Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, 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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:366252 original size:33 final size:32
Alignment explanation
Indices: 366190--366252 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
366180 CATAAGCTTT
*
366190 ATGATTGTTTCTTTGAATGTCTGAAATTGCTG
1 ATGATTGTTTCTTTGAATATCTGAAATTGCTG
* *
366222 ATGATTGATTTCTTAT-AATATTTGACATTGC
1 ATGATTG-TTTCTT-TGAATATCTGAAATTGC
366253 CTTCTGTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 7 0.27
33 18 0.69
34 1 0.04
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (32 bp):
ATGATTGTTTCTTTGAATATCTGAAATTGCTG
Found at i:375749 original size:3 final size:3
Alignment explanation
Indices: 375736--375767 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
375726 AAGAGGAGAT
*
375736 TCC TTC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
375768 TTCTTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:383050 original size:7 final size:7
Alignment explanation
Indices: 383034--383066 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
383024 TCCTCAATTT
383034 AAAAAT-
1 AAAAATA
383040 AAAAATA
1 AAAAATA
383047 AAAAATA
1 AAAAATA
383054 AAAAATA
1 AAAAATA
383061 AAAAAT
1 AAAAAT
383067 TAATTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:383466 original size:14 final size:14
Alignment explanation
Indices: 383442--383477 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
383432 GCAAACACAG
383442 TTTTC-TTTTTTCT
1 TTTTCTTTTTTTCT
383455 TTTTCTTTTTTTCT
1 TTTTCTTTTTTTCT
*
383469 TTTTATTTT
1 TTTTCTTTT
383478 GTTGCTCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTTTCT
Found at i:384259 original size:197 final size:196
Alignment explanation
Indices: 383897--384279 Score: 513
Period size: 197 Copynumber: 1.9 Consensus size: 196
383887 GAAGAAATTG
*
383897 CAAGCTTGTAAGTCAATCTTTCATAGCAATACTGATATCCATGATCAATATAGTAAGCACCTACC
1 CAAGCTTGTAAGTCAATCTTTCATAGCAATACTGATAGCCATGATCAATATAGTAAGCACCTACC
**
383962 ACTAAATCATGTGGTTGTGACACACACGATTTAGAAACACACAAATAAAATGCACAGCCCAGGAC
66 ACTAAATCATGTGGCCGTGA-ACACACGATTTAGAAACACACAAATAAAATG-ACA--CCAGGAC
*
384027 CAGGAACTTGGCATATCTGCATCCATGGTGTTTATGAAACCAATAACATACGCAGAGACAAGAAC
127 CAGAAACTTGGCATATCTGCATCCATGGTGTTTATGAAACCAATAACATACGCAGAGACAAGAAC
384092 ATCCC
192 ATCCC
* *
384097 CAAGCTTGTAAGTCAATCTTTCAGTAGCAAGATACTGATAGCCATGATCCATATGGTAAGCACCT
1 CAAGCTTGTAAGTCAATCTTTCA-TAGC-A-ATACTGATAGCCATGATCAATATAGTAAGCACCT
* ** * * * *
384162 ACCTGCT-AATCATGTGGCCGTTG-ATGCATGATTTAGAAACACGCAAATGAATTG-CA-CAGGA
63 ACC-ACTAAATCATGTGGCCG-TGAACACACGATTTAGAAACACACAAATAAAATGACACCAGGA
* * *
384223 CCAGAAACTTGGCATGTCTGCATCCATGGTGTTTATGAAGCCAATAACATATGCAGA
126 CCAGAAACTTGGCATATCTGCATCCATGGTGTTTATGAAACCAATAACATACGCAGA
384280 CACAGAAAAT
Statistics
Matches: 162, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
197 58 0.36
200 25 0.15
201 4 0.02
202 26 0.16
203 45 0.28
204 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (196 bp):
CAAGCTTGTAAGTCAATCTTTCATAGCAATACTGATAGCCATGATCAATATAGTAAGCACCTACC
ACTAAATCATGTGGCCGTGAACACACGATTTAGAAACACACAAATAAAATGACACCAGGACCAGA
AACTTGGCATATCTGCATCCATGGTGTTTATGAAACCAATAACATACGCAGAGACAAGAACATCC
C
Found at i:387138 original size:5 final size:5
Alignment explanation
Indices: 387121--387159 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
387111 AAGCAATGAA
* *
387121 ACAAC ACCAAA ACAAA ACAAC ACAAC ACAAC ACAAC ACA
1 ACAAC A-CAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACA
387160 GAGACAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAC
Found at i:392064 original size:16 final size:17
Alignment explanation
Indices: 392038--392070 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
392028 TTAATTTGTT
392038 AATAGAATAAAAAATAA
1 AATAGAATAAAAAATAA
*
392055 AATA-AATAAATAATAA
1 AATAGAATAAAAAATAA
392071 TTAAGGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AATAGAATAAAAAATAA
Found at i:392432 original size:28 final size:28
Alignment explanation
Indices: 392391--392660 Score: 260
Period size: 28 Copynumber: 9.5 Consensus size: 28
392381 TTTAACATGT
* *
392391 TTTGTCTAAATTTAGATAAGAAAATATG
1 TTTGTCTTAATTTAGACAAGAAAATATG
* *
392419 CTTGTTTTAATTTAGTTA-AAGAAACATAT-
1 TTTGTCTTAATTTAG--ACAAGAAA-ATATG
* * *
392448 TTTATCTTAATTTAGACTAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAATATG
* *
392476 TTTGTCTTAATTTAAACAAGAAAACATATT
1 TTTGTCTTAATTTAGACAAG-AAA-ATATG
*
392506 TTTTTCTTAATTTAGACAAGAAAATATG
1 TTTGTCTTAATTTAGACAAGAAAATATG
* *
392534 TTTGTTTTAATTTAGAAAAG-AAATATG
1 TTTGTCTTAATTTAGACAAGAAAATATG
* *
392561 TTTTGTCTTAATTTAAACAAGAAAAACATG
1 -TTTGTCTTAATTTAGACAAG-AAAATATG
* * *
392591 TATGTCTTAATTTAAGACAA-AAAATTTT
1 TTTGTCTTAATTT-AGACAAGAAAATATG
* *
392619 TTTGTCTTAATCTAGACAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAATATG
*
392647 TTTGTCTCAATTTA
1 TTTGTCTTAATTTA
392661 AGCGAGATAA
Statistics
Matches: 195, Mismatches: 35, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
27 17 0.09
28 105 0.54
29 36 0.18
30 37 0.19
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAAAATATG
Found at i:392677 original size:57 final size:57
Alignment explanation
Indices: 392384--392697 Score: 300
Period size: 57 Copynumber: 5.5 Consensus size: 57
392374 TAGTGGTTTT
* * * * * * *
392384 AACATGTTTTGTCTAAATTTAGATAAGAAAATATGCTTGTTTTAATTT-AGTTA-AAGA
1 AACATTTTTTATCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAG--ACAAGA
* *
392441 AACATATTTTATCTTAATTTAGACTAGAAAACATGTTTGTCTTAATTTAA-ACAAGAA
1 AACATTTTTTATCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAAG-A
* * * *
392498 AACATATTTTTTTCTTAATTTAGACAAGAAAATATGTTTGTTTTAATTT-AGAAAAGA
1 AACAT-TTTTTATCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAAGA
* * * * *
392555 AATATGTTTTGTCTTAATTTAAACAAGAAAAACATGTATGTCTTAATTTAAGACAA-A
1 AACATTTTTTATCTTAATTTAGACAAG-AAAACATGTTTGTCTTAATTTAAGACAAGA
* * * *
392612 AA-ATTTTTTTGTCTTAATCTAGACAAGAAAACATGTTTGTCTCAATTTAAG-CGAGA
1 AACA-TTTTTTATCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAAGA
*
392668 TAACATTTTTTATCTTAATTGATGACAAGA
1 -AACATTTTTTATCTTAATTTA-GACAAGA
392698 GTTCTATTAA
Statistics
Matches: 214, Mismatches: 31, Indels: 23
0.80 0.12 0.09
Matches are distributed among these distances:
55 3 0.01
56 46 0.21
57 109 0.51
58 56 0.26
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (57 bp):
AACATTTTTTATCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAAGA
Found at i:392684 original size:85 final size:85
Alignment explanation
Indices: 392437--392697 Score: 287
Period size: 85 Copynumber: 3.0 Consensus size: 85
392427 AATTTAGTTA
* *
392437 AAGAAACATA-TTTTATCTTAATTTAGACTAGAAAACATGTTTGTCTTAATTTAAACAAGAAAAC
1 AAGAAA-ATATTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAACAAGAAAAC
*
392501 ATATTTTTTTCTTAATTTAGAC
65 AT-TTTTTATCTTAATTTAGAC
* * * *
392523 AAGAAAATATGTTTGTTTTAATTTAGAAAAG-AAATATGTTTTGTCTTAATTTAAACAAGAAAAA
1 AAGAAAATATTTTTGTCTTAATTTAGACAAGAAAACATG-TTTGTCTTAATTTAAACAAG-AAAA
* * *
392587 CA-TGTATGTCTTAATTTAAGAC
64 CATTTTTTATCTTAATTT-AGAC
* * * * * *
392609 AA-AAAATTTTTTTGTCTTAATCTAGACAAGAAAACATGTTTGTCTCAATTTAAGCGAGATAACA
1 AAGAAAATATTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAACAAGAAAACA
*
392673 TTTTTTATCTTAATTGATGAC
66 TTTTTTATCTTAATTTA-GAC
392694 AAGA
1 AAGA
392698 GTTCTATTAA
Statistics
Matches: 144, Mismatches: 23, Indels: 16
0.79 0.13 0.09
Matches are distributed among these distances:
84 6 0.04
85 77 0.53
86 55 0.38
87 6 0.04
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (85 bp):
AAGAAAATATTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAACAAGAAAACA
TTTTTTATCTTAATTTAGAC
Found at i:402674 original size:2 final size:2
Alignment explanation
Indices: 402667--402699 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
402657 TGATATCACA
402667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
402700 TCACATTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:407248 original size:9 final size:9
Alignment explanation
Indices: 407231--407261 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
407221 GACCCATCAC
*
407231 CACCGCCAG
1 CACCACCAG
407240 CACCACCAG
1 CACCACCAG
407249 CACCACCAG
1 CACCACCAG
407258 CACC
1 CACC
407262 TCCACCGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.58, G:0.13, T:0.00
Consensus pattern (9 bp):
CACCACCAG
Found at i:411279 original size:12 final size:12
Alignment explanation
Indices: 411262--411286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
411252 TACAAGGAAT
411262 CTGCCTCCCTCC
1 CTGCCTCCCTCC
411274 CTGCCTCCCTCC
1 CTGCCTCCCTCC
411286 C
1 C
411287 GCAATCCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.68, G:0.08, T:0.24
Consensus pattern (12 bp):
CTGCCTCCCTCC
Found at i:424419 original size:5 final size:5
Alignment explanation
Indices: 424409--424434 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
424399 TAAAACTCAT
424409 ACCAA ACCAA ACCAA ACCAA ACCAA A
1 ACCAA ACCAA ACCAA ACCAA ACCAA A
424435 ATTTTGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCAA
Found at i:424878 original size:29 final size:28
Alignment explanation
Indices: 424845--424922 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
424835 TTCCTTATAT
* *
424845 TTGTTCACGTATAGCCTTTTCTCTTGTA
1 TTGTTCAAGTATAGCTTTTTCTCTTGTA
* * *
424873 CTTGTTCATGTACAACTTTTTCTCTTGTA
1 -TTGTTCAAGTATAGCTTTTTCTCTTGTA
424902 TCTGTTCAAGTATAGCTTTTT
1 T-TGTTCAAGTATAGCTTTTT
424923 TTTAGCTCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (28 bp):
TTGTTCAAGTATAGCTTTTTCTCTTGTA
Found at i:432962 original size:10 final size:8
Alignment explanation
Indices: 432921--432954 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
432911 GTAATTTTAG
432921 AATCATGT
1 AATCATGT
432929 AATCATGTT
1 AATCATG-T
432938 GAATCATGT
1 -AATCATGT
432947 AATCATGT
1 AATCATGT
432955 TACATCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (8 bp):
AATCATGT
Found at i:432962 original size:18 final size:18
Alignment explanation
Indices: 432920--432955 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
432910 AGTAATTTTA
432920 GAATCATGTAATCATGTT
1 GAATCATGTAATCATGTT
432938 GAATCATGTAATCATGTT
1 GAATCATGTAATCATGTT
432956 ACATCATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
GAATCATGTAATCATGTT
Found at i:435932 original size:2 final size:2
Alignment explanation
Indices: 435927--435955 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
435917 ATGGTGTGTG
435927 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
435956 GTACACACAC
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:436953 original size:6 final size:6
Alignment explanation
Indices: 436942--436968 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
436932 TTAATTTGCG
436942 CATTTC CATTTC CATTTC CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CAT
436969 GTTTTGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTTC
Found at i:443361 original size:28 final size:29
Alignment explanation
Indices: 443303--443362 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
443293 TTAAGTTTAT
* *
443303 AATATTAAATATTAAATTATAATACATAA
1 AATATTAAATATTAAATTACAATACACAA
*
443332 AATA-TAAATAGTTAAA-TACAATATACAA
1 AATATTAAATA-TTAAATTACAATACACAA
443360 AAT
1 AAT
443363 TAATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (29 bp):
AATATTAAATATTAAATTACAATACACAA
Found at i:443591 original size:15 final size:16
