Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 16
Found at i:2235575 original size:25 final size:25
Alignment explanation
Indices: 2235540--2235592 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2235530 ATGTTTATGT
* *
2235540 TTATTTAATTTATTTTATTA-TTTTA
1 TTATTTAATTT-TTTAATTAGGTTTA
*
2235565 TTATTTGATTTTTTAATTAGGTTTA
1 TTATTTAATTTTTTAATTAGGTTTA
2235590 TTA
1 TTA
2235593 ATTGTTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (25 bp):
TTATTTAATTTTTTAATTAGGTTTA
Found at i:2235583 original size:16 final size:17
Alignment explanation
Indices: 2235543--2235583 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2235533 TTTATGTTTA
*
2235543 TTTAATTTATTTTATTAT
1 TTTAA-TTATTTGATTAT
2235561 TTT-ATTATTTGATT-T
1 TTTAATTATTTGATTAT
2235576 TTTAATTA
1 TTTAATTA
2235584 GGTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 1 0.05
18 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTAATTATTTGATTAT
Found at i:2238857 original size:7 final size:7
Alignment explanation
Indices: 2238831--2238877 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
2238821 TTCGGGTTTT
2238831 TTTTC-C
1 TTTTCTC
*
2238837 TTTTTTC
1 TTTTCTC
2238844 TTCTTCTC
1 TT-TTCTC
2238852 TTTTCTC
1 TTTTCTC
2238859 TTCTTCTC
1 TT-TTCTC
2238867 TTTTCTC
1 TTTTCTC
2238874 TTTT
1 TTTT
2238878 TTTTCAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
6 4 0.11
7 19 0.53
8 13 0.36
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTCTC
Found at i:2238860 original size:15 final size:15
Alignment explanation
Indices: 2238836--2238875 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
2238826 GTTTTTTTTC
*
2238836 CTTTTTTCTTCTTCT
1 CTTTTCTCTTCTTCT
2238851 CTTTTCTCTTCTTCT
1 CTTTTCTCTTCTTCT
2238866 CTTTTCTCTT
1 CTTTTCTCTT
2238876 TTTTTTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
CTTTTCTCTTCTTCT
Found at i:2239547 original size:22 final size:23
Alignment explanation
Indices: 2239516--2239559 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2239506 ATTTTTATCC
2239516 TTTTCCTTTTT-TTGTTTCTTTTA
1 TTTTCCTTTTTCTT-TTTCTTTTA
2239539 TTTT-CTTTTTCTTTTTCTTTT
1 TTTTCCTTTTTCTTTTTCTTTT
2239560 TCTTCAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTCCTTTTTCTTTTTCTTTTA
Found at i:2239550 original size:6 final size:6
Alignment explanation
Indices: 2239539--2239563 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2239529 GTTTCTTTTA
2239539 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
2239564 CAAGCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:2241452 original size:20 final size:20
Alignment explanation
Indices: 2241424--2241471 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2241414 TTTGAAATGA
* * *
2241424 TATCCATACCTTCCCTTCGG
1 TATCGATACCTACCCGTCGG
2241444 TATCGATACCTACCCGTCGG
1 TATCGATACCTACCCGTCGG
2241464 TATCGATA
1 TATCGATA
2241472 TTGATTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (20 bp):
TATCGATACCTACCCGTCGG
Found at i:2254254 original size:47 final size:47
Alignment explanation
Indices: 2254122--2254383 Score: 224
Period size: 47 Copynumber: 5.8 Consensus size: 47
2254112 TCTTTTTTTG
* * *
2254122 TTTGGAAAATGTTTTGAGAAATCTTCTAAAATT-AT-TTT-TTTCC-
1 TTTGAAAAATATTTTGAGAGATCTTCTAAAATTAATCTTTCTTTCCT
* * * **
2254165 TTCGAAAAATATTTTTAGAGATCTTCTAAAATCAATAC-TTCTTTAAT
1 TTTGAAAAATATTTTGAGAGATCTTCTAAAATTAAT-CTTTCTTTCCT
* *
2254212 TTTGAAAAATATTTTGAGAGATTTTCTGAAATTAAGT-TTTCTTTCCT
1 TTTGAAAAATATTTTGAGAGATCTTCTAAAATTAA-TCTTTCTTTCCT
* * * * *
2254259 TTTGAAAATTGTTTCGAGAGA---TCTAAAATTAGTCTCTCTTTCCT
1 TTTGAAAAATATTTTGAGAGATCTTCTAAAATTAATCTTTCTTTCCT
* * * * * *
2254303 TTTG-AAAATATTTT-AAAGATATTATGAAATTAATCTTTGTTTTCT
1 TTTGAAAAATATTTTGAGAGATCTTCTAAAATTAATCTTTCTTTCCT
2254348 TTTGAAAAAT-TTTGTGAGAGATCTTCTAAAATTAAT
1 TTTGAAAAATATTT-TGAGAGATCTTCTAAAATTAAT
2254384 ATCTCATTTA
Statistics
Matches: 170, Mismatches: 35, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
42 4 0.02
43 35 0.21
44 24 0.14
45 26 0.15
46 9 0.05
47 71 0.42
48 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (47 bp):
TTTGAAAAATATTTTGAGAGATCTTCTAAAATTAATCTTTCTTTCCT
Found at i:2265777 original size:26 final size:27
Alignment explanation
Indices: 2265734--2265784 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2265724 TGGTGCATGA
2265734 ACTTCAATTTAGTCTATTT-TTTTAGT
1 ACTTCAATTTAGTCTATTTATTTTAGT
*
2265760 ACTTCTAATTTA-TTTATTTATTTTA
1 ACTTC-AATTTAGTCTATTTATTTTA
2265785 CAAATTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.61
Consensus pattern (27 bp):
ACTTCAATTTAGTCTATTTATTTTAGT
Found at i:2268764 original size:24 final size:24
Alignment explanation
Indices: 2268737--2268791 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
2268727 GTTTGGTTCG
*
2268737 ATTAATATTTAAA-AAATTGATTT-A
1 ATTAATA-TTAAAGAAAATG-TTTCA
2268761 ATTAACTATTAAAGAAAATGTTTCA
1 ATTAA-TATTAAAGAAAATGTTTCA
2268786 ATTAAT
1 ATTAAT
2268792 TTGATTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (24 bp):
ATTAATATTAAAGAAAATGTTTCA
Found at i:2268976 original size:25 final size:25
Alignment explanation
Indices: 2268945--2269022 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
2268935 ATTAAAAAAT
2268945 ATAATATTATTAAAATTATATTATA
1 ATAATATTATTAAAATTATATTATA
* * *
2268970 ATAATATTA--AATATTTTAATAATTA
1 ATAATATTATTAAAATTAT-ATTA-TA
* * *
2268995 ATAATTTTATTAAAATCATATTAAA
1 ATAATATTATTAAAATTATATTATA
2269020 ATA
1 ATA
2269023 TTAAATTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
23 6 0.15
24 3 0.08
25 23 0.57
26 3 0.08
27 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
ATAATATTATTAAAATTATATTATA
Found at i:2268990 original size:40 final size:39
Alignment explanation
Indices: 2268921--2269025 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 39
2268911 TATTTGAGTA
** * *
2268921 TATATTAACGTAATATTAAAAAATATAATATTATTAA-AAT
1 TATATTAAAATAATATTAAATATTATAATA--ATTAATAAT
* *
2268961 TATATTATAATAATATTAAATATTTTAATAATTAATAAT
1 TATATTAAAATAATATTAAATATTATAATAATTAATAAT
* *
2269000 TTTATTAAAATCATATTAAAATATTA
1 TATATTAAAATAATATT-AAATATTA
2269026 AATTAATATT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 5 0.09
39 17 0.32
40 31 0.58
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (39 bp):
TATATTAAAATAATATTAAATATTATAATAATTAATAAT
Found at i:2269024 original size:19 final size:19
Alignment explanation
Indices: 2268931--2269053 Score: 63
Period size: 19 Copynumber: 6.3 Consensus size: 19
2268921 TATATTAACG
* *
2268931 TAATATTAAAA-AATATAA
1 TAATATTAAAATATTAAAA
* *
2268949 TATTATTAAAATTATATTATAA
1 TAATATT-AAA--ATATTAAAA
**
2268971 TAATATT-AAATATTTTAA
1 TAATATTAAAATATTAAAA
* **
2268989 TAATTAATAATTTTATTAAAA
1 TAA-TATTAA-AATATTAAAA
* *
2269010 TCATATTAAAATATTAAAT
1 TAATATTAAAATATTAAAA
*
2269029 TAATATT-AAATAAATAAAA
1 TAATATTAAAAT-ATTAAAA
2269048 TAATAT
1 TAATAT
2269054 ACTTTTTTGA
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
18 21 0.26
19 30 0.38
20 8 0.10
21 9 0.11
22 12 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATATTAAAATATTAAAA
Found at i:2269041 original size:50 final size:51
Alignment explanation
Indices: 2268897--2269049 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 51
2268887 CAAACATTAT
* * *
2268897 ATATTATTATAAT-ATATT-TGAGTATATATTAACGTAATATTAAA-AAATATA
1 ATATTATTAAAATCATATTAT-AATA-ATATTAA-ATAATATTAAATAAATATA
* * *
2268948 ATATTATTAAAATTATATTATAATAATATTAAAT-AT-TTTAATAATTAATA
1 ATATTATTAAAATCATATTATAATAATATTAAATAATATTAAATAAAT-ATA
* *
2268998 ATTTTATTAAAATCATA-T-TAA-AATATTAAATTAATATTAAATAAATAAA
1 ATATTATTAAAATCATATTATAATAATATTAAA-TAATATTAAATAAATATA
2269047 ATA
1 ATA
2269050 ATATACTTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
47 9 0.11
48 8 0.10
49 12 0.14
50 27 0.32
51 19 0.23
52 8 0.10
53 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (51 bp):
ATATTATTAAAATCATATTATAATAATATTAAATAATATTAAATAAATATA
Found at i:2269045 original size:47 final size:49
Alignment explanation
Indices: 2268897--2269045 Score: 121
Period size: 51 Copynumber: 3.0 Consensus size: 49
2268887 CAAACATTAT
* * * *
2268897 ATATTATTATAAT-ATATT-TGAGTATATATTAACGTAATATTAAAAAATATA
1 ATATTATTAAAATCATATTAT-AATA-ATATTAA-ATAATATTAAATAA-ATA
* * *
2268948 ATATTATTAAAATTATATTATAATAATATTAAAT-ATTTTAATAATTAATA
1 ATATTATTAAAATCATATTATAATAATATTAAATAATATT-A-AATAAATA
*
2268998 ATTTTATTAAAATCATA-T-TAA-AATATTAAATTAATATTAAATAAATA
1 ATATTATTAAAATCATATTATAATAATATTAAA-TAATATTAAATAAATA
2269045 A
1 A
2269046 AATAATATAC
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
47 17 0.21
48 5 0.06
49 9 0.11
50 20 0.24
51 22 0.27
52 8 0.10
53 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (49 bp):
ATATTATTAAAATCATATTATAATAATATTAAATAATATTAAATAAATA
Found at i:2269167 original size:18 final size:18
Alignment explanation
Indices: 2269146--2269180 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2269136 ATAAAGAAAC
2269146 TAGAAAAATTAATTACTT
