Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 1 of 32
Found at i:1944 original size:22 final size:22
Alignment explanation
Indices: 1919--1966 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1909 CCCGAATCCT
* * *
1919 AAACCCTAGAACCTTAAACCCC
1 AAACCCAAAAACCCTAAACCCC
*
1941 AAACCCAAAAACCCTAAACCTC
1 AAACCCAAAAACCCTAAACCCC
1963 AAAC
1 AAAC
1967 TCGAACCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.40, G:0.02, T:0.10
Consensus pattern (22 bp):
AAACCCAAAAACCCTAAACCCC
Found at i:2025 original size:21 final size:21
Alignment explanation
Indices: 1950--2026 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
1940 CAAACCCAAA
* *
1950 AACCCTAAACCTC-AAACTCG
1 AACCCTAAACCCCTAACCTCG
* *
1970 AACCCT-AACCCCGACCCTCG
1 AACCCTAAACCCCTAACCTCG
* *
1990 AATCCC-CAACGCCTAACCTCG
1 AA-CCCTAAACCCCTAACCTCG
2011 AACCCTAAACCCCTAA
1 AACCCTAAACCCCTAA
2027 TACTTTATCA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
19 5 0.11
20 16 0.36
21 24 0.53
ACGTcount: A:0.34, C:0.47, G:0.06, T:0.13
Consensus pattern (21 bp):
AACCCTAAACCCCTAACCTCG
Found at i:2334 original size:15 final size:14
Alignment explanation
Indices: 2316--2350 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2306 TAAATATAAT
2316 TAATATAATAATTTA
1 TAATATAATAA-TTA
*
2331 TAATATGATAATTA
1 TAATATAATAATTA
2345 TAATAT
1 TAATAT
2351 TGTTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
TAATATAATAATTA
Found at i:6314 original size:25 final size:25
Alignment explanation
Indices: 6285--6334 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
6275 CTCTTACTTT
6285 TAAAGTCCAATC-TAGCACCAACATC
1 TAAAGTCCAA-CATAGCACCAACATC
*
6310 TAAAGTCCAACATAGCATCAACATC
1 TAAAGTCCAACATAGCACCAACATC
6335 AAAATAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.42, C:0.30, G:0.08, T:0.20
Consensus pattern (25 bp):
TAAAGTCCAACATAGCACCAACATC
Found at i:13949 original size:12 final size:12
Alignment explanation
Indices: 13930--13984 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
13920 TAATTATTAA
13930 AAAAATTAAAAT
1 AAAAATTAAAAT
* *
13942 AAATATTATAAT
1 AAAAATTAAAAT
13954 AAAAATTAAAAT
1 AAAAATTAAAAT
*
13966 AAAAAATAATAATT
1 AAAAATTAA-AA-T
13980 AAAAA
1 AAAAA
13985 ATATTGACGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
12 28 0.78
13 2 0.06
14 6 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAATTAAAAT
Found at i:13949 original size:24 final size:24
Alignment explanation
Indices: 13922--13968 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
13912 AAAAATATTA
13922 ATTATTAA-AAAAATTAAAATAAAT
1 ATTA-TAATAAAAATTAAAATAAAT
13946 ATTATAATAAAAATTAAAATAAA
1 ATTATAATAAAAATTAAAATAAA
13969 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTATAATAAAAATTAAAATAAAT
Found at i:14131 original size:29 final size:31
Alignment explanation
Indices: 14084--14143 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
14074 TAAAAATAAT
14084 TTTTTAAAAATTAAATATTT-AT-ATTTATA
1 TTTTTAAAAATTAAATATTTAATGATTTATA
*
14113 TTTTT-AAATTTAAAGTATTTAATGATTTATA
1 TTTTTAAAAATTAAA-TATTTAATGATTTATA
14144 AATTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 10 0.37
30 2 0.07
31 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTTTAAAAATTAAATATTTAATGATTTATA
Found at i:15123 original size:30 final size:30
Alignment explanation
Indices: 15089--15151 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
15079 TTATAAGTGC
*
15089 TTATTTGATTCAAAATAAAAATATAAGAAT
1 TTATTTGACTCAAAATAAAAATATAAGAAT
*
15119 TTATTTGACTCAAAATAAAAATATAAGAGT
1 TTATTTGACTCAAAATAAAAATATAAGAAT
15149 TTA
1 TTA
15152 ATTAAACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (30 bp):
TTATTTGACTCAAAATAAAAATATAAGAAT
Found at i:15165 original size:29 final size:30
Alignment explanation
Indices: 15099--15173 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
15089 TTATTTGATT
* **
15099 CAAAATAAAAATATAAGAATTTATTTGACT
1 CAAAATAAAAATATAAGAATTTAATTGAAA
*
15129 CAAAATAAAAATATAAGAGTTTAATT-AAA
1 CAAAATAAAAATATAAGAATTTAATTGAAA
* *
15158 CATAATAAAAGTATAA
1 CAAAATAAAAATATAA
15174 CGGCTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (30 bp):
CAAAATAAAAATATAAGAATTTAATTGAAA
Found at i:15773 original size:39 final size:39
Alignment explanation
Indices: 15692--15773 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
15682 TAAATATCAT
* * * *
15692 TTAA-ATAAAATAAATAAATTTAAAAATTACTTATATTG
1 TTAACATAAAATAAATAAATTTAAAAATTAATTACACTA
* *
15730 TTAACATAAAATGAATAAATTTATAAATTAATTACACTA
1 TTAACATAAAATAAATAAATTTAAAAATTAATTACACTA
15769 TTAAC
1 TTAAC
15774 CTTTTAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 4 0.11
39 33 0.89
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (39 bp):
TTAACATAAAATAAATAAATTTAAAAATTAATTACACTA
Found at i:15824 original size:21 final size:22
Alignment explanation
Indices: 15798--15839 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15788 AATATTACTG
*
15798 TTTTT-AAATTATATTTATTAT
1 TTTTTAAAATTATATTAATTAT
15819 TTTTTAAAATTATATTAATTA
1 TTTTTAAAATTATATTAATTA
15840 ATCTTACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTAAAATTATATTAATTAT
Found at i:16689 original size:251 final size:240
Alignment explanation
Indices: 16391--16941 Score: 640
Period size: 251 Copynumber: 2.2 Consensus size: 240
16381 NNNNNNNNNN
* * * * *
16391 AATTAACTTATTACGTTAACTCTTATATATTTACGTTAATATTTAAAATTTAATTATTCCA-TCT
1 AATTGACTTATTACGTTAACT-TTACACATTTACGTTAAAATTTAAAATTTAGTTATTCCACT-T
* * * *
16455 TTATAAGTTTTTACGTCAATTCTTATAATTTAACGTCAAGGCTT-TTCTATGTTAATTTTTAACT
64 TTATAAGATTTTACGTCAATTCTTATAATTTAACGTCAAGACTTATT-TATGTCAATTTTAAACT
* *
16519 ATAATTATTTTTATCTTTATTATTTTATATTTAAAAAATAAAATTTATATATTGTTAAATACTTT
128 ATAATTA-TTTTA---TTATT-TTTTATATTTAAAAAATAAAATTTATATATCGTTAAATAATTT
* * * *
16584 TA-ATCCGAGAATATAAATATAAATGTTTATTTTTTATTAAGATTAGAGTTTTTTATTT
188 TAGCT-CGAGAATATAAATATAAATATTTATTTTTTATTAAAATTA-A---ATTT-TTT
* * **
16642 AATTGACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTAAAATTTAGTTATTTTACTTT
1 AATTGACTTATTACGTTAACTTT-ACACATTTACGTTAAAATTTAAAATTTAGTTATTCCACTTT
* * * * *
16707 TATATGATTTTATGTCAATTGTTATAATTTTACGTCAAGACTTATTTATGTCAATTTTAAATTAT
65 TATAAGATTTTACGTCAATTCTTATAATTTAACGTCAAGACTTATTTATGTCAATTTTAAACTAT
* *
16772 AATTATTTTATTATTTTTTTTATTTAAAAATTAAAATTTATATATCGTTAAATAATTTTAGCTCG
130 AATTATTTTATTATTTTTTATATTTAAAAAATAAAATTTATATATCGTTAAATAATTTTAGCTCG
* *
16837 AGACTATAAATTTAAATATTTATTTTTTATTAAAATTAAATTTTTT
195 AGAATATAAATATAAATATTTATTTTTTATTAAAATTAAATTTTTT
* * * * *
16883 AATTGACTTGTTACGTTAACTTGTACTCATTTATGCTAAAATTTTAAATTTAGTTATTC
1 AATTGACTTATTACGTTAACTT-TACACATTTACGTTAAAATTTAAAATTTAGTTATTC
16942 TACCTTTACG
Statistics
Matches: 260, Mismatches: 35, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
241 52 0.20
242 4 0.02
245 1 0.00
246 77 0.30
247 6 0.02
250 7 0.03
251 110 0.42
252 3 0.01
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.51
Consensus pattern (240 bp):
AATTGACTTATTACGTTAACTTTACACATTTACGTTAAAATTTAAAATTTAGTTATTCCACTTTT
ATAAGATTTTACGTCAATTCTTATAATTTAACGTCAAGACTTATTTATGTCAATTTTAAACTATA
ATTATTTTATTATTTTTTATATTTAAAAAATAAAATTTATATATCGTTAAATAATTTTAGCTCGA
GAATATAAATATAAATATTTATTTTTTATTAAAATTAAATTTTTT
Found at i:27544 original size:55 final size:55
Alignment explanation
Indices: 27484--27595 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 55
27474 ATCACTTTCA
* *
27484 ATCAAAATCT-AAAAGAAAAATTCAAGAAAAAGATTAAAATTAACATACTTCTGAC
1 ATCAAAATCTAAAAAG-AAAATCCAAGAAAAAGATTAAAATTAACATACTTATGAC
*
27539 ATCAAAATCTAAAAAGAAAATCCAAGAAAAAGATTAAATTTAACATACTTATGAC
1 ATCAAAATCTAAAAAGAAAATCCAAGAAAAAGATTAAAATTAACATACTTATGAC
27594 AT
1 AT
27596 AAAGCAGGCT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
55 48 0.91
56 5 0.09
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.24
Consensus pattern (55 bp):
ATCAAAATCTAAAAAGAAAATCCAAGAAAAAGATTAAAATTAACATACTTATGAC
Found at i:29665 original size:3 final size:3
Alignment explanation
Indices: 29657--29681 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29647 TGCCATTGGA
29657 GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG G
29682 GTATGGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:29927 original size:9 final size:9
Alignment explanation
Indices: 29913--29938 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29903 TAAACTATGA
29913 GGTGGAGGT
1 GGTGGAGGT
29922 GGTGGAGGT
1 GGTGGAGGT
29931 GGTGGAGG
1 GGTGGAGG
29939 ACCTCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.69, T:0.19
Consensus pattern (9 bp):
GGTGGAGGT
Found at i:30082 original size:3 final size:3
Alignment explanation
Indices: 30074--30125 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
30064 GTGACACTAA
*
30074 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A-G AGG AGG TGG -GG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
*
30120 TGG AGG
1 AGG AGG
30126 TGCACATCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.29, C:0.00, G:0.67, T:0.04
Consensus pattern (3 bp):
AGG
Found at i:33073 original size:12 final size:12
Alignment explanation
Indices: 33049--33087 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
33039 AAAATATTAC
33049 AATTTTATAATTT
1 AATTTT-TAATTT
33062 AATTTTTAATTT
1 AATTTTTAATTT
*
33074 AATTTTTAAATT
1 AATTTTTAATTT
33086 AA
1 AA
33088 CAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AATTTTTAATTT
Found at i:33142 original size:15 final size:16
Alignment explanation
Indices: 33122--33151 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33112 ATAATTTAAA
33122 TTTAAATTT-TTTTAT
1 TTTAAATTTATTTTAT
33137 TTTAAATTTATTTTA
1 TTTAAATTTATTTTA
