Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 287 of 322
Found at i:95267768 original size:21 final size:21
Alignment explanation
Indices: 95267742--95267785 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
95267732 TTTAAGAAAT
*
95267742 TAATATAATAATATATTAATA
1 TAATATAATAATATAATAATA
95267763 TAATATAATAATATAATAATA
1 TAATATAATAATATAATAATA
95267784 TA
1 TA
95267786 CTAAAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATATAATAATATAATAATA
Found at i:95271137 original size:26 final size:26
Alignment explanation
Indices: 95271108--95271163 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
95271098 TGATACAAAT
95271108 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
95271134 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
95271160 TGAT
1 TGAT
95271164 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:95271232 original size:57 final size:57
Alignment explanation
Indices: 95271144--95271257 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
95271134 TGATAATGGT
95271144 TTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTAAATGA
1 TTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTAAATGA
*
95271201 TTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAATAATTAAATGA
1 TTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTAAATGA
95271258 ATGAAATATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.41
Consensus pattern (57 bp):
TTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTAAATGA
Found at i:95272686 original size:26 final size:26
Alignment explanation
Indices: 95272656--95272708 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
95272646 TTTATAGTTT
*
95272656 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
95272682 TACCCATAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
95272708 T
1 T
95272709 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:95284816 original size:44 final size:44
Alignment explanation
Indices: 95284740--95284843 Score: 104
Period size: 44 Copynumber: 2.4 Consensus size: 44
95284730 GGCTATATGA
* * * * *
95284740 GGCACTAAGTGTGCAATATCGAGATAATTTCAGTTTAAT-GTGAT
1 GGCACTAAGTGTGCGAGATCGAGATAACTTCAG-CTAATACTGAT
** *
95284784 GGCACTAAGTGTGCGAGATCGTTATAGCTTCAGCTAATCACTGAT
1 GGCACTAAGTGTGCGAGATCGAGATAACTTCAGCTAAT-ACTGAT
95284829 -GCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
95284844 ATTCTTAGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.08
44 42 0.84
45 4 0.08
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
GGCACTAAGTGTGCGAGATCGAGATAACTTCAGCTAATACTGAT
Found at i:95288314 original size:23 final size:23
Alignment explanation
Indices: 95288284--95288372 Score: 74
Period size: 23 Copynumber: 3.8 Consensus size: 23
95288274 AACCATATCA
95288284 GGAAGCTCACAAAGAGCCTATTG
1 GGAAGCTCACAAAGAGCCTATTG
* *
95288307 GGAAGCTC-CGAATAGCCATATATTG
1 GGAAGCTCACAAAGAGCC---TATTG
* ** *
95288332 GGAAGTTCA-AGCGAGCACTATCG
1 GGAAGCTCACAAAGAGC-CTATTG
95288355 GGAAGCTCACAAAGAGCC
1 GGAAGCTCACAAAGAGCC
95288373 ATATATCGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
22 7 0.14
23 21 0.43
24 5 0.10
25 15 0.31
26 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (23 bp):
GGAAGCTCACAAAGAGCCTATTG
Found at i:95288336 original size:48 final size:49
Alignment explanation
Indices: 95288278--95288383 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 49
95288268 ACAAAGAACC
* * * *
95288278 ATATCAGGAAGCTCACAAAGAGC-CTATTGGGAAGCTC-CGAATAGCCAT
1 ATATCGGGAAGCTCA-AAAGAGCACTATCGGGAAGCTCACAAAGAGCCAT
* * **
95288326 ATATTGGGAAGTTCAAGCGAGCACTATCGGGAAGCTCACAAAGAGCCAT
1 ATATCGGGAAGCTCAAAAGAGCACTATCGGGAAGCTCACAAAGAGCCAT
95288375 ATATCGGGA
1 ATATCGGGA
95288384 TGCTTTTAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
47 5 0.11
48 25 0.53
49 17 0.36
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (49 bp):
ATATCGGGAAGCTCAAAAGAGCACTATCGGGAAGCTCACAAAGAGCCAT
Found at i:95290506 original size:52 final size:52
Alignment explanation
Indices: 95290441--95291328 Score: 1749
Period size: 52 Copynumber: 17.1 Consensus size: 52
95290431 TGGTACAAAT
95290441 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
*
95290493 TGATAATGAGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290545 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290597 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290649 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290701 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290753 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290805 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290857 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290909 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95290961 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95291013 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95291065 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95291117 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95291169 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95291221 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* *
95291273 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
95291325 TGAT
1 TGAT
95291329 GGGCATTTCA
Statistics
Matches: 832, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 832 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:95293033 original size:54 final size:54
Alignment explanation
Indices: 95292949--95293818 Score: 1654
Period size: 54 Copynumber: 16.1 Consensus size: 54
95292939 AGGAAGCGTC
* * *
95292949 CTGGTGGCTATGCCACA-ATTATCTGATCTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293003 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293057 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293111 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293165 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293219 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293273 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293327 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293381 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293435 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293489 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293543 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293597 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293651 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
95293705 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
* * *
95293759 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCAC-AATATCTGTAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTG-AT
95293813 CTGGTG
1 CTGGTG
95293819 ACTTCGTCAC
Statistics
Matches: 808, Mismatches: 6, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
53 7 0.01
54 800 0.99
55 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACGATTATCTGAT
Found at i:95293814 original size:32 final size:27
Alignment explanation
Indices: 95292949--95293818 Score: 910
Period size: 27 Copynumber: 32.2 Consensus size: 27
95292939 AGGAAGCGTC
* *
95292949 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTACCACATA-TATCTGAT
* *
95292976 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTACCACATA-TATCTGAT
* *
95293003 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293030 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293057 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293084 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293111 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293138 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293165 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293192 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293219 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293246 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293273 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293300 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293327 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293354 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293381 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293408 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293435 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293462 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293489 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293516 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293543 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293570 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293597 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293624 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293651 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293678 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293705 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
* *
95293732 CTGGTGGCTATGCCACGAT-TATCTGAT
1 CTGGTGGCTCTACCAC-ATATATCTGAT
* *
95293759 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTACCACATATATCTGAT
95293786 CTGGTGGCTCTACCACA-ATATCTGTAT
1 CTGGTGGCTCTACCACATATATCTG-AT
95293813 CTGGTG
1 CTGGTG
95293819 ACTTCGTCAC
Statistics
Matches: 753, Mismatches: 60, Indels: 60
0.86 0.07 0.07
Matches are distributed among these distances:
26 35 0.05
27 689 0.92
28 29 0.04
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTACCACATATATCTGAT
Found at i:95295103 original size:3 final size:3
Alignment explanation
Indices: 95295089--95295137 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
95295079 TTTTATACTA
*
95295089 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
95295132 AA- AAT A
1 AAT AAT A
95295138 TTTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:95295111 original size:11 final size:11
Alignment explanation
Indices: 95295095--95295133 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
95295085 ACTAAATAAT
95295095 TAATAATAAAA
1 TAATAATAAAA
*
95295106 TAATAATGAAA
1 TAATAATAAAA
95295117 TAATAATAAAA
1 TAATAATAAAA
95295128 TAATAA
1 TAATAA
95295134 AATATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:95295120 original size:19 final size:19
Alignment explanation
Indices: 95295096--95295137 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
95295086 CTAAATAATT
*
95295096 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
95295115 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
95295134 AATA
1 AATA
95295138 TTTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:95296408 original size:6 final size:6
Alignment explanation
Indices: 95296397--95296493 Score: 53
