Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009575.1 Hibiscus syriacus cultivar Beakdansim tig00116943_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 458240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:125871 original size:25 final size:24
Alignment explanation
Indices: 125842--125899 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
125832 TTTAAAAATA
*
125842 TTTTTAAAAAGTATAT-ATAATATAG
1 TTTTTAAAAA-CATATGAT-ATATAG
*
125867 TTTTTGAAAACATATGATATATAG
1 TTTTTAAAAACATATGATATATAG
*
125891 CTTTTAAAA
1 TTTTTAAAA
125900 TATTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (24 bp):
TTTTTAAAAACATATGATATATAG
Found at i:125948 original size:12 final size:11
Alignment explanation
Indices: 125933--125980 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
125923 ATTATATATT
125933 TTTATTTATTTA
1 TTTA-TTATTTA
125945 TTTATTA-TTA
1 TTTATTATTTA
125955 -TTATTATTTA
1 TTTATTATTTA
*
125965 TATTATTACTTA
1 T-TTATTATTTA
125977 TTTA
1 TTTA
125981 ATTTTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 6 0.19
10 6 0.19
11 6 0.19
12 14 0.44
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:125977 original size:28 final size:28
Alignment explanation
Indices: 125922--125978 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
125912 AGAAATATAA
*
125922 TATTATATATTTTTATTTATTTATTTAT
1 TATTATATATTTTTATTTATTTACTTAT
125950 TATTAT-TATTATTTATATTA-TTACTTAT
1 TATTATATATT-TTTAT-TTATTTACTTAT
125978 T
1 T
125979 TAATTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 19 0.73
29 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TATTATATATTTTTATTTATTTACTTAT
Found at i:127496 original size:8 final size:8
Alignment explanation
Indices: 127483--127584 Score: 57
Period size: 8 Copynumber: 12.6 Consensus size: 8
127473 AAATTTAACA
127483 TTTTTTAT
1 TTTTTTAT
127491 TTTTTTA-
1 TTTTTTAT
127498 TTTTTTAT
1 TTTTTTAT
* *
127506 TTTTTCAC
1 TTTTTTAT
*
127514 TTTTTCACT
1 TTTTTTA-T
127523 TTTTCATT-T
1 TTTT--TTAT
127532 TTGTTTTAT
1 TT-TTTTAT
*
127541 TTTTTT-C
1 TTTTTTAT
* *
127548 TCTTTTAA
1 TTTTTTAT
**
127556 CATTTTAT
1 TTTTTTAT
*
127564 TTATTTAT
1 TTTTTTAT
*
127572 TTATTTAT
1 TTTTTTAT
127580 TTTTT
1 TTTTT
127585 CTCTTAAATT
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
7 12 0.16
8 48 0.66
9 10 0.14
10 2 0.03
11 1 0.01
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTTAT
Found at i:127588 original size:38 final size:37
Alignment explanation
Indices: 127476--127631 Score: 121
Period size: 35 Copynumber: 4.3 Consensus size: 37
127466 TTCTTTAAAA
* *
127476 TTTAACATTTTTTATTTTTTTATTTTTTATTTTTTCACT
1 TTTAACA--TTTTATTTATTTATTTTTTATTTTTTCTCT
* * *
127515 TTT-TCACTTT-TTCATTT-TTGTTTTATTTTTTTCTCT
1 TTTAACATTTTATTTATTTATT-TTTTA-TTTTTTCTCT
127551 TTTAACATTTTATTTATTTATTTATTTATTTTTTCTC-
1 TTTAACATTTTATTTATTTATTT-TTTATTTTTTCTCT
* ** * *
127588 -TTAA-ATTTAACAT-TTTATTCTTTAGTTTTT-TCT
1 TTTAACATTTTATTTATTTATTTTTTATTTTTTCTCT
127621 TTTAACATTTT
1 TTTAACATTTT
127632 TATATATAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
32 2 0.02
33 9 0.10
34 12 0.13
35 20 0.21
36 19 0.20
37 5 0.05
38 18 0.19
39 9 0.10
ACGTcount: A:0.19, C:0.10, G:0.01, T:0.71
Consensus pattern (37 bp):
TTTAACATTTTATTTATTTATTTTTTATTTTTTCTCT
Found at i:127654 original size:16 final size:15
Alignment explanation
Indices: 127623--127653 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
127613 TTTTTTCTTT
127623 TAACATTTTTATATA
1 TAACATTTTTATATA
127638 TAACATTTTT-TATA
1 TAACATTTTTATATA
127652 TA
1 TA
127654 TTTTCCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TAACATTTTTATATA
Found at i:127675 original size:26 final size:24
Alignment explanation
Indices: 127642--127695 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
127632 TATATATAAC
127642 ATTT-TTTATATATTTTCCTTCTTT
1 ATTTATTTATATATTTTCCTT-TTT
* *
127666 GATTTATTTATTTATTTTTCTTTTT
1 -ATTTATTTATATATTTTCCTTTTT
127691 ATTTA
1 ATTTA
127696 GTTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 7 0.27
26 14 0.54
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTATTTATATATTTTCCTTTTT
Found at i:137360 original size:22 final size:22
Alignment explanation
Indices: 137335--137396 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
137325 TTAATCAGTT
* * *
137335 TTCAAACGAATTCCAATGAGCA
1 TTCAAACCAAGTCCAATCAGCA
*
137357 TTCAGACCAAGTCCAATCAGCA
1 TTCAAACCAAGTCCAATCAGCA
137379 TT-AATACCAA-TCCAATCA
1 TTCAA-ACCAAGTCCAATCA
137397 ATAGTAAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 9 0.26
22 25 0.74
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (22 bp):
TTCAAACCAAGTCCAATCAGCA
Found at i:137394 original size:21 final size:22
Alignment explanation
Indices: 137346--137396 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
137336 TCAAACGAAT
* *
137346 TCCAATGAGCATTCAGACCAAG
1 TCCAATCAGCATTAAGACCAAG
*
137368 TCCAATCAGCATTAATACCAA-
1 TCCAATCAGCATTAAGACCAAG
137389 TCCAATCA
1 TCCAATCA
137397 ATAGTAAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (22 bp):
TCCAATCAGCATTAAGACCAAG
Found at i:141179 original size:21 final size:21
Alignment explanation
Indices: 141153--141204 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
141143 TGAATGTGCC
141153 TGATATGTATTATATGTGATG
1 TGATATGTATTATATGTGATG
141174 TGATATGTATTATATGTGATG
1 TGATATGTATTATATGTGATG
141195 TGATATGTAT
1 TGATATGTAT
141205 ATGCTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (21 bp):
TGATATGTATTATATGTGATG
Found at i:141190 original size:16 final size:18
Alignment explanation
Indices: 141153--141230 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 18
141143 TGAATGTGCC
141153 TGATATG-TAT-TATATG
1 TGATATGATATGTATATG
*
141169 TGATGTGATATGTATTATATG
1 TGATATGATATG---TATATG
*
141190 TGATGTGATATGTATATG
1 TGATATGATATGTATATG
141208 CT-ATAT-ATATGTTATATG
1 -TGATATGATATG-TATATG
141226 ATGAT
1 -TGAT
141231 GATTTATGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
16 6 0.12
17 8 0.16
18 16 0.31
19 3 0.06
21 18 0.35
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (18 bp):
TGATATGATATGTATATG
Found at i:141280 original size:30 final size:31
Alignment explanation
Indices: 141211--141281 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
141201 GTATATGCTA
* *
141211 TATATATG-TTATATGATGATGATTTATGTG
1 TATATATGAATATATGATGATAATTTATGTG
*
141241 TCTATATGAATATATGAT-ATAATTTATGTG
1 TATATATGAATATATGATGATAATTTATGTG
141271 -ATATAATGAAT
1 TATAT-ATGAAT
141282 GTGAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 3 0.09
30 24 0.69
31 8 0.23
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.46
Consensus pattern (31 bp):
TATATATGAATATATGATGATAATTTATGTG
Found at i:141685 original size:23 final size:23
Alignment explanation
Indices: 141655--141699 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
141645 GATATATGTG
*
141655 TTCTATGTGGTCTTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
141678 TTCTATGTGGTCCTTCGGGACA
1 TTCTATGTGGTCCTTCGGGACA
141700 AATTCTACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAT
Found at i:142543 original size:57 final size:56
Alignment explanation
Indices: 142480--142593 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 56
142470 ATTCATTTAT
*
142480 ATGCTTGCAGAAA-TCTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
1 ATGCTTGCAGAAATTC-ATGAAAATTAATCAAAAA-CAGTAAAGGTAAAAGCAGTAGC
* * *
142537 ATGCTTGCTGAAATTCATGAAAATTAATGAAAAACGGTAAAGGTAAAAGCAGTAGC
1 ATGCTTGCAGAAATTCATGAAAATTAATCAAAAACAGTAAAGGTAAAAGCAGTAGC
142593 A
1 A
142594 CCCTACAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 21 0.40