33152 AATTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTAAATTTATTTTAT
Found at i:33148 original size:11 final size:11
Alignment explanation
Indices: 33132--33156 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33122 TTTAAATTTT
33132 TTTATTTTAAA
1 TTTATTTTAAA
33143 TTTATTTTAAA
1 TTTATTTTAAA
33154 TTT
1 TTT
33157 TTTATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:35341 original size:57 final size:56
Alignment explanation
Indices: 35238--35500 Score: 171
Period size: 57 Copynumber: 4.7 Consensus size: 56
35228 TCAATAATAT
* * * * **
35238 ATTACCAACAAAAATTTCATTAATAATTTTTAAT-GAAATTATGTCGATAACAATTAA
1 ATTACTAATAAAAA-TTCATTGATAATTTTCAATAG-AATTCCGTCGATAACAATTAA
* * **
35295 ATTACAAATAAAAATATCATTGATAATTTTCATTAGAATTCCGTCGATAATGATTAA
1 ATTACTAATAAAAAT-TCATTGATAATTTTCAATAGAATTCCGTCGATAACAATTAA
* * ** * ** * *
35352 ATTATTAACAAAAACTTTGTTTATAATTTTCAATAGAATTCTAT-GGTAACAACTAA
1 ATTACTAATAAAAA-TTCATTGATAATTTTCAATAGAATTCCGTCGATAACAATTAA
* * * * * *
35408 ATTACTAATAAAAATTCCGTTAATAATTTTTAATGGAATTCCATCAATAAC--TT--
1 ATTACTAATAAAAATT-CATTGATAATTTTCAATAGAATTCCGTCGATAACAATTAA
* *
35461 ATTACCAATCAAAAATTCTATTGATAATTTTCGATA-AATT
1 ATTACTAAT-AAAAATTC-ATTGATAATTTTCAATAGAATT
35501 TTCATTAGAA
Statistics
Matches: 161, Mismatches: 38, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
53 13 0.08
54 19 0.12
55 3 0.02
56 43 0.27
57 81 0.50
58 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.38
Consensus pattern (56 bp):
ATTACTAATAAAAATTCATTGATAATTTTCAATAGAATTCCGTCGATAACAATTAA
Found at i:35447 original size:113 final size:109
Alignment explanation
Indices: 35183--35500 Score: 272
Period size: 110 Copynumber: 2.9 Consensus size: 109
35173 AAACCAACAA
* * * * **
35183 AAATAACTAACAAAAGTTCCGTTAGTAATTTTTAATGGAATTTTGTCAATAATATATTACCAACA
1 AAATTACTAATAAAAATTCCGTTAATAATTTTTAATGGAATTCCGTCAATAATATATTACCAACA
* *
35248 AAAATTTCATTAATAATTTTTAATGAAATTATGTCGATAACAATT
66 AAAATTTCATTAATAATTTTCAATGAAATTATG-CGATAACAACT
* * * * * * * *
35293 AAATTACAAATAAAAATAT-CATTGATAATTTTCATTAGAATTCCGTCGATAATGATTAAATTAT
1 AAATTACTAATAAAAAT-TCCGTTAATAATTTTTAATGGAATTCCGTCAATAAT-A-T--ATTAC
* * * *
35357 TAACAAAAACTTT-GTTTATAATTTTCAATAGAATTCTATG-G-TAACAACT
61 CAACAAAAA-TTTCATTAATAATTTTCAAT-GAAAT-TATGCGATAACAACT
*
35406 AAATTACTAATAAAAATTCCGTTAATAATTTTTAATGGAATTCCATCAATAACT-TATTACCAAT
1 AAATTACTAATAAAAATTCCGTTAATAATTTTTAATGGAATTCCGTCAATAA-TATATTACCAA-
* *
35470 CAAAAA-TTCTATTGATAATTTTCGAT-AAATT
64 CAAAAATTTC-ATTAATAATTTTCAATGAAATT
35501 TTCATTAGAA
Statistics
Matches: 161, Mismatches: 34, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
107 1 0.01
108 5 0.03
109 6 0.04
110 57 0.35
111 3 0.02
112 2 0.01
113 49 0.30
114 27 0.17
115 7 0.04
116 4 0.02
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (109 bp):
AAATTACTAATAAAAATTCCGTTAATAATTTTTAATGGAATTCCGTCAATAATATATTACCAACA
AAAATTTCATTAATAATTTTCAATGAAATTATGCGATAACAACT
Found at i:36289 original size:25 final size:25
Alignment explanation
Indices: 36252--36312 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
36242 TTAATACATG
36252 TATTATGT-ATTA-TGATTATATAAA-
1 TATTAT-TAATTATTGATT-TATAAAT
36276 TATTACTTAATTATTGATTTATAAAT
1 TATTA-TTAATTATTGATTTATAAAT
36302 TATTATTAATT
1 TATTATTAATT
36313 TATATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
24 6 0.18
25 17 0.52
26 10 0.30
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (25 bp):
TATTATTAATTATTGATTTATAAAT
Found at i:36315 original size:26 final size:26
Alignment explanation
Indices: 36262--36323 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
36252 TATTATGTAT
36262 TATGATTATATAAATATTACTTAATTA
1 TATGATT-TATAAATATTACTTAATTA
36289 T-TGATTTATAAATTATTA-TTAATTTA
1 TATGATTTATAAA-TATTACTTAA-TTA
36315 TAT-ATTTAT
1 TATGATTTAT
36324 TTAATTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 10 0.31
26 20 0.62
27 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TATGATTTATAAATATTACTTAATTA
Found at i:37752 original size:26 final size:27
Alignment explanation
Indices: 37716--37767 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
37706 TTGATGTCAG
* *
37716 TCTTCTTTTTCCTGCATCT-TCTTTGC
1 TCTTCATTTTCATGCATCTATCTTTGC
*
37742 TCTTCATTTTCATGCATGTATCTTTG
1 TCTTCATTTTCATGCATCTATCTTTG
37768 TTCATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.10, C:0.25, G:0.10, T:0.56
Consensus pattern (27 bp):
TCTTCATTTTCATGCATCTATCTTTGC
Found at i:39926 original size:109 final size:108
Alignment explanation
Indices: 39718--39913 Score: 258
Period size: 109 Copynumber: 1.8 Consensus size: 108
39708 GCCCATTTAC
* * * *
39718 TTTTATATTTAAATATCAGTTATGCAATTTTTAATGTTATAAAAGTAAATTTGTATACTAATTTT
1 TTTTATATTAAAATATCAATTATGCAATTTCTAATGTTATAAAAG-AAATTTCTATACTAATTTT
* * * *
39783 TTACATATTTGTTAATTTATAGGGTTCTTGATAAATATATTAAT
65 CTACATATTTATTAATTAATAGAGTTCTTGATAAATATATTAAT
39827 TTTTATATTAAAATATCAATTATGTC-A-TTCTAATGTTATAAAA-AAATTTCTATACTAA-TTT
1 TTTTATATTAAAATATCAATTATG-CAATTTCTAATGTTATAAAAGAAATTTCTATACTAATTTT
*
39888 CTATAT-TTTATTAATTAATAGAGTTC
65 CTACATATTTATTAATTAATAGAGTTC
39914 AGTTTAGAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
104 17 0.22
105 7 0.09
106 14 0.18
108 15 0.19
109 23 0.30
110 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (108 bp):
TTTTATATTAAAATATCAATTATGCAATTTCTAATGTTATAAAAGAAATTTCTATACTAATTTTC
TACATATTTATTAATTAATAGAGTTCTTGATAAATATATTAAT
Found at i:40919 original size:12 final size:12
Alignment explanation
Indices: 40902--40927 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40892 AAAATACAAT
40902 AATTATTCCTAA
1 AATTATTCCTAA
40914 AATTATTCCTAA
1 AATTATTCCTAA
40926 AA
1 AA
40928 AGTCTACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTATTCCTAA
Found at i:53256 original size:29 final size:29
Alignment explanation
Indices: 53224--53293 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
53214 CTCGTATACT
* **
53224 TGTTCACGTATAACTTTTTCTCTTGTACC
1 TGTTCACGTACAACTTCCTCTCTTGTACC
* * * *
53253 TGTTCATGTACAGCTTCCTCTTTTGTATC
1 TGTTCACGTACAACTTCCTCTCTTGTACC
53282 TGTTCACGTACA
1 TGTTCACGTACA
53294 GCTTTTCTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (29 bp):
TGTTCACGTACAACTTCCTCTCTTGTACC
Found at i:59330 original size:2 final size:2
Alignment explanation
Indices: 59323--59349 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59313 TTGGAGATTT
59323 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59350 TGCGTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60959 original size:43 final size:43
Alignment explanation
Indices: 60910--60998 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
60900 CAATGCAATC
*
60910 ATATTACAGTCAATGTATGTAATGTGATTACAGTCCAAAACCA
1 ATATTACAGCCAATGTATGTAATGTGATTACAGTCCAAAACCA
60953 ATATTACAGCCAATGTATGTAATGTGATTACAGTCCAAAACCA
1 ATATTACAGCCAATGTATGTAATGTGATTACAGTCCAAAACCA
60996 ATA
1 ATA
60999 CAATCACATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (43 bp):
ATATTACAGCCAATGTATGTAATGTGATTACAGTCCAAAACCA
Found at i:61107 original size:15 final size:15
Alignment explanation
Indices: 61087--61145 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
61077 TAATATTATA
61087 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
61102 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
* *
61117 A-TAATATAAGAATAAAA
1 ATTAAAAT-A-AA-AAAT
61134 ATTAAAATAAAA
1 ATTAAAATAAAA
61146 TAAAATGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 5 0.14
15 17 0.49
16 4 0.11
17 4 0.11
18 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:61133 original size:40 final size:40
Alignment explanation
Indices: 61075--61275 Score: 135
Period size: 40 Copynumber: 4.9 Consensus size: 40
61065 AAAAATATTT
*
61075 TATAATATTATAATTAAAATAAAA-AATATTAAAATAAAATA
1 TATAATATAATAA-TAAAATAAAAGAA-ATTAAAATAAAATA
* * * *
61116 TATAATATAAGAATAAAAATTAAAATAAAATAAAATGTAAAAAA
1 TATAATATAATAAT-AAAA-TAAAAGAAATTAAAA--TAAAATA
* **
61160 T-TAACATTTATATAATATAGGTAAAAGAAATTAAAATAAAATA
1 TAT-A-ATATA-ATAATA-AAATAAAAGAAATTAAAATAAAATA
* *
61203 TATAATATAA-AA-AATATATTAAAGAAATAAAAATAAAATA
1 TATAATATAATAATAA-A-ATAAAAGAAATTAAAATAAAATA
* * *
61243 TATAAGATTATAAT--AATAAAAGAAAATAAAATA
1 TATAATATAATAATAAAATAAAAGAAATTAAAATA
61276 TATGATATTA
Statistics
Matches: 125, Mismatches: 21, Indels: 31
0.71 0.12 0.18
Matches are distributed among these distances:
38 16 0.13
39 2 0.02
40 31 0.25
41 18 0.14
42 15 0.12
43 11 0.09
44 9 0.07
45 18 0.14
46 5 0.04
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.29
Consensus pattern (40 bp):
TATAATATAATAATAAAATAAAAGAAATTAAAATAAAATA
Found at i:61142 original size:20 final size:20
Alignment explanation
Indices: 61078--61388 Score: 88
Period size: 20 Copynumber: 15.6 Consensus size: 20
61068 AATATTTTAT
* *
61078 AATATTATAATTAAAATAAAA
1 AATATTA-AAATAAAATATAA
*
61099 AATATTAAAATAAAATATAT
1 AATATTAAAATAAAATATAA
*
61119 AATA-TAAGAATAAAA-ATTA
1 AATATTAA-AATAAAATATAA
*
61138 AA-A-TAAAATAAAATGTAA
1 AATATTAAAATAAAATATAA
*
61156 AAAATTAACATTTATATAATATAGGTAAA
1 AATATTAA-A---ATA-AA-ATA--T-AA
* *
61185 AGAAATTAAAATAAAATATAT
1 A-ATATTAAAATAAAATATAA
*
61206 AATA-TAAAA-AATATATTAA
1 AATATTAAAATAAAATA-TAA
* * *
61225 AGAAATAAAAATAAAATATAT
1 A-ATATTAAAATAAAATATAA
* *
61246 AAGATT---ATAATA-AT-A
1 AATATTAAAATAAAATATAA
* *
61261 AA-A-GAAAATAAAATATAT
1 AATATTAAAATAAAATATAA
* * *
61279 GATATTAAAA-ATATATTTAA
1 AATATTAAAATA-AAATATAA
**
61299 AATA-T--AATATTATATAA
1 AATATTAAAATAAAATATAA
61316 AA-ATTAATAATAAAAATATAA
1 AATATTAA-AAT-AAAATATAA
*
61337 ATATATTAAAAAGAAAATATAA
1 A-ATATT-AAAATAAAATATAA
*
61359 AATATTATAATAATAA-ATAA
1 AATATTAAAATAA-AATATAA
61379 AA-A-TAAAATA
1 AATATTAAAATA
