Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold188
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: 942289
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.27
Warning! 138643 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:163257 original size:20 final size:19
Alignment explanation
Indices: 163232--163285 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
163222 CTATCACTAT
163232 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
*
163252 TTGTATTGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
163272 TTGTATCGATACAT
1 TTGTATCGATACAT
163286 TGTTTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:167100 original size:19 final size:20
Alignment explanation
Indices: 167056--167105 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
167046 CTGCTAGTTT
**
167056 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
167076 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
167095 CATGTATCGAT
1 CATGTATCGAT
167106 GCATTGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:169494 original size:22 final size:21
Alignment explanation
Indices: 169459--169508 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
169449 GTTTTTGATG
*
169459 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
169479 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
169500 AATTTGAAG
1 ATTTTGAAG
169509 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:169505 original size:21 final size:22
Alignment explanation
Indices: 169466--169508 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
169456 ATGATTTTGA
* *
169466 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
169488 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
169509 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:169810 original size:18 final size:20
Alignment explanation
Indices: 169769--169821 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
169759 CTATAGACCC
169769 TAATTCACATCAAACAAGTA
1 TAATTCACATCAAACAAGTA
169789 TAATTCA-AT-AACACAA-TA
1 TAATTCACATCAA-ACAAGTA
*
169807 TAATTAAACATCAAA
1 TAATT-CACATCAAA
169822 TTCATCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 10 0.36
21 2 0.07
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (20 bp):
TAATTCACATCAAACAAGTA
Found at i:173897 original size:19 final size:19
Alignment explanation
Indices: 173857--173925 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
173847 CAGTTTCATA
**
173857 TATCGATACAATTGTCCATG
1 TATCGATACAA-TGAACATG
173877 TATCGATACAATGAACATG
1 TATCGATACAATGAACATG
* *
173896 TATCGATGCAAAGCATA-ATG
1 TATCGATACAATG-A-ACATG
173916 TATCGATACA
1 TATCGATACA
173926 TCTGGGTGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 17 0.40
20 24 0.57
21 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:176403 original size:20 final size:20
Alignment explanation
Indices: 176380--176447 Score: 118
Period size: 20 Copynumber: 3.3 Consensus size: 20
176370 CTGGACATGT
176380 TAAAAATGCATGAAACATAA
1 TAAAAATGCATGAAACATAA
176400 TAAAAAAATGCATGAAACATAA
1 T--AAAAATGCATGAAACATAA
176422 TAAAAATGCATGAAACATAA
1 TAAAAATGCATGAAACATAA
176442 TAAAAA
1 TAAAAA
176448 AATGCATGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
20 26 0.57
22 20 0.43
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (20 bp):
TAAAAATGCATGAAACATAA
Found at i:176409 original size:22 final size:22
Alignment explanation
Indices: 176381--176455 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
176371 TGGACATGTT
176381 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
176403 AAAAATGCATGAAACATAAT--
1 AAAAATGCATGAAACATAATAA
176423 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
176445 AAAAATGCATG
1 AAAAATGCATG
176456 GTCAAAGGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.39
22 31 0.61
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:177412 original size:20 final size:20
Alignment explanation
Indices: 177365--177439 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
177355 AAAAAGACAT
*
177365 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
177384 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
177405 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
177425 AATGTATCGATACAT
1 AATGTATCGATACAT
177440 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:177433 original size:40 final size:39
Alignment explanation
Indices: 177362--177439 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
177352 GGTAAAAAGA
* *
177362 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
177401 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
177440 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:178571 original size:3 final size:3
Alignment explanation
Indices: 178556--178592 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
178546 TCTGAGTCAC
* *
178556 CAT CAT TAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
178593 TTCTTTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:180295 original size:20 final size:20
Alignment explanation
Indices: 180270--180366 Score: 128
Period size: 19 Copynumber: 5.0 Consensus size: 20
180260 CTACCAGTTT
*
180270 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
180290 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
*
180309 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
* *
180329 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGTA
180348 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
180367 TCGATACAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
18 1 0.02
19 34 0.52
20 31 0.47
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:180320 original size:39 final size:39
Alignment explanation
Indices: 180270--180365 Score: 176
Period size: 39 Copynumber: 2.5 Consensus size: 39
180260 CTACCAGTTT
180270 CATGTATCGATACAATTGTCCATGTATCGATACAATGAA
1 CATGTATCGATACAATTGTCCATGTATCGATACAATGAA
*
180309 CATGTATCGATACAATTGTCCATGTATTGATACAATGAA
1 CATGTATCGATACAATTGTCCATGTATCGATACAATGAA
180348 CATGTATCGATAC-ATTGT
1 CATGTATCGATACAATTGT
180366 ATCGATACAA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
38 5 0.09
39 51 0.91
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (39 bp):
CATGTATCGATACAATTGTCCATGTATCGATACAATGAA
Found at i:180368 original size:13 final size:13
Alignment explanation
Indices: 180350--180374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180340 ACAATGAACA
180350 TGTATCGATACAT
1 TGTATCGATACAT
180363 TGTATCGATACA
1 TGTATCGATACA
180375 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:181038 original size:15 final size:15
Alignment explanation
Indices: 181018--181072 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
181008 TTCTCTAAAT
181018 AAGAAAAACAAAAA-A
1 AAGAAAAA-AAAAACA
181033 AAGAAAAAAAAAACA
1 AAGAAAAAAAAAACA
*
181048 AAGAAAAAAAAAGCA
1 AAGAAAAAAAAAACA
181063 AA-AAAAAAAA
1 AAGAAAAAAAA
181073 GAAGAAAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
14 13 0.34
15 25 0.66
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAACA
Found at i:181040 original size:10 final size:10
Alignment explanation
Indices: 181018--181070 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
181008 TTCTCTAAAT
181018 AAGAAAAACAA
1 AAGAAAAA-AA
181029 AA-AAAAGAAA
1 AAGAAAA-AAA
*
181039 AA-AAAAACA
1 AAGAAAAAAA
181048 AAGAAAAAAA
1 AAGAAAAAAA
181058 AAGCAAAAAAA
1 AAG-AAAAAAA
181069 AA
1 AA
181071 AAGAAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 4 0.11
10 21 0.57
11 12 0.32
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:181056 original size:26 final size:26
Alignment explanation
Indices: 181027--181081 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
181017 TAAGAAAAAC
181027 AAAAAAAAG-AAAAAAAAAACA-AAGA
1 AAAAAAAAGCAAAAAAAAAA-AGAAGA
181052 AAAAAAAAGCAAAAAAAAAAAGAAGA
1 AAAAAAAAGCAAAAAAAAAAAGAAGA
181078 AAAA
1 AAAA
181082 GCATGGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (26 bp):
AAAAAAAAGCAAAAAAAAAAAGAAGA
Found at i:181080 original size:15 final size:14
Alignment explanation
Indices: 181018--181081 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
181008 TTCTCTAAAT
181018 AAGAAAAACAAAAAA
1 AAGAAAAA-AAAAAA
181033 AAGAAAAAAAAAACA
1 AAGAAAAAAAAAA-A
*
181048 AAG-AAAAAAAAAG
1 AAGAAAAAAAAAAA
* *
181061 CA-AAAAAAAAAAG
1 AAGAAAAAAAAAAA
181074 AAGAAAAA
1 AAGAAAAA
181082 GCATGGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.28
14 19 0.44
15 12 0.28
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAAA
Found at i:181092 original size:1 final size:1
Alignment explanation
Indices: 181021--181072 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
181011 TCTAAATAAG
* * * * **
181021 AAAAACAAAAAAAAGAAAAAAAAAACAAAGAAAAAAAAAGCAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
181073 GAAGAAAAAG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:188324 original size:13 final size:13
Alignment explanation