57 29 0.56
58 2 0.04
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.23
Consensus pattern (56 bp):
ATGCTTGCAGAAATTCATGAAAATTAATCAAAAACAGTAAAGGTAAAAGCAGTAGC
Found at i:145093 original size:9 final size:9
Alignment explanation
Indices: 145081--145105 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
145071 GATCGGATTT
145081 ATCGGTTCA
1 ATCGGTTCA
145090 ATCGGTTCA
1 ATCGGTTCA
145099 ATCGGTT
1 ATCGGTT
145106 TAATTGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (9 bp):
ATCGGTTCA
Found at i:153948 original size:18 final size:17
Alignment explanation
Indices: 153925--153959 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
153915 TGATAGATCT
153925 GACCCGACCCGATTGACC
1 GACCCGACCCG-TTGACC
153943 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
153960 ACCGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.20, C:0.46, G:0.23, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGTTGACC
Found at i:155305 original size:15 final size:15
Alignment explanation
Indices: 155285--155314 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
155275 AAAATGCCTT
155285 TATGGTCTAGACTAA
1 TATGGTCTAGACTAA
155300 TATGGTCTAGACTAA
1 TATGGTCTAGACTAA
155315 GTAAATGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TATGGTCTAGACTAA
Found at i:157112 original size:18 final size:18
Alignment explanation
Indices: 157089--157123 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
157079 AGGGATTATC
157089 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
157107 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
157124 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:159691 original size:21 final size:22
Alignment explanation
Indices: 159653--159695 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
159643 TATGAGAAAT
159653 TGTTTCTAAAATATAAAAATGA
1 TGTTTCTAAAATATAAAAATGA
159675 TGTTTC-AAAAT-TGAAAAATGA
1 TGTTTCTAAAATAT-AAAAATGA
159696 AAATAAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (22 bp):
TGTTTCTAAAATATAAAAATGA
Found at i:163264 original size:22 final size:23
Alignment explanation
Indices: 163239--163287 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
163229 GGAATCAATA
* *
163239 CCCC-CTTGAATGGGAACTGATT
1 CCCCTCTTGAAGGGGAACCGATT
*
163261 CCCCTTTTGAAGGGGAACCGATT
1 CCCCTCTTGAAGGGGAACCGATT
163284 CCCC
1 CCCC
163288 ATAGGGGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.24
Consensus pattern (23 bp):
CCCCTCTTGAAGGGGAACCGATT
Found at i:163276 original size:23 final size:23
Alignment explanation
Indices: 163244--163287 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
163234 CAATACCCCC
* *
163244 TTGAATGGGAACTGATTCCCCTT
1 TTGAAGGGGAACCGATTCCCCTT
163267 TTGAAGGGGAACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
163288 ATAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCTT
Found at i:167420 original size:24 final size:24
Alignment explanation
Indices: 167319--167406 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
167309 TGAATTATGT
* *
167319 TATGATACCTGACATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
167343 TTTGATACTTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
167367 TATGATACTTGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
167391 AATGATACTTGACCTG
1 TATGATACTTGACCTG
167407 AATTATGTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:169518 original size:29 final size:30
Alignment explanation
Indices: 169472--169532 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
169462 ACGCCCGTTT
*
169472 TTCCAATTTAGTGACTAATGTTT-ATTTCG
1 TTCCAATTTAGTGACTAACGTTTCATTTCG
* * *
169501 TTCCAGTTTGGTGCCTAACGTTTCATTTCG
1 TTCCAATTTAGTGACTAACGTTTCATTTCG
169531 TT
1 TT
169533 ACTCAAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (30 bp):
TTCCAATTTAGTGACTAACGTTTCATTTCG
Found at i:170630 original size:55 final size:55
Alignment explanation
Indices: 170562--170758 Score: 353
Period size: 55 Copynumber: 3.6 Consensus size: 55
170552 ATTGTATGAA
170562 TGTGTATCGGTACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTGTAATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTGTAATT
*
170617 TGTGTATCGGTACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTGTTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTGTAATT
*
170672 TGTGTATCGATACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTGCTAA-T
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTG-TAATT
170727 TGTGTATCGGTACACTGA-GAGTGTATCGATAC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATAC
170759 CCCTAAGCAT
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
54 14 0.10
55 121 0.88
56 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACACCCAAAACATCGAGTGTAATT
Found at i:171194 original size:37 final size:37
Alignment explanation
Indices: 171144--171217 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
171134 CTATGAAAAT
171144 ATGGTATATGTGATTAAATGAAAATAACGATCAATAC
1 ATGGTATATGTGATTAAATGAAAATAACGATCAATAC
171181 ATGGTATATGTGATTAAATGAAAATAACGATCAATAC
1 ATGGTATATGTGATTAAATGAAAATAACGATCAATAC
171218 TTTTTATGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (37 bp):
ATGGTATATGTGATTAAATGAAAATAACGATCAATAC
Found at i:171489 original size:21 final size:21
Alignment explanation
Indices: 171464--171514 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
171454 GTCGAGGGTC
171464 TATGTGGTCCTTCGAGATAAT
1 TATGTGGTCCTTCGAGATAAT
*
171485 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTTCGAGATAAT
171506 TATGTGGTC
1 TATGTGGTC
171515 ATCTGGGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (21 bp):
TATGTGGTCCTTCGAGATAAT
Found at i:171522 original size:21 final size:21
Alignment explanation
Indices: 171464--171533 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
171454 GTCGAGGGTC
* *
171464 TATGTGGTCCTTCGAGATAAT
1 TATGTGGTCATTCGGGATAAT
*
171485 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCATTCGGGATAAT
*
171506 TATGTGGTCA-TCTGGGACAAT
1 TATGTGGTCATTC-GGGATAAT
171527 TATGTGG
1 TATGTGG
171534 CACTTTGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (21 bp):
TATGTGGTCATTCGGGATAAT
Found at i:175823 original size:4 final size:4
Alignment explanation
Indices: 175814--175852 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
175804 ATCTGGAATC
175814 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
175853 CTTCGTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:177055 original size:64 final size:64
Alignment explanation
Indices: 176968--177105 Score: 143
Period size: 64 Copynumber: 2.2 Consensus size: 64
176958 TGAAGGTATG
* * * **
176968 CATCGATGCACTACTGAAACATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGGATA
1 CATCGATGCACTACTGAAACATCGATGCACAAAAGGCATTCGATGT-TTCATTATTAATGGGATA
* * ** * ** *
177032 CATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATG
1 CATCGATGCACTACTGAAACATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATGGGATA
177096 CATCGATGCA
1 CATCGATGCA
177106 TGAATTGCAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
63 2 0.03
64 58 0.97
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
CATCGATGCACTACTGAAACATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATGGGATA
Found at i:177143 original size:45 final size:45
Alignment explanation
Indices: 177048--177151 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
177038 TGCACTCCTT
* *
177048 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
177093 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
177137 AGTGCATCGATGCAC
1 A-TGCATCGATGCAC
