Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 73 of 206
Found at i:20554603 original size:21 final size:21
Alignment explanation
Indices: 20554577--20554632 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
20554567 AACAGCGGTG
*
20554577 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
20554598 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
20554619 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
20554633 AACAATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:20555531 original size:19 final size:17
Alignment explanation
Indices: 20555503--20555553 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
20555493 CAACGTCAAC
20555503 AAATAATTTAAAAACTATA
1 AAATAATTTAAAAA--ATA
*
20555522 AAATATTTTAAAAAATA
1 AAATAATTTAAAAAATA
*
20555539 AAAAAATTTAAAAAA
1 AAATAATTTAAAAAA
20555554 AAAGCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 16 0.55
19 13 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAATTTAAAAAATA
Found at i:20555542 original size:18 final size:19
Alignment explanation
Indices: 20555503--20555553 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
20555493 CAACGTCAAC
*
20555503 AAATAATTTAAAAACTATA
1 AAATAATTTAAAAAATATA
*
20555522 AAATATTTTAAAAAATA-A
1 AAATAATTTAAAAAATATA
20555540 AAA-AATTTAAAAAA
1 AAATAATTTAAAAAA
20555554 AAAGCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 15 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAATTTAAAAAATATA
Found at i:20555831 original size:16 final size:17
Alignment explanation
Indices: 20555810--20555841 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20555800 AATTTATTAC
20555810 ATTTTTTGAAA-ATTTA
1 ATTTTTTGAAACATTTA
20555826 ATTTTTTGAAACATTT
1 ATTTTTTGAAACATTT
20555842 TAGGTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTTTTGAAACATTTA
Found at i:20556298 original size:37 final size:37
Alignment explanation
Indices: 20556239--20556319 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
20556229 ATTCTATAGA
*
20556239 GTCTGTGGCGAGATCCCAGATTGACTGCTGATGGTCAT
1 GTCT-TGGCGAGATCCCAGATTGACTGCTGACGGTCAT
* *
20556277 GTCTTGGCGAGATCTCGGATTGACTGCTGACGGTCAT
1 GTCTTGGCGAGATCCCAGATTGACTGCTGACGGTCAT
20556314 GTCTTG
1 GTCTTG
20556320 TTGATCAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.31
Consensus pattern (37 bp):
GTCTTGGCGAGATCCCAGATTGACTGCTGACGGTCAT
Found at i:20560459 original size:28 final size:30
Alignment explanation
Indices: 20560397--20560460 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
20560387 CCAACGTGAA
20560397 TATATTATGTTATAAAAAATATTATATTAAT
1 TATA-TATGTTATAAAAAATATTATATTAAT
* * *
20560428 TATATATGTTA-AATAAGTATTATA-TATT
1 TATATATGTTATAAAAAATATTATATTAAT
20560456 TATAT
1 TATAT
20560461 TAAATCACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 7 0.23
31 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
TATATATGTTATAAAAAATATTATATTAAT
Found at i:20560608 original size:39 final size:40
Alignment explanation
Indices: 20560564--20560656 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
20560554 AAAAATTATA
**
20560564 TTTAATAAAATAAAATATTTATTATATTTAT-TTGTGTTT
1 TTTAATAAAATAAAATATTTATTATATTTATGTAATGTTT
** * *
20560603 TTTAATGTAATGAAATATTTATTATGTTTATGGTAATGTTT
1 TTTAATAAAATAAAATATTTATTATATTTAT-GTAATGTTT
20560644 TTTAATATAAATA
1 TTTAATA-AAATA
20560657 TTTTTAATGC
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
39 27 0.64
41 12 0.29
42 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (40 bp):
TTTAATAAAATAAAATATTTATTATATTTATGTAATGTTT
Found at i:20562586 original size:42 final size:42
Alignment explanation
Indices: 20562540--20562657 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
20562530 ATCTTATGTG
* *
20562540 CCGAAGAAAACATATTGGCACGTAAGTGCATCATCAGATATA
1 CCGAAGAAAACATACTGGCACGTAAGTGCATCATCAGACATA
* * * **
20562582 CCGAAGAAAACATACTGGCACATGAGTGCATAATTGGACATA
1 CCGAAGAAAACATACTGGCACGTAAGTGCATCATCAGACATA
* * * *
20562624 CCGAAGCAATA-ATAGTGGCATGTAAATGCATCAT
1 CCGAAG-AAAACATACTGGCACGTAAGTGCATCAT
20562658 TGGCTACATC
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 58 0.95
43 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (42 bp):
CCGAAGAAAACATACTGGCACGTAAGTGCATCATCAGACATA
Found at i:20563255 original size:28 final size:28
Alignment explanation
Indices: 20563224--20563285 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
20563214 CTATTTAGTA
20563224 ACAGTAACAATGTAAGCCTTAGCCCAAT
1 ACAGTAACAATGTAAGCCTTAGCCCAAT
**
20563252 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTAAGCCTTAGCCCAAT
20563280 ACAGTA
1 ACAGTA
20563286 TCGGTACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (28 bp):
ACAGTAACAATGTAAGCCTTAGCCCAAT
Found at i:20563761 original size:81 final size:81
Alignment explanation
Indices: 20563647--20563796 Score: 203
Period size: 81 Copynumber: 1.9 Consensus size: 81
20563637 AAGGGTATAC
* * * * * * *
20563647 CAGTCATTTTACCCTGTGGGGGTATTTCGGTCATTTTACCCTGTGGGGGTAA-TTCGTTCATTTT
1 CAGTCATTTTACCCTATGGAGGTAATTCAGTCATTTTACCCTATGGAGATAATTTCGTT-ATTTT
20563711 ACCCTGTAGAGGTAATT
65 ACCCTGTAGAGGTAATT
* *
20563728 CAGTCATTTTACCCTATTGAGGTAATTCAGTCATTTTACCCTATGGAGATAATTTGGTTATTTTA
1 CAGTCATTTTACCCTATGGAGGTAATTCAGTCATTTTACCCTATGGAGATAATTTCGTTATTTTA
20563793 CCCT
66 CCCT
20563797 ACGGGGATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
81 54 0.92
82 5 0.08
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (81 bp):
CAGTCATTTTACCCTATGGAGGTAATTCAGTCATTTTACCCTATGGAGATAATTTCGTTATTTTA
CCCTGTAGAGGTAATT
Found at i:20563797 original size:27 final size:27
Alignment explanation
Indices: 20563649--20563810 Score: 173
Period size: 27 Copynumber: 6.0 Consensus size: 27
20563639 GGGTATACCA
* * *
20563649 GTCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGAGGTAATTCG
* *
20563676 GTCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGGAGGTAATTCG
* * * *
20563703 TTCATTTTACCCTGTAGAGGTAATTCA
1 GTCATTTTACCCTATGGAGGTAATTCG
* *
20563730 GTCATTTTACCCTATTGAGGTAATTCA
1 GTCATTTTACCCTATGGAGGTAATTCG
* *
20563757 GTCATTTTACCCTATGGAGATAATTTG
1 GTCATTTTACCCTATGGAGGTAATTCG
* *
20563784 GTTATTTTACCCTACGG-GGATAATTCG
1 GTCATTTTACCCTATGGAGG-TAATTCG
20563811 ATTATTTATT
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.01
27 117 0.99
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCTATGGAGGTAATTCG
Found at i:20567466 original size:42 final size:42
Alignment explanation
Indices: 20567331--20567553 Score: 169
Period size: 42 Copynumber: 5.3 Consensus size: 42
20567321 TTACACGCAT
* * * * * *
20567331 AGTGCATCATTGGATAAACCGAAGCAATCATACTGACACGTA
1 AGTGCATCATCGGATATACCGAAGAAAACATACTGGCATGTA
* * * * * * * * *
20567373 AATGTATCACCGAATGTACCAAAAAAAACATACCGACATGTA
1 AGTGCATCATCGGATATACCGAAGAAAACATACTGGCATGTA
*
20567415 AATGCATCATCGGATATACCGAAGAAAACATACTGGCATGTA
1 AGTGCATCATCGGATATACCGAAGAAAACATACTGGCATGTA
* ** *
20567457 AGTGCATCATCTGATATATTGAAGAAAACATACCGGCATGTA
1 AGTGCATCATCGGATATACCGAAGAAAACATACTGGCATGTA
** * * * * * *
20567499 CTTGTATCATCGAACATACCGAAGTAATA-ATACTAGCACGTA
1 AGTGCATCATCGGATATACCGAAG-AAAACATACTGGCATGTA
*
20567541 AGTGCATAATCGG
1 AGTGCATCATCGG
20567554 CTAGATCTAA
Statistics
Matches: 137, Mismatches: 43, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
42 134 0.98
43 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (42 bp):
AGTGCATCATCGGATATACCGAAGAAAACATACTGGCATGTA
Found at i:20569781 original size:20 final size:19
Alignment explanation
Indices: 20569744--20569783 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
20569734 AGATTACCAA
**
20569744 ATTAAATAATATTTCAAAT
1 ATTAAATAATATAACAAAT
20569763 ATTAAATAAATATAACAAAT
1 ATTAAAT-AATATAACAAAT
20569783 A
1 A
20569784 CTTGGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAATAATATAACAAAT
Found at i:20583939 original size:37 final size:37
Alignment explanation
Indices: 20583867--20583939 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
20583857 ATGACTAAAC
* *
20583867 AATTCAATAATATTAAATAATATAAAATGTGAAATTT
1 AATTCAATAATATTAAATAATATAAAATATAAAATTT
*
20583904 AATTTAATAATA-TAAATAATATATATAA-ATAAAATT
1 AATTCAATAATATTAAATAATATA-A-AATATAAAATT
20583940 ATTACTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 11 0.35
37 18 0.58
38 2 0.06
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (37 bp):
AATTCAATAATATTAAATAATATAAAATATAAAATTT
Found at i:20587374 original size:107 final size:110
Alignment explanation
Indices: 20587244--20587487 Score: 309
Period size: 109 Copynumber: 2.2 Consensus size: 110
20587234 AGACACTTTT
* * * *
20587244 TTTTTTTTACTTTGGGACACTGATGGCCGGCACCAATGT-ATT-TAAAAAATTTTGGGTGCTGGC
1 TTTTTTTTATTTTGGGACACTGATGGCCAGCACCAATGTCATTAAAAAAAATTTTGAGTGCTGGC
* *
20587307 CAGTAGATGGCTGACACCAAGTACAATTTTTAGCTC-CTAATGCA-
66 AAGTAGATGACTGACACCAAGTACAATTTTTAGCTCTC-AATGCAC
** *
20587351 TTTTTTTTATTTTGGGACACTGATAACCAGCACCAGTGTCATTAAAAAAAATTTTGAGTGCTGGC
1 TTTTTTTTATTTTGGGACACTGATGGCCAGCACCAATGTCATTAAAAAAAATTTTGAGTGCTGGC
* * *
20587416 AAGTAGATGACTGACACCAAGTACATTTTTTGGCTTTCAATGCAC
66 AAGTAGATGACTGACACCAAGTACAATTTTTAGCTCTCAATGCAC
*
20587461 TTTTTTTT-TGCTTTGGGATACTGATGG
1 TTTTTTTTAT--TTTGGGACACTGATGG
20587488 TTGACACCAC
