTTGGTTG
2394482 AAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCA
1 AAATGAAAATCGCAAC-AGAGAATGAC-ATCGCAACGCA
*
2394521 AAATGAAAATCGCAAC-GAG-A-GA-ATCGCAACGCG
1 AAATGAAAATCGCAACAGAGAATGACATCGCAACGCA
2394554 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
2394569 TGCGATTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
33 25 0.53
35 2 0.04
36 1 0.02
37 3 0.06
39 16 0.34
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (37 bp):
AAATGAAAATCGCAACAGAGAATGACATCGCAACGCA
Found at i:2394573 original size:19 final size:19
Alignment explanation
Indices: 2394481--2394573 Score: 88
Period size: 19 Copynumber: 5.1 Consensus size: 19
2394471 TCTTTTGGTT
*
2394481 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
2394500 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
2394520 AAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2394537 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2394553 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2394572 GA
1 GA
2394574 TTTTGGTTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 1 0.02
18 1 0.02
19 28 0.48
20 15 0.26
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2394665 original size:20 final size:20
Alignment explanation
Indices: 2394600--2394690 Score: 123
Period size: 20 Copynumber: 4.5 Consensus size: 20
2394590 CGATTATCTC
2394600 GTTGCGATTTTCA-TTTCGT
1 GTTGCGATTTTCATTTTCGT
2394619 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
2394639 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
2394660 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
2394680 GTTGCGATTTT
1 GTTGCGATTTT
2394691 AAGTTTAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
19 13 0.21
20 33 0.52
21 17 0.27
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:2395284 original size:20 final size:20
Alignment explanation
Indices: 2395252--2395364 Score: 88
Period size: 20 Copynumber: 5.6 Consensus size: 20
2395242 AAAAATCGCA
2395252 TTGCGATTTTACGTATTGTCG
1 TTGCGA-TTTACGTATTGTCG
* * *
2395273 TTGCGATTTACGGATACG-CA
1 TTGCGATTTACGTAT-TGTCG
*
2395293 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTGTCG
* *
2395313 TTGCGATTTATAG-ATACG-CG
1 TTGCGATTTA-CGTAT-TGTCG
* *
2395333 TTGCGATTTACATATTCTCG
1 TTGCGATTTACGTATTGTCG
*
2395353 TTACGATTTACG
1 TTGCGATTTACG
2395365 GATACGCGTT
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
20 62 0.89
21 8 0.11
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTGTCG
Found at i:2395314 original size:40 final size:40
Alignment explanation
Indices: 2395248--2395379 Score: 192
Period size: 40 Copynumber: 3.3 Consensus size: 40
2395238 CTTTAAAAAT
*
2395248 CGCATTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
**
2395289 CGCATTGCGATTTACGTATTCTCGTTGCGATTTATAGATA
1 CGCATTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * *
2395329 CGCGTTGCGATTTACATATTCTCGTTACGATTTACGGATA
1 CGCATTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
2395369 CGCGTTGCGAT
1 CGCATTGCGAT
2395380 AGTCAGAATC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.88
41 10 0.12
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGCATTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:2395360 original size:60 final size:62
Alignment explanation
Indices: 2395273--2395440 Score: 157
Period size: 60 Copynumber: 2.8 Consensus size: 62
2395263 CGTATTGTCG
** * * * * *
2395273 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTA-T-AG-ATACGCG
1 TTGCGATTTACATATTCGCGTTACGATTTACGTATTCGCGTTGCGATTTAGTCAGAAT-CGCA
* * *
2395333 TTGCGATTTACATATTCTCGTTACGATTTACGGATACGCGTTGCGA--TAGTCAGAATCGCA
1 TTGCGATTTACATATTCGCGTTACGATTTACGTATTCGCGTTGCGATTTAGTCAGAATCGCA
* * * * *
2395393 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTACATATTCGCGTTACGATTTACGTATTCGCGTTGCGATT
2395441 CTGGAAAATC
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 80 0.94
61 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (62 bp):
TTGCGATTTACATATTCGCGTTACGATTTACGTATTCGCGTTGCGATTTAGTCAGAATCGCA
Found at i:2395360 original size:80 final size:80
Alignment explanation
Indices: 2395252--2395440 Score: 222
Period size: 80 Copynumber: 2.4 Consensus size: 80
2395242 AAAAATCGCA
* * * * * *
2395252 TTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGCGAT--TTACGTATTCTCGTT
1 TTGCGA-TTTACATATTCTCGTTGCGATTTACGGATACGCATTGCGATAGTCA-G-AATCGCATT
2395315 GCGATTTATA-GATACGCG
63 GCGATTTATATG-TACGCG
* *
2395333 TTGCGATTTACATATTCTCGTTACGATTTACGGATACGCGTTGCGATAGTCAGAATCGCATTGCG
1 TTGCGATTTACATATTCTCGTTGCGATTTACGGATACGCATTGCGATAGTCAGAATCGCATTGCG
*
2395398 ATTTATATGTTCGCG
66 ATTTATATGTACGCG
* *
2395413 TTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTACATATTCTCGTTGCGATT
2395441 CTGGAAAATC
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
80 83 0.89
81 8 0.09
82 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (80 bp):
TTGCGATTTACATATTCTCGTTGCGATTTACGGATACGCATTGCGATAGTCAGAATCGCATTGCG
ATTTATATGTACGCG
Found at i:2395374 original size:20 final size:20
Alignment explanation
Indices: 2395271--2395379 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
2395261 TACGTATTGT
2395271 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * * *
2395291 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
**
2395311 CGTTGCGATTTATAGATACG
1 CGTTGCGATTTACGGATACG
** * *
2395331 CGTTGCGATTTACATATTCT
1 CGTTGCGATTTACGGATACG
*
2395351 CGTTACGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
2395371 CGTTGCGAT
1 CGTTGCGAT
2395380 AGTCAGAATC
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:2395411 original size:20 final size:20
Alignment explanation
Indices: 2395369--2395440 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2395359 TTTACGGATA
** * *
2395369 CGCGTTGCGATAGTCAGAAT
1 CGCGTTGCGATTTTCATATT
* *
2395389 CGCATTGCGATTTAT-ATGTT
1 CGCGTTGCGATTT-TCATATT
2395409 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
2395429 CGCGTTGCGATT
1 CGCGTTGCGATT
2395441 CTGGAAAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:2395437 original size:40 final size:40
Alignment explanation
Indices: 2395252--2395440 Score: 177
Period size: 40 Copynumber: 4.7 Consensus size: 40
2395242 AAAAATCGCA
* ** *
2395252 TTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACGCA
1 TTGCGA-TTTACATATTCG-CGTTGCGATTTATAGATACGCG
* *
2395293 TTGCGATTTACGTATTCTCGTTGCGATTTATAGATACGCG
1 TTGCGATTTACATATTCGCGTTGCGATTTATAGATACGCG
* * **
2395333 TTGCGATTTACATATTCTCGTTACGATTTACGGATACGCG
1 TTGCGATTTACATATTCGCGTTGCGATTTATAGATACGCG
* * * * *
2395373 TTGCGATAGT-CAGAATCGCATTGCGATTTATATG-TTCGCG
1 TTGCGAT-TTACATATTCGCGTTGCGATTTATA-GATACGCG
*
2395413 TTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTTACATATTCGCGTTGCGATT
2395441 CTGGAAAATC
Statistics
Matches: 123, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 114 0.93
41 8 0.07
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACATATTCGCGTTGCGATTTATAGATACGCG
Found at i:2401539 original size:16 final size:17
Alignment explanation
Indices: 2401504--2401541 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2401494 AACAAAATAG
