Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 29
Found at i:5642725 original size:23 final size:23
Alignment explanation
Indices: 5642680--5642725 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5642670 ACATTTTATA
*
5642680 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
5642703 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
5642726 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:5644295 original size:20 final size:21
Alignment explanation
Indices: 5644270--5644309 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5644260 CTATTTAACC
*
5644270 CTTTTACTTTTATC-ATCAAT
1 CTTTTAATTTTATCAATCAAT
5644290 CTTTTAATTTTATCAATCAA
1 CTTTTAATTTTATCAATCAA
5644310 ATCACTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (21 bp):
CTTTTAATTTTATCAATCAAT
Found at i:5644697 original size:27 final size:28
Alignment explanation
Indices: 5644634--5644766 Score: 115
Period size: 30 Copynumber: 4.5 Consensus size: 28
5644624 ATTAAAAATC
*
5644634 TATATTTTATTTTTATCTTAACTTATTAAA
1 TATATTTTATTTTTATTTTAACTTA--AAA
5644664 TATATTTTATTTTTATTTTAACTTAAAA
1 TATATTTTATTTTTATTTTAACTTAAAA
* * *
5644692 -CTATTTTAATCTTATTTTAACTTAAAA
1 TATATTTTATTTTTATTTTAACTTAAAA
* * *
5644719 AATATATCTCTTTCTTATTTTAACATTTAAAAA
1 TATAT-TTTATTT-TTATTTTAAC--TT-AAAA
* *
5644752 TATATCTTAATTTTA
1 TATATTTTATTTTTA
5644767 AAATAAAAGT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
27 24 0.29
28 6 0.07
29 3 0.04
30 34 0.41
31 3 0.04
32 5 0.06
33 8 0.10
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (28 bp):
TATATTTTATTTTTATTTTAACTTAAAA
Found at i:5644737 original size:30 final size:31
Alignment explanation
Indices: 5644701--5644758 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5644691 ACTATTTTAA
5644701 TCTTATTTTAAC-TTAAAAAATATATCTCTT
1 TCTTATTTTAACATTAAAAAATATATCTCTT
*
5644731 TCTTATTTTAACATTTAAAAATATATCT
1 TCTTATTTTAACATTAAAAAATATATCT
5644759 TAATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (31 bp):
TCTTATTTTAACATTAAAAAATATATCTCTT
Found at i:5644769 original size:18 final size:18
Alignment explanation
Indices: 5644743--5644849 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 18
5644733 TTATTTTAAC
*
5644743 ATTTAAAAATATATCTTA
1 ATTTTAAAATATATCTTA
* **
5644761 ATTTTAAAATAAAAGTATA
1 ATTTTAAAATATATCT-TA
* *
5644780 TATTTTAATATATATTTTA
1 -ATTTTAAAATATATCTTA
5644799 ACTTTTAAAATATATCTTA
1 A-TTTTAAAATATATCTTA
* * * *
5644818 GTTTTCATATATAT-TTG
1 ATTTTAAAATATATCTTA
*
5644835 ATCTTAAAAATATAT
1 AT-TTTAAAATATAT
5644850 TTATTATTAT
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
17 3 0.04
18 33 0.49
19 19 0.28
20 12 0.18
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTTTAAAATATATCTTA
Found at i:5644969 original size:30 final size:30
Alignment explanation
Indices: 5644933--5645013 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
5644923 AACGTATTAA
* *
5644933 ATATATTTTATTCTTTTTTTGATTTAAAAT
1 ATATATTTTATTCTTTTTTAGATTAAAAAT
* *
5644963 ATATATTTTAGTCTTATTTTAGCTTAAAAAT
1 ATATATTTTATTCTT-TTTTAGATTAAAAAT
*
5644994 ATTTTATTTT-TATCTTTTTT
1 A-TATATTTTAT-TCTTTTTT
5645014 GAGTCAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 14 0.33
31 17 0.40
32 11 0.26
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (30 bp):
ATATATTTTATTCTTTTTTAGATTAAAAAT
Found at i:5648181 original size:2 final size:2
Alignment explanation
Indices: 5648176--5648213 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5648166 AGGTTTAAAC
*
5648176 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5648214 GAACAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5652907 original size:16 final size:16
Alignment explanation
Indices: 5652871--5652918 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
5652861 TTTAACCCTA
*
5652871 GGTTGACTTTGACTAG
1 GGTTGACTTTGACCAG
* *
5652887 AGTTGACTTTGACCGG
1 GGTTGACTTTGACCAG
*
5652903 GGTTGATTTTGACCAG
1 GGTTGACTTTGACCAG
5652919 AAAGTCAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.31, T:0.35
Consensus pattern (16 bp):
GGTTGACTTTGACCAG
Found at i:5662204 original size:7 final size:7
Alignment explanation
Indices: 5662190--5662255 Score: 71
Period size: 7 Copynumber: 9.0 Consensus size: 7
5662180 AATCCCACAT
5662190 AAAGAAA
1 AAAGAAA
*
5662197 ATAGAAA
1 AAAGAAA
5662204 AAAG-AA
1 AAAGAAA
5662210 AAAGAAGA
1 AAAGAA-A
5662218 ATAAGAAGA
1 A-AAGAA-A
5662227 ATAAGAAA
1 A-AAGAAA
*
5662235 AAAGAAG
1 AAAGAAA
5662242 AAAGAAA
1 AAAGAAA
5662249 AAAGAAA
1 AAAGAAA
5662256 GAAATAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
6 6 0.12
7 28 0.54
8 4 0.08
9 14 0.27
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:5662227 original size:25 final size:23
Alignment explanation
Indices: 5662191--5662259 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
5662181 ATCCCACATA
5662191 AAGAAA-ATAGAAAAAAGAAAAAG
1 AAGAAAGA-AGAAAAAAGAAAAAG
*
5662214 AAGAATAAGAAG-AATAAGAAAAAAG
1 AAG-A-AAGAAGAAAAAAG-AAAAAG
*
5662239 AAGAAAGAAAAAAGAAAGAAA
1 AAGAAAGAAGAAA-AAAGAAA
5662260 TAAAAGTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
23 8 0.22
24 12 0.32
25 16 0.43
26 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAGAAAGAAGAAAAAAGAAAAAG
Found at i:5662250 original size:15 final size:15
Alignment explanation
Indices: 5662201--5662264 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 15
5662191 AAGAAAATAG
5662201 AAAAAAGAA-AAAGA
1 AAAAAAGAAGAAAGA
*
5662215 AGAATAAGAAGAATA-A
1 A-AAAAAGAAGAA-AGA
5662231 GAAAAAAGAAGAAAG-
1 -AAAAAAGAAGAAAGA
*
5662246 AAAAAAGAAAGAAATA
1 AAAAAAG-AAGAAAGA
5662262 AAA
1 AAA
5662265 GTTATAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
15 14 0.35
16 16 0.40
17 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (15 bp):
AAAAAAGAAGAAAGA
Found at i:5662264 original size:14 final size:14
Alignment explanation
Indices: 5662190--5662264 Score: 73
Period size: 14 Copynumber: 5.1 Consensus size: 14
5662180 AATCCCACAT
5662190 AAAGAA-AATAGAAA
1 AAAGAAGAA-AGAAA
5662204 AAAGAA-AAAGAAGA
1 AAAGAAGAAAGAA-A
5662218 ATAAGAAGAATAAGAAA
1 A-AAGAAG-A-AAGAAA
5662235 AAAGAAGAAAGAAA
1 AAAGAAGAAAGAAA
*
5662249 AAAGAAAGAAATAAA
1 AAAG-AAGAAAGAAA
5662264 A
1 A
5662265 GTTATAAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
13 4 0.07
14 20 0.37
15 16 0.30
16 6 0.11
17 3 0.06
18 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAGAAGAAAGAAA
Found at i:5669091 original size:27 final size:26
Alignment explanation
Indices: 5669058--5669153 Score: 93
Period size: 27 Copynumber: 3.6 Consensus size: 26
5669048 AAATTTTTAA
*
5669058 AAGTTAAAATAAGAAAAAGACATTTTT
1 AAGTTAAAATAA-AAAAAAACATTTTT
* ** *
5669085 TAGTTAAAATAATATTAAAATATTTTT
1 AAGTTAAAATAA-AAAAAAACATTTTT
* *
5669112 AAGTTAAAATAAAAAAAAATATTTAAT
1 AAGTTAAAATAAAAAAAAACATTT-TT
*
5669139 AAGTTAAGATAAAAA
1 AAGTTAAAATAAAAA
5669154 TATAATATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.18
27 47 0.82
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (26 bp):
AAGTTAAAATAAAAAAAAACATTTTT
Found at i:5669144 original size:54 final size:59
Alignment explanation
Indices: 5669050--5669177 Score: 142
Period size: 54 Copynumber: 2.2 Consensus size: 59
5669040 ATTAAGATAA
* * * *
5669050 ATTTTTAAAAGTTAAAATAAGAAAAAGACATTTTTTAGTTAAAAT-AATAT-TAA-A-AT
1 ATTTTT-AAAGTTAAAATAAGAAAAAAACATTTATAAGTTAAAATAAAAATATAATATAT
* *
5669106 ATTTTT-AAGTTAAAATAA-AAAAAAATATTTAATAAGTTAAGATAAAAATATAATATAT
1 ATTTTTAAAGTTAAAATAAGAAAAAAACATTT-ATAAGTTAAAATAAAAATATAATATAT
5669164 ATTTTTAAAGTTAA
1 ATTTTTAAAGTTAA
5669178 GATATGAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
53 10 0.17
54 21 0.35
55 4 0.07
56 9 0.15
57 1 0.02
58 8 0.13
59 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (59 bp):
ATTTTTAAAGTTAAAATAAGAAAAAAACATTTATAAGTTAAAATAAAAATATAATATAT
Found at i:5671175 original size:2 final size:2
Alignment explanation
Indices: 5671168--5671206 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5671158 TTTTCCTAAC
5671168 TA TA TA TA TA 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 TA TA TA TA TA T
5671207 GGAGTCTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5674952 original size:17 final size:17
Alignment explanation
Indices: 5674919--5674962 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5674909 TAGTTTGATT
*
5674919 AATGAACTAATTTTAATG
1 AATGAACT-ACTTTAATG
*
5674937 AATGAACTACTTTAATT
1 AATGAACTACTTTAATG
*
5674954 AGTGAACTA
1 AATGAACTA
5674963 TCAATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (17 bp):
AATGAACTACTTTAATG
Found at i:5679689 original size:25 final size:25
Alignment explanation
Indices: 5679631--5679698 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
5679621 TCGACCGGTT
5679631 CCAACCCGACCC---GACCCGTTGAC
1 CCAACCCGACCCGTTGA-CCGTTGAC
* *
5679654 CCAACCTGACCTGTTGACCGTTGAC
1 CCAACCCGACCCGTTGACCGTTGAC
**
5679679 CTGACCCGACCCGTTGACCG
1 CCAACCCGACCCGTTGACCG
5679699 AGTGATATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 10 0.28
25 24 0.67
26 2 0.06
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.16
Consensus pattern (25 bp):
CCAACCCGACCCGTTGACCGTTGAC
Found at i:5679743 original size:29 final size:29
Alignment explanation
Indices: 5679700--5679905 Score: 233
Period size: 29 Copynumber: 7.2 Consensus size: 29
5679690 CGTTGACCGA
*
