Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 14 of 27
Found at i:2015030 original size:16 final size:16
Alignment explanation
Indices: 2014985--2015062 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
2014975 TACGTTAATA
* *
2014985 ATTTATATTATATAAA
1 ATTTATATTATATTAT
*
2015001 ATTT-TA-AATA-TAT
1 ATTTATATTATATTAT
2015014 ATTTATATTATATTAT
1 ATTTATATTATATTAT
2015030 ATTT-TAATTAT-TT-T
1 ATTTAT-ATTATATTAT
*
2015044 ATATATATTATATTCAT
1 ATTTATATTATATT-AT
2015061 AT
1 AT
2015063 AATCGTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
13 5 0.10
14 14 0.29
15 11 0.22
16 16 0.33
17 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATATTATATTAT
Found at i:2017254 original size:2 final size:2
Alignment explanation
Indices: 2017247--2017278 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2017237 TTTGTAAGAG
2017247 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
2017279 GAAAATGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2019495 original size:32 final size:33
Alignment explanation
Indices: 2019441--2019504 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
2019431 AGATCAATTT
* *
2019441 ATAAATTTATTTTATTATTTTAAA-ATATTAAAA
1 ATAAATTTATATTAATATTTTAAATA-ATTAAAA
*
2019474 ATAATTTTATATTAATA-TTTAAATAATTAAA
1 ATAAATTTATATTAATATTTTAAATAATTAAA
2019505 TTTAGATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
ATAAATTTATATTAATATTTTAAATAATTAAAA
Found at i:2020079 original size:27 final size:28
Alignment explanation
Indices: 2020039--2020107 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
2020029 TAATATGAGT
2020039 ATATGAATATAATATA-AAAT-TATTAAA
1 ATATGAATATAATATATAAATAT-TTAAA
2020066 ATAT-AATATAAATATATAAATATTTAAA
1 ATATGAATAT-AATATATAAATATTTAAA
**
2020094 A-ATTTATATAATAT
1 ATATGAATATAATAT
2020108 GAATCATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 5 0.14
27 17 0.46
28 14 0.38
29 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATGAATATAATATATAAATATTTAAA
Found at i:2020088 original size:19 final size:19
Alignment explanation
Indices: 2020038--2020088 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
2020028 TTAATATGAG
*
2020038 TATATGAATATAATATAAA
1 TATATAAATATAATATAAA
2020057 -ATTATTAAAATATAATATAAA
1 TA-TA-T-AAATATAATATAAA
2020078 TATATAAATAT
1 TATATAAATAT
2020089 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 1 0.04
19 8 0.30
20 2 0.07
21 15 0.56
22 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TATATAAATATAATATAAA
Found at i:2020126 original size:33 final size:32
Alignment explanation
Indices: 2020066--2020155 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 32
2020056 AATTATTAAA
2020066 ATATAATATAAATATATAAATATTTAAAAATTT
1 ATATAATATAAATATATAAATATTT-AAAATTT
*
2020099 ATATAATATGAATCAT-TAAA-ATATTAAAATTT
1 ATATAATATAAAT-ATATAAATAT-TTAAAATTT
* *
2020131 ATATCGATATAAATTATTTAAATAT
1 ATAT-AATATAAA-TATATAAATAT
2020156 GATTATAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
32 13 0.27
33 26 0.54
34 7 0.15
35 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (32 bp):
ATATAATATAAATATATAAATATTTAAAATTT
Found at i:2020208 original size:46 final size:45
Alignment explanation
Indices: 2020137--2020240 Score: 106
Period size: 46 Copynumber: 2.2 Consensus size: 45
2020127 ATTTATATCG
*
2020137 ATATAAATTATTTAAATATGATTATAAT-AAAATA-AAATATATAAAT
1 ATATAAATT-TTAAAATATGATTATAATCAAAATATAAATA-AT-AAT
*
2020183 ATATAAATTTTAAAATAT-ATTTTATAATCAAATTATAAATAATAAT
1 ATATAAATTTTAAAATATGA--TTATAATCAAAATATAAATAATAAT
*
2020229 AAATAATATTTT
1 ATATAA-ATTTT
2020241 TGGCACGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
44 1 0.02
45 8 0.16
46 24 0.48
47 12 0.24
48 5 0.10
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (45 bp):
ATATAAATTTTAAAATATGATTATAATCAAAATATAAATAATAAT
Found at i:2028935 original size:18 final size:19
Alignment explanation
Indices: 2028899--2028937 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2028889 ATAATTAAAT
2028899 AAAATTTTAAATCAATTTA
1 AAAATTTTAAATCAATTTA
*
2028918 AAAATTTTAAA-CATTTTA
1 AAAATTTTAAATCAATTTA
2028936 AA
1 AA
2028938 TTATGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTTAAATCAATTTA
Found at i:2030476 original size:2 final size:2
Alignment explanation
Indices: 2030464--2030509 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2030454 GCACTTCATC
* *
2030464 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2030505 AT AT A
1 AT AT A
2030510 ACTTTTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2030693 original size:17 final size:17
Alignment explanation
Indices: 2030673--2030706 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2030663 AAATATTGAG
2030673 TATAAATATTTATTTAA
1 TATAAATATTTATTTAA
2030690 TATAAATATTTATTTAA
1 TATAAATATTTATTTAA
2030707 AAAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAAATATTTATTTAA
Found at i:2030744 original size:18 final size:18
Alignment explanation
Indices: 2030721--2030759 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2030711 ATTTAAAAAT
* * *
2030721 TATATTTTTATATTTAAA
1 TATATTATTAAATATAAA
2030739 TATATTATTAAATATAAA
1 TATATTATTAAATATAAA
2030757 TAT
1 TAT
2030760 TAAATACGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATTATTAAATATAAA
Found at i:2033361 original size:16 final size:15
Alignment explanation
Indices: 2033340--2033394 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
2033330 AAGTTGACTT
2033340 AAAAAATTATTTAATA
1 AAAAAATT-TTTAATA
2033356 AAAAAATTTATTAAT-
1 AAAAAATTT-TTAATA
*
2033371 AAATAATTTTTAAATA
1 AAAAAATTTTT-AATA
2033387 TAAAAAAT
1 -AAAAAAT
2033395 ATAATTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 2 0.06
15 12 0.36
16 13 0.39
17 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAAATTTTTAATA
Found at i:2033366 original size:17 final size:17
Alignment explanation
Indices: 2033340--2033394 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
2033330 AAGTTGACTT
2033340 AAAAAA-TTATTTAATA
1 AAAAAATTTATTTAATA
2033356 AAAAAATTTA-TTAAT-
1 AAAAAATTTATTTAATA
* *
2033371 AAATAATTT-TTAAATA
1 AAAAAATTTATTTAATA
2033387 TAAAAAAT
1 -AAAAAAT
2033395 ATAATTATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 12 0.38
16 11 0.34
17 9 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAAATTTATTTAATA
Found at i:2033710 original size:16 final size:15
Alignment explanation
Indices: 2033689--2033730 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2033679 AGGTGCTCTT
2033689 TATTAATATTTATTTA
1 TATTAATATTT-TTTA
2033705 TATTAATATTTTTTA
1 TATTAATATTTTTTA
*
2033720 AATATAATATT
1 TAT-TAATATT
2033731 AATAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATATTTTTTA
Found at i:2035256 original size:32 final size:31
Alignment explanation
Indices: 2035227--2035285 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2035217 TTTACTGACA
*
2035227 AAAAATAAT-ATTATAGATTTAA-AAAACTG
1 AAAAATAATAATTTTAGATTTAATAAAACTG
2035256 AAAAATTAATAATTTTAGATTTAATAAAAC
1 AAAAA-TAATAATTTTAGATTTAATAAAAC
2035286 AAACTAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 12 0.46
32 5 0.19
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (31 bp):
