Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 23
Found at i:5210964 original size:25 final size:25
Alignment explanation
Indices: 5210936--5211011 Score: 104
Period size: 25 Copynumber: 3.0 Consensus size: 25
5210926 TTTAAAATAA
5210936 TATTATTTTTATTTTTATTTTTATT
1 TATTATTTTTATTTTTATTTTTATT
5210961 TATTATTTTTATTTATTATTTTTA-T
1 TATTATTTTTATTT-TTATTTTTATT
5210986 TATTACTTATTTA-TTTTA-TTTTATT
1 TATTA-TT-TTTATTTTTATTTTTATT
5211011 T
1 T
5211012 TTTTAAACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.11
25 25 0.53
26 13 0.28
27 4 0.09
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (25 bp):
TATTATTTTTATTTTTATTTTTATT
Found at i:5210966 original size:13 final size:13
Alignment explanation
Indices: 5210936--5211001 Score: 100
Period size: 13 Copynumber: 5.1 Consensus size: 13
5210926 TTTAAAATAA
5210936 TATTATTTTTATT
1 TATTATTTTTATT
5210949 T-TTATTTTTATT
1 TATTATTTTTATT
5210961 TATTATTTTTATT
1 TATTATTTTTATT
5210974 TATTATTTTTA-T
1 TATTATTTTTATT
5210986 TATTACTTATTTATT
1 TATTA-TT-TTTATT
5211001 T
1 T
5211002 TATTTTATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
12 18 0.37
13 25 0.51
14 4 0.08
15 2 0.04
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTATTTTTATT
Found at i:5210985 original size:32 final size:32
Alignment explanation
Indices: 5210938--5211016 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
5210928 TAAAATAATA
* *
5210938 TTATTT-TTATTTTTATTTTTATTTA-TTATTT
1 TTATTTATTATTTTTATTATTACTTATTTA-TT
5210969 TTATTTATTATTTTTATTATTACTTATTTATT
1 TTATTTATTATTTTTATTATTACTTATTTATT
5211001 TTATTTTATT-TTTTTA
1 TTA-TTTATTATTTTTA
5211017 AACATGTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 6 0.14
32 28 0.65
33 9 0.21
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (32 bp):
TTATTTATTATTTTTATTATTACTTATTTATT
Found at i:5212223 original size:19 final size:20
Alignment explanation
Indices: 5212191--5212228 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5212181 TTTCTTCATT
5212191 TTTTTCATTAATTT-TTTCA
1 TTTTTCATTAATTTCTTTCA
5212210 TTTTT-ATTATATTTCTTTC
1 TTTTTCATTA-ATTTCTTTC
5212229 GAAATTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTCATTAATTTCTTTCA
Found at i:5212480 original size:43 final size:43
Alignment explanation
Indices: 5212416--5212511 Score: 183
Period size: 43 Copynumber: 2.2 Consensus size: 43
5212406 TGTAAGTTGT
5212416 AATTTCAATTGATCAAAGGTAAGCAATTTAAAATGAATTTTAA
1 AATTTCAATTGATCAAAGGTAAGCAATTTAAAATGAATTTTAA
*
5212459 AATTTCAATTGATCAATGGTAAGCAATTTAAAATGAATTTTAA
1 AATTTCAATTGATCAAAGGTAAGCAATTTAAAATGAATTTTAA
5212502 AATTTCAATT
1 AATTTCAATT
5212512 TAAATTTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (43 bp):
AATTTCAATTGATCAAAGGTAAGCAATTTAAAATGAATTTTAA
Found at i:5212487 original size:24 final size:24
Alignment explanation
Indices: 5212416--5212487 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
5212406 TGTAAGTTGT
*
5212416 AATTTCAATTGATCAAAGGTAAGC
1 AATTTCAATTGATCAATGGTAAGC
* * **
5212440 AATTT-AA--AATGAATTTTAA--
1 AATTTCAATTGATCAATGGTAAGC
5212459 AATTTCAATTGATCAATGGTAAGC
1 AATTTCAATTGATCAATGGTAAGC
5212483 AATTT
1 AATTT
5212488 AAAATGAATT
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
19 5 0.15
20 2 0.06
21 7 0.21
22 8 0.24
23 2 0.06
24 10 0.29
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (24 bp):
AATTTCAATTGATCAATGGTAAGC
Found at i:5213154 original size:3 final size:3
Alignment explanation
Indices: 5213148--5213182 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
5213138 AATAATAATA
5213148 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT A
5213183 CCTACCCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5217459 original size:19 final size:18
Alignment explanation
Indices: 5217406--5217463 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
5217396 AATCAAGAAC
*
5217406 AAAAAGAAAAAAAAAAGA
1 AAAAAGAAAAAAAAAATA
* *
5217424 AAAAAGTAAAGAGAAAATA
1 AAAAAG-AAAAAAAAAATA
*
5217443 AAAAAGAGAAACAAAAATA
1 AAAAAGA-AAAAAAAAATA
5217462 AA
1 AA
5217464 GGAAAAGGCG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 7 0.22
19 25 0.78
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAATA
Found at i:5219168 original size:85 final size:85
Alignment explanation
Indices: 5218920--5219149 Score: 354
Period size: 85 Copynumber: 2.7 Consensus size: 85
5218910 GAATCCAGTT
* * *
5218920 TAGCATAGCTCAAGGCGAGAAGGGTTACCTGTCAACAAAATCCTTCGAGTTCGATTCTA-TCAAC
1 TAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAAC
5218984 TCAAGGGCATATCAAATTAA
66 TCAAGGGCATATCAAATTAA
* * * * * *
5219004 CATCATAGCTCAAGGCGAGAATGGCTATCTGTCAACAAAAGCCTTCGAGTTTGATTCCATTCAAC
1 TAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAAC
5219069 TCAAGGGCATATCAAATTAA
66 TCAAGGGCATATCAAATTAA
* *
5219089 TAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAAACTTTCGAGTTCGATTCCATT
1 TAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATT
5219150 TAGCTCGAAG
Statistics
Matches: 129, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 51 0.40
85 78 0.60
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (85 bp):
TAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAAC
TCAAGGGCATATCAAATTAA
Found at i:5219626 original size:3 final size:3
Alignment explanation
Indices: 5219620--5219659 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5219610 AATAATAATA
5219620 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5219660 CCAACCCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5220324 original size:30 final size:30
Alignment explanation
Indices: 5220283--5220340 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5220273 ATTTGGTCCT
5220283 TTAACTTTCTATTGTTTGCTATTTTAGTCA
1 TTAACTTTCTATTGTTTGCTATTTTAGTCA
* *
5220313 TTAAGTTTCTATTTTTTGCTATTTTAGT
1 TTAACTTTCTATTGTTTGCTATTTTAGT
5220341 ATTTTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.60
Consensus pattern (30 bp):
TTAACTTTCTATTGTTTGCTATTTTAGTCA
Found at i:5220359 original size:30 final size:28
Alignment explanation
Indices: 5220282--5220397 Score: 74
Period size: 30 Copynumber: 3.9 Consensus size: 28
5220272 CATTTGGTCC
*
5220282 TTTAACTTTCTATTGTTTGCTATTTTAGTCA
1 TTTAAATTT-TATT-TTTGCTATTTTAGT-A
*
5220313 -TTAAGTTTCTATTTTTTGCTATTTTAGTA
1 TTTAAATTT-TA-TTTTTGCTATTTTAGTA
* * *
5220342 TTTTAAATGTTTATTTTTGCGA-TTCAGTCC
1 -TTTAAAT-TTTATTTTTGCTATTTTAGT-A
* *
5220372 TTTAAATTTTTATTTATGTTATTTTA
1 TTTAAA-TTTTATTTTTGCTATTTTA
5220398 ATCCTTTAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
29 22 0.32
30 36 0.52
31 9 0.13
32 2 0.03
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (28 bp):
