Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009065.1 Hibiscus syriacus cultivar Beakdansim tig00112488_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: 1198333
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:765261 original size:11 final size:11
Alignment explanation
Indices: 765231--765305 Score: 93
Period size: 11 Copynumber: 7.0 Consensus size: 11
765221 CATTTAAAAT
765231 TATTATTATTA
1 TATTATTATTA
**
765242 -AAAATTATTA
1 TATTATTATTA
765252 TATTATTATTA
1 TATTATTATTA
765263 TTATTA-TATTA
1 -TATTATTATTA
765274 T-TTATTATTA
1 TATTATTATTA
*
765284 TATTAATATTA
1 TATTATTATTA
765295 TATTATTATTA
1 TATTATTATTA
765306 CAAGCCCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 3 0.06
10 15 0.28
11 31 0.57
12 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTATTA
Found at i:766712 original size:23 final size:24
Alignment explanation
Indices: 766678--766722 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
766668 TATATATGAT
766678 AAATAATAA-TTT-ATATTTTTTA
1 AAATAATAATTTTAATATTTTTTA
*
766700 AAATAAATTATTTTAATATTTTT
1 AAAT-AATAATTTTAATATTTTT
766723 CAATATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 4 0.21
24 3 0.16
25 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATAATAATTTTAATATTTTTTA
Found at i:773725 original size:21 final size:21
Alignment explanation
Indices: 773709--773762 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
773699 GTGTTGCATT
773709 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
773730 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
773751 TCGCGTTGCGAT
1 TCGCGTTGCGAT
773763 GGTATACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGGAAA
Found at i:773861 original size:20 final size:20
Alignment explanation
Indices: 773833--773940 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
773823 AATTGGGAAA
*
773833 ATCGAAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
773853 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
773873 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
773894 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
773914 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
773934 TTCGCAA
1 ATCGCAA
773941 CGTGATTTAC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 57 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:773941 original size:20 final size:20
Alignment explanation
Indices: 773895--773947 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
773885 TAATACAAAA
*
773895 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
*
773915 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
773935 TCGCAACGTGATT
1 TCGCAACGAGATT
773948 TACATAGCGC
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:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:774541 original size:18 final size:19
Alignment explanation
Indices: 774498--774541 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
774488 GCAACGAGAT
*
774498 AATCGCAACGCGAAATAAA
1 AATCGCAAAGCGAAATAAA
* *
774517 AAACGCAAAGCGAAA-CAA
1 AATCGCAAAGCGAAATAAA
774535 AATCGCA
1 AATCGCA
774542 GTGCGATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.55, C:0.23, G:0.16, T:0.07
Consensus pattern (19 bp):
AATCGCAAAGCGAAATAAA
Found at i:774576 original size:19 final size:19
Alignment explanation
Indices: 774543--774719 Score: 153
Period size: 19 Copynumber: 9.8 Consensus size: 19
774533 AAAATCGCAG
774543 TGCGATTTT-ATTTCGCGT
1 TGCGATTTTCATTTCGCGT
774561 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
774580 TGCGATTTT-ATTT-GCGGT
1 TGCGATTTTCATTTCGC-GT
774598 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
774617 TGCGATTGTC--CT-G-GT
1 TGCGATTTTCATTTCGCGT
* **
774632 CGCGATAGTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
774651 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
**
774665 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
* *
774685 TGCGATTCTCATTATCTCGT
1 TGCGATTTTCATT-TCGCGT
774705 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
774720 AACCAAAAGA
Statistics
Matches: 130, Mismatches: 14, Indels: 29
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.08
15 10 0.08
16 3 0.02
17 6 0.05
18 25 0.19
19 42 0.32
20 33 0.25
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:774600 original size:37 final size:37
Alignment explanation
Indices: 774543--774719 Score: 154
Period size: 37 Copynumber: 4.9 Consensus size: 37
774533 AAAATCGCAG
774543 TGCGATTTTATTTCGCGTTGCGATTTTCATTTCGCGT
1 TGCGATTTTATTTCGCGTTGCGATTTTCATTTCGCGT
774580 TGCGATTTTATTT-GCGGTTGCGATTTTCATTTCGCGT
1 TGCGATTTTATTTCGC-GTTGCGATTTTCATTTCGCGT
* ** * **
774617 TGCGATTGT-CCT-G-GTCGCGATAGTCATTTCGCGT
1 TGCGATTTTATTTCGCGTTGCGATTTTCATTTCGCGT
* * **
774651 TGCGA---T-TCTCTCGTTGCGATAGTCATTTCCGCGT
1 TGCGATTTTATTTCGCGTTGCGATTTTCATTT-CGCGT
* *
774685 TGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 TGCGATT-TTATT-TCGCGTTGCGATTTTCATTTC
774720 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.03
33 15 0.13
34 33 0.28
36 4 0.03
37 42 0.36
39 2 0.02
40 18 0.15
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (37 bp):
TGCGATTTTATTTCGCGTTGCGATTTTCATTTCGCGT
Found at i:774644 original size:34 final size:33
Alignment explanation
Indices: 774606--774694 Score: 133
Period size: 34 Copynumber: 2.6 Consensus size: 33
774596 GTTGCGATTT
* *
774606 TCATTTCGCGTTGCGATTGTCCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCT-CTCGTCGCGATAG
*
774640 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
774673 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
774695 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 17 0.33
34 34 0.67
ACGTcount: A:0.11, C:0.26, G:0.25, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:774696 original size:20 final size:20
Alignment explanation
Indices: 774662--774719 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
774652 GCGATTCTCT
**
774662 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
774682 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
774702 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
774720 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:776773 original size:42 final size:42
Alignment explanation
Indices: 776713--776837 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
776703 GCCCGACTCA
* * *
776713 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
776755 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * * *
776797 ACTGTCATCGTTGAAGAGGTCCCTCTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GT-CCACTCCCACCGTTCAAGAG
776838 CCCGATTCAA
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 46 0.70
43 2 0.03
44 18 0.27
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:776793 original size:21 final size:21
Alignment explanation
Indices: 776769--776837 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
776759 TCATTCCTCG
776769 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
776790 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
776811 AGAGGTCCCTCTCCCACCATTCA
1 AGA-GTCCC-CTCCCACCGTTCA
776834 AGAG
1 AGAG
776838 CCCGATTCAA
Statistics
Matches: 33, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
21 18 0.55
22 4 0.12
23 11 0.33
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:778207 original size:14 final size:14
Alignment explanation
Indices: 778188--778223 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
778178 ATTGTTTAAT
778188 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
778202 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
778216 TGATTTGT
1 TGATTTGT
778224 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:778444 original size:33 final size:32
Alignment explanation
Indices: 778402--778528 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
778392 ATTAAATTCA
778402 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
778435 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
778468 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
778501 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
778529 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:778491 original size:66 final size:66
Alignment explanation
Indices: 778402--778527 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
778392 ATTAAATTCA
778402 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
778467 G
66 G
*
778468 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