5679700 GTGATATTTTAGTAATTATTTTTAAAATG
1 GTGATATTTTCGTAATTATTTTTAAAATG
*
5679729 GTGATATTTTGGTAATTATTTTTAAAATG
1 GTGATATTTTCGTAATTATTTTTAAAATG
* *
5679758 GTGATATTTTGGTAATTATTTTGAAAATG
1 GTGATATTTTCGTAATTATTTTTAAAATG
* **
5679787 GTGTTATTTTCGT-A--ATTTTTAAAAAA
1 GTGATATTTTCGTAATTATTTTTAAAATG
*
5679813 GTGATAATTTCGTAATT-TTTTTAAAAAT-
1 GTGATATTTTCGTAATTATTTTT-AAAATG
* * *
5679841 GTGATATTTTCATAATTAGTTTTAAAAAG
1 GTGATATTTTCGTAATTATTTTTAAAATG
* * *
5679870 GTGATATTTTAGTAAATATTTCTTAAAAGG
1 GTGATATTTTCGTAATTATTT-TTAAAATG
5679900 GTGATA
1 GTGATA
5679906 ATTGTGTAAA
Statistics
Matches: 151, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.13
27 1 0.01
28 25 0.17
29 92 0.61
30 13 0.09
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (29 bp):
GTGATATTTTCGTAATTATTTTTAAAATG
Found at i:5679878 original size:83 final size:84
Alignment explanation
Indices: 5679700--5679884 Score: 223
Period size: 83 Copynumber: 2.2 Consensus size: 84
5679690 CGTTGACCGA
** * *
5679700 GTGATATTTTAGTAATTATTTTTAAAATGGTGATATTTTGGTAATTATTTTTAAAATGGTGATAT
1 GTGATATTTTAGT-A--ATTTTTAAAAAAGTGATAATTTCGTAATTATTTTTAAAATGGTGATAT
** *
5679765 TTTGGTAATTATTTTGAAAATG
63 TTTCATAATTATTTTGAAAAAG
* *
5679787 GTGTTATTTTCGTAATTTTTAAAAAAGTGATAATTTCGTAATT-TTTTTAAAAAT-GTGATATTT
1 GTGATATTTTAGTAATTTTTAAAAAAGTGATAATTTCGTAATTATTTTT-AAAATGGTGATATTT
5679850 TCATAATTAGTTTT-AAAAAG
65 TCATAATTA-TTTTGAAAAAG
5679870 GTGATATTTTAGTAA
1 GTGATATTTTAGTAA
5679885 ATATTTCTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
83 39 0.46
84 34 0.40
86 1 0.01
87 11 0.13
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (84 bp):
GTGATATTTTAGTAATTTTTAAAAAAGTGATAATTTCGTAATTATTTTTAAAATGGTGATATTTT
CATAATTATTTTGAAAAAG
Found at i:5687134 original size:29 final size:28
Alignment explanation
Indices: 5687091--5687275 Score: 155
Period size: 29 Copynumber: 6.5 Consensus size: 28
5687081 CGTTGACCGA
5687091 GTGATATTTTAGTAATTATTTTTAAAATG
1 GTGATATTTT-GTAATTATTTTTAAAATG
* *
5687120 GTGATATTTTGGTAATGATTTTGAAAATG
1 GTGATATTTT-GTAATTATTTTTAAAATG
* **
5687149 GTGCTATTTT-T--TTAATTTTTAAAAAA
1 GTGATATTTTGTAATT-ATTTTTAAAATG
*
5687175 GTGATAATTTTGT-ATTTTTTTTAAAAT-
1 GTGAT-ATTTTGTAATTATTTTTAAAATG
** *
5687202 GTGATATTTTCGTAATTAGCTTTAAAAAG
1 GTGATATTTT-GTAATTATTTTTAAAATG
* *
5687231 GTGATATTTTAGTAAATATTTCTTAAAAGG
1 GTGATATTTT-GTAATTATTT-TTAAAATG
*
5687261 GTGATAATTGTGTAA
1 GTGAT-ATTTTGTAA
5687276 AATGGTTGAT
Statistics
Matches: 126, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.01
26 18 0.14
27 13 0.10
28 20 0.16
29 54 0.43
30 16 0.13
31 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (28 bp):
GTGATATTTTGTAATTATTTTTAAAATG
Found at i:5689380 original size:28 final size:25
Alignment explanation
Indices: 5689344--5689395 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
5689334 ATAGGGAATA
5689344 AAATAAAATAAATAAAGATAAAAAATG
1 AAATAAAATAAA-AAA-ATAAAAAATG
*
5689371 AAATAGAAATAAAAAAATAATAAAT
1 AAATA-AAATAAAAAAATAAAAAAT
5689396 AATAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 8 0.35
28 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (25 bp):
AAATAAAATAAAAAAATAAAAAATG
Found at i:5689382 original size:18 final size:17
Alignment explanation
Indices: 5689348--5689386 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5689338 GGAATAAAAT
5689348 AAAATAAATAAAGATAA
1 AAAATAAATAAAGATAA
5689365 AAAATGAAATAGAA-ATAA
1 AAAAT-AAATA-AAGATAA
5689383 AAAA
1 AAAA
5689387 ATAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (17 bp):
AAAATAAATAAAGATAA
Found at i:5689392 original size:3 final size:3
Alignment explanation
Indices: 5689386--5689438 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
5689376 GAAATAAAAA
*
5689386 AAT AAT AAAT AAT AAAT AAT AAT -AT AAT -AT AAT -AT AAG AA- AAT
1 AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5689429 AAT AAT AAT A
1 AAT AAT AAT A
5689439 TATACCATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
2 8 0.19
3 29 0.67
4 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5689397 original size:7 final size:7
Alignment explanation
Indices: 5689385--5689460 Score: 55
Period size: 7 Copynumber: 9.9 Consensus size: 7
5689375 AGAAATAAAA
5689385 AAATAAT
1 AAATAAT
5689392 AAATAAT
1 AAATAAT
5689399 AAATAAT
1 AAATAAT
5689406 AATATAAT
1 AA-ATAAT
5689414 ATAAT-AT
1 A-AATAAT
*
5689421 AAGAAAAT
1 AA-ATAAT
5689429 AATAATAAT
1 -A-AATAAT
*
5689438 ATATACCAT
1 AAATA--AT
5689447 AAATAAAT
1 AAAT-AAT
5689455 AAATAA
1 AAATAA
5689461 GAACAAGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
6 1 0.02
7 25 0.45
8 17 0.30
9 11 0.20
10 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (7 bp):
AAATAAT
Found at i:5689402 original size:28 final size:27
Alignment explanation
Indices: 5689344--5689409 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
5689334 ATAGGGAATA
* *
5689344 AAATAAAATAAATAAAGATAAAAAATG
1 AAATAAAATAAAAAAAAATAAAAAATG
*
5689371 AAATAGAAATAAAAAAATAATAAATAAT-
1 AAATA-AAATAAAAAAA-AATAAAAAATG
5689399 AAATAATAATA
1 AAATAA-AATA
5689410 TAATATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 19 0.58
29 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (27 bp):
AAATAAAATAAAAAAAAATAAAAAATG
Found at i:5689448 original size:26 final size:26
Alignment explanation
Indices: 5689396--5689456 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
5689386 AATAATAAAT
*
5689396 AATAAATAATAATATAATATAATATA
1 AATAAATAATAATATAATATAACATA
*
5689422 AGA-AAATAATAATA-ATATATACCATA
1 A-ATAAATAATAATATA-ATATAACATA
5689448 AATAAATAA
1 AATAAATAA
5689457 ATAAGAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 2 0.07
26 27 0.90
27 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (26 bp):
AATAAATAATAATATAATATAACATA
Found at i:5689472 original size:24 final size:24
Alignment explanation
Indices: 5689445--5689499 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
5689435 AATATATACC
*
5689445 ATAAATAA-ATAAATAAGAACAAGA
1 ATAAATAACAAAAATAAGAACAA-A
* * *
5689469 ATAAAAAACAAAAATAGGAATAAA
1 ATAAATAACAAAAATAAGAACAAA
5689493 ATAAATA
1 ATAAATA
5689500 TAAAGGCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (24 bp):
ATAAATAACAAAAATAAGAACAAA
Found at i:5691950 original size:23 final size:23
Alignment explanation
Indices: 5691901--5691951 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5691891 GCCTTGAGCT
* * **
5691901 AAGCTGCAAATAATAAGTTTTTT
1 AAGCTACAAATAATAAGTCTTCG
5691924 AAGCTACAAATAATAAGTCTTCG
1 AAGCTACAAATAATAAGTCTTCG
5691947 AAGCT
1 AAGCT
5691952 GAGCATAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (23 bp):
AAGCTACAAATAATAAGTCTTCG
Found at i:5692222 original size:169 final size:168
Alignment explanation
Indices: 5691944--5692764 Score: 722
Period size: 169 Copynumber: 4.9 Consensus size: 168
5691934 TAATAAGTCT
* * * * * * *
5691944 TCGAAGCTGAGCATAGCCGAACTCGAAGGTTTTTGGTTGGAAAATAACCCTTCTTA-CCTTGAGC
1 TCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC-TAGACTTGAGT
** * * * * * * ** *
5692008 TATATTGCAAATGATGTGCCGTTGAGATTAGCTTAGTTAAACTCAAAGGTATTTTGTTAACATAA
65 TATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTCAAACTCAAAGGTATTTTGTTGGCAGAA
* * *
5692073 AACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGTCC
130 AACCCTTCTCGACTTAAGTTATGCTACAAATGATGTG-CC
* * * *
5692113 TCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTT
1 TCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTT
* * * * * * *
5692178 ATGTTGCAAATAATATGTCATTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCA-AAT
66 ATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTCAAACTCAAAGGTATTTTGTTGGCAGAA-
* * * * *
5692242 AACCTTTCTTGCCTTGAGTTATGTTACAAATGATGTGCCC
130 AACCCTTCTCGACTTAAGTTATGCTACAAATGATGTG-CC
** * * * * * * * * * * *
5692282 TAAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGTTAGCATATAGCCTTTCTCGACTTAAGCT
1 TCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTT
* * * * * * *
5692347 ATGCTGCAAATGATATGACGTTTAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGGTGGCAGATA
66 ATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTCAAACTCAAAGGTATTTTGTTGGCAGAAA
* **
5692412 GCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCC
131 ACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCC
* * * * * * *
5692450 TTGGAGCTTAGCGTAGTCGAACTCGAAGGTCCTAGG-TGACAGATAACCCTTCTAGCCTTGAGTT
1 TCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTT
** * * * * * * * *
5692514 ATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTC-GAGG--GTCT-TTGGCAGAT
66 ATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGTCAAACTCAAAGGTATTTTGTTGGCAGAA
* *
5692575 AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
130 AACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCC
* * *
5692614 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTT
1 TCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTT
* * * **
5692679 ATGCTACAAATGATATG-CCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTGGCAGTT
66 ATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAGTCAAACTCAAAGGTATTTTGTTGGCAGAA
* * *
5692743 AGCCCTTCTAGCCTTAAGTTAT
130 AACCCTTCTCGACTTAAGTTAT
5692765 ATTACCGATA
Statistics
Matches: 532, Mismatches: 110, Indels: 21
0.80 0.17 0.03
Matches are distributed among these distances:
164 98 0.18