AAAAATAATAATTTTAGATTTAATAAAACTG
Found at i:2036251 original size:2 final size:2
Alignment explanation
Indices: 2036244--2036275 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2036234 ATAAAATCTC
2036244 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
2036276 GACAATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2036442 original size:11 final size:11
Alignment explanation
Indices: 2036407--2036474 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
2036397 TTATGACAAA
2036407 TATATT-ATAT
1 TATATTAATAT
*
2036417 TATTTTTAATAT
1 TA-TATTAATAT
*
2036429 TATATTAATTT
1 TATATTAATAT
2036440 TATATT--TAT
1 TATATTAATAT
* *
2036449 TA-AAT-ATTT
1 TATATTAATAT
2036458 TATATTAATAT
1 TATATTAATAT
2036469 TATATT
1 TATATT
2036475 TTTATATCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
8 2 0.04
9 8 0.18
10 4 0.09
11 25 0.56
12 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTAATAT
Found at i:2036448 original size:29 final size:28
Alignment explanation
Indices: 2036408--2036475 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
2036398 TATGACAAAT
* *
2036408 ATATTATATTATTTTTAATA-TTATATTA
1 ATATTATATT-TATTAAATATTTATATTA
*
2036436 ATTTTATATTTATTAAATATTTTATATTA
1 ATATTATATTTATTAAATA-TTTATATTA
2036465 ATATTATATTT
1 ATATTATATTT
2036476 TTATATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.21
28 9 0.26
29 18 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTATATTTATTAAATATTTATATTA
Found at i:2036457 original size:18 final size:19
Alignment explanation
Indices: 2036407--2036487 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 19
2036397 TTATGACAAA
2036407 TATATTATATT--AT-TTT
1 TATATTATATTAAATATTT
2036423 TAATATTATATT--A-ATTT
1 T-ATATTATATTAAATATTT
2036440 TATATT-TATTAAATATTT
1 TATATTATATTAAATATTT
*
2036458 TATATTAATATTATAT-TTT
1 TATATT-ATATTAAATATTT
*
2036477 TATATCATATT
1 TATATTATATT
2036488 TAAAATTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
15 4 0.07
16 6 0.11
17 16 0.29
18 15 0.27
19 8 0.14
20 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTATATTAAATATTT
Found at i:2036506 original size:40 final size:40
Alignment explanation
Indices: 2036421--2036507 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
2036411 TTATATTATT
* *
2036421 TTTAATATTATATTAATTTTATATTTATTAAATATTTTATA
1 TTTAATATTATATT-ATTTTATATATATTAAATATTTTAAA
2036462 -TTAATATTATA-T-TTTTATATCATATTTAAA-ATTATTAAA
1 TTTAATATTATATTATTTTATAT-ATA-TTAAATATT-TTAAA
2036501 TTTAATA
1 TTTAATA
2036508 ATGACTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
37 8 0.20
38 5 0.12
39 10 0.25
40 17 0.43
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (40 bp):
TTTAATATTATATTATTTTATATATATTAAATATTTTAAA
Found at i:2037972 original size:2 final size:2
Alignment explanation
Indices: 2037965--2037993 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2037955 TTCGAGAATT
2037965 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
2037994 GTATTATAAT
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:2038293 original size:16 final size:16
Alignment explanation
Indices: 2038272--2038302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2038262 TTTTTTTTAA
2038272 AAAAATTAAATATTTT
1 AAAAATTAAATATTTT
*
2038288 AAAAATTATATATTT
1 AAAAATTAAATATTT
2038303 ATATCTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAATTAAATATTTT
Found at i:2040134 original size:39 final size:35
Alignment explanation
Indices: 2040053--2040136 Score: 87
Period size: 39 Copynumber: 2.2 Consensus size: 35
2040043 AAATTAATGT
* *
2040053 ATATATAATAAAAAATTTTATTTTAATTTAATTATA
1 ATAT-TAATAAAAAATTTTATATTAATTTAATAATA
*
2040089 ACTATTAATATAAAAATTATTAATATTATTTTAAATAATA
1 A-TATTAATA-AAAAATT-TT-ATATTAATTT-AATAATA
2040129 ATATTAAT
1 ATATTAAT
2040137 TTTTGGACGA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
36 6 0.15
37 10 0.25
38 2 0.05
39 15 0.38
40 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (35 bp):
ATATTAATAAAAAATTTTATATTAATTTAATAATA
Found at i:2040607 original size:16 final size:17
Alignment explanation
Indices: 2040577--2040610 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2040567 GAAGCAAATG
*
2040577 TTTTTTTTCTTTTTCTT
1 TTTTTTTTCTCTTTCTT
2040594 TTTTTTTTC-CTTTCTT
1 TTTTTTTTCTCTTTCTT
2040610 T
1 T
2040611 CATTATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTTCTCTTTCTT
Found at i:2042731 original size:2 final size:2
Alignment explanation
Indices: 2042720--2042760 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2042710 TATACAATTC
2042720 AT AT -T 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
2042761 CTACGTAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2043299 original size:18 final size:20
Alignment explanation
Indices: 2043266--2043305 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2043256 TTTTTATATA
2043266 AAAAATTATAATTTAAAATT
1 AAAAATTATAATTTAAAATT
*
2043286 AAAAA-TAT-ATTTAAATTT
1 AAAAATTATAATTTAAAATT
2043304 AA
1 AA
2043306 TTTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 3 0.16
20 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTATAATTTAAAATT
Found at i:2044277 original size:23 final size:24
Alignment explanation
Indices: 2044227--2044279 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2044217 AACATTATAT
* *
2044227 ATTT-AAAATTAAAATATAATTAA
1 ATTTAAAAAATAAAATATAATAAA
*
2044250 TTTTAAAAAATAAAATATAA-AAA
1 ATTTAAAAAATAAAATATAATAAA
2044273 ATTTAAA
1 ATTTAAA
2044280 TTCGATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTTAAAAAATAAAATATAATAAA
Found at i:2052983 original size:19 final size:19
Alignment explanation
Indices: 2052961--2053020 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
2052951 ACGTGAAGGA
2052961 AAAGTTAACATTTGAAAGC
1 AAAGTTAACATTTGAAAGC
*
2052980 AAAGTTTTAA-ATAACGTGAAAGC
1 AAAG--TTAACAT---TTGAAAGC
2053003 AAAGTTAACATTTGAAAG
1 AAAGTTAACATTTGAAAG
2053021 GCATATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
19 10 0.30
20 2 0.06
21 8 0.24
22 2 0.06
23 11 0.33
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (19 bp):
AAAGTTAACATTTGAAAGC
Found at i:2053711 original size:2 final size:2
Alignment explanation
Indices: 2053704--2053735 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2053694 GTAACTTCAA
*
2053704 AT AT AT AT AT AA 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
2053736 TGTGTCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2054859 original size:18 final size:16
Alignment explanation
Indices: 2054836--2054879 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
2054826 AATCAATTTA
2054836 AAATTATATTTTACTATT
1 AAATTATATTTTA--ATT
*
2054854 AAATTAAATTTTAATT
1 AAATTATATTTTAATT
*
2054870 AATTTATATT
1 AAATTATATT
2054880 ATATTGAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTATATTTTAATT
Found at i:2055087 original size:23 final size:21
Alignment explanation
Indices: 2055049--2055095 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
2055039 TCTCAATATT
2055049 AATTAATTTTTCAAAAAAAATA
1 AATTAATTTTTC-AAAAAAATA
* *
2055071 AATTATATTTTTTAAAATAATA
1 AATTA-ATTTTTCAAAAAAATA
2055093 AAT
1 AAT
