Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:478105 original size:36 final size:37
Alignment explanation
Indices: 478039--478111 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
478029 GTTGAATTTA
*
478039 TATTATATAAAAAATTAGTTAATTAGTAGTTTAAGTTT
1 TATTATATAAAAAAATAGTT-ATTAGTAGTTTAAGTTT
*
478077 TATTATAATAAAAAAATAG-T-TTATTAGTTTAAGTT
1 TATTAT-ATAAAAAAATAGTTATTAGTAGTTTAAGTT
478112 ATATAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 14 0.44
38 7 0.22
39 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.47
Consensus pattern (37 bp):
TATTATATAAAAAAATAGTTATTAGTAGTTTAAGTTT
Found at i:478148 original size:13 final size:13
Alignment explanation
Indices: 478130--478158 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
478120 GAATAATTAT
478130 TTAAATTAGTTTA
1 TTAAATTAGTTTA
478143 TTAAATTAGTTTA
1 TTAAATTAGTTTA
478156 TTA
1 TTA
478159 TTATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (13 bp):
TTAAATTAGTTTA
Found at i:478245 original size:21 final size:22
Alignment explanation
Indices: 478220--478260 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
478210 GTTAATTAGT
478220 TTGTTAG-TTTAAGTTATATTA
1 TTGTTAGTTTTAAGTTATATTA
478241 TTGTTAGTTTTAAGTTATAT
1 TTGTTAGTTTTAAGTTATAT
478261 CCTATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (22 bp):
TTGTTAGTTTTAAGTTATATTA
Found at i:478498 original size:30 final size:31
Alignment explanation
Indices: 478462--478548 Score: 135
Period size: 30 Copynumber: 2.9 Consensus size: 31
478452 TAGTAGTAAA
* *
478462 TTATAATTAAA-AATCGTTTATTAGTTTAAG
1 TTATAATTAAATAATAGTTTATTAGTTGAAG
478492 TTATAA-TAAATAATAGTTTATTAGTTGAAG
1 TTATAATTAAATAATAGTTTATTAGTTGAAG
478522 TTAT-ATTAAATAATAGTTTATTAGTTG
1 TTATAATTAAATAATAGTTTATTAGTTG
478549 TTTAAGGGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.09
30 48 0.91
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.47
Consensus pattern (31 bp):
TTATAATTAAATAATAGTTTATTAGTTGAAG
Found at i:478517 original size:377 final size:376
Alignment explanation
Indices: 477761--478501 Score: 1068
Period size: 382 Copynumber: 1.9 Consensus size: 376
477751 AATTTTTTAT
*
477761 TTTATTTAAATTAGTTTATTATTTTAAATTATTAGTTTGTTAGTTTAGGGTTTAGGGTAAAACAA
1 TTTATTTAAATTAGTTTATTATTATAAATTATTAGTTTGTTAGTTTAGGGTTTAGGGTAAAACAA
* *
477826 TTACTTAATTAGTTTGTTAGTTTAAGTTATATTATTGTTAGTTTAAGTTCTATCATACATAAATA
66 TTACTTAATTAGTTTGTTAGTTTAAGTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATA
*
477891 AAAAATTATTTAATTAGTTTGTTTGATAGTTATAAATTAAAAAATAATAATTAATTAGTTTGTTT
131 AAAAATTATTTAATTAGTATGTTTGATAGTTATAAATTAAAAAATAATAATTAATTAG-TTGTTT
477956 GTTAGTCGTTAGTTATATATAAAAAATAGTTAATTAGTTTGTAGTTAGTTAAAAAATTAAGTTAT
195 GTTAGTCGTTAGTTATATATAAAAAATAGTTAATTAGTTTGTAGTTAGTTAAAAAATTAAGTTAT
* **
478021 ATTTGTTTGTTGAATTTATATTATATAAAAAATTAGTTAATTAGTAGTTTAAGTTTTATTATAAT
260 ATTTATTTGTTGAATTTATATTATATAAAAAATTAGTTAATTAGTAGTTTAAGTTAAATTATAAT
478086 AAAAAAATAGTTTATTAGTTTAAGTTATATAAAAGAATAATTATTTAAATTAG
325 AAAAAAATAGTTTATTAGTTTAAGTTATATAAAAGAATAATTATTT-AATTAG
* *
478139 TTTA-TTAAATTAGTTTATTATTATATATTATTAGTTTGTTGGTTTAGGGTTTAGGGTAAAACAA
1 TTTATTTAAATTAGTTTATTATTATAAATTATTAGTTTGTTAGTTTAGGGTTTAGGGTAAAAC--
* * *
478203 AAAATTAGTTAATTAGTTTGTTAGTTTAAGTTATATTATTGTTAGTTTTAAGTTATATCCTATAG
64 --AATTACTTAATTAGTTTGTTAGTTTAAGTTATATTATTGTTAG-TTTAAGTTATATCATACAG
* * *
478268 AAATAAAAAATTATTTAATTAGTATGTTTGATAGTTATATATTAATAAA-AATAATTAGTTAG-T
126 AAATAAAAAATTATTTAATTAGTATGTTTGATAGTTATAAATTAAAAAATAATAATTAATTAGTT
* *
478331 -TTT-TTAGTCGTTAGTTATATATAAAAAAAATA-TGTAATTAGTTTGT-GTTAGTTAAATAGTT
191 GTTTGTTAGTCGTTAGTTATATAT--AAAAAATAGT-TAATTAGTTTGTAGTTAGTTAAAAAATT
** *
478392 AAGTTGCCATA-TTATTTGTTGAATTTATATTATATAAAAAATTTAGTTAATTAGTTTTTTTAGT
253 AAGTT---ATATTTATTTGTTGAATTTATATTATATAAAAAA-TTAGTTAATTAGTAGTTTAAGT
* *
478456 AGTAAATTATAAT-TAAAAATCGTTTATTAGTTTAAGTTATAATAAA
314 --TAAATTATAATAAAAAAATAGTTTATTAGTTTAAGTTAT-ATAAA
478502 TAATAGTTTA
Statistics
Matches: 326, Mismatches: 22, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
377 74 0.23
378 26 0.08
379 21 0.06
380 29 0.09
381 76 0.23
382 86 0.26
383 14 0.04
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (376 bp):
TTTATTTAAATTAGTTTATTATTATAAATTATTAGTTTGTTAGTTTAGGGTTTAGGGTAAAACAA
TTACTTAATTAGTTTGTTAGTTTAAGTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATA
AAAAATTATTTAATTAGTATGTTTGATAGTTATAAATTAAAAAATAATAATTAATTAGTTGTTTG
TTAGTCGTTAGTTATATATAAAAAATAGTTAATTAGTTTGTAGTTAGTTAAAAAATTAAGTTATA
TTTATTTGTTGAATTTATATTATATAAAAAATTAGTTAATTAGTAGTTTAAGTTAAATTATAATA
AAAAAATAGTTTATTAGTTTAAGTTATATAAAAGAATAATTATTTAATTAG
Found at i:478543 original size:15 final size:15
Alignment explanation
Indices: 478498--478544 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
478488 TAAGTTATAA
478498 TAAATAATAGTTTAT
1 TAAATAATAGTTTAT
** *
478513 TAGTTGA-AGTTATAT
1 TAAATAATAGTT-TAT
478528 TAAATAATAGTTTAT
1 TAAATAATAGTTTAT
478543 TA
1 TA
478545 GTTGTTTAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (15 bp):
TAAATAATAGTTTAT
Found at i:479873 original size:23 final size:23
Alignment explanation
Indices: 479833--479876 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
479823 ATTAATTATT
*
479833 ATTTAAATTAACTATATTATTTG
1 ATTTAAATCAACTATATTATTTG
* *
479856 ATTTAAATCAATTTTATTATT
1 ATTTAAATCAACTATATTATT
479877 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATCAACTATATTATTTG
Found at i:481055 original size:59 final size:58
Alignment explanation
Indices: 480989--481264 Score: 334
Period size: 59 Copynumber: 4.8 Consensus size: 58
480979 TTTCAAAATG
*
480989 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATTATTAATATCAAAAC
1 ATTAAATATTAATAATAA-ATCATTATTACTAATCATTACTAATTATTAATATCAAAAC
* * * *
481048 ATTAAATATTAATAATAAATCATTATTACTAATTATTATTAAATTATTAATATTAAATC
1 ATTAAATATTAATAATAAATCATTATTACTAATCATTACT-AATTATTAATATCAAAAC
* *
481107 ATTAAATATTAATAATAAATCATTATTACTAATCATTACTAA--ATT--T-T--TAAT
1 ATTAAATATTAATAATAAATCATTATTACTAATCATTACTAATTATTAATATCAAAAC
* * * **
481158 ATTAAATATTAATAGTAAATCATTATTACTAATTATTACTATATTTTTAATATCAAATT
1 ATTAAATATTAATAATAAATCATTATTACTAATCATTACTA-ATTATTAATATCAAAAC
* *
481217 ATTAAATATTAATAATAAAT-ATTACTATTAATCATTACTAAATTATTA
1 ATTAAATATTAATAATAAATCATTATTACTAATCATTACT-AATTATTA
481265 TTATTATTTT
Statistics
Matches: 187, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
51 40 0.21
52 1 0.01
53 1 0.01
54 3 0.02
56 4 0.02
57 1 0.01
58 43 0.23
59 94 0.50
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (58 bp):
ATTAAATATTAATAATAAATCATTATTACTAATCATTACTAATTATTAATATCAAAAC
Found at i:481071 original size:21 final size:21
Alignment explanation
Indices: 481033--481131 Score: 93
Period size: 21 Copynumber: 4.9 Consensus size: 21
481023 CATTACTAAT
*
481033 TATTAAT-ATCAAAACATTAAA
1 TATTAATAAT-AAATCATTAAA
481054 TATTAATAATAAATCA-T---
1 TATTAATAATAAATCATTAAA
* * *
481071 TATTACTAAT-TATTATTAAA
1 TATTAATAATAAATCATTAAA
*
481091 TTATTAATATTAAATCATTAAA
1 -TATTAATAATAAATCATTAAA
481113 TATTAATAATAAATCATTA
1 TATTAATAATAAATCATTA
481132 TTACTAATCA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
16 3 0.05
17 10 0.16
20 1 0.02
21 38 0.61
22 10 0.16
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTAATAATAAATCATTAAA
Found at i:481101 original size:14 final size:14
Alignment explanation
Indices: 481079--481228 Score: 64
Period size: 14 Copynumber: 10.8 Consensus size: 14
481069 ATTATTACTA
*
481079 ATTATTATTAAATT
1 ATTAATATTAAATT
*
481093 ATTAATATTAAATC
1 ATTAATATTAAATT
*
481107 ATTAAATATT-AATA
1 ATT-AATATTAAATT
*
481121 ATAAATCATT--ATT
1 ATTAAT-ATTAAATT
*
481134 ACTAATCATTACTAAATT
1 ATTAAT-A-T--TAAATT
*
481152 TTTAATATTAAA-T
1 ATTAATATTAAATT
* *
481165 ATTAATAGTAAATC
1 ATTAATATTAAATT
* *
481179 ATTATTACT-AATT
1 ATTAATATTAAATT
*
481192 ATTACTA-T--ATT
1 ATTAATATTAAATT
* *
481203 TTTAATATCAAATT
1 ATTAATATTAAATT
481217 ATTAAATATTAA
1 ATT-AATATTAA
481229 TAATAAATAT
Statistics
Matches: 103, Mismatches: 21, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
11 8 0.08
12 1 0.01
13 31 0.30
14 40 0.39
15 13 0.13
16 2 0.02
17 1 0.01
18 7 0.07
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.47
Consensus pattern (14 bp):
ATTAATATTAAATT
Found at i:481116 original size:15 final size:14
Alignment explanation
Indices: 481048--481182 Score: 54
Period size: 14 Copynumber: 9.9 Consensus size: 14
481038 ATATCAAAAC
481048 ATTAAAT-ATTAAT
1 ATTAAATCATTAAT
* *
481061 AATAAATCATTATT
1 ATTAAATCATTAAT
* *
481075 ACTAATTATTATTAA-
1 ATTAA--ATCATTAAT
481090 ATTATTAAT-ATTAAAT
1 ATTA--AATCATT-AAT
481106 CATTAAAT-ATTAAT
1 -ATTAAATCATTAAT
* *
481120 AATAAATCATTATT
1 ATTAAATCATTAAT
*
481134 ACT-AATCA-T--T
1 ATTAAATCATTAAT
* **
481144 ACTAAATTTTTAAT
1 ATTAAATCATTAAT
481158 ATTAAAT-ATTAAT
1 ATTAAATCATTAAT
*
481171 AGTAAATCATTA
1 ATTAAATCATTA
481183 TTACTAATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
10 4 0.04
11 3 0.03
12 2 0.02
13 28 0.30
14 33 0.35
15 13 0.14
16 6 0.06
17 5 0.05
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (14 bp):
ATTAAATCATTAAT
Found at i:481134 original size:24 final size:24