177152 TACTAATGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 2 0.04
45 43 0.84
46 6 0.12
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (45 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:183310 original size:15 final size:15
Alignment explanation
Indices: 183290--183322 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
183280 CGTAGGACCC
*
183290 CTACATCCTGAAGGA
1 CTACATCCCGAAGGA
183305 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
183320 CTA
1 CTA
183323 TTATACCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:183486 original size:12 final size:12
Alignment explanation
Indices: 183467--183502 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
183457 TATCATGTTC
183467 TCATATCACATG
1 TCATATCACATG
* *
183479 TTATATCACATA
1 TCATATCACATG
183491 TCATATCACATG
1 TCATATCACATG
183503 AACATATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATATCACATG
Found at i:183893 original size:64 final size:64
Alignment explanation
Indices: 183806--184022 Score: 190
Period size: 64 Copynumber: 3.4 Consensus size: 64
183796 TAATGAAGGT
* * * * * **
183806 ATGCATCAATACACTACTGATGCATCGGTGCATAAAAGGTATTCAATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCAATGT-TTCATTATTAATGGG
* ** ** *
183870 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCAATGTTTCATTATTAATGGG
* ** * **
183934 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTC-ATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCAATG-TTTCATTATTAATGGG
**
183996 AGTGCATCGATGCACTACCAATGCATC
1 A-TGCATCGATGCACTACTTATGCATC
184023 AATACATCTT
Statistics
Matches: 129, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
62 2 0.02
63 32 0.25
64 95 0.74
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCAATGTTTCATTATTAATGGG
Found at i:185328 original size:20 final size:20
Alignment explanation
Indices: 185299--185343 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
185289 TATCAGTACA
*
185299 GTATCGGTACACTGAGGAGT
1 GTATCAGTACACTGAGGAGT
*
185319 GTATCAGTACATTGAGGAGT
1 GTATCAGTACACTGAGGAGT
185339 GTATC
1 GTATC
185344 GATACACCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (20 bp):
GTATCAGTACACTGAGGAGT
Found at i:185349 original size:20 final size:20
Alignment explanation
Indices: 185299--185350 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
185289 TATCAGTACA
*
185299 GTATCGGTACACTGAGGAGT
1 GTATCGATACACTGAGGAGT
*
185319 GTATC-AGTACATTGAGGAGT
1 GTATCGA-TACACTGAGGAGT
185339 GTATCGATACAC
1 GTATCGATACAC
185351 CCAAAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
GTATCGATACACTGAGGAGT
Found at i:185938 original size:22 final size:22
Alignment explanation
Indices: 185885--185939 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
185875 CCTTCGGGAC
* *
185885 AACTATGTGGCACTTCGGTGTA
1 AACTATATGGCACTTCGGTGCA
*
185907 ACCCTATATGGCACTTCGGTGCA
1 A-ACTATATGGCACTTCGGTGCA
185930 AACTATATGG
1 AACTATATGG
185940 TCCTCCGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (22 bp):
AACTATATGGCACTTCGGTGCA
Found at i:190173 original size:8 final size:8
Alignment explanation
Indices: 190160--190190 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
190150 TTCCCATATA
190160 TAATGGGG
1 TAATGGGG
190168 TAATGGGG
1 TAATGGGG
190176 TAATGGGG
1 TAATGGGG
190184 TAA-GGGG
1 TAATGGGG
190191 AGGTAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.26, C:0.00, G:0.52, T:0.23
Consensus pattern (8 bp):
TAATGGGG
Found at i:190804 original size:31 final size:31
Alignment explanation
Indices: 190769--190828 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
190759 GTGTTCTATG
190769 CGAGCTGTGACGAGAGGATAAAGCTTTGCTA
1 CGAGCTGTGACGAGAGGATAAAGCTTTGCTA
** *
190800 CGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 CGAGCTGTGACGAGAGGATAAAGCTTTGC
190829 ATGCGCCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (31 bp):
CGAGCTGTGACGAGAGGATAAAGCTTTGCTA
Found at i:190883 original size:21 final size:22
Alignment explanation
Indices: 190832--190883 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
190822 GCTTTGCATG
*
190832 CGCCATTCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
190854 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
190876 CG-CATGCA
1 CGCCATGCA
190884 TGCAGCGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.23, C:0.29, G:0.33, T:0.15
Consensus pattern (22 bp):
CGCCATGCACGTCGGAAGAGGT
Found at i:190968 original size:29 final size:29
Alignment explanation
Indices: 190929--191016 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
190919 AGGGCGCAGG
* * *
190929 ACAAGGACGCCCAGCGCGCATGGCGACCT
1 ACAAGGTCGCCCGGAGCGCATGGCGACCT
* * * * *
190958 ACCATGTCGCCTGGTGTGCATGGCGACCT
1 ACAAGGTCGCCCGGAGCGCATGGCGACCT
*
190987 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCGGAGCGCATGGCGACCT
191016 A
1 A
191017 TGCTGGGAAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.14
Consensus pattern (29 bp):
ACAAGGTCGCCCGGAGCGCATGGCGACCT
Found at i:193651 original size:21 final size:21
Alignment explanation
Indices: 193623--193665 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
193613 GAAAATAGAT
*
193623 TAAAAAAAACAGAATATACAAC
1 TAAAAAAGACAGAATA-ACAAC
*
193645 TAAAAAAGACATAATAACAAC
1 TAAAAAAGACAGAATAACAAC
193666 AATATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.14, G:0.05, T:0.14
Consensus pattern (21 bp):
TAAAAAAGACAGAATAACAAC
Found at i:203532 original size:18 final size:18
Alignment explanation
Indices: 203511--203551 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
203501 AGGCATTTGA
203511 TCCTCTGGAT-GTGCTTGT
1 TCCTCT-GATCGTGCTTGT
*
203529 TCCTCTGCTCGTGCTTGT
1 TCCTCTGATCGTGCTTGT
203547 TCCTC
1 TCCTC
203552 GTGTTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.02, C:0.32, G:0.22, T:0.44
Consensus pattern (18 bp):
TCCTCTGATCGTGCTTGT
Found at i:205131 original size:22 final size:22
Alignment explanation
Indices: 205099--205159 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
205089 CCAGAACCCC
205099 AGGGGGTATCGATTCCCCTACA
1 AGGGGGTATCGATTCCCCTACA
* * * *
205121 GGGGGGAATCGGTTCCCCTTCA
1 AGGGGGTATCGATTCCCCTACA
205143 AGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
205160 TCTGTACTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (22 bp):
AGGGGGTATCGATTCCCCTACA
Found at i:217324 original size:51 final size:49
Alignment explanation
Indices: 217258--217383 Score: 180
Period size: 51 Copynumber: 2.5 Consensus size: 49
217248 TTAGCAGTAA
**
217258 AGCGCGCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGT-GGGTAT
*
217308 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCG-CCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTAT
* *
217358 AGCACGGCCCCTGCAGCGCGCTATAC
1 AGCGC-GCCCCTGCACCGCGCTATAC
217384 CTGTATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
50 34 0.49
51 35 0.51
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.17
Consensus pattern (49 bp):
AGCGCGCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTAT
Found at i:217527 original size:20 final size:19
Alignment explanation
Indices: 217496--217534 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
217486 TTATCACACC
*
217496 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAATACTCT
217515 AAATTTCTCTCAAATACTCT
1 AAATTT-TCTCAAATACTCT
217535 CTTTTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTCTCAAATACTCT
Found at i:222391 original size:34 final size:34
Alignment explanation
Indices: 222344--222429 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 34
222334 ACCCGCCCCG
*
222344 ATTATATATATATATAATATAATATTTTTTATATTA