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
107 34 0.29
108 3 0.03
109 57 0.49
110 9 0.08
111 13 0.11
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (110 bp):
TTTTTTTTATTTTGGGACACTGATGGCCAGCACCAATGTCATTAAAAAAAATTTTGAGTGCTGGC
AAGTAGATGACTGACACCAAGTACAATTTTTAGCTCTCAATGCAC
Found at i:20588410 original size:21 final size:21
Alignment explanation
Indices: 20588384--20588432 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
20588374 AGTCCCACTT
20588384 TGATCCCAACAATGATTTCAA
1 TGATCCCAACAATGATTTCAA
*
20588405 TGATCCCAACGATGATTTCAA
1 TGATCCCAACAATGATTTCAA
20588426 TGATCCC
1 TGATCCC
20588433 GATTTGGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
TGATCCCAACAATGATTTCAA
Found at i:20591059 original size:3 final size:3
Alignment explanation
Indices: 20591051--20591146 Score: 183
Period size: 3 Copynumber: 32.0 Consensus size: 3
20591041 TGAAACAATC
*
20591051 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20591099 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20591147 ATCTAAGGTT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20591331 original size:4 final size:4
Alignment explanation
Indices: 20591322--20591374 Score: 97
Period size: 4 Copynumber: 13.0 Consensus size: 4
20591312 ATGATAACAA
20591322 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAACT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA-T
20591371 TAAT
1 TAAT
20591375 AATAACATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 44 0.92
5 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (4 bp):
TAAT
Found at i:20592565 original size:22 final size:21
Alignment explanation
Indices: 20592514--20592565 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
20592504 TATTTAAATG
* *
20592514 AAATGAGAAAAAAATAAATTT
1 AAATGAAAAAAAAAGAAATTT
*
20592535 CAATGGAAAAAAAAAGATAATTT
1 AAAT-GAAAAAAAAAGA-AATTT
20592558 AAATGAAA
1 AAATGAAA
20592566 TGGAAATGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (21 bp):
AAATGAAAAAAAAAGAAATTT
Found at i:20592573 original size:6 final size:6
Alignment explanation
Indices: 20592558--20592613 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
20592548 AAGATAATTT
20592558 AAAT-G AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAAT-G
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
20592604 AAAT-G AAATG
1 AAATGG AAATG
20592614 AAAAAAAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 14 0.29
6 35 0.71
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:20593154 original size:25 final size:26
Alignment explanation
Indices: 20593104--20593157 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
20593094 AGGAAATGAG
*
20593104 AAAATTTTGAAATTTAAATGAAATTT
1 AAAATTTTGAAATTGAAATGAAATTT
*
20593130 AAAATTTTGAAA-TGAAATGATATTT
1 AAAATTTTGAAATTGAAATGAAATTT
20593155 AAA
1 AAA
20593158 TTGAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (26 bp):
AAAATTTTGAAATTGAAATGAAATTT
Found at i:20593165 original size:24 final size:25
Alignment explanation
Indices: 20593119--20593165 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20593109 TTTGAAATTT
**
20593119 AAATGAAATTTAAAATTTTGAAATG
1 AAATGAAATTTAAAATTGAGAAATG
*
20593144 AAATGATATTT-AAATTGAGAAA
1 AAATGAAATTTAAAATTGAGAAA
20593166 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (25 bp):
AAATGAAATTTAAAATTGAGAAATG
Found at i:20593354 original size:21 final size:21
Alignment explanation
Indices: 20593329--20593375 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
20593319 ATATTAGGAA
20593329 AAAATAAATTTAAATGGAAAT
1 AAAATAAATTTAAATGGAAAT
20593350 AAAATAAATTTAAATGGAAAT
1 AAAATAAATTTAAATGGAAAT
*
20593371 GAAAT
1 AAAAT
20593376 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.28
Consensus pattern (21 bp):
AAAATAAATTTAAATGGAAAT
Found at i:20593552 original size:29 final size:28
Alignment explanation
Indices: 20593497--20593550 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
20593487 CCCAACGAGT
20593497 CTGAAACAAGCCTTTTTTTTCAATTTTAC
1 CTGAAACAAG-CTTTTTTTTCAATTTTAC
*
20593526 CTGAAACAAG-TTTTTTTTTAATTTT
1 CTGAAACAAGCTTTTTTTTCAATTTT
20593551 TTCCCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
29 10 0.42
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (28 bp):
CTGAAACAAGCTTTTTTTTCAATTTTAC
Found at i:20597355 original size:90 final size:89
Alignment explanation
Indices: 20597198--20597529 Score: 443
Period size: 90 Copynumber: 3.7 Consensus size: 89
20597188 ACAGATACAA
* * * * * *
20597198 TAAATATTAATACACAAAAATATAAAATTCAAA-TAAAAATAATACACACTAAATTAAATTTAAA
1 TAAA-ATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTAAA
* *
20597262 CACCCAACAAACTACAAACATATCAG
65 CACCCAACAAACTACAAACAGAT-GG
20597288 TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATAC-GAACTAAATTAAATTTAAA
1 TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAG-ACTAAATTAAATTTAAA
20597352 CACCCAACAAACTACAAACAGATGG
65 CACCCAACAAACTACAAACAGATGG
* * * * *
20597377 ATAAAATTAATGCATGAAATTTTTAAATTCAAACTATATATAACACAGACTAAATTAAATTTAAA
1 -TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTAAA
* *
20597442 CACACAACAAACTACAAAAAGATGGG
65 CACCCAACAAACTACAAACAGAT-GG
* * *
20597468 TAAAATTAAAACACGAAAATTTTAAATTCAAATTACATATAATACAGAGTAAATTAAATTTA
1 TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTA
20597530 CAGATACAAA
Statistics
Matches: 214, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
89 26 0.12
90 185 0.86
91 3 0.01
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (89 bp):
TAAAATTAATACACGAAAATTTTAAATTCAAACTACATATAATACAGACTAAATTAAATTTAAAC
ACCCAACAAACTACAAACAGATGG
Found at i:20598516 original size:118 final size:113
Alignment explanation
Indices: 20598196--20598505 Score: 314
Period size: 117 Copynumber: 2.7 Consensus size: 113
20598186 GTAGTGTCGG
* * * * * *
20598196 CCATCAGTGTCCCAAAGTAAAAAGAAAATTGCATTGGGAGACAAAAAATGTATTTGGTGCTGGCC
1 CCATCAGTGTCCCAAAGTAAAAAAAAAATTGCCTT-GGACACAAAAAATGTACTTGGTGCCGACC
* *
20598261 ATCTACTGGCCAACACCCCCCAAAAAATTTTTTTAATGGACACTGATGCTGG
65 ATCTACTGGCCAACA---CCCAAAAAATTTTTTTAATGGACACTGATGCCGA
* * * * * * **
20598313 CCATCAATGTCCCAAAGTAAAAAAAAAAATGTCTTAGGACTCGAAAAATGTACCTGGTATCGACC
1 CCATCAGTGTCCCAAAGTAAAAAAAAAATTGCCTT-GGACACAAAAAATGTACTTGGTGCCGACC
* * *
20598378 ATCTATTGGCCAACACCCAAAACAATTTTTTTTTAAATTGACACTGGTGCCGA
65 ATCTACTGGCCAACACCCAAAA-AA--TTTTTTT-AATGGACACTGATGCCGA
* * * *
20598431 CCATCAGTGTCCCAAAGTAAAAAAAAAATTACCTTGGAACCCAAAAAAGGTACTTGGTGCCAACC
1 CCATCAGTGTCCCAAAGTAAAAAAAAAATTGCCTTGG-ACACAAAAAATGTACTTGGTGCCGACC
*
20598496 ACCTACTGGC
65 ATCTACTGGC
20598506 ATGCACCCAA
Statistics
Matches: 155, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
114 7 0.05
115 2 0.01
117 73 0.47
118 73 0.47
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (113 bp):
CCATCAGTGTCCCAAAGTAAAAAAAAAATTGCCTTGGACACAAAAAATGTACTTGGTGCCGACCA
TCTACTGGCCAACACCCAAAAAATTTTTTTAATGGACACTGATGCCGA
Found at i:20599543 original size:9 final size:9
Alignment explanation
Indices: 20599531--20599573 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
20599521 TAAAAATTAA
20599531 TAAAAAAAT
1 TAAAAAAAT
20599540 TAAATAAAAT
1 TAAA-AAAAT
* *
20599550 TCAAAAATT
1 TAAAAAAAT
20599559 TAAAAAAAT
1 TAAAAAAAT
20599568 TAAAAA
1 TAAAAA
20599574 TGAATCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:20600413 original size:20 final size:20
Alignment explanation
Indices: 20600388--20600427 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20600378 CGTAAAATGA
*
20600388 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
20600408 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20600428 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20600417 original size:34 final size:34
Alignment explanation
Indices: 20600374--20600439 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
20600364 AGTAAAATGT
*
20600374 TTTTCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
20600407 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
20600440 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:20600443 original size:14 final size:15
Alignment explanation
Indices: 20600367--20600443 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
20600357 GATTGCCAGT
* *
20600367 AAAATGTTTTTC-GT
1 AAAATGATTTTCTGG
20600381 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
20600395 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
20600415 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
20600430 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
20600444 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.08
14 21 0.42
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:20601160 original size:111 final size:111
Alignment explanation
Indices: 20600966--20601295 Score: 642
Period size: 111 Copynumber: 3.0 Consensus size: 111
20600956 TGAAGTATTG
20600966 TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAATGT
1 TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAATGT
20601031 CTGTACATATTAACAAACTTTAATACAACAATACAACTACATGTTA
66 CTGTACATATTAACAAACTTTAATACAACAATACAACTACATGTTA
*
20601077 TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACATTACTTTTTCTAAATGT
1 TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAATGT
*
20601142 CTGTACATATTAACAAACTTTAATACAACAATACAACTACATGTTG
66 CTGTACATATTAACAAACTTTAATACAACAATACAACTACATGTTA
20601188 TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAATGT
1 TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAATGT
20601253 CTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 CTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
20601296 CATGGTATTG
Statistics
Matches: 216, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 216 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (111 bp):
TTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAATGT
CTGTACATATTAACAAACTTTAATACAACAATACAACTACATGTTA
Found at i:20602258 original size:145 final size:145
Alignment explanation
Indices: 20601995--20602305 Score: 590
Period size: 145 Copynumber: 2.2 Consensus size: 145
20601985 TTGTCATTCA
*
20601995 TGAAATGGTCCAAAAAAGTAGGAAGTAAATAAAATCTAACTGTACCAGGGTCAAAGGGAGATTTG
1 TGAAAGGGTCCAAAAAAGTAGGAAGTAAATAAAATCTAACTGTACCAGGGTCAAAGGGAGATTTG
20602060 AAGACTCATTTAAATTATTCTAGACTTGTCAAGGATGTAAGTATCAATGAGAAAGACATGAACGA
66 AAGACTCATTTAAATTATTCTAGACTTGTCAAGGATGTAAGTATCAATGAGAAAGACATGAACGA
20602125 GCAACTTCAATAGGT
131 GCAACTTCAATAGGT
20602140 TGAAAGGGTCCAAAAAAGTAGGAAGTAAATAAAATCTAACTGTACCAGGGTCAAAGGGAGATTTG
1 TGAAAGGGTCCAAAAAAGTAGGAAGTAAATAAAATCTAACTGTACCAGGGTCAAAGGGAGATTTG
20602205 AAGACTCATTTAAATTATTCTAGACTTGTCAAGGATGTAAGTATCAATGAGAAAGACATGAACGA
66 AAGACTCATTTAAATTATTCTAGACTTGTCAAGGATGTAAGTATCAATGAGAAAGACATGAACGA
20602270 GCAACTTCAATAGGT
131 GCAACTTCAATAGGT
*
20602285 TGAAAGGG-GCAAAAAA-TAGGA
1 TGAAAGGGTCCAAAAAAGTAGGA
20602306 CAAAATTATT
Statistics
Matches: 164, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
143 5 0.03
144 7 0.04
145 152 0.93
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (145 bp):
TGAAAGGGTCCAAAAAAGTAGGAAGTAAATAAAATCTAACTGTACCAGGGTCAAAGGGAGATTTG
AAGACTCATTTAAATTATTCTAGACTTGTCAAGGATGTAAGTATCAATGAGAAAGACATGAACGA
GCAACTTCAATAGGT
Found at i:20606258 original size:19 final size:20
Alignment explanation
Indices: 20606223--20606261 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
20606213 ATGATATATG
*
20606223 TAAAATATATATTTTTATTA
1 TAAAATATATATATTTATTA
20606243 TAAAAT-TATATATTTATTA
1 TAAAATATATATATTTATTA
20606262 GCTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATATATATATTTATTA
Found at i:20615872 original size:40 final size:41
Alignment explanation
Indices: 20615816--20615893 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 41
20615806 AGATAATCGC
*
20615816 TAGAAATTGTGGTATAT-CAAAATTTCTAAGTGAATATCCT
1 TAGAAATTGTGGTATATACAAAATTTCTAAGGGAATATCCT
* * *
20615856 TAGATATTTTGGTATATACCATAATTTCTAAGGGAATA
1 TAGAAATTGTGGTATATA-CAAAATTTCTAAGGGAATA
20615894 CCGATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 15 0.47
42 17 0.53
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (41 bp):
TAGAAATTGTGGTATATACAAAATTTCTAAGGGAATATCCT
Found at i:20616152 original size:146 final size:147
Alignment explanation
Indices: 20615833--20616179 Score: 376
Period size: 146 Copynumber: 2.4 Consensus size: 147
20615823 TGTGGTATAT
* * * * * *
20615833 CAAAATTTCTAAGTGAATATCCTTAGATATTTTGGTATATACCATAATTTCTAAGGGAATACCGA
1 CAAAATTTCTAAGAGCACATCCTTAGATATTTTGGTATATACCATAATTTCTAAAGAAATACCAA
* * * *
20615898 TATTTTTATGGAACCCCGTAAGAAATTTTGGTATACCAAAATAGTGTTGTATAAACTTATAACAA
66 TATTTCTATGGAACCCCGTAAGAAATTTTGATATACCAAAATACTGTTGTATAAACCTATAACAA
*
20615963 GATTTCTAACGAAATAC
131 GATTTCTAACAAAATAC
*** * * * **
20615980 CAAAATTTCTAAGAGGTTATCTTTAGATATTCTGGTATATACCTTAATTTCTAAAGAAATATTAA
1 CAAAATTTCTAAGAGCACATCCTTAGATATTTTGGTATATACCATAATTTCTAAAGAAATACCAA
* * * * *
20616045 TATTTCTATGGAACCTCGTTAG-AATTTTGATATACCAAAAT-CTGAATT-TATGAGCCTATACC
66 TATTTCTATGGAACCCCGTAAGAAATTTTGATATACCAAAATACTG--TTGTATAAACCTATAAC
* *
20616107 AAGATTTCTAATAAAATAT
129 AAGATTTCTAACAAAATAC
** * * *
20616126 CACTATTTCTAATAGCACATCCTTAGATATTTTGGTATATACTAAAATTTCTAA
1 CAAAATTTCTAAGAGCACATCCTTAGATATTTTGGTATATACCATAATTTCTAA
20616180 CAAGATGGTA
Statistics
Matches: 164, Mismatches: 34, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
145 2 0.01
146 87 0.53
147 75 0.46
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (147 bp):
CAAAATTTCTAAGAGCACATCCTTAGATATTTTGGTATATACCATAATTTCTAAAGAAATACCAA
TATTTCTATGGAACCCCGTAAGAAATTTTGATATACCAAAATACTGTTGTATAAACCTATAACAA
GATTTCTAACAAAATAC
Found at i:20616551 original size:20 final size:20
Alignment explanation
Indices: 20616528--20616578 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
20616518 AGTTTTTACC
20616528 AAAATTTCTAATGAAATACT
1 AAAATTTCTAATGAAATACT
20616548 AAAATTTCTAATGAAATACT
1 AAAATTTCTAATGAAATACT
20616568 AAAATTTCTAA
1 AAAATTTCTAA
20616579 GAACTTATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAATTTCTAATGAAATACT
Found at i:20623441 original size:6 final size:6
Alignment explanation
Indices: 20623430--20623455 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20623420 TTAAGAAAAG
20623430 TAGACA TAGACA TAGACA TAGACA TA
1 TAGACA TAGACA TAGACA TAGACA TA
20623456 TGATGATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (6 bp):
TAGACA
Found at i:20632467 original size:21 final size:21
Alignment explanation
Indices: 20632443--20632486 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20632433 GCAACCCAAT
*
20632443 TTTTATT-TTTATTATTATTTA
1 TTTTATTCTTTACT-TTATTTA
*
20632464 TTTTTTTCTTTACTTTATTTA
1 TTTTATTCTTTACTTTATTTA
20632485 TT
1 TT
20632487 ACTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTATTCTTTACTTTATTTA
Found at i:20632480 original size:17 final size:17
Alignment explanation
Indices: 20632460--20632501 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
20632450 TTTATTATTA
*
20632460 TTTATTTTTTTCTTTAC
1 TTTATTTTTTACTTTAC
* *
20632477 TTTATTTATTACTTTAT
1 TTTATTTTTTACTTTAC
20632494 TTTATTTT
1 TTTATTTT
20632502 ATTTTACTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTACTTTAC
Found at i:20632496 original size:27 final size:26
Alignment explanation
Indices: 20632450--20632513 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
20632440 AATTTTTATT
*
20632450 TTTATTATTATTTATTTTTTTCTTTAC
1 TTTATTATTATTTATTTTTAT-TTTAC
*
20632477 TTTATTTATTACTTTA-TTTTATTTTAT
1 TTTA-TTATTA-TTTATTTTTATTTTAC
20632504 TTTACTTATT
1 TTTA-TTATT
20632514 TGAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 17 0.53
28 11 0.34
29 4 0.12
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTATTATTATTTATTTTTATTTTAC
Found at i:20633544 original size:11 final size:11
Alignment explanation
Indices: 20633530--20633554 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20633520 AAAAAAAAGG
20633530 AAAAAAGAAAA
1 AAAAAAGAAAA
20633541 AAAAAAGAAAA
1 AAAAAAGAAAA
20633552 AAA
1 AAA
20633555 TAATTTGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:20638253 original size:50 final size:50
Alignment explanation
Indices: 20638178--20638351 Score: 186
Period size: 50 Copynumber: 3.5 Consensus size: 50
20638168 TTTGGAAAGT
*
20638178 AAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * ** **** * *
20638228 AAGATTTGCCGTTGTGGCTTTAATCTATTCCACTGCACCACCTGGGAAGT
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
*
20638278 AAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * *
20638328 AAAATTGGCCACTGTGGCTTTAAT
1 AAGATTCGCCATTGTAGCTTTAAT
20638352 TTATTCCACT
Statistics
Matches: 95, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
Found at i:20638347 original size:100 final size:100
Alignment explanation
Indices: 20638171--20638386 Score: 324
Period size: 100 Copynumber: 2.2 Consensus size: 100
20638161 CGTAACTTTT
* *
20638171 GGAAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTG
1 GGAAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAAATTGG
** *
20638236 CCGTTGTGGCTTTAATCTATTCCACTGCACCACCT
66 CCACTGTGGCTTTAATCTATTCCACTGCACCACCA
* * *
20638271 GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAAATTGG
1 GGAAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAAATTGG
* * **
20638336 CCACTGTGGCTTTAATTTATTCCACTGTACTGCCA
66 CCACTGTGGCTTTAATCTATTCCACTGCACCACCA
20638371 GGAAAGTAAGATTCGC
1 GGAAAGTAAGATTCGC
20638387 TATTCTCAGT
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (100 bp):
GGAAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAAATTGG
CCACTGTGGCTTTAATCTATTCCACTGCACCACCA
Found at i:20638509 original size:41 final size:41
Alignment explanation
Indices: 20638450--20638596 Score: 136
Period size: 41 Copynumber: 3.5 Consensus size: 41
20638440 TCTGCTCTGT
*
20638450 TGCAACCTCAGGGAGATAAGACCTGATGTGATATACTCTAC
1 TGCAACTTCAGGGAGATAAGACCTGATGTGATATACTCTAC
* * * * *
20638491 TGCAACTTCAGAGG-GATAAGATCTATTATTTCA-ATCCACTCCAC
1 TGCAACTTCAG-GGAGATAAGA-C-CTGATGTGATAT--ACTCTAC
* * * *
20638535 TGTAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTAT
1 TGCAACTTCAGGGAGATAAGACCTGATGTGATATACTCTAC
*
20638576 TGCAACTTCAGAGAGATAAGA
1 TGCAACTTCAGGGAGATAAGA
20638597 TCTTTTATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
41 41 0.50
42 9 0.11
43 9 0.11
44 23 0.28
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
