Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold395
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: 363785
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 3
Found at i:183010 original size:17 final size:16
Alignment explanation
Indices: 182987--183056 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
182977 TTCTCTTTTA
182987 AAAAAAAACAACAAAA-
1 AAAAAAAACAA-AAAAC
183003 ATAAAAAAACAAAAAAC
1 A-AAAAAAACAAAAAAC
*
183020 AAAAAAAACATAAAGAAA
1 AAAAAAAACA-AAA-AAC
*
183038 AAAAAAAAGAAAAAA-
1 AAAAAAAACAAAAAAC
183053 AAAA
1 AAAA
183057 GAGAATCTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
15 4 0.08
16 16 0.33
17 17 0.35
18 11 0.23
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAAAAACAAAAAAC
Found at i:183039 original size:30 final size:29
Alignment explanation
Indices: 182987--183056 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
182977 TTCTCTTTTA
*
182987 AAAAAAAACAACAAAAATAAAAAAACAAAA-
1 AAAAAAAA-AACAAAAAGAAAAAAA-AAAAG
*
183017 AACAAAAAAAACATAAAGAAAAAAAAAAAG
1 AA-AAAAAAAACAAAAAGAAAAAAAAAAAG
183047 AAAAAAAAAA
1 AAAAAAAAAA
183057 GAGAATCTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 12 0.33
30 18 0.50
31 6 0.17
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (29 bp):
AAAAAAAAAACAAAAAGAAAAAAAAAAAG
Found at i:184196 original size:54 final size:57
Alignment explanation
Indices: 184125--184253 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 57
184115 CTCCTTTCAC
*
184125 CCTTT-AGTCCTCAAAGAGCAGGACGCCTT-T-C-AAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTC-AAGAGCAGGACGCCTTCTCCTAAAGCCCACACAAATTGGTGGCA
184179 CCTTTCAGTCCTCAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCA
1 CCTTTCAGTCCTCAAGAGCAGGACGCCTTCTCC---TAAAGCCCACACAAATTGGTGGCA
*
184239 CTTTTCAGTCCTCAA
1 CCTTTCAGTCCTCAA
184254 AAGGATGCTT
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
54 21 0.32
55 8 0.12
56 1 0.02
60 36 0.55
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (57 bp):
CCTTTCAGTCCTCAAGAGCAGGACGCCTTCTCCTAAAGCCCACACAAATTGGTGGCA
Found at i:187160 original size:51 final size:51
Alignment explanation
Indices: 187084--187220 Score: 152
Period size: 51 Copynumber: 2.7 Consensus size: 51
187074 TTCATCTCGG
* * * *
187084 GGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATT-TCTCTTAATCGA
1 GGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTCTC-CATAATCGA
* * * *
187135 GGATACTCCAACTTCGATTTTATTTCTAAAACACCCATTCTCCATAATCGG
1 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTCTCCATAATCGA
* *
187186 GGATACTCTAACTCCGATTTTATTTCCAGAACACC
1 GGATACTCCAACTCCGATTTTATTTCCAAAACACC
187221 GACTTTTCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
51 69 0.96
52 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTCTCCATAATCGA
Found at i:187240 original size:51 final size:51
Alignment explanation
Indices: 187083--187248 Score: 142
Period size: 51 Copynumber: 3.3 Consensus size: 51
187073 TTTCATCTCG
* * * * **
187083 GGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATT-TCTCTTAATC-
1 GGGATACTCCAACT-CCGATTTTATTTCCAAAACACCCATTCTC-CACAATCA
* * * *
187133 GAGGATACTCCAACTTCGATTTTATTTCTAAAACACCCATTCTCCATAATCG
1 G-GGATACTCCAACTCCGATTTTATTTCCAAAACACCCATTCTCCACAATCA
* * * *
187185 GGGATACTCTAACTCCGATTTTATTTCCAGAACACCGACTT-TTCACAATCA
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCCA-TTCTCCACAATCA
187236 GGGATACTCCAAC
1 GGGATACTCCAAC
187249 CCCGTTATTT
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
50 1 0.01
51 88 0.93
52 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACACCCATTCTCCACAATCA
Found at i:187333 original size:76 final size:76
Alignment explanation
Indices: 187236--187381 Score: 197
Period size: 76 Copynumber: 1.9 Consensus size: 76
187226 TTCACAATCA
* *
187236 GGGATACTCCAACCCCGTTA-TTTCTAAGGGGACACTCCAA-CCTCGGTTTTATTTCTAAAACAT
1 GGGATACTCCAACCCCATTATTTTC-AAGGGGACACTCCAATCC-CGATTTTATTTCTAAAACAT
187299 CAATTTTTCATCG
64 CAATTTTTCATCG
* * * * *
187312 GGGATACTCCAACCCCATTATTTTCACGGGGATACTCCAATCCCGATTTTATTTTTGAAACATCT
1 GGGATACTCCAACCCCATTATTTTCAAGGGGACACTCCAATCCCGATTTTATTTCTAAAACATCA
187377 ATTTT
66 ATTTT
187382 CTATGATGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
76 55 0.90
77 6 0.10
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (76 bp):
GGGATACTCCAACCCCATTATTTTCAAGGGGACACTCCAATCCCGATTTTATTTCTAAAACATCA
ATTTTTCATCG
Found at i:189532 original size:11 final size:11
Alignment explanation
Indices: 189515--189547 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
189505 TAAAAAATTA
189515 AATAATTATTT
1 AATAATTATTT
*
189526 GATAATTATTT
1 AATAATTATTT
189537 AATAA-TATTT
1 AATAATTATTT
189547 A
1 A
189548 CGTGAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
AATAATTATTT
Found at i:193482 original size:18 final size:18
Alignment explanation
Indices: 193459--193494 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
193449 GCTAAGCCTT
193459 GGAGTCATTAGACGCTTC
1 GGAGTCATTAGACGCTTC
*
193477 GGAGTCATTGGACGCTTC
1 GGAGTCATTAGACGCTTC
193495 ATAACTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (18 bp):
GGAGTCATTAGACGCTTC
Found at i:196714 original size:13 final size:13
Alignment explanation
Indices: 196696--196721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
196686 CAAATGTATC
196696 GATACATTTTTTA
1 GATACATTTTTTA
196709 GATACATTTTTTA
1 GATACATTTTTTA
196722 TTGTATCGAT
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
GATACATTTTTTA
Found at i:196719 original size:64 final size:64
Alignment explanation
Indices: 196645--196770 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 64
196635 AAAATGTATC
*
196645 GATACATTTTTTATTGTATCAATAAATGTTGGGTTTTAGCCCAAATGTATCGATACATTTTTTA
1 GATACATTTTTTATTGTATCAATAAATGTTAGGTTTTAGCCCAAATGTATCGATACATTTTTTA
* *
196709 GATACATTTTTTATTGTATCGATACATGTTAGGTTTTAGCCCAAATGTATCGATACATTTTT
1 GATACATTTTTTATTGTATCAATAAATGTTAGGTTTTAGCCCAAATGTATCGATACATTTTT
196771 CATTGTATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (64 bp):
GATACATTTTTTATTGTATCAATAAATGTTAGGTTTTAGCCCAAATGTATCGATACATTTTTTA
Found at i:196821 original size:52 final size:51
Alignment explanation
Indices: 196709--196831 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
196699 ACATTTTTTA
* *
196709 GATACATTTTTTATTGTATCGATACATGTTAGGTTTTAGCCCAAATGTATC
1 GATACATTTTTCATTGTATCGATACATGTTAGCTTTTAGCCCAAATGTATC
* *
196760 GATACATTTTTCATTGTATCGATATAT-TCTAGCTTTTTGACCCAAATGTATC
1 GATACATTTTTCATTGTATCGATACATGT-TAGCTTTTAG-CCCAAATGTATC
*
196812 GATACATTTTTCAATGTATC
1 GATACATTTTTCATTGTATC
196832 AACACATGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 1 0.02
51 33 0.51
52 31 0.48
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (51 bp):
GATACATTTTTCATTGTATCGATACATGTTAGCTTTTAGCCCAAATGTATC
Found at i:198111 original size:19 final size:19
Alignment explanation
Indices: 198068--198140 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
198058 CACACTCAGA
*
198068 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
198088 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
198107 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
*
198127 TGTATTGATACATG
1 TGTATCGATACATG
198141 AGATTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:203332 original size:21 final size:22
Alignment explanation
Indices: 203296--203357 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
203286 AAAAAATGCC
203296 TTGATTAAGGGGGGAGAAATT-T
1 TTGATTAA-GGGGGAGAAATTCT
*
203318 TTGATTAAAGGGGAGAAATTCT
1 TTGATTAAGGGGGAGAAATTCT
*
203340 TTAATTAAGGGGGAGAAA
1 TTGATTAAGGGGGAGAAA
203358 AATGAAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 11 0.31
22 25 0.69
ACGTcount: A:0.37, C:0.02, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGATTAAGGGGGAGAAATTCT
Found at i:204011 original size:13 final size:13
Alignment explanation
Indices: 203990--204042 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
203980 CGATACATGG
*
203990 TACAATGTATCGA
1 TACATTGTATCGA
204003 TACATTGTATCGA
1 TACATTGTATCGA
204016 TACA-TG-AT-G-
1 TACATTGTATCGA
204025 -A-ATTGTATCGA
1 TACATTGTATCGA
204036 TACATTG
1 TACATTG
204043 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:204016 original size:33 final size:33
Alignment explanation
Indices: 203974--204042 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
203964 CTACCACTGT
*
203974 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
204007 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
204040 TTG
1 TTG
204043 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:204492 original size:13 final size:13
Alignment explanation
Indices: 204474--204499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
204464 TACAGCAAGT
204474 ATGTATCGATACA
1 ATGTATCGATACA
204487 ATGTATCGATACA
1 ATGTATCGATACA
204500 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:205697 original size:20 final size:19
Alignment explanation
Indices: 205643--205698 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
205633 AAACCCTTTA
*
205643 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
205663 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
205683 AATGTATCGATACATG
1 AAAGTATCGATACATG
205699 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:209869 original size:15 final size:15
Alignment explanation
Indices: 209849--209879 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
209839 TAAAAATGTC
*
209849 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
209864 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
209879 C
1 C
209880 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:211979 original size:13 final size:13
Alignment explanation
Indices: 211961--211996 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
211951 CATTTTTCTT
211961 TGTATCGATACAA
1 TGTATCGATACAA
*
211974 TGTATCGATACAC
1 TGTATCGATACAA
211987 TGTATCGATA
1 TGTATCGATA
211997 TAGGGGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:213899 original size:43 final size:43
Alignment explanation
Indices: 213843--213928 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
213833 AGATAAAGGG
213843 GAGAATGCGTGAATTATCTTATTAAGGGGGAGAATGTACGAAT
1 GAGAATGCGTGAATTATCTTATTAAGGGGGAGAATGTACGAAT
*
213886 GAGAATGCGTGAATTATTTTATTAAGGGGGAGAATGTACGAAT
1 GAGAATGCGTGAATTATCTTATTAAGGGGGAGAATGTACGAAT
