Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009622.1 Hibiscus syriacus cultivar Beakdansim tig00117011_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: 790348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 4
Found at i:5834 original size:109 final size:109
Alignment explanation
Indices: 5700--5917 Score: 368
Period size: 109 Copynumber: 2.0 Consensus size: 109
5690 ATAACATTGG
5700 AGAGTAAGTCATAAACTTATAATTAAAAACATTTAAAAAAAATC-AAAAGGGCTCCCCTCAAATA
1 AGAGTAAGTCATAAACTTATAATTAAAAACATTT-AAAAAAATCAAAAAGGGCTCCCCTCAAATA
5764 GTACATTCCAAACAAAAATTTGACTTTAAAAGCTTGACACTTAAA
65 GTACATTCCAAACAAAAATTTGACTTTAAAAGCTTGACACTTAAA
*
5809 AGAGTAATTCATAAACTTA-ACATTAAAAACATTTAAAAAAATCAAAAAGGGCTCCCCTCAAATA
1 AGAGTAAGTCATAAACTTATA-ATTAAAAACATTTAAAAAAATCAAAAAGGGCTCCCCTCAAATA
* * *
5873 GTGCATTCCAAACAAAATTTTGACTTTAAAAGCTTGATACTTAAA
65 GTACATTCCAAACAAAAATTTGACTTTAAAAGCTTGACACTTAAA
5918 CAAAATTGAA
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
108 10 0.10
109 93 0.90
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.27
Consensus pattern (109 bp):
AGAGTAAGTCATAAACTTATAATTAAAAACATTTAAAAAAATCAAAAAGGGCTCCCCTCAAATAG
TACATTCCAAACAAAAATTTGACTTTAAAAGCTTGACACTTAAA
Found at i:11208 original size:23 final size:21
Alignment explanation
Indices: 11168--11209 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
11158 GTCTATATAT
*
11168 ATATTTATTTTTATAAATAAG
1 ATATTTATTTTTAGAAATAAG
11189 ATATTTATTTACTTAGAAATA
1 ATATTTATTT--TTAGAAATA
11210 TCAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATTTATTTTTAGAAATAAG
Found at i:11289 original size:20 final size:18
Alignment explanation
Indices: 11252--11294 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11242 CCTGTTTCTT
*
11252 AATATTAAAAAATAAATA
1 AATATTAAAAAACAAATA
11270 AATATTAATAAAACATAATA
1 AATATTAA-AAAACA-AATA
*
11290 TATAT
1 AATAT
11295 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATTAAAAAACAAATA
Found at i:11312 original size:19 final size:19
Alignment explanation
Indices: 11284--11355 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
11274 TTAATAAAAC
* *
11284 ATAATATATATATATATAT
1 ATAATTTATAAATATATAT
* *
11303 ATAATTTATAAAAATAAAAT
1 ATAATTTATAAATAT-ATAT
* *
11323 ATTTATTTAAAAATAATATAT
1 A-TAATTTATAAAT-ATATAT
11344 ATAATTTATAAA
1 ATAATTTATAAA
11356 AGTAAAATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 12 0.30
20 13 0.32
21 13 0.32
22 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATTTATAAATATATAT
Found at i:11326 original size:17 final size:17
Alignment explanation
Indices: 11306--11369 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
11296 TATATATATA
11306 ATTTATAAAAATAAAAT
1 ATTTATAAAAATAAAAT
11323 ATTTATTTAAAAATAATATATAT
1 ATTTA--TAAAAAT-A-A-A-AT
*
11346 AATTTATAAAAGTAAAAT
1 -ATTTATAAAAATAAAAT
11364 ATTTAT
1 ATTTAT
11370 TTATTAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
17 11 0.28
18 2 0.05
19 8 0.21
20 2 0.05
21 2 0.05
22 7 0.18
23 2 0.05
24 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTATAAAAATAAAAT
Found at i:11352 original size:24 final size:22
Alignment explanation
Indices: 11297--11380 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
11287 ATATATATAT
11297 ATATATATAATTTATAAAAATA
1 ATATATATAATTTATAAAAATA
* *
11319 AAATAT-TTA-TT-TAAAAATA
1 ATATATATAATTTATAAAAATA
*
11338 ATATATATAATTTATAAAAGTA
1 ATATATATAATTTATAAAAATA
* *
11360 AAATAT-TTATTTATTAAAAAT
1 ATATATATAATTTA-TAAAAAT
11381 TTCAGAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
19 13 0.26
20 4 0.08
21 10 0.20
22 23 0.46
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
ATATATATAATTTATAAAAATA
Found at i:11377 original size:22 final size:20
Alignment explanation
Indices: 11306--11378 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
11296 TATATATATA
11306 ATTTATAAAAATAAAATATTT
1 ATTTAT-AAAATAAAATATTT
* *
11327 ATTTA-AAAATAATATATATA
1 ATTTATAAAATAAAATAT-TT
11347 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAA-TAAAATATTT
11368 ATTTATTAAAA
1 ATTTA-TAAAA
11379 ATTTCAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.25
20 6 0.14
21 15 0.34
22 12 0.27
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATAAAATATTT
Found at i:11593 original size:22 final size:22
Alignment explanation
Indices: 11567--11617 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
11557 AGAAATAGAA
* *
11567 TAAAATTGTATTAAATAATGAC
1 TAAAATAGCATTAAATAATGAC
* *
11589 TAAAATAGCATTTAATAATGGC
1 TAAAATAGCATTAAATAATGAC
11611 TAAAATA
1 TAAAATA
11618 AAAGGAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (22 bp):
TAAAATAGCATTAAATAATGAC
Found at i:13281 original size:3 final size:3
Alignment explanation
Indices: 13273--13353 Score: 58
Period size: 3 Copynumber: 27.0 Consensus size: 3
13263 CTGTAATATG
* * * *
13273 TAA TAA TAA TATT TAT TAA TAA -AA -ACA TAA TAA TAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * * *
13318 TAA TAA TAA TTA TAA CAA TTA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13354 AACGGGCAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
2 3 0.05
3 55 0.90
4 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:13353 original size:21 final size:21
Alignment explanation
Indices: 13299--13353 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
13289 TAATAAAAAC
* *
13299 ATAATAATAGTAATAATTATA
1 ATAATAATAATAACAATTATA
*
13320 ATAATAATTATAACAATTATA
1 ATAATAATAATAACAATTATA
*
13341 ATAATAAAAATAA
1 ATAATAATAATAA
13354 AACGGGCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAATAATAATAACAATTATA
Found at i:14117 original size:121 final size:120
Alignment explanation
Indices: 13819--14260 Score: 534
Period size: 121 Copynumber: 3.7 Consensus size: 120
13809 AACTCCATAA
* * * *
13819 GTGAT-GAATCAAG-ATAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTCCAGA
1 GTGATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
* * * *
13882 TGAGTTCTTCTCATTATGAACTTTTTATGGAAATGATGATGATGATCTATCTCCTTCT
66 TGAGTTCTTCTCATTATGAAC-TCTTCTGGAAAT--TGATGTTGATCTATCTCATTCT
* *
13940 GTGATAGAATTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
1 GTGATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
14005 TGAGTTCTTCTCATTATGAACTCCTTCTGGAAATTGATGTTGATCTATCTCATTCT
66 TGAGTTCTTCTCATTATGAACT-CTTCTGGAAATTGATGTTGATCTATCTCATTCT
* * * *
14061 GCGATAGAGTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGA
1 GTGATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
* * *
14126 TGAGTTCTTCTTATTATGAACAT-TTCTGG-AA---ATGTTGATCCA--TCA---A
66 TGAGTTCTTCTCATTATGAAC-TCTTCTGGAAATTGATGTTGATCTATCTCATTCT
* * * *
14172 GTGAT-GAATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCATTTTTCA
1 GTGATAGAA-TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-CTCTTCA
14235 GATGAGTTCTTCTCATTATGAACTCT
64 GATGAGTTCTTCTCATTATGAACTCT
14261 ACCTGGCAAT
Statistics
Matches: 288, Mismatches: 26, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
110 5 0.02
111 72 0.25
114 3 0.01
116 10 0.03
119 2 0.01
120 6 0.02
121 104 0.36
122 9 0.03
123 77 0.27
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (120 bp):
GTGATAGAATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
TGAGTTCTTCTCATTATGAACTCTTCTGGAAATTGATGTTGATCTATCTCATTCT
Found at i:16133 original size:75 final size:74
Alignment explanation
Indices: 15961--16134 Score: 172
Period size: 75 Copynumber: 2.3 Consensus size: 74
15951 TGTTATGGGT
* * * *
15961 CTTT-AGCATGCCCCAACATTGGCTAATACAGATGTTCAAAATGTACCAACATTCCTGATTCTGA
1 CTTTAAGCATACCCCAACATTTGCTAATACAAATGTTCAAAATGTACCAACATTCCTGAGTCTGA
16025 TTAAAAGAG
66 TTAAAAGAG
** * * * * *
16034 CTTTAAGCATGTCCCAGCATTTTGCTGATACAAATGTTCAAAATG-AGTCAATATTCTTGAGTCT
1 CTTTAAGCATACCCCAACA-TTTGCTAATACAAATGTTCAAAATGTA-CCAACATTCCTGAGTCT
* *
16098 GATTGAAATGGG
64 GATT-AAAAGAG
* *
16110 CTTTCAGTATACCCCAACATTTGCT
1 CTTTAAGCATACCCCAACATTTGCT
16135 TCTTGTTGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
73 4 0.05
74 13 0.16
75 45 0.56
76 19 0.23
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (74 bp):
CTTTAAGCATACCCCAACATTTGCTAATACAAATGTTCAAAATGTACCAACATTCCTGAGTCTGA
TTAAAAGAG
Found at i:20926 original size:12 final size:13
Alignment explanation
Indices: 20902--20930 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20892 AAATGAAAAA
20902 AAATGCAAAATGT
1 AAATGCAAAATGT
20915 AAATGC-AAATGT
1 AAATGCAAAATGT
20927 AAAT
1 AAAT
20931 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:22568 original size:28 final size:26
Alignment explanation
Indices: 22513--22570 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
22503 AAACATTAAT
*
22513 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
22539 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
22567 AAAA
1 AAAA
22571 GAAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:23205 original size:20 final size:18
Alignment explanation