778528 TAGTAATTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
G
Found at i:780804 original size:12 final size:12
Alignment explanation
Indices: 780787--780811 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
780777 TCTTCGGGGA
780787 CTTTTTCTTCTT
1 CTTTTTCTTCTT
780799 CTTTTTCTTCTT
1 CTTTTTCTTCTT
780811 C
1 C
780812 AGGATTATGA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:781973 original size:246 final size:246
Alignment explanation
Indices: 781550--782042 Score: 970
Period size: 246 Copynumber: 2.0 Consensus size: 246
781540 TGCGAAACTA
781550 AGACCTGTTGCCGGATGGGGAAGGATGTCGTTGGATATTGGAACGGATGTCGCCGGAGAGAGTGA
1 AGACCTGTTGCCGGATGGGGAAGGATGTCGTTGGATATTGGAACGGATGTCGCCGGAGAGAGTGA
781615 TAGATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTATAT
66 TAGATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTATAT
781680 ATACACAAAAATTTGGCTTGCGAAACTAAAACCTGTTGCGAACTTTGAAACTCGCATTGCGATTC
131 ATACACAAAAATTTGGCTTGCGAAACTAAAACCTGTTGCGAACTTTGAAACTCGCATTGCGATTC
781745 TGTATTATCTCGTTGCGAAAGGCAATCATTTGACCATCGCAATGCGAAATGC
196 TGTATTATCTCGTTGCGAAAGGCAATCATTTGACCATCGCAATGCG-AATGC
781797 AGACCTGTTGCCGGATGGGG-AGGATGTCGTTGGATATTGGAACGGATGTCGCCGGAGAGAGTGA
1 AGACCTGTTGCCGGATGGGGAAGGATGTCGTTGGATATTGGAACGGATGTCGCCGGAGAGAGTGA
781861 TAGATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTATAT
66 TAGATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTATAT
781926 ATACACAAAAATTTGGCTTGCGAAACTAAAACCTGTTGCGAACTTTGAAACTCGCATTGCGATTC
131 ATACACAAAAATTTGGCTTGCGAAACTAAAACCTGTTGCGAACTTTGAAACTCGCATTGCGATTC
781991 TGTATTATCTCGTTGCGAAAGGCAATCATTTGACCATCGCAATGCGAATGC
196 TGTATTATCTCGTTGCGAAAGGCAATCATTTGACCATCGCAATGCGAATGC
782042 A
1 A
782043 AATCGCAACG
Statistics
Matches: 246, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
245 6 0.02
246 220 0.89
247 20 0.08
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (246 bp):
AGACCTGTTGCCGGATGGGGAAGGATGTCGTTGGATATTGGAACGGATGTCGCCGGAGAGAGTGA
TAGATGGAGATGGAATGAGTTGCGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTATAT
ATACACAAAAATTTGGCTTGCGAAACTAAAACCTGTTGCGAACTTTGAAACTCGCATTGCGATTC
TGTATTATCTCGTTGCGAAAGGCAATCATTTGACCATCGCAATGCGAATGC
Found at i:782324 original size:20 final size:20
Alignment explanation
Indices: 782299--782336 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
782289 ATTCATTTGA
782299 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATAG
*
782319 CTATCGCAACGGGAAAAT
1 CTATCGCAACGCGAAAAT
782337 CGCAATGCGA
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:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATAG
Found at i:782399 original size:19 final size:19
Alignment explanation
Indices: 782377--782420 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
782367 TTTCTCGTTA
782377 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
782396 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
782415 CGATTT
1 CGATTT
782421 CTCGTTGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:784342 original size:19 final size:19
Alignment explanation
Indices: 784262--784377 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 19
784252 TAGTTTACTT
* *
784262 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
784282 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
784301 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
784321 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
784340 TCGC-A-TCG--AT-AAAA
1 TCGCAACGCGAAATGAAAA
784354 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
784372 TCGCAA
1 TCGCAA
784378 TGACAAAATA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 12 0.15
19 23 0.29
20 29 0.37
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:784386 original size:32 final size:33
Alignment explanation
Indices: 784320--784394 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
784310 GGAAATGGCT
* *
784320 ATCGCAATGCGAAATGAAAATCGCATCGATAAA
1 ATCGCAACGCGAAATGAAAATCGCATCGACAAA
784353 ATCGCAACGCGAAATG-AAATCGCAAT-GACAAA
1 ATCGCAACGCGAAATGAAAATCGC-ATCGACAAA
*
784385 ATAGCAACGC
1 ATCGCAACGC
784395 AAAACACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 21 0.55
33 17 0.45
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCATCGACAAA
Found at i:784446 original size:14 final size:14
Alignment explanation
Indices: 784427--784484 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
784417 TTTCATTTCG
784427 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
784441 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
784457 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
784473 CGTTGCGATTTT
1 CGTTGCGATTTT
784485 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:784491 original size:33 final size:33
Alignment explanation
Indices: 784414--784500 Score: 158
Period size: 32 Copynumber: 2.7 Consensus size: 33
784404 ATCGCATTGT
*
784414 GATTTTCATTTCGCGTTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
784447 GA-TTTCATTTCGCATTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
784479 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCATTGCGAT
784501 AGCCATTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 31 0.60
33 21 0.40
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
Found at i:784507 original size:19 final size:19
Alignment explanation
Indices: 784485--784528 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
784475 TTGCGATTTT
*
784485 CATTTCGCATTGCGATAGC
1 CATTTCCCATTGCGATAGC
* *
784504 CATTTTCCCGTTGCGATAGT
1 CA-TTTCCCATTGCGATAGC
784524 CATTT
1 CATTT
784529 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (19 bp):
CATTTCCCATTGCGATAGC
Found at i:785039 original size:18 final size:18
Alignment explanation
Indices: 785013--785057 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
785003 GTCGATCAGA
*
785013 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
785031 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
785049 TGATGGCTC
1 TGATGGCTC
785058 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:786332 original size:19 final size:20
Alignment explanation
Indices: 786308--786349 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
786298 AATAGTTTCT
786308 GAAAATG-AAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
786327 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
786347 GAA
1 GAA
786350 TTCGACTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.10
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:786647 original size:20 final size:21
Alignment explanation
Indices: 786622--786670 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
786612 TCTGAGAGAT
786622 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
786642 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
786664 AGAGATG
1 GGAGATG
786671 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:786656 original size:22 final size:22
Alignment explanation
Indices: 786629--786672 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
786619 GATGGAGATA
*
786629 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
786651 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
786673 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:786885 original size:20 final size:20
Alignment explanation
Indices: 786860--786953 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
786850 GATTATGTAT
786860 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
786880 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
786900 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
786921 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
786941 TATCGCATTGCGA
1 TATCGCGTTGCGA
786954 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:786925 original size:41 final size:41
Alignment explanation
Indices: 786880--786957 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
786870 CGAAAGTCAG
* * *
786880 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
786921 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
786958 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:786954 original size:20 final size:20
Alignment explanation
Indices: 786840--786954 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
786830 CGTTTTGAAA
*
786840 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
786861 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
786881 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