213929 TTGTTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (43 bp):
GAGAATGCGTGAATTATCTTATTAAGGGGGAGAATGTACGAAT
Found at i:214515 original size:20 final size:19
Alignment explanation
Indices: 214461--214516 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
214451 AAACCCTTTA
*
214461 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
214481 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
214501 AATGTATCGATACATG
1 AAAGTATCGATACATG
214517 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:214605 original size:13 final size:13
Alignment explanation
Indices: 214587--214611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
214577 ACATAAAATC
214587 TGTATCGATACAA
1 TGTATCGATACAA
214600 TGTATCGATACA
1 TGTATCGATACA
214612 CAAAAAATAT
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:214625 original size:34 final size:34
Alignment explanation
Indices: 214568--214666 Score: 166
Period size: 34 Copynumber: 3.0 Consensus size: 34
214558 TAGCCAAACT
* *
214568 TGTATCGAT--ACATAAAATCTGTATCGATACAA
1 TGTATCGATACACAAAAAATATGTATCGATACAA
214600 TGTATCGATACACAAAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATATGTATCGATACAA
214634 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACACAAAAAATATGTATCGATACA
214667 TAACGGCTAG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.14
34 54 0.86
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAATATGTATCGATACAA
Found at i:214638 original size:13 final size:13
Alignment explanation
Indices: 214620--214645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
214610 CACAAAAAAT
214620 ATGTATCGATACA
1 ATGTATCGATACA
214633 ATGTATCGATACA
1 ATGTATCGATACA
214646 CAAAAAATAT
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:218883 original size:12 final size:14
Alignment explanation
Indices: 218854--218882 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
218844 GGAATGGATC
218854 TTTGTTGAGTGTTT
1 TTTGTTGAGTGTTT
218868 TTTGTTGA-TGTTT
1 TTTGTTGAGTGTTT
218881 TT
1 TT
218883 GGATGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.69
Consensus pattern (14 bp):
TTTGTTGAGTGTTT
Found at i:219419 original size:20 final size:20
Alignment explanation
Indices: 219374--219450 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
219364 GAAAACCTGG
*
219374 AATGTATCGATACA--AAGCA
1 AATGTATCGATACATTTA-CA
*
219393 AATTGTATCGATACATTTCCA
1 AA-TGTATCGATACATTTACA
*
219414 AATGTATCGATACATTTACT
1 AATGTATCGATACATTTACA
* *
219434 TATATATCGATACATTT
1 AATGTATCGATACATTT
219451 TTTTCGACCA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.04
20 43 0.88
21 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTTACA
Found at i:219522 original size:20 final size:20
Alignment explanation
Indices: 219497--219535 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
219487 CATTTGAGAC
*
219497 ATGTATCGATACATTCACTT
1 ATGTATCAATACATTCACTT
219517 ATGTATCAATACATTCACT
1 ATGTATCAATACATTCACT
219536 AATTATATCG
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:0.21, G:0.08, T:0.38
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:220532 original size:13 final size:13
Alignment explanation
Indices: 220514--220539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
220504 TTCTATAATT
220514 TGTATCGATACAA
1 TGTATCGATACAA
220527 TGTATCGATACAA
1 TGTATCGATACAA
220540 AACTACCTTC
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):
TGTATCGATACAA
Found at i:224988 original size:79 final size:78
Alignment explanation
Indices: 224640--224974 Score: 435
Period size: 79 Copynumber: 4.2 Consensus size: 78
224630 AATATCGAAT
* *
224640 TTTTCATCATAGGGATACTCCAACCTCATTATTTTCGAAGGGATACTCCAACCCCATTTTTATTT
1 TTTTCATC-TCGGGATACTCCAACCCCATTATTTTCGAAGGGATACTCCAACCCCATTTTTATTT
224705 T-AAAATATTAAAA
65 TCAAAATATTAAAA
* *
224718 TTTTCATCTCAGGGATACTCCAACCCCATTATTTTCGAAGGGATACTTCAACCCTATTTTTATTT
1 TTTTCATCTC-GGGATACTCCAACCCCATTATTTTCGAAGGGATACTCCAACCCCATTTTTATTT
*
224783 CCAAAATATTAAAA
65 TCAAAATATTAAAA
* * *
224797 TTTTCGTCTCGAGGATACTCTAACCCCATTATTTTC-AAGGGGATACTCCAACCCCGTTTTTA-T
1 TTTTCATCTCG-GGATACTCCAACCCCATTATTTTCGAA-GGGATACTCCAACCCCATTTTTATT
*
224860 TTCTAAAGTATTAAAA
64 TTC-AAAATATTAAAA
* * * *
224876 TTTTCATCTCGAGGATACTCCAAACCCATTA-TTTCTGAGGGGATACTCTAATCCCATTTTTATT
1 TTTTCATCTCG-GGATACTCCAACCCCATTATTTTC-GAAGGGATACTCCAACCCCATTTTTATT
*
224940 TTCAAAATATTAAAT
64 TTCAAAATATTAAAA
224955 TTTTCATCATCGGTGATACT
1 TTTTCATC-TCGG-GATACT
224975 TCAATCTCGT
Statistics
Matches: 226, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
77 1 0.00
78 69 0.31
79 142 0.63
80 14 0.06
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (78 bp):
TTTTCATCTCGGGATACTCCAACCCCATTATTTTCGAAGGGATACTCCAACCCCATTTTTATTTT
CAAAATATTAAAA
Found at i:224988 original size:158 final size:157
Alignment explanation
Indices: 224637--225012 Score: 473
Period size: 157 Copynumber: 2.4 Consensus size: 157
224627 TATAATATCG
* * *
224637 AATTTTTCATCATAGGGATACTCCAACCTCATTATTTTCGAA-GGGATACTCCAACCCCATTTTT
1 AATTTTTCATCATCGGGATACTTCAACCTCATTATTTTC-AAGGGGATACTCCAACCCCGTTTTT
*
224701 ATTTTAAAATATTAAAATTTTCATCTCAGGGATACTCCAACCCCATTATTTTCGAAGGGATACTT
65 ATTTTAAAATATTAAAATTTTCATCTCAGGGATACTCCAAACCCATTATTTTCGAAGGGATACTT
224766 CAACCCTATTTTTATTTCCAAAATATTA
130 CAACCCTATTTTTATTTCCAAAATATTA
* * *
224794 AAATTTTCGTC-TCGAGGATAC-TCTAACCCCATTATTTTCAAGGGGATACTCCAACCCCGTTTT
1 AATTTTTCATCATCG-GGATACTTC-AACCTCATTATTTTCAAGGGGATACTCCAACCCCGTTTT
* *
224857 TATTTCTAAAGTATTAAAATTTTCATCTC-GAGGATACTCCAAACCCATTA-TTTCTGAGGGGAT
64 TATTT-TAAAATATTAAAATTTTCATCTCAG-GGATACTCCAAACCCATTATTTTC-GAAGGGAT
*
224920 AC-TCTAATCCC-ATTTTTATTTTCAAAATATTA
126 ACTTC-AA-CCCTATTTTTATTTCCAAAATATTA
* * * * *
224952 AATTTTTCATCATCGGTGATACTTCAATCTC-GTA-TTTAAAGGGGACACTCCAACCCTGTTT
1 AATTTTTCATCATCGG-GATACTTCAACCTCATTATTTTCAAGGGGATACTCCAACCCCGTTT
225013 CTTTTTGAAT
Statistics
Matches: 190, Mismatches: 18, Indels: 22
0.83 0.08 0.10
Matches are distributed among these distances:
156 5 0.03
157 85 0.45
158 83 0.44
159 15 0.08
160 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (157 bp):
AATTTTTCATCATCGGGATACTTCAACCTCATTATTTTCAAGGGGATACTCCAACCCCGTTTTTA
TTTTAAAATATTAAAATTTTCATCTCAGGGATACTCCAAACCCATTATTTTCGAAGGGATACTTC
AACCCTATTTTTATTTCCAAAATATTA
Found at i:225032 original size:158 final size:158
Alignment explanation
Indices: 224652--225012 Score: 391
Period size: 158 Copynumber: 2.3 Consensus size: 158
224642 TTCATCATAG
* * * * * * * *
224652 GGATACTCCAACCTCATTATTTTCGAA-GGGATACTCCAACCCCATTTTTATTT-TAAAATATTA
1 GGATACTCTAACCCCAGTATTTT-AAAGGGGACACTCCAACCCCGTTTTTATTTCGAAACTATTA
*
224715 AAATTTTCATCTCAGGGATACTCCAACCCCATTATTTTCGAAGGGATACTTCAACCCTATTTTTA
65 AAATTTTCATCTCAGGGATACTCCAAACCCATTATTTTCGAAGGGATACTTCAACCCTATTTTTA
*
224780 TTTCCAAAATATTAAAATTTTCGTCTCGA
130 TTTCCAAAATATTAAAATTTTCATCTCGA
* * * * *
224809 GGATACTCTAACCCCATTATTTTCAAGGGGATACTCCAACCCCGTTTTTATTTCTAAAGTATTAA
1 GGATACTCTAACCCCAGTATTTTAAAGGGGACACTCCAACCCCGTTTTTATTTCGAAACTATTAA
*
224874 AATTTTCATCTC-GAGGATACTCCAAACCCATTA-TTTCTGAGGGGATAC-TCTAATCCC-ATTT
66 AATTTTCATCTCAG-GGATACTCCAAACCCATTATTTTC-GAAGGGATACTTC-AA-CCCTATTT
* *
224935 TTATTTTCAAAATATTAAATTTTTCATCATCG-
127 TTATTTCCAAAATATTAAAATTTTCATC-TCGA
* * *
224967 GTGATACT-TCAATCTC-GTA-TTTAAAGGGGACACTCCAACCCTGTTT
1 G-GATACTCT-AACCCCAGTATTTTAAAGGGGACACTCCAACCCCGTTT
225013 CTTTTTGAAT
Statistics
Matches: 179, Mismatches: 16, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
156 2 0.01
157 77 0.43
158 84 0.47
159 16 0.09
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (158 bp):
GGATACTCTAACCCCAGTATTTTAAAGGGGACACTCCAACCCCGTTTTTATTTCGAAACTATTAA
AATTTTCATCTCAGGGATACTCCAAACCCATTATTTTCGAAGGGATACTTCAACCCTATTTTTAT
TTCCAAAATATTAAAATTTTCATCTCGA
Found at i:229215 original size:32 final size:33
Alignment explanation
Indices: 229157--229218 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
229147 CATACAGATG
*
229157 TATCGATACATTATGCTTTGTATCGATACATTA
1 TATCGATACATTATGCATTGTATCGATACATTA
229190 TATCGATACATGT-T-CATTGTATCGATACA
1 TATCGATACAT-TATGCATTGTATCGATACA
229219 CGGACAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (33 bp):
TATCGATACATTATGCATTGTATCGATACATTA
Found at i:229234 original size:20 final size:19
Alignment explanation
Indices: 229184--229238 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
229174 TTGTATCGAT
* *
229184 ACATTATATCGATACATGT
1 ACATTATATCGATACACGG
* *
229203 TCATTGTATCGATACACGG
1 ACATTATATCGATACACGG
229222 ACAATTATATCGATACA
1 AC-ATTATATCGATACA
229239 TGAGATTCGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (19 bp):
ACATTATATCGATACACGG
Found at i:229295 original size:20 final size:20
Alignment explanation
Indices: 229270--229307 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
229260 TACCACTGTT
229270 TGTATCGATACATGGTATAG
1 TGTATCGATACATGGTATAG
*
229290 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
229308 TGATATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGGTATAG
Found at i:230523 original size:10 final size:10
Alignment explanation
Indices: 230508--230597 Score: 58
Period size: 10 Copynumber: 8.6 Consensus size: 10
230498 AGTAAATCAA
230508 CAACAAGTAG
1 CAACAAGTAG
* *
230518 CAACAAGCAC
1 CAACAAGTAG
*
230528 CAAGTGAAGTAG
1 CAA--CAAGTAG
*
230540 CAACAAGCAG
1 CAACAAGTAG
*
230550 CAACAAATAG
1 CAACAAGTAG
230560 CAACACAGTAAG
1 CAACA-AGT-AG
*
230572 CAAAATAGTAG
1 CAACA-AGTAG
230583 CAAACAA--AG
1 C-AACAAGTAG
230592 CAACAA
1 CAACAA
230598 CGAATAGCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
8 5 0.08
9 3 0.05
10 29 0.47
11 6 0.10
12 19 0.31
ACGTcount: A:0.53, C:0.22, G:0.17, T:0.08
Consensus pattern (10 bp):
CAACAAGTAG
Found at i:230606 original size:45 final size:43
Alignment explanation
Indices: 230535--230624 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 43
230525 CACCAAGTGA
* *
230535 AGTAGCAACAAGCAGCAACAAATAGCAACACAGTAAGCAAAAT
1 AGTAGCAACAAGCAACAACAAATAGCAACACAGCAAGCAAAAT
*
230578 AGTAGCAAACAAAGCAACAACGAATAGCAACACAGCAAGCAAAAT
1 AGTAGC-AAC-AAGCAACAACAAATAGCAACACAGCAAGCAAAAT
230623 AG
1 AG
230625 CAAGCAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 6 0.14
44 3 0.07
45 33 0.79
ACGTcount: A:0.54, C:0.21, G:0.17, T:0.08
Consensus pattern (43 bp):
AGTAGCAACAAGCAACAACAAATAGCAACACAGCAAGCAAAAT
Found at i:230635 original size:11 final size:11
Alignment explanation