2055096 ATAAATCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAATTTTTCAAAAAAATA
Found at i:2055878 original size:19 final size:19
Alignment explanation
Indices: 2055854--2055912 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
2055844 TAAAAATATT
2055854 ATAAATATTACACAAATAA
1 ATAAATATTACACAAATAA
* *
2055873 ATAAAT-TTA-A-ATAT-T
1 ATAAATATTACACAAATAA
2055888 ATAAATATTACACAAATAA
1 ATAAATATTACACAAATAA
2055907 ATAAAT
1 ATAAAT
2055913 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 2 0.06
18 6 0.19
19 12 0.38
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAATATTACACAAATAA
Found at i:2055888 original size:34 final size:34
Alignment explanation
Indices: 2055847--2055922 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
2055837 TATAATATAA
2055847 AAATATTATAAATATTACACAAATAAATAAATTT
1 AAATATTATAAATATTACACAAATAAATAAATTT
2055881 AAATATTATAAATATTACACAAATAAATAAATTT
1 AAATATTATAAATATTACACAAATAAATAAATTT
*
2055915 AAAAATTA
1 AAATATTA
2055923 AGCAGCTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (34 bp):
AAATATTATAAATATTACACAAATAAATAAATTT
Found at i:2057827 original size:2 final size:2
Alignment explanation
Indices: 2057820--2057846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2057810 TGCGCAGGTA
2057820 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2057847 TTACCATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2061244 original size:10 final size:10
Alignment explanation
Indices: 2061226--2061262 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2061216 CAGTAGCCAA
2061226 CCCCTCCCCC-
1 CCCC-CCCCCT
2061236 CCCCCCCCCT
1 CCCCCCCCCT
2061246 CCCCCCCCCT
1 CCCCCCCCCT
2061256 CCCCCCC
1 CCCCCCC
2061263 TTCTTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.19
10 21 0.81
ACGTcount: A:0.00, C:0.92, G:0.00, T:0.08
Consensus pattern (10 bp):
CCCCCCCCCT
Found at i:2061246 original size:15 final size:16
Alignment explanation
Indices: 2061226--2061260 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
2061216 CAGTAGCCAA
2061226 CCCCTCCCCCCCCC-C
1 CCCCTCCCCCCCCCTC
2061241 CCCCTCCCCCCCCCTC
1 CCCCTCCCCCCCCCTC
2061257 CCCC
1 CCCC
2061261 CCTTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.00, C:0.91, G:0.00, T:0.09
Consensus pattern (16 bp):
CCCCTCCCCCCCCCTC
Found at i:2066343 original size:2 final size:2
Alignment explanation
Indices: 2066330--2066360 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2066320 ATTGTATTTC
*
2066330 AT AT AT AC 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 A
2066361 GTAGTGTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2077489 original size:2 final size:2
Alignment explanation
Indices: 2077482--2077514 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2077472 TTCACACCAT
2077482 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 T
2077515 CCTGCGTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2077972 original size:12 final size:11
Alignment explanation
Indices: 2077940--2078023 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
2077930 AAAAATTTAA
2077940 ATTTTATAA-T
1 ATTTTATAATT
2077950 ATTTTATTAATT
1 ATTTTA-TAATT
2077962 ATTATTATAATT
1 ATT-TTATAATT
*
2077974 ATTTTAT-TTT
1 ATTTTATAATT
**
2077984 ATTTTATTTTT
1 ATTTTATAATT
***
2077995 ATAAAATAATT
1 ATTTTATAATT
* *
2078006 ATTTTATTATA
1 ATTTTATAATT
2078017 ATTTTAT
1 ATTTTAT
2078024 TCTATTTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 15 0.25
11 29 0.49
12 12 0.20
13 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTATAATT
Found at i:2078425 original size:2 final size:2
Alignment explanation
Indices: 2078418--2078447 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2078408 TAGACTAATA
2078418 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
2078448 GCAGACGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2080209 original size:21 final size:24
Alignment explanation
Indices: 2080183--2080227 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
2080173 ATTGGTCAAA
2080183 TTTAAAAAT-TTTA-AAT-TAATT
1 TTTAAAAATATTTATAATATAATT
2080204 TTTAAAAATATTTATAATATAATT
1 TTTAAAAATATTTATAATATAATT
2080228 AAATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 3 0.14
24 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAAAATATTTATAATATAATT
Found at i:2080276 original size:26 final size:26
Alignment explanation
Indices: 2080243--2080308 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
2080233 TAAATATTTA
2080243 TTTATTAAATAC-TAATTTAAT-TAAT
1 TTTATTAAA-ACTTAATTTAATCTAAT
*
2080268 TTTAATTAAAACTTATTTTAATCTAAT
1 TTT-ATTAAAACTTAATTTAATCTAAT
2080295 TTTATTAAAA-TTAA
1 TTTATTAAAACTTAA
2080309 AATTTATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 8 0.22
26 21 0.58
27 7 0.19
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTATTAAAACTTAATTTAATCTAAT
Found at i:2080954 original size:20 final size:19
Alignment explanation
Indices: 2080931--2080982 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2080921 ATATAAAGCA
2080931 TAAATTATTTTTATATTTAT
1 TAAA-TATTTTTATATTTAT
* * *
2080951 TAAAAATATTATATATTTTT
1 TAAATAT-TTTTATATTTAT
2080971 TAAATATTTTTA
1 TAAATATTTTTA
2080983 ATGTTGTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAATATTTTTATATTTAT
Found at i:2082142 original size:2 final size:2
Alignment explanation
Indices: 2082135--2082162 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2082125 AGATAATGGG
2082135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2082163 AAGGGTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2082854 original size:19 final size:17
Alignment explanation
Indices: 2082812--2082855 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
2082802 TTTAAGATAG
2082812 ATTTGAAAAAATATTTTT
1 ATTT-AAAAAATATTTTT
*
2082830 AATTAAAATAATATATTTT
1 ATTTAAAA-AATAT-TTTT
2082849 ATTTAAA
1 ATTTAAA
2082856 TTTATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTAAAAAATATTTTT
Found at i:2082856 original size:18 final size:18
Alignment explanation
Indices: 2082817--2082855 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2082807 GATAGATTTG
2082817 AAAA-AATATTTTTAATT
1 AAAATAATATTTTTAATT
*
2082834 AAAATAATATATTTTATTT
1 AAAATAATAT-TTTTAATT
2082853 AAA
1 AAA
2082856 TTTATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATAATATTTTTAATT
Found at i:2083665 original size:18 final size:18
Alignment explanation
Indices: 2083644--2083683 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2083634 AAAAAATTAA
2083644 TTAAATAAAAATATAATT
1 TTAAATAAAAATATAATT
** *
2083662 TTAAATAATTATTTAATT
1 TTAAATAAAAATATAATT
2083680 TTAA
1 TTAA
2083684 TTCAAAGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATAAAAATATAATT
Found at i:2083699 original size:2 final size:2
Alignment explanation
Indices: 2083692--2083716 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2083682 AATTCAAAGT
2083692 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 T
2083717 TTAAGCCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2084246 original size:20 final size:19
Alignment explanation
Indices: 2084217--2084254 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2084207 TAAACAGATC