786901 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
786922 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
786942 ATCGCATTGCGAT
1 ATCGCATTGCGAT
786955 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:786973 original size:41 final size:41
Alignment explanation
Indices: 786880--786975 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
786870 CGAAAGTCAG
* * * ** *
786880 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
786921 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
786963 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
786976 TTTCTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:786987 original size:20 final size:20
Alignment explanation
Indices: 786907--787055 Score: 140
Period size: 20 Copynumber: 7.3 Consensus size: 20
786897 AAGTATCTCG
786907 TTGCGATTTT-TTATTATCGCA
1 TTGCGATTTTCTTA-T-TCGCA
** *
786928 TTGCGATAGTCAGTA-TCGCA
1 TTGCGATTTTC-TTATTCGCA
** *
786948 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT-CTTATTCGCA
*
786969 TTGCGATTTTCTTATTCGCG
1 TTGCGATTTTCTTATTCGCA
786989 TTGCGATTTTCTTATTCGCA
1 TTGCGATTTTCTTATTCGCA
** *
787009 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT-CTTATTCGCA
*
787030 TTGCGATTTACTTATTCGCA
1 TTGCGATTTTCTTATTCGCA
787050 TTGCGA
1 TTGCGA
787056 ATTGGGAAAA
Statistics
Matches: 105, Mismatches: 18, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
20 64 0.61
21 39 0.37
23 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTCTTATTCGCA
Found at i:786993 original size:41 final size:41
Alignment explanation
Indices: 786943--787055 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 41
786933 ATAGTCAGTA
* * **
786943 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTT-CTTAT
1 TCGCGTTGCGATTTT-CCAATTCGCATTGCGATTTTCCCAAT
**
786984 TCGCGTTGCGATTTTCTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCAATTCGCATTGCGATTTTCCCAAT
* **
787025 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCGTTGCGATTTTCCAATTCGCATTGCGA
787056 ATTGGGAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
40 17 0.27
41 47 0.73
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCAATTCGCATTGCGATTTTCCCAAT
Found at i:786993 original size:61 final size:61
Alignment explanation
Indices: 786905--787055 Score: 216
Period size: 61 Copynumber: 2.5 Consensus size: 61
786895 GTAAGTATCT
786905 CGTTGCGATTTT-TTATTATCGCATTGCGATAGTCAGTA-TCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTTCTTA-T-TCGCATTGCGATAGTC-GTATTCGCATTGCGATTTTCCCAATTCG
* ** *
786967 CGTTGCGATTTTCTTATTCGCGTTGCGATTTTCTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTTCTTATTCGCATTGCGATAGTCGTATTCGCATTGCGATTTTCCCAATTCG
*
787028 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTTCTTATTCGCATTGCGA
787056 ATTGGGAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
60 2 0.02
61 63 0.78
62 13 0.16
63 3 0.04
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (61 bp):
CGTTGCGATTTTCTTATTCGCATTGCGATAGTCGTATTCGCATTGCGATTTTCCCAATTCG
Found at i:790700 original size:22 final size:22
Alignment explanation
Indices: 790651--790704 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
790641 AAAGTGTCTT
* *
790651 AGCACTGATACTAAAGTGCCAC
1 AGCACTGATACTAAAATACCAC
* **
790673 AACACTGATACTAAAATATTAC
1 AGCACTGATACTAAAATACCAC
790695 AGCACTGATA
1 AGCACTGATA
790705 TGAAAGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (22 bp):
AGCACTGATACTAAAATACCAC
Found at i:790732 original size:22 final size:22
Alignment explanation
Indices: 790697--790757 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
790687 AATATTACAG
**
790697 CACTGATATGAAAGTGCATTCA
1 CACTGATACAAAAGTGCATTCA
* * *
790719 CACTGATTCAAAAGTGTATTCG
1 CACTGATACAAAAGTGCATTCA
*
790741 CACTGCTACAAAAGTGC
1 CACTGATACAAAAGTGC
790758 CATAGCACTG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (22 bp):
CACTGATACAAAAGTGCATTCA
Found at i:791064 original size:20 final size:20
Alignment explanation
Indices: 791039--791087 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
791029 GAGCCTGTCA
791039 GTATCGATACTAACCTTAGG
1 GTATCGATACTAACCTTAGG
**
791059 GTATCGATACTGGCCTTAGG
1 GTATCGATACTAACCTTAGG
791079 GTATCGATA
1 GTATCGATA
791088 TTGGACTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
GTATCGATACTAACCTTAGG
Found at i:791096 original size:20 final size:20
Alignment explanation
Indices: 791039--791106 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
791029 GAGCCTGTCA
*
791039 GTATCGATACT-AACCTTAGG
1 GTATCGATACTGGA-CTTAGG
*
791059 GTATCGATACTGGCCTTAGG
1 GTATCGATACTGGACTTAGG
*
791079 GTATCGATATTGGACTTA--
1 GTATCGATACTGGACTTAGG
791097 GTATCGATAC
1 GTATCGATAC
791107 CAATTTTATC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.21
20 33 0.79
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GTATCGATACTGGACTTAGG
Found at i:796224 original size:21 final size:21
Alignment explanation
Indices: 796200--796240 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
796190 CATCCCTCGT
796200 CTTAACATACGCAAAAAAGGC
1 CTTAACATACGCAAAAAAGGC
*
796221 CTTAATATACGCAAAAAAGG
1 CTTAACATACGCAAAAAAGG
796241 TCTCCGTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.17
Consensus pattern (21 bp):
CTTAACATACGCAAAAAAGGC
Found at i:807199 original size:19 final size:20
Alignment explanation
Indices: 807163--807204 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
807153 GTGTAAATGA
*
807163 ATTTCAAGATTTTATATTCG
1 ATTTCAAGATTATATATTCG
807183 ATTTCAA-ATTATATATTCG
1 ATTTCAAGATTATATATTCG
807202 ATT
1 ATT
807205 AAATTATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTCAAGATTATATATTCG
Found at i:813190 original size:23 final size:23
Alignment explanation
Indices: 813147--813190 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
813137 ATACACTATG
* *
813147 AATGTGTACCGATATATTCCTTA
1 AATGTGTACCGATACACTCCTTA
*
813170 AATGTGTATCGATACACTCCT
1 AATGTGTACCGATACACTCCT
813191 AGGTATACCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (23 bp):
AATGTGTACCGATACACTCCTTA
Found at i:813631 original size:13 final size:13
Alignment explanation
Indices: 813613--813651 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
813603 GTCATAAATC
813613 TATGACGCGCATT
1 TATGACGCGCATT
*
813626 TATGACACGCATT
1 TATGACGCGCATT
813639 TATGACGCGCATT
1 TATGACGCGCATT
813652 GCGCGTCATT
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:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:813786 original size:85 final size:85
Alignment explanation
Indices: 813623--813787 Score: 224
Period size: 85 Copynumber: 1.9 Consensus size: 85
813613 TATGACGCGC
* * * *
813623 ATTTATGACACGCATTTATGACGCGCATTGCGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
1 ATTTATGACACGCATTTATGACGCACATTGCGCGTCATTGAAGCACACATCATAAATAAAGATGA
* *
813688 CACATATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
** *
813708 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCACACATCATTAAA-AAAGATG
1 ATTTATGACACGCATTTATGACGCACATTGCGCGTCATTGAAGCACACATCA-TAAATAAAGATG
*
813772 ACACGCATTCGTGTGT
65 ACACACATTCGTGTGT
813788 TGTGATCGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
85 65 0.94
86 4 0.06
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACGCACATTGCGCGTCATTGAAGCACACATCATAAATAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:819268 original size:15 final size:15
Alignment explanation
Indices: 819248--819277 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
819238 ACATTTTGAA
*
819248 TGTTTTGGATTTTTG
1 TGTTTTGGATGTTTG
819263 TGTTTTGGATGTTTG
1 TGTTTTGGATGTTTG
819278 GATATTTTAT
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:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (15 bp):
TGTTTTGGATGTTTG
Found at i:819300 original size:24 final size:24
Alignment explanation
Indices: 819241--819313 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
819231 TGTTAAAACA
* *
819241 TTTTGAATGTTTTGGAT-TTTTGT
1 TTTTGAATGGTTTGGATATTTTAT
*
819264 GTTTTGGAT-GTTTGGATATTTTAT
1 -TTTTGAATGGTTTGGATATTTTAT
* *
819288 TTTTGAATGGTTTGAATATTTAAT
1 TTTTGAATGGTTTGGATATTTTAT
819312 TT
1 TT
819314 GAACTTCATG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (24 bp):
TTTTGAATGGTTTGGATATTTTAT
Found at i:824325 original size:18 final size:16
Alignment explanation
Indices: 824302--824336 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
824292 TATGGAATTT
824302 TTCCTTAATCTCTATTCA
1 TTCCTTAAT-TCT-TTCA
