Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008419.1 Hibiscus syriacus cultivar Beakdansim tig00111199_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: 1038719
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 5
Found at i:210183 original size:106 final size:103
Alignment explanation
Indices: 209958--210276 Score: 381
Period size: 105 Copynumber: 3.0 Consensus size: 103
209948 TTTATTTTTT
* * *
209958 AGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTGAAAACAAATTCGAAATTTGTATTCTC
1 AGAAAACAACCTCAAATGAGATCAACTTTGTTTAATGTG-AAACAAATTCAAAATTTGTA-TCTC
*
210023 AAAGGAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAA
64 AAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
* * * * * * * *
210063 AAAAAACAATCTCAAGTGAGATTAATTTTTGTTT-CTAGTGAATCAAATTCAAAATTTGTATATC
1 AGAAAACAACCTCAAATGAGATCAA-CTTTGTTTAAT-GTGAAACAAATTCAAAATTTGTATCTC
* * *
210127 AAAGGAAAAAAATGTCTCGAGCAAGACGAAGTTTGTTTT-AA
64 AAAGG--AAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
*** *
210168 GAGAAAGTGACCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCA
1 -AGAAAACAACCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCA
*
210233 AAGGAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAA
65 AAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
210272 AGAAA
1 AGAAA
210277 TTGTCTCAAG
Statistics
Matches: 180, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
103 33 0.18
104 10 0.06
105 80 0.44
106 57 0.32
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (103 bp):
AGAAAACAACCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAA
AGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA
Found at i:210660 original size:4 final size:4
Alignment explanation
Indices: 210651--211203 Score: 1011
Period size: 4 Copynumber: 138.8 Consensus size: 4
210641 TTTATGTATC
*
210651 ATGT ATGT ATG- -TGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
210697 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
210745 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
210793 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
210841 ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
210889 ATGT ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
210937 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
210985 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
211033 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
211081 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
211129 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
211177 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
211204 CTTTTCTCAA
Statistics
Matches: 537, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
2 2 0.00
4 535 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:212390 original size:21 final size:23
Alignment explanation
Indices: 212355--212397 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
212345 TGTCTGTGCT
212355 ATTTTTCCACTTTTTGTTCTTTG
1 ATTTTTCCACTTTTTGTTCTTTG
*
212378 ATTTTT-C-CTTTTTTTTCTTT
1 ATTTTTCCACTTTTTGTTCTTT
212398 TCTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.07, C:0.16, G:0.05, T:0.72
Consensus pattern (23 bp):
ATTTTTCCACTTTTTGTTCTTTG
Found at i:212394 original size:10 final size:9
Alignment explanation
Indices: 212364--212416 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
212354 TATTTTTCCA
*
212364 CTTTTTGTT
1 CTTTTTTTT
212373 CTTTGATTTTT
1 CTTT--TTTTT
212384 CCTTTTTTTT
1 -CTTTTTTTT
212394 CTTTTCTTTT
1 CTTTT-TTTT
212404 C-TTTTTTT
1 CTTTTTTTT
212412 CTTTT
1 CTTTT
212417 CTTTGCTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 5 0.13
9 15 0.39
10 10 0.26
11 4 0.11
12 4 0.11
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:212400 original size:5 final size:5
Alignment explanation
Indices: 212380--212420 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
212370 GTTCTTTGAT
212380 TTTTCC TTTT- TTTTC TTTTC TTTTC -TTT- TTTTC TTTTC TTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
212421 GCTGTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
4 10 0.31
5 18 0.56
6 4 0.12
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:212403 original size:21 final size:20
Alignment explanation
Indices: 212364--212420 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
212354 TATTTTTCCA
* **
212364 CTTTTTGTTCTTTGATTTTT
1 CTTTTTTTTCTTTTCTTTTT
212384 CCTTTTTTTTCTTTTC-TTTT
1 -CTTTTTTTTCTTTTCTTTTT
212404 C-TTTTTTTCTTTTCTTT
1 CTTTTTTTTCTTTTCTTT
212421 GCTGTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
20 4 0.12
21 12 0.38
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (20 bp):
CTTTTTTTTCTTTTCTTTTT
Found at i:212411 original size:13 final size:13
Alignment explanation
Indices: 212379--212420 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
212369 TGTTCTTTGA
* *
212379 TTTTTCCTTTTTT
1 TTTTTTCTTTTCT
212392 TTCTTTTCTTTTCT
1 TT-TTTTCTTTTCT
212406 TTTTTTCTTTTCT
1 TTTTTTCTTTTCT
212419 TT
1 TT
212421 GCTGTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:212436 original size:30 final size:33
Alignment explanation
Indices: 212400--212487 Score: 103
Period size: 34 Copynumber: 2.7 Consensus size: 33
212390 TTTTCTTTTC
*
212400 TTTTCTTT-TTT-TCTTT-TCTTTGCTGTTTG-T
1 TTTTCTTTGTTTAT-TTTCTCTTTGCTCTTTGAT
212430 TTTTCTTTGTTTATTTTCTCTTTGCTCTTTGACT
1 TTTTCTTTGTTTATTTTCTCTTTGCTCTTTGA-T
* *
212464 TTTTCTTTGCTCATTTTCTCTTTG
1 TTTTCTTTGTTTATTTTCTCTTTG
212488 TTTTTTTTCG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 8 0.16
31 6 0.12
32 13 0.26
34 23 0.46
ACGTcount: A:0.03, C:0.17, G:0.09, T:0.70
Consensus pattern (33 bp):
TTTTCTTTGTTTATTTTCTCTTTGCTCTTTGAT
Found at i:212453 original size:15 final size:15
Alignment explanation
Indices: 212423--212496 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
212413 TTTTCTTTGC
*
212423 TGTTTGTTTT-TCTT
1 TGTTTATTTTCTCTT
212437 TGTTTATTTTCTCTT
1 TGTTTATTTTCTCTT
212452 TGCTCTTTGACTTTT-TCTT
1 TG---TTT-A-TTTTCTCTT
* *
212471 TGCTCATTTTCTCTT
1 TGTTTATTTTCTCTT
*
212486 TGTTTTTTTTC
1 TGTTTATTTTC
212497 GTTCTCTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
14 13 0.28
15 19 0.40
16 1 0.02
18 3 0.06
19 7 0.15
20 4 0.09
ACGTcount: A:0.04, C:0.16, G:0.09, T:0.70
Consensus pattern (15 bp):
TGTTTATTTTCTCTT
Found at i:217846 original size:34 final size:32
Alignment explanation
Indices: 217789--217860 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
217779 CTTGGCTTGC
*
217789 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTCT
217820 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
217854 TTTCTTT
1 TTTCTTT
217861 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:218599 original size:19 final size:21
Alignment explanation
Indices: 218549--218600 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
218539 GAAACCCCTT
218549 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
218570 TTAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
218589 TGAAGATACATG
1 TGAAAATACATG
218601 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:222816 original size:19 final size:15
Alignment explanation
Indices: 222774--222808 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
222764 CATAAGAATT
222774 GAAAATAAAGTGCTC
1 GAAAATAAAGTGCTC
222789 GAAAATAAAGTGCTC
1 GAAAATAAAGTGCTC
222804 GAAAA
1 GAAAA
222809 CAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.17
Consensus pattern (15 bp):
GAAAATAAAGTGCTC
Found at i:223961 original size:21 final size:22
Alignment explanation
Indices: 223911--223961 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
223901 TAAAGTGATC
* *
223911 AATAATAACAAAATTGGTAGAA
1 AATAATAATAAAACTGGTAGAA
*
223933 AA-AGTAATAAAACTGGTA-AA
1 AATAATAATAAAACTGGTAGAA
223953 AATAATAAT
1 AATAATAAT
223962 GTTTTTGGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.24
Consensus pattern (22 bp):
AATAATAATAAAACTGGTAGAA
Found at i:224293 original size:86 final size:86
Alignment explanation
Indices: 224146--224321 Score: 289
Period size: 86 Copynumber: 2.0 Consensus size: 86
224136 TAAAAAGTGC
* * * * *
224146 CTTAATAAAAGCTAAAGAAGTGTGACCGTCTGTCTGGTTATGAAGAAAATATATGATAATAGAAA
1 CTTAATAAAAGCTAAAGAAGCGTGACCGTATGTCTGATCATGAAGAAAATATATGAGAATAGAAA
224211 TTCTACTAAAAGATAAGCTCT