2084217 AAATTTAAATTTAAATAAA
1 AAATTTAAATTTAAATAAA
2084236 AAATTTAAAATTTAAATAA
1 AAATTT-AAATTTAAATAA
2084255 TCATATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTAAATTTAAATAAA
Found at i:2084757 original size:2 final size:2
Alignment explanation
Indices: 2084752--2084786 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2084742 CTTCGTTCAT
2084752 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2084787 TTTCTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2090226 original size:17 final size:18
Alignment explanation
Indices: 2090191--2090229 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2090181 AGATTTCATA
2090191 ATTTTTATATTCGTATTAT
1 ATTTTTATATTC-TATTAT
2090210 ATTTTTATATT-TATTAT
1 ATTTTTATATTCTATTAT
2090227 ATT
1 ATT
2090230 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTTTATATTCTATTAT
Found at i:2090238 original size:11 final size:9
Alignment explanation
Indices: 2090191--2090242 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 9
2090181 AGATTTCATA
2090191 ATTT-TTAT
1 ATTTATTAT
2090199 ATTCGTATTAT
1 ATT--TATTAT
2090210 ATTT-TTAT
1 ATTTATTAT
2090218 ATTTATTAT
1 ATTTATTAT
2090227 ATTATAATTAT
1 ATT-T-ATTAT
2090238 ATTTA
1 ATTTA
2090243 AAATATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 11 0.29
9 9 0.24
10 3 0.08
11 15 0.39
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTATTAT
Found at i:2090248 original size:20 final size:19
Alignment explanation
Indices: 2090214--2090253 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2090204 TATTATATTT
**
2090214 TTATATTTATTATATTATAA
1 TTATATTTAAAATATT-TAA
2090234 TTATATTTAAAATATTTAA
1 TTATATTTAAAATATTTAA
2090253 T
1 T
2090254 ATTTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATTTAAAATATTTAA
Found at i:2090310 original size:6 final size:6
Alignment explanation
Indices: 2090299--2090343 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2090289 AATAAATAAA
*
2090299 TATATT TATATT TATATT TA-A-T TAT-TT TTTATAT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT-T TATATT TATAT
2090344 GATATGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
4 3 0.09
5 4 0.12
6 21 0.64
7 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:2090746 original size:25 final size:23
Alignment explanation
Indices: 2090718--2090780 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 23
2090708 TTTTTAAAAA
*
2090718 ATATTTTATATTTGTGTAAATATTT
1 ATATTTTATATTT-T-AAAATATTT
*
2090743 ATATTATATAAATTTTAAAATATTT
1 ATATT-T-TATATTTTAAAATATTT
2090768 ATATATTTATATT
1 ATAT-TTTATATT
2090781 ATTTTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 5 0.16
25 18 0.56
26 3 0.09
27 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
ATATTTTATATTTTAAAATATTT
Found at i:2090792 original size:14 final size:14
Alignment explanation
Indices: 2090775--2090807 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2090765 TTTATATATT
*
2090775 TATATTATTTTTAA
1 TATATTATATTTAA
2090789 TATATTATATTTAA
1 TATATTATATTTAA
2090803 TATAT
1 TATAT
2090808 CAAATCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATATTTAA
Found at i:2102286 original size:26 final size:26
Alignment explanation
Indices: 2102246--2102311 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
2102236 CTCATTATTG
*
2102246 ACACGACACGCTTACCTGATACACAA
1 ACACGACACGATTACCTGATACACAA
* * *
2102272 ACACGATACGATTACTTGATACACGA
1 ACACGACACGATTACCTGATACACAA
2102298 ACACGACACGATTA
1 ACACGACACGATTA
2102312 ATTAATTATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (26 bp):
ACACGACACGATTACCTGATACACAA
Found at i:2103842 original size:12 final size:12
Alignment explanation
Indices: 2103825--2103849 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2103815 CTTCATACAG
2103825 AACCAGAGAAGA
1 AACCAGAGAAGA
2103837 AACCAGAGAAGA
1 AACCAGAGAAGA
2103849 A
1 A
2103850 TGCACACCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.24, T:0.00
Consensus pattern (12 bp):
AACCAGAGAAGA
Found at i:2105578 original size:2 final size:2
Alignment explanation
Indices: 2105571--2105601 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2105561 TTGGAAATGA
*
2105571 TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2105602 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2105606 original size:2 final size:2
Alignment explanation
Indices: 2105601--2105625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2105591 TCTATCTCTC
2105601 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 T
2105626 CAATCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2106578 original size:34 final size:34
Alignment explanation
Indices: 2106515--2106732 Score: 242
Period size: 34 Copynumber: 6.4 Consensus size: 34
2106505 CATGTATACG
* **
2106515 TTGTTGATTAAAT-GGTGATTTGGTAGTTTATTA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * * *
2106548 TTGTTGATTAAATGGGTGATTTGATGGTTTATCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
2106582 TTGTTGACTAAATGGGAGATTTGATAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
2106616 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
2106650 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * **
2106684 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGTCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
2106718 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2106733 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
33 16 0.10
34 141 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:2106657 original size:102 final size:101
Alignment explanation
Indices: 2106515--2106732 Score: 301
Period size: 102 Copynumber: 2.1 Consensus size: 101
2106505 CATGTATACG
** * ** * * *
2106515 TTGTTGATTAAATGGTGATTTGGTAGTTTATTATTGTTGATTAAATGGGTGATTTGATGGTTTAT
1 TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTAC
2106580 CATTGTTGACTAAATGGGAGATTTGATAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGATAGCTTACCA
*
2106616 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTA
* * * **
2106681 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGTCA
65 CCATTGTTGACTAAATGGGAGATTTGATAGCTTACCA
2106718 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2106733 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 15 0.15
102 87 0.85
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTAC
CATTGTTGACTAAATGGGAGATTTGATAGCTTACCA
Found at i:2111177 original size:34 final size:34
Alignment explanation
Indices: 2111120--2111338 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
2111110 AAGTGGGAGA
*
2111120 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
2111153 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGTC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2111187 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2111221 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2111255 ATTATTGATTAAATGGGTGATTTGGTGGATTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2111289 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2111323 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2111339 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 141 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2111263 original size:102 final size:101
