Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 37
Found at i:4119305 original size:17 final size:17
Alignment explanation
Indices: 4119246--4119306 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
4119236 TCATAAAACT
4119246 TAATATTATTATTTTTA
1 TAATATTATTATTTTTA
*
4119263 AAATATT-TTATTTATTA
1 TAATATTATTATTT-TTA
4119280 TTAA-A-TATTATTTTTA
1 -TAATATTATTATTTTTA
*
4119296 TAATTTTATTA
1 TAATATTATTA
4119307 ATAAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 3 0.08
16 10 0.28
17 21 0.58
18 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATATTATTATTTTTA
Found at i:4119442 original size:23 final size:23
Alignment explanation
Indices: 4119393--4119461 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
4119383 GTGTTACATT
* * * **
4119393 ATATTTTAAAAATATTAAGTATT
1 ATATTTTAAATATATTTATTAAA
4119416 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
4119439 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
4119462 TATTAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 27 0.71
24 11 0.29
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:4119499 original size:19 final size:19
Alignment explanation
Indices: 4119431--4119499 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
4119421 TTAAATATAT
*
4119431 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATT-TA
**
4119450 TTATTATATTAATATTAAATA
1 TTATTA-A-TAATATTATTTA
*
4119471 -TATAAATAATATTATTTA
1 TTATTAATAATATTATTTA
4119489 TTATTAATAAT
1 TTATTAATAAT
4119500 TTAATATTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 10 0.26
19 16 0.41
20 5 0.13
21 1 0.03
22 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (19 bp):
TTATTAATAATATTATTTA
Found at i:4119504 original size:24 final size:24
Alignment explanation
Indices: 4119472--4119613 Score: 75
Period size: 24 Copynumber: 6.0 Consensus size: 24
4119462 TATTAAATAT
4119472 ATAA-ATAATATTATTTATTATTA
1 ATAATATAATATTATTTATTATTA
* * * *
4119495 ATAATTTAATATTCTATGA-AATTA
1 ATAATATAATATTAT-TTATTATTA
*
4119519 ATAA-ATAATATAATTT-TT-TTA
1 ATAATATAATATTATTTATTATTA
* * *
4119540 ATAATTTATTA-TATATTATTAAAATA
1 ATAATATAATATTAT-TTATT--ATTA
* * *
4119566 AAAATATAATATAATATATTATT-
1 ATAATATAATATTATTTATTATTA
4119589 ATAATATAATTGATTATTT-TTATTA
1 ATAATATAA-T-ATTATTTATTATTA
4119614 TATTATTAAA
Statistics
Matches: 84, Mismatches: 22, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
21 9 0.11
22 7 0.08
23 21 0.25
24 24 0.29
25 7 0.08
26 14 0.17
27 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
ATAATATAATATTATTTATTATTA
Found at i:4119637 original size:22 final size:23
Alignment explanation
Indices: 4119609--4119677 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
4119599 TGATTATTTT
4119609 TATTATATTATTAAAAATA-TAA
1 TATTATATTATTAAAAATATTAA
*
4119631 TATTATATTATTAGAAATATTAA
1 TATTATATTATTAAAAATATTAA
* * *
4119654 TAAATATATT-TTAAATATTTTAA
1 T-ATTATATTATTAAAAATATTAA
4119677 T
1 T
4119678 TAAAATGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 18 0.45
23 15 0.38
24 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
TATTATATTATTAAAAATATTAA
Found at i:4119912 original size:42 final size:42
Alignment explanation
Indices: 4119856--4119943 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
4119846 TTCTACCAAC
** *
4119856 CAAACACTGGAAAATATTTTTCGAAAAATAAATTACGTAAAA
1 CAAACACTGGAAAATATTTTTAAAAAAACAAATTACGTAAAA
* *
4119898 CAAACA-TGAGAAAATATTTTTAAAAAAACGAATTACGTGAAA
1 CAAACACTG-GAAAATATTTTTAAAAAAACAAATTACGTAAAA
4119940 CAAA
1 CAAA
4119944 AATAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (42 bp):
CAAACACTGGAAAATATTTTTAAAAAAACAAATTACGTAAAA
Found at i:4121775 original size:35 final size:35
Alignment explanation
Indices: 4121729--4121818 Score: 162
Period size: 35 Copynumber: 2.6 Consensus size: 35
4121719 GTTTTTAAAT
4121729 AAAATTTGAGTTATAAAAAAAGATTTAAATAATTC
1 AAAATTTGAGTTATAAAAAAAGATTTAAATAATTC
* *
4121764 AAATTTTGAGTTATAAAATAAGATTTAAATAATTC
1 AAAATTTGAGTTATAAAAAAAGATTTAAATAATTC
4121799 AAAATTTGAGTTATAAAAAA
1 AAAATTTGAGTTATAAAAAA
4121819 TATGGAGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAATTTGAGTTATAAAAAAAGATTTAAATAATTC
Found at i:4133429 original size:34 final size:36
Alignment explanation
Indices: 4133382--4133483 Score: 154
Period size: 37 Copynumber: 2.9 Consensus size: 36
4133372 TTTCGTCCTA
* *
4133382 CTAGGATTGAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
4133417 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
4133452 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
4133484 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:4133467 original size:37 final size:35
Alignment explanation
Indices: 4133382--4133481 Score: 148
Period size: 34 Copynumber: 2.8 Consensus size: 35
4133372 TTTCGTCCTA
* * *
4133382 CTAGGATTGAAACTCCTAAAAATATGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
4133417 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAA-TTT
4133452 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
4133482 GAGTTCTACT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 28 0.47
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:4133507 original size:37 final size:37
Alignment explanation
Indices: 4133379--4133517 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 37
4133369 ATTTTTCGTC
* * *
4133379 CTACTAGGATTGAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
4133416 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
4133450 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * * *
4133487 CTACTATTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4133518 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
34 30 0.34
35 1 0.01
36 1 0.01
37 55 0.63
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:4133818 original size:23 final size:22
Alignment explanation
Indices: 4133787--4133850 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
4133777 TTTTCTTTTT
4133787 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
4133810 ATTTTATGT-AT-TTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
4133832 -TTTA-GTATATATTTTTTTT
1 TTTTATGTA-ATATTTTTTTT
4133851 TTTAGATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
19 2 0.06
20 4 0.11
21 10 0.28
22 12 0.33
23 4 0.11
24 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:4133821 original size:20 final size:20
Alignment explanation
Indices: 4133797--4133850 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
4133787 TTTTCATGTA
4133797 ATATTTTTTTTACATTT-TAT
1 ATATTTTTTTTAC-TTTATAT
*
4133817 GTATTTCTTTTTTACTTTAGTAT
1 ATA-TT-TTTTTTACTTTA-TAT
4133840 ATATTTTTTTT
1 ATATTTTTTTT
4133851 TTTAGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 2 0.07
21 11 0.39
22 10 0.36
23 5 0.18
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (20 bp):
ATATTTTTTTTACTTTATAT
Found at i:4133851 original size:23 final size:22
Alignment explanation
Indices: 4133800--4133866 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
4133790 TCATGTAATA
*
4133800 TTTTTTTTACATTTTATGTATT
1 TTTTTTTTACATTTTATATATT
*
4133822 TCTTTTTTAC-TTTAGTATATATTT
1 TTTTTTTTACATTT--TATATA-TT
* *
4133846 TTTTTTTTAGATTATATATAT
1 TTTTTTTTACATTTTATATAT
4133867 AAATATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 3 0.08
22 10 0.28
23 11 0.31
24 10 0.28
25 2 0.06
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTTTTTACATTTTATATATT
Found at i:4133908 original size:35 final size:32
Alignment explanation
Indices: 4133864--4133948 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
4133854 AGATTATATA
*
4133864 TATAAATATATTATTTTTTATCAGTTTTATTAATT
1 TATATATATATTATTTTTTA--A-TTTTATTAATT
* *
4133899 TATATATATATTTACTTTTTAATTTTTTTAATT
1 TATATATATA-TTATTTTTTAATTTTATTAATT
4133932 T-TATATATATTATTTTT
1 TATATATATATTATTTTT
4133949 ACTTTTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 7 0.16
32 8 0.18
33 11 0.24
34 1 0.02
35 9 0.20
36 9 0.20
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (32 bp):
TATATATATATTATTTTTTAATTTTATTAATT
Found at i:4133939 original size:30 final size:31
Alignment explanation
Indices: 4133888--4133978 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 31
4133878 TTTTTATCAG
*
4133888 TTTTATTAATTTATATATATATTTACTTTTTAAT
1 TTTTATTAA--TATTTATATATTTA-TTTTTAAT
*
4133922 TTTT-TTAAT-TTTATATATATTATTTTTACT
1 TTTTATTAATATTTATATAT-TTATTTTTAAT
* * *
4133952 TTTTATTATTATTTATTTATTTGTTTT
1 TTTTATTAATATTTATATATTTATTTT
4133979 ATTTCTATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
30 19 0.39
31 14 0.29
32 8 0.16
33 4 0.08
34 4 0.08
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.70
Consensus pattern (31 bp):
TTTTATTAATATTTATATATTTATTTTTAAT
Found at i:4133950 original size:37 final size:33
Alignment explanation
Indices: 4133888--4133971 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 33
4133878 TTTTTATCAG
4133888 TTTTATTAATTTATATATATATTTACTTTTTAA
1 TTTTATTAATTTATATATATATTTACTTTTTAA
*
4133921 TTTTTTTAATTTTATATATATTATTTTTACTTTTT-A
1 TTTTATTAA-TTTATATATA-TA--TTTACTTTTTAA
*
4133957 TTATTATTTATTTAT
