Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001709.1 Hibiscus syriacus cultivar Beakdansim tig00003435_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: 1326839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:119459 original size:22 final size:20
Alignment explanation
Indices: 119413--119469 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
119403 AATTAACTAT
119413 TTATAATTAAATTATAGTAA
1 TTATAATTAAATTATAGTAA
*
119433 TTATATATTATAATTATAATTAA
1 TTATA-ATTA-AATTAT-AGTAA
119456 -TATAATTAATATTA
1 TTATAATTAA-ATTA
119470 ATATAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.19
21 12 0.38
22 10 0.31
23 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTATAATTAAATTATAGTAA
Found at i:119482 original size:15 final size:15
Alignment explanation
Indices: 119431--119613 Score: 90
Period size: 15 Copynumber: 11.5 Consensus size: 15
119421 AAATTATAGT
*
119431 AATTATA-TATTAT-
1 AATTATATTAATATA
119444 AATTATAATTAATAT-
1 AATTAT-ATTAATATA
119459 AATTAATATTAATATA
1 AATT-ATATTAATATA
119475 AATTATATGT--TATA
1 AATTATAT-TAATATA
119489 AATTATATAGTATATTTTATA
1 AATTATAT--TA-A---TATA
*
119510 AACTATAGTTAATAT-
1 AATTATA-TTAATATA
119525 AATTAATATTAATATA
1 AATT-ATATTAATATA
* *
119541 ATATAGTTTATAAACTATA
1 A-AT--TATATTAA-TATA
* *
119560 TACTATATTAATATA
1 AATTATATTAATATA
*
119575 AATTATAGTTAAGATA
1 AATTATA-TTAATATA
* *
119591 AATAACATTAATATA
1 AATTATATTAATATA
*
119606 AACTATAT
1 AATTATAT
119614 AGTACATTAA
Statistics
Matches: 132, Mismatches: 18, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
13 6 0.05
14 13 0.10
15 54 0.41
16 32 0.24
17 2 0.02
18 6 0.05
19 6 0.05
20 2 0.02
21 10 0.08
22 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTATATTAATATA
Found at i:119636 original size:20 final size:21
Alignment explanation
Indices: 119595--119636 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
119585 AAGATAAATA
119595 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
119617 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
119637 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:119816 original size:22 final size:19
Alignment explanation
Indices: 119723--119825 Score: 61
Period size: 20 Copynumber: 5.1 Consensus size: 19
119713 GGTTACGTAT
*
119723 ATAGTTTATATAACATATAA
1 ATAGTTTATAT-ACATATAC
*
119743 ATAGATTGTATATATATATATAC
1 ATAG--T-T-TATATACATATAC
*
119766 TATAGGTTATAT--ATAT--
1 -ATAGTTTATATACATATAC
119782 ATAGTTTATATACACTATAC
1 ATAGTTTATATACA-TATAC
119802 ATAGTTTATACATACATGATAC
1 ATAGTTTAT--ATACAT-ATAC
119824 AT
1 AT
119826 GTACTATAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
15 10 0.15
17 1 0.02
18 7 0.11
20 18 0.27
21 2 0.03
22 12 0.18
23 7 0.11
24 9 0.14
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (19 bp):
ATAGTTTATATACATATAC
Found at i:119862 original size:37 final size:37
Alignment explanation
Indices: 119814--119884 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
119804 AGTTTATACA
*
119814 TACATGATACATGTACTATAAGTTACA-TATATAGTT
1 TACATGATACATATACTATAAGTTACATTATATAGTT
*
119850 TACATGTATACATATACTATATGTTACATTATATA
1 TACATG-ATACATATACTATAAGTTACATTATATA
119885 TATTAACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 6 0.19
37 19 0.61
38 6 0.19
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (37 bp):
TACATGATACATATACTATAAGTTACATTATATAGTT
Found at i:119912 original size:7 final size:7
Alignment explanation
Indices: 119902--119947 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
119892 TATGGTTTAT
119902 GTTTAGG
1 GTTTAGG
**
119909 GTTTATT
1 GTTTAGG
**
119916 GTTTAAA
1 GTTTAGG
119923 GTTTAGG
1 GTTTAGG
119930 GTTTAGG
1 GTTTAGG
119937 GTTTAGG
1 GTTTAGG
119944 GTTT
1 GTTT
119948 TTATAAACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (7 bp):
GTTTAGG
Found at i:119947 original size:21 final size:21
Alignment explanation
Indices: 119902--119941 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
119892 TATGGTTTAT
**
119902 GTTTAGGGTTTATTGTTTAAA
1 GTTTAGGGTTTAGGGTTTAAA
119923 GTTTAGGGTTTAGGGTTTA
1 GTTTAGGGTTTAGGGTTTA
119942 GGGTTTTTAT
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:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTTTAAA
Found at i:120421 original size:82 final size:81
Alignment explanation
Indices: 120333--120490 Score: 262
Period size: 82 Copynumber: 1.9 Consensus size: 81
120323 TTAGTTATAC
* *
120333 ATATATATATATACTATATTAATATAAATTATAACATATAAACTATATATTTTATATAGTTTATA
1 ATATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTT-TATAGTTTATA
120398 CATATATAGTTTTTTTT
65 CATATATAGTTTTTTTT
***
120415 ATATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTATAGTTTATAC
1 ATATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTTATAGTTTATAC
120480 ATATATAGTTT
66 ATATATAGTTT
120491 ATATACATAG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
81 23 0.32
82 48 0.68
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (81 bp):
ATATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTTATAGTTTATAC
ATATATAGTTTTTTTT
Found at i:120486 original size:15 final size:14
Alignment explanation
Indices: 120468--120668 Score: 91
Period size: 13 Copynumber: 14.1 Consensus size: 14
120458 TATATACTTT
120468 TATAGTTTATACATA
1 TATAGTTTATA-ATA
120483 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
120496 CATAGTTTAT-ATA
1 TATAGTTTATAATA
120509 TATAGTTCATATAA-A
1 TATAGTT--TATAATA
* *
120524 CATAATTTATATATA
1 TATAGTTTATA-ATA
120539 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
120557 TATAGTTTAT-AT-
1 TATAGTTTATAATA
** * *
120569 TATA-AATATAGTT
1 TATAGTTTATAATA
*
120582 TATAATTT-TATATA
1 TATAGTTTATA-ATA
*
120596 CATAGTTTAT-ATA
1 TATAGTTTATAATA
*
120609 TATAGTTCACATAA-A
1 TATAGTT--TATAATA
*
120624 TATAATTTAT-ATA
1 TATAGTTTATAATA
*
120637 TA-ATTTATAATAATTA
1 TATAGTT-T-ATAA-TA
120653 TATAGTTTATAATA
1 TATAGTTTATAATA
120667 TA
1 TA
120669 AATATAATTT
Statistics
Matches: 142, Mismatches: 21, Indels: 47
0.68 0.10 0.22
Matches are distributed among these distances:
11 3 0.02
12 9 0.06
13 47 0.33
14 16 0.11
15 40 0.28
16 10 0.07
17 7 0.05
18 10 0.07
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:120497 original size:17 final size:16
Alignment explanation
Indices: 120458--120499 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
120448 TTTTATAAAC
* *
120458 TATATACTTTTATAGT
1 TATATACATATATAGT
120474 T-TATACATATATAGTT
1 TATATACATATATAG-T
120490 TATATACATA
1 TATATACATA
120500 GTTTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 3 0.14
17 8 0.36
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (16 bp):
TATATACATATATAGT
Found at i:120511 original size:28 final size:27
Alignment explanation
Indices: 120469--120663 Score: 93
Period size: 28 Copynumber: 6.9 Consensus size: 27
120459 ATATACTTTT
*
120469 ATAGTTTATACATATATAGTTTATATA
1 ATAGTTTATATATATATAGTTTATATA
*
120496 CATAG-TT-TATATATATAGTTCATATAAA
1 -ATAGTTTATATATATATAGTT--TATATA
*
120524 CATAATTTATATATATATAGCTTATAATAATTA
1 -ATAGTTTATATATATATAG-TT-T-AT-A-TA
120557 TATAGTTTATATTATAAATATAG-TT-TAT-
1 -ATAGTTTATA-TAT--ATATAGTTTATATA
*
120585 A-A-TTT-TATATACATAGTTTATATA
1 ATAGTTTATATATATATAGTTTATATA
* * * *
120609 TATAGTTCACATAAATATAATTTATAT-
1 -ATAGTTTATATATATATAGTTTATATA
*
120636 ATAATTTATAATAATTATATAGTTTATA
1 ATAGTTTAT-AT-A-TATATAGTTTATA
120664 ATATAAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
21 5 0.04
22 2 0.02
23 6 0.05
24 2 0.02
25 4 0.03
26 20 0.16
27 7 0.05
28 28 0.22
29 14 0.11
30 14 0.11
31 5 0.04
32 1 0.01
33 11 0.09
34 4 0.03
36 6 0.05
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (27 bp):
ATAGTTTATATATATATAGTTTATATA
Found at i:120522 original size:81 final size:82
Alignment explanation
Indices: 120335--120523 Score: 249
Period size: 82 Copynumber: 2.3 Consensus size: 82
120325 AGTTATACAT
* *** *
120335 ATATATATATACTATATTAATATAAATTATAACATATAAACTATATATTTTATATAGTTTATACA
1 ATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTATATAGTTTATACA
* * *
120400 TATATAGTTTTTTTTAT
66 TATATAGTTTTATATAC
120417 ATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTT-TATAGTTTATACA
1 ATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTATATAGTTTATACA
120481 TATATAG-TTTATATAC
66 TATATAGTTTTATATAC
* *
120497 ATAGTTTATATA-TATAGTTCATATAAA
1 ATA-TATATATACTATA-TTAATATAAA
120524 CATAATTTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
80 13 0.14
81 36 0.38
82 46 0.48
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (82 bp):
ATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTATATAGTTTATACA
TATATAGTTTTATATAC
Found at i:120639 original size:11 final size:11
Alignment explanation
Indices: 120623--120705 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
120613 GTTCACATAA
120623 ATATAATTTAT
1 ATATAATTTAT
120634 ATATAATTTAT
1 ATATAATTTAT
120645 A-ATAATTATAT
1 ATATAATT-TAT
* *
120656 AGTTTATAATATAA
1 A---TATAATTTAT
*
120670 ATATAATTTCT
1 ATATAATTTAT
120681 ATATAATTT-T
1 ATATAATTTAT
* *
120691 ATATTATATAT
1 ATATAATTTAT
120702 ATAT
1 ATAT
120706 TATATTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
10 14 0.24
11 37 0.63
14 3 0.05
15 5 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (11 bp):
ATATAATTTAT
Found at i:120647 original size:18 final size:18
Alignment explanation
Indices: 120624--120678 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
120614 TTCACATAAA
120624 TATAATTTATATATAATT
1 TATAATTTATATATAATT
* *
120642 TATAA-TAATTATATAGTT
1 TATAATTTA-TATATAATT
* *
120660 TATAATATAAATATAATT
1 TATAATTTATATATAATT
120678 T
1 T
120679 CTATATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 2 0.07
18 26 0.90
19 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATAATTTATATATAATT
Found at i:120694 original size:100 final size:98
Alignment explanation
Indices: 120488--120674 Score: 315
Period size: 100 Copynumber: 1.9 Consensus size: 98
120478 ACATATATAG