61389 TATGATATTA
Statistics
Matches: 217, Mismatches: 37, Indels: 75
0.66 0.11 0.23
Matches are distributed among these distances:
14 1 0.00
15 2 0.01
16 8 0.04
17 25 0.12
18 21 0.10
19 20 0.09
20 57 0.26
21 32 0.15
22 17 0.08
23 5 0.02
24 8 0.04
25 4 0.02
26 5 0.02
28 1 0.00
29 4 0.02
30 7 0.03
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AATATTAAAATAAAATATAA
Found at i:61308 original size:32 final size:32
Alignment explanation
Indices: 61228--61382 Score: 92
Period size: 33 Copynumber: 4.9 Consensus size: 32
61218 ATATTAAAGA
* * * *
61228 AATAAAAATAAAATATATAAGATTATAA-TAAT
1 AATAAAAATATAATATAT-ATATAAAAATTAAT
* *
61260 AAAAGAAAATAAAATATATGATATTAAAAA-T-AT
1 AATA-AAAATATAATATAT-ATA-TAAAAATTAAT
* *
61293 ATTTAAAATATAATAT-TATATAAAAATTAAT
1 AATAAAAATATAATATATATATAAAAATTAAT
*
61324 AATAAAAATATAA-ATATAT-TAAAAA-GAA-
1 AATAAAAATATAATATATATATAAAAATTAAT
* *
61352 AATATAAAATATTATAATAATAAATAAAAAT
1 AATA-AAAATATAAT-AT-ATATATAAAAAT
61383 AAAATATATG
Statistics
Matches: 98, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.04
29 16 0.16
30 12 0.12
31 19 0.19
32 17 0.17
33 25 0.26
34 5 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (32 bp):
AATAAAAATATAATATATATATAAAAATTAAT
Found at i:61334 original size:21 final size:22
Alignment explanation
Indices: 61310--61383 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
61300 ATATAATATT
61310 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATTAATAATAAAA
61331 ATATAAATATATTAA-AA-AGAAA
1 ATATAAA-ATATTAATAATA-AAA
61353 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAATAA-AA
61375 ATA-AAAATA
1 ATATAAAATA
61384 AAATATATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.02
21 22 0.47
22 19 0.40
23 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (22 bp):
ATATAAAATATTAATAATAAAA
Found at i:61370 original size:113 final size:113
Alignment explanation
Indices: 61230--61455 Score: 384
Period size: 113 Copynumber: 2.0 Consensus size: 113
61220 ATTAAAGAAA
* *
61230 TAAAAATAAAATATATAAGATTATAATAATAAA-AGAAAATAAAATATATGATATTAAAAATATA
1 TAAAAAGAAAATATAAAAGATTATAATAATAAATA-AAAATAAAATATATGATATTAAAAATATA
61294 TTTAA-AATATAATATTATATAAAAATTAATAATAAAAATATAAATATAT
65 TTTAAGAA-ATAATATTATATAAAAATTAATAATAAAAATATAAATATAT
*
61343 TAAAAAGAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
1 TAAAAAGAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
*
61408 TTAAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATAT
66 TTAAGAAATAATATTATATAAAAATTAATAATAAAAATATAAATATAT
61456 ACAATTCCAA
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
113 104 0.97
114 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (113 bp):
TAAAAAGAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
TTAAGAAATAATATTATATAAAAATTAATAATAAAAATATAAATATAT
Found at i:61432 original size:16 final size:15
Alignment explanation
Indices: 61270--61448 Score: 77
Period size: 16 Copynumber: 12.5 Consensus size: 15
61260 AAAAGAAAAT
*
61270 AAAATATATGATATTA
1 AAAATATATTATA-TA
61286 AAAATATATT-TA-A
1 AAAATATATTATATA
*
61299 AATATAATATTATATA
1 AAAAT-ATATTATATA
*
61315 AAAAT-TAATA-ATA
1 AAAATATATTATATA
*
61328 AAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
*
61345 AAAAGA-A--A-ATA
1 AAAATATATTATATA
*
61356 TAAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
61371 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
*
61383 AAAATATATGATATTA
1 AAAATATATTATA-TA
61399 AAAATATATT-TA-A
1 AAAATATATTATATA
*
61412 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
61428 AAAAT-TAATA-ATA
1 AAAATATATTATATA
61441 AAAATATA
1 AAAATATA
61449 AATATATACA
Statistics
Matches: 127, Mismatches: 13, Indels: 48
0.68 0.07 0.26
Matches are distributed among these distances:
10 1 0.01
11 11 0.09
12 3 0.02
13 30 0.24
14 24 0.19
15 17 0.13
16 33 0.26
17 8 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:63016 original size:15 final size:15
Alignment explanation
Indices: 62996--63049 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
62986 TTTTCTCTAT
* *
62996 AATCACATTGCTTGC
1 AATCACATTACTTAC
63011 AATCACATTACTTAC
1 AATCACATTACTTAC
* *
63026 AATCACATAACTTAT
1 AATCACATTACTTAC
*
63041 AATTACATT
1 AATCACATT
63050 GTATTATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (15 bp):
AATCACATTACTTAC
Found at i:63469 original size:16 final size:16
Alignment explanation
Indices: 63448--63481 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
63438 TGTCTATTGG
63448 CTTTTGCTCTCTCTCT
1 CTTTTGCTCTCTCTCT
63464 CTTTTGCTCTCTCTCT
1 CTTTTGCTCTCTCTCT
63480 CT
1 CT
63482 AGTGCCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.38, G:0.06, T:0.56
Consensus pattern (16 bp):
CTTTTGCTCTCTCTCT
Found at i:90331 original size:6 final size:7
Alignment explanation
Indices: 90314--90343 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
90304 AGTTCTCCAA
90314 TTTTTTG
1 TTTTTTG
90321 TTTTTTG
1 TTTTTTG
90328 TTTTTTG
1 TTTTTTG
90335 TTTTTTG
1 TTTTTTG
90342 TT
1 TT
90344 GTTGTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:101916 original size:40 final size:39
Alignment explanation
Indices: 101864--101944 Score: 117
Period size: 40 Copynumber: 2.1 Consensus size: 39
101854 AATTCATTCT
* * *
101864 TGGGACAAAACTTCAAAGAATATCAATTTAATGTCATTA
1 TGGGAAAAAACTTCAAAGAAGATCAATCTAATGTCATTA
*
101903 TGGGAAAATAACTTCAAAGAAGATCTATCTAATGTCATTA
1 TGGGAAAA-AACTTCAAAGAAGATCAATCTAATGTCATTA
101943 TG
1 TG
101945 AGAATCGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 7 0.19
40 30 0.81
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (39 bp):
TGGGAAAAAACTTCAAAGAAGATCAATCTAATGTCATTA
Found at i:106869 original size:2 final size:2
Alignment explanation
Indices: 106862--106886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
106852 CTGAGAATGA
106862 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
106887 AAAGAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114727 original size:25 final size:25
Alignment explanation
Indices: 114693--114743 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
114683 AGAGTTGTTA
114693 GAGCAGTTGAAGAAAGAATGTGCCT
1 GAGCAGTTGAAGAAAGAATGTGCCT
114718 GAGCAGTTGAAGAAAGAATGTGCCT
1 GAGCAGTTGAAGAAAGAATGTGCCT
114743 G
1 G
114744 TCTAGCCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (25 bp):
GAGCAGTTGAAGAAAGAATGTGCCT
Found at i:119680 original size:13 final size:13
Alignment explanation
Indices: 119662--119686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119652 CGAAACGAGG
119662 AGAGAGAGAGAGC
1 AGAGAGAGAGAGC
119675 AGAGAGAGAGAG
1 AGAGAGAGAGAG
119687 TCATGGAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.48, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAGAGC
Found at i:125283 original size:2 final size:2
Alignment explanation
Indices: 125276--125322 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
125266 GCTCAGAAGA
*
125276 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT CT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
125318 GT GT G
1 GT GT G
125323 AGAAAGAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.02, G:0.49, T:0.49
Consensus pattern (2 bp):
GT
Found at i:141441 original size:2 final size:2
Alignment explanation
Indices: 141434--141459 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
141424 TGTTCCCCAA
141434 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
141460 GCAAGTGCAA
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:153828 original size:2 final size:2
Alignment explanation
Indices: 153821--153848 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
153811 TTCTTTAGCA
153821 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
153849 GCACGATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154838 original size:3 final size:3
Alignment explanation
Indices: 154823--154854 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
154813 CATTTACGGG
*
154823 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
154855 GGACTAGTTT
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:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:179696 original size:31 final size:29
Alignment explanation
Indices: 179658--179782 Score: 102
Period size: 31 Copynumber: 4.3 Consensus size: 29
179648 ATAATATTAT
179658 AATTAAAATAAATATATAATATAAGAATAAA
1 AATTAAAATAAATATATAATAT-AGAA-AAA
*
179689 AATTAAAATAAA-ATA-AA-ATA-TAAAA
1 AATTAAAATAAATATATAATATAGAAAAA
**
179714 AATT--AATATTTATATAATATAGATAAAACA
1 AATTAAAATAAATATATAATATAG--AAAA-A
179744 AATTAAAATAAAATATATAATATA-AAAAA
1 AATTAAAAT-AAATATATAATATAGAAAAA
179773 TATATTAAAA
1 -A-ATTAAAA
179783 AATAAAAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
23 4 0.05
24 3 0.04
25 9 0.12
26 4 0.05
27 1 0.01
28 2 0.03
29 6 0.08
30 13 0.17
31 19 0.25
32 3 0.04
33 12 0.16
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (29 bp):
AATTAAAATAAATATATAATATAGAAAAA
Found at i:179781 original size:12 final size:14
Alignment explanation
Indices: 179698--180122 Score: 109
Period size: 14 Copynumber: 29.9 Consensus size: 14
179688 AAATTAAAAT
*
179698 AAAATAAAATATAA
1 AAAATATAATATAA
*
179712 AAAAT-TAATATTTAT
1 AAAATATAATA--TAA
*
179727 ATAATATAGATA-AA
1 AAAATATA-ATATAA
*
179741 ACAAAT-TAAAATAA
1 A-AAATATAATATAA
*
179755 AATATATAATATAA
1 AAAATATAATATAA
179769 AAAATAT-AT-TAA
1 AAAATATAATATAA
*
179781 AAAATA-AAAATAA
1 AAAATATAATATAA
*
179794 AATATATAAAACTATAA
1 AA-A-ATATAA-TATAA
*
179811 TAATAA-ATAAAAATAA
1 -AA-AATAT-AATATAA
* * * *
179827 AATATATGACATTA
1 AAAATATAATATAA
*
179841 AAAATAT-ATTTAA
1 AAAATATAATATAA
* *
179854 AATATGATATTATATA