Indices: 230611--230652 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
230601 ATAGCAACAC
230611 AGCAAGCAAAAT
1 AGCAAGC-AAAT
230623 AGCAAGCAAAT
1 AGCAAGCAAAT
**
230634 AGCAAGCAAGC
1 AGCAAGCAAAT
230645 AGCAAGCA
1 AGCAAGCA
230653 CGAAGAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 21 0.75
12 7 0.25
ACGTcount: A:0.52, C:0.21, G:0.21, T:0.05
Consensus pattern (11 bp):
AGCAAGCAAAT
Found at i:230697 original size:32 final size:35
Alignment explanation
Indices: 230627--230699 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 35
230617 CAAAATAGCA
* *
230627 AGCAA-ATAGCAAGCAAGCAGCAAGCACGAAGAAGT
1 AGCAAGATAGCAAGCAA-CAACAAGCACGAAGAAAT
230662 AGCAAGATAGCAAGCAA-AACAAGCAC-AA-AAAT
1 AGCAAGATAGCAAGCAACAACAAGCACGAAGAAAT
230694 AGCAAG
1 AGCAAG
230700 TAAAAAGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 9 0.26
33 2 0.06
34 8 0.23
35 5 0.14
36 11 0.31
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.05
Consensus pattern (35 bp):
AGCAAGATAGCAAGCAACAACAAGCACGAAGAAAT
Found at i:232431 original size:202 final size:201
Alignment explanation
Indices: 232043--232433 Score: 475
Period size: 202 Copynumber: 1.9 Consensus size: 201
232033 CCAGGGTCCA
232043 CTTTTATACCGAAAGTGGGCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAGTCCTTTA
1 CTTTTATACCGAAAGTGGGCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAGTCCTTTA
* *
232108 GGGTTGCCGAGAAACTTTTACATCGAAGGTATACCCTAGGGGCATTTTCATACCTTTCTAAAACC
66 GGGTTGCAGAGAAACTTTTACATCGAAGGTATACCCTAGGGGCATTTTCATA-CTTTCAAAAACC
* * * *
232173 AACTCCTAGGTCGTTACCGAGTCCGCTTTTATGTCGAAAGTAGATATTTTGGATAGGTTGTATCC
130 AACTCCTAGGTCGTCACCGAGTCCGCTTTTATGTCCAAAGTAGACATTTAGGATAGGTTGTATCC
232238 AGGTTTG
195 AGGTTTG
* * * *
232245 CTTTTATGCCGAAGGTGGGCATTTAGGATCGGTTCATCCTATCTCTAGTCTTTTTAAGTCCTTTA
1 CTTTTATACCGAAAGTGGGCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAGTCCTTTA
* * * * *
232310 GGGTTGTTAG-GATACTTTTACGTCGAAGGTATACCCGTATGGGCA-TTTCGTGA-TTTCCAAAA
66 GGGTTG-CAGAGAAACTTTTACATCGAAGGTATACCC-TAGGGGCATTTTCAT-ACTTT-CAAAA
* * * * * * * * * *
232372 ATCGAGTCTTAGGTTGTCATCGGGTTCGCTTTTATG-CCAAAGGTGGGCATTTAGGATAGGTT
127 ACCAACTCCTAGGTCGTCACCGAGTCCGCTTTTATGTCCAAA-GTAGACATTTAGGATAGGTT
232434 CGTCCCATCT
Statistics
Matches: 159, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
201 7 0.04
202 143 0.90
203 9 0.06
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (201 bp):
CTTTTATACCGAAAGTGGGCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAGTCCTTTA
GGGTTGCAGAGAAACTTTTACATCGAAGGTATACCCTAGGGGCATTTTCATACTTTCAAAAACCA
ACTCCTAGGTCGTCACCGAGTCCGCTTTTATGTCCAAAGTAGACATTTAGGATAGGTTGTATCCA
GGTTTG
Found at i:232636 original size:155 final size:151
Alignment explanation
Indices: 232240--232987 Score: 448
Period size: 155 Copynumber: 4.8 Consensus size: 151
232230 TTGTATCCAG
* * * * * ** *
232240 GTTTGCTTTTATGCCGAAGGTGGGCATTTAGGATCGGTTCATC-CTATCTCTAGT-CTTTTTAAG
1 GTTTGCTTTTATGCCAAAGGTAGGTATTTAGGATAGGTTCATCGCT-TATAAAATCCTTTTTAAG
* * * * *
232303 TCCTTT-AGGGTTGTTAGGATACTTTTACGTCGAAGGTATACCCGTATGGGCATTTCGTGATTTC
65 TCCTTTAAGGG-TATT-GGGTACTTTTACGTCGAAGGTAT-CCCGTA-GGGCATTTTGTAATTTT
** * * * * *
232367 CAAAAATCGAGTCTTAGGTTGTCATCGG
126 TTAGAA-CAAGTCATAGGTT-TCACCGA
* * * * * * * ** * *
232395 GTTCGCTTTTATGCCAAAGGTGGGCATTTAGGATAGGTTCGTCCCATCTCTAGT-CTTTGTAAGT
1 GTTTGCTTTTATGCCAAAGGTAGGTATTTAGGATAGGTTCATCGCTTATAAAATCCTTTTTAAGT
*
232459 CCTTT-AGGG--TTGCCGAGATACTTTTACGTCGAAGGTATAACCGTAAGGGCATATTTGTAATT
66 CCTTTAAGGGTATTG--G-G-TACTTTTACGTCGAAGGTAT-CCCGT-AGGGCAT-TTTGTAATT
* *
232521 TTTTATAACAACTCATAGGTCTTCACCGA
124 TTTTAGAACAAGTCATAGGT-TTCACCGA
* * *
232550 GTTTGCTTTTATGTCAAAGGTAGATATTTAGGATAGGTTCATCGCTTATAAAATCCTTTTTCAGT
1 GTTTGCTTTTATGCCAAAGGTAGGTATTTAGGATAGGTTCATCGCTTATAAAATCCTTTTTAAGT
** * * *
232615 CCTTTAAGGGTATTGGGTACTTTTACACCGAAAGTATCCCCTGT-GAGCATTTT-CATATTTTTC
66 CCTTTAAGGGTATTGGGTACTTTTACGTCGAAGGTAT-CCC-GTAGGGCATTTTGTA-ATTTTT-
** *
232678 TAGAACTAAGTTTTAGGTTTTCA-CTA
127 TAGAAC-AAGTCATAGG-TTTCACCGA
* * * * * * ** *
232704 GGTCTGCTTTTATGCCTATGGTGGGTATTTAGGATAGGTTCATCCCATTTTGGAATCATTTTTAA
1 -GTTTGCTTTTATGCCAAAGGTAGGTATTTAGGATAGGTTCATCGC-TTATAAAATCCTTTTTAA
* * * * * * *
232769 GTCCTTT-AGGGATTTTGGGCACTTCTATGTCGAAGATATCCCTTAGGGGTATTTTTGTAATTTT
64 GTCCTTTAAGGG-TATTGGGTACTTTTACGTCGAAGGTATCCCGTA-GGGCA-TTTTGTAATTTT
* *
232833 TTAGAACCAAGTCCTAAGTTGTCACCG-
126 TTAGAA-CAAGTCATAGGTT-TCACCGA
* * **
232860 GATTTGCTTTTATGCCGAAGGTAGGTATTTAGGATAGG-T-AT-GTCTCATCTAATCCTTTTTAA
1 G-TTTGCTTTTATGCCAAAGGTAGGTATTTAGGATAGGTTCATCG-CTTATAAAATCCTTTTTAA
* * * *
232922 GACCTTTAAGGGTATTAGGTACTTTTACGTCGAAGTTATCCTC-TAGGGGCATTTTCATAATTTT
64 GTCCTTTAAGGGTATTGGGTACTTTTACGTCGAAGGTATCC-CGTA-GGGCATTTT-GTAATTTT
232986 TT
126 TT
232988 TTTAACTTAG
Statistics
Matches: 469, Mismatches: 92, Indels: 66
0.75 0.15 0.11
Matches are distributed among these distances:
151 1 0.00
152 7 0.01
153 68 0.14
154 21 0.04
155 231 0.49
156 120 0.26
157 17 0.04
158 1 0.00
159 3 0.01
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (151 bp):
GTTTGCTTTTATGCCAAAGGTAGGTATTTAGGATAGGTTCATCGCTTATAAAATCCTTTTTAAGT
CCTTTAAGGGTATTGGGTACTTTTACGTCGAAGGTATCCCGTAGGGCATTTTGTAATTTTTTAGA
ACAAGTCATAGGTTTCACCGA
Found at i:235270 original size:2 final size:2
Alignment explanation
Indices: 235265--235293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
235255 CTTTTGTGTG
235265 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 T
235294 TCGTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:236545 original size:17 final size:17
Alignment explanation
Indices: 236492--236552 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
236482 CAAAAAAAAG
236492 AAAAGAAAAATG-G-AA
1 AAAAGAAAAATGTGCAA
*
236507 ATGAA-AAAAATGTGCAA
1 A-AAAGAAAAATGTGCAA
*
236524 TAAAGAAAAA-GTGCAAA
1 AAAAGAAAAATGTGC-AA
236541 AAAAGAAAAATG
1 AAAAGAAAAATG
236553 AAAGACGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 8 0.22
16 9 0.25
17 18 0.50
18 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.18, T:0.11
Consensus pattern (17 bp):
AAAAGAAAAATGTGCAA
Found at i:237689 original size:44 final size:44
Alignment explanation
Indices: 237641--237778 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 44
237631 GTCTCAACTA
* *
237641 CATTTGCATTTTAGATGACATTGGTATTTGCATCATTACATATG
1 CATTTGCATTTTAGATGACATTGGCATTTGCATCATTTCATATG
* * * * * *
237685 CATTTTCCCCTTTGTTGATG-C-TT-GCATTTGTATCATTTTACATG
1 CA-TTT-GCATTT-TAGATGACATTGGCATTTGCATCATTTCATATG
* * *
237729 CTTTTGCA-TTCAGATAACATTGGCATTTGCATCATTTCATATG
1 CATTTGCATTTTAGATGACATTGGCATTTGCATCATTTCATATG
237772 CATTTGC
1 CATTTGC
237779 TACCTGATGC
Statistics
Matches: 70, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
40 3 0.04
41 3 0.04
42 3 0.04
43 27 0.39
44 19 0.27
45 5 0.07
46 5 0.07
47 5 0.07
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (44 bp):
CATTTGCATTTTAGATGACATTGGCATTTGCATCATTTCATATG
Found at i:238656 original size:48 final size:47
Alignment explanation
Indices: 238580--238687 Score: 171
Period size: 48 Copynumber: 2.3 Consensus size: 47
238570 TTGGCTGTAT
* *
238580 CTAGCCAAACTCTTTCATCCCTCATTTGACTGTATTGGAGTTAGGGC
1 CTAGTCAAACTCTTTCATCCCTCATTTGACTATATTGGAGTTAGGGC
* *
238627 CTAGTCAAACTCTTTACATCCCTCTTTTGACTATATTGGTGTTAGGGC
1 CTAGTCAAACTCTTT-CATCCCTCATTTGACTATATTGGAGTTAGGGC
238675 CTAGTCAAACTCT
1 CTAGTCAAACTCT
238688 CCTCTTTCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
47 14 0.25
48 42 0.75
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (47 bp):
CTAGTCAAACTCTTTCATCCCTCATTTGACTATATTGGAGTTAGGGC
Found at i:238739 original size:44 final size:43
Alignment explanation
Indices: 238690--238945 Score: 223
Period size: 44 Copynumber: 5.8 Consensus size: 43
238680 CAAACTCTCC
* *
238690 TCTTTCCTGTTTGACATATGGTTACAACCCTGGTCAGATTCTTT
1 TCTTT-CTGTTTGACATATAGTTACCACCCTGGTCAGATTCTTT
* * * *
238734 TCTTTCCGATTTGACATATAGTTACCACCTTGGTCA-AATCTACCT
1 TCTTTCTG-TTTGACATATAGTTACCACCCTGGTCAGATTCT--TT
* * * *
238779 CCTTTTTGTCTAACATATAGTTACCACCCTGGTCAGATTCTTT
1 TCTTTCTGTTTGACATATAGTTACCACCCTGGTCAGATTCTTT
* * **
238822 TCATTT-TGATTTGACATATAGTTACCACCTTGGTCA-AATCTGCC
1 TC-TTTCTG-TTTGACATATAGTTACCACCCTGGTCAGATTCT-TT
* *
238866 TCTTTCCTGTATGACATATTGTTACCACCCTGGTCAGATTCTTT
1 TCTTT-CTGTTTGACATATAGTTACCACCCTGGTCAGATTCTTT
* * *
238910 TCATTCTAATTTGACGTAT-GTTTACCACCCTGGTCA
1 TCTTTCT-GTTTGACATATAG-TTACCACCCTGGTCA
238946 AATCTACCAC
Statistics
Matches: 169, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
43 20 0.12
44 133 0.79
45 16 0.09
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (43 bp):
TCTTTCTGTTTGACATATAGTTACCACCCTGGTCAGATTCTTT
Found at i:238982 original size:176 final size:175
Alignment explanation
Indices: 238678--239077 Score: 496
Period size: 176 Copynumber: 2.3 Consensus size: 175
238668 TTAGGGCCTA
* * *
238678 GTCAAACTCTCCTCTTTCCTGTTTGACATATGGTTACAACCCTGGTCAGATTCTTTTCTTTCCGA
1 GTCAAA-TCTCCTCTTTCCTGTATGACATATGGTTACAACCCTGGTCAGATTCTTTTCATTCCAA
* * * * *
238743 TTTGACATATAGTTACCACCTTGGTCAAATCTACCTCCTTTTTGTCTAACATATAGTTACCACCC
65 TTTGACATATAGTTACCACCCTGGTCAAATCTACCACCCTCTTATCTAACATATAGTTACCACCC
* *
238808 TGGTCAGATTCTTTTCATTTTGATTTGACATATAGTTACCACCTTG
130 TGGTCAAATTCTTTTCATTCTGATTTGACATATAGTTACCACCTTG
* * *
238854 GTCAAATCTGCCTCTTTCCTGTATGACATATTGTTACCACCCTGGTCAGATTCTTTTCATTCTAA
1 GTCAAATCT-CCTCTTTCCTGTATGACATATGGTTACAACCCTGGTCAGATTCTTTTCATTCCAA
* * *
238919 TTTGACGTAT-GTTTACCACCCTGGTCAAATCTACCACCCTCTTATCTAACGTATGGTTACCACC
65 TTTGACATATAG-TTACCACCCTGGTCAAATCTACCACCCTCTTATCTAACATATAGTTACCACC
* * ** *
238983 TTGGTTAAATTCTTTTCATTCTGATTTGATGTATGGTTACCACCTTG
129 CTGGTCAAATTCTTTTCATTCTGATTTGACATATAGTTACCACCTTG
* * * * * * * *
239030 GTTAAATCTAACTCCTTACTGTTTGACGTATGGTTATAACCCTTGTCA
1 GTCAAATCT-CCTCTTTCCTGTATGACATATGGTTACAACCCTGGTCA
239078 AATGATTTGC
Statistics
Matches: 190, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
175 4 0.02
176 186 0.98
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (175 bp):
GTCAAATCTCCTCTTTCCTGTATGACATATGGTTACAACCCTGGTCAGATTCTTTTCATTCCAAT
TTGACATATAGTTACCACCCTGGTCAAATCTACCACCCTCTTATCTAACATATAGTTACCACCCT
GGTCAAATTCTTTTCATTCTGATTTGACATATAGTTACCACCTTG
Found at i:239017 original size:44 final size:44
Alignment explanation
Indices: 238699--239080 Score: 213
Period size: 44 Copynumber: 8.7 Consensus size: 44
238689 CTCTTTCCTG
* * * * *
238699 TTTGACATATGGTTACAACCCTGGTCAGATTCTTTTCTTTCCGA