*
120488 TTTATATACATAGTTTATATATATAGTTCATATAAACATAATTTATATATATATAGCTTATAATA
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATATA--TTATAATA
*
120553 ATTATATAGTTTATATTATAAATATAGTTTATAAT
64 ATTATATAGTTTATAATATAAATATAGTTTATAAT
*
120588 TTTATATACATAGTTTATATATATAGTTCACATAAATATAATTTATATATA-AT-TTATAATAAT
1 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATATATTATAATAAT
120651 TATATAGTTTATAATATAAATATA
66 TATATAGTTTATAATATAAATATA
120675 ATTTCTATAT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
96 33 0.39
99 2 0.02
100 49 0.58
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (98 bp):
TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATATATTATAATAAT
TATATAGTTTATAATATAAATATAGTTTATAAT
Found at i:125260 original size:24 final size:24
Alignment explanation
Indices: 125188--125267 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
125178 ATTTCAAACT
* * *
125188 TGAATTATGTTCTAATACATT-ACC
1 TGAATTCTGTTCTAATTC-TTGATC
*
125212 TGAATTCTGTTCTAATTTTTGATC
1 TGAATTCTGTTCTAATTCTTGATC
* *
125236 TGGATTCTGTTCTGATATCTT-ATC
1 TGAATTCTGTTCTAAT-TCTTGATC
125260 TGAATTCT
1 TGAATTCT
125268 ATTTTGATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 2 0.04
24 41 0.89
25 3 0.07
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTAATTCTTGATC
Found at i:129899 original size:12 final size:12
Alignment explanation
Indices: 129879--129996 Score: 100
Period size: 12 Copynumber: 9.8 Consensus size: 12
129869 AATACATTAC
*
129879 CTGAATTCTGTT
1 CTGATTTCTGTT
*
129891 CTGATTTCTGAT
1 CTGATTTCTGTT
129903 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
129915 CTGATTTCTGAT
1 CTGATTTCTGTT
129927 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
129939 CTGATATCTGAT
1 CTGATTTCTGTT
129951 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
129963 CTGATATCT-TAT
1 CTGATTTCTGT-T
*
129975 CTGAATTCTGTT
1 CTGATTTCTGTT
*
129987 TTGATTTCTG
1 CTGATTTCTG
129997 ATATATCCGT
Statistics
Matches: 84, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
11 7 0.08
12 70 0.83
13 7 0.08
ACGTcount: A:0.15, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:129901 original size:7 final size:6
Alignment explanation
Indices: 129883--129998 Score: 70
Period size: 7 Copynumber: 19.3 Consensus size: 6
129873 CATTACCTGA
129883 ATTCTG -TTCTG ATTTCTG A-TCTGG ATTCTG -TTCTG ATTTCTG A-TCTGG
1 ATTCTG ATTCTG A-TTCTG ATTCT-G ATTCTG ATTCTG A-TTCTG ATTCT-G
*
129931 ATTCTG -TTCTG ATATCTG A-TCTGG ATTCTG -TTCTG ATATCTT A-TCTG
1 ATTCTG ATTCTG AT-TCTG ATTCT-G ATTCTG ATTCTG AT-TCTG ATTCTG
*
129978 AATTCTG -TTTTG ATTTCTG AT
1 -ATTCTG ATTCTG A-TTCTG AT
129999 ATATCCGTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 36
0.69 0.03 0.28
Matches are distributed among these distances:
5 36 0.41
6 13 0.15
7 39 0.44
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:129910 original size:24 final size:24
Alignment explanation
Indices: 129883--129998 Score: 187
Period size: 24 Copynumber: 4.8 Consensus size: 24
129873 CATTACCTGA
129883 ATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATTTCTGATCTGG
129907 ATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATTTCTGATCTGG
*
129931 ATTCTGTTCTGATATCTGATCTGG
1 ATTCTGTTCTGATTTCTGATCTGG
* * *
129955 ATTCTGTTCTGATATCTTATCTGA
1 ATTCTGTTCTGATTTCTGATCTGG
*
129979 ATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATTTCTGAT
129999 ATATCCGTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (24 bp):
ATTCTGTTCTGATTTCTGATCTGG
Found at i:129915 original size:48 final size:47
Alignment explanation
Indices: 129863--129998 Score: 173
Period size: 48 Copynumber: 2.8 Consensus size: 47
129853 ACTTGAATTT
*
129863 TGTTCTAATACATTACCTGAATTCTGTTCTGATTTCTGATCTGGATTC
1 TGTTCTAATAC-TTATCTGAATTCTGTTCTGATTTCTGATCTGGATTC
* * * * *
129911 TGTTCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGGATTC
1 TGTTCT-AATACTTATCTGAATTCTGTTCTGATTTCTGATCTGGATTC
* *
129959 TGTTCTGATATCTTATCTGAATTCTGTTTTGATTTCTGAT
1 TGTTCTAATA-CTTATCTGAATTCTGTTCTGATTTCTGAT
129999 ATATCCGTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
47 1 0.01
48 69 0.95
49 3 0.04
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (47 bp):
TGTTCTAATACTTATCTGAATTCTGTTCTGATTTCTGATCTGGATTC
Found at i:131597 original size:12 final size:12
Alignment explanation
Indices: 131580--131629 Score: 57
Period size: 12 Copynumber: 4.0 Consensus size: 12
131570 TTGTACTTAT
131580 TTTTATTTTTTA
1 TTTTATTTTTTA
131592 TTTTATGTTGTTT-
1 TTTTAT-TT-TTTA
*
131605 TTACTATTTTTTA
1 TT-TTATTTTTTA
131618 TTTTATTTTTTA
1 TTTTATTTTTTA
131630 AATTAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 18 0.56
13 8 0.25
14 6 0.19
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:139598 original size:31 final size:29
Alignment explanation
Indices: 139538--139599 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
139528 ATTTGGTGTA
*
139538 ATACATAAATTTTAATTTATTGTAATTAT
1 ATACACAAATTTTAATTTATTGTAATTAT
139567 ATACACAATATTTTAATTTTAATT-TAATTAT
1 ATACACAA-ATTTTAA-TTT-ATTGTAATTAT
139598 AT
1 AT
139600 GTAGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 7 0.24
31 12 0.41
32 3 0.10
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (29 bp):
ATACACAAATTTTAATTTATTGTAATTAT
Found at i:139710 original size:29 final size:29
Alignment explanation
Indices: 139665--139729 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
139655 TATATAAAAG
* * * *
139665 TAAATATAATTATTTATTTACATACTAAA
1 TAAATATAAATAGTTATGTACATAATAAA
* *
139694 TAAATATAAATAGTTATGTATATAATATA
1 TAAATATAAATAGTTATGTACATAATAAA
139723 TAAATAT
1 TAAATAT
139730 TTATTTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAATATAAATAGTTATGTACATAATAAA
Found at i:139725 original size:23 final size:23
Alignment explanation
Indices: 139693--139742 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
139683 TACATACTAA
139693 ATAA-ATATAAATAGTTATGTAT
1 ATAATATATAAATAGTTATGTAT
* *
139715 ATAATATATAAATATTTATTTAT
1 ATAATATATAAATAGTTATGTAT
139738 ATAAT
1 ATAAT
139743 GGTGTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
ATAATATATAAATAGTTATGTAT
Found at i:142054 original size:31 final size:31
Alignment explanation
Indices: 141999--142057 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
141989 ATGCCGCTAA
*
141999 AGACTCGTACTTTAGTGGCGTTTTTATATAT
1 AGACTCGTACTTTAGTGGCATTTTTATATAT
*
142030 AGACTTGTACTTTAGTGAG-ATTTTTATA
1 AGACTCGTACTTTAGTG-GCATTTTTATA
142058 CAAACGTCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (31 bp):
AGACTCGTACTTTAGTGGCATTTTTATATAT
Found at i:142125 original size:40 final size:41
Alignment explanation
Indices: 142027--142133 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 41
142017 CGTTTTTATA
* * * *
142027 TATAGACTTGTACTTTAGTGAG-ATTTTTATACAAACGTCGT
1 TATACACTTGTACTTTAGTG-GCGTTTATATACAAACGCCGT
* *
142068 TATACAGTTGTATTTTAGTGGCGTTTATATAC-AACGCCGT
1 TATACACTTGTACTTTAGTGGCGTTTATATACAAACGCCGT
* *
142108 TATACACTCGTACTTTAGTGACGTTT
1 TATACACTTGTACTTTAGTGGCGTTT
142134 GTGTTACAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 30 0.55
41 25 0.45
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (41 bp):
TATACACTTGTACTTTAGTGGCGTTTATATACAAACGCCGT
Found at i:142232 original size:28 final size:28
Alignment explanation
Indices: 142227--142406 Score: 171
Period size: 28 Copynumber: 5.9 Consensus size: 28
142217 ATACCAAACT
142227 CCAAACCCCAAACCCATCTGCTTCACTA
1 CCAAACCCCAAACCCATCTGCTTCACTA
*
142255 CCAAACCCCAAACTCATCTGCTTCACTACCAAA
1 CCAAACCCCAAACCCATCTGCTTCACT-----A
*
142288 CTCCAAACCCCAAATCCATCTGCTTCACTA
1 --CCAAACCCCAAACCCATCTGCTTCACTA
* **
142318 CCAAACTCCAAACCCCAGACCTATCTGCTTTGCTA
1 CCAAACCCCAAA---C---CC-ATCTGCTTCACTA
*
142353 CCAAACCCCAAACCCATCTACTTCACTA
1 CCAAACCCCAAACCCATCTGCTTCACTA
*
142381 CTAAACCCCAAACCCATCTGCTTCAC
1 CCAAACCCCAAACCCATCTGCTTCAC
142407 GGCCATTTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
28 71 0.57
29 2 0.02
30 1 0.01
32 1 0.01
33 1 0.01
34 2 0.02
35 47 0.38
ACGTcount: A:0.32, C:0.44, G:0.04, T:0.20
Consensus pattern (28 bp):
CCAAACCCCAAACCCATCTGCTTCACTA
Found at i:142244 original size:35 final size:35
Alignment explanation
Indices: 142198--142367 Score: 219
Period size: 35 Copynumber: 5.1 Consensus size: 35
142188 CCGCGTTTTA
*
142198 CCCAAACCCATCTGCTTCAATACCAAACTCCAAAC
1 CCCAAACCCATCTGCTTCACTACCAAACTCCAAAC
142233 CCCAAACCCATCTGCTTCACT-----A--CCAAAC
1 CCCAAACCCATCTGCTTCACTACCAAACTCCAAAC
*
142261 CCCAAACTCATCTGCTTCACTACCAAACTCCAAAC
1 CCCAAACCCATCTGCTTCACTACCAAACTCCAAAC
*
142296 CCCAAATCCATCTGCTTCACTACCAAACTCCAAAC
1 CCCAAACCCATCTGCTTCACTACCAAACTCCAAAC
* * ** *
142331 CCCAGACCTATCTGCTTTGCTACCAAACCCCAAAC
1 CCCAAACCCATCTGCTTCACTACCAAACTCCAAAC
142366 CC
1 CC
142368 ATCTACTTCA
Statistics
Matches: 118, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
28 26 0.22
30 1 0.01
33 1 0.01
35 90 0.76
ACGTcount: A:0.33, C:0.44, G:0.04, T:0.19
Consensus pattern (35 bp):
CCCAAACCCATCTGCTTCACTACCAAACTCCAAAC
Found at i:142276 original size:63 final size:63
Alignment explanation
Indices: 142198--142405 Score: 244
Period size: 63 Copynumber: 3.3 Consensus size: 63
142188 CCGCGTTTTA
142198 CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAAC
1 CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAAC
* * *
142261 CCCAAACTCATCTGCTTCACTACCAAACTCCAAACCCCAAATCCATCTGCTTCACTACCAAAC
1 CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAAC
* * * **** * *
142324 TCCAAACCC--CAGACCTATC--TGCTTTGCTACCAAACCCCAAACCCATCTACTTCACTACTAA
1 CCCAAACCCATCTG--CT-TCAATACCAAACT-CCAAACCCCAAACCCATCTGCTTCACTACCAA
142385 AC
62 AC
142387 CCCAAACCCATCTGCTTCA
1 CCCAAACCCATCTGCTTCA
142406 CGGCCATTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
61 2 0.02
62 6 0.05
63 110 0.90
64 2 0.02
65 2 0.02
ACGTcount: A:0.33, C:0.43, G:0.04, T:0.20
Consensus pattern (63 bp):
CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAAC
Found at i:142361 original size:98 final size:98
Alignment explanation
Indices: 142198--142395 Score: 306
Period size: 98 Copynumber: 2.0 Consensus size: 98
142188 CCGCGTTTTA
142198 CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAACCC
1 CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAACCC
* * *
142263 CAAACTCATCTGCTTCACTACCAAACTCCAAAC
66 CAAACCCATCTACTTCACTACCAAACCCCAAAC
* * * * **
142296 CCCAAATCCATCTGCTTCACTACCAAACTCCAAACCCCAGACCTATCTGCTTTGCTACCAAACCC
1 CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAACCC
*
142361 CAAACCCATCTACTTCACTACTAAACCCCAAAC
66 CAAACCCATCTACTTCACTACCAAACCCCAAAC
142394 CC
1 CC
142396 ATCTGCTTCA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.33, C:0.44, G:0.04, T:0.19
Consensus pattern (98 bp):
CCCAAACCCATCTGCTTCAATACCAAACTCCAAACCCCAAACCCATCTGCTTCACTACCAAACCC
CAAACCCATCTACTTCACTACCAAACCCCAAAC
Found at i:146091 original size:42 final size:42
Alignment explanation
Indices: 145976--146319 Score: 265
Period size: 43 Copynumber: 8.2 Consensus size: 42
145966 TGCATATTTG
* *
145976 GCGGCGTTTGTTCTAAAAACGCCGCTATAGAACTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
146018 GCGACGTTTGTATTCAAAAACGCCGTTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * *
146061 GCGGCATTTGTTCCAAAAACGCTGTTATAGATCTGA-CTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
146102 ------TTTGTATCCAAAAAGCGTCGCTATATGA-CTGACCTCTT
1 GCGGCGTTTGT-TCCAAAAA-CGCCGCTATA-GATCTGACCTTTT
* ** *
146140 GTGGCGTTTTGTTTTAAAAACGCCGCTATAGATCTAACCTTTT
1 GCGGCG-TTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* ** * * *
146183 GCGACGTTTGTTCTGAAAATGCTGCTATAGATCTCTACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * * * ** * * *
146226 GCGACGTTTATTCCGAAAACACC-AAATAGATATCGACCCTTA
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
146268 GAGGCGTTTGTTCCAAAAACGCCGCGATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
146311 GCGGCGTTT
1 GCGGCGTTT
146320 TTTGTTTTCA
Statistics
Matches: 238, Mismatches: 48, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
35 5 0.02
36 8 0.03
37 11 0.05
38 6 0.03
41 5 0.02
42 90 0.38
43 101 0.42
44 7 0.03
45 5 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:146159 original size:122 final size:120
Alignment explanation
Indices: 145982--146216 Score: 294
Period size: 122 Copynumber: 1.9 Consensus size: 120
145972 TTTGGCGGCG
* * *
145982 TTTGTTCTAAAAACGCCGCTATAGAACTGACCTTTTGCGACGTTTGTATTCAAAAACGCCGTTAT
1 TTTGTTCCAAAAACGCCGCTATAGAACTGACCTCTTGCGACGTTTGTATTCAAAAACGCCGCTAT
* * *
146047 AGATCTGACCTTTTGCGGCATTTGTTCCAAAAACGCTGTTATAGATCTGACTTTT
66 AGATCTAACCTTTTGCGACATTTGTTCCAAAAACGCTGCTATAGATCTGACTTTT
* * * *
146102 TTTGTATCCAAAAAGCGTCGCTATATG-ACTGACCTCTTGTGGCGTTTTGT-TTTAAAAACGCCG
1 TTTGT-TCCAAAAA-CGCCGCTATA-GAACTGACCTCTTGCGACG-TTTGTATTCAAAAACGCCG
* ** *
146165 CTATAGATCTAACCTTTTGCGACGTTTGTTCTGAAAATGCTGCTATAGATCT
62 CTATAGATCTAACCTTTTGCGACATTTGTTCCAAAAACGCTGCTATAGATCT
146217 CTACCTTTTG
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
120 5 0.05
121 7 0.07
122 79 0.81
123 6 0.06
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (120 bp):
TTTGTTCCAAAAACGCCGCTATAGAACTGACCTCTTGCGACGTTTGTATTCAAAAACGCCGCTAT
AGATCTAACCTTTTGCGACATTTGTTCCAAAAACGCTGCTATAGATCTGACTTTT
Found at i:146170 original size:80 final size:78
Alignment explanation
Indices: 146024--146174 Score: 178
Period size: 80 Copynumber: 1.9 Consensus size: 78
146014 TTTTGCGACG
* * * * *
146024 TTTGTATTCAAAAACGCCGTTATAGATCTGACCTTTTGCGGCATTTGTTCCAAAAACGCTGTTAT
1 TTTGTATCCAAAAACGCCGCTATAGATCTGACCTCTTGCGGCATTTGTTCCAAAAACGCCGCTAT
146089 AGATCTGACTTTT
66 AGATCTGACTTTT
* * * **
146102 TTTGTATCCAAAAAGCGTCGCTATATGA-CTGACCTCTTGTGGCGTTTTGTTTTAAAAACGCCGC
1 TTTGTATCCAAAAA-CGCCGCTATA-GATCTGACCTCTTGCGGC-ATTTGTTCCAAAAACGCCGC
146166 TATAGATCT
63 TATAGATCT
146175 AACCTTTTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
78 13 0.22
79 21 0.35
80 26 0.43
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (78 bp):
TTTGTATCCAAAAACGCCGCTATAGATCTGACCTCTTGCGGCATTTGTTCCAAAAACGCCGCTAT
AGATCTGACTTTT
Found at i:146453 original size:19 final size:21
Alignment explanation
Indices: 146415--146453 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
146405 AGCGGCGCTT
*
146415 AAAAACGCCGCTATAGAACTA
1 AAAAACGCCGCTATAAAACTA
146436 AAAAACGCCG-T-TAAAACT
1 AAAAACGCCGCTATAAAACT
146454 CTATTTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAACGCCGCTATAAAACTA
Found at i:148164 original size:10 final size:9
Alignment explanation
Indices: 148141--148174 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
148131 GTTTTTACTG
148141 TTTTTTTGT
1 TTTTTTTGT
148150 TTTTTTTGT
1 TTTTTTTGT
148159 TTTTTTT-T
1 TTTTTTTGT
148167 TATTTTTT
1 T-TTTTTT
148175 AAAATTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 2 0.08
9 22 0.92
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:148172 original size:17 final size:17
Alignment explanation
Indices: 148107--148173 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
148097 ATTGTACTTA
*
148107 TTTTTTTATTTTTTATT-
1 TTTTTTTGTTTTTT-TTG
* * **
148124 TTATGTTGTTTTTACTG
1 TTTTTTTGTTTTTTTTG
148141 TTTTTTTGTTTTTTTTG
1 TTTTTTTGTTTTTTTTG
148158 TTTTTTT-TTTATTTTT
1 TTTTTTTGTTT-TTTTT
148174 TAAAATTAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 4 0.10
17 35 0.90
ACGTcount: A:0.07, C:0.01, G:0.07, T:0.84
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTG
Found at i:150755 original size:31 final size:29
Alignment explanation
Indices: 150695--150756 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
150685 ATTTGGTGTA
*
150695 ATACATAAATTTTAATTTATTGTAATTAT
1 ATACACAAATTTTAATTTATTGTAATTAT
150724 ATACACAATATTTTAATTTTAATT-TAATTAT
1 ATACACAA-ATTTTAA-TTT-ATTGTAATTAT
150755 AT
1 AT
150757 GTAGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 7 0.24
31 12 0.41
32 3 0.10
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (29 bp):
ATACACAAATTTTAATTTATTGTAATTAT
Found at i:150882 original size:23 final size:23
Alignment explanation
Indices: 150850--150899 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
150840 TACTTACTAA
150850 ATAA-ATATAAATAGTTATGTAT
1 ATAATATATAAATAGTTATGTAT
* *
150872 ATAATATATAAATATTTATTTAT
1 ATAATATATAAATAGTTATGTAT
150895 ATAAT
1 ATAAT
150900 GGTGTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
ATAATATATAAATAGTTATGTAT
Found at i:154434 original size:18 final size:19
Alignment explanation
Indices: 154388--154434 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
154378 GGACCCTTGG
*
154388 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAA
154407 TGCATCGATGCA-TAA-AA
1 TGCATCGATGCACTAAGAA
154424 TGCATTCGATG
1 TGCA-TCGATG
154435 TTTTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAA
Found at i:154535 original size:45 final size:46
Alignment explanation
Indices: 154447--154537 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
154437 TTGAAAAAGC
* *
154447 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
154493 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
154538 TTCGATGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:154582 original size:20 final size:20
Alignment explanation
Indices: 154557--154594 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
154547 TGAAAAAATA
154557 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
154577 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
154595 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:159955 original size:12 final size:12
Alignment explanation
Indices: 159940--160005 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
159930 GTTATTTAAA
159940 CGGGTATTGGGC
1 CGGGTATTGGGC
*
159952 CGGGTATTGGGT
1 CGGGTATTGGGC
* *
159964 CAGGTATTGGGT
1 CGGGTATTGGGC
159976 C-GGTATTGGGC
1 CGGGTATTGGGC
* * *
159987 CGGGAATCGGGA
1 CGGGTATTGGGC
159999 CGGGTAT
1 CGGGTAT
160006 ATATATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 10 0.22
12 36 0.78
ACGTcount: A:0.14, C:0.14, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:160061 original size:24 final size:25
Alignment explanation
Indices: 160005--160061 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
159995 GGGACGGGTA
160005 TATATATATTTAAATTAAATATATAT
1 TATAT-TATTTAAATTAAATATATAT
*
160031 T-TTTTATTTAAATTAAAT-T-TAT
1 TATATTATTTAAATTAAATATATAT
160053 TAATATTAT
1 T-ATATTAT
160062 ATATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.15
23 1 0.04
24 19 0.70
25 2 0.07
26 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATTATTTAAATTAAATATATAT
Found at i:160123 original size:13 final size:12
Alignment explanation
Indices: 160092--160128 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
160082 TTTTAATATT
*
160092 TATCGGGTCGGG
1 TATCGGGGCGGG
160104 TATCGGGGCGGG
1 TATCGGGGCGGG
160116 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
160129 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:160190 original size:6 final size:6
Alignment explanation
Indices: 160179--160203 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
160169 AAATGGGTTT
160179 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
160204 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:161715 original size:21 final size:21
Alignment explanation
Indices: 161689--161728 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
161679 AAGATTATTT
161689 TCATTTTT-TAATTTTGAAACA
1 TCATTTTTGT-ATTTTGAAACA
161710 TCATTTTTGTATTTTGAAA
1 TCATTTTTGTATTTTGAAA
161729 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTGTATTTTGAAACA
Found at i:163745 original size:8 final size:8
Alignment explanation
Indices: 163732--163813 Score: 51
Period size: 8 Copynumber: 9.6 Consensus size: 8
163722 CACGGTCTTG
163732 TGCATCGA
1 TGCATCGA
*
163740 TGCATCAAA
1 TGCATC-GA
*
163749 TGCACCG-
1 TGCATCGA
163756 TGCATCGA
1 TGCATCGA
*
163764 TGCATCAAA
1 TGCATC-GA
163773 TGCA-CTGA