1 TT-TTATTAATTTAT
4133972 TTGTTTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 8 0.19
34 10 0.23
35 2 0.05
36 8 0.19
37 15 0.35
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
TTTTATTAATTTATATATATATTTACTTTTTAA
Found at i:4133970 original size:21 final size:22
Alignment explanation
Indices: 4133922--4133970 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
4133912 ACTTTTTAAT
4133922 TTTTTTAATTTTATATATATTA
1 TTTTTTAATTTTATATATATTA
*
4133944 -TTTTTACTTTT-TAT-TATTA
1 TTTTTTAATTTTATATATATTA
4133963 TTTATTTA
1 TTT-TTTA
4133971 TTTGTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTTATATATATTA
Found at i:4134132 original size:15 final size:15
Alignment explanation
Indices: 4134114--4134143 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4134104 TATTTATTTC
4134114 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
4134129 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
4134144 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:4136097 original size:18 final size:18
Alignment explanation
Indices: 4136074--4136113 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
4136064 TTCCTTCAAG
4136074 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
4136092 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
4136110 TCTG
1 TCTG
4136114 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:4136647 original size:8 final size:8
Alignment explanation
Indices: 4136634--4136672 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
4136624 GAACATTTCA
*
4136634 TGCATTCT
1 TGCATTTT
4136642 TGCA-TTT
1 TGCATTTT
4136649 TGCATTTT
1 TGCATTTT
*
4136657 TGCCTTTT
1 TGCATTTT
4136665 TGCATTTT
1 TGCATTTT
4136673 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:4137816 original size:13 final size:13
Alignment explanation
Indices: 4137798--4137840 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
4137788 CAATCAGAAT
4137798 AAAAAAGGCAAAA
1 AAAAAAGGCAAAA
4137811 AAAAAAGTAGCAAAA
1 AAAAAAG--GCAAAA
4137826 AACAAAA-GCAAAA
1 AA-AAAAGGCAAAA
4137839 AA
1 AA
4137841 GAACAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.56
15 8 0.30
16 4 0.15
ACGTcount: A:0.77, C:0.09, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAAAAGGCAAAA
Found at i:4137838 original size:24 final size:23
Alignment explanation
Indices: 4137829--4137873 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4137819 AGCAAAAAAC
4137829 AAAAGCAAAAAAGAACAAAAAGAA
1 AAAAG-AAAAAAGAACAAAAAGAA
* *
4137853 AAAAGAAAAAGGGACAAAAAG
1 AAAAGAAAAAAGAACAAAAAG
4137874 CACATGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.76, C:0.07, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAAGAACAAAAAGAA
Found at i:4138489 original size:22 final size:22
Alignment explanation
Indices: 4138461--4138504 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4138451 AGCTACCCTA
4138461 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
4138483 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
4138505 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:4138973 original size:18 final size:18
Alignment explanation
Indices: 4138939--4138974 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4138929 TCAACATCAA
* *
4138939 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATCTTTGG
4138957 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
4138975 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:4139577 original size:22 final size:22
Alignment explanation
Indices: 4139546--4139614 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
4139536 AAACATTTCC
4139546 CTTGAAATAAATTTTCGTCTCT
1 CTTGAAATAAATTTTCGTCTCT
*
4139568 CTTGAGAT-AA--TT--TC-C-
1 CTTGAAATAAATTTTCGTCTCT
4139583 CTTGAAATAAATTTTCGTCTCT
1 CTTGAAATAAATTTTCGTCTCT
*
4139605 CTTGAGATAA
1 CTTGAAATAA
4139615 TTTCCCTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 2 0.05
18 2 0.05
19 2 0.05
20 2 0.05
21 3 0.08
22 16 0.43
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (22 bp):
CTTGAAATAAATTTTCGTCTCT
Found at i:4139676 original size:36 final size:36
Alignment explanation
Indices: 4139540--4139741 Score: 314
Period size: 37 Copynumber: 5.5 Consensus size: 36
4139530 CATTGAAAAC
*
4139540 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACA
*
4139577 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACA
*
4139614 ATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACA
*
4139651 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
*
4139687 TTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
*
4139723 GTTTCCCTTGAAACTAAAT
1 ATTTCCCTTGAAA-TAAAT
4139742 ATTTAAATAT
Statistics
Matches: 157, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
36 69 0.44
37 81 0.52
38 7 0.04
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (36 bp):
ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
Found at i:4139822 original size:37 final size:36
Alignment explanation
Indices: 4139754--4139875 Score: 158
Period size: 36 Copynumber: 3.4 Consensus size: 36
4139744 TTAAATATGT
*
4139754 TTTCT-TTGAAACAAATTTCGT-TCCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCT-CCCTTGAGACAG
* * * *
4139789 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
4139826 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
4139862 TTACTCTTGAAACA
1 TTTCTCTTGAAACA
4139876 CAAAATCTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 5 0.07
36 40 0.53
37 29 0.39
38 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:4140664 original size:105 final size:105
Alignment explanation
Indices: 4140482--4141095 Score: 943
Period size: 105 Copynumber: 5.9 Consensus size: 105
4140472 AAATACTTGG
* *
4140482 AGTTCAACTTCACGACGAAGGGTCCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
4140547 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* *
4140587 AGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
*
4140652 TCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* *
4140692 AGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
*
4140757 TCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* *
4140797 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAACCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
*
4140862 TCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* **
4140902 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATT
1 AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
* *
4140962 TCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
66 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * * * ** *
4141002 AGTTCAACTTCACAACGAATGGACGGCTAG-TTGTCAACAAACAATTTCCCGGTTCCAGAGCCAA
1 AGTTCAACTTCACGACGAAGGGACCGCT-GCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAA
* *
4141066 TTTCAACTTCACGACGGAGGATATTGGACT
64 TTTCAACTTCACAACGAAGGATATTGGACT
4141096 TGGAACAATG
Statistics
Matches: 473, Mismatches: 29, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
100 81 0.17
101 4 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 342 0.72
106 36 0.08
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
Found at i:4141690 original size:34 final size:36
Alignment explanation
Indices: 4141643--4141744 Score: 154
Period size: 37 Copynumber: 2.9 Consensus size: 36
4141633 TTTCGTCCTA
* *
4141643 CTAGGATTGAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
4141678 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
4141713 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
4141745 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:4141728 original size:37 final size:35
Alignment explanation
Indices: 4141643--4141742 Score: 148
Period size: 34 Copynumber: 2.8 Consensus size: 35
4141633 TTTCGTCCTA
* * *
4141643 CTAGGATTGAAACTCCTAAAAATATGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
4141678 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAA-TTT
4141713 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
4141743 GAGTTCTACT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 28 0.47
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:4141770 original size:37 final size:37
Alignment explanation
Indices: 4141640--4141753 Score: 144
Period size: 37 Copynumber: 3.2 Consensus size: 37
4141630 ATTTTTCGTC
* * *
4141640 CTACTAGGATTGAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
4141677 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
4141711 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
4141748 CTACTA
1 CTACTA
4141754 TTATTTAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
34 30 0.45
35 1 0.01
36 1 0.01
37 35 0.52
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:4142074 original size:23 final size:22
Alignment explanation
Indices: 4142043--4142104 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
4142033 TTTTCTTTTT
4142043 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
4142066 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
4142089 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