2401504 AGATGACAGCTATAACAA
1 AGATGACAGC-ATAACAA
*
2401522 AGATGACAG-ATAAGAA
1 AGATGACAGCATAACAA
2401538 AGAT
1 AGAT
2401542 AATAAGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (17 bp):
AGATGACAGCATAACAA
Found at i:2401562 original size:60 final size:60
Alignment explanation
Indices: 2401491--2401612 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
2401481 AGACGACGAC
2401491 AACAACAAAATAGAGATGACAGCTATAACAAAGATGACAGATAAGAAAGATAATAAGAGG
1 AACAACAAAATAGAGATGACAGCTATAACAAAGATGACAGATAAGAAAGATAATAAGAGG
2401551 AACAACAAAATAGAGATGACAGCTATAACAAAGATGACAGATAAGAAAGATAATAAGAGG
1 AACAACAAAATAGAGATGACAGCTATAACAAAGATGACAGATAAGAAAGATAATAAGAGG
2401611 AA
1 AA
2401613 TAAAATTAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.57, C:0.10, G:0.20, T:0.13
Consensus pattern (60 bp):
AACAACAAAATAGAGATGACAGCTATAACAAAGATGACAGATAAGAAAGATAATAAGAGG
Found at i:2401599 original size:16 final size:17
Alignment explanation
Indices: 2401564--2401601 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2401554 AACAAAATAG
2401564 AGATGACAGCTATAACAA
1 AGATGACAGC-ATAACAA
*
2401582 AGATGACAG-ATAAGAA
1 AGATGACAGCATAACAA
2401598 AGAT
1 AGAT
2401602 AATAAGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (17 bp):
AGATGACAGCATAACAA
Found at i:2406112 original size:3 final size:3
Alignment explanation
Indices: 2406104--2406135 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2406094 TGTAAAAAAT
2406104 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2406136 GTACGATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2409670 original size:20 final size:20
Alignment explanation
Indices: 2409647--2409698 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2409637 AACGCGATCC
2409647 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2409667 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2409687 CCAAAATCGCAA
1 CCAGAATCGCAA
2409699 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2409796 original size:20 final size:20
Alignment explanation
Indices: 2409754--2409946 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
2409744 GATTTTCCAT
* ** *
2409754 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2409774 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
2409794 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2409814 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2409834 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2409854 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2409874 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
2409894 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
2409915 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2409935 AATCGCAACGCG
1 AATCGCAACGCG
2409947 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 123 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2409837 original size:60 final size:60
Alignment explanation
Indices: 2409754--2409946 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2409744 GATTTTCCAT
* ** * *
2409754 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTA
* * ***
2409814 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTA
* ** *
2409874 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGTA
2409935 AATCGCAACGCG
1 AATCGCAACGCG
2409947 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGTA
Found at i:2410366 original size:33 final size:33
Alignment explanation
Indices: 2410327--2410397 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2410317 TTCACTTAGA
*
2410327 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2410360 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2410393 TTTCA
1 TTTCA
2410398 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2410537 original size:14 final size:14
Alignment explanation
Indices: 2410518--2410572 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2410508 AGAATGACTG
2410518 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2410532 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2410551 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2410565 TCGCAACG
1 TCGCAACG
2410573 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2410555 original size:33 final size:33
Alignment explanation
Indices: 2410518--2410588 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2410508 AGAATGACTG
**
2410518 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2410551 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2410584 TCGCA
1 TCGCA
2410589 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2410606 original size:19 final size:19
Alignment explanation
Indices: 2410584--2410681 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2410574 GAAACCAAAA
*
2410584 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2410603 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2410617 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2410636 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2410650 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2410669 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2410682 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2410625 original size:14 final size:14
Alignment explanation
Indices: 2410606--2410695 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2410596 TTTCATTTCG
2410606 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2410620 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2410639 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2410653 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2410670 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2410686 CGTTGCGATT
1 CGTTGCGATT
2410696 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2410631 original size:33 final size:33
Alignment explanation
Indices: 2410589--2410703 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2410579 CAAAATCGCA
2410589 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2410622 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2410655 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2410688 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2410704 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2412559 original size:93 final size:93
Alignment explanation
Indices: 2412400--2413058 Score: 1302
Period size: 93 Copynumber: 7.1 Consensus size: 93
2412390 TAGATTGCTT
*
2412400 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412465 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2412493 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412558 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2412586 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412651 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2412679 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412744 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2412772 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412837 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2412864 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412929 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2412957 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2413022 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2413050 AGTAAATTT