TGCAACTTCAGGGAGATAAGACCTGATGTGATATACTCTAC
Found at i:20638552 original size:85 final size:85
Alignment explanation
Indices: 20638450--20638637 Score: 304
Period size: 85 Copynumber: 2.2 Consensus size: 85
20638440 TCTGCTCTGT
* * *
20638450 TGCAACCTCAGGGAGATAAGACCTGATGTGATATACTCTACTGCAACTTCAGAGGGATAAGATCT
1 TGCAACTTCAGGGAGATAAGACCTGATGCGATATACTCTACTGCAACTTCAGAGAGATAAGATCT
20638515 ATTATTTCAATCCACTCCAC
66 ATTATTTCAATCCACTCCAC
* * *
20638535 TGTAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTATTGCAACTTCAGAGAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGACCTGATGCGATATACTCTACTGCAACTTCAGAGAGATAAGATCT
* *
20638600 TTTATTTTAATCCACTCCAC
66 ATTATTTCAATCCACTCCAC
20638620 TGCAACTTCAGGGAGATA
1 TGCAACTTCAGGGAGATA
20638638 GGATTACTGG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (85 bp):
TGCAACTTCAGGGAGATAAGACCTGATGCGATATACTCTACTGCAACTTCAGAGAGATAAGATCT
ATTATTTCAATCCACTCCAC
Found at i:20638636 original size:44 final size:44
Alignment explanation
Indices: 20638484--20638637 Score: 163
Period size: 44 Copynumber: 3.6 Consensus size: 44
20638474 GATGTGATAT
*
20638484 ACTCTACTGCAACTTCAGAGG-GATAAGATCTATTATTTCAATCC
1 ACTCCACTGCAACTTCAG-GGAGATAAGATCTATTATTTCAATCC
* * * * * *
20638528 ACTCCACTGTAACTTCAGGGAGATAAGA-C-CTGA-TGCGATCT
1 ACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTCAATCC
* * * * *
20638569 ACTCTATTGCAACTTCAGAGAGATAAGATCTTTTATTTTAATCC
1 ACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTCAATCC
20638613 ACTCCACTGCAACTTCAGGGAGATA
1 ACTCCACTGCAACTTCAGGGAGATA
20638638 GGATTACTGG
Statistics
Matches: 86, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 29 0.34
42 3 0.03
43 5 0.06
44 49 0.57
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (44 bp):
ACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTCAATCC
Found at i:20638785 original size:217 final size:216
Alignment explanation
Indices: 20638542--20638954 Score: 591
Period size: 217 Copynumber: 1.9 Consensus size: 216
20638532 CACTGTAACT
* * *
20638542 TCAGGGAGATAAGACCTGATGCGATCTACTCTATTGCAACTTCAGAGAGATAAGATCTTTTATTT
1 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGACCTTTTATTT
* * * *
20638607 TAATCCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTTCAATGTAC-TCCACTGTA-TC
66 TAACCCACTCCACTGCAACTTCAGGGAGATAGGATGACTGGCTTAAATCTACTTCC-C--TACTC
* *
20638670 CTCAGGG-AGGTAAAA-TCTGCCATCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTG
128 CT-AGGGAAGATAAAATTC-GCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
20638733 TTTCTTCAGTCTGCTCCGCTGCAACC
191 TTTCTTCAGTCTGCTCCGCTGCAACC
*
20638759 TCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGCAACTTCAAAGAGATAAGACCTTTTATTT
1 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGACCTTTTATTT
** * * * *
20638824 TAACCCGTTCCACTGCAACTTCAGGGAGATATGATGAGTGGCTTAAATCTGCTTCCCTACTCCTG
66 TAACCCACTCCACTGCAACTTCAGGGAGATAGGATGACTGGCTTAAATCTACTTCCCTACTCCTA
* *
20638889 GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTTCT
131 GGGAAGATAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTTCT
20638954 T
196 T
20638955 TGACCTATTC
Statistics
Matches: 174, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
215 5 0.03
216 59 0.34
217 107 0.61
218 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (216 bp):
TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGACCTTTTATTT
TAACCCACTCCACTGCAACTTCAGGGAGATAGGATGACTGGCTTAAATCTACTTCCCTACTCCTA
GGGAAGATAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTTCT
TCAGTCTGCTCCGCTGCAACC
Found at i:20638996 original size:130 final size:130
Alignment explanation
Indices: 20638845--20639185 Score: 565
Period size: 130 Copynumber: 2.6 Consensus size: 130
20638835 ACTGCAACTT
* *
20638845 CAGGGAGATATGATGAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC
1 CAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC
* * *
20638910 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTTCTTTGACCTATTCCACTGTTGAC
66 TTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTTTCTTCGACCTATTCCACTGCTGAC
*
20638975 CAGGGAGATAGGATTAGTGGCTTAAATATGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC
1 CAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC
**
20639040 TTCGATCAACTCCACTACTACTTAGGGAGATAAGATCTGTTTCTTCGACCTATTCCACTGCTGAC
66 TTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTTTCTTCGACCTATTCCACTGCTGAC
* * * *
20639105 CAGAGAGATAGGATTAGTGGCTTAAATCTTCTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTT
1 CAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC
*
20639170 TTCGATCTGCTTCACT
66 TTCGATCTGCTCCACT
20639186 GTGGTGTAGG
Statistics
Matches: 195, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 195 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (130 bp):
CAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTC
TTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTTTCTTCGACCTATTCCACTGCTGAC
Found at i:20646998 original size:108 final size:107
Alignment explanation
Indices: 20646836--20647125 Score: 492
Period size: 107 Copynumber: 2.7 Consensus size: 107
20646826 CTAAACGTGG
*
20646836 AATCGAAACCCAGTACCTTAGGGCACGTTCTTCGAATTTCCAAACGCAAAATATTGCCTTATTTT
1 AATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTT
*
20646901 GAAAATTTTTGAAAATGATATTAAG-TCATTTGGTCGAACGAGA
66 GAAAATTTTTG-AAAGGATATTAAGCT-ATTTGGTCGAACGAGA
*
20646944 AATCGAAACCCAATACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTT
1 AATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTT
*
20647009 GAAAATTTTTGAAAGGATATTTAGCTATTTGGTCGAACGAGA
66 GAAAATTTTTGAAAGGATATTAAGCTATTTGGTCGAACGAGA
* *
20647051 AATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCTAAATATTGCCTTAATTT
1 AATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTT
20647116 GAAATATTTT
66 GAAA-ATTTT
20647126 CCTTTTTGAA
Statistics
Matches: 173, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
107 93 0.54
108 80 0.46
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (107 bp):
AATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTT
GAAAATTTTTGAAAGGATATTAAGCTATTTGGTCGAACGAGA
Found at i:20647081 original size:107 final size:108
Alignment explanation
Indices: 20646807--20647125 Score: 500
Period size: 108 Copynumber: 3.0 Consensus size: 108
20646797 AAAATTCAAG
* * * * *
20646807 AGGATATTTAGCAATTTGG-CTAAACGTGGAATCGAAACCCAGTACCTTAGGGCACGTTCTTCGA
1 AGGATATTTAGCTATTTGGTC-GAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
20646871 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
65 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
* * *
20646915 ATGATATTAAG-TCATTTGGTCGAACGAGAAATCGAAACCCAATACCTTAGGGCACGTTCCTCGA
1 AGGATATTTAGCT-ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
20646979 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTG-AA
65 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
20647022 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
* *
20647087 TTTCCAAACGCTAAATATTGCCTTAATTTGAAATATTTT
66 TTTCCAAACGCAAAATATTGCCTTATTTTGAAA-ATTTT
20647126 CCTTTTTGAA
Statistics
Matches: 194, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
107 93 0.48
108 100 0.52
109 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
Found at i:20647629 original size:3 final size:3
Alignment explanation
Indices: 20647621--20647710 Score: 67
Period size: 3 Copynumber: 30.0 Consensus size: 3
20647611 TAAGTAATTA
* * * *
20647621 AAT AAT AAT AA- CAT AAAT ACT AAT AAT AAT AAC AA- AGAT ACT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * * *
20647666 AAT AAT AAT AAT AAT AAT AAT ATT ATT ATT ATT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20647711 GTTAAAAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.03
3 67 0.93
4 3 0.04
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20647647 original size:21 final size:21
Alignment explanation
Indices: 20647621--20647673 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
20647611 TAAGTAATTA
20647621 AATAATAATAACATAA-ATACT
1 AATAATAATAACA-AAGATACT
20647642 AATAATAATAACAAAGATACT
1 AATAATAATAACAAAGATACT
20647663 AATAATAATAA
1 AATAATAATAA
20647674 TAATAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAATAATAACAAAGATACT
Found at i:20648935 original size:19 final size:19
Alignment explanation
Indices: 20648913--20648959 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
20648903 CTTTGGTTTG
*
20648913 TAATTGGGTAG-TTGGGGTT
1 TAATTGGGTAGTTTAGGG-T
**
20648932 TAATTGTTTAGTTTAGGGT
1 TAATTGGGTAGTTTAGGGT
20648951 TAATTGGGT
1 TAATTGGGT
20648960 TTTGGGCTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (19 bp):
TAATTGGGTAGTTTAGGGT
Found at i:20649552 original size:123 final size:123
Alignment explanation
Indices: 20649360--20649622 Score: 490
Period size: 123 Copynumber: 2.1 Consensus size: 123
20649350 TTCAATGTAC
*
20649360 TCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTCAATGTGCTCCACTTTAGGGGATAAGAT
1 TCCACTGTAATCTCAGGGAGGTAAAATCTGCCATCTTCAATGTGCTCCACTTTAGGGGATAAGAT
* *
20649425 CTGAAACGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGT
66 CTGAAACAATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGT
20649483 TCCACTGTAATCTCAGGGAGGTAAAATCTGCCATCTTCAATGTGCTCCACTTTAGGGGATAAGAT
1 TCCACTGTAATCTCAGGGAGGTAAAATCTGCCATCTTCAATGTGCTCCACTTTAGGGGATAAGAT
*
20649548 CTGAAACAATCTACTCTACTGTAACCTCAGATAAATAAGATCCTTTATTTTAATCCGT
66 CTGAAACAATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGT
20649606 TCCACTGTAATCTCAGG
1 TCCACTGTAATCTCAGG
20649623 AAGATAGGAT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 136 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (123 bp):
TCCACTGTAATCTCAGGGAGGTAAAATCTGCCATCTTCAATGTGCTCCACTTTAGGGGATAAGAT
CTGAAACAATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGT
Found at i:20649746 original size:175 final size:174
Alignment explanation
Indices: 20649556--20650204 Score: 1102
Period size: 175 Copynumber: 3.7 Consensus size: 174
20649546 ATCTGAAACA
* * *
20649556 ATCTACTCTACTGTAACCTCAGATAAATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
* *
20649621 GGAAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAA-TC
66 GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
*
20649685 TTCCGATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCG
131 TT-CG-TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGACGCG
* **
20649731 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAGCCCGCTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
*
20649796 GGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
66 GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
*
20649861 TTCGTCTGCTCCACTGTAATATCAGGGAGATAAGACCTGACGCG
131 TTCGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGACGCG
20649905 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
*
20649970 GGGAGATAGGATTACTAGCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
66 GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
* *
20650035 TTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACGCG
131 TTC-GTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGACGCG
* *
20650080 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
* *
20650145 GGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCTGA
66 GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
20650205 CGCGATCTTN
Statistics
Matches: 448, Mismatches: 24, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
174 166 0.37
175 278 0.62
176 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (174 bp):
ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
TTCGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGACGCG
Found at i:20649802 original size:44 final size:44
Alignment explanation
Indices: 20649433--20650201 Score: 308
Period size: 44 Copynumber: 17.8 Consensus size: 44
20649423 ATCTGAAACG
* * * *
20649433 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* * * * ** *
20649477 ATCCGTTCCACTGTAATCTCAGGGAGGTAAAAT-CTGCCATCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTAT-TTTA
* * ***
20649522 ATGTGCTCCAC--T--T-T-AGGG-GATAAGAT-C-TGA-AACA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* * * ** *
20649556 ATCTACTCTACTGTAACCTCAGATAAATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* * * * * * *
20649600 ATCCGTTCCACTGTAATCTCAGGAAGATAGGAT--TACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTA
* * ** **
20649644 ATCTACTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATCTTCCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTAT-TT-TA
* ***
20649690 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-CC-TGA-TGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* * *
20649731 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTA
** * * * *
20649775 GCCCGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTATCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTAT-TTTA
* ** *
20649819 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTATT-TTA
* * * ****
20649864 GTCTGCTCCACTGTAATATCAGGGAGATAAGA-CC-TGA-CGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* * * *
20649905 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* * * * **
20649949 ATCCGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTA
* ** *
20649993 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTATT-TT-A
* * * * ****
20650039 GTCTGTTCCACTGTAATCTCAGGGAAATAAGA-CC-TGA-CGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
* ** *
20650080 ATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTA
* * * *
20650124 ATCCGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTATCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTAT-TTTA
* *
20650168 ATCTGCTCCGCTGTAATCTCAGAGAGATAAGATC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC
20650202 TGACGCGATC
Statistics
Matches: 524, Mismatches: 156, Indels: 89
0.68 0.20 0.12
Matches are distributed among these distances:
34 10 0.02
36 2 0.00
38 7 0.01
39 5 0.01
40 5 0.01
41 87 0.17
42 12 0.02
43 22 0.04
44 258 0.49
45 54 0.10
46 62 0.12
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA
Found at i:20650179 original size:349 final size:349
Alignment explanation
Indices: 20649556--20650204 Score: 1156
Period size: 349 Copynumber: 1.9 Consensus size: 349
20649546 ATCTGAAACA
* *
20649556 ATCTACTCTACTGTAACCTCAGATAAATAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
20649621 GGAAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATCT
66 GGAAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATCT
* *
20649686 TCCGATCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTC
131 TCCGATCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTACTGTAACTTC
*
20649751 AGAGAGATAAGATCCTTTATTTTAGCCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCT
196 AGAGAGATAAGATCCTTTATTTTAACCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCT
*
20649816 TCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGTCTGCTCCACTGTAAT
261 TCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCTGAAATTCTTCGTCTGCTCCACTGTAAT
20649881 ATCAGGGAGATAAGACCTGACGCG
326 ATCAGGGAGATAAGACCTGACGCG
*
20649905 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
1 ATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
* * *
20649970 GGGAGATAGGATTACTAGCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
66 GGAAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAA-TC
* * *
20650035 TT-CGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTT
130 TTCCGATCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTACTGTAACTT
*
20650099 CAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATC
195 CAGAGAGATAAGATCCTTTATTTTAACCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATC
20650164 TTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCTGA
260 TTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCTGA
20650205 CGCGATCTTN
Statistics
Matches: 285, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
349 281 0.99
350 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (349 bp):
ATCTACTCTACTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
GGAAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATCT
TCCGATCTGCTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTACTGTAACTTC
AGAGAGATAAGATCCTTTATTTTAACCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCT
TCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCTGAAATTCTTCGTCTGCTCCACTGTAAT
ATCAGGGAGATAAGACCTGACGCG
Found at i:20652551 original size:7 final size:8
Alignment explanation
Indices: 20652521--20652549 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
20652511 ATTTTTGATT
20652521 TTTTTTGA
1 TTTTTTGA
20652529 TTTTTTGA
1 TTTTTTGA
20652537 TTTTTTGA
1 TTTTTTGA
20652545 TTTTT
1 TTTTT
20652550 GAATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (8 bp):
TTTTTTGA
Found at i:20657391 original size:107 final size:108
Alignment explanation
Indices: 20657117--20657435 Score: 500
Period size: 108 Copynumber: 3.0 Consensus size: 108
20657107 AAAATTCAAG
* * * * *
20657117 AGGATATTTAGCAATTTGG-CTAAACGTGAAATCGAAACCCAGTACCTTAGGGCACGTTCTTTGA
1 AGGATATTTAGCTATTTGGTC-GAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
20657181 ATTTCCAAACACAAAATATTGCCTTATTTTGAAAATTTTTGAAA
65 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
* *
20657225 AGGATATTAAG-TCATTTGGTCGAACGAGAAATCGAAACCCAATACCTTAGGGCACGTTCCTCGA
1 AGGATATTTAGCT-ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
20657289 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTG-AA
65 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
20657332 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
* *
20657397 TTTCCAAACGCTAAATATTGCCTTAATTTGAAATATTTT
66 TTTCCAAACGCAAAATATTGCCTTATTTTGAAA-ATTTT
20657436 CCTTTTTGAA
Statistics
Matches: 195, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
107 94 0.48
108 100 0.51
109 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
Found at i:20657945 original size:3 final size:3
Alignment explanation
Indices: 20657937--20658020 Score: 82
Period size: 3 Copynumber: 28.0 Consensus size: 3
20657927 AAGTAATTAA
* * * *
20657937 AAT AAT AAT AAT AA- CAT AAAT ACT AAT AAT AAT AAC AA- AGAT ACT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* *