Indices: 188306--188330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188296 CATATTACTT
188306 TGTATCGATACAG
1 TGTATCGATACAG
188319 TGTATCGATACA
1 TGTATCGATACA
188331 TGATCTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:191629 original size:58 final size:57
Alignment explanation
Indices: 191539--191658 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 57
191529 CAAAAAAATA
*
191539 AAAACCTTTTGCATTCTTCCAATATTCTAGTAAGGTGAGAAAAATATTTTGTATTTTT
1 AAAACCTTTTGCATTCTTCCAATATTCTAGTAAGGTGAGAAAAACATTTTG-ATTTTT
*
191597 AAAACCTTTTGCATTCTTCCAATATTCTAGTAAGGTGAGAAAGACATTTTGATTTTT
1 AAAACCTTTTGCATTCTTCCAATATTCTAGTAAGGTGAGAAAAACATTTTGATTTTT
191654 AAAAC
1 AAAAC
191659 TTTGTATGTT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 11 0.18
58 49 0.82
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (57 bp):
AAAACCTTTTGCATTCTTCCAATATTCTAGTAAGGTGAGAAAAACATTTTGATTTTT
Found at i:192645 original size:10 final size:10
Alignment explanation
Indices: 192630--192655 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
192620 CTCATATAAA
192630 CATCAATTTT
1 CATCAATTTT
192640 CATCAATTTT
1 CATCAATTTT
192650 CATCAA
1 CATCAA
192656 ATTCTTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (10 bp):
CATCAATTTT
Found at i:197905 original size:23 final size:23
Alignment explanation
Indices: 197879--197923 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
197869 AGCCTTAACA
197879 TTTGCAAACGGTGT-TGTTTCCCC
1 TTTGCAAACGGTGTAT-TTTCCCC
* *
197902 TTTGTAAATGGTGTATTTTCCC
1 TTTGCAAACGGTGTATTTTCCC
197924 TTTAATGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (23 bp):
TTTGCAAACGGTGTATTTTCCCC
Found at i:200020 original size:2 final size:2
Alignment explanation
Indices: 200013--200045 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
200003 AGAAAAATTC
200013 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
200046 CAGCTTGGAG
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:200260 original size:119 final size:119
Alignment explanation
Indices: 200049--200267 Score: 330
Period size: 119 Copynumber: 1.8 Consensus size: 119
200039 TATATATCAG
*
200049 CTTGGAGTTAAAGATATATTTAGCATGGCCAAATGCATACCTCGACTTAGAGCTAAAATGTATTT
1 CTTGGAGTTAAAGATATATTTAGCATGACCAAATGCATACCTCGACTTAGAGCTAAAATGTATTT
* * *
200114 GAAATTAACTTTACGATGCCCAATGCATATACAAAAATTCTATGCATACCTCAA
66 GAAATGAACTGTACAATGCCCAATGCATATACAAAAATTCTATGCATACCTCAA
* * * *
200168 CTTGGAGTTAAAGATATATTTAGCTTGACCAAATGCATTCCTCGACTTGGAGCTAAAATTTATTT
1 CTTGGAGTTAAAGATATATTTAGCATGACCAAATGCATACCTCGACTTAGAGCTAAAATGTATTT
* * * *
200233 GAAATGAACTGTGCAATGTCCAGTGCATGTACAAA
66 GAAATGAACTGTACAATGCCCAATGCATATACAAA
200268 TATGTATATC
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 88 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (119 bp):
CTTGGAGTTAAAGATATATTTAGCATGACCAAATGCATACCTCGACTTAGAGCTAAAATGTATTT
GAAATGAACTGTACAATGCCCAATGCATATACAAAAATTCTATGCATACCTCAA
Found at i:200773 original size:21 final size:21
Alignment explanation
Indices: 200702--200773 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
200692 TTTAACAATT
* *
200702 TGTATTGATACAATAAG-GTAA
1 TGTATCGATAC-ATAAGTGAAA
200723 TGTATCGATACATAAGTGAAA
1 TGTATCGATACATAAGTGAAA
***
200744 -GTATCGATACATGCTTGAAA
1 TGTATCGATACATAAGTGAAA
*
200764 TGTGTCGATA
1 TGTATCGATA
200774 TAGGGCCATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 22 0.51
21 21 0.49
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:203897 original size:20 final size:20
Alignment explanation
Indices: 203874--203945 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
203864 TTATGCCTTG
*
203874 TATCGATACATGGATAATTA
1 TATCGATACATGGACAATTA
203894 TATCGATACATGGACAATTA
1 TATCGATACATGGACAATTA
*
203914 TATTGATACATGGACAATTA
1 TATCGATACATGGACAATTA
203934 TATCGATACATG
1 TATCGATACATG
203946 AAACTGGCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:205644 original size:3 final size:3
Alignment explanation
Indices: 205629--205662 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
205619 AACCATCAAA
*
205629 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
205663 GAGACTCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:210160 original size:20 final size:21
Alignment explanation
Indices: 210135--210177 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
210125 AATTTTTCAG
210135 AATGTATCGATACAT-TGAAA
1 AATGTATCGATACATCTGAAA
210155 AATGTATCGATACATCTGAAA
1 AATGTATCGATACATCTGAAA
210176 AA
1 AA
210178 CCCAGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.28
Consensus pattern (21 bp):
AATGTATCGATACATCTGAAA
Found at i:210361 original size:21 final size:22
Alignment explanation
Indices: 210337--210386 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
210327 ATCAAATCTT
* *
210337 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
210358 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
210380 --TCAAAAT
1 CTTCAAAAT
210387 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:212574 original size:989 final size:989
Alignment explanation
Indices: 210658--215605 Score: 9520
Period size: 989 Copynumber: 5.0 Consensus size: 989
210648 AGCAGCCACC
210658 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
1 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
210723 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
66 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
*
210788 TCCTGCTCAAAGACGCACTTGAGGT-CTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
131 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
* *
210852 GTTGTTTCCGAACCCAAGCTAACCTCAAACACTTCAACCAAACTTTCTCACGGTTGGCTGTCCGA
196 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
210917 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTTATTTTTTGACACT
261 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGAC-TTTTTTTTTATTTTTTGACACT
210982 TGAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAG
325 TGAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAG
* *
211047 CTTTTCTTAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTACTATTCATTCCTAC
390 CTTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTAC
211112 CTCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGA
455 CTCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGA
211177 GGGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCC
520 GGGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCC
211242 TTCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAA
585 TTCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAA
211307 TACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAA
650 TACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAA
211372 CCTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATG
715 CCTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATG
**
211437 GCATGATCCTTAGTCACTTCTTCGAGGCCAATGGTATTGACATGTCATGCGATGTCGGGATTCTT
780 GCATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCGGGATTCTT
*
211502 ATTTCTCGATCACGCATCATCGATTCCCAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCG
845 ATTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCG
211567 ATCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATG
910 ATCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATG
211632 GAAGAAGATGCTCCT
975 GAAGAAGATGCTCCT
211647 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
1 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
*
211712 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATA
66 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
*
211777 ACCTGCTCAAAGACGTACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
131 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
*
211842 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACATCCTCACGGTTGGCTGTCCGA
196 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
211907 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
261 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
*
211972 GAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGTGAGAACCTTGTCCGAGC
326 GAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAGC
212037 TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
391 TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
212102 TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
456 TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
212167 GGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
521 GGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
212232 TCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAAT
586 TCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAAT
*
212297 ACTTAACCCTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
651 ACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
212362 CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
716 CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
* * *