TTTAAATTTTATTTTTGCTATTTTAGTA
Found at i:5225221 original size:2 final size:2
Alignment explanation
Indices: 5225216--5225255 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5225206 ACACACACAC
5225216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5225256 TGGAACAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5227963 original size:42 final size:42
Alignment explanation
Indices: 5227916--5228006 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
5227906 GTGCATGGCG
5227916 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
1 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
5227958 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
1 GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
5228000 GCATGGC
1 GCATGGC
5228007 TGTGCATGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.14, C:0.20, G:0.43, T:0.23
Consensus pattern (42 bp):
GCATGGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCT
Found at i:5228097 original size:29 final size:27
Alignment explanation
Indices: 5228030--5228112 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 27
5228020 TGCAACGTGG
5228030 GTAGGTCGCCAGGGAATCCCACGACATT
1 GTAGGTCGCCAGGG-ATCCCACGACATT
*
5228058 GTAGGTCGCCAGGGCATCCCAGCGATATT
1 GTAGGTCGCCAGGG-ATCCCA-CGACATT
5228087 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTCGCC-AGGGATCCC-ACGAC
5228113 CTATGCCTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 20 0.41
29 24 0.49
30 5 0.10
ACGTcount: A:0.24, C:0.29, G:0.30, T:0.17
Consensus pattern (27 bp):
GTAGGTCGCCAGGGATCCCACGACATT
Found at i:5228195 original size:12 final size:11
Alignment explanation
Indices: 5228175--5228210 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
5228165 GAAATCAGCT
5228175 GCATTATTGCA
1 GCATTATTGCA
*
5228186 GCACTTATTGCT
1 GCA-TTATTGCA
5228198 GCATTATTGCA
1 GCATTATTGCA
5228209 GC
1 GC
5228211 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:5228426 original size:8 final size:9
Alignment explanation
Indices: 5228396--5228433 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5228386 GGTAAGTTTT
5228396 TTTTAATTA
1 TTTTAATTA
5228405 TTTTAATTA
1 TTTTAATTA
*
5228414 GTTT-ATTA
1 TTTTAATTA
5228422 TTTTAAATTA
1 TTTT-AATTA
5228432 TT
1 TT
5228434 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:5228572 original size:27 final size:27
Alignment explanation
Indices: 5228520--5228577 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
5228510 TAAAAAAAAA
*
5228520 TTAATTAGTGTTTAGTTAGTCTAATAT
1 TTAATTAGTGTTTAGTTAGTCTAATAG
5228547 TTAATTAGT-TTGTAGTTAGT-TAAATAG
1 TTAATTAGTGTT-TAGTTAGTCT-AATAG
5228574 TTAA
1 TTAA
5228578 GTTATATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (27 bp):
TTAATTAGTGTTTAGTTAGTCTAATAG
Found at i:5228684 original size:35 final size:38
Alignment explanation
Indices: 5228607--5228684 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 38
5228597 TTTATATTAT
* ** *
5228607 ATAAAAAATTAGTTTATTAGTAGTTTAAGTTTTATTATA
1 ATAAAAAATTAGTTTATTA-TAGTTTAAGTTATAAAAGA
5228646 ATAAAAAA-TAGTTTA-T-TAGTTTAAGTTATAAAAGA
1 ATAAAAAATTAGTTTATTATAGTTTAAGTTATAAAAGA
5228681 ATAA
1 ATAA
5228685 TTATTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 19 0.54
37 1 0.03
38 7 0.20
39 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (38 bp):
ATAAAAAATTAGTTTATTATAGTTTAAGTTATAAAAGA
Found at i:5228794 original size:21 final size:22
Alignment explanation
Indices: 5228760--5228809 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
5228750 ACAAAAAATT
5228760 AGTTA-ATTAGTTGTTAGTTTA
1 AGTTATATTAGTTGTTAGTTTA
5228781 AGTTATATTA-TTGTTAGTTTA
1 AGTTATATTAGTTGTTAGTTTA
5228802 AGTTATAT
1 AGTTATAT
5228810 CATATAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (22 bp):
AGTTATATTAGTTGTTAGTTTA
Found at i:5229060 original size:29 final size:29
Alignment explanation
Indices: 5228985--5229087 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 29
5228975 ATTAGTTAAT
*
5228985 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT--TAAATTAT-ATTAAAGAA
* *
5229016 TCA-TTTATTAATTTAATTTATATTAAAGAA
1 T-AGTTTATT-AGTTAAATTATATTAAAGAA
*
5229046 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAGTTTATTAGTTAA-ATTATATTAAAGAA
5229076 TAG-TTATTAGTT
1 TAGTTTATTAGTT
5229088 GTTTAAGGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
29 21 0.34
30 32 0.52
31 6 0.10
32 3 0.05
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.48
Consensus pattern (29 bp):
TAGTTTATTAGTTAAATTATATTAAAGAA
Found at i:5230386 original size:24 final size:24
Alignment explanation
Indices: 5230357--5230403 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5230347 TTTAATTATT
*
5230357 ATTTAAATTAACTATATTATTTTG
1 ATTTAAATAAACTATATTATTTTG
* *
5230381 ATTTAAATAAATTTTATTATTTT
1 ATTTAAATAAACTATATTATTTT
5230404 TGTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTAAATAAACTATATTATTTTG
Found at i:5231409 original size:14 final size:14
Alignment explanation
Indices: 5231390--5231437 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
5231380 TTCAAGTCGT
5231390 AAATCATTACTATC
1 AAATCATTACTATC
5231404 AAATCATTAC--T-
1 AAATCATTACTATC
*
5231415 AAATCATTAATATC
1 AAATCATTACTATC
5231429 AAATCATTA
1 AAATCATTA
5231438 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:5231462 original size:49 final size:52
Alignment explanation
Indices: 5231406--5232093 Score: 523
Period size: 60 Copynumber: 12.4 Consensus size: 52
5231396 TTACTATCAA
* *
5231406 ATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTA-T
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTACT
5231457 -T-ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATTACT
*
5231513 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-AATTTC-
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTACT
* *
5231564 ATTATTACT-AATCATTACTATCAAATCATTAAAAATTAATAAT-AATTTC-
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTACT
* * * *
5231613 ATTATTACT-AATCATTACTAAATCAAAT-ATCAATCATTATTAATAAT-AATTTC-
1 ATCATTACTAAATCATTACT--ATCAAATCATTAA--A-AATTAATAATAAATTACT
* *
5231666 ATTATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATT
1 ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATTACT
* *
5231724 AATCATTACTAAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATTACT
*
5231784 AATCATTACTAAATCATTACTATAAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATTACT
* *
5231844 AATCATTACTAAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATTACT
5231904 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A---A--ATTACT