Alignment explanation
Indices: 2111120--2111338 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
2111110 AAGTGGGAGA
** * * * *
2111120 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGATTA
*
2111185 TCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2111221 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGATT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGATT
* * *
2111286 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2111323 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2111339 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGATTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2112063 original size:2 final size:2
Alignment explanation
Indices: 2112056--2112089 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2112046 CTCGACGGTT
2112056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2112090 AAATTTCCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2112807 original size:154 final size:154
Alignment explanation
Indices: 2112521--2112830 Score: 584
Period size: 154 Copynumber: 2.0 Consensus size: 154
2112511 GGCATGGTTC
2112521 ACGATACATTGAAGAATACAATTCCTGAAGCTGTGTTTTATTGGTAAGTCAGAGAGGCCAAGATG
1 ACGATACATTGAAGAATACAATTCCTGAAGCTGTGTTTTATTGGTAAGTCAGAGAGGCCAAGATG
* *
2112586 TCACTGCCCAACAACTTTTATGTCCAAGTAGGAAGGAGAGAGGTAAATTGTTTAGAATATCACCT
66 TCACTGCCCAACAACTTATATGTCCAAGTAGGAAGGAGAGAGGTAAATTGTTTAGAATATCAACT
2112651 TTTACTGTTGCAATTCTTTCTTTT
131 TTTACTGTTGCAATTCTTTCTTTT
2112675 ACGATACATTGAAGAATACAATTCCTGAAGCTGTGTTTTATTGGTAAGTCAGAGAGGCCAAGATG
1 ACGATACATTGAAGAATACAATTCCTGAAGCTGTGTTTTATTGGTAAGTCAGAGAGGCCAAGATG
* *
2112740 TCACTGCCCAACAACTTATCTGTCCAAGTAGGAAGGAGAGAGGTAAATTGTTTAGAATATTAACT
66 TCACTGCCCAACAACTTATATGTCCAAGTAGGAAGGAGAGAGGTAAATTGTTTAGAATATCAACT
2112805 TTTACTGTTGCAATTCTTTCTTTT
131 TTTACTGTTGCAATTCTTTCTTTT
2112829 AC
1 AC
2112831 ATGCATCAAT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 152 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (154 bp):
ACGATACATTGAAGAATACAATTCCTGAAGCTGTGTTTTATTGGTAAGTCAGAGAGGCCAAGATG
TCACTGCCCAACAACTTATATGTCCAAGTAGGAAGGAGAGAGGTAAATTGTTTAGAATATCAACT
TTTACTGTTGCAATTCTTTCTTTT
Found at i:2116405 original size:34 final size:34
Alignment explanation
Indices: 2116359--2116543 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
2116349 GTAAAAACCA
*
2116359 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2116393 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2116427 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2116461 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2116495 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2116528 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2116544 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2120636 original size:19 final size:19
Alignment explanation
Indices: 2120609--2120671 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2120599 TCACGTGTAC
* *
2120609 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2120628 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2120647 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2120666 AGTACC
1 AGTACC
2120672 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2121024 original size:34 final size:34
Alignment explanation
Indices: 2120978--2121161 Score: 255
Period size: 34 Copynumber: 5.4 Consensus size: 34
2120968 GTAAAAACCA
*
2120978 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2121012 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2121046 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2121080 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2121114 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2121147 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2121162 ATGTTTCATG
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2126527 original size:44 final size:42
Alignment explanation
Indices: 2126469--2126550 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
2126459 AAAACTTTAA
* * *
2126469 AAATAAAATAATTTAATGTAAAATTTAATTTTTTATTTATCATT
1 AAATAAAATAATTTAA--TAAAATTAAAATTTTTACTTATCATT
2126513 AAAT-AAATATATTTAATAAAATTAAAATTTTTACTTAT
1 AAATAAAATA-ATTTAATAAAATTAAAATTTTTACTTAT
2126551 AAATGAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 19 0.56
43 5 0.15
44 10 0.29
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (42 bp):
AAATAAAATAATTTAATAAAATTAAAATTTTTACTTATCATT
Found at i:2126560 original size:43 final size:42
Alignment explanation
Indices: 2126469--2126574 Score: 99
Period size: 42 Copynumber: 2.5 Consensus size: 42
2126459 AAAACTTTAA
* * * * *
2126469 AAATAAA-ATAATTTAATGTAAAATTTAATTTTTTATTTATCATT
1 AAATAAATAT-ATTTAA--TAAAATTAAAATTTTTACTTATAATG
2126513 AAATAAATATATTTAATAAAATTAAAATTTTTACTTATAAATG
1 AAATAAATATATTTAATAAAATTAAAATTTTTACTTAT-AATG
*
2126556 AAATAACTAT-TCTTAATAA
1 AAATAAATATAT-TTAATAA
2126575 TAAAAAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 20 0.38
43 18 0.34
44 13 0.25
45 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (42 bp):
AAATAAATATATTTAATAAAATTAAAATTTTTACTTATAATG
Found at i:2132658 original size:33 final size:33
Alignment explanation
Indices: 2132615--2132686 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
2132605 TATATATATT
* * *
2132615 TAAATTAAATTATTAA-ATATATAAATATTAATA
1 TAAATAAAATT-TTAATATATATAAATAATAAAA
* *
2132648 TAAATAAAATTTTAATATTTTTAAATAATAAAA
1 TAAATAAAATTTTAATATATATAAATAATAAAA
2132681 TAAATA
1 TAAATA
2132687 TCAATTTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAATAAAATTTTAATATATATAAATAATAAAA
Found at i:2133216 original size:22 final size:22
Alignment explanation
Indices: 2133185--2133238 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
2133175 TTTTACTATT
2133185 CATCACTGTTTATGTATCGATA
1 CATCACTGTTTATGTATCGATA
*
2133207 CATCAATGTTTATGTATCGATA
1 CATCACTGTTTATGTATCGATA
2133229 CATCACTGTT
1 CATCACTGTT
2133239 CATCACTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (22 bp):
CATCACTGTTTATGTATCGATA
Found at i:2133341 original size:73 final size:73
Alignment explanation
Indices: 2133208--2133347 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
2133198 GTATCGATAC
* * * * *
2133208 ATCAATGTTTATGTATCGATACATCACTGTTCATCACTATATATTGAGCCCAATGCCTATAATTT
1 ATCAATGTTCATGTATCCATACATCACTGTTCATCACTATACATTAAGCCCAACGCCTATAATTT
2133273 TACTGTTT
66 TACTGTTT
* * *
2133281 ATCATTGTTCATGTATCCATACATCACTGTTCATCACTATACATTAAGTCCAACGGCTATAATTT
1 ATCAATGTTCATGTATCCATACATCACTGTTCATCACTATACATTAAGCCCAACGCCTATAATTT
2133346 TA
66 TA
2133348 AATGTATGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (73 bp):
ATCAATGTTCATGTATCCATACATCACTGTTCATCACTATACATTAAGCCCAACGCCTATAATTT
TACTGTTT
Found at i:2134785 original size:31 final size:33
Alignment explanation
Indices: 2134728--2134811 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 33
2134718 TCATGTTTAA
*
2134728 AATATTTTATATTTTATATAAATTTTAATATATT
1 AATATTTTATA-TTTATATAAATTTTAAAATATT
2134762 AATATTTTATA-TTATA-AAATTTTAAAATATT