212427 CATGATCCTTAGTCACTTCTTAGAGGCCAGCGGTATTGATATGTCATGCGATGTCAGGATTCTTA
781 CATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCGGGATTCTTA
212492 TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
846 TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
212557 TCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATGG
911 TCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATGG
212622 AAGAAGATGCTCCT
976 AAGAAGATGCTCCT
*
212636 TCCAGGTCGTGATCGGCACTCCCAAGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
1 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
212701 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
66 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
212766 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
131 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
212831 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
196 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
212896 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
261 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
*
212961 GAGATGTTTGGTTGGATTACATTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAGC
326 GAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAGC
213026 TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
391 TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
213091 TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
456 TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
213156 GGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
521 GGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
*
213221 TCCACCTCATGATCATTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAAT
586 TCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAAT
213286 ACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
651 ACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
213351 CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
716 CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
*
213416 CATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCAGGATTCTTA
781 CATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCGGGATTCTTA
213481 TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
846 TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
* *
213546 TCATCCTCGACAACGTGATGTTTCTGCTCCACAAGAAGATGAGCAAGAGGAACCACAACAAATGG
911 TCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATGG
213611 AAGAAGATGCTCCT
976 AAGAAGATGCTCCT
* *
213625 TCCAGGTCGTGATCGGCACTCCCAAGTCGTAACTGGGCAGCTCCCACACCCACTGCCTAAACCAC
1 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
*
213690 CCGAAACTATCCTATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
66 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
213755 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
131 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
213820 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
196 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
213885 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
261 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
*
213950 GAGATGTTTGGTTGGATTACATTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAGC
326 GAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAGC
214015 TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
391 TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
214080 TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
456 TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
* *
214145 GGAGAGATCAAAGAAGGGATGGCTCCTTGAATCACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
521 GGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
* *
214210 TCCAACTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGGCACCTAAT
586 TCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAAT
214275 ACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
651 ACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
214340 CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
716 CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
*
214405 CATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTTGGGATTCTTA
781 CATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCGGGATTCTTA
214470 TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
846 TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
*
214535 TCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAAGATGAGCAAGAGGAACCACAACAAATGG
911 TCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATGG
214600 AAGAAGATGCTCCT
976 AAGAAGATGCTCCT
*
214614 TTCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
1 TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
*
214679 CCGAAACTATCCCATTTTACACTGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
66 CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
*
214744 ACCTGCTCAAAGACGCACTTAAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
131 ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
214809 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
196 GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
214874 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTTATTTTTTGACACT
261 CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGAC-TTTTTTTTTATTTTTTGACACT
214939 TGAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAG
325 TGAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAG
215004 CTTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTAC
390 CTTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTAC
215069 CTCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGA
455 CTCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGA
215134 GGGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCC
520 GGGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCC
215199 TTCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAA
585 TTCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAA
215264 TACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAA
650 TACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAA
*
215329 CCTCGCCTACTTCATTTTCACCAACATTATTCGCGACTTGGAAGGCACTTCGGCTATTCTCCATG
715 CCTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATG
*
215394 GCATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTTGGGATTCTT
780 GCATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCGGGATTCTT
215459 ATTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCG
845 ATTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCG
* *
215524 ATCATCCTCGATAGCGTGATGTTTCTGCTCCACAAAAGGATGAGCAAGAGGAACCACAACAAATG
910 ATCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATG
215589 GAAGAAGATGCTCCT
975 GAAGAAGATGCTCCT
215604 TC
1 TC
215606 TCCTCCTCTT
Statistics
Matches: 3903, Mismatches: 54, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
989 3081 0.79
990 822 0.21
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (989 bp):
TCCAGGTCGTGATCGGCACTCCCAGGTCGTAACCGGGCAGCTCCCACACCCACTGCCTAAACCAC
CCGAAACTATCCCATTTTACACCGAAACACTTTTTAACCAAACCGATGGCTCATCGAATGAAATT
ACCTGCTCAAAGACGCACTTGAGGTGCTTCTTCGTCAAATCCTCAAAATCAAACCTTCTTCGAAG
GTTGTTTCCGAACCCAAGCTAACCTCGAACACTTCAACCAAACTTCCTCACGGTTGGCTGTCCGA
CCATGTCGCGCAATCGATATGAAATATCTCAAGTCTTTTGACTTTTTTTTTATTTTTTGACACTT
GAGATGTTTGGTTGGATTACACTCTTAAGCTTAAATGTATCAGTTCGCGAGAACCTTGTCCGAGC
TTTTCTCAGTAACGCTCGTCTCGAGCATAACTATAGCAACGAAGTTATTGCTATTCATTCCTACC
TCATGGATCAAGACTTGATCTTTCCCCCCTCCATTTTAGTCGATGCACTAAACATGCCATATGAG
GGAGAGATCAAAGAAGGGATGGCTCCTCGAAACACTAGAGTTCCCCTAAATAAAGCCATTCGCCT
TCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATCTTCTGACCGTTCGACACCTAAT
ACTTAACACTCAGTAACTCCGATTACTAGTGGCTTCACATGATCCGAACAAGTCAATGGCCTAAC
CTCGCCTACTTCATTTTCACCAACATTATTCGCGACTCGGAAGGCACTTCGGCTATTCTCCATGG
CATGATCCTTAGTCACTTCTTCGAGGCCAGCGGTATTGACATGTCATGCGATGTCGGGATTCTTA
TTTCTCGATCACGCATCATCGATTCCAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAACCGA
TCATCCTCGACAGCGTGATGTTTCTGCTCCACAAGAGGATGAGCAAGAGGAACCACAACAAATGG
AAGAAGATGCTCCT
Found at i:221389 original size:15 final size:16
Alignment explanation
Indices: 221362--221391 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
221352 TTTAAAAATT
221362 AAAAAATTAATTAATA
1 AAAAAATTAATTAATA
221378 AAAAAATT-ATTAAT
1 AAAAAATTAATTAAT
221392 TATCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTAATTAATA
Found at i:221682 original size:22 final size:22
Alignment explanation
Indices: 221657--221704 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
221647 AAAAAAATCG
*
221657 ATTT-AAATTTTATTTATTATAA
1 ATTTGAAATTTTATTT-TTAAAA
**
221679 ATTTGTCATTTTATTTTTAAAA
1 ATTTGAAATTTTATTTTTAAAA
221701 ATTT
1 ATTT
221705 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTGAAATTTTATTTTTAAAA
Found at i:221785 original size:21 final size:21
Alignment explanation
Indices: 221759--221816 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 21
221749 TAGATGTAAT