165 48 0.09
167 40 0.08
168 73 0.14
169 272 0.51
170 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (168 bp):
TCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTT
ATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTCAAACTCAAAGGTATTTTGTTGGCAGAAA
ACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCC
Found at i:5692228 original size:84 final size:83
Alignment explanation
Indices: 5691948--5692764 Score: 687
Period size: 84 Copynumber: 9.8 Consensus size: 83
5691938 AAGTCTTCGA
* * * * * * * * *
5691948 AGCTGAGCATAGCCGAACTCGAAGGTTTTTGGTTGGAAAATAACCCTTCT-TACCTTGAGCTATA
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA-CTTAAGTTATG
*
5692012 TTGCAAATGATGTGCCGTTG
65 CTGCAAATGATGTGCC-TTG
* * * ** * * * ** * * * * *
5692032 AGATTAGCTTAGTTAAACTCAAAGGTATTTTGTTAACATAAAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
5692097 TACAAATGATGTGTCCTCG
66 TGCAAATGATGTG-CCTTG
* *
5692116 AAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATG
1 -AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * * *
5692181 TTGCAAATAATATGTCATTG
65 CTGCAAATGATGTG-CCTTG
* * * * * * *
5692201 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAAATAACCTTTCTTGCCTTGAGTTATGT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* **
5692266 TACAAATGATGTGCCCTAAA
66 TGCAAATGATGTG-CCT-TG
* * * * * * * * *
5692286 AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGTTAGCATATAGCCTTTCTCGACTTAAGCTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* * *
5692351 TGCAAATGATATGACGTTT
66 TGCAAATGATGTG-CCTTG
* *
5692370 AGCTGAGCGTAGTCGAACTCGAAGGTATTTTGG-TGGCAGATAGCCCTTCTCGACTTAAGTTATG
1 AGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
5692434 CTGTAAATGATGTGCCTTGG
65 CTGCAAATGATGTGCCTT-G
* * * * * * *
5692454 AGCTTAGCGTAGTCGAACTCGAAGGTCCTAGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
** *
5692518 TATAAATGATGTGCCCTCG
66 TGCAAATGATGTG-CCTTG
* * * * *
5692537 AAGCTGAGTGTAATCAAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATG
1 -AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
5692598 CTGCAAATGATGTGCCTTGG
65 CTGCAAATGATGTGCCTT-G
* * *
5692618 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
5692683 TACAAATGATATGCCTTGG
66 TGCAAATGATGTGCCTT-G
* * * * * *
5692702 AGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGG-TGGCAGTTAGCCCTTCTAGCCTTAAGTTAT
1 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
5692765 ATTACCGATA
Statistics
Matches: 587, Mismatches: 131, Indels: 30
0.78 0.18 0.04
Matches are distributed among these distances:
80 26 0.04
81 39 0.07
82 1 0.00
83 46 0.08
84 337 0.57
85 138 0.24
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (83 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCTTG
Found at i:5692657 original size:248 final size:251
Alignment explanation
Indices: 5692073--5692764 Score: 901
Period size: 248 Copynumber: 2.8 Consensus size: 251
5692063 GTTAACATAA
* * * * * * *
5692073 AACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGTCCTCGAAGCTGAGCGTAGTCGAACTCG
1 AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACCTTGAAGCTGAGCGTAGTCGAACTCG
* * * *
5692138 AGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGTTGCAAATAATATGTCATT-GA
66 AAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTGGA
* * * *
5692202 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAAATAACCTTTCTTGCCTTGAGTTATGTT
130 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
* * *
5692267 ACAAATGATGTGCCCTAAAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGTTAGCAT
194 ACAAATGATGTGCCCTAAAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTCAGCAT
* * * *
5692325 ATAGCCTTTCTCGACTTAAGCTATGCTGCAAATGATATGACGTT-TAGCTGAGCGTAGTCGAACT
1 A-A-CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACCTTGAAGCTGAGCGTAGTCGAACT
* * *
5692389 CGAAGGTATTTTGG-TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTG
64 CGAAGGT-CTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTG
* * * * *
5692453 GAGCTTAGCGTAGTCGAACTCGAAGGTCCTAGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
128 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* **
5692518 TATAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGG-CAG-AT
193 TACAAATGATGTGCCCTAAAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTCAGCAT
*
5692575 AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCG
1 AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACCTTGAAGCTGAGCGTAGTCGAACTCG
* * * * *
5692639 AAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCTTGGAG
66 AAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG
* * * *
5692704 CTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTGGCAGTTAGCCCTTCTAGCCTTAAGTTAT
131 CTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTAT
5692765 ATTACCGATA
Statistics
Matches: 379, Mismatches: 54, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
247 8 0.02
248 127 0.34
249 30 0.08
250 3 0.01
251 2 0.01
252 78 0.21
253 96 0.25
254 35 0.09
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (251 bp):
AACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGACCTTGAAGCTGAGCGTAGTCGAACTCG
AAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG
CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTAC
AAATGATGTGCCCTAAAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGTCAGCAT
Found at i:5694065 original size:95 final size:94
Alignment explanation
Indices: 5693897--5694082 Score: 282
Period size: 95 Copynumber: 2.0 Consensus size: 94
5693887 ATATGTAAAC
* * *
5693897 ACCTTTATCAAGTTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTTCCTTAGAGGG
1 ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGG
*
5693962 ACATCTCAAGCTTTATTGTATAGTATAATT
66 ACAACTCAAGCTTTATTGTATA-TATAATT
* * * * *
5693992 ACCTTTATCAGGCTAGTTGAATATTATCCATAAAGTCGGGGCATTTAACCAATTGCTTTAGAGGG
1 ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGG
5694057 ACAACTCAAGCTTTATTGTATATATA
66 ACAACTCAAGCTTTATTGTATATATA
5694083 TAATATTATA
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 4 0.05
95 78 0.95
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (94 bp):
ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATATATAATT
Found at i:5696853 original size:10 final size:11
Alignment explanation
Indices: 5696835--5696868 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
5696825 GATGCAAAAG
5696835 ATGAAAATAAA
1 ATGAAAATAAA
5696846 AT-AAAATAAA
1 ATGAAAATAAA
5696856 ATGAAAATGAAA
1 ATGAAAAT-AAA
5696868 A
1 A
5696869 GAGTTAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 7 0.33
12 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (11 bp):
ATGAAAATAAA
Found at i:5697981 original size:13 final size:13
Alignment explanation
Indices: 5697965--5698022 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
5697955 CAAAATAAAT
5697965 AAAATAAATATAA
1 AAAATAAATATAA
*
5697978 AAAATGAAATAGAA
1 AAAAT-AAATATAA
* *
5697992 ATAA-AAATA-AG
1 AAAATAAATATAA
5698003 AAAAT-AATATAA
1 AAAATAAATATAA
5698015 GAAAATAA
1 -AAAATAA
5698023 TAATAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
11 8 0.23
12 6 0.17
13 10 0.29
14 11 0.31
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:5697999 original size:39 final size:38
Alignment explanation
Indices: 5697956--5698094 Score: 108
Period size: 39 Copynumber: 3.6 Consensus size: 38
5697946 GGAAGCAAAC
5697956 AAAATAAATAAAATAAATATAAAAAATGAAATAGAAATA
1 AAAATAAATAAAATAAATATAAAAAATGAAATA-AAATA
* * *
5697995 AAAAT-AAGAAAAT-AATATAAGAAAATAATAATAATATA
1 AAAATAAATAAAATAAATATAA-AAAATGA-AATAAAATA
** * *
5698033 TACCATAAAT-AAATAAATA-AGAACAA-GAAAAAAAATA
1 -AAAATAAATAAAATAAATATA-AAAAATGAAATAAAATA
*
5698070 AAAATTGGAATAAAATAAATATAAA
1 AAAA-T-AAATAAAATAAATATAAA
5698095 TATAAACCCA
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
36 2 0.03
37 15 0.19
38 21 0.27
39 31 0.40
40 8 0.10
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (38 bp):
AAAATAAATAAAATAAATATAAAAAATGAAATAAAATA
Found at i:5698014 original size:19 final size:18
Alignment explanation
Indices: 5697965--5698032 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
5697955 CAAAATAAAT
*
5697965 AAAATAAATATAAAAAATG
1 AAAAT-AATATAAAAAAAG
*
5697984 -AAATAGAAATAAAAATAAG
1 AAAATA-ATATAAAAA-AAG
* *
5698003 AAAATAATATAAGAAAAT
1 AAAATAATATAAAAAAAG
5698021 AATAATAATATA
1 AA-AATAATATA
5698033 TACCATAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 1 0.03
18 16 0.40
19 18 0.45
20 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAATAATATAAAAAAAG
Found at i:5698024 original size:13 final size:14
Alignment explanation
Indices: 5697965--5698022 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 14
5697955 CAAAATAAAT
5697965 AAAATAAATATAA-
1 AAAATAAATATAAG
*
5697978 AAAATGAA-AT-AG
1 AAAATAAATATAAG
*
5697990 -AAATAAAAATAAG
1 AAAATAAATATAAG
5698003 AAAAT-AATATAAG
1 AAAATAAATATAAG
5698016 AAAATAA
1 AAAATAA
5698023 TAATAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.19
12 4 0.11
13 21 0.57
14 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AAAATAAATATAAG
Found at i:5698334 original size:19 final size:18
Alignment explanation
Indices: 5698310--5698345 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5698300 ACGTTAGGAG