Indices: 23168--23210 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
23158 TTTATTTCTT
*
23168 AATATTAAAAAATAAATA
1 AATATTAAAAAACAAATA
23186 AATATTAATAAAACATAATA
1 AATATTAA-AAAACA-AATA
*
23206 TATAT
1 AATAT
23211 ATATATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATTAAAAAACAAATA
Found at i:23238 original size:17 final size:17
Alignment explanation
Indices: 23218--23281 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
23208 TATATATATA
23218 ATTTATAAAAATAAAAT
1 ATTTATAAAAATAAAAT
23235 ATTTATTTAAAAATAATATATAT
1 ATTTA--TAAAAAT-A-A-A-AT
*
23258 AATTTATAAAAGTAAAAT
1 -ATTTATAAAAATAAAAT
23276 ATTTAT
1 ATTTAT
23282 TTATTAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
17 11 0.28
18 2 0.05
19 8 0.21
20 2 0.05
21 2 0.05
22 7 0.18
23 2 0.05
24 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTATAAAAATAAAAT
Found at i:23247 original size:19 final size:19
Alignment explanation
Indices: 23223--23284 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 19
23213 ATATAATTTA
23223 TAAAAATAAAATATTTATT
1 TAAAAATAAAATATTTATT
* *
23242 TAAAAATAATATATATAATT
1 TAAAAATAAAATAT-TTATT
23262 TATAAAAGTAAAATATTTATT
1 TA-AAAA-TAAAATATTTATT
23283 TA
1 TA
23285 TTAAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.36
20 6 0.17
21 10 0.28
22 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAAATAAAATATTTATT
Found at i:23267 original size:22 final size:21
Alignment explanation
Indices: 23211--23293 Score: 89
Period size: 22 Copynumber: 3.9 Consensus size: 21
23201 TAATATATAT
23211 ATATATAATTTATAAAAATAAA
1 ATAT-TAATTTATAAAAATAAA
* *
23233 ATATTTA-TT-TAAAAATAAT
1 ATATTAATTTATAAAAATAAA
*
23252 ATATATAATTTATAAAAGTAAA
1 ATAT-TAATTTATAAAAATAAA
*
23274 ATATTTATTTATTAAAAATA
1 ATATTAATTTA-TAAAAATA
23294 TCAGAAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 13 0.26
20 4 0.08
21 10 0.20
22 23 0.46
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
ATATTAATTTATAAAAATAAA
Found at i:25243 original size:3 final size:3
Alignment explanation
Indices: 25235--25333 Score: 65
Period size: 3 Copynumber: 33.0 Consensus size: 3
25225 ATGTAATATG
* * * * *
25235 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
25280 TAA CAA TTA TAA TAA TAA TTA CAA CAA TTA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
25328 AAA TAA
1 TAA TAA
25334 AACGGGCAAA
Statistics
Matches: 72, Mismatches: 22, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
2 2 0.03
3 68 0.94
4 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25265 original size:27 final size:27
Alignment explanation
Indices: 25235--25298 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
25225 ATGTAATATG
* *
25235 TAATAATAATATTTATTAATAA-AAATA
1 TAATAATAATAATAATT-ATAACAAATA
* *
25262 TAATAATAGTAATAATTATAACAATTA
1 TAATAATAATAATAATTATAACAAATA
25289 TAATAATAAT
1 TAATAATAAT
25299 TACAACAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TAATAATAATAATAATTATAACAAATA
Found at i:25297 original size:21 final size:21
Alignment explanation
Indices: 25271--25318 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
25261 ATAATAATAG
*
25271 TAATAATTATAACAATTATAA
1 TAATAATTACAACAATTATAA
25292 TAATAATTACAACAATTATAA
1 TAATAATTACAACAATTATAA
25313 TAATAA
1 TAATAA
25319 AAATAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATAATTACAACAATTATAA
Found at i:36207 original size:39 final size:39
Alignment explanation
Indices: 36153--36235 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
36143 GTTGTGTTTA
36153 TGTGCCTCCGCTTGCATTGTACACATCTATTATGCAATT
1 TGTGCCTCCGCTTGCATTGTACACATCTATTATGCAATT
* *
36192 TGTGCCTCTGCTTGCATTGTATACATCTATTATGCAATT
1 TGTGCCTCCGCTTGCATTGTACACATCTATTATGCAATT
36231 TGTGC
1 TGTGC
36236 TTTAAGTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (39 bp):
TGTGCCTCCGCTTGCATTGTACACATCTATTATGCAATT
Found at i:42427 original size:33 final size:33
Alignment explanation
Indices: 42376--42455 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
42366 GTCATCCGAT
* * * *
42376 CGAGTTATACGAGAGCATTCGAGGTCA-TCCGAG
1 CGAGCTATGCGAGGGCATTCGAGGGCAGT-CGAG
42409 CGAGC-ACTGCGAGGGCATTCGAGGGCAGTCGAG
1 CGAGCTA-TGCGAGGGCATTCGAGGGCAGTCGAG
42442 CGAGCTATGCGAGG
1 CGAGCTATGCGAGG
42456 AAATCTAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 1 0.03
33 37 0.93
34 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.38, T:0.16
Consensus pattern (33 bp):
CGAGCTATGCGAGGGCATTCGAGGGCAGTCGAG
Found at i:51922 original size:7 final size:7
Alignment explanation
Indices: 51910--51956 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
51900 AAGGGTTTAA
51910 GGCTTAG
1 GGCTTAG
51917 GGCTTAG
1 GGCTTAG
51924 GGCTTAG
1 GGCTTAG
51931 GGCTTAG
1 GGCTTAG
*
51938 GGTTTAG
1 GGCTTAG
*
51945 GGTTTAG
1 GGCTTAG
51952 GGCTT
1 GGCTT
51957 GTAGTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.13, C:0.11, G:0.43, T:0.34
Consensus pattern (7 bp):
GGCTTAG
Found at i:51925 original size:21 final size:21
Alignment explanation
Indices: 51901--51956 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
51891 AATTAGATTA
*
51901 AGGGTTTAAGGCTTAGGGCTT
1 AGGGTTTAGGGCTTAGGGCTT
* *
51922 AGGGCTTAGGGCTTAGGGTTT
1 AGGGTTTAGGGCTTAGGGCTT
51943 AGGGTTTAGGGCTT
1 AGGGTTTAGGGCTT
51957 GTAGTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.09, G:0.41, T:0.34
Consensus pattern (21 bp):
AGGGTTTAGGGCTTAGGGCTT
Found at i:53401 original size:20 final size:20
Alignment explanation
Indices: 53376--53416 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53366 TTTCTGGGCA
* *
53376 AGGGGAATCGGTACCCATTC
1 AGGGGAACCGATACCCATTC
*
53396 AGGGGAACCGATACCCCTTC
1 AGGGGAACCGATACCCATTC
53416 A
1 A
53417 AACGAACAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCATTC
Found at i:54252 original size:31 final size:31
Alignment explanation
Indices: 54214--54338 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
54204 AGGGTCGAGG
54214 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
54245 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
54276 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
54307 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
54338 G
1 G
54339 GTCTTCAGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:60520 original size:19 final size:19
Alignment explanation
Indices: 60496--60541 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
60486 ATGGTGTACT
*
60496 GATGCATAGGTAGTGCATC
1 GATGCACAGGTAGTGCATC
60515 GATGCACAGGTAGTGCATC
1 GATGCACAGGTAGTGCATC
*
60534 GATACACA
1 GATGCACA
60542 CGTTAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (19 bp):
GATGCACAGGTAGTGCATC
Found at i:60930 original size:2 final size:2
Alignment explanation
Indices: 60923--60959 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
60913 AATCATATGA
*
60923 AT AT AT AT AT AT AT AT AT AT A- AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60960 CTAATTCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:61984 original size:18 final size:18
Alignment explanation
Indices: 61961--61995 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61951 CGAAACAATC
61961 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
61979 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
61996 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:62811 original size:11 final size:11
Alignment explanation
Indices: 62795--62828 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
62785 CATTTCGGAC
62795 TCGGATCCGGG
1 TCGGATCCGGG
*
62806 TCGGATCCAGG
1 TCGGATCCGGG
*
62817 TCGGATACGGG
1 TCGGATCCGGG
62828 T
1 T
62829 TGGGGGTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.21
Consensus pattern (11 bp):
TCGGATCCGGG
Found at i:67335 original size:14 final size:14
Alignment explanation
Indices: 67318--67344 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
67308 GATTGGGTTA
67318 AACATAAATGAACG
1 AACATAAATGAACG
67332 AACATAAATGAAC
1 AACATAAATGAAC
67345 ATAACTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:70819 original size:26 final size:25
Alignment explanation
Indices: 70766--70825 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
70756 TAAGGGTTTG
* *
70766 TTTAGTTTTAGAAAATATTTTTATT
1 TTTACTTTTAGAAAACATTTTTATT
70791 TTTA-TTTTCAGAAAACAGTTTTTATT
1 TTTACTTTT-AGAAAACA-TTTTTATT
70817 TTTACTTTT
1 TTTACTTTT
70826 TTGAAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 11 0.35
26 12 0.39
27 4 0.13
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (25 bp):
TTTACTTTTAGAAAACATTTTTATT
Found at i:71526 original size:16 final size:16
Alignment explanation
Indices: 71473--71523 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
71463 AAATTAAGAG
*
71473 AATATTTAAAT-TTAA
1 AATATTTAATTATTAA
*
71488 AATATAAATAATTATTAA
1 AATAT--TTAATTATTAA
71506 AATATTTAATATATTAA
1 AATATTTAAT-TATTAA
71523 A
1 A
71524 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.17