221759 TTAAAATATTTAATTTTTA-TA
1 TTAAAATATTTAA-TTTTACTA
*
221780 TTAAAATATATTTATTTTACTA
1 TTAAAATAT-TTAATTTTACTA
221802 TATAAATATATTTAA
1 T-TAAA-ATATTTAA
221817 ATAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 14 0.45
22 6 0.19
23 7 0.23
24 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAATATTTAATTTTACTA
Found at i:222236 original size:5 final size:5
Alignment explanation
Indices: 222212--222356 Score: 56
Period size: 5 Copynumber: 29.6 Consensus size: 5
222202 TATTAATCAA
* *
222212 TATATT TATAA TATATT TATAT TATTTT TATAT TATAAT TATAT T-TA-
1 TATA-T TATAT TATA-T TATAT TA-TAT TATAT TAT-AT TATAT TATAT
* * * *
222259 AATAT TATA- TATTT TAAAT T-TAT CATATT TATAT T-T-T T-TAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT
* * * * * * *
222305 TATATT TATGT TATAT TTTAT TTTTT TATGT T-TAT AATA- TATAA TATAT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
222354 TAT
1 TAT
222357 GTATAAATAA
Statistics
Matches: 104, Mismatches: 22, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
3 3 0.03
4 17 0.16
5 59 0.57
6 25 0.24
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:222247 original size:16 final size:16
Alignment explanation
Indices: 222223--222321 Score: 56
Period size: 18 Copynumber: 5.7 Consensus size: 16
222213 ATATTTATAA
222223 TATATTTATATTATTTT
1 TATA-TTATATTATTTT
222240 TATATTATAATTATATTT
1 TATATTAT-ATTAT-TTT
*
222258 AAATATTATA-TATTTT
1 -TATATTATATTATTTT
* *
222274 AAATTTATCATATTTATATTT
1 ---TATATTATA-TTAT-TTT
* *
222295 TTTATTATATTATATT
1 TATATTATATTATTTT
*
222311 TATGTTATATT
1 TATATTATATT
222322 TTATTTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
16 18 0.27
17 16 0.24
18 19 0.29
19 7 0.11
20 3 0.05
21 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
TATATTATATTATTTT
Found at i:222296 original size:23 final size:24
Alignment explanation
Indices: 222234--222313 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 24
222224 ATATTTATAT
* * *
222234 TATTTTTATATTATAATTATATTTA
1 TATTTATATATTTTAATTATA-TCA
*
222259 AATATTATATATTTTAAATT-TATCA
1 TAT-TTATATATTTT-AATTATATCA
* *
222284 TATTTATAT-TTTTTATTATATTA
1 TATTTATATATTTTAATTATATCA
222307 TATTTAT
1 TATTTAT
222314 GTTATATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
22 3 0.07
23 15 0.33
24 6 0.13
25 6 0.13
26 11 0.24
27 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTTATATATTTTAATTATATCA
Found at i:222320 original size:11 final size:11
Alignment explanation
Indices: 222212--222326 Score: 81
Period size: 11 Copynumber: 10.1 Consensus size: 11
222202 TATTAATCAA
*
222212 TATATTTATAA
1 TATATTTATAT
222223 TATATTTATAT
1 TATATTTATAT
*
222234 TATTTTTATAT
1 TATATTTATAT
*
222245 TATAATTATATT
1 TATATTTATA-T
222257 TAAATATTATATAT
1 T--ATATT-TATAT
* *
222271 TTTAAATT-TAT
1 TAT-ATTTATAT
*
222282 CATATTTATAT
1 TATATTTATAT
* *
222293 TTTTTATTATAT
1 TATAT-TTATAT
*
222305 TATATTTATGT
1 TATATTTATAT
222316 TATATTT-TAT
1 TATATTTATAT
222326 T
1 T
222327 TTTTTATGTT
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
10 6 0.08
11 49 0.61
12 13 0.16
13 2 0.03
14 6 0.08
15 4 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:222345 original size:26 final size:26
Alignment explanation
Indices: 222217--222346 Score: 79
Period size: 26 Copynumber: 4.8 Consensus size: 26
222207 ATCAATATAT
* * *
222217 TTATAATATATTTATATTATTTTTATA
1 TTATATTATATTTATAATATATTT-TA
222244 TTATAATTATATTTAAATATTATATATTTTAAA
1 TTAT-ATTATATTT--ATA--ATATATTTT--A
*
222277 TT-TATCATATTTAT-AT-T-TTTTA
1 TTATATTATATTTATAATATATTTTA
**
222299 TTATATTATATTTATGTTATATTTTA
1 TTATATTATATTTATAATATATTTTA
* * *
222325 TTTTTTTATGTTTATAATATAT
1 TTATATTATATTTATAATATAT
222347 AATATATTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
22 3 0.04
23 11 0.14
24 5 0.06
25 2 0.02
26 24 0.30
27 4 0.05
28 8 0.10
29 2 0.02
30 3 0.04
31 9 0.11
32 7 0.09
33 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.63
Consensus pattern (26 bp):
TTATATTATATTTATAATATATTTTA
Found at i:222572 original size:2 final size:2
Alignment explanation
Indices: 222565--222599 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
222555 CTGTCACTTT
222565 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
222600 TAAAATCCTA
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:227755 original size:21 final size:21
Alignment explanation
Indices: 227731--227771 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
227721 TCTAGTAATA
*
227731 TTAAAACTTCATCAAATTATT
1 TTAAAAATTCATCAAATTATT
**
227752 TTAAAAATTGTTCAAATTAT
1 TTAAAAATTCATCAAATTAT
227772 GAGACTGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAAAATTCATCAAATTATT
Found at i:228263 original size:2 final size:2
Alignment explanation
Indices: 228256--228293 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
228246 ACCTGAACTA
228256 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
228294 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230406 original size:15 final size:15
Alignment explanation
Indices: 230386--230414 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
230376 ATTAACTGTA
230386 TGATAAGGCTTGTCT
1 TGATAAGGCTTGTCT
230401 TGATAAGGCTTGTC
1 TGATAAGGCTTGTC
230415 CTGTATACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.38
Consensus pattern (15 bp):
TGATAAGGCTTGTCT
Found at i:231473 original size:23 final size:24
Alignment explanation
Indices: 231417--231474 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
231407 TAGGTGAAGA
231417 TAGGGGTGAGAAAGATAACTATAG
1 TAGGGGTGAGAAAGATAACTATAG
* * * *
231441 TAGGGGTGAGAGAGATGATTCTAG
1 TAGGGGTGAGAAAGATAACTATAG
231465 T-GGGGTGAGA
1 TAGGGGTGAGA
231475 TAGAATACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.33, C:0.03, G:0.41, T:0.22
Consensus pattern (24 bp):
TAGGGGTGAGAAAGATAACTATAG
Found at i:232484 original size:31 final size:29
Alignment explanation
Indices: 232449--232506 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
232439 TTTCCTATAA
*
232449 GGTTTGATTGAGAAGATTATGTCTCTTGTAG
1 GGTTTGA-TGAGAAGACTATGTC-CTTGTAG
*
232480 GGTTTGATGAGGAGACTATGTCCTTGT
1 GGTTTGATGAGAAGACTATGTCCTTGT
232507 TGCCCAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 13 0.52
31 7 0.28
ACGTcount: A:0.21, C:0.09, G:0.31, T:0.40
Consensus pattern (29 bp):
GGTTTGATGAGAAGACTATGTCCTTGTAG
Found at i:233383 original size:23 final size:23
Alignment explanation
Indices: 233344--233400 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
233334 TTTAGTAGTC
* *
233344 ACAAAATATTTACAGCTATTAAA
1 ACAAAAAATATACAGCTATTAAA
*
233367 ACAGAAAATATACAGCTATTAAA
1 ACAAAAAATATACAGCTATTAAA
233390 ACAAAAAATAT
1 ACAAAAAATAT
233401 CTCTTCCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (23 bp):
ACAAAAAATATACAGCTATTAAA
Found at i:240642 original size:2 final size:2
Alignment explanation
Indices: 240635--240667 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
240625 AACGTTAACT
240635 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
240668 GAATTTGACT
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:242140 original size:20 final size:21
Alignment explanation
Indices: 242094--242142 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
242084 TACAAAAAAC
*
242094 TTTTATTTGTTGATGATTCAT
1 TTTTATTTGTTCATGATTCAT
** *
242115 AATTATTT-TTCATGTTTCAT
1 TTTTATTTGTTCATGATTCAT
242135 TTTTATTT
1 TTTTATTT
242143 ATGATCTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.65
Consensus pattern (21 bp):
TTTTATTTGTTCATGATTCAT
Found at i:243823 original size:16 final size:17
Alignment explanation
Indices: 243788--243825 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
243778 TAGAATTCAT
243788 ATTTTCAAACAAAGTTA
1 ATTTTCAAACAAAGTTA
* *
243805 ATTTTGAAA-AAATTTA
1 ATTTTCAAACAAAGTTA
243821 ATTTT
1 ATTTT
243826 TGAAGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTTTCAAACAAAGTTA
Found at i:244333 original size:18 final size:19
Alignment explanation
Indices: 244310--244349 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
244300 ATAGTATTCT
244310 TTTTA-TTAAATAAAATTA
1 TTTTATTTAAATAAAATTA
* *
244328 TTTTATTTAAGTAATATTA
1 TTTTATTTAAATAAAATTA
244347 TTT
1 TTT
244350 AATAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTATTTAAATAAAATTA
Found at i:251385 original size:51 final size:50
Alignment explanation
Indices: 251261--251394 Score: 187
Period size: 50 Copynumber: 2.7 Consensus size: 50
251251 ATTTGCTTGC
* * * * *
251261 ATGTATCGATACATTGATTAATATATCGATACATTTGGGTAAAATCCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCAGA
* * *
251311 ACGTATCGATATAATGAAGAATGTATCGATACATCTGGGTAAAAACCTAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACC-AGA
251362 ATGTATCGATACAATGAATAATGTATCGATACA
1 ATGTATCGATACAATGAATAATGTATCGATACA
251395 AACAGTAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 39 0.54
51 33 0.46
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACCAGA
Found at i:252340 original size:21 final size:21
Alignment explanation
Indices: 252316--252383 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
252306 AAGGATGATA
252316 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* *
252337 AAGGCTAG-CGATAT--TGAACTTA
1 AAGG-T-GCCAATATGCTG-A-TTC
*
252359 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATATGCTGATTC
252380 AAGG
1 AAGG
252384 CTAACGACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
20 3 0.09
21 16 0.46
22 13 0.37
23 3 0.09
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:252375 original size:43 final size:43
Alignment explanation
Indices: 252314--252395 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
252304 AGAAGGATGA
* *
252314 TAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGAACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCTAACGACATTGAACT
*
252357 TAAAGGTGCCAATGTGCTGATTCAAGGCTAACGACATTG
1 TAAAGGTGCCAATATGCTGATTCAAGGCTAACGACATTG
252396 GGCTTAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCTAACGACATTGAACT
Found at i:252518 original size:31 final size:31
Alignment explanation
Indices: 252415--252594 Score: 121
Period size: 32 Copynumber: 5.7 Consensus size: 31
252405 GGAGATGCCC
* * *
252415 CCAACTTATGTGGGTTTTTGAAAGGGTTGCCA
1 CCAACTTGTGTGGG-CTTTGAAAGGGTTGCTA
*** * * *
252447 TTGACTTGTG-GGGCTTTAAGAAGGGTTACCA
1 CCAACTTGTGTGGGCTTTGA-AAGGGTTGCTA
*** * * *
252478 CCCGTTTGTGTGGGCTTTGAAGGGGTTGTTG
1 CCAACTTGTGTGGGCTTTGAAAGGGTTGCTA
*
252509 CCAACTTGTGTGGGCTTCAGAAAGGGTTGCTA
1 CCAACTTGTGTGGGCTT-TGAAAGGGTTGCTA
* * *
252541 CCGACTTGTGTGGGCTTTAGAAA-GGTTCACCA
1 CCAACTTGTGTGGGCTTT-GAAAGGGTT-GCTA
*
252573 CTAACTTGTGTGGGCTTTGAAA
1 CCAACTTGTGTGGGCTTTGAAA
252595 AAGGTTGCCA
Statistics
Matches: 112, Mismatches: 31, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
30 4 0.04
31 46 0.41
32 62 0.55
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.33
Consensus pattern (31 bp):
CCAACTTGTGTGGGCTTTGAAAGGGTTGCTA
Found at i:252615 original size:32 final size:32
Alignment explanation
Indices: 252509--252634 Score: 85
Period size: 32 Copynumber: 3.9 Consensus size: 32
252499 GGGGTTGTTG
* * * *
252509 CCAACTTGTGTGGGC-TTCAGAAAGGGTTGCTA
1 CCAACCTGTGTGGGCTTTGA-AAAAGGTTGCCA
* * * *
252541 CCGACTTGTGTGGGCTTT-AGAAAGGTTCACCA
1 CCAACCTGTGTGGGCTTTGAAAAAGGTT-GCCA
* *
252573 CTAACTTGTGTGGGCTTTGAAAAAGGTTGCCA
1 CCAACCTGTGTGGGCTTTGAAAAAGGTTGCCA
* ** * *
252605 CCAGCCTGTGTAAGTTTTGGAAAAGGTTGC
1 CCAACCTGTGTGGGCTTTGAAAAAGGTTGC
252635 GATCGACTTA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
31 6 0.08
32 59 0.79
33 10 0.13
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (32 bp):
CCAACCTGTGTGGGCTTTGAAAAAGGTTGCCA
Found at i:252882 original size:28 final size:28
Alignment explanation
Indices: 252838--252906 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
252828 ACAGCAAGTA
*
252838 CCACTGA-TTGTGAACTTCGAAAAGATG
1 CCACTGACTTGTGGACTTCGAAAAGATG
* *
252865 CCACTGACTTGTGGACTTCGAAGAGGTG
1 CCACTGACTTGTGGACTTCGAAAAGATG
*
252893 CCACTGACTAGTGG
1 CCACTGACTTGTGG
252907 GCTTTGTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 7 0.19
28 30 0.81
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (28 bp):
CCACTGACTTGTGGACTTCGAAAAGATG
Found at i:252992 original size:14 final size:13
Alignment explanation
Indices: 252960--252998 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
252950 TTTCTAACAC
252960 AGTTCTTGACAAA
1 AGTTCTTGACAAA
252973 AGTTCTTGACGAAA
1 AGTTCTTGAC-AAA
*
252987 ATTTCTTGACAA
1 AGTTCTTGACAA
252999 CAATTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
AGTTCTTGACAAA
Found at i:253003 original size:14 final size:13
Alignment explanation
Indices: 252962--253004 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
252952 TCTAACACAG
*
252962 TTCTTGACAAAAG
1 TTCTTGACAAAAT
252975 TTCTTGACGAAAAT
1 TTCTTGAC-AAAAT
252989 TTCTTGACAACAAT
1 TTCTTGACAA-AAT
253003 TT
1 TT
253005 TGTTGACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (13 bp):
TTCTTGACAAAAT
Found at i:263576 original size:20 final size:21
Alignment explanation
Indices: 263551--263601 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
263541 CGATACACTA
*
263551 TATCGATACATG-ACCA-AATG
1 TATCGATACATGTA-AAGAATG
*
263571 TATCGATACTTGTAAAGAATG
1 TATCGATACATGTAAAGAATG
263592 TATCGATACA
1 TATCGATACA
263602 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (21 bp):
TATCGATACATGTAAAGAATG
Found at i:263679 original size:13 final size:13
Alignment explanation
Indices: 263661--263686 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263651 TACACACAAG
263661 ATGTATCGATACA
1 ATGTATCGATACA
263674 ATGTATCGATACA
1 ATGTATCGATACA
263687 TCCCAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:263703 original size:33 final size:32
Alignment explanation
Indices: 263643--263706 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
263633 CTTAACTGTT
*
263643 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
263675 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
263707 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:265285 original size:3 final size:3
Alignment explanation
Indices: 265271--265307 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
265261 CATCAAGGAC
*
265271 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
265308 GTGACTCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:269592 original size:13 final size:13
Alignment explanation
Indices: 269574--269600 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
269564 TACAGCAAGT
269574 ATGTATCGATACA
1 ATGTATCGATACA
269587 ATGTATCGATACA
1 ATGTATCGATACA
269600 A
1 A
269601 CAAAAACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:269597 original size:32 final size:33
Alignment explanation
Indices: 269556--269619 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
269546 TAGCCAAACT
* **
269556 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACAACAAAAACTGTATCGATACAA
269588 TGTATCGATACAACAAAAACTGTATCGATACA
1 TGTATCGATACAACAAAAACTGTATCGATACA
269620 TTGGTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
TGTATCGATACAACAAAAACTGTATCGATACAA
Found at i:271842 original size:21 final size:21
Alignment explanation
Indices: 271809--271853 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
271799 TTGCAAGTTG
*
271809 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
271831 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
271851 AAA
1 AAA
271854 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:274897 original size:13 final size:13
Alignment explanation
Indices: 274879--274903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274869 CATAAAATGT
274879 TGTATCGATACAA
1 TGTATCGATACAA
274892 TGTATCGATACA
1 TGTATCGATACA
274904 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:274901 original size:33 final size:33
Alignment explanation
Indices: 274859--274925 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
274849 TTCAACGATT
274859 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
274892 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
274925 T
1 T
274926 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:274984 original size:13 final size:13
Alignment explanation
Indices: 274966--274990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274956 ATTACTCAAA
274966 TGTATCGATACAT
1 TGTATCGATACAT
274979 TGTATCGATACA
1 TGTATCGATACA
274991 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:275092 original size:52 final size:52
Alignment explanation
Indices: 274999--275126 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
274989 CACTGATCTT
*
274999 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
*
275050 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
275102 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
275127 TCATATTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 18 0.25
52 51 0.71
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:279368 original size:20 final size:21
Alignment explanation
Indices: 279299--279376 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
279289 AATGTCCAAA
*
279299 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
279319 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
279344 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
279364 TTGTATCGATACA
1 ATGTATCGATACA
279377 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:279383 original size:13 final size:13
Alignment explanation
Indices: 279365--279402 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
279355 CATTTTTCTT
279365 TGTATCGATACAA
1 TGTATCGATACAA
*
279378 TGTATCGATACAC
1 TGTATCGATACAA
279391 TGTATCGATACA
1 TGTATCGATACA
279403 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:281877 original size:20 final size:20
Alignment explanation
Indices: 281854--281947 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
281844 AGAATTCAAA