20657982 AAT AAT AAT AAT AAT AAT AAT AAT ATT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20658021 GTTAAAAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20657965 original size:21 final size:21
Alignment explanation
Indices: 20657939--20657992 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
20657929 GTAATTAAAA
20657939 TAATAATAATAACATAA-ATAC
1 TAATAATAATAACA-AAGATAC
20657960 TAATAATAATAACAAAGATAC
1 TAATAATAATAACAAAGATAC
20657981 TAATAATAATAA
1 TAATAATAATAA
20657993 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
TAATAATAATAACAAAGATAC
Found at i:20658025 original size:15 final size:15
Alignment explanation
Indices: 20657982--20658032 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
20657972 CAAAGATACT
* *
20657982 AATAATAATAATAAT
1 AATAATAATATTAAA
20657997 AATAATAATATTAAA
1 AATAATAATATTAAA
*
20658012 AATAATAATGTTAAA
1 AATAATAATATTAAA
20658027 AATAAT
1 AATAAT
20658033 TAGCTAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAATAATATTAAA
Found at i:20658966 original size:15 final size:15
Alignment explanation
Indices: 20658946--20658984 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
20658936 CTACTGCTTG
20658946 TGTTCTTTGCTCTCT
1 TGTTCTTTGCTCTCT
20658961 TGTTCTTTGCTCTCT
1 TGTTCTTTGCTCTCT
*
20658976 TATTCTTTG
1 TGTTCTTTG
20658985 TTTTGTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.03, C:0.23, G:0.13, T:0.62
Consensus pattern (15 bp):
TGTTCTTTGCTCTCT
Found at i:20659261 original size:19 final size:19
Alignment explanation
Indices: 20659239--20659285 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
20659229 CTTTGGTTTG
*
20659239 TAATTGGGTAG-TTGGGGTT
1 TAATTGGGTAGTTTAGGG-T
**
20659258 TAATTGTTTAGTTTAGGGT
1 TAATTGGGTAGTTTAGGGT
20659277 TAATTGGGT
1 TAATTGGGT
20659286 TTTGGGCTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (19 bp):
TAATTGGGTAGTTTAGGGT
Found at i:20665228 original size:3 final size:3
Alignment explanation
Indices: 20665220--20665284 Score: 105
Period size: 3 Copynumber: 21.7 Consensus size: 3
20665210 AGTCCTATTT
20665220 AAG AAG AAG AA- AGAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
20665265 AAG AAG AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AA
20665285 TAGACTATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20666868 original size:28 final size:29
Alignment explanation
Indices: 20666806--20666869 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
20666796 AAATAAACCA
*
20666806 AACTTATTAAAAATCCTAAAAATAAATTT
1 AACTTATTAAAAACCCTAAAAATAAATTT
* *
20666835 ATCTTATT-AAAACCCTAAATAT-AATTCT
1 AACTTATTAAAAACCCTAAAAATAAATT-T
20666863 AACTTAT
1 AACTTAT
20666870 AAGGACCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 19 0.63
29 7 0.23
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (29 bp):
AACTTATTAAAAACCCTAAAAATAAATTT
Found at i:20667047 original size:41 final size:42
Alignment explanation
Indices: 20666912--20667066 Score: 151
Period size: 41 Copynumber: 3.7 Consensus size: 42
20666902 AATTTATTAG
* * * *
20666912 AAAACTTAA-ATATAATTTAG-AAATTAAATTCTACCCTATT
1 AAAACTTAAGATCTAATTTAGCAAAATAAATTCTAACATATT
20666952 AAAACTTAA-ATCTAATTTAAAGCAAAATAAAATTCTAACCA-ATT
1 AAAACTTAAGATCTAATTT--AGCAAAAT-AAATTCTAA-CATATT
* * * *
20666996 ACAACCTAAGACCTAATTTAG-AAAATAAATTCTAACATAGT
1 AAAACTTAAGATCTAATTTAGCAAAATAAATTCTAACATATT
*
20667037 AAAACTTAAGATCTAAATT-GCAAAATAAAT
1 AAAACTTAAGATCTAATTTAGCAAAATAAAT
20667067 CCTGACCGAT
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
40 20 0.21
41 35 0.37
42 7 0.07
43 6 0.06
44 18 0.19
45 9 0.09
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (42 bp):
AAAACTTAAGATCTAATTTAGCAAAATAAATTCTAACATATT
Found at i:20670708 original size:151 final size:152
Alignment explanation
Indices: 20670433--20670728 Score: 540
Period size: 151 Copynumber: 2.0 Consensus size: 152
20670423 TGGCTTCTTA
20670433 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCCGAATATTATTGAGTTTGAT
1 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCCGAATATTATTGAGTTTGAT
*
20670498 TACTCTTTAAAAGTTATAAGTGAGAAAATCTTAACTTATTTTCTTTGTCTCCTAGAGTTGTTTAT
66 TACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTATTTTCTTTGTCTCCTAGAGTTGTTTAT
20670563 TTTATTGCGAGTGCATAACGGC
131 TTTATTGCGAGTGCATAACGGC
* * *
20670585 GAGCCTTAGGTCAACTTTGTTAGAAATTGATCCTACAT-TTTTTTCGAATATTATTGAGTTTGAT
1 GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCCGAATATTATTGAGTTTGAT
*
20670649 TACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTGTTTTCTTTGTCTCCTAGAGTTGTTTAT
66 TACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTATTTTCTTTGTCTCCTAGAGTTGTTTAT
20670714 TTTATTGCGAGTGCA
131 TTTATTGCGAGTGCA
20670729 AAATGATGAG
Statistics
Matches: 139, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
151 103 0.74
152 36 0.26
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (152 bp):
GAGCCTTAGGTCAACTTTGTTAGAAAGTGATCCCACATCTTTTTCCGAATATTATTGAGTTTGAT
TACTCTTTAAAAGTTACAAGTGAGAAAATCTTAACTTATTTTCTTTGTCTCCTAGAGTTGTTTAT
TTTATTGCGAGTGCATAACGGC
Found at i:20673581 original size:26 final size:27
Alignment explanation
Indices: 20673546--20673607 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
20673536 TTTCTCGAAA
*
20673546 TTTACCAGGGGTAAAATCT-TC-AAAAT
1 TTTACTAGGGGTAAAAT-TGTCAAAAAT
20673572 TTTACTAGGGGTAAAATTGTCAAAAAT
1 TTTACTAGGGGTAAAATTGTCAAAAAT
*
20673599 TTTATTAGG
1 TTTACTAGG
20673608 CTAAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 1 0.03
26 18 0.56
27 13 0.41
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (27 bp):
TTTACTAGGGGTAAAATTGTCAAAAAT
Found at i:20673993 original size:9 final size:9
Alignment explanation
Indices: 20673979--20674033 Score: 56
Period size: 9 Copynumber: 5.6 Consensus size: 9
20673969 AAATAGAGAG
*
20673979 AATTTTTCC
1 AATTTTACC
20673988 AATTTTACC
1 AATTTTACC
20673997 AATTTCTATTGACC
1 AA--T-T-TT-ACC
20674011 AATTTTACC
1 AATTTTACC
20674020 AATTTTACC
1 AATTTTACC
20674029 AATTT
1 AATTT
20674034 CTATTAAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 27 0.68
10 2 0.05
11 2 0.05
12 2 0.05
13 2 0.05
14 5 0.12
ACGTcount: A:0.31, C:0.20, G:0.02, T:0.47
Consensus pattern (9 bp):
AATTTTACC
Found at i:20686741 original size:57 final size:56
Alignment explanation
Indices: 20686672--20687158 Score: 346
Period size: 57 Copynumber: 8.6 Consensus size: 56
20686662 CCACTTAAAA
* * *
20686672 CCTTAAAGAGGTGGATTATATAAAGTCCATATTAGAAAGATGTGACTATCAACTTTG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTA-AAAGGTGTGACTATCAACTTTG
* *
20686729 CCTTAAAGAGGTG-A--AT-T--AGTCGATCTTAAAGAGGTTTGACTATCAACTTCT-
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAA-AGGTGTGACTATCAACTT-TG
* * * * *
20686780 CCTTAAAGAGGTGAATTCTATAAAGTCCATTTTAAAAAAGGCGTGACTATCAATTTTT
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTT--AAAAGGTGTGACTATCAACTTTG
* * * *
20686838 CCTTAAAGAGGTGAATTATATAAAGTCCATATTAAAGAGGCGTGATTATCAA-TTTT
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAA-AGGTGTGACTATCAACTTTG
* * * * ** ***
20686894 CCTTCAGAGAGATGAATTATATAAAATCCATCTTAAAGAGGTATGGTTAT-TTGTGTCT-
1 CCTT-AAAGAGGTGAATTATATAAAGTCCATCTTAAA-AGGTGTGACTATCAACT-T-TG
* * * * * *
20686952 CCTTAAAGAGGTGGATTATATAAATTCCATTTTAAGGAGGTGTGATTATCAACTTTA
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAA-AAGGTGTGACTATCAACTTTG
* * * * * ** * *
20687009 CTTTAAAAAAAGTGAACTACATAAAGTCCATCTTAAAGAGGCATGACTATGAACTTCG
1 CCTT-AAAGAGGTGAATTATATAAAGTCCATCTTAAA-AGGTGTGACTATCAACTTTG
* * * * * * *
20687067 CCTTAAAGAGGTGAATCATATAGAGTCCATGTTAAATATGTGTGACTATTAGCTTCG
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAA-AGGTGTGACTATCAACTTTG
* * *
20687124 CTTTAAATAGTTGAATTATATAAAGTCCATCTTAA
1 CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAA
20687159 GAAAGTTTGA
Statistics
Matches: 341, Mismatches: 68, Indels: 42
0.76 0.15 0.09
Matches are distributed among these distances:
50 2 0.01
51 38 0.11
52 2 0.01
53 1 0.00
54 3 0.01
55 1 0.00
56 13 0.04
57 184 0.54
58 93 0.27
59 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (56 bp):
CCTTAAAGAGGTGAATTATATAAAGTCCATCTTAAAAGGTGTGACTATCAACTTTG
Found at i:20686924 original size:115 final size:113
Alignment explanation
Indices: 20686672--20687163 Score: 361
Period size: 115 Copynumber: 4.3 Consensus size: 113
20686662 CCACTTAAAA
* * * * *** *
20686672 CCTTAAAGAGGTGGATTATATAAAGTCCATATTAGAAAGATGTGACTATCAACTTTGCCTTAAAG
1 CCTTAAAGAGATGAATTATATAAAGTCCATCTTAAAAAGGCATGACTATCAACTTCGCCTTAAAG
* * * * *
20686737 AGGTG-A--AT-T--AGTCGATCTTAAAGAGGTTTGACTATCAACTTCT
66 AGGTGAATTATATAAAGTCCATATTAAAGAGGTGTGATTATCAA-TTTT
* * * * * **
20686780 CCTTAAAGAGGTGAATTCTATAAAGTCCATTTTAAAAAAGGCGTGACTATCAATTTTTCCTTAAA
1 CCTTAAAGAGATGAATTATATAAAGTCCATCTT-AAAAAGGCATGACTATCAACTTCGCCTTAAA
*
20686845 GAGGTGAATTATATAAAGTCCATATTAAAGAGGCGTGATTATCAATTTT
65 GAGGTGAATTATATAAAGTCCATATTAAAGAGGTGTGATTATCAATTTT
* * * * ** *** *
20686894 CCTTCAGAGAGATGAATTATATAAAATCCATCTTAAAGAGGTATGGTTAT-TTGTGTCTCCTTAA
1 CCTT-AAAGAGATGAATTATATAAAGTCCATCTTAAAAAGGCATGACTATCAACT-TCGCCTTAA
* * * * *
20686958 AGAGGTGGATTATATAAATTCCATTTTAAGGAGGTGTGATTATCAACTTTA
64 AGAGGTGAATTATATAAAGTCCATATTAAAGAGGTGTGATTATCAA-TTTT
* * * * * * *