5231963 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 -ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT-A----A--ATTACT
* *
5232023 AATCATTACT--ATCAAATTACTATCAAATCATTAAATATTAATAAT-AATTTC-
1 -ATCATTACTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAAATTACT
5232074 ATCATTACT-AATCATTACTA
1 ATCATTACTAAATCATTACTA
5232094 AATCTTATAA
Statistics
Matches: 574, Mismatches: 30, Indels: 68
0.85 0.04 0.10
Matches are distributed among these distances:
48 32 0.06
49 82 0.14
50 23 0.04
51 17 0.03
52 13 0.02
53 35 0.06
54 2 0.00
55 5 0.01
56 1 0.00
57 3 0.01
58 4 0.01
59 72 0.13
60 285 0.50
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (52 bp):
ATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAAATTACT
Found at i:5231637 original size:60 final size:60
Alignment explanation
Indices: 5231567--5232097 Score: 621
Period size: 60 Copynumber: 9.2 Consensus size: 60
5231557 TAATTTCATT
5231567 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
5231626 ATTACTAAATCA--AATATC-AATCATT----ATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * * * * * *
5231679 ATTACT--ATCA--AATCATTAAA-AATTAATAA-TAAT-TTCA-TT-ATTATTAATCATT
1 ATTACTAAATCATTACT-ATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * *
5231731 ACTA--AA-TCATTATTATCAAATCATTA-AAAATTATTAAT---GATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATC---ATTAAA-AATTAATAATAATTTCATTATTACTAATC
*
5231788 ATTACTAAATCATTACTATAAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
5231848 ATTACTAAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
5231908 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTT-ATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
5231967 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
5232027 ATTACT--ATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
5232087 ATTACTAAATC
1 ATTACTAAATC
5232098 TTATAAACAC
Statistics
Matches: 407, Mismatches: 34, Indels: 59
0.81 0.07 0.12
Matches are distributed among these distances:
51 10 0.02
52 23 0.06
53 40 0.10
54 2 0.00
55 7 0.02
56 5 0.01
57 31 0.08
58 11 0.03
59 67 0.16
60 208 0.51
62 3 0.01
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:5231738 original size:46 final size:48
Alignment explanation
Indices: 5231517--5231742 Score: 314
Period size: 49 Copynumber: 4.6 Consensus size: 48
5231507 ATTACTAATC
5231517 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACT-AATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATT
5231567 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATT
* *
5231616 ATTACTAATCATTACTAAATCAAAT-ATCAATCATTATTAATAATAATTTCATT
1 ATTACTAATCATTAC---ATCAAATCATTAA--A-AATTAATAATAATTTCATT
5231669 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAC-ATCAAATCATTAAAAATTAATAATAATTTCATT
*
5231718 ATTATTAATCATTAC-T-AAATCATTA
1 ATTACTAATCATTACATCAAATCATTA
5231743 TTATCAAATC
Statistics
Matches: 163, Mismatches: 7, Indels: 16
0.88 0.04 0.09
Matches are distributed among these distances:
46 9 0.06
47 1 0.01
49 90 0.55
50 11 0.07
51 14 0.09
52 5 0.03
53 33 0.20
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATTACTAATCATTACATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:5231800 original size:11 final size:11
Alignment explanation
Indices: 5231778--5231984 Score: 55
Period size: 11 Copynumber: 17.6 Consensus size: 11
5231768 TGATTTCATT
5231778 ATTACT-AATC
1 ATTACTAAATC
5231788 ATTACTAAATC
1 ATTACTAAATC
5231799 ATTACTATAAAATC
1 ATTAC--T-AAATC
* *
5231813 ATTA-AAAATT
1 ATTACTAAATC
* * *
5231823 AATAATAATTTC
1 ATTACTAA-ATC
*
5231835 ATTATTACTAATC
1 ATTACTA--AATC
5231848 ATTACTAAATC
1 ATTACTAAATC
*
5231859 ATTATTATCAAATC
1 ATTA--CT-AAATC
* *
5231873 ATTA-AAAATT
1 ATTACTAAATC
* **
5231883 ATTAATGATTTC
1 ATTACT-AAATC
*
5231895 ATTATTACTAATC
1 ATTACTA--AATC
5231908 ATTACTAAATC
1 ATTACTAAATC
5231919 ATTACTATCAAATC
1 ATTAC--T-AAATC
* *
5231933 ATTA-AAAATT
1 ATTACTAAATC
* * *
5231943 AATAATAATTTATT
1 ATTACTAA---ATC
5231957 ATTACT-AATC
1 ATTACTAAATC
5231967 ATTACTAAATC
1 ATTACTAAATC
5231978 ATTACTA
1 ATTACTA
5231985 TCAAATCATT
Statistics
Matches: 146, Mismatches: 28, Indels: 45
0.67 0.13 0.21
Matches are distributed among these distances:
10 36 0.25
11 42 0.29
12 13 0.09
13 20 0.14
14 35 0.24
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:5231812 original size:120 final size:119
Alignment explanation
Indices: 5231669--5232101 Score: 746
Period size: 120 Copynumber: 3.6 Consensus size: 119
5231659 TAATTTCATT
*
5231669 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
5231734 AAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
66 AAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
*
5231788 ATTACTAAATCATTACTATAAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
5231853 TAAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
65 TAAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
5231908 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTT-ATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* * *
5231972 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
65 TAAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
* *
5232027 ATTACT-ATCAAATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTA
1 ATTACTAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
5232091 CTAAATC-TTAT
64 CTAAATCATTAT
5232102 AAACACATAG
Statistics
Matches: 301, Mismatches: 9, Indels: 8
0.95 0.03 0.03
Matches are distributed among these distances:
117 3 0.01
119 119 0.40
120 179 0.59
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (119 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
Found at i:5231989 original size:239 final size:237
Alignment explanation
Indices: 5231669--5232101 Score: 744
Period size: 239 Copynumber: 1.8 Consensus size: 237
5231659 TAATTTCATT
*
5231669 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
* * *
5231734 AAATCATTATTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATCATTACTAAATC
66 AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT--ATC
*
5231799 -ATTACTATAAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTA
129 AATTACTATAAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTACTAAATC-TTA
5231863 TTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
193 TTATCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
5231908 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTT-ATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
5231972 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCA
65 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATC-