16 4 0.14
17 11 0.38
18 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTTAATTATTAA
Found at i:98210 original size:2 final size:2
Alignment explanation
Indices: 98203--98264 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
98193 TAGGTGTATG
98203 AT AT AT AT AT AT AT A- AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98243 AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
98265 GCAAAAATGG
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 54 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:98798 original size:28 final size:28
Alignment explanation
Indices: 98758--98825 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
98748 AAAAGTATGT
98758 CAGCGATGGTGGTTGTGCCCAGAAAAAG
1 CAGCGATGGTGGTTGTGCCCAGAAAAAG
98786 CAGCGATGGTGGTTGTGCCCAGAAAAAG
1 CAGCGATGGTGGTTGTGCCCAGAAAAAG
98814 CAGCGATGGTGG
1 CAGCGATGGTGG
98826 GTTAGGGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (28 bp):
CAGCGATGGTGGTTGTGCCCAGAAAAAG
Found at i:99481 original size:37 final size:35
Alignment explanation
Indices: 99409--99483 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 35
99399 AGTTTCAATA
*
99409 TTATGATTTTTAATTTAAAAAAAATGTAATAAATT
1 TTATGATTTTTAATTTAAAAAAAATGAAATAAATT
99444 TTAT-ATTTTATAATATTAAAAAATAATGAAA-ATAATT
1 TTATGATTTT-TAAT-TTAAAAAA-AATGAAATA-AATT
99481 TTA
1 TTA
99484 AAATACCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
34 5 0.14
35 8 0.23
36 9 0.26
37 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (35 bp):
TTATGATTTTTAATTTAAAAAAAATGAAATAAATT
Found at i:101708 original size:16 final size:14
Alignment explanation
Indices: 101673--101699 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
101663 AATTGTGTTA
101673 TAAATATATTTTTT
1 TAAATATATTTTTT
101687 TAAATATATTTTT
1 TAAATATATTTTT
101700 ATTGAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAAATATATTTTTT
Found at i:107284 original size:16 final size:16
Alignment explanation
Indices: 107265--107300 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
107255 TTAGAGATTA
107265 ATCCTTTTACTTTTTG
1 ATCCTTTTACTTTTTG
107281 ATCCTTTTACTTTTTG
1 ATCCTTTTACTTTTTG
107297 ATCC
1 ATCC
107301 CTCTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.06, T:0.58
Consensus pattern (16 bp):
ATCCTTTTACTTTTTG
Found at i:109255 original size:28 final size:28
Alignment explanation
Indices: 109224--109314 Score: 114
Period size: 28 Copynumber: 3.2 Consensus size: 28
109214 TGAATTAAAT
* *
109224 TGAATATTGAATGCATTTCATGCATCGA
1 TGAACATTAAATGCATTTCATGCATCGA
*
109252 TGAACA-TACCATGCATTTCATGCATCGA
1 TGAACATTA-AATGCATTTCATGCATCGA
109280 TGAACA-TAACATGCATTTCATGCATCGA
1 TGAACATTAA-ATGCATTTCATGCATCGA
*
109308 TGTACAT
1 TGAACAT
109315 ACCATGCACC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 54 0.98
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (28 bp):
TGAACATTAAATGCATTTCATGCATCGA
Found at i:109315 original size:28 final size:28
Alignment explanation
Indices: 109234--109322 Score: 160
Period size: 28 Copynumber: 3.2 Consensus size: 28
109224 TGAATATTGA
109234 ATGCATTTCATGCATCGATGAACATACC
1 ATGCATTTCATGCATCGATGAACATACC
*
109262 ATGCATTTCATGCATCGATGAACATAAC
1 ATGCATTTCATGCATCGATGAACATACC
*
109290 ATGCATTTCATGCATCGATGTACATACC
1 ATGCATTTCATGCATCGATGAACATACC
109318 ATGCA
1 ATGCA
109323 CCGATGCACT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (28 bp):
ATGCATTTCATGCATCGATGAACATACC
Found at i:109375 original size:46 final size:45
Alignment explanation
Indices: 109318--109424 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
109308 TGTACATACC
* * * *
109318 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-T-AAAACATCGAATACACTTG
* * *
109364 ATGCATCGATGCACTCTGGCTATTTTAAATCATCGAATACACTTG
1 ATGCATCGATGCACTCAGGATATTTTAAAACATCGAATACACTTG
109409 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
109425 TTAGTGCGCC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 32 0.60
46 18 0.34
47 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTAAAACATCGAATACACTTG
Found at i:123960 original size:18 final size:18
Alignment explanation
Indices: 123928--123966 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
123918 ACATGTACAA
*
123928 AAAAAAAGGTATTCCAGC
1 AAAAAAAGGTATTCCAAC
123946 AAAAAAAGG-ATTTCCAAC
1 AAAAAAAGGTA-TTCCAAC
123964 AAA
1 AAA
123967 CATGCCTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (18 bp):
AAAAAAAGGTATTCCAAC
Found at i:124630 original size:39 final size:39
Alignment explanation
Indices: 124585--124659 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
124575 AACTTATTCA
* *
124585 AGTATATAACTATCAAAGCACCAAAGAAATGAAGAACGG
1 AGTATATAACCATCAAAGAACCAAAGAAATGAAGAACGG
**
124624 AGTATATAACCATCAAAGAACCATGGAAATGAAGAA
1 AGTATATAACCATCAAAGAACCAAAGAAATGAAGAA
124660 TGGATTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.16
Consensus pattern (39 bp):
AGTATATAACCATCAAAGAACCAAAGAAATGAAGAACGG
Found at i:128524 original size:21 final size:21
Alignment explanation
Indices: 128498--128545 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
128488 ACTCGTCATA
*
128498 TTTTTAATTTTTTA-ATTAAT
1 TTTTTAATTTTATAGATTAAT
128518 TTATTTAATTTTATAGATTAAT
1 TT-TTTAATTTTATAGATTAAT
128540 TTTTTA
1 TTTTTA
128546 TAATCACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTAATTTTATAGATTAAT
Found at i:130380 original size:12 final size:12
Alignment explanation
Indices: 130363--130407 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
130353 AAACGTTATC
130363 ATATTATATAAT
1 ATATTATATAAT
130375 ATATTATATAAT
1 ATATTATATAAT
130387 ATATTCATAT-AT
1 ATATT-ATATAAT
*
130399 ATATAATAT
1 ATATTATAT
130408 TTACATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 23 0.74
13 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTATATAAT
Found at i:130408 original size:17 final size:17
Alignment explanation
Indices: 130361--130408 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
130351 TTAAACGTTA
130361 TCATAT-TATATAATA-
1 TCATATATATATAATAT
130376 T-AT-TATATA-ATATAT
1 TCATATATATATA-ATAT
130391 TCATATATATATAATAT
1 TCATATATATATAATAT
130408 T
1 T
130409 TACATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 2 0.07
16 2 0.07
17 11 0.41
18 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
TCATATATATATAATAT
Found at i:130414 original size:19 final size:20
Alignment explanation
Indices: 130373--130419 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
130363 ATATTATATA
130373 ATATATTATATAATATATTC
1 ATATATTATATAATATATTC
130393 ATATA-TATATAATAT-TTAC
1 ATATATTATATAATATATT-C
130412 ATAT-TTAT
1 ATATATTAT
130420 TCTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 5 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTATATAATATATTC
Found at i:143084 original size:105 final size:105
Alignment explanation
Indices: 142902--143781 Score: 1609
Period size: 105 Copynumber: 8.4 Consensus size: 105
142892 AGGTTTTACC
* * *
142902 CAGAGTCAATATCAACTTCACAACGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
142967 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
143007 CAGAGCCAATTTCAACTTCACAACGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
143072 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
143112 CAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
143177 ACGAAGGGACCGCTGGTTGTTAACAAATATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
143217 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
143282 ACGAAGGGACCGCTGGTTGTTAACAAACATTTCTC-AGTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
143321 CCAGAGCCAATTTCAACTTCACAACGAAGAATATTGGATTCCAGACAACGCAAGTTCAACTTCAC
1 -CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
143386 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
143427 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
143492 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
143532 CAGAGCCAATTTTAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
143597 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
143637 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
143702 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
143742 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
143782 GGAACAATAC
Statistics
Matches: 751, Mismatches: 22, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
104 3 0.00
105 745 0.99
106 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:144286 original size:12 final size:12
Alignment explanation
Indices: 144269--144313 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
144259 AAACGTTATC
144269 ATATTATATAAT
1 ATATTATATAAT
144281 ATATTATATAAT
1 ATATTATATAAT
144293 ATATTCATAT-AT
1 ATATT-ATATAAT
*
144305 ATATAATAT
1 ATATTATAT
144314 TTACATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 23 0.74
13 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTATATAAT
Found at i:144314 original size:17 final size:17
Alignment explanation
Indices: 144267--144314 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
144257 TTAAACGTTA
144267 TCATAT-TATATAATA-
1 TCATATATATATAATAT
144282 T-AT-TATATA-ATATAT
1 TCATATATATATA-ATAT
144297 TCATATATATATAATAT
1 TCATATATATATAATAT
144314 T
1 T
144315 TACATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 2 0.07
16 2 0.07
17 11 0.41
18 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
TCATATATATATAATAT
Found at i:144320 original size:19 final size:20
Alignment explanation
Indices: 144279--144325 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
144269 ATATTATATA
144279 ATATATTATATAATATATTC
1 ATATATTATATAATATATTC
144299 ATATA-TATATAATAT-TTAC
1 ATATATTATATAATATATT-C
144318 ATAT-TTAT
1 ATATATTAT
144326 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 5 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTATATAATATATTC
Found at i:156762 original size:37 final size:37
Alignment explanation
Indices: 156704--156850 Score: 224
Period size: 37 Copynumber: 3.9 Consensus size: 37
156694 ATAATGTTAG
*
156704 AGTTTTACTAAGGATTCAAACTCCTAAAAATAAGATAA
1 AGTTTTACT-ATGATTCAAACTCCTAAAAATAAGATAA
*
156742 AGTTTTACTATGATTCAAACTCCTAAAAATATGATAGA
1 AGTTTTACTATGATTCAAACTCCTAAAAATAAGATA-A
* *
156780 A-TTTTACTATGATTCAAACTCCTAAAAATATGATAG
1 AGTTTTACTATGATTCAAACTCCTAAAAATAAGATAA
*
156816 AGTTTTATTATGATTCAAACTCCTAAAAATAAGAT
1 AGTTTTACTATGATTCAAACTCCTAAAAATAAGAT
156851 TCATAAGCAT
Statistics
Matches: 102, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
36 1 0.01
37 90 0.88
38 11 0.11
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (37 bp):
AGTTTTACTATGATTCAAACTCCTAAAAATAAGATAA
Found at i:157301 original size:18 final size:17
Alignment explanation
Indices: 157264--157307 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
157254 TTTTATTTTG
**
157264 TTTTATTTTTTTAATTTA
1 TTTTA-TTTTTTAAAATA
157282 TTATTATTTTTTAAAATA
1 TT-TTATTTTTTAAAATA
157300 TTTTATTT
1 TTTTATTT
157308 ATATACATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 14 0.61
19 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTAAAATA
Found at i:157385 original size:22 final size:23
Alignment explanation
Indices: 157337--157388 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
157327 TTTTTTTATC
157337 TTATTTTATTTCATTTCTCTACCA
1 TTATTTTATTT-ATTTCTCTACCA
*
157361 TTATTATTATTT-TTTCTCT-CTA
1 TTATT-TTATTTATTTCTCTACCA
157383 TTATTT
1 TTATTT
157389 ATCTATACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 7 0.27
24 5 0.19
25 6 0.23
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATTTTATTTATTTCTCTACCA
Found at i:162194 original size:25 final size:25
Alignment explanation
Indices: 162160--162210 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
162150 CCAGTAGCAA
162160 AAAGCATCGATTATTAACTATCATT
1 AAAGCATCGATTATTAACTATCATT
162185 AAAGCATCGATTATTAACTATCATT
1 AAAGCATCGATTATTAACTATCATT
162210 A
1 A
162211 CACTGATAAG
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:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (25 bp):
AAAGCATCGATTATTAACTATCATT
Found at i:164358 original size:2 final size:2
Alignment explanation
Indices: 164351--164426 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
164341 CAATCAAAGA
164351 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
164393 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
164427 ACTAATCTCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:165828 original size:100 final size:100
Alignment explanation
Indices: 165706--165905 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
165696 ATCTTAAACC
165706 TTAATTAAATGATATAGTATTAATTTAAAGGGTAAATTATTTATTTGGCCATTCAATTATTATTA
1 TTAATTAAATGATATAGTATTAATTTAAAGGGTAAATTATTTATTTGGCCATTCAATTATTATTA
165771 TTTTTCTATTTTAATCATTACTAAAATTATTTTTT
66 TTTTTCTATTTTAATCATTACTAAAATTATTTTTT
165806 TTAATTAAATGATATAGTATTAATTTAAAGGGTAAATTATTTATTTGGCCATTCAATTATTATTA
1 TTAATTAAATGATATAGTATTAATTTAAAGGGTAAATTATTTATTTGGCCATTCAATTATTATTA
165871 TTTTTCTATTTTAATCATTACTAAAATTATTTTTT
66 TTTTTCTATTTTAATCATTACTAAAATTATTTTTT
165906 CTTATCAATC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (100 bp):
TTAATTAAATGATATAGTATTAATTTAAAGGGTAAATTATTTATTTGGCCATTCAATTATTATTA
TTTTTCTATTTTAATCATTACTAAAATTATTTTTT
Found at i:168657 original size:24 final size:24
Alignment explanation
Indices: 168630--168678 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
168620 GCATGCTTTT
168630 TCACAATAAACTAAGCACTTTGAC
1 TCACAATAAACTAAGCACTTTGAC
*
168654 TCACAGTAAACTAAGCACTTTGAC
1 TCACAATAAACTAAGCACTTTGAC
168678 T
1 T
168679 GTCATTTTTG
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:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (24 bp):
TCACAATAAACTAAGCACTTTGAC
Found at i:168778 original size:16 final size:16
Alignment explanation
Indices: 168745--168785 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
168735 GTTTACTTCA
168745 GAATGATT-AAGAGCT
1 GAATGATTCAAGAGCT
168760 GAATGATTCAA-ATGCT
1 GAATGATTCAAGA-GCT
168776 GAATGATTCA
1 GAATGATTCA
168786 GAGGCTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAGAGCT
Found at i:169285 original size:34 final size:29
Alignment explanation
Indices: 169216--169273 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
169206 GGACTTTTTT
169216 TTTGTTTCTTTTGAATTTTCATATATTAA
1 TTTGTTTCTTTTGAATTTTCATATATTAA
169245 TTTGTTTCTTTTGAATTTTCATATATTAA
1 TTTGTTTCTTTTGAATTTTCATATATTAA
169274 GCTCCATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (29 bp):
TTTGTTTCTTTTGAATTTTCATATATTAA
Found at i:169299 original size:3 final size:3
Alignment explanation
Indices: 169287--169964 Score: 931
Period size: 3 Copynumber: 233.0 Consensus size: 3
169277 CCATTGTTTT
169287 AGA AGAA AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA
1 AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169332 AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
169378 AG- AGA AAA AGA AG- AGA CG- AGA AG- AGA AGA AGA AG- AGA AGA AGAA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A
169422 AGA A-A AG- AGAA AGA AGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA
169467 AGA AGA AGA AGA AGAA AGA AGA AGA AGA A-A AGA AGA AGA AGA A-A
1 AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169511 AGA AGA AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169557 AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA GAGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA
169602 AGA AGA AGA AG- AGA AGAA AGA AGA AG- AGA AGA AGA AGAA AGA AGGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AG-A AGA A-GA
169648 A-A AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AG- AGA AGA A-A AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
169691 AGAA AGA AG- AGA AGA AAA AAA AGA GAGAA AGA AGA AG- AGA AGA A-A
1 AG-A AGA AGA AGA AGA AGA AGA AGA -AG-A AGA AGA AGA AGA AGA AGA
* *
169736 ATA AGA AAA AGA AG- AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169782 A-A AGA AGA AGAA AGA AGA AGA AGA A-A AG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169825 AGA AGA AGA AGA AGA AGA A-A AG- AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169871 AGA AGA AGA AGA AGA A-A A-A AGA AGA AGA AGA AGA AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
169915 AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
169962 AGA
1 AGA
169965 GACCATGTAC
Statistics
Matches: 618, Mismatches: 9, Indels: 96
0.85 0.01 0.13
Matches are distributed among these distances:
2 69 0.11
3 510 0.83
4 38 0.06
5 1 0.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:173612 original size:37 final size:37
Alignment explanation
Indices: 173536--173612 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
173526 TTTTTATATT
*
173536 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
173573 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
173610 TTT
1 TTT
173613 GTAATAGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:173835 original size:21 final size:21
Alignment explanation
Indices: 173784--173836 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
173774 ATTATGACTA
173784 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
173805 TCGCGTTGCGATTTTTCCAA-T
1 TCGCAATGCGA-TTTTCCAATT
173826 TCGCAATGCGA
1 TCGCAATGCGA
173837 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:173851 original size:20 final size:21
Alignment explanation
Indices: 173826--173877 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
173816 TTTTTCCAAT
*
173826 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
173846 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
173867 TCGCAATGCGA
1 TCGCAATGCGA
173878 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:173891 original size:20 final size:20
Alignment explanation