1 AGTAAATTT
2413059 ATCCATTCAA
Statistics
Matches: 564, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 92 0.16
93 472 0.84
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2412986 original size:278 final size:279
Alignment explanation
Indices: 2412400--2413058 Score: 1302
Period size: 278 Copynumber: 2.4 Consensus size: 279
2412390 TAGATTGCTT
*
2412400 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412465 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2412530 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
2412595 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
196 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
2412660 GTTTTGTCTTTTGGTTGAA
261 GTTTTGTCTTTTGGTTGAA
2412679 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2412744 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2412809 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
2412873 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
196 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
2412938 GTTTTGTCTTTTGGTTGAA
261 GTTTTGTCTTTTGGTTGAA
2412957 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2413022 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
2413059 ATCCATTCAA
Statistics
Matches: 379, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
278 222 0.59
279 157 0.41
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (279 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
GTTTTGTCTTTTGGTTGAA
Found at i:2413142 original size:19 final size:19
Alignment explanation
Indices: 2413102--2413236 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
2413092 TAGTTTACTT
* *
2413102 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2413122 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2413141 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2413160 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2413174 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2413193 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
**
2413207 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2413226 TCGCAATGCGA
1 TCGCAACGCGA
2413237 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2413177 original size:14 final size:14
Alignment explanation
Indices: 2413158--2413214 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2413148 GCGAAATGAA
2413158 AATCGCAACGACAG
1 AATCGCAACGACAG
*
2413172 AATCGCAACGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
2413191 AATCGCAACGAAAG
1 AATCGCAACGACAG
2413205 AATCGCAACG
1 AATCGCAACG
2413215 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:2413181 original size:33 final size:33
Alignment explanation
Indices: 2413139--2413231 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
2413129 GCGAAACCAA
*
2413139 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
2413172 AATCGCAACGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2413205 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2413232 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2413228 original size:52 final size:54
Alignment explanation
Indices: 2413102--2413236 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 54
2413092 TAGTTTACTT
*
2413102 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
*
2413160 TCGCAA-CGACA-G--AATCGCAACGCGAAACCAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
2413207 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
2413237 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 39 0.57
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:2413254 original size:19 final size:19
Alignment explanation
Indices: 2413232--2413360 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2413222 AAAATCGCAA
2413232 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2413251 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2413265 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2413284 TGCGATTAT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2413298 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2413317 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2413336 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2413356 TGCGA
1 TGCGA
2413361 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2413274 original size:33 final size:33
Alignment explanation
Indices: 2413232--2413323 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2413222 AAAATCGCAA
2413232 TGCGATTTTGGTTTCGCGTTGCGATCT-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGAT-TATGTCGT
2413265 TGCGATTTTGGTTTCGCGTTGCGATTATGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTATGTCGT
**
2413298 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2413324 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTATGTCGT
Found at i:2415303 original size:14 final size:14
Alignment explanation
Indices: 2415284--2415319 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2415274 ATTGTTTAAT
2415284 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2415298 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2415312 TGATTTGT
1 TGATTTGT
2415320 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2415442 original size:19 final size:19
Alignment explanation
Indices: 2415426--2415526 Score: 133
Period size: 19 Copynumber: 5.6 Consensus size: 19
2415416 AAAAATGACT
2415426 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2415445 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2415464 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
2415478 ATCGCAATGTGAAATG-AA
1 ATCGCAATGCGAAATGAAA
2415496 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2415516 ATCGCAATGCG
1 ATCGCAATGCG
2415527 TTTATAATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 2 0.03
18 11 0.15
19 34 0.48
20 12 0.17
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2415573 original size:52 final size:52
Alignment explanation
Indices: 2415533--2415800 Score: 384
Period size: 52 Copynumber: 5.0 Consensus size: 52
2415523 TGCGTTTATA
2415533 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--TT-
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2415582 ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
2415637 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2415694 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2415746 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2415799 AT
1 AT
2415801 GTTGGGATTT
Statistics
Matches: 206, Mismatches: 2, Indels: 18
0.91 0.01 0.08
Matches are distributed among these distances:
47 6 0.03
49 9 0.04
50 4 0.02
52 92 0.45
53 17 0.08
54 6 0.03
55 9 0.04
57 63 0.31
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2415579 original size:19 final size:19
Alignment explanation
Indices: 2415555--2415828 Score: 363