*
281854 GTATCGATACATGTCGCAAT
1 GTATCGATACATGTAGCAAT
* **
281874 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTAGCA-AT
*
281895 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTAGCAAT
* **
281915 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTAGCA-AT
281936 GTATCGATACAT
1 GTATCGATACAT
281948 TTCTTGGCAG
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGTAGCAAT
Found at i:281898 original size:21 final size:21
Alignment explanation
Indices: 281872--281947 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
281862 ACATGTCGCA
281872 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
281893 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
281913 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
281934 ATGTATCGATACAT
1 ATGTATCGATACAT
281948 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:281905 original size:41 final size:41
Alignment explanation
Indices: 281854--281947 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
281844 AGAATTCAAA
281854 GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
*
281895 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
281936 GTATCGATACAT
1 GTATCGATACAT
281948 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (41 bp):
GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
Found at i:283184 original size:8 final size:8
Alignment explanation
Indices: 283171--283196 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
283161 GTTTGTTTAA
283171 ATTTTGTG
1 ATTTTGTG
283179 ATTTTGTG
1 ATTTTGTG
283187 ATTTTGTG
1 ATTTTGTG
283195 AT
1 AT
283197 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:285991 original size:20 final size:20
Alignment explanation
Indices: 285948--285999 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
285938 CTTAACTGTT
*
285948 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
285967 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
285987 TGTATCGATACAT
1 TGTATCGATACAT
286000 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:290823 original size:28 final size:28
Alignment explanation
Indices: 290663--291009 Score: 360
Period size: 28 Copynumber: 12.0 Consensus size: 28
290653 CGTTCATCTC
*
290663 TTCAAAGCCCACAAGTC-GTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
290690 TTCAAAGCCTACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
290719 TTCAAAGCCCACACGAGTCAGTGGCAACTCCT
1 TTCAAAGCCCACA--AGTCAGTGGC-A-TCCT
* * *
290751 TTCAAAGCCTACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
290780 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
290808 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
290836 TTCAAAGCCCACAAGTCAATGACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
290865 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
290893 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
290921 TTCAAAGCCCA-ACAGTTAGTGGCACCCT
1 TTCAAAGCCCACA-AGTCAGTGGCATCCT
* * *
290949 TTCAAGGGCCACACAAGTC-GTGGTAACTCTT
1 TTCAA-AGCC-CACAAGTCAGTGG-CA-TCCT
*
290980 TTCAAAGCCCACACAAGTTAGTGGCA-CCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
291009 T
1 T
291010 GTTTTAAAAA
Statistics
Matches: 270, Mismatches: 36, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.06
28 115 0.43
29 74 0.27
30 16 0.06
31 28 0.10
32 21 0.08
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:290862 original size:85 final size:85
Alignment explanation
Indices: 290663--291007 Score: 403
Period size: 85 Copynumber: 4.0 Consensus size: 85
290653 CGTTCATCTC
* * * *
290663 TTCAAAGCCCACAAGTC-GTGGCAC-CCTTTCAAAGCCTACAAGTTAGTGGCACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAG
290726 CCCACACGAGTCAGTGGCAACTCCT
65 CCCACA--AGTCAGTGGC-AC-CCT
* * *
290751 TTCAAAGCCTACAAGTTAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
*
290816 CCACAAGTTAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* *
290836 TTCAAAGCCCACAAGTCAATGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
290901 CCACAAGTCAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* * * * *
290921 TTCAAAGCCCA-ACAGTTAGTGGCAC-CCTTTCAAGGGCCACACAAGTC-GTGGTAACTCTTTTC
1 TTCAAAGCCCACA-AGTCAGTGGCACTCTTTTCAA-AGCC-CACAAGTCAGTGG-CA-TCCTTTC
*
290983 AAAGCCCACACAAGTTAGTGGCACC
61 AAAG-CC-CACAAGTCAGTGGCACC
291008 TTGTTTTAAA
Statistics
Matches: 226, Mismatches: 22, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
84 8 0.04
85 109 0.48
86 11 0.05
87 19 0.08
88 17 0.08
89 39 0.17
90 23 0.10
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
CCACAAGTCAGTGGCACCCT
Found at i:290868 original size:57 final size:57
Alignment explanation
Indices: 290663--291007 Score: 432
Period size: 57 Copynumber: 6.0 Consensus size: 57
290653 CGTTCATCTC
* *
290663 TTCAAAGCCCACAAGTC-GTGGCAC-CCTTTCAAAGCCTACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCT
* *
290719 TTCAAAGCCCACACGAGTCAGTGGCAACTCCTTTCAAAGCCTACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCT
*
290780 TTTAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
* * * * *
290836 TTCAAAGCCCACAAGTCAATGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
290893 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCA-ACAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA-AGTTAGTGGCACCCT
* * *
290949 TTCAAGGGCCACACAAGTC-GTGGTAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAA-AGCC-CACAAGTCAGTGG-CACTCCTTTCAAAG-CC-CACAAGTTAGTGGCACC
291008 TTGTTTTAAA
Statistics
Matches: 258, Mismatches: 17, Indels: 23
0.87 0.06 0.08
Matches are distributed among these distances:
55 1 0.00
56 67 0.26
57 87 0.34
58 15 0.06
59 24 0.09
60 4 0.02
61 59 0.23
62 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
Found at i:292130 original size:13 final size:13
Alignment explanation
Indices: 292112--292137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
292102 TACAGCAAGT
292112 ATGTATCGATACA
1 ATGTATCGATACA
292125 ATGTATCGATACA
1 ATGTATCGATACA
292138 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:294385 original size:21 final size:21
Alignment explanation
Indices: 294352--294396 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
294342 TTGCAAGTTG
*
294352 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
294374 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
294394 AAA
1 AAA
294397 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:298323 original size:20 final size:20
Alignment explanation
Indices: 298244--298323 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
298234 AATGTCCAAA
*
298244 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
298264 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
298289 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
298309 TTGTATCGATACATT
1 ATGTATCGATACATT
298324 GTATTGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:298327 original size:13 final size:13
Alignment explanation
Indices: 298309--298347 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
298299 ACATTTTTCT
298309 TTGTATCGATACA
1 TTGTATCGATACA
*
298322 TTGTATTGATACA
1 TTGTATCGATACA
*
298335 CTGTATCGATACA
1 TTGTATCGATACA
298348 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:300825 original size:20 final size:20
Alignment explanation
Indices: 300802--300895 Score: 89
Period size: 21 Copynumber: 4.6 Consensus size: 20
300792 AGAATTCAAA
* *
300802 GTATCGATAAATGTCGCAAT
1 GTATCGATACATGTAGCAAT
* **
300822 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTAGCA-AT
*
300843 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTAGCAAT
* **
300863 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTAGCA-AT
300884 GTATCGATACAT
1 GTATCGATACAT
300896 TTCTTGGCAG
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 29 0.49
21 30 0.51
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGTAGCAAT
Found at i:300846 original size:21 final size:21
Alignment explanation
Indices: 300820--300895 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
300810 AAATGTCGCA
300820 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
300841 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
300861 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
300882 ATGTATCGATACAT
1 ATGTATCGATACAT
300896 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:300893 original size:41 final size:41
Alignment explanation
Indices: 300802--300895 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
300792 AGAATTCAAA
*
300802 GTATCGATAAATGTCGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
*
300843 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
300884 GTATCGATACAT
1 GTATCGATACAT
300896 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (41 bp):
GTATCGATACATGTCGCAATGTATCGATACATGAAAAAGAT
Found at i:300952 original size:13 final size:13
Alignment explanation
Indices: 300934--300959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300924 TACAGCAAGT