1 ATTATATATATA-AT-ATATAATATATTTTATATTA
* * *
222380 ATTATATATATAATTTTTTATATATTTTATATTA
1 ATTATATATATAATATATAATATATTTTATATTA
*
222414 ATTATATATAAAATAT
1 ATTATATATATAATAT
222430 TTTTGGGTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
34 30 0.68
35 2 0.05
36 12 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
ATTATATATATAATATATAATATATTTTATATTA
Found at i:222409 original size:25 final size:27
Alignment explanation
Indices: 222345--222411 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
222335 CCCGCCCCGA
*
222345 TTATATA-TATATATAATATAATATTT
1 TTATATATTTTATATAATATAATATTT
222371 TT-TATATTAATTATAT-ATATAAT-TTT
1 TTATATATT--TTATATAATATAATATTT
222397 TTATATATTTTATAT
1 TTATATATTTTATAT
222412 TAATTATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 10 0.28
26 8 0.22
27 13 0.36
28 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATATATTTTATATAATATAATATTT
Found at i:222429 original size:18 final size:18
Alignment explanation
Indices: 222350--222430 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 18
222340 CCCGATTATA
222350 TATATATATAATA-TAA-
1 TATATATATAATATTAAT
* *
222366 TAT-T-TTTTATATTAAT
1 TATATATATAATATTAAT
*
222382 TATATATATAAT-TT-TT
1 TATATATATAATATTAAT
* *
222398 TATATATTTTATATTAAT
1 TATATATATAATATTAAT
*
222416 TATATATAAAATATT
1 TATATATATAATATT
222431 TTTGGGTTCG
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.10
15 4 0.08
16 17 0.35
17 5 0.10
18 17 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATATAATATTAAT
Found at i:222803 original size:31 final size:31
Alignment explanation
Indices: 222742--222807 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
222732 TAAGAGAAAA
* *
222742 TAGT-CCTAACGTTATCGATTCGTTCAATTT
1 TAGTCCCTAACGTTATCGATCCATTCAATTT
* **
222772 TAGTCCCTAATGTTATCGATCCATTTGATTT
1 TAGTCCCTAACGTTATCGATCCATTCAATTT
222803 TAGTC
1 TAGTC
222808 TCTCATCTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.44
Consensus pattern (31 bp):
TAGTCCCTAACGTTATCGATCCATTCAATTT
Found at i:223005 original size:5 final size:5
Alignment explanation
Indices: 222995--223144 Score: 300
Period size: 5 Copynumber: 30.0 Consensus size: 5
222985 ACTATTCACA
222995 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
223045 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
223095 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
223145 GTTGTGCAAG
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 145 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:227840 original size:5 final size:5
Alignment explanation
Indices: 227830--227861 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
227820 TAATATTTTT
227830 TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
227862 TTATATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:229321 original size:31 final size:30
Alignment explanation
Indices: 229290--229345 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
229280 CATAATATTA
*
229290 TATTAAAA-TATTAAAAAAATAAAAATAAT
1 TATTAAAATTATTAAAAAAACAAAAATAAT
*
229319 TATTAAAATTATTTAAAAAACAAAAAT
1 TATTAAAATTATTAAAAAAACAAAAAT
229346 TTGAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (30 bp):
TATTAAAATTATTAAAAAAACAAAAATAAT
Found at i:230466 original size:22 final size:22
Alignment explanation
Indices: 230441--230502 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
230431 GTGAAATTTT
*
230441 TCCCGAACGATCTATGTAGATG
1 TCCCGAAGGATCTATGTAGATG
* * **
230463 TCCCGAAGGTTCTCTGTATTTG
1 TCCCGAAGGATCTATGTAGATG
*
230485 TCCCGAAGGACCTATGTA
1 TCCCGAAGGATCTATGTA
230503 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (22 bp):
TCCCGAAGGATCTATGTAGATG
Found at i:235512 original size:22 final size:22
Alignment explanation
Indices: 235446--235512 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
235436 GGCATGTGAA
* * *
235446 ATTTGTCTCGAATGACCTATAT
1 ATTTGTCCCGAAGGACCTATGT
* * *
235468 ATATATCCCGAAGGACCTCTGT
1 ATTTGTCCCGAAGGACCTATGT
235490 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
235512 A
1 A
235513 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:237311 original size:16 final size:16
Alignment explanation
Indices: 237290--237324 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
237280 TTACTCTACT
237290 TGTTATGAACCTGACC
1 TGTTATGAACCTGACC
237306 TGTTATGAACCTGACC
1 TGTTATGAACCTGACC
237322 TGT
1 TGT
237325 AAATGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (16 bp):
TGTTATGAACCTGACC
Found at i:237898 original size:20 final size:20
Alignment explanation
Indices: 237731--237891 Score: 205
Period size: 20 Copynumber: 8.0 Consensus size: 20
237721 AAATTCGCGT
237731 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
* * ** *
237751 CGCAAATTTGGAAAATCGCAA
1 TGCGAA-TACGTAAATCGCAA
* *
237772 TGCGATTACGTAAATCGTAA
1 TGCGAATACGTAAATCGCAA
237792 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
237812 TGTGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
* *
237832 TGCGAATACATAAATTGCAA
1 TGCGAATACGTAAATCGCAA
*
237852 TACGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
237872 TGCGAATATGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
237892 CATGAATCTG
Statistics
Matches: 117, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
20 103 0.88
21 14 0.12
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
TGCGAATACGTAAATCGCAA
Found at i:238121 original size:22 final size:22
Alignment explanation
Indices: 238095--238159 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
238085 GCGACATCCG
*
238095 TCCCCATCTCCGACAAAATCAA
1 TCCCCATCTCCGACGAAATCAA
* *
238117 TCCCCATCTCCGACGATATCAG
1 TCCCCATCTCCGACGAAATCAA
* *
238139 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
238160 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.40, G:0.11, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAA
Found at i:238534 original size:20 final size:20
Alignment explanation
Indices: 238509--238561 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
238499 CGATTTTCAT
238509 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
238529 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
238549 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
238562 TTTTATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:238569 original size:20 final size:20
Alignment explanation
Indices: 238546--238584 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
238536 TGCGATAGTC
238546 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
238566 ATTTTCGTGTTGCGATTTT
1 ATTTTCGTGTTGCGATTTT
238585 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:238591 original size:20 final size:20
Alignment explanation
Indices: 238548--238591 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
238538 CGATAGTCAT
* *
238548 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTGCGATTTTAAG
238568 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
238588 TTTC
1 TTTC
238592 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:240485 original size:20 final size:20
Alignment explanation
Indices: 240473--240510 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
240463 ATCGCAATGT
240473 GAAAATGACTATCGCAACAC
1 GAAAATGACTATCGCAACAC
*
240493 GAAAATGACTATCACAAC
1 GAAAATGACTATCGCAAC
240511 GAGAGAATCG
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:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:240575 original size:20 final size:20
Alignment explanation
Indices: 240550--240643 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
240540 CAACAACAAA
*