1 AAAAT-ATAATATA-A
179870 AAAAT-TAATCAT-A
1 AAAATATAAT-ATAA
*
179883 TAAATATAAATATATTA
1 AAAATAT-AATATA--A
*
179900 AAAATA-AA-ATAT
1 AAAATATAATATAA
*
179912 AAAATATTATAATAA
1 AAAATATAAT-ATAA
* *
179927 TAAATA-AAAATAA
1 AAAATATAATATAA
* * * *
179940 AATATATGACATTA
1 AAAATATAATATAA
*
179954 AAAATAT-ATTTAA
1 AAAATATAATATAA
*
179967 GAAATGATATTATATAA
1 -AAA--ATATAATATAA
*
179984 AAATTAATAATATAA
1 AAAAT-ATAATATAA
*
179999 ATATAA-AT-ATATTA
1 A-A-AATATAATATAA
*
180013 AAAATA-AA-ATAT
1 AAAATATAATATAA
*
180025 AAAATATTATAATAA
1 AAAATATAAT-ATAA
* *
180040 TAAATA-AAAATAA
1 AAAATATAATATAA
* * *
180053 AATATATGATATTA
1 AAAATATAATATAA
*
180067 AAAATAT-ATTTAA
1 AAAATATAATATAA
* *
180080 GAAATGATATTATATA
1 AAAAT-ATAATATA-A
*
180096 AAAAT-TAATAAAA
1 AAAATATAATATAA
180109 AAAATATAAATATA
1 AAAATAT-AATATA
180123 TTAAACTTAT
Statistics
Matches: 294, Mismatches: 70, Indels: 93
0.64 0.15 0.20
Matches are distributed among these distances:
12 26 0.09
13 66 0.22
14 88 0.30
15 61 0.21
16 27 0.09
17 22 0.07
18 4 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (14 bp):
AAAATATAATATAA
Found at i:179785 original size:33 final size:33
Alignment explanation
Indices: 179748--179833 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
179738 AAAACAAATT
* *
179748 AAAATAAAATATATAATATA-AAAAATATATTAA
1 AAAATAAAA-ATAAAATATATAAAAATATAATAA
*
179781 AAAATAAAAATAAAATATATAAAACTATAATAA
1 AAAATAAAAATAAAATATATAAAAATATAATAA
*
179814 TAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
179834 GACATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 9 0.19
33 39 0.81
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAAATATAATAA
Found at i:179832 original size:23 final size:24
Alignment explanation
Indices: 179661--179832 Score: 68
Period size: 23 Copynumber: 7.4 Consensus size: 24
179651 ATATTATAAT
179661 TAAAATA-AATATATAATATAAGAATA
1 TAAAATATAATA-ATAA-ATAA-AATA
179687 -AAAAT-TAA-AATAAAATAAAATA
1 TAAAATATAATAAT-AAATAAAATA
* ** *
179709 TAAAAAATTAAT-ATTTATATAATA
1 TAAAATA-TAATAATAAATAAAATA
* *
179733 T-AGATA-AA-ACA-AATTAAAATA
1 TAAAATATAATA-ATAAATAAAATA
179754 -AAATATATAAT-ATAAA-AAATATA
1 TAAA-ATATAATAATAAATAAA-ATA
* * *
179777 TTAAAAAATAAAAATAAA--ATATA
1 -TAAAATATAATAATAAATAAAATA
179800 TAAAACTATAATAATAAATAAAA-A
1 TAAAA-TATAATAATAAATAAAATA
179824 TAAAATATA
1 TAAAATATA
179833 TGACATTAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 43
0.64 0.11 0.25
Matches are distributed among these distances:
21 9 0.08
22 17 0.16
23 37 0.34
24 23 0.21
25 22 0.20
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (24 bp):
TAAAATATAATAATAAATAAAATA
Found at i:179923 original size:113 final size:113
Alignment explanation
Indices: 179785--180127 Score: 609
Period size: 113 Copynumber: 3.0 Consensus size: 113
179775 TATTAAAAAA
*
179785 TAAAAATAAAATATATAAA-ACTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATA
1 TAAAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATA
*
179849 TTTAA-AATATGATATTATATAAAAATTAATCATATAAATATAAATATAT
65 TTTAAGAA-ATGATATTATATAAAAATTAATAATATAAATATAAATATAT
179898 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
179963 TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
66 TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
*
180011 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
1 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
* *
180076 TTAAGAAATGATATTATATAAAAATTAATAAAAAAAATATAAATATAT
66 TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
180124 TAAA
1 TAAA
180128 CTTATATTTT
Statistics
Matches: 223, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
112 3 0.01
113 218 0.98
114 2 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (113 bp):
TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
TTAAGAAATGATATTATATAAAAATTAATAATATAAATATAAATATAT
Found at i:179940 original size:33 final size:34
Alignment explanation
Indices: 179891--180074 Score: 119
Period size: 33 Copynumber: 5.2 Consensus size: 34
179881 TATAAATATA
*
179891 AATATATTAAAAATAAAATATAAAATATTATAAT
1 AATATAATAAAAATAAAATATAAAATATTATAAT
** *
179925 AATA-AATAAAAATAAAATATATGACATTA-AA-
1 AATATAATAAAAATAAAATATAAAATATTATAAT
* *
179956 AATATATTTAAGAAATGATATTATATAAAAATTAATAATATAAATAT
1 AATATA-ATAA-AAAT-A-A-AATAT-AAAA-T-AT--TAT--A-AT
*
180003 AAATATATTAAAAATAAAATATAAAATATTATAAT
1 -AATATAATAAAAATAAAATATAAAATATTATAAT
**
180038 AATA-AATAAAAATAAAATATATGATATTA-AA-
1 AATATAATAAAAATAAAATATAAAATATTATAAT
180069 AATATA
1 AATATA
180075 TTTAAGAAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
31 8 0.07
32 6 0.05
33 46 0.39
34 12 0.10
35 3 0.03
36 2 0.02
37 4 0.03
38 5 0.04
40 4 0.03
41 1 0.01
42 6 0.05
43 4 0.03
44 1 0.01
45 2 0.02
46 5 0.04
47 4 0.03
48 6 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (34 bp):
AATATAATAAAAATAAAATATAAAATATTATAAT
Found at i:180003 original size:6 final size:6
Alignment explanation
Indices: 179992--180058 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
179982 AAAAATTAAT
* *
179992 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
180042 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
180059 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:180100 original size:16 final size:15
Alignment explanation
Indices: 179825--180100 Score: 68
Period size: 16 Copynumber: 19.3 Consensus size: 15
179815 AAATAAAAAT
* *
179825 AAAATATATGACATTA
1 AAAATATATTATA-TA
179841 AAAATATATT-TA-A
1 AAAATATATTATATA
*
179854 AATATGATATTATATA
1 AAAAT-ATATTATATA
*
179870 AAAAT-TAATCATATA
1 AAAATAT-ATTATATA
* *
179885 AATATA-AATATATTA
1 AAAATATATTATA-TA
179900 AAAATA-A--A-ATA
1 AAAATATATTATATA
*
179911 TAAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
179926 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
* *
179938 AAAATATATGACATTA
1 AAAATATATTATA-TA
179954 AAAATATATT-TA-A
1 AAAATATATTATATA
*
179967 GAAATGATATTATATA
1 AAAAT-ATATTATATA
*
179983 AAAAT-TAATA-ATA
1 AAAATATATTATATA
* *
179996 TAAATATAAATATATTA
1 AAAATAT-ATTATA-TA
180013 AAAATA-A--A-ATA
1 AAAATATATTATATA
*
180024 TAAA-ATATTATAATA
1 AAAATATATTAT-ATA
*
180039 ATAAATA-A--AAAT-
1 A-AAATATATTATATA
*
180051 AAAATATATGATATTA
1 AAAATATATTATA-TA
180067 AAAATATATT-TA-A
1 AAAATATATTATATA
*
180080 GAAATGATATTATATA
1 AAAAT-ATATTATATA
180096 AAAAT
1 AAAAT
180101 TAATAAAAAA
Statistics
Matches: 193, Mismatches: 27, Indels: 80
0.64 0.09 0.27
Matches are distributed among these distances:
10 2 0.01
11 22 0.11
12 6 0.03
13 30 0.16
14 31 0.16
15 42 0.22
16 51 0.26
17 9 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:180301 original size:15 final size:15
Alignment explanation
Indices: 180277--180315 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
180267 TTTTCCCTGT
180277 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
180292 AATCATATTACTTGT
1 AATCACATTACTTGC
180307 AATCACATT
1 AATCACATT
180316 GCATTGTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:186536 original size:24 final size:24
Alignment explanation
Indices: 186487--186536 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
186477 AATTTTCTTC
* **
186487 AAAAGAAATACTAGTATAATGGAT
1 AAAAAAAATACTAGTATAATAAAT
186511 AAAAAAAATACCTAGT-TAATAAAT
1 AAAAAAAATA-CTAGTATAATAAAT
186535 AA
1 AA
186537 GATAACATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (24 bp):
AAAAAAAATACTAGTATAATAAAT
Found at i:187086 original size:2 final size:2
Alignment explanation
Indices: 187079--187105 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
187069 AGGAGAAAGA
187079 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
187106 TCTAATTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:188382 original size:8 final size:8
Alignment explanation
Indices: 188369--188394 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
188359 GCAATGGGTG
188369 TTTTGAAA
1 TTTTGAAA
188377 TTTTGAAA
1 TTTTGAAA
188385 TTTTGAAA
1 TTTTGAAA
188393 TT
1 TT
188395 CCACATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (8 bp):
TTTTGAAA
Found at i:190153 original size:36 final size:36
Alignment explanation
Indices: 190097--190169 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
190087 TTTAGTTGTA
* * **
190097 TGTCTACAGCAAGGACATTAATGTCACATAACAATG
1 TGTCCACAACAAGGACATTAATAACACATAACAATG
*
190133 TGTCCACAACAAGGACATTAATAACACATAATAATG
1 TGTCCACAACAAGGACATTAATAACACATAACAATG
190169 T
1 T
190170 ATCCTCGAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (36 bp):
TGTCCACAACAAGGACATTAATAACACATAACAATG
Found at i:195023 original size:21 final size:21
Alignment explanation
Indices: 194981--195024 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
194971 TTACATTATT
*
194981 TTTTAATTAAAAATATATAAA
1 TTTTAATTAAAAATATAAAAA
*
195002 TTTTATTTAATAAATA-AAAAA
1 TTTTAATTAA-AAATATAAAAA
195023 TT
1 TT
195025 ACGTACCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTAATTAAAAATATAAAAA
Found at i:197000 original size:30 final size:30
Alignment explanation
Indices: 196933--197002 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
196923 TTTAATGATG
* * * *
196933 GACAAAATATTTATTTCTTTTAAGACATTT
1 GACATAATATTTACTTCTTTTAAAACACTT
* * *
196963 TATATAATATTTACTTCTTTTAAAATACTT
1 GACATAATATTTACTTCTTTTAAAACACTT
196993 GACATAATAT
1 GACATAATAT
197003 GCATACATAC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (30 bp):
GACATAATATTTACTTCTTTTAAAACACTT
Found at i:207767 original size:23 final size:23
Alignment explanation
Indices: 207708--207759 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
207698 TTGTTAGATA
207708 AGCATTGTATATTTATTATGGTT
1 AGCATTGTATATTTATTATGGTT