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCTGA
* * * * * * *
238743 TTTGACATATAGTTACCACCTTGGTCAAA-TCTACCTCCTTTTTG-
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCT--TTTCATTCTGA
* * * * * *
238787 TCTAACATATAGTTACCACCCTGGTCAGATTCTTTTCATTTTGA
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCTGA
* * * ** *
238831 TTTGACATATAGTTACCACCTTGGTCAAA-TCTGCCTCTTTCCTG-
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCT-TTTCATT-CTGA
* * * * *
238875 TATGACATATTGTTACCACCCTGGTCAGATTCTTTTCATTCTAA
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCTGA
* ** * *
238919 TTTGACGTATGTTTACCACCCTGGTCAAA-TC-TACCACCCTCTTA
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCTTTTCA--TTCTGA
* * * *
238963 TCTAACGTATGGTTACCACCTTGGTTAAATTCTTTTCATTCTGA
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCTGA
* * * ** *
239007 TTTGATGTATGGTTACCACCTTGGTTAAA-TCTAACTCCTTACTG-
1 TTTGACGTATGGTTACCACCCTGGTCAAATTCT-TTTCATT-CTGA
** *
239051 TTTGACGTATGGTTATAACCCTTGTCAAAT
1 TTTGACGTATGGTTACCACCCTGGTCAAAT
239081 GATTTGCATT
Statistics
Matches: 262, Mismatches: 61, Indels: 29
0.74 0.17 0.08
Matches are distributed among these distances:
42 3 0.01
43 20 0.08
44 217 0.83
45 19 0.07
46 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (44 bp):
TTTGACGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCTGA
Found at i:239092 original size:88 final size:87
Alignment explanation
Indices: 238678--239065 Score: 422
Period size: 88 Copynumber: 4.4 Consensus size: 87
238668 TTAGGGCCTA
* * * *
238678 GTCAAACTCT-CCTCTTTCCTGTTTGACATATGGTTACAACCCTGGTCAGATTCTTTTCTTTCCG
1 GTCAAA-TCTACCTCCTT-CTGTTTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTG
*
238742 ATTTGACATATAGTTACCACCTTG
64 ATTTGACGTATAGTTACCACCTTG
* * * * *
238766 GTCAAATCTACCTCCTTTTTGTCTAACATATAGTTACCACCCTGGTCAGATTCTTTTCATTTTGA
1 GTCAAATCTACCTCC-TTCTGTTTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGA
*
238831 TTTGACATATAGTTACCACCTTG
65 TTTGACGTATAGTTACCACCTTG
* * * * *
238854 GTCAAATCTGCCTCTTTCCTGTATGACATATTGTTACCACCCTGGTCAGATTCTTTTCATTCTAA
1 GTCAAATCTACCTCCTT-CTGTTTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGA
*
238919 TTTGACGTAT-GTTTACCACCCTG
65 TTTGACGTATAG-TTACCACCTTG
* * * * * * *
238942 GTCAAATCTACCACCCTCT-TATCTAACGTATGGTTACCACCTTGGTTAAATTCTTTTCATTCTG
1 GTCAAATCTACCTCCTTCTGT-T-TGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTG
* *
239006 ATTTGATGTATGGTTACCACCTTG
64 ATTTGACGTATAGTTACCACCTTG
* * *
239030 GTTAAATCTAACTCCTTACTGTTTGACGTATGGTTA
1 GTCAAATCTACCTCCTT-CTGTTTGACATATGGTTA
239066 TAACCCTTGT
Statistics
Matches: 253, Mismatches: 38, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
86 1 0.00
87 8 0.03
88 237 0.94
89 6 0.02
90 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (87 bp):
GTCAAATCTACCTCCTTCTGTTTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGAT
TTGACGTATAGTTACCACCTTG
Found at i:239240 original size:42 final size:41
Alignment explanation
Indices: 239178--239336 Score: 153
Period size: 41 Copynumber: 3.8 Consensus size: 41
239168 CCCATCAGTT
*
239178 TTGACCCGA-GAGACTCCTTCACCTTTTGTCTGCCCATCGACC
1 TTGA-CCGAGGAGACTTCTTCACCTTTT-TCTGCCCATCGACC
* * * *
239220 TTGATCGAGGAAACTTCTTCACCTTTTTTCTGCCCGTCG-GC
1 TTGACCGAGGAGACTTCTTCACC-TTTTTCTGCCCATCGACC
* * *
239261 TTGACCTG-GGAGACTTCTTTACCTTTTTTTGCCCATCGACT
1 TTGACC-GAGGAGACTTCTTCACCTTTTTCTGCCCATCGACC
* * *
239302 TTGACCTAAGAGACTTCTTTACCTTTTCTCTGCCC
1 TTGACCGAGGAGACTTCTTCACCTTTT-TCTGCCC
239337 GTCAGCTTTA
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
40 13 0.14
41 46 0.48
42 33 0.34
43 4 0.04
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36
Consensus pattern (41 bp):
TTGACCGAGGAGACTTCTTCACCTTTTTCTGCCCATCGACC
Found at i:239358 original size:42 final size:42
Alignment explanation
Indices: 239161--239667 Score: 311
Period size: 42 Copynumber: 12.1 Consensus size: 42
239151 CTTTGATCCC
* * * * *
239161 TTGTCTACCCATCAGTTTTGACCC-GAGAGACTCCTTCACCTT
1 TTGTCTGCCCGTCAGCTTTGACCCAG-GAGACTTCTTTACCTT
* * * * * *
239203 TTGTCTGCCCATC-GACCTTGATCGAGGAAACTTCTTCACCTT
1 TTGTCTGCCCGTCAG-CTTTGACCCAGGAGACTTCTTTACCTT
* * **
239245 TTTTCTGCCCGTCGGC-TTGACCTGGGAGACTTCTTTACCTT
1 TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCTTTACCTT
* * * *
239286 TT-TTTGCCCATC-GACTTTGACCTAAGAGACTTCTTTACCTT
1 TTGTCTGCCCGTCAG-CTTTGACCCAGGAGACTTCTTTACCTT
* * * * *
239327 TTCTCTGCCCGTCAGCTTTAATCTAGGAGACTTCTTTATCC-A
1 TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCTTTA-CCTT
* * *
239369 TTGT-TACCCGTCAGCTTTGACCCAAGAGACTTCTTTACCCT
1 TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCTTTACCTT
* * *
239410 TTG-CTTGCCAGTCGGCTTTGACCCATGAGACTTCTTTACCCTT
1 TTGTC-TGCCCGTCAGCTTTGACCCAGGAGACTTCTTTA-CCTT
* * ** * *
239453 TT-CCTGCCCATCAAATTTGACCCGGGAGACTT-TGTTACCCT
1 TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCT-TTACCTT
* * * *
239494 TTGTCTGCCCGTCAACTTTGACTCAGGAGACTTCCTTATCTT
1 TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCTTTACCTT
* * * * * *
239536 CTATCTGGCCGTCAACTTTGACCCAAGAGACTTCTTTATCTT
1 TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCTTTACCTT
* ** * * * *
239578 TTGTCTGCACC-TCGGCTCAGACCCAAGAGACTTTTTTATCTA
1 TTGTCTGC-CCGTCAGCTTTGACCCAGGAGACTTCTTTACCTT
* * * * *
239620 TTGTCTACCTC-TC-GACTTAGACCCAGGAGATTTCTTTATCAT
1 TTGTCTGCC-CGTCAG-CTTTGACCCAGGAGACTTCTTTACCTT
239662 TTGTCT
1 TTGTCT
239668 ACTCGTCGAC
Statistics
Matches: 372, Mismatches: 74, Indels: 38
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.00
40 11 0.03
41 87 0.23
42 260 0.70
43 13 0.03
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.36
Consensus pattern (42 bp):
TTGTCTGCCCGTCAGCTTTGACCCAGGAGACTTCTTTACCTT
Found at i:239396 original size:83 final size:83
Alignment explanation
Indices: 239187--239585 Score: 331
Period size: 83 Copynumber: 4.8 Consensus size: 83
239177 TTTGACCCGA
* * * * * * * * * *
239187 GAGACTCCTTCACCTTTTGTCTGCCCATCGACCTTGATCGAGGAAACTTCTTCACCTTTTTTCTG
1 GAGACTTCTTTACCTTTT-TCTGCCCATCAACTTTGACCCAAGAGACTTCTTTACCTTTTCTCTG
* *
239252 CCCGTCGGC-TTGACCTGG
65 CCCGTCAGCTTTGACCTAG
* * *
239270 GAGACTTCTTTACCTTTTTTTGCCCATCGACTTTGACCTAAGAGACTTCTTTACCTTTTCTCTGC
1 GAGACTTCTTTACCTTTTTCTGCCCATCAACTTTGACCCAAGAGACTTCTTTACCTTTTCTCTGC
* *
239335 CCGTCAGCTTTAATCTAG
66 CCGTCAGCTTTGACCTAG
* * * * * *
239353 GAGACTTCTTTATCCATTGT-TACCCGTCAGCTTTGACCCAAGAGACTTCTTTACCCTTTGCT-T
1 GAGACTTCTTTA-CCTTTTTCTGCCCATCAACTTTGACCCAAGAGACTTCTTTA-CCTTTTCTCT
* * * *
239416 GCCAGTCGGCTTTGACCCAT
64 GCCCGTCAGCTTTGACCTAG
* * ** * *
239436 GAGACTTCTTTACCCTTTTCCTGCCCATCAAATTTGACCCGGGAGACTT-TGTTACCCTTTGTCT
1 GAGACTTCTTTA-CCTTTTTCTGCCCATCAACTTTGACCCAAGAGACTTCT-TTACCTTTTCTCT
*
239500 GCCCGTCAACTTTGA-CTCAG
64 GCCCGTCAGCTTTGACCT-AG
* * * * * * *
239520 GAGACTTCCTTATCTTCTATCTGGCCGTCAACTTTGACCCAAGAGACTTCTTTATCTTTTGTCTG
1 GAGACTTCTTTACCTT-TTTCTGCCCATCAACTTTGACCCAAGAGACTTCTTTACCTTTTCTCTG
239585 C
65 C
239586 ACCTCGGCTC
Statistics
Matches: 250, Mismatches: 57, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
82 46 0.18
83 103 0.41
84 100 0.40
85 1 0.00
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (83 bp):
GAGACTTCTTTACCTTTTTCTGCCCATCAACTTTGACCCAAGAGACTTCTTTACCTTTTCTCTGC
CCGTCAGCTTTGACCTAG
Found at i:239481 original size:125 final size:125
Alignment explanation
Indices: 239270--239585 Score: 309
Period size: 125 Copynumber: 2.5 Consensus size: 125
239260 CTTGACCTGG
** *
239270 GAGACTTCTTTACCTTTTTTTGCCCATCGACTTTGACCTAAGAGACTTCTTTACCTTTTCTCTGC
1 GAGACTTCTTTACCTTTGCTTGCCCATCGACTTTGACCCAAGAGACTTCTTTACCTTTTCTCTGC
* ** * * * *
239335 CCGTCAGCTTTAATCTAGGAGACTTCT-TTATCCATTGT-TACCCGTCAGCTTTGACCCAA
66 CCATCAAATTTAACCCAGGAGACTT-TGTTACCCATTGTCTACCCGTCAACTTTGACCCAA
* *
239394 GAGACTTCTTTACCCTTTGCTTG-CCAGTCGGCTTTGACCCATGAGACTTCTTTACCCTTTTC-C
1 GAGACTTCTTTA-CCTTTGCTTGCCCA-TCGACTTTGACCCAAGAGACTTCTTTA-CCTTTTCTC
* * * * * *
239457 TGCCCATCAAATTTGACCCGGGAGACTTTGTTACCCTTTGTCTGCCCGTCAACTTTGACTCAG
63 TGCCCATCAAATTTAACCCAGGAGACTTTGTTACCCATTGTCTACCCGTCAACTTTGACCCAA
* * * * * * * *
239520 GAGACTTCCTTATCTTCT-ATCTGGCCGTCAACTTTGACCCAAGAGACTTCTTTATCTTTTGTCT
1 GAGACTTCTTTACCTT-TGCT-TGCCCATCGACTTTGACCCAAGAGACTTCTTTACCTTTTCTCT
239584 GC
64 GC
239586 ACCTCGGCTC
Statistics
Matches: 156, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
124 16 0.10
125 72 0.46
126 66 0.42
127 2 0.01
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (125 bp):
GAGACTTCTTTACCTTTGCTTGCCCATCGACTTTGACCCAAGAGACTTCTTTACCTTTTCTCTGC
CCATCAAATTTAACCCAGGAGACTTTGTTACCCATTGTCTACCCGTCAACTTTGACCCAA
Found at i:239668 original size:42 final size:41
Alignment explanation
Indices: 239555--239704 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 41
239545 CGTCAACTTT
* * *
239555 GACCCAAGAGACTTCTTTATCTTTTGTCTGCAC-CTCGGCTCA
1 GACCCAAGAGATTTCTTTATC-TTTGTCTAC-CTCTCGACTCA
*
239597 GACCCAAGAGACTTT-TTTATCTATTGTCTACCTCTCGACTTA
1 GACCCAAGAGA-TTTCTTTATCT-TTGTCTACCTCTCGACTCA
* *
239639 GACCCAGGAGATTTCTTTATCATTTGTCTA-CTCGTCGACTCC
1 GACCCAAGAGATTTCTTTATC-TTTGTCTACCTC-TCGACTCA
* * * *
239681 GACCCAGGAAACTTCTTCATCTTT
1 GACCCAAGAGATTTCTTTATCTTT
239705 TTTTCCCATC
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
41 11 0.12
42 78 0.85
43 3 0.03
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (41 bp):
GACCCAAGAGATTTCTTTATCTTTGTCTACCTCTCGACTCA
Found at i:241537 original size:32 final size:32
Alignment explanation
Indices: 241477--241569 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
241467 AAGCAGCAAC
* ** * *
241477 AAGTAGTAACAAGCAGTAAAGAACAGCAAGCA
1 AAGTAGCAACAAGCAACAACGAATAGCAAGCA
*
241509 AA-TCAGCAATAAGCAACAACGAATAGCAAGCA
1 AAGT-AGCAACAAGCAACAACGAATAGCAAGCA
* *
241541 AAGTAGCAACAAGCAGCAAGGAATAGCAA
1 AAGTAGCAACAAGCAACAACGAATAGCAA
241570 CACAGCAAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
31 1 0.02
32 48 0.96
33 1 0.02
ACGTcount: A:0.53, C:0.18, G:0.20, T:0.09
Consensus pattern (32 bp):
AAGTAGCAACAAGCAACAACGAATAGCAAGCA
Found at i:241558 original size:22 final size:21
Alignment explanation
Indices: 241533--241625 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 21
241523 AACAACGAAT
241533 AGCAAGCAAAGTAGCAACAAGC
1 AGCAAGCAAA-TAGCAACAAGC
*
241555 AGCAAG-GAATAGCAAC-A-C
1 AGCAAGCAAATAGCAACAAGC
* *
241573 AGCAAGCAAAATAGCACGCAAAAC
1 AGCAAGC-AAATAGCA-AC-AAGC
241597 AGC-AGCAAATAGCAAGCAAGC