1 TAGAAAAATTAATTACTT
2269164 TAGAAAAATTAATTACT
1 TAGAAAAATTAATTACT
2269181 ACTATCAAAT
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:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
TAGAAAAATTAATTACTT
Found at i:2269254 original size:41 final size:42
Alignment explanation
Indices: 2269168--2269248 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
2269158 TTACTTTAGA
* * *
2269168 AAAATTAATTACTACTATCAAATACTGAAAAATATTTTTCAT
1 AAAATAAATTACTACTATCAAACACTAAAAAATATTTTTCAT
*
2269210 AAAATAAATTA-TAACTATTAAACACTAAAAAATATTTTT
1 AAAATAAATTACT-ACTATCAAACACTAAAAAATATTTTT
2269249 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (42 bp):
AAAATAAATTACTACTATCAAACACTAAAAAATATTTTTCAT
Found at i:2269260 original size:41 final size:42
Alignment explanation
Indices: 2269181--2269260 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
2269171 ATTAATTACT
* * *
2269181 ACTATCAAATACTGAAAAATATTTTTCATAAAATAAATTATA
1 ACTATCAAACACTAAAAAATATTTTTCATAAAAAAAATTATA
* *
2269223 ACTATTAAACACTAAAAAATATTTTT-TTAAAAAAAATT
1 ACTATCAAACACTAAAAAATATTTTTCATAAAAAAAATT
2269261 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 10 0.30
42 23 0.70
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (42 bp):
ACTATCAAACACTAAAAAATATTTTTCATAAAAAAAATTATA
Found at i:2272473 original size:15 final size:15
Alignment explanation
Indices: 2272450--2272479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2272440 CATTGAGTCC
2272450 TTTAAAATTTAAATT
1 TTTAAAATTTAAATT
*
2272465 TTTATAATTTAAATT
1 TTTAAAATTTAAATT
2272480 AATAATGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAAATTTAAATT
Found at i:2280289 original size:55 final size:54
Alignment explanation
Indices: 2280219--2280428 Score: 267
Period size: 55 Copynumber: 3.8 Consensus size: 54
2280209 TTGCATTTAC
*
2280219 CGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTGTATGAATTA
1 CGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTTTATGAATTA
* * * *
2280273 TCGTATTGGCATTATGTGTGCAACCCCACGTAATTCATAACGAATTTATGAATTA
1 -CGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTTTATGAATTA
* * * *
2280328 CCGTATTGGCACTATGTGTGCAACCCCACGTAATCCATAAGGAGTTTGTGAATTA
1 -CGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTTTATGAATTA
* ** * *
2280383 CTGTATTGGCGCTATGTGTGCAAAACCACATAATTTATAATAAGTT
1 C-GTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTT
2280429 GAATATTCAA
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 1 0.01
55 134 0.99
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
CGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTTTATGAATTA
Found at i:2280417 original size:110 final size:110
Alignment explanation
Indices: 2280215--2280422 Score: 301
Period size: 110 Copynumber: 1.9 Consensus size: 110
2280205 TATGTTGCAT
* *
2280215 TTACCGTATTGGCACTATGTGTGCAACCCCACATAATTCATAATGAGTGTATGAATTATCGTATT
1 TTACCGTATTGGCACTATGTGTGCAACCCCACATAATCCATAAGGAGTGTATGAATTATCGTATT
* ** *
2280280 GGCATTATGTGTGCAACCCCACGTAATTCATAACGAATTTATGAA
66 GGCACTATGTGTGCAAAACCACATAATTCATAACGAATTTATGAA
* * *
2280325 TTACCGTATTGGCACTATGTGTGCAACCCCACGTAATCCATAAGGAGTTTGTGAATTA-CTGTAT
1 TTACCGTATTGGCACTATGTGTGCAACCCCACATAATCCATAAGGAGTGTATGAATTATC-GTAT
* *
2280389 TGGCGCTATGTGTGCAAAACCACATAATTTATAA
65 TGGCACTATGTGTGCAAAACCACATAATTCATAA
2280423 TAAGTTGAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
109 1 0.01
110 85 0.99
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (110 bp):
TTACCGTATTGGCACTATGTGTGCAACCCCACATAATCCATAAGGAGTGTATGAATTATCGTATT
GGCACTATGTGTGCAAAACCACATAATTCATAACGAATTTATGAA
Found at i:2282232 original size:18 final size:18
Alignment explanation
Indices: 2282209--2282248 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2282199 TTTTTTTGAT
*
2282209 TTTCTGATTCATGG-TTAA
1 TTTCTGATT-AAGGATTAA
2282227 TTTCTGATTAAGGATTAA
1 TTTCTGATTAAGGATTAA
2282245 TTTC
1 TTTC
2282249 CTCAAGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (18 bp):
TTTCTGATTAAGGATTAA
Found at i:2283976 original size:17 final size:17
Alignment explanation
Indices: 2283934--2283976 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2283924 CCAGCATCGT
2283934 TTATTTTAGTTATATAA
1 TTATTTTAGTTATATAA
*
2283951 TTATATTTA-TTATTTAA
1 TTAT-TTTAGTTATATAA
2283968 TATATTTTA
1 T-TATTTTA
2283977 CACTTTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTATTTTAGTTATATAA
Found at i:2284102 original size:27 final size:27
Alignment explanation
Indices: 2284064--2284116 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2284054 ATGAAGATCT
*
2284064 TGATGCTGTGGACTTTCAAGTTCAAAA
1 TGATGCTATGGACTTTCAAGTTCAAAA
*
2284091 TGATGCTATGGAGTTTCAAGTTCAAA
1 TGATGCTATGGACTTTCAAGTTCAAA
2284117 GTCGTCATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAGTTCAAAA
Found at i:2285863 original size:664 final size:664
Alignment explanation
Indices: 2284595--2285923 Score: 2604
Period size: 664 Copynumber: 2.0 Consensus size: 664
2284585 AATTAATAAT
2284595 ATAAATTTACTATAATTTAAATCTACAAAGTTAGCTTGCAGCGAGAGGAAACTCAATAGGAGCGG
1 ATAAATTTACTATAATTTAAATCTACAAAGTTAGCTTGCAGCGAGAGGAAACTCAATAGGAGCGG
*
2284660 TTGTAATATGCATAAAAAATGGAAAACGATATCACGCCCATGATTGGAGTAAGAATAAACAACCC
66 TTGTAATAGGCATAAAAAATGGAAAACGATATCACGCCCATGATTGGAGTAAGAATAAACAACCC
2284725 TATATCTGCATTTTGCCCTCTAACCACTATGGTCTCCTTATAAAGTTCACGATATAAAAAAGAAA
131 TATATCTGCATTTTGCCCTCTAACCACTATGGTCTCCTTATAAAGTTCACGATATAAAAAAGAAA
*
2284790 AATTATTGAACCCAATTATACTGGCGATATACGAAGAAATCTTCCAATACTGAAGGATACTAGGT
196 AATTATTGAACCCAATTATACTGGCGATATACAAAGAAATCTTCCAATACTGAAGGATACTAGGT
2284855 GTGCACCAAATTCCCAGATTTATCCGATAACAAGATCCCTCTAATCAATGTCATAAGATATGCTC
261 GTGCACCAAATTCCCAGATTTATCCGATAACAAGATCCCTCTAATCAATGTCATAAGATATGCTC
2284920 GGGCTGCAAATATCGCCTCTTGTTCTGTTGATTGTTCATATACTCTAAATTCTTTCTCCAACCAC
326 GGGCTGCAAATATCGCCTCTTGTTCTGTTGATTGTTCATATACTCTAAATTCTTTCTCCAACCAC
*
2284985 GTCATTTGTATCCACAACCCATCGGTGACATCGATTGGAGGCTCCTTTCCGAATAAATAAAAAAT
391 GTCATTTGTATCCACAACCCATCGGTGACATCGATTGGAGGCTCCATTCCGAATAAATAAAAAAT
2285050 AAGCTTATCTCACTTATAATTTTTGCGAAGCACCAATGGAACACCATTAATCGAAGCACCAAGTT
456 AAGCTTATCTCACTTATAATTTTTGCGAAGCACCAATGGAACACCATTAATCGAAGCACCAAGTT
2285115 GATAAGCGACATCTTCTACTGTTATGGTTGTTTCACCACAAGGAAAATAGAATGTATGAGTTTTG
521 GATAAGCGACATCTTCTACTGTTATGGTTGTTTCACCACAAGGAAAATAGAATGTATGAGTTTTG
2285180 GGCCTCTAACATTCAATCAGTACCAATATCAGTGTCGACATCACCTTAAAACTACGAAACATGTG
586 GGCCTCTAACATTCAATCAGTACCAATATCAGTGTCGACATCACCTTAAAACTACGAAACATGTG
2285245 GTAGGATACAATCC
651 GTAGGATACAATCC
2285259 ATAAATTTACTATAATTTAAATCTACAAAGTTAGCTTGCAGCGAGAGGAAACTCAATAGGAGCGG
1 ATAAATTTACTATAATTTAAATCTACAAAGTTAGCTTGCAGCGAGAGGAAACTCAATAGGAGCGG
2285324 TTGTAATAGGCATAAAAAATGGAAAACGATATCACGCCCATGATTGGAGTAAGAATAAACAACCC
66 TTGTAATAGGCATAAAAAATGGAAAACGATATCACGCCCATGATTGGAGTAAGAATAAACAACCC
2285389 TATATCTGCATTTTGCCCTCTAACCACTATGGTCTCCTTATAAAGTTCACGATATAAAAAAGAAA
131 TATATCTGCATTTTGCCCTCTAACCACTATGGTCTCCTTATAAAGTTCACGATATAAAAAAGAAA
2285454 AATTATTGAACCCAATTATACTGGCGATATACAAAGAAATCTTCCAATACTGAAGGATACTAGGT
196 AATTATTGAACCCAATTATACTGGCGATATACAAAGAAATCTTCCAATACTGAAGGATACTAGGT
*
2285519 GTGCACCAAATTCCCAGATTTATCCGATAACAAGATCCCTCTAATCAATGTTATAAGATATGCTC
261 GTGCACCAAATTCCCAGATTTATCCGATAACAAGATCCCTCTAATCAATGTCATAAGATATGCTC
*
2285584 GGGCTGCAAATATCGCCTCTTGTTCTGTTGATTGTTCATATACTCTAAATTCTTTCTCCAACCAT
326 GGGCTGCAAATATCGCCTCTTGTTCTGTTGATTGTTCATATACTCTAAATTCTTTCTCCAACCAC
*
2285649 GTCATTTGTATCCACAACCCATCGGTGACATCGATTGGAGGCTCCATTCTGAATAAATAAAAAAT
391 GTCATTTGTATCCACAACCCATCGGTGACATCGATTGGAGGCTCCATTCCGAATAAATAAAAAAT
2285714 AAGCTTATCTCACTTATAATTTTTGCGAAGCACCAATGGAACACCATTAATCGAAGCACCAAGTT
456 AAGCTTATCTCACTTATAATTTTTGCGAAGCACCAATGGAACACCATTAATCGAAGCACCAAGTT
2285779 GATAAGCGACATCTTCTACTGTTATGGTTGTTTCACCACAAGGAAAATAGAATGTATGAGTTTTG
521 GATAAGCGACATCTTCTACTGTTATGGTTGTTTCACCACAAGGAAAATAGAATGTATGAGTTTTG
2285844 GGCCTCTAACATTCAATCAGTACCAATATCAGTGTCGACATCACCTTAAAACTACGAAACATGTG
586 GGCCTCTAACATTCAATCAGTACCAATATCAGTGTCGACATCACCTTAAAACTACGAAACATGTG
2285909 GTAGGATACAATCC
651 GTAGGATACAATCC
2285923 A
1 A
2285924 GATTGTTAAA
Statistics
Matches: 659, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
664 659 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (664 bp):
ATAAATTTACTATAATTTAAATCTACAAAGTTAGCTTGCAGCGAGAGGAAACTCAATAGGAGCGG
TTGTAATAGGCATAAAAAATGGAAAACGATATCACGCCCATGATTGGAGTAAGAATAAACAACCC
TATATCTGCATTTTGCCCTCTAACCACTATGGTCTCCTTATAAAGTTCACGATATAAAAAAGAAA
AATTATTGAACCCAATTATACTGGCGATATACAAAGAAATCTTCCAATACTGAAGGATACTAGGT
GTGCACCAAATTCCCAGATTTATCCGATAACAAGATCCCTCTAATCAATGTCATAAGATATGCTC
GGGCTGCAAATATCGCCTCTTGTTCTGTTGATTGTTCATATACTCTAAATTCTTTCTCCAACCAC
GTCATTTGTATCCACAACCCATCGGTGACATCGATTGGAGGCTCCATTCCGAATAAATAAAAAAT
AAGCTTATCTCACTTATAATTTTTGCGAAGCACCAATGGAACACCATTAATCGAAGCACCAAGTT
GATAAGCGACATCTTCTACTGTTATGGTTGTTTCACCACAAGGAAAATAGAATGTATGAGTTTTG
GGCCTCTAACATTCAATCAGTACCAATATCAGTGTCGACATCACCTTAAAACTACGAAACATGTG