5698310 AAGAAATAATAATAAAAAA
1 AAGAAATAATAA-AAAAAA
*
5698329 AAGAAATAGTAAAAAAA
1 AAGAAATAATAAAAAAA
5698346 TATAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AAGAAATAATAAAAAAAA
Found at i:5698352 original size:17 final size:16
Alignment explanation
Indices: 5698321--5698373 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
5698311 AGAAATAATA
*
5698321 ATAAAAAAA-AGAAAT
1 ATAAAAAAATATAAAT
5698336 AGTAAAAAAATATAAAT
1 A-TAAAAAAATATAAAT
* *
5698353 A-AATAAAATATATAT
1 ATAAAAAAATATAAAT
5698368 ATAAAA
1 ATAAAA
5698374 TAGTAGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 14 0.45
16 11 0.35
17 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (16 bp):
ATAAAAAAATATAAAT
Found at i:5698416 original size:2 final size:2
Alignment explanation
Indices: 5698403--5698440 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5698393 AAAAGGTAAA
*
5698403 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5698441 GTCCTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5698568 original size:12 final size:13
Alignment explanation
Indices: 5698538--5698577 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
5698528 TATATGTAAC
5698538 AAATAAATAATATA
1 AAAT-AATAATATA
5698552 AAATAATAATA-A
1 AAATAATAATATA
5698564 AAATAATAATATA
1 AAATAATAATATA
5698577 A
1 A
5698578 GGATCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
13 9 0.36
14 4 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATATA
Found at i:5700694 original size:21 final size:21
Alignment explanation
Indices: 5700665--5700704 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5700655 AGCTCAACTA
* *
5700665 TATTGAAATAGTTTATTTGGT
1 TATTAAAATAATTTATTTGGT
5700686 TATTAAAATAATTTATTTG
1 TATTAAAATAATTTATTTG
5700705 ATAATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (21 bp):
TATTAAAATAATTTATTTGGT
Found at i:5703446 original size:2 final size:2
Alignment explanation
Indices: 5703439--5703475 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5703429 ATTTTTAACA
5703439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5703476 ATTTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5705163 original size:18 final size:18
Alignment explanation
Indices: 5705129--5705164 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5705119 ATATAGAGTA
*
5705129 GTATCGGTACCCCTTTTG
1 GTATCGGTACCACTTTTG
*
5705147 GTATCGGTACCATTTTTG
1 GTATCGGTACCACTTTTG
5705165 CATTCTGGAA
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:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (18 bp):
GTATCGGTACCACTTTTG
Found at i:5706655 original size:19 final size:20
Alignment explanation
Indices: 5706619--5706666 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5706609 TCAAAATCCT
* *
5706619 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
5706639 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
5706658 CTTTCAAAA
1 TTTTCAAAA
5706667 AATCATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:5707700 original size:18 final size:19
Alignment explanation
Indices: 5707652--5707700 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
5707642 TTAGACCCTT
*
5707652 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
5707671 AGTGCATCGATGCA-TAA-
1 AGTGCATCGATGCACTAAG
5707688 AGTGCATTCGATG
1 AGTGCA-TCGATG
5707701 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 13 0.46
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:5707809 original size:65 final size:65
Alignment explanation
Indices: 5707673--5707831 Score: 225
Period size: 65 Copynumber: 2.5 Consensus size: 65
5707663 GCACTAAGAG
* *
5707673 TGCATCGATGCATAAAGTGCATTCGATG-TTTCAAAATAACCTGAGTGCAACGATGCATGTCTTA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCAACGATGCATGTATTA
* * * *
5707737 TGCATCGATACATAAAATGCATTCGATGTTTTTATAAA-AACCTGAGTGTATCGATGCATGGTAT
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAACCTGAGTGCAACGATGCAT-GTAT
5707801 TA
64 TA
5707803 -GCATCGATGCATAAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
5707832 CAATTTATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 26 0.31
65 51 0.60
66 8 0.09
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (65 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAACCTGAGTGCAACGATGCATGTATTA
Found at i:5707872 original size:65 final size:65
Alignment explanation
Indices: 5707672--5707873 Score: 184
Period size: 65 Copynumber: 3.1 Consensus size: 65
5707662 TGCACTAAGA
* ** * * **
5707672 GTGCATCGATGCATAAAGTGCATTCGATGTTTCAAAATA-AC-CTGAGTGCAACGATGCATGTCT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATACAATGAGTGCATCGATGCATGGAT
5707735 T
65 T
* * * *
5707736 ATGCATCGATACATAAAATGCATTCGATGTT---TTTATAAAAACCTGAGTGTATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTAT-ACAA--TGAGTGCATCGATGCATGG
5707798 TATT
63 -ATT
* *
5707802 -AGCATCGATGCATAAAATGCATTCGATGTTCAATTTATTCAATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATACAATGAGTGCATCGATGCATGGATT
5707865 GGTGCATCG
1 -GTGCATCG
5707874 GTACACTCTT
Statistics
Matches: 110, Mismatches: 17, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
60 2 0.02
62 1 0.01
63 5 0.05
64 41 0.37
65 52 0.47
66 2 0.02
67 2 0.02
68 5 0.05
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATACAATGAGTGCATCGATGCATGGATT
Found at i:5708703 original size:20 final size:20
Alignment explanation
Indices: 5708678--5708741 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
5708668 ACCCGATGGA
5708678 TGCATCGATGCATGTCCTTG
1 TGCATCGATGCATGTCCTTG
*
5708698 TGCATCGATG---G---AT-
1 TGCATCGATGCATGTCCTTG
5708711 -GCATCGATGCATGTCCTTG
1 TGCATCGATGCATGTCCTTG
5708730 TGCATCGATGCA
1 TGCATCGATGCA
5708742 CATTCAAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
12 9 0.26
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
20 21 0.62
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATGTCCTTG
Found at i:5708712 original size:32 final size:32
Alignment explanation
Indices: 5708671--5708739 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
5708661 TCCTAAAACC
5708671 CGATGGATGCATCGATGCATGTCCTTGTGCAT
1 CGATGGATGCATCGATGCATGTCCTTGTGCAT
5708703 CGATGGATGCATCGATGCATGTCCTTGTGCAT
1 CGATGGATGCATCGATGCATGTCCTTGTGCAT
5708735 CGATG
1 CGATG
5708740 CACATTCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (32 bp):
CGATGGATGCATCGATGCATGTCCTTGTGCAT
Found at i:5708788 original size:44 final size:45
Alignment explanation
Indices: 5708707--5708828 Score: 137
Period size: 45 Copynumber: 2.8 Consensus size: 45
5708697 GTGCATCGAT
* * * *
5708707 GGATGCATCGATGCA-TGTCCTTGTGCATCGATGCACATTC-AA-
1 GGATGCATCGATGCACTTTCATAGTGTATCGATGCACATTCAAAG
*
5708749 GGAGTGCATCGGTGCA-TCTTCAT-GATGTATCGATGCACATTCAAAG
1 GGA-TGCATCGATGCACT-TTCATAG-TGTATCGATGCACATTCAAAG
5708795 GGATGCATCGATGCACTTTCATAGTGTATCGATG
1 GGATGCATCGATGCACTTTCATAGTGTATCGATG
5708829 TATTAAGCAC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
42 3 0.04
43 13 0.19
44 19 0.28
45 28 0.41
46 5 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (45 bp):
GGATGCATCGATGCACTTTCATAGTGTATCGATGCACATTCAAAG
Found at i:5708791 original size:21 final size:23
Alignment explanation
Indices: 5708729--5708815 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
5708719 GCATGTCCTT
5708729 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
5708752 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
5708774 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
5708796 GATGCATCGATGCACTTTCA
1 G-TGCATCGATGCACATTCA
5708816 TAGTGTATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
22 3 0.06
23 18 0.35
24 16 0.31
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:5708827 original size:21 final size:23
Alignment explanation
Indices: 5708733--5708828 Score: 69
Period size: 21 Copynumber: 4.3 Consensus size: 23
5708723 GTCCTTGTGC
*
5708733 ATCGATGCACATTC-AAGGAGTGC
1 ATCGATGCACATTCAAAGGA-TGT
* *
5708756 ATCGGTGCATC-TTC--ATGATGT
1 ATCGATGCA-CATTCAAAGGATGT
*
5708777 ATCGATGCACATTCAAAGGGATGC
1 ATCGATGCACATTCAAA-GGATGT
* *
5708801 ATCGATGCACTTTCATA-G-TGT
1 ATCGATGCACATTCAAAGGATGT
5708822 ATCGATG
1 ATCGATG
5708829 TATTAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 22 0.37
22 4 0.07
23 12 0.20
24 20 0.34
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (23 bp):
ATCGATGCACATTCAAAGGATGT
Found at i:5712659 original size:21 final size:21
Alignment explanation
Indices: 5712633--5712674 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5712623 GAGATTATTT
*
5712633 TCATTTTTCA-ATTTTAAAATA
1 TCATTTTT-ATATTTAAAAATA
5712654 TCATTTTTATATTTAAAAATA
1 TCATTTTTATATTTAAAAATA
5712675 GTTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TCATTTTTATATTTAAAAATA
Found at i:5714607 original size:19 final size:17
Alignment explanation
Indices: 5714583--5714631 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5714573 TTTGACCCTT
*
5714583 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TAA
*
5714601 GAGTGCACCGATGCATAA
1 -AGTGCATCGATGCATAA
5714619 AGTGCATTCGATG
1 AGTGCA-TCGATG
5714632 TTTGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (17 bp):
AGTGCATCGATGCATAA
Found at i:5714672 original size:45 final size:46
Alignment explanation
Indices: 5714601--5714707 Score: 146
Period size: 45 Copynumber: 2.3 Consensus size: 46