207731 AGCATTGTATATTTATTATGGTT
1 AGCATTGTATATTTATTATGGTT
207754 AGCATT
1 AGCATT
207760 ATAAATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (23 bp):
AGCATTGTATATTTATTATGGTT
Found at i:212438 original size:14 final size:14
Alignment explanation
Indices: 212411--212450 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
212401 AAAGGTAAAG
212411 TTTTTATTTA-ATT
1 TTTTTATTTATATT
212424 TTTTTATTTATA-T
1 TTTTTATTTATATT
*
212437 TTTTTAATTATATT
1 TTTTTATTTATATT
212451 CTATTTGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 22 0.92
14 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:212595 original size:15 final size:16
Alignment explanation
Indices: 212575--212608 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
212565 TGTTATGTGG
*
212575 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
212590 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
212606 ATT
1 ATT
212609 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:214179 original size:21 final size:20
Alignment explanation
Indices: 214128--214182 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
214118 TCATATATAA
*
214128 ATTTTATTTTTTACT-TGTC
1 ATTTTATTTTTTATTATGTC
*
214147 A-TAT-TTTTTTATTATGTAC
1 ATTTTATTTTTTATTATGT-C
214166 ATTTTATTTTTTATTAT
1 ATTTTATTTTTTATTAT
214183 TTTAATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
19 3 0.10
20 2 0.07
21 11 0.38
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (20 bp):
ATTTTATTTTTTATTATGTC
Found at i:214387 original size:15 final size:14
Alignment explanation
Indices: 214362--214404 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
214352 GAGATAATTG
214362 TAATTTTTTTAATA
1 TAATTTTTTTAATA
*
214376 TAATTTTATTTATTA
1 TAATTTT-TTTAATA
*
214391 TATATATTTTTAAT
1 TA-ATTTTTTTAAT
214405 GACTCTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TAATTTTTTTAATA
Found at i:217916 original size:42 final size:44
Alignment explanation
Indices: 217856--217944 Score: 137
Period size: 42 Copynumber: 2.1 Consensus size: 44
217846 GTTACTGAAA
* * *
217856 ACTGAAGCTTTGTTATAGAAGCTCTCTC-C-TGTTTTTCTTCCT
1 ACTGAAGCTTAGTGATAGAAGCTCTCTCTCTTGTTTCTCTTCCT
217898 ACTGAAGCTTAGTGATAGAAGCTCTCTCTCTTGTTTCTCTTCCT
1 ACTGAAGCTTAGTGATAGAAGCTCTCTCTCTTGTTTCTCTTCCT
217942 ACT
1 ACT
217945 ATTTCTTCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 26 0.62
43 1 0.02
44 15 0.36
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (44 bp):
ACTGAAGCTTAGTGATAGAAGCTCTCTCTCTTGTTTCTCTTCCT
Found at i:223373 original size:2 final size:2
Alignment explanation
Indices: 223366--223391 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
223356 ATGAAAAGCA
223366 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
223392 GGGTGGCAGC
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:238712 original size:2 final size:2
Alignment explanation
Indices: 238705--238736 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
238695 TTCAACTCAA
238705 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
238737 TGGAAAAATA
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):
AT
Found at i:239714 original size:20 final size:20
Alignment explanation
Indices: 239676--239735 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
239666 TCTCGCTCAA
*
239676 ATTTAATTATAT-ATGAATT
1 ATTTAATTTTATGATGAATT
*
239695 ATTTAATTTTATGTTGAATT
1 ATTTAATTTTATGATGAATT
* *
239715 TTTTAACTATTATGATGAATT
1 ATTTAA-TTTTATGATGAATT
239736 TGCATGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 11 0.32
20 11 0.32
21 12 0.35
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTAATTTTATGATGAATT
Found at i:240790 original size:30 final size:30
Alignment explanation
Indices: 240752--240830 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
240742 TTAAAAATTT
*
240752 AAATAAATTTTCATATTATTATTTTAAATT
1 AAATAAATTTTCATATTATTATTTTAAATC
* * *
240782 ATATAAATTTTTATATTTTTATTTTAAATC
1 AAATAAATTTTCATATTATTATTTTAAATC
240812 AAATAAATTTTACA-ATTAT
1 AAATAAATTTT-CATATTAT
240831 GACTGATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATAAATTTTCATATTATTATTTTAAATC
Found at i:255869 original size:6 final size:6
Alignment explanation
Indices: 255861--255903 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
255851 TCTCTTTTTG
* *
255861 GCCTTG GCC-TT GGCTTT GCCTTT GCCTTT GCCTTT GCCTTT GC
1 GCCTTT GCCTTT GCCTTT GCCTTT GCCTTT GCCTTT GCCTTT GC
255904 TGCTGCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 3 0.09
6 30 0.91
ACGTcount: A:0.00, C:0.33, G:0.23, T:0.44
Consensus pattern (6 bp):
GCCTTT
Found at i:258511 original size:6 final size:6
Alignment explanation
Indices: 258500--258524 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
258490 TAAATAAAAA
258500 GGAGAG GGAGAG GGAGAG GGAGAG G
1 GGAGAG GGAGAG GGAGAG GGAGAG G
258525 CTTTGGCGTT
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:259973 original size:17 final size:17
Alignment explanation
Indices: 259947--259980 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
259937 AAGTGTAATC
259947 AATGGATGACTTATTTT
1 AATGGATGACTTATTTT
*
259964 AATGGTTGACTTATTTT
1 AATGGATGACTTATTTT
259981 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (17 bp):
AATGGATGACTTATTTT
Found at i:260131 original size:2 final size:2
Alignment explanation
Indices: 260121--260155 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
260111 CTTACAAAAA
*
260121 AT AT A- AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
260156 GAGAAGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:261142 original size:2 final size:2
Alignment explanation
Indices: 261135--261161 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
261125 ATTTAGAAAC
261135 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
261162 CACAGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:264262 original size:18 final size:19
Alignment explanation
Indices: 264231--264267 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
264221 GATGATTTAA
264231 TTCAATTACGTTTT-AATT
1 TTCAATTACGTTTTCAATT
264249 TTCAATTGAC-TTTTCAATT
1 TTCAATT-ACGTTTTCAATT
264268 AATCTTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (19 bp):
TTCAATTACGTTTTCAATT
Found at i:271301 original size:21 final size:21
Alignment explanation
Indices: 271277--271316 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
271267 TTACTTCTTC
*
271277 ATATTAACAAATATTAAATAT
1 ATATTAAAAAATATTAAATAT
*
271298 ATATTAAAAAATTTTAAAT
1 ATATTAAAAAATATTAAAT
271317 TTTAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATTAAAAAATATTAAATAT
Found at i:288885 original size:15 final size:15
Alignment explanation
Indices: 288865--288895 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
288855 CAAATAATCC
*
288865 ATGCTTTCCATGCTT
1 ATGCTTCCCATGCTT
288880 ATGCTTCCCATGCTT
1 ATGCTTCCCATGCTT
288895 A
1 A
288896 AATTTGCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (15 bp):
ATGCTTCCCATGCTT
Found at i:288907 original size:24 final size:24
Alignment explanation
Indices: 288880--288928 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
288870 TTCCATGCTT
288880 ATGCTTCCCATGCTTAAATTTGCC
1 ATGCTTCCCATGCTTAAATTTGCC
*
288904 ATGCTTCCCATGCTTGAATTTGCC
1 ATGCTTCCCATGCTTAAATTTGCC
288928 A
1 A
288929 CCATGATGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (24 bp):
ATGCTTCCCATGCTTAAATTTGCC
Found at i:301892 original size:62 final size:59
Alignment explanation
Indices: 301826--302141 Score: 269
Period size: 56 Copynumber: 5.5 Consensus size: 59
301816 TTAAAATAAG
301826 TTTAATATATATTATATTTTTTATTATTAATTTTTATATAATATCATATTTCTAAATATATT
1 TTTAATATATATTATA-TTTTTATTATTAATTTTTATATAATATCAT-TTT-TAAATATATT
* * *
301888 TTTAATATCATA-TAT-TTATTT-TTATTTA-TTTT-TATAATAT--TTTATATAT-TATT
1 TTTAATAT-ATATTATATT-TTTATTATTAATTTTTATATAATATCATTTTTAAATATATT
301941 TTTAATATAT-TTATA-TTTTATTATTAATTTTTATATAATATCATTCTTT-AATATATT
1 TTTAATATATATTATATTTTTATTATTAATTTTTATATAATATCATT-TTTAAATATATT
* * * * *
301998 TTTAATGT-CA-TATA-TTTTATT-TTTATTTATTAT-T-ATAAT-ATTTTTATATTTATT
1 TTTAATATATATTATATTTTTATTATTAATTT-TTATATAAT-ATCATTTTTAAATATATT
* *
302052 TTTGATATAT-TTATATTTATATTATTAA-TTTTATATAATATCATATTTTAAATATATT
1 TTTAATATATATTATATTTTTATTATTAATTTTTATATAATATCAT-TTTTAAATATATT
302110 TTTAATGTCATATATT-TATTTTTTATTTATTA
1 TTTAA--T-ATATATTATA-TTTTTA-TTATTA
302142 TTATAATTTT
Statistics
Matches: 205, Mismatches: 20, Indels: 57
0.73 0.07 0.20
Matches are distributed among these distances:
51 3 0.01
52 12 0.06
53 19 0.09
54 29 0.14
55 19 0.09
56 31 0.15
57 20 0.10
58 23 0.11
59 4 0.02
60 9 0.04
61 9 0.04
62 18 0.09
63 9 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (59 bp):
TTTAATATATATTATATTTTTATTATTAATTTTTATATAATATCATTTTTAAATATATT
Found at i:301915 original size:10 final size:10
Alignment explanation
Indices: 301900--301958 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
301890 TAATATCATA
301900 TATTTATTTT
1 TATTTATTTT
301910 TATTTATTTT
1 TATTTATTTT
*
301920 TATAATATTTT
1 TAT-TTATTTT
301931 ATATATTATTTT
1 -TAT-TTATTTT
* *
301943 TAATATATTTA
1 T-ATTTATTTT
301954 TATTT
1 TATTT
301959 TATTATTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
10 16 0.39
11 13 0.32
12 12 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTATTTT
Found at i:301928 original size:11 final size:11
Alignment explanation
Indices: 301904--302063 Score: 52
Period size: 11 Copynumber: 14.5 Consensus size: 11
301894 ATCATATATT
*
301904 TATTTTTAT-T
1 TATTTTTATAA
301914 TATTTTTATAA
1 TATTTTTATAA
301925 TA-TTTTAT-A
1 TATTTTTATAA
*
301934 TATTATTTTTAA
1 TATT-TTTATAA
*
301946 TATATTTAT-A
1 TATTTTTATAA
301956 T-TTTATTATTAA