Period size: 6 Copynumber: 16.5 Consensus size: 6
95296387 CAAAACAAAT
* * * *
95296397 AAAAGA AAAAG- AATAGA AAAAGAA ACAAAGTTA AAATGA AACAG- AGAAGA
1 AAAAGA AAAAGA AAAAGA AAAAG-A A-AAAG--A AAAAGA AAAAGA AAAAGA
* * *
95296447 AAAAG- -AAAGG AAAAGA AAAAG- -AAAGG AAAAGA AAAAGA GAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
95296491 AAA
1 AAA
95296494 GGAGAAAAGT
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
4 8 0.12
5 7 0.10
6 43 0.62
7 2 0.03
8 7 0.10
9 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:95296459 original size:22 final size:22
Alignment explanation
Indices: 95296399--95296502 Score: 58
Period size: 22 Copynumber: 4.7 Consensus size: 22
95296389 AAACAAATAA
*
95296399 AAGAAAAA-GAATAGAAAA-AG
1 AAGAAAAAGGAAAAGAAAAGAG
* *
95296419 AA-ACAAAGTTAAAATGAAACAGAG
1 AAGAAAAAG-GAAAA-GAAA-AGAG
*
95296443 AAGAAAAA-GAAAGGAAAAGA-
1 AAGAAAAAGGAAAAGAAAAGAG
95296463 AA-AAGAAAGGAAAAGAAAAAGAG
1 AAGAA-AAAGGAAAAG-AAAAGAG
*
95296486 AAAGAAAAGGAGAAAAG
1 -AAGAAAAAG-GAAAAG
95296503 TTAGGGATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
19 6 0.10
20 7 0.11
21 11 0.17
22 14 0.22
23 4 0.06
24 9 0.14
25 12 0.19
ACGTcount: A:0.71, C:0.02, G:0.23, T:0.04
Consensus pattern (22 bp):
AAGAAAAAGGAAAAGAAAAGAG
Found at i:95296464 original size:5 final size:5
Alignment explanation
Indices: 95296447--95296494 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
95296437 ACAGAGAAGA
* *
95296447 AAAAG AAAGG AAAAG AAAAAG AAAGG AAAAG AAAAAG AGAAAG AAAAG
1 AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG -AAAAG A-AAAG AAAAG
95296495 GAGAAAAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 21 0.58
6 15 0.42
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:95296464 original size:16 final size:16
Alignment explanation
Indices: 95296443--95296494 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
95296433 TGAAACAGAG
95296443 AAGAAAAAGAAAGGAA
1 AAGAAAAAGAAAGGAA
95296459 AAGAAAAAGAAAGGAA
1 AAGAAAAAGAAAGGAA
*
95296475 AAGAAAAAGAGAAAGAA
1 AAGAAAAAGA-AAGGAA
95296492 AAG
1 AAG
95296495 GAGAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 26 0.76
17 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAGGAA
Found at i:95296493 original size:11 final size:11
Alignment explanation
Indices: 95296434--95296500 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
95296424 AAGTTAAAAT
95296434 GAAACAGAG-AA
1 GAAA-AGAGAAA
95296445 GAAAA-AGAAA
1 GAAAAGAGAAA
*
95296455 GGAAAAGAAAAA
1 -GAAAAGAGAAA
*
95296467 GAAAGGA-AAA
1 GAAAAGAGAAA
95296477 GAAAAAGAGAAA
1 G-AAAAGAGAAA
95296489 GAAAAGGAGAAA
1 GAAAA-GAGAAA
95296501 AGTTAGGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
9 2 0.04
10 7 0.15
11 24 0.51
12 14 0.30
ACGTcount: A:0.72, C:0.01, G:0.27, T:0.00
Consensus pattern (11 bp):
GAAAAGAGAAA
Found at i:95296498 original size:12 final size:12
Alignment explanation
Indices: 95296450--95296500 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
95296440 GAGAAGAAAA
95296450 AGAAAGGAAAA-G
1 AGAAA-GAAAAGG
*
95296462 AAAAAG-AAAGG
1 AGAAAGAAAAGG
*
95296473 A-AAAGAAAAAG
1 AGAAAGAAAAGG
95296484 AGAAAGAAAAGG
1 AGAAAGAAAAGG
95296496 AGAAA
1 AGAAA
95296501 AGTTAGGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 7 0.21
11 8 0.24
12 18 0.55
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAGG
Found at i:95297043 original size:29 final size:29
Alignment explanation
Indices: 95297011--95297067 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
95297001 AAAGATAGAG
95297011 TCGACGAGGAATAACTTGAAAGTTTCTAC
1 TCGACGAGGAATAACTTGAAAGTTTCTAC
95297040 TCGACGAGGAATAACTTGAAAGTTTCTA
1 TCGACGAGGAATAACTTGAAAGTTTCTA
95297068 GTTTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (29 bp):
TCGACGAGGAATAACTTGAAAGTTTCTAC
Found at i:95306948 original size:13 final size:13
Alignment explanation
Indices: 95306926--95306958 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
95306916 AATGGTTTGT
95306926 TTAT-TAAACTAA
1 TTATCTAAACTAA
95306938 TTATCTAAACTAA
1 TTATCTAAACTAA
*
95306951 TTAACTAA
1 TTATCTAA
95306959 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:95310304 original size:29 final size:30
Alignment explanation
Indices: 95310245--95310302 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
95310235 TCCGAGCCTT
*
95310245 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
95310275 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
95310303 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:95310532 original size:13 final size:13
Alignment explanation
Indices: 95310514--95310545 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
95310504 TTTCCAGCAA
95310514 TTATGAATTTATT
1 TTATGAATTTATT
95310527 TTATGAATTTATT
1 TTATGAATTTATT
*
95310540 TGATGA
1 TTATGA
95310546 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:95310720 original size:50 final size:50
Alignment explanation
Indices: 95310640--95310824 Score: 361
Period size: 50 Copynumber: 3.7 Consensus size: 50
95310630 ATTTGGGTAA
*
95310640 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
95310690 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
95310740 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
95310790 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
95310825 TTTGGCATGT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:95326072 original size:18 final size:18
Alignment explanation
Indices: 95326036--95326069 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
95326026 GAGCCGAAAG
95326036 GGGCCATATGGGCCCAAT
1 GGGCCATATGGGCCCAAT
95326054 GGGCC-TATGGGCCCAA
1 GGGCCATATGGGCCCAA
95326070 ATGAATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (18 bp):
GGGCCATATGGGCCCAAT
Found at i:95326301 original size:27 final size:27
Alignment explanation
Indices: 95326282--95326438 Score: 224
Period size: 27 Copynumber: 5.8 Consensus size: 27
95326272 ATTACCAAAG
* *
95326282 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
95326309 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
95326336 TACCCTCAATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
95326363 TACCCTCAATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
95326390 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
95326417 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
95326439 TAAAATACTC
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 118 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:95326379 original size:81 final size:81
Alignment explanation
Indices: 95326258--95326438 Score: 238
Period size: 81 Copynumber: 2.2 Consensus size: 81
95326248 ACTAAAATGT
* * * * *
95326258 CCTCAATTTGTAAAATTACCAAAGTACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTAT
1 CCTCAATTTATAAAATTACCAAAGTACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTAC
95326323 AGAATTA-CTATTTTAC
66 AGAATTATC-ATTTTAC
* ***
95326339 CCTCAATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTAC
1 CCTCAATTTATAAAATTACCAAAGTACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTAC
*
95326404 AGAATTATCGTTTTAC
66 AGAATTATCATTTTAC
* *
95326420 CCTCGATTTACAAAATTAC
1 CCTCAATTTATAAAATTAC
95326439 TAAAATACTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 85 0.99
82 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (81 bp):
CCTCAATTTATAAAATTACCAAAGTACCCTCAATTTACAGAATTACCATTTTACCCTCGATTTAC
AGAATTATCATTTTAC
Found at i:95326462 original size:27 final size:27
Alignment explanation
Indices: 95326417--95326584 Score: 144
Period size: 27 Copynumber: 6.2 Consensus size: 27
95326407 ATTATCGTTT
* ** *
95326417 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
* *** * *
95326444 TACTCTTGGTTTGTGAAATTACCGAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
95326471 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
** *
95326498 TACCACT-GGTTTGTGAAATTACCAAAA
1 TACC-CTCAATTTGTAAAATTACCAAAA
95326525 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
* **
95326552 TACACCT-GATTTACAAAATTA-CAGAAA
1 TAC-CCTCAATTTGTAAAATTACCA-AAA
95326579 TACCCT
1 TACCCT
95326585 TAACTTTCTA
Statistics
Matches: 114, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
26 7 0.06
27 102 0.89
28 5 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
TACCCTCAATTTGTAAAATTACCAAAA
Found at i:95326464 original size:54 final size:54
Alignment explanation
Indices: 95326417--95326554 Score: 188
Period size: 54 Copynumber: 2.6 Consensus size: 54
95326407 ATTATCGTTT
* * *
95326417 TACCCTCGATTTACAAAATTACTAAAATACTC-TTGGTTTGTGAAATTACCGAAA
1 TACCCTCAATTTACAAAATTACCAAAATAC-CACTGGTTTGTGAAATTACCGAAA
** *
95326471 TACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCAAAA
1 TACCCTCAATTTACAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
**
95326525 TACCCTCAATTTGTAAAATTACCAAAATAC
1 TACCCTCAATTTACAAAATTACCAAAATAC
95326555 ACCTGATTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 76 0.99
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
TACCCTCAATTTACAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
Found at i:95326571 original size:54 final size:54
Alignment explanation
Indices: 95326459--95326640 Score: 190
Period size: 54 Copynumber: 3.3 Consensus size: 54
95326449 TTGGTTTGTG
* * ***
95326459 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCACTGATTTACA
95326513 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATA-CACCTGATTTACA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCA-CTGATTTACA
* * * * *
95326567 AAATTA-CAGAAATACCCTTAACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACCA-AAATACCCTCAA-TTTGT-AAAATTACCA-AAATACCACTGATTTACA
**
95326623 AAATTACTGAAATACCCT
1 AAATTACCAAAATACCCT
95326641 TGGTTTGTAG
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
53 4 0.04
54 63 0.58
55 5 0.05
56 35 0.32
57 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCACTGATTTACA
Found at i:95326634 original size:27 final size:27
Alignment explanation
Indices: 95326595--95326646 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
95326585 TAACTTTCTA
95326595 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
95326622 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
95326647 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:95326764 original size:27 final size:27
Alignment explanation
Indices: 95326687--95326764 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
95326677 ACATGACTAA
* *
95326687 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
95326714 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
95326741 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