Period size: 19 Copynumber: 15.4 Consensus size: 19
2415545 GATTCTCTCG
2415555 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415574 TTGCGA--TT-ATTTCG--
1 TTGCGATTTTCATTTCGCA
2415588 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415607 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415645 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415664 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415683 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2415702 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2415716 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2415735 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2415754 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2415768 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2415788 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2415802 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2415821 TTGCGATT
1 TTGCGATT
2415829 GTATTTTCCG
Statistics
Matches: 228, Mismatches: 6, Indels: 42
0.83 0.02 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 139 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2418129 original size:12 final size:12
Alignment explanation
Indices: 2418112--2418136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2418102 TCTTCGGGGA
2418112 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2418124 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2418136 C
1 C
2418137 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2418345 original size:24 final size:24
Alignment explanation
Indices: 2418311--2418357 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2418301 CTGAAACATC
2418311 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2418335 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2418358 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2419068 original size:20 final size:20
Alignment explanation
Indices: 2419040--2419408 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2419030 AAATTTCAGT
* * * *
2419040 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2419060 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2419080 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2419100 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2419120 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2419140 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2419160 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2419180 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2419200 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2419220 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2419240 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2419260 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2419280 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2419300 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2419320 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2419340 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2419360 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2419380 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2419400 GTTGCGATT
1 GTTGCGATT
2419409 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2420845 original size:20 final size:21
Alignment explanation
Indices: 2420820--2420863 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
2420810 GAAATTAAGT
2420820 TTCCATATT-ACTCTTC-TCTC
1 TTCCATATTCA-TCTTCTTCTC
*
2420840 TTCCATCTTCATCTTCTTCTC
1 TTCCATATTCATCTTCTTCTC
2420861 TTC
1 TTC
2420864 TCCACGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.11, C:0.36, G:0.00, T:0.52
Consensus pattern (21 bp):
TTCCATATTCATCTTCTTCTC
Found at i:2422828 original size:18 final size:18
Alignment explanation
Indices: 2422795--2422835 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2422785 TATGCTTATA
2422795 TGAT-ATAAATGAATTAG
1 TGATAATAAATGAATTAG
*
2422812 TGATAATAATATG-ATTAT
1 TGATAATAA-ATGAATTAG
2422830 TGATAA
1 TGATAA
2422836 ATATGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 14 0.67
19 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (18 bp):
TGATAATAAATGAATTAG
Found at i:2423395 original size:21 final size:19
Alignment explanation
Indices: 2423368--2423414 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
2423358 CTGTTCACGG
*
2423368 TACTGTTCATACGGTATTGT
1 TACTGTTCATACCGTATT-T
*
2423388 TCACTGTTCATGCCGTATTT
1 T-ACTGTTCATACCGTATTT
2423408 TACTGTT
1 TACTGTT
2423415 TATAAAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 15 0.62
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (19 bp):
TACTGTTCATACCGTATTT
Found at i:2425847 original size:82 final size:82
Alignment explanation
Indices: 2425725--2425915 Score: 208
Period size: 82 Copynumber: 2.3 Consensus size: 82
2425715 GCCGCTATAG
* * * *
2425725 AGTAGTA-TTGTAGCGGCGTTTTTTATATAAACGCCGCAATAGGTACATATGTAGTGGTGTTT-T
1 AGTAGTACTT-TAGCGACG-TTTTTATATAAACGCCGCAATAAGTACATATATAGTGGCGTTTAT
2425788 T-TCAACAAACACCACAACAA
64 TAT-AA-AAACACCACAACAA
* * * *
2425808 AGTAGTACTTTAGTGACGTTTTTATATAAACTCCGCAATAAGTTCATCTATAGTGGCGTTTATTA
1 AGTAGTACTTTAGCGACGTTTTTATATAAACGCCGCAATAAGTACATATATAGTGGCGTTTATTA
* * *
2425873 TAAAAACGCCACAATAG
66 TAAAAACACCACAACAA
* *
2425890 ATTAGTACTTTAGCGGCGTTTTTATA
1 AGTAGTACTTTAGCGACGTTTTTATA
2425916 AAAATGCCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
82 71 0.78
83 17 0.19
84 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (82 bp):
AGTAGTACTTTAGCGACGTTTTTATATAAACGCCGCAATAAGTACATATATAGTGGCGTTTATTA
TAAAAACACCACAACAA
Found at i:2425915 original size:41 final size:41
Alignment explanation
Indices: 2425688--2425930 Score: 151
Period size: 41 Copynumber: 5.9 Consensus size: 41
2425678 CACAAAATGA
* *
2425688 TACTTTAGCGGCGTTTCTTA-AACAAACGCCGCTATAGAGTAG
1 TACTTTAGCGGCGTTT-TTATAA-AAACGCCACAATAGAGTAG
* * *
2425730 TA-TTGTAGCGGCGTTTTTTATATAAACGCCGCAATAG-GTACA
1 TACTT-TAGCGGCG-TTTTTATAAAAACGCCACAATAGAGTA-G
* * * * * *
2425772 TA-TGTAGTGGTGTTTTT-TCAACAAACACCACAACAAAGTAG
1 TACTTTAGCGGCGTTTTTAT-AA-AAACGCCACAATAGAGTAG
* * * * *
2425813 TACTTTAGTGACGTTTTTATATAAACTCCGCAATA-AGT--
1 TACTTTAGCGGCGTTTTTATAAAAACGCCACAATAGAGTAG
* * *
2425851 TCATCTATAGTGGCGTTTATTATAAAAACGCCACAATAGATTAG
1 T-A-CTTTAGCGGCGTTT-TTATAAAAACGCCACAATAGAGTAG
* *
2425895 TACTTTAGCGGCGTTTTTATAAAAATGCCATAATAG
1 TACTTTAGCGGCGTTTTTATAAAAACGCCACAATAG
2425931 GATTCACCTA
Statistics
Matches: 157, Mismatches: 29, Indels: 31
0.72 0.13 0.14
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 21 0.13
41 67 0.43
42 59 0.38
43 6 0.04
44 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTTTATAAAAACGCCACAATAGAGTAG
Found at i:2425952 original size:41 final size:40
Alignment explanation
Indices: 2425818--2425954 Score: 116
Period size: 41 Copynumber: 3.4 Consensus size: 40
2425808 AGTAGTACTT
* * * * *
2425818 TAGTGACGTTTTTATATAAACTCCGCAATA-AGTTCATCTA
1 TAGTGGCGTTTTTATAAAAACGCCACAATAGA-TTCAACTA
*
2425858 TAGTGGCGTTTATTATAAAAACGCCACAATAGATT-AGTACTT
1 TAGTGGCGTTT-TTATAAAAACGCCACAATAGATTCA--ACTA