240550 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
240570 ATCGCAATGCGAAAACGACT
1 ATCGCAATGCGAAAATGACT
240590 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
240610 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
240630 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
240644 TGAAAATCGC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:240605 original size:40 final size:40
Alignment explanation
Indices: 240550--240660 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
240540 CAACAACAAA
*
240550 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAACGACT
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAACGACT
***
240590 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAACGACT
** *
240630 ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGA
240661 TTCTCTCGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 17 0.27
40 47 0.73
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAAAATGACTATCGCAATGCGAAAACGACT
Found at i:240753 original size:40 final size:40
Alignment explanation
Indices: 240667--240755 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
240657 GCGATTCTCT
*
240667 CGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCACATTGCGATAGTCAAATTCG
* ** **
240707 CATTGCGATAGTCATTTTCACATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCACATTGCGATAGTCAAATTCG
*
240747 TGTTGCGAT
1 CGTTGCGAT
240756 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCACATTGCGATAGTCAAATTCG
Found at i:240755 original size:20 final size:20
Alignment explanation
Indices: 240669--240740 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
240659 GATTCTCTCG
240669 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
240689 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
240709 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCAAATTCGCA
240729 TTGCGATAGTCA
1 TTGCGATAGTCA
240741 TTTTCGTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:241330 original size:21 final size:21
Alignment explanation
Indices: 241239--241343 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
241229 GACTCACCTG
*
241239 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
241261 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
241281 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
241302 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
241323 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
241344 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:241336 original size:42 final size:42
Alignment explanation
Indices: 241236--241346 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
241226 CCCGACTCAC
* * * *
241236 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
241278 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
241320 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
241347 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:242746 original size:14 final size:14
Alignment explanation
Indices: 242727--242762 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
242717 ATTGTTTAAT
242727 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
242741 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
242755 TGATTTGT
1 TGATTTGT
242763 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:242925 original size:33 final size:34
Alignment explanation
Indices: 242868--242943 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
242858 AAAACAGTCG
242868 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
242902 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
242935 CGTTGCGAT
1 CGTTGCGAT
242944 AGTTATTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:242952 original size:33 final size:33
Alignment explanation
Indices: 242868--242963 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 33
242858 AAAACAGTCG
*
242868 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATGTTCA-TTTCGCATTGCGATTCACT
* *
242902 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATGTTCATTTCGCATTGCGATTCACT
*
242935 CGTTGCGATAGTT-ATTTCCGCGTTGCGAT
1 CGTTGCGAT-GTTCATTT-CGCATTGCGAT
242964 AGTCAATTCC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATGTTCATTTCGCATTGCGATTCACT
Found at i:242960 original size:20 final size:20
Alignment explanation
Indices: 242935--243009 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
242925 GCGATTCTCT
*
242935 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
242955 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
242975 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
242995 TGTTGCAATAGTCAT
1 CGTTGCGATAGTCAT
243010 ATTCGTGTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:243016 original size:20 final size:21
Alignment explanation
Indices: 242936--243023 Score: 103
Period size: 20 Copynumber: 4.4 Consensus size: 21
242926 CGATTCTCTC
* *
242936 GTTGCGATAGTTAT-TTCCGC
1 GTTGCGATAGTCATATTCCGT
*
242956 GTTGCGATAGTCA-ATTCCGC
1 GTTGCGATAGTCATATTCCGT
242976 GTTGCGATAGTCAT-TTCCGT
1 GTTGCGATAGTCATATTCCGT
*
242996 GTTGCAATAGTCATATT-CGT
1 GTTGCGATAGTCATATTCCGT
*
243016 GTTACGAT
1 GTTGCGAT
243024 TTCCGCGTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
GTTGCGATAGTCATATTCCGT
Found at i:246367 original size:20 final size:20
Alignment explanation
Indices: 246342--246388 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
246332 AAATTCAGTA
246342 TTGCGATAGTCAGAATC-TCG
1 TTGCGATAGTCAGAATCGT-G
*
246362 TTGCGATAGTCAGATTCGTG
1 TTGCGATAGTCAGAATCGTG
246382 TTGCGAT
1 TTGCGAT
246389 TTACGTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGTG
Found at i:246398 original size:20 final size:20
Alignment explanation
Indices: 246382--246528 Score: 213
Period size: 20 Copynumber: 7.3 Consensus size: 20
246372 CAGATTCGTG
246382 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
246402 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
246422 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
246442 TTGCAATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
246462 ATGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** * *
246482 TTGCGATTTTCCAAATCCGCG
1 TTGCGA-TTTACGTATTCGCA
246503 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
246523 TTGCGA
1 TTGCGA
246529 ATTAGGAAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 96 0.87
21 14 0.13
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:246427 original size:60 final size:58
Alignment explanation
Indices: 246362--246528 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 58
246352 CAGAATCTCG
* *
246362 TTGCGATAGTCAGATTCGTGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
* * * *
246422 TTGCGATTTACGTATTCGCATTGCAATTTACGTATTCGCAATGCGATTTACGTAATCGCA
1 TTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
* *
246482 TTGCGATTTTCCAAATCCGCGTTGCGATTTACGTATTCGCATTGCGA
1 TTGCGA--TT-CAGATTCGCGTTGCGATTTACGTATTCGCATTGCGA
246529 ATTAGGAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 55 0.61
61 29 0.32
62 2 0.02
63 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (58 bp):
TTGCGATTCAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
Found at i:246549 original size:21 final size:21
Alignment explanation
Indices: 246525--246570 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
246515 TATTCGCATT
246525 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
246546 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
246567 GCGA
1 GCGA
246571 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:248189 original size:24 final size:24
Alignment explanation