Alignment explanation
Indices: 443560--443593 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
443550 AATATTTTTT
*
443560 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
443576 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
443591 AAT
1 AAT
443594 CTATATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:443749 original size:22 final size:22
Alignment explanation
Indices: 443715--443763 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
443705 ATATATGATC
443715 AAATAGAATATAAT-TAAAAAA
1 AAATAGAATATAATATAAAAAA
*
443736 TAAATA-AATAATAATATAAATAA
1 -AAATAGAAT-ATAATATAAAAAA
443759 AAATA
1 AAATA
443764 TTACTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 15 0.62
23 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATAGAATATAATATAAAAAA
Found at i:443756 original size:12 final size:12
Alignment explanation
Indices: 443724--443764 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
443714 CAAATAGAAT
*
443724 ATAAT-TAAAAA
1 ATAATATAAATA
443735 ATAA-ATAAATA
1 ATAATATAAATA
443746 ATAATATAAATA
1 ATAATATAAATA
*
443758 AAAATAT
1 ATAATAT
443765 TACTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:443904 original size:14 final size:14
Alignment explanation
Indices: 443876--443914 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
443866 TTTATTTTTT
*
443876 AATTATATT-AAAA
1 AATTATTTTAAAAA
443889 AATTATTTTAAAAA
1 AATTATTTTAAAAA
443903 AATTA-TTTAAAA
1 AATTATTTTAAAA
443915 TATATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTATTTTAAAAA
Found at i:447095 original size:18 final size:19
Alignment explanation
Indices: 447072--447107 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
447062 ATATAAAAAA
447072 ATTAA-TTAAATTTTTTTG
1 ATTAATTTAAATTTTTTTG
447090 ATTAATTTAAATTTTTTT
1 ATTAATTTAAATTTTTTT
447108 AAAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
ATTAATTTAAATTTTTTTG
Found at i:447236 original size:2 final size:2
Alignment explanation
Indices: 447229--447255 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
447219 TCATCATGAC
447229 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 T
447256 GATTTTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:447647 original size:16 final size:16
Alignment explanation
Indices: 447615--447645 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
447605 ATATCTTTTT
447615 TTATTAATTTAAAAAA
1 TTATTAATTTAAAAAA
447631 TTATT-ATTTAAAAAA
1 TTATTAATTTAAAAAA
447646 ATAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTAATTTAAAAAA
Found at i:449842 original size:7 final size:7
Alignment explanation
Indices: 449830--449872 Score: 77
Period size: 7 Copynumber: 6.0 Consensus size: 7
449820 AAATAATAAT
449830 AAAAATA
1 AAAAATA
449837 AAAAATA
1 AAAAATA
449844 AAAAATA
1 AAAAATA
449851 AAAAATA
1 AAAAATA
449858 AAAAATA
1 AAAAATA
449865 AAATAATA
1 AAA-AATA
449873 GTCGTAGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 31 0.89
8 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:449856 original size:21 final size:22
Alignment explanation
Indices: 449824--449872 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
449814 TACTTGAAAT
449824 AATAAT-AAAAATAAAAAATAA
1 AATAATAAAAAATAAAAAATAA
449845 AA-AATAAAAAATAAAAAATAA
1 AATAATAAAAAATAAAAAATAA
449866 AATAATA
1 AATAATA
449873 GTCGTAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (22 bp):
AATAATAAAAAATAAAAAATAA
Found at i:457977 original size:14 final size:14
Alignment explanation
Indices: 457949--458014 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
457939 TATATATTAC
*
457949 TAATAAAATTTAAAT
1 TAAT-AAATTAAAAT
457964 TAATAAATTAAAAT
1 TAATAAATTAAAAT
**
457978 TAATTCA-T-AAA-
1 TAATAAATTAAAAT
457989 -AATAAATTAAAAT
1 TAATAAATTAAAAT
*
458002 TAA-AAATCAAAAT
1 TAATAAATTAAAAT
458015 CATATTTAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
10 4 0.10
11 1 0.02
12 6 0.15
13 10 0.24
14 16 0.39
15 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAAATTAAAAT
Found at i:458013 original size:24 final size:24
Alignment explanation
Indices: 457965--458014 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
457955 AATTTAAATT
**
457965 AATAAATTAAAATTAATTCATAAA
1 AATAAATTAAAATTAATAAATAAA
*
457989 AATAAATTAAAATTAA-AAATCAA
1 AATAAATTAAAATTAATAAATAAA
458012 AAT
1 AAT
458015 CATATTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAAATTAAAATTAATAAATAAA
Found at i:467043 original size:7 final size:7
Alignment explanation
Indices: 467031--467064 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
467021 GCATCCGCAT
*
467031 GGCATTG
1 GGCATTA
467038 GGCATTA
1 GGCATTA
467045 GGCATTA
1 GGCATTA
467052 GGCATTA
1 GGCATTA
467059 GGCATT
1 GGCATT
467065 GGGTTACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (7 bp):
GGCATTA
Found at i:467050 original size:14 final size:14
Alignment explanation
Indices: 467031--467067 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
467021 GCATCCGCAT
467031 GGCATTGGGCATTA
1 GGCATTGGGCATTA
*
467045 GGCATTAGGCATTA
1 GGCATTGGGCATTA
467059 GGCATTGGG
1 GGCATTGGG
467068 TTACTTCGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.27
Consensus pattern (14 bp):
GGCATTGGGCATTA
Found at i:482115 original size:20 final size:21
Alignment explanation
Indices: 482077--482116 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
482067 GATAATATAA
*
482077 TATTTAAAAAAACTCTTAAAC
1 TATTTAAAAAAAATCTTAAAC
482098 TATTTAAAAAAAAT-TTAAA
1 TATTTAAAAAAAATCTTAAA
482117 TAAGTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
TATTTAAAAAAAATCTTAAAC
Found at i:482484 original size:86 final size:86
Alignment explanation
Indices: 482366--482538 Score: 276
Period size: 86 Copynumber: 2.0 Consensus size: 86
482356 TTACACAAAA
* *
482366 TTTTCTTGTGAAATCCATAAAATTATTATTAATATATAACAATAGCAACTT-AGAAAAATAATAC
1 TTTTCTTATGAAATCCATAAAATTATTATTAATAGATAACAATAGCAACTTCA-AAAAATAATAC
482430 TACTTAAAAAGACAAATTTGTT
65 TACTTAAAAAGACAAATTTGTT
* *
482452 TTTTCTTATGAAATCTATAAAATTATTGTTAATAGATAACAATAGCAACTTCAAAAAATAATACT
1 TTTTCTTATGAAATCCATAAAATTATTATTAATAGATAACAATAGCAACTTCAAAAAATAATACT
**
482517 ACTTAAAAAGGTAAATTTGTT
66 ACTTAAAAAGACAAATTTGTT
482538 T
1 T
482539 CATTAAACAA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 79 0.99
87 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (86 bp):
TTTTCTTATGAAATCCATAAAATTATTATTAATAGATAACAATAGCAACTTCAAAAAATAATACT
ACTTAAAAAGACAAATTTGTT
Found at i:483912 original size:17 final size:16
Alignment explanation
Indices: 483886--483928 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
483876 CGGCGACTCC
*
483886 TTTTT-TTTTTTTCAT
1 TTTTTGTTTTTTTTAT
*
483901 TTTTTGTTTTTTTTGT
1 TTTTTGTTTTTTTTAT
483917 TTTTATGTTTTT
1 TTTT-TGTTTTT
483929 GTGGGGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.05, C:0.02, G:0.07, T:0.86
Consensus pattern (16 bp):
TTTTTGTTTTTTTTAT
Found at i:483919 original size:23 final size:22
Alignment explanation
Indices: 483886--483930 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
483876 CGGCGACTCC
*
483886 TTTTTTTTTTTTCAT-TTTTTG
1 TTTTTTTTTTTTTATGTTTTTG
483907 TTTTTTTTGTTTTTATGTTTTTG
1 TTTTTTTT-TTTTTATGTTTTTG
483930 T
1 T
483931 GGGGTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTTTTTATGTTTTTG
Found at i:487272 original size:2 final size:2
Alignment explanation
Indices: 487265--487300 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
487255 GAATATCAGG
*
487265 TC TC TC TC TC TC CC 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
487301 ACACACACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:490714 original size:35 final size:36
Alignment explanation
Indices: 490652--490723 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
490642 TCAAATTTTT
**
490652 ATAATTTTATTTTAAATTAAATAAATTTATATAATTA
1 ATAATTTTATTTTAAAAAAAATAAATTT-TATAATTA
* *
490689 ATAA-TTT-TTTTAAAAAAAATTAATTTTATGATTA
1 ATAATTTTATTTTAAAAAAAATAAATTTTATAATTA
490723 A
1 A
490724 CAAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 8 0.26
35 16 0.52
36 3 0.10
37 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (36 bp):
ATAATTTTATTTTAAAAAAAATAAATTTTATAATTA
Found at i:490723 original size:22 final size:23
Alignment explanation
Indices: 490698--490740 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
490688 AATAATTTTT
490698 TTAAAAAAAATTAATT-TTATGA
1 TTAAAAAAAATTAATTATTATGA
*
490720 TTAACAAAAATTAATTATTAT
1 TTAAAAAAAATTAATTATTAT
490741 TTGTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTAAAAAAAATTAATTATTATGA
Found at i:495939 original size:16 final size:16
Alignment explanation
Indices: 495920--495952 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
495910 AAATTAGAAT
495920 CAATAATTAAGATAGC
1 CAATAATTAAGATAGC
495936 CAATAATTAAGATAGC
1 CAATAATTAAGATAGC
495952 C
1 C
495953 TTCATTACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.24
Consensus pattern (16 bp):
CAATAATTAAGATAGC
Found at i:499400 original size:16 final size:16
Alignment explanation
Indices: 499379--499409 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
499369 AAATTAGAAT
499379 CAATAATTAAGATAAC
1 CAATAATTAAGATAAC
499395 CAATAATTAAGATAA
1 CAATAATTAAGATAA
499410 GTTTCATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
CAATAATTAAGATAAC
Found at i:508101 original size:18 final size:16
Alignment explanation
Indices: 508068--508115 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
508058 AATAGAATTG
508068 AAAAAAATAAATAAAT
1 AAAAAAATAAATAAAT
508084 AAAAATAATAATATAAAT
1 AAAAA-AATAA-ATAAAT
*
508102 AAATAAATTAAATA
1 AAA-AAAATAAATA
508116 TAAACTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.18
17 8 0.29
18 13 0.46
19 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAAATAAATAAAT
Found at i:508113 original size:5 final size:4
Alignment explanation
Indices: 508072--508115 Score: 52
Period size: 4 Copynumber: 10.2 Consensus size: 4
508062 GAATTGAAAA
*
508072 AAAT AAAT AAAT AAAA ATAAT AATAT AAAT AAAT AAATT AAAT A
1 AAAT AAAT AAAT AAAT A-AAT AA-AT AAAT AAAT AAA-T AAAT A
508116 TAAACTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 24 0.69
5 11 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:508252 original size:16 final size:17
Alignment explanation
Indices: 508233--508267 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
508223 TTATAAAATC
*
508233 ATTATATT-ATTTTTTA
1 ATTATATTAATTATTTA
508249 ATTATATTAATTATTTA
1 ATTATATTAATTATTTA
508266 AT
1 AT
508268 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATATTAATTATTTA
Found at i:509556 original size:6 final size:6
Alignment explanation
Indices: 509522--509569 Score: 51
Period size: 6 Copynumber: 7.3 Consensus size: 6
509512 ACGTCAAGAT
*
509522 TTTTTA TTTGTTA TTTTTA TTATAATTA TTTTTA TTTTTA TTATTA TT
1 TTTTTA TTT-TTA TTTTTA TT-T--TTA TTTTTA TTTTTA TTTTTA TT
509570 CATTTATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
6 24 0.65
7 7 0.19
8 1 0.03
9 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:509558 original size:21 final size:22
Alignment explanation
Indices: 509525--509574 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
509515 TCAAGATTTT
509525 TTATTTGTTATTTTTATTATAA
1 TTATTTGTTATTTTTATTATAA
*
509547 TTATTT-TTATTTTTATTATTA
1 TTATTTGTTATTTTTATTATAA
509568 TTCATTT
1 TT-ATTT
509575 ATAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTATTTGTTATTTTTATTATAA
Found at i:509989 original size:251 final size:249
Alignment explanation