66 TTCTACTAAAAGATAAGCTCT
* *
224232 CTTAATAAAAGCTAAGGAAGCGTGATCGTATGTCTGATCATGAAGAAAATATATGAGAATAGAAA
1 CTTAATAAAAGCTAAAGAAGCGTGACCGTATGTCTGATCATGAAGAAAATATATGAGAATAGAAA
224297 TTCTACTAAAAGATAAGCTCT
66 TTCTACTAAAAGATAAGCTCT
224318 CTTA
1 CTTA
224322 TATATTTTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (86 bp):
CTTAATAAAAGCTAAAGAAGCGTGACCGTATGTCTGATCATGAAGAAAATATATGAGAATAGAAA
TTCTACTAAAAGATAAGCTCT
Found at i:224681 original size:16 final size:14
Alignment explanation
Indices: 224660--224704 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 14
224650 TTTAAATTTC
224660 AAATATAAAAATATT
1 AAATATAAAAA-ATT
224675 GAAATATTCAAAAAATT
1 -AAATA-T-AAAAAATT
224692 AAATATAAAAAAT
1 AAATATAAAAAAT
224705 ACTAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.26
15 1 0.04
16 10 0.37
17 4 0.15
18 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
AAATATAAAAAATT
Found at i:224721 original size:32 final size:31
Alignment explanation
Indices: 224660--224726 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
224650 TTTAAATTTC
**
224660 AAATATAAAAATATTGAAATATTCAAAAAATT
1 AAATATAAAAATATAAAAATATT-AAAAAATT
224692 AAATATAAAAAATACTAAAAATATT-AAAAATT
1 AAATAT-AAAAATA-TAAAAATATTAAAAAATT
224724 AAA
1 AAA
224727 AAATTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 16 0.52
33 7 0.23
34 8 0.26
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (31 bp):
AAATATAAAAATATAAAAATATTAAAAAATT
Found at i:225051 original size:24 final size:24
Alignment explanation
Indices: 225023--225069 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
225013 ATAATTAGAA
225023 AACATAATAAGCT-TCGACTAATTC
1 AACATAAT-AGCTCTCGACTAATTC
* *
225047 AACATTATAGGTCTCGACTAATT
1 AACATAATAGCTCTCGACTAATT
225070 TAAATTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (24 bp):
AACATAATAGCTCTCGACTAATTC
Found at i:225144 original size:7 final size:7
Alignment explanation
Indices: 225125--225176 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
225115 AGTGTTGATA
225125 ATATGTAT
1 ATATGT-T
225133 ATATGTT
1 ATATGTT
225140 ATATG-T
1 ATATGTT
225146 ATATGTT
1 ATATGTT
225153 ATATG-T
1 ATATGTT
*
225159 ATATTTT
1 ATATGTT
*
225166 ATATGTA
1 ATATGTT
225173 ATAT
1 ATAT
225177 ATCAGTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
6 11 0.28
7 22 0.56
8 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (7 bp):
ATATGTT
Found at i:225150 original size:13 final size:13
Alignment explanation
Indices: 225132--225172 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
225122 ATAATATGTA
225132 TATATGTTATATG
1 TATATGTTATATG
225145 TATATGTTATATG
1 TATATGTTATATG
*
225158 TATATTTTATATG
1 TATATGTTATATG
225171 TA
1 TA
225173 ATATATCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TATATGTTATATG
Found at i:225241 original size:2 final size:2
Alignment explanation
Indices: 225234--225266 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
225224 TATAACCTAT
225234 TA TA TA 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 TA TA TA T
225267 TAGTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:225323 original size:24 final size:24
Alignment explanation
Indices: 225296--225351 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
225286 ATATATATTC
**
225296 AATTTTTTTAGTAATTTAATTTTT
1 AATTTTTTTAGTAATTTAACATTT
* *
225320 AA--TTTTTAGTATTTTTACATTT
1 AATTTTTTTAGTAATTTAACATTT
225342 AATTTTTTTA
1 AATTTTTTTA
225352 AAAAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 18 0.69
24 8 0.31
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (24 bp):
AATTTTTTTAGTAATTTAACATTT
Found at i:225818 original size:57 final size:57
Alignment explanation
Indices: 225723--225858 Score: 209
Period size: 57 Copynumber: 2.4 Consensus size: 57
225713 CGATTTTAAC
* *
225723 CAACTATCGCAACGCGAATTCCTTTTTCGCAACACTAATTACCGCTATAGGTAAACA
1 CAACTATCGCAACGCGAATTTCTTTTTCGCAACACTAATTACCGATATAGGTAAACA
* * *
225780 CAACTATCGCAACGCGAATTTCTTTTTCGCCACGCTAATTACTGATATAGGTAAACA
1 CAACTATCGCAACGCGAATTTCTTTTTCGCAACACTAATTACCGATATAGGTAAACA
* *
225837 TAACTATTGCAACGCGAATTTC
1 CAACTATCGCAACGCGAATTTC
225859 GCAAATCGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (57 bp):
CAACTATCGCAACGCGAATTTCTTTTTCGCAACACTAATTACCGATATAGGTAAACA
Found at i:226301 original size:13 final size:14
Alignment explanation
Indices: 226283--226311 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
226273 TTGTCAAATT
226283 CGGATTTTTT-TAC
1 CGGATTTTTTCTAC
226296 CGGATTTTTTCTAC
1 CGGATTTTTTCTAC
226310 CG
1 CG
226312 TGTTTACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (14 bp):
CGGATTTTTTCTAC
Found at i:226474 original size:57 final size:57
Alignment explanation
Indices: 226358--226553 Score: 306
Period size: 57 Copynumber: 3.5 Consensus size: 57
226348 CGAATTCGAT
* *
226358 TTGCGAAAACGAAATTCGTGTTGCGATAG-TGTGTTTACCTATATCGGTAATTAGCG
1 TTGCGAAAACGAAATTCGCGTTGCGATAGTTGTGTTTACCTATAGCGGTAATTAGCG
* *
226414 TTGCGAAAAAGAAATTCGCGTTGCGATAGTTGTGTTTACCTATAGCAGTAATTAGCG
1 TTGCGAAAACGAAATTCGCGTTGCGATAGTTGTGTTTACCTATAGCGGTAATTAGCG
* *
226471 TTGCGAGAACGAAATTCGCGTTGCGATAGTTATGTTTACCTAT-GTCGGTAATTAGCG
1 TTGCGAAAACGAAATTCGCGTTGCGATAGTTGTGTTTACCTATAG-CGGTAATTAGCG
*
226528 TTGCGAAAACGAAATTCGCATTGCGA
1 TTGCGAAAACGAAATTCGCGTTGCGA
226554 ATTTGGACAC
Statistics
Matches: 128, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
56 28 0.22
57 100 0.78
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (57 bp):
TTGCGAAAACGAAATTCGCGTTGCGATAGTTGTGTTTACCTATAGCGGTAATTAGCG
Found at i:228834 original size:24 final size:24
Alignment explanation
Indices: 228802--228857 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
228792 GGATTGTGGG
228802 ATTCCCATGGGATGGGAATCCCAC
1 ATTCCCATGGGATGGGAATCCCAC
228826 ATTCCCATGGGATGGGAATCCCAC
1 ATTCCCATGGGATGGGAATCCCAC
228850 ATTCCCAT
1 ATTCCCAT
228858 ATTTGATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (24 bp):
ATTCCCATGGGATGGGAATCCCAC
Found at i:229426 original size:18 final size:19
Alignment explanation
Indices: 229403--229459 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 19
229393 CCAGTAATCC
229403 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
229421 TATTCCCACTGGTAATCTTT
1 TATT-CCACTGGTAATCTTT
229441 TATTCTCACTGGTAATCTT
1 TATTC-CACTGGTAATCTT
229460 ACATTCCGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 29 0.81
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:229465 original size:20 final size:20
Alignment explanation
Indices: 229409--229459 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
229399 ATCCTATTCC
229409 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
*
229429 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCCCA
229449 CTGGTAATCTT
1 CTGGTAATCTT
229460 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:229828 original size:40 final size:40
Alignment explanation
Indices: 229774--229849 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
229764 ATAAAATAAA
*
229774 AAAAGTGTAGCACTTAACACATACTTACACCGGTGTGACT
1 AAAAGTGTAGCACTTAACACATACTTACACCAGTGTGACT
* *
229814 AAAAGTGTATCACTTAACACATATTTACACCAGTGT
1 AAAAGTGTAGCACTTAACACATACTTACACCAGTGT
229850 AAGTATCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (40 bp):
AAAAGTGTAGCACTTAACACATACTTACACCAGTGTGACT
Found at i:235007 original size:95 final size:94
Alignment explanation
Indices: 234806--235068 Score: 343
Period size: 95 Copynumber: 2.8 Consensus size: 94
234796 AGAGTATCCT
*
234806 TACTACTAA-TCTAAGTAGTATCGATATCATATATGGTATCGGTACC-TTCTAGCATTCTGTTTT
1 TACTAC-AACTCTAAGTAGTATCGATATCATATATGGTATCGATACCATT-TAGCATTCTGTTTT
* * * * * *
234869 GACAGTATTGGTACTGCATCAGCAGTATCGG
64 GACAGTATCGGTACTACACCAGAAGCATCGA
* *
234900 TACTACTACTCTAAATAGTATCGATATCATATATGGTATCGATACCATGTTAGCATTCTGTTTTG
1 TACTACAACTCTAAGTAGTATCGATATCATATATGGTATCGATACCAT-TTAGCATTCTGTTTTG
*
234965 ACAGTATCGGTATTAC-CCGAGAAGCATCGA
65 ACAGTATCGGTACTACACC-AGAAGCATCGA
* *
234995 TATTACAACTCTAAGTAGTATCGATATCATATATGGTATCGATACCAATTTAGCATTATGTTTTG
1 TACTACAACTCTAAGTAGTATCGATATCATATATGGTATCGATACC-ATTTAGCATTCTGTTTTG
*
235060 ACGGTATCG
65 ACAGTATCG
235069 ATACCAATTT
Statistics
Matches: 149, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
93 1 0.01
94 42 0.28
95 103 0.69
96 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (94 bp):