Alignment explanation
Indices: 481082--481185 Score: 72
Period size: 24 Copynumber: 4.3 Consensus size: 24
481072 ATTACTAATT
*
481082 ATTATTAAATTATTAATATTAAATC
1 ATTATTAAA-TATTAATAATAAATC
481107 ---ATTAAATATTAATAATAAATC
1 ATTATTAAATATTAATAATAAATC
* ** *
481128 ATTATTACTAATCATTACTAA-ATTTTT
1 ATTATTA--AAT-ATTAATAATA-AATC
* *
481155 AATATTAAATATTAATAGTAAATC
1 ATTATTAAATATTAATAATAAATC
481179 ATTATTA
1 ATTATTA
481186 CTAATTATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 17
0.67 0.14 0.19
Matches are distributed among these distances:
21 14 0.24
22 6 0.10
24 17 0.29
25 4 0.07
26 4 0.07
27 14 0.24
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (24 bp):
ATTATTAAATATTAATAATAAATC
Found at i:481185 original size:110 final size:109
Alignment explanation
Indices: 480984--481270 Score: 358
Period size: 110 Copynumber: 2.5 Consensus size: 109
480974 AATAATTTCA
* * * *
480984 AAATGATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATTATTAATATCAAAACA
1 AAATCATTAAATATTAATAATAA-AT-ATTACTACTAATCATTACTAA--ATT-AT-T---AATA
* *
481049 TTAAATATTAATAATAAATCATTATTACTAATTATTATTAAATTATTAATATT
57 TTAAATATTAATAATAAATCATTATTACTAATTATTACTAAATTATTAATATC
* *
481102 AAATCATTAAATATTAATAATAAATCATTATTACTAATCATTACTAAATTTTTAATATTAAATAT
1 AAATCATTAAATATTAATAATAAAT-ATTACTACTAATCATTACTAAATTATTAATATTAAATAT
* * *
481167 TAATAGTAAATCATTATTACTAATTATTACTATATTTTTAATATC
65 TAATAATAAATCATTATTACTAATTATTACTAAATTATTAATATC
* * *
481212 AAATTATTAAATATTAATAATAAATATTACTATTAATCATTACTAAATTATTATTATTA
1 AAATCATTAAATATTAATAATAAATATTACTACTAATCATTACTAAATTATTAATATTA
481271 TTTTAAATAT
Statistics
Matches: 155, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
109 30 0.19
110 75 0.48
113 1 0.01
114 1 0.01
115 3 0.02
117 23 0.15
118 22 0.14
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (109 bp):
AAATCATTAAATATTAATAATAAATATTACTACTAATCATTACTAAATTATTAATATTAAATATT
AATAATAAATCATTATTACTAATTATTACTAAATTATTAATATC
Found at i:481194 original size:27 final size:27
Alignment explanation
Indices: 481113--481195 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
481103 AATCATTAAA
481113 TATTAATAATAAATCATTATTACTAAT
1 TATTAATAATAAATCATTATTACTAAT
* * ** * * *
481140 CA-T--TACTAAATTTTTAATATTAAA
1 TATTAATAATAAATCATTATTACTAAT
*
481164 TATTAATAGTAAATCATTATTACTAAT
1 TATTAATAATAAATCATTATTACTAAT
481191 TATTA
1 TATTA
481196 CTATATTTTT
Statistics
Matches: 39, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
24 16 0.41
25 1 0.03
26 1 0.03
27 21 0.54
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (27 bp):
TATTAATAATAAATCATTATTACTAAT
Found at i:481628 original size:52 final size:52
Alignment explanation
Indices: 481572--481698 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 52
481562 TTATTCCATA
* * *
481572 ATTATTAGTAATAATTATTAAATCATAA-GTATAAAATCATT-ATTATAATTTC
1 ATTATTACTAATAATTATTAAATCATAATG-ATAAAAT-ATTAATAATAACTTC
*
481624 ATTATTACTAATAATTATT--ATCA-AATGATTAAATATTAATAATAACTTC
1 ATTATTACTAATAATTATTAAATCATAATGATAAAATATTAATAATAACTTC
* * *
481673 ATTATTATTAATCATTACTAAATCAT
1 ATTATTACTAATAATTATTAAATCAT
481699 TCTTATCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
48 3 0.05
49 33 0.52
50 5 0.08
51 4 0.06
52 18 0.29
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (52 bp):
ATTATTACTAATAATTATTAAATCATAATGATAAAATATTAATAATAACTTC
Found at i:481736 original size:62 final size:59
Alignment explanation
Indices: 481627--481814 Score: 191
Period size: 60 Copynumber: 3.3 Consensus size: 59
481617 TAATTTCATT
* *
481627 ATTACTAATAATTATTATCAAATGATTAAATATTAATAATAACTTCATTATTATTAATC
1 ATTACTAATAATTATTATCAAATCATTAAATATTAATAATAACTTCATTATTACTAATC
* *
481686 ATTACTAAATCATTCTTATCAAATCATTAAATATTAAAATAATAACTTCATTATTAC---T-
1 ATTACT-AATAATTATTATCAAATCATTAAATATT--AATAATAACTTCATTATTACTAATC
* * * *
481744 A--A-T--T-GTTACTATCAAAACATTAAATATTAATAATAA-ATCATTATTACTAATC
1 ATTACTAATAATTATTATCAAATCATTAAATATTAATAATAACTTCATTATTACTAATC
481796 ATTACTAAATAATTATTAT
1 ATTACT-AATAATTATTAT
481815 AATTTTAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 28
0.73 0.08 0.20
Matches are distributed among these distances:
48 10 0.10
49 8 0.08
51 21 0.20
52 2 0.02
54 1 0.01
55 2 0.02
56 1 0.01
58 2 0.02
59 13 0.12
60 25 0.24
62 19 0.18
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (59 bp):
ATTACTAATAATTATTATCAAATCATTAAATATTAATAATAACTTCATTATTACTAATC
Found at i:481757 original size:111 final size:110
Alignment explanation
Indices: 481616--481814 Score: 299
Period size: 111 Copynumber: 1.8 Consensus size: 110
481606 AATCATTATT
* * ** * *
481616 ATAATTTCATTATTACTAATAATTATTATCAAATGATTAAATATTAATAATAACTTCATTATTAT
1 ATAACTTCATTATTACTAATAATTACTATCAAAACATTAAATATTAATAATAA-ATCATTATTAC
* *
481681 TAATCATTACTAAATCATTCTTATCAAATCATTAAATATTAAAATA
65 TAATCATTACTAAATAATTATTATCAAATCATTAAATATTAAAATA
**
481727 ATAACTTCATTATTACTAATTGTTACTATCAAAACATTAAATATTAATAATAAATCATTATTACT
1 ATAACTTCATTATTACTAATAATTACTATCAAAACATTAAATATTAATAATAAATCATTATTACT
481792 AATCATTACTAAATAATTATTAT
66 AATCATTACTAAATAATTATTAT
481815 AATTTTAAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
110 31 0.40
111 47 0.60
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.43
Consensus pattern (110 bp):
ATAACTTCATTATTACTAATAATTACTATCAAAACATTAAATATTAATAATAAATCATTATTACT
AATCATTACTAAATAATTATTATCAAATCATTAAATATTAAAATA
Found at i:481802 original size:48 final size:50
Alignment explanation
Indices: 481686--481861 Score: 152
Period size: 48 Copynumber: 3.6 Consensus size: 50
481676 ATTATTAATC
* *
481686 ATTACTAAATCATT-CTTATCAAATCATTAAATATTAAAATAATAACTTCATT
1 ATTACT-AATCATTAC-TATCAAAACATTAAATATT-AAATAATAACATCATT
**
481738 ATTACTAATTGTTACTATCAAAACATTAAATATT-AATAATAA-ATCATT
1 ATTACTAATCATTACTATCAAAACATTAAATATTAAATAATAACATCATT
* * *
481786 ATTACTAATCATTACTA--AATAATTATTATAATTTTAAAT-ATAAAATCATT
1 ATTACTAATCATTACTATCAA-AA-CATTA-AATATTAAATAATAACATCATT
* * *
481836 ATTA--AATCATGATTATCAAATCATTA
1 ATTACTAATCATTACTATCAAAACATTA
481862 CTAAATCAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
46 2 0.02
47 2 0.02
48 37 0.36
49 18 0.17
50 15 0.14
51 23 0.22
52 7 0.07
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (50 bp):
ATTACTAATCATTACTATCAAAACATTAAATATTAAATAATAACATCATT
Found at i:484946 original size:21 final size:20
Alignment explanation
Indices: 484916--484975 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
484906 TTTTATTTTT
484916 TTAAATATCAAACAAATTTG
1 TTAAATATCAAACAAATTTG
* *
484936 TTAATTAATCAATCAAATTTG
1 TTAAAT-ATCAAACAAATTTG
*
484957 TTAAATATCAAATAAATTT
1 TTAAATATCAAACAAATTT
484976 AAATATCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (20 bp):
TTAAATATCAAACAAATTTG
Found at i:485059 original size:17 final size:17
Alignment explanation
Indices: 485037--485095 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
485027 AGATTATAAA
485037 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
*
485054 TTAAACAACAATAAATATTT
1 TTAAACAA-AAT--ATTTTT
*
485074 TTAAACACAATATTTTT
1 TTAAACAAAATATTTTT
485091 TTAAA
1 TTAAA
485096 TGAGAATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 18 0.50
18 3 0.08
19 3 0.08
20 12 0.33
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:485587 original size:28 final size:30
Alignment explanation
Indices: 485547--485609 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
485537 ATTTTTTATA
485547 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
485577 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
485605 TAATA
1 TAATA
485610 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:485616 original size:28 final size:28
Alignment explanation
Indices: 485551--485674 Score: 103
Period size: 28 Copynumber: 4.4 Consensus size: 28
485541 TTTATATAAT
*
485551 ATAATATATAACTTAAACTAACAAACTA
1 ATAATTTATAACTTAAACTAACAAACTA
*
485579 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-TTATAACTTAAACTAACAAACTA
* *
485607 ATAATTTAT-ACTAACAACCTAATTAAACCTA
1 ATAATTTATAACTTA-AA-CTAA-CAAA-CTA
** *
485638 A-ACCTTA-AACCCTAAACTAACAAACTA
1 ATAATTTATAA-CTTAAACTAACAAACTA
485665 ATAATTTATA
1 ATAATTTATA
485675 TAATAAACTA
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
27 10 0.13
28 39 0.51
29 11 0.14
30 10 0.13
31 6 0.08
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (28 bp):
ATAATTTATAACTTAAACTAACAAACTA
Found at i:485619 original size:21 final size:21
Alignment explanation
Indices: 485586--485629 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
485576 CTAATATAAT
485586 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* * *
485607 ATAATTTATACTAACAACCTA
1 ATAACTTAAACTAACAAACTA
485628 AT
1 AT
485630 TAAACCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:486160 original size:29 final size:29
Alignment explanation
Indices: 486126--486196 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
486116 GGTCGCACGG
486126 ATGCCATGGCGACGTCCTTCCTCGCCCGA
1 ATGCCATGGCGACGTCCTTCCTCGCCCGA
*
486155 ATGCCATGGCGACGTCCTTCCTCGCCCGG
1 ATGCCATGGCGACGTCCTTCCTCGCCCGA
486184 ATGCCATGGCGAC
1 ATGCCATGGCGAC