1 AGCAAGCAAATAGCAA-CAAGC
241618 AGCAAGCA
1 AGCAAGCA
241626 CGAAGAAGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
18 7 0.12
19 1 0.02
20 14 0.24
21 9 0.16
22 19 0.33
23 4 0.07
24 4 0.07
ACGTcount: A:0.51, C:0.24, G:0.22, T:0.04
Consensus pattern (21 bp):
AGCAAGCAAATAGCAACAAGC
Found at i:241581 original size:64 final size:63
Alignment explanation
Indices: 241464--241623 Score: 141
Period size: 64 Copynumber: 2.5 Consensus size: 63
241454 CGAACAACAA
* * * * * * *
241464 ACAAAGCAGCAAC-AAGTAGTAACAAGCAGTAAAGAACAGCAAGCAAATCAGCAATA-AGCA-
1 ACAAAACAGCAGCAAAGTAGCAACAAGCAGCAAGGAACAGCAAGCAAAGCAGCAAAATAGCAC
* * *
241524 ACAACGAATAGCAAGCAAAGTAGCAACAAGCAGCAAGGAATAGCAA-CACAGCAAGCAAAATAGC
1 ACAA--AACAGC-AGCAAAGTAGCAACAAGCAGCAAGGAACAGCAAGCAAAGC-AGCAAAATAGC
241588 AC
62 AC
*
241590 GCAAAACAGCAGCAAA-TAGCAAGCAAGCAGCAAG
1 ACAAAACAGCAGCAAAGTAGCAA-CAAGCAGCAAG
241624 CACGAAGAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
60 4 0.05
62 10 0.12
63 23 0.29
64 36 0.45
65 4 0.05
66 3 0.04
ACGTcount: A:0.52, C:0.22, G:0.20, T:0.06
Consensus pattern (63 bp):
ACAAAACAGCAGCAAAGTAGCAACAAGCAGCAAGGAACAGCAAGCAAAGCAGCAAAATAGCAC
Found at i:241585 original size:20 final size:19
Alignment explanation
Indices: 241533--241588 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
241523 AACAACGAAT
*
241533 AGCAAGCAAAGTAGCAACA
1 AGCAAGCAAAATAGCAACA
241552 AGC-AGCAAGGAATAGCAACA
1 AGCAAGCAA--AATAGCAACA
241572 CAGCAAGCAAAATAGCA
1 -AGCAAGCAAAATAGCA
241589 CGCAAAACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.16
19 3 0.09
20 16 0.50
21 3 0.09
22 5 0.16
ACGTcount: A:0.52, C:0.21, G:0.21, T:0.05
Consensus pattern (19 bp):
AGCAAGCAAAATAGCAACA
Found at i:243290 original size:156 final size:154
Alignment explanation
Indices: 242895--243439 Score: 519
Period size: 156 Copynumber: 3.5 Consensus size: 154
242885 AATCATCATT
* * * * * *
242895 TCTAATCTTTTTACGTCCTTTAAGGTTGCCAGAATACTTTTACGTCAATGGTATAGCCATAAGGG
1 TCTAGTCTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTACGTCAA-GGTATA-CCGTAAGGG
* * * *
242960 CATTTTCATAATTTCCTA-AACCGAGTCTTAGGTTGTCA-TCGGGTTCACTTTTCTGCCGAAAGT
64 CATTTTCATAATTTTCTAGAACCGAGTCCTAGGTTGTCACTC-GGTCCACTTTTATGCCGAAAGT
*
243023 GGGCATTTAGGATAGGTTCATCCCATC
128 GGACATTTAGGATAGGTTCATCCCATC
* * *
243050 TCTAGTC-TTTTAAGTCCTTTAGGGTTGCTGAGATACTTTTACGTATAAGGTATACCTGTAAGGG
1 TCTAGTCTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTACGT-CAAGGTATACC-GTAAGGG
* ** *
243114 CATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTGTCACTAC-GTCCGTTTTTATGCCGAAGGT
64 CATTTTCATAATTTTCTAGAACCGAGTCCTAGGTTGTCACT-CGGTCCACTTTTATGCCGAAAGT
243178 GGACATTTCA-GATAGGTTCATCCCATC
128 GGACATTT-AGGATAGGTTCATCCCATC
* *
243205 TTTAGTCTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCGTAGGGG
1 TCTAGTCTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTACGTC-AAGGTATAC-CGTAAGGG
* * * * * * * * *
243270 TATTTTCATAATTTTCTAGAACCAACTCCTAGGTCGTCAC-CAAGTTCACTTGTATGTCGAAGGT
64 CATTTTCATAATTTTCTAGAACCGAGTCCTAGGTTGTCACTC-GGTCCACTTTTATGCCGAAAGT
* * * * *
243334 AGATATTTTGGATAGGTTCATCCCTTT
128 GGACATTTAGGATAGGTTCATCCCATC
** * * * ** * * * * *
243361 TAAAATCCTTTTTACGTCCTTTAGGGGTGTTGGG-CACTTTTACGGTGAAGGTATCCCCTAAAGG
1 TCTAGT-CTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTAC-GTCAAGGTATACCGTAAGGG
243425 CATTTTCATAATTTT
64 CATTTTCATAATTTT
243440 TTGGGTTTAG
Statistics
Matches: 324, Mismatches: 52, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
153 2 0.01
154 60 0.19
155 92 0.28
156 143 0.44
157 27 0.08
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (154 bp):
TCTAGTCTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTACGTCAAGGTATACCGTAAGGGCA
TTTTCATAATTTTCTAGAACCGAGTCCTAGGTTGTCACTCGGTCCACTTTTATGCCGAAAGTGGA
CATTTAGGATAGGTTCATCCCATC
Found at i:247616 original size:10 final size:10
Alignment explanation
Indices: 247601--247661 Score: 77
Period size: 10 Copynumber: 5.9 Consensus size: 10
247591 TTTGAATATG
247601 AATAAAAATA
1 AATAAAAATA
*
247611 AATAAAACTA
1 AATAAAAATA
*
247621 ATTTAAAAATA
1 A-ATAAAAATA
*
247632 ATTAAAAATA
1 AATAAAAATA
247642 AATAAAAACTA
1 AATAAAAA-TA
247653 AATAAAAAT
1 AATAAAAAT
247662 CTCTAAGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
10 27 0.60
11 18 0.40
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (10 bp):
AATAAAAATA
Found at i:247629 original size:21 final size:20
Alignment explanation
Indices: 247601--247661 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
247591 TTTGAATATG
*
247601 AATAAAAATAAATAAAACTA
1 AATAAAAATAAATAAAAATA
* *
247621 ATTTAAAAATAATTAAAAATA
1 A-ATAAAAATAAATAAAAATA
247642 AATAAAAACTAAATAAAAAT
1 AATAAAAA-TAAATAAAAAT
247662 CTCTAAGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAAAAATAAATAAAAATA
Found at i:247641 original size:31 final size:31
Alignment explanation
Indices: 247603--247661 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
247593 TGAATATGAA
*
247603 TAAAAATAAAT-AAAACTAATTTAAAAATAAT
1 TAAAAATAAATAAAAACTAA-ATAAAAATAAT
247634 TAAAAATAAATAAAAACTAAATAAAAAT
1 TAAAAATAAATAAAAACTAAATAAAAAT
247662 CTCTAAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (31 bp):
TAAAAATAAATAAAAACTAAATAAAAATAAT
Found at i:247649 original size:11 final size:11
Alignment explanation
Indices: 247604--247660 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
247594 GAATATGAAT
247604 AAAAATAAAT-
1 AAAAATAAATA
* * *
247614 AAAACTAATTT
1 AAAAATAAATA
*
247625 AAAAAT-AATT
1 AAAAATAAATA
247635 AAAAATAAATA
1 AAAAATAAATA
*
247646 AAAACTAAATA
1 AAAAATAAATA
247657 AAAA
1 AAAA
247661 TCTCTAAGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
10 17 0.44
11 22 0.56
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:251086 original size:20 final size:20
Alignment explanation
Indices: 251064--251134 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
251054 TAACTAGATG
* *
251064 TATCGATACATTTAAAAATG
1 TATCGATACATTCAAAAATA
* * *
251084 TATCAATACATTCATACATA
1 TATCGATACATTCAAAAATA
* *
251104 TATCGATAAATTGAAAAATA
1 TATCGATACATTCAAAAATA
251124 TATCGATACAT
1 TATCGATACAT
251135 CTGGGTAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (20 bp):
TATCGATACATTCAAAAATA
Found at i:254732 original size:21 final size:21
Alignment explanation
Indices: 254703--254751 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
254693 AGTGACCGAA
*
254703 ATTTTGGAGTCACCACCGATC
1 ATTTCGGAGTCACCACCGATC
* *
254724 ATTTCGGAGTCGCCATCGATC
1 ATTTCGGAGTCACCACCGATC
254745 ATTTCGG
1 ATTTCGG
254752 GCTAGGCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (21 bp):
ATTTCGGAGTCACCACCGATC
Found at i:259807 original size:13 final size:13
Alignment explanation
Indices: 259786--259823 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
259776 AGTATATGAT
259786 TTTAA-TATTTAA
1 TTTAATTATTTAA
*
259798 TTTAATTATTTTA
1 TTTAATTATTTAA
*
259811 TGTAATTATTTAA
1 TTTAATTATTTAA
259824 AAAGTGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
TTTAATTATTTAA
Found at i:264506 original size:13 final size:13
Alignment explanation
Indices: 264488--264517 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
264478 ACAATTCTTC
264488 ATGTATCGATACA
1 ATGTATCGATACA
264501 ATGTATCGATACA
1 ATGTATCGATACA
264514 ATGT
1 ATGT
264518 CCCATGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:264512 original size:33 final size:33
Alignment explanation
Indices: 264470--264533 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
264460 TGGGCATAAC
* *
264470 GTATCGATACAAT-TCTTCATGTATCGATACAAT
1 GTATCGATACAATGTC-CCATGAATCGATACAAT
264503 GTATCGATACAATGTCCCATGAATCGATACA
1 GTATCGATACAATGTCCCATGAATCGATACA
264534 TTTCACTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (33 bp):
GTATCGATACAATGTCCCATGAATCGATACAAT
Found at i:266826 original size:21 final size:22
Alignment explanation
Indices: 266783--266826 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
266773 TTAGGGAATA
*
266783 AAAAAAAACCTAAAGATCTAAG
1 AAAAAAAACCTAAAGATCAAAG
* *
266805 AAAAACAACCTAAA-ATGAAAG
1 AAAAAAAACCTAAAGATCAAAG
266826 A
1 A
266827 TTTGAAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAAAAACCTAAAGATCAAAG
Found at i:270733 original size:20 final size:19
Alignment explanation
Indices: 270708--270745 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
270698 TCCCGTAGCT
*
270708 ATGTATCGATACAATTCATA
1 ATGTATCAATAC-ATTCATA
270728 ATGTATCAATACATTCAT
1 ATGTATCAATACATTCAT
270746 TTGAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
ATGTATCAATACATTCATA
Found at i:270907 original size:32 final size:33
Alignment explanation
Indices: 270866--270927 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
270856 ATTGTCCATG
*
270866 TATCGATACAATGAAT-ATGTATCGATACAATA
1 TATCGATACAAAGAATAATGTATCGATACAATA
*
270898 TATCGATACAAAGCATAATGTATCGATACA
1 TATCGATACAAAGAATAATGTATCGATACA
270928 TCTGGGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (33 bp):
TATCGATACAAAGAATAATGTATCGATACAATA
Found at i:272426 original size:13 final size:13
Alignment explanation
Indices: 272408--272433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
272398 ACATTAAAAT
272408 TGTATCGATATAA
1 TGTATCGATATAA
272421 TGTATCGATATAA
1 TGTATCGATATAA
272434 ATTTGATTGT
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:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:273976 original size:22 final size:21
Alignment explanation
Indices: 273951--274000 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
273941 CCAATTCATC
273951 ATTTTCTACT-TGCAACTCATTT
1 ATTTTCTACTCT--AACTCATTT
* *
273973 ATTTTCTGCTCTAATTCATTT
1 ATTTTCTACTCTAACTCATTT
273994 ATTTTCT
1 ATTTTCT
274001 TTTCTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.60
22 9 0.36
23 1 0.04
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTTCTACTCTAACTCATTT
Found at i:273993 original size:21 final size:21
Alignment explanation
Indices: 273967--274021 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
273957 TACTTGCAAC
273967 TCATTTATTTTCTGCTCTAAT
1 TCATTTATTTTCTGCTCTAAT
**
273988 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTGCTCTAAT
* *
274009 TCACTTAATTTCT
1 TCATTTATTTTCT
274022 TTTCAAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTGCTCTAAT
Found at i:276359 original size:33 final size:32
Alignment explanation
Indices: 276296--276360 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