TACTACAACTCTAAGTAGTATCGATATCATATATGGTATCGATACCATTTAGCATTCTGTTTTGA
CAGTATCGGTACTACACCAGAAGCATCGA
Found at i:235071 original size:33 final size:33
Alignment explanation
Indices: 235029--235107 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
235019 TATCATATAT
235029 GGTATCGATACCAATTTAGCATTATGTTTTGAC
1 GGTATCGATACCAATTTAGCATTATGTTTTGAC
235062 GGTATCGATACCAATTTAGCATTATGTTTTGAC
1 GGTATCGATACCAATTTAGCATTATGTTTTGAC
*
235095 AGTATCGATACCA
1 GGTATCGATACCA
235108 TAACTCAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (33 bp):
GGTATCGATACCAATTTAGCATTATGTTTTGAC
Found at i:235125 original size:21 final size:21
Alignment explanation
Indices: 235095--235140 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
235085 ATGTTTTGAC
235095 AGTATCGATACCA-TAACTCAG
1 AGTATCGATACCACT-ACTCAG
* *
235116 AGTATTGATACTACTACTCAG
1 AGTATCGATACCACTACTCAG
235137 AGTA
1 AGTA
235141 GTTAAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCACTACTCAG
Found at i:237556 original size:5 final size:5
Alignment explanation
Indices: 237546--237581 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
237536 GAGATAAGCC
237546 ATATG ATATG A-ATG ATATG ATATG A-ATG ATATG ATA
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATA
237582 AGAAGCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (5 bp):
ATATG
Found at i:237562 original size:9 final size:10
Alignment explanation
Indices: 237546--237581 Score: 58
Period size: 9 Copynumber: 3.8 Consensus size: 10
237536 GAGATAAGCC
237546 ATATGATATG
1 ATATGATATG
237556 A-ATGATATG
1 ATATGATATG
237565 ATATGA-ATG
1 ATATGATATG
237574 ATATGATA
1 ATATGATA
237582 AGAAGCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (10 bp):
ATATGATATG
Found at i:237565 original size:14 final size:14
Alignment explanation
Indices: 237546--237581 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
237536 GAGATAAGCC
237546 ATATGATATGAATG
1 ATATGATATGAATG
237560 ATATGATATGAATG
1 ATATGATATGAATG
237574 ATATGATA
1 ATATGATA
237582 AGAAGCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.36
Consensus pattern (14 bp):
ATATGATATGAATG
Found at i:239629 original size:13 final size:13
Alignment explanation
Indices: 239613--239638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
239603 TGAGATAATG
239613 TTGAGAGAGGGTT
1 TTGAGAGAGGGTT
239626 TTGAGAGAGGGTT
1 TTGAGAGAGGGTT
239639 CAACGATTGA
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:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (13 bp):
TTGAGAGAGGGTT
Found at i:239884 original size:20 final size:20
Alignment explanation
Indices: 239812--239884 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
239802 ATAGTAATAG
*
239812 TATCGATACTGGATGAACAA
1 TATCGATACTAGATGAACAA
* *
239832 TATCGATACTAAGAAAGAATAA
1 TATCGATACT-AG-ATGAACAA
239854 TATCGATACTAGATGAACAA
1 TATCGATACTAGATGAACAA
239874 TATCGATACTA
1 TATCGATACTA
239885 TGTGCACAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
22 16 0.35
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (20 bp):
TATCGATACTAGATGAACAA
Found at i:240503 original size:80 final size:80
Alignment explanation
Indices: 240410--240570 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
240400 AGATTGTCAG
* *
240410 TGATGAAGAAGATGATCCCATGGACCTCTTTCTTTCGGTTCTGAGGAAAATTATTGTGAAGGTGA
1 TGATGAAGAAGATGATCCCATGGACCTCTTTCTTTCAGTTCTGAGGAAAATTATTGTGAAAGTGA
240475 CACTTGATCCCAACT
66 CACTTGATCCCAACT
240490 TGATGAAGAAGATGATCCCATGGACCTCTTTCTTTCAGTTCTGAGGAAAATTATTGTGAAAGTGA
1 TGATGAAGAAGATGATCCCATGGACCTCTTTCTTTCAGTTCTGAGGAAAATTATTGTGAAAGTGA
240555 CACTTGATCCCAACT
66 CACTTGATCCCAACT
240570 T
1 T
240571 TTTCCTTCCC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (80 bp):
TGATGAAGAAGATGATCCCATGGACCTCTTTCTTTCAGTTCTGAGGAAAATTATTGTGAAAGTGA
CACTTGATCCCAACT
Found at i:249752 original size:17 final size:18
Alignment explanation
Indices: 249730--249763 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
249720 TCTTTAATGT
249730 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
249747 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
249764 TATTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:249795 original size:29 final size:30
Alignment explanation
Indices: 249730--249800 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
249720 TCTTTAATGT
249730 ATATTTTA-TT-ATATTTAATATTTTGTTA
1 ATATTTTATTTAATATTTAATATTTTGTTA
*
249758 GTATTTTATTTAACTATTTAA-ATTTT-TTA
1 ATATTTTATTTAA-TATTTAATATTTTGTTA
249787 ATATTTTATTTAAT
1 ATATTTTATTTAAT
249801 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 17 0.45
30 6 0.16
31 7 0.18
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (30 bp):
ATATTTTATTTAATATTTAATATTTTGTTA
Found at i:253398 original size:31 final size:31
Alignment explanation
Indices: 253360--253453 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
253350 AGGGTCGAGG
253360 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
253391 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
253422 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
253453 G
1 G
253454 GTCTTTCGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:257429 original size:31 final size:31
Alignment explanation
Indices: 257391--257471 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
257381 AGGGTCGAGG
257391 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
* *
257422 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
*
257453 GTTTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
257472 AATCTATGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATAGACT
Found at i:261665 original size:22 final size:21
Alignment explanation
Indices: 261640--261691 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
261630 GAACGAAAAT
**
261640 ATAACATAAATTTTTTTTACAC
1 ATAACATAAA-TAATTTTACAC
*
261662 ATAAACGTAAATAATTTTACAC
1 AT-AACATAAATAATTTTACAC
261684 ATAA-ATAA
1 ATAACATAA
261692 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 13 0.52
23 7 0.28
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAACATAAATAATTTTACAC
Found at i:261690 original size:16 final size:14
Alignment explanation
Indices: 261669--261710 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
261659 CACATAAACG
261669 TAAATAATTTTACACA
1 TAAATAATTTTA-A-A
261685 TAAATAA-TTTAAA
1 TAAATAATTTTAAA
261698 TAATATAATTTTA
1 TAA-ATAATTTTA
261711 TATTATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 5 0.21
15 8 0.33
16 7 0.29
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATAATTTTAAA
Found at i:273513 original size:16 final size:17
Alignment explanation
Indices: 273485--273520 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
273475 TAATTAATTA
273485 TTTTTATTCTAATATTT
1 TTTTTATTCTAATATTT
273502 TTTTTATT-TAATATTT
1 TTTTTATTCTAATATTT
273518 TTT
1 TTT
273521 AAAGTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATTCTAATATTT
Found at i:273521 original size:14 final size:16
Alignment explanation
Indices: 273485--273520 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
273475 TAATTAATTA
273485 TTTTTATTCTAATATTT
1 TTTTTATTCTAATA-TT
273502 TTTTTATT-TAATATT
1 TTTTTATTCTAATATT
273517 TTTT
1 TTTT
273521 AAAGTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATTCTAATATT
Found at i:273565 original size:15 final size:14
Alignment explanation
Indices: 273525--273639 Score: 56
Period size: 16 Copynumber: 7.7 Consensus size: 14
273515 TTTTTTAAAG
273525 TTATTATATATATAT
1 TTATTATAT-TATAT
*
273540 TTATAACTATTATAT
1 TTATTA-TATTATAT
*
273555 TTATTATTATTTTA-
1 TTATTA-TATTATAT
*
273569 TTATTA-ACGTATAT
1 TTATTATA-TTATAT
*
273583 ATA-TATATATATAT
1 TTATTATAT-TATAT
*
273597 ATATATATATATATAT
1 TTAT-TATAT-TATAT
*
273613 ATATATATATATATAT
1 TTAT-TATAT-TATAT
*
273629 ATATATATATT
1 TTAT-TATATT
273640 CTTTTTTACT
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 17 0.20
15 22 0.26
16 40 0.47
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.55
Consensus pattern (14 bp):
TTATTATATTATAT
Found at i:273585 original size:2 final size:2
Alignment explanation
Indices: 273578--273638 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
273568 ATTATTAACG
273578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