Indices: 248162--248216 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
248152 TTAAAAGGTC
*
248162 AATTTTACTCCTCACTCTACTGAA
1 AATTTGACTCCTCACTCTACTGAA
* *
248186 AATTTGAGTCTTCACTCTACTGAA
1 AATTTGACTCCTCACTCTACTGAA
248210 AATTTGA
1 AATTTGA
248217 TTCTTATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (24 bp):
AATTTGACTCCTCACTCTACTGAA
Found at i:248221 original size:24 final size:24
Alignment explanation
Indices: 248173--248221 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
248163 ATTTTACTCC
248173 TCACTCTACTGAAAATTTGAGTCT
1 TCACTCTACTGAAAATTTGAGTCT
*
248197 TCACTCTACTGAAAATTTGATTCT
1 TCACTCTACTGAAAATTTGAGTCT
248221 T
1 T
248222 ATACTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (24 bp):
TCACTCTACTGAAAATTTGAGTCT
Found at i:251182 original size:2 final size:2
Alignment explanation
Indices: 251175--251205 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
251165 AAAATTTTAA
251175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
251206 AGCACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:251779 original size:53 final size:53
Alignment explanation
Indices: 251542--251779 Score: 287
Period size: 53 Copynumber: 4.5 Consensus size: 53
251532 ATTAAGGGTC
* * * * *
251542 AGGGTTAGAGAAGATGAACAAAGACAGAATATGAAGATGCTCGATTTGGGTTT
1 AGGGTTAGAGAAGATAAATAAAGATAGAAGATGAAGAGGCTCGATTTGGGTTT
* * * *
251595 AAGGTTAGAGAAGATTAATAGAGACAGAAGATGAAGAGGCTCGATTTGGGTTT
1 AGGGTTAGAGAAGATAAATAAAGATAGAAGATGAAGAGGCTCGATTTGGGTTT
* * *
251648 AGGGTTAAAGAAGATAAATAAAGATATAAGATGAAGAGGCTCGATTTTGGTTT
1 AGGGTTAGAGAAGATAAATAAAGATAGAAGATGAAGAGGCTCGATTTGGGTTT
* * * * * *
251701 GGGGTTAGAAAAGATAAACAAAGATAGAAGATGAAGAGGCTAGGTTAGGGTTT
1 AGGGTTAGAGAAGATAAATAAAGATAGAAGATGAAGAGGCTCGATTTGGGTTT
* * *
251754 AGGATTAGAGAATATAAATAGAGATA
1 AGGGTTAGAGAAGATAAATAAAGATA
251780 TAAACTAAAT
Statistics
Matches: 157, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 157 1.00
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.24
Consensus pattern (53 bp):
AGGGTTAGAGAAGATAAATAAAGATAGAAGATGAAGAGGCTCGATTTGGGTTT
Found at i:251806 original size:106 final size:105
Alignment explanation
Indices: 251575--251826 Score: 265
Period size: 106 Copynumber: 2.4 Consensus size: 105
251565 ACAGAATATG
* * * * * * *
251575 AAGATGCTCGATTTGGGTTTAAGGTTAGAGAAGATTAATAGAGACAGAAGATGAAGAGGCTCGAT
1 AAGAGGCTCGATTAGGGTTT-GGGTTAGAGAAGATAAACAAAGACAGAAGATGAAGAGGCTAGAT
* * *
251640 TTGGGTTTAGGGTTAAAGAAGATAAATAAAGATATAAGATG
65 TAGGGTTTAGGATTAAAGAAGATAAATAAAGATATAAGATA
** * * *
251681 AAGAGGCTCGATTTTGGTTTGGGGTTAGAAAAGATAAACAAAGATAGAAGATGAAGAGGCTAGGT
1 AAGAGGCTCGATTAGGGTTT-GGGTTAGAGAAGATAAACAAAGACAGAAGATGAAGAGGCTAGAT
* * *
251746 TAGGGTTTAGGATTAGAGAATATAAATAGAGATATAA-ACTA
65 TAGGGTTTAGGATTAAAGAAGATAAATAAAGATATAAGA-TA
* * *
251787 AATAGGGTC-AGTTAGGGTTTGGGTTAGAGAAGATGAACAA
1 AAGAGGCTCGA-TTAGGGTTTGGGTTAGAGAAGATAAACAA
251827 TTGTGGGTTT
Statistics
Matches: 121, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
105 20 0.17
106 101 0.83
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.26
Consensus pattern (105 bp):
AAGAGGCTCGATTAGGGTTTGGGTTAGAGAAGATAAACAAAGACAGAAGATGAAGAGGCTAGATT
AGGGTTTAGGATTAAAGAAGATAAATAAAGATATAAGATA
Found at i:252438 original size:31 final size:34
Alignment explanation
Indices: 252400--252482 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 34
252390 TATATATGTT
252400 TATACTAAT-AA-AT-TAATATATAGTTTATATA
1 TATACTAATGAACATATAATATATAGTTTATATA
252431 TATACTAATGAACTATATAATATATAGTTTAT-T-
1 TATACTAATGAAC-ATATAATATATAGTTTATATA
252464 TAT-CTTAATGAACTATATA
1 TATAC-TAATGAAC-ATATA
252483 GTTTATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
31 9 0.19
32 3 0.06
33 17 0.36
34 3 0.06
35 15 0.32
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (34 bp):
TATACTAATGAACATATAATATATAGTTTATATA
Found at i:252473 original size:33 final size:35
Alignment explanation
Indices: 252413--252482 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 35
252403 ACTAATAAAT
252413 TAATATATAGTTTATATATATACTAATGAACTATA
1 TAATATATAGTTTATATATATACTAATGAACTATA
252448 TAATATATAGTTTAT-T-TAT-CTTAATGAACTATA
1 TAATATATAGTTTATATATATAC-TAATGAACTATA
252481 TA
1 TA
252483 GTTTATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 1 0.03
33 17 0.50
34 1 0.03
35 15 0.44
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (35 bp):
TAATATATAGTTTATATATATACTAATGAACTATA
Found at i:256174 original size:23 final size:23
Alignment explanation
Indices: 256148--256196 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
256138 TCTATTAAAA
*
256148 TAAAATTATT-ATATTATATATTT
1 TAAAATTATTAATA-AATATATTT
256171 TAAAATTATTAATAAATATATTT
1 TAAAATTATTAATAAATATATTT
256194 TAA
1 TAA
256197 GAAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAAATTATTAATAAATATATTT
Found at i:256211 original size:23 final size:24
Alignment explanation
Indices: 256149--256217 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
256139 CTATTAAAAT
*
256149 AAAATTATT-ATATTATATATTTT-
1 AAAATTATTAATA-AATATATTTTA
256172 AAAATTATTAATAAATATATTTTA
1 AAAATTATTAATAAATATATTTTA
*
256196 AGAAATT-TTTAT-AATAT-TTTTA
1 A-AAATTATTAATAAATATATTTTA
256218 TACTATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.12
23 23 0.56
24 8 0.20
25 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
AAAATTATTAATAAATATATTTTA
Found at i:260673 original size:31 final size:31
Alignment explanation
Indices: 260635--260701 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
260625 TATATTTTTC
*
260635 TTTTTATTATTTTA-GTCTTTAACATTTTATT
1 TTTTTATTATTTTATGT-TTTAACATTTTAAT
*
260666 TTTTTATTATTTTATGTTTTAACGTTTTAAT
1 TTTTTATTATTTTATGTTTTAACATTTTAAT
260697 TTTTT
1 TTTTT
260702 GTCAAAACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (31 bp):
TTTTTATTATTTTATGTTTTAACATTTTAAT
Found at i:260951 original size:32 final size:33
Alignment explanation
Indices: 260874--260951 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 33
260864 ATCAAAAAGG
*
260874 ATGATGTGAT-ATGTGTCACATTACTCAAAGTA
1 ATGATGTGATCATGTGTCACATCACTCAAAGTA
* *
260906 ATGATATGA-CATGTGTCACATCATTCAAAGTA
1 ATGATGTGATCATGTGTCACATCACTCAAAGTA
260938 ATGATGT-ATCATGT
1 ATGATGTGATCATGT
260952 TAACAATTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (33 bp):
ATGATGTGATCATGTGTCACATCACTCAAAGTA
Found at i:261087 original size:29 final size:29
Alignment explanation
Indices: 261045--261103 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
261035 TAGTAATATC
261045 ACATATGTACATTTAATTCACAAAATGTA
1 ACATATGTACATTTAATTCACAAAATGTA
261074 ACATATGTACATTTAATTCACAAAATGTA
1 ACATATGTACATTTAATTCACAAAATGTA
261103 A
1 A
261104 GATTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (29 bp):
ACATATGTACATTTAATTCACAAAATGTA
Found at i:261298 original size:29 final size:29
Alignment explanation
Indices: 261256--261314 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
261246 TAGTAATATC
261256 ACATATGTACATTTAATTCACAAAATGTA
1 ACATATGTACATTTAATTCACAAAATGTA
261285 ACATATGTACATTTAATTCACAAAATGTA
1 ACATATGTACATTTAATTCACAAAATGTA
261314 A
1 A
261315 GATTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (29 bp):
ACATATGTACATTTAATTCACAAAATGTA
Found at i:262981 original size:6 final size:6
Alignment explanation
Indices: 262974--263027 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
262964 CGCTTCTCTT
* *
262974 CATCTT CATCTC CATCTC CATCTC CATCTC CATCATCC TCATCTC TATCTC
1 CATCTC CATCTC CATCTC CATCTC CATCTC CATC-T-C -CATCTC CATCTC
263025 CAT
1 CAT
263028 AACCATTTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 34 0.81