* *
5232037 AATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAATCTTAT
129 AATTACTATAAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTACTAAATCTTAT
5232102 AAACACATAG
Statistics
Matches: 184, Mismatches: 7, Indels: 7
0.93 0.04 0.04
Matches are distributed among these distances:
237 3 0.02
238 4 0.02
239 138 0.75
240 39 0.21
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (237 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAA
TTACTATAAAATCATTAAAAATTAATAATAATTTCATCATTACTAATCATTACTAAATCTTATTA
TCAAATCATTAAAAATTATTAATGATTTCATTATTACTAATC
Found at i:5234970 original size:28 final size:28
Alignment explanation
Indices: 5234939--5234992 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
5234929 ATAATCTAAT
*
5234939 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
5234967 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
5234993 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:5234999 original size:28 final size:28
Alignment explanation
Indices: 5234935--5234999 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
5234925 TTATATAATC
*
5234935 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
5234963 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
5234991 TAATTTATA
1 TAATATATA
5235000 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:5235002 original size:21 final size:21
Alignment explanation
Indices: 5234969--5235017 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5234959 TTAATATAAT
5234969 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
5234990 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
5235011 ATTAACT
1 A-TAACT
5235018 AAATTTCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:5235691 original size:29 final size:29
Alignment explanation
Indices: 5235652--5235754 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
5235642 GGACGCCGGC
* *
5235652 GTGCATGGCGACCTATAAGGTCGCCGGGA
1 GTGCTTGGCGACCTATAAGGTCGCTGGGA
* *
5235681 TTGCTTGGCGACCTACAAGGTCGCTGGGA
1 GTGCTTGGCGACCTATAAGGTCGCTGGGA
* * *
5235710 GTGCATGGCGACCTTGTAA-GTCGCTTGGA
1 GTGCTTGGCGACC-TATAAGGTCGCTGGGA
5235739 GTGCTTGGCGACCTAT
1 GTGCTTGGCGACCTAT
5235755 GGTTGGGTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 2 0.03
29 57 0.92
30 3 0.05
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.24
Consensus pattern (29 bp):
GTGCTTGGCGACCTATAAGGTCGCTGGGA
Found at i:5235800 original size:12 final size:12
Alignment explanation
Indices: 5235783--5235807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5235773 CCATGCACGA
5235783 CACGATCCTCGT
1 CACGATCCTCGT
5235795 CACGATCCTCGT
1 CACGATCCTCGT
5235807 C
1 C
5235808 GGGAGCCACA
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:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (12 bp):
CACGATCCTCGT
Found at i:5235822 original size:18 final size:18
Alignment explanation
Indices: 5235799--5235834 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5235789 CCTCGTCACG
5235799 ATCCTCGTCGGGAGCCAC
1 ATCCTCGTCGGGAGCCAC
5235817 ATCCTCGTCGGGAGCCAC
1 ATCCTCGTCGGGAGCCAC
5235835 GTCGTAGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.17
Consensus pattern (18 bp):
ATCCTCGTCGGGAGCCAC
Found at i:5236299 original size:14 final size:14
Alignment explanation
Indices: 5236280--5236314 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5236270 TAAAATAATT
5236280 ATATTTTCTTA-AAA
1 ATATTTTC-TAGAAA
5236294 ATATTTTCTAGAAA
1 ATATTTTCTAGAAA
5236308 ATATTTT
1 ATATTTT
5236315 ACGGTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATTTTCTAGAAA
Found at i:5236703 original size:27 final size:25
Alignment explanation
Indices: 5236668--5236757 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 25
5236658 ATTATATTAA
5236668 TATTAAATACATAAATAATATTATTCTT
1 TATTAAATA-ATAAATAATATTA-T-TT
* *
5236696 TATT-AATAATTTAATAATGTTATTT
1 TATTAAATAA-TAAATAATATTATTT
*
5236721 TATTAAATTAATAAATAATATAAATTT
1 TATTAAA-TAATAAATAATAT-TATTT
5236748 TATT-AATAAT
1 TATTAAATAAT
5236758 TTATTATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
25 10 0.19
26 14 0.26
27 25 0.47
28 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTAAATAATAAATAATATTATTT
Found at i:5236772 original size:53 final size:53
Alignment explanation
Indices: 5236668--5236772 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
5236658 ATTATATTAA
* * *
5236668 TATTAAATACATAAATAATATTATTCTTTATTAATAATTTAATAATGTTATTT
1 TATTAAATACATAAATAATATAAATCTTTATTAATAATTTAATAATATTATTT
*
5236721 TATTAAATTA-ATAAATAATATAAAT-TTTATTAATAATTTATTATATATTATT
1 TATTAAA-TACATAAATAATATAAATCTTTATTAATAATTTAATA-ATATTATT
5236773 AAAATAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
52 17 0.37
53 27 0.59
54 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (53 bp):
TATTAAATACATAAATAATATAAATCTTTATTAATAATTTAATAATATTATTT
Found at i:5236868 original size:55 final size:53
Alignment explanation
Indices: 5236747--5236868 Score: 126
Period size: 55 Copynumber: 2.3 Consensus size: 53
5236737 AATATAAATT
5236747 TTATTAATAATTT-ATT--ATATATTATTAAAATAAAAAAATATAATATCTTATA
1 TTATTAA-AATTTAATTGAATATATTATTAAAATAAAAAAATATAATATC-TATA
* * * * *
5236799 TTATTATACTTTAATTGAATATTTTATTATAATATTAAAAATATAATATC-ATA
1 TTATTAAAATTTAATTGAATATATTATTAAAATA-AAAAAATATAATATCTATA
5236852 TTATTAGAAATATTAAT
1 TTATTA-AAAT-TTAAT
5236869 AAATTTTTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
51 4 0.07
52 9 0.16
53 9 0.16
54 16 0.28
55 19 0.33
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (53 bp):
TTATTAAAATTTAATTGAATATATTATTAAAATAAAAAAATATAATATCTATA
Found at i:5241974 original size:22 final size:22
Alignment explanation
Indices: 5241952--5241992 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5241942 TCATAATTAT
5241952 TTAAAAA-ATTAAATAAAAATA
1 TTAAAAATATTAAATAAAAATA
*
5241973 TTAAAAATATTTAATAAAAA
1 TTAAAAATATTAAATAAAAA
5241993 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAATATTAAATAAAAATA
Found at i:5248142 original size:44 final size:44
Alignment explanation
Indices: 5248053--5248238 Score: 250
Period size: 44 Copynumber: 4.3 Consensus size: 44
5248043 TGGTACATTG
* ** *
5248053 TTATGGATAAATGACAAGTATATTGGT-AAATAAGCTTACGTGC
1 TTATGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
5248096 TTATAGATTAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
1 TTATGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * * *
5248140 TTATGGATAAATAGCAAGTACATTGGTAAAATAAGCTTACGAGC
1 TTATGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
5248184 TTATGGATTAATGGTAAGTATTTTGGTAAAATAAGCTTATGAGC