20687009 CTTTAAAAAAAGTGAACTACATAAAGTCCATCTTAAAGAGGCATGACTATGAACTTCGCCTTAAA
1 CCTTAAAGAGA-TGAATTATATAAAGTCCATCTTAAAAAGGCATGACTATCAACTTCGCCTTAAA
* * * * * * * **
20687074 GAGGTGAATCATATAGAGTCCATGTTAAATATGTGTGACTAT-TAGCTT
65 GAGGTGAATTATATAAAGTCCATATTAAAGAGGTGTGATTATCAATTTT
* *
20687122 CGCTTTAAATAGTTGAATTATATAAAGTCCATCTTAAGAAAG
1 C-C-TTAAAGAGATGAATTATATAAAGTCCATCTTAA-AAAG
20687164 TTTGACATCA
Statistics
Matches: 301, Mismatches: 68, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
108 30 0.10
109 32 0.11
110 1 0.00
112 2 0.01
113 4 0.01
114 94 0.31
115 137 0.46
116 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (113 bp):
CCTTAAAGAGATGAATTATATAAAGTCCATCTTAAAAAGGCATGACTATCAACTTCGCCTTAAAG
AGGTGAATTATATAAAGTCCATATTAAAGAGGTGTGATTATCAATTTT
Found at i:20688004 original size:35 final size:35
Alignment explanation
Indices: 20687955--20688054 Score: 119
Period size: 35 Copynumber: 2.9 Consensus size: 35
20687945 CTACTGGTTT
* * * *
20687955 TTTGGGGCGGCACCGTGTAAACGATATATAGGTCC
1 TTTGGGACGACACCGTGTAAACGATATACAAGTCC
* * *
20687990 TTTGGGATGACACCGTGTAAACGGTATACAAGTCT
1 TTTGGGACGACACCGTGTAAACGATATACAAGTCC
* *
20688025 TTTGGGGCGACACTGTGTAAACGATATACA
1 TTTGGGACGACACCGTGTAAACGATATACA
20688055 TGTAACATCC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (35 bp):
TTTGGGACGACACCGTGTAAACGATATACAAGTCC
Found at i:20691959 original size:38 final size:35
Alignment explanation
Indices: 20691905--20691975 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 35
20691895 CCTCATGGGT
20691905 GTTTTGAAAAATTATTTTATTTTAAATTTGTTTTTAA
1 GTTTTGAAAAATTA-TTTATTTTAAATTT-TTTTTAA
*
20691942 GTTTT-AAAATATCTATTTATTTTTAATTTTTTTT
1 GTTTTGAAAA-AT-TATTTATTTTAAATTTTTTTT
20691976 GAAAAAGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 9 0.29
37 20 0.65
38 2 0.06
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (35 bp):
GTTTTGAAAAATTATTTATTTTAAATTTTTTTTAA
Found at i:20692917 original size:21 final size:21
Alignment explanation
Indices: 20692843--20692910 Score: 127
Period size: 21 Copynumber: 3.2 Consensus size: 21
20692833 GCTCGGTCAC
20692843 ACGGGTGTATGTCTCCTCCAT
1 ACGGGTGTATGTCTCCTCCAT
20692864 ACGGGTGTATGTCTCCTCCAT
1 ACGGGTGTATGTCTCCTCCAT
*
20692885 ACGGGTGTGTGTCTCCTCCAT
1 ACGGGTGTATGTCTCCTCCAT
20692906 ACGGG
1 ACGGG
20692911 CGTGTGTAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.31
Consensus pattern (21 bp):
ACGGGTGTATGTCTCCTCCAT
Found at i:20704634 original size:22 final size:22
Alignment explanation
Indices: 20704606--20704703 Score: 124
Period size: 22 Copynumber: 4.5 Consensus size: 22
20704596 TTTATTGTTC
*
20704606 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
20704628 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
20704650 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
20704672 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
20704694 AAACATGAGA
1 AAACATGAGA
20704704 TGAAAGTATG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:20706551 original size:61 final size:58
Alignment explanation
Indices: 20706451--20706590 Score: 172
Period size: 61 Copynumber: 2.3 Consensus size: 58
20706441 GATTATTGTT
* ** *
20706451 ATTAAATTTTAATAGGATTATTATTAAATATGATGTAATAAAAATAAAAATAAATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATGTAATAAAAAT---AATAAATAATTTA
* *
20706512 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATGTAATAAAAATAATAAATAATTTA
* *
20706570 GTAATATTCTTAATATAATTA
1 ATTATATT-TTAATATAATTA
20706591 ATTTTATATT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 18 0.26
59 12 0.17
61 40 0.57
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATGTAATAAAAATAATAAATAATTTA
Found at i:20706620 original size:23 final size:23
Alignment explanation
Indices: 20706594--20706637 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
20706584 ATAATTAATT
20706594 TTATATTA-AATTATATTAAAAGA
1 TTAT-TTATAATTATATTAAAAGA
**
20706617 TTATTTATTTTTATATTAAAA
1 TTATTTATAATTATATTAAAA
20706638 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTTATAATTATATTAAAAGA
Found at i:20716542 original size:21 final size:21
Alignment explanation
Indices: 20716516--20716555 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20716506 ACTTTCTTGA
*
20716516 AAAACAAACTTAAAAATGGTG
1 AAAACAAACCTAAAAATGGTG
20716537 AAAACAAACCTAAAAATGG
1 AAAACAAACCTAAAAATGG
20716556 ACAAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAACAAACCTAAAAATGGTG
Found at i:20718835 original size:20 final size:20
Alignment explanation
Indices: 20718810--20718847 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20718800 ATACAAATTA
20718810 TTATTCCTAGAAAATAAAAT
1 TTATTCCTAGAAAATAAAAT
* *
20718830 TTATTCTTGGAAAATAAA
1 TTATTCCTAGAAAATAAA
20718848 TTCGCACTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (20 bp):
TTATTCCTAGAAAATAAAAT
Found at i:20719269 original size:17 final size:17
Alignment explanation
Indices: 20719231--20719272 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
20719221 TGAATGTGAC
* *
20719231 TCATTTATCTAATTTTA
1 TCATTTCTCTAATTTCA
*
20719248 CCATTTCTCTAATTTCA
1 TCATTTCTCTAATTTCA
20719265 TCATTTCT
1 TCATTTCT
20719273 ATTCATTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (17 bp):
TCATTTCTCTAATTTCA
Found at i:20724052 original size:9 final size:9
Alignment explanation
Indices: 20724038--20724128 Score: 55
Period size: 9 Copynumber: 9.9 Consensus size: 9
20724028 CACTTCTAAG
20724038 TAATTTTTA
1 TAATTTTTA
20724047 TAATTTTT-
1 TAATTTTTA
*
20724055 GAATATTTTA
1 TAAT-TTTTA
20724065 TAAGATTTTTAA
1 T-A-ATTTTT-A
*
20724077 TAATTTTAA
1 TAATTTTTA
20724086 TAATTTTT-
1 TAATTTTTA
*
20724094 TAA-TTCTA
1 TAATTTTTA
*
20724102 TAATTATTTT
1 TAATT-TTTA
*
20724112 TTATTTTT-
1 TAATTTTTA
20724120 TGAATTTTT
1 T-AATTTTT
20724129 TTATTTATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.05
8 10 0.16
9 30 0.47
10 11 0.17
11 6 0.09
12 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
TAATTTTTA
Found at i:20724093 original size:20 final size:19
Alignment explanation
Indices: 20724042--20724097 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
20724032 TCTAAGTAAT
*
20724042 TTTTATAATTTTTGAAT-A
1 TTTTATAATTTTTTAATAA
*
20724060 TTTTATAAGATTTTTAATAA
1 TTTTATAA-TTTTTTAATAA
20724080 TTTTAATAATTTTTTAAT
1 TTTT-ATAATTTTTTAAT
20724098 TCTATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.25
19 7 0.22
20 13 0.41
21 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTTAATAA
Found at i:20724106 original size:16 final size:15
Alignment explanation
Indices: 20724085--20724146 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
20724075 AATAATTTTA
20724085 ATAATTTTTTAATTCT
1 ATAATTTTTTAATT-T
*
20724101 ATAATTATTTTTTATTTT
1 AT-A--ATTTTTTAATTT
* *
20724119 TTGAATTTTTTTATTT
1 AT-AATTTTTTAATTT
20724135 ATAATTTTTTAA
1 ATAATTTTTTAA
20724147 AAAAATTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
15 9 0.25
16 13 0.36
17 1 0.03
18 3 0.08
19 10 0.28
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (15 bp):
ATAATTTTTTAATTT
Found at i:20728830 original size:25 final size:25
Alignment explanation
Indices: 20728802--20728851 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20728792 GAAGGGTTGT
20728802 ATGGCTGGAGAATCTTAAGAATAAA
1 ATGGCTGGAGAATCTTAAGAATAAA
20728827 ATGGCTGGAGAATCTTAAGAATAAA
1 ATGGCTGGAGAATCTTAAGAATAAA
20728852 GGTGGTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (25 bp):
ATGGCTGGAGAATCTTAAGAATAAA
Found at i:20753070 original size:21 final size:21
Alignment explanation
Indices: 20753044--20753085 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20753034 CTTATTAAAG
20753044 AGACTTAGTATACTTGGAAGT
1 AGACTTAGTATACTTGGAAGT
20753065 AGACTTAGTATACTTGGAAGT
1 AGACTTAGTATACTTGGAAGT
20753086 GACACCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
AGACTTAGTATACTTGGAAGT
Found at i:20756057 original size:105 final size:104
Alignment explanation
Indices: 20755867--20756109 Score: 366
Period size: 105 Copynumber: 2.3 Consensus size: 104
20755857 NNNNNNNNNN
* * *
20755867 GATTT-ATGGGTGGTGCTATGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTAT
1 GATTTCATTGGTGGTGCTAAGTGCGT-ATCCACCATATCTTTGAAATGTAAAAGGGGGTTGCTAT
* *
20755931 GTGCTGATTCCCCGGAGGGGTTGCTAAGTGCTGATTCCCT
65 GTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
20755971 GATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATG-AAAAGGGGGGTTGCTA
1 GATTTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTTTGAAATGTAAAA-GGGGGTTGCTA
20756035 TGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
64 TGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
* *
20756076 GA-TTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 GATTTCATTGGTGGTGCTAAGTGC-GTATCCACCA
20756110 ATAACGGCTA
Statistics
Matches: 128, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
104 36 0.28
105 91 0.71
106 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (104 bp):
GATTTCATTGGTGGTGCTAAGTGCGTATCCACCATATCTTTGAAATGTAAAAGGGGGTTGCTATG
TGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
Found at i:20765934 original size:45 final size:45
Alignment explanation
Indices: 20765838--20766024 Score: 157