1 TATTT-TTA-TAA
301968 T-TTTTATATAA
1 TATTTT-TATAA
301979 TATCATTCTT-TAA
1 TAT--TT-TTATAA
301992 TATATTTT-TAA
1 TAT-TTTTATAA
* * * **
302003 TGTCATATATTT
1 TAT-TTTTATAA
*
302015 TATTTTTAT-T
1 TATTTTTATAA
*
302025 TATTATTATAA
1 TATTTTTATAA
*
302036 TATTTTTATATT
1 TATTTTTATA-A
302048 TATTTTTGAT-A
1 TATTTTT-ATAA
302059 TATTT
1 TATTT
302064 ATATTTATAT
Statistics
Matches: 115, Mismatches: 19, Indels: 31
0.70 0.12 0.19
Matches are distributed among these distances:
9 5 0.04
10 30 0.26
11 43 0.37
12 25 0.22
13 8 0.07
14 3 0.03
15 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:302060 original size:111 final size:111
Alignment explanation
Indices: 301826--302167 Score: 523
Period size: 112 Copynumber: 3.0 Consensus size: 111
301816 TTAAAATAAG
301826 TTTAATATATATTATATTTTTTATTATTAATTTTTATATAATATCATATTTCTAAATATATTTTT
1 TTTAATATAT-TTATA--TTTTATTATTAATTTTTATATAATATCATATTT-TAAATATATTTTT
* *
301891 AATATCATATATTTATTTTTATTTATTTTTATAATA-TTTTATATATTATT
62 AATGTCATATATTTATTTTTATTTATTATTATAATATTTTTATAT-TTATT
301941 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCAT-TCTTT-AATATATTTTTAAT
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATAT-TTTAAATATATTTTTAAT
302004 GTCATATATTTTATTTTTATTTATTATTATAATATTTTTATATTTATT
65 GTCATATA-TTTATTTTTATTTATTATTATAATATTTTTATATTTATT
*
302052 TTTGATATATTTATATTTATATTATTAA-TTTTATATAATATCATATTTTAAATATATTTTTAAT
1 TTTAATATATTTATATTT-TATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
*
302116 GTCATATATTTATTTTTTATTTATTATTATAAT-TTTATATATTTTATT
65 GTCATATATTTA-TTTTTATTTATTATTATAATATTTTTATA-TTTATT
302164 TTTA
1 TTTA
302168 TTTCTTTAAT
Statistics
Matches: 214, Mismatches: 5, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
110 21 0.10
111 78 0.36
112 100 0.47
114 5 0.02
115 10 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (111 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATG
TCATATATTTATTTTTATTTATTATTATAATATTTTTATATTTATT
Found at i:302136 original size:27 final size:27
Alignment explanation
Indices: 301884--302167 Score: 108
Period size: 27 Copynumber: 10.3 Consensus size: 27
301874 TTTCTAAATA
301884 TATTTTTAATATCATATATTTA-TTTT
1 TATTTTTAATATCATATATTTATTTTT
** * * *
301910 TATTTATTTTTATAATAT-TTTATATAT
1 TATTT-TTAATATCATATATTTATTTTT
*
301937 TATTTTTAATAT-ATTTATATTTTATTATT
1 TATTTTTAATATCA--TATA-TTTATTTTT
* * * *
301966 AATTTTT-ATATAATATCATTCT-TTAATA
1 TATTTTTAATATCATAT-ATT-TATT-TTT
*
301994 TATTTTTAATGTCATATATTT-TATTTT
1 TATTTTTAATATCATATATTTAT-TTTT
* * * *
302021 TATTTATTATTATAATATTTTTA-TATT
1 TATTT-TTAATATCATATATTTATTTTT
*
302048 TATTTTTGATATAT-TTATATTTATATTATT
1 TATTTTT-A-ATATCATATATTTAT-TT-TT
* ** *
302078 AATTTTATATAATATCATAT-TTTA-AATA
1 TA-TTT-T-TAATATCATATATTTATTTTT
*
302106 TATTTTTAATGTCATATATTTATTTTT
1 TATTTTTAATATCATATATTTATTTTT
*
302133 TATTTATTATTAT-A-AT-TTTATATATTT
1 TATTT-TTAATATCATATATTTAT-T-TTT
302160 TATTTTTA
1 TATTTTTA
302168 TTTCTTTAAT
Statistics
Matches: 192, Mismatches: 38, Indels: 56
0.67 0.13 0.20
Matches are distributed among these distances:
25 16 0.08
26 27 0.14
27 68 0.35
28 40 0.21
29 21 0.11
30 3 0.02
31 11 0.06
32 5 0.03
33 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (27 bp):
TATTTTTAATATCATATATTTATTTTT
Found at i:302156 original size:10 final size:9
Alignment explanation
Indices: 301907--302201 Score: 69
Period size: 8 Copynumber: 34.7 Consensus size: 9
301897 ATATATTTAT
*
301907 TTTTATTTA
1 TTTTATATA
301916 TTTTTATAATA
1 -TTTTAT-ATA
301927 TTTTATATA
1 TTTTATATA
301936 --TTAT-T-
1 TTTTATATA
*
301941 TTTAATATA
1 TTTTATATA
*
301950 -TTTATATT
1 TTTTATATA
301958 TTATTAT-TAA
1 TT-TTATAT-A
301968 TTTT-TATA
1 TTTTATATA
**
301976 TAATATCAT-
1 TTTTAT-ATA
301985 TCTTTAATATA
1 T-TTT-ATATA
301996 TTTT-TA-A
1 TTTTATATA
* *
302003 TGTCATATA
1 TTTTATATA
302012 -TTT-TAT-
1 TTTTATATA
*
302018 TTTTATTTA
1 TTTTATATA
302027 TTATTATAATA
1 TT-TTAT-ATA
302038 TTTT-TATA
1 TTTTATATA
302046 -TTTAT-T-
1 TTTTATATA
*
302052 TTTGATATA
1 TTTTATATA
*
302061 TTTATATTTA
1 TTT-TATATA
*
302071 TATTAT-TAA
1 TTTTATAT-A
302080 TTTTATATA
1 TTTTATATA
*
302089 --ATATCATA
1 TTTTAT-ATA
302097 TTTTAAATATA
1 TTTT--ATATA
302108 TTTT-TA-A
1 TTTTATATA
* *
302115 TGTCATATA
1 TTTTATATA
302124 -TTTAT-T-
1 TTTTATATA
*
302130 TTTTATTTA
1 TTTTATATA
302139 TTATTATA-A
1 TT-TTATATA
302148 TTTTATATA
1 TTTTATATA
302157 -TTT-TAT-
1 TTTTATATA
* *
302163 TTTTATTTC
1 TTTTATATA
*
302172 TTTAATATA
1 TTTTATATA
302181 TTTT-TATA
1 TTTTATATA
302189 --TTATATA
1 TTTTATATA
302196 TTTTAT
1 TTTTAT
302202 TTTAATTGTT
Statistics
Matches: 207, Mismatches: 32, Indels: 93
0.62 0.10 0.28
Matches are distributed among these distances:
6 3 0.01
7 46 0.22
8 49 0.24
9 47 0.23
10 44 0.21
11 16 0.08
12 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:302156 original size:33 final size:33
Alignment explanation
Indices: 302119--302203 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
302109 TTTTAATGTC
*
302119 ATATATTTATTTTTTATTTA-TTATTATAATTTT
1 ATATATTTATTTTTTATTTATTTAATAT-ATTTT
*
302152 ATATATTT-TATTTTTATTTCTTTAATATATTTT
1 ATATATTTAT-TTTTTATTTATTTAATATATTTT
*
302185 -TATATTATATATTTTATTT
1 ATATATT-TATTTTTTATTT
302204 TAATTGTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
32 7 0.16
33 31 0.69
34 7 0.16
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTATTTTTTATTTATTTAATATATTTT
Found at i:302214 original size:82 final size:81
Alignment explanation
Indices: 302140--302288 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 81
302130 TTTTATTTAT
* *
302140 TATTATA-ATTTTATATATTTTAT-TTTTATT-TCTTTAA-TATATTTTTATATTATATATTTTA
1 TATTATATATGTTA-ATATTTTATATTTTATTAT-TTTAATTATATTCTTATATTATATA-TTTA
302201 TTTTAATTGTTTTTACCTA
63 TTTTAATTGTTTTTACCTA
* *
302220 TATTATATATGTTAATTTTTTATATTTTATTATTTTAATTTTATTCTTATATTATATATTTATTT
1 TATTATATATGTTAATATTTTATATTTTATTATTTTAATTATATTCTTATATTATATATTTATTT
302285 TAAT
66 TAAT
302289 ATTTATTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
80 15 0.25
81 28 0.46
82 18 0.30
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (81 bp):
TATTATATATGTTAATATTTTATATTTTATTATTTTAATTATATTCTTATATTATATATTTATTT
TAATTGTTTTTACCTA
Found at i:302228 original size:48 final size:46
Alignment explanation
Indices: 302155--302301 Score: 128
Period size: 49 Copynumber: 3.2 Consensus size: 46
302145 TAATTTTATA
* * * *
302155 TATTTTATTTTTATTTCT-T-TAATATATTTTTATATTATATATTT
1 TATTTTAATTTTATTCCTATATTATATATTTTTATTTTATATATTT
* *
302199 TATTTTAATTGTTTTTACCTATATTATATATGTTAATT-TTTTATATTTTAT
1 TATTTTAATT-TTATT-CCTATATTATATAT-TT--TTATTTTATATATT-T
*
302250 TATTTTAATTTTATTCTTATATTATATA--TTTATTTTA-ATA-TT
1 TATTTTAATTTTATTCCTATATTATATATTTTTATTTTATATATTT
302292 TATTTTAATT
1 TATTTTAATT
302302 ATAATATTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
42 11 0.13
43 1 0.01
44 13 0.15
45 9 0.11
46 3 0.04
47 1 0.01
48 7 0.08
49 14 0.16
50 13 0.15
51 13 0.15
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (46 bp):
TATTTTAATTTTATTCCTATATTATATATTTTTATTTTATATATTT
Found at i:302247 original size:7 final size:7
Alignment explanation
Indices: 302218--302292 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
302208 TGTTTTTACC
*
302218 TATATTA
1 TATATTT
302225 TATATGTT
1 TATAT-TT
* *
302233 AATTTTT
1 TATATTT
302240 TATATTT
1 TATATTT
302247 TATTATTT
1 TA-TATTT
302255 TA-ATTT
1 TATATTT
*
302261 TAT-TCT
1 TATATTT
*
302267 TATATTA
1 TATATTT
302274 TATA-TT
1 TATATTT
302280 TAT-TTT
1 TATATTT
*
302286 AATATTT
1 TATATTT
302293 ATTTTAATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
6 19 0.37
7 22 0.42
8 11 0.21
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (7 bp):
TATATTT
Found at i:302248 original size:33 final size:32
Alignment explanation
Indices: 302185--302248 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
302175 AATATATTTT
* *
302185 TATATTATATATTTTATTTTAATTGTTTTTACC
1 TATATTATATATTTAATTTT-ATTATTTTTACC
302218 TATATTATATATGTTAATTTT-TTATATTTTA
1 TATATTATATAT-TTAATTTTATTAT-TTTTA
302249 TTATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 17 0.63
34 7 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (32 bp):
TATATTATATATTTAATTTTATTATTTTTACC
Found at i:302261 original size:22 final size:22
Alignment explanation
Indices: 302218--302261 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
302208 TGTTTTTACC
302218 TATATTATATATGTTAATTTTT
1 TATATTATATATGTTAATTTTT
* *
302240 TATATTTTATTATTTTAATTTT
1 TATATTATA-TATGTTAATTTT
302262 ATTCTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TATATTATATATGTTAATTTTT
Found at i:302292 original size:12 final size:12
Alignment explanation
Indices: 302275--302300 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
302265 CTTATATTAT
302275 ATATTTATTTTA
1 ATATTTATTTTA
302287 ATATTTATTTTA
1 ATATTTATTTTA
302299 AT
1 AT
302301 TATAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTATTTTA
Found at i:302303 original size:51 final size:51
Alignment explanation
Indices: 302189--302285 Score: 132
Period size: 49 Copynumber: 2.0 Consensus size: 51
302179 TATTTTTATA
* *
302189 TTATATATT-TTATTTTAATTGTTTTTACCTATATTATATATGTTAATTTT
1 TTATATTTTATTATTTTAATTGTTATTACCTATATTATATATGTTAATTTT
*
302239 TTATATTTTATTATTTTAATT-TTATT-CTTATATTATATAT-TT-ATTTT
1 TTATATTTTATTATTTTAATTGTTATTACCTATATTATATATGTTAATTTT
302286 AATATTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 5 0.12
48 2 0.05
49 13 0.30
50 12 0.28
51 11 0.26
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (51 bp):
TTATATTTTATTATTTTAATTGTTATTACCTATATTATATATGTTAATTTT
Found at i:302309 original size:30 final size:30