4142105 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:4142101 original size:24 final size:23
Alignment explanation
Indices: 4142058--4142103 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
4142048 ATGTAATATT
*
4142058 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
4142081 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
4142104 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:4142169 original size:42 final size:39
Alignment explanation
Indices: 4142120--4142223 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 39
4142110 TTTTAGATTA
*
4142120 TATATATAAATATATTATTTTTTATTATCAGTTTTATTAATT
1 TATATAT-AATATATTATTTTTT-TT-TAAGTTTTATTAATT
* *
4142162 TATATATATATATATATATTTACTTTTTTAATTTTTTTTAATT
1 TATATATA-ATATAT-TATTT--TTTTTTAAGTTTTATTAATT
4142205 T-TATAT-ATATATTATTTTT
1 TATATATAATATATTATTTTT
4142224 ACTTTTTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
37 2 0.04
39 5 0.09
40 6 0.11
41 1 0.02
42 18 0.33
43 18 0.33
44 2 0.04
45 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (39 bp):
TATATATAATATATTATTTTTTTTTAAGTTTTATTAATT
Found at i:4142170 original size:44 final size:43
Alignment explanation
Indices: 4142117--4142250 Score: 114
Period size: 44 Copynumber: 3.0 Consensus size: 43
4142107 TTTTTTTAGA
*
4142117 TTATATATATAAATATATTATTTTTTATTATCAGTTTTATTAAT
1 TTATATATATAAATATATTATTTTTTATTAT-AATTTTATTAAT
* *
4142161 TTATATATATATATATA-TATTTACTTT-TT-TAATTTTTTTTAAT
1 TTATATATATAAATATATTATTT--TTTATTATAA-TTTTATTAAT
* * * *
4142204 TT-TATATATATATTATTTTTACTTTTTTATTATTATTTTATTTAT
1 TTATATATATA-AATA-TATTA-TTTTTTATTATAATTTTATTAAT
4142249 TT
1 TT
4142251 GTTTTATTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
42 9 0.12
43 19 0.26
44 22 0.31
45 17 0.24
46 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (43 bp):
TTATATATATAAATATATTATTTTTTATTATAATTTTATTAAT
Found at i:4142181 original size:46 final size:44
Alignment explanation
Indices: 4142117--4142250 Score: 143
Period size: 46 Copynumber: 3.0 Consensus size: 44
4142107 TTTTTTTAGA
*
4142117 TTATATATATAAATATATTA-TTTTTTATTATCAGTTTTATTAATT
1 TTATATATATATATATATTACTTTTTTATTAT-A-TTTTATTAATT
*
4142162 TATATATATATATATATATTTACTTTTTTA--AT-TTTTTTTAATT
1 T-TATATATATATATATA-TTACTTTTTTATTATATTTTATTAATT
* *
4142205 TTATATATATAT-TATTTTTACTTTTTTATTATTATTTTATTTATT
1 TTATATATATATATA-TATTACTTTTTTATTA-TATTTTATTAATT
4142250 T
1 T
4142251 GTTTTATTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
41 13 0.17
42 12 0.16
43 12 0.16
44 1 0.01
45 11 0.14
46 17 0.22
47 3 0.04
48 7 0.09
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (44 bp):
TTATATATATATATATATTACTTTTTTATTATATTTTATTAATT
Found at i:4142231 original size:25 final size:24
Alignment explanation
Indices: 4142203--4142279 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
4142193 TTTTTTTTAA
4142203 TTTTATATATATATTATTTTTACTT-
1 TTTTAT-TATATATT-TTTTTACTTC
* *
4142228 TTTTATTAT-TATTTTATTTATTTG
1 TTTTATTATATATTTT-TTTACTTC
*
4142252 TTTTATTTCTATATTTTTTT-CTTC
1 TTTTA-TTATATATTTTTTTACTTC
4142276 TTTT
1 TTTT
4142280 TCTTTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 14 0.32
25 12 0.27
26 6 0.14
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTTATTATATATTTTTTTACTTC
Found at i:4142402 original size:15 final size:15
Alignment explanation
Indices: 4142384--4142413 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4142374 TATTTATTTC
4142384 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
4142399 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
4142414 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:4145939 original size:6 final size:6
Alignment explanation
Indices: 4145928--4145954 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4145918 ATGATATGAG
4145928 TGTGGT TGTGGT TGTGGT TGTGGT TGT
1 TGTGGT TGTGGT TGTGGT TGTGGT TGT
4145955 CTTGTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TGTGGT
Found at i:4151850 original size:20 final size:19
Alignment explanation
Indices: 4151827--4151872 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
4151817 CGATATAATA
4151827 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
4151847 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
4151867 GGTAAA
1 GGTAAA
4151873 GCGCTACCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:4155351 original size:201 final size:201
Alignment explanation
Indices: 4155116--4155855 Score: 1293
Period size: 201 Copynumber: 3.7 Consensus size: 201
4155106 GTAAAATTTA
4155116 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* * *
4155181 TAAATATACCGATTTTATTAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
*
4155246 CGATACTTTTGGTCCAGAATGGATGCCAAAATGGGTGAACGCATAAAGTGTCGATACATTTTC-A
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
4155310 AAAGTTG
196 AAAG-TG
*
4155317 TCGATCCCAGAAACATATGCATCAATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
4155382 TAAATATATCGGTTTTATGAGAGAATAGGTCTACAATATGTATCGACACTTTTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
*
4155447 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGAGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
4155512 AAAGTG
196 AAAGTG
* * *
4155518 TCGATCCCAAAAACATATGCATCCATAAGTATAATGTAATAAGTAAATTTACAATGTTACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
4155583 TAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
*
4155648 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGATGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
4155713 AAAGTG
196 AAAGTG
* * * * *
4155719 TCGATCCTAGAAACATATGCATCTATAAGCATAATGTAATAGGTAAATTTACAATGAAACCAGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
4155784 TAAATATACCGGTTTTATGAGAGAATAGGTCTATAACATGTATCGACACTTTTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
4155849 CGATACT
131 CGATACT
4155856 AATTTAAATA
Statistics
Matches: 511, Mismatches: 27, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
201 506 0.99
202 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (201 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
AAAGTG
Found at i:4158948 original size:251 final size:250
Alignment explanation
Indices: 4158488--4158979 Score: 634
Period size: 251 Copynumber: 2.0 Consensus size: 250
4158478 TAAAGTTTCT
*
4158488 CATAAAGTGTCGATCCATATATAAAAAGTAACGACTCAAAAAACATCAAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATATATAAAAAGT-ACGACTCAAAAAACATCAAAACCCATAATTATAAT
* *
4158553 GTAATGGGTAATTTTTCAATAAAACCTGTATAAATATACCGGTTTTATGAAAAATATGTCTACAA
65 GTAATAGGTAATTTTTCAATAAAACCTGTATAAATATACCGGTTTTATGAAAAATAGGTCTACAA
* * *
4158618 CATTTATCGACACTTATTAGTATTGCGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGGG
130 CATGTATCGACACTTATTAATATTGCGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGGGGG
** * *
4158683 AACCTACAAAGTGTCGATACATTTTCATAGAGTGTCGAT-CCAAAAGGGTTACACG
195 AACAAACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAGGGTTACACG
* * * *
4158738 CATAAAGTGTCGATACATTTATTAAAAATGT-CGA-TCCCAAAAACATCGAAACTCATAATTATA
1 CATAAAGTGTCGATACATATA-TAAAAA-GTACGACT-CAAAAAACATCAAAACCCATAATTATA
* * * * *
4158801 ATGTAATATGTAATTTTGT-AATATAA-CTGGTATACATATACCGGTTTTGTGAGATAATAGGTC
63 ATGTAATAGGTAATTTT-TCAATAAAACCT-GTATAAATATACCGGTTTTATGA-AAAATAGGTC
* * * * *
4158864 TATAATATGTATTGACACTTATTAATATTGTGTCGATAATTTTTGTCCATAATGGATGCCAAAAA
125 TACAACATGTATCGACACTTATTAATATTGCGTCGATAATTTTTGTCCAGAATGGATGCCAAAAA
** * *
4158929 GGGTTAACAAATAAAGTGTCGATACATTTTCAAAAAGTGTTGATCCCAAAA
190 GGGGGAACAAACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAA
4158980 ACATCGAAAC
Statistics
Matches: 207, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
249 3 0.01
250 88 0.43
251 108 0.52
252 8 0.04
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (250 bp):
CATAAAGTGTCGATACATATATAAAAAGTACGACTCAAAAAACATCAAAACCCATAATTATAATG
TAATAGGTAATTTTTCAATAAAACCTGTATAAATATACCGGTTTTATGAAAAATAGGTCTACAAC
ATGTATCGACACTTATTAATATTGCGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGGGGGA
ACAAACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAGGGTTACACG
Found at i:4162313 original size:87 final size:87
Alignment explanation
Indices: 4162213--4162375 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
4162203 AAATAGGTCA
4162213 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
*
4162278 CCGGTTAAATGCCTATTTTATT
66 CCAGTTAAATGCCTATTTTATT
* *
4162300 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
4162365 CCAGTTAAATG
66 CCAGTTAAATG
4162376 ATATAACATT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTAATAATATTT
CCAGTTAAATGCCTATTTTATT
Found at i:4162347 original size:23 final size:23
Alignment explanation
Indices: 4162297--4162341 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4162287 TGCCTATTTT
*
4162297 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
4162320 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
4162342 TGTTATTGTA
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:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:4164888 original size:20 final size:21
Alignment explanation