GTAGGATACAATCC
Found at i:2300883 original size:23 final size:23
Alignment explanation
Indices: 2300812--2300885 Score: 59
Period size: 26 Copynumber: 3.2 Consensus size: 23
2300802 ATTATAATAT
2300812 AAATTATAATATACAATTTAA-A
1 AAATTATAATATACAATTTAACA
*
2300834 AAA--AGT-ATATA-AATTAAAGCATAA
1 AAATTA-TAATATACAATTTAA-C---A
2300858 AAATTATAATATACAATTTAACA
1 AAATTATAATATACAATTTAACA
2300881 AAATT
1 AAATT
2300886 CATATAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 19
0.66 0.03 0.31
Matches are distributed among these distances:
19 6 0.15
20 6 0.15
21 1 0.03
22 3 0.08
23 6 0.15
24 4 0.10
25 1 0.03
26 7 0.17
27 6 0.15
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (23 bp):
AAATTATAATATACAATTTAACA
Found at i:2302073 original size:32 final size:33
Alignment explanation
Indices: 2302035--2302119 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 33
2302025 TATCAATTAC
*
2302035 ATTCTAAACCCCAAA-TCTAAAATACTTCAATT
1 ATTCTAAACCCCAAATTCCAAAATACTTCAATT
*
2302067 ATTCTAAACCTCAAATTCCAAAATACTTCAATT
1 ATTCTAAACCCCAAATTCCAAAATACTTCAATT
**
2302100 ATATGCCCAACCCCAAATTC
1 AT-T-CTAAACCCCAAATTC
2302120 ATAATCCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 14 0.31
33 18 0.40
34 1 0.02
35 12 0.27
ACGTcount: A:0.41, C:0.28, G:0.01, T:0.29
Consensus pattern (33 bp):
ATTCTAAACCCCAAATTCCAAAATACTTCAATT
Found at i:2302825 original size:15 final size:15
Alignment explanation
Indices: 2302805--2302834 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2302795 TACAACTCGA
2302805 TTTTAACTTGAATTT
1 TTTTAACTTGAATTT
*
2302820 TTTTAAGTTGAATTT
1 TTTTAACTTGAATTT
2302835 ATGAAATTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (15 bp):
TTTTAACTTGAATTT
Found at i:2303180 original size:35 final size:36
Alignment explanation
Indices: 2303141--2303223 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 36
2303131 GGGGTTGGGC
2303141 ATGTAATTGA-AGTA-TTTTGGAATTT-GAGGTTTAGA
1 ATGTAATTGATA-TATTTTTGGAATTTAG-GGTTTAGA
*
2303176 ATGTAATTGATATATTTTTTTGAATTTAGGGTTTAGA
1 ATGTAATTGATATA-TTTTTGGAATTTAGGGTTTAGA
*
2303213 ATATAATTGAT
1 ATGTAATTGAT
2303224 GACTGTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 12 0.29
36 1 0.02
37 28 0.67
38 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (36 bp):
ATGTAATTGATATATTTTTGGAATTTAGGGTTTAGA
Found at i:2303723 original size:28 final size:28
Alignment explanation
Indices: 2303690--2303746 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2303680 ACCGTCATTT
*
2303690 TTTTAAACACTAACTTGATGACATAATA
1 TTTTAAACACTAACTCGATGACATAATA
** *
2303718 TTTTAAGTACTAACTCGATGTCATAATA
1 TTTTAAACACTAACTCGATGACATAATA
2303746 T
1 T
2303747 AAATATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (28 bp):
TTTTAAACACTAACTCGATGACATAATA
Found at i:2304461 original size:23 final size:23
Alignment explanation
Indices: 2304435--2304491 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
2304425 TTTATGGAAT
2304435 TAATTTTTTTTAAAGAAAATATA
1 TAATTTTTTTTAAAGAAAATATA
2304458 TAATTTTTTTTAAAGAAAATATA
1 TAATTTTTTTTAAAGAAAATATA
2304481 TAATTTTTTTT
1 TAATTTTTTTT
2304492 CAATTTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TAATTTTTTTTAAAGAAAATATA
Found at i:2309278 original size:15 final size:15
Alignment explanation
Indices: 2309258--2309287 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2309248 TGAAATGAGA
*
2309258 TTTTAGATTTTTTAT
1 TTTTAGATATTTTAT
2309273 TTTTAGATATTTTAT
1 TTTTAGATATTTTAT
2309288 AAAATATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTTAGATATTTTAT
Found at i:2319373 original size:29 final size:28
Alignment explanation
Indices: 2319314--2319373 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2319304 AAATAGTACA
* *
2319314 AAATAGTAAAAATAGAAACTTAAGGTCT
1 AAATAGCAAAAATAGAAACTTAAGGGCT
* *
2319342 AAATAGCAAAAATAGGAACTTTAGGGGCT
1 AAATAGCAAAAATAGAAAC-TTAAGGGCT
2319371 AAA
1 AAA
2319374 ATAAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (28 bp):
AAATAGCAAAAATAGAAACTTAAGGGCT
Found at i:2319412 original size:29 final size:30
Alignment explanation
Indices: 2319378--2319450 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
2319368 GCTAAAATAA
* *
2319378 ATAAAACAAAAATTTTAGGGA-CAAAAT-G
1 ATAAAACAAAAACTTCAGGGACCAAAATGG
2319406 ATAAAA-AAGAAACTTCAGGGACCAAAATGG
1 ATAAAACAA-AAACTTCAGGGACCAAAATGG
2319436 ATAAAACAAAAACTT
1 ATAAAACAAAAACTT
2319451 AAAGAACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 2 0.05
28 16 0.41
29 6 0.15
30 13 0.33
31 2 0.05
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.18
Consensus pattern (30 bp):
ATAAAACAAAAACTTCAGGGACCAAAATGG
Found at i:2319463 original size:30 final size:29
Alignment explanation
Indices: 2319358--2319578 Score: 100
Period size: 30 Copynumber: 7.6 Consensus size: 29
2319348 CAAAAATAGG
* * *
2319358 AACTTTAGGGGCTAAAATAAATAAAACAAA
1 AACTTAAGGGACTAAAAT-GATAAAACAAA
* *
2319388 AATTTTAGGGAC-AAAATGATAAAA-AAGA
1 AACTTAAGGGACTAAAATGATAAAACAA-A
* *
2319416 AACTTCAGGGACCAAAATGGATAAAACAAA
1 AACTTAAGGGACTAAAAT-GATAAAACAAA
* * *
2319446 AACTTAAAGAACTAAAATAGA-AAAATAGAA
1 AACTTAAGGGACTAAAAT-GATAAAACA-AA
* * *
2319476 AA-TT-AGGGA-TAAAATAATAATTACAGA
1 AACTTAAGGGACTAAAATGATAA-AACAAA
* * ***
2319503 AAGTTAAAGGG-CTAAAA-AATACAAACTGG
1 AACTT-AAGGGACTAAAATGATA-AAACAAA
* * *
2319532 AATTTAAGGGACTAAACTAATAAAAACAAA
1 AACTTAAGGGACTAAAATGAT-AAAACAAA
2319562 AACTTAAAGGG-CTAAAA
1 AACTT-AAGGGACTAAAA
2319579 CAACATAAAC
Statistics
Matches: 148, Mismatches: 27, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
26 1 0.01
27 13 0.09
28 29 0.20
29 33 0.22
30 64 0.43
31 8 0.05
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (29 bp):
AACTTAAGGGACTAAAATGATAAAACAAA
Found at i:2319595 original size:59 final size:56
Alignment explanation
Indices: 2319438--2319607 Score: 128
Period size: 59 Copynumber: 2.9 Consensus size: 56
2319428 CAAAATGGAT
** * *
2319438 AAAACAAAAACTTAAAGAACTAAAATAGAAAAATAGAAAATT-AGGGA-TAAAATAATA
1 AAAACAAAAACTTAAAGGGCTAAAA-A-AAAAACA-AAATTTAAGGGACTAAAATAATA
** * * ** *
2319495 ATTACAGAAAGTTAAAGGGCTAAAAAATACAAACTGGAATTTAAGGGACTAAACTAATA
1 AAAACAAAAACTTAAAGGGCTAAAAAA-A-AAAC-AAAATTTAAGGGACTAAAATAATA
* *
2319554 AAAACAAAAACTTAAAGGGCTAAAACAACATAAACAAAATTTAAAGTACTAAAA
1 AAAACAAAAACTTAAAGGGCTAAAA-AA-A-AAACAAAATTTAAGGGACTAAAA
2319608 CAAATACAAA
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
55 1 0.01
56 2 0.02
57 26 0.31
58 5 0.06
59 44 0.52
60 7 0.08
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (56 bp):
AAAACAAAAACTTAAAGGGCTAAAAAAAAAACAAAATTTAAGGGACTAAAATAATA
Found at i:2321254 original size:3 final size:3
Alignment explanation
Indices: 2321248--2321279 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2321238 AAAAATAATA
*
2321248 ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2321280 AATTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2322293 original size:39 final size:38
Alignment explanation
Indices: 2322236--2322342 Score: 116
Period size: 35 Copynumber: 2.9 Consensus size: 38
2322226 CAGAATTGGA
* * *
2322236 AAATTGTCTCAAGTGAGACAACATTTGTTTTTTTTAAAG
1 AAATTGTTTCAAGCGAGACAA-AATTGTTTTTTTTAAAG
*
2322275 AAATTGTTTCAAGCGAGACAAAATTG---TTTTTAGAG
1 AAATTGTTTCAAGCGAGACAAAATTGTTTTTTTTAAAG
*
2322310 AAATTGTCTT-AAGCGAGACAAAGTT-TTTTTTTT
1 AAATTGT-TTCAAGCGAGACAAAATTGTTTTTTTT
2322343 GAGAAAACGA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
35 29 0.49
36 2 0.03
37 5 0.08
38 4 0.07
39 19 0.32
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (38 bp):
AAATTGTTTCAAGCGAGACAAAATTGTTTTTTTTAAAG
Found at i:2322550 original size:38 final size:37
Alignment explanation
Indices: 2322500--2322584 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
2322490 AAATTTTTGG
2322500 TAAAATGTCTCAAGCGAGA-AAGAATTTGTTTTAAAGA
1 TAAAATGTCTCAAGCGAGACAA-AATTTGTTTTAAAGA
*
2322537 TAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
1 TAAAA-TGTCTCAAGCGAGACAAAATTTGTTTTAAAGA
*
2322575 -AAACTGTCTC
1 TAAAATGTCTC
2322585 TAGCAAGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 6 0.14
37 8 0.18
38 28 0.64
39 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (37 bp):
TAAAATGTCTCAAGCGAGACAAAATTTGTTTTAAAGA
Found at i:2323823 original size:35 final size:35
Alignment explanation
Indices: 2323784--2323913 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 35
2323774 CTTGTCCTAT
* *
2323784 CTTTTTCT-TTGTTTTTCTTTTGTTCTTTT-TCTTTG
1 CTTTTTCTCTT-TGTTTCTTTTCTT-TTTTCTCTTTG
2323819 CTTTTTCTCTTTGTTTCTTTTCTTTTTTCTCTTTG
1 CTTTTTCTCTTTGTTTCTTTTCTTTTTTCTCTTTG
*
2323854 TTCTTGTTTTCTCTTTGCTTCTTTCTCTTTGTTATTTGCTCTTTG
1 --C-T-TTTTCTCTTTGTTTCTTT-TC--T-TT-TTT-CTCTTTG
*
2323899 CTTTTTTTCTTTGTT
1 CTTTTTCTCTTTGTT
2323914 GTGACTTGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
34 4 0.05
35 25 0.32
36 2 0.03
37 1 0.01
38 1 0.01
39 17 0.22
40 2 0.03
41 11 0.14
42 2 0.03
43 3 0.04
44 3 0.04
45 7 0.09