5714591 GGTGCACTAA
* * * * *
5714601 GAGTGCACCGATGCATAAAGTGCATTCGATG-TTTGA-AAATAGCCT
1 GAGTGCATCGATGCATAAAATACATTCGATGCTTTCATAAA-AACCT
5714646 GAGTGCATCGATGCATAAAATACATTCGATGCTTTCATAAAAACCT
1 GAGTGCATCGATGCATAAAATACATTCGATGCTTTCATAAAAACCT
5714692 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
5714708 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 28 0.51
46 24 0.44
47 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATACATTCGATGCTTTCATAAAAACCT
Found at i:5721513 original size:21 final size:22
Alignment explanation
Indices: 5721489--5721529 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5721479 AGGAACTTAA
5721489 ATATAAAATAA-TGATATGAAC
1 ATATAAAATAAGTGATATGAAC
* *
5721510 ATATAAGATAAGTTATATGA
1 ATATAAAATAAGTGATATGA
5721530 TAAAGATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATAAAATAAGTGATATGAAC
Found at i:5722155 original size:30 final size:31
Alignment explanation
Indices: 5722084--5722184 Score: 109
Period size: 30 Copynumber: 3.3 Consensus size: 31
5722074 GAGTCGAGGG
* * * *
5722084 TTACCTATGTCTTTCGAGACATATGGATAGT
1 TTACCTATGTCCTTCGGGACATATGGACAGA
*
5722115 TTACTTATGTCCTTCGGGAC-T-TGGACAGGA
1 TTACCTATGTCCTTCGGGACATATGGACA-GA
*
5722145 TTACCTATGTCCTTCAGGACATATGGACA-A
1 TTACCTATGTCCTTCGGGACATATGGACAGA
*
5722175 CTACCTATGT
1 TTACCTATGT
5722185 TTTTCGGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.08
30 30 0.51
31 18 0.31
32 6 0.10
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGA
Found at i:5723693 original size:20 final size:20
Alignment explanation
Indices: 5723668--5723710 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5723658 TCTTAAGGAA
5723668 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* * *
5723688 CATTTAGGATCATGTAGTTG
1 CATTTAGGACCATATAGATG
5723708 CAT
1 CAT
5723711 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:5725952 original size:4 final size:4
Alignment explanation
Indices: 5725943--5726113 Score: 162
Period size: 4 Copynumber: 42.8 Consensus size: 4
5725933 TTTTTAAAAA
5725943 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * *
5725991 GTAC ATAC GTAC ATAC GTAC ATAC GTAC GTAC GTAC ATAT ATAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * * *
5726039 ATAC TTAG GTAC ATAC GTAC GTAC ATAC GTAC GTAT ATAC GTAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
5726087 GTAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
5726114 GTTTTAAAAA
Statistics
Matches: 140, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 140 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:5726959 original size:25 final size:26
Alignment explanation
Indices: 5726923--5726989 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 26
5726913 TGATGTGGAC
*
5726923 TTTCAA-TTCAAAGTGATGC-TGAAG
1 TTTCAAGTTCAAAGTGATACATGAAG
5726947 TTTCAAGTTCAAAGTGATACTATGAAG
1 TTTCAAGTTCAAAGTGATAC-ATGAAG
5726974 TTTCAAGTTCAAAGTG
1 TTTCAAGTTCAAAGTG
5726990 GTGATGGTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 6 0.15
25 12 0.31
27 21 0.54
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (26 bp):
TTTCAAGTTCAAAGTGATACATGAAG
Found at i:5729039 original size:25 final size:25
Alignment explanation
Indices: 5729005--5729060 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
5728995 AATGCTGTGT
*
5729005 TTTTTTATTTAATGTGAAGTAATAA
1 TTTTTTATTTAATGTAAAGTAATAA
* *
5729030 TTTTTTATTTTATGTAAAGTAATGA
1 TTTTTTATTTAATGTAAAGTAATAA
5729055 TTTTTT
1 TTTTTT
5729061 GTTATTTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (25 bp):
TTTTTTATTTAATGTAAAGTAATAA
Found at i:5733188 original size:30 final size:30
Alignment explanation
Indices: 5733148--5733242 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
5733138 TTAAGAATTT
* *
5733148 AAATGATATTTTATTTAAAATTTAGGGTTA
1 AAATTATATTTTATTTAAAATTTAGTGTTA
*
5733178 AAATTATATTTTATCTAAAATTTAGTGTT-
1 AAATTATATTTTATTTAAAATTTAGTGTTA
* *
5733207 AAATTAATATTTTA-TGAAAATTTAGTGATA
1 AAATT-ATATTTTATTTAAAATTTAGTGTTA
5733237 AAATTA
1 AAATTA
5733243 AAAATTAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 18 0.32
30 39 0.68
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (30 bp):
AAATTATATTTTATTTAAAATTTAGTGTTA
Found at i:5734271 original size:15 final size:13
Alignment explanation
Indices: 5734250--5734290 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
5734240 TTTTACCGGA
5734250 TAAAAAACCGGTT
1 TAAAAAACCGGTT
5734263 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
5734277 TAAAAAACCGGTT
1 TAAAAAACCGGTT
5734290 T
1 T
5734291 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:5734281 original size:12 final size:12
Alignment explanation
Indices: 5734244--5734289 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
5734234 GGTTTTTTTT
*
5734244 ACCGGATAAAAA
1 ACCGGTTAAAAA
5734256 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
5734271 ACCGGTTAAAAA
1 ACCGGTTAAAAA
5734283 ACCGGTT
1 ACCGGTT
5734290 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:5736601 original size:21 final size:21
Alignment explanation
Indices: 5736577--5736616 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5736567 TTTATTTTAT
5736577 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
5736598 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
5736617 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:5736664 original size:33 final size:33
Alignment explanation
Indices: 5736611--5736709 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
5736601 TTTGTTTCAA
5736611 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
5736643 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
5736676 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
5736709 T
1 T
5736710 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:5736738 original size:13 final size:13
Alignment explanation
Indices: 5736695--5736749 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
5736685 TTGGAAGTAT
5736695 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
5736708 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
5736722 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
5736735 TTAAGTATTTGAA
1 TTAAGTATTTCAA
5736748 TT
1 TT
5736750 TATTGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:5737206 original size:21 final size:18
Alignment explanation
Indices: 5737161--5737194 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5737151 GGTTTTTTAT
5737161 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
5737178 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
5737195 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:5737314 original size:15 final size:17
Alignment explanation
Indices: 5737288--5737319 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5737278 TTCTATGGGA
5737288 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
5737304 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
5737320 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:5738323 original size:18 final size:19
Alignment explanation
Indices: 5738300--5738342 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
5738290 ATTAATTTAA
5738300 ATAAAAT-TGATAATTTATT
1 ATAAAATATGAT-ATTTATT
*
5738319 A-AAAATATTATATTTATT
1 ATAAAATATGATATTTATT
5738337 ATAAAA
1 ATAAAA
5738343 ATAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAAAATATGATATTTATT
Found at i:5739065 original size:30 final size:28
Alignment explanation
Indices: 5738998--5739083 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
5738988 ACTGTAAACA
** *
5738998 CCATTTTTCAACACCAACACTTACCACC
1 CCATTTTTCAACACCAACACCCACCATC
5739026 CCATTTTTCAACACCAACACCCACCATC
1 CCATTTTTCAACACCAACACCCACCATC
* * *
5739054 CTATTTTTTTCAACATCAAC-CCCATCATC
1 CCA--TTTTTCAACACCAACACCCACCATC
5739083 C
1 C
5739084 ATTGTTCTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
28 27 0.54
29 9 0.18
30 14 0.28
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (28 bp):
CCATTTTTCAACACCAACACCCACCATC
Found at i:5742483 original size:66 final size:65
Alignment explanation
Indices: 5742397--5742525 Score: 168
Period size: 66 Copynumber: 2.0 Consensus size: 65
5742387 TTCGACTCGT
** * * * *
5742397 TGTTCGTTAAGTTTGTTAAAATTTTACTTGACTTATGCTCATTAAAAAAATTTGTTGCTAAACTT
1 TGTTCGTTAACCTCGTTAAAATTTTACTCGACTCATGCTCATT-AAAAAACTTGTTGCTAAACTT
5742462 G
65 G
* * *
5742463 TGTTCGTTAACCTCGTTAAAATTTTACTCGACTCGTGCTCGTTAAAAAACTTGTTGCTCAACT
1 TGTTCGTTAACCTCGTTAAAATTTTACTCGACTCATGCTCATTAAAAAACTTGTTGCTAAACT
5742526 CGTGCTCATT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
65 18 0.33
66 36 0.67
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (65 bp):
TGTTCGTTAACCTCGTTAAAATTTTACTCGACTCATGCTCATTAAAAAACTTGTTGCTAAACTTG
Found at i:5743021 original size:15 final size:17
Alignment explanation
Indices: 5742983--5743026 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
5742973 TGTAAAGGTC
5742983 TCAAGTCGAGCTCGAAT
1 TCAAGTCGAGCTCGAAT
**
5743000 TTGAGTCGAG-TC-AAT
1 TCAAGTCGAGCTCGAAT
5743015 TCAAGTCGAGCT
1 TCAAGTCGAGCT
5743027 TTTATCGAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 11 0.50
16 3 0.14
17 8 0.36
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (17 bp):
TCAAGTCGAGCTCGAAT
Found at i:5745419 original size:9 final size:9
Alignment explanation