1 TGCATC-GA
163781 GTGCATCGA
1 -TGCATCGA
*
163790 TGCATGGTA
1 TGCATCG-A
163799 TGTGCATCGA
1 --TGCATCGA
163809 TGCAT
1 TGCAT
163814 AAAATGCATT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
7 6 0.11
8 25 0.44
9 18 0.32
10 2 0.04
11 6 0.11
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (8 bp):
TGCATCGA
Found at i:163763 original size:24 final size:25
Alignment explanation
Indices: 163731--163794 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
163721 GCACGGTCTT
*
163731 GTGCATCGATGCATCAAATGCAC-C
1 GTGCATCGATGCATCAAATGCACGA
163755 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCAC-GA
163781 GTGCATCGATGCAT
1 GTGCATCGATGCAT
163795 GGTATGTGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
24 23 0.62
26 14 0.38
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
GTGCATCGATGCATCAAATGCACGA
Found at i:163866 original size:20 final size:20
Alignment explanation
Indices: 163841--163878 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
163831 TGAAAAAATA
163841 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
163861 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
163879 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:165605 original size:29 final size:30
Alignment explanation
Indices: 165573--165634 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
165563 ATTTGGTGTA
*
165573 ATACATAA-ATTTTAATTTT-TTGTAATTAT
1 ATACACAATATTTTAATTTTATT-TAATTAT
165602 ATACACAATATTTTAATTTTAATTTAATTAT
1 ATACACAATATTTTAATTTT-ATTTAATTAT
165633 AT
1 AT
165635 GTAGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 11 0.38
31 9 0.31
32 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (30 bp):
ATACACAATATTTTAATTTTATTTAATTAT
Found at i:165745 original size:29 final size:29
Alignment explanation
Indices: 165697--165764 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
165687 AATTATGTAA
* * * *
165697 AAATAAATATAATTATTTATTTACATACT
1 AAATAAATATAAATAGTTATGTACATAAT
*
165726 AAATAAATATAAATAGTTATGTATATAAT
1 AAATAAATATAAATAGTTATGTACATAAT
*
165755 ACATAAATAT
1 AAATAAATAT
165765 TTATTTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (29 bp):
AAATAAATATAAATAGTTATGTACATAAT
Found at i:165760 original size:23 final size:23
Alignment explanation
Indices: 165734--165778 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
165724 CTAAATAAAT
165734 ATAAATAGTTATGTATATAATAC
1 ATAAATAGTTATGTATATAATAC
* *
165757 ATAAATATTTATTTATATAATA
1 ATAAATAGTTATGTATATAATA
165779 GTGTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAAATAGTTATGTATATAATAC
Found at i:167006 original size:20 final size:20
Alignment explanation
Indices: 166973--167018 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
166963 AGTTTGCTAG
166973 TAGTTAAGGCTGTTAATGTT
1 TAGTTAAGGCTGTTAATGTT
* *
166993 TAGTTGAGGTTGTTAATGTT
1 TAGTTAAGGCTGTTAATGTT
167013 TAGTTA
1 TAGTTA
167019 CAAAGTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (20 bp):
TAGTTAAGGCTGTTAATGTT
Found at i:168118 original size:36 final size:36
Alignment explanation
Indices: 168071--168175 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
168061 TGAAAAAGAA
*
168071 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAAGT
*
168107 GAACGGAAGGAAGCATCGTCACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAAGT
*
168143 GAACGGAATGAAGCATCGGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAA
168176 TTGATCATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTTCGATTCAAAGT
Found at i:168418 original size:20 final size:20
Alignment explanation
Indices: 168385--168430 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
168375 AGTTTGATAG
168385 TAGTTAAGGCTGTTAATGTT
1 TAGTTAAGGCTGTTAATGTT
* *
168405 TAGTTGAGGTTGTTAATGTT
1 TAGTTAAGGCTGTTAATGTT
168425 TAGTTA
1 TAGTTA
168431 CAAAGTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (20 bp):
TAGTTAAGGCTGTTAATGTT
Found at i:171312 original size:74 final size:74
Alignment explanation
Indices: 171218--171359 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 74
171208 GGAAGAGCAA
* * * *
171218 TTACCCCTCCCAATTTTGATGGTCTAACTACATTTTAGGTCATTGATTATTATAAAACCATTATA
1 TTACCCCTCCCAACTTTGATGATCTAACTACATTTTAAGTCACTGATTATTATAAAACCATTATA
171283 ATTAAGCTT
66 ATTAAGCTT
* * *
171292 TTACCCCTCTCAACTTTGATGATCTAATTACATTTTAAGTCACTGATTATTATAAAATCATTATA
1 TTACCCCTCCCAACTTTGATGATCTAACTACATTTTAAGTCACTGATTATTATAAAACCATTATA
171357 ATT
66 ATT
171360 GAGCCCTTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (74 bp):
TTACCCCTCCCAACTTTGATGATCTAACTACATTTTAAGTCACTGATTATTATAAAACCATTATA
ATTAAGCTT
Found at i:173914 original size:26 final size:26
Alignment explanation
Indices: 173865--173915 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
173855 ATCTGACGTG
* * *
173865 GCAGTTTCTAGAAGGTCCAGTCAGCA
1 GCAGTTTCTAAAAGATCCAATCAGCA
*
173891 GCAGTTTCTAAAAGATCTAATCAGC
1 GCAGTTTCTAAAAGATCCAATCAGC
173916 GCGCCTTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (26 bp):
GCAGTTTCTAAAAGATCCAATCAGCA
Found at i:175045 original size:14 final size:14
Alignment explanation
Indices: 175026--175062 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
175016 ATAATCATCT
*
175026 CACAGGGCTTATAC
1 CACAGGGCCTATAC
175040 CACAGGGCCTATAC
1 CACAGGGCCTATAC
175054 CACAGGGCC
1 CACAGGGCC
175063 ACCAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.35, G:0.24, T:0.14
Consensus pattern (14 bp):
CACAGGGCCTATAC
Found at i:175722 original size:74 final size:74
Alignment explanation
Indices: 175596--175761 Score: 215
Period size: 74 Copynumber: 2.2 Consensus size: 74
175586 GGAAGAACAA
* * * * *
175596 TTACTCCTCCCAACTTTGATGGTCTAATTACATTTTGGGTCATTGATAATTATAAAATCATTATA
1 TTACCCCTCCCAAATTTGATGATCTAATTACATTTTGGGTCACTGATAATTATAAAATCATTAAA
*
175661 ATTAAGCAT
66 ATTAAGCAC
* * *
175670 TTACCCCTCCCAAATTTGATGATCTAATTATATTTTTGGTCACTGATAATTATATAATCATTAAA
1 TTACCCCTCCCAAATTTGATGATCTAATTACATTTTGGGTCACTGATAATTATAAAATCATTAAA
* *
175735 ATTGAGCCC
66 ATTAAGCAC
*
175744 TTATCCCTCCTCAAATTT
1 TTACCCCTCC-CAAATTT
175762 TGTTGTATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 72 0.91
75 7 0.09
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (74 bp):
TTACCCCTCCCAAATTTGATGATCTAATTACATTTTGGGTCACTGATAATTATAAAATCATTAAA
ATTAAGCAC
Found at i:184836 original size:28 final size:28
Alignment explanation
Indices: 184796--184850 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
184786 GTGGGTACTA
184796 TTCATCACTATTCACTGCTACAATAATG
1 TTCATCACTATTCACTGCTACAATAATG
*
184824 TTCATCACTATTCACTGCTACAGTAAT
1 TTCATCACTATTCACTGCTACAATAAT
184851 TTCCGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.36
Consensus pattern (28 bp):
TTCATCACTATTCACTGCTACAATAATG
Found at i:185303 original size:46 final size:46
Alignment explanation
Indices: 185240--185448 Score: 269
Period size: 46 Copynumber: 4.8 Consensus size: 46
185230 TATAAAATTT
* * *
185240 CTTATCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
185285 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
185331 CTTACCATTTAATTCCATAAGCTCGTAAACTTATTTTAACAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
185377 CTTACCATTTAA-T-C-----C-CATAAGCTTATTTTACCAATATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
185415 CTTGCCA-TT-ATTCCATAAGCTCGTAATCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
185449 GCATGCTTAC
Statistics
Matches: 144, Mismatches: 11, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
36 1 0.01
37 3 0.02
38 27 0.19
39 1 0.01
43 1 0.01
44 12 0.08
45 10 0.07
46 89 0.62
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:192975 original size:17 final size:18
Alignment explanation
Indices: 192953--192986 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
192943 TTGGAAGGTC
*
192953 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
192970 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
192987 ACAGAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:194179 original size:12 final size:12
Alignment explanation
Indices: 194159--194228 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
194149 GATACATTAC
*
194159 CTGAATTCTGTT
1 CTGATTTCTGTT
*
194171 CTGATTTCTGAT
1 CTGATTTCTGTT
194183 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
194195 CTGATATCTGAT
1 CTGATTTCTGTT
*
194207 CTGAATTCTGTT
1 CTGATTTCTGTT
*
194219 TTGATTTCTG
1 CTGATTTCTG
194229 ATATCTCTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:194190 original size:24 final size:24
Alignment explanation
Indices: 194159--194230 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
194149 GATACATTAC
194159 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
194183 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
194207 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
194231 ATCTCTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:194193 original size:48 final size:49
Alignment explanation
Indices: 194122--194230 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
194112 AAATATTTTA
* *
194122 TCTGATTTCCGA-CTTGAATTCTGTTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATATC-TGACCTGAATTCTGT
* * *
194170 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTATGATATCTGACCTGAATTCTGT
*
194218 TTTGATTTCTGAT
1 TCTGATTTCTGAT
194231 ATCTCTATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 51 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTATGATATCTGACCTGAATTCTGT
Found at i:198016 original size:17 final size:18
Alignment explanation
Indices: 197994--198027 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
197984 TTGGAAGGTC
*
197994 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
198011 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
198028 ACAGAATCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:199215 original size:12 final size:12
Alignment explanation
Indices: 199200--199259 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