Indices: 509546--510323 Score: 1062
Period size: 251 Copynumber: 3.1 Consensus size: 249
509536 TTTTATTATA
* * *
509546 ATTATTTTTATTTTTATTATTATTCATTTATAAATTAAAATTTGTAAACCATTAA-ATACTTTAA
1 ATTATTTTTATCTTTACTATTATTTATTTATAAATTAAAATTTGTAAACCA-TAATATACTTTAA
* * *
509610 ACTTGAGAAAATAGATTTAAATGTTTAATTTCTTATAAAATTATGTTTATTTGACTTAATTGACT
65 ACTTGAGAATATAAATTTAAATGTTTAATTTCTTATAAAATTATATTTATTTGACTTAATTGACT
*
509675 TGTTACGTTAAATCTATCACTTTACATCAATATTTTGAAAATAGTTATTCCACTTTTATAATTTT
130 TGTTACGTTAAATCTATCACTTTACATCAATATTTTGACAATAGTTATTCCA-TTTTATAATTTT
509740 TTATGA-TAATTATTATAAGTTTATATCAAGGTTTTTCAACTACTAATTTTCACTATG
194 TTAT-ATTAATTATTATAAGTTTATATCAAGGTTTTTCAACTACTAATTTTC-CTATG
*
509797 ATTATTTTTATCTTTACTATTATTTATTTATAAATTAAAATTTGTAAACCGTAATATACTTTAAA
1 ATTATTTTTATCTTTACTATTATTTATTTATAAATTAAAATTTGTAAACCATAATATACTTTAAA
*
509862 CTTGAGAATATAAATTTAAATGTTTAATTTCTTATAAAATTATATTTATTTGACTTAATTAACTT
66 CTTGAGAATATAAATTTAAATGTTTAATTTCTTATAAAATTATATTTATTTGACTTAATTGACTT
*
509927 GTTACGTTAAATCTATCACTTTACATAAATATTTTGACAATAGTTATTCCATATTTATAATTTTT
131 GTTACGTTAAATCTATCACTTTACATCAATATTTTGACAATAGTTATTCCAT-TTTATAATTTTT
** *
509992 TATATTAATTATTATAAGTTTACGTCAAGATTTTTCAACTACTAATTTTCGCTATG
195 TATATTAATTATTATAAGTTTATATCAAGGTTTTTCAACTACTAATTTTC-CTATG
* * * *
510048 ATTATTTGTATCCTTACTATTATTTATTCATTAATTAAAATTTGTAAACCATAATATACTTTAAA
1 ATTATTTTTATCTTTACTATTATTTATTTATAAATTAAAATTTGTAAACCATAATATACTTTAAA
* * * *
510113 CTTGAGAATATAAATTTAAATATTTAATTTTTTAAAAAATTATTTTTATTTGACTTAATTGACTT
66 CTTGAGAATATAAATTTAAATGTTTAATTTCTTATAAAATTATATTTATTTGACTTAATTGACTT
* * * ** * * * *
510178 ATTATGTTAAATCTCAT-AATTTAGGTCAATATTTTGACAATATTTGTTTCTC-CTTTATAATAT
131 GTTACGTTAAATCT-ATCACTTTACATCAATATTTTGACAATAGTT-ATTC-CATTTTATAATTT
* * * * * * *
510241 TTTACATTAATTCTT-TCAATTTTATATCAAGGTTTTTCAACAACTATTTTTTCTTATA
193 TTTATATTAATTATTAT-AAGTTTATATCAAGGTTTTTCAACTACTA-ATTTTCCTATG
* * *
510299 ATTATTTCTATCATTACTACTATTT
1 ATTATTTTTATCTTTACTATTATTT
510324 CATAAAAATT
Statistics
Matches: 472, Mismatches: 47, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
250 6 0.01
251 455 0.96
252 10 0.02
253 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (249 bp):
ATTATTTTTATCTTTACTATTATTTATTTATAAATTAAAATTTGTAAACCATAATATACTTTAAA
CTTGAGAATATAAATTTAAATGTTTAATTTCTTATAAAATTATATTTATTTGACTTAATTGACTT
GTTACGTTAAATCTATCACTTTACATCAATATTTTGACAATAGTTATTCCATTTTATAATTTTTT
ATATTAATTATTATAAGTTTATATCAAGGTTTTTCAACTACTAATTTTCCTATG
Found at i:516045 original size:15 final size:15
Alignment explanation
Indices: 516025--516059 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
516015 ATCTTGGACA
516025 ATTTGATCATGGGTT
1 ATTTGATCATGGGTT
**
516040 ATTTGATTGTGGGTT
1 ATTTGATCATGGGTT
516055 ATTTG
1 ATTTG
516060 CTTATTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.29, T:0.51
Consensus pattern (15 bp):
ATTTGATCATGGGTT
Found at i:516501 original size:21 final size:20
Alignment explanation
Indices: 516477--516520 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
516467 AATTTAGTAA
* *
516477 AATTTAGGATTTAGTTATATT
1 AATTAAGGATTTA-TTAAATT
*
516498 AATTAAGGTTTTATTAAATT
1 AATTAAGGATTTATTAAATT
516518 AAT
1 AAT
516521 CCAAGGACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
AATTAAGGATTTATTAAATT
Found at i:516768 original size:8 final size:8
Alignment explanation
Indices: 516740--516810 Score: 61
Period size: 8 Copynumber: 8.5 Consensus size: 8
516730 TATAGGGAGT
*
516740 TAATTAAA
1 TAATTAAG
*
516748 TAATTTAG
1 TAATTAAG
516756 TTAATTAAG
1 -TAATTAAG
516765 TAATGTAATG
1 TAAT-TAA-G
**
516775 TCTTTAAG
1 TAATTAAG
516783 TAATTAAG
1 TAATTAAG
*
516791 TAATTAAT
1 TAATTAAG
*
516799 TAAATAAG
1 TAATTAAG
516807 TAAT
1 TAAT
516811 ATTTAATAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
8 33 0.67
9 13 0.27
10 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.10, T:0.42
Consensus pattern (8 bp):
TAATTAAG
Found at i:517445 original size:72 final size:72
Alignment explanation
Indices: 517328--517475 Score: 287
Period size: 72 Copynumber: 2.1 Consensus size: 72
517318 AAAATAGTTA
517328 ATGAAGTTAGAGTAGAAAATCCATATGCTAAAATGGTTATGGATGCATTGCAACTGGAGTTTCAG
1 ATGAAGTTAGAGTAGAAAATCCATATGCTAAAATGGTTATGGATGCATTGCAACTGGAGTTTCAG
517393 TTCAATG
66 TTCAATG
*
517400 ATGAAGTTAGAGTAGAAAATCCATATGCTAAAATGGTTATGGATGCTTTGCAACTGGAGTTTCAG
1 ATGAAGTTAGAGTAGAAAATCCATATGCTAAAATGGTTATGGATGCATTGCAACTGGAGTTTCAG
517465 TTCAATG
66 TTCAATG
517472 ATGA
1 ATGA
517476 GAGTCAAGAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (72 bp):
ATGAAGTTAGAGTAGAAAATCCATATGCTAAAATGGTTATGGATGCATTGCAACTGGAGTTTCAG
TTCAATG
Found at i:520662 original size:16 final size:16
Alignment explanation
Indices: 520641--520673 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
520631 TTTAGGGGTT
520641 TTAGGCATTACATGAC
1 TTAGGCATTACATGAC
*
520657 TTAGGCATTGCATGAC
1 TTAGGCATTACATGAC
520673 T
1 T
520674 GGTTGATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (16 bp):
TTAGGCATTACATGAC
Found at i:520977 original size:90 final size:89
Alignment explanation
Indices: 520868--521043 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 89
520858 TATGTGATTG
* * * * ** *
520868 ATTTTTGGTTATTGCATGACTAGTTTATAGGGCATTATTTGATTGATTTTTAAGCATTGCATGAT
1 ATTTTTAGTCATTGCATGACTAGTTGATAAGGCATTACGTGACTGATTTTTAAGCATTGCATGAT
* *
520933 TGTTTGATAGGGTATTGCATAACTA
66 TGGTTGATA-GGCATTGCATAACTA
* *
520958 ATTTTTAGTCATTGCATGACTAGTTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCGTGAT
1 ATTTTTAGTCATTGCATGACTAGTTGATAAGGCATTACGTGACTGATTTTTAAGCATTGCATGAT
521023 TGGTTGATAGGCATTGCATAA
66 TGGTTGATAGGCATTGCATAA
521044 TTGATTGATA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 11 0.15
90 64 0.85
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (89 bp):
ATTTTTAGTCATTGCATGACTAGTTGATAAGGCATTACGTGACTGATTTTTAAGCATTGCATGAT
TGGTTGATAGGCATTGCATAACTA
Found at i:521029 original size:45 final size:45
Alignment explanation
Indices: 520843--521037 Score: 162
Period size: 45 Copynumber: 4.4 Consensus size: 45
520833 TATTGTGTGG
* * *
520843 CTGGTTGAT-AGGCATTATGTGATTGATTTTT-GGTTATTGCATGA
1 CTGGTTGATAAGGCATTACGTGACTGATTTTTAGG-CATTGCATGA
* * * ** * *
520887 CTAGTTTATAGGGCATTATTTGATTGATTTTTAAGCATTGCATGA
1 CTGGTTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCATGA
* * * * * * * * *
520932 TTGTTTGATAGGGTATTGCATAACTAATTTTTAGTCATTGCATGA
1 CTGGTTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCATGA
* *
520977 CTAGTTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCGTGA
1 CTGGTTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCATGA
*
521022 TTGGTTGAT-AGGCATT
1 CTGGTTGATAAGGCATT
521038 GCATAATTGA
Statistics
Matches: 117, Mismatches: 32, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
44 14 0.12
45 102 0.87
46 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (45 bp):
CTGGTTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCATGA
Found at i:521033 original size:22 final size:22
Alignment explanation
Indices: 520967--521288 Score: 126
Period size: 22 Copynumber: 14.3 Consensus size: 22
520957 AATTTTTAGT
* *
520967 CATTGCATGACTAGTTGATAAGG
1 CATTGCGTGACTGGTTGAT-AGG
* * **
520990 CATTACGTGACTGATTTTTAGG
1 CATTGCGTGACTGGTTGATAGG
*
521012 CATTGCGTGATTGGTTGATAGG
1 CATTGCGTGACTGGTTGATAGG
* * * *
521034 CATTGCATAATTGATTGATAGGG
1 CATTGCGTGACTGGTTGATA-GG
* * *
521057 CATTGTGTGGCTTGTTTG-TAGGG
1 CATTGCGTGAC-TGGTTGATA-GG
** * ** *
521080 CATTGTATGACTAGTTTTTAAG
1 CATTGCGTGACTGGTTGATAGG
* * ** *
521102 CATTGTGTGACTAGTTTTTAGT
1 CATTGCGTGACTGGTTGATAGG
* *
521124 CATTGCATGACTAGTTGATAGGG
1 CATTGCGTGACTGGTTGATA-GG
** *
521147 CATTATGTGATTGGTTGATAGG
1 CATTGCGTGACTGGTTGATAGG
* * *
521169 CATTACGTGATTGATTGATAGG
1 CATTGCGTGACTGGTTGATAGG
* *
521191 ACATTGCGTGAATGGCTTGCA-GGG
1 -CATTGCGTGACTGG-TTG-ATAGG
* * *
521215 CATTGCGTAACTGATTGATGGGG
1 CATTGCGTGACTGGTTGAT-AGG
* * * **
521238 TATTACGTGATTGGTTTTTAGGG
1 CATTGCGTGACTGGTTGATA-GG
* **
521261 CATTGCGTGACTGTTTTCTAGG
1 CATTGCGTGACTGGTTGATAGG
521283 CATTGC
1 CATTGC
521289 TTGGATATTA
Statistics
Matches: 228, Mismatches: 61, Indels: 21
0.74 0.20 0.07
Matches are distributed among these distances:
21 1 0.00
22 109 0.48
23 107 0.47
24 10 0.04
25 1 0.00
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (22 bp):
CATTGCGTGACTGGTTGATAGG
Found at i:521059 original size:45 final size:45
Alignment explanation
Indices: 520921--521273 Score: 162
Period size: 45 Copynumber: 7.8 Consensus size: 45
520911 TGATTTTTAA
* * * * * **
520921 GCATTGCATGATTGTTTGATAGGGTATTGCATAACTAATTTTTA-G
1 GCATTGCGTGATTGGTTGATA-GGCATTGCATGACTGATTGATAGG
* * * * * * **
520966 TCATTGCATGACTAGTTGATAAGGCATTACGTGACTGATTTTTA-G
1 GCATTGCGTGATTGGTTGAT-AGGCATTGCATGACTGATTGATAGG
* *
521011 GCATTGCGTGATTGGTTGATAGGCATTGCATAATTGATTGATAGG
1 GCATTGCGTGATTGGTTGATAGGCATTGCATGACTGATTGATAGG
* * * * ** *
521056 GCATTGTGTGGCTTGTTTG-TAGGGCATTGTATGACT-AGTTTTTA-A
1 GCATTGCGT-GATTGGTTGATA-GGCATTGCATGACTGA-TTGATAGG
* * * ** *
521101 GCATTGTGTGACTAGTTTTTAGTCATTGCATGACT-AGTTGATAGG
1 GCATTGCGTGATTGGTTGATAGGCATTGCATGACTGA-TTGATAGG
** * * *
521146 GCATTATGTGATTGGTTGATAGGCATTACGTGATTGATTGATAGG
1 GCATTGCGTGATTGGTTGATAGGCATTGCATGACTGATTGATAGG
* * * * * *
521191 ACATTGCGTGAATGGCTTGCA-GGGCATTGCGTAACTGATTGATGGG
1 GCATTGCGTGATTGG-TTG-ATAGGCATTGCATGACTGATTGATAGG
* * ** *
521237 GTATTACGTGATTGGTTTTTAGGGCATTGCGTGACTG
1 GCATTGCGTGATTGGTTGATA-GGCATTGCATGACTG
521274 TTTTCTAGGC
Statistics
Matches: 232, Mismatches: 64, Indels: 23
0.73 0.20 0.07
Matches are distributed among these distances:
44 39 0.17
45 120 0.52
46 72 0.31
47 1 0.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (45 bp):
GCATTGCGTGATTGGTTGATAGGCATTGCATGACTGATTGATAGG
Found at i:521082 original size:90 final size:89
Alignment explanation
Indices: 520890--521288 Score: 254
Period size: 90 Copynumber: 4.4 Consensus size: 89
520880 TGCATGACTA
* ** * * * * *
520890 GTTTATAGGGCATTATTTGATTGATTTTTAAGCATTGCATGATTGTTTGATAGGGTATTGCATAA
1 GTTTGTAGGGCATTACGTGACTGATTTTTAGGCATTGCGTGATTGGTTGATA-GGCATTGCATAA
* ** * * * *
520955 CTAATTTTTA-GTCATTGCATGACTA
65 CTGATTGATAGGGCATTACGTGA-TT
*
520980 G-TTGATAAGGCATTACGTGACTGATTTTTAGGCATTGCGTGATTGGTTGATAGGCATTGCATAA
1 GTTTG-TAGGGCATTACGTGACTGATTTTTAGGCATTGCGTGATTGGTTGATAGGCATTGCATAA
* ** *
521044 TTGATTGATAGGGCATTGTGTGGCTT
65 CTGATTGATAGGGCATTACGT-GATT
*** * * * * ** * *
521070 GTTTGTAGGGCATTGTATGACT-AGTTTTTAAGCATTGTGTGACTAGTTTTTAGTCATTGCATGA
1 GTTTGTAGGGCATTACGTGACTGA-TTTTTAGGCATTGCGTGATTGGTTGATAGGCATTGCATAA
*
521134 CT-AGTTGATAGGGCATTATGTGATT
65 CTGA-TTGATAGGGCATTACGTGATT
* * ** * * *
521159 GGTTGATA-GGCATTACGTGATTGATTGATAGGACATTGCGTGAATGGCTTGCA-GGGCATTGCG
1 GTTTG-TAGGGCATTACGTGACTGATTTTTAGG-CATTGCGTGATTGG-TTG-ATAGGCATTGCA
* *
521222 TAACTGATTGATGGGGTATTACGTGATT
62 TAACTGATTGATAGGGCATTACGTGATT
* *
521250 GGTTTTTAGGGCATTGCGTGACTG-TTTTCTAGGCATTGC
1 -GTTTGTAGGGCATTACGTGACTGATTTT-TAGGCATTGC
521289 TTGGATATTA
Statistics
Matches: 235, Mismatches: 59, Indels: 29
0.73 0.18 0.09
Matches are distributed among these distances:
89 43 0.18
90 126 0.54
91 45 0.19
92 21 0.09
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.40
Consensus pattern (89 bp):
GTTTGTAGGGCATTACGTGACTGATTTTTAGGCATTGCGTGATTGGTTGATAGGCATTGCATAAC
TGATTGATAGGGCATTACGTGATT
Found at i:521163 original size:23 final size:23
Alignment explanation
Indices: 521137--521270 Score: 110
Period size: 23 Copynumber: 5.9 Consensus size: 23