ACGTcount: A:0.01, C:0.18, G:0.08, T:0.73
Consensus pattern (35 bp):
CTTTTTCTCTTTGTTTCTTTTCTTTTTTCTCTTTG
Found at i:2323837 original size:21 final size:21
Alignment explanation
Indices: 2323811--2323913 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
2323801 TTTTGTTCTT
2323811 TTTCTTTGCTTTTTCTCTTTG
1 TTTCTTTGCTTTTTCTCTTTG
*
2323832 TTTCTTTTCTTTTTTCTCTTTG
1 TTTCTTTGC-TTTTTCTCTTTG
2323854 -TTC-TTG--TTTTCTCTTTG
1 TTTCTTTGCTTTTTCTCTTTG
* *
2323871 CTTCTTT-CTCTTTGT-TATTTG
1 TTTCTTTGCT-TTT-TCTCTTTG
* *
2323892 -CTCTTTGCTTTTTTTCTTTG
1 TTTCTTTGCTTTTTCTCTTTG
2323912 TT
1 TT
2323914 GTGACTTGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
17 11 0.17
18 3 0.05
19 3 0.05
20 15 0.23
21 21 0.32
22 13 0.20
ACGTcount: A:0.01, C:0.18, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTCTTTGCTTTTTCTCTTTG
Found at i:2323848 original size:22 final size:22
Alignment explanation
Indices: 2323796--2323855 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
2323786 TTTTCTTTGT
*
2323796 TTTTCTTTTGT-TC-TT-TTTC
1 TTTTCTTTTTTCTCTTTGTTTC
*
2323815 TTTGC-TTTTTCTCTTTGTTTC
1 TTTTCTTTTTTCTCTTTGTTTC
2323836 TTTTCTTTTTTCTCTTTGTT
1 TTTTCTTTTTTCTCTTTGTT
2323856 CTTGTTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
20 2 0.06
21 8 0.24
22 14 0.41
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTCTTTTTTCTCTTTGTTTC
Found at i:2323865 original size:17 final size:17
Alignment explanation
Indices: 2323838--2323877 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2323828 TTTGTTTCTT
2323838 TTCTTTTTTCTCTTTG-
1 TTCTTTTTTCTCTTTGC
2323854 TTCTTGTTTTCTCTTTGC
1 TTCTT-TTTTCTCTTTGC
2323872 TTCTTT
1 TTCTTT
2323878 CTCTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.72
Consensus pattern (17 bp):
TTCTTTTTTCTCTTTGC
Found at i:2323869 original size:66 final size:66
Alignment explanation
Indices: 2323783--2323910 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 66
2323773 TCTTGTCCTA
*
2323783 TCTTTTTCTTTGTTTTTCTTTTG-TTCTTTTTCTTTGCTT-TTT-CTCTTTG-TTTCTTTTCTTT
1 TCTTTTTCTTTGTTTTTC-TTTGCTTCTTTCTCTTTG-TTATTTGCTCTTTGCTTT-TTTTCTTT
2323844 TTTC
63 TTTC
2323848 TCTTTGTTC-TTGTTTTCTCTTTGCTTCTTTCTCTTTGTTATTTGCTCTTTGCTTTTTTTCTTT
1 TCTTT-TTCTTTGTTTT-TCTTTGCTTCTTTCTCTTTGTTATTTGCTCTTTGCTTTTTTTCTTT
2323911 GTTGTGACTT
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
65 18 0.32
66 20 0.36
67 15 0.27
68 3 0.05
ACGTcount: A:0.01, C:0.18, G:0.08, T:0.73
Consensus pattern (66 bp):
TCTTTTTCTTTGTTTTTCTTTGCTTCTTTCTCTTTGTTATTTGCTCTTTGCTTTTTTTCTTTTTT
C
Found at i:2323876 original size:39 final size:39
Alignment explanation
Indices: 2323796--2323903 Score: 114
Period size: 39 Copynumber: 2.7 Consensus size: 39
2323786 TTTTCTTTGT
*
2323796 TTTTCTTTTGTTCTTTTTCTTTGCTTTTTCTCTTTGTTTC
1 TTTTCTTTTGTTCTTTTTCTTTGC-TTTTCTCTTTGCTTC
*
2323836 TTTTCTTTTTTCTCTTTGTTC-TTG-TTTTCTCTTTGCTTC
1 TTTTCTTTTGT-TCTTT-TTCTTTGCTTTTCTCTTTGCTTC
* *
2323875 -TTTCTCTTTGTTATTTGCTCTTTGCTTTT
1 TTTTCT-TTTGTTCTTT-TTCTTTGCTTTT
2323904 TTTCTTTGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
38 12 0.21
39 21 0.36
40 14 0.24
41 8 0.14
42 3 0.05
ACGTcount: A:0.01, C:0.19, G:0.08, T:0.72
Consensus pattern (39 bp):
TTTTCTTTTGTTCTTTTTCTTTGCTTTTCTCTTTGCTTC
Found at i:2323880 original size:14 final size:13
Alignment explanation
Indices: 2323785--2323911 Score: 85
Period size: 13 Copynumber: 9.8 Consensus size: 13
2323775 TTGTCCTATC
2323785 TTTT-TCTTTG-T
1 TTTTCTCTTTGCT
2323796 TTTTCT-TTTG-T
1 TTTTCTCTTTGCT
*
2323807 TCTTTTTCTTTGCT
1 T-TTTCTCTTTGCT
2323821 TTTTCTCTTTG--
1 TTTTCTCTTTGCT
2323832 -TTTCT-TTT-CTT
1 TTTTCTCTTTGC-T
2323843 TTTTCTCTTTGTTCTT
1 TTTTCTCTTTG--C-T
2323859 GTTTTCTCTTTGCT
1 -TTTTCTCTTTGCT
2323873 TCTTTCTCTTTG-T
1 T-TTTCTCTTTGCT
2323886 TATTTGCTCTTTGCT
1 T-TTT-CTCTTTGCT
*
2323901 TTTTTTCTTTG
1 TTTTCTCTTTG
2323912 TTGTGACTTG
Statistics
Matches: 96, Mismatches: 4, Indels: 30
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.03
10 5 0.05
11 10 0.10
12 10 0.10
13 28 0.29
14 23 0.24
15 3 0.03
16 3 0.03
17 11 0.11
ACGTcount: A:0.01, C:0.17, G:0.09, T:0.73
Consensus pattern (13 bp):
TTTTCTCTTTGCT
Found at i:2323913 original size:52 final size:51
Alignment explanation
Indices: 2323809--2323909 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 51
2323799 TCTTTTGTTC
* * * *
2323809 TTTTTCTTTGCTTTTTCTCTTTGTTTCTTTTCTTTTTTCTCTTTGTTCTTG
1 TTTTTCTTTGCTTTTTCTCTTTGTTTATTTGCTCTTTGCTCTTTGTTCTTG
*
2323860 TTTTCTCTTTGCTTCTTTCTCTTTG-TTATTTGCTCTTTGCT-TTTTTTCTT
1 TTTT-TCTTTGCTT-TTTCTCTTTGTTTATTTGCTCTTTGCTCTTTGTTCTT
2323910 TGTTGTGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
51 12 0.28
52 21 0.49
53 10 0.23
ACGTcount: A:0.01, C:0.19, G:0.08, T:0.72
Consensus pattern (51 bp):
TTTTTCTTTGCTTTTTCTCTTTGTTTATTTGCTCTTTGCTCTTTGTTCTTG
Found at i:2327576 original size:21 final size:22
Alignment explanation
Indices: 2327552--2327592 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2327542 ACATATGATG
*
2327552 TAAAATAA-AATATTTACAACA
1 TAAAATAACAACATTTACAACA
2327573 TAAAATAACAACATTTACAA
1 TAAAATAACAACATTTACAA
2327593 TATGTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAACAACATTTACAACA
Found at i:2328034 original size:30 final size:29
Alignment explanation
Indices: 2327944--2328034 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
2327934 TACCAACTGG
* *
2327944 AATTTAAGGGACTAAAATAATAAAAACCAAA
1 AATTTAAAGGACTAAAATAGT-AAAA-CAAA
* * * *
2327975 AACTTAAAGGGCTAAAACAGCATAAACAAA
1 AATTTAAAGGACTAAAATAGTA-AAACAAA
*
2328005 ATTTTAAAGGACTAAAATAGTAAATACAAA
1 AATTTAAAGGACTAAAATAGTAAA-ACAAA
2328035 TAAAATAGAG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 2 0.04
30 27 0.57
31 18 0.38
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (29 bp):
AATTTAAAGGACTAAAATAGTAAAACAAA
Found at i:2329684 original size:3 final size:3
Alignment explanation
Indices: 2329676--2329798 Score: 246
Period size: 3 Copynumber: 41.0 Consensus size: 3
2329666 TAACAAAATG
2329676 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
2329724 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
2329772 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2329799 CAACAACAAT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 120 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2341193 original size:19 final size:20
Alignment explanation
Indices: 2341169--2341219 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2341159 TGGCCAAGAG
*
2341169 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
2341188 CATGTATTTTC-TTCAAAAAT
1 CATGTATTTTCATT-AAAAAT
2341208 CATGTATTTTCA
1 CATGTATTTTCA
2341220 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 16 0.57
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:2347958 original size:17 final size:18
Alignment explanation
Indices: 2347936--2347977 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
2347926 CTTTCAATTA
2347936 TTTATTTAATTATTAT-T
1 TTTATTTAATTATTATCT
*
2347953 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
2347971 TTTATTT
1 TTTATTT
2347978 TTAAAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2356081 original size:6 final size:6
Alignment explanation
Indices: 2356046--2356075 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2356036 TGTATGCTCC
2356046 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
2356076 GAAAAAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:2357870 original size:21 final size:21
Alignment explanation
Indices: 2357824--2357870 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2357814 TAAAATCTTT
* *
2357824 TCTTTATTTTTACTTTAAATC
1 TCTTTATTATTACTTTAAATA
*
2357845 GCTTTAATTATTA-TTTAAATA
1 TCTTT-ATTATTACTTTAAATA
2357866 TCTTT
1 TCTTT
2357871 TTACCAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.60
Consensus pattern (21 bp):
TCTTTATTATTACTTTAAATA
Found at i:2359095 original size:22 final size:21
Alignment explanation
Indices: 2359068--2359114 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
2359058 TCATTTTTTA
*
2359068 AAAAAATAAATAAATATGCAAT
1 AAAAAATAAATAAAAATG-AAT
*
2359090 AAAAAATAATTAAAAATGAAT
1 AAAAAATAAATAAAAATGAAT
2359111 AAAA
1 AAAA
2359115 TTCAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAATAAATAAAAATGAAT
Found at i:2359112 original size:32 final size:33
Alignment explanation
Indices: 2359069--2359136 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
2359059 CATTTTTTAA
2359069 AAAAATAAATAAATATGCAATAAAAA-ATAAT-T
1 AAAAATAAATAAA-ATGCAATAAAAATATAATGT
* *
2359101 AAAAATGAATAAAATTCAATAAAAATATAATGT
1 AAAAATAAATAAAATGCAATAAAAATATAATGT
2359134 AAA
1 AAA
2359137 GCTAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 11 0.34
32 17 0.53
33 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (33 bp):
AAAAATAAATAAAATGCAATAAAAATATAATGT
Found at i:2359704 original size:10 final size:10
Alignment explanation