95326765 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:95327650 original size:24 final size:25
Alignment explanation
Indices: 95327574--95327643 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
95327564 AGGAAGTGCT
* *
95327574 AAAAA-GGCTATGCCCCAGTTTACC
1 AAAAAGGGCTTTGCCCCAGTTTATC
* *
95327598 GAAAAGGGTTTTGCCCCAGTTTATC
1 AAAAAGGGCTTTGCCCCAGTTTATC
95327623 AAAAAGGGCTTTGCCCCAGTT
1 AAAAAGGGCTTTGCCCCAGTT
95327644 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 4 0.10
25 35 0.90
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAAGGGCTTTGCCCCAGTTTATC
Found at i:95327656 original size:24 final size:24
Alignment explanation
Indices: 95327573--95327656 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
95327563 GAGGAAGTGC
* *
95327573 TAAAAAGGCTATGCCCCAGTTTACC
1 TAAAAAGGCTTTGCCCCAGTTTA-T
* * *
95327598 GAAAAGGGTTTTGCCCCAGTTTAT
1 TAAAAAGGCTTTGCCCCAGTTTAT
*
95327622 CAAAAAGGGCTTTGCCCCAG-TTAT
1 TAAAAA-GGCTTTGCCCCAGTTTAT
95327646 TAAAAGAGGCT
1 TAAAA-AGGCT
95327657 AGGCCTCTAG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 16 0.33
25 32 0.67
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (24 bp):
TAAAAAGGCTTTGCCCCAGTTTAT
Found at i:95327912 original size:31 final size:31
Alignment explanation
Indices: 95327864--95327945 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
95327854 GCTTACAGTG
*
95327864 AAGGCTTC-GTCCAGTGATATGATTTATGAA
1 AAGGCTTCGGCCCAGTGATATGATTTATGAA
95327894 AAGGCTTCGGCCCAGTGATATGATTTATGAA
1 AAGGCTTCGGCCCAGTGATATGATTTATGAA
*
95327925 ATGGCTTCGGCCCAGT-ATATG
1 AAGGCTTCGGCCCAGTGATATG
95327946 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 13 0.27
31 36 0.73
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTGATATGATTTATGAA
Found at i:95328044 original size:33 final size:33
Alignment explanation
Indices: 95327951--95328044 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
95327941 ATATGTCGAG
*
95327951 ACTGAATTAGGGCTTAGGCCCATATTGCTACTGTT
1 ACTGAA-TAGGGCTTAGGCCCAGATTG-TACTGTT
* * *
95327986 --T--A-AGGGCTAAGGCCCAGACTATACTGTT
1 ACTGAATAGGGCTTAGGCCCAGATTGTACTGTT
*
95328014 ACTGAATAGGGCTTTGGCCCAGATTGTACTG
1 ACTGAATAGGGCTTAGGCCCAGATTGTACTG
95328045 ACACTGTGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
28 7 0.15
29 15 0.33
30 1 0.02
31 1 0.02
32 1 0.02
33 21 0.46
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (33 bp):
ACTGAATAGGGCTTAGGCCCAGATTGTACTGTT
Found at i:95334194 original size:24 final size:25
Alignment explanation
Indices: 95334119--95334201 Score: 93
Period size: 24 Copynumber: 3.5 Consensus size: 25
95334109 CTATCCAGAG
*
95334119 CTTCCCGA-TATGGTTCTTTGTAAA
1 CTTCCCGATTATGGTTCTTTGTGAA
* *
95334143 CTT-CCTAATATGGTTCTTTGTGAA
1 CTTCCCGATTATGGTTCTTTGTGAA
* *
95334167 CTTCCCGATTATGGCTCTTT-TGAG
1 CTTCCCGATTATGGTTCTTTGTGAA
95334191 CTTCCC-ATTAT
1 CTTCCCGATTAT
95334202 ATAGCCCGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 8 0.16
24 30 0.59
25 13 0.25
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (25 bp):
CTTCCCGATTATGGTTCTTTGTGAA
Found at i:95339050 original size:50 final size:49
Alignment explanation
Indices: 95338974--95339073 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 49
95338964 ACATTTTACA
* *
95338974 ACTTTTGCAAAGTGGTCCCTATAAGGGTTTTTCATGAAAATCACCTAGG
1 ACTTTTGCAAAATGGTCCCTACAAGGGTTTTTCATGAAAATCACCTAGG
*
95339023 NACTTTTGCAAAATGGTCCCTACAAGGGTTTTTCATGAAAGTCACCTAGG
1 -ACTTTTGCAAAATGGTCCCTACAAGGGTTTTTCATGAAAATCACCTAGG
95339073 A
1 A
95339074 AAAGATGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (49 bp):
ACTTTTGCAAAATGGTCCCTACAAGGGTTTTTCATGAAAATCACCTAGG
Found at i:95341046 original size:13 final size:13
Alignment explanation
Indices: 95341024--95341100 Score: 75
Period size: 13 Copynumber: 5.9 Consensus size: 13
95341014 TTTGGCAATA
95341024 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
95341037 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
* * *
95341050 C-TGTGAAAAAATA
1 CTTTTG-AAAAGTG
* *
95341063 CTTTTGAGAAGTA
1 CTTTTGAAAAGTG
*
95341076 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
95341089 CTTTTGAAAAGT
1 CTTTTGAAAAGT
95341101 TTGGTTTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
12 2 0.04
13 47 0.90
14 3 0.06
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:95343639 original size:12 final size:12
Alignment explanation
Indices: 95343622--95343655 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
95343612 TTATTTTATT
95343622 TAAATATAAATA
1 TAAATATAAATA
*
95343634 TAAATATTAATA
1 TAAATATAAATA
*
95343646 TTAATATAAA
1 TAAATATAAA
95343656 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATATAAATA
Found at i:95343641 original size:25 final size:24
Alignment explanation
Indices: 95343595--95343655 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
95343585 GGGGGGTTTA
* **
95343595 ATTTAATATTAATATATTTATTTT
1 ATTTAATATAAATATAAATATTTT
*
95343619 ATTTAAATATAAATATAAATA-TTA
1 ATTT-AATATAAATATAAATATTTT
95343643 ATATTAATATAAA
1 AT-TTAATATAAA
95343656 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAATATAAATATAAATATTTT
Found at i:95344527 original size:4 final size:4
Alignment explanation
Indices: 95344518--95344544 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
95344508 TTAGTAAAAC
95344518 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
95344545 ACGTTTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:95345282 original size:23 final size:22
Alignment explanation
Indices: 95345256--95345299 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
95345246 AAACAATAGC
* *
95345256 GAAATAAAATTAAAAACCACAAT
1 GAAACAAAAGTAAAAA-CACAAT
*
95345279 GAAACAATAGTAAAAACACAA
1 GAAACAAAAGTAAAAACACAA
95345300 AAAAAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (22 bp):
GAAACAAAAGTAAAAACACAAT
Found at i:95355161 original size:19 final size:19
Alignment explanation
Indices: 95355121--95355163 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
95355111 TTTTTGTAAG
* *
95355121 TTTTATAATTTTTCATTAA
1 TTTTATAACTTTTAATTAA
95355140 TTTTATATACTTTTAATT-A
1 TTTTATA-ACTTTTAATTAA
95355159 TTTTA
1 TTTTA
95355164 ATAAATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAACTTTTAATTAA
Found at i:95362379 original size:12 final size:12
Alignment explanation
Indices: 95362344--95362379 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
95362334 ACTAGTCCTT
95362344 TAATTATCATGA
1 TAATTATCATGA
95362356 TAATT-TCATGA
1 TAATTATCATGA
*
95362367 TAATTATCTTGA
1 TAATTATCATGA
95362379 T
1 T
95362380 TGAGAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (12 bp):
TAATTATCATGA
Found at i:95364503 original size:13 final size:13
Alignment explanation
Indices: 95364432--95364565 Score: 76
Period size: 13 Copynumber: 10.0 Consensus size: 13
95364422 TATCTATATC
*
95364432 CATATAAACATTT
1 CATATAATCATTT
* *
95364445 CGTATAAACATTT
1 CATATAATCATTT
95364458 CATATAA-CTATTT
1 CATATAATC-ATTT
* *
95364471 CTATATAGCTGA-TT
1 C-ATATA-ATCATTT
95364485 CATATAATCATTT
1 CATATAATCATTT
*
95364498 CGTAT-ATCTATTT
1 CATATAATC-ATTT
*
95364511 CCATATAATCAATT
1 -CATATAATCATTT
*
95364525 CATATAACCATTT
1 CATATAATCATTT
* * *
95364538 TATGTATTCATTTTT
1 CATATAATCA--TTT
*
95364553 CATATAACCATTT
1 CATATAATCATTT
95364566 GGTATATTTA
Statistics
Matches: 92, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
12 6 0.07
13 58 0.63
14 15 0.16
15 13 0.14
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:95364515 original size:27 final size:26
Alignment explanation
Indices: 95364421--95364530 Score: 84
Period size: 27 Copynumber: 4.1 Consensus size: 26
95364411 TCCCTTTTAC
* *
95364421 ATATCTATATCCATATAAACATTTCGT
1 ATATCTAT-TTCATATAATCATTTCGT
*
95364448 ATAAAC-ATTTCATATAA-CTATTTC-T
1 AT-ATCTATTTCATATAATC-ATTTCGT
95364473 ATATAGCTGA-TTCATATAATCATTTCGT
1 ATAT--CT-ATTTCATATAATCATTTCGT
* *
95364501 ATATCTATTTCCATATAATCAATTCAT
1 ATATCTATTT-CATATAATCATTTCGT
95364528 ATA
1 ATA
95364531 ACCATTTTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
24 1 0.01
25 5 0.07
26 18 0.26
27 35 0.51
28 9 0.13
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (26 bp):
ATATCTATTTCATATAATCATTTCGT
Found at i:95364526 original size:40 final size:40
Alignment explanation
Indices: 95364421--95364537 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 40
95364411 TCCCTTTTAC
* * *
95364421 ATATCTATATCCATATAAACATTTCGTATAAACATTTCAT
1 ATATCTATTTCCATATAAACAATTCATATAAACATTTCAT
* * * * * *
95364461 ATAACTATTTCTATAT-AGCTGATTCATATAATCATTTCGT
1 ATATCTATTTCCATATAAAC-AATTCATATAAACATTTCAT
* *
95364501 ATATCTATTTCCATATAATCAATTCATATAACCATTT
1 ATATCTATTTCCATATAAACAATTCATATAAACATTT
95364538 TATGTATTCA
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
39 2 0.03
40 57 0.93
41 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (40 bp):
ATATCTATTTCCATATAAACAATTCATATAAACATTTCAT
Found at i:95364537 original size:27 final size:27
Alignment explanation
Indices: 95364485--95364537 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
95364475 ATAGCTGATT
* * * *
95364485 CATATAATCATTTCGTATATCTATTTC
1 CATATAATCAATTCATATAACCATTTC
95364512 CATATAATCAATTCATATAACCATTT
1 CATATAATCAATTCATATAACCATTT
95364538 TATGTATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (27 bp):
CATATAATCAATTCATATAACCATTTC
Found at i:95364573 original size:28 final size:28
Alignment explanation
Indices: 95364523--95364579 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
95364513 ATATAATCAA
* *
95364523 TTCATATAACCATTTTATGTATTCATTT
1 TTCATATAACCATTTGATATATTCATTT
* *
95364551 TTCATATAACCATTTGGTATATTTATTT
1 TTCATATAACCATTTGATATATTCATTT
95364579 T
1 T
95364580 CTACTCGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.54
Consensus pattern (28 bp):
TTCATATAACCATTTGATATATTCATTT
Found at i:95367275 original size:57 final size:57
Alignment explanation
Indices: 95367187--95367300 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
95367177 TAAGGGTACG
*
95367187 CAGAGAGACAATTGGGAAAAAGCTTTTGGGAAAACTTGATTGATTAAGACAATACCC
1 CAGAGAGACAATTGGGAAAAAGCTTTTGGGAAAACTCGATTGATTAAGACAATACCC
95367244 CAGAGAGACAATTGGGAAAAAGCTTTTGGGAAAACTCGATTGATTAAGACAATACCC
1 CAGAGAGACAATTGGGAAAAAGCTTTTGGGAAAACTCGATTGATTAAGACAATACCC
95367301 AAGGAAAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (57 bp):
CAGAGAGACAATTGGGAAAAAGCTTTTGGGAAAACTCGATTGATTAAGACAATACCC
Found at i:95369618 original size:47 final size:47
Alignment explanation
Indices: 95369549--95369640 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
95369539 AAGACCCCCT
*
95369549 ACACTTAAGATGTACATTGCCCTCAATGTACAAAGATAGATATATAG
1 ACACTTAAGATGTACATTGCCCTCAATGTACAAAGATAGACATATAG
95369596 ACACTTAAGATGTACATTGCCCTCAATGTACAAAGATAGACATAT