824320 TTCCTTAATTCTTTCA
1 TTCCTTAATTCTTTCA
824336 T
1 T
824337 AACTTCTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (16 bp):
TTCCTTAATTCTTTCA
Found at i:826347 original size:16 final size:16
Alignment explanation
Indices: 826326--826361 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
826316 TCCATAAAGA
826326 AAAATAATAAAGAAAC
1 AAAATAATAAAGAAAC
* *
826342 AAAATAATAATGTAAC
1 AAAATAATAAAGAAAC
826358 AAAA
1 AAAA
826362 CTTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAATAATAAAGAAAC
Found at i:835493 original size:21 final size:21
Alignment explanation
Indices: 835445--835493 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
835435 CCGAAATAAT
*
835445 AAAAAAATATTATTTTTATTC
1 AAAAAAATATTATTTTAATTC
*
835466 AATAAAAATATTGA-TTTAATTG
1 AA-AAAAATATT-ATTTTAATTC
835488 AAAAAA
1 AAAAAA
835494 TAATATATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAAAAATATTATTTTAATTC
Found at i:839858 original size:18 final size:19
Alignment explanation
Indices: 839835--839871 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
839825 CCAGTAATCA
839835 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
839853 TATTCCAACTGGTAATCTT
1 TATTCC-ACTGGTAATCTT
839872 ACATTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:840504 original size:24 final size:23
Alignment explanation
Indices: 840475--840520 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
840465 CGTTTATTAA
*
840475 ATAAACGAACACGAATGAACGAAT
1 ATAAACGAACAC-AATAAACGAAT
840499 ATAAACGAACACAATAAACGAA
1 ATAAACGAACACAATAAACGAA
840521 CAACTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (23 bp):
ATAAACGAACACAATAAACGAAT
Found at i:840530 original size:13 final size:13
Alignment explanation
Indices: 840474--840522 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
840464 TCGTTTATTA
840474 AATAAACGAACAC
1 AATAAACGAACAC
*
840487 GAATGAACG-A-A-
1 -AATAAACGAACAC
*
840498 TATAAACGAACAC
1 AATAAACGAACAC
840511 AATAAACGAACA
1 AATAAACGAACA
840523 ACTCAAACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
10 6 0.21
11 1 0.04
12 2 0.07
13 12 0.43
14 7 0.25
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.10
Consensus pattern (13 bp):
AATAAACGAACAC
Found at i:840752 original size:29 final size:29
Alignment explanation
Indices: 840720--840780 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
840710 TCAACAAAAC
*
840720 AATCTTCTTGAAATCCAAACAACTTCAAT
1 AATCTTCTTGAAATCAAAACAACTTCAAT
840749 AATCTTCTTGAAATCAAAACAACTTCAAT
1 AATCTTCTTGAAATCAAAACAACTTCAAT
840778 AAT
1 AAT
840781 ATTTGTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.31
Consensus pattern (29 bp):
AATCTTCTTGAAATCAAAACAACTTCAAT
Found at i:846684 original size:32 final size:32
Alignment explanation
Indices: 846633--846695 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
846623 TTGAGGAAAG
**
846633 AAAATTAATTTTTGAAAAATAGATATCTTGAA
1 AAAATTAAGCTTTGAAAAATAGATATCTTGAA
*
846665 AAAATTAAGCTTTGGAAAATAGATATCTTGA
1 AAAATTAAGCTTTGAAAAATAGATATCTTGA
846696 GCTAACTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.35
Consensus pattern (32 bp):
AAAATTAAGCTTTGAAAAATAGATATCTTGAA
Found at i:851161 original size:18 final size:18
Alignment explanation
Indices: 851138--851176 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
851128 CTATTCAGGG
* *
851138 TGATGATCTTGATATAGA
1 TGATGATCATGATAAAGA
*
851156 TGATGATGATGATAAAGA
1 TGATGATCATGATAAAGA
851174 TGA
1 TGA
851177 CGACGATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (18 bp):
TGATGATCATGATAAAGA
Found at i:851202 original size:18 final size:18
Alignment explanation
Indices: 851147--851203 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
851137 GTGATGATCT
*
851147 TGATATAGATGATGATGA
1 TGATATAGATGAAGATGA
* * *
851165 TGATAAAGATGACGACGA
1 TGATATAGATGAAGATGA
*
851183 TGATATTGATGAAGATGA
1 TGATATAGATGAAGATGA
851201 TGA
1 TGA
851204 GGATGAGGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (18 bp):
TGATATAGATGAAGATGA
Found at i:851208 original size:15 final size:15
Alignment explanation
Indices: 851190--851253 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
851180 CGATGATATT
851190 GATGAAGATGATGAG
1 GATGAAGATGATGAG
* *
851205 GATGAGGATGAGGAG
1 GATGAAGATGATGAG
* * *
851220 GAAGAGGATGACGAG
1 GATGAAGATGATGAG
*
851235 GAAGAAGATGATGAG
1 GATGAAGATGATGAG
851250 GATG
1 GATG
851254 TTGATGAAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.39, C:0.02, G:0.45, T:0.14
Consensus pattern (15 bp):
GATGAAGATGATGAG
Found at i:851241 original size:18 final size:18
Alignment explanation
Indices: 851214--851248 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
851204 GGATGAGGAT
*
851214 GAGGAGGAAGAGGATGAC
1 GAGGAAGAAGAGGATGAC
*
851232 GAGGAAGAAGATGATGA
1 GAGGAAGAAGAGGATGA
851249 GGATGTTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.09
Consensus pattern (18 bp):
GAGGAAGAAGAGGATGAC
Found at i:852947 original size:11 final size:11
Alignment explanation
Indices: 852922--852952 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
852912 TATAAAATCC
852922 GGTTGAACC-T
1 GGTTGAACCAT
852932 GGTTGAACCAT
1 GGTTGAACCAT
852943 GGTTGAACCA
1 GGTTGAACCA
852953 GTGAACCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (11 bp):
GGTTGAACCAT
Found at i:853197 original size:16 final size:16
Alignment explanation
Indices: 853178--853208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
853168 TTTGGTCGAC
*
853178 GAAATGTAAGATTATT
1 GAAATGTAAAATTATT
853194 GAAATGTAAAATTAT
1 GAAATGTAAAATTAT
853209 ATTTGGGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (16 bp):
GAAATGTAAAATTATT
Found at i:854344 original size:20 final size:20
Alignment explanation
Indices: 854277--854347 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
854267 CTCAAGAGGA
* *
854277 GTATCAATACT-ACAGGGTTG
1 GTATCGATACTCA-AGGGGTG
*
854297 GTATCGAAACTCAAGGGGTG
1 GTATCGATACTCAAGGGGTG
854317 GTATCGATACTCAAGGGGTG
1 GTATCGATACTCAAGGGGTG
854337 GTATCGATACT
1 GTATCGATACT
854348 GGGATCACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 45 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCAAGGGGTG
Found at i:854504 original size:15 final size:15
Alignment explanation
Indices: 854480--854510 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
854470 TATAATTTTG
854480 CCTTGAGTATCGATA
1 CCTTGAGTATCGATA
*
854495 CCTTGGGTATCGATA
1 CCTTGAGTATCGATA
854510 C
1 C
854511 TAGCAGGTGG
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:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (15 bp):
CCTTGAGTATCGATA
Found at i:860283 original size:21 final size:22
Alignment explanation
Indices: 860259--860315 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
860249 ATTGTCCAGA
*
860259 GGGAACCGATTTCTCCCCAAGG
1 GGGAACCGATTCCTCCCCAAGG
*
860281 GGAAACCGATTCCTCCCCAAGG
1 GGGAACCGATTCCTCCCCAAGG
*
860303 GGGTACCGATTCC
1 GGGAACCGATTCC
860316 CCCTAAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCTCCCCAAGG
Found at i:862814 original size:42 final size:42
Alignment explanation
Indices: 862767--862950 Score: 314
Period size: 42 Copynumber: 4.3 Consensus size: 42
862757 CATATTCGCA
* *
862767 TTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
862809 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
862851 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
862893 TTGCGATAGTCCAAGTTCGCGTTTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCG--TTGCGATTTATTCCAAATTCG
862937 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
862951 ATTTGTTGCG
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
42 100 0.75
44 34 0.25
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:862826 original size:19 final size:19
Alignment explanation
Indices: 862767--863011 Score: 150
Period size: 21 Copynumber: 11.7 Consensus size: 19
862757 CATATTCGCA
862767 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
862788 TTGTGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
862809 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
862830 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
862851 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
862872 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
862893 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
862914 TTTTGCGATTTATTCCAAATTCG
1 --TTGCGA--TAGTCCAAGTTCG
* *
862937 TTGCGATAGTCCAAATTTG
1 TTGCGATAGTCCAAGTTCG
* *
862956 TTGCGATAGT-CGACTATCG