1 TTATGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
5248228 TTATGG-TTAAT
1 TTATGGATTAAT
5248239 AAATGGTAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
43 27 0.22
44 97 0.78
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (44 bp):
TTATGGATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:5248201 original size:88 final size:87
Alignment explanation
Indices: 5248053--5248233 Score: 283
Period size: 88 Copynumber: 2.1 Consensus size: 87
5248043 TGGTACATTG
* *
5248053 TTATGGATAAATGACAAGTATATTGGTAAATAAGCTTACGTGCTTATAGATTAATGGTAAGTATA
1 TTATGGATAAATGACAAGTACATTGGTAAATAAGCTTACGAGCTTATAGATTAATGGTAAGTATA
5248118 ATGGTAAAATAAGCTTACGAGC
66 ATGGTAAAATAAGCTTACGAGC
*
5248140 TTATGGATAAAT-AGCAAGTACATTGGTAAAATAAGCTTACGAGCTTATGGATTAATGGTAAGTA
1 TTATGGATAAATGA-CAAGTACATTGGT-AAATAAGCTTACGAGCTTATAGATTAATGGTAAGTA
** *
5248204 TTTTGGTAAAATAAGCTTATGAGC
64 TAATGGTAAAATAAGCTTACGAGC
5248228 TTATGG
1 TTATGG
5248234 TTAATAAATG
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
86 1 0.01
87 24 0.28
88 61 0.71
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.33
Consensus pattern (87 bp):
TTATGGATAAATGACAAGTACATTGGTAAATAAGCTTACGAGCTTATAGATTAATGGTAAGTATA
ATGGTAAAATAAGCTTACGAGC
Found at i:5248744 original size:22 final size:22
Alignment explanation
Indices: 5248702--5248757 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
5248692 GATGCACTAT
*
5248702 TCACTATTCACGGGTAATGTTCA
1 TCACTATTCA-TGGTAATGTTCA
* *
5248725 TCACTGTTCATGGTACTGTTCA
1 TCACTATTCATGGTAATGTTCA
5248747 TCACTATTCAT
1 TCACTATTCAT
5248758 AAAAAAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (22 bp):
TCACTATTCATGGTAATGTTCA
Found at i:5250383 original size:18 final size:16
Alignment explanation
Indices: 5250332--5250376 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 16
5250322 ATTTCCCCCC
5250332 AATTCTCTTTCATCCCT
1 AATTCTC-TTCATCCCT
5250349 AATTGCTGCTTCATCCCT
1 AATT-CT-CTTCATCCCT
5250367 AATTCTCTTC
1 AATTCTCTTC
5250377 CAATCCCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.15
17 6 0.23
18 15 0.58
19 1 0.04
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.44
Consensus pattern (16 bp):
AATTCTCTTCATCCCT
Found at i:5250388 original size:18 final size:16
Alignment explanation
Indices: 5250328--5250388 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 16
5250318 GTTAATTTCC
5250328 CCCCAATTCTCTTTCAT
1 CCCCAATTCTC-TTCAT
*
5250345 CCCTAATTGCTGCTTCAT
1 CCCCAATT-CT-CTTCAT
*
5250363 CCCTAATTCTCTTCCAAT
1 CCCCAATTCTCTT-C-AT
5250381 CCCCAATT
1 CCCCAATT
5250389 ACTTCCCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.08
17 10 0.26
18 24 0.63
19 1 0.03
ACGTcount: A:0.20, C:0.39, G:0.03, T:0.38
Consensus pattern (16 bp):
CCCCAATTCTCTTCAT
Found at i:5252162 original size:32 final size:32
Alignment explanation
Indices: 5252117--5252220 Score: 156
Period size: 32 Copynumber: 3.2 Consensus size: 32
5252107 CAACTGCTTT
*
5252117 GCATTATCTAAATAT-AGCTTTGACTCGACTCA
1 GCATTATCCAAATATGA-CTTTGACTCGACTCA
5252149 GCATTATCCAAATATGACTTTGACTCGACTCA
1 GCATTATCCAAATATGACTTTGACTCGACTCA
* **
5252181 GCATTATCCAAATATGACTTTGACTCTACTGT
1 GCATTATCCAAATATGACTTTGACTCGACTCA
5252213 GCATTATC
1 GCATTATC
5252221 TATATGCAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 66 0.99
33 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (32 bp):
GCATTATCCAAATATGACTTTGACTCGACTCA
Found at i:5261068 original size:20 final size:20
Alignment explanation
Indices: 5261043--5261092 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5261033 TTTTCCCAAT
*
5261043 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
5261063 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
5261083 TCGCAATGCG
1 TCGCAATGCG
5261093 CATGCGATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:5261155 original size:20 final size:21
Alignment explanation
Indices: 5261130--5261181 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
5261120 TAATAAAAAA
*
5261130 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTAACTT
5261150 TCGCAAC-ACGATACTAACTT
1 TCGCAACGACGATACTAACTT
5261170 TCGCAACG-CGAT
1 TCGCAACGACGAT
5261182 TTACTTAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
TCGCAACGACGATACTAACTT
Found at i:5261743 original size:19 final size:19
Alignment explanation
Indices: 5261697--5261761 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
5261687 CGAGAATGAG
* *
5261697 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
* *
5261717 TATTGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
5261736 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
5261755 AATCGCA
1 AATCGCA
5261762 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
19 28 0.76
20 9 0.24
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:5261834 original size:39 final size:38
Alignment explanation
Indices: 5261757--5261927 Score: 163
Period size: 39 Copynumber: 4.6 Consensus size: 38
5261747 GAAACCAAAA
* *
5261757 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
5261795 TCGCGTTGCGATTTTAATTTCGCAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
* * * **
5261834 TCGCGTTGCGA--TT-GTCT-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
** * *
5261867 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTAATTT-CGCGTTGCGATTTTCATT
* *
5261906 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTAATTTC
5261928 AACCAAAAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
33 23 0.21
35 2 0.02
36 4 0.04
37 2 0.02
38 22 0.20
39 39 0.36
40 17 0.16
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:5261904 original size:20 final size:19
Alignment explanation
Indices: 5261757--5261927 Score: 190
Period size: 19 Copynumber: 9.1 Consensus size: 19
5261747 GAAACCAAAA
*
5261757 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5261776 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5261795 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
5261814 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
5261834 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
5261850 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
5261867 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
5261886 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5261906 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5261926 TC
1 TC
5261928 AACCAAAAGA
Statistics
Matches: 133, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 68 0.51
20 50 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5264007 original size:21 final size:21
Alignment explanation