1 ACACTTAAGATGTACATTGCCCTCAATGTACAAAGATAGACATAT
95369641 TAAAAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (47 bp):
ACACTTAAGATGTACATTGCCCTCAATGTACAAAGATAGACATATAG
Found at i:95376466 original size:598 final size:598
Alignment explanation
Indices: 95375245--95377036 Score: 3293
Period size: 598 Copynumber: 3.0 Consensus size: 598
95375235 AGTAACGGCG
* * * * *
95375245 CCAAAAACTTGGTACGTGATATTTGCGGCAGGTTTTAAAGATTTATAATTAATCATTCTTGAAAC
1 CCAAAAACGTGGTACGTGATATTCGCGACAGGTTTTAAAGATTTATGATTAATCGTTCTTGAAAC
* * * *
95375310 TAACTATTATCACGATGAAGG-AAGTGTACCTATTGAACAGTAGTATAGCTTTAGCAAGACCGAA
66 TAACTATTATCACAATAAAGGCAAGTGTACCTATCGAACAGTAGTATAGCTTTAGCAAGACCGGA
* *
95375374 TTATCAAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
131 TTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
*
95375439 T-AGGAGATTTGTTTATCTAGACTAATTAACTAAACTAAGGGTGCACAGACAGAAAATTGGGAAA
196 TAAGG-GATTTGTTTATATAGACTAATTAACTAAACTAAGGGTGCACAGACAGAAAATTGGGAAA
95375503 AAGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTT
260 AAGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTT
* *
95375568 GTTATTTGACTCTGAATCAGACGATTTATTCATTTGACTTGATCCGTAGAAATCCCTAAGTTATA
325 GTTATTTGACTCTGAATCAGACGATTTATTCATTTGACTTGATCTGTAGAAATCTCTAAGTTATA
95375633 TTATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGGTTGATTAATTGAAATCTCTTTCTAAT
390 TTATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGGTTGATTAATTGAAATCTCTTTCTAAT
* * *
95375698 TAATGCCCTAGTGTTGCATTAACTCGATCTATAGATCC-CGTTATTAGGTTTCACCCTAATCCGG
455 TAACGCACTAGTGTTGCATTAACTCGATCTATGGATCCTC-TTATTAGGTTTCACCCTAATCCGG
95375762 CAAAATCTTATCACCCTATCTCTAAGTGTGCAATCGACTCCACTTAATTACGACAAATTTACTCT
519 CAAAATCTTATCACCCTATCTCTAAGTGTGCAATCGACTCCACTTAATTACGACAAATTTACTCT
95375827 TAGACAGGGTCTATC
584 TAGACAGGGTCTATC
95375842 CCAAAAACGTGGTACGTGATATTCGCGACAGGTTTTAAAGATTTATGATTAATCGTTCTTGAAAC
1 CCAAAAACGTGGTACGTGATATTCGCGACAGGTTTTAAAGATTTATGATTAATCGTTCTTGAAAC
*
95375907 TAACTATTATCACAATAAAGGCAAGTGTACCTATCAAACAGTAGTATAGCTTTAGCAAGACCGGA
66 TAACTATTATCACAATAAAGGCAAGTGTACCTATCGAACAGTAGTATAGCTTTAGCAAGACCGGA
95375972 TTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
131 TTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
*
95376037 TAAGGGATTTGTTTATATAGACTAATTAACTAAACTAAGGGTGCACAAACAGAAAATTGGGAAAA
196 TAAGGGATTTGTTTATATAGACTAATTAACTAAACTAAGGGTGCACAGACAGAAAATTGGGAAAA
95376102 AGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTTG
261 AGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTTG
*
95376167 TTATTTGACTCTGAATTAGACGATTTATTCATTTGACTTGATCTGTAGAAATCTCTAAGTTATAT
326 TTATTTGACTCTGAATCAGACGATTTATTCATTTGACTTGATCTGTAGAAATCTCTAAGTTATAT
95376232 TATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGGTTGATTAATTGAAATCTCTTTCTAATT
391 TATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGGTTGATTAATTGAAATCTCTTTCTAATT
95376297 AACGCACTAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCA
456 AACGCACTAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCA
95376362 AAATCTTATCACCCTATCTCTAAGTGTGCAATCGACTCCACTTAATTACGACAAATTTACTCTTA
521 AAATCTTATCACCCTATCTCTAAGTGTGCAATCGACTCCACTTAATTACGACAAATTTACTCTTA
95376427 GACAGGGTCTATC
586 GACAGGGTCTATC
95376440 CCAAAAACGTGGTACGTGATATTCGCGACAGGTTTTAAAGATTTATGATTAATCGTTCTTGAAAC
1 CCAAAAACGTGGTACGTGATATTCGCGACAGGTTTTAAAGATTTATGATTAATCGTTCTTGAAAC
*
95376505 TAACTATTATCACAATAAAGGCAAGTGTACCTATCGAACAGTAGTATAACTTTAGCAAGACCGGA
66 TAACTATTATCACAATAAAGGCAAGTGTACCTATCGAACAGTAGTATAGCTTTAGCAAGACCGGA
95376570 TTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
131 TTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
95376635 TAAGGGATTTGTTTATATAGACTAATTAACTAAACTAAGGGTGCACAGACAGAAAATTGGGAAAA
196 TAAGGGATTTGTTTATATAGACTAATTAACTAAACTAAGGGTGCACAGACAGAAAATTGGGAAAA
95376700 AGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTTG
261 AGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTTG
95376765 TTATTTGACTCTGAATCAGACGATTTATTCATTTGACTTGATCTGTAGAAATCTCTAAGTTATAT
326 TTATTTGACTCTGAATCAGACGATTTATTCATTTGACTTGATCTGTAGAAATCTCTAAGTTATAT
*
95376830 TATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGATTGATTAATTGAAATCTCTTTCTAATT
391 TATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGGTTGATTAATTGAAATCTCTTTCTAATT
95376895 AACGCACTAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCA
456 AACGCACTAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCA
* * * * *
95376960 AAATCTTATCACCCTATCTCTAGGCGTGCAATCGACTCCGCTTAATTACAAAAAATTTACTCTTA
521 AAATCTTATCACCCTATCTCTAAGTGTGCAATCGACTCCACTTAATTACGACAAATTTACTCTTA
*
95377025 GACAGAGTCTAT
586 GACAGGGTCTAT
95377037 TCCTCCTTTG
Statistics
Matches: 1161, Mismatches: 31, Indels: 5
0.97 0.03 0.00
Matches are distributed among these distances:
597 79 0.07
598 1078 0.93
599 4 0.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (598 bp):
CCAAAAACGTGGTACGTGATATTCGCGACAGGTTTTAAAGATTTATGATTAATCGTTCTTGAAAC
TAACTATTATCACAATAAAGGCAAGTGTACCTATCGAACAGTAGTATAGCTTTAGCAAGACCGGA
TTGTCGAACCCAAAGGAACCAAGAGTACTAGTAATTACTTTCTTTTTATTATCTAACCTAAAAAT
TAAGGGATTTGTTTATATAGACTAATTAACTAAACTAAGGGTGCACAGACAGAAAATTGGGAAAA
AGCTTTTGGGAAAACTCGATTGATTAAGACAATACCCAAGGAAAAATCCACCTAGACTTCACTTG
TTATTTGACTCTGAATCAGACGATTTATTCATTTGACTTGATCTGTAGAAATCTCTAAGTTATAT
TATTATCTCTCTCGAGACTAATAACGTCTAACCCTAGGTTGATTAATTGAAATCTCTTTCTAATT
AACGCACTAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCA
AAATCTTATCACCCTATCTCTAAGTGTGCAATCGACTCCACTTAATTACGACAAATTTACTCTTA
GACAGGGTCTATC
Found at i:95378495 original size:859 final size:859
Alignment explanation
Indices: 95376837--95378558 Score: 3444
Period size: 859 Copynumber: 2.0 Consensus size: 859
95376827 TATTATTATC
95376837 TCTCTCGAGACTAATAACGTCTAACCCTAGATTGATTAATTGAAATCTCTTTCTAATTAACGCAC
1 TCTCTCGAGACTAATAACGTCTAACCCTAGATTGATTAATTGAAATCTCTTTCTAATTAACGCAC
95376902 TAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCAAAATCTT
66 TAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCAAAATCTT
95376967 ATCACCCTATCTCTAGGCGTGCAATCGACTCCGCTTAATTACAAAAAATTTACTCTTAGACAGAG
131 ATCACCCTATCTCTAGGCGTGCAATCGACTCCGCTTAATTACAAAAAATTTACTCTTAGACAGAG
95377032 TCTATTCCTCCTTTGAATAAGAGCATTAACTTGAATCAATATCCTAGAATATTATAACAAGAAAT
196 TCTATTCCTCCTTTGAATAAGAGCATTAACTTGAATCAATATCCTAGAATATTATAACAAGAAAT
95377097 AAGAACACATAATTAAGAACAAGTCAAATATTTATCATACAATTCAGATAATAAAAACAAGATCC
261 AAGAACACATAATTAAGAACAAGTCAAATATTTATCATACAATTCAGATAATAAAAACAAGATCC
95377162 GTCTTAGGTTTCATTCCCCTTAGGTATTTAGGGGGTTTAGTTCATAATTATAAAAGAAAACATCT
326 GTCTTAGGTTTCATTCCCCTTAGGTATTTAGGGGGTTTAGTTCATAATTATAAAAGAAAACATCT
95377227 CAGAAGAATAATGAATACAAAACATAAAGAAAAGCCAAAACCCCTGAATGGAAATTGAAGGGAGA
391 CAGAAGAATAATGAATACAAAACATAAAGAAAAGCCAAAACCCCTGAATGGAAATTGAAGGGAGA
95377292 TCTTCAGTCTTGATGATGAATCCGGCTTCTGAGATGGACCAATCATCTTCCCTTGAGTAATTTCT
456 TCTTCAGTCTTGATGATGAATCCGGCTTCTGAGATGGACCAATCATCTTCCCTTGAGTAATTTCT
95377357 TGCCTCCTACTCCGTGTCTCTCTTCTAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAGAATGCC
521 TGCCTCCTACTCCGTGTCTCTCTTCTAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAGAATGCC
95377422 TAAGAGCCCTTAAAAGTGGCATTTTTCCGAGTAGGACTATACTTGGGCTCGGGAGGGGCACGCCC
586 TAAGAGCCCTTAAAAGTGGCATTTTTCCGAGTAGGACTATACTTGGGCTCGGGAGGGGCACGCCC
95377487 TTGTGACACACCCGTGTGCGATTACTCCAGCCCGTGGTCAAAGCTGTTGAATAGGCACGGACGTG
651 TTGTGACACACCCGTGTGCGATTACTCCAGCCCGTGGTCAAAGCTGTTGAATAGGCACGGACGTG
95377552 TAGTCTACCCGTGTAAGTCATGCTTCGATCCTGCCAAATGGACAAGGCCGTGTGACACGCCCGTG
716 TAGTCTACCCGTGTAAGTCATGCTTCGATCCTGCCAAATGGACAAGGCCGTGTGACACGCCCGTG
95377617 TGAGGAAGTCCAAGCCGTGTTGATTTCTCACGTGGGTTCATTCTCTCCTTTTTTTGGCCCGTTTC
781 TGAGGAAGTCCAAGCCGTGTTGATTTCTCACGTGGGTTCATTCTCTCCTTTTTTTGGCCCGTTTC
95377682 TAGCTCTTTTTTGT
846 TAGCTCTTTTTTGT
95377696 TCTCTCGAGACTAATAACGTCTAACCCTAGATTGATTAATTGAAATCTCTTTCTAATTAACGCAC
1 TCTCTCGAGACTAATAACGTCTAACCCTAGATTGATTAATTGAAATCTCTTTCTAATTAACGCAC
95377761 TAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCAAAATCTT
66 TAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCAAAATCTT
95377826 ATCACCCTATCTCTAGGCGTGCAATCGACTCCGCTTAATTACAAAAAATTTACTCTTAGACAGAG
131 ATCACCCTATCTCTAGGCGTGCAATCGACTCCGCTTAATTACAAAAAATTTACTCTTAGACAGAG
95377891 TCTATTCCTCCTTTGAATAAGAGCATTAACTTGAATCAATATCCTAGAATATTATAACAAGAAAT
196 TCTATTCCTCCTTTGAATAAGAGCATTAACTTGAATCAATATCCTAGAATATTATAACAAGAAAT
95377956 AAGAACACATAATTAAGAACAAGTCAAATATTTATCATACAATTCAGATAATAAAAACAAGATCC
261 AAGAACACATAATTAAGAACAAGTCAAATATTTATCATACAATTCAGATAATAAAAACAAGATCC
95378021 GTCTTAGGTTTCATTCCCCTTAGGTATTTAGGGGGTTTAGTTCATAATTATAAAAGAAAACATCT
326 GTCTTAGGTTTCATTCCCCTTAGGTATTTAGGGGGTTTAGTTCATAATTATAAAAGAAAACATCT
95378086 CAGAAGAATAATGAATACAAAACATAAAGAAAAGCCAAAACCCCTGAATGGAAATTGAAGGGAGA
391 CAGAAGAATAATGAATACAAAACATAAAGAAAAGCCAAAACCCCTGAATGGAAATTGAAGGGAGA
95378151 TCTTCAGTCTTGATGATGAATCCGGCTTCTGAGATGGACCAATCATCTTCCCTTGAGTAATTTCT
456 TCTTCAGTCTTGATGATGAATCCGGCTTCTGAGATGGACCAATCATCTTCCCTTGAGTAATTTCT
95378216 TGCCTCCTACTCCGTGTCTCTCTTCTAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAGAATGCC
521 TGCCTCCTACTCCGTGTCTCTCTTCTAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAGAATGCC
95378281 TAAGAGCCCTTAAAAGTGGCATTTTTCCGAGTAGGACTATACTTGGGCTCGGGAGGGGCACGCCC
586 TAAGAGCCCTTAAAAGTGGCATTTTTCCGAGTAGGACTATACTTGGGCTCGGGAGGGGCACGCCC
95378346 TTGTGACACACCCGTGTGCGATTACTCCAGCCCGTGGTCAAAGCTGTTGAATAGGCACGGACGTG
651 TTGTGACACACCCGTGTGCGATTACTCCAGCCCGTGGTCAAAGCTGTTGAATAGGCACGGACGTG
95378411 TAGTCTACCCGTGTAAGTCATGCTTCGATCCTGCCAAATGGACAAGGCCGTGTGACACGCCCGTG
716 TAGTCTACCCGTGTAAGTCATGCTTCGATCCTGCCAAATGGACAAGGCCGTGTGACACGCCCGTG
95378476 TGAGGAAGTCCAAGCCGTGTTGATTTCTCACGTGGGTTCATTCTCTCCTTTTTTTGGCCCGTTTC
781 TGAGGAAGTCCAAGCCGTGTTGATTTCTCACGTGGGTTCATTCTCTCCTTTTTTTGGCCCGTTTC
95378541 TAGCTCTTTTTTGT
846 TAGCTCTTTTTTGT
95378555 TCTC
1 TCTC
95378559 CTATGCTCAC
Statistics
Matches: 863, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
859 863 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (859 bp):
TCTCTCGAGACTAATAACGTCTAACCCTAGATTGATTAATTGAAATCTCTTTCTAATTAACGCAC
TAGTGTTGCATTAACTCGATCTATGGATCCTCTTATTAGGTTTCACCCTAATCCGGCAAAATCTT
ATCACCCTATCTCTAGGCGTGCAATCGACTCCGCTTAATTACAAAAAATTTACTCTTAGACAGAG
TCTATTCCTCCTTTGAATAAGAGCATTAACTTGAATCAATATCCTAGAATATTATAACAAGAAAT
AAGAACACATAATTAAGAACAAGTCAAATATTTATCATACAATTCAGATAATAAAAACAAGATCC
GTCTTAGGTTTCATTCCCCTTAGGTATTTAGGGGGTTTAGTTCATAATTATAAAAGAAAACATCT
CAGAAGAATAATGAATACAAAACATAAAGAAAAGCCAAAACCCCTGAATGGAAATTGAAGGGAGA
TCTTCAGTCTTGATGATGAATCCGGCTTCTGAGATGGACCAATCATCTTCCCTTGAGTAATTTCT
TGCCTCCTACTCCGTGTCTCTCTTCTAAGTGCCTCCTCAGGTGTTTAAATAGGCTTTAGAATGCC
TAAGAGCCCTTAAAAGTGGCATTTTTCCGAGTAGGACTATACTTGGGCTCGGGAGGGGCACGCCC
TTGTGACACACCCGTGTGCGATTACTCCAGCCCGTGGTCAAAGCTGTTGAATAGGCACGGACGTG