486197 ATACCCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.14, C:0.39, G:0.27, T:0.20
Consensus pattern (29 bp):
ATGCCATGGCGACGTCCTTCCTCGCCCGA
Found at i:486612 original size:19 final size:19
Alignment explanation
Indices: 486585--486624 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
486575 TATATTTAAT
*
486585 ATTTAATTTAAAATAATAA
1 ATTTAATTTAAAAGAATAA
*
486604 ATTTTATTTAAAAGAATAA
1 ATTTAATTTAAAAGAATAA
486623 AT
1 AT
486625 ATGAATGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTAATTTAAAAGAATAA
Found at i:486980 original size:2 final size:2
Alignment explanation
Indices: 486973--487001 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
486963 ACTATCAGAT
486973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
487002 TATCAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:487090 original size:16 final size:13
Alignment explanation
Indices: 487045--487087 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 13
487035 ATTTAATCTA
487045 TATTTATAAAAAT
1 TATTTATAAAAAT
487058 TATTATATAAAAAT
1 TATT-TATAAAAAT
487072 TATTGTATAATAAAT
1 TATT-TATAA-AAAT
487087 T
1 T
487088 TATAACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 4 0.15
14 18 0.67
15 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TATTTATAAAAAT
Found at i:488393 original size:19 final size:18
Alignment explanation
Indices: 488311--488401 Score: 62
Period size: 19 Copynumber: 4.7 Consensus size: 18
488301 GGTTTCGTAA
488311 AATATTATTTAAATTTAAAT
1 AATATTATTTAAA--TAAAT
488331 AGATA--ATTTAAA-AAAT
1 A-ATATTATTTAAATAAAT
*
488347 AATATTACTTCAAATAAACTATT
1 AATATTA-TTTAAAT-AA--A-T
488370 AATATTATTTCAAATAAAT
1 AATATTATTT-AAATAAAT
*
488389 AATATGATTTAAA
1 AATATTATTTAAA
488402 AATTAAATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 22
0.70 0.04 0.27
Matches are distributed among these distances:
15 3 0.05
16 5 0.09
17 1 0.02
18 8 0.14
19 17 0.29
20 4 0.07
21 3 0.05
22 5 0.09
23 12 0.21
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
AATATTATTTAAATAAAT
Found at i:488410 original size:21 final size:19
Alignment explanation
Indices: 488384--488423 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
488374 TTATTTCAAA
488384 TAAATAATATGATTTAAAAAT
1 TAAATAA-AT-ATTTAAAAAT
*
488405 TAAATAAATATTTTAAAAT
1 TAAATAAATATTTAAAAAT
488424 ATTTTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TAAATAAATATTTAAAAAT
Found at i:488492 original size:23 final size:24
Alignment explanation
Indices: 488432--488492 Score: 56
Period size: 23 Copynumber: 2.6 Consensus size: 24
488422 ATATTTTCAT
* *
488432 AATAT-TATAAATATACTTTTTAG
1 AATATATATAAATAAACTTTATAG
* *
488455 AATA-ATTTAGTATAAACTTTATA-
1 AATATATATA-AATAAACTTTATAG
488478 AATATATATAAATAA
1 AATATATATAAATAA
488493 TTATTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (24 bp):
AATATATATAAATAAACTTTATAG
Found at i:489335 original size:18 final size:17
Alignment explanation
Indices: 489312--489346 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
489302 AATATTATTT
489312 CAACTTTAATTTAGATCA
1 CAACTTTAATTTA-ATCA
*
489330 CAACTTTAGTTTAATCA
1 CAACTTTAATTTAATCA
489347 ATTTCCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (17 bp):
CAACTTTAATTTAATCA
Found at i:489406 original size:28 final size:27
Alignment explanation
Indices: 489369--489423 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
489359 CAACTTTTAT
489369 TATTGATAAATAAACTCACTTACATTAA
1 TATTGATAAATAAACTCACTTAC-TTAA
*
489397 TATTGTTAAATAAACTCACTTACTTAA
1 TATTGATAAATAAACTCACTTACTTAA
489424 GGAAAGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (27 bp):
TATTGATAAATAAACTCACTTACTTAA
Found at i:489711 original size:23 final size:23
Alignment explanation
Indices: 489667--489712 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
489657 CAATATTTTA
***
489667 TTTTAAATAATTTATCTTTATAT
1 TTTTAAATAATTTATAACTATAT
*
489690 TTTTAACTAATTTATAACTATAT
1 TTTTAAATAATTTATAACTATAT
489713 ATTGAGTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAAATAATTTATAACTATAT
Found at i:490620 original size:73 final size:73
Alignment explanation
Indices: 490484--490620 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
490474 TTTTAAGTTT
* * ** * *
490484 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTTAAACACTTGAAAATATGGTAATTCAG
1 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCAAAAACATGATAATTCAG
490549 TGGGCTCC
66 TGGGCTCC
*
490557 AATAATTAAAAAATATTTTTAAACATATTTTTTT-TATTAAAAAACTCAAAAACATGATGATTCA
1 AATAATTAAAAAATATTTTTAAACATATTTTTTTAT-TTAAAAAACTCAAAAACATGATAATTCA
490621 ATGGACCCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 1 0.02
73 55 0.98
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.40
Consensus pattern (73 bp):
AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTAAAAAACTCAAAAACATGATAATTCAG
TGGGCTCC
Found at i:491235 original size:31 final size:31
Alignment explanation
Indices: 491197--491263 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
491187 GCGGGAATGA
*
491197 TCCCTAATATTATTGATTCATTAGCTTTTAG
1 TCCCTAATATTATTGATTCATTAGATTTTAG
*
491228 TCCCTAATATTATTGATTCATTCGATTTTAG
1 TCCCTAATATTATTGATTCATTAGATTTTAG
491259 TCCCT
1 TCCCT
491264 CATTCACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (31 bp):
TCCCTAATATTATTGATTCATTAGATTTTAG
Found at i:492658 original size:26 final size:26
Alignment explanation
Indices: 492621--492670 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
492611 AACTTTTCAA
492621 AAATTAATAAAAGAATAA-TTACATGG
1 AAATTAATAAAA-AATAATTTACATGG
492647 AAATTGAA-AAAAAATAATTTACAT
1 AAATT-AATAAAAAATAATTTACAT
492671 AAAGGCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.23
26 15 0.68
27 2 0.09
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (26 bp):
AAATTAATAAAAAATAATTTACATGG
Found at i:493351 original size:3 final size:3
Alignment explanation
Indices: 493345--493374 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
493335 TTTTTTCTTC
493345 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
493375 GAAAAATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:502583 original size:44 final size:43
Alignment explanation
Indices: 502478--502583 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 43
502468 TTCTTAATTT
* *
502478 TTTTTATCTTTATAATTGATGCCTCTAATTCTTGTAATCCTAC
1 TTTTTATCTTTATAATTGATGCATCTAATTCTTGTAATCATAC
* * * *
502521 TTTTTATCTTTACAATTGATGTATTTAATT-TTTTCAATCATACC
1 TTTTTATCTTTATAATTGATGCATCTAATTCTTGT-AATCATA-C
502565 TTTTTA-CATTTATAATTGA
1 TTTTTATC-TTTATAATTGA
502584 CGATCCTAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
42 3 0.06
43 33 0.62
44 17 0.32
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (43 bp):
TTTTTATCTTTATAATTGATGCATCTAATTCTTGTAATCATAC
Found at i:502703 original size:42 final size:42
Alignment explanation
Indices: 502546--502812 Score: 196
Period size: 42 Copynumber: 6.4 Consensus size: 42
502536 TTGATGTATT
* * **
502546 TAATTTTTTCAATCAT-ACCTTTTTACATTTATAATTGACGATCC
1 TAATTTTTTCAATC-TCA-CTTTTTACCTTTATAATT-AGGCCCC
* * * * *
502590 TAAGTTTTTCAATCTCACTTTGTAACTTTATAATT-GAGCTCT
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTAG-GCCCC
* * * *
502632 TGA-TTTTTCAATCTCTCTTTCTACATTTATAATTACGGCCCC
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTA-GGCCCC
* *
502674 TAATTTTTT-AATATCACTTTTTACCTTTATAATTGAGG-CCA
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAATT-AGGCCCC
* * *
502715 TAATTTTTTCAATCCCAC-TTTTAACTTATATAATTTAGGCCCT
1 TAATTTTTTCAATCTCACTTTTTACCTT-TATAA-TTAGGCCCC
*
502758 TAATTTTTTCAATCTCACCTTTTA-CTTTA-AATTTGAGG--CC
1 TAATTTTTTCAATCTCACTTTTTACCTTTATAA-TT-AGGCCCC
502798 TAATTTTTT-AATCTC
1 TAATTTTTTCAATCTC
502813 TGTAAGGCCC
Statistics
Matches: 185, Mismatches: 26, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
39 6 0.03
40 10 0.05
41 51 0.28
42 52 0.28
43 47 0.25
44 19 0.10
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (42 bp):
TAATTTTTTCAATCTCACTTTTTACCTTTATAATTAGGCCCC
Found at i:502708 original size:83 final size:81
Alignment explanation
Indices: 502546--502812 Score: 244
Period size: 84 Copynumber: 3.2 Consensus size: 81
502536 TTGATGTATT
** *
502546 TAATTTTTTCAATCATACCTTTTTACATTTATAATTGAC-GATCCTAAGTTTTTCAATCTCACTT
1 TAATTTTTTCAATC-T-CC-TTTTACATTTATAATT-ACGGCCCCTAA-TTTTTTAATCTCACTT
* *
502610 TGTAACTTTATAATTGA-GCTCT
61 T-TTACTTTATAATTGAGGC-CA
* *
502632 TGA-TTTTTCAATCTCTCTTTCTACATTTATAATTACGGCCCCTAATTTTTTAATATCACTTTTT
1 TAATTTTTTCAATCTC-CTTT-TACATTTATAATTACGGCCCCTAATTTTTTAATCTCACTTTTT
502696 ACCTTTATAATTGAGGCCA
64 A-CTTTATAATTGAGGCCA
* * *
502715 TAATTTTTTCAATCCCACTTTTA-ACTTATATAATTTA-GGCCCTTAATTTTTTCAATCTCACCT
1 TAATTTTTTCAATCTC-CTTTTACA-TT-TATAA-TTACGGCCCCTAATTTTTT-AATCTCACTT
502778 TTTACTTTA-AATTTGAGGCC-
61 TTTACTTTATAA-TTGAGGCCA
502798 TAATTTTTT-AATCTC
1 TAATTTTTTCAATCTC
502813 TGTAAGGCCC
Statistics
Matches: 156, Mismatches: 14, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
82 8 0.05
83 51 0.33
84 70 0.45
85 25 0.16
86 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (81 bp):
TAATTTTTTCAATCTCCTTTTACATTTATAATTACGGCCCCTAATTTTTTAATCTCACTTTTTAC
TTTATAATTGAGGCCA