Indices: 173866--173980 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
173856 AATTGGGAAA
*
173866 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
173886 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
173907 ATCGCAACACGATACTGAAT
1 ATCGCAACGCGATACTGACT
* * *
173927 TTTGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
173947 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
173967 TTCGCAACGAGATA
1 ATCGCAACGCGATA
173981 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.78
21 14 0.18
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:173908 original size:41 final size:41
Alignment explanation
Indices: 173863--174000 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
173853 GCGAATTGGG
* *
173863 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * * *
173904 AAAATCGCAACACGATACTGAATTTTGCAACGCGATACTTAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
173946 --TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
173985 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
174001 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 29 0.37
41 43 0.55
42 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:174513 original size:20 final size:20
Alignment explanation
Indices: 174454--174517 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
174444 GCGATTTTAG
* *
174454 TTTCGCGTTGCGGTAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
174474 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
174494 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
174514 TTTC
1 TTTC
174518 AGAAACTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:174708 original size:25 final size:24
Alignment explanation
Indices: 174654--174708 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
174644 TGTTTATTAT
* *
174654 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
174678 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
174704 TGTTT
1 TGTTT
174709 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:175857 original size:18 final size:18
Alignment explanation
Indices: 175836--175883 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
175826 TCCACTTCGG
175836 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
175854 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
175872 GAGCCATCACCT
1 GAGCCATCACCT
175884 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:176458 original size:20 final size:19
Alignment explanation
Indices: 176424--176478 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
176414 TAGTTTACTT
*
176424 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
176443 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
*
176463 TCGCAATGCGAAATGA
1 TCGCAACGCGAAATGA
176479 AAATCGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:176536 original size:19 final size:19
Alignment explanation
Indices: 176486--176539 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
176476 TGAAAATCGC
*
176486 ATTTTCATTTTGCATTGCG
1 ATTTTCATTTCGCATTGCG
*
176505 A-TTT--TGTCG--TTGCG
1 ATTTTCATTTCGCATTGCG
176519 ATTTTCATTTCGCATTGCG
1 ATTTTCATTTCGCATTGCG
176538 AT
1 AT
176540 AGCCATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
14 6 0.22
15 3 0.11
16 3 0.11
17 4 0.15
18 3 0.11
19 8 0.30
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.50
Consensus pattern (19 bp):
ATTTTCATTTCGCATTGCG
Found at i:176548 original size:39 final size:40
Alignment explanation
Indices: 176505--176597 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
176495 TTGCATTGCG
***
176505 ATTTTGTCGTTGCGATTTTCATTT-CGCATTGCGATAGCC
1 ATTTTGTCGTTGCGATAGCCATTTCCGCATTGCGATAGCC
* *
176544 ATTTTGT-GTTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTTGTCGTTGCGATAGCCATTTCCGCATTGCGATAGCC
176583 ATTTTCG-CGTTGCGA
1 ATTTT-GTCGTTGCGA
176598 AAGTAAGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 13 0.28
39 25 0.54
40 8 0.17
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (40 bp):
ATTTTGTCGTTGCGATAGCCATTTCCGCATTGCGATAGCC
Found at i:176576 original size:20 final size:19
Alignment explanation
Indices: 176524--176597 Score: 94
Period size: 20 Copynumber: 3.8 Consensus size: 19
176514 TTGCGATTTT
*
176524 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
* *
176543 CATTTTGTGTTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
176562 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
176582 CATTTTCGCGTTGCGA
1 CA-TTTCGCGTTGCGA
176598 AAGTAAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 21 0.45
20 23 0.49
21 3 0.06
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:176608 original size:20 final size:20
Alignment explanation
Indices: 176568--176623 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
176558 TAGCCATTTC
* * *
176568 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
176588 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
176608 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
176624 AATATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:176998 original size:21 final size:20
Alignment explanation
Indices: 176972--177040 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
176962 CTGTCATCCC
176972 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* *
176993 TCAAGAGGCCCCTATCATC-T
1 TCAAGAGTCCCCT-CCATCGT
* *
177013 CTCAAGAGTCCCCCCCACCGT
1 -TCAAGAGTCCCCTCCATCGT
177034 TCAAGAG
1 TCAAGAG
177041 GCCACTGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 11 0.28
21 27 0.69
22 1 0.03
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:177052 original size:41 final size:42
Alignment explanation
Indices: 176962--177052 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
176952 CCCGACTCAC
* *
176962 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* * *
177004 CTATCATCTCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
177045 CTGTCATC
1 CTGTCATC
177053 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:178631 original size:14 final size:14
Alignment explanation
Indices: 178612--178664 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
178602 GAAACTGACT
178612 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
178626 ATCGCAATGCGAAATGAA
1 ATCGCAA--CGAGA-G-A
*
178644 ATCGCAACGAGAAA
1 ATCGCAACGAGAGA
178658 ATCGCAA
1 ATCGCAA
178665 TGCGATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 15 0.47
16 8 0.25
17 1 0.03
18 8 0.25
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:178698 original size:14 final size:14
Alignment explanation
Indices: 178676--178705 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
178666 GCGATTTTCA
178676 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
*
178690 TTTCTCATTGCGAT
1 TTTCGCATTGCGAT
178704 TT
1 TT
178706 CATTTTCGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (14 bp):
TTTCGCATTGCGAT
Found at i:178731 original size:20 final size:20
Alignment explanation
Indices: 178706--178744 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
178696 ATTGCGATTT
* *
178706 CATTTTCGCGTTGCGATAGC
1 CATTTTCGCATTACGATAGC
178726 CATTTTCGCATTACGATAG
1 CATTTTCGCATTACGATAG
178745 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (20 bp):
CATTTTCGCATTACGATAGC
Found at i:179759 original size:20 final size:20
Alignment explanation
Indices: 179653--179767 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
179643 GATTCTGTAT
*
179653 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
179673 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
179693 AATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
179713 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
179734 TATCGCGTTGCGATGGTCAG
1 TATCGCGTTGCGATAGTCAG
*
179754 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
179768 TTTCCAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.76
21 14 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:179786 original size:41 final size:41
Alignment explanation
Indices: 179694--179788 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
179684 GAAAGTCAGA
* * ** *
179694 ATCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
* *
179735 ATCGCGTTGCGATGGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT-CAAAT
179777 -TCGCATTGCGAT
1 ATCGCATTGCGAT
179789 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
Found at i:179800 original size:20 final size:21
Alignment explanation
Indices: 179756--179807 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
179746 ATGGTCAGTA
*
179756 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
179777 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
179797 TCGCATTGCGA
1 TCGCATTGCGA
179808 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:179849 original size:21 final size:22
Alignment explanation
Indices: 179797--179849 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