273620 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
273639 TCTTTTTTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:273931 original size:4 final size:4
Alignment explanation
Indices: 273917--274024 Score: 69
Period size: 4 Copynumber: 26.2 Consensus size: 4
273907 TACTTTTTTC
* * *
273917 TTAT CTTAT TTAT TTAT CTAT TTAT TTAA TTAT TTAT TTAT TT-T TTCT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * *
273965 TCTCT TTAT TT-T TATAT TTCCT TTAT CT-T TGAT TTAT TTACT CATAT
1 T-TAT TTAT TTAT T-TAT TT-AT TTAT TTAT TTAT TTAT TTA-T -TTAT
274012 TTAT TTAT TTAT T
1 TTAT TTAT TTAT T
274025 CATGTATATA
Statistics
Matches: 82, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
3 6 0.07
4 59 0.72
5 15 0.18
6 2 0.02
ACGTcount: A:0.21, C:0.09, G:0.01, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:284391 original size:9 final size:9
Alignment explanation
Indices: 284377--284412 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
284367 GCCCTAAGTT
284377 GAAAAAAAA
1 GAAAAAAAA
284386 GAAAAAAAA
1 GAAAAAAAA
*
284395 GGAAAAAAA
1 GAAAAAAAA
*
284404 CAAAAAAAA
1 GAAAAAAAA
284413 TTGTTTATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:284510 original size:29 final size:30
Alignment explanation
Indices: 284451--284510 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
284441 CCCTAAATTG
* *
284451 AAAAAAGAAAAGGAAAAGAGAAAAAAGATA
1 AAAAAACAAAAGGAAAAGAGAAAAAAAATA
284481 AAAAAACAAAA-GAAAA-AGAAAAGAAAATA
1 AAAAAACAAAAGGAAAAGAGAAAA-AAAATA
284510 A
1 A
284511 GGTGGGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 11 0.41
30 10 0.37
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (30 bp):
AAAAAACAAAAGGAAAAGAGAAAAAAAATA
Found at i:285908 original size:106 final size:105
Alignment explanation
Indices: 285592--285983 Score: 443
Period size: 99 Copynumber: 3.8 Consensus size: 105
285582 ATCGTGCACA
* *
285592 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGT---C-AAC--TTTCCAATT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCAATT
* * *
285651 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTCGACC
66 TCAGATCCAATTTCAACTTCACAACGAAAGATATTAGACC
* * *
285691 CAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAACAAATAA----C--TT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCAATT
* * *
285750 TCAGAGT-CAATTTTAACTTCACAACG-AAGTATATTGGACT
66 TCAGA-TCCAATTTCAACTTCACAACGAAAG-ATATTAGACC
* * * * *
285790 CAAGACAGCACAAGCTTAACTTCACGGCGAAGGGGCGGCTGACTGTTAATAAACAATTCCCCAAT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATT-TCCAAT
* **
285855 TTTAGATCCAATTTCAACTTCACAGTGAAAGATATTAGACC
65 TTCAGATCCAATTTCAACTTCACAACGAAAGATATTAGACC
* *
285896 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAACAATTTTCCAGT
1 CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAA-TTTCCAAT
* *
285961 TCCAGAACCAATTTCAACTTCAC
65 TTCAGATCCAATTTCAACTTCAC
285984 GACGGAGGAT
Statistics
Matches: 242, Mismatches: 33, Indels: 29
0.80 0.11 0.10
Matches are distributed among these distances:
98 2 0.01
99 124 0.51
101 1 0.00
102 1 0.00
103 2 0.01
104 1 0.00
105 1 0.00
106 105 0.43
107 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAAGACAACACAAGCTCAACTTCACGGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCAATT
TCAGATCCAATTTCAACTTCACAACGAAAGATATTAGACC
Found at i:287872 original size:17 final size:17
Alignment explanation
Indices: 287850--287883 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
287840 ATATATATTA
287850 ATTATTTTTATTCTAAT
1 ATTATTTTTATTCTAAT
*
287867 ATTATTTTTATTTTAAT
1 ATTATTTTTATTCTAAT
287884 GTTTTTTAAA
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:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATTTTTATTCTAAT
Found at i:287931 original size:53 final size:57
Alignment explanation
Indices: 287866--287973 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 57
287856 TTTATTCTAA
* *
287866 TATTATTTTTATT-TTAATGTT-TT-TTAAAGT-TAT-TATATATATATATTTATAAC
1 TATTATATTTATTATT-ATGTTATTATTAAAGTATATATATATATATATATATATAAC
* *
287919 TATTATATTTATTATTATTTTATTATTAACGTATATATATATATATATATATATA
1 TATTATATTTATTATTATGTTATTATTAAAGTATATATATATATATATATATATA
287974 TATATATTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 16 0.35
54 4 0.09
55 6 0.13
56 3 0.07
57 17 0.37
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (57 bp):
TATTATATTTATTATTATGTTATTATTAAAGTATATATATATATATATATATATAAC
Found at i:287957 original size:2 final size:2
Alignment explanation
Indices: 287950--287980 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
287940 ATTATTAACG
287950 TA TA 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 TA TA T
287981 TCTTTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:288259 original size:24 final size:24
Alignment explanation
Indices: 288232--288309 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
288222 TATGTACATA
*
288232 TTATTTCTTTACTTTTTTCTTATC
1 TTATTTATTTACTTTTTTCTTATC
*
288256 TTATTTATTTATCTATTTAT-TTA-C
1 TTATTTATTTA-CT-TTTTTCTTATC
* *
288280 TTATTTATATA-TTTTTTCTTCTC
1 TTATTTATTTACTTTTTTCTTATC
288303 TTTATTT
1 -TTATTT
288310 TTCTATTTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.09
22 3 0.07
23 1 0.02
24 27 0.61
25 5 0.11
26 4 0.09
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTTATTTACTTTTTTCTTATC
Found at i:288265 original size:4 final size:4
Alignment explanation
Indices: 288251--288381 Score: 61
Period size: 4 Copynumber: 31.8 Consensus size: 4
288241 TACTTTTTTC
* * * *
288251 TTAT CTTAT TTAT TTAT CTAT TTAT TTAC TTAT TTAT ATAT TT-T TTCT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * *
288299 TCTCT TTAT TT-T TCTAT TTCCT TTAT CT-T TGAT TTAT TTACT CATAT
1 T-TAT TTAT TTAT T-TAT TT-AT TTAT TTAT TTAT TTAT TTA-T -TTAT
* * * *
288346 TTAT TTAT TTCT TTAT TCAT GTAT ATAT TGTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTA
288382 AATCTATGAC
Statistics
Matches: 95, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
3 6 0.06
4 68 0.72
5 19 0.20
6 2 0.02
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:294649 original size:22 final size:22
Alignment explanation
Indices: 294624--294668 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
294614 ACTCTATGAC
294624 TTGATGCTTTGTGAATTATTCT
1 TTGATGCTTTGTGAATTATTCT
294646 TTGATGCTTTGTGAATTATTCT
1 TTGATGCTTTGTGAATTATTCT
294668 T
1 T
294669 ACACGATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.56
Consensus pattern (22 bp):
TTGATGCTTTGTGAATTATTCT
Found at i:295706 original size:41 final size:40
Alignment explanation
Indices: 295647--295728 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
295637 TGGCCTTGCT
* *
295647 TATTTAATAAAAAGGCCAGGCCTAGGCCTTTTTAAAAGCC
1 TATTTAATAAAAAGGCCAGGCCTAGGCCTATTAAAAAGCC
* *
295687 TATTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAAGCC
1 TATTTAA-TAAAAAGGCCAGGCCTAGGCCTATTAAAAAGCC
295728 T
1 T
295729 TATAAGCCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 7 0.19
41 30 0.81
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (40 bp):
TATTTAATAAAAAGGCCAGGCCTAGGCCTATTAAAAAGCC
Found at i:295891 original size:17 final size:17
Alignment explanation
Indices: 295869--295901 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
295859 AACTTTTAAA
295869 CAGGCTTTTAAACAGGT
1 CAGGCTTTTAAACAGGT
295886 CAGGCTTTTAAACAGG
1 CAGGCTTTTAAACAGG
295902 CCCAGGCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (17 bp):
CAGGCTTTTAAACAGGT
Found at i:297916 original size:32 final size:32
Alignment explanation
Indices: 297879--297964 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 32
297869 ACAACAGTAC
*
297879 CAGTGTTGTATTCAGATAATGCACAAT-AGTGT
1 CAGTGTTGCATTCAGATAATGCAC-ATCAGTGT
* *
297911 TAGTGTTGCATTCAGATAGTGC-CATCAGTGT
1 CAGTGTTGCATTCAGATAATGCACATCAGTGT
* *
297942 CAATGTTGCATTTAGATAATGCA
1 CAGTGTTGCATTCAGATAATGCA
297965 TAAAACTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 24 0.53
32 19 0.42
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (32 bp):
CAGTGTTGCATTCAGATAATGCACATCAGTGT
Found at i:309211 original size:2 final size:2
Alignment explanation
Indices: 309199--309235 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
309189 TATTAGAAAA
309199 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