Alignment explanation
Indices: 302179--302301 Score: 51
Period size: 33 Copynumber: 4.0 Consensus size: 30
302169 TTCTTTAATA
*
302179 TATTTTTATATTATATATTTTATTTTAATTGT
1 TATTCTTATATTATATA-TTTATTTTAATT-T
* * *
302211 TTTTACCTATATTATATATGTTAATTTT--TTA
1 TATT-CTTATATTATATAT-TT-ATTTTAATTT
* *
302242 TATT-TTATTATTTTA-ATTTTATTCTTATATTA
1 TATTCTTA-TATTATATA-TTTATT-TTA-ATTT
*
302274 TATAT-TTATTTTA-ATATTTATTTTAATT
1 TAT-TCTTATATTATATATTTATTTTAATT
302302 ATAATATTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 25
0.68 0.09 0.24
Matches are distributed among these distances:
28 3 0.04
29 10 0.14
30 10 0.14
31 10 0.14
32 16 0.23
33 17 0.24
34 5 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (30 bp):
TATTCTTATATTATATATTTATTTTAATTT
Found at i:302603 original size:15 final size:15
Alignment explanation
Indices: 302556--302609 Score: 72
Period size: 15 Copynumber: 3.4 Consensus size: 15
302546 CGTTTGGTAC
302556 ATTACAATGCAATGTG
1 ATTACAA-GCAATGTG
*
302572 ATTACAGGTCTAATGTG
1 ATTACAAG-C-AATGTG
302589 ATTACAAGCAATGTG
1 ATTACAAGCAATGTG
302604 ATTACA
1 ATTACA
302610 GGGAACATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 13 0.38
16 8 0.24
17 13 0.38
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (15 bp):
ATTACAAGCAATGTG
Found at i:302801 original size:54 final size:56
Alignment explanation
Indices: 302783--302931 Score: 170
Period size: 56 Copynumber: 2.7 Consensus size: 56
302773 TAATTTTATA
302783 TAATATCATTTTTAAATATATTTTTAATATCA-TATATTTTATT-TT-A-TTTAT-
1 TAATATCATTTTTAAATATATTTTTAATATCATTATATTTTATTATTAATTTTATA
* * * *
302834 TATTATAATATTTTATATTTTATTTTTAATAT-ATTTATATTTT-TTATTAATTTTATA
1 TAATATCAT-TTTTA-AATATATTTTTAATATCA-TTATATTTTATTATTAATTTTATA
302891 TAATATCATTTCTTAAATATATTTTTAATATCA-TATATTTT
1 TAATATCATTT-TTAAATATATTTTTAATATCATTATATTTT
302932 TAATATATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
51 7 0.09
52 6 0.08
53 16 0.20
54 10 0.12
55 9 0.11
56 21 0.26
57 11 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (56 bp):
TAATATCATTTTTAAATATATTTTTAATATCATTATATTTTATTATTAATTTTATA
Found at i:302805 original size:27 final size:27
Alignment explanation
Indices: 302775--302989 Score: 95
Period size: 27 Copynumber: 8.2 Consensus size: 27
302765 TTTATTATTA
302775 ATTTTATATAATATCATTTTTAAATAT
1 ATTTTATATAATATCATTTTTAAATAT
* * *
302802 A-TTT-T-TAATATCATATATTTTATTTT
1 ATTTTATATAATATCAT-T-TTTAAATAT
* * * *
302828 A-TTTAT-TATTATAATATTTTATATTTT
1 ATTTTATATAATATCAT-TTTTA-AATAT
* * *
302855 ATTTTTAATATATTTAT-ATTTTTTATTA-
1 A-TTTT-ATATA-ATATCATTTTTAAATAT
302883 ATTTTATATAATATCATTTCTTAAATAT
1 ATTTTATATAATATCATTT-TTAAATAT
*
302911 ATTTTTAATATCATAT-ATTTTT-AATAT
1 A-TTTT-ATATAATATCATTTTTAAATAT
* *
302938 A-TTTATAT--T-TTATTATT--A-AT
1 ATTTTATATAATATCATTTTTAAATAT
302958 -TTTTATATAATATCATTTCTTAAATAT
1 ATTTTATATAATATCATTT-TTAAATAT
302985 ATTTT
1 ATTTT
302990 TAATGTCATA
Statistics
Matches: 149, Mismatches: 15, Indels: 47
0.71 0.07 0.22
Matches are distributed among these distances:
20 9 0.06
21 2 0.01
22 7 0.05
23 4 0.03
24 15 0.10
25 8 0.05
26 26 0.17
27 34 0.23
28 8 0.05
29 14 0.09
30 14 0.09
31 4 0.03
32 4 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTTATATAATATCATTTTTAAATAT
Found at i:302872 original size:32 final size:32
Alignment explanation
Indices: 302790--302889 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
302780 ATATAATATC
* **
302790 ATTTTTAAATATATTTTTAATATCATATATTTT
1 ATTTTT-AATATATTTATAATATTTTATATTTT
*
302823 A-TTTT-ATTTATTATTATAATATTTTATATTTT
1 ATTTTTAATATA-T-TTATAATATTTTATATTTT
*
302855 ATTTTTAATATATTTAT-ATTTTTTATTAATTTT
1 ATTTTTAATATATTTATAATATTTTA-T-ATTTT
302888 AT
1 AT
302890 ATAATATCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
30 4 0.07
31 8 0.15
32 26 0.47
33 13 0.24
34 4 0.07
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (32 bp):
ATTTTTAATATATTTATAATATTTTATATTTT
Found at i:302920 original size:25 final size:25
Alignment explanation
Indices: 302891--302998 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
302881 TAATTTTATA
302891 TAATATCATTTCTTAAATATATTTT
1 TAATATCATTTCTTAAATATATTTT
* * *
302916 TAATATCATATATTTTTAATATATTTA
1 TAATATCAT-T-TCTTAAATATATTTT
* * *
302943 T-ATTTTA-TTATT-AAT-T-TTTAT
1 TAATATCATTTCTTAAATATATTT-T
302964 ATAATATCATTTCTTAAATATATTTT
1 -TAATATCATTTCTTAAATATATTTT
*
302990 TAATGTCAT
1 TAATATCAT
302999 ATATTTTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
20 3 0.05
21 1 0.02
22 4 0.06
23 7 0.11
24 5 0.08
25 20 0.32
26 7 0.11
27 16 0.25
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (25 bp):
TAATATCATTTCTTAAATATATTTT
Found at i:302926 original size:16 final size:15
Alignment explanation
Indices: 302907--303098 Score: 83
Period size: 16 Copynumber: 13.1 Consensus size: 15
302897 CATTTCTTAA
302907 ATATATTTTTAATAT
1 ATATATTTTTAATAT
302922 CATATATTTTTAATAT
1 -ATATATTTTTAATAT
* *
302938 ATTTATATTTTATTAT
1 ATATAT-TTTTAATAT
302954 -TA-ATTTTT-ATAT
1 ATATATTTTTAATAT
302966 AATATCATTTCTT-A-A-
1 -ATAT-ATTT-TTAATAT
*
302981 ATATATTTTTAATGT
1 ATATATTTTTAATAT
302996 CATATA-TTTT-AT-T
1 -ATATATTTTTAATAT
* *
303009 -TTTATTTATTATTAT
1 ATATATTT-TTAATAT
303024 A-ATA-TTTT-ATAT
1 ATATATTTTTAATAT
* *
303036 -TTTATTTTTGATAT
1 ATATATTTTTAATAT
* *
303050 ATTTATATTT-ATAT
1 ATATATTTTTAATAT
303064 -TATTAATTTTTAATAT
1 ATA-T-ATTTTTAATAT
*
303080 AATCATATTTTAAATAT
1 -AT-ATATTTTTAATAT
303097 AT
1 AT
303099 TTTATGTCAT
Statistics
Matches: 137, Mismatches: 14, Indels: 50
0.68 0.07 0.25
Matches are distributed among these distances:
11 3 0.02
12 12 0.09
13 19 0.14
14 22 0.16
15 26 0.19
16 39 0.28
17 13 0.09
18 2 0.01
19 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (15 bp):
ATATATTTTTAATAT
Found at i:302945 original size:54 final size:54
Alignment explanation
Indices: 302742--302945 Score: 190
Period size: 54 Copynumber: 3.8 Consensus size: 54
302732 TTAATTATTA
** *
302742 AAATATAAGTTTAATATAT-TATTTTTATTATTAATTTTATATAATATCATTTTT
1 AAATATATTTTTAATATATATATTTTTAATA-TAATTTTATATAATATCATTTTT
* * * *
302796 AAATATATTTTTAATATCATATA-TTTT-ATTTTA-TTTAT-TATTATAATATTTT
1 AAATATATTTTTAATAT-ATATATTTTTAATATAATTTTATATAATATCAT-TTTT
* * *
302848 ATATTTTATTTTTAATATATTTATATTTTTTAT-TAATTTTATATAATATCATTTCTT
1 A-AATATATTTTTAATATA--TATATTTTTAATATAATTTTATATAATATCATTT-TT
302905 AAATATATTTTTAATATCATATATTTTTAATAT-A-TTTATAT
1 AAATATATTTTTAATAT-ATATATTTTTAATATAATTTTATAT
302946 TTTATTATTA
Statistics
Matches: 122, Mismatches: 15, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
51 7 0.06
52 11 0.09
53 16 0.13
54 27 0.22
55 24 0.20
56 26 0.21
57 11 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (54 bp):
AAATATATTTTTAATATATATATTTTTAATATAATTTTATATAATATCATTTTT
Found at i:302975 original size:28 final size:29
Alignment explanation
Indices: 302927--303089 Score: 126
Period size: 28 Copynumber: 5.7 Consensus size: 29
302917 AATATCATAT
*
302927 ATTTTTAATATATTTATATTT-TATTATTA
1 ATTTTTAATATA-ATATATTTATATTATTA
* * *
302956 ATTTTT-ATATAATATCATTTCT-TAAATA
1 ATTTTTAATATAATAT-ATTTATATTATTA
* * *
302984 TATTTTTAATGTCATATATTT-TATT-TTT
1 -ATTTTTAATATAATATATTTATATTATTA
*
303012 ATTTATTATTATAATAT-TTTATATT-TT-
1 ATTT-TTAATATAATATATTTATATTATTA
* *
303039 ATTTTTGATATATTTATATTTATATTATTA
1 ATTTTTAATATA-ATATATTTATATTATTA
303069 ATTTTTAATATAATCATATTT
1 ATTTTTAATATAAT-ATATTT
303090 TAAATATATT
Statistics
Matches: 106, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
26 6 0.06
27 17 0.16
28 38 0.36
29 21 0.20
30 24 0.23
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTTTAATATAATATATTTATATTATTA
Found at i:302980 original size:74 final size:74
Alignment explanation
Indices: 302854--303035 Score: 281
Period size: 74 Copynumber: 2.5 Consensus size: 74
302844 TTTTATATTT
302854 TATTTTTAATATATTTATATTTT-TTATTAA-TTTTATATAATATCATTTCTTAAATATATTTTT
1 TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
302917 AATATCATA
66 AATATCATA
302926 TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
1 TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
*
302991 AATGTCATA
66 AATATCATA
303000 TA-TTTT-AT-T-TTTAT-TTATTATTA-TAATATTTTATAT
1 TATTTTTAATATATTTATATT-TTATTATTAAT-TTTTATAT
303036 TTTATTTTTG
Statistics
Matches: 105, Mismatches: 1, Indels: 10
0.91 0.01 0.09
Matches are distributed among these distances:
69 6 0.06
70 19 0.18
71 1 0.01
72 25 0.24
73 11 0.10
74 43 0.41
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (74 bp):
TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
AATATCATA
Found at i:303029 original size:26 final size:25
Alignment explanation
Indices: 302999--303136 Score: 82
Period size: 27 Copynumber: 5.1 Consensus size: 25
302989 TTAATGTCAT
302999 ATATTTTATTTTTATTTATTATTATA
1 ATATTTTATTTTTATTT-TTATTATA
*
303025 ATATTTTATATTTTATTTTTGATATATTT
1 ATATTTTAT-TTTTATTTTT-AT-TA-TA
* *
303054 ATATTTATATTATTAATTTTTAATATA
1 ATATTT-TATT-TTTATTTTTATTATA
***
303081 ATCATATTT-TAAATATATTTTATGTCAT-
1 AT-AT-TTTATTTTTAT-TTTTAT-T-ATA
*
303109 ATATTTTATTTTTATTTATTATTTTA
1 ATATTTTATTTTTATTT-TTATTATA
303135 AT
1 AT
303137 TTTATATATT
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
25 1 0.01
26 21 0.25
27 29 0.34
28 10 0.12
29 13 0.15
30 11 0.13
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (25 bp):
ATATTTTATTTTTATTTTTATTATA
Found at i:303035 original size:7 final size:7
Alignment explanation
Indices: 302998--303143 Score: 57
Period size: 6 Copynumber: 21.7 Consensus size: 7
302988 TTTAATGTCA
302998 TATATTT
1 TATATTT
303005 TAT-TTT
1 TATATTT
303011 TAT-TTAT
1 TATATT-T
*
303018 TAT-TAT
1 TATATTT
*
303024 AATATTT