TAGTCTACCCGTGTAAGTCATGCTTCGATCCTGCCAAATGGACAAGGCCGTGTGACACGCCCGTG
TGAGGAAGTCCAAGCCGTGTTGATTTCTCACGTGGGTTCATTCTCTCCTTTTTTTGGCCCGTTTC
TAGCTCTTTTTTGT
Found at i:95379406 original size:21 final size:20
Alignment explanation
Indices: 95379377--95379415 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
95379367 TATAGGCAGC
95379377 AAAAACATGCCAGTTCATAT
1 AAAAACATGCCAGTTCATAT
*
95379397 AAAAATCATGCCATTTCAT
1 AAAAA-CATGCCAGTTCAT
95379416 CTTCAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.28
Consensus pattern (20 bp):
AAAAACATGCCAGTTCATAT
Found at i:95380568 original size:42 final size:42
Alignment explanation
Indices: 95380516--95380633 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
95380506 ATGTTATAGT
*
95380516 ATATCAATGCCAATAG-CCCAGCTATGGTCTTACACGAATCTC
1 ATATCGATGCCAAT-GTCCCAGCTATGGTCTTACACGAATCTC
* *
95380558 ATATTGATGCCAATGTCCCAGAC-ATGGTTTTACACGAATCTC
1 ATATCGATGCCAATGTCCCAG-CTATGGTCTTACACGAATCTC
* *
95380600 GTATCGATGCCAATGTCCCAGATATGGTCTTACA
1 ATATCGATGCCAATGTCCCAGCTATGGTCTTACA
95380634 TGAAATCACA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGCTATGGTCTTACACGAATCTC
Found at i:95389245 original size:46 final size:43
Alignment explanation
Indices: 95389193--95389406 Score: 148
Period size: 46 Copynumber: 4.7 Consensus size: 43
95389183 ATTGTGGGCT
95389193 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGTA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTA-GA-AGTA
* * *
95389239 AGTGTAAGACCACGTCTGGGAAATGGCATCGG--CATTGAGACAAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCATT-AG--AAGT--A
* ** *
95389287 AGTGTAAGATATGTCTGGGACATGCATCGGCCTCAGGACGTAAGCA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTA-G-AAGTA
* *
95389333 AGTGTAAGACATGTCTGGGACATGCATCGG-CTATGA-AATGTA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAGAA-GTA
*
95389375 TCAGTGTAAAACCATGTCTGGGACATGACATC
1 --AGTGTAAGA-CATGTCTGGGACATG-CATC
95389407 TGCAACTTGC
Statistics
Matches: 136, Mismatches: 16, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
44 11 0.08
45 21 0.15
46 53 0.39
47 24 0.18
48 20 0.15
49 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (43 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAGAAGTA
Found at i:95400678 original size:79 final size:78
Alignment explanation
Indices: 95400547--95400709 Score: 301
Period size: 79 Copynumber: 2.1 Consensus size: 78
95400537 ACCAGATATA
95400547 ATATTCTTTTGGTGCAGGACTTATGGACTAATGAAACTCTACCACCACCGGAGCATCATCCTCCA
1 ATATTCTTTTGGTGCAGGACTTATGGACTAATGAAACTCTACCACCACCGGAGCATCATCCTCCA
95400612 CCCTCACACCGAT
66 CCCTCACACCGAT
*
95400625 NATATTCTTTTGGTGCAGGACTTATGGACTAATGAAACTCTACCACCACCGGAGTATCATCCTCC
1 -ATATTCTTTTGGTGCAGGACTTATGGACTAATGAAACTCTACCACCACCGGAGCATCATCCTCC
95400690 ACCCTCACACCGAT
65 ACCCTCACACCGAT
95400704 -TATTCT
1 ATATTCT
95400710 CTAAAAATCC
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
77 6 0.07
79 77 0.93
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (78 bp):
ATATTCTTTTGGTGCAGGACTTATGGACTAATGAAACTCTACCACCACCGGAGCATCATCCTCCA
CCCTCACACCGAT
Found at i:95416901 original size:49 final size:49
Alignment explanation
Indices: 95416836--95416932 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
95416826 TCTGAATAAG
* *
95416836 AGCTTATCTTGAATCAGTATCCTAGGATATGAATACAAGAATTAAGAAA
1 AGCTTATCTTGAATCAGTATCCTAGGATATCAAAACAAGAATTAAGAAA
*
95416885 AGCTTATCTTGAATCAGTATCCTGGGATATCAAAACAAGAATTAAGAA
1 AGCTTATCTTGAATCAGTATCCTAGGATATCAAAACAAGAATTAAGAA
95416933 CACAAAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (49 bp):
AGCTTATCTTGAATCAGTATCCTAGGATATCAAAACAAGAATTAAGAAA
Found at i:95416943 original size:14 final size:15
Alignment explanation
Indices: 95416919--95416948 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
95416909 GGATATCAAA
95416919 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
95416934 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
95416948 A
1 A
95416949 AGTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:95422760 original size:470 final size:470
Alignment explanation
Indices: 95421879--95423288 Score: 2703
Period size: 470 Copynumber: 3.0 Consensus size: 470
95421869 GTCAGGACTT
* * *
95421879 AATCAGGAATTCTAAGAATTTTTTACAAGATTTCAAAAATTTTCTAACTTACGAGGCTGACACGC
1 AATCAGGAATTCTAAGAAGTTTTTACAGGATTTCAAAAATTTTCTAACTTACGAGGATGACACGC
*
95421944 TCGTGTGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCATGTAACTTCTCTGACTT
66 TCGT-TGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCGTGTAACTTCTCTGACTT
**
95422009 GTGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGCATGGTCAATTAATTCATTTCGAAATT
130 GTGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGTGTGGTCAATTAATTCATTTCGAAATT
*
95422074 AGGTGCAGGTTTCACACGGCCAAGACACATGCCTATGTTCTAGGCCATGTAGCATACACGCTCGT
195 AGGTGCAGGTTTCACACGGCCAAGACACATACCTATGTTCTAGGCCATGTAGCATACACGCTCGT
95422139 GTCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACAC
260 GTCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACAC
95422204 GGCCTAACCACACGCCCATGTACCTGGCCATGTGTCACACACGGTCTAGACACACACTCGTGTGT
325 GGCCTAACCACACGCCCATGTACCTGGCCATGTGTCACACACGGTCTAGACACACACTCGTGTGT
95422269 CTATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGAC
390 CTATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGAC
95422334 CTGCACTAAAACTCAA
455 CTGCACTAAAACTCAA
95422350 AATCAGGAATTCTAAGAAGTTTTTACAGGATTTCAAAAATTTTCTAACTTACGAGGATGACACGC
1 AATCAGGAATTCTAAGAAGTTTTTACAGGATTTCAAAAATTTTCTAACTTACGAGGATGACACGC
95422415 TCGTTGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCGTGTAACTTCTCTGACTTG
66 TCGTTGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCGTGTAACTTCTCTGACTTG
95422480 TGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGTGTGGTCAATTAATTCATTTCGAAATTA
131 TGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGTGTGGTCAATTAATTCATTTCGAAATTA
95422545 GGTGCAGGTTTCACACGGCCAAGACACATACCTATGTTCTAGGCCATGTAGCATACACGCTCGTG
196 GGTGCAGGTTTCACACGGCCAAGACACATACCTATGTTCTAGGCCATGTAGCATACACGCTCGTG
95422610 TCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACACG
261 TCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACACG
95422675 GCCTAACCACACGCCCATGTACCTGGCCATGTGTCACACACGGTCTAGACACACACTCGTGTGTC
326 GCCTAACCACACGCCCATGTACCTGGCCATGTGTCACACACGGTCTAGACACACACTCGTGTGTC
95422740 TATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGACC
391 TATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGACC
95422805 TGCACTAAAACTCAA
456 TGCACTAAAACTCAA
95422820 AATCAGGAATTCTAAGAAGTTTTTACAGGATTTCAAAAATTTTCTAACTTACGAGGATGACACGC
1 AATCAGGAATTCTAAGAAGTTTTTACAGGATTTCAAAAATTTTCTAACTTACGAGGATGACACGC
95422885 TCGTTGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCGTGTAACTTCTCTGACTTG
66 TCGTTGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCGTGTAACTTCTCTGACTTG
95422950 TGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGTGTGGTCAATTAATTCATTTCGAAATTA
131 TGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGTGTGGTCAATTAATTCATTTCGAAATTA
95423015 GGTGCAGGTTTCACACGGCCAAGACACATACCTATGTTCTAGGCCATGTAGCATACACGCTCGTG
196 GGTGCAGGTTTCACACGGCCAAGACACATACCTATGTTCTAGGCCATGTAGCATACACGCTCGTG
95423080 TCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACACG
261 TCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACACG
* * * *
95423145 GCCTAACCATACGTCCATGTACCAGGCCATGTGTCACACACGGTCTAGAGACACACTCGTGTGTC
326 GCCTAACCACACGCCCATGTACCTGGCCATGTGTCACACACGGTCTAGACACACACTCGTGTGTC
95423210 TATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGACC
391 TATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGACC
*
95423275 TACACTAAAACTCA
456 TGCACTAAAACTCA
95423289 CATCCATTAA
Statistics
Matches: 927, Mismatches: 12, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
470 861 0.93
471 66 0.07
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (470 bp):
AATCAGGAATTCTAAGAAGTTTTTACAGGATTTCAAAAATTTTCTAACTTACGAGGATGACACGC
TCGTTGACCCTAGGACACGCCCGTGCTATAGAGCATGTTCGACTTCGTGTAACTTCTCTGACTTG
TGCACATGGCCATGCCACACGCCCGTGTGCTAGGTCGTGTGGTCAATTAATTCATTTCGAAATTA
GGTGCAGGTTTCACACGGCCAAGACACATACCTATGTTCTAGGCCATGTAGCATACACGCTCGTG
TCTCTACCTGTATGCTCAATTCTGAGCATTCTATTTTCTTAAATTTAAGGTGCAGGGGACACACG
GCCTAACCACACGCCCATGTACCTGGCCATGTGTCACACACGGTCTAGACACACACTCGTGTGTC
TATCCATGTGGACGAAATAAAGCCATTTCTAGTTTCATTTCTCACCCAAAATCACACCAATGACC
TGCACTAAAACTCAA
Found at i:95424541 original size:52 final size:52
Alignment explanation
Indices: 95424481--95424584 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
95424471 TCTATGGATT
95424481 CCCTTATTAGGTTTCACCCTAATCTGGCAAAATTTTATCACCCTACCTCTAG
1 CCCTTATTAGGTTTCACCCTAATCTGGCAAAATTTTATCACCCTACCTCTAG
*
95424533 CCCTTATTAGGTTTCACCCTAATCTGGCAAAATTTTATCACCCTATCTCTAG
1 CCCTTATTAGGTTTCACCCTAATCTGGCAAAATTTTATCACCCTACCTCTAG
95424585 GCATGCAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.36
Consensus pattern (52 bp):
CCCTTATTAGGTTTCACCCTAATCTGGCAAAATTTTATCACCCTACCTCTAG
Found at i:95425154 original size:13 final size:13
Alignment explanation
Indices: 95425136--95425163 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
95425126 CTGCCAAAGG
95425136 GACACGCCCGTGT
1 GACACGCCCGTGT
95425149 GACACGCCCGTGT
1 GACACGCCCGTGT
95425162 GA
1 GA
95425164 GAAAGTCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.14
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:95425683 original size:59 final size:59
Alignment explanation
Indices: 95425591--95425708 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
95425581 TAAGTGATTA
95425591 CCTTTGATCAAAATGTCACAGAGTTTAACACCCTCACTAAAGATTCACTGC-AATCACTC
1 CCTTTGATCAAAATGTCACAGAGTTTAACACCCTCACTAAAGATTCACT-CAAATCACTC
95425650 CCTTTGATCAAAATGTCACAGAGTTTAACACCCTCACTAAAGATTCACTCAAATCACTC
1 CCTTTGATCAAAATGTCACAGAGTTTAACACCCTCACTAAAGATTCACTCAAATCACTC
95425709 AAGGTGTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 1 0.02
59 57 0.98
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (59 bp):
CCTTTGATCAAAATGTCACAGAGTTTAACACCCTCACTAAAGATTCACTCAAATCACTC
Found at i:95440919 original size:44 final size:44
Alignment explanation
Indices: 95440871--95440962 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
95440861 ACACATAATT
95440871 AAGAACAAGTCAAATATTTATCATACAATTCAGATAATAATAAA
1 AAGAACAAGTCAAATATTTATCATACAATTCAGATAATAATAAA
95440915 AAGAACAAGTCAAATATTTATCATACAATTCAGATAATAATAAA
1 AAGAACAAGTCAAATATTTATCATACAATTCAGATAATAATAAA
95440959 AAGA
1 AAGA
95440963 TCCATCTTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (44 bp):
AAGAACAAGTCAAATATTTATCATACAATTCAGATAATAATAAA
Found at i:95444579 original size:32 final size:32
Alignment explanation
Indices: 95444538--95444600 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