Found at i:502924 original size:27 final size:27
Alignment explanation
Indices: 502889--502951 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
502879 AACCTTATAC
502889 ATAGGCTTGGGCTAAGTGAGCATTCAT
1 ATAGGCTTGGGCTAAGTGAGCATTCAT
502916 ATAGGCTTGGGCTAAGTGAGCATTCAT
1 ATAGGCTTGGGCTAAGTGAGCATTCAT
*
502943 TTAGGCTTG
1 ATAGGCTTG
502952 AGTTTGGCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (27 bp):
ATAGGCTTGGGCTAAGTGAGCATTCAT
Found at i:506557 original size:28 final size:28
Alignment explanation
Indices: 506521--506591 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
506511 ACTAATTAAT
506521 ATATGAAC-AATCAAATGAATTAATAAACA
1 ATAT-AACAAATCAAATGAATTAATAAA-A
** *
506550 ATATAACAAAT-AAATTTATTAATAAAT
1 ATATAACAAATCAAATGAATTAATAAAA
*
506577 ATA-AACGAATCAAAT
1 ATATAACAAATCAAAT
506592 ATATCTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 6 0.17
27 7 0.19
28 16 0.44
29 7 0.19
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.28
Consensus pattern (28 bp):
ATATAACAAATCAAATGAATTAATAAAA
Found at i:507865 original size:36 final size:36
Alignment explanation
Indices: 507820--507891 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
507810 AATGGGAGAA
507820 AGAAATGATTTTTGGGATGATTTTGAAGCTAAATGG
1 AGAAATGATTTTTGGGATGATTTTGAAGCTAAATGG
507856 AGAAATGATTTTTGGGATGATTTTGAAGCTAAATGG
1 AGAAATGATTTTTGGGATGATTTTGAAGCTAAATGG
507892 GCTAGGGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (36 bp):
AGAAATGATTTTTGGGATGATTTTGAAGCTAAATGG
Found at i:513072 original size:30 final size:29
Alignment explanation
Indices: 513025--513082 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
513015 TTTCTTACCC
513025 AACTTTCAATTTGATCAATTTGCTCACTG
1 AACTTTCAATTTGATCAATTTGCTCACTG
513054 AACTTTACAA-TTGAATCAATTTGCTCACT
1 AACTTT-CAATTTG-ATCAATTTGCTCACT
513083 CGACCGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (29 bp):
AACTTTCAATTTGATCAATTTGCTCACTG
Found at i:523217 original size:54 final size:54
Alignment explanation
Indices: 523130--523237 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
523120 TGGTAAACTA
* *
523130 TGTATTTAGTTACCCAATTATTCTCGCATATTTTTATTACCAAACTATTACTTT
1 TGTATTTAGTTACCCAATTATTCTCACACATTTTTATTACCAAACTATTACTTT
* * * *
523184 TGTATTTAGTTATCCAATTATTCTTACACATTTTTGTTACTAAACTATTACTTT
1 TGTATTTAGTTACCCAATTATTCTCACACATTTTTATTACCAAACTATTACTTT
523238 GGTTCTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (54 bp):
TGTATTTAGTTACCCAATTATTCTCACACATTTTTATTACCAAACTATTACTTT
Found at i:523836 original size:30 final size:30
Alignment explanation
Indices: 523802--523858 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
523792 ACTAATAACA
523802 TGAAAACTGTTTTACGTAAAATGAATTACT
1 TGAAAACTGTTTTACGTAAAATGAATTACT
** *
523832 TGAAATTTGTTTTATGTAAAATGAATT
1 TGAAAACTGTTTTACGTAAAATGAATT
523859 TCATTTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (30 bp):
TGAAAACTGTTTTACGTAAAATGAATTACT
Found at i:524081 original size:42 final size:40
Alignment explanation
Indices: 524008--524087 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 40
523998 CGTAAAATGA
*
524008 ATTATTATTTTTATAAAAATAATAAATTATATTAATTATTT
1 ATTATTATTATTATAAAAATAATAAATTATATT-ATTATTT
524049 ATTATATATTATTA-AAAATATAATACAA-TATATTATTAT
1 ATTAT-TATTATTATAAAA-ATAATA-AATTATATTATTAT
524088 AATATAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
41 14 0.40
42 19 0.54
43 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
ATTATTATTATTATAAAAATAATAAATTATATTATTATTT
Found at i:524133 original size:17 final size:19
Alignment explanation
Indices: 524110--524159 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 19
524100 TTTATATTAC
524110 TATAATATTAAAA-ATATA
1 TATAATATTAAAATATATA
524128 -ATAATATTAAAATTATATA
1 TATAATATTAAAA-TATATA
524147 TATATATATTAAA
1 TATA-ATATTAAA
524160 TATTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.43
19 5 0.18
20 3 0.11
21 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAATATTAAAATATATA
Found at i:524329 original size:27 final size:27
Alignment explanation
Indices: 524273--524331 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
524263 GAAAAATATT
*
524273 TAAAAATATTTTACGAAAAATTAGATAA
1 TAAAAATATTTTAC-AAAAATTAGAAAA
524301 TAAAATATATTTTA-AAAAATTTA-AAAA
1 TAAAA-ATATTTTACAAAAA-TTAGAAAA
524328 TAAA
1 TAAA
524332 TTACATTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 12 0.43
28 8 0.29
29 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
TAAAAATATTTTACAAAAATTAGAAAA
Found at i:524397 original size:15 final size:15
Alignment explanation
Indices: 524377--524407 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
524367 AGAAAAATGT
524377 AAAAAACATTTTCTA
1 AAAAAACATTTTCTA
524392 AAAAAACATTTTCTA
1 AAAAAACATTTTCTA
524407 A
1 A
524408 CTATAAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAAACATTTTCTA
Found at i:528408 original size:105 final size:105
Alignment explanation
Indices: 528103--528393 Score: 377
Period size: 105 Copynumber: 2.8 Consensus size: 105
528093 AAAGTTGAAC
* *
528103 AAGTTCTTCTCATTATGAACTTCTTCTCCTTT-AGGACGAGTTCTTCTCATTATGAACTCTTCTG
1 AAGTTCTTCTCATTACGAA-TT-TTCTCCTTTAAGG-TGAGTTCTTCTCATTATGAACTCTTCTG
* * ** *
528167 GAAATGTCGATTCACCTTCTTCTAGGGTAAATTTGAAAGGAAC
63 GAAATGTTGGTTCACCTTCTTCTAGGGTGGATTTGAAAGGAAA
* * * ** * * * *
528210 ATGCTCTTCACATTACGAACCTTCTCATTTAAGATGAGTTCTTCTCACTATGAACTCTTTTGGAA
1 AAGTTCTTCTCATTACGAATTTTCTCCTTTAAGGTGAGTTCTTCTCATTATGAACTCTTCTGGAA
*
528275 ATGTTGGTTCACATTCTTCTAGGGTGGATTTGAAAGGAAA
66 ATGTTGGTTCACCTTCTTCTAGGGTGGATTTGAAAGGAAA
* *
528315 AAGTTATTCTCATCACGAATTTTCTCCTTTAAGGTGAGTTCTTCTCATTATGAACTCTTCTGGAA
1 AAGTTCTTCTCATTACGAATTTTCTCCTTTAAGGTGAGTTCTTCTCATTATGAACTCTTCTGGAA
528380 ATGTTGGTTCACCT
66 ATGTTGGTTCACCT
528394 CTTTCTGCGG
Statistics
Matches: 154, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
105 137 0.89
106 2 0.01
107 15 0.10
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (105 bp):
AAGTTCTTCTCATTACGAATTTTCTCCTTTAAGGTGAGTTCTTCTCATTATGAACTCTTCTGGAA
ATGTTGGTTCACCTTCTTCTAGGGTGGATTTGAAAGGAAA
Found at i:529364 original size:11 final size:11
Alignment explanation
Indices: 529340--529408 Score: 77
Period size: 12 Copynumber: 6.1 Consensus size: 11
529330 TCTCAAACCC
529340 TCATTTTTCTTT
1 TCATTTTT-TTT
*
529352 TCATTTTTATT
1 TCATTTTTTTT
529363 TCATTTTTTTTT
1 TCA-TTTTTTTT
**
529375 TCATTTTTTCA
1 TCATTTTTTTT
529386 TC-TTTTTTTT
1 TCATTTTTTTT
529396 TCATTTTTCTTT
1 TCATTTTT-TTT
529408 T
1 T
529409 TCACTTTTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.17
11 18 0.38
12 22 0.46
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (11 bp):
TCATTTTTTTT
Found at i:529369 original size:23 final size:22
Alignment explanation
Indices: 529340--529403 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 22
529330 TCTCAAACCC
*
529340 TCATTTTTCTTTTCATTTTTATT
1 TCATTTTTTTTTTCATTTTT-TT
529363 TCATTTTTTTTTTCA--TTTTT
1 TCATTTTTTTTTTCATTTTTTT
529383 TCATCTTTTTTTTTCATTTTT
1 TCAT-TTTTTTTTTCATTTTT
529404 CTTTTTCACT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 6 0.16
21 14 0.38
23 17 0.46
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (22 bp):
TCATTTTTTTTTTCATTTTTTT
Found at i:529394 original size:13 final size:13
Alignment explanation
Indices: 529378--529417 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
529368 TTTTTTTTCA
529378 TTTTTTCATCTTT
1 TTTTTTCATCTTT
529391 TTTTTTCAT-TTT
1 TTTTTTCATCTTT
529403 TCTTTTTCA-CTTT
1 T-TTTTTCATCTTT
529416 TT
1 TT
529418 CATTCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCATCTTT
Found at i:529404 original size:20 final size:20
Alignment explanation
Indices: 529340--529403 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 20
529330 TCTCAAACCC
*
529340 TCATTTTTCTTTTCATTTTTATT
1 TCATTTTTTTTTTCA--TTT-TT
529363 TCATTTTTTTTTTCATTTTT
1 TCATTTTTTTTTTCATTTTT
529383 TCATCTTTTTTTTTCATTTTT
1 TCAT-TTTTTTTTTCATTTTT
529404 CTTTTTCACT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 6 0.15
21 19 0.49
23 14 0.36
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (20 bp):
TCATTTTTTTTTTCATTTTT
Found at i:529409 original size:34 final size:33
Alignment explanation
Indices: 529355--529420 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
529345 TTTCTTTTCA
*
529355 TTTTTATTTCATTTTTTTTTTCATTTTTTCATC
1 TTTTTATTTCATTTTTTTTTTCACTTTTTCATC
*
529388 TTTTTTTTTCATTTTTCTTTTTCACTTTTTCAT
1 TTTTTATTTCATTTTT-TTTTTCACTTTTTCAT
529421 TCATTCATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (33 bp):
TTTTTATTTCATTTTTTTTTTCACTTTTTCATC
Found at i:529431 original size:26 final size:26
Alignment explanation
Indices: 529379--529437 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
529369 TTTTTTTCAT
** *
529379 TTTTTCATCTTTTTTTTTCATTTTTC
1 TTTTTCATCTTTTTCATTCATTATTC
529405 TTTTTCA-CTTTTTCATTCATTCATTC
1 TTTTTCATCTTTTTCATTCATT-ATTC
*
529431 TTCTTCA
1 TTTTTCA
529438 AGCATAGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTCATCTTTTTCATTCATTATTC
Found at i:532973 original size:14 final size:14
Alignment explanation
Indices: 532951--532984 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