Indices: 5745405--5745430 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5745395 ACCTTGTTCA
5745405 TCATCTTGT
1 TCATCTTGT
5745414 TCATCTTGT
1 TCATCTTGT
5745423 TCATCTTG
1 TCATCTTG
5745431 ATCAAGAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.54
Consensus pattern (9 bp):
TCATCTTGT
Found at i:5746370 original size:18 final size:18
Alignment explanation
Indices: 5746343--5746377 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5746333 TGATTAAAAG
5746343 TATAGAACTTTATTAAAC
1 TATAGAACTTTATTAAAC
*
5746361 TATAGTACTTTATTAAA
1 TATAGAACTTTATTAAA
5746378 GTACTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (18 bp):
TATAGAACTTTATTAAAC
Found at i:5749540 original size:20 final size:20
Alignment explanation
Indices: 5749517--5749702 Score: 161
Period size: 20 Copynumber: 9.3 Consensus size: 20
5749507 AATATATAAA
5749517 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5749537 TCGCAACACAGAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5749557 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
5749577 TTGCAACAC-TGAAGTCAAAT
1 TCGCAACACAT-AAGTCAAAT
* **
5749597 TCGCAACGCGAATCTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
* **
5749617 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
*
5749637 TCGCAACACAGAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
5749657 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5749677 TCGCAACGCGA-AAGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
5749697 TCGCAA
1 TCGCAA
5749703 AGCGCGTTTA
Statistics
Matches: 141, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
18 4 0.03
19 3 0.02
20 126 0.89
21 5 0.04
22 2 0.01
23 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:5749583 original size:60 final size:60
Alignment explanation
Indices: 5749492--5749702 Score: 240
Period size: 60 Copynumber: 3.5 Consensus size: 60
5749482 ACCCAGTTTC
*
5749492 CAAATTCGCAACGCGAATA-TATAAATCGCAACACATAAGTCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATAGTA-AATTCGCAACACATAAGTCAAATTCGCAACACAGAAGT
* *
5749552 CAAATTCGCAACGCG-ATAGTCAAATTTGCAACAC-TGAAGTCAAATTCGCAACGC-GAA-T
1 CAAATTCGCAACGCGAATAGT-AAATTCGCAACACAT-AAGTCAAATTCGCAACACAGAAGT
* * *
5749610 CTGTAAA-TCGCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAATTCGCAACACATAAGT
1 C---AAATTCGCAACGCGAA-TAGTAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGT
5749672 CAAATTCGCAACGCGAA-AGTCAAATTCGCAA
1 CAAATTCGCAACGCGAATAGT-AAATTCGCAA
5749703 AGCGCGTTTA
Statistics
Matches: 128, Mismatches: 9, Indels: 28
0.78 0.05 0.17
Matches are distributed among these distances:
58 4 0.03
59 13 0.10
60 96 0.75
61 10 0.08
62 5 0.04
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (60 bp):
CAAATTCGCAACGCGAATAGTAAATTCGCAACACATAAGTCAAATTCGCAACACAGAAGT
Found at i:5749840 original size:20 final size:20
Alignment explanation
Indices: 5749814--5749865 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5749804 TCGATAATTA
5749814 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
5749834 TCGTTGCGAATTTGTAAATC
1 GCGTTGCGAATTTGAAAATC
*
5749854 GCGTTGCTAATT
1 GCGTTGCGAATT
5749866 ACCGATATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:5749921 original size:20 final size:20
Alignment explanation
Indices: 5749896--5749937 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5749886 CTATTGCAAT
5749896 GCGATTTACAAATTCACAAC
1 GCGATTTACAAATTCACAAC
* *
5749916 GCGATTTTCAAATTCGCAAC
1 GCGATTTACAAATTCACAAC
5749936 GC
1 GC
5749938 TAATTACCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (20 bp):
GCGATTTACAAATTCACAAC
Found at i:5750000 original size:57 final size:57
Alignment explanation
Indices: 5749912--5750075 Score: 292
Period size: 57 Copynumber: 2.9 Consensus size: 57
5749902 TACAAATTCA
5749912 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACAATCG
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACAATCG
* *
5749969 CAACGCGATTTTCAAATTCGCAACGCTAATTATCGATATAGGTAAACAGTACTATCG
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACAATCG
* *
5750026 CAACGCGATTTACAAATTCACAACGCTAATTACCGATATAGGTAAACAGT
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
5750076 GTTGCGAAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 102 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (57 bp):
CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACAATCG
Found at i:5750093 original size:13 final size:13
Alignment explanation
Indices: 5750075--5750099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5750065 AGGTAAACAG
5750075 TGTTGCGAAAATT
1 TGTTGCGAAAATT
5750088 TGTTGCGAAAAT
1 TGTTGCGAAAAT
5750100 AAACGCGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
TGTTGCGAAAATT
Found at i:5750134 original size:20 final size:20
Alignment explanation
Indices: 5750109--5750254 Score: 106
Period size: 20 Copynumber: 7.3 Consensus size: 20
5750099 TAAACGCGCT
*
5750109 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
*
5750129 TTGCG-ATTT-ACAAATTCGTG
1 TTGCGAATTTGAC--TTTCGTG
* *
5750149 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC--TTTCGTG
5750169 TTGCGAATTTGAC-TTCAGTG
1 TTGCGAATTTGACTTTC-GTG
* * *
5750189 TTGCGAATTTGAGTATCGCG
1 TTGCGAATTTGACTTTCGTG
* *
5750209 TTGTGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
*
5750229 TTACGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
5750249 TTGCGA
1 TTGCGA
5750255 TTTAAAGATT
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
18 2 0.02
19 9 0.09
20 83 0.81
21 6 0.06
22 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGTG
Found at i:5750239 original size:40 final size:40
Alignment explanation
Indices: 5750164--5750240 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
5750154 ATTTACAGAT
*
5750164 TCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGAGTA
1 TCGCGTTGCGAATTTGACTTCAGTGTTACGAATTTGAGTA
* **
5750204 TCGCGTTGTGAATTTGACTTTTGTGTTACGAATTTGA
1 TCGCGTTGCGAATTTGACTTCAGTGTTACGAATTTGA
5750241 CTTCTGTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTCAGTGTTACGAATTTGAGTA
Found at i:5750273 original size:20 final size:20
Alignment explanation
Indices: 5750248--5750378 Score: 65
Period size: 20 Copynumber: 6.5 Consensus size: 20
5750238 TGACTTCTGT
5750248 GTTGCG-ATTTAAAGATTCGC
1 GTTGCGAATTTAAA-ATTCGC
5750268 GTTGCGAATTTGGAAAA-TCGC
1 GTTGCGAATTT--AAAATTCGC
** *
5750289 AATGCG-ATTTACATATTCGC
1 GTTGCGAATTTA-AAATTCGC
* *
5750309 GTTGCGAATTTAGAAACT-GG
1 GTTGCGAATTTA-AAATTCGC
* ** *
5750329 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAATTTAAAATTCGC
* * *
5750349 GTCGCGAATTTGAGA-TCGC
1 GTTGCGAATTTAAAATTCGC
*
5750368 GTTGCAAATTT
1 GTTGCGAATTT
5750379 GTTGGTCATT
Statistics
Matches: 82, Mismatches: 22, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
18 1 0.01
19 17 0.21
20 40 0.49
21 20 0.24
22 1 0.01
23 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTAAAATTCGC
Found at i:5750963 original size:21 final size:22
Alignment explanation
Indices: 5750939--5750979 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5750929 GAAATAAAAG
*
5750939 AAGGAA-AGGGAGAAAAATGTA
1 AAGGAAGAGAGAGAAAAATGTA
*
5750960 AAGGAAGAGAGATAAAAATG
1 AAGGAAGAGAGAGAAAAATG
5750980 GAGAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.10
Consensus pattern (22 bp):
AAGGAAGAGAGAGAAAAATGTA
Found at i:5753042 original size:6 final size:6
Alignment explanation
Indices: 5753031--5754009 Score: 1917
Period size: 6 Copynumber: 163.2 Consensus size: 6
5753021 TATGCTTGTA
5753031 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753079 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753127 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
*
5753175 TATATC TATATC TATATC TATATC TATATA TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753223 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753271 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753319 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATCTC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATA--TC
5753369 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753417 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753465 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753513 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753561 --TATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753607 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753655 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753703 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753751 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753799 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753847 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753895 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753943 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
5753991 TATATC TATATC TATATC T
1 TATATC TATATC TATATC T
5754010 TTTTACCTCT
Statistics
Matches: 967, Mismatches: 2, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.00
6 957 0.99
8 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:5758384 original size:18 final size:18
Alignment explanation
Indices: 5758361--5758399 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5758351 TTTCTATCCA
*
5758361 CCAGCACGAGCACATGCT