* * * *
2425900 TAGCGGCGTTTTTATAAAAATGCCATAATAGGATTCACCTA
1 TAGTGGCGTTTTTATAAAAACGCCACAATA-GATTCAACTA
*
2425941 TAGTGGTGTTTTTA
1 TAGTGGCGTTTTTA
2425955 CCAATAAATA
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
40 11 0.14
41 49 0.63
42 17 0.22
43 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (40 bp):
TAGTGGCGTTTTTATAAAAACGCCACAATAGATTCAACTA
Found at i:2429212 original size:22 final size:22
Alignment explanation
Indices: 2429169--2429213 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2429159 CGTTTGTAAT
**
2429169 AAAAAACGCCGCTATAGTTCTA
1 AAAAAACGCCGCTATAAATCTA
*
2429191 AAAAAATGCCGCTATAAATCTA
1 AAAAAACGCCGCTATAAATCTA
2429213 A
1 A
2429214 CATTTTACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (22 bp):
AAAAAACGCCGCTATAAATCTA
Found at i:2430192 original size:16 final size:17
Alignment explanation
Indices: 2430165--2430200 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2430155 GATATTAGAA
2430165 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
2430182 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
2430198 AAA
1 AAA
2430201 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:2430375 original size:22 final size:22
Alignment explanation
Indices: 2430347--2430388 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2430337 ATATTTCAGA
*
2430347 TAATTTAAAGTTTGTTGCGGCG
1 TAATTTAAAGTGTGTTGCGGCG
*
2430369 TAATTTATAGTGTGTTGCGG
1 TAATTTAAAGTGTGTTGCGG
2430389 TGTTACGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (22 bp):
TAATTTAAAGTGTGTTGCGGCG
Found at i:2431478 original size:6 final size:6
Alignment explanation
Indices: 2431467--2431493 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2431457 TCCCCTCTAG
2431467 TAGGAT TAGGAT TAGGAT TAGGAT TAG
1 TAGGAT TAGGAT TAGGAT TAGGAT TAG
2431494 ATTTAGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TAGGAT
Found at i:2441401 original size:12 final size:13
Alignment explanation
Indices: 2441384--2441417 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2441374 TTTCTTTTAT
2441384 TTTTTAAAATA-A
1 TTTTTAAAATACA
2441396 TTTTTAAAATACA
1 TTTTTAAAATACA
*
2441409 ATTTTAAAA
1 TTTTTAAAA
2441418 GATATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTTAAAATACA
Found at i:2449063 original size:41 final size:42
Alignment explanation
Indices: 2449001--2449086 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
2448991 TGGCCTGGCC
* * *
2449001 TATTTAACTAAACAGGTCAGACCCAGGCCTTTTTAAAAG-CT
1 TATTTAACTAAACAGGCCAGACCCAGGCCTATTAAAAAGCCT
**
2449042 TATTTAACTAAACAGGCCAGACTTAGGCCTATTAAAAAGCCT
1 TATTTAACTAAACAGGCCAGACCCAGGCCTATTAAAAAGCCT
2449084 TAT
1 TAT
2449087 AAGCCTGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 34 0.87
42 5 0.13
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (42 bp):
TATTTAACTAAACAGGCCAGACCCAGGCCTATTAAAAAGCCT
Found at i:2456227 original size:5 final size:5
Alignment explanation
Indices: 2456217--2456246 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2456207 AAAAGATTAT
*
2456217 AATAA AATAA AGTAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
2456247 TAAACAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:2456801 original size:2 final size:2
Alignment explanation
Indices: 2456794--2456836 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2456784 TAAATGGAAA
*
2456794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2456836 A
1 A
2456837 ATAAATGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2456907 original size:5 final size:5
Alignment explanation
Indices: 2456899--2456959 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
2456889 AATAATAGAG
* * * * *
2456899 AAATA AAATA ATACA AAATA AGATA TAATA ATAGTA AACA-A AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA A-AATA AA-ATA AAATA AAATA
2456950 AAATA AAATA
1 AAATA AAATA
2456960 GTAAAAACAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
4 1 0.02
5 38 0.88
6 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:2456926 original size:22 final size:23
Alignment explanation
Indices: 2456884--2456936 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
2456874 AGGGGAAAAT
*
2456884 ATAATAATAATAGAGAAATAA-A
1 ATAATAAAAATAGAGAAATAATA
*
2456906 ATAATACAAAATA-AGATATAATA
1 ATAATA-AAAATAGAGAAATAATA
*
2456929 ATAGTAAA
1 ATAATAAA
2456937 CAAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.25
Consensus pattern (23 bp):
ATAATAAAAATAGAGAAATAATA
Found at i:2456943 original size:36 final size:36
Alignment explanation
Indices: 2456887--2456983 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 36
2456877 GGAAAATATA
*
2456887 ATAATAATAGAGAAATAAAATAATACAAAATAAGAT
1 ATAATAATAGAGAAATAAAATAAAACAAAATAAGAT
* *
2456923 ATAATAATAGTA-AACA-AAAATAAAATAAAATAAAAT
1 ATAATAATAG-AGAA-ATAAAATAAAACAAAATAAGAT
* * *
2456959 AGTAAAAACAAAG-AATAAAATAAAA
1 A-TAATAATAGAGAAATAAAATAAAA
2456984 ATATGAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
35 1 0.02
36 41 0.82
37 8 0.16
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (36 bp):
ATAATAATAGAGAAATAAAATAAAACAAAATAAGAT
Found at i:2456949 original size:31 final size:30
Alignment explanation
Indices: 2456913--2456983 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 30
2456903 AAAATAATAC
2456913 AAAATAAGATATAATAATAGT-AAACAAA-AAT
1 AAAATAA-A-ATAA-AATAGTAAAACAAAGAAT
2456944 AAAATAAAATAAAATAGTAAAAACAAAGAAT
1 AAAATAAAATAAAATAGT-AAAACAAAGAAT
2456975 AAAATAAAA
1 AAAATAAAA
2456984 ATATGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.16
29 4 0.11
30 8 0.22
31 19 0.51
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (30 bp):
AAAATAAAATAAAATAGTAAAACAAAGAAT
Found at i:2458969 original size:108 final size:106
Alignment explanation
Indices: 2458772--2459032 Score: 299
Period size: 108 Copynumber: 2.4 Consensus size: 106
2458762 TGTATTGTTC
* * * ** * *
2458772 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTA-GAACTGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTGAATGAAATAGAAATTGTTTATTGACA
* * * * *
2458836 GCCAGTCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCT
66 GCCAGTCGCCCCTTCGCTATAAAGTTGAGCTTGTATTATCT
* *
2458877 CGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTGAATGAAATAGAAATGTTGTTTGTTGA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTGAATGAAATAGAAA--TTGTTTATTGA
* *
2458942 CAGTCAGTCGCCCCTTCGTTATAAAGTTGAGCTTGTATTATCT
64 CAGCCAGTCGCCCCTTCGCTATAAAGTTGAGCTTGTATTATCT
* * * *
2458985 CGAGTCTAATATTCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGA--CTGAATGAAA
2459033 CTGGGAAGCC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
105 35 0.27
106 8 0.06
108 77 0.59
110 10 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTGAATGAAATAGAAATTGTTTATTGACA
GCCAGTCGCCCCTTCGCTATAAAGTTGAGCTTGTATTATCT
Found at i:2460240 original size:13 final size:12
Alignment explanation
Indices: 2460222--2460257 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
2460212 ACCCTAAACG
2460222 TTTTTTCTCTTTT
1 TTTTTTCT-TTTT
2460235 TTTTTTCTTTTT
1 TTTTTTCTTTTT
2460247 TCTTTTTCTTT
1 T-TTTTTCTTT