Indices: 2359689--2359713 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2359679 TTTGTAAAAG
2359689 AATATTTAAA
1 AATATTTAAA
2359699 AATATTTAAA
1 AATATTTAAA
2359709 AATAT
1 AATAT
2359714 GAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATTTAAA
Found at i:2360420 original size:21 final size:22
Alignment explanation
Indices: 2360396--2360456 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
2360386 TTTACATTAT
2360396 ATTTTTATTTGA-ATTTTATT-C
1 ATTTTTATTT-ATATTTTATTGC
* *
2360417 ATTTTTAATTATTTTTTATTGC
1 ATTTTTATTTATATTTTATTGC
*
2360439 ATTTTTATTTATTTTTTA
1 ATTTTTATTTATATTTTA
2360457 AAAAAGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.03
21 16 0.46
22 18 0.51
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (22 bp):
ATTTTTATTTATATTTTATTGC
Found at i:2360433 original size:32 final size:34
Alignment explanation
Indices: 2360386--2360454 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
2360376 ATTTTTTAGC
2360386 TTTACATTATATTTTTATTTG-AATTTTATTCATT
1 TTTACATTATATTTTTA-TTGCAATTTTATTCATT
* *
2360420 TTTA-ATTAT-TTTTTATTGCATTTTTATTTATT
1 TTTACATTATATTTTTATTGCAATTTTATTCATT
2360452 TTT
1 TTT
2360455 TAAAAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.09
32 20 0.62
33 5 0.16
34 4 0.12
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (34 bp):
TTTACATTATATTTTTATTGCAATTTTATTCATT
Found at i:2360441 original size:22 final size:21
Alignment explanation
Indices: 2360409--2360456 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
2360399 TTTATTTGAA
2360409 TTTTATTCATTTTTAATTATT
1 TTTTATTCATTTTTAATTATT
*
2360430 TTTTATTGCATTTTTATTTATT
1 TTTTATT-CATTTTTAATTATT
2360452 TTTTA
1 TTTTA
2360457 AAAAAGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTCATTTTTAATTATT
Found at i:2361210 original size:2 final size:2
Alignment explanation
Indices: 2361205--2361236 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2361195 AATTTTTTGT
2361205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2361237 CACCCTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2364443 original size:33 final size:33
Alignment explanation
Indices: 2364406--2364564 Score: 191
Period size: 33 Copynumber: 4.9 Consensus size: 33
2364396 AAATAATCAT
*
2364406 GACTTTTGGAGGCAACCT-TTGGCGAAGAGACAC
1 GACTTTTGGAGGC-ACCTCTTGGTGAAGAGACAC
*
2364439 GACTTTTGGAGGCACCTCTTGGTGAAGAGACAT
1 GACTTTTGGAGGCACCTCTTGGTGAAGAGACAC
*
2364472 AACTTTTGGAGGCACCTCTTGGTGAAGAGACA-
1 GACTTTTGGAGGCACCTCTTGGTGAAGAGACAC
* * * *
2364504 -ACCTTTAGAGGCACCTCTTGGTGAAGATAGAC
1 GACTTTTGGAGGCACCTCTTGGTGAAGAGACAC
* *
2364536 GAAC-TTTGGATGCATCTCTTGGTGAAGAG
1 G-ACTTTTGGAGGCACCTCTTGGTGAAGAG
2364565 TCATGACTCT
Statistics
Matches: 111, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
31 27 0.24
32 4 0.04
33 78 0.70
34 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (33 bp):
GACTTTTGGAGGCACCTCTTGGTGAAGAGACAC
Found at i:2364544 original size:64 final size:65
Alignment explanation
Indices: 2364407--2364564 Score: 198
Period size: 64 Copynumber: 2.4 Consensus size: 65
2364397 AATAATCATG
* * *
2364407 ACTTTTGGAGGCAACCT-TTGGCGAAGAGACACGACTTTTGGAGGCACCTCTTGGTGAAGAGACA
1 ACTTTTGGAGGC-ACCTCTTGGTGAAGAGACAC-ACCTTTAGAGGCACCTCTTGGTGAAGAGACA
*
2364471 TA
64 GA
2364473 ACTTTTGGAGGCACCTCTTGGTGAAGAGACA-ACCTTTAGAGGCACCTCTTGGTGAAGATAGAC-
1 ACTTTTGGAGGCACCTCTTGGTGAAGAGACACACCTTTAGAGGCACCTCTTGGTGAAG--AGACA
2364536 GA
64 GA
* *
2364538 AC-TTTGGATGCATCTCTTGGTGAAGAG
1 ACTTTTGGAGGCACCTCTTGGTGAAGAG
2364565 TCATGACTCT
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
64 47 0.57
65 7 0.08
66 29 0.35
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (65 bp):
ACTTTTGGAGGCACCTCTTGGTGAAGAGACACACCTTTAGAGGCACCTCTTGGTGAAGAGACAGA
Found at i:2364741 original size:44 final size:43
Alignment explanation
Indices: 2364643--2364771 Score: 168
Period size: 44 Copynumber: 3.0 Consensus size: 43
2364633 CTCATAGCTG
* * ** * * *
2364643 TTGGTGTAAAGAAGTATGTCCCTTGGTTCATTCTCTTAGCCAT
1 TTGGTGTGAAGAAGCATGTCCCTTATTTGAATCTCCTAGCCAT
*
2364686 TTGGTGTGAAGAAGCATGTCCCTTAATTTGAATCTCCTAGTCAT
1 TTGGTGTGAAGAAGCATGTCCCTT-ATTTGAATCTCCTAGCCAT
2364730 TTGGTGTGAAGAAGCATGTCCCTTGATTTGAATCTCCTAGCC
1 TTGGTGTGAAGAAGCATGTCCCTT-ATTTGAATCTCCTAGCC
2364772 GTTGGAATGA
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 22 0.29
44 53 0.71
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (43 bp):
TTGGTGTGAAGAAGCATGTCCCTTATTTGAATCTCCTAGCCAT
Found at i:2368269 original size:14 final size:16
Alignment explanation
Indices: 2368237--2368282 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
2368227 GATTTCATGA
*
2368237 ATATTGTTTATCTGAT
1 ATATTATTTATCTGAT
2368253 ATATTATTTA-CTG-T
1 ATATTATTTATCTGAT
* *
2368267 ATATTTTTTATATGAT
1 ATATTATTTATCTGAT
2368283 CATTTGTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 10 0.40
15 5 0.20
16 10 0.40
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (16 bp):
ATATTATTTATCTGAT
Found at i:2371023 original size:27 final size:27
Alignment explanation
Indices: 2370993--2371051 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
2370983 ACCATCAGTA
*
2370993 TTACTAGTGACTTTGAAATATCACTGG
1 TTACTAGTGACTCTGAAATATCACTGG
*
2371020 TTACTAGTGACTCTGAAATATCATTGG
1 TTACTAGTGACTCTGAAATATCACTGG
2371047 TTACT
1 TTACT
2371052 TTACCATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (27 bp):
TTACTAGTGACTCTGAAATATCACTGG
Found at i:2375162 original size:13 final size:14
Alignment explanation
Indices: 2375139--2375167 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2375129 TTCATATATC
2375139 ATCCACTTATCAAA
1 ATCCACTTATCAAA
2375153 ATCC-CTTATCAAA
1 ATCCACTTATCAAA
2375166 AT
1 AT
2375168 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (14 bp):
ATCCACTTATCAAA
Found at i:2380833 original size:38 final size:37
Alignment explanation
Indices: 2380778--2380897 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 37
2380768 ATATCAATTA
*
2380778 AGCACTTCAATGCAAATGGTGCGCACAACCTTATGTGT
1 AGCACTTC-ATGCAAATGGTGCGCACGACCTTATGTGT
* * * *
2380816 AGCACTTCGATGAAAATGGAGGGTACGACCTTATGTGT
1 AGCACTTC-ATGCAAATGGTGCGCACGACCTTATGTGT
* * *
2380854 AGCACTTCAGTGCATATGGTGTGCATGACCTTATGTGT
1 AGCACTTCA-TGCAAATGGTGCGCACGACCTTATGTGT
2380892 AAGCAC
1 -AGCAC
2380898 CACGGTGCAT
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
37 1 0.01
38 62 0.91
39 5 0.07
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (37 bp):
AGCACTTCATGCAAATGGTGCGCACGACCTTATGTGT
Found at i:2386765 original size:103 final size:103
Alignment explanation
Indices: 2386586--2386779 Score: 316
Period size: 103 Copynumber: 1.9 Consensus size: 103
2386576 TTTTATATCA
* * * *
2386586 GAATAATCATAGTTACAGGTTAACAATATAATAAGTGAAATATGACTATCATCATACACAATACA
1 GAATAATCATAATTACAGATTAACAAAATAATAAGCGAAATATGACTATCATCATACACAATACA
*
2386651 CGTATAAATTTAGCACAAGGGTGAGGCATATGCACTCG
66 CATATAAATTTAGCACAAGGGTGAGGCATATGCACTCG
* *
2386689 GAATAATCATAATTACATATTAACAAAATAATAAGCGAAATATGACTATCATCATACATAATACA
1 GAATAATCATAATTACAGATTAACAAAATAATAAGCGAAATATGACTATCATCATACACAATACA
*
2386754 CATATAAATTTATCACAAGGGTGAGG
66 CATATAAATTTAGCACAAGGGTGAGG
2386780 GACACACCTA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (103 bp):
GAATAATCATAATTACAGATTAACAAAATAATAAGCGAAATATGACTATCATCATACACAATACA
CATATAAATTTAGCACAAGGGTGAGGCATATGCACTCG
Found at i:2393427 original size:12 final size:12
Alignment explanation
Indices: 2393410--2393451 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2393400 ATATTTTATC
2393410 TGATTTCTGCTT
1 TGATTTCTGCTT
*
2393422 TGATTTTTG-TT
1 TGATTTCTGCTT
*
2393433 CTGATTTCTGCTC
1 -TGATTTCTGCTT
2393446 TGATTT
1 TGATTT
2393452 ATGATATCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.88
13 1 0.04
ACGTcount: A:0.10, C:0.14, G:0.17, T:0.60
Consensus pattern (12 bp):
TGATTTCTGCTT
Found at i:2393690 original size:64 final size:64
Alignment explanation
Indices: 2393573--2393736 Score: 248
Period size: 64 Copynumber: 2.6 Consensus size: 64
2393563 ACTGGTAATT
* * *
2393573 CCTTATGGA-CCTAAGGCAACT--CTT-GGGTGGACTCCTTGGCTTAATGGGCCTAGTGGTAAGA
1 CCTTATGGACCCTAAGGC-ACTCCCTTAGGGTGGGCTCCTTGGCCTAATAGGCCTAGTGGTAAGA
*
2393634 CCTTATGGACCCTAAGGCACTCCCTTAGGGTGGGCTCCTTGGCCTAATAGGTCTAGTGGTAAGA
1 CCTTATGGACCCTAAGGCACTCCCTTAGGGTGGGCTCCTTGGCCTAATAGGCCTAGTGGTAAGA
2393698 CCTTATGGACCCTAAGGCACTCCCTTAGGGT-GGCTCCTT
1 CCTTATGGACCCTAAGGCACTCCCTTAGGGTGGGCTCCTT
2393737 TGATGTATGC
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
61 12 0.13
62 8 0.08
63 11 0.12
64 64 0.67
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (64 bp):
CCTTATGGACCCTAAGGCACTCCCTTAGGGTGGGCTCCTTGGCCTAATAGGCCTAGTGGTAAGA
Found at i:2396372 original size:22 final size:22
Alignment explanation
Indices: 2396344--2396393 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2396334 TATAGTTAAA
*
2396344 GGATAAATGTCAGGAATTATGT
1 GGATAAATGTAAGGAATTATGT
2396366 GGATAAATGTAAGGAATTATGT
1 GGATAAATGTAAGGAATTATGT