1 TTGCGATAGTCCAAGT-TCG
* *
862975 CATTGCGATTTATTCCAAATTCG
1 --TTGCGA--TAGTCCAAGTTCG
862998 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
863012 AATCGCAACG
Statistics
Matches: 179, Mismatches: 23, Indels: 46
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.02
19 58 0.32
21 64 0.36
23 42 0.23
24 3 0.02
25 9 0.05
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:862831 original size:21 final size:21
Alignment explanation
Indices: 862761--862966 Score: 153
Period size: 21 Copynumber: 9.8 Consensus size: 21
862751 GATTTACATA
*
862761 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
862782 TTCGCGTTGTGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
862805 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
862824 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
862847 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
862866 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
862889 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
862908 TTCGCGTTTTGCGATTTATTCCAAA
1 TTCGCG--TTGCGA--TAGTCCAAG
*
862933 TT--CGTTGCGATAGTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
862952 TT--TGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
862967 GACTATCGCA
Statistics
Matches: 152, Mismatches: 17, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
19 50 0.33
21 57 0.38
23 36 0.24
25 9 0.06
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:863836 original size:21 final size:21
Alignment explanation
Indices: 863762--863884 Score: 101
Period size: 21 Copynumber: 5.9 Consensus size: 21
863752 CGTTGCGATT
*
863762 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
*
863781 TTGGAATAAATCGCAATGCGAA-
1 TTGGACT--ATCGCAATGCGAAC
* *
863803 TATGTA-AATCGCAATGCGAAC
1 T-TGGACTATCGCAATGCGAAC
* **
863824 CTGGACTATCGCAACACGAAC
1 TTGGACTATCGCAATGCGAAC
*
863845 TTGGACTATCTCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
863866 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
863885 TTTACATATT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.07
20 16 0.20
21 52 0.63
22 1 0.01
23 7 0.09
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:863923 original size:41 final size:42
Alignment explanation
Indices: 863893--864063 Score: 174
Period size: 41 Copynumber: 4.1 Consensus size: 42
863883 GATTTACATA
*
863893 TTCGCATTGCGATAGTCCAAGTTCGTATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCAAGTTCGTATTGCGATAGTACA-AG
** *
863934 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGTATTGCGATAGTACAAG
* * *
863976 TTCGCATTGCGAT-TTACATA-TTC-TCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCA-AGTTCGT-ATTGCGATAGTACAAG
** *
864017 TTCGCATTGCGATAGTCCAAGTTCGCGTTACGATAGT-CGAAG
1 TTCGCATTGCGATAGTCCAAGTTCGTATTGCGATAGTAC-AAG
864059 TTCGC
1 TTCGC
864064 GTTACGAATC
Statistics
Matches: 109, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
41 69 0.63
42 40 0.37
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (42 bp):
TTCGCATTGCGATAGTCCAAGTTCGTATTGCGATAGTACAAG
Found at i:863925 original size:62 final size:62
Alignment explanation
Indices: 863893--864042 Score: 273
Period size: 62 Copynumber: 2.4 Consensus size: 62
863883 GATTTACATA
*
863893 TTCGCATTGCGATAGTCCAAGTTCGTATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
* *
863955 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCTCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
864017 TTCGCATTGCGATAGTCCAAGTTCGC
1 TTCGCATTGCGATAGTCCAAGTTCGC
864043 GTTACGATAG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
Found at i:864070 original size:21 final size:21
Alignment explanation
Indices: 863893--864063 Score: 206
Period size: 21 Copynumber: 8.2 Consensus size: 21
863883 GATTTACATA
863893 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
863914 TTCGTATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
863934 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
863955 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
863976 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
*
863996 TTCTCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
864017 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
864038 TTCGCGTTACGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
864059 TTCGC
1 TTCGC
864064 GTTACGAATC
Statistics
Matches: 127, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
20 32 0.25
21 95 0.75
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:867830 original size:20 final size:21
Alignment explanation
Indices: 867768--867827 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
867758 TTAGTGCAGA
867768 GGGAATCGATACCCCT-GAAG
1 GGGAATCGATACCCCTCGAAG
* * * *
867788 GGGAACCGATTCCCCCCGTAG
1 GGGAATCGATACCCCTCGAAG
867809 GGGAATCGATACCCCTCGA
1 GGGAATCGATACCCCTCGA
867828 GGGTTTTGGA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.25, C:0.32, G:0.28, T:0.15
Consensus pattern (21 bp):
GGGAATCGATACCCCTCGAAG
Found at i:873859 original size:27 final size:28
Alignment explanation
Indices: 873796--873879 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
873786 CGTAAACACT
873796 TAAAATATTATTATT--TATATGTTTAA
1 TAAAATATTATTATTAATATATGTTTAA
873822 TATTAATATATTATT-TTAATATCAT-TTTAA
1 TA--AA-ATATTATTATTAATAT-ATGTTTAA
* *
873852 TAAAATATTAATTATTAATTTATATTTA
1 TAAAATATT-ATTATTAATATATGTTTA
873880 TAGATAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
26 2 0.04
27 5 0.10
28 11 0.23
29 18 0.38
30 10 0.21
31 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TAAAATATTATTATTAATATATGTTTAA
Found at i:873863 original size:41 final size:40
Alignment explanation
Indices: 873818--873908 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 40
873808 ATTTATATGT
873818 TTAATATTAATATATTATTT-TA-ATATCATTTTAATAAAATA
1 TTAATATTAATATA-TATTTATAGATA--ATTTTAATAAAATA
* *
873859 TTAATTATTAATTTATATTTATAGATAATTTTAATAATATA
1 TTAA-TATTAATATATATTTATAGATAATTTTAATAAAATA
873900 TATAATATT
1 T-TAATATT
873909 TTTATTTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
41 27 0.61
42 14 0.32
43 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (40 bp):
TTAATATTAATATATATTTATAGATAATTTTAATAAAATA
Found at i:873989 original size:23 final size:23
Alignment explanation
Indices: 873941--873990 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
873931 AATTATTAAC
* *
873941 AAAAGTAATATTTTAAATTTTAT
1 AAAAATAATATTTTAAATATTAT
*
873964 AAAAATAATATTATTGAATATT-T
1 AAAAATAATATT-TTAAATATTAT
873987 AAAA
1 AAAA
873991 TATACTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
AAAAATAATATTTTAAATATTAT
Found at i:874058 original size:21 final size:22
Alignment explanation
Indices: 874005--874060 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
873995 CTCCTTAAAG
874005 TATAATATAATATTATTATTTTAA
1 TATAA-ATAATATTATTATTTT-A
*
874029 TATTTAATAATATTATTATTTT-
1 TA-TAAATAATATTATTATTTTA
874051 TATAAATAAT
1 TATAAATAAT
874061 TCTTATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 7 0.24
22 2 0.07
24 18 0.62
25 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATAAATAATATTATTATTTTA
Found at i:874060 original size:24 final size:24
Alignment explanation
Indices: 874011--874060 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
874001 AAAGTATAAT
**
874011 ATAATATTATTATTTTAATATTTA
1 ATAATATTATTATTTTAATAAATA
*
874035 ATAATATTATTATTTTTATAAATA
1 ATAATATTATTATTTTAATAAATA
874059 AT
1 AT
874061 TCTTATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAATATTATTATTTTAATAAATA
Found at i:875784 original size:44 final size:45
Alignment explanation
Indices: 875607--875827 Score: 293
Period size: 45 Copynumber: 5.0 Consensus size: 45
875597 CAGATTTGAA
* * * * * * *
875607 ATTTATGTTTTAATCCGTTTGGTCAAATTACGTTTCAAGCCTCTT
1 ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTT
875652 ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTT
1 ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTT
* **
875697 ATTTTTGTTTTATTTCATATGGTCAAATTATGTTCCAAGCCCCTT
1 ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTT
*
875742 ATTTTTGTTTTATTTCGTAT-GTCAAATTACATTCCAAACCCCTT
1 ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTT
* * * *
875786 A-TTTTGTTTTATTTTGTATGGTCAAATTTCATGCAAAGCCCC
1 ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCC
875828 CATATTTCCC
Statistics
Matches: 156, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
43 17 0.11
44 40 0.26