2460258 CTTCGACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:2471748 original size:21 final size:20
Alignment explanation
Indices: 2471717--2471802 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
2471707 AAAACCAGAA
*
2471717 CCCTAGGGGGGTATCGATTC
1 CCCTAGGGGGGAATCGATTC
*
2471737 CCCTATGGGGGGAATCGGTTC
1 CCCTA-GGGGGGAATCGATTC
* * *
2471758 CTCTTCAAAGGGGGAATCGGTTC
1 C-C--CTAGGGGGGAATCGATTC
*
2471781 CCTCAAGGGGGG-ATCGATTC
1 CC-CTAGGGGGGAATCGATTC
2471801 CC
1 CC
2471803 TCTGCACCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.25
21 23 0.41
22 2 0.04
23 15 0.27
24 2 0.04
ACGTcount: A:0.17, C:0.26, G:0.34, T:0.23
Consensus pattern (20 bp):
CCCTAGGGGGGAATCGATTC
Found at i:2471790 original size:20 final size:21
Alignment explanation
Indices: 2471744--2471804 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2471734 TTCCCCTATG
2471744 GGGGGAATCGGTTCCTCTTCAAA
1 GGGGGAATCGGTTCC-C-TCAAA
2471767 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2471787 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2471805 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 1 0.03
23 15 0.42
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2475138 original size:14 final size:14
Alignment explanation
Indices: 2475119--2475157 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2475109 TAATGGGGAG
2475119 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
2475133 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
2475147 GAATCTCTGCA
1 TAATCCCTGCA
2475158 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:2483199 original size:4 final size:4
Alignment explanation
Indices: 2483192--2483257 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
2483182 AACAGATGGA
* * *
2483192 AAAT AAAT AAA- AATAA AAAT AAAT AAAA AAAT AAACCT AATT AAA- AAAT
1 AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAA--T AAAT AAAT AAAT
2483241 -AAT -AAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
2483258 ACTAATAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
3 11 0.22
4 35 0.69
5 2 0.04
6 3 0.06
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:2483213 original size:12 final size:12
Alignment explanation
Indices: 2483191--2483295 Score: 51
Period size: 12 Copynumber: 8.5 Consensus size: 12
2483181 AAACAGATGG
2483191 AAAATAAATAAA-
1 AAAA-AAATAAAT
2483203 AATAAAAATAAAT
1 AA-AAAAATAAAT
2483216 AAAAAAATAAACCT
1 AAAAAAATAAA--T
**
2483230 AATTAAA-AAAT
1 AAAAAAATAAAT
2483241 AATAATAAATAAAT
1 AA-AA-AAATAAAT
*
2483255 --AAAACT-AAT
1 AAAAAAATAAAT
2483264 AAGAAAAAT-AAT
1 AA-AAAAATAAAT
*
2483276 AAAAGAAAAGAAAT
1 -AAA-AAAATAAAT
2483290 AAAAAA
1 AAAAAA
2483296 CGATAATAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
9 3 0.04
10 3 0.04
11 5 0.07
12 30 0.41
13 19 0.26
14 13 0.18
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:2483253 original size:17 final size:16
Alignment explanation
Indices: 2483191--2483253 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
2483181 AAACAGATGG
2483191 AAAATAAAT-AAAAAT
1 AAAATAAATAAAAAAT
2483206 AAAAATAAATAAAAAAAT
1 -AAAATAAAT-AAAAAAT
* *
2483224 AAACCTAATTAAAAAAT
1 AAA-ATAAATAAAAAAT
2483241 AATAATAAATAAA
1 AA-AATAAATAAA
2483254 TAAAACTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.23
17 19 0.49
18 11 0.28
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAATAAAAAAT
Found at i:2483263 original size:17 final size:16
Alignment explanation
Indices: 2483200--2483270 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 16
2483190 GAAAATAAAT
*
2483200 AAAAATAAAAATAAATAA
1 AAAAATAAAACT-AAT-A
*
2483218 AAAAATAAACCTAATTA
1 AAAAATAAAACTAA-TA
2483235 AAAAAT--AA-TAATA
1 AAAAATAAAACTAATA
2483248 AATAAATAAAACTAATA
1 AA-AAATAAAACTAATA
2483265 AGAAAA
1 A-AAAA
2483271 ATAATAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
13 4 0.09
14 7 0.16
15 1 0.02
16 2 0.05
17 18 0.41
18 12 0.27
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (16 bp):
AAAAATAAAACTAATA
Found at i:2483264 original size:13 final size:11
Alignment explanation
Indices: 2483191--2483279 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 11
2483181 AAACAGATGG
*
2483191 AAAATAA-ATA
1 AAAATAATAAA
2483201 AAAATAA-AAA
1 AAAATAATAAA
* *
2483211 TAAATAAAAAA
1 AAAATAATAAA
*
2483222 ATAAACCTAATTAA
1 A-AAA--TAATAAA
2483236 AAAATAAT-AA
1 AAAATAATAAA
* *
2483246 TAAATAA-ATA
1 AAAATAATAAA
*
2483256 AAACTAATAAGA
1 AAAATAATAA-A
2483268 AAAATAATAAA
1 AAAATAATAAA
2483279 A
1 A
2483280 GAAAAGAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
10 29 0.48
11 10 0.16
12 13 0.21
13 3 0.05
14 6 0.10
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.20
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:2483277 original size:35 final size:33
Alignment explanation
Indices: 2483197--2483293 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 33
2483187 ATGGAAAATA
* *
2483197 AATAAAAATAAAAATAAATAAAAAAATAAACCT
1 AATAAAAATAATAATAAATAAAAAAATAAAACT
* *
2483230 AATTAAAA-AATAAT-AATAAATAAATAAAACT
1 AATAAAAATAATAATAAATAAAAAAATAAAACT
*
2483261 AATAAGAAA-AATAATAAAAGAAAAGAAATAAAA
1 AATAA-AAATAATAAT-AAATAAAA-AAATAAAA
2483294 AACGATAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 19 0.36
32 14 0.26
33 7 0.13
34 5 0.09
35 8 0.15
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (33 bp):
AATAAAAATAATAATAAATAAAAAAATAAAACT
Found at i:2483293 original size:9 final size:8
Alignment explanation
Indices: 2483191--2483295 Score: 54
Period size: 8 Copynumber: 12.8 Consensus size: 8
2483181 AAACAGATGG
2483191 AAAATAAAT
1 AAAA-AAAT
2483200 AAAAATAA-
1 AAAAA-AAT
*
2483208 AAATAAAT
1 AAAAAAAT
2483216 AAAAAAAT
1 AAAAAAAT
**
2483224 AAACCTAAT
1 AAA-AAAAT
*
2483233 TAAAAAAT
1 AAAAAAAT
*
2483241 --AATAAT
1 AAAAAAAT
*
2483247 AAATAAAT
1 AAAAAAAT
*
2483255 AAAACTAAT
1 AAAA-AAAT
2483264 AAGAAAAAT
1 AA-AAAAAT
* *
2483273 AATAAAAG
1 AAAAAAAT
2483281 AAAAGAAAT
1 AAAA-AAAT
2483290 AAAAAA
1 AAAAAA
2483296 CGATAATAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
6 5 0.07
7 2 0.03
8 34 0.48
9 28 0.39
10 2 0.03
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2483331 original size:20 final size:21
Alignment explanation
Indices: 2483300--2483347 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
2483290 AAAAAACGAT
* *
2483300 AATAAAGT-AAGGTTAAAA-C
1 AATAAAATAAAGGGTAAAATC
*
2483319 AATTAAATAAAGGGTAAAATC
1 AATAAAATAAAGGGTAAAATC
2483340 AATAAAAT
1 AATAAAAT
2483348 TTAAAGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.23
Consensus pattern (21 bp):
AATAAAATAAAGGGTAAAATC
Found at i:2483736 original size:2 final size:2
Alignment explanation
Indices: 2483729--2483803 Score: 92
Period size: 2 Copynumber: 41.0 Consensus size: 2
2483719 AAATAAATGA
2483729 AT AT AT AT AT AT A- AT A- AT A- AT A- AT A- AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2483764 AT AT AC 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
2483804 TAAATACTAA
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
1 7 0.11
2 57 0.89
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2483847 original size:5 final size:5