521127 TGCATGACTA
*
521137 GTTGATAGGGCATTATGTGATTG
1 GTTGATAGGGCATTACGTGATTG
521160 GTTGATA-GGCATTACGTGATTG
1 GTTGATAGGGCATTACGTGATTG
* * * *
521182 ATTGATAGGACATTGCGTGAATG
1 GTTGATAGGGCATTACGTGATTG
* * * *
521205 GCTTG-CAGGGCATTGCGTAACTG
1 G-TTGATAGGGCATTACGTGATTG
* * *
521228 ATTGATGGGGTATTACGTGATTG
1 GTTGATAGGGCATTACGTGATTG
** *
521251 GTTTTTAGGGCATTGCGTGA
1 GTTGATAGGGCATTACGTGA
521271 CTGTTTTCTA
Statistics
Matches: 85, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
22 23 0.27
23 59 0.69
24 3 0.04
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.35
Consensus pattern (23 bp):
GTTGATAGGGCATTACGTGATTG
Found at i:522932 original size:33 final size:33
Alignment explanation
Indices: 522887--522949 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
522877 ACCTACAATC
*
522887 AATGCAGTTGGAGATCCAACAAGAGATGCAGTT
1 AATGCAGCTGGAGATCCAACAAGAGATGCAGTT
522920 AATGCAGCTGGAGATCCAACAAGAGATGCA
1 AATGCAGCTGGAGATCCAACAAGAGATGCA
522950 ATGTTGGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (33 bp):
AATGCAGCTGGAGATCCAACAAGAGATGCAGTT
Found at i:524780 original size:22 final size:22
Alignment explanation
Indices: 524755--524895 Score: 128
Period size: 22 Copynumber: 6.4 Consensus size: 22
524745 TTTTCTAGGT
**
524755 ATTGCATGATGGATTTTTAAGG
1 ATTGCATGATCAATTTTTAAGG
* *
524777 ATTGCATAATCAATTTTTAAGC
1 ATTGCATGATCAATTTTTAAGG
*
524799 ATTGCTTGA-CTAATTTTT-AGG
1 ATTGCATGATC-AATTTTTAAGG
* *
524820 TATTGCATGACCAATTTTTAGGG
1 -ATTGCATGATCAATTTTTAAGG
524843 ATTGCATGATCAATTTTT-AGG
1 ATTGCATGATCAATTTTTAAGG
* * *
524864 TATTGCGTGAT-TATTTTTAAAGT
1 -ATTGCATGATCAATTTTT-AAGG
524887 ATTGCATGA
1 ATTGCATGA
524896 CCCTAAGAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
21 11 0.11
22 81 0.84
23 5 0.05
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (22 bp):
ATTGCATGATCAATTTTTAAGG
Found at i:524824 original size:66 final size:65
Alignment explanation
Indices: 524731--524897 Score: 190
Period size: 66 Copynumber: 2.5 Consensus size: 65
524721 TGTGACTTGG
* ** ***
524731 GCATTGTGTGATTGTTTTCTAGGTATTGCATGATGGATTTTTAAGGATTGCATAATCAATTTTTA
1 GCATTGCGTGATAATTTT-TAGGTATTGCATGACCAATTTTTAAGGATTGCATAATCAATTTTTA
524796 A
65 A
* * *
524797 GCATTGCTTGACTAATTTTTAGGTATTGCATGACCAATTTTTAGGGATTGCATGATCAATTTTTA
1 GCATTGCGTGA-TAATTTTTAGGTATTGCATGACCAATTTTTAAGGATTGCATAATCAATTTTTA
*
524862 G
65 A
* * *
524863 GTATTGCGTGATTATTTTTAAAGTATTGCATGACC
1 GCATTGCGTGATAATTTTT-AGGTATTGCATGACC
524898 CTAAGAAATA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
65 7 0.08
66 73 0.86
67 5 0.06
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (65 bp):
GCATTGCGTGATAATTTTTAGGTATTGCATGACCAATTTTTAAGGATTGCATAATCAATTTTTAA
Found at i:530689 original size:21 final size:19
Alignment explanation
Indices: 530665--530705 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
530655 AATTCAAAAC
530665 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
530686 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
530705 A
1 A
530706 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:535736 original size:18 final size:18
Alignment explanation
Indices: 535713--535750 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
535703 AAAAGGCCTA
*
535713 AGCCATCCCCTATACTTG
1 AGCCATCCCCTAAACTTG
*
535731 AGCCATCCTCTAAACTTG
1 AGCCATCCCCTAAACTTG
535749 AG
1 AG
535751 ATACTTGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.26
Consensus pattern (18 bp):
AGCCATCCCCTAAACTTG
Found at i:538855 original size:194 final size:195
Alignment explanation
Indices: 538526--538916 Score: 563
Period size: 194 Copynumber: 2.0 Consensus size: 195
538516 CCAAAAGATA
**
538526 TAGTCAAGAGCAAGGAATTGATTATGATGAAACCCATGCTTCGATAGCTAGACTAGAGGTAATTA
1 TAGTCAAGAGCAAGGAATAAATTATGATGAAACCCATGCTTCGATAGCTAGACTAGAGGTAATTA
* *
538591 GAATGTTATTAGCCTTTGCATGCTATATGAGCTTTAAACTATATCAAATGGATGCCAACAATGGT
66 GAATGTTATTAGCCTTTGCATGCTATATGAACTTTAAACTATATCAAATGGATACCAACAATGGT
* *
538656 TTTCTAAATAGGTTAATCTATAAGGAAATATATGTTGAACAACCACCCTGCTTT-AAGCCCAACT
131 TTTCTAAATAGGTTAATCAATAAGGAAATATATGTTGAACAACCACCCGGCTTTAAAGCCCAACT
** * *
538720 TAGTCAAGAAG-AAGGAATAAATTATGATGAAACTTATGCTTCGGTAGCTAGACTATAGGTAATT
1 TAGTCAAG-AGCAAGGAATAAATTATGATGAAACCCATGCTTCGATAGCTAGACTAGAGGTAATT
* * * **
538784 AGAATGTTATTAGCCTTTGCGTGCTCTATGAACTTTAAACTATTTCAAATGGATATTAA-AAGTG
65 AGAATGTTATTAGCCTTTGCATGCTATATGAACTTTAAACTATATCAAATGGATACCAACAA-TG
* * * *
538848 TTTTTCTAAATTGGTTAATCAATAAGGAAGTATATGTTGAACAACCAGCCGGCTTTGAAAGCCCA
129 GTTTTCTAAATAGGTTAATCAATAAGGAAATATATGTTGAACAACCACCCGGCTTT-AAAGCCCA
538913 ACT
193 ACT
538916 T
1 T
538917 TTCCAAATCA
Statistics
Matches: 174, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
193 2 0.01
194 159 0.91
195 2 0.01
196 11 0.06
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (195 bp):
TAGTCAAGAGCAAGGAATAAATTATGATGAAACCCATGCTTCGATAGCTAGACTAGAGGTAATTA
GAATGTTATTAGCCTTTGCATGCTATATGAACTTTAAACTATATCAAATGGATACCAACAATGGT
TTTCTAAATAGGTTAATCAATAAGGAAATATATGTTGAACAACCACCCGGCTTTAAAGCCCAACT
Found at i:540649 original size:20 final size:20
Alignment explanation
Indices: 540624--540662 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
540614 ATGCAAGAAC
540624 ATGTATCAATACACCCCAAT
1 ATGTATCAATACACCCCAAT
*
540644 ATGTATCAATACATCCCAA
1 ATGTATCAATACACCCCAA
540663 CTAATGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (20 bp):
ATGTATCAATACACCCCAAT
Found at i:545947 original size:21 final size:21
Alignment explanation
Indices: 545914--545956 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
545904 TGCACGTTGA
*
545914 TTAGTTTAATTTAAGTTATTT
1 TTAGTTTAATTTAAGCTATTT
*
545935 TTAG-TTAATTTTATGCTATTT
1 TTAGTTTAA-TTTAAGCTATTT
545956 T
1 T
545957 GCTTGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (21 bp):
TTAGTTTAATTTAAGCTATTT
Found at i:547265 original size:18 final size:20
Alignment explanation
Indices: 547219--547266 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
547209 TTAGTCTTTG
547219 TTAATTAGTTTAGTTTTCTAA
1 TTAATTA-TTTAGTTTTCTAA
547240 TTAA--ATTTAG-TTT-TAA
1 TTAATTATTTAGTTTTCTAA
547256 TTAATTATTTA
1 TTAATTATTTA
547267 TGAAATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
18 10 0.40
19 1 0.04
21 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
TTAATTATTTAGTTTTCTAA
Found at i:549212 original size:3 final size:3
Alignment explanation
Indices: 549204--549235 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
549194 GTTAGCTTTT
549204 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
549236 GGAAGAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:550706 original size:18 final size:20
Alignment explanation
Indices: 550660--550707 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
550650 TTAGTCTTCG
550660 TTAATTAGTTTAGTTTTCTAA
1 TTAATTA-TTTAGTTTTCTAA
550681 TTAA--ATTTAG-TTT-TAA
1 TTAATTATTTAGTTTTCTAA
550697 TTAATTATTTA
1 TTAATTATTTA
550708 CAAAATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
18 10 0.40
19 1 0.04
21 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
TTAATTATTTAGTTTTCTAA
Found at i:556280 original size:251 final size:249
Alignment explanation
Indices: 555586--556708 Score: 1121
Period size: 251 Copynumber: 4.5 Consensus size: 249
555576 TATTCCATTT
* * **
555586 TTATAATTTTTTACTTTAATTCTTACAGCTTTA-AACTAAGGTTTTTCAACTATTATTTTTCACT
1 TTATAATTTTTTACATTAATT-TTACAACTTTATGTC-AAGGTTTTTCAACTATTATTTTTCACT
* * * *
555650 ATAATTATTTTTATCCTTACTATTATACATTTATAAATTATAATTTGTAAACCATTAAATACTTC
64 ATAATTATTTTTATCCTTATTATTATTCATTTATAAATTAAAATTTGTAAACCA-TAAA-A-TAC
* * * *
555715 ATTTAAACTTGAGAATATAAATTTATATATTTAATTTTTTAAAAAATTATGTTTATTTGATATAA
126 -TTTAAAC-TCAAAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGATATAA
* * * *
555780 TTGACTTGTTATGCTAAATCTCACATGTTTTCATTAATATTTTGATAATTTTTGTTCCACC
189 TTGACTTGTTACGTTAAATCTCACATGTTTACGTTAATATTTTGATAATTTTTGTTCCACC
* * * * * * * * *
555841 TTCATAACTTTATGCGTTAATTCTCACAACTTTATATCAAGGCTTTTCAACTACTAATTTTCACT
1 TT-ATAATTTTTTACATTAATT-TTACAACTTTATGTCAAGGTTTTTCAACTATTATTTTTCACT
* * * *
555906 ATAATTGTTTTCATCCTTATTATTATTCTTTTATAAATTAAAATTTGTAAACCATTAAATACTTT
64 ATAATTATTTTTATCCTTATTATTATTCATTTATAAATTAAAATTTGTAAACCATAAAATACTTT
555971 AAACTCGAAAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGACT-TAATTG
129 AAACTC-AAAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGA-TATAATTG
* * * * * *
556035 ATTTGTTACGTTAAATCTCACATGCTTACCTTAATAATATGATAATGTTTGTTCCACC
192 ACTTGTTACGTTAAATCTCACATGTTTACGTTAATATTTTGATAATTTTTGTTCCACC
*
556093 TTGATAATTTTTTACATTAATGTTTACAATTTTATGTCAAGGTTTTTCAACTATTATTTTTCACT
1 TT-ATAATTTTTTACATTAAT-TTTACAACTTTATGTCAAGGTTTTTCAACTATTATTTTTCACT
* * *
556158 AT-ATTTTTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCATAAAATACTTT
64 ATAATTATTTTTATCCTTATTATTATTCATTTATAAATTAAAATTTGTAAACCATAAAATACTTT
* ** * * * *
556222 AAACTCAAGTATATAAATTTAAATGGTTAATTTTTTAAAATATTATGTTTAGTTGACT-TAATAG
129 AAACTCAA-AATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGA-TATAATTG
* * * * * * * * ** *
556286 ACTTGTTAGGTTAAATCGCATATATTTATGTTCACATTTTGACAATACTTGTTCCACAT
192 ACTTGTTACGTTAAATCTCACATGTTTACGTTAATATTTTGATAATTTTTGTTCCAC-C
* * ** * * * ** * ** * *
556345 TTATAA-TTTTTACGTTGATCCTACATCTATACGTCAATATTTTTC-AGTCACAAATTCTCACTA
1 TTATAATTTTTTACATTAATTTTACAACTTTATGTCAAGGTTTTTCAACT-ATTATTTTTCACTA
* * ** ** * *
556408 TAATTATTTTTATCCTTATTATAATTCTTTTATAAATTAAAATTTAAAAATTATTAAATAATTTA
65 TAATTATTTTTATCCTTATTATTATTCATTTATAAATTAAAATTTGTAAACCATAAAATACTTTA
* *
556473 AACTCAAAATATAAATTTAAATGTTTAATTTTTTAAAAATTTATATTTATTTGATATAATTGACT
130 AACTCAAAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGATATAATTGACT
* * * * ** *
556538 TATTACATTAAATCTCATACGTTTACGTTAATATTTTG-GCATTTCTTGTTTCACC
195 TGTTACGTTAAATCTCACATGTTTACGTTAATATTTTGATAATTT-TTGTTCCACC
* * * * *
556593 TTATTAATTTCTTATATTAATTTTTACAGCTTTATGTCAAGGTATTTC-ACT-TGCTATTTTTTA
1 TTA-TAATTTTTTACATTAA-TTTTACAACTTTATGTCAAGGTTTTTCAACTAT--TATTTTTCA
* * *
556656 CTATAATTATTTTTATCTTTATTATTATTCATTTATAAATCAAAATTTTTAAA
62 CTATAATTATTTTTATCCTTATTATTATTCATTTATAAATTAAAATTTGTAAA
556709 ATTGCTTATT
Statistics
Matches: 709, Mismatches: 143, Indels: 36
0.80 0.16 0.04
Matches are distributed among these distances:
248 8 0.01
249 118 0.17
250 80 0.11
251 230 0.32
252 164 0.23
253 4 0.01
254 1 0.00
255 5 0.01
256 97 0.14
257 2 0.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.48
Consensus pattern (249 bp):
TTATAATTTTTTACATTAATTTTACAACTTTATGTCAAGGTTTTTCAACTATTATTTTTCACTAT
AATTATTTTTATCCTTATTATTATTCATTTATAAATTAAAATTTGTAAACCATAAAATACTTTAA
ACTCAAAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGATATAATTGACTT
GTTACGTTAAATCTCACATGTTTACGTTAATATTTTGATAATTTTTGTTCCACC
Found at i:557627 original size:15 final size:15
Alignment explanation
Indices: 557602--557637 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
557592 GATAAAAAAT
557602 AAAAATAATTATATTG
1 AAAAATAATTA-ATTG
557618 AAAAAT-ATTAATTG
1 AAAAATAATTAATTG
557632 AAAAAT
1 AAAAAT
557638 CTTAACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 4 0.20
16 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAAATAATTAATTG
Found at i:557633 original size:14 final size:14
Alignment explanation
Indices: 557602--557642 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
557592 GATAAAAAAT
557602 AAAAATAATTATATTG
1 AAAAAT-ATTA-ATTG
557618 AAAAATATTAATTG
1 AAAAATATTAATTG
*
557632 AAAAATCTTAA
1 AAAAATATTAA