179787 ATTTACTTAT
179797 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
179818 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
179839 TCGCATTGCGA
1 TCGCATTGCGA
179850 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:186891 original size:68 final size:66
Alignment explanation
Indices: 186710--186899 Score: 209
Period size: 68 Copynumber: 2.8 Consensus size: 66
186700 CAAAGGTGGA
* * * * *
186710 ATGGAGGTGGATGATGGTAGAGACGGTGATGGTTGATATGGATAGTGATGTTGTGATGTTGGTGG
1 ATGGAGGTGGAT-ATGGTAGAGA-TGTGATGGTTGAT-TGGAGAGTGATGTTGTAATGATGATGG
186775 TGAG
63 TGAG
* * * *
186779 ATAGAGGTGGATGCTGGTAGGGATGGTAATGGTTGATTGGAGAGTGATGTTGTAATGATGATGGT
1 ATGGAGGTGGAT-ATGGTAGAGAT-GTGATGGTTGATTGGAGAGTGATGTTGTAATGATGATGGT
*
186844 GAT
64 GAG
* *
186847 ATGGAGGTGCATATTGGTAGAGATGTGATGGTTGATGTGAAGAGTGATGTTGT
1 ATGGAGGTGGATA-TGGTAGAGATGTGATGGTTGAT-TGGAGAGTGATGTTGT
186900 GAAGGAGTAC
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
67 11 0.11
68 60 0.59
69 31 0.30
ACGTcount: A:0.24, C:0.02, G:0.42, T:0.33
Consensus pattern (66 bp):
ATGGAGGTGGATATGGTAGAGATGTGATGGTTGATTGGAGAGTGATGTTGTAATGATGATGGTGA
G
Found at i:191979 original size:16 final size:16
Alignment explanation
Indices: 191958--191999 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
191948 TTACTATTCA
191958 CATGAATAGTGAATTT
1 CATGAATAGTGAATTT
191974 CATGAATAGTGAATTT
1 CATGAATAGTGAATTT
**
191990 TGTGAATAGT
1 CATGAATAGT
192000 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (16 bp):
CATGAATAGTGAATTT
Found at i:206954 original size:37 final size:37
Alignment explanation
Indices: 206913--206986 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
206903 AATAAGTGTT
206913 CAATTTTTACCTAATGAATCAATTAAATTTAAATTAA
1 CAATTTTTACCTAATGAATCAATTAAATTTAAATTAA
*
206950 CAATTTTTATCTAATGAATCAATTAAATTTAAATTAA
1 CAATTTTTACCTAATGAATCAATTAAATTTAAATTAA
206987 GTCTAACATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (37 bp):
CAATTTTTACCTAATGAATCAATTAAATTTAAATTAA
Found at i:208790 original size:16 final size:16
Alignment explanation
Indices: 208769--208802 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
208759 ATGTGATAAA
208769 TTCTAATATATT-TTTT
1 TTCTAA-ATATTATTTT
208785 TTCTAAATATTATTTT
1 TTCTAAATATTATTTT
208801 TT
1 TT
208803 ATTAATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCTAAATATTATTTT
Found at i:208800 original size:15 final size:16
Alignment explanation
Indices: 208769--208801 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
208759 ATGTGATAAA
*
208769 TTCTAATATATTTTTT
1 TTCTAATATATTATTT
208785 TTCTAA-ATATTATTT
1 TTCTAATATATTATTT
208800 TT
1 TT
208802 TATTAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTAATATATTATTT
Found at i:210749 original size:17 final size:16
Alignment explanation
Indices: 210722--210763 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
210712 GTTGATTGTG
210722 GGAAGAAAGGAAGAATAA
1 GGAA-AAAGGAAGAA-AA
210740 GGAAAAAGGAAGAAAA
1 GGAAAAAGGAAGAAAA
*
210756 AGAAAAAG
1 GGAAAAAG
210764 AGAGGACCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (16 bp):
GGAAAAAGGAAGAAAA
Found at i:211196 original size:49 final size:49
Alignment explanation
Indices: 211124--211234 Score: 222
Period size: 49 Copynumber: 2.3 Consensus size: 49
211114 TTGCCTCTCT
211124 TTCTCCTTGCTTTCTTAAAATCTTGTAGCAGAAGGGTGCTAACTCAACC
1 TTCTCCTTGCTTTCTTAAAATCTTGTAGCAGAAGGGTGCTAACTCAACC
211173 TTCTCCTTGCTTTCTTAAAATCTTGTAGCAGAAGGGTGCTAACTCAACC
1 TTCTCCTTGCTTTCTTAAAATCTTGTAGCAGAAGGGTGCTAACTCAACC
211222 TTCTCCTTGCTTT
1 TTCTCCTTGCTTT
211235 TCATTAATAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (49 bp):
TTCTCCTTGCTTTCTTAAAATCTTGTAGCAGAAGGGTGCTAACTCAACC
Found at i:212324 original size:6 final size:6
Alignment explanation
Indices: 212301--212390 Score: 60
Period size: 6 Copynumber: 15.0 Consensus size: 6
212291 CCACATTCTT
* *
212301 CATCTA CAT-TA CCATCTA CATCTA CATC-A CCGTCTA CTTCTA CATC-A
1 CATCTA CATCTA -CATCTA CATCTA CATCTA -CATCTA CATCTA CATCTA
* * * * * *
212348 CCATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATCTA
1 -CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA CATCTA
212391 TATCACCTCC
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
5 4 0.05
6 66 0.90
7 3 0.04
ACGTcount: A:0.24, C:0.42, G:0.01, T:0.32
Consensus pattern (6 bp):
CATCTA
Found at i:212324 original size:18 final size:18
Alignment explanation
Indices: 212301--212390 Score: 76
Period size: 18 Copynumber: 5.0 Consensus size: 18
212291 CCACATTCTT
212301 CATCTACATTACCATCTA
1 CATCTACATTACCATCTA
* *
212319 CATCTACATCACCGTCTA
1 CATCTACATTACCATCTA
* * *
212337 CTTCTACATCACCATCTC
1 CATCTACATTACCATCTA
* *
212355 CATCTCCATCT-CCATCTC
1 CATCTACAT-TACCATCTA
*
212373 CATCTCCATCT-CCATCTA
1 CATCTACAT-TACCATCTA
212391 TATCACCTCC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.24, C:0.42, G:0.01, T:0.32
Consensus pattern (18 bp):
CATCTACATTACCATCTA
Found at i:216387 original size:54 final size:54
Alignment explanation
Indices: 216303--216414 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
216293 ATTGCATCGA
* *
216303 AGTGCCGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATTGCACATAT
1 AGTGCCGAAATGGAAATTCACAAACACATTATGAATACCATGGATTGCACATAT
*** * * *
216357 AGTGCCGAAATGGTTGTTCATAAACACATTATGAATACCATGGGTTGCACATTT
1 AGTGCCGAAATGGAAATTCACAAACACATTATGAATACCATGGATTGCACATAT
216411 AGTG
1 AGTG
216415 TCAAAAATGC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (54 bp):
AGTGCCGAAATGGAAATTCACAAACACATTATGAATACCATGGATTGCACATAT
Found at i:219409 original size:39 final size:39
Alignment explanation
Indices: 219300--219418 Score: 122
Period size: 39 Copynumber: 3.1 Consensus size: 39
219290 TTGACCTTTT
* * *
219300 ATTTATAA-TTCTAAAATTATTTCAC-TCTAACATTCAAA
1 ATTTCTAATTTCTTAAATTATTTCACAT-TAACATTCTAA
* *
219338 ATTTCTAATTTTTTAAATT-TTACCACCA-TAACATTCTAA
1 ATTTCTAATTTCTTAAATTATT-TCA-CATTAACATTCTAA
219377 A-TTCTTAATTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTTC-TAATTTCTTAAATTATTTCACATTAACATTCTAA
219416 ATT
1 ATT
219419 ATTTTTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
38 14 0.21
39 48 0.73
40 4 0.06
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (39 bp):
ATTTCTAATTTCTTAAATTATTTCACATTAACATTCTAA
Found at i:229109 original size:19 final size:20
Alignment explanation
Indices: 229085--229127 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
229075 AGCATTTATC
*
229085 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
229104 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
229124 TTCA
1 TTCA
229128 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:229532 original size:35 final size:35
Alignment explanation
Indices: 229493--229569 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
229483 TTCCATTTTT
*
229493 ACGCCTATAACATCACCATCTTCCATTACCATTGC
1 ACGCCTATAACATCACCATCTTCCATCACCATTGC
* * * *
229528 ACGCCTATATCATTACCATCTTCTATCACCATTTC
1 ACGCCTATAACATCACCATCTTCCATCACCATTGC
229563 ACGCCTA
1 ACGCCTA
229570 AATAACCACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.31
Consensus pattern (35 bp):
ACGCCTATAACATCACCATCTTCCATCACCATTGC
Found at i:233234 original size:20 final size:20
Alignment explanation
Indices: 233209--233253 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
233199 GCCAAGAGCA
*
233209 TTTCATTAAAAATTATGTAT
1 TTTCATTAAAAATCATGTAT
*
233229 TTTCATTAAAAATCATGTGT
1 TTTCATTAAAAATCATGTAT
233249 TTTCA
1 TTTCA
233254 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTCATTAAAAATCATGTAT
Found at i:240481 original size:24 final size:24
Alignment explanation
Indices: 240449--240541 Score: 177
Period size: 24 Copynumber: 3.9 Consensus size: 24
240439 CAAATGGCTC
240449 GTTCGTTCATTTATGTTAATTTAT
1 GTTCGTTCATTTATGTTAATTTAT
240473 GTTCGTTCATTTATGTTAATTTAT
1 GTTCGTTCATTTATGTTAATTTAT
240497 GTTCGTTCATTTATGTTAATTTAT
1 GTTCGTTCATTTATGTTAATTTAT
*
240521 GTTCGTTCATTTATGCTAATT
1 GTTCGTTCATTTATGTTAATT
240542 GAACGTTCGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (24 bp):
GTTCGTTCATTTATGTTAATTTAT
Found at i:240486 original size:14 final size:14
Alignment explanation
Indices: 240467--240535 Score: 64
Period size: 14 Copynumber: 5.5 Consensus size: 14
240457 ATTTATGTTA
240467 ATTTATGTTCGTTC
1 ATTTATGTTCGTTC
*
240481 ATTTA---T-GTTA
1 ATTTATGTTCGTTC
240491 ATTTATGTTCGTTC
1 ATTTATGTTCGTTC
*
240505 ATTTA---T-GTTA
1 ATTTATGTTCGTTC
240515 ATTTATGTTCGTTC
1 ATTTATGTTCGTTC
240529 ATTTATG
1 ATTTATG
240536 CTAATTGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
10 16 0.37
11 2 0.05
13 2 0.05
14 23 0.53
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.58
Consensus pattern (14 bp):
ATTTATGTTCGTTC
Found at i:240864 original size:24 final size:24
Alignment explanation
Indices: 240832--240889 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
240822 TTTTGCATCC