45 99 0.63
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (45 bp):
ATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTT
Found at i:875834 original size:89 final size:89
Alignment explanation
Indices: 875651--875834 Score: 266
Period size: 89 Copynumber: 2.1 Consensus size: 89
875641 TCAAGCCTCT
*
875651 TATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAGCCCCTTATTTTTGTTTTATTTCATA
1 TATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAACCCCTTATTTTTGTTTTATTTCATA
* *
875716 TGGTCAAATTATGTTCCAAGCCCCT
66 TGGTCAAATTATG-TCAAAGCCCCA
**
875741 TATTTTTGTTTTATTTCGTAT-GTCAAATTACATTCCAAACCCCTTA-TTTTGTTTTATTTTGTA
1 TATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAACCCCTTATTTTTGTTTTATTTCATA
875804 TGGTCAAATTTCATG-CAAAGCCCCCA
66 TGGTCAAA-TT-ATGTCAAAG-CCCCA
875830 TATTT
1 TATTT
875835 CCCCCTGATT
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
88 27 0.31
89 35 0.41
90 24 0.28
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.48
Consensus pattern (89 bp):
TATTTTTGTTTTATTTCGTATGGTCAAATTACATTCCAAACCCCTTATTTTTGTTTTATTTCATA
TGGTCAAATTATGTCAAAGCCCCA
Found at i:876617 original size:20 final size:20
Alignment explanation
Indices: 876594--876649 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
876584 TTTGAAACTT
876594 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
876614 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
876634 AAATTCGCAACGCGAA
1 AAATTCGCAACACGAA
876650 TTTAGTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.48, C:0.21, G:0.16, T:0.14
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:876669 original size:19 final size:20
Alignment explanation
Indices: 876645--876697 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
876635 AATTCGCAAC
876645 GCGAATTT-AGTTTCACGTT
1 GCGAATTTAAGTTTCACGTT
* * **
876664 GCGAATTTCATTTTCGTGTT
1 GCGAATTTAAGTTTCACGTT
876684 GCGAATTTAAGTTT
1 GCGAATTTAAGTTT
876698 AAAAAACTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (20 bp):
GCGAATTTAAGTTTCACGTT
Found at i:878250 original size:42 final size:42
Alignment explanation
Indices: 878186--878324 Score: 206
Period size: 42 Copynumber: 3.3 Consensus size: 42
878176 CCCCCCACTT
* * * *
878186 CGAGTGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
*
878228 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCTACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
* * *
878270 CGAGAGCCATTACCTGATCGAGTCGATTATACACCTCCACAT
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
878312 CGAGAGCCATCAC
1 CGAGAGCCATCAC
878325 TTATTCCATC
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.27, C:0.35, G:0.19, T:0.19
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:878468 original size:21 final size:21
Alignment explanation
Indices: 878441--878490 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
878431 GTTAGGGGAG
878441 TTACGTGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
* *
878462 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
878483 TTACGTGA
1 TTACGTGA
878491 CGACAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:878549 original size:21 final size:21
Alignment explanation
Indices: 878441--878556 Score: 60
Period size: 21 Copynumber: 5.5 Consensus size: 21
878431 GTTAGGGGAG
878441 TTACGTGATGAGGT-CAGTACT
1 TTACGTGATGAGGTACAGT-CT
* *
878462 TTGCGTGATGAGGT-CGGTACT
1 TTACGTGATGAGGTACAGT-CT
* ** * *
878483 TTACGTGACGA-CAATAGTGCA
1 TTACGTGATGAGGTACAGT-CT
**
878504 TGGCGTGATGAGGTACAGTCT
1 TTACGTGATGAGGTACAGTCT
* *
878525 TTACGTGGTGAGGTAGATGTC-
1 TTACGTGATGAGGTACA-GTCT
*
878546 TTACGCGATGA
1 TTACGTGATGA
878557 CAATGGTGCT
Statistics
Matches: 69, Mismatches: 23, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
21 62 0.90
22 7 0.10
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (21 bp):
TTACGTGATGAGGTACAGTCT
Found at i:878550 original size:63 final size:63
Alignment explanation
Indices: 878444--878603 Score: 148
Period size: 63 Copynumber: 2.5 Consensus size: 63
878434 AGGGGAGTTA
* * *
878444 CGTGATGAGGTCAGTACTTTGCGTGATGAGGTCGGTACTTTACGTGACGACAATAGTGCATGG
1 CGTGATGAGGTCAGTACTTTACGTGATGAGGTAGGTACTTTACGCGACGACAATAGTGCATGG
* * * * *
878507 CGTGATGAGGTACAGT-CTTTACGTGGTGAGGTAGATGT-C-TTACGCGATGACAATGGTGCTTT
1 CGTGATGAGGT-CAGTACTTTACGTGATGAGGTAG--GTACTTTACGCGACGACAATAGTGCATG
*
878569 A
63 G
* * *
878570 CGTGGTGAGGT-ATCTACTTTATGTGATGAGGTAG
1 CGTGATGAGGTCA-GTACTTTACGTGATGAGGTAG
878604 CCGCTCTACG
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 70 0.89
64 5 0.06
65 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (63 bp):
CGTGATGAGGTCAGTACTTTACGTGATGAGGTAGGTACTTTACGCGACGACAATAGTGCATGG
Found at i:879268 original size:21 final size:21
Alignment explanation
Indices: 879195--879269 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
879185 CAGTTTCCAG
* *
879195 ATTCGCAACGCGATTTTGACT-
1 ATTCGCAATGCGATTTT-CCTA
* * *
879216 A-TCGCATTACGATTTTCCAA
1 ATTCGCAATGCGATTTTCCTA
**
879236 ATTCGCGTTGCGATTTTCCTA
1 ATTCGCAATGCGATTTTCCTA
879257 ATTCGCAATGCGA
1 ATTCGCAATGCGA
879270 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.31
21 28 0.67
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCCTA
Found at i:879284 original size:20 final size:20
Alignment explanation
Indices: 879259--879324 Score: 107
Period size: 20 Copynumber: 3.3 Consensus size: 20
879249 TTTTCCTAAT
879259 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
879279 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
879299 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
879319 TCGCAA
1 TCGCAA
879325 CGTGAATCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:879331 original size:20 final size:20
Alignment explanation
Indices: 879259--879334 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
879249 TTTTCCTAAT
879259 TCGCAATGCGAATAC-GTAAA
1 TCGCAATGCGAAT-CTGTAAA
**
879279 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATCTGTAAA
879299 TCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
* *
879319 TCGCAACGTGAATCTG
1 TCGCAATGCGAATCTG
879335 ACTATCGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATCTGTAAA
Found at i:879341 original size:20 final size:20
Alignment explanation
Indices: 879318--879384 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
879308 GAATCTGTAA
* *
879318 ATCGCAACGTGAATCTGACT
1 ATCGCAACGAGATTCTGACT
879338 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
879358 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
879378 ATCGCAA
1 ATCGCAA
879385 TACTGAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:879342 original size:40 final size:40
Alignment explanation
Indices: 879259--879385 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 40
879249 TTTTCCTAAT
* ** *
879259 TCGCAATGCGAATAC-GTAAATCGCAATGCGAATAAGTA-AA
1 TCGCAATGCGAAT-CTGTAAATCGCAACGCGAATCTG-ACTA
*
879299 TCGCAATGCGAATCTGTAAATCGCAACGTGAATCTGACTA
1 TCGCAATGCGAATCTGTAAATCGCAACGCGAATCTGACTA
* * * * *
879339 TCGCAACGAGATTCTG-ACTATCGCAACGCGATTCTGACTA
1 TCGCAATGCGAATCTGTA-AATCGCAACGCGAATCTGACTA
879379 TCGCAAT
1 TCGCAAT
879386 ACTGAATTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.04
40 69 0.96
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (40 bp):
TCGCAATGCGAATCTGTAAATCGCAACGCGAATCTGACTA
Found at i:882689 original size:20 final size:20
Alignment explanation
Indices: 882664--882757 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
882654 GACATTCATT
882664 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCAGAA-A
*
882684 TGACTATCGCAACACAGAAA
1 TGACTATCGCAACGCAGAAA
**
882704 TGACTATCGCAA-TAAGGAAA
1 TGACTATCGCAACGCA-GAAA
* * *
882724 TGGCTATCGCAATGCGGAAA
1 TGACTATCGCAACGCAGAAA
882744 TGACTATCGCAACG
1 TGACTATCGCAACG
882758 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 58 0.94
21 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCAGAAA
Found at i:882768 original size:14 final size:14
Alignment explanation
Indices: 882749--882802 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
882739 GGAAATGACT
882749 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
882763 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
882782 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
882796 ATCGCAA
1 ATCGCAA
882803 TGTGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:882772 original size:34 final size:34
Alignment explanation
Indices: 882729--882822 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 34