557643 CACAAAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.58
15 4 0.17
16 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (14 bp):
AAAAATATTAATTG
Found at i:558752 original size:505 final size:498
Alignment explanation
Indices: 557343--558977 Score: 1388
Period size: 505 Copynumber: 3.2 Consensus size: 498
557333 TATTTTATCC
* * * * * * *
557343 TAAAAATAATTAT-AGTGAAAAATAGCAATTGAAAAACATTAACATAAAACTATAAGAGTAAATG
1 TAAAAATAATTATCA-TGAAAATTAGTAGTTGAAAAACTTTAACGTAAAACTATAAGAATTAAT-
** * * * * * **
557407 TTAAAAAT--TAAGAAGATGGAACAAGTATTATGAGAATATT-AATGTAAACGTGTGAGATTTAA
64 AAAAAAATAATAA-AAG-TGGAACAA-AATTGTCAAAATATTGAA-ATAAATATGTGAGATTTAA
*
557469 AGTAACAAGTCAATTAAGTCAACTAAACATAATTTTTGAAAACTTAAACATTTAAATTTATATTC
125 A-TAACAAGTCAATTAAGTCAACTAAACATAATTTTTGAAAAATTAAACATTTAAATTTATATTC
* * * *
557534 TCAAGTTTAAAGTAT-TTAATAGTTTACAAATTTTAATTTATAAAAGAATAATAGCAAGGATAAA
189 TCGAGTTTAAAGTATCATAA-ATTTTACAAATTTTAATTTATAAATGAATAAT----A--AT-AA
* * * * *
557598 AAATAAAAATAATTATATTGAAAAATATTAATTGAAAAATCTTAACACAAAACTGTAAGAATTAA
246 GAACAAAAATAATTATAGTGAAAAATAATAATTGAAAAATATTAACACAAAACTGTAAGAATTAA
* * * * * * * * * *
557663 TGTAAAAAAGTATAAAAGTTGAATAAACACTATAAAAATATTGACATAAATATGTAAGATTTAAC
311 TGTAAAAAATTATAAAAGTAGAATAAGCATTGTCAAAATATTAACGTTAATATGTGAGATTTAAC
* * *
557728 GTAACAAATGAATTATGTCAAATAAACATAATTTTTTAAAAAGTTAAGCATTTAAATTTATATTC
376 GTAACAAATCAATTAAGTCAAATAAACATAATTTTTTAAAAATTTAA-CATTT-AATTTATATTC
** * * **
557793 TTGAGTTTAAAATATATAACGGTTTATAAATTTTAATTTATAAAAGAATAATAGTAAGGT
439 TCAAGTTTAAAATATATAACGATTTATAAATTTTAATATATAAAAGAATAATAGTAAGAA
* * *
557853 TAAGAATAATTATCATGAAAATTAGTAGTTGAAAAACTTTAACGTAAACCTGTAAGAATTAATAA
1 TAAAAATAATTATCATGAAAATTAGTAGTTGAAAAACTTTAACGTAAAACTATAAGAATTAATAA
* * * *
557918 AAAAATTATAAAAGTGGAACAAAATTGTGAAAATATTGATATAAATATGTGAGATTTAATATAAT
66 AAAAATAATAAAAGTGGAACAAAATTGTCAAAATATTGAAATAAATATGTGAGATTTAA-ATAAC
* * *
557983 AAATCAATTACGTCAACTAAACATAACTTTTTGAAAAATTAAACATTAAAATTTATACTT-TCGA
130 AAGTCAATTAAGTCAACTAAACATAA-TTTTTGAAAAATTAAACATTTAAATTTATA-TTCTCGA
* * *
558047 GTTTAAAGCAT--TTAATGGTTTACAAATTTTAA--T-T---T--ATAA-AATAAGGACAAAAAT
193 GTTTAAAGTATCATAAAT--TTTACAAATTTTAATTTATAAATGAATAATAATAAGAACAAAAAT
* * * ** * * * * *
558101 AATGATGGTGACACTTAGTAATTAAAAAATATTAACATAAACCTGTAAGAATTAATATAAAAAAT
256 AATTATAGTGAAAAATAATAATTGAAAAATATTAACACAAAACTGTAAGAATTAATGTAAAAAAT
* * * * *
558166 TATAAAGGTAGAATAAGCATTGTCAAAATATTAATG-TAGATGTGTGAGATTTAACGTAATAAGT
321 TATAAAAGTAGAATAAGCATTGTCAAAATATTAACGTTA-ATATGTGAGATTTAACGTAACAAAT
* * *
558230 CAATTATA-CCAAATAAACATAATTGTTTGAAAATTTAACATTTAATTTTATATTCTCAAGTTTA
385 CAATTA-AGTCAAATAAACATAATTTTTTAAAAATTTAACATTTAA-TTTATATTCTCAAGTTTA
* * *
558294 AAGCAT-TAT-ACGATTTATGAATTTTAATATATAAATGAATAATAGTGAGAA
448 AA--ATATATAACGATTTATAAATTTTAATATATAAAAGAATAATAGTAAGAA
** * * *
558345 TAAAAATAATTATGGTGAAAATTATTAGTT-AAAAGA-TCTTGATGTAAAACTATAAGAATTAAC
1 TAAAAATAATTATCATGAAAATTAGTAGTTGAAAA-ACT-TTAACGTAAAACTATAAGAATTAA-
* * ** ** *
558408 TTAGAAAATAATAATGGTGGAACATGCATTGTCAAAATATTGAAATAAATGT-TGGAAGATTTAA
63 TAAAAAAATAATAAAAGTGGAACA-AAATTGTCAAAATATTGAAATAAATATGT-G-AGATTTAA
** * * * *
558472 CATAACAAGTCAATTATTTGAAATAAATATAATTTTTTTAAAAATTAAACATTTAAATTTATATT
125 -ATAACAAGTCAATTAAGTCAACTAAACATAA-TTTTTGAAAAATTAAACATTTAAATTTATATT
* *
558537 CTCGAGTTTAAAGTATCATACAATTTTGCAACTTTTAATTTATAAATGAATAATAATAAGAACAA
188 CTCGAGTTTAAAGTATCATA-AATTTTACAAATTTTAATTTATAAATGAATAATAATAAGAACAA
* * * * *
558602 AAATAATTATAGTGAAAAATAATAGTTGAAAAACT-TTGACGCAAAACTATAAGAATTAAGGTAA
252 AAATAATTATAGTGAAAAATAATAATTGAAAAA-TATTAACACAAAACTGTAAGAATTAATGTAA
* * * * **
558666 AAAATTATAAAAGTGGAACAAGCATTGTCATAATATTAACGTTAATATATGAGATTTAGTGTAAC
316 AAAATTATAAAAGTAGAATAAGCATTGTCAAAATATTAACGTTAATATGTGAGATTTAACGTAAC
* ** *
558731 AAATTAATTAAGTCAAATAAACATAATTTTTTTTAAATTAAACATTTGAATTTATATTCTCAAGT
381 AAATCAATTAAGTCAAATAAACATAATTTTTTAAAAATTTAACATTT-AATTTATATTCTCAAGT
* * * * * * *
558796 TTGGATTAAGTATTTAATGGTTTACAAATTTTAATTTATAAATA-AATAATAGTAAAAGA
445 TT--A--AAATATATAACGATTTATAAATTTTAATATATAAA-AGAATAATAGTAAGA-A
* * * * * * *
558855 TAAAAACAATTAT-AGTGAAAAATAGCA-TTAGAAAATC-TTAATG-CAAACTTGTAAGAATTAA
1 TAAAAATAATTATCA-TGAAAATTAGTAGTT-GAAAAACTTTAACGTAAAAC-TATAAGAATTAA
* * * * ** *
558916 TATAAAAAATTAT-AAAGATTGAAAAAACATTTTCAAAATATTGACGTAAATGTGTGAGATTT
63 TA-AAAAAATAATAAAAG-TGGAACAAA-ATTGTCAAAATATTGAAATAAATATGTGAGATTT
558978 GATGTAATAG
Statistics
Matches: 900, Mismatches: 171, Indels: 110
0.76 0.14 0.09
Matches are distributed among these distances:
491 7 0.01
492 106 0.12
493 163 0.18
494 29 0.03
495 74 0.08
496 13 0.01
497 1 0.00
498 4 0.00
499 1 0.00
501 4 0.00
502 1 0.00
504 5 0.01
505 164 0.18
506 6 0.01
507 4 0.00
508 72 0.08
509 159 0.18
510 79 0.09
511 8 0.01
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34
Consensus pattern (498 bp):
TAAAAATAATTATCATGAAAATTAGTAGTTGAAAAACTTTAACGTAAAACTATAAGAATTAATAA
AAAAATAATAAAAGTGGAACAAAATTGTCAAAATATTGAAATAAATATGTGAGATTTAAATAACA
AGTCAATTAAGTCAACTAAACATAATTTTTGAAAAATTAAACATTTAAATTTATATTCTCGAGTT
TAAAGTATCATAAATTTTACAAATTTTAATTTATAAATGAATAATAATAAGAACAAAAATAATTA
TAGTGAAAAATAATAATTGAAAAATATTAACACAAAACTGTAAGAATTAATGTAAAAAATTATAA
AAGTAGAATAAGCATTGTCAAAATATTAACGTTAATATGTGAGATTTAACGTAACAAATCAATTA
AGTCAAATAAACATAATTTTTTAAAAATTTAACATTTAATTTATATTCTCAAGTTTAAAATATAT
AACGATTTATAAATTTTAATATATAAAAGAATAATAGTAAGAA
Found at i:558813 original size:751 final size:748
Alignment explanation
Indices: 557441--558837 Score: 1714
Period size: 751 Copynumber: 1.9 Consensus size: 748
557431 GTATTATGAG
* *
557441 AATATTAATGTAAACGTGTGAGATTTAAAGTAACAAGTCAATTAAGTCAACTAAACATAATTTTT
1 AATATTAATGTAAACGTGTGAGATTTAAAGTAACAAGTCAATTAAGCCAAATAAACATAATTTTT
*
557506 GAAAACTTAAACATTTAAATTTATATTCTCAAGTTTAAAGTATTTAATAGTTTACAAATTTTAAT
66 GAAAACTTAAACATTTAAATTTATATTCTCAAGTTTAAAGCATTTAATAGTTTACAAATTTTAAT
* *
557571 TTATAAAAGAATAATAGCAAGGATAAAAAATAAAAATAATTATATTGAAAAATATTAATTGAAAA
131 ATATAAAAGAATAAT---AAGGATAAAAAATAAAAATAATTATAGTGAAAAATATTAATTGAAAA
* * *
557636 ATCTTAACACAAAACTGTAAGAATTAATGTAAAAAAGTATAAAAGTTGAATAAACACTATAAAAA
193 ATCTTAACACAAAACTATAAGAATTAATGTAAAAAAGTATAAAAGTGGAACAAACACTATAAAAA
* * * *
557701 TATTGACATAAATATGTAAGATTTAACGTAACAAATGAATTATGTCAAATAAACATAATTTTTTA
258 TATTGAAATAAATATGGAAGATTTAACATAACAAATCAATTATGTCAAATAAACATAATTTTTTA
* * **
557766 AAAAGTTAAGCATTTAAATTTATATTCTTGAGTTTAAAATATATAACGGTTTATAAATTTTAATT
323 AAAAGTTAAACATTTAAATTTATATTCTCGAGTTTAAAATATATAACAATTTATAAATTTTAATT
* *** * * *
557831 TATAAAAGAATAATAGTAAGGTTAAGAATAATTATCATGAAAATTAGTAGTTGAAAAACTTTAAC
388 TATAAAAGAATAATAATAAGAACAAAAATAATTATCATGAAAAATAATAGTTGAAAAACTTTAAC
* * * * * *
557896 GTAAACCTGTAAGAATTAATAAAAAAATTATAAAAGTGGAACAAAATTGTGAAAATATTGATATA
453 GCAAAACTATAAGAATTAATAAAAAAATTATAAAAGTGGAACAAAATTGTCAAAATATTAACATA
* * * *
557961 AATATGTGAGATTTAATATAATAAATCAATTACGTCAACTAAACATAACTTTTTGAAAAATTAAA
518 AATATATGAGATTTAATATAACAAATCAATTAAGTCAAATAAACATAACTTTTTGAAAAATTAAA
*
558026 CATTAAAATTTATACTTTCGAGTTTAAAGCATTTAATGGTTTACAAATTTTAATTTATAAAATAA
583 CATTAAAATTTATACTTTCAAGTTTAAAGCATTTAATGGTTTACAAATTTTAATTTATAAAATAA
558091 GGACAAAAATAATGATGGTGACACTTAGTAATTAAAAAATATTAACATAAACCTGTAAGAATTAA
648 GGACAAAAATAATGATGGTGACACTTAGTAATTAAAAAATATTAACATAAACCTGTAAGAATTAA
558156 TATAAAAAATTATAAAGGTAGAATAAGCATTGTCAA
713 TATAAAAAATTATAAAGGTAGAATAAGCATTGTCAA
* * * *
558192 AATATTAATGTAGATGTGTGAGATTTAACGTAATAAGTCAATTATA-CCAAATAAACATAATTGT
1 AATATTAATGTAAACGTGTGAGATTTAAAGTAACAAGTCAATTA-AGCCAAATAAACATAATT-T
* * **
558256 TTGAAAA-TTTAACATTTAATTTTATATTCTCAAGTTTAAAGCA-TT-ATACGATTTATGAATTT
64 TTGAAAACTTAAACATTTAAATTTATATTCTCAAGTTTAAAGCATTTAATA-G-TTTACAAATTT
* * * * * *
558318 TAATATATAAATGAATAAT-A-G-T-GAGAATAAAAATAATTATGGTGAAAATTATTAGTT-AAA
127 TAATATATAAAAGAATAATAAGGATAAAAAATAAAAATAATTATAGTGAAAAATATTAATTGAAA
* *** * ** ** * * *
558378 AGATCTTGATGTAAAACTATAAGAATTAACT-TAGAAAA-TAATAATGGTGGAACATGCATTGTC
192 A-ATCTTAACACAAAACTATAAGAATTAA-TGTAAAAAAGT-ATAAAAGTGGAACAAACACTATA
* * * * *
558441 AAAATATTGAAATAAATGTTGGAAGATTTAACATAACAAGTCAATTATTTGAAATAAATATAATT
254 AAAATATTGAAATAAAT-ATGGAAGATTTAACATAACAAATCAATTATGTCAAATAAACATAA-T
*
558506 TTTTTAAAAA-TTAAACATTTAAATTTATATTCTCGAGTTTAAAGTATCAT-ACAATTT-TGCAA
317 TTTTTAAAAAGTTAAACATTTAAATTTATATTCTCGAGTTTAAAATAT-ATAACAATTTAT--AA
* *
558568 CTTTTAATTTATAAATGAATAATAATAAGAACAAAAATAATTAT-AGTGAAAAATAATAGTTGAA
379 ATTTTAATTTATAAAAGAATAATAATAAGAACAAAAATAATTATCA-TGAAAAATAATAGTTGAA
* *
558632 AAACTTTGACGCAAAACTATAAGAATTAAGGT-AAAAAATTATAAAAGTGGAACAAGCATTGTCA
443 AAACTTTAACGCAAAACTATAAGAATTAA--TAAAAAAATTATAAAAGTGGAACAA-AATTGTCA
* * * * * *
558696 TAATATTAACGTTAATATATGAGATTTAGTGTAACAAATTAATTAAGTCAAATAAACATAA-TTT
505 AAATATTAACATAAATATATGAGATTTAATATAACAAATCAATTAAGTCAAATAAACATAACTTT
*** ** *
558760 TTTTTAAATTAAACATTTGAATTTATA-TTCTCAAGTTTGGATTAAGTATTTAATGGTTTACAAA
570 TTGAAAAATTAAACATTAAAATTTATACTT-TCAAGTTT--A--AAGCATTTAATGGTTTACAAA
558824 TTTTAATTTATAAA
630 TTTTAATTTATAAA
558838 TAAATAATAG
Statistics
Matches: 543, Mismatches: 82, Indels: 42
0.81 0.12 0.06
Matches are distributed among these distances:
743 5 0.01
744 88 0.16
745 79 0.15
746 96 0.18
747 56 0.10
748 56 0.10
749 4 0.01
750 3 0.01
751 147 0.27
752 9 0.02
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (748 bp):
AATATTAATGTAAACGTGTGAGATTTAAAGTAACAAGTCAATTAAGCCAAATAAACATAATTTTT
GAAAACTTAAACATTTAAATTTATATTCTCAAGTTTAAAGCATTTAATAGTTTACAAATTTTAAT
ATATAAAAGAATAATAAGGATAAAAAATAAAAATAATTATAGTGAAAAATATTAATTGAAAAATC
TTAACACAAAACTATAAGAATTAATGTAAAAAAGTATAAAAGTGGAACAAACACTATAAAAATAT
TGAAATAAATATGGAAGATTTAACATAACAAATCAATTATGTCAAATAAACATAATTTTTTAAAA
AGTTAAACATTTAAATTTATATTCTCGAGTTTAAAATATATAACAATTTATAAATTTTAATTTAT
AAAAGAATAATAATAAGAACAAAAATAATTATCATGAAAAATAATAGTTGAAAAACTTTAACGCA
AAACTATAAGAATTAATAAAAAAATTATAAAAGTGGAACAAAATTGTCAAAATATTAACATAAAT
ATATGAGATTTAATATAACAAATCAATTAAGTCAAATAAACATAACTTTTTGAAAAATTAAACAT
TAAAATTTATACTTTCAAGTTTAAAGCATTTAATGGTTTACAAATTTTAATTTATAAAATAAGGA
CAAAAATAATGATGGTGACACTTAGTAATTAAAAAATATTAACATAAACCTGTAAGAATTAATAT
AAAAAATTATAAAGGTAGAATAAGCATTGTCAA
Found at i:559902 original size:15 final size:15
Alignment explanation
Indices: 559884--559925 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
559874 TCAATCAATA
559884 ATTTTTATTATAATT
1 ATTTTTATTATAATT
* *
559899 ATTTTTATTTTTATT
1 ATTTTTATTATAATT
*
559914 ATTCTT-TTATAA
1 ATTTTTATTATAA
559926 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTATTATAATT
Found at i:560431 original size:255 final size:251
Alignment explanation
Indices: 559892--561418 Score: 830
Period size: 255 Copynumber: 6.1 Consensus size: 251
559882 TAATTTTTAT
** *
559892 TATAATTATTTTTATTTTTATTA-TTCT-TTTATAAATTAAAATTTAGAAACCATT-AA-A-TAT
1 TATAATTATTTTTATCCTTATTATTTCTATTTATAAATTAAAATTT-GAAACCGTTAAATACTAT
*
559952 TTTAAACTTGAGAATATAAATTTAAATGTTTAATTTTTTAAAAAATTATATTTATTTGACTTATT
65 TTTAAACTTGAGAATATAAATTTAAATGTTTAA-TTTTTAAAAAATTATATTTATTTGACTTAAT
* * * * * * *
560017 TGATTTGTTATATTTAATCTCATACATTTACGTTAATATTCTGACAATACTTGTTCTACTTTTAT
129 TAAGTTGTTACATTAAATCTCA-ACATTTACATTAATATTCTGACAATACTTATTCCACTTTTAT
* * * * * *
560082 AATTTTTTATATTAATTCTTATAACTTTAAGTTAAGGTTTTTCAATTACTATTTTTCAC
193 AATTTTTTACATTAATTCATACAACTTTAAGTTAAAGTTTTTCAACTACTATCTTTCAC
* *
560141 TATAATTATTTTTATCCTTACTATTATTTATTTATAAATTAAAATTTGTAAACCGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATT-TCTATTTATAAATTAAAATTTG-AAACCGTTAAATAC-T
**
560206 ATTTTAAACTCAAGAATATAAATTTAAATGTTTAATTTTCTAAAAAATTATATTTATTTGACTTA