Indices: 5263983--5264049 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5263973 TCATTCCTCG
5263983 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5264004 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5264025 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5264046 AGAG
1 AGAG
5264050 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5264007 original size:42 final size:42
Alignment explanation
Indices: 5263961--5264049 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
5263951 CCTTTTGTTG
* *
5263961 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
5264003 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
5264045 AAGAG
1 AAGAG
5264050 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:5265421 original size:14 final size:14
Alignment explanation
Indices: 5265402--5265437 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5265392 ATTGTTTAAT
5265402 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5265416 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
5265430 TGATTTGT
1 TGATTTGT
5265438 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:5265638 original size:19 final size:19
Alignment explanation
Indices: 5265616--5265733 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
5265606 CGAAATTAAA
5265616 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5265635 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
5265650 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5265668 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5265683 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
5265701 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
5265720 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
5265734 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:5265662 original size:33 final size:33
Alignment explanation
Indices: 5265620--5265713 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
5265610 ATTAAATTCG
5265620 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
5265653 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
5265686 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5265714 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:5269399 original size:14 final size:14
Alignment explanation
Indices: 5269380--5269416 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5269370 CATCAATTAA
5269380 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5269394 ACAAATCATCTTTT
1 ACAAATCAACATTT
5269408 ACAAATCAA
1 ACAAATCAA
5269417 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:5269805 original size:20 final size:20
Alignment explanation
Indices: 5269780--5269830 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5269770 ATTCATTTGA
*
5269780 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
5269800 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
5269820 TTATCGCAACG
1 CTATCGCAACG
5269831 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:5269880 original size:14 final size:15
Alignment explanation
Indices: 5269860--5269932 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
5269850 TGAAAATCGC
5269860 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
5269875 -TTGCGATTTTCAGTTCG
1 ATTGCGATTTTC---TCG
*
5269892 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
5269910 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
5269926 -TTGCGAT
1 ATTGCGAT
5269933 AGCCATTTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:5269909 original size:18 final size:18
Alignment explanation
Indices: 5269856--5269920 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
5269846 GAAATGAAAA
*
5269856 TCGCATTGCGATTT--TC
1 TCGCATTGCGATTTCATT
*
5269872 TCG--TTGCGATTTTCAGT
1 TCGCATTGCGA-TTTCATT
5269889 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
5269907 TCGCATTGCGATTT
1 TCGCATTGCGATTT
5269921 TCTCGTTGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.15
15 3 0.07
16 3 0.07
17 3 0.07
18 20 0.49
19 6 0.15
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:5270058 original size:14 final size:14
Alignment explanation
Indices: 5270039--5270075 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5270029 CATCAATTAA
5270039 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5270053 ACAAATCATCTTTT
1 ACAAATCAACATTT
5270067 ACAAATCAA
1 ACAAATCAA
5270076 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:5271969 original size:20 final size:19
Alignment explanation
Indices: 5271934--5272000 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
5271924 GAAACTTAAA
5271934 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
5271953 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
5271973 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
5271992 ATCGCAACG
1 ATCGCAACG
5272001 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5272008 original size:14 final size:14
Alignment explanation
Indices: 5271989--5272046 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5271979 ATGCGAAATG
5271989 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5272003 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
5272019 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
5272035 AAAATCGCAACG
1 AAAATCGCAACG
5272047 CGAAACACAA
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:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5272031 original size:32 final size:33
Alignment explanation
Indices: 5271973--5272051 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
5271963 GGAAATGGCT
*
5271973 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
5272006 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
5272038 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
5272052 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:5272080 original size:19 final size:17
Alignment explanation
Indices: 5272058--5272153 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
5272048 GAAACACAAA
5272058 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
5272077 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
5272093 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
5272109 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
5272125 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
5272142 TCGCATTGCGAT
1 TCGC-TTGCGAT
5272154 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:5272099 original size:14 final size:14
Alignment explanation
Indices: 5272080--5272137 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5272070 TTTCATTTCG