1 CCAGCACCAGCACATGCT
5758379 CCAGCACCAGCACATGCT
1 CCAGCACCAGCACATGCT
5758397 CCA
1 CCA
5758400 CTTACCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.44, G:0.18, T:0.10
Consensus pattern (18 bp):
CCAGCACCAGCACATGCT
Found at i:5759288 original size:18 final size:17
Alignment explanation
Indices: 5759267--5759301 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5759257 CATTCGTAAA
5759267 TTTTTAAGTACTTTATTT
1 TTTTTAA-TACTTTATTT
*
5759285 TTTTTAATATTTTATTT
1 TTTTTAATACTTTATTT
5759302 CAGTCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATACTTTATTT
Found at i:5767388 original size:15 final size:15
Alignment explanation
Indices: 5767368--5767398 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5767358 AACTCTTAGG
5767368 AGAGACTTGAGACAA
1 AGAGACTTGAGACAA
5767383 AGAGACTTGAGACAA
1 AGAGACTTGAGACAA
5767398 A
1 A
5767399 ATGATAGAAA
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:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (15 bp):
AGAGACTTGAGACAA
Found at i:5768386 original size:186 final size:186
Alignment explanation
Indices: 5768063--5768629 Score: 965
Period size: 186 Copynumber: 3.0 Consensus size: 186
5768053 TCATCTCCAG
*
5768063 ATTGACCCGATTTCCTCAACGCGAAGGAA-AAGTGTCATAATTTATCGAAAATGACCCGATCTCT
1 ATTGACCCGATTTCCTCAACGCGAAGGAACAA-TGTCATAATTTATCGAAAACGACCCGATCTCT
* * *
5768127 TCAACACGGATGAGCAGTGACGTCTTCAAAATCAAATTGACCCGATCTCCTCAACACGAAGGAGC
65 TCAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCAACACGAAGGAGC
* *
5768192 AATGTCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAA
130 AGTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAA
* * *
5768249 ATTGATCCGATTTCCTCAACGCGAAGGAACAATGTCACAATTTATCGAAAACGACCTGATCTCTT
1 ATTGACCCGATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTT
*
5768314 CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCAACACGAAGGAACA
66 CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCAACACGAAGGAGCA
*
5768379 GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCATATTGTCCCCAA
131 GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAA
*
5768435 ATTGACCCGATTTCCTCAACACGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTT
1 ATTGACCCGATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTT
* * * *
5768500 TAACACGGATGAGTAGTGTCGTCTTCAACATCAAATCGACCTGATCTCCTCAACATGAAGGAGCA
66 CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCAACACGAAGGAGCA
5768565 GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCCAA
131 GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGT-CCCCAA
5768622 ATTGACCC
1 ATTGACCC
5768630 TTAGATAGCC
Statistics
Matches: 358, Mismatches: 21, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
186 342 0.96
187 16 0.04
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (186 bp):
ATTGACCCGATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTT
CAACACGGATGAGCAGTGTCGTCTTCAACATCAAATTGACCTGATCTCCTCAACACGAAGGAGCA
GTGTCATCCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAA
Found at i:5768991 original size:18 final size:18
Alignment explanation
Indices: 5768968--5769002 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5768958 ATTTTCTGTC
5768968 CACCAGCACATGCTCCAG
1 CACCAGCACATGCTCCAG
5768986 CACCAGCACATGCTCCA
1 CACCAGCACATGCTCCA
5769003 CTTACCAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.46, G:0.14, T:0.11
Consensus pattern (18 bp):
CACCAGCACATGCTCCAG
Found at i:5775026 original size:37 final size:37
Alignment explanation
Indices: 5774950--5775026 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
5774940 TTTTTATATT
*
5774950 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
5774987 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
5775024 TTT
1 TTT
5775027 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:5775202 original size:20 final size:20
Alignment explanation
Indices: 5775177--5775229 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5775167 ATTTCCTAGG
5775177 AATCTTTTATTCCCACTGGT
1 AATCTTTTATTCCCACTGGT
5775197 AATCTTTTATTCCCACTGGT
1 AATCTTTTATTCCCACTGGT
*
5775217 AATCTTATATTCC
1 AATCTTTTATTCC
5775230 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.45
Consensus pattern (20 bp):
AATCTTTTATTCCCACTGGT
Found at i:5783105 original size:128 final size:128
Alignment explanation
Indices: 5782840--5783098 Score: 484
Period size: 128 Copynumber: 2.0 Consensus size: 128
5782830 GGAGAAAAGT
5782840 CTCAAGGTAATCTATTCCATACATTTGAGTGTACCCTTTAGCAATCAATCTTTCTTTGTACCTCT
1 CTCAAGGTAATCTATTCCATACATTTGAGTGTACCCTTTAGCAATCAATCTTTCTTTGTACCTCT
*
5782905 CCAAAGAACCATTTGATTTATACTTTACTGTGAACACACATCGACATTCCACTGGTGTCTTCC
66 CCAAAGAACCATTTGATTTATACTTTACTGTGAACACACATCGACATCCCACTGGTGTCTTCC
5782968 CTCAAGGTAATCTATTCCATACATTTGAGTGTACCCTTTAGCAATCAATCTTTCTTTGTACCTCT
1 CTCAAGGTAATCTATTCCATACATTTGAGTGTACCCTTTAGCAATCAATCTTTCTTTGTACCTCT
*
5783033 CCAAAGAACCATTTGATTTATA-TTTCACTGTGAACACCCATCGACATCCCACTGGTGTCTTCC
66 CCAAAGAACCATTTGATTTATACTTT-ACTGTGAACACACATCGACATCCCACTGGTGTCTTCC
5783096 CTC
1 CTC
5783099 TTGGTAACTC
Statistics
Matches: 128, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
127 3 0.02
128 125 0.98
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.36
Consensus pattern (128 bp):
CTCAAGGTAATCTATTCCATACATTTGAGTGTACCCTTTAGCAATCAATCTTTCTTTGTACCTCT
CCAAAGAACCATTTGATTTATACTTTACTGTGAACACACATCGACATCCCACTGGTGTCTTCC
Found at i:5797609 original size:25 final size:25
Alignment explanation
Indices: 5797548--5797609 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
5797538 AGTTTTAATC
* * *
5797548 AAAAATTATTTTTTATTATTATATT
1 AAAAATTATATTTTAATATTATACT
*
5797573 AAAAATGAATATTTTAATA-TATTACT
1 AAAAAT-TATATTTTAATATTA-TACT
5797599 AAAAATTATAT
1 AAAAATTATAT
5797610 GACAAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AAAAATTATATTTTAATATTATACT
Found at i:5798237 original size:21 final size:21
Alignment explanation
Indices: 5798208--5798261 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5798198 TAAAATGTTA
*
5798208 AAAAAGATTAAAATATTCTTT
1 AAAATGATTAAAATATTCTTT
5798229 AAAATGATTAAAATATTCTTT
1 AAAATGATTAAAATATTCTTT
5798250 AAAAT-ATTAAAA
1 AAAATGATTAAAA
5798262 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAATGATTAAAATATTCTTT
Found at i:5798522 original size:16 final size:18
Alignment explanation
Indices: 5798475--5798525 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
5798465 TTTGTTTTAC
5798475 GGAATGTAAGATTACCAGTA
1 GGAA-GTAAGATTACCAG-A
5798495 GGAATGTAAGATTACCA-A
1 GGAA-GTAAGATTACCAGA
5798513 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
5798526 TGATAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGA
Found at i:5798742 original size:37 final size:37
Alignment explanation
Indices: 5798669--5798743 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
5798659 GTTGGAAGAT
* *
5798669 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
5798706 ATTTATATATATATT-TTTAAAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTGAAAATCATAAA
5798743 A
1 A
5798744 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 16 0.47
38 16 0.47
39 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:5800803 original size:30 final size:30
Alignment explanation
Indices: 5800764--5800839 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
5800754 TCATATATTC
5800764 GGTC-GGTTGGG-GCGGTGAAACTTTATTTT
1 GGTCGGGTTGGGCG-GGTGAAACTTTATTTT
*
5800793 GGTCGGGTTGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTTGGGCGGGTGAAACTTTATTTT
* *
5800823 GGTCGGGTCGGTCGGGT
1 GGTCGGGTTGGGCGGGT
5800840 TTTTTAAGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 4 0.09
30 38 0.88
31 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.42, T:0.36
Consensus pattern (30 bp):
GGTCGGGTTGGGCGGGTGAAACTTTATTTT
Found at i:5801108 original size:38 final size:38
Alignment explanation
Indices: 5801063--5801136 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
5801053 TCGGGTTGGG
5801063 TTTTTAAGTGTGATATTCGGGTCAAATCGGGTCGGGGT
1 TTTTTAAGTGTGATATTCGGGTCAAATCGGGTCGGGGT
* *
5801101 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGG
1 TTTTTAAGTGTGATATTCGGGTCAAATCGGGTCGGG
5801137 TTTGGGGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.36
Consensus pattern (38 bp):
TTTTTAAGTGTGATATTCGGGTCAAATCGGGTCGGGGT
Found at i:5809169 original size:6 final size:6
Alignment explanation
Indices: 5809158--5809214 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
5809148 ATCAGTCATC
* *
5809158 TCTTCA TCTTCA TCTTCAGA TCTGT-A CCATTCA TCTTTA TCTTCA TCTTCA
1 TCTTCA TCTTCA TCTTC--A TCT-TCA TC-TTCA TCTTCA TCTTCA TCTTCA
5809209 TCTTCA
1 TCTTCA
5809215 GACCATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 34 0.81
7 3 0.07
8 4 0.10
9 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (6 bp):
TCTTCA
Found at i:5819843 original size:28 final size:28
Alignment explanation
Indices: 5819803--5819866 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
5819793 GGATGGTGGT
5819803 TTTGCTTTCTTACAGATCATTGATTCGC
1 TTTGCTTTCTTACAGATCATTGATTCGC
5819831 TTTGCTTTCTTACAGATCATTGATTCGC
1 TTTGCTTTCTTACAGATCATTGATTCGC
5819859 TTTGCTTT
1 TTTGCTTT
5819867 GACAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.50
Consensus pattern (28 bp):
TTTGCTTTCTTACAGATCATTGATTCGC