2396388 GGATAA
1 GGATAA
2396394 GAAATTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (22 bp):
GGATAAATGTAAGGAATTATGT
Found at i:2397333 original size:12 final size:12
Alignment explanation
Indices: 2397315--2397350 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2397305 TGGATATTTT
2397315 CTCTGATTTCTG
1 CTCTGATTTCTG
* *
2397327 TTCTGATTTCTA
1 CTCTGATTTCTG
2397339 CTCTGATTTCTG
1 CTCTGATTTCTG
2397351 ATATCTCCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.14, T:0.53
Consensus pattern (12 bp):
CTCTGATTTCTG
Found at i:2403388 original size:21 final size:22
Alignment explanation
Indices: 2403351--2403392 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2403341 ATGCACAAAG
*
2403351 TCGGATAAAAAATCGATCCGGA
1 TCGGATAAAAAACCGATCCGGA
2403373 TCGGAT-AAAAACCGATCCGG
1 TCGGATAAAAAACCGATCCGG
2403393 TTTTTCACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (22 bp):
TCGGATAAAAAACCGATCCGGA
Found at i:2404647 original size:188 final size:188
Alignment explanation
Indices: 2404330--2404705 Score: 752
Period size: 188 Copynumber: 2.0 Consensus size: 188
2404320 TCTATTTCAC
2404330 TACACATGGGAGCTATGTTCTACGAGCGTCATCCAATATCATATAAAATACCACAAGTAGAAAAG
1 TACACATGGGAGCTATGTTCTACGAGCGTCATCCAATATCATATAAAATACCACAAGTAGAAAAG
2404395 CAACATATATAAATGGTATTCTCAAAAAAAATTGAGAATTACATATCAAAAGTATAACCCCACAT
66 CAACATATATAAATGGTATTCTCAAAAAAAATTGAGAATTACATATCAAAAGTATAACCCCACAT
2404460 GTCACACCCTAATCTAGGGGTTAAAAGTTTTCCAAAAGTTAATATTTTTTATTAAAGG
131 GTCACACCCTAATCTAGGGGTTAAAAGTTTTCCAAAAGTTAATATTTTTTATTAAAGG
2404518 TACACATGGGAGCTATGTTCTACGAGCGTCATCCAATATCATATAAAATACCACAAGTAGAAAAG
1 TACACATGGGAGCTATGTTCTACGAGCGTCATCCAATATCATATAAAATACCACAAGTAGAAAAG
2404583 CAACATATATAAATGGTATTCTCAAAAAAAATTGAGAATTACATATCAAAAGTATAACCCCACAT
66 CAACATATATAAATGGTATTCTCAAAAAAAATTGAGAATTACATATCAAAAGTATAACCCCACAT
2404648 GTCACACCCTAATCTAGGGGTTAAAAGTTTTCCAAAAGTTAATATTTTTTATTAAAGG
131 GTCACACCCTAATCTAGGGGTTAAAAGTTTTCCAAAAGTTAATATTTTTTATTAAAGG
2404706 GCCAATTTTA
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 188 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (188 bp):
TACACATGGGAGCTATGTTCTACGAGCGTCATCCAATATCATATAAAATACCACAAGTAGAAAAG
CAACATATATAAATGGTATTCTCAAAAAAAATTGAGAATTACATATCAAAAGTATAACCCCACAT
GTCACACCCTAATCTAGGGGTTAAAAGTTTTCCAAAAGTTAATATTTTTTATTAAAGG
Found at i:2410720 original size:43 final size:40
Alignment explanation
Indices: 2410634--2410780 Score: 120
Period size: 43 Copynumber: 3.5 Consensus size: 40
2410624 ACCCTAAAGA
* * *
2410634 ACCATCATCTCATAATCCAACTGAACTGACCTCTCAGCGATAT
1 ACCATCATCACATCATCCAAC-GAACTG-CCTCTCA-CAATAT
2410677 ACCATCATCACATCATCCAATCGAACTGCCCTCTCACTAATAT
1 ACCATCATCACATCATCCAA-CGAACTG-CCTCTCAC-AATAT
** * * *
2410720 ATTACCATCACATCATCCAACCAAACAT-CCTCGC-CAATAT
1 ACCATCATCACATCATCCAA-CGAAC-TGCCTCTCACAATAT
2410760 ACCA-CAATCACATCATCCAAC
1 ACCATC-ATCACATCATCCAAC
2410781 TGAATCACCC
Statistics
Matches: 88, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
39 2 0.02
40 21 0.24
41 1 0.01
42 6 0.07
43 56 0.64
44 2 0.02
ACGTcount: A:0.35, C:0.37, G:0.05, T:0.23
Consensus pattern (40 bp):
ACCATCATCACATCATCCAACGAACTGCCTCTCACAATAT
Found at i:2411121 original size:21 final size:20
Alignment explanation
Indices: 2411041--2411122 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
2411031 CTCAAATCAG
*
2411041 TTTCCAGATTCGCAACGCGAT
1 TTTCCA-ATTCGCAATGCGAT
**
2411062 TATGACAA-TCGCAATGCGAT
1 T-TTCCAATTCGCAATGCGAT
* *
2411082 TTTCCAATTTTGCATTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
2411103 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
2411123 ATAAGTAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.08
20 12 0.25
21 25 0.52
22 7 0.15
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:2411159 original size:21 final size:21
Alignment explanation
Indices: 2411112--2411184 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
2411102 TTTTCCCAAT
* *
2411112 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
* *
2411132 TCACAATGCGAATTTTGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
2411153 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
2411174 TCGCAACGCGA
1 TCGCAATGCGA
2411185 TAATACAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 11 0.24
21 34 0.76
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:2411220 original size:20 final size:20
Alignment explanation
Indices: 2411195--2411267 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2411185 TAATACAAAA
2411195 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
2411215 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
*
2411235 TCGCAACGCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
2411255 TCGCAACGAGATA
1 TCGCAACGCGATA
2411268 ATACCTAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:2411809 original size:20 final size:20
Alignment explanation
Indices: 2411760--2411818 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2411750 TTTATTCTCT
* **
2411760 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
2411780 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
2411800 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
2411819 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2412009 original size:25 final size:24
Alignment explanation
Indices: 2411955--2412009 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2411945 TGTTTATTAT
* *
2411955 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2411979 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2412005 TGTTT
1 TGTTT
2412010 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2413124 original size:18 final size:18
Alignment explanation
Indices: 2413103--2413150 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2413093 TCCACTTCGG
2413103 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2413121 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2413139 GAGCCATCACCT
1 GAGCCATCACCT
2413151 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2413745 original size:19 final size:20
Alignment explanation
Indices: 2413691--2413746 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
2413681 TAGTTTACTT
* *
2413691 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2413711 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
2413731 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
2413747 AAAGTACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2413971 original size:12 final size:12
Alignment explanation
Indices: 2413952--2413985 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2413942 CTCTCCGGCG
2413952 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2413964 ATATCCGTTCCT
1 ACATCCGTTCCT
2413976 ACATCC-TTCC
1 ACATCCGTTCC
2413986 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2414567 original size:24 final size:24
Alignment explanation
Indices: 2414540--2414593 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2414530 GTATTCAAAA
*
2414540 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2414564 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2414588 TTTGAT
1 TTTGAT
2414594 GTTGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2414785 original size:12 final size:12
Alignment explanation
Indices: 2414768--2414792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2414758 ATATAATCCT
2414768 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2414780 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2414792 G
1 G
2414793 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2417142 original size:19 final size:18
Alignment explanation
Indices: 2417120--2417211 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
2417110 GGAAATTACT
2417120 ATCGCAATGCGAAACGAAA
1 ATCGCAATGCGAAA-GAAA
*
2417139 ATCGCAA--CG--AGATA
1 ATCGCAATGCGAAAGAAA
*
2417153 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAA-GAAA
*
2417172 ATCGCAA--CG--AGAGA
1 ATCGCAATGCGAAAGAAA
2417186 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAA-GAAA
2417205 ATCGCAA
1 ATCGCAA
2417212 CGAGGGAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 26 0.46
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAAGAAA
Found at i:2417172 original size:33 final size:33
Alignment explanation
Indices: 2417120--2417244 Score: 196
Period size: 33 Copynumber: 3.8 Consensus size: 33
2417110 GGAAATTACT
* *
2417120 ATCGCAATGCGAAACGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2417153 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2417186 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2417219 ATTGCAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2417245 ATCGAATTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2417305 original size:33 final size:33
Alignment explanation
Indices: 2417263--2417387 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 33
2417253 TAGTTTCGCA
* * *