300934 ATGTATCGATACA
1 ATGTATCGATACA
300947 ATGTATCGATACA
1 ATGTATCGATACA
300960 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:306368 original size:13 final size:13
Alignment explanation
Indices: 306350--306376 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
306340 ACATGCTGCC
306350 TTGTATCGATACA
1 TTGTATCGATACA
306363 TTGTATCGATACA
1 TTGTATCGATACA
306376 T
1 T
306377 GTTCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:306409 original size:21 final size:20
Alignment explanation
Indices: 306362--306417 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
306352 GTATCGATAC
**
306362 ATTGTATCGATACATGTTCA
1 ATTGTATCGATACATGGACA
306382 A-TGTATCGATACATGGACAA
1 ATTGTATCGATACATGGAC-A
*
306402 ATTGTATCGTTACATG
1 ATTGTATCGATACATG
306418 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.48
20 3 0.10
21 13 0.42
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:310298 original size:33 final size:33
Alignment explanation
Indices: 310241--310305 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
310231 TAGCCAAACT
* * *
310241 TGTATCGATACACCAAAGTATGTATTGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
310274 TGTATCGATACACAAAAA-ATTGTATCGATACA
1 TGTATCGATACACAAAAATA-TGTATCGATACA
310306 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:314370 original size:15 final size:15
Alignment explanation
Indices: 314350--314380 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
314340 TAAAAATGTC
*
314350 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
314365 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
314380 C
1 C
314381 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:316471 original size:13 final size:13
Alignment explanation
Indices: 316453--316490 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
316443 CATTTTTCTT
316453 TGTATCGATACAA
1 TGTATCGATACAA
*
316466 TGTATCGATACAC
1 TGTATCGATACAA
316479 TGTATCGATACA
1 TGTATCGATACA
316491 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:316645 original size:20 final size:19
Alignment explanation
Indices: 316604--316646 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
316594 ATCTTTTGCA
316604 AAATTCTTGTTTTTCACTTC
1 AAATTCTTGTTTTTCAC-TC
316624 AAATTACTTCGTTTTTCA-TC
1 AAATT-CTT-GTTTTTCACTC
316644 AAA
1 AAA
316647 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (19 bp):
AAATTCTTGTTTTTCACTC
Found at i:319064 original size:13 final size:13
Alignment explanation
Indices: 319046--319071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
319036 ACACCAAAGT
319046 ATGTATCGATACA
1 ATGTATCGATACA
319059 ATGTATCGATACA
1 ATGTATCGATACA
319072 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:319069 original size:33 final size:33
Alignment explanation
Indices: 319027--319090 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
319017 TAGCCAAACT
* *
319027 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
319060 TGTATCGATACACAAAAAATTGTATCGATAC
1 TGTATCGATACACAAAAAATTGTATCGATAC
319091 CTTGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:320286 original size:13 final size:13
Alignment explanation
Indices: 320268--320292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320258 CAATTTTTTG
320268 TGTATCGATACAT
1 TGTATCGATACAT
320281 TGTATCGATACA
1 TGTATCGATACA
320293 AGTTTGGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:323732 original size:13 final size:13
Alignment explanation
Indices: 323714--323741 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
323704 CAACATTCCC
323714 TGTATCGATACAT
1 TGTATCGATACAT
323727 TGTATCGATACAT
1 TGTATCGATACAT
323740 TG
1 TG
323742 GGTACTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:325654 original size:56 final size:57
Alignment explanation
Indices: 325540--325659 Score: 222
Period size: 57 Copynumber: 2.1 Consensus size: 57
325530 TGAAAATAAA
325540 TTTTTACATAATTTTTACATAAAGGGGAGAAGATAACTGTTTAAGGGGGAGACTTTT
1 TTTTTACATAATTTTTACATAAAGGGGAGAAGATAACTGTTTAAGGGGGAGACTTTT
* *
325597 TTTTTACATAATTTTTACATAAGGGGGAGAAGATAACTGTTTAAGGGGGAGATTTTT
1 TTTTTACATAATTTTTACATAAAGGGGAGAAGATAACTGTTTAAGGGGGAGACTTTT
325654 TTTTTA
1 TTTTTA
325660 AAGGAAAAAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (57 bp):
TTTTTACATAATTTTTACATAAAGGGGAGAAGATAACTGTTTAAGGGGGAGACTTTT
Found at i:326208 original size:20 final size:20
Alignment explanation
Indices: 326185--326257 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
326175 CACACCCAGA
326185 TGTATCGATACATGCTGCCT
1 TGTATCGATACATGCTGCCT
326205 TGTATCGATACATGCTGCCT
1 TGTATCGATACATGCTGCCT
* **
326225 TGTATCGATACATG-TTCAA
1 TGTATCGATACATGCTGCCT
326244 TGTATCGATACATG
1 TGTATCGATACATG
326258 GACAAATTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
19 16 0.32
20 34 0.68
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTGCCT
Found at i:326270 original size:21 final size:20
Alignment explanation
Indices: 326224--326278 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
326214 ACATGCTGCC
**
326224 TTGTATCGATACATGTTCAA
1 TTGTATCGATACATGGACAA
326244 -TGTATCGATACATGGACAAA
1 TTGTATCGATACATGGAC-AA
326264 TTGTATCGATACATG
1 TTGTATCGATACATG
326279 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 15 0.48
20 2 0.06
21 14 0.45
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:326344 original size:13 final size:13
Alignment explanation
Indices: 326323--326353 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
326313 CGATACATGG
*
326323 TACAATGTATCGA
1 TACATTGTATCGA
326336 TACATTGTATCGA
1 TACATTGTATCGA
326349 TACAT
1 TACAT
326354 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:326349 original size:33 final size:32
Alignment explanation
Indices: 326307--326373 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
326297 CTATGACTAT
326307 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
326340 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
326373 T
1 T
326374 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:329239 original size:79 final size:79
Alignment explanation
Indices: 329142--329389 Score: 250
Period size: 79 Copynumber: 3.1 Consensus size: 79
329132 AACGGGGTCA
* ** * * * *
329142 GAGTA-CCCCTTAAGAAATAACATGGTTAGAGTATCCCTAATGGTGGAAAATCGATGTTTTAGGA
1 GAGTATCCCCTTAA-AAATAACAAGGTTAGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAA
*
329206 GTAAAA-TCAAGGTTG
65 ATAAAACT-AAGGTTG
* * * *
329221 GAGTATCCCCTCAAAAATAACAAGATTAAAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAA
1 GAGTATCCCCTTAAAAATAACAAGGTTAGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAA
**
329286 TAAAACTGGGGTTG
66 TAAAACTAAGGTTG
* * * *
329300 GAGTATCCCCTTAGAAATAACAGGGCTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTT-GAAA
1 GAGTATCCCCTTAAAAATAACAAGGTTAGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAG-AA
* ** *
329364 ATGAAACCGAGGTTA
65 ATAAAACTAAGGTTG
329379 GAGTATCCCCT
1 GAGTATCCCCT
329390 CGGAAATAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
78 1 0.01
79 131 0.94
80 8 0.06
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (79 bp):
GAGTATCCCCTTAAAAATAACAAGGTTAGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAA
TAAAACTAAGGTTG
Found at i:331827 original size:50 final size:50
Alignment explanation
Indices: 331720--331851 Score: 203
Period size: 50 Copynumber: 2.7 Consensus size: 50
331710 AAAAATGCCT
* *
331720 GAATGTATCGATACATTGAAAAATGTATCGAT-CATCTAGGTAAAACCCA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCAA
* *
331769 GAATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAACCAA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCAA
* *
331819 GAATGTATCAATACAATGAACAATGTATCGATA
1 GAATGTATCGATACAATGAAAAATGTATCGATA
331852 GAAATTGTGA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 30 0.39
50 46 0.61
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (50 bp):
GAATGTATCGATACAATGAAAAATGTATCGATACATCTAGGTAAAACCAA
Found at i:332970 original size:52 final size:52
Alignment explanation
Indices: 332875--333129 Score: 247
Period size: 52 Copynumber: 5.0 Consensus size: 52
332865 ATGAAAAAGG
* * * * * *
332875 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAAAGATGCGAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
* *
332927 TGTCAATGTGCTGATTCACA-GCCAGCGACATTAGACTTGAAGATGAGAAGAA
1 TGCCAATGTGCTGATTCA-AGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
* * * *
332979 TGCCAATGTGCTGATTCAAGGCTAACGACATTAGGCTTAGGAATG-TTA-AAG-A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTA--AA-GATGAGAAGAA
* * * *
333031 TGCCAATATGCTAATTCAAGGCCAGTGATATTAGACTTAAAGATGATG--G--
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGA-GAAGAA
**
333080 TGCCAATGTGCTGATTCAAGGCCAATGACATTAGACTTAAAGATGAGAAG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAG
333130 GATGATAAAG
Statistics
Matches: 167, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
48 1 0.01
49 43 0.26
50 6 0.04