95444528 TATGGTGCCT
95444538 ATGAAAATGGAGAATTAGGAAAAAGGATGAGC
1 ATGAAAATGGAGAATTAGGAAAAAGGATGAGC
*
95444570 ATGAAAATGGAGAATTAGGAAAGAGGATGAG
1 ATGAAAATGGAGAATTAGGAAAAAGGATGAG
95444601 TAAGACGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.02, G:0.33, T:0.16
Consensus pattern (32 bp):
ATGAAAATGGAGAATTAGGAAAAAGGATGAGC
Found at i:95444591 original size:16 final size:16
Alignment explanation
Indices: 95444540--95444591 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
95444530 TGGTGCCTAT
95444540 GAAAATGGAGAATTAG
1 GAAAATGGAGAATTAG
* ** *
95444556 GAAAAAGGATG-AGCAT
1 GAAAATGGA-GAATTAG
95444572 GAAAATGGAGAATTAG
1 GAAAATGGAGAATTAG
95444588 GAAA
1 GAAA
95444592 GAGGATGAGT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.31, T:0.15
Consensus pattern (16 bp):
GAAAATGGAGAATTAG
Found at i:95449475 original size:26 final size:26
Alignment explanation
Indices: 95449443--95449550 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
95449433 TGAAATGCCC
*
95449443 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
95449469 ATTATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
95449495 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
95449521 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
95449547 ATCA
1 ATCA
95449551 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:95461516 original size:46 final size:48
Alignment explanation
Indices: 95461414--95461732 Score: 221
Period size: 46 Copynumber: 6.7 Consensus size: 48
95461404 ACATTATGAG
* * * ** ***
95461414 AGCCAATGTAAGACCATGTCTGGTACATGGCATCGGCATTAAGACAAA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA
**
95461462 AGATAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA
* * * *
95461508 AGCCAGTGTAAGA-TATGTCTAGGACATGG-ATTGG-CTATGAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGTA
** * * * *
95461553 -GTTAGTGTAAGACCATGTTTGGGACATGGCATCGACAC-AGATATGTGA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGATGT-A
* * *
95461601 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATTACG-A
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-GATGTA
* * * *
95461650 TAGTCAGTGTAAGACCAAGTCTGGGACATGGCATC-GACT-TA-ATGGATA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT-G-TA
* *
95461698 AGCTAGTGCAAGACCATGTCTGGGACATGGCATCG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
95461733 ACATTCTACC
Statistics
Matches: 213, Mismatches: 42, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
44 10 0.05
45 16 0.08
46 57 0.27
47 45 0.21
48 15 0.07
49 34 0.16
50 33 0.15
51 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA
Found at i:95461672 original size:49 final size:50
Alignment explanation
Indices: 95461556--95461735 Score: 181
Period size: 49 Copynumber: 3.7 Consensus size: 50
95461546 GAGATGTGTT
* **
95461556 AGTGTAAGACCATGTTTGGGACATGGCATCGACACAGATATGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATACGAGAGCC
* * * *
95461606 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTC-GAT-TACGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GACACAGATATACGAGAGCC
* ** ** * *
95461655 AGTGTAAGACCAAGTCTGGGACATGGCATCGACTTA-ATGGA-TA-AGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATACGAGAGCC
*
95461702 AGTGCAAGACCATGTCTGGGACATGGCATCGACA
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACA
95461736 TTCTACCATA
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
47 33 0.30
48 6 0.05
49 36 0.33
50 32 0.29
51 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATACGAGAGCC
Found at i:95461675 original size:99 final size:96
Alignment explanation
Indices: 95461556--95461731 Score: 246
Period size: 96 Copynumber: 1.8 Consensus size: 96
95461546 GAGATGTGTT
* * * *
95461556 AGTGTAAGACCATGTTTGGGACATGGCATCGACACAGATATGTGA-GAGCCAGTGTAAGACCATG
1 AGTGTAAGACCAAGTCTGGGACATGGCATCG--ACAGA-ATG-GATAAGCCAGTGCAAGACCATG
95461620 TCTGGGACATGGCATCAGCCTCGATTACGATAGTC
62 TCTGGGACATGGCATCAGCCTCGATTACGATAGTC
** *
95461655 AGTGTAAGACCAAGTCTGGGACATGGCATCGACTTAATGGATAAGCTAGTGCAAGACCATGTCTG
1 AGTGTAAGACCAAGTCTGGGACATGGCATCGACAGAATGGATAAGCCAGTGCAAGACCATGTCTG
95461720 GGACATGGCATC
66 GGACATGGCATC
95461732 GACATTCTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 2 0.03
96 35 0.51
97 3 0.04
99 29 0.42
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (96 bp):
AGTGTAAGACCAAGTCTGGGACATGGCATCGACAGAATGGATAAGCCAGTGCAAGACCATGTCTG
GGACATGGCATCAGCCTCGATTACGATAGTC
Found at i:95461724 original size:47 final size:46
Alignment explanation
Indices: 95461420--95461734 Score: 189
Period size: 47 Copynumber: 6.7 Consensus size: 46
95461410 TGAGAGCCAA
* * * * * *
95461420 TGTAAGACCATGTCTGGTACATGGCATCGGCATTAA-GACAAAAGATAG
1 TGTAAGACCATGTCTGGGACATGGCATCGAC-TGAATG--GATAGCTAG
* * *
95461468 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATC-GACT-GA-ATGGATAGCTAG
* * * * * *
95461514 TGTAAGA-TATGTCTAGGACATGG-ATTGGCT--ATGAGATGTGTTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTGAATG-GAT-AGCTAG
* * * *
95461558 TGTAAGACCATGTTTGGGACATGGCATCGACACAGATATGTGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCG--ACTGA-ATG-GATAGCTAG
* * *
95461608 TGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATTACGATAG-TCAG
1 TGTAAGACCATGTCTGGGACATGGCATC-GACT-GAAT-GGATAGCT-AG
* *
95461657 TGTAAGACCAAGTCTGGGACATGGCATCGACTTAATGGATAAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTGAATGGAT-AGCTAG
*
95461704 TGCAAGACCATGTCTGGGACATGGCATCGAC
1 TGTAAGACCATGTCTGGGACATGGCATCGAC
95461735 ATTCTACCAT
Statistics
Matches: 207, Mismatches: 39, Indels: 43
0.72 0.13 0.15
Matches are distributed among these distances:
41 3 0.01
42 1 0.00
44 10 0.05
45 16 0.08
46 37 0.18
47 53 0.26
48 13 0.06
49 36 0.17
50 32 0.15
51 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACTGAATGGATAGCTAG
Found at i:95463711 original size:40 final size:40
Alignment explanation
Indices: 95463656--95463797 Score: 171
Period size: 40 Copynumber: 3.6 Consensus size: 40
95463646 TATTTGGATG
*
95463656 ATAACCGGGCTAAGTCCCGAAGTCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
95463696 ATAACCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * * *
95463736 AGAGCCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* * *
95463776 ATATCC-GGTTAAATCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
95463798 TACTTGGCTT
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 15 0.17
40 73 0.83
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:95468301 original size:47 final size:47
Alignment explanation
Indices: 95468230--95468397 Score: 273
Period size: 47 Copynumber: 3.6 Consensus size: 47
95468220 CCCTTCGGGA
* * * *
95468230 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
95468277 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
95468324 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
95468371 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
95468398 TATTCAAATA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 113 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:95468308 original size:25 final size:25
Alignment explanation
Indices: 95468280--95468358 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
95468270 ACTCGGCCCT
95468280 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
95468305 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
95468327 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
95468352 ATCACAT
1 ATCACAT
95468359 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:95473773 original size:15 final size:16
Alignment explanation
Indices: 95473753--95473785 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
95473743 ATATATATTT
95473753 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
95473768 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
95473785 T
1 T
95473786 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:95473871 original size:22 final size:22
Alignment explanation
Indices: 95473832--95473890 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
95473822 GTTTTAAGAA
*
95473832 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
95473853 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
95473875 AT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
95473891 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:95473907 original size:26 final size:24
Alignment explanation
Indices: 95473861--95473920 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
95473851 ATTTGTTTTA
95473861 ATATTTATTTTTATATTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
95473885 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
95473911 TTTTTTATTT
1 ATATTTATTT
95473921 AATGAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.25
26 18 0.56
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:95478573 original size:21 final size:21
Alignment explanation
Indices: 95478547--95478588 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
95478537 GATCAACCGC
95478547 TACCAAACAAATACTATAATA
1 TACCAAACAAATACTATAATA
*
95478568 TACCAAACAACTACTATAATA
1 TACCAAACAAATACTATAATA
95478589 GTGCATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (21 bp):
TACCAAACAAATACTATAATA
Found at i:95488993 original size:23 final size:25
Alignment explanation
Indices: 95488950--95488999 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
95488940 ATGGGAAAGA
*
95488950 AAAAAATAAGTTAGGGAATTAG-GG
1 AAAAAATAAGTTAGAGAATTAGAGG
*
95488974 AAAAATTAAGTTAGAG-ATTAGAGG
1 AAAAAATAAGTTAGAGAATTAGAGG
95488998 AA
1 AA
95489000 TAAGGGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.22
Consensus pattern (25 bp):
AAAAAATAAGTTAGAGAATTAGAGG
Found at i:95500864 original size:31 final size:31
Alignment explanation
Indices: 95500829--95500892 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
95500819 AGAATGTTAC
95500829 GAAAGCCCCTTCGAAAAAGTTAGTAGAGCGT
1 GAAAGCCCCTTCGAAAAAGTTAGTAGAGCGT
** *
95500860 GAAAGCCTTTTCGAAAAAGTTAGTGGAGCGT
1 GAAAGCCCCTTCGAAAAAGTTAGTAGAGCGT
95500891 GA
1 GA
95500893 GTCTGATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (31 bp):
GAAAGCCCCTTCGAAAAAGTTAGTAGAGCGT
Found at i:95503553 original size:4 final size:4
Alignment explanation
Indices: 95503532--95503570 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
95503522 ACAAAGATCT
* *
95503532 ATAC ATGC ATAG ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
95503571 TATATATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:95508376 original size:18 final size:18
Alignment explanation
Indices: 95508353--95508387 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
95508343 AGTGAGAATA