240832 GTTCGTTTATGCTCGTTCATTTGT
1 GTTCGTTTATGCTCGTTCATTTGT
240856 GTTCGTTTATGCTCGTTCATTTGT
1 GTTCGTTTATGCTCGTTCATTTGT
240880 GTTCGTTTAT
1 GTTCGTTTAT
240890 CATTTAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.09, C:0.16, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGCTCGTTCATTTGT
Found at i:243970 original size:41 final size:42
Alignment explanation
Indices: 243917--244002 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 42
243907 GTTGGGAAAC
243917 AGTTTAGTGAGACGGGGTCTGAGGAAGGCGATAATA-GGGGA
1 AGTTTAGTGAGACGGGGTCTGAGGAAGGCGATAATAGGGGGA
243958 AGTTTAGTGAGACGGGGTCTGAGGAAGGCGATAATAGGGGGA
1 AGTTTAGTGAGACGGGGTCTGAGGAAGGCGATAATAGGGGGA
244000 AGT
1 AGT
244003 CAGATTATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 36 0.82
42 8 0.18
ACGTcount: A:0.29, C:0.07, G:0.44, T:0.20
Consensus pattern (42 bp):
AGTTTAGTGAGACGGGGTCTGAGGAAGGCGATAATAGGGGGA
Found at i:245208 original size:37 final size:37
Alignment explanation
Indices: 245161--245236 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
245151 ACTAGTCTCT
245161 AACTCTCATCCTTCTTTTCAGAGACTACAAGAAACTA
1 AACTCTCATCCTTCTTTTCAGAGACTACAAGAAACTA
*** *
245198 AACTCTCATCCTTCTTTTCTTTGGCTACAAGAAACTA
1 AACTCTCATCCTTCTTTTCAGAGACTACAAGAAACTA
245235 AA
1 AA
245237 ACAGAGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (37 bp):
AACTCTCATCCTTCTTTTCAGAGACTACAAGAAACTA
Found at i:250748 original size:21 final size:21
Alignment explanation
Indices: 250724--250788 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
250714 TCAAAGCAAC
250724 ATTTTTAAATGATAAGTAACG
1 ATTTTTAAATGATAAGTAACG
* *
250745 A-TTTTAACATG-TCAAATCAA-T
1 ATTTTTAA-ATGAT-AAGT-AACG
*
250766 ATTTTTAAATGACAAGTAACG
1 ATTTTTAAATGATAAGTAACG
250787 AT
1 AT
250789 AATGATTGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
20 9 0.27
21 16 0.48
22 8 0.24
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (21 bp):
ATTTTTAAATGATAAGTAACG
Found at i:250760 original size:42 final size:42
Alignment explanation
Indices: 250699--250788 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
250689 TGCACTTTTA
*
250699 AACGATTTTAACATCTCAAAGCAACATTTTTAAATGATAAGT
1 AACGATTTTAACATCTCAAAGCAACATTTTTAAATGACAAGT
* * *
250741 AACGATTTTAACATGTCAAATCAATATTTTTAAATGACAAGT
1 AACGATTTTAACATCTCAAAGCAACATTTTTAAATGACAAGT
250783 AACGAT
1 AACGAT
250789 AATGATTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (42 bp):
AACGATTTTAACATCTCAAAGCAACATTTTTAAATGACAAGT
Found at i:251289 original size:20 final size:20
Alignment explanation
Indices: 251253--251290 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
251243 AAAGAAATAT
*
251253 TAAAAATATATAGAAAATCA
1 TAAAAATATATAAAAAATCA
*
251273 TAAAAATATTTAAAAAAT
1 TAAAAATATATAAAAAAT
251291 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAATATATAAAAAATCA
Found at i:251312 original size:20 final size:20
Alignment explanation
Indices: 251287--251386 Score: 59
Period size: 20 Copynumber: 5.0 Consensus size: 20
251277 AATATTTAAA
251287 AAATAAAATAAAATAAAAAC
1 AAATAAAATAAAATAAAAAC
*
251307 AAAT-AAA-CAAATAAAAAAC
1 AAATAAAATAAAAT-AAAAAC
251326 AAATCAAAGGA-AAAAT-AAAA-
1 AAAT-AAA--ATAAAATAAAAAC
* **
251346 TAATAATAATAATAATAAATGC
1 AAATAA-AATAA-AATAAAAAC
251368 AAA-AAAATAATAATAAAAA
1 AAATAAAATAA-AATAAAAA
251387 GTATTAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
18 5 0.08
19 17 0.27
20 23 0.37
21 10 0.16
22 2 0.03
23 5 0.08
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (20 bp):
AAATAAAATAAAATAAAAAC
Found at i:251443 original size:3 final size:3
Alignment explanation
Indices: 251437--251462 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
251427 AAAAAAGGTA
251437 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
251463 AATGATTAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:251506 original size:10 final size:10
Alignment explanation
Indices: 251491--251526 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
251481 ATGAAATTGG
251491 AAATAAAAAT
1 AAATAAAAAT
251501 AAATAAAAA-
1 AAATAAAAAT
251510 AAATAAAAAT
1 AAATAAAAAT
251520 AAATAAA
1 AAATAAA
251527 TAAAGACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:253245 original size:84 final size:84
Alignment explanation
Indices: 252999--254459 Score: 1570
Period size: 84 Copynumber: 17.4 Consensus size: 84
252989 AAATCGATAA
* * * * * * *
252999 TTTTGTCGACAGATAGCCCTTCTTGCATTGAGCTATGCTGTAAATTTGATTTTCCTCT-GAG-TA
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATGTGCCT-TGGAGCT-
** *
253062 GAATGTAATCGAACTCGAAGGTC
62 GAGCGTAGTCGAACTCGAAGGTC
* * * * *
253085 --TTGATTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTG
1 TTTTG-TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTGGAGCTG
*
253148 AGCGTAGTTGAACTCGAAGGTC
63 AGCGTAGTCGAACTCGAAGGTC
* * * * * * *
253170 TTTGGTTGGTAGATAGCTCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGCCTTTGAGCTGAGC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
253235 GTAGTCGAACTTGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * * * *
253254 TTTGGTTGGCAGATATCCCTTCTCGACTTAAGCTATGATGTAAATGATGTTCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
253319 GTAATCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * *
253338 TTTTGTTGGCAAATAACCCTTATAGCCTTGAGTTATGCAGCAAATGATGTGCCTTTGAGTTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
253403 GTAATCGAATTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
253422 TTTTGTTGGTAGATAGCCCTTCTCA-ACTTAAGTTATGCTGCAAATGATGTGCCTCT-GAGCTGA
1 TTTTGTTGGCAGATAGCCCTTCT-AGCCTTGAGCTATGCTGCAAATGATGTGCCT-TGGAGCTGA
*
253485 GCGTAGTCGAACTCGAAGGTA
64 GCGTAGTCGAACTCGAAGGTC
* * * * *
253506 TTTTGTTGGCAAATAGCTCTTCTTA-CCTTGAGCTATGTTGCAAATGATGTGCCTTGAAGCTTAG
1 TTTTGTTGGCAGATAGCCCTTC-TAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* *
253570 CGTAGTCGAACTCGAAAGTA
65 CGTAGTCGAACTCGAAGGTC
* * * * * * * * * *
253590 TTTGGTTAGCAAATAACTCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTGGAGCTAAAC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
253655 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * *
253674 TTTTTGGTGGAAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAAT-ATTATGCATTTGAGCTGA
1 -TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGA
* * *
253738 GTGTAATCGAACTCGAATGTC
64 GCGTAGTCGAACTCGAAGGTC
* * * *
253759 TTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATGCTGCAAATGTTGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
253824 GTAGTCGAACTCGAAGG--
66 GTAGTCGAACTCGAAGGTC
* * * *
253841 TTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
253906 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * * * * *
253925 TTTGGTTGGAAGATAACCCTTCTAGCCTTGAGTTATGATGAAAATGATGCGCCTTGGAGCTGAAC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
253990 GTAGTAGAACTCAAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
254009 TTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGTTATGCTGC--A--ATGTGCCTTGGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
254070 GTAGTCGAACTTGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
254089 TTTTGTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT-ATTGTGCCTTTGAGCTGAG
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAG
* *
254153 TGTAATCGAACTCGAAGGTC
65 CGTAGTCGAACTCGAAGGTC
* * *
254173 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT--ACATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
254236 GTAGTCGAACTCGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* * * * *
254255 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
254320 GTAGTAGAACTCGAAGGTA
66 GTAGTCGAACTCGAAGGTC
* * * * *
254339 TTTTGTTGGCAAATAGCCCTTCTTGGCTTGGGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
254404 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
254423 TTTTGTTGCCAGATAACCCTTCTAGCCTTGAGTTATG
1 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATG
254460 GTGTTAATAG
Statistics
Matches: 1169, Mismatches: 184, Indels: 46
0.84 0.13 0.03
Matches are distributed among these distances:
80 67 0.06
82 147 0.13
83 5 0.00
84 776 0.66
85 138 0.12
86 34 0.03
87 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (84 bp):
TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:254209 original size:414 final size:417
Alignment explanation
Indices: 252999--254459 Score: 1759
Period size: 414 Copynumber: 3.5 Consensus size: 417
252989 AAATCGATAA
* * * * * * *
252999 TTTTGTCGACAGATAGCCCTTCTTG-CATTGAGCTATGCTGTAAATTTGATTTTCCTCTGAG-TA
1 TTTTGTTGGCAGATAGCCCTTCTCGAC-TTAAGCTATGCTGCAAA--TGATGTGCCTCTGAGCT-
** * * * * * * *
253062 GAATGTAATCGAACTCGAAGGT-CTTGATTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTA
62 GAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAAATAGCCCTTCTAGCCTTGAGCTATGTTG-A
* * * * * * * *
253126 AATTTGATATGCCTTTGAGCTGAGCGTAGTTGAACTCGAAGGTC-TTTGGTTGGTAGATAGCTCT