63 ATTTTAAACTTGAGAATATAAATTTAAATGTTTAATTTT-TAAAAAATTATATTTATTTGACTTA
* *
560271 ATTAAGTTGTTGCATTAAATCTC-ACATGTTACATTAATATTTTGACAATACTTATTCCACTTTT
127 ATTAAGTTGTTACATTAAATCTCAACAT-TTACATTAATATTCTGACAATACTTATTCCACTTTT
* * * *
560335 ATAATTTTTTACGTTAATTCATACAATTTTATA-TTAAAGTTTTTTAACTATTGA-CTTTCAC
191 ATAATTTTTTACATTAATTCATACAACTTTA-AGTTAAAGTTTTTCAACTACT-ATCTTTCAC
* * *
560396 TATAATTATTTTTATCCCTATTATTTCTCATTTAT--A--AAAATTTAAAAACTGTTAAATAC--
1 TATAATTATTTTTATCCTTATTATTTCT-ATTTATAAATTAAAATTT-GAAACCGTTAAATACTA
* *
560455 -GTCAAACTTGAGAATATAAATTTAAATGTTTAATTTTTAAAAAAATTATATTTATTTGA-TATA
64 TTTTAAACTTGAGAATATAAATTTAAATGTTTAATTTTT-AAAAAATTATATTTATTTGACT-TA
** * * * ** * **
560518 ATTAACCTATTACGTTAAATCTCACACCTTTATGTTAATATTTTGATATTTCTCGTCCCACCTTA
127 ATTAAGTTGTTACATTAAATCTCA-ACATTTACATTAATATTCTG--A---C-AAT---A-CTTA
* * * * *
560583 TT-AATTTTTACGTTAATTCTTATAGTTTTATATTAATTC-TAACAACTTTATA-TCAAAATTTT
181 TTCCACTTTTA---TAA----T-T--TTTTACATTAATTCAT-ACAACTTTA-AGTTAAAGTTTT
* *
560645 TCAATTGCTAT-TTTCAC
234 TCAACTACTATCTTTCAC
* * * * *
560662 TATAATTATTTTTATTC-TATTATTAT-TGTTTATAAATT----TAT-AAA--TTTTAA-A-TAT
1 TATAATTATTTTTATCCTTATTATT-TCTATTTATAAATTAAAATTTGAAACCGTTAAATACTAT
* * * * * * *
560716 GTTAAACTCGAGAATA-ATATTTAAAT-TTTAATTGTTCAAAAAAGAATTATCTCT-TTTGATTT
65 TTTAAACTTGAGAATATAAATTTAAATGTTTAATT-TT--TAAAA-AATTATATTTATTTGACTT
* * * * * * * * *
560778 AA-TGACTTATTTA-ATTAAATC-CACACGTTTACATTGATATT-T-ATAATATTTTTTTCACTT
126 AATTAAGTT-GTTACATTAAATCTCA-ACATTTACATTAATATTCTGACAATACTTATTCCACTT
* ** * *
560838 TT-TAATTTTTT--ATAAATTGTTACAA-TTTACA-TGAAAGTTTTTCAACTA--A-ATTTCAC
189 TTATAATTTTTTACATTAATTCATACAACTTTA-AGTTAAAGTTTTTCAACTACTATCTTTCAC
* * * * * *
560894 TATATTTATTTTATAT--TTTTTATTATTTATTTAAAAATAAAAATTTGAAAAC-TTAAATAC--
1 TATAATTATTTT-TATCCTTATTATT-TCTATTTATAAATTAAAATTTGAAACCGTTAAATACTA
** * * * *
560954 --TTAAACTCAATAATATAAATTTAAA--TATAATTTTTTAAAAATTATATTTATTTGACGTAAT
64 TTTTAAACTTGAGAATATAAATTTAAATGTTTAATTTTTAAAAAATTATATTTATTTGACTTAAT
* * * ** * * * *
561015 TAACTTGTTAC-GTAAATCTTATATGTTTA-GTTAATATT-TTACAATTCTTGTGTCC-CTTTTA
129 TAAGTTGTTACATTAAATCTCA-ACATTTACATTAATATTCTGACAATACTTAT-TCCACTTTTA
* * * *
561076 TAATTTATATA-ATTAATTC-T-CACACTTTACG-TCAAG-CTTTCAACTACTAAT-TTTCAC
192 TAATTT-TTTACATTAATTCATACA-ACTTTAAGTTAAAGTTTTTCAACTACT-ATCTTTCAC
* * **
561133 TATAATGATTTTTACCCTTATTATTATTCT-TTTATAAATTAAAATTTGTAAACTATTAAATAC-
1 TATAATTATTTTTATCCTTATTA-T-TTCTATTTATAAATTAAAATTTG-AAACCGTTAAATACT
* *
561196 --TTTAAACTTGAAAATATAAATTTAAATATTTAATTTTTTTAAAAAA-TATATTTATTTGACTT
63 ATTTTAAACTTGAGAATATAAATTTAAATGTTTAA--TTTTTAAAAAATTATATTTATTTGACTT
* * * * * * * ** * *
561258 AATTAATTTTTTTACCTTAAATCTCACACGTTTACCTTAATATTCTAACAGTGTTTGTTCCACAT
126 AATTAA-GTTGTTACATTAAATCTCA-ACATTTACATTAATATTCTGACAATACTTATTCCACTT
** ** * * * * *
561323 TTATAA--TTTTATGTTAATTTTTAC-AGTTTTACTTAAAGTTTTTAAACTACTATTTTTCAC
189 TTATAATTTTTTACATTAATTCATACAACTTTAAGTTAAAGTTTTTCAACTACTATCTTTCAC
* *
561383 TATAA-TAGTTTTATCCTTACTATTAT-TATTTATAAA
1 TATAATTATTTTTATCCTTATTATT-TCTATTTATAAA
561419 CCATTAAATA
Statistics
Matches: 1000, Mismatches: 168, Indels: 221
0.72 0.12 0.16
Matches are distributed among these distances:
232 26 0.03
233 20 0.02
234 46 0.05
235 34 0.03
236 22 0.02
237 32 0.03
238 23 0.02
239 22 0.02
240 23 0.02
241 6 0.01
242 9 0.01
243 22 0.02
244 3 0.00
245 4 0.00
246 23 0.02
247 98 0.10
248 55 0.05
249 54 0.05
250 41 0.04
251 24 0.02
252 24 0.02
253 4 0.00
254 8 0.01
255 113 0.11
256 78 0.08
257 7 0.01
258 7 0.01
259 24 0.02
260 29 0.03
261 29 0.03
262 12 0.01
264 8 0.01
265 9 0.01
266 26 0.03
267 35 0.04
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (251 bp):
TATAATTATTTTTATCCTTATTATTTCTATTTATAAATTAAAATTTGAAACCGTTAAATACTATT
TTAAACTTGAGAATATAAATTTAAATGTTTAATTTTTAAAAAATTATATTTATTTGACTTAATTA
AGTTGTTACATTAAATCTCAACATTTACATTAATATTCTGACAATACTTATTCCACTTTTATAAT
TTTTTACATTAATTCATACAACTTTAAGTTAAAGTTTTTCAACTACTATCTTTCAC
Found at i:560593 original size:247 final size:249
Alignment explanation
Indices: 559910--561417 Score: 751
Period size: 247 Copynumber: 6.1 Consensus size: 249
559900 TTTTTATTTT
* * * * *
559910 TATTATTCTTTTATAAATTAAAATTTAGAAACCATTAAATA-TTTTAAACTTGAGAATATAAATT
1 TATTATTCATTTAT-AA-TAAAATTTAAAAACCGTTAAATACTGTCAAACTTGAGAATATAAATT
* * * * *
559974 TAAATGTTTAATTTTTTAAAAAATTATATTTATTTGACTTATTTGATTTGTTATATTTAATCTCA
64 TAAATGTTTAA-TTTTTAAAAAATTATATTTATTTGACTTAATTAACTTGTTACATTAAATCTCA
* * * **
560039 TACATTTACGTTAATATTCTGACAATACTTGTTCTACTTTTATAATTTTTTATATTAATTCTTAT
128 CAC-TTTACGTTAATATTTTGACAATACTTGTTCCACTTTTATAATTTTTTACGTTAATTCTTAT
* * * * *
560104 AACTTTA-AGTTAAGGTTTTTCAATTACTATTTTTCACTATAATTATTTTTATCCTTAC
192 AATTTTATA-TTAAAGTTTTTCAACTACTATCTTTCACTATAATTATTTTTATCCCTAC
* ** * * **
560162 TATTATTTATTTATAAATTAAAATTTGTAAACCGTTAAATACTTATTTTAAACTCAAGAATATAA
1 TATTATTCATTTAT-AA-TAAAATTTAAAAACCGTTAAATAC---TGTCAAACTTGAGAATATAA
* *
560227 ATTTAAATGTTTAATTTTCTAAAAAATTATATTTATTTGACTTAATTAAGTTGTTGCATTAAATC
61 ATTTAAATGTTTAATTTT-TAAAAAATTATATTTATTTGACTTAATTAACTTGTTACATTAAATC
* * *
560292 TCACA-TGTTACATTAATATTTTGACAATACTTATTCCACTTTTATAATTTTTTACGTTAATTCA
125 TCACACT-TTACGTTAATATTTTGACAATACTTGTTCCACTTTTATAATTTTTTACGTTAATTCT
* * * *
560356 TACAATTTTATATTAAAGTTTTTTAACTATTGA-CTTTCACTATAATTATTTTTATCCCTAT
189 TATAATTTTATATTAAAGTTTTTCAACTACT-ATCTTTCACTATAATTATTTTTATCCCTAC
*
560417 TATT-TCTCATTTAT-A-AAAATTTAAAAACTGTTAAATAC-GTCAAACTTGAGAATATAAATTT
1 TATTAT-TCATTTATAATAAAATTTAAAAACCGTTAAATACTGTCAAACTTGAGAATATAAATTT
* * *
560478 AAATGTTTAATTTTTAAAAAAATTATATTTATTTGA-TATAATTAACCTATTACGTTAAATCTCA
65 AAATGTTTAATTTTT-AAAAAATTATATTTATTTGACT-TAATTAACTTGTTACATTAAATCTCA
* * * * * * *
560542 CACCTTTATGTTAATATTTTGATATTTCTCGTCCCAC-CTTATTAA-TTTTTACGTTAATTCTTA
128 CA-CTTTACGTTAATATTTTGACAATACTTGTTCCACTTTTA-TAATTTTTTACGTTAATTCTTA
* * * * * * ** ** * *
560605 TAGTTTTATATT-AA--TTCT-AACAACTTTATATCAAAATTTTTCAATTGCTATTTTCACTA-
191 TAATTTTATATTAAAGTTTTTCAACTACTATCTTTCACTATAATT--ATT--T-TTATCCCTAC
* * *** * * * *
560664 TAATTATTTTTATTCTATTATTATTGTTTATAAA--TTTATAA-A-TTTTAAA-TATGTTA-AAC
1 T-ATTA--TTCATT-TA-TAATAAAATTTAAAAACCGTTA-AATACTGTCAAACT-TG--AGAA-
* * ** * * * * * *
560723 TCGAGAATAATATTTAAATTTTAATTGTTCAAAAAAGAATTATCTCT-TTTGATTTAA-TGACTT
56 T--A-TA-AAT-TTAAATGTTTAATTTTTAAAAA----ATTATATTTATTTGACTTAATTAACTT
* * * * * * *
560786 ATTTA-ATTAAATC-CACACGTTTACATTGATA-TTT-ATAATATTTTTTTCACTTTT-TAATTT
112 -GTTACATTAAATCTCACAC-TTTACGTTAATATTTTGACAATACTTGTTCCACTTTTATAATTT
* * * * * * *
560846 TTTA--TAAATTGTTACAA-TTTACATGAAAGTTTTTCAACTA--A-ATTTCACTATATTTATTT
175 TTTACGTTAATTCTTATAATTTTATATTAAAGTTTTTCAACTACTATCTTTCACTATAATTATTT
* **
560905 TATAT--TTTT
240 T-TATCCCTAC
* * * ** *
560914 TATTATTTATTTAAAAATAAAAATTTGAAAA-C-TTAAATACT-T-AAACTCAATAATATAAATT
1 TATTATTCATTT-ATAAT-AAAATTTAAAAACCGTTAAATACTGTCAAACTTGAGAATATAAATT
* * * * * *
560975 TAAA--TATAATTTTTTAAAAATTATATTTATTTGACGTAATTAACTTGTTAC-GTAAATCTTAT
64 TAAATGTTTAATTTTTAAAAAATTATATTTATTTGACTTAATTAACTTGTTACATTAAATCTCAC
* * * * *
561037 ATGTTTA-GTTAATATTTT-ACAATTCTTGTGTCC-CTTTTATAATTTATATA-ATTAATTCTCA
129 A-CTTTACGTTAATATTTTGACAATACTTGT-TCCACTTTTATAATTT-TTTACGTTAATTCTTA
* * ** * * * *
561098 -CACTTTA-CGTCAAG-CTTTCAACTACTAAT-TTTCACTATAATGATTTTTA-CCCTTAT
191 TAATTTTATATTAAAGTTTTTCAACTACT-ATCTTTCACTATAATTATTTTTATCCC-TAC
* ** ** * *
561154 TATTATTCTTTTATAAATTAAAATTTGTAAACTATTAAATACT-TTAAACTTGAAAATATAAATT
1 TATTATTCATTTAT-AA-TAAAATTTAAAAACCGTTAAATACTGTCAAACTTGAGAATATAAATT
* * * *
561218 TAAATATTTAATTTTTTTAAAAAA-TATATTTATTTGACTTAATTAATTTTTTTACCTTAAATCT
64 TAAATGTTTAA--TTTTTAAAAAATTATATTTATTTGACTTAATTAA-CTTGTTACATTAAATCT
* * * * ** * * *
561282 CACACGTTTACCTTAATATTCTAACAGTGTTTGTTCCACATTTATAA--TTTTATGTTAATTTTT
126 CACAC-TTTACGTTAATATTTTGACAATACTTGTTCCACTTTTATAATTTTTTACGTTAATTCTT
* * * * * * *
561345 ACAGTTTTA-CTTAAAGTTTTTAAACTACTATTTTTCACTATAA-TAGTTTTATCCTTAC
190 ATAATTTTATATTAAAGTTTTTCAACTACTATCTTTCACTATAATTATTTTTATCCCTAC
561403 TATTATT-ATTTATAA
1 TATTATTCATTTATAA
561418 ACCATTAAAT
Statistics
Matches: 958, Mismatches: 199, Indels: 203
0.70 0.15 0.15
Matches are distributed among these distances:
233 7 0.01
234 22 0.02
235 26 0.03
236 17 0.02
237 19 0.02
238 13 0.01
239 22 0.02
240 28 0.03
241 2 0.00
242 11 0.01
243 33 0.03
244 5 0.01
245 9 0.01
246 33 0.03
247 149 0.16
248 65 0.07
249 44 0.05
250 45 0.05
251 27 0.03
252 47 0.05
253 8 0.01
254 18 0.02
255 134 0.14
256 82 0.09
257 19 0.02
258 17 0.02
259 26 0.03
260 11 0.01
261 11 0.01
262 8 0.01
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (249 bp):
TATTATTCATTTATAATAAAATTTAAAAACCGTTAAATACTGTCAAACTTGAGAATATAAATTTA
AATGTTTAATTTTTAAAAAATTATATTTATTTGACTTAATTAACTTGTTACATTAAATCTCACAC
TTTACGTTAATATTTTGACAATACTTGTTCCACTTTTATAATTTTTTACGTTAATTCTTATAATT
TTATATTAAAGTTTTTCAACTACTATCTTTCACTATAATTATTTTTATCCCTAC
Found at i:560686 original size:17 final size:18
Alignment explanation
Indices: 560661--560694 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
560651 GCTATTTTCA
560661 CTATAATTATT-TTTATT
1 CTATAATTATTGTTTATT
*
560678 CTATTATTATTGTTTAT
1 CTATAATTATTGTTTAT
560695 AAATTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (18 bp):
CTATAATTATTGTTTATT
Found at i:561631 original size:219 final size:217
Alignment explanation
Indices: 561214--561631 Score: 497
Period size: 219 Copynumber: 1.9 Consensus size: 217
561204 TGAAAATATA
* * * * *
561214 AATTTAAATATTTAATTTTTTTAAAAAATATATTTATTTGACTTAATTAATTTTTTTACCTTAAA
1 AATTTAAATATTTAATTTTCTAAAAAAATATATTTATTTAACTTAATTAATTTTGTTACATTAAA
* * * **
561279 TCTCACACGTTTACCTTAATATTCTAACAGTGTTTGTTCCACATTTATAATTTTATGTTAATTTT
66 TCTCACACATTTACCTTAATATTCTAACAATATTTGTTCCACATTTATAATTTTATGTTAATTCA
* *
561344 TACAGTTTTACTTAAAGTTTTTAAACTACTATTTTTCACTATAATAGTTTTATCCTTACTATTAT
131 TACAGTTTTACTTAAAGTTTTTAAACTACTAATTTTCACTATAATAGTTTTATCCTTA-TAGTAT
561409 TATTTATAAACCATTAAATACTT
195 TATTTATAAACCATTAAATACTT
* * *
561432 AATTTAAATGTTTAATTTTCTAAAAAAATTATTTTTATTTAACTTAATTGACTTTATGTTA-ATT
1 AATTTAAATATTTAATTTTCTAAAAAAA-TATATTTATTTAACTTAATT-AATTT-TGTTACATT
* * * * *
561496 AAATCTCATATATTTA-GTTAATATTTTAACAATATTTGTTCCAC-TTTATAATTTTTTATTTTA
63 AAATCTCACACATTTACCTTAATATTCTAACAATATTTGTTCCACATTTATAA--TTTTATGTTA
* * * *
561559 ATTCATACGGTTTTGCGTTGAAGTTTTTAAACTA-TAAATTTTCACTATAATTATTTTTATCC-T
126 ATTCATACAGTTTTAC-TTAAAGTTTTTAAACTACT-AATTTTCACTATAA-TAGTTTTATCCTT
561622 -TAGTATTATT
188 ATAGTATTATT
561632 CTTTTACAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
218 32 0.19
219 51 0.30
220 41 0.24
221 34 0.20
222 10 0.06
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (217 bp):
AATTTAAATATTTAATTTTCTAAAAAAATATATTTATTTAACTTAATTAATTTTGTTACATTAAA
TCTCACACATTTACCTTAATATTCTAACAATATTTGTTCCACATTTATAATTTTATGTTAATTCA
TACAGTTTTACTTAAAGTTTTTAAACTACTAATTTTCACTATAATAGTTTTATCCTTATAGTATT
ATTTATAAACCATTAAATACTT
Found at i:563141 original size:18 final size:18
Alignment explanation
Indices: 563118--563152 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
563108 CAAATTTCAA
563118 AATTTTA-AAGATTTTACC
1 AATTTTACAA-ATTTTACC
563136 AATTTTACAAATTTTAC
1 AATTTTACAAATTTTAC
563153 GCCAACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTTTACAAATTTTACC
Found at i:579687 original size:33 final size:33
Alignment explanation
Indices: 579608--579696 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
579598 GACCAACTTT
*
579608 AATAGTGGCATTCACATCATCACCATAAACTCT