95508353 AGGAACCCAAAATCATTC
1 AGGAACCCAAAATCATTC
95508371 AGGAACCCAAAATCATT
1 AGGAACCCAAAATCATT
95508388 TTGACATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (18 bp):
AGGAACCCAAAATCATTC
Found at i:95510636 original size:23 final size:23
Alignment explanation
Indices: 95510553--95510640 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 23
95510543 TTAGTGCCAA
* *
95510553 TCTGGTGTGTTTGGGTAGATTAT
1 TCTGGTGTGTTTGGTTGGATTAT
* * *
95510576 TATGGTGTGTTTGAG-AGGATCAT
1 TCTGGTGTGTTTG-GTTGGATTAT
95510599 TCTGGTGTGTTTGGTTGGATTAT
1 TCTGGTGTGTTTGGTTGGATTAT
*
95510622 TCCGGTGTGTTTGGTTGGA
1 TCTGGTGTGTTTGGTTGGA
95510641 ATCCGTGTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.02
23 53 0.96
24 1 0.02
ACGTcount: A:0.12, C:0.06, G:0.36, T:0.45
Consensus pattern (23 bp):
TCTGGTGTGTTTGGTTGGATTAT
Found at i:95511463 original size:7 final size:7
Alignment explanation
Indices: 95511451--95511491 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
95511441 AGTTTTTCTT
95511451 TAAAAAA
1 TAAAAAA
95511458 TAAAAAA
1 TAAAAAA
95511465 TAAAAAA
1 TAAAAAA
95511472 TAAAAAA
1 TAAAAAA
95511479 TAATAAAA
1 TAA-AAAA
95511487 TAAAA
1 TAAAA
95511492 TAAAAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:95511477 original size:21 final size:22
Alignment explanation
Indices: 95511452--95511497 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
95511442 GTTTTTCTTT
95511452 AAAAAATAAAAAATAA-AAAAT
1 AAAAAATAAAAAATAATAAAAT
*
95511473 AAAAAAT-AATAA-AATAAAAT
1 AAAAAATAAAAAATAATAAAAT
95511493 AAAAA
1 AAAAA
95511498 TTTTCGGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 14 0.61
21 7 0.30
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAAAATAAAAAATAATAAAAT
Found at i:95520479 original size:29 final size:29
Alignment explanation
Indices: 95520431--95520509 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
95520421 TTACACTTAC
*
95520431 TGAAATGTGAATAATGAATAAATTGAAAT
1 TGAAATGTGAATAGTGAATAAATTGAAAT
*
95520460 TGAAATGTGAATAGTAAATAAATTGAAAT
1 TGAAATGTGAATAGTGAATAAATTGAAAT
95520489 TGAAATGTGAATAGTGAATAA
1 TGAAATGTGAATAGTGAATAA
95520510 TGATTATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (29 bp):
TGAAATGTGAATAGTGAATAAATTGAAAT
Found at i:95521610 original size:41 final size:42
Alignment explanation
Indices: 95521513--95521760 Score: 410
Period size: 42 Copynumber: 6.0 Consensus size: 42
95521503 TCATTTTCTA
* * * * *
95521513 ATGCCATAGTCTAACTATGGTCTTACACATATTCACATATCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCG
*
95521555 ATGCGATAGCCCAGCTATGGTCTTACACGTAATCACATA-CG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCG
*
95521596 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCG
95521638 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA-CG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCG
*
95521679 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCG
95521721 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAT
1 ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATAT
95521761 TGCCATGGTC
Statistics
Matches: 193, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
41 79 0.41
42 114 0.59
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (42 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCG
Found at i:95521652 original size:83 final size:83
Alignment explanation
Indices: 95521513--95521759 Score: 431
Period size: 83 Copynumber: 3.0 Consensus size: 83
95521503 TCATTTTCTA
* * * * * * *
95521513 ATGCCATAGTCTAACTATGGTCTTACACATATTCACATATCGATGCGATAGCCCAGCTATGGTCT
1 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCGATGCCATAGCCCAGCTATGGTCT
95521578 TACACGTAATCACATACG
66 TACACGTAATCACATACG
95521596 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCGATGCCATAGCCCAGCTATGGTCT
1 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCGATGCCATAGCCCAGCTATGGTCT
95521661 TACACGTAATCACATACG
66 TACACGTAATCACATACG
95521679 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCGATGCCATAGCCCAGCTATGGTCT
1 ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCGATGCCATAGCCCAGCTATGGTCT
95521744 TACACGTAATCACATA
66 TACACGTAATCACATA
95521760 TTGCCATGGT
Statistics
Matches: 157, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 157 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (83 bp):
ATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCGATGCCATAGCCCAGCTATGGTCT
TACACGTAATCACATACG
Found at i:95531100 original size:85 final size:85
Alignment explanation
Indices: 95530957--95531125 Score: 320
Period size: 85 Copynumber: 2.0 Consensus size: 85
95530947 CATAGAAGGG
* *
95530957 AAAAGTGATCATCATGTCATAAAACATAAGAATAAGGGATGAAGTTTAATTCCCGAGCCTAGGGG
1 AAAAGTGATCAGCATGTCATAAAACATAAGAATAACGGATGAAGTTTAATTCCCGAGCCTAGGGG
95531022 CAAAAGTGTAAATATGCAAT
66 CAAAAGTGTAAATATGCAAT
95531042 AAAAGTGATCAGCATGTCATAAAACATAAGAATAACGGATGAAGTTTAATTCCCGAGCCTAGGGG
1 AAAAGTGATCAGCATGTCATAAAACATAAGAATAACGGATGAAGTTTAATTCCCGAGCCTAGGGG
95531107 CAAAAGTGTAAATATGCAA
66 CAAAAGTGTAAATATGCAA
95531126 AAGTTTAAGG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (85 bp):
AAAAGTGATCAGCATGTCATAAAACATAAGAATAACGGATGAAGTTTAATTCCCGAGCCTAGGGG
CAAAAGTGTAAATATGCAAT
Found at i:95532424 original size:46 final size:46
Alignment explanation
Indices: 95532374--95532549 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
95532364 TGGTTGAGCA
95532374 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
95532420 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
95532465 CATCCGAACTCGTTCAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
95532513 CCCGAGCTCGTTGAGTTGTGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
95532550 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:95532530 original size:93 final size:93
Alignment explanation
Indices: 95532371--95532542 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
95532361 GGATGGTTGA
* * *
95532371 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
95532436 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
95532464 GCATCCGAACTCGTTCAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
95532529 TGTGTCCGAGTTCG
66 TGAGTCCGAGTTCG
95532543 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTCAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:95537943 original size:16 final size:15
Alignment explanation
Indices: 95537901--95537943 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
95537891 CTTAATTTGT
95537901 TCTTT-CTATTTATG
1 TCTTTACTATTTATG
*
95537915 TCTTTATTGATTTATG
1 TCTTTACT-ATTTATG
95537931 CTCTTTACTATTT
1 -TCTTTACTATTT
95537944 CTCTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 5 0.21
15 1 0.04
16 11 0.46
17 7 0.29
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.63
Consensus pattern (15 bp):
TCTTTACTATTTATG
Found at i:95539482 original size:6 final size:6
Alignment explanation
Indices: 95539466--95539505 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
95539456 CATTGAGTCC
*
95539466 ATTTAT CTTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
95539506 TAATTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:95539511 original size:18 final size:18
Alignment explanation
Indices: 95539473--95539543 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
95539463 TCCATTTATC
95539473 TTTATATTTATA-TTTATA
1 TTTATATTTATATTTTA-A
95539491 TTTATATTTATATTTTAA
1 TTTATATTTATATTTTAA
* * * *
95539509 TTTTTCTTTTTATGTTTAT
1 TTTATATTTATAT-TTTAA
* *
95539528 TTTGTCTTTATATTTT
1 TTTATATTTATATTTT
95539544 GAACTCTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 26 0.58
19 19 0.42
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATATTTATATTTTAA
Found at i:95539530 original size:12 final size:12
Alignment explanation
Indices: 95539466--95539542 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
95539456 CATTGAGTCC
*
95539466 ATTTATCTTTAT
1 ATTTATTTTTAT
*
95539478 ATTTATATTTAT
1 ATTTATTTTTAT
*
95539490 ATTTATATTTAT
1 ATTTATTTTTAT
*
95539502 ATTTTAATTTTTCT
1 A-TTT-ATTTTTAT
* *
95539516 TTTTATGTTTAT
1 ATTTATTTTTAT
* *
95539528 -TTTGTCTTTAT
1 ATTTATTTTTAT
95539539 ATTT
1 ATTT
95539543 TGAACTCTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.17
12 33 0.61
13 6 0.11
14 6 0.11
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (12 bp):
ATTTATTTTTAT
Found at i:95539874 original size:30 final size:30
Alignment explanation
Indices: 95539840--95539901 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
95539830 GGACATGGTT
* *
95539840 GTGTGGCCAGCTCGTGGGGATCCCACGGCC
1 GTGTGGCCAGCCCGTAGGGATCCCACGGCC
95539870 GTGTGGCCAGCCCGTAGGGATCCCACGGCC
1 GTGTGGCCAGCCCGTAGGGATCCCACGGCC
95539900 GT
1 GT
95539902 TGCAATTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.11, C:0.34, G:0.39, T:0.16
Consensus pattern (30 bp):
GTGTGGCCAGCCCGTAGGGATCCCACGGCC
Found at i:95546438 original size:33 final size:33
Alignment explanation
Indices: 95546401--95546480 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
95546391 GAGGTGTACA
95546401 TTCCTTTTCAAGTGGTACACACAAAGTATACCT
1 TTCCTTTTCAAGTGGTACACACAAAGTATACCT
*
95546434 TTCCTTTTCATA-TGGTATACACAAAGTATACCT
1 TTCCTTTTCA-AGTGGTACACACAAAGTATACCT
** *
95546467 AACCTTTCCAAGTG
1 TTCCTTTTCAAGTG
95546481 TACCACTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 39 0.95
34 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (33 bp):
TTCCTTTTCAAGTGGTACACACAAAGTATACCT
Found at i:95549531 original size:39 final size:39
Alignment explanation
Indices: 95549436--95549892 Score: 701
Period size: 39 Copynumber: 11.6 Consensus size: 39
95549426 TTGAATGATG
*
95549436 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
95549474 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
95549515 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
95549554 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
95549593 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
95549632 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
95549671 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
95549710 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
95549749 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
** * *
95549788 TCCGGGCTAAGCCAAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
95549827 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
95549866 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
95549893 AACGAGGAGC
Statistics
Matches: 393, Mismatches: 18, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
39 325 0.83
40 56 0.14
41 11 0.03
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:95550252 original size:60 final size:60
Alignment explanation