1 AATATTTTATATTTATATAAATTTTAAAATATT
* * *
2134793 CATATATATATATATATAT
1 AATAT-TTTATATTTATAT
2134812 TCATATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 18 0.42
32 10 0.23
33 4 0.09
34 11 0.26
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
AATATTTTATATTTATATAAATTTTAAAATATT
Found at i:2134817 original size:6 final size:5
Alignment explanation
Indices: 2134795--2134859 Score: 53
Period size: 5 Copynumber: 12.2 Consensus size: 5
2134785 AAAATATTCA
2134795 TATAT ATATAT ATATAT TCATAT TATAT T-T-T TAATAT TATAT TATATTT
1 TATAT -TATAT -TATAT T-ATAT TATAT TATAT T-ATAT TATAT TATA--T
*
2134844 TATAT TATAT TTTAT T
1 TATAT TATAT TATAT T
2134860 TTTACATCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 26 0.50
6 18 0.35
7 5 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:2134848 original size:12 final size:12
Alignment explanation
Indices: 2134799--2134858 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
2134789 TATTCATATA
2134799 TATATATATATATT
1 TATAT-TATAT-TT
*
2134813 CATATTATATTT
1 TATATTATATTT
2134825 T-TA--ATA--T
1 TATATTATATTT
2134832 TATATTATATTT
1 TATATTATATTT
2134844 TATATTATATTT
1 TATATTATATTT
2134856 TAT
1 TAT
2134859 TTTTACATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 3 0.08
10 3 0.08
11 2 0.05
12 18 0.46
13 5 0.13
14 4 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTATATTT
Found at i:2134855 original size:31 final size:34
Alignment explanation
Indices: 2134794--2134856 Score: 96
Period size: 31 Copynumber: 1.9 Consensus size: 34
2134784 TAAAATATTC
2134794 ATATATATATATATATATTCATATTATATTTTTA
1 ATATATATATATATATATTCATATTATATTTTTA
*
2134828 ATAT-TATAT-TATAT-TTTATATTATATTTT
1 ATATATATATATATATATTCATATTATATTTT
2134857 ATTTTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.50
32 5 0.18
33 5 0.18
34 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (34 bp):
ATATATATATATATATATTCATATTATATTTTTA
Found at i:2135115 original size:20 final size:20
Alignment explanation
Indices: 2135088--2135134 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2135078 CCAAATTAAA
**
2135088 TATATTTAATTCTAAAATTT
1 TATATTTAATTAAAAAATTT
* *
2135108 TTTATTTATTTAAAAAATTT
1 TATATTTAATTAAAAAATTT
2135128 TATATTT
1 TATATTT
2135135 TTATATTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTTAATTAAAAAATTT
Found at i:2135183 original size:16 final size:17
Alignment explanation
Indices: 2135148--2135186 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2135138 TATTAATATT
* *
2135148 TAAATATTTTATAAACA
1 TAAATATTTTAAAAAAA
2135165 TAAATA-TTTAAAAAAA
1 TAAATATTTTAAAAAAA
2135181 TAAATA
1 TAAATA
2135187 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATATTTTAAAAAAA
Found at i:2135336 original size:22 final size:22
Alignment explanation
Indices: 2135311--2135352 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2135301 GGAGTGATAT
2135311 TGAAAATGTATTATAGTTATTA
1 TGAAAATGTATTATAGTTATTA
** *
2135333 TGAATTTGTATTATATTTAT
1 TGAAAATGTATTATAGTTAT
2135353 ATATTTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TGAAAATGTATTATAGTTATTA
Found at i:2135365 original size:27 final size:27
Alignment explanation
Indices: 2135342--2135393 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
2135332 ATGAATTTGT
*
2135342 ATTATATTTATA-TATTTTATAATTTA
1 ATTATATTTAAATTATTTTATAATTTA
2135368 ATTATATTTAAATTATTTTAT-ATTTA
1 ATTATATTTAAATTATTTTATAATTTA
2135394 TATAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTATATTTAAATTATTTTATAATTTA
Found at i:2135387 original size:20 final size:20
Alignment explanation
Indices: 2135343--2135401 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
2135333 TGAATTTGTA
**
2135343 TTATATTTATATATTTTATAAT
1 TTATATTTATATAAATTAT--T
*
2135365 TTA-ATTATATTTAAATTATT
1 TTATATT-TATATAAATTATT
2135385 TTATATTTATATAAATT
1 TTATATTTATATAAATT
2135402 TTAATATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 13 0.42
21 6 0.19
22 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATTTATATAAATTATT
Found at i:2139501 original size:2 final size:2
Alignment explanation
Indices: 2139494--2139533 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2139484 TTACTCTTAA
2139494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2139534 CTTATTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2141135 original size:18 final size:19
Alignment explanation
Indices: 2141112--2141148 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2141102 TCAGGTGTAT
*
2141112 CTGGTGGTGGTGG-AGGGG
1 CTGGTGGTCGTGGAAGGGG
2141130 CTGGTGGTCGTGGAAGGGG
1 CTGGTGGTCGTGGAAGGGG
2141149 TCGTGGTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.08, C:0.08, G:0.62, T:0.22
Consensus pattern (19 bp):
CTGGTGGTCGTGGAAGGGG
Found at i:2141604 original size:2 final size:2
Alignment explanation
Indices: 2141597--2141627 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2141587 AAGCCAAGAT
2141597 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2141628 TTTTGGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2143996 original size:2 final size:2
Alignment explanation
Indices: 2143989--2144025 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2143979 ATGTTGTAAA
2143989 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
2144026 GGAGGTAACA
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:2146514 original size:2 final size:2
Alignment explanation
Indices: 2146507--2146535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2146497 AGATAGGATC
2146507 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 A
2146536 AAATTTATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2148322 original size:62 final size:62
Alignment explanation
Indices: 2148256--2148374 Score: 170
Period size: 62 Copynumber: 1.9 Consensus size: 62
2148246 AAATTTTTCG
*
2148256 TTTAATTGATATATAACTAT-ATTACTAATTA-AGCGAAAATTAATCTAAAATTATAACTCTAC
1 TTTAATTGATATATAACTATAATGA-TAATTAGA-CGAAAATTAATCTAAAATTATAACTCTAC
* * *
2148318 TTTAATTGGTATATAACTATAATGATAATTAGATGAGAATTAATCTAAAATTATAAC
1 TTTAATTGATATATAACTATAATGATAATTAGACGAAAATTAATCTAAAATTATAAC
2148375 AATTTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
62 47 0.92
63 4 0.08
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (62 bp):
TTTAATTGATATATAACTATAATGATAATTAGACGAAAATTAATCTAAAATTATAACTCTAC
Found at i:2148524 original size:16 final size:15
Alignment explanation
Indices: 2148495--2148533 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2148485 TACTTTTACA
2148495 ATATATAATATCAAC
1 ATATATAATATCAAC
* *
2148510 ATATGATAATTTCAAT
1 ATAT-ATAATATCAAC
2148526 ATATATAA
1 ATATATAA
2148534 GTATTAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (15 bp):
ATATATAATATCAAC
Found at i:2149188 original size:20 final size:21
Alignment explanation
Indices: 2149152--2149196 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2149142 TATATATTTT
2149152 ATAAT-TTACTTTAAATATAA
1 ATAATATTACTTTAAATATAA
*
2149172 ATAATATTAGTTT-AATATAA
1 ATAATATTACTTTAAATATAA
2149192 A-AATA
1 ATAATA
2149197 CTGTTTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAATATTACTTTAAATATAA
Found at i:2152619 original size:15 final size:16