309236 TAAATTACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:310278 original size:2 final size:2
Alignment explanation
Indices: 310271--310315 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
310261 GCAAATTTAA
310271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
310313 AT A
1 AT A
310316 ATTGAGTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:313383 original size:40 final size:40
Alignment explanation
Indices: 313326--313407 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
313316 TGCAAGTTTA
* * *
313326 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACAATTCGATGTATATGGTGGACACAACCTTATGTG
* *
313366 TAATACAATTCGATGTATATGGTGGACACGATCTTATGTG
1 TAATACAATTCGATGTATATGGTGGACACAACCTTATGTG
313406 TA
1 TA
313408 GCACTACGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (40 bp):
TAATACAATTCGATGTATATGGTGGACACAACCTTATGTG
Found at i:313644 original size:45 final size:45
Alignment explanation
Indices: 313506--313716 Score: 309
Period size: 45 Copynumber: 4.7 Consensus size: 45
313496 GGTAATCATG
* * *
313506 AAAATAAGCCTATGAGCTTATGGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* ** *
313550 AAAATAAGGTTACGAGCTTATATAACAAAT-GTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
313594 AAAATAAGCTTACGAGCTTGTGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
313639 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
313684 AAAATAAGCTTACAAGCTTATGGGATAAATGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGT
313717 GAGAAATTTT
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
44 58 0.39
45 91 0.61
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:313656 original size:89 final size:90
Alignment explanation
Indices: 313506--313716 Score: 309
Period size: 89 Copynumber: 2.4 Consensus size: 90
313496 GGTAATCATG
* * * *
313506 AAAATAAGCCTATGAGCTTATGGAAT-AATGGCAAGTATATTGGTAAAATAAGGTTACGAGCTTA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
313570 TATAACAAAT-GTAAGTATATTGGT
66 TAGAACAAATGGTAAGTATATTGGT
*
313594 AAAATAAGCTTACGAGCTTGTGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * *
313659 TGGAATAAATGGTAAGTATTTTGGT
66 TAGAACAAATGGTAAGTATATTGGT
* *
313684 AAAATAAGCTTACAAGCTTATGGGATAAATGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGT
313717 GAGAAATTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
88 23 0.21
89 43 0.39
90 43 0.39
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (90 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TAGAACAAATGGTAAGTATATTGGT
Found at i:317298 original size:10 final size:10
Alignment explanation
Indices: 317283--317320 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
317273 GTCTAAGAGC
317283 TCATATAGGA
1 TCATATAGGA
317293 TCATATA-GA
1 TCATATAGGA
*
317302 TGCATTTAGGA
1 T-CATATAGGA
317313 TCATATAG
1 TCATATAG
317321 TTGCATGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (10 bp):
TCATATAGGA
Found at i:317313 original size:20 final size:20
Alignment explanation
Indices: 317288--317326 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
317278 AGAGCTCATA
317288 TAGGATCATATAGATGCATT
1 TAGGATCATATAGATGCATT
*
317308 TAGGATCATATAGTTGCAT
1 TAGGATCATATAGATGCAT
317327 GTGGTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
TAGGATCATATAGATGCATT
Found at i:323617 original size:20 final size:20
Alignment explanation
Indices: 323588--323626 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
323578 AGAGCTCATA
*
323588 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
323608 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
323627 ATGGTGAAAG
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:328545 original size:39 final size:39
Alignment explanation
Indices: 328466--328547 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
328456 CGTTTATGTG
* * *
328466 CGTTTATTAAATGAACGAACATGAACAAGATTTTGTGTT
1 CGTTTATTAAATGAACGAACATGAACAAGAGTCTGCGTT
*
328505 CGTTTAATTAAATGAACGAACGTGAACATAG-GTCT-CGTT
1 CGTTT-ATTAAATGAACGAACATGAACA-AGAGTCTGCGTT
328544 CGTT
1 CGTT
328548 CATTTACGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 12 0.32
40 23 0.62
41 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (39 bp):
CGTTTATTAAATGAACGAACATGAACAAGAGTCTGCGTT
Found at i:328562 original size:33 final size:33
Alignment explanation
Indices: 328525--328597 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
328515 AATGAACGAA
328525 CGTGAACATAGGTCTCGTTCGTTCATTTACGTT
1 CGTGAACATAGGTCTCGTTCGTTCATTTACGTT
328558 CGTGAACATAGGTCTCGTTCGTTCATTTACGTT
1 CGTGAACATAGGTCTCGTTCGTTCATTTACGTT
328591 CGTGAAC
1 CGTGAAC
328598 GTTCGGTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (33 bp):
CGTGAACATAGGTCTCGTTCGTTCATTTACGTT
Found at i:328621 original size:14 final size:14
Alignment explanation
Indices: 328597--328652 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
328587 CGTTCGTGAA
*
328597 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
*
328611 TGTTCGATTATGTT
1 CGTTCGATTATGTT
*
328625 CGTTCGTTTATGTT
1 CGTTCGATTATGTT
*
328639 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
328653 TAACCCAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:329748 original size:16 final size:15
Alignment explanation
Indices: 329727--329778 Score: 77
Period size: 16 Copynumber: 3.3 Consensus size: 15
329717 GTCTCCAACG
329727 TTTATGTTCGTGTTC
1 TTTATGTTCGTGTTC
329742 ATTTATGTTCGTGTTC
1 -TTTATGTTCGTGTTC
*
329758 GTTATGTTCGTGTTC
1 TTTATGTTCGTGTTC
329773 GTTTAT
1 -TTTAT
329779 TTATTAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 14 0.42
16 19 0.58
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.58
Consensus pattern (15 bp):
TTTATGTTCGTGTTC
Found at i:329764 original size:15 final size:15
Alignment explanation
Indices: 329728--329775 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
329718 TCTCCAACGT
*
329728 TTATGTTCGTGTTCAT
1 TTATGTTCGTGTTC-G
329744 TTATGTTCGTGTTCG
1 TTATGTTCGTGTTCG
329759 TTATGTTCGTGTTCG
1 TTATGTTCGTGTTCG
329774 TT
1 TT
329776 TATTTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.56
Consensus pattern (15 bp):
TTATGTTCGTGTTCG
Found at i:329866 original size:16 final size:16
Alignment explanation
Indices: 329845--329877 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
329835 AAAAAAAATT
329845 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
329861 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
329877 T
1 T
329878 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:331377 original size:25 final size:24
Alignment explanation
Indices: 331345--331392 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
331335 TTATGTTAAA
331345 AATGAATTTATAATAATTTAAAAAG
1 AATGAATTTATAA-AATTTAAAAAG
*
331370 AATGAATTTATAAAATTTTAAAA
1 AATGAATTTATAAAATTTAAAAA
331393 TATAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
AATGAATTTATAAAATTTAAAAAG
Found at i:331457 original size:8 final size:8
Alignment explanation
Indices: 331430--331457 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
331420 ATAAAAATAT
331430 TTTTAAAA
1 TTTTAAAA
331438 TTTTAAAA
1 TTTTAAAA
331446 TTTTAAAA
1 TTTTAAAA
331454 TTTT
1 TTTT
331458 CAGGAAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:333302 original size:209 final size:209
Alignment explanation
Indices: 332942--333359 Score: 809
Period size: 209 Copynumber: 2.0 Consensus size: 209
332932 ATTCGTTTGT
* *
332942 AAGGATTTGAGAGTCAATTACATGTGGGGAATGGTAAACACCCCCACAACATCCAAAATTGATAC
1 AAGGATTTGAGAGTCAATTACACGTGGGGAAGGGTAAACACCCCCACAACATCCAAAATTGATAC
333007 TTCTTGGTTATATATTGTCTAAGTAGTGGAACTTTATATATTCAAATCTAAAATTTAAATTACGA
66 TTCTTGGTTATATATTGTCTAAGTAGTGGAACTTTATATATTCAAATCTAAAATTTAAATTACGA
333072 TCCTTTTATTTCGATGAATTTAGAAAACGAGTGAATTTTTTTAAAAAAATATTCGTCTCAATGAA
131 TCCTTTTATTTCGATGAATTTAGAAAACGAGTGAATTTTTTTAAAAAAATATTCGTCTCAATGAA
*
333137 AAGTATTTAGTTCA
196 AAGTATTTAATTCA
333151 AAGGATTTGAGAGTCAATTACACGTGGGGAAGGGTAAACACCCCCACAACATCCAAAATTGATAC
1 AAGGATTTGAGAGTCAATTACACGTGGGGAAGGGTAAACACCCCCACAACATCCAAAATTGATAC
333216 TTCTTGGTTATATATTGTCTAAGTAGTGGAACTTTATATATTCAAATCTAAAATTTAAATTACGA
66 TTCTTGGTTATATATTGTCTAAGTAGTGGAACTTTATATATTCAAATCTAAAATTTAAATTACGA
333281 TCCTTTTATTTCGATGAATTTAGAAAACGAGTGAATTTTTTTAAAAAAATATTCGTCTCAATGAA
131 TCCTTTTATTTCGATGAATTTAGAAAACGAGTGAATTTTTTTAAAAAAATATTCGTCTCAATGAA