Indices: 4164863--4164955 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
4164853 TTTTCCCAAT
*
4164863 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4164883 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
4164904 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
4164924 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
4164945 TCGCAATGCGA
1 TCGCAATGCGA
4164956 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4164908 original size:41 final size:41
Alignment explanation
Indices: 4164863--4164955 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
4164853 TTTTCCCAAT
4164863 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4164904 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4164945 TCGCAATGCGA
1 TCGCAATGCGA
4164956 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:4164968 original size:41 final size:41
Alignment explanation
Indices: 4164882--4165016 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
4164872 GAATAAGTAA
** *
4164882 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
4164923 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
4164964 ATCGCAATGCGATAAT-AAAAAATTGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
4165005 TTCGCAACGCGA
1 ATCGCAACGCGA
4165017 TACTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:4164969 original size:20 final size:20
Alignment explanation
Indices: 4164944--4165037 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
4164934 AATTGGGAAA
*
4164944 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
4164964 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
* *
4164985 ATTGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
4165005 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
4165025 TTCGCAACGCGAT
1 ATCGCAACGCGAT
4165038 TTACATAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:4165612 original size:19 final size:19
Alignment explanation
Indices: 4165552--4165632 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
4165542 TTCGAGAATG
4165552 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
4165572 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
4165588 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
4165605 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
4165624 AAAATCGCA
1 AAAATCGCA
4165633 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:4165650 original size:19 final size:19
Alignment explanation
Indices: 4165628--4165736 Score: 173
Period size: 19 Copynumber: 5.7 Consensus size: 19
4165618 GAAACCAAAA
*
4165628 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
4165647 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
* *
4165666 TCACGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATT
4165685 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
*
4165704 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTTATT
4165724 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4165737 GTCTGGTCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 65 0.78
20 18 0.22
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:4165756 original size:33 final size:33
Alignment explanation
Indices: 4165719--4165806 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
4165709 GTTGCGATTT
* *
4165719 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
4165752 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
4165785 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
4165807 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:4165808 original size:20 final size:20
Alignment explanation
Indices: 4165774--4165831 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
4165764 GCGATTCTCT
**
4165774 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
4165794 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
4165814 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
4165832 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:4167892 original size:42 final size:42
Alignment explanation
Indices: 4167833--4167953 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
4167823 CCGACTCGCC
* * *
4167833 TATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCT
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCT
* * * *
4167875 TATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCAT
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCT
* ** * *
4167917 TGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
4167954 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (42 bp):
TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCT
Found at i:4169331 original size:14 final size:14
Alignment explanation
Indices: 4169312--4169347 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4169302 ATTGTTTAAT
4169312 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4169326 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4169340 TGATTTGT
1 TGATTTGT
4169348 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:4169549 original size:19 final size:19
Alignment explanation
Indices: 4169527--4169677 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
4169517 CGAAATTAAA
4169527 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4169546 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4169561 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
4169579 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
4169593 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4169612 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4169627 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
4169645 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4169664 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4169678 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4169573 original size:33 final size:32
Alignment explanation
Indices: 4169531--4169657 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
4169521 ATTAAATTCG
4169531 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
4169564 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
4169597 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
4169630 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4169658 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:4169620 original size:66 final size:66
Alignment explanation
Indices: 4169524--4169656 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
4169514 ACGCGAAATT
*
4169524 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4169589 G
66 G
*
4169590 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4169655 G
66 G
4169656 A
1 A
4169657 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:4171956 original size:12 final size:12
Alignment explanation
Indices: 4171939--4171963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4171929 TCTTCGGGGA
4171939 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4171951 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4171963 C
1 C
4171964 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:4172172 original size:24 final size:24
Alignment explanation
Indices: 4172138--4172191 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
4172128 CTGAAACATC
* * *
4172138 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTAATGACCAAG
*
4172162 ATCAAAGTCCGGGTAATGACCAAG
1 ATCAAAATCCGGGTAATGACCAAG
4172186 ATCAAA
1 ATCAAA
4172192 TACTGACTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGGTAATGACCAAG
Found at i:4173269 original size:20 final size:20
Alignment explanation
Indices: 4173244--4173301 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
4173234 ATTCATTTGA
4173244 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4173264 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
4173284 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
4173302 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:4173344 original size:14 final size:14
Alignment explanation
Indices: 4173325--4173382 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
4173315 GAAAATCGCA
4173325 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
4173339 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
4173356 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
4173372 TTGCGATTTTC
1 TTGCGATTTTC
4173383 ATTTCGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 22 0.56
16 3 0.08
17 3 0.08
19 11 0.28
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:4173344 original size:33 final size:33
Alignment explanation
Indices: 4173307--4173377 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
4173297 AAAATCGCAA
4173307 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
4173340 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
4173373 TGCGA
1 TGCGA
4173378 TTTTCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:4173361 original size:19 final size:19
Alignment explanation
Indices: 4173320--4173454 Score: 173
Period size: 19 Copynumber: 7.6 Consensus size: 19
4173310 GAAATGAAAA
4173320 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