532941 GAAATGAATG
532951 TAAAAAATGAAGAA
1 TAAAAAATGAAGAA
*
532965 TAAAGAATGAAGAA
1 TAAAAAATGAAGAA
532979 TGAAAA
1 T-AAAA
532985 TGTAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (14 bp):
TAAAAAATGAAGAA
Found at i:536219 original size:21 final size:21
Alignment explanation
Indices: 536178--536219 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
536168 CGACTATTCG
* *
536178 TTATAATTGATCGATTTATCA
1 TTATAACTGATCGATTAATCA
536199 TTATAACTGAT-GACTTAATCA
1 TTATAACTGATCGA-TTAATCA
536220 AGTGTAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (21 bp):
TTATAACTGATCGATTAATCA
Found at i:537664 original size:149 final size:148
Alignment explanation
Indices: 537420--537725 Score: 441
Period size: 149 Copynumber: 2.1 Consensus size: 148
537410 ATCTTAAAAG
* * * * *
537420 TTCGGTACTCTAGTTTCTTTAGCTTTTAATGCATGATTTCCCGCGCTTTAATCGTTTTCAAGATT
1 TTCGGTACTCTAGCTCCTTTAGCTTTTAATGCATGACTTCCCGAGCTTTAATCATTTTCAAGATT
* * * * * *
537485 AATGTGCAACCTTCCCGGTGTTTTATTCGTTGTTTCCATTATGCAGTTTGTTGGCTCCATACTTG
66 AATGCGCAACCTTCCCAGTGCTTTACTCGTTATTTCCATTATGCAGTTTGTTGGCTCCATACCTG
537550 TTTAAGTTATTTTGAATA
131 TTTAAGTTATTTTGAATA
* *
537568 TTCGGTACTCTAGCTCCTTTAGCTTTTAATGCATGACCTTCCCGATCTTTATTCATTTTCAAGAT
1 TTCGGTACTCTAGCTCCTTTAGCTTTTAATGCATGA-CTTCCCGAGCTTTAATCATTTTCAAGAT
* * *
537633 TAATGCGCGACCTTCCCATTGCTTTACTCGTTATTTCCGTTATGCAGTTTGTTGGCTCCATACCT
65 TAATGCGCAACCTTCCCAGTGCTTTACTCGTTATTTCCATTATGCAGTTTGTTGGCTCCATACCT
*
537698 GTTTAGGTTATTTTGAATA
130 GTTTAAGTTATTTTGAATA
*
537717 TTCAGTACT
1 TTCGGTACT
537726 ATAGTTTTGT
Statistics
Matches: 139, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
148 34 0.24
149 105 0.76
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (148 bp):
TTCGGTACTCTAGCTCCTTTAGCTTTTAATGCATGACTTCCCGAGCTTTAATCATTTTCAAGATT
AATGCGCAACCTTCCCAGTGCTTTACTCGTTATTTCCATTATGCAGTTTGTTGGCTCCATACCTG
TTTAAGTTATTTTGAATA
Found at i:541017 original size:64 final size:64
Alignment explanation
Indices: 540938--541077 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 64
540928 CGGATCTTGG
* * *
540938 CAGGTCGGGTAAAATCGGATACAGGTCA-ATTCAGGTTGATTTGATACCAGATCCAGATCGGGTT
1 CAGGTCGGGTCAAATCAG-TACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
* * * * * *
541002 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACATCAGATCCAGATCGGGTT
1 CAGGTCGGGTCAAATCAGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
*
541066 CATGTCGGGTCA
1 CAGGTCGGGTCA
541078 TTTTCAGTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 6 0.09
64 58 0.91
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (64 bp):
CAGGTCGGGTCAAATCAGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
Found at i:541791 original size:17 final size:18
Alignment explanation
Indices: 541769--541818 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
541759 ATATTATATA
541769 TATATATAA-TATAAAAT
1 TATATATAACTATAAAAT
*
541786 TATATATAAACTATATAAT
1 TATATAT-AACTATAAAAT
541805 TAT-TATAAACTATA
1 TATATAT-AACTATA
541819 TATATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.23
18 13 0.43
19 10 0.33
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATATAACTATAAAAT
Found at i:541813 original size:18 final size:18
Alignment explanation
Indices: 541778--541917 Score: 77
Period size: 18 Copynumber: 7.3 Consensus size: 18
541768 ATATATATAA
*
541778 TATAAAATTATATATAAAC
1 TATATAATTAT-TATAAAC
541797 TATATAATTATTATAAAC
1 TATATAATTATTATAAAC
* **
541815 TATATATATAAATTAT-ATT
1 TATATA-AT-TATTATAAAC
* * *
541834 TATGTGCACTATATATAAAAC
1 TATAT-AATTAT-TAT-AAAC
**
541855 TATGTATATAAAATTATAAAC
1 TA--TATA-ATTATTATAAAC
*
541876 TATAT-TTATATTATAAAC
1 TATATAAT-TATTATAAAC
*
541894 TATATAATTATTATAAGC
1 TATATAATTATTATAAAC
541912 TATATA
1 TATATA
541918 TAAATTATGT
Statistics
Matches: 91, Mismatches: 19, Indels: 23
0.68 0.14 0.17
Matches are distributed among these distances:
18 44 0.48
19 25 0.27
20 5 0.05
21 9 0.10
22 3 0.03
23 5 0.05
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TATATAATTATTATAAAC
Found at i:541885 original size:21 final size:18
Alignment explanation
Indices: 541867--542047 Score: 77
Period size: 18 Copynumber: 9.9 Consensus size: 18
541857 TGTATATAAA
*
541867 ATTATAAACTATATTTAT
1 ATTATAAACTATATATAT
541885 ATTATAAACTATATA-ATT
1 ATTATAAACTATATATA-T
* *
541903 ATTATAAGCTATATATAA
1 ATTATAAACTATATATAT
*** *
541921 ATTAT-GTTTATGTGAACTAT
1 ATTATAAACTATAT--A-TAT
*
541941 ATATATAAACTATGTATAT
1 AT-TATAAACTATATATAT
* * * *
541960 A-AACTATA-TATGTATAA
1 ATTA-TAAACTATATATAT
* * **
541977 ACTACAAAAAATATATAGT
1 ATTATAAACTATATATA-T
*
541996 -TTATAAAATATTATATAT
1 ATTATAAACTA-TATATAT
*
542014 ATTAATATACTATATATAT
1 ATT-ATAAACTATATATAT
542033 A-TATAAACTATATAT
1 ATTATAAACTATATAT
542048 GTATAAACTA
Statistics
Matches: 123, Mismatches: 26, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
17 29 0.24
18 53 0.43
19 22 0.18
20 11 0.09
21 3 0.02
22 5 0.04
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTATAAACTATATATAT
Found at i:541908 original size:97 final size:95
Alignment explanation
Indices: 541785--541962 Score: 295
Period size: 95 Copynumber: 1.9 Consensus size: 95
541775 TAATATAAAA
*
541785 TTATATATAAACTATATAATTATTATAAACTATATATATAAATTATATTTATGTGCACTATATAT
1 TTATATATAAACTATATAATTATTATAAAC--TATATATAAATTATATTTATGTGAACTATATAT
541850 A-AAACTATGTATATAAAATTATAAACTATAT
64 ATAAACTATGTATATAAAATTATAAACTATAT
* *
541881 TTATATTATAAACTATATAATTATTATAAGCTATATATAAATTATGTTTATGTGAACTATATATA
1 TTATA-TATAAACTATATAATTATTATAAACTATATATAAATTATATTTATGTGAACTATATATA
541946 TAAACTATGTATATAAA
65 TAAACTATGTATATAAA
541963 CTATATATGT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
95 32 0.42
96 21 0.27
97 24 0.31
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (95 bp):
TTATATATAAACTATATAATTATTATAAACTATATATAAATTATATTTATGTGAACTATATATAT
AAACTATGTATATAAAATTATAAACTATAT
Found at i:541924 original size:18 final size:17
Alignment explanation
Indices: 541859--541925 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 17
541849 TAAAACTATG
541859 TATATAAAATTATAAAC
1 TATATAAAATTATAAAC
* *
541876 TATATTTATATTATAAAC
1 TATA-TAAAATTATAAAC
* *
541894 TATATAATTATTATAAGC
1 TATATAA-AATTATAAAC
541912 TATATATAAATTAT
1 TATATA-AAATTAT
541926 GTTTATGTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.14
18 35 0.83
19 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TATATAAAATTATAAAC
Found at i:541960 original size:15 final size:15
Alignment explanation
Indices: 541912--541980 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 15
541902 TATTATAAGC
*
541912 TATATATAAATTATG
1 TATATATAAACTATG
* * *
541927 TTTATGTGAACTA--
1 TATATATAAACTATG
541940 TATATATAAACTATG
1 TATATATAAACTATG
*
541955 --TATATAAACTATA
1 TATATATAAACTATG
*
541968 TATGTATAAACTA
1 TATATATAAACTA
541981 CAAAAAATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
13 22 0.54
15 19 0.46
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (15 bp):
TATATATAAACTATG
Found at i:542012 original size:2 final size:2
Alignment explanation
Indices: 542003--542177 Score: 100
Period size: 2 Copynumber: 88.0 Consensus size: 2
541993 AGTTTATAAA
*
542003 AT AT -T AT AT AT AT -T A- AT AT ACT AT AT AT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
* * * * *
542044 AT AT GT AT AA ACT AT AT AA ACT AT AT AGT TT AT AT GT -T AT A-
1 AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * **
542085 AT TT AT AT -T ACT AT AGT AT AT AT GT AT GC AT A- ACT A- AT AT
1 AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT
*
542125 A- AGT AT AT AT AG A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
542166 AT AT AT AT AT AT
1 AT AT AT AT AT AT
542178 TAAAGAAATA
Statistics
Matches: 134, Mismatches: 20, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
1 10 0.07
2 112 0.84
3 12 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:542061 original size:17 final size:16
Alignment explanation
Indices: 542007--542061 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
541997 TATAAAATAT
*
542007 TATATATATTAATATAC
1 TATATATATT-ATAAAC
542024 TATATATATATATAAAC
1 TATATATAT-TATAAAC
*
542041 TATATAT-GTATAAAC
1 TATATATATTATAAAC
542056 TATATA
1 TATATA
542062 AACTATATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 13 0.37
17 21 0.60
18 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (16 bp):
TATATATATTATAAAC
Found at i:542092 original size:77 final size:77
Alignment explanation
Indices: 541955--542107 Score: 216
Period size: 77 Copynumber: 2.0 Consensus size: 77
541945 ATAAACTATG
*
541955 TATATAAACTATATATGTATAAACTACAAAAAATATATAGTTTATAAAATATTATATATATTAAT
1 TATATAAACTATATATGTATAAACTACAAAAAATATATAGTTTATAAAATATAATATATATTAAT
542020 ATACTATATATA
66 ATACTATATATA
* * * *** * *
542032 TATATAAACTATATATGTATAAACTATATAAACTATATAGTTTATATGTTATAATTTATATTACT
1 TATATAAACTATATATGTATAAACTACAAAAAATATATAGTTTATAAAATATAATATATATTAAT
*
542097 ATAGTATATAT
66 ATACTATATAT
542108 GTATGCATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (77 bp):
TATATAAACTATATATGTATAAACTACAAAAAATATATAGTTTATAAAATATAATATATATTAAT