Found at i:5820882 original size:14 final size:14
Alignment explanation
Indices: 5820863--5820889 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5820853 TAAAAAAATT
5820863 ATATACATAAATAC
1 ATATACATAAATAC
5820877 ATATACATAAATA
1 ATATACATAAATA
5820890 TTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATACATAAATAC
Found at i:5822408 original size:24 final size:24
Alignment explanation
Indices: 5822362--5822408 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5822352 ATTTAATATC
* *
5822362 AACACAAACAACATTGACTATTAA
1 AACACAAACAACATTAACAATTAA
**
5822386 AACACAATTAACATTAACAATTA
1 AACACAAACAACATTAACAATTA
5822409 CTAGAACATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.23
Consensus pattern (24 bp):
AACACAAACAACATTAACAATTAA
Found at i:5822422 original size:18 final size:18
Alignment explanation
Indices: 5822395--5822434 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5822385 AAACACAATT
* *
5822395 AACATTAACAATTACTAG
1 AACATCAACAATTACTAA
5822413 AACATCAACAATTACTAA
1 AACATCAACAATTACTAA
5822431 AACA
1 AACA
5822435 CACTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.03, T:0.23
Consensus pattern (18 bp):
AACATCAACAATTACTAA
Found at i:5822512 original size:25 final size:25
Alignment explanation
Indices: 5822462--5822557 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
5822452 AGGGTAACAT
* * * *
5822462 AATTAGTATTAACAATCATTAACAC
1 AATTAATATTAACAATTACTACCAC
* **
5822487 ATTTAATGCTAACAATTACTACCAC
1 AATTAATATTAACAATTACTACCAC
*
5822512 AATTAATATTAATAATTACTACCAC
1 AATTAATATTAACAATTACTACCAC
*
5822537 AACTAATATTAACAATTACTA
1 AATTAATATTAACAATTACTA
5822558 TTCTTTAACC
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (25 bp):
AATTAATATTAACAATTACTACCAC
Found at i:5826651 original size:44 final size:44
Alignment explanation
Indices: 5826548--5826638 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
5826538 CCAGTAGTCT
5826548 CTAAAAACTCATTTTGAACCCTTAGTGATGAAGATCACAGTTAG
1 CTAAAAACTCATTTTGAACCCTTAGTGATGAAGATCACAGTTAG
5826592 CTAAAAACTCATTTTGAACCCTTAGTGATGAAGATCACAGTTAG
1 CTAAAAACTCATTTTGAACCCTTAGTGATGAAGATCACAGTTAG
5826636 CTA
1 CTA
5826639 GGAATTCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (44 bp):
CTAAAAACTCATTTTGAACCCTTAGTGATGAAGATCACAGTTAG
Found at i:5831195 original size:141 final size:139
Alignment explanation
Indices: 5830923--5831180 Score: 353
Period size: 141 Copynumber: 1.9 Consensus size: 139
5830913 AAAGCAAAAT
* * *
5830923 TCAAAATAAATCAAACCCATCAAAACCAAAGGTATCCTAACACTAAATCCAGTGTTTATAATAAC
1 TCAAAAGAAACCAAACCCATCAAAACCAAAGCTATCCTAACACTAAATCCAGTGTTTATAATAAC
* *
5830988 TCGTTAACATATACGAAAGGAAAATTAAGCAAAATTAACAAAAGATTCAATGAAACGGGAGAAAA
66 TC--TAACATATACAAAAGGAAAATTAAGCAAAATTAACAAAAGATTCAATGAAACGGGAAAAAA
5831053 AAAAGTAACAG
129 AAAAGTAACAG
* * * * *
5831064 TCAAAAGAAACCAAACCCATTAAAACCAAAGCTATCCTAATACTAAATTCAGTGTTTATCATCAC
1 TCAAAAGAAACCAAACCCATCAAAACCAAAGCTATCCTAACACTAAATCCAGTGTTTATAATAAC
*
5831129 TC-AA-A-A-ACAAATATGGAGAATTAAGCAAAATTAACAAAAGATTCAATGAAAC
66 TCTAACATATACAAA-A-GGAAAATTAAGCAAAATTAACAAAAGATTCAATGAAAC
5831181 AAAAGGGAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
135 4 0.04
136 2 0.02
137 38 0.36
138 2 0.02
141 59 0.56
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.21
Consensus pattern (139 bp):
TCAAAAGAAACCAAACCCATCAAAACCAAAGCTATCCTAACACTAAATCCAGTGTTTATAATAAC
TCTAACATATACAAAAGGAAAATTAAGCAAAATTAACAAAAGATTCAATGAAACGGGAAAAAAAA
AAGTAACAG
Found at i:5832640 original size:9 final size:8
Alignment explanation
Indices: 5832629--5832658 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
5832619 TAATTGTTTA
5832629 AAAATATT
1 AAAATATT
5832637 AAAATATT
1 AAAATATT
5832645 AAAATATT
1 AAAATATT
5832653 AAAATA
1 AAAATA
5832659 AACTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:5832729 original size:11 final size:10
Alignment explanation
Indices: 5832707--5832765 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
5832697 TTCACTTTTT
*
5832707 TAAAAATAAA
1 TAAAAATGAA
5832717 TAAAAATGCAA
1 TAAAAATG-AA
5832728 TAAAAATGAA
1 TAAAAATGAA
5832738 TTAAAAATGAA
1 -TAAAAATGAA
* *
5832749 TAAAATTCAA
1 TAAAAATGAA
5832759 TAAAAAT
1 TAAAAAT
5832766 ATAATGTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 23 0.53
11 20 0.47
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (10 bp):
TAAAAATGAA
Found at i:5832733 original size:21 final size:20
Alignment explanation
Indices: 5832707--5832765 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
5832697 TTCACTTTTT
5832707 TAAAAATAAATAAAAATGCAA
1 TAAAAATAAATAAAAATG-AA
*
5832728 TAAAAATGAATTAAAAATGAA
1 TAAAAAT-AAATAAAAATGAA
* *
5832749 TAAAATTCAATAAAAAT
1 TAAAAATAAATAAAAAT
5832766 ATAATGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.24
21 15 0.45
22 10 0.30
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
TAAAAATAAATAAAAATGAA
Found at i:5832916 original size:14 final size:14
Alignment explanation
Indices: 5832897--5832923 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5832887 GTTGTTAAAA
5832897 AATAATAATTCATG
1 AATAATAATTCATG
5832911 AATAATAATTCAT
1 AATAATAATTCAT
5832924 TTGATCCCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (14 bp):
AATAATAATTCATG
Found at i:5834145 original size:21 final size:21
Alignment explanation
Indices: 5834090--5834138 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
5834080 GGGAGCGTCA
5834090 GTGCATCGATGCATACACAAG
1 GTGCATCGATGCATACACAAG
5834111 GTGCATCGATGCATACACAAG
1 GTGCATCGATGCATACACAAG
5834132 GTGCATC
1 GTGCATC
5834139 AGTGCATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
GTGCATCGATGCATACACAAG
Found at i:5834402 original size:65 final size:64
Alignment explanation
Indices: 5834208--5834411 Score: 220
Period size: 65 Copynumber: 3.2 Consensus size: 64
5834198 CTAAGAGTGT
* * *
5834208 ATCGATGCATGAAGTGCATTCGATGTTTCAA-AATATCCTGAGTGCATCGATGCATGGCTTGTAC
1 ATCGATGCATAAAATGCATTCGATGTTTCAATAATATCCTGAGTGCATCGATGCATGG-TTGTGC
* * *
5834272 ATCGATGCATCAAATGCATTCGATGTTTTC-ATAA-AGCCCTGAGTGCATCTATGCATGGTATGT
1 ATCGATGCATAAAATGCATTCGATG-TTTCAATAATA-TCCTGAGTGCATCGATGCATGGT-TGT
5834335 GC
63 GC
* * *
5834337 ATCGATGCATAAAATGCATTCGATG-TTCAATTTATTTCATG-GTGCATCGATGCATGGATTGGT
1 ATCGATGCATAAAATGCATTCGATGTTTCAA-TAATATCCTGAGTGCATCGATGCATGG-TT-GT
5834400 GC
63 GC
*
5834402 ATCGGTGCAT
1 ATCGATGCAT
5834412 CACTTTGAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
63 3 0.03
64 43 0.36
65 73 0.61
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (64 bp):
ATCGATGCATAAAATGCATTCGATGTTTCAATAATATCCTGAGTGCATCGATGCATGGTTGTGC
Found at i:5835012 original size:2 final size:2
Alignment explanation
Indices: 5835005--5835067 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
5834995 CAAACCAAAC
5835005 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5835047 CA CA -A CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA
5835068 TATATATATA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5835072 original size:2 final size:2
Alignment explanation
Indices: 5835067--5835122 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5835057 ACACACACAC
5835067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5835109 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5835123 TAAGTTCAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5837150 original size:23 final size:23
Alignment explanation
Indices: 5837120--5837201 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
5837110 GCATGGCCTT
5837120 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
* * **
5837143 GTGCATCGGTGCACCTTC-A-TT
1 GTGCATCGATGCACATTCAAGGC
* * *
5837164 GTGTATCGATGCATATTCAAGGG
1 GTGCATCGATGCACATTCAAGGC
*
5837187 GATGAATCGATGCAC
1 G-TGCATCGATGCAC
5837202 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 14 0.32
22 2 0.05
23 17 0.39
24 11 0.25
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGC
Found at i:5843070 original size:83 final size:82
Alignment explanation
Indices: 5842982--5843179 Score: 215
Period size: 83 Copynumber: 2.4 Consensus size: 82
5842972 GTTGGACCCT
* * * *
5842982 TAGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAG-CC
1 TAGTGCATCGATGCA-TAAGAGTGCATCGATGCATCAAATGCATTCAATGTTTTCAAAA-AGCCC
5843045 TGAGTGCATCGATGCATGG
64 TGAGTGCATCGATGCATGG
* * * *
5843064 CTAGTGCATCGATGCAT-GGCTTGTGCATCGATGTATCAAATGCATTCAATGTTTTCATAAAGCC
1 -TAGTGCATCGATGCATAAG--AGTGCATCGATGCATCAAATGCATTCAATGTTTTCAAAAAGCC
*
5843128 CTGAGTGCATCTATGCATGG
63 CTGAGTGCATCGATGCATGG
*
5843148 TATGTGCATCGATGCATAA-AATGCATTCGATG
1 TA-GTGCATCGATGCATAAGAGTGCA-TCGATG
5843180 TTCATTTTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
81 1 0.01
82 5 0.05
83 49 0.51
84 41 0.43
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (82 bp):
TAGTGCATCGATGCATAAGAGTGCATCGATGCATCAAATGCATTCAATGTTTTCAAAAAGCCCTG
AGTGCATCGATGCATGG
Found at i:5843071 original size:19 final size:19
Alignment explanation
Indices: 5843047--5843096 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
5843037 AAATAGCCTG
5843047 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGGCT
5843066 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGGCT
*
5843085 TGTGCATCGATG
1 AGTGCATCGATG
5843097 TATCAAATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGCATGGCT
Done.