4173336 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4173353 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
4173369 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4173386 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4173405 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4173424 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
4173443 TCGCGTTGCGAT
1 TCGCATTGCGAT
4173455 AGTCTGTTTT
Statistics
Matches: 105, Mismatches: 4, Indels: 17
0.83 0.03 0.13
Matches are distributed among these distances:
14 22 0.21
16 6 0.06
17 6 0.06
19 71 0.68
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4173378 original size:33 final size:33
Alignment explanation
Indices: 4173320--4173437 Score: 182
Period size: 33 Copynumber: 3.4 Consensus size: 33
4173310 GAAATGAAAA
4173320 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
4173353 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
4173386 TCGCATTGCGATTTTCATTTTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC----T-CGTTGCGATTTTCATT
4173424 TCGCATTGCGATTT
1 TCGCATTGCGATTT
4173438 CCATTTCGCG
Statistics
Matches: 79, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
33 49 0.62
37 1 0.01
38 29 0.37
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:4175479 original size:20 final size:19
Alignment explanation
Indices: 4175444--4175510 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4175434 GAAACTTAAA
4175444 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
4175463 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
4175483 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
4175502 ATCGCAACG
1 ATCGCAACG
4175511 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:4175518 original size:14 final size:14
Alignment explanation
Indices: 4175499--4175556 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4175489 ATGCGAAATG
4175499 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4175513 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
4175529 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4175545 AAAATCGCAACG
1 AAAATCGCAACG
4175557 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:4175541 original size:32 final size:33
Alignment explanation
Indices: 4175483--4175561 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
4175473 GGAAATGGCT
*
4175483 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4175516 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
4175548 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
4175562 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:4175590 original size:19 final size:18
Alignment explanation
Indices: 4175568--4175715 Score: 77
Period size: 14 Copynumber: 8.6 Consensus size: 18
4175558 GAAACACAAA
*
4175568 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
4175587 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
4175603 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
4175619 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
*
4175635 T--CGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
*
4175649 T--CGTTGCAATTTTCATT
1 TCGCGTTGCGA-TTTCATT
* **
4175666 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGAT-TTCATT
*
4175685 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGAT-TTCATT
*
4175705 TCGTGTTGCGA
1 TCGCGTTGCGA
4175716 AAGTAAACTA
Statistics
Matches: 105, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
14 32 0.30
15 3 0.03
16 6 0.06
17 2 0.02
18 15 0.14
19 30 0.29
20 17 0.16
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:4175609 original size:14 final size:14
Alignment explanation
Indices: 4175590--4175661 Score: 90
Period size: 14 Copynumber: 4.9 Consensus size: 14
4175580 TTTCATTTCG
4175590 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4175604 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4175620 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
4175636 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4175650 CGTTGCAATTTT
1 CGTTGCGATTTT
4175662 CATTTCGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
14 36 0.71
16 4 0.08
18 11 0.22
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4175620 original size:32 final size:32
Alignment explanation
Indices: 4175573--4175646 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
4175563 ACAAATCGCA
4175573 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
4175606 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
4175638 TTGCGATTT
1 TTGCGATTT
4175647 TGTCGTTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 35 0.85
33 6 0.15
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.49
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:4175696 original size:20 final size:19
Alignment explanation
Indices: 4175662--4175715 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
4175652 TTGCAATTTT
*
4175662 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4175681 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
4175701 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
4175716 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4176214 original size:18 final size:18
Alignment explanation
Indices: 4176188--4176232 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4176178 GTCAATCAGA
* *
4176188 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
4176206 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4176224 TGATGGCTC
1 TGATGGCTC
4176233 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:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:4177577 original size:20 final size:20
Alignment explanation
Indices: 4177552--4177589 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4177542 AATAGTTTCT
4177552 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
4177572 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
4177590 GAGAGAATCG
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:4178155 original size:20 final size:20
Alignment explanation
Indices: 4178042--4178155 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
4178032 CGCTTTGAAA
4178042 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
4178062 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
4178082 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
4178102 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
4178123 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
4178143 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4178156 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:4178173 original size:21 final size:21
Alignment explanation
Indices: 4178144--4178236 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
4178134 ATAGTAAGTA
4178144 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
4178165 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
4178185 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
4178206 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
4178226 TCGCATTGCGA
1 TCGCATTGCGA
4178237 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:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:4178174 original size:41 final size:41
Alignment explanation
Indices: 4178083--4178217 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
4178073 AAAGTCAGTA
* * * ** *
4178083 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
4178123 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
4178165 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
4178206 TCGCGTTGCGAT
1 TCGCGTTGCGAT
4178218 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:4178218 original size:41 final size:41
Alignment explanation
Indices: 4178144--4178236 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
4178134 ATAGTAAGTA
4178144 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
4178185 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
4178226 TCGCATTGCGA
1 TCGCATTGCGA
4178237 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:4182603 original size:87 final size:87
Alignment explanation
Indices: 4182457--4182619 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
4182447 TATGTTATAT
4182457 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
4182522 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * * *
4182544 TATTTAACGGGAAATATTATCAAGTACAATAACATATTATGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
4182609 AGCGCTTATAT
66 AGCGCTTATAT
4182620 TGACTTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:4186317 original size:169 final size:169
Alignment explanation
Indices: 4186035--4186520 Score: 697
Period size: 169 Copynumber: 2.8 Consensus size: 169
4186025 GTATATTTAT
*
4186035 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACA
1 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAAA
*
4186100 CTTTTTGACAAGGTATCGACACATTTTTCTTCTATTCTGGACATAAAGTACCGACACAATATTAA
66 CTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAA
4186165 AAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAA
131 AAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAA
4186204 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAAA
1 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAAA
* *
4186269 CTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCCGGATATAAAGTACCGACACAATATTAA
66 CTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAA
* *
4186334 AAAGTGTCGATATAGGTTGTAGACCTATTTGCTCATAAA
131 AAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAA
*
4186373 ACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1 ACC-G------------G-TTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG
* * * * *
4186438 TTTTTTCAA--TCGATACTTTTTGAAAAGGTATCGACACATTTTTCTTTCATTCTGGACATAAAG
52 ---TGTAAATGTCGAAACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
4186501 TACCGACACAATATTAAAAA
114 TACCGACACAATATTAAAAA
4186521 ATGTGAAAAC
Statistics
Matches: 286, Mismatches: 14, Indels: 19
0.90 0.04 0.06
Matches are distributed among these distances:
169 166 0.58
170 1 0.00
182 1 0.00
183 45 0.16
184 69 0.24
186 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (169 bp):
ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAAA
CTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAA
AAAGTATCGATATAGGTTGTAGACCTATTCGCTCATAAA
Found at i:4188092 original size:200 final size:200
Alignment explanation
Indices: 4187754--4188715 Score: 1698
Period size: 200 Copynumber: 4.8 Consensus size: 200
4187744 AACATTAAAC
* * * *
4187754 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
4187818 AAAAATTACCTAATA-ATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
4187882 GGATCGACACTTT-TTGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
130 GGATCGACACTTTATT-GTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
4187946 CTACAAA
194 CTACAAA
* *
4187953 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
4188018 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
4188083 GATCGACACTTTATTGTTGCGCCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
4188148 ACAAA
196 ACAAA
*
4188153 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
4188218 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
4188283 GATCGACACTTTATTGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
4188348 ACAAA
196 ACAAA
*
4188353 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
4188418 AAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTTATCGGATCGACAC-TTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
4188482 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGATCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
4188547 ACAAA
196 ACAAA
* *
4188552 AGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
4188617 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
4188682 GATCGACACTTTATGGTTGCACCTTGTTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
4188716 ATTTTAAATT
Statistics
Matches: 733, Mismatches: 26, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
199 258 0.35
200 473 0.65
201 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:4188556 original size:399 final size:400
Alignment explanation
Indices: 4187754--4188715 Score: 1709
Period size: 399 Copynumber: 2.4 Consensus size: 400
4187744 AACATTAAAC
* * * *
4187754 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
*
4187818 AAAAATTACCTAATA-ATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
4187882 GGATCGACACTTT-TTGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
130 GGATCGACACTTTATT-GTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
4187946 CTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTT
194 CTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTT
*
4188011 AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTT
259 AGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTT
*
4188076 ATATATGGATCGACACTTTATTGTTGCGCCCTGTTTGCCATTCATTCTGGACCAAAAATATCGAC
324 ATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGAC
4188141 ACAAACTACAAA
389 ACAAACTACAAA
*
4188153 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
4188218 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
4188283 GATCGACACTTTATTGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
*
4188348 ACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAA-TCGGTATACTTGTACCGGTTA
196 ACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACT-GGTATACTTGTACCGGTTA
*
4188412 GATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTTATCGGATCGACAC-TTTTA
260 GATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTA
*
4188476 TATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGATCAAAAATATCGACA
325 TATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACA
4188541 CAAACTACAAA
390 CAAACTACAAA
* *
4188552 AGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
4188617 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
4188682 GATCGACACTTTATGGTTGCACCTTGTTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
4188716 ATTTTAAATT
Statistics
Matches: 539, Mismatches: 20, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
399 305 0.57
400 232 0.43
401 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (400 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAAAGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAG
ATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTAT
ATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACAC
AAACTACAAA
Found at i:4188960 original size:18 final size:18
Alignment explanation
Indices: 4188937--4188997 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
4188927 TCTCATTCAT
*
4188937 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
4188955 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
4188974 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
4188993 AATTA
1 AATTA
4188998 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:4188973 original size:19 final size:19
Alignment explanation
Indices: 4188949--4188997 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
4188939 TTATATTCAC
4188949 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
4188968 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
4188987 ATACAAAATTA
1 ATACAAAATTA
4188998 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:4192389 original size:161 final size:162
Alignment explanation
Indices: 4192118--4192452 Score: 492
Period size: 161 Copynumber: 2.1 Consensus size: 162
4192108 ATTTTGATAT
* ** * *
4192118 CGGTTTTATCATATTTTTAAATGTTATATTGTTGTGGATCGATATATTTTTTTAAAGTATCGACA
1 CGGTTTTATCATATTTTTAAATGGTATATCATTGTGGATCGATACATTTTTTAAAAGTATCGACA
* *
4192183 CATTATAGGCGCTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGTAT
66 CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAT
* * *
4192247 CGACACTTTCAATATATTCGGTAACGTTTTAC
131 CGACACTTTAAATATATCCGATAACGTTTTAC
** *
4192279 CGGTTTTATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACA
1 CGGTTTTATCATATTTTTAAATGGTATATCATTGTGGATCGATACATTTTTTAAAAGTATCGACA
* ** *
4192344 CTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAGTAT
66 CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAT
* *
4192409 CGACACTTTAAATGTATCCGATAGCGTTTTAC
131 CGACACTTTAAATATATCCGATAACGTTTTAC
4192441 CGGTTTTATCAT
1 CGGTTTTATCAT
4192453 TTCAATACCG
Statistics
Matches: 154, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
161 107 0.69
162 47 0.31
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (162 bp):
CGGTTTTATCATATTTTTAAATGGTATATCATTGTGGATCGATACATTTTTTAAAAGTATCGACA
CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAT
CGACACTTTAAATATATCCGATAACGTTTTAC
Found at i:4199180 original size:2 final size:2
Alignment explanation
Indices: 4199173--4199218 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4199163 ATTTAATTAG
4199173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4199215 TA TA
1 TA TA
4199219 GACTGTTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4199263 original size:33 final size:33
Alignment explanation
Indices: 4199226--4199291 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
4199216 ATAGACTGTT
*
4199226 AGTTAGCCTAATTCTATAACACTTTGTCCACTA
1 AGTTAGCCTAATTCTATAACACTGTGTCCACTA
4199259 AGTTAGCCTAATTCTATAACACTGTGTCCACTA
1 AGTTAGCCTAATTCTATAACACTGTGTCCACTA
4199292 GGTGTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (33 bp):
AGTTAGCCTAATTCTATAACACTGTGTCCACTA
Found at i:4213685 original size:19 final size:20
Alignment explanation
Indices: 4213653--4213691 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4213643 GTATGCATAT
* *
4213653 TTAAAAAATTATATTTAAAC
1 TTAAAAAATAATATCTAAAC
4213673 TTAAAAAA-AATATCTAAAC
1 TTAAAAAATAATATCTAAAC
4213692 AATGTGAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAATAATATCTAAAC
Found at i:4229814 original size:161 final size:162
Alignment explanation
Indices: 4229543--4229877 Score: 492
Period size: 161 Copynumber: 2.1 Consensus size: 162
4229533 ATTTTGATAT
* ** * *
4229543 CGGTTTTATCATATTTTTAAATGTTATATTGTTGTGGATCGATATATTTTTTTAAAGTATCGACA