ATACTATATATA
Found at i:542440 original size:18 final size:18
Alignment explanation
Indices: 542414--542484 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
542404 ATAGTATGTG
542414 TATACATGTAATGTAAAC
1 TATACATGTAATGTAAAC
* **
542432 TATATATGTAACTTATAGTATATG
1 TATACATGT-A---AT-GTA-AAC
542456 TATACATGTAATGTAAAC
1 TATACATGTAATGTAAAC
*
542474 TATATATGTAA
1 TATACATGTAA
542485 CTTATAGTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 19 0.47
19 4 0.10
20 2 0.05
22 2 0.05
23 4 0.10
24 9 0.22
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (18 bp):
TATACATGTAATGTAAAC
Found at i:542449 original size:42 final size:42
Alignment explanation
Indices: 542391--542500 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
542381 ACAATAGTTA
*
542391 ATATATGTAACTTATAGTATGTGTATACATGTAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
542433 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
*
542475 ATATATGTAACTTATAGTACATGTAT
1 ATATATGTAACTTATAGTATATGTAT
542501 GTATAAACTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (42 bp):
ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
Found at i:542648 original size:20 final size:19
Alignment explanation
Indices: 542616--542665 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
542606 TATAAAAAAC
542616 TCTAAACCCTAAACTTGATAA
1 TCTAAA-CCTAAACTTGA-AA
*
542637 TCTAAACCTAAACTTTAAA
1 TCTAAACCTAAACTTGAAA
542656 TCCTAAACCT
1 T-CTAAACCT
542666 TAACCCTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.11
20 18 0.67
21 6 0.22
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (19 bp):
TCTAAACCTAAACTTGAAA
Found at i:544416 original size:22 final size:22
Alignment explanation
Indices: 544388--544436 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
544378 CACACTGGTT
544388 ATCTCTCATTTATCTCATTTTG
1 ATCTCTCATTTATCTCATTTTG
*
544410 ATCTCTCATTTCTCTCATTTTG
1 ATCTCTCATTTATCTCATTTTG
544432 ATCTC
1 ATCTC
544437 ACTAGCTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.53
Consensus pattern (22 bp):
ATCTCTCATTTATCTCATTTTG
Found at i:544538 original size:34 final size:33
Alignment explanation
Indices: 544460--544563 Score: 145
Period size: 33 Copynumber: 3.1 Consensus size: 33
544450 TTCTCTCAAA
* *
544460 TTCTCTATTTTTGGTTGATAATCGAATCATTTT
1 TTCTCTATTTTTGGTTGATATTCGAATCTTTTT
544493 TTCTCTATTTTTGGTTGATATTCGAATCTTTTT
1 TTCTCTATTTTTGGTTGATATTCGAATCTTTTT
* * *
544526 TTCTCTGTTTTTTGGTTGATATTTGAATCCTTTCT
1 TTCTCT-ATTTTTGGTTGATATTCGAAT-CTTTTT
544561 TTC
1 TTC
544564 AAGGGTTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 37 0.58
34 19 0.30
35 8 0.12
ACGTcount: A:0.15, C:0.13, G:0.12, T:0.59
Consensus pattern (33 bp):
TTCTCTATTTTTGGTTGATATTCGAATCTTTTT
Found at i:544922 original size:102 final size:99
Alignment explanation
Indices: 544735--544962 Score: 339
Period size: 102 Copynumber: 2.3 Consensus size: 99
544725 AAGAGGTAAC
* *
544735 TAAAATGTTTAATTTGTTGCTACTGTTGATTTGTTTGTGTTGGTTTTTCATTCGGATTACTTCTA
1 TAAACTGTTTAATTTGTTGCTACTGTTGATTTGTTTGTGTTGGTTGTTCATTCGGATTACTTCTA
* *
544800 TAAGGTTGTTAGATGCCTTTATTTAGAGTTTAAA
66 TAAGGTTGTTAGATGCCTTTATTTACAATTTAAA
* **
544834 TAAACTGTTCAATTTGTTGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATTGTTT
1 TAAACTGTTTAATTTGTTGCTACTGTTGATTTG-TT-TG-TGTTGGTTGTTCATTCGGATTACTT
* * *
544899 TTATAAGGTTGTTAGCTGTCTTTATTTACAATTTAAA
63 CTATAAGGTTGTTAGATGCCTTTATTTACAATTTAAA
544936 TAAACTGTTTAATTTGTTGCTACTGTT
1 TAAACTGTTTAATTTGTTGCTACTGTT
544963 CGTTGTTTAT
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
99 31 0.27
100 2 0.02
101 2 0.02
102 80 0.70
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (99 bp):
TAAACTGTTTAATTTGTTGCTACTGTTGATTTGTTTGTGTTGGTTGTTCATTCGGATTACTTCTA
TAAGGTTGTTAGATGCCTTTATTTACAATTTAAA
Found at i:548106 original size:14 final size:14
Alignment explanation
Indices: 548087--548134 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
548077 ATTTTTTCTT
548087 TATATAAATTAAAC
1 TATATAAATTAAAC
*
548101 TATAT-AATT-TA-
1 TATATAAATTAAAC
548112 TATA-AAATTAAAC
1 TATATAAATTAAAC
*
548125 TATATTAATT
1 TATATAAATT
548135 TTCCTTCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 8 0.30
14 9 0.33
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:548124 original size:24 final size:24
Alignment explanation
Indices: 548085--548135 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
548075 TTATTTTTTC
548085 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
548108 TTTATATAAAATTAAACTATATTAA
1 TTTATAT-AAATTAAACTATATTAA
548133 TTT
1 TTT
548136 TCCTTCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:548462 original size:33 final size:32
Alignment explanation
Indices: 548393--548472 Score: 115
Period size: 33 Copynumber: 2.5 Consensus size: 32
548383 TTACAGGTCC
* * *
548393 GGTTAAAAACATGTCAGGTTAAAAACAGGTCA
1 GGTTGAAAACAGGTCAGGTTAAAAACAAGTCA
*
548425 GGTTGAAAACAGGTCAGGTTGAAAAACAAGTCG
1 GGTTGAAAACAGGTCAGGTT-AAAAACAAGTCA
548458 GGTTGAAAACAGGTC
1 GGTTGAAAACAGGTC
548473 GGGTAATACC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 18 0.42
33 25 0.58
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (32 bp):
GGTTGAAAACAGGTCAGGTTAAAAACAAGTCA
Found at i:548476 original size:16 final size:16
Alignment explanation
Indices: 548385--548472 Score: 113
Period size: 16 Copynumber: 5.4 Consensus size: 16
548375 CGGATCATTT
* *
548385 ACAGGTCCGGTTAAAA
1 ACAGGTCAGGTTGAAA
* *
548401 ACATGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
548417 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
548433 ACAGGTCAGGTTGAAAA
1 ACAGGTCAGGTTG-AAA
* *
548450 ACAAGTCGGGTTGAAA
1 ACAGGTCAGGTTGAAA
548466 ACAGGTC
1 ACAGGTC
548473 GGGTAATACC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
16 50 0.78
17 14 0.22
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:551666 original size:3 final size:3
Alignment explanation
Indices: 551658--551712 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
551648 GGCATGTTTG
**
551658 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA
*
551704 TAA CAA TAA
1 TAA TAA TAA
551713 ATAAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:551701 original size:25 final size:24
Alignment explanation
Indices: 551675--551722 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
551665 AATAATTTTA
551675 ATAATAATAAAT-AATAAATAAAATA
1 ATAATAA-AAATAAATAAA-AAAATA
*
551700 ATAATAACAATAAATAAAAAAAT
1 ATAATAAAAATAAATAAAAAAAT
551723 GGGTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
ATAATAAAAATAAATAAAAAAATA
Found at i:551719 original size:22 final size:22
Alignment explanation
Indices: 551674--551718 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
551664 TAATAATTTT
*
551674 AATAATAATAAATAATAAATAA
1 AATAATAATAAACAATAAATAA
551696 AATAATAAT-AACAATAAATAA
1 AATAATAATAAACAATAAATAA
551717 AA
1 AA
551719 AAATGGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
AATAATAATAAACAATAAATAA
Found at i:552142 original size:124 final size:123
Alignment explanation
Indices: 551940--552258 Score: 477
Period size: 124 Copynumber: 2.6 Consensus size: 123
551930 GTAATCTAGC
*
551940 AAAGGTTGAACAAGCTCTTCTCATTGTGAACTTC---TTCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCTTCTTCAGATGAGTTCTTCTCATTA
* *
552002 TGAAC-TCCTTCTGGAAATGCTGATGATGATATATCTCCTTCTGTGATAGAGTCATGCA
66 TGAACTTTC-TCTGGAAAAGCTGATGATGATATATCTCCTTCTGTGATAGAGTCATGCA
*
552060 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTC-TTCTTCAGATGAGTTCTTCTCATT
* * *
552125 ATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCA
65 ATGAACTTTCTCTGGAAAAGCTGATGATGATATATCTCCTTCTGTGATAGAGTCATGCA
** * *
552184 AAAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTTC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-TTTCTTCTTCAGATGAGTTCTTCTCATT
552248 ATGAACTTTCT
65 ATGAACTTTCT
552259 TCTTCTTTCT
Statistics
Matches: 181, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
120 32 0.18
123 36 0.20
124 107 0.59
125 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (123 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGCTGATGATGATATATCTCCTTCTGTGATAGAGTCATGCA
Found at i:552252 original size:39 final size:41
Alignment explanation
Indices: 552198--552296 Score: 139
Period size: 44 Copynumber: 2.4 Consensus size: 41
552188 GTTGAACAAA
552198 TTCTTCTCATTATGAA-ATTCTTCTTTC-TCTTCAGATAAG
1 TTCTTCTCATTATGAATATTCTTCTTTCTTCTTCAGATAAG
* *
552237 TTCTTCTCATTATGAACTTTCTTCTTCTTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAA---TATTCTTCTTTCTTCTTCAGATAAG
552281 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
552297 CTTTCTCTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
39 16 0.30
43 10 0.19
44 27 0.51
ACGTcount: A:0.20, C:0.21, G:0.08, T:0.51
Consensus pattern (41 bp):
TTCTTCTCATTATGAATATTCTTCTTTCTTCTTCAGATAAG
Found at i:552283 original size:44 final size:43
Alignment explanation
Indices: 552215--552302 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 43
552205 CATTATGAAA
552215 TTCTTCTTTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC
1 TTCTTCTTTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC
*
552258 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC
1 TTCTTCTTTC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTC
552302 T
1 T
552303 CTGGAAAAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 10 0.23
44 33 0.77
ACGTcount: A:0.17, C:0.23, G:0.08, T:0.52
Consensus pattern (43 bp):
TTCTTCTTTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC
Found at i:552392 original size:113 final size:113
Alignment explanation
Indices: 552238--552535 Score: 510
Period size: 113 Copynumber: 2.6 Consensus size: 113
552228 TCAGATAAGT
552238 TCTTCTCATTATGAACTTTCTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 TCTTCTCATTATGAA----CTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
552303 CTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
62 CTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
552355 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
552420 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAGCAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
552468 TCTTCTCATTATGAACTTCTTC-TTCATTCTTCATATGAGTTCTTCTCATTATGAACTCTT-TCT
1 TCTTCTCATTATGAACTTCTTCTTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
552531 GGAAA
64 GGAAA
552536 TTTTGATCCA
Statistics
Matches: 177, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
112 3 0.02
113 157 0.89
114 2 0.01
117 15 0.08
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:557894 original size:11 final size:11
Alignment explanation
Indices: 557874--557906 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
557864 CTTGATTCAA
*
557874 TTTTCCTTTTT
1 TTTTCTTTTTT
557885 TTTTCTTTTTT
1 TTTTCTTTTTT
557896 TTTTCTTTTTT
1 TTTTCTTTTTT
557907 CATTCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:557904 original size:18 final size:18
Alignment explanation
Indices: 557879--557921 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
557869 TTCAATTTTC
* *
557879 CTTT-TTTTTTCTTTTTT
1 CTTTCTTTTTTCATTCTT
*
557896 TTTTCTTTTTTCATTCTT
1 CTTTCTTTTTTCATTCTT
557914 CTTTCTTT
1 CTTTCTTT
557922 GCTGGATGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (18 bp):
CTTTCTTTTTTCATTCTT
Found at i:559863 original size:14 final size:14
Alignment explanation
Indices: 559844--559927 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 14
559834 AAATGTAATT
559844 ATGTAAAAATGAAA
1 ATGTAAAAATGAAA
* *
559858 ATGTAAATA-CAAA
1 ATGTAAAAATGAAA
*
559871 CAT-AAAAAATGAAA
1 -ATGTAAAAATGAAA
*
559885 ATGT--AAATGCAA
1 ATGTAAAAATGAAA
* **
559897 ATGTAAATATGTGA
1 ATGTAAAAATGAAA
* *
559911 ATGTAACAATAAAA
1 ATGTAAAAATGAAA
559925 ATG
1 ATG
559928 CAAATTGTAT
Statistics
Matches: 50, Mismatches: 15, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
12 11 0.22
13 9 0.18
14 30 0.60
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (14 bp):
ATGTAAAAATGAAA
Found at i:559903 original size:27 final size:27
Alignment explanation
Indices: 559844--559903 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
559834 AAATGTAATT
559844 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAATGTAAATACAA
** *
559870 ACATAAAAAATGAAAATGTAAATGCAA
1 ATGTAAAAAATGAAAATGTAAATACAA
559897 ATGTAAA
1 ATGTAAA
559904 TATGTGAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.22
Consensus pattern (27 bp):
ATGTAAAAAATGAAAATGTAAATACAA
Found at i:559997 original size:7 final size:7
Alignment explanation
Indices: 559963--560004 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
559953 ACAAAAGTAT
559963 AAATGCA
1 AAATGCA
* *
559970 CAATGAA
1 AAATGCA
559977 AAATGCA
1 AAATGCA
559984 AAGATGCA
1 AA-ATGCA
559992 AAATGC-
1 AAATGCA
559998 AAATGCA
1 AAATGCA
560005 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:561510 original size:19 final size:17
Alignment explanation
Indices: 561486--561542 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 17
561476 TTAATACCTG
561486 AATAAAATAAAAAAATATT
1 AATAAAATAAAAAAA-A-T
561505 AATAAAATAATATAAAAAT
1 AATAAAATAA-A-AAAAAT
561524 AATAAGTAATAAAAAAAAT
1 AATAA--AATAAAAAAAAT
561543 TTGAAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 22 0.65
20 3 0.09
21 9 0.26
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAAAATAAAAAAAAT
Found at i:561527 original size:14 final size:13
Alignment explanation
Indices: 561486--561540 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 13
561476 TTAATACCTG
*
561486 AATAAAATAAAAA
1 AATAATATAAAAA
*
561499 AAT-AT-TAATAA
1 AATAATATAAAAA
561510 AATAATATAAAAA
1 AATAATATAAAAA
561523 TAATAAGTAATAAAAA
1 -AATAA-T-ATAAAAA
561539 AA
1 AA
561541 ATTTGAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 8 0.24
12 3 0.09
13 8 0.24
14 5 0.15
15 3 0.09
16 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
AATAATATAAAAA
Found at i:568791 original size:3 final size:3
Alignment explanation
Indices: 568783--568837 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
568773 GACCTGTTTG
**
568783 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA
*
568829 TAA CAA TAA
1 TAA TAA TAA
568838 ATAAAAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:568844 original size:22 final size:22
Alignment explanation
Indices: 568799--568843 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
568789 TAATAATTTT
*
568799 AATAATAATAAATAATAAATAA
1 AATAATAATAAACAATAAATAA
568821 AATAATAAT-AACAATAAATAA
1 AATAATAATAAACAATAAATAA
568842 AA
1 AA
568844 AATGGGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
AATAATAATAAACAATAAATAA
Found at i:569844 original size:22 final size:21
Alignment explanation
Indices: 569809--569850 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
569799 CATAATTATT
569809 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
569830 TAAAAATATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
569851 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:574680 original size:79 final size:82
Alignment explanation
Indices: 574590--574760 Score: 233
Period size: 80 Copynumber: 2.1 Consensus size: 82
574580 TAGATGCTTT
* * *
574590 TCAATATATTTCATAAAGTAAAG-CATCTTAAGATTTGATAGAGCTTTTAGCTAG-ATTTTT-TT
1 TCAATATATTTCATAAAGTAAAGTAATCTTAAGATTTGATAGAACTTTTAGCTAGAATTTTTCCT
* *
574652 TATATTCTTGACTTTTC
66 TATATTCTTGACATCTC
* * * *
574669 TCAATATATTTCATATAGTAAAGTAATCTTCAGTTTTGATGGAACTTTTAGCTAGAATTTTTCCT
1 TCAATATATTTCATAAAGTAAAGTAATCTTAAGATTTGATAGAACTTTTAGCTAGAATTTTTCCT
574734 TATATTCTTGACATCTC
66 TATATTCTTGACATCTC
574751 TCAATA-ATTT
1 TCAATATATTT
574761 TTTTTTTTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 22 0.28
80 26 0.32
81 10 0.12
82 22 0.28
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (82 bp):
TCAATATATTTCATAAAGTAAAGTAATCTTAAGATTTGATAGAACTTTTAGCTAGAATTTTTCCT
TATATTCTTGACATCTC
Found at i:574995 original size:24 final size:23
Alignment explanation
Indices: 574974--575017 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
574964 AGGGTGAATT
574974 TTAAAAAATTATAAGAAGTGAAG
1 TTAAAAAATTATAAGAAGTGAAG
* *
574997 TTATAAAATTTTAAGAA-TGAA
1 TTAAAAAATTATAAGAAGTGAA
575018 AATAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.32
Consensus pattern (23 bp):
TTAAAAAATTATAAGAAGTGAAG
Found at i:575058 original size:22 final size:22
Alignment explanation
Indices: 575020--575067 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
575010 AGAATGAAAA
* * *
575020 TAAATTATCAATAAAAATATTT
1 TAAATTATAAATAAAAAAAATT
575042 TAAATT-TAAATATAAAAAAATT
1 TAAATTATAAATA-AAAAAAATT
575064 TAAA
1 TAAA
575068 ATTTTAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTATAAATAAAAAAAATT
Found at i:589027 original size:21 final size:21
Alignment explanation
Indices: 589003--589063 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
588993 GAGTCGAGGG
589003 ATATCAGTGGTCCTTCGGGAC
1 ATATCAGTGGTCCTTCGGGAC
* *
589024 ATATCAGTGGTCTTTCGGGGC
1 ATATCAGTGGTCCTTCGGGAC
589045 --AT-AGTGGTCCTTCGGGAC
1 ATATCAGTGGTCCTTCGGGAC
589063 A
1 A
589064 AATATTCAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
21 19 0.54
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (21 bp):
ATATCAGTGGTCCTTCGGGAC
Found at i:592367 original size:17 final size:17
Alignment explanation
Indices: 592345--592411 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 17
592335 ACTACACATG
592345 AAGAAATAAAAAAAAAA
1 AAGAAATAAAAAAAAAA
592362 AAGAAATAATAATAATAAAA
1 AAGAAATAA-AA-AA-AAAA
*
592382 AA-ATAATAAAAAAATGAA
1 AAGA-AATAAAAAAA-AAA
*
592400 AAGAAAGAAAAA
1 AAGAAATAAAAA
592412 CATGACCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 10 0.24
18 15 0.36
19 6 0.14
20 11 0.26
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (17 bp):
AAGAAATAAAAAAAAAA
Found at i:592401 original size:20 final size:18
Alignment explanation
Indices: 592348--592411 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
592338 ACACATGAAG
*
592348 AAATAAAAAAA-AAAAAG
1 AAATAAAAAAATAAAAAA
*
592365 AAATAATAATAATAAAAAA
1 AAATAA-AAAAATAAAAAA
* *
592384 ATAATAAAAAAATGAAAAG
1 A-AATAAAAAAATAAAAAA
*
592403 AAAGAAAAA
1 AAATAAAAA
592412 CATGACCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 6 0.16