Alignment explanation
Indices: 2483839--2483911 Score: 85
Period size: 5 Copynumber: 14.0 Consensus size: 5
2483829 AATAATAGAG
* *
2483839 AAATA AAATA ATACA AAATA AGATATA ATAATA AACA-A AAATA AAATA
1 AAATA AAATA AAATA AAATA A-A-ATA A-AATA AA-ATA AAATA AAATA
2483887 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
2483912 GTAAAAACAA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
4 1 0.02
5 47 0.80
6 6 0.10
7 5 0.08
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:2483859 original size:15 final size:15
Alignment explanation
Indices: 2483829--2483911 Score: 78
Period size: 15 Copynumber: 5.3 Consensus size: 15
2483819 AAAATACAAT
*
2483829 AATAATAGAGAAATAA
1 AATAATATA-AAATAA
*
2483845 AATAATACAAAATAA
1 AATAATATAAAATAA
2483860 GATATAATAATAAACA-AA
1 -A-ATAAT-ATAAA-ATAA
*
2483878 AATAAAATAAAATAA
1 AATAATATAAAATAA
*
2483893 AATAAAATAAAATAA
1 AATAATATAAAATAA
2483908 AATA
1 AATA
2483912 GTAAAAACAA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.02
15 32 0.54
16 13 0.22
17 6 0.10
18 6 0.10
19 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (15 bp):
AATAATATAAAATAA
Found at i:2498887 original size:26 final size:27
Alignment explanation
Indices: 2498858--2498928 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 27
2498848 TATTTTTATT
2498858 ATATATTAATAAAATAATATTAA-AAA
1 ATATATTAATAAAATAATATTAATAAA
* *
2498884 ATATCTTATCATAAAA-ATTATTAATAAA
1 ATATATTA--ATAAAATAATATTAATAAA
* *
2498912 ATAGAGTAATTAAAATA
1 ATATATTAA-TAAAATA
2498929 GGAGCAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
26 8 0.23
27 12 0.34
28 15 0.43
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (27 bp):
ATATATTAATAAAATAATATTAATAAA
Found at i:2498912 original size:12 final size:13
Alignment explanation
Indices: 2498858--2498928 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 13
2498848 TATTTTTATT
2498858 ATATATTAATAAA
1 ATATATTAATAAA
2498871 ATAATATTAA-AAA
1 AT-ATATTAATAAA
*
2498884 ATATCTTATCATAAA
1 ATATATTA--ATAAA
2498899 A-ATTATTAATAAA
1 ATA-TATTAATAAA
* *
2498912 ATAGAGTAATTAAA
1 ATATATTAA-TAAA
2498926 ATA
1 ATA
2498929 GGAGCAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
12 5 0.11
13 17 0.36
14 17 0.36
15 8 0.17
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (13 bp):
ATATATTAATAAA
Found at i:2508481 original size:56 final size:57
Alignment explanation
Indices: 2508385--2508491 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 57
2508375 TGCACATACT
* *
2508385 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCACCAGCC
1 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCAAATGCATTTCATGCACCAGCC
*
2508442 ATGCATCGATGCACTCTG-GCTATTT-TG-AAACATCAAATGCATTTCATGCA
1 ATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCAAATGCATTTCATGCA
2508492 TCGGTGCACT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
56 22 0.49
57 20 0.44
58 3 0.07
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (57 bp):
ATGCATCGATGCACTCAGAGTTTTATGAAAACATCAAATGCATTTCATGCACCAGCC
Found at i:2515958 original size:21 final size:21
Alignment explanation
Indices: 2515916--2515959 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2515906 ACCCCTGGAG
* *
2515916 CTAGTTCTTCACGAGCTTCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
2515937 CTAGCTCTTCTCGCGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
2515958 CT
1 CT
2515960 CCTCCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.41, G:0.14, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:2517141 original size:65 final size:64
Alignment explanation
Indices: 2517023--2517230 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 64
2517013 TTTCAAAGTG
* * * **
2517023 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAAACCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
*
2517086 CC
63 TC
* * *
2517088 ATGAATCGATGCACAAACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGTATGCATT
1 ATGCATCGATGCACAAACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
*
2517151 TG
63 TC
* * *
2517153 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
*
2517217 ATGCATCGGTGCAC
1 ATGCATCGATGCAC
2517231 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 49 0.41
65 63 0.53
66 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:2519406 original size:2 final size:2
Alignment explanation
Indices: 2519399--2519424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2519389 GAAATACTTA
2519399 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
2519425 TGAAGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2519826 original size:3 final size:3
Alignment explanation
Indices: 2519818--2519904 Score: 167
Period size: 3 Copynumber: 29.3 Consensus size: 3
2519808 GTTTCAAAAT
2519818 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2519866 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2519905 GAGGAAAGTG
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2520253 original size:19 final size:20
Alignment explanation
Indices: 2520219--2520256 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2520209 ACCGCTAAAG
2520219 AACCGGTTGGGAACCGACAA
1 AACCGGTTGGGAACCGACAA
*
2520239 AACCGG-TGTGAACCGACA
1 AACCGGTTGGGAACCGACA
2520257 GTTCAAGCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.26, G:0.29, T:0.11
Consensus pattern (20 bp):
AACCGGTTGGGAACCGACAA
Found at i:2523719 original size:100 final size:102
Alignment explanation
Indices: 2523506--2523765 Score: 349
Period size: 100 Copynumber: 2.6 Consensus size: 102
2523496 TAGTTTGAGG
*
2523506 AATAAAATAAAATGTTAGTAA-GTTAGTATGAACAATAAAAATAAAATGTT---A-GTTAGTATG
1 AATAAAATAAAA-GTTAG-AATGTTAGTATGAACAATAAAAATAAAAAGTTAGAATGTTAGTATG
* *
2523566 AACAACAAAAATATAAAAAGTTAGAATGTTAGTATGAAC
64 AACAACAAAAATATAAAAAGTTAGAATGTTAATACGAAC
* *
2523605 ACTAAAAATAAAAAGTTAGAATGTTAGTATGAACAATAAAAATAAAAAATTAGAATGTTAGTATG
1 AAT-AAAAT-AAAAGTTAGAATGTTAGTATGAACAATAAAAATAAAAAGTTAGAATGTTAGTATG
*
2523670 AACAATAAAAATA-AAAAA-TTAGAATGTTAATACGAAC
64 AACAACAAAAATATAAAAAGTTAGAATGTTAATACGAAC
* *
2523707 AATAAAATAAAAGTTAGAATGTTAGTACGAACAGT-AAAAT-AAAAGTTAGAATGTTAGTA
1 AATAAAATAAAAGTTAGAATGTTAGTATGAACAATAAAAATAAAAAGTTAGAATGTTAGTA
2523766 AGTTAGTAAT
Statistics
Matches: 144, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
98 18 0.12
99 9 0.06
100 62 0.43
101 9 0.06
102 19 0.13
103 6 0.04
104 21 0.15
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (102 bp):
AATAAAATAAAAGTTAGAATGTTAGTATGAACAATAAAAATAAAAAGTTAGAATGTTAGTATGAA
CAACAAAAATATAAAAAGTTAGAATGTTAATACGAAC
Found at i:2523763 original size:32 final size:34
Alignment explanation
Indices: 2523509--2523765 Score: 334
Period size: 34 Copynumber: 7.7 Consensus size: 34
2523499 TTTGAGGAAT
*
2523509 AAAATAAAATGTTAGTAA-GTTAGTATGAACAATA
1 AAAATAAAAAGTTAG-AATGTTAGTATGAACAATA
* *
2523543 AAAATAAAATGTT---A-GTTAGTATGAACAACAA
1 AAAATAAAAAGTTAGAATGTTAGTATGAACAA-TA
*
2523574 AAATATAAAAAGTTAGAATGTTAGTATGAACACTA
1 AAA-ATAAAAAGTTAGAATGTTAGTATGAACAATA
2523609 AAAATAAAAAGTTAGAATGTTAGTATGAACAATA
1 AAAATAAAAAGTTAGAATGTTAGTATGAACAATA
*