276286 TTTGAAACAA
* *
276296 TGTATCGATACAATTCATCATTTATTGATACAT
1 TGTATCGATACAATTCA-CATGTATCGATACAT
276329 TGTATCGATACAATGTGC-CATGTATCGATACA
1 TGTATCGATACAAT-T-CACATGTATCGATACA
276361 AACAGTGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAATTCACATGTATCGATACAT
Found at i:276455 original size:32 final size:33
Alignment explanation
Indices: 276414--276476 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
276404 ATTCTCCATG
*
276414 TATCGATACAATG-A-ACATGTATCGATACATTT
1 TATCGATACAAAGCATA-ATGTATCGATACATTT
276446 TATCGATACAAAGCATAATGTATCGATACAT
1 TATCGATACAAAGCATAATGTATCGATACAT
276477 CTGGGTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.43
33 15 0.54
34 1 0.04
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (33 bp):
TATCGATACAAAGCATAATGTATCGATACATTT
Found at i:276522 original size:82 final size:82
Alignment explanation
Indices: 276425--276591 Score: 298
Period size: 82 Copynumber: 2.0 Consensus size: 82
276415 ATCGATACAA
* *
276425 TGAACATGTATCGATACATTTTATCGATACAAAGCATAATGTATCGATACATCTGGGTGTGTATC
1 TGAACATGTATCGATACATTGTATCGATACAAAGCATAATGTATCAATACATCTGGGTGTGTATC
*
276490 GATACATTCAAGGATTT
66 AATACATTCAAGGATTT
*
276507 TGAACATGTATCGATACATTGTATCGATACAAAGCATAATGTATCAATACATCTGGGTGTGTATT
1 TGAACATGTATCGATACATTGTATCGATACAAAGCATAATGTATCAATACATCTGGGTGTGTATC
276572 AATACATTCAAGGATTT
66 AATACATTCAAGGATTT
276589 TGA
1 TGA
276592 TCTTTGTAGC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (82 bp):
TGAACATGTATCGATACATTGTATCGATACAAAGCATAATGTATCAATACATCTGGGTGTGTATC
AATACATTCAAGGATTT
Found at i:276531 original size:13 final size:13
Alignment explanation
Indices: 276513--276537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
276503 ATTTTGAACA
276513 TGTATCGATACAT
1 TGTATCGATACAT
276526 TGTATCGATACA
1 TGTATCGATACA
276538 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:277416 original size:13 final size:13
Alignment explanation
Indices: 277398--277422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277388 ACACATAGTA
277398 TGTATCGATACAT
1 TGTATCGATACAT
277411 TGTATCGATACA
1 TGTATCGATACA
277423 CCATAAAATG
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:277419 original size:32 final size:33
Alignment explanation
Indices: 277378--277445 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
277368 GTAGCTAAAC
**
277378 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
277410 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
277443 TTG
1 TTG
277446 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:281527 original size:15 final size:15
Alignment explanation
Indices: 281509--281538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
281499 CCAAATTGAG
281509 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
281524 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
281539 ATTGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:281534 original size:16 final size:16
Alignment explanation
Indices: 281498--281538 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
281488 GATAAAAATG
* *
281498 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
281514 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
281529 TCC-AAATGAA
1 TCCAAAATGAA
281539 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:283045 original size:8 final size:8
Alignment explanation
Indices: 283030--283061 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
283020 ATTTGATTAA
283030 ATTTTGTG
1 ATTTTGTG
*
283038 AGTTTGTG
1 ATTTTGTG
283046 ATTTTGTG
1 ATTTTGTG
283054 ATTTTGTG
1 ATTTTGTG
283062 TTGAATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.59
Consensus pattern (8 bp):
ATTTTGTG
Found at i:283282 original size:13 final size:13
Alignment explanation
Indices: 283264--283302 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
283254 ACAGCATTTT
283264 TTGTATCGATACA
1 TTGTATCGATACA
283277 TTGTATCGATACA
1 TTGTATCGATACA
*
283290 CTGTATCGATACA
1 TTGTATCGATACA
283303 GTGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:283479 original size:20 final size:20
Alignment explanation
Indices: 283444--283484 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
283434 CAAAATTCTT
283444 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
283466 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
283485 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:288434 original size:13 final size:13
Alignment explanation
Indices: 288412--288450 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
288402 ATAATCCCCC
* *
288412 TGTATTGATACAG
1 TGTATCGATACAA
288425 TGTATCGATACAA
1 TGTATCGATACAA
288438 TGTATCGATACAA
1 TGTATCGATACAA
288451 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:295822 original size:13 final size:13
Alignment explanation
Indices: 295804--295829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295794 GCAACTAAAC
295804 TTGTATCGATACA
1 TTGTATCGATACA
295817 TTGTATCGATACA
1 TTGTATCGATACA
295830 CCATAAAATG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:298554 original size:20 final size:21
Alignment explanation
Indices: 298525--298565 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
298515 CTATTTTGTT
298525 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
298544 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
298566 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:298720 original size:13 final size:13
Alignment explanation
Indices: 298704--298735 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
298694 CCTTGTATGA
298704 ATACAGTGTATCG
1 ATACAGTGTATCG
*
298717 ATACAATGTATCG
1 ATACAGTGTATCG
298730 ATACAG
1 ATACAG
298736 AGAATGCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (13 bp):
ATACAGTGTATCG
Found at i:303862 original size:13 final size:13
Alignment explanation
Indices: 303844--303868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303834 ATTACTCAAA
303844 TGTATCGATACAT
1 TGTATCGATACAT
303857 TGTATCGATACA
1 TGTATCGATACA
303869 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:304005 original size:52 final size:52
Alignment explanation
Indices: 303877--303997 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
303867 CACTGATCTT
*
303877 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAACTATAAAA
* *
303929 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAACTATAAAA
303981 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
303998 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATAAACTATAAAA
Found at i:308622 original size:13 final size:13
Alignment explanation
Indices: 308604--308629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
308594 ACATTTTGTG
308604 ATGTATCGATACA
1 ATGTATCGATACA
308617 ATGTATCGATACA
1 ATGTATCGATACA
308630 TTTTGTGCGT
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:308647 original size:32 final size:33
Alignment explanation
Indices: 308582--308649 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
308572 CGTTACAAGC
*
308582 CAATGTATCGATACATTTTGTGATGTATCGATA
1 CAATGTATCGATACATTTTGTGACGTATCGATA
308615 CAATGTATCGATACATTTTGTG-CGTATCGATA
1 CAATGTATCGATACATTTTGTGACGTATCGATA
308647 CAA
1 CAA
308650 GTTTGGCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATTTTGTGACGTATCGATA
Found at i:309202 original size:32 final size:31
Alignment explanation
Indices: 309160--309220 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 31
309150 CATTGGGTTT
*
309160 AGAAGGGTTGCCACCAAATTGTGTAGGCTTTGG
1 AGAAGGGTTGCCACC-AACT-TGTAGGCTTTGG
309193 AGAA-GGTTGCCACCAACTTGTAGGCTTT
1 AGAAGGGTTGCCACCAACTTGTAGGCTTT
309221 AAAAGGATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
31 3 0.11
32 10 0.37
33 4 0.15
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (31 bp):
AGAAGGGTTGCCACCAACTTGTAGGCTTTGG
Found at i:309587 original size:141 final size:140
Alignment explanation
Indices: 309215--309704 Score: 506
Period size: 141 Copynumber: 3.5 Consensus size: 140
309205 CCAACTTGTA
* * * * * *
309215 GGCTTTAAAAGGATGCCACTGATTTGTTGGCTTTGAAAGGGTGCCACTAACTTGTGGGC-TTCAA
1 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAA
* * * * * *
309279 AAGGGTGCCACTGACTTCTGGGCTTCGAAAAGG-TGCCAC-AACTTGTGGGCTTTGAAAGGGTGC
66 AAGGATGCCACTAACATGT-GGCTT-TAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGC
*
309342 CA-TCGACTTTTG
129 CACT-GACTTATG
* * * * *
309354 GGCTTTGAGAGAGGTTGCCACCGACTTGTGTGGGC-TTAAAGGGGTGTCACTAACTTGTGGGCTT
1 GGCTTTGA-A-AGGATGCCACTGAC-T-TGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTT
* * * *
309418 TGAGAAGGATGCCACTGACTCATG-GGCTTTAAAAGGATGCCACTGACATGTGGGCTTTGAAAAG
62 TGAAAAGGATGCCACT-A-ACATGTGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAG
309482 GTGCCACTGACTTATG
125 GTGCCACTGACTTATG
* * * * *
309498 GGCTTTGAAAGGATGCCACTGACATGTAGCCTTTAAAAGGATGCCATTGACTTGTGGGCTTTGAA
1 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAA
* * * *
309563 AAGGATGCCACTAACATGTCGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAATGATGCC
66 AAGGATGCCACTAACATGT-GGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCC
*
309628 ACTGACTTGTG
130 ACTGACTTATG
* * * * * *
309639 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAATGATACCACTGACTTATGGGCTTTGAA
1 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAA
309704 A
66 A
309705 TGGGTCGTAT
Statistics
Matches: 290, Mismatches: 48, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
139 11 0.04
140 7 0.02
141 156 0.54
142 43 0.15
143 32 0.11
144 38 0.13
145 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (140 bp):
GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAA
AAGGATGCCACTAACATGTGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCA
CTGACTTATG
Found at i:309592 original size:113 final size:114
Alignment explanation
Indices: 309208--309704 Score: 487
Period size: 113 Copynumber: 4.4 Consensus size: 114
309198 GTTGCCACCA
* ** * * *
309208 ACTTGTAGGCTTT-AAAAGGATGCCACTGATTTGTTGGCTTTG-AAAGGGTGCCACTAACTTGTG
1 ACTTGTGGGCTTTGAAAAGGATGCCACTGACATGTGGGCTTTGAAAAGGATGCCACTAACTTATG
** * * * *
309271 GGCTTCAAAAGGGTGCCACTGACTTCTGGGCTTCGAAAAGG-TGCCAC-A
66 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTT-TAAAAGGATGCCACTG
* * * * * **
309319 ACTTGTGGGCTTTG-AAAGGGTGCCA-TCGACTTTTGGGCTTTGAGAGAGGTTGCCACCGACTTG
1 ACTTGTGGGCTTTGAAAAGGATGCCACT-GACATGTGGGCTTTGA-AAAGGATGCCACTAAC-T-