2417263 TTGCGATTTT-AGTTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTATCTCG
* * *
2417296 TTGCGATTTTTATTTCGCATTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
2417329 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
2417362 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2417388 AGTAATTTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 83 0.99
34 1 0.01
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCG
Found at i:2417353 original size:19 final size:18
Alignment explanation
Indices: 2417251--2417387 Score: 91
Period size: 19 Copynumber: 8.0 Consensus size: 18
2417241 GCAAATCGAA
2417251 TTTAGTTTCGCATTGCGAT
1 TTTA-TTTCGCATTGCGAT
*
2417270 TTTAGTTTCGCGTTGCGA-
1 TTTA-TTTCGCATTGCGAT
*
2417288 TTT-TGTCG--TTGCGATT
1 TTTATTTCGCATTGCGA-T
2417304 TTTATTTCGCATTGCGA-
1 TTTATTTCGCATTGCGAT
* * *
2417321 -TTCTCTAG--TTGCGAT
1 TTTATTTCGCATTGCGAT
2417336 TTTCATTTCGCATTGCGA-
1 TTT-ATTTCGCATTGCGAT
*
2417354 -TTATCTCG--TTGCGAT
1 TTTATTTCGCATTGCGAT
2417369 TTTCATTTCGCATTGCGAT
1 TTT-ATTTCGCATTGCGAT
2417388 AGTAATTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
14 18 0.20
16 21 0.23
17 14 0.15
18 3 0.03
19 36 0.39
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.47
Consensus pattern (18 bp):
TTTATTTCGCATTGCGAT
Found at i:2417513 original size:14 final size:15
Alignment explanation
Indices: 2417494--2417530 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
2417484 CATCAATTAA
2417494 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
2417508 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
2417522 ACAAATCAA
1 ACAAATCAA
2417531 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:2419395 original size:91 final size:90
Alignment explanation
Indices: 2419221--2419405 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
2419211 ATTTCAAACT
* *
2419221 TTCAACCAAAAGACAAAACAAAGACGAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2419286 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
2419314 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
2419378 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
2419405 T
1 T
2419406 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:2421117 original size:20 final size:19
Alignment explanation
Indices: 2421090--2421277 Score: 110
Period size: 19 Copynumber: 10.8 Consensus size: 19
2421080 TCTTTTGGTT
2421090 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2421109 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2421130 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2421149 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
2421163 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
2421182 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
2421196 GAAATGACTATCGCAAC--
1 GAAATGAAAATCGCAACGA
*
2421213 G--A-GAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
2421229 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2421248 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
2421262 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2421278 TGCGATTTTG
Statistics
Matches: 130, Mismatches: 17, Indels: 44
0.68 0.09 0.23
Matches are distributed among these distances:
14 40 0.31
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 42 0.32
20 30 0.23
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2421158 original size:14 final size:14
Alignment explanation
Indices: 2421139--2421260 Score: 64
Period size: 14 Copynumber: 7.6 Consensus size: 14
2421129 GGAAATGACT
2421139 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2421153 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
*
2421170 CTATCGCAATGAGAGA
1 --ATCGCAACGAGAGA
*
2421186 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
*
2421203 CTATCGCAACGAGAAA
1 --ATCGCAACGAGAGA
*
2421219 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
2421238 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2421252 ATCGCAACG
1 ATCGCAACG
2421261 CGAAATGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
14 33 0.39
15 1 0.01
16 12 0.14
17 13 0.15
18 1 0.01
19 25 0.29
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2421172 original size:33 final size:33
Alignment explanation
Indices: 2421118--2421277 Score: 257
Period size: 33 Copynumber: 4.8 Consensus size: 33
2421108 AGATAATGAA
2421118 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
*
2421152 AATCGCAACGCGAAATGACTATCGCAATGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
*
2421185 AATCGCAACGCGAAATGACTATCGCAACGAGAA
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
2421218 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
2421251 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
2421278 TGCGATTTTG
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 109 0.91
34 11 0.09
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:2421225 original size:66 final size:66
Alignment explanation
Indices: 2421090--2421277 Score: 259
Period size: 66 Copynumber: 2.7 Consensus size: 66
2421080 TCTTTTGGTT
*
2421090 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAGAAT
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC-GAAATGACTATCGCAACGAGAAAAT
2421155 CGCAACGC
59 CGCAACGC
** *
2421163 GAAATGACTATCGCAATGAGAGAATCGCAACGCGAAATGACTATCGCAACGAGAAAATCGCAACG
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACTATCGCAACGAGAAAATCGCAACG
2421228 C
66 C
**
2421229 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACTATCGCAA
2421278 TGCGATTTTG
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
66 76 0.72
67 11 0.10
69 1 0.01
70 1 0.01
73 17 0.16
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (66 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACTATCGCAACGAGAAAATCGCAACG
C
Found at i:2421920 original size:20 final size:20
Alignment explanation
Indices: 2421897--2421990 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
2421887 CTACAGTAAG
2421897 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
* *
2421917 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACAT
* *
2421937 AATTCGCATTGCTATTTACTT
1 -ATTCGCATTGCGATTTACAT
* * *
2421958 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
2421978 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2421991 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:2421946 original size:41 final size:40
Alignment explanation
Indices: 2421897--2421990 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
2421887 CTACAGTAAG
* *
2421897 ATTCGCATTGCGATTTACATATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACATAATCGCATTGCGATTTACCT
* * * *
2421937 AATTCGCATTGCTATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACATAATCGCATTGCGATTTACCT
2421978 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2421991 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 12 0.26
41 34 0.74
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACATAATCGCATTGCGATTTACCT
Found at i:2422011 original size:21 final size:21
Alignment explanation
Indices: 2421987--2422042 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2421977 TATTCGCATT
*
2421987 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
2422008 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
2422028 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
2422043 TGCATTGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:2422084 original size:20 final size:20
Alignment explanation
Indices: 2422044--2422092 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2422034 TAGGAAAATT
*
2422044 GCATTGCAATAGTCAGTATC
1 GCATTGCGATAGTCAGTATC
2422064 GCATTGCGATAGTCA-TAATC
1 GCATTGCGATAGTCAGT-ATC
*
2422084 GCGTTGCGA
1 GCATTGCGA
2422093 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
GCATTGCGATAGTCAGTATC
Found at i:2423632 original size:31 final size:32
Alignment explanation
Indices: 2423592--2423654 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
2423582 ATCCTCAGAG
* *
2423592 AATGGAGGAAACCCTAATGGTATCCTT-CGAT
1 AATGCAGGAAACCCTAATGGTAACCTTACGAT
* *
2423623 AATGCAGGAAACCTTACTGGTAACCTTACGAT
1 AATGCAGGAAACCCTAATGGTAACCTTACGAT
2423655 CTCTCCAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (32 bp):
AATGCAGGAAACCCTAATGGTAACCTTACGAT
Found at i:2429833 original size:51 final size:49
Alignment explanation
Indices: 2429722--2429833 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 49
2429712 AACTAATGAC
* * *
2429722 TAAAATAATAATAAACTAAAGATAAGTTTTTATTCTATCATAATTTCTAA
1 TAAAATAATAATAAACTAAAGATAAGTTTTAATTATAT-ATAATTCCTAA
* *
2429772 TAAAACAATAATAAACT-AAGAATAATGTTTTAACTTGATAT-TCATTCCTAA
1 TAAAATAATAATAAACTAAAG-ATAA-GTTTTAA-TT-ATATATAATTCCTAA
2429823 TAAAATAATAA
1 TAAAATAATAA
2429834 ATATAATTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
49 3 0.06
50 20 0.38
51 24 0.46
52 2 0.04
53 3 0.06
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (49 bp):