1 CGGTTTTATCATATTTTTAAATGGTATATCATTGTGGATCGATACATTTTTTAAAAGTATCGACA
* *
4229608 CATTATAGGCGCTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGTAT
66 CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAT
* * *
4229672 CGACACTTTCAATATATTCGGTAACGTTTTAC
131 CGACACTTTAAATATATCCGATAACGTTTTAC
** *
4229704 CGGTTTTATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACA
1 CGGTTTTATCATATTTTTAAATGGTATATCATTGTGGATCGATACATTTTTTAAAAGTATCGACA
* ** *
4229769 CTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAGTAT
66 CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAT
* *
4229834 CGACACTTTAAATGTATCCGATAGCGTTTTAC
131 CGACACTTTAAATATATCCGATAACGTTTTAC
4229866 CGGTTTTATCAT
1 CGGTTTTATCAT
4229878 TTCAATACCG
Statistics
Matches: 154, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
161 107 0.69
162 47 0.31
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (162 bp):
CGGTTTTATCATATTTTTAAATGGTATATCATTGTGGATCGATACATTTTTTAAAAGTATCGACA
CATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAT
CGACACTTTAAATATATCCGATAACGTTTTAC
Found at i:4236604 original size:2 final size:2
Alignment explanation
Indices: 4236597--4236637 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4236587 ATTTAATTAG
4236597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4236638 GACTGTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4236687 original size:33 final size:33
Alignment explanation
Indices: 4236645--4236710 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
4236635 ATAGACTGTT
*
4236645 AGTTAGCCTAATTCTATAACACTTTGTCCACTA
1 AGTTAGCCTAATTCTATAACACTGTGTCCACTA
4236678 AGTTAGCCTAATTCTATAACACTGTGTCCACTA
1 AGTTAGCCTAATTCTATAACACTGTGTCCACTA
4236711 GGTGTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (33 bp):
AGTTAGCCTAATTCTATAACACTGTGTCCACTA
Found at i:4253617 original size:19 final size:20
Alignment explanation
Indices: 4253585--4253623 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4253575 GTATGCATAT
* *
4253585 TTAAAAAATTATATTTAAAC
1 TTAAAAAATAATATCTAAAC
4253605 TTAAAAAA-AATATCTAAAC
1 TTAAAAAATAATATCTAAAC
4253624 AATGTGAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAAATAATATCTAAAC
Found at i:4275562 original size:21 final size:21
Alignment explanation
Indices: 4275511--4275563 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
4275501 ATTATGACTA
4275511 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
4275532 TCACGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
4275553 TCGCAATGCGA
1 TCGCAATGCGA
4275564 ATTTGAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:4275577 original size:21 final size:21
Alignment explanation
Indices: 4275553--4275750 Score: 97
Period size: 21 Copynumber: 9.6 Consensus size: 21
4275543 TTTTCCCAAT
4275553 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATTTGAAAAA
* **
4275574 TCGCAATGCG-ATACTG-ACTA
1 TCGCAATGCGAAT-TTGAAAAA
*
4275594 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGAAAAA
* ** *
4275615 TCGCAATGCAAATTT-ACGTAT
1 TCGCAATGCGAATTTGA-AAAA
** * * * *
4275636 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGAATTTGAAAAA
** *
4275657 TCGCAATGCGAATACG-TAAA
1 TCGCAATGCGAATTTGAAAAA
*
4275677 TCGCAACGCG-A-TT-AAGTAAA
1 TCGCAATGCGAATTTGAA--AAA
* *
4275697 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTTGAAAAA
** *
4275718 TCGCAATGCGAATACG-TAAA
1 TCGCAATGCGAATTTGAAAAA
4275738 TCGCAATGCGAAT
1 TCGCAATGCGAAT
4275751 CTTACTATCG
Statistics
Matches: 132, Mismatches: 34, Indels: 23
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 56 0.42
21 72 0.55
22 2 0.02
23 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTTGAAAAA
Found at i:4275682 original size:20 final size:20
Alignment explanation
Indices: 4275657--4275768 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
4275647 TTTTCATAAT
4275657 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
4275677 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
4275697 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
4275718 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
4275738 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
4275758 TCGCAATGCGA
1 TCGCAATGCGA
4275769 TTTACATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:4275719 original size:41 final size:41
Alignment explanation
Indices: 4275657--4275750 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
4275647 TTTTCATAAT
* *
4275657 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
4275697 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
4275738 TCGCAATGCGAAT
1 TCGCAATGCGAAT
4275751 CTTACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 12 0.25
41 36 0.75
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:4275721 original size:103 final size:104
Alignment explanation
Indices: 4275535--4275726 Score: 264
Period size: 103 Copynumber: 1.9 Consensus size: 104
4275525 TCCAATTTCA
* ** * *
4275535 CGTTGCGATTTTCCCAATTCGCAATGCGAATTTGAAAAATCGCAATGCGATACTGACTATCGCAA
1 CGTTGCGATTTTCACAATTCGCAATGCGAATACGAAAAATCGCAACGCGATACTGACAATCGCAA
*
4275600 TGCGAATTTGGAAAATCGCAATGCAAATTTACGTATTCG
66 TGCGAATTAGGAAAATCGCAATGCAAATTTACGTATTCG
* * *
4275639 CGTTGCGATTTTCATAATTCGCAATGCGAATACG-TAAATCGCAACGCGATTA-AGTA-AATCGC
1 CGTTGCGATTTTCACAATTCGCAATGCGAATACGAAAAATCGCAACGCGA-TACTG-ACAATCGC
4275701 AATGCGAATTAGGAAAATCGCAATGC
64 AATGCGAATTAGGAAAATCGCAATGC
4275727 GAATACGTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
103 44 0.57
104 33 0.43
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (104 bp):
CGTTGCGATTTTCACAATTCGCAATGCGAATACGAAAAATCGCAACGCGATACTGACAATCGCAA
TGCGAATTAGGAAAATCGCAATGCAAATTTACGTATTCG
Found at i:4276320 original size:19 final size:19
Alignment explanation
Indices: 4276282--4276348 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
4276272 TTCGAGAATG
*
4276282 AAAATCGCAACACGGAAATA
1 AAAATCGCAACGC-GAAATA
**
4276302 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
4276321 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
4276340 AAAATCGCA
1 AAAATCGCA
4276349 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:4276371 original size:19 final size:19
Alignment explanation
Indices: 4276344--4276508 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
4276334 GAAACCAAAA
*
4276344 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
4276363 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4276382 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4276401 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
4276415 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
4276434 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
4276448 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
4276467 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
4276487 ATCTCGTTGAGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
4276507 TC
1 TC
4276509 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
14 20 0.17
16 4 0.03
17 5 0.04
19 59 0.50
20 30 0.25
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4276423 original size:14 final size:14
Alignment explanation
Indices: 4276404--4276459 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
4276394 TTTCATTTCG
4276404 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4276418 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
4276437 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4276451 CGTTGCGAT
1 CGTTGCGAT
4276460 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4276433 original size:33 final size:33
Alignment explanation
Indices: 4276385--4276483 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
4276375 TTTCATTTCG
**
4276385 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
4276418 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
4276451 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
4276484 ATTATCTCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.76
34 15 0.24
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:4278677 original size:42 final size:42
Alignment explanation
Indices: 4278601--4278689 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
4278591 GACTCGCCTG
* * *
4278601 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
4278643 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
4278685 TCATC
1 TCATC
4278690 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:4280089 original size:14 final size:14
Alignment explanation
Indices: 4280070--4280105 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4280060 ATTGTTTAAT
4280070 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
4280084 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
4280098 TGATTTGT
1 TGATTTGT
4280106 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:4280272 original size:19 final size:19
Alignment explanation
Indices: 4280250--4280400 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
4280240 CGAAATTAAA
4280250 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4280269 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4280284 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