2523643 AAAATAAAAAATTAGAATGTTAGTATGAACAATA
1 AAAATAAAAAGTTAGAATGTTAGTATGAACAATA
* * *
2523677 AAAATAAAAAATTAGAATGTTAATACGAACAAT-
1 AAAATAAAAAGTTAGAATGTTAGTATGAACAATA
* *
2523710 AAAAT-AAAAGTTAGAATGTTAGTACGAACAGT-
1 AAAATAAAAAGTTAGAATGTTAGTATGAACAATA
2523742 AAAAT-AAAAGTTAGAATGTTAGTA
1 AAAATAAAAAGTTAGAATGTTAGTA
2523766 AGTTAGTAAT
Statistics
Matches: 206, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
30 15 0.07
31 4 0.02
32 57 0.28
33 5 0.02
34 107 0.52
35 5 0.02
36 13 0.06
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (34 bp):
AAAATAAAAAGTTAGAATGTTAGTATGAACAATA
Found at i:2523785 original size:134 final size:134
Alignment explanation
Indices: 2523509--2523765 Score: 348
Period size: 134 Copynumber: 1.9 Consensus size: 134
2523499 TTTGAGGAAT
** ** * *
2523509 AAAATAAAATGTTAGTAA-GTTAGTATGAACAATAAAAATAAAATGTTAGTTAGTATGAACAACA
1 AAAATAAAAAATTAG-AATGTTAGTATGAACAATAAAAATAAAAAATTAGATAGTATAAACAACA
*
2523573 AAAATATAAAAAGTTAGAATGTTAGTATGAACACTAAAAATAAAAAGTTAGAATGTTAGTATGAA
65 AAAATATAAAAAGTTAGAATGTTAGTACGAACACTAAAAATAAAAAGTTAGAATGTTAGTATGAA
2523638 CAATA
130 CAATA
2523643 AAAATAAAAAATTAGAATGTTAGTATGAACAATAAAAATAAAAAATTAGA-ATGT-TAATACGAA
1 AAAATAAAAAATTAGAATGTTAGTATGAACAATAAAAATAAAAAATTAGATA-GTATAA-AC-AA
*
2523706 CAATAAA-AT-AAAAGTTAGAATGTTAGTACGAACAGT-AAAAT-AAAAGTTAGAATGTTAGTA
63 CAA-AAATATAAAAAGTTAGAATGTTAGTACGAACACTAAAAATAAAAAGTTAGAATGTTAGTA
2523766 AGTTAGTAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
132 19 0.17
133 10 0.09
134 71 0.65
135 7 0.06
136 3 0.03
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (134 bp):
AAAATAAAAAATTAGAATGTTAGTATGAACAATAAAAATAAAAAATTAGATAGTATAAACAACAA
AAATATAAAAAGTTAGAATGTTAGTACGAACACTAAAAATAAAAAGTTAGAATGTTAGTATGAAC
AATA
Found at i:2526907 original size:13 final size:13
Alignment explanation
Indices: 2526889--2526939 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
2526879 ATATTAATCC
*
2526889 CTATTTTTATTTT
1 CTATTTTTATCTT
2526902 CTATTTTTATCCTT
1 CTATTTTTAT-CTT
* *
2526916 CTTTTTTTCTCTT
1 CTATTTTTATCTT
2526929 CT-TTTTT-TCTT
1 CTATTTTTATCTT
2526940 TTCCATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.12
12 5 0.15
13 15 0.44
14 10 0.29
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (13 bp):
CTATTTTTATCTT
Found at i:2538424 original size:10 final size:10
Alignment explanation
Indices: 2538409--2538463 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
2538399 ATCAAAGACA
*
2538409 AAAATAAAAT
1 AAAATAAAAC
*
2538419 AAAATAAAAT
1 AAAATAAAAC
*
2538429 AAGAATAGAAC
1 AA-AATAAAAC
* *
2538440 GAGATAAAAC
1 AAAATAAAAC
2538450 AAAATAAAAC
1 AAAATAAAAC
2538460 AAAA
1 AAAA
2538464 CAAGATAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
10 30 0.81
11 7 0.19
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:2539300 original size:36 final size:34
Alignment explanation
Indices: 2539232--2539371 Score: 155
Period size: 36 Copynumber: 4.2 Consensus size: 34
2539222 ATGATAATAG
* *
2539232 GTTAGTATAAACAATAAAAATAAAAAGTTAGAAT
1 GTTAGTATGAACAATAAAAATAAAAAATTAGAAT
2539266 GTTAGTATGAACAATAAAAATAAAAAAAATTAGAAT
1 GTTAGTATGAACAATAAAAAT--AAAAAATTAGAAT
* *
2539302 GTTAGTACGAACAAT--AAA-AAAAAGTTAGAAT
1 GTTAGTATGAACAATAAAAATAAAAAATTAGAAT
* ** *
2539333 TTTAGTACAAACAAT-AAAAT-AAAAGTTAGAAT
1 GTTAGTATGAACAATAAAAATAAAAAATTAGAAT
2539365 GTTAGTA
1 GTTAGTA
2539372 AGTTAGTGAT
Statistics
Matches: 95, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
31 25 0.26
32 21 0.22
34 23 0.24
36 26 0.27
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.26
Consensus pattern (34 bp):
GTTAGTATGAACAATAAAAATAAAAAATTAGAAT
Found at i:2539330 original size:31 final size:31
Alignment explanation
Indices: 2539253--2539371 Score: 148
Period size: 31 Copynumber: 3.6 Consensus size: 31
2539243 CAATAAAAAT
*
2539253 AAAAAGTTAGAATGTTAGTATGAACAATAAAAATAA
1 AAAAAGTTAGAATGTTAGTACGAACAAT----A-AA
*
2539289 AAAAAATTAGAATGTTAGTACGAACAATAAA
1 AAAAAGTTAGAATGTTAGTACGAACAATAAA
* *
2539320 AAAAAGTTAGAATTTTAGTACAAACAATAAA
1 AAAAAGTTAGAATGTTAGTACGAACAATAAA
2539351 ATAAAAGTTAGAATGTTAGTA
1 A-AAAAGTTAGAATGTTAGTA
2539372 AGTTAGTGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
31 31 0.41
32 19 0.25
36 26 0.34
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.26
Consensus pattern (31 bp):
AAAAAGTTAGAATGTTAGTACGAACAATAAA
Found at i:2541129 original size:20 final size:22
Alignment explanation
Indices: 2541101--2541155 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
2541091 TTACAAACAC
*
2541101 AACATCAAACAA-TAAAG-AAA
1 AACAACAAACAACTAAAGTAAA
**
2541121 AACAACAAACAACTTCAGTAAA
1 AACAACAAACAACTAAAGTAAA
2541143 ACACAACAAACAA
1 A-ACAACAAACAA
2541156 ACTCAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 4 0.14
23 11 0.38
ACGTcount: A:0.65, C:0.22, G:0.04, T:0.09
Consensus pattern (22 bp):
AACAACAAACAACTAAAGTAAA
Found at i:2542256 original size:21 final size:23
Alignment explanation
Indices: 2542207--2542256 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2542197 TCATAAGGAT
2542207 CGTGTCACAAGAACAGAGGAAAAA
1 CGTGTCACAAGAACAGA-GAAAAA
*
2542231 CGTGTCACAAGAGCAGA-AAAAA
1 CGTGTCACAAGAACAGAGAAAAA
2542253 -GTGT
1 CGTGT
2542257 ATCACAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
24 16 0.64
ACGTcount: A:0.46, C:0.16, G:0.26, T:0.12
Consensus pattern (23 bp):
CGTGTCACAAGAACAGAGAAAAA
Found at i:2544137 original size:21 final size:22
Alignment explanation
Indices: 2544106--2544146 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2544096 TCTTATAATT
2544106 TATTCGAATTC-GATTTGATTAA
1 TATTCGAATTCAGA-TTGATTAA
2544128 TATTC-AATTCAGATTGATT
1 TATTCGAATTCAGATTGATT
2544147 CGAGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (22 bp):
TATTCGAATTCAGATTGATTAA
Found at i:2548084 original size:22 final size:21
Alignment explanation
Indices: 2548053--2548093 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2548043 GAATCATCAT
*
2548053 TTTTGGCTGGATTTTGTTTTCC
1 TTTTGGCTGG-GTTTGTTTTCC
*
2548075 TTTTGTCTGGGTTTGTTTT
1 TTTTGGCTGGGTTTGTTTT
2548094 AGAATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.02, C:0.10, G:0.24, T:0.63
Consensus pattern (21 bp):
TTTTGGCTGGGTTTGTTTTCC
Found at i:2548106 original size:34 final size:34
Alignment explanation
Indices: 2548063--2548146 Score: 150
Period size: 34 Copynumber: 2.5 Consensus size: 34
2548053 TTTTGGCTGG
*
2548063 ATTTTGTTTTCCTTTTGTCTGGGTTTGTTTTAGA
1 ATTTTGTTTTCCTTTTGTCTGGGTTTATTTTAGA
2548097 ATTTTGTTTTCCTTTTGTCTGGGTTTATTTTAGA
1 ATTTTGTTTTCCTTTTGTCTGGGTTTATTTTAGA
*
2548131 ATTTTGTTTTACTTTT
1 ATTTTGTTTTCCTTTT
2548147 AATGTTGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.11, C:0.08, G:0.17, T:0.64
Consensus pattern (34 bp):
ATTTTGTTTTCCTTTTGTCTGGGTTTATTTTAGA
Found at i:2552588 original size:2 final size:2
Alignment explanation
Indices: 2552583--2552632 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2552573 TTTTGTGTAC
2552583 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
2552625 AT AT AT AT
1 AT AT AT AT
2552633 TTGTTTATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.