Alignment explanation
Indices: 2152601--2152642 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
2152591 ATATATTATA
2152601 TTTATATTTAA-AATT
1 TTTATATTTAATAATT
2152616 TTTACATATTTAATAATT
1 TTT--ATATTTAATAATT
2152634 TTT-TATTTA
1 TTTATATTTA
2152643 TATTTACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 9 0.38
17 8 0.33
18 7 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATATTTAATAATT
Found at i:2152900 original size:20 final size:19
Alignment explanation
Indices: 2152871--2152920 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 19
2152861 TATTATTATG
*
2152871 TATTAAAAATAATACATAAA
1 TATTATAAATAATACAT-AA
2152891 TATTATAAAT--TACATAA
1 TATTATAAATAATACATAA
*
2152908 TAATATAATATAA
1 TATTATAA-ATAA
2152921 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 9 0.36
18 7 0.28
20 9 0.36
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTATAAATAATACATAA
Found at i:2153711 original size:34 final size:34
Alignment explanation
Indices: 2153668--2153818 Score: 212
Period size: 34 Copynumber: 4.4 Consensus size: 34
2153658 ATTTGGTAGT
* *
2153668 TTGTTGATTAAATGGAAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
*
2153702 TTGTTGATTAAATAGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
2153736 TTATTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * *
2153770 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2153804 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2153819 TGATTTTTAC
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 102 1.00
ACGTcount: A:0.27, C:0.07, G:0.26, T:0.40
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
Found at i:2158298 original size:34 final size:34
Alignment explanation
Indices: 2158232--2158416 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
2158222 AAGTGGGAGA
* *
2158232 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2158265 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2158299 ATTGTTGATTAAATAGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2158333 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2158367 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2158401 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2158417 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2159622 original size:2 final size:2
Alignment explanation
Indices: 2159615--2159653 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2159605 GTTTCTGTTT
2159615 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
2159654 GGACGTTGTT
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:2159803 original size:2 final size:2
Alignment explanation
Indices: 2159793--2159835 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2159783 AACTGGTGTG
*
2159793 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2159835 T
1 T
2159836 GCTGTACACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2172306 original size:17 final size:17
Alignment explanation
Indices: 2172278--2172331 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2172268 TATAATTAAA
2172278 ATTAAA-TAAAAATATT
1 ATTAAATTAAAAATATT
* *
2172294 ATTAAATTAAAAAAATA
1 ATTAAATTAAAAATATT
*
2172311 ATTTAAATCATAAAATATT
1 A-TTAAATTA-AAAATATT
2172330 AT
1 AT
2172332 ATTCAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.20
17 9 0.30
18 8 0.27
19 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAATTAAAAATATT
Found at i:2172325 original size:18 final size:19
Alignment explanation
Indices: 2172283--2172339 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
2172273 TTAAAATTAA
* *
2172283 ATAAAAATATTATTAAATT
1 ATAAAAATAATATTAAATC
*
2172302 AAAAAAATAAT-TTAAATC
1 ATAAAAATAATATTAAATC
*
2172320 ATAAAATATTATATTCAAAT
1 ATAAAA-ATAATATT-AAAT
2172340 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 11 0.37
19 13 0.43
20 2 0.07
21 4 0.13
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAAATAATATTAAATC
Found at i:2172759 original size:31 final size:34
Alignment explanation
Indices: 2172686--2172759 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 34
2172676 ATTGCATTTT
* **
2172686 TATAA-ATATTATTTTAATTAACATTATTAATCA
1 TATAATATATTATTTTAATTAACATTATAAAAAA
2172719 T-TAAT-TATTATTTT-ATTAA-ATT-TAAAAAA
1 TATAATATATTATTTTAATTAACATTATAAAAAA
2172748 TATAATATATTA
1 TATAATATATTA
2172760 AGTATAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
29 5 0.14
30 7 0.20
31 10 0.29
32 12 0.34
33 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (34 bp):
TATAATATATTATTTTAATTAACATTATAAAAAA
Found at i:2182135 original size:3 final size:3
Alignment explanation
Indices: 2182127--2182167 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2182117 TCCCTACACA
2182127 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2182168 ATCAACAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2187541 original size:97 final size:97
Alignment explanation
Indices: 2187375--2187565 Score: 337
Period size: 97 Copynumber: 2.0 Consensus size: 97
2187365 AACAACTTTC
* *
2187375 GTAACATGTCAATTCTATAATTTGTTTAGTTGAAAGTGAAAATTAAGATATTAGAATTTAAAGTT
1 GTAACATGTCAATTCTATAATTTGTTTAGTTGAAAGAGAAAATTAAGACATTAGAATTTAAAGTT
* *
2187440 CCTTGGAAGATAGTCTCTTCTAAGAAATTTTA
66 CCTTGCAAGATAGACTCTTCTAAGAAATTTTA
*
2187472 GTAACATGTCAATTCTATAATTTGTTTAGTTGAAAGAGAAAATTAAGACATTAGACTTTAAAGTT
1 GTAACATGTCAATTCTATAATTTGTTTAGTTGAAAGAGAAAATTAAGACATTAGAATTTAAAGTT
2187537 CCTTGCAAGATAGACTCTTCTAAGAAATT
66 CCTTGCAAGATAGACTCTTCTAAGAAATT
2187566 CCCGAGCCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (97 bp):
GTAACATGTCAATTCTATAATTTGTTTAGTTGAAAGAGAAAATTAAGACATTAGAATTTAAAGTT
CCTTGCAAGATAGACTCTTCTAAGAAATTTTA
Found at i:2188010 original size:2 final size:2
Alignment explanation
Indices: 2188003--2188048 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2187993 ACAACTAAAA
2188003 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2188045 TC TC
1 TC TC
2188049 ATGCAGACTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2206397 original size:10 final size:10
Alignment explanation
Indices: 2206382--2206406 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2206372 TTTTTAATAC
2206382 AAATATTAAA
1 AAATATTAAA
2206392 AAATATTAAA
1 AAATATTAAA
2206402 AAATA
1 AAATA
2206407 AAACTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATATTAAA
Found at i:2206667 original size:21 final size:22
Alignment explanation
Indices: 2206641--2206701 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
2206631 TAAACATATT
*
2206641 TATTTAAAAATAAATATAATAA
1 TATTTAAAAATAAATATAAAAA
*
2206663 T-TTTAAAAAT-AATACAAAAA
1 TATTTAAAAATAAATATAAAAA
*
2206683 TATTAAAAAATAAA-ATAAA
1 TATTTAAAAATAAATATAAA
2206702 TACACTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TATTTAAAAATAAATATAAAAA
Found at i:2206772 original size:3 final size:3
Alignment explanation
Indices: 2206764--2206812 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
2206754 AATAACTTTT
2206764 ATA ATA ATA ATA ATA ATA ACT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
2206809 ATA A
1 ATA A
2206813 AACACCGACG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2216896 original size:13 final size:14