* * * * *
309382 TGTGGGC-TT-AAAGGGGTGTCACTAACTTGTGGGCTTTGAGAAGGATGCCACTG
62 TATGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTT-AAAAGGATGCCACTG
** *
309435 ACTCATGGGCTTT-AAAAGGATGCCACTGACATGTGGGCTTTGAAAAGG-TGCCACTGACTTATG
1 ACTTGTGGGCTTTGAAAAGGATGCCACTGACATGTGGGCTTTGAAAAGGATGCCACTAACTTATG
* * * *
309498 GGCTTTGAAAGGATGCCACTGACATGTAGCCTTTAAAAGGATGCCATTG
66 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTG
* *
309547 ACTTGTGGGCTTTGAAAAGGATGCCACTAACATGTCGGCTTTG-AAAGGATGCCACTAACTTATG
1 ACTTGTGGGCTTTGAAAAGGATGCCACTGACATGTGGGCTTTGAAAAGGATGCCACTAACTTATG
* * *
309611 GGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
66 GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTG
* * * *
309660 ACTTGTGGGCTTTG-AAATGATACCACTGACTTATGGGCTTTGAAA
1 ACTTGTGGGCTTTGAAAAGGATGCCACTGACATGTGGGCTTTGAAA
309705 TGGGTCGTAT
Statistics
Matches: 319, Mismatches: 50, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
110 1 0.00
111 34 0.11
112 57 0.18
113 135 0.42
114 39 0.12
115 17 0.05
116 35 0.11
117 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (114 bp):
ACTTGTGGGCTTTGAAAAGGATGCCACTGACATGTGGGCTTTGAAAAGGATGCCACTAACTTATG
GGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTG
Found at i:309706 original size:28 final size:28
Alignment explanation
Indices: 309185--309704 Score: 512
Period size: 28 Copynumber: 18.4 Consensus size: 28
309175 AAATTGTGTA
* ** *
309185 GGCTTTGGAGAAGGTTGCCACCAACTTGTA
1 GGCTTT-GA-AAGGATGCCACTGACTTGTG
* * *
309215 GGCTTTAAAAGGATGCCACTGATTTGTT
1 GGCTTTGAAAGGATGCCACTGACTTGTG
* *
309243 GGCTTTGAAAGGGTGCCACTAACTTGTG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
** * *
309271 GGCTTCAAAAGGGTGCCACTGACTTCTG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
* *
309299 GGCTTCGAAAAGG-TGCCAC-AACTTGTG
1 GGCTTTG-AAAGGATGCCACTGACTTGTG
* *
309326 GGCTTTGAAAGGGTGCCA-TCGACTTTTG
1 GGCTTTGAAAGGATGCCACT-GACTTGTG
* *
309354 GGCTTTGAGAGAGGTTGCCACCGACTTGTGTG
1 GGCTTTGA-A-AGGATGCCACTGAC-T-TGTG
* * *
309386 GGC-TT-AAAGGGGTGTCACTAACTTGTG
1 GGCTTTGAAA-GGATGCCACTGACTTGTG
**
309413 GGCTTTGAGAAGGATGCCACTGACTCATG
1 GGCTTTGA-AAGGATGCCACTGACTTGTG
* *
309442 GGCTTTAAAAGGATGCCACTGACATGTG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
*
309470 GGCTTTGAAAAGG-TGCCACTGACTTATG
1 GGCTTTG-AAAGGATGCCACTGACTTGTG
* *
309498 GGCTTTGAAAGGATGCCACTGACATGTA
1 GGCTTTGAAAGGATGCCACTGACTTGTG
* * *
309526 GCCTTTAAAAGGATGCCATTGACTTGTG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
* * *
309554 GGCTTTGAAAAGGATGCCACTAACATGTC
1 GGCTTTG-AAAGGATGCCACTGACTTGTG
* *
309583 GGCTTTGAAAGGATGCCACTAACTTATG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
*
309611 GGCTTTGAAATGATGCCACTGACTTGTG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
*
309639 GGCTTTGAAAGGGTGCCACTGACTTGTG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
* * *
309667 GGCTTTGAAATGATACCACTGACTTATG
1 GGCTTTGAAAGGATGCCACTGACTTGTG
309695 GGCTTTGAAA
1 GGCTTTGAAA
309705 TGGGTCGTAT
Statistics
Matches: 408, Mismatches: 66, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
26 5 0.01
27 29 0.07
28 278 0.68
29 67 0.16
30 20 0.05
31 3 0.01
32 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (28 bp):
GGCTTTGAAAGGATGCCACTGACTTGTG
Found at i:319773 original size:20 final size:20
Alignment explanation
Indices: 319748--319785 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
319738 CTGCCAAGGA
*
319748 AATGTATCGATACATTATTT
1 AATGTATCAATACATTATTT
319768 AATGTATCAATACATTAT
1 AATGTATCAATACATTAT
319786 ATCGATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (20 bp):
AATGTATCAATACATTATTT
Found at i:319859 original size:20 final size:19
Alignment explanation
Indices: 319834--319907 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
319824 TTTACCCAGA
319834 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
319854 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
319874 TGTCTCGATACATTTT-AT
1 TGTATCGATACATTTTCAT
*
319892 AATGTATCAATACATT
1 --TGTATCGATACATT
319908 CAGGCACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 42 0.91
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:322262 original size:51 final size:50
Alignment explanation
Indices: 322205--322473 Score: 274
Period size: 51 Copynumber: 5.3 Consensus size: 50
322195 TCTCGCCTCA
* *
322205 GGGATACTCCAATCCCGGTTTCATTT-TCAAAACATCAATTTTTCTTAATCG
1 GGGATACTCCAA-CCCGATTTTATTTCT-AAAACATCAATTTTTCTTAATCG
* ** * * * * * *
322256 AGGATACTCCAACTCCGATTTTACCTCTAAAGCCTCGA-TTTACTGCAACCG
1 GGGATACTCCAAC-CCGATTTTATTTCTAAAACATCAATTTTTCT-TAATCG
* *
322307 GGGATACTCCAATCCCGATTTTATCTCCAAAACATCAATTTTTCTTAATCG
1 GGGATACTCCAA-CCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCG
* * * * *
322358 GGGATACTCCAACTCTGATTTTATTTCTAAAATACCAATTTTTCATAATTG
1 GGGATACTCCAAC-CCGATTTTATTTCTAAAACATCAATTTTTCTTAATCG
*
322409 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAAT-G
1 GGGATACTCCAA-CCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCG
322459 AGGGATACTCCAACC
1 -GGGATACTCCAACC
322474 TCGTTATTTT
Statistics
Matches: 180, Mismatches: 30, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
50 10 0.06
51 162 0.90
52 8 0.04
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (50 bp):
GGGATACTCCAACCCGATTTTATTTCTAAAACATCAATTTTTCTTAATCG
Found at i:322387 original size:102 final size:101
Alignment explanation
Indices: 322205--322472 Score: 317
Period size: 102 Copynumber: 2.6 Consensus size: 101
322195 TCTCGCCTCA
* * * *
322205 GGGATACTCCAATCCCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCGAGGATACTCCAACT
1 GGGATACTCCAATCCCGATTTTATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACT
* *
322270 CCGATTTTACCTCT-AAAGCCTCGATTTACTGC-AACCG
66 CCGATTTTACCTCTAAAAGAC-CAATTT--TGCAAACCG
*
322307 GGGATACTCCAATCCCGATTTTATCTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACT
1 GGGATACTCCAATCCCGATTTTATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACT
* ** * * **
322372 CTGATTTTATTTCTAAAATACCAATTTTTCATAATTG
66 CCGATTTTACCTCTAAAAGACCAATTTTGCA-AACCG
* * *
322409 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAAT-GAGGGATACTCCAAC
1 GGGATACTCCAATCCCGATTTTATTTCCAAAACATCAATTTTTCTTAATCG-GGGATACTCCAAC
322473 CTCGTTATTT
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
100 2 0.01
101 1 0.01
102 137 0.95
103 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (101 bp):
GGGATACTCCAATCCCGATTTTATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACT
CCGATTTTACCTCTAAAAGACCAATTTTGCAAACCG
Found at i:322586 original size:51 final size:51
Alignment explanation
Indices: 322506--322602 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
322496 CTAACCCCAG
*
322506 TTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACACTCCAACTCCGA
1 TTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACAATCCAACTCCGA
* * * * *
322557 TTTTATTT-TCAAAACACTAATTTTTCACAATCGGGGATAATCCAAC
1 TTTTATTTCT-AAAACACCAATTCTCCACAATCAGGGACAATCCAAC
322603 CCCGTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.03
51 38 0.97
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (51 bp):
TTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACAATCCAACTCCGA
Found at i:322594 original size:130 final size:129
Alignment explanation
Indices: 322356--322633 Score: 332
Period size: 130 Copynumber: 2.1 Consensus size: 129
322346 TTTTCTTAAT
* * * * * * ** *
322356 CGGGGATACTCCAA-CTCTGATTTTATTTCTAAAATACCAATTTTTCATAATTGGGGATACTCCA
1 CGGGGATACTCCAACCCCAG-TTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACACTCCA
* * *
322420 ACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATGAGGGATACTCCAACCTCGTTATTTTC
65 ACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATGAGGGATAATCCAACCCCGTTA-TTTC
322485 GA
129 -A
*
322487 -GGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACACTCCAA
1 CGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACACTCCAA
*
322551 CTCCGATTTTATTT-TCAAAACA-CTAATTTTTCACAATCG-GGGATAATCCAACCCCGTTATTT
66 CCCCGATTTTATTTCT-AAAACATC-AATTTTTCACAAT-GAGGGATAATCCAACCCCGTTATTT
322613 CA
128 CA
322615 TCGGGGATACTCCAACCCC
1 -CGGGGATACTCCAACCCC
322634 GTTATTTTCG
Statistics
Matches: 126, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
128 1 0.01
129 6 0.05
130 115 0.91
131 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (129 bp):
CGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTCTCCACAATCAGGGACACTCCAA
CCCCGATTTTATTTCTAAAACATCAATTTTTCACAATGAGGGATAATCCAACCCCGTTATTTCA
Found at i:322622 original size:28 final size:27
Alignment explanation
Indices: 322586--322662 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 27
322576 ATTTTTCACA
*
322586 ATCGGGGATAATCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
322613 CATCGGGGATACTCCAACCCCGTTATTT
1 -ATCGGGGATACTCCAACCCCGTTATTT
322641 -TCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
322663 GCTTTATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.04
28 44 0.96
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTATTT
Found at i:322710 original size:51 final size:50
Alignment explanation
Indices: 322646--322763 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 50
322636 TATTTTCGAG
*
322646 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC
1 GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATC
* * * *
322696 AGGGATACTTCAACCCCGGCCTTATTTCTAAGATATTGATTTCTCATAATC
1 -GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATC
322747 GAGGA-ACTCCAACCCCG
1 G-GGATACTCCAACCCCG
322764 TTATTTTTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 12 0.20
51 48 0.80
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (50 bp):
GGGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATC
Found at i:324246 original size:13 final size:13
Alignment explanation
Indices: 324228--324252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
324218 ACACAAAGTA
324228 TGTATCGATACAG
1 TGTATCGATACAG
324241 TGTATCGATACA
1 TGTATCGATACA
324253 CAAAAAATTG
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:330381 original size:13 final size:13
Alignment explanation
Indices: 330363--330388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
330353 ACATTTTTCT
330363 TTGTATCGATACA
1 TTGTATCGATACA
330376 TTGTATCGATACA
1 TTGTATCGATACA
330389 GGGGGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:332212 original size:21 final size:20