126 AA-ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTTGGCAGATAACCCT
* * * *
253190 TCTTGCCTTGAGCTATGTTGCAAATAATGTGCCTTTGAGCTGAGCGTAGTCGAACTTGAAGGTCT
190 TCTAGCCTTGAGTTATGCTGC--A-AATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCT
* * * * * *
253255 TTGGTTGGCAGATATCCCTTCTCGACTTAAGCTATGATGTAAATGA-TGTTCCTTTGAGCTGAGT
252 TTTGTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT-ATTGTGCCTTTGAGCTGAGT
* * *
253319 GTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATAGCCTTGAGTTATGCAGCAAATG
316 GTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* * * * *
253384 ATGTGCCTTTGAGTTGAGTGTAATCGAATTCGAAGGT
381 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
253421 CTTTTGTTGGTAGATAGCCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAG
1 -TTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAG
* * *
253486 CGTAGTCGAACTCGAAGGTATTTTGTTGGCAAATAGCTCTTCTTA-CCTTGAGCTATGTTGCAAA
65 CGTAGTCGAACTCGAAGGTATTTGGTTGGCAAATAGCCCTTC-TAGCCTTGAGCTATGTTGAAAA
* * * * * *
253550 TGATGTGCCTTGAAGCTTAGCGTAGTCGAACTCGAAA-GT-ATTTGGTTAGCAAATAACTCTTCT
129 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAAGGTCTTTTGGTTGGCAGATAACCCTTCT
* * * *
253613 AGCCTTGAGTTATGCTACAAATGATATGCCTTGGAGCTAAACGTAGTCGAACTCGAAGGTCTTTT
193 AGCCTTGAGTTATGCTGCAAATG---TGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTC-TTT
* * * * * * *
253678 TGGTGGAAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAATATTATGCATTTGAGCTGAGTGTA
254 TGTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATATTGTGCCTTTGAGCTGAGTGTA
* * *
253743 ATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATGCTGCAAATGTTG
319 ATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
253808 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-
384 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * * *
253841 TTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCT-TGGAGCTGAG
1 TTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCT-GAGCTGAG
* * * *
253905 CGTAGTCGAACTCGAAGGTCTTTGGTTGG-AAGATAACCCTTCTAGCCTTGAGTTATGATGAAAA
65 CGTAGTCGAACTCGAAGGTATTTGGTTGGCAA-ATAGCCCTTCTAGCCTTGAGCTATGTTGAAAA
* * * *
253969 TGATGCGCCTTGGAGCTGAACGTAGTAGAACTCAAAGGTCTTTTGG-TGGCAGATAGCCCTTCTA
129 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTTGGCAGATAACCCTTCTA
*
254033 GCCTTGAGTTATGCTGC-AATGTGCCTTGGAGCTGAGTGTAGTCGAACTTGAAGGTCTTTTGTTG
194 GCCTTGAGTTATGCTGCAAATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTG
*
254097 GTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATATTGTGCCTTTGAGCTGAGTGTAATCGA
259 GAAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATATTGTGCCTTTGAGCTGAGTGTAATCGA
*
254162 ACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCT--ACATGATGTGCCT
324 ACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
254225 TGGAGCTGAGCGTAGTCGAACTCGAAGGT
389 TGGAGCTGAGCGTAGTCGAACTCGAAGGT
* *
254254 ATTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCT-TGGAGCTGA
1 -TTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCT-GAGCTGA
* * * * * *
254318 GCGTAGTAGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGGCTTGGGCTATGTTGCAAA
64 GCGTAGTCGAACTCGAAGGTATTTGGTTGGCAAATAGCCCTTCTAGCCTTGAGCTATGTTGAAAA
* *
254383 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-GTTGCCAGATAACCCTTCTA
129 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTTGGCAGATAACCCTTCTA
254447 GCCTTGAGTTATG
194 GCCTTGAGTTATG
254460 GTGTTAATAG
Statistics
Matches: 886, Mismatches: 132, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
412 39 0.04
413 1 0.00
414 289 0.33
415 33 0.04
417 4 0.00
418 13 0.01
419 164 0.19
420 100 0.11
421 176 0.20
422 31 0.03
423 35 0.04
424 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (417 bp):
TTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGC
GTAGTCGAACTCGAAGGTATTTGGTTGGCAAATAGCCCTTCTAGCCTTGAGCTATGTTGAAAATG
ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTTGGCAGATAACCCTTCTAGC
CTTGAGTTATGCTGCAAATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGA
AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATATTGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGT
Found at i:259287 original size:21 final size:21
Alignment explanation
Indices: 259262--259363 Score: 70
Period size: 20 Copynumber: 4.7 Consensus size: 21
259252 AGAAAGAAAG
259262 AAAAATTAAAAATATATATAA
1 AAAAATTAAAAATATATATAA
259283 AAAAATCATAAAAATATTTTAATATAA
1 AAAAAT--TAAAAATA---T-ATATAA
259310 AAAAATCATAAAAA-A-ATA-AA
1 AAAAAT--TAAAAATATATATAA
* *
259330 AAAAATAAAAAAAATA-ATAA
1 AAAAATTAAAAATATATATAA
259350 AAATAA-TAAAAATA
1 AAA-AATTAAAAATA
259364 AATCAAAGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
18 5 0.07
19 2 0.03
20 20 0.29
21 11 0.16
23 8 0.12
26 2 0.03
27 20 0.29
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATTAAAAATATATATAA
Found at i:259331 original size:9 final size:9
Alignment explanation
Indices: 259303--259408 Score: 88
Period size: 9 Copynumber: 11.2 Consensus size: 9
259293 AAAATATTTT
259303 AATATAAAAA
1 AATA-AAAAA
259313 AATCATAAAAA
1 AAT-A-AAAAA
259324 AATAAAAAA
1 AATAAAAAA
259333 AATAAAAAA
1 AATAAAAAA
*
259342 AATAATAAA
1 AATAAAAAA
*
259351 AATAATAAA
1 AATAAAAAA
*
259360 AATAAATCAA
1 AATAAA-AAA
** *
259370 AGGAAAAAT
1 AATAAAAAA
*
259379 AA-AATAAA
1 AATAAAAAA
259387 AATACAAAAA
1 AATA-AAAAA
259397 AATAACAAAA
1 AATAA-AAAA
259407 AA
1 AA
259409 AAGTATTAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
8 6 0.08
9 40 0.50
10 24 0.30
11 10 0.12
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:259397 original size:21 final size:19
Alignment explanation
Indices: 259303--259409 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 19
259293 AAAATATTTT
*
259303 AATATAAAAAAATCATAAAAA
1 AATA-AAAAAAAT-AAAAAAA
259324 AATAAAAAAAATAAAAAAAA
1 AATAAAAAAAAT-AAAAAAA
* *
259344 TAATAAAAATAATAAAAATA
1 -AATAAAAAAAATAAAAAAA
259364 AATCAAAGGAAAAATAAAATAAA
1 AAT-AAA--AAAAATAAAA-AAA
259387 AATACAAAAAAATAACAAAAA
1 AATA-AAAAAAATAA-AAAAA
259408 AA
1 AA
259410 AGTATTAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
19 3 0.04
20 23 0.32
21 28 0.38
22 12 0.16
23 7 0.10
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (19 bp):
AATAAAAAAAATAAAAAAA
Found at i:259409 original size:27 final size:26
Alignment explanation
Indices: 259306--259407 Score: 98
Period size: 27 Copynumber: 3.7 Consensus size: 26
259296 ATATTTTAAT
*
259306 ATAAAAAAATCATAAAAAAATAAAAAAA
1 ATAAAAAAA--ATAAAAAAATAATAAAA
259334 ATAAAAAAAATAATAAAAATAATAAAA
1 ATAAAAAAAATAA-AAAAATAATAAAA
* **
259361 ATAAATCAAAGGAAAAATAA-AATAAAA
1 ATAAA-AAAAATAAAAA-AATAATAAAA
259388 ATACAAAAAAATAACAAAAA
1 ATA-AAAAAAATAA-AAAAA
259408 AAAGTATTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 4 0.06
27 37 0.60
28 21 0.34
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (26 bp):
ATAAAAAAAATAAAAAAATAATAAAA
Found at i:259471 original size:3 final size:3
Alignment explanation
Indices: 259465--259507 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
259455 ATAAGAGGTA
259465 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
259508 TGATTAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:259549 original size:4 final size:4
Alignment explanation
Indices: 259540--259598 Score: 86
Period size: 4 Copynumber: 14.8 Consensus size: 4
259530 TTGGAAATAA
259540 AAAT AAAT -AA- AAAT GAAAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT -A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
259588 AAAT AAAT AAA
1 AAAT AAAT AAA
259599 AAGGACCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 4 0.08
4 42 0.82
5 2 0.04
6 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:261958 original size:14 final size:14
Alignment explanation
Indices: 261941--261968 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
261931 ATCATAACAA
261941 AATTATATAACTAT
1 AATTATATAACTAT
261955 AATTATATAACTAT
1 AATTATATAACTAT
261969 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:268281 original size:3 final size:3
Alignment explanation
Indices: 268273--268368 Score: 165
Period size: 3 Copynumber: 32.0 Consensus size: 3
268263 CCATATTGAT
*
268273 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
268321 TTA TTA TTA TAA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
268369 AATATATTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:281223 original size:7 final size:7
Alignment explanation
Indices: 281193--281246 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
281183 ATTATGCTTG
281193 AAGAGAAA
1 AAGA-AAA
281201 AAGAAAA
1 AAGAAAA
*
281208 GAAAAAAA
1 -AAGAAAA
281216 AAGGAAAA
1 AA-GAAAA
281224 AAGAAAA
1 AAGAAAA
*
281231 AA-AAAG
1 AAGAAAA
281237 AAGAAAA
1 AAGAAAA
281244 AAG
1 AAG
281247 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 5 0.13
7 18 0.46
8 16 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Done.