4280302 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
4280316 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
4280335 TTCGCAATGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4280350 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
4280368 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
4280387 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
4280401 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4280296 original size:33 final size:32
Alignment explanation
Indices: 4280254--4280380 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
4280244 ATTAAATTCG
4280254 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
4280287 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
4280320 CGTTGCGATTTTCATTTCGCAATGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
4280353 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4280381 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:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:4280330 original size:66 final size:66
Alignment explanation
Indices: 4280247--4280379 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
4280237 ACGCGAAATT
*
4280247 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4280312 G
66 G
*
4280313 AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
4280378 G
66 G
4280379 A
1 A
4280380 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:4282692 original size:12 final size:12
Alignment explanation
Indices: 4282675--4282711 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
4282665 TCTTCGGGGA
4282675 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4282687 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4282699 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4282711 C
1 C
4282712 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:4282920 original size:24 final size:24
Alignment explanation
Indices: 4282886--4282939 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4282876 CTGAAACATC
*
4282886 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
4282910 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4282934 ATCAAA
1 ATCAAA
4282940 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4283748 original size:20 final size:21
Alignment explanation
Indices: 4283723--4283774 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4283713 TTTTCCTAAT
*
4283723 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGCAAA
* **
4283743 TCGCAATGCAAATTTGGCAAA
1 TCGCAATGCGAATTAAGCAAA
4283764 TCGCAATGCGA
1 TCGCAATGCGA
4283775 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGCAAA
Found at i:4283796 original size:20 final size:20
Alignment explanation
Indices: 4283763--4283841 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
4283753 AATTTGGCAA
* *
4283763 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
4283783 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
4283804 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
4283824 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
4283842 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:4283848 original size:20 final size:20
Alignment explanation
Indices: 4283801--4283850 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
4283791 GAGATAATAC
4283801 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
4283821 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
4283841 AAAATCGCAA
1 AAAATCGCAA
4283851 TCATCTCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:4283975 original size:20 final size:20
Alignment explanation
Indices: 4283950--4284027 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
4283940 ATTCATTTGA
*
4283950 CTATCGCAACGCGAAAATGG
1 CTATCGCAACTCGAAAATGG
* * *
4283970 CTATCGTAATTCG-AAATGAA
1 CTATCGCAACTCGAAAATG-G
**
4283990 AAATCGCAACTCGAAAATGG
1 CTATCGCAACTCGAAAATGG
*
4284010 CTATCGCAACTAGAAAAT
1 CTATCGCAACTCGAAAAT
4284028 CGCAATGCGA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 5 0.11
20 34 0.77
21 5 0.11
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
CTATCGCAACTCGAAAATGG
Found at i:4284087 original size:19 final size:19
Alignment explanation
Indices: 4284046--4284132 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
4284036 GAAATGAAAA
4284046 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
4284062 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
4284079 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4284098 TCGCATTGCGATTGTCATT
1 TCGCATTGCGATTTTCATT
4284117 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
4284133 TCATTGCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
14 10 0.16
16 3 0.05
17 3 0.05
19 46 0.74
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4284118 original size:38 final size:33
Alignment explanation
Indices: 4284046--4284162 Score: 126
Period size: 38 Copynumber: 3.4 Consensus size: 33
4284036 GAAATGAAAA
* *
4284046 TCGCATTGCGATTTTCTCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCTCGTTGCGATTGTCATT
4284079 TCGCATTGCGATTTTCATTTCGCATTGCGATTGTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTGTCATT
* *
4284117 TCGCATTGCGATTTTCTCATTGCGATAGTCAGTT
1 TCGCATTGCGATTTTCTCGTTGCGATTGTCA-TT
**
4284151 TCGTGTTGCGAT
1 TCGCATTGCGAT
4284163 AGTCTGTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
33 27 0.38
34 12 0.17
35 2 0.03
36 3 0.04
38 28 0.39
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTGTCATT
Found at i:4285760 original size:40 final size:42
Alignment explanation
Indices: 4285716--4285806 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
4285706 CCTCTTCAAC
* *
4285716 GATGACAGTGGCCTCTTGAAC-GGTGG-GGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAAGTGGAGGGGACTCTTGAGG
* *
4285756 GATGATAGGGGCCTCTTGAACAATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAAGTGGAGGGGACTCTTGAGG
*
4285798 AATGACAGG
1 GATGACAGG
4285807 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 19 0.44
41 3 0.07
42 21 0.49
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACAAGTGGAGGGGACTCTTGAGG
Found at i:4286169 original size:20 final size:20
Alignment explanation
Indices: 4286144--4286216 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
4286134 GAAGAATAGT
*
4286144 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
4286164 TTACTTTCGCAACACGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
4286184 TAACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
4286204 TGACTATCGCAAC
1 TTACTTTCGCAAC
4286217 GCGGAAATGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:4286217 original size:20 final size:20
Alignment explanation
Indices: 4286170--4286256 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
4286160 AAACTTACTT
* * *
4286170 TCGCAACACGAAAATAACTA
1 TCGCAACGCGGAAATGACTA
4286190 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
4286210 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
4286230 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
4286249 TCGCAACG
1 TCGCAACG
4286257 ACAAAATCGC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 14 0.24
20 44 0.76
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:4286324 original size:14 final size:14
Alignment explanation
Indices: 4286305--4286363 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
4286295 TTTCATTTCG
4286305 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4286319 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
4286336 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4286352 CGTTGCGATTTT
1 CGTTGCGATTTT
4286364 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4286333 original size:33 final size:33
Alignment explanation
Indices: 4286294--4286379 Score: 154
Period size: 33 Copynumber: 2.6 Consensus size: 33
4286284 GCATTACGAT
*
4286294 TTTTCATTTCGCGTTGCGATTTTGTCGTTGCGA
1 TTTTCATTTCGCATTGCGATTTTGTCGTTGCGA
4286327 TTTTCATTTCGCATTGCGATTTTGTCGTTGCGA
1 TTTTCATTTCGCATTGCGATTTTGTCGTTGCGA
*
4286360 TTTTCATTTTGCATTGCGAT
1 TTTTCATTTCGCATTGCGAT
4286380 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (33 bp):
TTTTCATTTCGCATTGCGATTTTGTCGTTGCGA
Found at i:4286976 original size:18 final size:18
Alignment explanation
Indices: 4286953--4287000 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
4286943 CGGGTCGATC
* *
4286953 AGGTGATTGCTCTGGGTG
1 AGGTGATAGCTCTGGATG
4286971 AGGTGATAGCTCTGGATG
1 AGGTGATAGCTCTGGATG
*
4286989 AGGTGATGGCTC
1 AGGTGATAGCTC
4287001 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.42, T:0.29
Consensus pattern (18 bp):
AGGTGATAGCTCTGGATG
Found at i:4288345 original size:20 final size:20
Alignment explanation
Indices: 4288320--4288362 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4288310 AATAGTTTCT
4288320 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
4288340 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
4288360 GAA
1 GAA
4288363 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Done.