333346 AAGTATTTAATTCA
196 AAGTATTTAATTCA
333360 CCCGGTTTTA
Statistics
Matches: 206, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 206 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (209 bp):
AAGGATTTGAGAGTCAATTACACGTGGGGAAGGGTAAACACCCCCACAACATCCAAAATTGATAC
TTCTTGGTTATATATTGTCTAAGTAGTGGAACTTTATATATTCAAATCTAAAATTTAAATTACGA
TCCTTTTATTTCGATGAATTTAGAAAACGAGTGAATTTTTTTAAAAAAATATTCGTCTCAATGAA
AAGTATTTAATTCA
Found at i:333658 original size:17 final size:16
Alignment explanation
Indices: 333624--333663 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
333614 AAAACACAAT
333624 AAATATTTATTTATTA
1 AAATATTTATTTATTA
*
333640 AAATAATTTCATTTATAA
1 AAAT-ATTT-ATTTATTA
333658 AAATAT
1 AAATAT
333664 GAAAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTTATTTATTA
Found at i:338370 original size:16 final size:16
Alignment explanation
Indices: 338346--338376 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
338336 TATCTCTTAT
*
338346 TCTCTTGTTCATATAA
1 TCTCATGTTCATATAA
338362 TCTCATGTTCATATA
1 TCTCATGTTCATATA
338377 TCTTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
TCTCATGTTCATATAA
Found at i:338721 original size:18 final size:20
Alignment explanation
Indices: 338676--338751 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
338666 TGAATATTTT
338676 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTGATTG
* *
338696 TTCCGAAGAACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
* *
338714 TCCCGAAGGACCATTGTTTG
1 TCCCGAAGGACCACTGATTG
* *
338734 TCCTGAAAGACCACTGAT
1 TCCCGAAGGACCACTGAT
338752 AATCCCTCGA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.32
19 1 0.02
20 29 0.66
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATTG
Found at i:339665 original size:2 final size:2
Alignment explanation
Indices: 339658--339695 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
339648 CATGAATTAG
*
339658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
339696 GATTTACTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:343764 original size:21 final size:21
Alignment explanation
Indices: 343729--343786 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
343719 GTGGCACCTA
* *
343729 AGAAGTTGAAGGAGTTGAAGG
1 AGAAATTGCAGGAGTTGAAGG
*
343750 TGAAATTGCAGGAGTTGAAGG
1 AGAAATTGCAGGAGTTGAAGG
*
343771 AGAAATTGCAAGAGTT
1 AGAAATTGCAGGAGTT
343787 ATTGGATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.36, T:0.22
Consensus pattern (21 bp):
AGAAATTGCAGGAGTTGAAGG
Found at i:354729 original size:29 final size:29
Alignment explanation
Indices: 354662--354722 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
354652 CTCACAGTCC
354662 CTTTAATACAATCTACAATATCCTTAGTA
1 CTTTAATACAATCTACAATATCCTTAGTA
354691 CTTTAATACAATCTACAATATCCTTAGTA
1 CTTTAATACAATCTACAATATCCTTAGTA
354720 CTT
1 CTT
354723 CTATACACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (29 bp):
CTTTAATACAATCTACAATATCCTTAGTA
Found at i:356534 original size:28 final size:28
Alignment explanation
Indices: 356479--356534 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
356469 TGTTCCTTAG
* ** *
356479 AATTTTATAAGTTTAAGTTCGTCTCTAA
1 AATTTTATAAATTTAAGTTCACCCCTAA
356507 AATTTTATAAATTTAAGTTCACCCCTAA
1 AATTTTATAAATTTAAGTTCACCCCTAA
356535 CATAAAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (28 bp):
AATTTTATAAATTTAAGTTCACCCCTAA
Found at i:359653 original size:2 final size:2
Alignment explanation
Indices: 359646--359680 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
359636 CCAAACAAAT
359646 TA TA TA TA 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 TA TA TA TA T
359681 GATTAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:360137 original size:28 final size:28
Alignment explanation
Indices: 360095--360153 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
360085 ACTTGTTGTA
*
360095 TAAAATGTCACACTAAACCTCTCAAAAT
1 TAAAATGTCAAACTAAACCTCTCAAAAT
360123 TAAAATGTCAAACTAAACCTCTCAAAAT
1 TAAAATGTCAAACTAAACCTCTCAAAAT
360151 TAA
1 TAA
360154 CAATTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.25
Consensus pattern (28 bp):
TAAAATGTCAAACTAAACCTCTCAAAAT
Found at i:364350 original size:21 final size:20
Alignment explanation
Indices: 364323--364421 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
364313 AATCAGTTTC
364323 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
364344 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
364365 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
364385 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
364406 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
364422 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:364437 original size:40 final size:40
Alignment explanation
Indices: 364388--364697 Score: 367
Period size: 40 Copynumber: 7.8 Consensus size: 40
364378 CGATTTTCCA
* * * ** *
364388 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATC-CGT
* * * *
364428 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGT
* * * *
364468 ATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAA--CGATAATCCGT
* * * *
364508 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
364548 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
364588 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
* *
364628 AAATCGCAACGAGAATCTGTAAATCGCAATGATAATCCAT
1 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
*
364668 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCTGTAAATCGCAAC
364698 ACTGAAATTT
Statistics
Matches: 248, Mismatches: 16, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.01
39 1 0.00
40 241 0.97
41 1 0.00
42 3 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
Found at i:364450 original size:20 final size:20
Alignment explanation
Indices: 364388--364697 Score: 279
Period size: 20 Copynumber: 15.5 Consensus size: 20
364378 CGATTTTCCA
* ** *
364388 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
364408 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
364428 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
364448 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
364468 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
364488 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
364508 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
364528 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
364548 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
364568 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
364588 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
364608 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
364628 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* * *
364648 AAATCGCAATG-ATAATCCAT
1 AAATCGCAACGCGT-ATCCGT
* * *
364668 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
364688 AAATCACAAC
1 AAATCGCAAC
364698 ACTGAAATTT
Statistics
Matches: 238, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.01
20 234 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:364474 original size:60 final size:60
Alignment explanation
Indices: 364388--364697 Score: 320
Period size: 60 Copynumber: 5.2 Consensus size: 60
364378 CGATTTTCCA
* ** * * * *
364388 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATC-CGTAAATCGCAACGAGTATCCGT
* * * * * *
364448 AAATCGCAACGTGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGT
* * * * * *
364508 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGT
*
364568 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGAGT-ATCCGT
* * * * * * *
364628 AAATCGCAACGAGAATCTGTAAATCGCAATGATAATCCATAAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGT
*
364688 AAATCACAAC
1 AAATCGCAAC
364698 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
60 209 1.00
61 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGAGTATCCGT
Found at i:365419 original size:24 final size:24
Alignment explanation
Indices: 365380--365426 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
365370 AAATTTGGTC
365380 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
365404 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
365427 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:367909 original size:33 final size:34