199190 GATACATTAC
199200 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
199212 CTGATTTCTGAT
1 CTGAATTCTGTT
*
199224 CTGGATTCTGTT
1 CTGAATTCTGTT
*
199236 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
199248 CTGAATTCTGTT
1 CTGAATTCTGTT
199260 TTGATTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:199219 original size:48 final size:48
Alignment explanation
Indices: 199163--199266 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
199153 AAATATTTTA
* *
199163 TCTGATTTCCGA-CTTGAATTTTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* * *
199211 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
199259 TTTGATTT
1 TCTGATTT
199267 ATGATATCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:199231 original size:24 final size:24
Alignment explanation
Indices: 199200--199271 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
199190 GATACATTAC
199200 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
199224 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
199248 CTGAATTCTGTTTTGATTTATGAT
1 CTGAATTCTGTTCTGATTTCTGAT
199272 ATCTCTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:203145 original size:25 final size:25
Alignment explanation
Indices: 203117--203166 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
203107 GAAAAGTCAA
203117 ATTGAATGCTTCAATTTTGGCAGCC
1 ATTGAATGCTTCAATTTTGGCAGCC
*
203142 ATTGAATGCTTCAATTTTGTCAGCC
1 ATTGAATGCTTCAATTTTGGCAGCC
203167 GGCGACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (25 bp):
ATTGAATGCTTCAATTTTGGCAGCC
Found at i:207723 original size:25 final size:25
Alignment explanation
Indices: 207689--207738 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
207679 GAAAAGTCAA
207689 ATTGAATGCTTCAATTTTGGCAGCC
1 ATTGAATGCTTCAATTTTGGCAGCC
* *
207714 ATTGGATGCTTCAATTTTGGTAGCC
1 ATTGAATGCTTCAATTTTGGCAGCC
207739 GGCGGCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (25 bp):
ATTGAATGCTTCAATTTTGGCAGCC
Found at i:215170 original size:19 final size:19
Alignment explanation
Indices: 215155--215195 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
215145 ATCTTTTCTT
215155 AAAA-TCATTTTATTTTTC
1 AAAATTCATTTTATTTTTC
215173 AAAATTCATTTT-TGTTTTC
1 AAAATTCATTTTAT-TTTTC
215192 AAAA
1 AAAA
215196 GAATTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (19 bp):
AAAATTCATTTTATTTTTC
Found at i:218439 original size:18 final size:18
Alignment explanation
Indices: 218416--218458 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
218406 CTTTAATTTA
*
218416 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
218434 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
218452 TTTATTT
1 TTTATTT
218459 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:221939 original size:22 final size:20
Alignment explanation
Indices: 221907--221962 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
221897 CCGGAAGGGG
* *
221907 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-AG-A
*
221929 GTATCGATACCATGGTAAGA
1 GTATCGATACCATAGTAAGA
*
221949 GTATCAATACCATA
1 GTATCGATACCATA
221963 CAACATCGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 15 0.52
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (20 bp):
GTATCGATACCATAGTAAGA
Found at i:221959 original size:95 final size:94
Alignment explanation
Indices: 221830--222028 Score: 283
Period size: 95 Copynumber: 2.1 Consensus size: 94
221820 ATACCAATGA
* * * * *
221830 GGTAGTATCGATACCATCGTAAGGGTATCGATACC-TGGCAACATCGAATCTAAAATTGGTATCT
1 GGTAGTATCGATACCATCGTAAGAGTATCAATACCAT-ACAACATCGAAGCTAAAATTGGTATCG
*
221894 ATACCGGAAGGGGGTATCGGTACCATAGTAT
65 ATACCAG-AGGGGGTATCGGTACCATAGTAT
*
221925 GGTAGTATCGATACCATGGTAAGAGTATCAATACCATACAACATCGAAGCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATCGTAAGAGTATCAATACCATACAACATCGAAGCTAAAATTGGTATCGA
*
221990 TACCAGAGGGGGTATCTGTACCATAGTAT
66 TACCAGAGGGGGTATCGGTACCATAGTAT
* *
222019 AGAAGTATCG
1 GGTAGTATCG
222029 GTACTAGGGT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 30 0.32
95 62 0.67
96 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (94 bp):
GGTAGTATCGATACCATCGTAAGAGTATCAATACCATACAACATCGAAGCTAAAATTGGTATCGA
TACCAGAGGGGGTATCGGTACCATAGTAT
Found at i:222539 original size:45 final size:45
Alignment explanation
Indices: 222426--222709 Score: 419
Period size: 45 Copynumber: 6.3 Consensus size: 45
222416 ATAATAATAC
* * *
222426 ATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAACGT
1 ATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGT
*
222471 ATAT-GGTACATTATCAACAGAAAAGTATCCTATAGTTGAAATGT
1 ATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGT
*
222515 ATATGGGTACATTATCAAAAGAAAAGTATGCTATAGTTGAAATGT
1 ATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGT
* * *
222560 ATATGGGTACATTATTAACAGAAAAGTATGTTATAATTGAAATGT
1 ATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGT
* *
222605 ATATGGGTACATTATCAAAAAAAAAGTATGCTATAGTTGAAATGT
1 ATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGT
* * *
222650 ATATGGGTACATTATCAACAGAAAATTATGGC-ATAGCTGAAATGC
1 ATATGGGTACATTATCAACAGAAAAGTAT-GCTATAGTTGAAATGT
*
222695 ATATGGGTGCATTAT
1 ATATGGGTACATTAT
222710 TGGCATAAAA
Statistics
Matches: 216, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
44 40 0.19
45 174 0.81
46 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (45 bp):
ATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGT
Found at i:225253 original size:2 final size:2
Alignment explanation
Indices: 225246--225278 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
225236 ATTAGGTCAG
*
225246 AT AT AT AT AT AT AA 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 A
225279 GTTTTTCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:225582 original size:2 final size:2
Alignment explanation
Indices: 225575--225622 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
225565 TAACGAAAAG
225575 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
225617 AT AT AT
1 AT AT AT
225623 GGTTATGCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229424 original size:19 final size:19
Alignment explanation
Indices: 229386--229475 Score: 85
Period size: 19 Copynumber: 4.5 Consensus size: 19
229376 CGCGATTCAG
229386 AGAATCGCAATGCGATCTTCCA
1 AGAATCGCAAT---ATCTTCCA
229408 AGAATCGCAATATCTTCCA
1 AGAATCGCAATATCTTCCA
**
229427 AGAATCGCAA-CGCGATT-CA
1 AGAATCGCAATATC--TTCCA
*
229446 GAGAATCGCAATGTCTTCCA
1 -AGAATCGCAATATCTTCCA
229466 AGAATCGCAA
1 AGAATCGCAA
229476 CGCGATTCAG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.02
19 32 0.54
20 14 0.24
21 1 0.02
22 11 0.19
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
AGAATCGCAATATCTTCCA
Found at i:229452 original size:20 final size:20
Alignment explanation
Indices: 229309--229495 Score: 124
Period size: 20 Copynumber: 9.4 Consensus size: 20
229299 TGACCAACAA
229309 AATCGCAACGCGATATCA-A-
1 AATCGCAACGCGAT-TCAGAG
* *
229328 AATCGCAACGCGATTTAGAA
1 AATCGCAACGCGATTCAGAG
** ** *
229348 AATCGCAACATTGA-AAAGAA
1 AATCGCAAC-GCGATTCAGAG
229368 AATCGCAACGCGATTCAGAG
1 AATCGCAACGCGATTCAGAG
*
229388 AATCGCAATGCGATCTTCCA-AG
1 AATCGCAACGCGA--TT-CAGAG
**
229410 AATCGCAATATC--TTCCA-AG
1 AATCGCAA-CGCGATT-CAGAG
229429 AATCGCAACGCGATTCAGAG
1 AATCGCAACGCGATTCAGAG
*
229449 AATCGCAATGTC--TTCCA-AG
1 AATCGCAACG-CGATT-CAGAG
229468 AATCGCAACGCGATTCAGAG
1 AATCGCAACGCGATTCAGAG
229488 AATCGCAA
1 AATCGCAA
229496 AACGGTCAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 31
0.74 0.09 0.17
Matches are distributed among these distances:
18 4 0.03
19 49 0.36
20 64 0.47
21 3 0.02
22 12 0.09
23 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGATTCAGAG
Found at i:229463 original size:39 final size:39
Alignment explanation
Indices: 229386--229495 Score: 168
Period size: 39 Copynumber: 2.8 Consensus size: 39
229376 CGCGATTCAG
*
229386 AGAATCGCAATGCGATCTTCCA-AGAATCGCAATATCTTCCA
1 AGAATCGCAACGCGA--TT-CAGAGAATCGCAATATCTTCCA
*
229427 AGAATCGCAACGCGATTCAGAGAATCGCAATGTCTTCCA
1 AGAATCGCAACGCGATTCAGAGAATCGCAATATCTTCCA
229466 AGAATCGCAACGCGATTCAGAGAATCGCAA
1 AGAATCGCAACGCGATTCAGAGAATCGCAA
229496 AACGGTCAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
38 2 0.03
39 50 0.76
41 14 0.21
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (39 bp):
AGAATCGCAACGCGATTCAGAGAATCGCAATATCTTCCA
Found at i:230457 original size:20 final size:20
Alignment explanation
Indices: 230434--230621 Score: 122
Period size: 20 Copynumber: 9.4 Consensus size: 20
230424 TTTGACCGTT
230434 TTGCGATTCTCTGAATCGCG
1 TTGCGATTCTCTGAATCGCG
*
230454 TTGCGATTCT-TGGAA--GACA
1 TTGCGATTCTCT-GAATCG-CG
230473 TTGCGATTCTCTGAATCGCG
1 TTGCGATTCTCTGAATCGCG
*
230493 TTGCGATTCT-TGGAA--GACA
1 TTGCGATTCTCT-GAATCG-CG
*
230512 TTGCGATTCTCTAAATCGCG
1 TTGCGATTCTCTGAATCGCG
* *
230532 TTGCGATTCT-TGGAAGATCACA
1 TTGCGATTCTCT-G-A-ATCGCG
* *
230554 TTGCAATTCTCTGAATCGTG
1 TTGCGATTCTCTGAATCGCG
* ** *
230574 TTGCGATTTTCT-TTTCAACG
1 TTGCGATTCTCTGAATC-GCG
* * *
230594 TTGCAATTTTCTAAATCGCG
1 TTGCGATTCTCTGAATCGCG
230614 TTGCGATT
1 TTGCGATT
230622 TTGTTGGTCA
Statistics
Matches: 129, Mismatches: 23, Indels: 32
0.70 0.12 0.17
Matches are distributed among these distances:
18 2 0.02
19 32 0.25
20 74 0.57
21 6 0.05
22 14 0.11
23 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTGAATCGCG
Found at i:230477 original size:39 final size:39
Alignment explanation
Indices: 230434--230581 Score: 242
Period size: 39 Copynumber: 3.7 Consensus size: 39
230424 TTTGACCGTT
230434 TTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGACA
1 TTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGACA
230473 TTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGACA
1 TTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGACA
*
230512 TTGCGATTCTCTAAATCGCGTTGCGATTCTTGGAAGATCACA
1 TTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAG---ACA
* *