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (6 bp):
CATCTC
Found at i:263039 original size:33 final size:33
Alignment explanation
Indices: 262973--263039 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
262963 TCGCTTCTCT
* **
262973 TCATCTTCATCTCCATCTCCATCTCCATCTCCA
1 TCATCCTCATCTCCATCTCCATAACCATCTCCA
* *
263006 TCATCCTCATCTCTATCTCCATAACCATTTCCA
1 TCATCCTCATCTCCATCTCCATAACCATCTCCA
263039 T
1 T
263040 AATCATTTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (33 bp):
TCATCCTCATCTCCATCTCCATAACCATCTCCA
Found at i:263862 original size:19 final size:19
Alignment explanation
Indices: 263838--263874 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
263828 GTTTGAGTTA
263838 AAAAAATGGAAGACATGTT
1 AAAAAATGGAAGACATGTT
*
263857 AAAAAATGGAATACATGT
1 AAAAAATGGAAGACATGT
263875 AGCTACGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (19 bp):
AAAAAATGGAAGACATGTT
Found at i:265069 original size:21 final size:21
Alignment explanation
Indices: 265044--265100 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
265034 CGTAGAATTT
265044 GTCCCGAAAGACCACTTAGAA
1 GTCCCGAAAGACCACTTAGAA
265065 GTCCCGAAAGACCACTTAGAA
1 GTCCCGAAAGACCACTTAGAA
*
265086 GTCCCGAAGGACCAC
1 GTCCCGAAAGACCAC
265101 ATATAACACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.35, C:0.32, G:0.21, T:0.12
Consensus pattern (21 bp):
GTCCCGAAAGACCACTTAGAA
Found at i:268955 original size:38 final size:37
Alignment explanation
Indices: 268913--268984 Score: 117
Period size: 38 Copynumber: 1.9 Consensus size: 37
268903 CGGGACGAGT
*
268913 TTTTTTTAAGTTTGATATTCGAGTCGGGTCAGGTTAGG
1 TTTTTTTAAGTGTGATATTCGAGTCGGGTC-GGTTAGG
*
268951 TTTTTTTAAGTGTGATATTCGGGTCGGGTCGGTT
1 TTTTTTTAAGTGTGATATTCGAGTCGGGTCGGTT
268985 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (37 bp):
TTTTTTTAAGTGTGATATTCGAGTCGGGTCGGTTAGG
Found at i:269087 original size:28 final size:28
Alignment explanation
Indices: 269045--269111 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
269035 CAGGTTCAGG
* * *
269045 TCGGGTCTGGTTTTTTTAAGTTTGATAT
1 TCGGGTCAGGTTTTTTAAAGTGTGATAT
* *
269073 TTGGGTC-GGGTTTTTAAAGTGTGATAT
1 TCGGGTCAGGTTTTTTAAAGTGTGATAT
269100 TCGGGTCAGGTT
1 TCGGGTCAGGTT
269112 CAGGTTTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.15, C:0.07, G:0.31, T:0.46
Consensus pattern (28 bp):
TCGGGTCAGGTTTTTTAAAGTGTGATAT
Found at i:275221 original size:65 final size:64
Alignment explanation
Indices: 275100--275305 Score: 197
Period size: 65 Copynumber: 3.2 Consensus size: 64
275090 TTTTTCTGAG
* * * *
275100 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATACACCAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
275162 ATT
62 ATT
* * * *
275165 TCATGCATCGATTCA-CATACCATGCACCGTTGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATACACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
275228 TT
63 TT
* * * * *
275230 TGATGCATCGATACACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCAGT
1 TGATGCATCGATACACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
275294 TGATGCATCGAT
1 TGATGCATCGAT
275306 GCACTAAGGG
Statistics
Matches: 117, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 43 0.37
65 66 0.56
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATACACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:282074 original size:21 final size:21
Alignment explanation
Indices: 282032--282075 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
282022 ACTCCGGGAG
* *
282032 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
282053 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
282074 CT
1 CT
282076 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:284664 original size:19 final size:20
Alignment explanation
Indices: 284629--284675 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
284619 CTAAATCCTT
* *
284629 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATTCCATTTTAGC
284649 TTTCAAAA-TCCATTTTAGC
1 TTTCAAAATTCCATTTTAGC
284668 TTTCAAAA
1 TTTCAAAA
284676 GAAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (20 bp):
TTTCAAAATTCCATTTTAGC
Found at i:293416 original size:2 final size:2
Alignment explanation
Indices: 293409--293433 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
293399 ACATTACATT
293409 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 T
293434 GGCTTCCGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:303926 original size:60 final size:55
Alignment explanation
Indices: 303798--303930 Score: 151
Period size: 55 Copynumber: 2.3 Consensus size: 55
303788 CTATGATTAT
* * * *
303798 CAAGAACATACACATACGCAAACGAATAACTGCATACTTAAAAAATGAAAAAAAA
1 CAAGAACAAACACATACGAAAACGAATAAATGCATACTTAAAAAAAGAAAAAAAA
* *
303853 CAAGAACAGACACATACGAAATTACGAATAAATGTATACTTAGAAAAGAAAAGAAAAAAAA
1 CAAGAACAAACACATACGAAA--ACGAATAAATGCATACTT---AAA-AAAAGAAAAAAAA
303914 -AAGAACAAACACATACG
1 CAAGAACAAACACATACG
303931 CACGAATTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
55 19 0.29
57 16 0.24
60 19 0.29
61 12 0.18
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (55 bp):
CAAGAACAAACACATACGAAAACGAATAAATGCATACTTAAAAAAAGAAAAAAAA
Found at i:304423 original size:21 final size:21
Alignment explanation
Indices: 304397--304436 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
304387 TATAATGTAA
* *
304397 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
304418 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
304437 TAATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:309023 original size:12 final size:12
Alignment explanation
Indices: 309006--309030 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
308996 CAGGATATAT
309006 AGCGGCGTTTTC
1 AGCGGCGTTTTC
309018 AGCGGCGTTTTC
1 AGCGGCGTTTTC
309030 A
1 A
309031 AAGCAAACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (12 bp):
AGCGGCGTTTTC
Found at i:309220 original size:41 final size:41
Alignment explanation
Indices: 309175--309272 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
309165 TACATATAAG
*
309175 TACTTTAGTGGCGTTTTAAAACAAACACCGCCATAGAATCC
1 TACTTTAGTGGAGTTTTAAAACAAACACCGCCATAGAATCC
*
309216 TACTTTAGTGGTGTTTTAAAACAAACACCGCCATAGAATCC
1 TACTTTAGTGGAGTTTTAAAACAAACACCGCCATAGAATCC
309257 TACTTTAGTGGAGTTT
1 TACTTTAGTGGAGTTT
309273 GTTAGTAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (41 bp):
TACTTTAGTGGAGTTTTAAAACAAACACCGCCATAGAATCC
Found at i:309308 original size:42 final size:42
Alignment explanation
Indices: 309261--309440 Score: 258
Period size: 42 Copynumber: 4.3 Consensus size: 42
309251 GAATCCTACT
*
309261 TTAGTGGAGTTTGTTAGTAAAACGCCGCAATAGAGACAAACC
1 TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACC
* * * * * *
309303 TTAGTGGTGTTTGTCACTAAAACGCCGCTATAGAGTCATACC
1 TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACC
*
309345 TTAGTGGCGTTTGTTA-TAAAAACGCCGCAATAGAGGC-AA-C
1 TTAGTGGCGTTTGTTAGT-AAAACGCCGCAATAGAGACAAACC
309385 TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACC
1 TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACC
309427 TTAGTGGCGTTTGT
1 TTAGTGGCGTTTGT
309441 CACTAGTGGC
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
40 35 0.29
41 5 0.04
42 82 0.67
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (42 bp):
TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACC
Found at i:309428 original size:82 final size:84
Alignment explanation
Indices: 309261--309440 Score: 258
Period size: 82 Copynumber: 2.2 Consensus size: 84
309251 GAATCCTACT
* *
309261 TTAGTGGAGTTTGTTAGTAAAACGCCGCAATAGAGACAAACCTTAGTGGTGTTTGTCACTAAAAC