882719 GGAAATGGCT
**
882729 ATCGCAATGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
882763 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
882796 ATCGCAATGTGAAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
882823 TGTGAAATGA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:882786 original size:19 final size:19
Alignment explanation
Indices: 882762--882848 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
882752 GCAACGAGAG
882762 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
882781 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
882795 AATCGCAATGTGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
882815 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
882834 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
882849 CTAGTTTCGC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 2 0.04
19 29 0.51
20 14 0.25
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:882901 original size:34 final size:34
Alignment explanation
Indices: 882858--882953 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
882848 ACTAGTTTCG
882858 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
882892 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
* ** *
882925 CGTTGCTATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
882954 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:883078 original size:14 final size:14
Alignment explanation
Indices: 883059--883095 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
883049 CATCAATTAA
883059 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
883073 ACAAATCATCTTTT
1 ACAAATCAACATTT
883087 ACAAATCAA
1 ACAAATCAA
883096 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:884532 original size:21 final size:22
Alignment explanation
Indices: 884508--884557 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
884498 TGACAGTGGC
*
884508 CTCTTGAATGG-TGAGAGGGGA
1 CTCTTGAAGGGATGAGAGGGGA
* *
884529 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAAGGGATGAGAGGGGA
884550 CTCTTGAA
1 CTCTTGAA
884558 CGATAGGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
CTCTTGAAGGGATGAGAGGGGA
Found at i:885134 original size:20 final size:20
Alignment explanation
Indices: 885068--885252 Score: 177
Period size: 20 Copynumber: 9.4 Consensus size: 20
885058 CAAACTTAAA
885068 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
885088 ATCACAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
885108 ATTGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
885128 ATCGCAATGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
*
885148 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
885162 ATCGCAATGCGCGAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
885184 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
885204 ATCGTAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
885224 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
885244 ATCGCAACG
1 ATCGCAACG
885253 AGAGAATCGC
Statistics
Matches: 136, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.05
16 2 0.01
18 4 0.03
19 4 0.03
20 112 0.82
22 7 0.05
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:885203 original size:96 final size:96
Alignment explanation
Indices: 885067--885268 Score: 318
Period size: 96 Copynumber: 2.1 Consensus size: 96
885057 TCAAACTTAA
* * *
885067 AATCGCAA--CGCGAAAATGACTATCACAACACGGAAATGACTATTGCAACGCGGAAATGACTAT
1 AATCGCAATGCGCGAAAATGACTATCACAACACGAAAATGACTATCGCAACGCGAAAATGACTAT
885130 CGCAATGCAAATTTGACTATCGCAACGAGAG
66 CGCAATGCAAATTTGACTATCGCAACGAGAG
* * * *
885161 AATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATGACTATCGTAATGCGAAAATGACTAT
1 AATCGCAATGCGCGAAAATGACTATCACAACACGAAAATGACTATCGCAACGCGAAAATGACTAT
*
885226 CGCAATGCGAATTTGACTATCGCAACGAGAG
66 CGCAATGCAAATTTGACTATCGCAACGAGAG
885257 AATCGCAATGCG
1 AATCGCAATGCG
885269 ATTTTCATTT
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 8 0.08
96 90 0.92
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (96 bp):
AATCGCAATGCGCGAAAATGACTATCACAACACGAAAATGACTATCGCAACGCGAAAATGACTAT
CGCAATGCAAATTTGACTATCGCAACGAGAG
Found at i:885320 original size:20 final size:20
Alignment explanation
Indices: 885295--885383 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
885285 GCGATTCTTT
885295 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
885315 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
**
885335 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
**
885355 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
*
885375 CGTTGCGAT
1 CATTGCGAT
885384 TTTGTTGTTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCG
Found at i:885393 original size:14 final size:14
Alignment explanation
Indices: 885368--885411 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
885358 TGCGATAGTC
*
885368 ATTTTCGCGTTGCG
1 ATTTTCTCGTTGCG
* * *
885382 ATTTTGTTGTTGCA
1 ATTTTCTCGTTGCG
885396 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
885410 AT
1 AT
885412 AGTCATTTTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTCTCGTTGCG
Found at i:887356 original size:20 final size:20
Alignment explanation
Indices: 887298--887385 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
887288 GAAACTTAAA
**
887298 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
887318 ATCGCAACACAAAAATGACT
1 ATCGCAACACGAAAATGACT
887338 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* ** **
887358 ATTGCAACGTGAATTTGACT
1 ATCGCAACACGAAAATGACT
887378 ATCGCAAC
1 ATCGCAAC
887386 GCAAGAATCG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:887680 original size:22 final size:22
Alignment explanation
Indices: 887618--887683 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
887608 TTTCTGACCG
* *
887618 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
887640 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
887662 TGATTTCGTCAGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
887684 GGATGTCTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:887935 original size:21 final size:21
Alignment explanation
Indices: 887911--887955 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
887901 ATTCGCATTT
887911 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* *
887932 CGAATTTGGAAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
887953 CGA
1 CGA
887956 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:889158 original size:20 final size:20
Alignment explanation
Indices: 889133--889170 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
889123 TACACTTTCG
889133 CAACGCGAAAGTAAAATTCT
1 CAACGCGAAAGTAAAATTCT
*
889153 CAACGCGAAAGTCAAATT
1 CAACGCGAAAGTAAAATT
889171 TGCGTTGTGA
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:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (20 bp):
CAACGCGAAAGTAAAATTCT
Found at i:891766 original size:22 final size:22
Alignment explanation
Indices: 891749--891837 Score: 178
Period size: 22 Copynumber: 4.0 Consensus size: 22
891739 CTCGTATAAA
891749 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
891771 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
891793 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
891815 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
891837 T
1 T
891838 ATGTCCATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:892173 original size:29 final size:29
Alignment explanation
Indices: 892131--892200 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
892121 TTCTGCATAA
**
892131 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
892160 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
892189 TCATGTCATGTA
1 TCATGTCATGTA
892201 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:892651 original size:67 final size:67
Alignment explanation
Indices: 892502--892652 Score: 196
Period size: 68 Copynumber: 2.2 Consensus size: 67
892492 TTTTCTCATG
* * *
892502 GGGGAATCGGTTCCCCCCCCTTGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
*
892567 GAG
65 GAA
** * * *
892570 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTT
1 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
892634 GAA
65 GAA
892637 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
892653 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
67 30 0.41
68 43 0.59