230554 TTGCAATTCTCTGAATCGTGTTGCGATT
1 TTGCGATTCTCTGAATCGCGTTGCGATT
230582 TTCTTTTCAA
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
39 74 0.73
42 28 0.27
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (39 bp):
TTGCGATTCTCTGAATCGCGTTGCGATTCTTGGAAGACA
Found at i:230478 original size:19 final size:19
Alignment explanation
Indices: 230454--230521 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
230444 CTGAATCGCG
230454 TTGCGATTCTTGGAAGACA
1 TTGCGATTCTTGGAAGACA
*
230473 TTGCGATTCTCT-GAATCG-CG
1 TTGCGATTCT-TGGAA--GACA
230493 TTGCGATTCTTGGAAGACA
1 TTGCGATTCTTGGAAGACA
230512 TTGCGATTCT
1 TTGCGATTCT
230522 CTAAATCGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
18 1 0.02
19 25 0.60
20 15 0.36
21 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (19 bp):
TTGCGATTCTTGGAAGACA
Found at i:233980 original size:32 final size:31
Alignment explanation
Indices: 233943--234027 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
233933 GAAAGTTTCG
*
233943 GGGCCACAGGGCCTACCTAAGAACACATCTTA
1 GGGCCACAGGGCCTACCTAAGAACA-ATCTCA
* ** *
233975 TGGCCACAGGGCCTACCCGAGAATAATCTCA
1 GGGCCACAGGGCCTACCTAAGAACAATCTCA
* *
234006 GGGCCGCAGAGCCTACCTAAGA
1 GGGCCACAGGGCCTACCTAAGA
234028 GTCACATTAG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
31 22 0.51
32 21 0.49
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (31 bp):
GGGCCACAGGGCCTACCTAAGAACAATCTCA
Found at i:243880 original size:18 final size:18
Alignment explanation
Indices: 243844--243882 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
243834 CTTTAATTTA
*
243844 TTTATTTAATCATTTTCT
1 TTTATTTAATCATTATCT
243862 TTTATTTAATTC-TTATCT
1 TTTATTTAA-TCATTATCT
243880 TTT
1 TTT
243883 TAAAAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTAATCATTATCT
Found at i:247996 original size:201 final size:200
Alignment explanation
Indices: 247574--248755 Score: 1367
Period size: 201 Copynumber: 5.8 Consensus size: 200
247564 GCGAAGTTTA
* * * *
247574 AAAAAGTATCGACACAAATTTAAAAAGTGTTGATACATTATGTCGACCTATTTTCTCATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC
*
247639 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCAATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTTT
* * *
247704 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTT-GGCATTCATT
131 TTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTACACCTCGTTTGGGCATTCATT
*
247768 CTGAAC
195 CTGGAC
* * *
247774 AAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGCAGACATATTTTTCTCATAAAAC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATA-TTTTCTCATAAAAC
* *
247839 CGGTATATTTATATCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTCTCGATGTT
65 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTT
* * *
247904 TTTGGGATCGGTACGATTT-TAAATGTATCGACACTTTATTCGTACACCTCGTTTGGGCATTGAT
130 TTTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATTCGTACACCTCGTTTGGGCATTCAT
*
247968 TATGGAC
194 TCTGGAC
* * * * * * *
247975 AAAAAGTATCGCCAAAAATTTAAAAAGTGTCGATACATTATGTTGACCA-ATTTTCTAATTATAT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGA-CATATTTTCTCATAAAAC
* * * * * * * * *
248039 TGGTATGTTTCTACCAGTAATATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTC
65 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTT
** * ** *
248104 TTTGGGATCGATACTTTTAATAAATGTATCGACACTTTACGCGTCCACCTTATTTGGACATTCAT
130 TTTGGGATCGATACTTTT-ATAAATGTATCGACACTTTATTCGTACACCTCGTTTGGGCATTCAT
248169 TCTGGAC
194 TCTGGAC
* * *
248176 AAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC
* * *
248241 GGTGTATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTTT
* * * *
248306 TTGGGATCGAT-GTTTT-T---GGGATCGATACTTTTTATAAAT-GTATCAACACTTTATGCGTG
131 TTGGGATCGATACTTTTATAAATGTATCGACAC--TTTAT---TCGTA-C-AC-C----T-C--G
**
248365 CACCTAGTTTTGCATTCATTCTGGAC
181 ----T--TTGGGCATTCATTCTGGAC
* * * * *
248391 AAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTTATAAAACT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC
* *
248456 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTATCGGTCTCCATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTTT
* * *
248521 TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGT-GTGCACCTCGTTTTGACATTCAT
131 TTGGGATCGATACTTTT-ATAAATGTATCGACACTTTAT-TCGTACACCTCGTTTGGGCATTCAT
248585 TCTGGAC
194 TCTGGAC
* ** * * *
248592 AATAAGTATCGACACAAATTTATCAAGTGTCGATACATTGTATAGACATATTTTCTCATGAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC
* * * *
248657 AGTAAATTTCTACCGGTTACATTGTAAATTTACCTACTACATTATAATTATCGGTCTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTTT
* *
248722 TTGGGATCGATACTTTTTATAAACGTATCAACAC
131 TTGGGATCGATAC-TTTTATAAATGTATCGACAC
248756 ATTTGTTTAC
Statistics
Matches: 829, Mismatches: 119, Indels: 67
0.82 0.12 0.07
Matches are distributed among these distances:
195 8 0.01
197 4 0.00
198 1 0.00
199 5 0.01
200 159 0.19
201 468 0.56
202 7 0.01
203 1 0.00
206 1 0.00
207 1 0.00
209 1 0.00
210 1 0.00
213 1 0.00
214 1 0.00
215 148 0.18
216 5 0.01
217 3 0.00
218 1 0.00
219 5 0.01
221 8 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (200 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACATATTTTCTCATAAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCGATGTTT
TTGGGATCGATACTTTTATAAATGTATCGACACTTTATTCGTACACCTCGTTTGGGCATTCATTC
TGGAC
Found at i:248317 original size:15 final size:15
Alignment explanation
Indices: 248297--248331 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
248287 ATTATCAGTC
248297 TCGATGTTTTTGGGA
1 TCGATGTTTTTGGGA
248312 TCGATGTTTTTGGGA
1 TCGATGTTTTTGGGA
248327 TCGAT
1 TCGAT
248332 ACTTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.31, T:0.46
Consensus pattern (15 bp):
TCGATGTTTTTGGGA
Found at i:248337 original size:16 final size:15
Alignment explanation
Indices: 248297--248338 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
248287 ATTATCAGTC
*
248297 TCGATGTTTTTGGGA
1 TCGATCTTTTTGGGA
*
248312 TCGATGTTTTTGGGA
1 TCGATCTTTTTGGGA
248327 TCGATACTTTTT
1 TCGAT-CTTTTT
248339 ATAAATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.14, C:0.10, G:0.26, T:0.50
Consensus pattern (15 bp):
TCGATCTTTTTGGGA
Found at i:248529 original size:416 final size:416
Alignment explanation
Indices: 247896--248732 Score: 1190
Period size: 416 Copynumber: 2.0 Consensus size: 416
247886 ATTATCGGTC
* * * *
247896 TCGATGTTTTTGGGATCGGTACGATTTTAAATGTATCGACACTTTATTCGTACACCTCGTTTGGG
1 TCGATGTTTTTGGGATCGATACGATTTTAAATGTATCAACACTTTATGCGTACACCTAGTTTGGG
* * *
247961 CATTGATTATGGACAAAAAGTATCGCCAAAAATTTAAAAAGTGTCGATACATTATGTTGACCAAT
66 CATTCATTATGGACAAAAAGTATCGACAAAAATTTAAAAAGTGTCGATACATTATGTAGACCAAT
* * * * * * *
248026 TTTCTAATTATATTGGTATGTTTCTACCAGTAATATTGTAAATTTACCTATTACATTATAATTAT
131 TTTCTAATAAAACTGGTATATTTATACCAGTAACATTGTAAATTTACCTATTAAATTATAATTAT
* * * *
248091 GGGTTTCGATGTCTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTACGCGTCCACCTTA
196 CGGTCTCCATGTCTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTACGCGTCCACCTCA
* *
248156 TTTGGACATTCATTCTGGACAAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATGTTG
261 TTTGGACATTCATTCTGGACAAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATATAG
* * ** * *
248221 ACCTATTTTCTCATAAAACCGGTGTATTTATACTGGTTACATTGTAAATTTACCTATTACATTAT
326 ACATATTTTCTCATAAAACCAGTAAATTTATACCGGTTACATTGTAAATTTACCTACTACATTAT
248286 AATTATCAGTCTCGATGTTTTTGGGA
391 AATTATCAGTCTCGATGTTTTTGGGA
** * *
248312 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTGCACCTAGTTT-T
1 TCGATGTTTTTGGGATCGATACGATTT-TAAATGTATCAACACTTTATGCGTACACCTAGTTTGG
* * * * *
248376 GCATTCATTCTGGACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGACCTA
65 GCATTCATTATGGACAAAAAGTATCGACAAAAATTTAAAAAGTGTCGATACATTATGTAGACCAA
* * *
248441 TTTTCTTATAAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTATAATTA
130 TTTTCTAATAAAACTGGTATATTTATACCAGTAACATTGTAAATTTACCTATTAAATTATAATTA
* * * *
248506 TCGGTCTCCATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTC
195 TCGGTCTCCATGTCTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTACGCGTCCACCTC
* * * * ** *
248571 GTTTTGACATTCATTCTGGACAATAAGTATCGACACAAATTTATCAAGTGTCGATACATTGTATA
260 ATTTGGACATTCATTCTGGACAAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATATA
* *
248636 GACATATTTTCTCATGAAACCAGTAAATTTCTACCGGTTACATTGTAAATTTACCTACTACATTA
325 GACATATTTTCTCATAAAACCAGTAAATTTATACCGGTTACATTGTAAATTTACCTACTACATTA
*
248701 TAATTATCGGTCTCGATGTTTTTGGGA
390 TAATTATCAGTCTCGATGTTTTTGGGA
248728 TCGAT
1 TCGAT
248733 ACTTTTTATA
Statistics
Matches: 368, Mismatches: 52, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
416 337 0.92
417 31 0.08
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (416 bp):
TCGATGTTTTTGGGATCGATACGATTTTAAATGTATCAACACTTTATGCGTACACCTAGTTTGGG
CATTCATTATGGACAAAAAGTATCGACAAAAATTTAAAAAGTGTCGATACATTATGTAGACCAAT
TTTCTAATAAAACTGGTATATTTATACCAGTAACATTGTAAATTTACCTATTAAATTATAATTAT
CGGTCTCCATGTCTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTACGCGTCCACCTCA
TTTGGACATTCATTCTGGACAAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATATAG
ACATATTTTCTCATAAAACCAGTAAATTTATACCGGTTACATTGTAAATTTACCTACTACATTAT
AATTATCAGTCTCGATGTTTTTGGGA
Found at i:248732 original size:617 final size:602
Alignment explanation
Indices: 247574--248755 Score: 1706
Period size: 617 Copynumber: 1.9 Consensus size: 602
247564 GCGAAGTTTA
* * *
247574 AAAAAGTATCGACACAAATTTAAAAAGTGTTGATACATTATGTCGACCTATTTTCTCATAAAACT
1 AAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATGTCGACCTATTTTCTCATAAAACC
*
247639 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCTCAATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCTCAATGTTT
*
247704 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
131 TTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
247769 TGAACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGCAGACATATTTTTCTCAT
196 TGAACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGCAGACATATTTTTCTCAT
* * *
247834 AAAACCGGTATATTTATATCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTCTCG
261 AAAACCGGTATATTTATACCGGTTACATTATAAATTTACCTATTAAATTATAATTATCGGTCTCC
* *
247899 ATGTTTTTGGGATCGGTACGATTTTAAATGTATCGACACTTTATTCGTACACCTCGTTTGGGCAT
326 ATGTTTTTGGGATCGATACGATTTTAAATGTATCGACACTTTATTCGTACACCTCGTTTGGACAT
* * * *
247964 TGATTATGGACAAAAAGTATCGCCAAAAATTTAAAAAGTGTCGATACATTATGTTGACCAATTTT
391 TCATTATGGACAAAAAGTATCGACAAAAATTTAAAAAGTGTCGATACATTATATAGACCAATTTT
* * *** ** * * *
248029 CTAATTATATTGGTATGTTTCTACCAGTAATATTGTAAATTTACCTATTACATTATAATTATGGG
456 CTAATGAAACCAGTAAATTTCTACCAGTAACATTGTAAATTTACCTACTACATTATAATTATCGG
* * *
248094 TTTCGATGTCTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTACGCGTCCACCTTATTT
521 TCTCGATGTCTTTGGGATCGATACTTTTAATAAACGTATCAACACTTTACGCGTCCACCTTATTT
248159 GGACATTCATTCTGGAC
586 GGACATTCATTCTGGAC
*
248176 AAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTCATAAAACC
1 AAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATGTCGACCTATTTTCTCATAAAACC
* *
248241 GGTGTATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCTC-------
248306 TTGGGATCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTGCACCTA
124 -----A---ATGTTTTTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTGCACCTA
* * *
248371 GTTTTGCATTCATTCTGGACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAG
181 GTTTGGCATTCATTCTGAACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGCAG
* * * *
248436 ACCTA-TTTTCTTATAAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAAATTA
246 ACATATTTTTCTCATAAAACCGGTATATTTATACCGGTTACATTATAAATTTACCTATTAAATTA
*
248500 TAATTATCGGTCTCCATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGT-G
311 TAATTATCGGTCTCCATGTTTTTGGGATCGATACGATTT--TAAATGTATCGACACTTTAT-TCG
* * * * * **
248563 TGCACCTCGTTTTGACATTCATTCTGGACAATAAGTATCGACACAAATTTATCAAGTGTCGATAC
373 TACACCTCGTTTGGACATTCATTATGGACAAAAAGTATCGACAAAAATTTAAAAAGTGTCGATAC
* * * *
248628 ATTGTATAGA-CATATTTTCTCATGAAACCAGTAAATTTCTACCGGTTACATTGTAAATTTACCT
438 ATTATATAGACCA-ATTTTCTAATGAAACCAGTAAATTTCTACCAGTAACATTGTAAATTTACCT
* *
248692 ACTACATTATAATTATCGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAACGTATCAACAC
502 ACTACATTATAATTATCGGTCTCGATGTCTTTGGGATCGATACTTTTAATAAACGTATCAACAC
248756 ATTTGTTTAC
Statistics
Matches: 510, Mismatches: 51, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
602 116 0.23
614 1 0.00
615 3 0.01
616 88 0.17
617 301 0.59
618 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (602 bp):
AAAAAGTATAGACACAAATTTAAAAAGTGTCGATACATTATGTCGACCTATTTTCTCATAAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTCTCAATGTTT
TTGGGATCGATACTTTTTATAAATGTATCAACACTTTATGCGTGCACCTAGTTTGGCATTCATTC
TGAACAAAATGTATCGACACAAATTTAGAAAGTGTCGATACATTATGCAGACATATTTTTCTCAT
AAAACCGGTATATTTATACCGGTTACATTATAAATTTACCTATTAAATTATAATTATCGGTCTCC
ATGTTTTTGGGATCGATACGATTTTAAATGTATCGACACTTTATTCGTACACCTCGTTTGGACAT
TCATTATGGACAAAAAGTATCGACAAAAATTTAAAAAGTGTCGATACATTATATAGACCAATTTT
CTAATGAAACCAGTAAATTTCTACCAGTAACATTGTAAATTTACCTACTACATTATAATTATCGG
TCTCGATGTCTTTGGGATCGATACTTTTAATAAACGTATCAACACTTTACGCGTCCACCTTATTT
GGACATTCATTCTGGAC
Found at i:249175 original size:19 final size:20
Alignment explanation
Indices: 249134--249183 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
249124 TTACATTCAC
249134 ATACAAAATTACAAAATAGT
1 ATACAAAATTACAAAATAGT
*
249154 ATACAAAATTA-TAAATCA-T
1 ATACAAAATTACAAAAT-AGT
249173 ATACAAAATTA
1 ATACAAAATTA
249184 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (20 bp):
ATACAAAATTACAAAATAGT
Found at i:250750 original size:18 final size:18
Alignment explanation
Indices: 250727--250766 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
250717 TTCCTCTTCG
*
250727 CTTCCTCCATGTTTTCTT
1 CTTCCTCCATATTTTCTT
250745 CTTCCTCCATATTTTCTT
1 CTTCCTCCATATTTTCTT
250763 CTTC
1 CTTC
250767 ATATTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.35, G:0.03, T:0.55
Consensus pattern (18 bp):
CTTCCTCCATATTTTCTT
Found at i:251141 original size:15 final size:15
Alignment explanation
Indices: 251121--251153 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
251111 ACTCTGTTTT
251121 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
*
251136 CCCTCACCTTCATCC
1 CCCTCACCGTCATCC
251151 CCC
1 CCC
251154 ATTACTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.64, G:0.03, T:0.21
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:253798 original size:182 final size:180
Alignment explanation
Indices: 253491--254151 Score: 796
Period size: 182 Copynumber: 3.6 Consensus size: 180
253481 TACGCGTACT
* * * *
253491 TATTAAAGTATCGACACTTTCAAAATA-TCTGGTAGCGCTTTATCGGTTTTGTCATTTCGAGATC
1 TATTAAAGTATCAACACTTTCAACATATTC-GGTAGCGCTTTACCGGTTTTGTCATTTCGAGACC
* * *
253555 GGTTTTGTCATTTTTTTACCTGTTATATTCTTATGAATCGATACATTTTTATAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTT-TAAAGTATCGACAC
*
253620 TTTATAGGCGCTATTACTTATTCTCTTTTAAATTCCAAAAGCGTCGATACTTA
128 TTTATAGGCGCTATTACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
253673 TATTAAAGTATCAACAATGTT-AACATATTCGGTAGTGCTTTACCAGTTTTGTCATTTCGAGACC
1 TATTAAAGTATCAACACT-TTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACC
* *
253737 AGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGACACATTTTTGAAAGGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT-AAA-GTATCGACAC
*
253802 TTTATAGGCGCTATTAC-TACTTCTCTTTTAAATTCCAAAAGTTTCGATACTTA
128 TTTATAGGCGCTATTACTTA-TTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
253855 TATTAAAGTATCGAA-ACTTTCAATATATCTC-GTAGCACTTTTCTGGTTTTTTCATTTCGAGAC
1 TATTAAAGTATC-AACACTTTCAACATAT-TCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGAC
* * *
253918 CGGTTTTGTCATATTTTAACATGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGATA
64 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT--TAAAGTATCGACA
* * *
253983 CTTTATAGGCACTGTTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
127 CTTTATAGGCGCTATTACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * * ** * * * * *
254037 T-TTCAATCTAATCGATACTTTTGACATATTCAGTAGCGCTTTACCGATTTTATCATAAT-GAAA
1 TATT-AAAGT-ATCAACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCAT-TTCGAGA
* * *
254100 CCGGTTTTGTCATATTTTTACTTGTTATATTGCTATGGATTGATACATTTTT
63 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
254152 TATTTGTACC
Statistics
Matches: 415, Mismatches: 48, Indels: 33
0.84 0.10 0.07
Matches are distributed among these distances:
180 1 0.00
181 14 0.03
182 304 0.73
183 94 0.23
184 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (180 bp):
TATTAAAGTATCAACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAAAGTATCGACACTTT
ATAGGCGCTATTACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:255320 original size:43 final size:43
Alignment explanation
Indices: 255273--255467 Score: 164
Period size: 42 Copynumber: 4.6 Consensus size: 43
255263 CAATAGGTCA
* * *
255273 AGATCTATAGCGGCATTTTTTGAACAAACGCCATAAAAAGTTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAAGTCG
** * *
255316 AGATCTATAATGACGTTTTTGGAACAAACGCCGT-AAAAGATC-
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAAG-TCG
* * * * *
255358 ATATCTATAGCAGTGTTTTTGGAATAAACGCCA-CAAAAGATCG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAAG-TCG
* ** * *
255401 -TATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCA
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAAGTCG
* * *
255443 AGTTCTATAGCGACATTTTTGGAAC
1 AGATCTATAGCGGCGTTTTTGGAAC
255468 TATAATAAAT
Statistics
Matches: 121, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
42 68 0.56
43 53 0.44
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (43 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCATAAAAAGTCG
Found at i:264334 original size:2 final size:2
Alignment explanation
Indices: 264327--264401 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
264317 AAGATGTATT
264327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264369 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
264402 TCTTGTTTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:264713 original size:15 final size:15
Alignment explanation
Indices: 264695--264776 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
264685 TTCCGGAAAA
264695 TGAATTACTGGAATT
1 TGAATTACTGGAATT
264710 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
264725 TGAATTTCTGGAAAA
1 TGAATTACTGGAATT
264740 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
264755 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
264769 TGAATTAC
1 TGAATTAC
264777 ATTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:264729 original size:30 final size:29
Alignment explanation
Indices: 264695--264776 Score: 128
Period size: 30 Copynumber: 2.8 Consensus size: 29
264685 TTCCGGAAAA
**
264695 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATT-CTGGAAAATGAATTACTGGAATT
264725 TGAATTTCTGGAAAATGAATTACTGGAATT
1 TGAA-TTCTGGAAAATGAATTACTGGAATT
264755 TGAATTCTGGAAAATGAATTAC
1 TGAATTCTGGAAAATGAATTAC
264777 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
29 18 0.37
30 29 0.59
31 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (29 bp):
TGAATTCTGGAAAATGAATTACTGGAATT
Found at i:264782 original size:20 final size:20
Alignment explanation
Indices: 264759--264808 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
264749 GGAATTTGAA
264759 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
264779 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
264799 TTCTGGAAAA
1 TTCTGGAAAA
264809 CGTTTTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:265096 original size:16 final size:17
Alignment explanation
Indices: 265075--265106 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
265065 TAATAGTGAT
265075 ATATTA-TATTTTAAAA
1 ATATTAGTATTTTAAAA
265091 ATATTAGTATTTTAAA