Indices: 95550159--95550281 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
95550149 GCATATGAAA
*
95550159 TTATCCGTTTAGCTATATGAATGCTATACTTTTGTTGTGCTGGAATTCATTGCTCATAAC
1 TTATCCGTTTAGCTATATGAATGCTATACTTTTGTTGTGCTGGAATTCATTGCTCAAAAC
95550219 TTATCCGTTTAGCTATATGAATGCTATACTTTTGTTGTGCTGGAATTCATTGCTCAAAAC
1 TTATCCGTTTAGCTATATGAATGCTATACTTTTGTTGTGCTGGAATTCATTGCTCAAAAC
95550279 TTA
1 TTA
95550282 CTAAGCATAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (60 bp):
TTATCCGTTTAGCTATATGAATGCTATACTTTTGTTGTGCTGGAATTCATTGCTCAAAAC
Found at i:95554793 original size:108 final size:108
Alignment explanation
Indices: 95554604--95554820 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
95554594 ACTCGAGCCA
95554604 CTTGCGTTGCCTCAAATTCAAGTCTTTCTGTGCCATTAAATACTTCAGACTTTTATGGTCAGTGT
1 CTTGCGTTGCCTCAAATTCAAGTCTTTCTGTGCCATTAAATACTTCAGACTTTTATGGTCAGTGT
95554669 AAATATAAAATTTTTCACCATATAAATAATGCCGCTATATTTT
66 AAATATAAAATTTTTCACCATATAAATAATGCCGCTATATTTT
95554712 CTTGCGTTGCCTCAAATTCAAGTCTTTCTGTGCCATTAAATACTTCAGACTTTTATGGTCAGTGT
1 CTTGCGTTGCCTCAAATTCAAGTCTTTCTGTGCCATTAAATACTTCAGACTTTTATGGTCAGTGT
95554777 AAATATAAAATTTTTCACCATATAAATAATGCCGCTATATTTT
66 AAATATAAAATTTTTCACCATATAAATAATGCCGCTATATTTT
95554820 C
1 C
95554821 AATGGAAACA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (108 bp):
CTTGCGTTGCCTCAAATTCAAGTCTTTCTGTGCCATTAAATACTTCAGACTTTTATGGTCAGTGT
AAATATAAAATTTTTCACCATATAAATAATGCCGCTATATTTT
Found at i:95557650 original size:44 final size:44
Alignment explanation
Indices: 95557579--95557666 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
95557569 CAGGAAACCA
*
95557579 TTTATCCAACATTTCAACGAAAACCTCTTTAGCATATTCACTTC
1 TTTATCCAACATTTCAAAGAAAACCTCTTTAGCATATTCACTTC
*
95557623 TTTATCCAACATTTCAAAGAAAGCCTCTTTAGCATATTCACTTC
1 TTTATCCAACATTTCAAAGAAAACCTCTTTAGCATATTCACTTC
95557667 GACTCTCTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (44 bp):
TTTATCCAACATTTCAAAGAAAACCTCTTTAGCATATTCACTTC
Found at i:95559323 original size:40 final size:40
Alignment explanation
Indices: 95559278--95559469 Score: 217
Period size: 40 Copynumber: 4.8 Consensus size: 40
95559268 ATAACCACAA
* * *
95559278 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
* *
95559318 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
* * * *
95559358 GTACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATATCAACTC
* * *
95559398 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGAT-ATATCAACTC
* * *
95559438 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT
95559470 CATTCAAATG
Statistics
Matches: 134, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 129 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATATCAACTC
Found at i:95562738 original size:33 final size:33
Alignment explanation
Indices: 95562668--95562780 Score: 90
Period size: 33 Copynumber: 3.5 Consensus size: 33
95562658 GGTGTACATT
* **
95562668 CCTTTTCAAGTGGTACATACAAAGTATACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
* *
95562701 CCTTTTCATA-TGGTATACACAATGTATACCTAA
1 CCTTTTCA-AGTGGTACACACAAAGTATACCTAA
** * *
95562734 CC-TTTCTAAGT-ACACACACAAAGTGTACATAA
1 CCTTTTC-AAGTGGTACACACAAAGTATACCTAA
*
95562766 CC-TTTCAAGTTGTAC
1 CCTTTTCAAGTGGTAC
95562781 CACTTGGGTA
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
31 4 0.06
32 28 0.44
33 30 0.48
34 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTATACCTAA
Found at i:95563973 original size:13 final size:13
Alignment explanation
Indices: 95563955--95563980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95563945 ACACATAATT
95563955 GATAAAAATTTTC
1 GATAAAAATTTTC
95563968 GATAAAAATTTTC
1 GATAAAAATTTTC
95563981 ATGCAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GATAAAAATTTTC
Found at i:95568019 original size:7 final size:7
Alignment explanation
Indices: 95568003--95568041 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
95567993 CTAAAGCTAC
*
95568003 CACTTAT
1 CACTTGT
95568010 CACTTGT
1 CACTTGT
95568017 CACTTGT
1 CACTTGT
95568024 CACTTGT
1 CACTTGT
*
95568031 CACTTAT
1 CACTTGT
95568038 CACT
1 CACT
95568042 GATTAGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:95568026 original size:14 final size:14
Alignment explanation
Indices: 95568003--95568041 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
95567993 CTAAAGCTAC
95568003 CACTTATCACTTGT
1 CACTTATCACTTGT
*
95568017 CACTTGTCACTTGT
1 CACTTATCACTTGT
95568031 CACTTATCACT
1 CACTTATCACT
95568042 GATTAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.41
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:95572294 original size:21 final size:22
Alignment explanation
Indices: 95572250--95572294 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
95572240 CCCAGATTTG
**
95572250 AAAAGATTAGAATAATATTGAA
1 AAAAGATTAGAATAATATCAAA
*
95572272 AAAAG-TTAGAGTAATATCAAA
1 AAAAGATTAGAATAATATCAAA
95572293 AA
1 AA
95572295 GAGTACTCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAAGATTAGAATAATATCAAA
Found at i:95575178 original size:31 final size:31
Alignment explanation
Indices: 95575140--95575198 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
95575130 ACAAATGACA
95575140 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
*
95575171 AGTGAAAAGTGGTAGCTTCTGCTACCTG
1 AGTGAAAAGTGGTAGCTTCAGCTACCTG
95575199 CTAAAATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:95576363 original size:30 final size:30
Alignment explanation
Indices: 95576315--95576372 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
95576305 CAAGCCAATT
* *
95576315 CCACACGGGCTGAGCACACTCCCGTGTGAA
1 CCACACGGGCTGAGCACACGCCCATGTGAA
95576345 CCACACGGGCTG-GCCACACGCCCATGTG
1 CCACACGGGCTGAG-CACACGCCCATGTG
95576373 CCTGCCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.21, C:0.40, G:0.28, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGAGCACACGCCCATGTGAA
Found at i:95579020 original size:47 final size:48
Alignment explanation
Indices: 95578961--95579091 Score: 165
Period size: 47 Copynumber: 2.8 Consensus size: 48
95578951 TTCGATCGAT
* * *
95578961 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTTATC-CCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCCA
* * * * * *
95579008 GAGTACCAATACCATGGCCCGTAGCCAAATTAAGGTATCTCCTCTCTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCCA
*
95579056 AAATACCTATACCATGGCCCGTAGCCAAATCAAGGT
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGT
95579092 GTAACACCCC
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
47 37 0.53
48 33 0.47
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCCA
Found at i:95580049 original size:27 final size:28
Alignment explanation
Indices: 95580019--95580086 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
95580009 GTGATGAAGT
95580019 CACCAGATACAGATAT-TGTGGCAGAGC
1 CACCAGATACAGATATATGTGGCAGAGC
95580046 CACCAGA-ACAGATATATGTGGCAGAGC
1 CACCAGATACAGATATATGTGGCAGAGC
95580073 CACCAGAT-CAGATA
1 CACCAGATACAGATA
95580087 ATNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 8 0.21
27 31 0.79
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (28 bp):
CACCAGATACAGATATATGTGGCAGAGC
Found at i:95594276 original size:26 final size:26
Alignment explanation
Indices: 95594246--95594301 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
95594236 TGAAATTCCC
95594246 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
95594272 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
95594298 ATCA
1 ATCA
95594302 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:95599269 original size:5 final size:5
Alignment explanation
Indices: 95599259--95599313 Score: 92
Period size: 5 Copynumber: 11.0 Consensus size: 5
95599249 TAAAGTATAT
* *
95599259 TATTA TATTA TATTA TATTA TATTA TGTTA TATTA GATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
95599309 TATTA
1 TATTA
95599314 ACTAATAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:95600029 original size:14 final size:16
Alignment explanation
Indices: 95600000--95600032 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
95599990 GTATTTTAAT
95600000 TAAAATGCATGGTAAG
1 TAAAATGCATGGTAAG
95600016 TAAAATG-A-GGTAAG
1 TAAAATGCATGGTAAG
95600030 TAA
1 TAA
95600033 TTGATATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.48, C:0.03, G:0.24, T:0.24
Consensus pattern (16 bp):
TAAAATGCATGGTAAG
Found at i:95600110 original size:23 final size:21
Alignment explanation
Indices: 95600084--95600128 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
95600074 GTGTATATGG
95600084 TTATTGGAATTGAATATGATTAT
1 TTATTGGAATTGAA-ATG-TTAT
*
95600107 TTATTTGAATTGAAATGTTAT
1 TTATTGGAATTGAAATGTTAT
95600128 T
1 T
95600129 AGTGAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
TTATTGGAATTGAAATGTTAT
Found at i:95600146 original size:29 final size:29
Alignment explanation
Indices: 95600114--95600195 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
95600104 TATTTATTTG
*
95600114 AATTGAAATGTTATTAGTGAATAAATTGA
1 AATTGAAATGTAATTAGTGAATAAATTGA
* *
95600143 AATTGAAATGTGAA-TAGTAAATTAATTGA
1 AATTGAAATGT-AATTAGTGAATAAATTGA
95600172 AATTGAAATGTGAATT-GTGAATAA
1 AATTGAAATGT-AATTAGTGAATAA
95600196 TGATTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.35
Consensus pattern (29 bp):
AATTGAAATGTAATTAGTGAATAAATTGA
Found at i:95600635 original size:24 final size:24
Alignment explanation
Indices: 95600608--95600654 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
95600598 AACATGGTTT
95600608 TATGAAATGATTATTGATATAATG
1 TATGAAATGATTATTGATATAATG
*
95600632 TATGAAATGGTTATTGATATAAT
1 TATGAAATGATTATTGATATAAT
95600655 TAGACTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (24 bp):
TATGAAATGATTATTGATATAATG
Found at i:95601430 original size:28 final size:28
Alignment explanation
Indices: 95601366--95601421 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
95601356 TTTCTAGAAT
95601366 ACCGAATTTGGTCTCGATCTGGTTCTAA
1 ACCGAATTTGGTCTCGATCTGGTTCTAA
95601394 ACCGAATTTGGTCTCGATCTGGTTCTAA
1 ACCGAATTTGGTCTCGATCTGGTTCTAA
95601422 CATGTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (28 bp):
ACCGAATTTGGTCTCGATCTGGTTCTAA
Found at i:95605398 original size:24 final size:25
Alignment explanation
Indices: 95605371--95605428 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
95605361 TATGCTCTTT
* * *
95605371 CGAGCTATA-AACGGTAAGCTCCTC
1 CGAGCTAAATAACGGTAAGCTCATA
*
95605395 CGAGATGAAATAACGGTAAGCTCATA
1 CGAGCT-AAATAACGGTAAGCTCATA
95605421 CGAGCTAA
1 CGAGCTAA
95605429 GAATCAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 5 0.19
25 4 0.15
26 18 0.67
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (25 bp):
CGAGCTAAATAACGGTAAGCTCATA
Done.