51 1 0.01
52 107 0.64
53 4 0.02
54 4 0.02
55 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAA
Found at i:333072 original size:43 final size:43
Alignment explanation
Indices: 333024--333124 Score: 112
Period size: 49 Copynumber: 2.2 Consensus size: 43
333014 CTTAGGAATG
* *
333024 TTAAAGATGCCAATATGCTAATTCAAGGCCAGTGATATTAGAC
1 TTAAAGATGCCAATATGCTAATTCAAGGCCAATGACATTAGAC
* *
333067 TTAAAGATGATGGTGCCAATGTGCTGATTCAAGGCCAATGACATTAGAC
1 TT-AA-A-GA---TGCCAATATGCTAATTCAAGGCCAATGACATTAGAC
333116 TTAAAGATG
1 TTAAAGATG
333125 AGAAGGATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
43 4 0.08
44 2 0.04
45 1 0.02
46 4 0.08
47 1 0.02
48 2 0.04
49 34 0.71
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (43 bp):
TTAAAGATGCCAATATGCTAATTCAAGGCCAATGACATTAGAC
Found at i:333217 original size:43 final size:43
Alignment explanation
Indices: 333135--333217 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
333125 AGAAGGATGA
* * *
333135 TAAAGGTGCCAATATACTGATTCAAGGCTAGCGATATTGGATT
1 TAAAGGTGCCAATATACTGATTCAAGGCCAACGACATTGGATT
* *
333178 TAAAGGTGCCAATGTGA-TGATTGAAGGCCAACGACATTGG
1 TAAAGGTGCCAATAT-ACTGATTCAAGGCCAACGACATTGG
333218 GCTTAGAAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (43 bp):
TAAAGGTGCCAATATACTGATTCAAGGCCAACGACATTGGATT
Found at i:333276 original size:32 final size:32
Alignment explanation
Indices: 333231--333480 Score: 238
Period size: 32 Copynumber: 7.9 Consensus size: 32
333221 TAGAAGGATA
*
333231 TGCCCCCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
333263 TGCCACTAACTTGTGTGGGC-TTTAAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGA-AAGGGT
* * * *
333295 TACCACCAGCTTGTATGGG-TTTTGAAGGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
333326 TGCCACCAACTTGTGCGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* ** **
333358 TGCAACTGACTTGTGTGGGCTTCAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* * * * **
333390 CGCCACTAGCTTGTATGGGC-TTTGAAGAATGT
1 TGCCACCAACTTGTGTGGGCTTTTGAA-AGGGT
* *
333422 TGCCACCAATTTGTGTGGGCTTTGGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
333454 TGCCACCGACTTGTGTAGGC-TTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTTGAAA
333481 AAGCGTTCTC
Statistics
Matches: 172, Mismatches: 41, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
31 34 0.20
32 133 0.77
33 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
Found at i:333388 original size:95 final size:96
Alignment explanation
Indices: 333222--333475 Score: 323
Period size: 95 Copynumber: 2.6 Consensus size: 96
333212 CATTGGGCTT
* * * *
333222 AGAAGGATATGCCCCCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACTAACTTGTGTGGGCTTTA
1 AGAAGG-T-TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACTGACTTGTGTGGGCTTCA
* *
333287 AGAAGGGTTACCACCAGCTTGTATGGGTTTTGA
64 AGAAGGGTCACCACCAGCTTGTATGGGCTTTGA
* * *
333320 AG-GGGTTGCCACCAACTTGTGCGGGCTTTAGAAAGGGTTGCAACTGACTTGTGTGGGCTTC-AG
1 AGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACTGACTTGTGTGGGCTTCAAG
* *
333383 AAAGGGTCGCCACTAGCTTGTATGGGCTTTGA
66 -AAGGGTCACCACCAGCTTGTATGGGCTTTGA
* * * * *
333415 AGAATGTTGCCACCAATTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGTAGGCTT
1 AGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACTGACTTGTGTGGGCTT
333476 TGAAAAAGCG
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
94 2 0.01
95 78 0.58
96 51 0.38
97 2 0.01
98 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (96 bp):
AGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACTGACTTGTGTGGGCTTCAAG
AAGGGTCACCACCAGCTTGTATGGGCTTTGA
Found at i:334655 original size:16 final size:14
Alignment explanation
Indices: 334612--334659 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
334602 TGCAAATACA
*
334612 CATGAATTGGAATG
1 CATGAATAGGAATG
**
334626 CATGAATACAAATG
1 CATGAATAGGAATG
334640 CTTATGAATAGGAATG
1 C--ATGAATAGGAATG
334656 CATG
1 CATG
334660 CGAAAACTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 15 0.56
16 12 0.44
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (14 bp):
CATGAATAGGAATG
Found at i:335564 original size:62 final size:61
Alignment explanation
Indices: 335467--335595 Score: 222
Period size: 62 Copynumber: 2.1 Consensus size: 61
335457 ATAGTGAACT
335467 TTGAATTAGTAAAACTTAAGGTTTTTATTTTCAAAATTCATTTAAGAATTTAAGGATTATAG
1 TTGAATTAGTAAAACTTAAGGTTTTTATTTTCAAAATTCATTTAAGAA-TTAAGGATTATAG
* * *
335529 TTGAATTATTAAAACTTAGGGTTTTTATTTTCAAAATTCATTTAAGGATTAAGGATTATAG
1 TTGAATTAGTAAAACTTAAGGTTTTTATTTTCAAAATTCATTTAAGAATTAAGGATTATAG
335590 TTGAAT
1 TTGAAT
335596 ATTGATAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
61 19 0.30
62 45 0.70
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (61 bp):
TTGAATTAGTAAAACTTAAGGTTTTTATTTTCAAAATTCATTTAAGAATTAAGGATTATAG
Found at i:338372 original size:34 final size:35
Alignment explanation
Indices: 338303--338375 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
338293 AGTGTTTGTG
*
338303 GAAAGAATAAGCACAAAGGAATACAAATGAGCTTT
1 GAAAGAATAAGCACAAAGGAATACAAAAGAGCTTT
* **
338338 GAAAGAATAA-CAACAAA-GAATATAAAAGCTCTTT
1 GAAAGAATAAGC-ACAAAGGAATACAAAAGAGCTTT
338372 GAAA
1 GAAA
338376 TATAGAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (35 bp):
GAAAGAATAAGCACAAAGGAATACAAAAGAGCTTT
Found at i:339602 original size:31 final size:32
Alignment explanation
Indices: 339566--339635 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
339556 AGATAAAGTG
* *
339566 AAATATGAATCAATAAACAA-TTTGATGTAGA
1 AAATATGAATCAATAAACAACATTCATGTAGA
339597 AAATATGAATCAATAAACAAGCATTCATGTAGA
1 AAATATGAATCAATAAACAA-CATTCATGTAGA
339630 AAATAT
1 AAATAT
339636 CAAGACATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 20 0.57
33 15 0.43
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (32 bp):
AAATATGAATCAATAAACAACATTCATGTAGA
Found at i:341357 original size:20 final size:20
Alignment explanation
Indices: 341329--341380 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
341319 TAGTACCCAT
* *
341329 GTATCGATACAAAGAACTTA
1 GTATAGATACAAAGAACTCA
*
341349 GTATGGATACAAAGAACTCA
1 GTATAGATACAAAGAACTCA
341369 GTATAGATACAA
1 GTATAGATACAA
341381 TGTATTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.23
Consensus pattern (20 bp):
GTATAGATACAAAGAACTCA
Found at i:344220 original size:19 final size:19
Alignment explanation
Indices: 344176--344229 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
344166 TGTCAATTTT
**
344176 ATGTATCGATACAATTCATG
1 ATGTATCGATA-AATTCAAC
344196 ATGTATCGATATAATT-AAC
1 ATGTATCGATA-AATTCAAC
344215 ATGTATCGATAAATT
1 ATGTATCGATAAATT
344230 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 15 0.48
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (19 bp):
ATGTATCGATAAATTCAAC
Found at i:344257 original size:33 final size:32
Alignment explanation
Indices: 344197--344258 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
344187 CAATTCATGA
**
344197 TGTATCGATATAATTAACATGTATCGATAAAT
1 TGTATCGATATAAGCAACATGTATCGATAAAT
*
344229 TGTATCGATACTAAGCAATATGTATCGATA
1 TGTATCGATA-TAAGCAACATGTATCGATA
344259 TATCTGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATATAAGCAACATGTATCGATAAAT
Found at i:344753 original size:20 final size:20
Alignment explanation
Indices: 344730--344767 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
344720 ATAACTCAAG
344730 AGGATCATT-AAAAAAGTTCA
1 AGGAT-ATTCAAAAAAGTTCA
*
344750 AGGATATTCAATAAAGTT
1 AGGATATTCAAAAAAGTT
344768 TCGAAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (20 bp):
AGGATATTCAAAAAAGTTCA
Found at i:346585 original size:23 final size:24
Alignment explanation
Indices: 346540--346586 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
346530 TCAAAAGATT
*
346540 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
346564 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
346587 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:350408 original size:19 final size:18
Alignment explanation
Indices: 350384--350446 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
350374 AGCGATACAT
350384 TGTATCGATACAATACTTA
1 TGTATCGATACAA-ACTTA
350403 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
350416 TGTATCGCTACAACACTTA
1 TGTATCGATACAA-ACTTA
350435 TGTATCGATACA
1 TGTATCGATACA
350447 TTTATTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:350412 original size:32 final size:32
Alignment explanation
Indices: 350362--350448 Score: 131
Period size: 32 Copynumber: 2.7 Consensus size: 32
350352 ATTTCCTTGG
*
350362 CAATAGCTT-TGTAGCGATACATTGTATCGATA
1 CAATA-CTTATGTATCGATACATTGTATCGATA
*
350394 CAATACTTATGTATCGATACATTGTATCGCTA
1 CAATACTTATGTATCGATACATTGTATCGATA
*
350426 CAACACTTATGTATCGATACATT
1 CAATACTTATGTATCGATACATT
350449 TATTGTTTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
31 3 0.06
32 48 0.94
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (32 bp):
CAATACTTATGTATCGATACATTGTATCGATA
Done.