Alignment explanation
Indices: 367858--368022 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
367848 CGGAAATTAC
* *
367858 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
367891 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
367925 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
367963 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
367996 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
368023 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 50 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:367941 original size:19 final size:19
Alignment explanation
Indices: 367872--368060 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
367862 GCAACGAGAG
367872 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
367891 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
367905 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
367925 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
367944 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
367963 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
367977 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
367996 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
368015 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
368029 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
368048 AATCGCATTGCGA
1 AATCGCAATGCGA
368061 TTCTCCCGTT
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 84 0.58
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:367999 original size:52 final size:52
Alignment explanation
Indices: 367858--368060 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
367848 CGGAAATTAC
*
367858 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
367905 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
367963 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
368015 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
368061 TTCTCCCGTT
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 85 0.61
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:368109 original size:19 final size:19
Alignment explanation
Indices: 368069--368166 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
368059 GATTCTCCCG
368069 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
368089 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
368108 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
368122 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
368141 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
368160 TTGCGAT
1 TTGCGAT
368167 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:368163 original size:52 final size:53
Alignment explanation
Indices: 368050--368166 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
368040 GAAATTAAAA
368050 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
368103 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
368155 TCGCATTGCGAT
1 TCGCATTGCGAT
368167 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:368292 original size:14 final size:14
Alignment explanation
Indices: 368273--368309 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
368263 CATCAATTAC
368273 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
368287 ACAAATCATCTTTT
1 ACAAATCAACTTTT
368301 ACAAATCAA
1 ACAAATCAA
368310 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:370273 original size:19 final size:19
Alignment explanation
Indices: 370233--370298 Score: 105
Period size: 19 Copynumber: 3.4 Consensus size: 19
370223 TAGTTTACTT
* *
370233 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
370253 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
370272 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
370291 TCGCAACG
1 TCGCAACG
370299 ACAGAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 31 0.70
20 13 0.30
ACGTcount: A:0.45, C:0.30, G:0.15, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:370308 original size:14 final size:14
Alignment explanation
Indices: 370289--370345 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
370279 GCGAAACCAA
*
370289 AATCGCAACGACAG
1 AATCGCAACGAAAG
370303 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
370320 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
370336 AATCGCAACG
1 AATCGCAACG
370346 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:370316 original size:33 final size:33
Alignment explanation
Indices: 370270--370362 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
370260 GCGAAACCAA
** *
370270 AATCGCAACGCGAAACCAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
370303 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
370336 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
370363 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:370327 original size:19 final size:18
Alignment explanation
Indices: 370249--370367 Score: 101
Period size: 19 Copynumber: 6.8 Consensus size: 18
370239 CACGAAACTT
*
370249 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-G
*
370268 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-G
*
370287 AAAATCGCAA--CGACAG
1 AAAATCGCAACGCGAAAG
*
370303 --AATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAA-G
370320 AAAATCGCAA--CGAAAG
1 AAAATCGCAACGCGAAAG
370336 --AATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-G
*
370353 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
370368 TTTTGGTTTC
Statistics
Matches: 86, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 11 0.13
19 49 0.57
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAG
Found at i:370385 original size:19 final size:19
Alignment explanation
Indices: 370363--370491 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
370353 AAAATCGCAA
370363 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
370382 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
370396 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
370415 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
370429 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
370448 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
370467 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
370487 TGCGA
1 TGCGA
370492 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:370405 original size:33 final size:33
Alignment explanation
Indices: 370363--370454 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
370353 AAAATCGCAA
370363 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
370396 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
370429 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
370455 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:370656 original size:93 final size:93
Alignment explanation
Indices: 370539--371192 Score: 1258
Period size: 93 Copynumber: 7.1 Consensus size: 93
370529 ATGGATTGCA
*
370539 TTAC-TTCAACCAAAAGGCAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
370603 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
370631 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
370696 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
370724 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
370789 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
370817 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
370881 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
370909 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
370974 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
371002 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
371067 TAGCAGGATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
371095 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
371160 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
371188 TTACT
1 TTACT
371193 AAGCAATCTA
Statistics
Matches: 554, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 95 0.17
93 459 0.83
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:371066 original size:278 final size:279
Alignment explanation
Indices: 370539--371192 Score: 1258
Period size: 278 Copynumber: 2.4 Consensus size: 279
370529 ATGGATTGCA
*
370539 TTAC-TTCAACCAAAAGGCAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