TAAAATAATAATAAACTAAAGATAAGTTTTAATTATATATAATTCCTAA
Found at i:2431682 original size:18 final size:21
Alignment explanation
Indices: 2431659--2431705 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 21
2431649 ATTTTTTTTT
2431659 CAAAAAAAC-AAAA-AAAGG-
1 CAAAAAAACAAAAACAAAGGC
2431677 CAAAAAAACAAAAACAAAGGC
1 CAAAAAAACAAAAACAAAGGC
2431698 CAAAAAAA
1 CAAAAAAA
2431706 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.35
19 4 0.15
20 5 0.19
21 8 0.31
ACGTcount: A:0.77, C:0.15, G:0.09, T:0.00
Consensus pattern (21 bp):
CAAAAAAACAAAAACAAAGGC
Found at i:2431711 original size:10 final size:10
Alignment explanation
Indices: 2431659--2431712 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
2431649 ATTTTTTTTT
2431659 CAAAAAAA--
1 CAAAAAAAGC
*
2431667 CAAAAAAAGG
1 CAAAAAAAGC
2431677 CAAAAAAA-C
1 CAAAAAAAGC
*
2431686 AAAAACAAAGGC
1 CAAAA-AAA-GC
2431698 CAAAAAAAGC
1 CAAAAAAAGC
2431708 CAAAA
1 CAAAA
2431713 TTTCAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 8 0.21
9 4 0.11
10 18 0.47
11 3 0.08
12 5 0.13
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:2436280 original size:11 final size:11
Alignment explanation
Indices: 2436266--2436296 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2436256 TTTCAAAAAA
2436266 AAAAAAAAACC
1 AAAAAAAAACC
2436277 AAAAAAAAACC
1 AAAAAAAAACC
2436288 AAAAAAAAA
1 AAAAAAAAA
2436297 AAACAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:2436297 original size:25 final size:24
Alignment explanation
Indices: 2436263--2436318 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2436253 TGTTTTCAAA
2436263 AAAAAAAAAAAACCAAAAAAAAACC
1 AAAAAAAAAAAA-CAAAAAAAAACC
*
2436288 AAAAAAAAAAAACAAAAAAAATCC
1 AAAAAAAAAAAACAAAAAAAAACC
*
2436312 CAAAAAA
1 AAAAAAA
2436319 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAAACAAAAAAAAACC
Found at i:2436318 original size:1 final size:1
Alignment explanation
Indices: 2436260--2436308 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
2436250 TTTTGTTTTC
** ** *
2436260 AAAAAAAAAAAAAAACCAAAAAAAAACCAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2436309 TCCCAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2444553 original size:15 final size:17
Alignment explanation
Indices: 2444533--2444565 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2444523 TCTAAGTAAC
2444533 TAATAAA-TAAA-ATAA
1 TAATAAACTAAAGATAA
2444548 TAATAAACTAAAGATAA
1 TAATAAACTAAAGATAA
2444565 T
1 T
2444566 GTTTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
TAATAAACTAAAGATAA
Found at i:2456855 original size:38 final size:38
Alignment explanation
Indices: 2456801--2456889 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
2456791 AATCTTTTAA
* * * *
2456801 ATTTGGGATTTTTAGTTTGATTATTTTATTTTTATCTT
1 ATTTAGGATTTATAGTTTGAATATTTTATTATTATCTT
*
2456839 ATTTAGGATTTATAGTTTGAATATTTTATTATTATTTT
1 ATTTAGGATTTATAGTTTGAATATTTTATTATTATCTT
*
2456877 ATTTAGGAATTAT
1 ATTTAGGATTTAT
2456890 TTATTTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.61
Consensus pattern (38 bp):
ATTTAGGATTTATAGTTTGAATATTTTATTATTATCTT
Found at i:2460215 original size:20 final size:20
Alignment explanation
Indices: 2460187--2460226 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2460177 TTTTATATTC
*
2460187 ATTTTATATTTAATTAATTT
1 ATTTCATATTTAATTAATTT
2460207 ATTTCATATTTAATTAATTT
1 ATTTCATATTTAATTAATTT
2460227 TTATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTCATATTTAATTAATTT
Found at i:2466667 original size:3 final size:3
Alignment explanation
Indices: 2466622--2466647 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2466612 GATGGAGAAA
2466622 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2466648 AGTTTACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2469689 original size:20 final size:20
Alignment explanation
Indices: 2469666--2469705 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2469656 ACATTTTTTG
2469666 TAAACTA-CACGTTTTGTTCC
1 TAAACTATCAC-TTTTGTTCC
2469686 TAAACTATCACTTTTGTTCC
1 TAAACTATCACTTTTGTTCC
2469706 ATTTTCGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (20 bp):
TAAACTATCACTTTTGTTCC
Found at i:2480968 original size:14 final size:15
Alignment explanation
Indices: 2480942--2480972 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2480932 TTGATCAAAT
2480942 CAATTTGACTTGACC
1 CAATTTGACTTGACC
2480957 CAATTTGA-TTGACC
1 CAATTTGACTTGACC
2480971 CA
1 CA
2480973 TTGACTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (15 bp):
CAATTTGACTTGACC
Found at i:2484573 original size:18 final size:18
Alignment explanation
Indices: 2484550--2484594 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2484540 TTCATGCATC
2484550 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
*
2484568 TAGTTCATTGAATAATGT
1 TAGTTCATTGAATAAAGT
2484586 TAGTTCATT
1 TAGTTCATT
2484595 AATCAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:2488575 original size:31 final size:32
Alignment explanation
Indices: 2488525--2488591 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
2488515 CATTTTTTTT
* *
2488525 CTTTAAGGGCTCTTTTTGAACACCACTATGAG
1 CTTTAAAGGCTCTTTTTGAACACCACTATGAA
* *
2488557 CTTTAAAGGCT-TTTTTGAACATCATTATGAA
1 CTTTAAAGGCTCTTTTTGAACACCACTATGAA
2488588 CTTT
1 CTTT
2488592 TTTTATCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (32 bp):
CTTTAAAGGCTCTTTTTGAACACCACTATGAA
Found at i:2500574 original size:30 final size:30
Alignment explanation
Indices: 2500482--2500578 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
2500472 AATACATGGT
2500482 AAAA-TTGGAGATCCATAATATAAAAACA-A
1 AAAATTTGGAGATCCATAATATAAAAA-ATA
** * ****
2500511 AAAATTTAAAGATGACCATAATACAGCCCATA
1 AAAATTTGGAGAT--CCATAATATAAAAAATA
*
2500543 AAAGTTTGGAGATCCATAATATAAAAAATA
1 AAAATTTGGAGATCCATAATATAAAAAATA
2500573 AAAATT
1 AAAATT
2500579 GAAAGATAAC
Statistics
Matches: 48, Mismatches: 16, Indels: 7
0.68 0.23 0.10
Matches are distributed among these distances:
29 4 0.08
30 23 0.48
31 1 0.02
32 20 0.42
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (30 bp):
AAAATTTGGAGATCCATAATATAAAAAATA
Found at i:2501051 original size:42 final size:42
Alignment explanation
Indices: 2500989--2501075 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
2500979 GCTAGGCGTG
* *
2500989 TTAGGGATGATTTTTTGGACACCAACCTCATATAATGAAATC
1 TTAGGGATGATTTTTCGGACAACAACCTCATATAATGAAATC
*
2501031 TTAGGGATGATTTTTCGGACAACAACGTCATATAATGAAATC
1 TTAGGGATGATTTTTCGGACAACAACCTCATATAATGAAATC
2501073 TTA
1 TTA
2501076 TGATTATCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (42 bp):
TTAGGGATGATTTTTCGGACAACAACCTCATATAATGAAATC
Found at i:2510376 original size:65 final size:64
Alignment explanation
Indices: 2510243--2510398 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 64
2510233 CTAAGAGTGT
* * *
2510243 ATCGATACATAAAATGCATTCGATGTTTTAAAATAGCATGTGTGCATCGATGCATGACTTGTGC
1 ATCGATGCATAAAATGCATTCGATGTTTTAAAATACCATGAGTGCATCGATGCATGACTTGTGC
* * *
2510307 ATCGATGCATAAAATGCATTCTATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATG-GTATGT
1 ATCGATGCATAAAATGCATTCGATGTTTT-A-AAATACCATGAGTGCATCGATGCATGACT-TGT
2510370 GC
63 GC
*
2510372 ATCGATGCATATAATGCATTCGATGTT
1 ATCGATGCATAAAATGCATTCGATGTT
2510399 CAATTTATTC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.35
65 50 0.62
66 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (64 bp):
ATCGATGCATAAAATGCATTCGATGTTTTAAAATACCATGAGTGCATCGATGCATGACTTGTGC
Found at i:2510438 original size:65 final size:63
Alignment explanation
Indices: 2510243--2510440 Score: 192
Period size: 65 Copynumber: 3.1 Consensus size: 63
2510233 CTAAGAGTGT
* *
2510243 ATCGATACATAAAATGCATTCGATGTTTT-A-AAATAGCATGTGTGCATCGATGCAT-GACTTGT
1 ATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-C-TGAGTGCATCGATGCATGGA-TTGT
2510305 GC
62 GC
*
2510307 ATCGATGCATAAAATGCATTCTATGTTTTCATAAAACCCTGAGTGCATCGATGCATGG-TATGTG
1 ATCGATGCATAAAATGCATTCGATGTTTTCATAAAA--CTGAGTGCATCGATGCATGGAT-TGTG
2510371 C
63 C
* * **
2510372 ATCGATGCATATAATGCATTCGATGTTCAATTTATTCAA-TG-GTGCATCGATGCATGGATTGAT
1 ATCGATGCATAAAATGCATTCGATGTT---TTCATAAAACTGAGTGCATCGATGCATGGATTG-T
2510435 GC
62 GC
2510437 ATCG
1 ATCG
2510441 GTACACTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
64 46 0.40
65 58 0.50
66 5 0.04
68 6 0.05
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (63 bp):
ATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTGAGTGCATCGATGCATGGATTGTGC
Found at i:2515650 original size:24 final size:24
Alignment explanation
Indices: 2515620--2515674 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
2515610 CGACAAACAT
2515620 TTTTCTTATTTCTTTTAAACTCAA
1 TTTTCTTATTTCTTTTAAACTCAA
2515644 TTTTCTTATTTCTTTTAAACTCAA
1 TTTTCTTATTTCTTTTAAACTCAA
2515668 TTTTCTT
1 TTTTCTT
2515675 TCATTCAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTCTTATTTCTTTTAAACTCAA
Done.