1 TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGTCACTAAAAC
* * *
309326 GCCGCTATAGAGTCATACC
66 GCCGCAATAGAGACAAACC
* * *
309345 TTAGTGGCGTTTGTTA-TAAAAACGCCGCAATAGAGGC-AA-CTTAGTGGCGTTTGTTAGTAAAA
1 TTAGTGGCGTTTGTTAGT-AAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGTCACTAAAA
309407 CGCCGCAATAGAGACAAACC
65 CGCCGCAATAGAGACAAACC
309427 TTAGTGGCGTTTGT
1 TTAGTGGCGTTTGT
309441 CACTAGTGGC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
82 51 0.59
83 3 0.03
84 33 0.38
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (84 bp):
TTAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGTCACTAAAAC
GCCGCAATAGAGACAAACC
Found at i:309449 original size:16 final size:16
Alignment explanation
Indices: 309428--309461 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
309418 AGACAAACCT
309428 TAGTGGCGTTTGTCAC
1 TAGTGGCGTTTGTCAC
309444 TAGTGGCGTTTGTCAC
1 TAGTGGCGTTTGTCAC
309460 TA
1 TA
309462 AAACGCCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.38
Consensus pattern (16 bp):
TAGTGGCGTTTGTCAC
Found at i:309476 original size:58 final size:58
Alignment explanation
Indices: 309386--309498 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
309376 AGAGGCAACT
* *
309386 TAGTGGCGTTTGTTAGTAAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGTCAC
1 TAGTGGCGTTTGTCACTAAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGTCAC
* * * *
309444 TAGTGGCGTTTGTCACTAAAACGCCGCTATAGAGCCATACCTTAGTGGTGTTTGT
1 TAGTGGCGTTTGTCACTAAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGT
309499 TATAAAAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (58 bp):
TAGTGGCGTTTGTCACTAAAACGCCGCAATAGAGACAAACCTTAGTGGCGTTTGTCAC
Found at i:309518 original size:42 final size:42
Alignment explanation
Indices: 309444--309585 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 42
309434 CGTTTGTCAC
* * * * *
309444 TAGTGGCGTTTGTCACT-AAAACGCCGCTATAGAGCCATACCT
1 TAGTGGTGTTTGTTA-TAAAAACGTCGCAATAGAGGCATACCT
*
309486 TAGTGGTGTTTGTTATAAAAATGTCGCAATAGAGGC-TAACCT
1 TAGTGGTGTTTGTTATAAAAACGTCGCAATAGAGGCAT-ACCT
* * ** * * * *
309528 TAGTGGCGTTTGTTGTTGAAACGTCGCAGTAGAGGTACACGT
1 TAGTGGTGTTTGTTATAAAAACGTCGCAATAGAGGCATACCT
309570 TAGTGGTGTTTGTTAT
1 TAGTGGTGTTTGTTAT
309586 TACAACGCCG
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
41 2 0.03
42 78 0.98
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
TAGTGGTGTTTGTTATAAAAACGTCGCAATAGAGGCATACCT
Found at i:309527 original size:100 final size:98
Alignment explanation
Indices: 309346--309540 Score: 268
Period size: 100 Copynumber: 2.0 Consensus size: 98
309336 AGTCATACCT
* *
309346 TAGTGGCGTTTGTTATAAAAACGCCGCAATAGAGGCAACTTAGTGGCGTTTGTTAGTAAAACGCC
1 TAGTGGCGTTTGTCATAAAAACGCCGCAATAGAGCCAACTTAGTGGCGTTTGTTAGTAAAACGCC
309411 GCAATAGAGACAAACCTTAGTGGCGTTTGTCAC
66 GCAATAGAGACAAACCTTAGTGGCGTTTGTCAC
* *
309444 TAGTGGCGTTTGTCACT-AAAACGCCGCTATAGAGCCATACCTTAGTGGTGTTTGTTA-TAAAAA
1 TAGTGGCGTTTGTCA-TAAAAACGCCGCAATAGAGCCA-A-CTTAGTGGCGTTTGTTAGT-AAAA
* * * *
309507 TGTCGCAATAGAGGCTAACCTTAGTGGCGTTTGT
62 CGCCGCAATAGAGACAAACCTTAGTGGCGTTTGT
309541 TGTTGAAACG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
98 32 0.38
99 3 0.04
100 50 0.59
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (98 bp):
TAGTGGCGTTTGTCATAAAAACGCCGCAATAGAGCCAACTTAGTGGCGTTTGTTAGTAAAACGCC
GCAATAGAGACAAACCTTAGTGGCGTTTGTCAC
Found at i:309682 original size:19 final size:19
Alignment explanation
Indices: 309658--309702 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
309648 ACCTTTCTTC
309658 CTTCATCCTCAACGAGCAT
1 CTTCATCCTCAACGAGCAT
309677 CTTCATCCTCAACGAGCAT
1 CTTCATCCTCAACGAGCAT
309696 CTTCATC
1 CTTCATC
309703 AAATCGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.09, T:0.29
Consensus pattern (19 bp):
CTTCATCCTCAACGAGCAT
Found at i:309742 original size:21 final size:21
Alignment explanation
Indices: 309716--309763 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
309706 TCGACATGCT
* *
309716 AGTCACCACCGTCGCGCCGCC
1 AGTCACCACCGTCACACCGCC
*
309737 AGTCACCACCGTCACACTGCC
1 AGTCACCACCGTCACACCGCC
309758 AGTCAC
1 AGTCAC
309764 TCCTCAAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.12
Consensus pattern (21 bp):
AGTCACCACCGTCACACCGCC
Found at i:313391 original size:20 final size:20
Alignment explanation
Indices: 313362--313404 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
313352 ATTCCACCAC
313362 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
313382 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
313402 ATG
1 ATG
313405 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:318304 original size:12 final size:12
Alignment explanation
Indices: 318283--318319 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
318273 TCGAAGCTGA
*
318283 AGCGAAAGAAGC
1 AGCGAGAGAAGC
318295 AGCGAGAGAAGC
1 AGCGAGAGAAGC
*
318307 AGAGAGAGAAGC
1 AGCGAGAGAAGC
318319 A
1 A
318320 TCATTTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.38, T:0.00
Consensus pattern (12 bp):
AGCGAGAGAAGC
Found at i:322641 original size:2 final size:2
Alignment explanation
Indices: 322634--322664 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
322624 ATTTAATCCA
322634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
322665 ATTGTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:324731 original size:23 final size:23
Alignment explanation
Indices: 324700--324745 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
324690 ATCCATCCAT
*
324700 GCATGCATGTATGTGTTATATGG
1 GCATCCATGTATGTGTTATATGG
324723 GCATCCATGTATGTGTTATATGG
1 GCATCCATGTATGTGTTATATGG
324746 TTATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (23 bp):
GCATCCATGTATGTGTTATATGG
Found at i:327718 original size:18 final size:18
Alignment explanation
Indices: 327695--327746 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
327685 GAACACTTAC
327695 TTTTAAGGCAAATCTACT
1 TTTTAAGGCAAATCTACT
327713 TTTTAAGGCAAATCTACT
1 TTTTAAGGCAAATCTACT
327731 TTTTAAGGCAAATCTA
1 TTTTAAGGCAAATCTA
327747 ATTATAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTAAGGCAAATCTACT
Found at i:327804 original size:3 final size:3
Alignment explanation
Indices: 327796--327839 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
327786 AACTATTTAA
*
327796 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAA TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
327840 TTTTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:327828 original size:23 final size:23
Alignment explanation
Indices: 327796--327839 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
327786 AACTATTTAA
*
327796 TATTATTATTATTATATTATTAT
1 TATTAATATTATTATATTATTAT
*
327819 TATTAATATTATTATTTTATT
1 TATTAATATTATTATATTATT
327840 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTAATATTATTATATTATTAT
Found at i:329273 original size:26 final size:26
Alignment explanation
Indices: 329230--329283 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
329220 AAGTAAACCA
* *
329230 CCCAAGGGGTCATCCAATGTTTGTAT
1 CCCAAGGGGCCATACAATGTTTGTAT
329256 CCCAAGGGGCCATACAATGTTTGTAT
1 CCCAAGGGGCCATACAATGTTTGTAT
329282 CC
1 CC
329284 TTTTGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (26 bp):
CCCAAGGGGCCATACAATGTTTGTAT
Found at i:329768 original size:2 final size:2
Alignment explanation
Indices: 329761--329788 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
329751 CACGTGAGTA
329761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329789 TAGCTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.