370603 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
370668 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
370733 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
370798 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
370817 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
370881 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
370946 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
*
371011 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGGAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
371076 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
371095 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
371160 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
371193 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
278 280 0.76
279 90 0.24
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:372916 original size:14 final size:14
Alignment explanation
Indices: 372894--372991 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 14
372884 TGGTTGAAAT
372894 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
372908 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
*
372926 TGAAAATCGCAACTA
1 -GAAAATCGCAACGA
*
372941 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
372959 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
372974 GATAATCGCAACGC
1 GAAAATCGCAACGA
372988 GAAA
1 GAAA
372992 TGAAAATCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
14 35 0.54
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.31
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:372929 original size:33 final size:33
Alignment explanation
Indices: 372889--373003 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
372879 TCTTTTGGTT
372889 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
372922 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
372955 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
372988 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
373004 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:372935 original size:19 final size:19
Alignment explanation
Indices: 372911--373008 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
372901 GCAACGAGAG
372911 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
372930 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
372944 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
372963 AATCGCAA--CG--A-GAT
1 AATCGCAACGCGAAATGAA
372977 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
372996 AATCGCAATGCGA
1 AATCGCAACGCGA
373009 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:373039 original size:14 final size:14
Alignment explanation
Indices: 373020--373076 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
373010 TTTGGTTTCG
373020 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
373034 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
373053 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
373067 CGTTGCGATT
1 CGTTGCGATT
373077 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:373052 original size:33 final size:33
Alignment explanation
Indices: 373004--373084 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
372994 AAAATCGCAA
**
373004 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
373037 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
373070 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
373085 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:373087 original size:21 final size:21
Alignment explanation
Indices: 373061--373136 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
373051 CGCGTTGCGA
373061 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
373082 TTCTCTCGTTGCGACAATCA-
1 TTCTCTCGTTGCGATTTTCAT
373102 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
373123 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
373137 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:373117 original size:41 final size:41
Alignment explanation
Indices: 373060--373137 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
373050 TCGCGTTGCG
*
373060 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAATC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAATC
373101 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
373138 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAATC
Found at i:373258 original size:33 final size:33
Alignment explanation
Indices: 373216--373286 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
373206 AATACTAACT
*
373216 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
373249 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
373282 TGAAA
1 TGAAA
373287 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:373520 original size:22 final size:22
Alignment explanation
Indices: 373468--373522 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
373458 TGGTTGTGAG
**
373468 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
373490 GAAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
373512 GGATTTCTTCG
1 GGATTTCTTCG
373523 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:373694 original size:20 final size:20
Alignment explanation
Indices: 373669--373822 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
373659 CTTTAAATAT
373669 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
373689 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
373711 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
373730 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
373750 CACGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
373770 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
373790 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
373810 CGCGTTGCGATTT
1 CGCGTTGCGATTT
373823 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.83
21 15 0.14
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:373801 original size:40 final size:40
Alignment explanation
Indices: 373668--373822 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
373658 GCTTTAAATA
*
373668 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
373709 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* * *
373749 ACACGTTACGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
373789 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
373823 TGGAAAATCG
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
40 64 0.68
41 30 0.32
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:373839 original size:21 final size:21
Alignment explanation
Indices: 373809--373891 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
373799 ATTTTCATAT
*
373809 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
373830 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
373851 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
373872 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
373892 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:373882 original size:42 final size:43
Alignment explanation
Indices: 373789--373887 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
373779 ATTTATGTGT
* *
373789 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
373830 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
373872 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
373888 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:374337 original size:15 final size:14
Alignment explanation
Indices: 374300--374344 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
374290 ATATGTGTAA
374300 AATATTA-AA-TAT
1 AATATTATAATTAT
*
374312 AATA-AATAATTATT
1 AATATTATAATTA-T
374326 AATATTATAATTAT
1 AATATTATAATTAT
374340 AATAT
1 AATAT
374345 ATTTTGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 6 0.22
13 2 0.07
14 11 0.41
15 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTATAATTAT
Found at i:376590 original size:18 final size:18
Alignment explanation
Indices: 376567--376603 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
376557 TATTCAAGGT
376567 TTATGAATACAAGTTCAC
1 TTATGAATACAAGTTCAC
376585 TTATGAATACAAGTTCAC
1 TTATGAATACAAGTTCAC
376603 T
1 T
376604 CCCATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
TTATGAATACAAGTTCAC
Done.