18 11 0.29
19 16 0.42
20 5 0.13
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (18 bp):
AAATAAAAAAATAAAAAA
Found at i:593142 original size:11 final size:11
Alignment explanation
Indices: 593126--593151 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
593116 CAAGGAAGAG
593126 GAACAACAAAA
1 GAACAACAAAA
593137 GAACAACAAAA
1 GAACAACAAAA
593148 GAAC
1 GAAC
593152 CTAAGGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (11 bp):
GAACAACAAAA
Found at i:603640 original size:20 final size:20
Alignment explanation
Indices: 603611--603649 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
603601 ATTTCACCAC
*
603611 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
603631 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
603650 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:604749 original size:153 final size:151
Alignment explanation
Indices: 604466--604771 Score: 497
Period size: 153 Copynumber: 2.0 Consensus size: 151
604456 TATAATTTCT
604466 TTTTCTATGATTTGATTCAGACTGATTTCTACCGTATTCTCCATAAAATTGTTCATGGTCTTTTT
1 TTTTCTATGATTTGATTCAGACTGATTTCTACCGTATTCTCCATAAAATTGTTCATGGTCTTTTT
604531 TTCGTTCTAGAGATTGATTTATTAGCTTAACCTTTCTTCTTCATTCAAGAAAGAAAATGGCATAA
66 TTCGTTCTAGAGATTGATTTATTAGCTTAACCTTTCTTCTTCATTCAAGAAAGAAAATGGCATAA
*
604596 TGACTAGAGTTTAGCGAGATG
131 TGACGAGAGTTTAGCGAGATG
* * * *
604617 TTTTCATATGATTTGATTCCA-ACTTATTTTTATCGTATTCTTCATAAAATTGTTCATGGTCTTT
1 TTTTC-TATGATTTGATT-CAGACTGATTTCTACCGTATTCTCCATAAAATTGTTCATGGTC-TT
* **
604681 TTTTTCGTTCTAGAGATTGATTTGTTAGCTTAACCTTTCTTCTTCATTCAAGAAAGAAAATGTTA
63 TTTTTCGTTCTAGAGATTGATTTATTAGCTTAACCTTTCTTCTTCATTCAAGAAAGAAAATGGCA
*
604746 TAATGACGAGAGTTTAGTGAGATG
128 TAATGACGAGAGTTTAGCGAGATG
604770 TT
1 TT
604772 CTAGTCATGG
Statistics
Matches: 143, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
151 5 0.03
152 48 0.34
153 90 0.63
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (151 bp):
TTTTCTATGATTTGATTCAGACTGATTTCTACCGTATTCTCCATAAAATTGTTCATGGTCTTTTT
TTCGTTCTAGAGATTGATTTATTAGCTTAACCTTTCTTCTTCATTCAAGAAAGAAAATGGCATAA
TGACGAGAGTTTAGCGAGATG
Found at i:610229 original size:19 final size:19
Alignment explanation
Indices: 610205--610244 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
610195 ACTATCTCCA
610205 TCACCGAACAATCATTCAC
1 TCACCGAACAATCATTCAC
610224 TCACCGAACAATCATTCAC
1 TCACCGAACAATCATTCAC
610243 TC
1 TC
610245 GATAACGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.38, G:0.05, T:0.23
Consensus pattern (19 bp):
TCACCGAACAATCATTCAC
Found at i:610890 original size:32 final size:32
Alignment explanation
Indices: 610840--610908 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
610830 ACCGGGGTAT
* *
610840 CGGGTACCCGATTCCCGGGTATCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* * *
610872 CGGGTACCTGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
610904 CGGGT
1 CGGGT
610909 CGGGACACGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.32, G:0.28, T:0.20
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:612526 original size:19 final size:19
Alignment explanation
Indices: 612502--612546 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
612492 GTGCATGCAA
612502 CGTCCACCACCAGCCCCAC
1 CGTCCACCACCAGCCCCAC
612521 CGTCCACCACCAGCCCCAC
1 CGTCCACCACCAGCCCCAC
*
612540 CGCCCAC
1 CGTCCAC
612547 TGCTTAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.64, G:0.11, T:0.04
Consensus pattern (19 bp):
CGTCCACCACCAGCCCCAC
Found at i:617388 original size:18 final size:19
Alignment explanation
Indices: 617365--617410 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
617355 ATTATAAAAT
617365 TATAAATAAAGAAATAAA-
1 TATAAATAAAGAAATAAAG
* *
617383 TATAAATAAATAATTAAAG
1 TATAAATAAAGAAATAAAG
617402 T-TAAATAAA
1 TATAAATAAA
617411 TTAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TATAAATAAAGAAATAAAG
Found at i:617393 original size:14 final size:13
Alignment explanation
Indices: 617366--617432 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
617356 TTATAAAATT
*
617366 ATAAA-TAAAGAA
1 ATAAATTAAATAA
617378 ATAAATATAAATAA
1 ATAAAT-TAAATAA
617392 AT-AATTAAAGTTAA
1 ATAAATTAAA--TAA
*
617406 ATAAATTAATTTAA
1 ATAAATTAA-ATAA
617420 ATTAAATTAAATA
1 A-TAAATTAAATA
617433 CTATATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 9 0.20
13 3 0.07
14 19 0.42
15 14 0.31
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
ATAAATTAAATAA
Found at i:617424 original size:5 final size:5
Alignment explanation
Indices: 617394--617431 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
617384 ATAAATAAAT
*
617394 AATTA AAGTTA AA-TA AATTA ATTTA AATTA AATTA AAT
1 AATTA AA-TTA AATTA AATTA AATTA AATTA AATTA AAT
617432 ACTATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:617442 original size:5 final size:5
Alignment explanation
Indices: 617434--617659 Score: 395
Period size: 5 Copynumber: 45.0 Consensus size: 5
617424 AATTAAATAC
617434 TATAT TATAT TATAT TATAT TATATT ATATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATA-T -TATAT TATAT TATAT TATAT TATAT
617486 TATAT TATAT TATAT TATAT TATAT TATA- TATAT TATAT ATATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TA-TAT TATAT
617537 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA- TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
617586 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
617636 TATAT TATAT TATAT TATA- TATAT
1 TATAT TATAT TATAT TATAT TATAT
617660 ACATTTTTTT
Statistics
Matches: 214, Mismatches: 0, Indels: 14
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.06
5 189 0.88
6 6 0.03
7 7 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:618627 original size:21 final size:20
Alignment explanation
Indices: 618593--618636 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
618583 TTAATATTTT
*
618593 TAATATTTAATAAACAATTA
1 TAATATTTAATAAACAATAA
* *
618613 TAATATTTTATTAAATAATAA
1 TAATA-TTTAATAAACAATAA
618634 TAA
1 TAA
618637 CACCATCGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATTTAATAAACAATAA
Found at i:618951 original size:17 final size:18
Alignment explanation
Indices: 618919--618960 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
618909 GATTTCAATT
*
618919 TAAATATTACATTTAATA
1 TAAAAATTACATTTAATA
*
618937 TAAAAATTA-ATTTAATC
1 TAAAAATTACATTTAATA
618954 TAAAAAT
1 TAAAAAT
618961 AATCTACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAATTACATTTAATA
Found at i:619337 original size:19 final size:20
Alignment explanation
Indices: 619288--619338 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
619278 TCTCTTCTTA
* *
619288 TTTCTTT-TTCCTTCCTCTT
1 TTTCTTTCTTTCTTCCTCCT
619307 TTTCTCTTCTTTCTT-CTCCT
1 TTTCT-TTCTTTCTTCCTCCT
619327 TTTCTTTCTTTC
1 TTTCTTTCTTTC
619339 ACTCCAGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTCTTTCTTTCTTCCTCCT
Found at i:619702 original size:23 final size:23
Alignment explanation
Indices: 619658--619702 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
619648 GTGACCGCGT
* * *
619658 CACGAGTGTTGCGTGTAGGGGGC
1 CACGAGTGTTGCATGCAAGGGGC
619681 CACGAGTGTTGCATGCAAGGGG
1 CACGAGTGTTGCATGCAAGGGG
619703 AAGACGCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.20
Consensus pattern (23 bp):
CACGAGTGTTGCATGCAAGGGGC
Found at i:619866 original size:40 final size:40
Alignment explanation
Indices: 619811--619930 Score: 159
Period size: 40 Copynumber: 3.0 Consensus size: 40
619801 TGCGTATTCG
* * *
619811 AGGGGAGCAGGTAAGGCATATATACTCCAATACGTCTTCC
1 AGGGGAGCAGGTAAGGCACATAGACTCCAATACGTCTTCA
619851 AGGGGAGCAGGTAAGGCACATAGACTCCAATACGTCTTCA
1 AGGGGAGCAGGTAAGGCACATAGACTCCAATACGTCTTCA
* * * * *
619891 AAGGGAGCATGGTAAGTCGCATGGACTGCAATACGTCTTC
1 AGGGGAGCA-GGTAAGGCACATAGACTCCAATACGTCTTC
619931 GAGATTCACT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 45 0.63
41 26 0.37
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.21
Consensus pattern (40 bp):
AGGGGAGCAGGTAAGGCACATAGACTCCAATACGTCTTCA
Found at i:623818 original size:44 final size:44
Alignment explanation
Indices: 623746--623834 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
623736 AGGCGTGACA
* * *
623746 ATTGCCTGAACCGAAAGATCAATATGAGAAAAGCTGAAAACACC
1 ATTGCATGAACCGAAAGAACAATATGAGAAAAGCAGAAAACACC
*
623790 ATTGCATGAACCGAAAGAACAATCTGAGAAAAGCAGAAAACACC
1 ATTGCATGAACCGAAAGAACAATATGAGAAAAGCAGAAAACACC
623834 A
1 A
623835 GGATGACAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.13
Consensus pattern (44 bp):
ATTGCATGAACCGAAAGAACAATATGAGAAAAGCAGAAAACACC
Found at i:626401 original size:30 final size:30
Alignment explanation
Indices: 626367--626446 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
626357 TGGTGCTCAT
* *
626367 GTTCTTGCTGATTAATCAAGTCATCAATAG
1 GTTCTTGCTGATCAATCAAGTCATCAACAG
* * *
626397 GTTCTTGCTGAACAATCAGGTCATCAACAT
1 GTTCTTGCTGATCAATCAAGTCATCAACAG
626427 GTTCTTGCTGATCAA-CAAGT
1 GTTCTTGCTGATCAATCAAGT
626447 TATTGCTGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 4 0.09
30 39 0.91
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (30 bp):
GTTCTTGCTGATCAATCAAGTCATCAACAG
Done.