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:892662 original size:21 final size:21
Alignment explanation
Indices: 892632--892673 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
892622 ATTCATTTCG
* *
892632 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
892653 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
892674 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:894018 original size:24 final size:23
Alignment explanation
Indices: 893987--894038 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
893977 AAACATCATC
893987 AAAATCCGAGTATTGACCAAGAT
1 AAAATCCGAGTATTGACCAAGAT
*
894010 AAAAGTCCGGGTATTGACCAAGAT
1 AAAA-TCCGAGTATTGACCAAGAT
*
894034 CAAAT
1 AAAAT
894039 TTCGAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (23 bp):
AAAATCCGAGTATTGACCAAGAT
Found at i:894813 original size:16 final size:16
Alignment explanation
Indices: 894791--894830 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
894781 ATCATTGGAG
*
894791 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
894807 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
894823 AAAAATTA
1 AAAAATTA
894831 GAGACGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:895011 original size:20 final size:20
Alignment explanation
Indices: 894986--895155 Score: 84
Period size: 20 Copynumber: 8.4 Consensus size: 20
894976 AAATAAAAGC
894986 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
895006 TGTTGC-AAATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* **
895026 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* * *
895046 AGTTGCG-AATTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
** *
895066 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
*
895086 TGTTGCGAAA-AAGAAATTCG
1 TGTTGCGAAATTA-AAATTCG
* *
895106 CGTTGCG-AATTCAGAAA-TCA
1 TGTTGCGAAATT-A-AAATTCG
* * *
895126 AGTTGCGAATTTGAAATTCCG
1 TGTTGCGAAATTAAAATT-CG
895147 TGTTGCGAA
1 TGTTGCGAA
895156 TTTGGAAATC
Statistics
Matches: 113, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.01
19 24 0.21
20 58 0.51
21 27 0.24
22 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:895070 original size:60 final size:60
Alignment explanation
Indices: 894987--895122 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 60
894977 AATAAAAGCT
* *
894987 GTTGCGAAATTA-AAATTCGTGTTGC-AAATTCGAAAATCGAGTTGCGAAAACA-AAATTCGA
1 GTTGCG-AATTAGAAAATCGTGTTGCGAAA-ACGAAAATCGAGTTGCGAAAA-AGAAATTCGA
* * * * * *
895047 GTTGCGAATTAGAAAATCTTGTTGCGAAAAGGAAACTTGTGTTGCGAAAAAGAAATTCGC
1 GTTGCGAATTAGAAAATCGTGTTGCGAAAACGAAAATCGAGTTGCGAAAAAGAAATTCGA
895107 GTTGCGAATTCAGAAA
1 GTTGCGAATT-AGAAA
895123 TCAAGTTGCG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 6 0.09
60 50 0.78
61 8 0.12
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (60 bp):
GTTGCGAATTAGAAAATCGTGTTGCGAAAACGAAAATCGAGTTGCGAAAAAGAAATTCGA
Found at i:895091 original size:40 final size:40
Alignment explanation
Indices: 894987--895114 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
894977 AATAAAAGCT
** * *
894987 GTTGCGAAATTAAAATTCGTGTTGCAAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* **
895027 GTTGCGAAAACAAAATTCGAGTTGCGAATTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* * ** * *
895067 GTTGCGAAAAGGAAACTT-GTGTTGCGAAAAAGAAATTCGC
1 GTTGCGAAAA-CAAAATTCGTGTTGCGAATTAGAAAATCGA
895107 GTTGCGAA
1 GTTGCGAA
895115 TTCAGAAATC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 67 0.93
41 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:895164 original size:41 final size:40
Alignment explanation
Indices: 895098--895179 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
895088 TTGCGAAAAA
895098 GAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
1 GAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
* ** **
895138 GAAATTCCGTGTTGCGAATTTGGAAATCGCGTTGCGAATTT
1 GAAATT-CGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
895179 G
1 G
895180 GAAAATCTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 6 0.17
41 30 0.83
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (40 bp):
GAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
Found at i:895173 original size:20 final size:21
Alignment explanation
Indices: 895098--895343 Score: 104
Period size: 20 Copynumber: 12.0 Consensus size: 21
895088 TTGCGAAAAA
**
895098 GAAATTCGCGTTGCGAATTCA
1 GAAATTCGCGTTGCGAATTTG
**
895119 GAAA-TCAAGTTGCGAATTT-
1 GAAATTCGCGTTGCGAATTTG
*
895138 GAAATTCCGTGTTGCGAATTTG
1 GAAATT-CGCGTTGCGAATTTG
895160 GAAA-TCGCGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
* * * * **
895180 GAAAATCTCATTACGAGA--AA
1 GAAATTCGCGTTGCGA-ATTTG
895200 GAAATTCGCGTTGC-AA-TTG
1 GAAATTCGCGTTGCGAATTTG
* *
895219 CAGAAACT-GAGTTGCGAATTTG
1 --GAAATTCGCGTTGCGAATTTG
** **
895241 GAAAACCGCGTTGCAGAA--AA
1 GAAATTCGCGTTGC-GAATTTG
* * *
895261 GAAATTCGAGTTGCAAATTTC
1 GAAATTCGCGTTGCGAATTTG
* * * *
895282 AAAACT-GAGTTGCGAATCTGG
1 GAAATTCGCGTTGCGAAT-TTG
*
895303 GAAATTCGCGTTGCGAAATTG
1 GAAATTCGCGTTGCGAATTTG
*
895324 G--AGTCTGCGTTGCGAATTTG
1 GAAATTC-GCGTTGCGAATTTG
895344 TTGCTCATTT
Statistics
Matches: 166, Mismatches: 42, Indels: 35
0.68 0.17 0.14
Matches are distributed among these distances:
18 1 0.01
19 10 0.06
20 85 0.51
21 50 0.30
22 20 0.12
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:895213 original size:61 final size:61
Alignment explanation
Indices: 895138--895298 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
895128 TTGCGAATTT
* * * *
895138 GAAATTCCGTGTTGCGAATTTG-GAAA-TCGCGTTGCGAATTTGGAAAATCTCATTAC-GAGAAA
1 GAAATT-CGAGTTGC-AATTTGAGAAACT-GAGTTGCGAATTTGGAAAACCGCATTACAGA-AAA
* * *
895200 GAAATTCGCGTTGCAA-TTGCAGAAACTGAGTTGCGAATTTGGAAAACCGCGTTGCAGAAAA
1 GAAATTCGAGTTGCAATTTG-AGAAACTGAGTTGCGAATTTGGAAAACCGCATTACAGAAAA
*
895261 GAAATTCGAGTTGCAAATTTCA-AAACTGAGTTGCGAAT
1 GAAATTCGAGTTGC-AATTTGAGAAACTGAGTTGCGAAT
895299 CTGGGAAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
59 3 0.04
60 2 0.02
61 66 0.78
62 12 0.14
63 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (61 bp):
GAAATTCGAGTTGCAATTTGAGAAACTGAGTTGCGAATTTGGAAAACCGCATTACAGAAAA
Found at i:895274 original size:102 final size:101
Alignment explanation
Indices: 895095--895280 Score: 227
Period size: 102 Copynumber: 1.8 Consensus size: 101
895085 GTGTTGCGAA
* * **
895095 AAAGAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTTGAAATTCCGTGTTGCGAATTTG
1 AAAGAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTTGAAATACCGCGTTGCGAA-TAA
* *
895160 GAAATCGCGTTGCGAATTTGGAAAATCTCATTACGAG
65 GAAATCGAGTTGCAAATTTGGAAAATCTCATTACGAG
*
895197 AAAGAAATTCGCGTTGC-AATTGCAGAAA-CTGAGTTGCGAATTTGGAAA-ACCGCGTTGCAGAA
1 AAAGAAATTCGCGTTGCGAATT-CAGAAATC-AAGTTGCGAATTT-GAAATACCGCGTTGC-GAA
895259 -AAGAAATTCGAGTTGCAAATTT
62 TAAGAAA-TCGAGTTGCAAATTT
895281 CAAAACTGAG
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
101 9 0.12
102 56 0.78
103 7 0.10
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (101 bp):
AAAGAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTTGAAATACCGCGTTGCGAATAAG
AAATCGAGTTGCAAATTTGGAAAATCTCATTACGAG
Found at i:895964 original size:15 final size:15
Alignment explanation
Indices: 895941--895984 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
895931 TAAATTAAGC
* *
895941 ATCAAAATTAATATT
1 ATCACAATTAATATA
895956 ATCACAATTCAA-ATA
1 ATCACAATT-AATATA
895971 ATCACAATTAATAT
1 ATCACAATTAATAT
895985 CAAGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCACAATTAATATA
Found at i:896814 original size:17 final size:18
Alignment explanation
Indices: 896792--896841 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
896782 GATATTTTAA
896792 TTTTAAATAAATTAAT-T
1 TTTTAAATAAATTAATAT
*
896809 TTTTAAATTAATTAATAT
1 TTTTAAATAAATTAATAT
896827 TTTT-AATAAA-TAATA
1 TTTTAAATAAATTAATA
896842 AATAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 20 0.67
18 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTAAATAAATTAATAT
Found at i:897291 original size:23 final size:20
Alignment explanation
Indices: 897240--897294 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 20
897230 ATAACATCCG
897240 ATATTAATATTTCTAATAAAA
1 ATATTAATATTT-TAATAAAA
897261 A-A-TAATATTTTAAATACCAAA
1 ATATTAATATTTT-AATA--AAA
897282 ATATTAATATTTT
1 ATATTAATATTTT
897295 TGATAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.03
19 12 0.41
20 1 0.03
21 5 0.17
22 1 0.03
23 9 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTAATATTTTAATAAAA
Done.