5272080 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5272094 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
5272110 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
5272126 CGTTGCGATTTT
1 CGTTGCGATTTT
5272138 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5272144 original size:33 final size:33
Alignment explanation
Indices: 5272063--5272153 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
5272053 ACAAATCGCA
5272063 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
5272096 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
5272128 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
5272154 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:5272172 original size:20 final size:19
Alignment explanation
Indices: 5272138--5272192 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5272128 TTGCGATTTT
*
5272138 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5272157 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5272177 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5272193 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5272691 original size:18 final size:18
Alignment explanation
Indices: 5272665--5272709 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5272655 GTCGATCAGA
*
5272665 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
5272683 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
5272701 TGATGGCTC
1 TGATGGCTC
5272710 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:5274050 original size:20 final size:20
Alignment explanation
Indices: 5274025--5274062 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5274015 AATAGTTTCT
5274025 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
5274045 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
5274063 TATCGCAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:5274360 original size:22 final size:22
Alignment explanation
Indices: 5274320--5274363 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5274310 GATTTAGATA
*
5274320 GACGGATTTCGCCGAAGATGGG
1 GACGGATTTCGCAGAAGATGGG
5274342 GACGGATTTCGTCAG-AGATGGG
1 GACGGATTTCG-CAGAAGATGGG
5274364 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCAGAAGATGGG
Found at i:5274598 original size:20 final size:20
Alignment explanation
Indices: 5274549--5274600 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
5274539 GATTATGTAT
*
5274549 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
5274569 -ATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
5274588 TATCTCGTTGCGA
1 TATCGCGTTGCGA
5274601 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:5274634 original size:20 final size:20
Alignment explanation
Indices: 5274529--5274642 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
5274519 CGCTTTGAAA
*
5274529 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
5274550 ATCGCGTTGCGAAAGTCAG-
1 ATCGCATTGCGATAGTCAGT
* * *
5274569 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
5274589 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
5274610 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5274630 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5274643 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
19 20 0.27
20 30 0.41
21 24 0.32
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5274661 original size:41 final size:41
Alignment explanation
Indices: 5274570--5274704 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
5274560 GAAAGTCAGA
* * * ** *
5274570 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
5274610 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
5274652 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
5274693 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5274705 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:5274675 original size:20 final size:20
Alignment explanation
Indices: 5274631--5274723 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
5274621 ATAGTCAGTA
* **
5274631 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
5274652 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
5274672 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
5274693 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
5274713 TCGCATTGCGA
1 TCGCATTGCGA
5274724 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:5274705 original size:41 final size:41
Alignment explanation
Indices: 5274631--5274726 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
5274621 ATAGTCAGTA
*
5274631 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
5274672 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
5274713 TCGCATTGCGAATT
1 TCGCATTGCGAATT
5274727 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:5279383 original size:23 final size:23
Alignment explanation
Indices: 5279357--5279401 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5279347 TATACTCTAA
*
5279357 CTCGTGTTACATTTATTAATTAG
1 CTCGTGTTAAATTTATTAATTAG
5279380 CTCGTGTTAAATTTATTAATTA
1 CTCGTGTTAAATTTATTAATTA
5279402 ACTCTCGTAG
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:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (23 bp):
CTCGTGTTAAATTTATTAATTAG
Found at i:5279704 original size:25 final size:23
Alignment explanation
Indices: 5279676--5279722 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
5279666 AATGAATAAG
*
5279676 ATTAGTATATAAATTATAAATTATA
1 ATTAATATATAAA-TAT-AATTATA
*
5279701 ATTAATATATTAATATAATTAT
1 ATTAATATATAAATATAATTAT
5279723 TATCAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAATATATAAATATAATTATA
Found at i:5280326 original size:41 final size:41
Alignment explanation
Indices: 5280281--5280376 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
5280271 TGATTTTCCC
*
5280281 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGA
*
5280322 AATTCGCAATGCGAATAAGTAAATCGCAAATCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGA
*
5280363 AAATCGCAATGCGA
1 AATTCGCAATGCGA
5280377 TACTGACTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGA
Found at i:5280330 original size:21 final size:20
Alignment explanation
Indices: 5280284--5280376 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
5280274 TTTTCCCAAT
*
5280284 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
5280304 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
5280324 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
**
5280345 TCGCAAAT-CGAATTGGGAAAA
1 TCGC-AATGCGAATAAGG-AAA
5280366 TCGCAATGCGA
1 TCGCAATGCGA