Alignment explanation
Indices: 332166--332214 Score: 89
Period size: 20 Copynumber: 2.4 Consensus size: 20
332156 AGAGAATAGA
332166 TGTATGTGCAAATAAATTTT
1 TGTATGTGCAAATAAATTTT
332186 TGTATGTGCAAATAAATTTT
1 TGTATGTGCAAATAAATTTT
332206 TGATATGTG
1 TG-TATGTG
332215 TGTAAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (20 bp):
TGTATGTGCAAATAAATTTT
Found at i:332994 original size:13 final size:13
Alignment explanation
Indices: 332976--333001 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
332966 TACACAAAGT
332976 ATGTATCGATACA
1 ATGTATCGATACA
332989 ATGTATCGATACA
1 ATGTATCGATACA
333002 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:332999 original size:32 final size:33
Alignment explanation
Indices: 332958--333021 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
332948 TAGCCAAACT
**
332958 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
332990 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
333022 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:334845 original size:19 final size:20
Alignment explanation
Indices: 334802--334851 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
334792 CACATCCAGA
* *
334802 TGTATCGATACATTATGCTT
1 TGTATCGATACATGATGCAT
334822 TGTATCGATACATGAT-CAT
1 TGTATCGATACATGATGCAT
*
334841 TGTATCAATAC
1 TGTATCGATAC
334852 TTACACAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:339531 original size:21 final size:20
Alignment explanation
Indices: 339505--339543 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
339495 CGGTCAAAAC
339505 TCTAGAAAGTATCGATACACA
1 TCTAG-AAGTATCGATACACA
*
339526 TCTAGATGTATCGATACA
1 TCTAGAAGTATCGATACA
339544 TTATGCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
TCTAGAAGTATCGATACACA
Found at i:340811 original size:164 final size:164
Alignment explanation
Indices: 340462--340799 Score: 376
Period size: 164 Copynumber: 2.0 Consensus size: 164
340452 TGAGCTTTGA
* *
340462 AAAATTCATTCATTTTCATGGATTTTTGAATTTTTTCCTTGACACTCCCTTTTTTTCGAAATACG
1 AAAATTCATTCATTTTCATGGATTTTTGAA-TTTTTCCTTGAAACT-CCTTTTTTTCGAAAAACG
* * **
340527 GAGTTTTCTTCTTCGTAAATTTTTTCGAGAGCATTTTTGTTAGTTTTTAATTTAAAAATTCATAA
64 AAGTTTTCTTCTCCGTAAATTTTTTCGAGAGCATTTTTGTTAGTTTAAAATTTAAAAATTCATAA
* * * *
340592 AATATTATTATTTAATTCATATTAAATCAATTTTCT
129 AATATTATCATTAAATTCATATTAAACCAATTTTCG
* * *
340628 AAAATTCATTCATTTTCATGGATTTTTGAATTTTTCCTTGAAAGT-TTTCTTTTTCGAAAAACTA
1 AAAATTCATTCATTTTCATGGATTTTTGAATTTTTCCTTGAAACTCCTT-TTTTTCGAAAAACGA
* * * * * * *
340692 AGTTTTGTTCTCCGTAAATTTTTTTG-GGGGATTTTT-TTCGATTTAAAATTTTTAAAATTCATC
65 AGTTTTCTTCTCCGTAAATTTTTTCGAGAGCATTTTTGTTAG-TTTAAAA-TTTAAAAATTCATA
* * * * *
340755 TAATGTTGTCATTAAATTCATATTAAACCAGTTTTGG
128 AAATATTATCATTAAATTCATATTAAACCAATTTTCG
*
340792 AAGATTCA
1 AAAATTCA
340800 AATTATTTCA
Statistics
Matches: 143, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
162 3 0.02
163 15 0.10
164 82 0.57
165 13 0.09
166 30 0.21
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (164 bp):
AAAATTCATTCATTTTCATGGATTTTTGAATTTTTCCTTGAAACTCCTTTTTTTCGAAAAACGAA
GTTTTCTTCTCCGTAAATTTTTTCGAGAGCATTTTTGTTAGTTTAAAATTTAAAAATTCATAAAA
TATTATCATTAAATTCATATTAAACCAATTTTCG
Found at i:342473 original size:158 final size:158
Alignment explanation
Indices: 342266--342706 Score: 611
Period size: 158 Copynumber: 2.8 Consensus size: 158
342256 TCAGTGGTAA
* *
342266 AAATAAATATTAATCATTTTTTAATCTTTTATATTCCTATGGGGGTCCGTAGGGGTATAAAAGAT
1 AAATAAATATCAATCA-TTTTTAATCTTTTATATTCCTATAGGGGTCCGTAGGGGTATAAAAGAT
342331 TTTAAAAACTTTTCGTATCTTTTCAGGTTTCCATTAAGATACAAAATGATATTTTTCAAA-AATA
65 TTTAAAAACTTTTCGTATCTTTTC-GGTTTCCATTAAGATACAAAATGATATTTTTCAAAGAATA
* **
342395 AATAAAATTAAATTAACACTTTCATAATTG
129 AATAAAATTAAATTAACACTCTCATAACCG
*
342425 AAATAAATATCAATCATTTTTAATCTTTTATATTCCTATAGGGATCCGTAGGGGTATAAAAGATT
1 AAATAAATATCAATCATTTTTAATCTTTTATATTCCTATAGGGGTCCGTAGGGGTATAAAAGATT
* * * *
342490 TCAAAATCTTTTCGTATCTTTTCGGGTTTCCATTAAGGTACGAAATGATATTTTT-AAAGAATAA
66 TTAAAAACTTTTCGTATCTTTTC-GGTTTCCATTAAGATACAAAATGATATTTTTCAAAGAATAA
* *
342554 ATAAAATTAAATTAATACTCTCGTAACCG
130 ATAAAATTAAATTAACACTCTCATAACCG
* * * *
342583 AGAGAAACT-TCAAT-TTTTTTAATCTTTTATATTCCTATAGGGGTCCGTAGGGGTATAAAAGGT
1 AAATAAA-TATCAATCATTTTTAATCTTTTATATTCCTATAGGGGTCCGTAGGGGTATAAAAGAT
* * * * *
342646 TTTAAAAACTTTTTGTATCGTTTCGGTTTTTCGTTAAGATACAAAATGATTTTTTTGCAAA
65 TTTAAAAACTTTTCGTATCTTTTCGG-TTTCCATTAAGATACAAAATGATATTTTT-CAAA
342707 TTAAAAAATC
Statistics
Matches: 250, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
156 2 0.01
157 93 0.37
158 136 0.54
159 19 0.08
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (158 bp):
AAATAAATATCAATCATTTTTAATCTTTTATATTCCTATAGGGGTCCGTAGGGGTATAAAAGATT
TTAAAAACTTTTCGTATCTTTTCGGTTTCCATTAAGATACAAAATGATATTTTTCAAAGAATAAA
TAAAATTAAATTAACACTCTCATAACCG
Found at i:348650 original size:79 final size:79
Alignment explanation
Indices: 348485--349062 Score: 831
Period size: 79 Copynumber: 7.3 Consensus size: 79
348475 TTTTAGAGAT
* * * * * *
348485 AATAACGGGGCTAGAGTATCCCTGATTATGAAAAATTGATG-TTTAGAAATAAAATCAGGGTTGG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGG
* *
348549 AGTATCCCTTCGAA
66 AGTATCCCCTCGGA
* *
348563 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAATCGGGGTTGT
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGG
*
348628 AGTATCCCCGCGGA
66 AGTATCCCCTCGGA
* * * *
348642 AACAACGGGGTTGGAGTATCCTCGATTACGAAAAATTGAA-GTTTTAGAAATAAAACCGAGGTTG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATT-AATGTTTTAGAAATAAAACCGGGGTTG
*
348706 GAGTATCCCCGCGGA
65 GAGTATCCCCTCGGA
* * *
348721 AATAACGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGG
348786 AGTATCCCCTCGGA
66 AGTATCCCCTCGGA
* *
348800 AATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTGAA-GTTTTAGAAATAAAATCGGGGTTG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATT-AATGTTTTAGAAATAAAACCGGGGTTG
*
348864 GAGTATCCCCTCGAA
65 GAGTATCCCCTCGGA
* * * * *
348879 AATAACTGGGTTAGAGTATCGCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAGGGTTGG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGG
348944 AGTATCCCCTCGGA
66 AGTATCCCCTCGGA
** *
348958 AATAATAGTGTTGGAGTATCCCCGATTATGAAAAATTGAA-GTTTTAGAAATAAAACCGGGGTTG
1 AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATT-AATGTTTTAGAAATAAAACCGGGGTTG
349022 GAGTATCCCCTCGGA
65 GAGTATCCCCTCGGA
349037 AATAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
349063 GATTAACGGG
Statistics
Matches: 451, Mismatches: 43, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
78 39 0.09
79 408 0.90
80 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGGGTTGG
AGTATCCCCTCGGA
Found at i:349077 original size:27 final size:28
Alignment explanation
Indices: 349014--349089 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
349004 GAAATAAAAC
***
349014 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
349042 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
349069 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
349090 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:350514 original size:35 final size:35
Alignment explanation
Indices: 350486--350794 Score: 532
Period size: 35 Copynumber: 8.9 Consensus size: 35
350476 TTTATTTTTT
350486 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
* *
350521 ATGCCCATCACTCCATGCCTCCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
350556 ATG-CCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
* *
350590 ATGCCCATCATTCCATGCCTCCACTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
350625 ATGCCCATCATCCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
350660 ATGCCCATCATTCCATGCCTTCATTTTTATATAT-T
1 ATGCCCATCATTCCATGCCTTCATTTTTATAT-TCC
350695 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
350730 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
1 ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
*
350765 ATGCCCATCATTCCATGCCTTCTTTTTTAT
1 ATGCCCATCATTCCATGCCTTCATTTTTAT
350795 TATTTTTTTT
Statistics
Matches: 258, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
34 33 0.13
35 224 0.87
36 1 0.00
ACGTcount: A:0.20, C:0.32, G:0.06, T:0.42
Consensus pattern (35 bp):
ATGCCCATCATTCCATGCCTTCATTTTTATATTCC
Found at i:350821 original size:12 final size:13
Alignment explanation
Indices: 350801--350829 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
350791 TTATTATTTT
350801 TTTTGAATTTTAA
1 TTTTGAATTTTAA
350814 TTTT-AATTTTAA
1 TTTTGAATTTTAA
350826 TTTT
1 TTTT
350830 TGATTTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:351558 original size:19 final size:20
Alignment explanation
Indices: 351534--351587 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
351524 ATCAATACAT
351534 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTCTA
** *
351553 TGTATCGATACATTTACTCTT
1 TGTATCGATACA-AAACTCTA
351574 TGTATCGATACAAA
1 TGTATCGATACAAA
351588 TTGTAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTCTA
Found at i:352626 original size:88 final size:88
Alignment explanation
Indices: 352426--352646 Score: 288
Period size: 88 Copynumber: 2.5 Consensus size: 88
352416 TGTCAAAACA
* * *
352426 AGGTTGAAATATCCCTTC-ACAATAGTAAGGATGGAG-TTTCCCTAAGGATAAAATTATACAAAG
1 AGGTTGGAGTATCCCTTCGA-AATAGTGAGGATGGAGTTTTCCC-AAGGATAAAATTATACAAAG
* *
352489 GAAAATTTGAATTTTTGTTAGAATG
64 AAAAATTTGAATTTTTGTTAGAAAG
* * *
352514 AGGTTGGAGTATCCCCATAG-AATAGTGAGGACGGAGTTTTCCCAAGGATAAAATTATACAAAGA
1 AGGTTGGAGTAT-CCCTTCGAAATAGTGAGGATGGAGTTTTCCCAAGGATAAAATTATACAAAGA
352578 AAAATTTGAATTTTTGTTAGAACAG
65 AAAATTTGAATTTTTGTTAGAA-AG
* *
352603 -GGTTGGAGTATCCCTTCGAAATAGTGAAGATGGAGTTTCCCCAA
1 AGGTTGGAGTATCCCTTCGAAATAGTGAGGATGGAGTTTTCCCAA
352647 AATTGGAAAT
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
87 5 0.04
88 99 0.86
89 11 0.10
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (88 bp):
AGGTTGGAGTATCCCTTCGAAATAGTGAGGATGGAGTTTTCCCAAGGATAAAATTATACAAAGAA
AAATTTGAATTTTTGTTAGAAAG
Found at i:360953 original size:20 final size:20
Alignment explanation
Indices: 360928--360968 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
360918 ATAAAAAGAT
360928 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
360948 AGAATGTATTGATACATTGA
1 AGAATGTATCGATACATTGA
360968 A
1 A
360969 AAAAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Done.