1 AATAGTGGCATTCACATCATCACCATAAACTCC
* * * * *
579641 ACTAATGGGATTCACATCATCACCATAGATTCC
1 AATAGTGGCATTCACATCATCACCATAAACTCC
*
579674 AATAGTGACATTCACATCATCAC
1 AATAGTGGCATTCACATCATCAC
579697 TGGCAACATT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.27
Consensus pattern (33 bp):
AATAGTGGCATTCACATCATCACCATAAACTCC
Found at i:584468 original size:3 final size:3
Alignment explanation
Indices: 584460--584497 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
584450 AATGATAACA
584460 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 AA
584498 ATGTATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:584763 original size:27 final size:27
Alignment explanation
Indices: 584733--584824 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
584723 AAGGGTGATC
*
584733 CAAGCACAAAAGCGCTCAAGGTCGTTT
1 CAAGCACAGAAGCGCTCAAGGTCGTTT
584760 CAAGCACAGAAGTAC-CT-AATGGT-GTTT
1 CAAGCACAGAAG--CGCTCAA-GGTCGTTT
* *
584787 CAAGCACAGAAGCG-TCTAAGGGCCTTT
1 CAAGCACAGAAGCGCTC-AAGGTCGTTT
*
584814 CAAGCATAGAA
1 CAAGCACAGAA
584825 ACGTCTAGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 44 0.81
28 5 0.09
29 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
CAAGCACAGAAGCGCTCAAGGTCGTTT
Found at i:589089 original size:6 final size:6
Alignment explanation
Indices: 589078--589128 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
589068 AACAAGGACA
589078 GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG
1 GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG
589126 GAG
1 GAG
589129 CTGCAAGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GAGATG
Found at i:591719 original size:57 final size:57
Alignment explanation
Indices: 591647--591760 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
591637 TCAAGTAAGA
591647 AATTAAGTGAAATCCATATGCCATTGAAGTCATGGCTCTTCAGAATTGCACTGTAAT
1 AATTAAGTGAAATCCATATGCCATTGAAGTCATGGCTCTTCAGAATTGCACTGTAAT
591704 AATTAAGTGAAATCCATATGCCATTGAAGTCATGGCTCTTCAGAATTGCACTGTAAT
1 AATTAAGTGAAATCCATATGCCATTGAAGTCATGGCTCTTCAGAATTGCACTGTAAT
591761 CAATCTGTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (57 bp):
AATTAAGTGAAATCCATATGCCATTGAAGTCATGGCTCTTCAGAATTGCACTGTAAT
Found at i:598181 original size:62 final size:62
Alignment explanation
Indices: 598084--598207 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
598074 AAAAGAAGAA
*
598084 GACATGAACAGAATAATCATTGTTTAAACTGTAGTAGCGATATTAACGAAATACCTTATGAT
1 GACATGAACAGAATAATCATTGTTTAAACTATAGTAGCGATATTAACGAAATACCTTATGAT
* * *
598146 GACATGAACAGAATAATCGTTGTTTAAACTATAGTAGTGATATTAATGAAATACCTTATGAT
1 GACATGAACAGAATAATCATTGTTTAAACTATAGTAGCGATATTAACGAAATACCTTATGAT
598208 ATACCTATTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (62 bp):
GACATGAACAGAATAATCATTGTTTAAACTATAGTAGCGATATTAACGAAATACCTTATGAT
Found at i:603351 original size:62 final size:62
Alignment explanation
Indices: 603272--603396 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
603262 GACAAACAAC
* * *
603272 AATTGAATAAAGCTAAAAATGTAGTGTACAAAGAAATCTTCCAAAATTTATATTAAGGTTAG
1 AATTGAATAAAACTAAAAATGTAGTGTACAAAGAAATCCTCCAAAATTTACATTAAGGTTAG
603334 AATTGAATAAAACTAAAAATGTAGTGTACAAAGAAATCCTCCAAAATTTACATTAAGGTTAG
1 AATTGAATAAAACTAAAAATGTAGTGTACAAAGAAATCCTCCAAAATTTACATTAAGGTTAG
603396 A
1 A
603397 CTTTTTTTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (62 bp):
AATTGAATAAAACTAAAAATGTAGTGTACAAAGAAATCCTCCAAAATTTACATTAAGGTTAG
Found at i:606790 original size:19 final size:19
Alignment explanation
Indices: 606757--606797 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
606747 AGAACTATAA
606757 TCTTGATCTTCCAAA-TCT
1 TCTTGATCTTCCAAATTCT
*
606775 TCTTGAATCTTTCAAATTCT
1 TCTTG-ATCTTCCAAATTCT
606795 TCT
1 TCT
606798 CAAGTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 9 0.45
20 6 0.30
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.49
Consensus pattern (19 bp):
TCTTGATCTTCCAAATTCT
Found at i:608052 original size:74 final size:74
Alignment explanation
Indices: 607859--608055 Score: 225
Period size: 74 Copynumber: 2.7 Consensus size: 74
607849 AGACAAAGTG
* * * * * *
607859 CTCTTAATTGACAAACCATACTTCTTAGTCGATTAAGTCTTCTCTATCCTGTAATTGAATTCTCT
1 CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTGTCCTGTAATTAAAGTCTCT
*** * *
607924 GGTAGTGAG
66 AACAGTAAA
* * * *
607933 TTCTTAGTTGACTAACCATGCTTCTTAATCGATTAAGTTTTCTCTGTCTTGTAATTAAAGTCTCT
1 CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTGTCCTGTAATTAAAGTCTCT
607998 AACAGTAAA
66 AACAGTAAA
* *
608007 CTCTTAGTTGACTAACTATG-TTACTTAGTCGACTAAGTCTTCTCTGTCC
1 CTCTTAGTTGACTAACCATGCTT-CTTAGTCGATTAAGTCTTCTCTGTCC
608056 CGCAATCTAC
Statistics
Matches: 101, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
73 2 0.02
74 99 0.98
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (74 bp):
CTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTCTTCTCTGTCCTGTAATTAAAGTCTCT
AACAGTAAA
Found at i:612253 original size:93 final size:93
Alignment explanation
Indices: 612090--612283 Score: 336
Period size: 93 Copynumber: 2.1 Consensus size: 93
612080 CTCAAAGACT
*
612090 TGGTCTGCAGCAAGACATTTGTCTCTCAAATCAGTAGTTCATATATGTGTGTGCACATGTGCAAG
1 TGGTCTGCAGCAAGACATTTGTCTCTCAAATCAGTAGTTCATAAATGTGTGTGCACATGTGCAAG
* *
612155 TATCTGCATGCATGCAAAAGTGTGTGCA
66 CATCTGCATGCATGCAAAAGTATGTGCA
* *
612183 TGGTCTGCAGCAAGACTTTTGTCTCTCAAATCAGTAGTTCATAAATGTGTGTGCACATGTGTAAG
1 TGGTCTGCAGCAAGACATTTGTCTCTCAAATCAGTAGTTCATAAATGTGTGTGCACATGTGCAAG
612248 CATCTGCATGCATGCAAAAGTATGTGCA
66 CATCTGCATGCATGCAAAAGTATGTGCA
612276 TGG-CTGCA
1 TGGTCTGCA
612284 TGTGACTCAC
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 5 0.05
93 91 0.95
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (93 bp):
TGGTCTGCAGCAAGACATTTGTCTCTCAAATCAGTAGTTCATAAATGTGTGTGCACATGTGCAAG
CATCTGCATGCATGCAAAAGTATGTGCA
Found at i:617916 original size:215 final size:218
Alignment explanation
Indices: 617509--617963 Score: 623
Period size: 215 Copynumber: 2.1 Consensus size: 218
617499 TAATTATAAA
* *
617509 ATATATAAATTAAATATATGTGTATATGTATAATATATTATTTTATTATATATAAAAAATTAATG
1 ATATATAAATT-AA-ATATGTGTATATATATAATATATTACTTTATTATATATAAAAAATTAATG
* * * *
617574 GCACAACTTATATGTTATAATATTTTAATTTTTATATAAAAGTTTGTATAAATAATAACTAATTA
64 ACACAACTTATATATTATAATATTTTAA---TTATATAAAAGTTTATATAAATAATAACTAAGTA
* *
617639 TAAATACTATGTTATAAAAATTAAGACGATAACTAATAAAATTATTAAGTGTAATAATATAAATA
126 TAAATAATATGTTATAAAAACTAAGACGATAACTAATAAAATTATTAAGTGTAATAATATAAATA
* *
617704 AAATCTATTATAAGTTTTAGTAATACTT
191 AAATCTATTATAAGTTATAATAATACTT
*
617732 ATATATAAATTAAATATGTGTATATATATAATATATTACTTTATTATGTATATATAAAATTAATG
1 ATATATAAATTAAATATGTGTATATATATAATATATTACTTTATTA--TATATAAAAAATTAATG
*
617797 ACACAACTTATATATTATAATATTTT-A-TA-A-CAAA-TTTATATAAATAATAACTAAGTATAA
64 ACACAACTTATATATTATAATATTTTAATTATATAAAAGTTTATATAAATAATAACTAAGTATAA
* * * ** * *
617857 ATAATATGTTATAAAAACTAGGATGATAATTAATAAGGTTATTAAGTGTAATCATATAAATAAAG
129 ATAATATGTTATAAAAACTAAGACGATAACTAATAAAATTATTAAGTGTAATAATATAAATAAAA
*
617922 TTTATTATAAGTTATAATAATACTT
194 TCTATTATAAGTTATAATAATACTT
*
617947 ATGTATAAATTAAATAT
1 ATATATAAATTAAATAT
617964 ACATAATATA
Statistics
Matches: 209, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
215 118 0.56
216 3 0.01
217 1 0.00
218 2 0.01
221 31 0.15
222 3 0.01
223 51 0.24
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.42
Consensus pattern (218 bp):
ATATATAAATTAAATATGTGTATATATATAATATATTACTTTATTATATATAAAAAATTAATGAC
ACAACTTATATATTATAATATTTTAATTATATAAAAGTTTATATAAATAATAACTAAGTATAAAT
AATATGTTATAAAAACTAAGACGATAACTAATAAAATTATTAAGTGTAATAATATAAATAAAATC
TATTATAAGTTATAATAATACTT
Found at i:618229 original size:16 final size:16
Alignment explanation
Indices: 618208--618241 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
618198 TTAGTATATT
*
618208 TTAAGTATATTATCAA
1 TTAAGTATACTATCAA
*
618224 TTAAGTTTACTATCAA
1 TTAAGTATACTATCAA
618240 TT
1 TT
618242 TTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
TTAAGTATACTATCAA
Found at i:622982 original size:21 final size:21
Alignment explanation
Indices: 622958--623000 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
622948 CTCTATTTAA
*
622958 TTTTACTCAAACTC-TTAAAT
1 TTTTTCTCAAACTCTTTAAAT
* *
622978 TTTTTTTCTAACTCTTTAAAT
1 TTTTTCTCAAACTCTTTAAAT
622999 TT
1 TT
623001 CTCCACACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTCTCAAACTCTTTAAAT
Found at i:623047 original size:18 final size:19
Alignment explanation
Indices: 623020--623056 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
623010 TCTTTCCCTT
623020 TCTTTATTTTTATC-TTTC
1 TCTTTATTTTTATCATTTC
*
623038 TCTTTTTTTTTATCATTTC
1 TCTTTATTTTTATCATTTC
623057 ATTGTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (19 bp):
TCTTTATTTTTATCATTTC
Found at i:624240 original size:17 final size:17
Alignment explanation
Indices: 624218--624253 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
624208 ACGCTTGCTT
*
624218 TAGACCTCCCAATTTTA
1 TAGACCTCACAATTTTA
*
624235 TAGACCTCATAATTTTA
1 TAGACCTCACAATTTTA
624252 TA
1 TA
624254 TAATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (17 bp):
TAGACCTCACAATTTTA
Found at i:624289 original size:22 final size:22
Alignment explanation
Indices: 624249--624308 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
624239 CCTCATAATT
*
624249 TTATATAATATAATTAATTATA
1 TTATATAATATAATAAATTATA
624271 TTATATACATATAA-AAATTA-A
1 TTATATA-ATATAATAAATTATA
624292 --A-ATAAT-TAATAAATTAT
1 TTATATAATATAATAAATTAT
624309 TTCTTAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 3 0.09
19 1 0.03
21 1 0.03
22 12 0.35
23 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTATATAATATAATAAATTATA
Found at i:626338 original size:40 final size:40
Alignment explanation
Indices: 626294--626371 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
626284 TTTAACCATG
** *
626294 AAAAGGTAATGATGTTGTGAAGTTATGCTTCCTCCTCTTA
1 AAAAGGTAATGACATTGTGAAGTTATGCTTACTCCTCTTA
* * *
626334 AAAAGGTAGTGACATTGTGAGGTTGTGCTTACTCCTCT
1 AAAAGGTAATGACATTGTGAAGTTATGCTTACTCCTCT
626372 CGAAAAGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (40 bp):
AAAAGGTAATGACATTGTGAAGTTATGCTTACTCCTCTTA
Found at i:630373 original size:21 final size:20
Alignment explanation
Indices: 630347--630402 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
630337 TTAAAGCTTG
*
630347 AGGGTCGACTACAACACTTCT
1 AGGGTC-ACTACAACACTCCT
**
630368 AGGGTCAACTGTAACACTCCT
1 AGGGTC-ACTACAACACTCCT
630389 AGGGTCACCTACAA
1 AGGGTCA-CTACAA
630403 AGCTCATAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (20 bp):
AGGGTCACTACAACACTCCT
Found at i:632011 original size:2 final size:2
Alignment explanation
Indices: 632004--632047 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
631994 TCTTTTCTTG
632004 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
632046 AT
1 AT
632048 TCCTTGATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643040 original size:26 final size:25
Alignment explanation
Indices: 642969--643048 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 25
642959 GAATCGAGGC
*
642969 ATCCATCCACTTTTGATGATAAGATT
1 ATCCAT-CACTTTTGATGGTAAGATT
* * *
642995 ATCCATTCGCTTCTGGTGGTAAGATT
1 ATCCA-TCACTTTTGATGGTAAGATT
*
643021 ATCCATCAACTTTTGATGGTAAAATT
1 ATCCATC-ACTTTTGATGGTAAGATT
643047 AT
1 AT
643049 TGTTAGAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.05
26 41 0.93
27 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (25 bp):
ATCCATCACTTTTGATGGTAAGATT