1 ATATTAGTATTTTAAA
265107 TATCTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATTAGTATTTTAAAA
Found at i:265172 original size:26 final size:24
Alignment explanation
Indices: 265121--265184 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 24
265111 TTTACTAAAA
265121 TATTATTGAAATATATAAATAATAT
1 TATTATT-AAATATATAAATAATAT
265146 TCATTATTAAATATATAAA-AATTTAT
1 T-ATTATTAAATATATAAATAA--TAT
265172 TATATATTAAATA
1 TAT-TATTAAATA
265185 AAAATATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.06
25 14 0.40
26 19 0.54
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TATTATTAAATATATAAATAATAT
Found at i:265192 original size:55 final size:53
Alignment explanation
Indices: 265124--265272 Score: 128
Period size: 54 Copynumber: 2.7 Consensus size: 53
265114 ACTAAAATAT
*
265124 TATTGAAATATATAAATAATATTCATTATTAAATATATAAAAATTTATTATATATTAA
1 TATT-AAAAATATAAAT-ATATT-ATTATTAAATATATAAAAA-TTATTATATA-TAA
* ** *
265182 -A-TAAAAATAT-AATATCTTATATTATTATAATATA-ATTAATTATTTTATATAA
1 TATTAAAAATATAAATAT-AT-TATTATTA-AATATATAAAAATTATTATATATAA
265234 TATTAAAAATATAATATTATATTATTA-TAAATATATAAA
1 TATTAAAAATATAA-A-TATATTATTATTAAATATATAAA
265273 TATATTTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
52 3 0.04
53 18 0.24
54 26 0.35
55 20 0.27
56 3 0.04
57 4 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (53 bp):
TATTAAAAATATAAATATATTATTATTAAATATATAAAAATTATTATATATAA
Found at i:265223 original size:18 final size:19
Alignment explanation
Indices: 265189--265234 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
265179 TAAATAAAAA
*
265189 TATAATAT-CTTATATTAT
1 TATAATATAATTATATTAT
265207 TATAATATAATTA-ATTAT
1 TATAATATAATTATATTAT
*
265225 T-TTATATAAT
1 TATAATATAAT
265235 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 14 0.56
19 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATATAATTATATTAT
Found at i:265238 original size:15 final size:16
Alignment explanation
Indices: 265200--265253 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 16
265190 ATAATATCTT
265200 ATATTATTATAATATA
1 ATATTATTATAATATA
*
265216 ATTAATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
265233 ATATTA--AAAATATA
1 ATATTATTATAATATA
265247 ATATTAT
1 ATATTAT
265254 ATTATTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.35
15 4 0.13
16 2 0.06
17 8 0.26
18 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:265278 original size:19 final size:21
Alignment explanation
Indices: 265233--265286 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
265223 ATTTTATATA
* *
265233 ATATTAAAAATATAATATTAT
1 ATATTATAAATATAATATAAT
265254 ATTATTATAAATAT-ATA-AAT
1 A-TATTATAAATATAATATAAT
*
265274 ATATTTTAAATAT
1 ATATTATAAATAT
265287 TTTAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 4 0.14
22 11 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTATAAATATAATATAAT
Found at i:265534 original size:42 final size:42
Alignment explanation
Indices: 265475--265594 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
265465 ATGAATTACA
*
265475 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
265517 TTCCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
265559 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
265595 TTCAGGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:269791 original size:37 final size:37
Alignment explanation
Indices: 269737--269880 Score: 202
Period size: 37 Copynumber: 3.9 Consensus size: 37
269727 TTCTTTCAAG
*
269737 CAAATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC
1 CAAATCAAGACTTCACAAAAGAGTAGTGAAGCAATGC
* * *
269774 CAAATCAAG-CATGCACAAAAGAGTATTCAAGCAATGC
1 CAAATCAAGAC-TTCACAAAAGAGTAGTGAAGCAATGC
* * *
269811 CAAATCAAGACTTCGCAAAAGAGTAGTAAAGCAATGT
1 CAAATCAAGACTTCACAAAAGAGTAGTGAAGCAATGC
269848 CAAATCAAGACTTCACAAAA-AGTAGTGAAGCAA
1 CAAATCAAGACTTCACAAAAGAGTAGTGAAGCAA
269881 GATCTGATCA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
36 13 0.14
37 81 0.85
38 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (37 bp):
CAAATCAAGACTTCACAAAAGAGTAGTGAAGCAATGC
Found at i:270081 original size:19 final size:21
Alignment explanation
Indices: 270049--270136 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 21
270039 TGAGTGACGT
270049 TTATATATATTATTATTATAC
1 TTATATATATTATTATTATAC
270070 TTATATTATATTATTATATATA-
1 TTATA-TATATTATTAT-TATAC
* *
270092 TAATAAATATAATAAATATTATTATAT
1 T--T--ATAT-AT-ATTATTATTATAC
270119 TTATAT-TATTATTATTAT
1 TTATATATATTATTATTAT
270137 TCTCAATGGT
Statistics
Matches: 56, Mismatches: 2, Indels: 19
0.73 0.03 0.25
Matches are distributed among these distances:
20 10 0.18
21 6 0.11
22 12 0.21
23 8 0.14
24 1 0.02
25 2 0.04
26 9 0.16
27 8 0.14
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATATATTATTATTATAC
Found at i:282245 original size:21 final size:21
Alignment explanation
Indices: 282221--282277 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
282211 TTTACACTTA
282221 GGGAACCGATCCCCTATGAGG
1 GGGAACCGATCCCCTATGAGG
282242 GGGAACCGATCCCCTATGAGG
1 GGGAACCGATCCCCTATGAGG
282263 GGGAACCGATTCCCC
1 GGGAACCGA-TCCCC
282278 CCACGCTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.14
Consensus pattern (21 bp):
GGGAACCGATCCCCTATGAGG
Found at i:285076 original size:36 final size:36
Alignment explanation
Indices: 285030--285102 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
285020 ATGTTCATGA
*
285030 ATAAGCTCGTTTA-TCGACTCATTTATCAACTCATTT
1 ATAAGCTCGTTTACT-GACTCATTTATAAACTCATTT
* *
285066 ATAAGTTCGTTTACTGATTCATTTATAAACTCATTT
1 ATAAGCTCGTTTACTGACTCATTTATAAACTCATTT
285102 A
1 A
285103 CTGGGTTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (36 bp):
ATAAGCTCGTTTACTGACTCATTTATAAACTCATTT
Found at i:285102 original size:24 final size:24
Alignment explanation
Indices: 285060--285105 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
285050 ATTTATCAAC
** *
285060 TCATTTATAAGTTCGTTTACTGAT
1 TCATTTATAAACTCATTTACTGAT
285084 TCATTTATAAACTCATTTACTG
1 TCATTTATAAACTCATTTACTG
285106 GGTTCTCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (24 bp):
TCATTTATAAACTCATTTACTGAT
Found at i:301561 original size:15 final size:15
Alignment explanation
Indices: 301543--301572 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
301533 AAAAGTAAAT
301543 CATAAAAAAACTTAA
1 CATAAAAAAACTTAA
*
301558 CATAAAAAGACTTAA
1 CATAAAAAAACTTAA
301573 TACTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (15 bp):
CATAAAAAAACTTAA
Found at i:304432 original size:15 final size:15
Alignment explanation
Indices: 304414--304443 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
304404 AAAAGTAAAT
304414 CATAAAAAAACTTAA
1 CATAAAAAAACTTAA
*
304429 CATAAAAAGACTTAA
1 CATAAAAAAACTTAA
304444 TACTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (15 bp):
CATAAAAAAACTTAA
Found at i:304641 original size:21 final size:20
Alignment explanation
Indices: 304616--304671 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
304606 TCAGAAAATA
304616 AAAAAATAAAAAATAATAAT
1 AAAAAATAAAAAATAATAAT
* * *
304636 AGAAAACTAAAAAATTATCAT
1 A-AAAAATAAAAAATAATAAT
304657 -AAAAATGAAAAAATA
1 AAAAAAT-AAAAAATA
304672 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 16 0.55
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAAAATAAAAAATAATAAT
Found at i:304661 original size:20 final size:19
Alignment explanation
Indices: 304612--304671 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
304602 CTTTTCAGAA
304612 AATAA-AAAAATAAAAAAT
1 AATAATAAAAATAAAAAAT
304630 AATAATAGAAAACTAAAAAAT
1 AATAATA-AAAA-TAAAAAAT
* *
304651 TATCATAAAAATGAAAAAAT
1 AATAATAAAAAT-AAAAAAT
304671 A
1 A
304672 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 5 0.14
19 2 0.06
20 15 0.43
21 13 0.37
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (19 bp):
AATAATAAAAATAAAAAAT
Found at i:309025 original size:20 final size:20
Alignment explanation
Indices: 308996--309055 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
308986 ACCCCATTGA
*
308996 CCGTTGACCGACTTTGACTC
1 CCGTTAACCGACTTTGACTC
309016 CCGTTAACCGACTTTGACTC
1 CCGTTAACCGACTTTGACTC
309036 CCGTTAACCGACTATTGACT
1 CCGTTAACCGACT-TTGACT
309056 TTTTTTGGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 32 0.84
21 6 0.16
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (20 bp):
CCGTTAACCGACTTTGACTC
Found at i:314565 original size:31 final size:30
Alignment explanation
Indices: 314527--314611 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 30
314517 TAAGGCGACC
* * *
314527 CTTGGGTAGGCTCTGCGGCCCTGAGATTTTT
1 CTTGGGTAGGCTC-GCGGCCCCGAGAATGTT
*
314558 CTTGGGTAGGCCTCCGTGGCCCCGAGAATGTT
1 CTTGGGTAGG-CT-CGCGGCCCCGAGAATGTT
*
314590 CTTGTGTAGGCTCGCAGGCCCC
1 CTTGGGTAGGCTCGC-GGCCCC
314612 AAGGTACTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.04
31 18 0.40
32 24 0.53
33 1 0.02
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (30 bp):
CTTGGGTAGGCTCGCGGCCCCGAGAATGTT
Found at i:316506 original size:27 final size:27
Alignment explanation
Indices: 316476--316545 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
316466 TGCTGTGGAC
316476 TTTCAAGTTCAAAGTGATACTATGAAG
1 TTTCAAGTTCAAAGTGATACTATGAAG
316503 TTTCAAGTTCAAAGTGATACTATGAAG
1 TTTCAAGTTCAAAGTGATACTATGAAG
316530 TTTCAAGTTCAAAGTG
1 TTTCAAGTTCAAAGTG
316546 GTGATGGCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (27 bp):
TTTCAAGTTCAAAGTGATACTATGAAG
Found at i:317125 original size:35 final size:35
Alignment explanation
Indices: 317085--317165 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
317075 CCACTATAAC
317085 AAATGCCGCAACAATTAACGGCATTTGTGAACAAA
1 AAATGCCGCAACAATTAACGGCATTTGTGAACAAA
* * * *
317120 AAATGCCACAACCATTAGCGGCGTTTGTGAACAAA
1 AAATGCCGCAACAATTAACGGCATTTGTGAACAAA
*
317155 AAAAGCCGCAA
1 AAATGCCGCAA
317166 TAAGCCGTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (35 bp):
AAATGCCGCAACAATTAACGGCATTTGTGAACAAA
Done.