Alignment explanation
Indices: 2216880--2216908 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2216870 TATCTTTGAG
2216880 TTTT-TTTTTTAAA
1 TTTTATTTTTTAAA
2216893 TTTTATTTTTTAAA
1 TTTTATTTTTTAAA
2216907 TT
1 TT
2216909 GATAGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTTAAA
Found at i:2219834 original size:21 final size:22
Alignment explanation
Indices: 2219805--2219850 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2219795 TGTTCAGACA
** *
2219805 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2219827 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2219848 AGT
1 AGT
2219851 TTTAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2221788 original size:28 final size:27
Alignment explanation
Indices: 2221733--2221803 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2221723 GCCACCCATT
*
2221733 TGTTTGTCAAAAATGATGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
2221760 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
2221788 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
2221804 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:2228115 original size:23 final size:23
Alignment explanation
Indices: 2228089--2228157 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
2228079 ATGATCAAGA
*
2228089 TAAAAAATATTAAAAATTAATTT
1 TAAAAAATATTAAAAATTAAATT
* *
2228112 TAAAAAAAATTAAATAAGTGAAATT
1 TAAAAAATATTAAA-AA-TTAAATT
2228137 TAAAAAATA-TATAAAATTAAA
1 TAAAAAATATTA-AAAATTAAA
2228158 ATTTTGTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 17 0.45
24 6 0.16
25 15 0.39
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
TAAAAAATATTAAAAATTAAATT
Found at i:2228151 original size:26 final size:23
Alignment explanation
Indices: 2228089--2228161 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 23
2228079 ATGATCAAGA
* *
2228089 TAAAAAATATTAAAAATTAATTT
1 TAAAAAATATTAAAAATGAAATT
*
2228112 TAAAAAAAATTAAATAAGTGAAATT
1 TAAAAAATATTAAA-AA-TGAAATT
* *
2228137 TAAAAAATATATAAAATTAAAATT
1 TAAAAAATAT-TAAAAATGAAATT
2228161 T
1 T
2228162 TGTATGATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
23 13 0.32
24 9 0.22
25 15 0.37
26 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
TAAAAAATATTAAAAATGAAATT
Found at i:2228894 original size:10 final size:11
Alignment explanation
Indices: 2228881--2228953 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
2228871 TATATTTTAA
2228881 TATATT-TATT
1 TATATTATATT
2228891 TATATTATATT
1 TATATTATATT
* *
2228902 T-TAACTATTTT
1 TAT-ATTATATT
2228913 TATATTTCATATT
1 TATA-TT-ATATT
2228926 T-TATTATATT
1 TATATTATATT
* *
2228936 TTTAATTATTTT
1 TAT-ATTATATT
2228948 TATATT
1 TATATT
2228954 TCATTCCTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 13 0.26
11 19 0.38
12 13 0.26
13 5 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTATATT
Found at i:2228900 original size:17 final size:16
Alignment explanation
Indices: 2228862--2228954 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 16
2228852 ATTAATAACT
2228862 TATATTTAATATATTTTAA
1 TATATTTAAT-TA-TTT-A
*
2228881 TATATTTATTTATATTA
1 TATATTTAATTAT-TTA
* *
2228898 TAT-TTTAACTATTTT
1 TATATTTAATTATTTA
*
2228913 TATATTTCATATTTTATTA
1 TATATTT-A-ATTAT-TTA
* *
2228932 TATTTTTAATTATTTT
1 TATATTTAATTATTTA
2228948 TATATTT
1 TATATTT
2228955 CATTCCTGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.09
16 18 0.31
17 10 0.17
18 8 0.14
19 17 0.29
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATTTAATTATTTA
Found at i:2228950 original size:35 final size:33
Alignment explanation
Indices: 2228861--2228958 Score: 119
Period size: 35 Copynumber: 2.9 Consensus size: 33
2228851 CATTAATAAC
2228861 TTATA-TTTAATATATTTTAATATATTT-ATTTATA
1 TTATATTTTAAT-TATTTT--TATATTTCATTTATA
* *
2228895 TTATATTTTAACTATTTTTATATTTCATATTTTA
1 TTATATTTTAATTATTTTTATATTTCAT-TTATA
2228929 TTATATTTTTAATTATTTTTATATTTCATT
1 TTATA-TTTTAATTATTTTTATATTTCATT
2228959 CCTGTTCCTT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
32 7 0.12
33 2 0.04
34 21 0.37
35 27 0.47
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (33 bp):
TTATATTTTAATTATTTTTATATTTCATTTATA
Found at i:2232355 original size:18 final size:18
Alignment explanation
Indices: 2232329--2232364 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2232319 TAGGTATTCC
2232329 GTCAGGGTAGACAAGCCA
1 GTCAGGGTAGACAAGCCA
* *
2232347 GTCATGGTAGATAAGCCA
1 GTCAGGGTAGACAAGCCA
2232365 TTCCAAGAAA
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:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (18 bp):
GTCAGGGTAGACAAGCCA
Found at i:2235112 original size:47 final size:47
Alignment explanation
Indices: 2235044--2235141 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
2235034 AAGTCATTGC
2235044 AAAA-TTAGAAGTCCAAAACCCATTGAAATGGCTTGGATCATGTATG
1 AAAATTTAGAAGTCCAAAACCCATTGAAATGGCTTGGATCATGTATG
2235090 AAAATTTAGAAGTCCAAAACCCATTGAAATGGCTTGGATCATGTATG
1 AAAATTTAGAAGTCCAAAACCCATTGAAATGGCTTGGATCATGTATG
2235137 AAAAT
1 AAAAT
2235142 GATTAACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 4 0.08
47 47 0.92
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (47 bp):
AAAATTTAGAAGTCCAAAACCCATTGAAATGGCTTGGATCATGTATG
Found at i:2244829 original size:19 final size:19
Alignment explanation
Indices: 2244786--2244831 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
2244776 TTAAACTTTT
*
2244786 TATTTATAAATTAGAAAAA
1 TATTTATAAATAAGAAAAA
* *
2244805 TA-TTATTAATAATAAAAA
1 TATTTATAAATAAGAAAAA
2244823 TATTTATAA
1 TATTTATAA
2244832 TGATAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TATTTATAAATAAGAAAAA
Found at i:2244832 original size:18 final size:18
Alignment explanation
Indices: 2244786--2244837 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
2244776 TTAAACTTTT
* *
2244786 TATTTATAAATTAGAAAAA
1 TATTTAT-AATAATAAAAA
2244805 TA-TTATTAATAATAAAAA
1 TATTTA-TAATAATAAAAA
*
2244823 TATTTATAATGATAA
1 TATTTATAATAATAA
2244838 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TATTTATAATAATAAAAA
Found at i:2245741 original size:11 final size:11
Alignment explanation
Indices: 2245725--2245785 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
2245715 CAAAATTTAC
2245725 ATATTTATATA
1 ATATTTATATA
2245736 ATATTTATA-A
1 ATATTTATATA
* *
2245746 TATTTTTATATT
1 -ATATTTATATA
*
2245758 ATAATTATATTTA
1 AT-ATT-TATATA
2245771 ATATATTATATA
1 ATAT-TTATATA
2245783 ATA
1 ATA
2245786 AATTTTAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
10 1 0.03
11 19 0.49
12 12 0.31
13 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTATATA
Found at i:2245748 original size:20 final size:20
Alignment explanation
Indices: 2245725--2245785 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
2245715 CAAAATTTAC
2245725 ATATTTATATAATATTTATA
1 ATATTTATATAATATTTATA
* * * *
2245745 ATATTTTTATATTA-TAATT
1 ATATTTATATAATATTTATA
2245764 ATATTTA-AT-ATATTATATA
1 ATATTTATATAATATT-TATA
2245783 ATA
1 ATA
2245786 AATTTTAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 2 0.06
18 3 0.10
19 14 0.45
20 12 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTATATAATATTTATA
Done.