1 TATATTT
303031 TATATTT
1 TATATTT
303038 TAT-TTT
1 TATATTT
303044 TGATATATT
1 T-ATAT-TT
303053 TATA-TT
1 TATATTT
303059 TATATTAT
1 TATATT-T
303067 TA-ATTTT
1 TATA-TTT
*
303074 TAATATAAT
1 T-ATAT-TT
*
303083 CATATTT
1 TATATTT
*
303090 TA-A--A
1 TATATTT
303094 TATATTT
1 TATATTT
* **
303101 TATGTCA
1 TATATTT
303108 TATATTT
1 TATATTT
303115 TAT-TTT
1 TATATTT
*
303121 TAT-TTA
1 TATATTT
303127 T-TATTT
1 TATATTT
303133 TA-ATTT
1 TATATTT
303139 TATAT
1 TATAT
303144 ATTTTTTTAT
Statistics
Matches: 104, Mismatches: 18, Indels: 34
0.67 0.12 0.22
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
6 40 0.38
7 40 0.38
8 15 0.14
9 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (7 bp):
TATATTT
Found at i:303101 original size:28 final size:27
Alignment explanation
Indices: 302742--302941 Score: 110
Period size: 27 Copynumber: 7.4 Consensus size: 27
302732 TTAATTATTA
**
302742 AAATATAAGTTTAATAT-AT-TATTTT
1 AAATATATTTTTAATATAATATATTTT
* * *
302767 TATTATTAATTTT-ATATAATATCATTTTT
1 AAATA-TATTTTTAATATAATAT-A-TTTT
*
302796 AAATATATTTTTAATATCATATATTTT
1 AAATATATTTTTAATATAATATATTTT
* * *
302823 -ATTTTATTTATTATTAT-A-ATATTTT
1 AAATATATTT-TTAATATAATATATTTT
* * *
302848 ATATTTTATTTTTAATATATTTATATTTT
1 A-AATATATTTTTAATATA-ATATATTTT
** *
302877 TTAT-TAATTTT-ATATAATATCATTTCTT
1 AAATATATTTTTAATATAATAT-A-TT-TT
*
302905 AAATATATTTTTAATATCATATATTTT
1 AAATATATTTTTAATATAATATATTTT
*
302932 TAATATATTT
1 AAATATATTT
302942 ATATTTTATT
Statistics
Matches: 136, Mismatches: 22, Indels: 32
0.72 0.12 0.17
Matches are distributed among these distances:
25 17 0.12
26 28 0.21
27 39 0.29
28 15 0.11
29 29 0.21
30 8 0.06
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (27 bp):
AAATATATTTTTAATATAATATATTTT
Found at i:303111 original size:184 final size:184
Alignment explanation
Indices: 302751--303253 Score: 625
Period size: 180 Copynumber: 2.8 Consensus size: 184
302741 AAAATATAAG
302751 TTTAATATA-TTATTTTTATTATTAA-TTTTATATAATATCATTT-TTAAATATATTTTTAATAT
1 TTTAATATATTTATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT
302813 CATATATTTTA-TTTTATTTATTATTATAATATTTTATATTTTATTTTTAATATATTTATATTTT
66 CATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTT-ATATATTTATATTTT
302877 -TTATTAA-TTTT-ATATAATATCATTTCTTAAATATATTTTTAATATCATATATT
130 ATTATTAATTTTTAATATAATATCATTTCTTAAATATATTTTTAATATCATATA-T
*
302930 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATG
1 TTTAATATATTTAT-TTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
302995 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTGATATATTTATATTT
65 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTT-ATATATTTATATTT
*
303060 ATATTATTAATTTTTAATAT-A-ATCATATT-TTAAATATA-TTTT-ATGTCATATAT
129 -TATTATTAATTTTTAATATAATATCAT-TTCTTAAATATATTTTTAATATCATATAT
** * * * *
303113 TTT-AT-T-TTTATTTATTATT-TTAATTTTATATATTTTTTTATTTCTTTAATATATTTTTTAT
1 TTTAATATATTTATTT-TTATTATTAATTTT-TATATAATATCATTTCTTAAATATATTTTTAAT
* * * * *
303174 AT-ATATATATTTATTTTAATTTGTT-TTATCTATATTATATAAATATTAATTTTT-TATATTT-
64 ATCATATAT-TTTATTTTTATTTATTATTAT-AATATT-T-TATAT-TTTATTTTTATATATTTA
303235 TATTTTATT-TTAATTTTTA
124 TATTTTATTATTAATTTTTA
303254 TTTTATATTA
Statistics
Matches: 292, Mismatches: 15, Indels: 35
0.85 0.04 0.10
Matches are distributed among these distances:
178 10 0.03
179 33 0.11
180 66 0.23
181 21 0.07
182 24 0.08
183 41 0.14
184 60 0.21
185 5 0.02
186 21 0.07
187 7 0.02
188 4 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (184 bp):
TTTAATATATTTATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT
CATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATTTTTATATATTTATATTTTA
TTATTAATTTTTAATATAATATCATTTCTTAAATATATTTTTAATATCATATAT
Found at i:303120 original size:19 final size:17
Alignment explanation
Indices: 303096--303155 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 17
303086 ATTTTAAATA
303096 TATTTTATGTCATATATTT
1 TATTTTAT-TCAT-TATTT
*
303115 TATTTTTATTTATTATTT
1 TA-TTTTATTCATTATTT
*
303133 TAATTTTATAT-ATTTTTT
1 T-ATTTTAT-TCATTATTT
303151 TATTT
1 TATTT
303156 CTTTAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 4 0.11
18 19 0.53
19 7 0.19
20 6 0.17
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TATTTTATTCATTATTT
Found at i:303133 original size:18 final size:18
Alignment explanation
Indices: 303110--303276 Score: 77
Period size: 18 Copynumber: 9.4 Consensus size: 18
303100 TTATGTCATA
*
303110 TATTTTATTTTTATTTAT
1 TATTTTATTTTTATATAT
*
303128 TATTTTAATTTTATATAT
1 TATTTTATTTTTATATAT
*
303146 TTTTTTATTTCTT-TA-A-
1 TATTTTATTT-TTATATAT
*
303162 TA-TAT-TTTTTATATAT
1 TATTTTATTTTTATATAT
303178 ATATATTTA-TTTTA-AT-T
1 -TAT-TTTATTTTTATATAT
*
303195 TGTTTTATCTATATTATATA-
1 TATTTTAT-T-T-TTATATAT
* * *
303215 AATATTAATTTTTTATATTT
1 TAT-TTTA-TTTTTATATAT
* *
303235 TATTTTATTTTAAT-TTT
1 TATTTTATTTTTATATAT
*
303252 TATTTTA-TATTATATACT
1 TATTTTATTTTTATATA-T
303270 TATTTTA
1 TATTTTA
303277 ATTATAATAT
Statistics
Matches: 112, Mismatches: 18, Indels: 38
0.67 0.11 0.23
Matches are distributed among these distances:
13 2 0.02
14 5 0.04
15 7 0.06
16 7 0.06
17 16 0.14
18 43 0.38
19 21 0.19
20 6 0.05
21 4 0.04
22 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (18 bp):
TATTTTATTTTTATATAT
Found at i:303145 original size:110 final size:112
Alignment explanation
Indices: 302926--303148 Score: 350
Period size: 110 Copynumber: 2.0 Consensus size: 112
302916 TAATATCATA
302926 TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
1 TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
302991 AATGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTT
66 AATGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTT
*
303038 TATTTTTGATATATTTATATTTATATTATTAATTTTTA-AT-ATAATCATATT-TTAAATATA-T
1 TATTTTTAATATATTTATATTT-TATTATTAATTTTTATATAAT-ATCAT-TTCTTAAATATATT
*
303099 TTT-ATGTCATATATTTTATTTTTATTTATTATTTTAAT-TTTATATATTT
63 TTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTT
303148 T
1 T
303149 TTTATTTCTT
Statistics
Matches: 105, Mismatches: 2, Indels: 10
0.90 0.02 0.09
Matches are distributed among these distances:
109 3 0.03
110 42 0.40
111 6 0.06
112 37 0.35
113 17 0.16
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (112 bp):
TATTTTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTT
AATGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTT
Found at i:303245 original size:17 final size:17
Alignment explanation
Indices: 303225--303276 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
303215 AATATTAATT
303225 TTTTATATTTTATTTTA
1 TTTTATATTTTATTTTA
303242 TTTTA-ATTTTTATTTTA
1 TTTTATA-TTTTATTTTA
* *
303259 TATTATATACTTATTTTA
1 TTTTATAT-TTTATTTTA
303277 ATTATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 1 0.03
17 20 0.67
18 9 0.30
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATTTTATTTTA
Found at i:307540 original size:57 final size:57
Alignment explanation
Indices: 307479--307592 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
307469 TCTGCTTTCC
307479 TTAGTCTTGTATTGCCTGTCAGAGTCAGAGTCTTCAGATGAATAAGAATACTTGTGT
1 TTAGTCTTGTATTGCCTGTCAGAGTCAGAGTCTTCAGATGAATAAGAATACTTGTGT
307536 TTAGTCTTGTATTGCCTGTCAGAGTCAGAGTCTTCAGATGAATAAGAATACTTGTGT
1 TTAGTCTTGTATTGCCTGTCAGAGTCAGAGTCTTCAGATGAATAAGAATACTTGTGT
307593 CTTCTCTTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (57 bp):
TTAGTCTTGTATTGCCTGTCAGAGTCAGAGTCTTCAGATGAATAAGAATACTTGTGT
Found at i:307668 original size:3 final size:3
Alignment explanation
Indices: 307660--307711 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
307650 TAACCCTGCC
* *
307660 TCT TCT TCT TCT TCT TCT TCT CCT TCT TCT TCT TGGT T-T TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT
*
307705 TCC TCT T
1 TCT TCT T
307712 TGACCTTCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.00, C:0.33, G:0.04, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:323897 original size:15 final size:15
Alignment explanation
Indices: 323843--323890 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
323833 TTGATTACTA
*
323843 AATAAGTTTAAAAAT
1 AATAATTTTAAAAAT
323858 CAATAATTTTTAAAAAT
1 -AATAA-TTTTAAAAAT
323875 AATAATTTTAAAAAT
1 AATAATTTTAAAAAT
323890 A
1 A
323891 TTTATTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.37
16 10 0.33
17 9 0.30
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
AATAATTTTAAAAAT
Found at i:329370 original size:13 final size:13
Alignment explanation
Indices: 329352--329377 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329342 GCTAAAATTA
329352 AAAAAAACAAAAC
1 AAAAAAACAAAAC
329365 AAAAAAACAAAAC
1 AAAAAAACAAAAC
329378 CTTATCTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:334617 original size:2 final size:2
Alignment explanation
Indices: 334610--334648 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
334600 ACGGTAGGAA
334610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
334649 AATCAGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:334740 original size:2 final size:2
Alignment explanation
Indices: 334682--334721 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
334672 GGGAGTCACC
334682 AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
334722 CCGGGGGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:344665 original size:12 final size:12
Alignment explanation
Indices: 344643--344667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
344633 GAGGAAAACC
344643 TAATTTAAAAGT
1 TAATTTAAAAGT
344655 TAATTTAAAAGT
1 TAATTTAAAAGT
344667 T
1 T
344668 GTTTCGTGGA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TAATTTAAAAGT
Done.