5280377 TACTGACTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:5280411 original size:21 final size:20
Alignment explanation
Indices: 5280362--5280412 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5280352 TCGAATTGGG
* *
5280362 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
5280382 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
5280403 AAAATCGCAA
1 AAAATCGCAA
5280413 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:5280432 original size:20 final size:21
Alignment explanation
Indices: 5280407--5280458 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
5280397 TAATAAAAAA
*
5280407 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTAACTT
5280427 TCGCAAC-ACGATACTAACTT
1 TCGCAACGACGATACTAACTT
5280447 TCGCAACG-CGAT
1 TCGCAACGACGAT
5280459 TTACTTAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
TCGCAACGACGATACTAACTT
Found at i:5280439 original size:41 final size:41
Alignment explanation
Indices: 5280362--5280439 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
5280352 TCGAATTGGG
* * **
5280362 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
5280403 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
5280440 CTAACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:5280997 original size:19 final size:19
Alignment explanation
Indices: 5280954--5281018 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
5280944 CGAGAATGAG
* *
5280954 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
5280974 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
5280993 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
5281012 AATCGCA
1 AATCGCA
5281019 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:5281036 original size:19 final size:19
Alignment explanation
Indices: 5281014--5281184 Score: 181
Period size: 19 Copynumber: 9.1 Consensus size: 19
5281004 GAAACCAAAA
*
5281014 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5281033 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
5281052 TTGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
5281071 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
5281091 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
5281107 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
5281124 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
5281143 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5281163 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5281183 TC
1 TC
5281185 AACAAAAGAC
Statistics
Matches: 131, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 66 0.50
20 50 0.38
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5281091 original size:39 final size:38
Alignment explanation
Indices: 5281014--5281184 Score: 154
Period size: 39 Copynumber: 4.6 Consensus size: 38
5281004 GAAACCAAAA
* *
5281014 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
*
5281052 TTGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
* * * **
5281091 TCGCGTTGCGA--TT-GTCT-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
** * *
5281124 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTAATTT-CGCGTTGCGATTTTCATT
* *
5281163 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTAATTTC
5281185 AACAAAAGAC
Statistics
Matches: 107, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
33 23 0.21
35 2 0.02
36 4 0.04
37 2 0.02
38 21 0.20
39 38 0.36
40 17 0.16
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:5283253 original size:21 final size:21
Alignment explanation
Indices: 5283229--5283295 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5283219 TCATTCCTCG
5283229 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5283250 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5283271 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5283292 AGAG
1 AGAG
5283296 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5283253 original size:42 final size:42
Alignment explanation
Indices: 5283173--5283295 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
5283163 GCCCGACTCG
* * *
5283173 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGACC
* * * *
5283215 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGACC
* * ** * *
5283257 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
5283296 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGACC
Found at i:5284665 original size:14 final size:14
Alignment explanation
Indices: 5284646--5284681 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5284636 ATTGTTTAAT
5284646 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5284660 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
5284674 TGATTTGT
1 TGATTTGT
5284682 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:5284882 original size:19 final size:19
Alignment explanation
Indices: 5284860--5284977 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
5284850 CGAAATTAAA
5284860 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5284879 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
5284894 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5284912 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5284927 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
5284945 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
5284964 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
5284978 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:5284906 original size:33 final size:33
Alignment explanation
Indices: 5284864--5284957 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
5284854 ATTAAATTCG
5284864 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
5284897 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
5284930 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5284958 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:5287257 original size:12 final size:12
Alignment explanation
Indices: 5287240--5287264 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5287230 TCTTCGGGGA
5287240 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5287252 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5287264 C
1 C
5287265 AGGATTATAT
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:5288631 original size:14 final size:14
Alignment explanation
Indices: 5288612--5288648 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5288602 CATCAATTAA
5288612 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5288626 ACAAATCATCTTTT
1 ACAAATCAACATTT
5288640 ACAAATCAA
1 ACAAATCAA
5288649 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
Done.