Found at i:643429 original size:19 final size:19
Alignment explanation
Indices: 643405--643444 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
643395 GAGAAATATA
643405 AGAGAAAGTATTTAAAGGG
1 AGAGAAAGTATTTAAAGGG
643424 AGAGAAAGTATTTAAAGGG
1 AGAGAAAGTATTTAAAGGG
643443 AG
1 AG
643445 TAAGAAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (19 bp):
AGAGAAAGTATTTAAAGGG
Found at i:644811 original size:29 final size:29
Alignment explanation
Indices: 644779--644841 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
644769 TTTTAAATTA
*
644779 TTTTAAAAAATTTGATATAAATTTTTAT-T
1 TTTTAAAAAATTTCAT-TAAATTTTTATAT
* **
644808 TTTTATAACGTTTCATTAAATTTTTATAT
1 TTTTAAAAAATTTCATTAAATTTTTATAT
644837 TTTTA
1 TTTTA
644842 TTTCTAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTTAAAAAATTTCATTAAATTTTTATAT
Found at i:656607 original size:90 final size:90
Alignment explanation
Indices: 656454--656633 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
656444 ATTCTCTATT
656454 ATAAAATATGACTAGCTGGTCTTCTGATGTAGATGTTTGTATGTGTTCAAATCCAACCATTACCT
1 ATAAAATATGACTAGCTGGTCTTCTGATGTAGATGTTTGTATGTGTTCAAATCCAACCATTACCT
656519 CATAATCACCTTGGATTCTATCCTC
66 CATAATCACCTTGGATTCTATCCTC
*
656544 ATAAATTATGACTAGCTGGTCTTCTGATGTAGATGTTTGTATGTGTTCAAATCCAACCATTACCT
1 ATAAAATATGACTAGCTGGTCTTCTGATGTAGATGTTTGTATGTGTTCAAATCCAACCATTACCT
656609 CATAATCACCTTGGATTCTATCCTC
66 CATAATCACCTTGGATTCTATCCTC
656634 TTGGATTTAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (90 bp):
ATAAAATATGACTAGCTGGTCTTCTGATGTAGATGTTTGTATGTGTTCAAATCCAACCATTACCT
CATAATCACCTTGGATTCTATCCTC
Found at i:661147 original size:2 final size:2
Alignment explanation
Indices: 661140--661165 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
661130 TCTTCTTCTG
661140 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
661166 TCCAAGACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:662428 original size:14 final size:15
Alignment explanation
Indices: 662401--662432 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
662391 CAAAATGATA
662401 AATAATATTTTAATT
1 AATAATATTTTAATT
662416 AATAATA-TTTAATT
1 AATAATATTTTAATT
662430 AAT
1 AAT
662433 TATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATTTTAATT
Found at i:662431 original size:18 final size:17
Alignment explanation
Indices: 662410--662444 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
662400 AAATAATATT
662410 TTAATTAATAATATTTAA
1 TTAATTAATAAT-TTTAA
*
662428 TTAATTATTAATTTTAA
1 TTAATTAATAATTTTAA
662445 AAAATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTAATAATTTTAA
Found at i:674198 original size:83 final size:84
Alignment explanation
Indices: 674091--674264 Score: 224
Period size: 83 Copynumber: 2.1 Consensus size: 84
674081 AACATATAAT
* * * * * *
674091 AATTTTTTCATTATGATATGTAATAACTAAATCTCTAATATTACCTGTAACAATTACATTTTTTA
1 AATTTTTTCAATATGATAAGTAATAACTAAATCTCTAACATAACATATAACAATTACATTTTTTA
674156 ATATGATATGTAATAATTA
66 ATATGATATGTAATAATTA
* * * * * *
674175 TATTTTTT-AATATGATAAGTAATAACTAAATTTTTAACATAATATATAATAATTATATTTTTTA
1 AATTTTTTCAATATGATAAGTAATAACTAAATCTCTAACATAACATATAACAATTACATTTTTTA
*
674239 ATATGATGTGTAATAATTA
66 ATATGATATGTAATAATTA
674258 AATTTTT
1 AATTTTT
674265 AACATAATAT
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
83 69 0.91
84 7 0.09
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (84 bp):
AATTTTTTCAATATGATAAGTAATAACTAAATCTCTAACATAACATATAACAATTACATTTTTTA
ATATGATATGTAATAATTA
Found at i:674209 original size:55 final size:54
Alignment explanation
Indices: 674150--674359 Score: 237
Period size: 55 Copynumber: 3.9 Consensus size: 54
674140 ACAATTACAT
* * * * *
674150 TTTTTAATATGATATGTAATAATTATATTTTTTAATATGATAAGTAATAACTAAA
1 TTTTTAACATAATATATAATAATTATATTTTTTAATATGACATGTAATAA-TAAA
**
674205 TTTTTAACATAATATATAATAATTATATTTTTTAATATGATGTGTAATAATTAAA
1 TTTTTAACATAATATATAATAATTATATTTTTTAATATGACATGTAATAA-TAAA
* * * *
674260 TTTTTAACATAATATATAACAA--ATATATTTTAACATGACATGTAATAAT-TA
1 TTTTTAACATAATATATAATAATTATATTTTTTAATATGACATGTAATAATAAA
* * * **
674311 TTTTTAATATAACATATAATAATTAAATTTTAGAATATGACATGTAATA
1 TTTTTAACATAATATATAATAATTATATTTTTTAATATGACATGTAATA
674360 CTGTGATAAC
Statistics
Matches: 133, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
51 20 0.15
52 1 0.01
53 42 0.32
55 70 0.53
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (54 bp):
TTTTTAACATAATATATAATAATTATATTTTTTAATATGACATGTAATAATAAA
Found at i:674304 original size:53 final size:53
Alignment explanation
Indices: 674126--674359 Score: 211
Period size: 55 Copynumber: 4.3 Consensus size: 53
674116 ACTAAATCTC
* * * * * * * *
674126 TAATATTACCTGTAACAATTACATTTTTTAATATGATATGTAATAATTATATTTTT
1 TAATATGACATGTAATAATTA-AATTTTTAACATAATATATAATAA--ATATATTT
* * * *
674182 TAATATGATAAGTAATAACTAAATTTTTAACATAATATATAATAATTATATTTTT
1 TAATATGACATGTAATAATTAAATTTTTAACATAATATATAATAA--ATATATTT
** *
674237 TAATATGATGTGTAATAATTAAATTTTTAACATAATATATAACAAATATATTT
1 TAATATGACATGTAATAATTAAATTTTTAACATAATATATAATAAATATATTT
* * * * *
674290 TAACATGACATGTAATAATT--ATTTTTAATATAACATATAATAATTAAATTT
1 TAATATGACATGTAATAATTAAATTTTTAACATAATATATAATAAATATATTT
674341 TAGAATATGACATGTAATA
1 T--AATATGACATGTAATA
674360 CTGTGATAAC
Statistics
Matches: 152, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
51 27 0.18
53 39 0.26
55 71 0.47
56 15 0.10
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (53 bp):
TAATATGACATGTAATAATTAAATTTTTAACATAATATATAATAAATATATTT
Found at i:674358 original size:28 final size:27
Alignment explanation
Indices: 674102--674359 Score: 198
Period size: 28 Copynumber: 9.5 Consensus size: 27
674092 ATTTTTTCAT
* * *
674102 TATGATATGTAATAACTAAATCTCTAA
1 TATGATATGTAATAATTAAATTTTTAA
* ** * *
674129 TATTACCTGTAACAATTACATTTTTTAA
1 TATGATATGTAATAATTA-AATTTTTAA
*
674157 TATGATATGTAATAATTATATTTTTTAA
1 TATGATATGTAATAATTA-AATTTTTAA
* *
674185 TATGATAAGTAATAACTAAATTTTTAA
1 TATGATATGTAATAATTAAATTTTTAA
* * * *
674212 CATAATATATAATAATTATATTTTTTAA
1 TATGATATGTAATAATTA-AATTTTTAA
*
674240 TATGATGTGTAATAATTAAATTTTTAA
1 TATGATATGTAATAATTAAATTTTTAA
* * * * * *
674267 CATAATATATAACAAATATA-TTTTAA
1 TATGATATGTAATAATTAAATTTTTAA
* *
674293 CATGACATGTAATAATT--ATTTTTAA
1 TATGATATGTAATAATTAAATTTTTAA
* * * *
674318 TATAACATATAATAATTAAATTTTAGAA
1 TATGATATGTAATAATTAAATTTT-TAA
*
674346 TATGACATGTAATA
1 TATGATATGTAATA
674360 CTGTGATAAC
Statistics
Matches: 180, Mismatches: 45, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
24 1 0.01
25 20 0.11
26 18 0.10
27 60 0.33
28 81 0.45
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (27 bp):
TATGATATGTAATAATTAAATTTTTAA
Found at i:688405 original size:26 final size:26
Alignment explanation
Indices: 688376--688425 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
688366 AAAAATATTT
* *
688376 TATTAGAAATTTGTCAAAATTTTGAA
1 TATTAAAAATTCGTCAAAATTTTGAA
*
688402 TATTAAAAATTCGTCAGAATTTTG
1 TATTAAAAATTCGTCAAAATTTTG
688426 TTTGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (26 bp):
TATTAAAAATTCGTCAAAATTTTGAA
Found at i:693057 original size:30 final size:32
Alignment explanation
Indices: 693010--693071 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
693000 AATTAATAAT
*
693010 TTTTTATTTTATATATTAATTAAATTTTTATA
1 TTTTTATTTTATATATTAAATAAATTTTTATA
693042 TTTTTA-TTT-TATATTAAATAAATTTTTATA
1 TTTTTATTTTATATATTAAATAAATTTTTATA
693072 ACTAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 20 0.69
31 3 0.10
32 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTTTATTTTATATATTAAATAAATTTTTATA
Found at i:694443 original size:41 final size:38
Alignment explanation
Indices: 694378--694456 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
694368 AACTTAATTT
**
694378 TAATGAAAGAAGAGGAGAAGAAGATGATGGAGTTGGAGAGA
1 TAATGAAAGAAGACAAGAA-AA-A-GATGGAGTTGGAGAGA
*
694419 TAATGGAAGAAGACAAGAAAAAGATGGAGTTGGAGAGA
1 TAATGAAAGAAGACAAGAAAAAGATGGAGTTGGAGAGA
694457 GATTAAAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 16 0.46
39 1 0.03
40 2 0.06
41 16 0.46
ACGTcount: A:0.48, C:0.01, G:0.37, T:0.14
Consensus pattern (38 bp):
TAATGAAAGAAGACAAGAAAAAGATGGAGTTGGAGAGA
Found at i:699055 original size:26 final size:26
Alignment explanation
Indices: 699019--699170 Score: 119
Period size: 26 Copynumber: 5.9 Consensus size: 26
699009 TTATGACATT
699019 CATCCACTTCTGGTGGTAAAATTATC
1 CATCCACTTCTGGTGGTAAAATTATC
* * *
699045 CATCCACTTCTGGTTGCAAAATTGTC
1 CATCCACTTCTGGTGGTAAAATTATC
* ** **
699071 CTTAGA-TTCTTATGGTAAAATTATC
1 CATCCACTTCTGGTGGTAAAATTATC
* *
699096 CATCCACTTCTTGTGGTAAAATTATT
1 CATCCACTTCTGGTGGTAAAATTATC
* ** * * * *
699122 CTTAGA-TTCTGATGATAAAATTTTT
1 CATCCACTTCTGGTGGTAAAATTATC
* *
699147 CATCCACTTCTAGTGATAAAATTA
1 CATCCACTTCTGGTGGTAAAATTA
699171 ATCTTAGAAT
Statistics
Matches: 95, Mismatches: 29, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
25 35 0.37
26 60 0.63
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (26 bp):
CATCCACTTCTGGTGGTAAAATTATC
Found at i:699090 original size:25 final size:25
Alignment explanation
Indices: 699062--699143 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
699052 TTCTGGTTGC
*
699062 AAAATTGTCCTTAGATTCTTATGGT
1 AAAATTATCCTTAGATTCTTATGGT
* ** *
699087 AAAATTATCCATCCACTTCTTGTGGT
1 AAAATTATCCTTAGA-TTCTTATGGT
* * *
699113 AAAATTATTCTTAGATTCTGATGAT
1 AAAATTATCCTTAGATTCTTATGGT
699138 AAAATT
1 AAAATT
699144 TTTCATCCAC
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
25 24 0.55
26 20 0.45
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (25 bp):
AAAATTATCCTTAGATTCTTATGGT
Found at i:699117 original size:51 final size:51
Alignment explanation
Indices: 699026--699178 Score: 182
Period size: 51 Copynumber: 3.0 Consensus size: 51
699016 ATTCATCCAC
* * * * *
699026 TTCTGGTGGTAAAATTATCCATCCACTTCTGGTTGCAAAATTGTCCTTAGA
1 TTCTGATGGTAAAATTATCCATCCACTTCTAGTGGTAAAATTATCCTTAGA
* * *
699077 TTCTTATGGTAAAATTATCCATCCACTTCTTGTGGTAAAATTATTCTTAGA
1 TTCTGATGGTAAAATTATCCATCCACTTCTAGTGGTAAAATTATCCTTAGA
* * * *
699128 TTCTGATGATAAAATTTTTCATCCACTTCTAGTGATAAAATTAAT-CTTAGA
1 TTCTGATGGTAAAATTATCCATCCACTTCTAGTGGTAAAATT-ATCCTTAGA
699179 ATTAAAATAG
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 86 0.98
52 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (51 bp):
TTCTGATGGTAAAATTATCCATCCACTTCTAGTGGTAAAATTATCCTTAGA
Found at i:701092 original size:17 final size:17
Alignment explanation
Indices: 701054--701094 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
701044 TGGATGGATT
701054 AAATCATAATCTTAATCC
1 AAATC-TAATCTTAATCC
701072 -AATCTAAT-TTATATCC
1 AAATCTAATCTTA-ATCC
701088 AAATCTA
1 AAATCTA
701095 GATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 10 0.48
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATCTAATCTTAATCC
Found at i:701103 original size:2 final size:2
Alignment explanation
Indices: 701096--701120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
701086 CCAAATCTAG
701096 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 A
701121 AAATCAAATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:702089 original size:20 final size:20
Alignment explanation
Indices: 702064--702104 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
702054 TTCTTATATT
702064 TCTTTATTAGTCATCCATTC
1 TCTTTATTAGTCATCCATTC
*
702084 TCTTTATTATTCATCCATTC
1 TCTTTATTAGTCATCCATTC
702104 T
1 T
702105 TAGTGGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (20 bp):
TCTTTATTAGTCATCCATTC
Done.