Period size: 45 Copynumber: 4.2 Consensus size: 45
20765828 TTGGAAATAT
* * * ** **
20765838 AGGTGGATGCTATGTGCTGATTCCAC-CTGATATTAATGAAAATAA
1 AGGTGGTTGCTATGTGCTGATTTCACAC-GGTACCAATGAGTATAA
* * *
20765883 AAGTGGTTGCTATGTGCTGATTTCA-ATGGATACCAATG-GTTATAT
1 AGGTGGTTGCTATGTGCTGATTTCACACGG-TACCAATGAG-TATAA
* * *
20765928 AGGTGGTTGCTATGTGCTGATTTCACCCGGTTCCATTGAGTATAA
1 AGGTGGTTGCTATGTGCTGATTTCACACGGTACCAATGAGTATAA
* * *
20765973 AGGTGGTTGCTATGTGCTGATTTCAC-CGAGTACTATTGACTATAA
1 AGGTGGTTGCTATGTGCTGATTTCACACG-GTACCAATGAGTATAA
*
20766018 GGGTGGT
1 AGGTGGT
20766025 GATGTGTACT
Statistics
Matches: 116, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
44 3 0.03
45 110 0.95
46 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (45 bp):
AGGTGGTTGCTATGTGCTGATTTCACACGGTACCAATGAGTATAA
Found at i:20765973 original size:90 final size:90
Alignment explanation
Indices: 20765834--20765997 Score: 231
Period size: 90 Copynumber: 1.8 Consensus size: 90
20765824 ATCGTTGGAA
* *
20765834 ATATAGGTGGATGCTATGTGCTGATTCCACCTGATATTAATGAAAATAAAAGTGGTTGCTATGTG
1 ATATAGGTGGATGCTATGTGCTGATTCCACCCGATATCAATGAAAATAAAAGTGGTTGCTATGTG
20765899 CTGATTTCAATGGATACCAATGGTT
66 CTGATTTCAATGGATACCAATGGTT
* * * * ** *
20765924 ATATAGGTGGTTGCTATGTGCTGATTTCACCCGGT-TCCATTGAGTATAAAGGTGGTTGCTATGT
1 ATATAGGTGGATGCTATGTGCTGATTCCACCCGATAT-CAATGAAAATAAAAGTGGTTGCTATGT
20765988 GCTGATTTCA
65 GCTGATTTCA
20765998 CCGAGTACTA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
89 1 0.02
90 63 0.98
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (90 bp):
ATATAGGTGGATGCTATGTGCTGATTCCACCCGATATCAATGAAAATAAAAGTGGTTGCTATGTG
CTGATTTCAATGGATACCAATGGTT
Found at i:20786039 original size:3 final size:3
Alignment explanation
Indices: 20786031--20786076 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
20786021 AAACAAGCTT
20786031 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20786077 AGGGTAAAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20787048 original size:81 final size:81
Alignment explanation
Indices: 20786900--20787059 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 81
20786890 GCTTTGGTTA
* ** ** *
20786900 AGTAGTAAATTTAAAGTTTTATCAATCCAATTGGTGTGGGTTCAAACCCCACAATATGCATAATT
1 AGTAGTAAATTTAAAGTTTTATAAATCCAATTAATGCAGGTTCAAACCCCACAATATACATAATT
20786965 TTA-TGAGTTTTTGTTG
66 TTATTG-GTTTTTGTTG
* * * *
20786981 AGTAGTAAATTTAAAGTTTTATAAATCCAATTAATGCATGTTCAAATCCCACATTATACATACTT
1 AGTAGTAAATTTAAAGTTTTATAAATCCAATTAATGCAGGTTCAAACCCCACAATATACATAATT
20787046 TTATTGGTTTTTGT
66 TTATTGGTTTTTGT
20787060 GAAAATGAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
81 66 0.97
82 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (81 bp):
AGTAGTAAATTTAAAGTTTTATAAATCCAATTAATGCAGGTTCAAACCCCACAATATACATAATT
TTATTGGTTTTTGTTG
Found at i:20790837 original size:11 final size:11
Alignment explanation
Indices: 20790823--20790898 Score: 61
Period size: 11 Copynumber: 7.1 Consensus size: 11
20790813 ATTAAACTTA
*
20790823 ATTACTTTAAT
1 ATTAATTTAAT
20790834 ATTAAATTTAAT
1 ATT-AATTTAAT
20790846 -TTAATATT-AT
1 ATTAAT-TTAAT
20790856 ATTAATTTAAT
1 ATTAATTTAAT
**
20790867 ATTAAGATAAT
1 ATTAATTTAAT
*
20790878 A--ATTTTAAT
1 ATTAATTTAAT
*
20790887 ATTAAATTAAT
1 ATTAATTTAAT
20790898 A
1 A
20790899 AAATCCTATC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
9 6 0.12
10 7 0.14
11 31 0.61
12 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (11 bp):
ATTAATTTAAT
Found at i:20790848 original size:5 final size:6
Alignment explanation
Indices: 20790829--20790898 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
20790819 CTTAATTACT
20790829 TTAATA TTAA-A TTTAAT- TTAATA TT-ATA TTAAT- TTAATA TTAAGATA
1 TTAATA TTAATA -TTAATA TTAATA TTAATA TTAATA TTAATA TT-A-ATA
* *
20790876 ATAATT TTAATA TTAA-A TTAATA
1 TTAATA TTAATA TTAATA TTAATA
20790899 AAATCCTATC
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
5 21 0.40
6 25 0.48
7 2 0.04
8 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:20790860 original size:16 final size:16
Alignment explanation
Indices: 20790822--20790897 Score: 89
Period size: 17 Copynumber: 4.4 Consensus size: 16
20790812 GATTAAACTT
*
20790822 AATTACTTTAATATTA
1 AATTAATTTAATATTA
20790838 AATTTAATTTAATATTA
1 AA-TTAATTTAATATTA
*
20790855 TATTAATTTAATATTA
1 AATTAATTTAATATTA
20790871 AGATAATAATTTTAATATTA
1 A-AT--TAA-TTTAATATTA
20790891 AATTAAT
1 AATTAAT
20790898 AAAATCCTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
16 17 0.33
17 19 0.37
19 5 0.10
20 11 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (16 bp):
AATTAATTTAATATTA
Found at i:20798513 original size:30 final size:30
Alignment explanation
Indices: 20798477--20798539 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
20798467 TAGCAGTACA
* *
20798477 GTGTGGGCCTGAGCCCATTATAGTAACAGT
1 GTGTGGGCCTGAGCCCAATATAGTAACAAT
*
20798507 GTGTGGGCCTTAGCCCAATATAGTAACAAT
1 GTGTGGGCCTGAGCCCAATATAGTAACAAT
20798537 GTG
1 GTG
20798540 GGTTTTAGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (30 bp):
GTGTGGGCCTGAGCCCAATATAGTAACAAT
Found at i:20798548 original size:28 final size:29
Alignment explanation
Indices: 20798474--20798560 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 29
20798464 CAGTAGCAGT
* *
20798474 ACAG-TGTGGGCCTGAGCCCATTATAGTA
1 ACAGATGTGGGCCTTAGCCCAATATAGTA
*
20798502 ACAGTGTGTGGGCCTTAGCCCAATATAGTA
1 ACAG-ATGTGGGCCTTAGCCCAATATAGTA
** *
20798532 ACA-ATGTGGGTTTTAGCCCAATACAGTA
1 ACAGATGTGGGCCTTAGCCCAATATAGTA
20798560 A
1 A
20798561 TCAGTACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
28 26 0.51
30 25 0.49
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (29 bp):
ACAGATGTGGGCCTTAGCCCAATATAGTA
Found at i:20798939 original size:27 final size:25
Alignment explanation
Indices: 20798922--20799225 Score: 205
Period size: 27 Copynumber: 11.3 Consensus size: 25
20798912 GGGTATAACA
*
20798922 GTCATTTTACCCTATAGGTGTATTTC
1 GTCATTTTACCCT-TAGGGGTATTTC
20798948 GGTCATTTTACCCTTCAGGGGTATTTC
1 -GTCATTTTACCCTT-AGGGGTATTTC
*
20798975 GATCATTTTACCCTTTGGGGGTATTTC
1 G-TCATTTTACCC-TTAGGGGTATTTC
* * *
20799002 GGTTATTTTACCCTTCGAGAGTATTTC
1 -GTCATTTTACCCTTAG-GGGTATTTC
* *
20799029 GGTCATTTTACCCTTCGAGAGTATTTC
1 -GTCATTTTACCCTTAG-GGGTATTTC
* ** * *
20799056 GGTTATTTTATTCATCGAGGGTATTTC
1 -GTCATTTTACCCTTAG-GGGTATTTC
*
20799083 GATCATTTTACCCTTCAAGGGTATTTC
1 G-TCATTTTACCCTT-AGGGGTATTTC
*
20799110 GATCATTTTACCCTTCAAGGGTATTTC
1 G-TCATTTTACCCTT-AGGGGTATTTC
* * *
20799137 GGTTATTTTACCCTTCGAGAGTATTTC
1 -GTCATTTTACCCTTAG-GGGTATTTC
*
20799164 GGTCATTTTAGCCATT-GAGGGTATTTC
1 -GTCATTTTA-CCCTTAG-GGGTATTTC
* * *
20799191 GGTCATTTTACCTTTTGAGGGTAATTTG
1 -GTCATTTTACCCTTAG-GGGT-ATTTC
20799219 GTCATTT
1 GTCATTT
20799226 ATTGACCTCT
Statistics
Matches: 239, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
26 10 0.04
27 217 0.91
28 12 0.05
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (25 bp):
GTCATTTTACCCTTAGGGGTATTTC
Found at i:20799212 original size:81 final size:81
Alignment explanation
Indices: 20798922--20799213 Score: 358
Period size: 81 Copynumber: 3.6 Consensus size: 81
20798912 GGGTATAACA
* *
20798922 GTCATTTTACCCTAT--AGGTGTATTTCGGTCATTTTACCCTTC-AGGGGTATTTCGATCATTTT
1 GTCATTTTACCCT-TCGAGG-GTATTTCGGTCATTTTACCCTTCGA-GGGTATTTCGGTTATTTT
* *
20798984 ACCCTTTGGGGGTATTTCG
63 ACCCTTCGAGGGTATTTCG
* * * **
20799003 GTTATTTTACCCTTCGAGAGTATTTCGGTCATTTTACCCTTCGAGAGTATTTCGGTTATTTTATT
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACC
*
20799068 CATCGAGGGTATTTCG
66 CTTCGAGGGTATTTCG
* * * *
20799084 ATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCGGTTATTTTACC
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACC
*
20799149 CTTCGAGAGTATTTCG
66 CTTCGAGGGTATTTCG
* * *
20799165 GTCATTTTAGCCATT-GAGGGTATTTCGGTCATTTTACCTTTTGAGGGTA
1 GTCATTTTA-CCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTA
20799214 ATTTGGTCAT
Statistics
Matches: 179, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 171 0.96
82 7 0.04
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (81 bp):
GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACC
CTTCGAGGGTATTTCG
Found at i:20799222 original size:54 final size:53
Alignment explanation
Indices: 20798922--20799225 Score: 335
Period size: 54 Copynumber: 5.6 Consensus size: 53
20798912 GGGTATAACA
*
20798922 GTCATTTTACCCTAT--AGGTGTATTTCGGTCATTTTACCCTTCAGGGGTATTTCG
1 GTCATTTTACCCT-TCGAGG-GTATTTCGGTCATTTTACCCTTGA-GGGTATTTCG
* * * * *
20798976 ATCATTTTACCCTTTGGGGGTATTTCGGTTATTTTACCCTTCGAGAGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTT-GAGGGTATTTCG
* * * * *
20799030 GTCATTTTACCCTTCGAGAGTATTTCGGTTATTTTATTCATCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA-CCCTTGAGGGTATTTCG
* * * *
20799084 ATCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTT-GAGGGTATTTCG
* * *
20799138 GTTATTTTACCCTTCGAGAGTATTTCGGTCATTTTAGCCATTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA-CCCTTGAGGGTATTTCG
* *
20799192 GTCATTTTACCTTTTGAGGGTAATTT-GGTCATTT
1 GTCATTTTACCCTTCGAGGGT-ATTTCGGTCATTT
20799226 ATTGACCTCT
Statistics
Matches: 210, Mismatches: 33, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
53 3 0.01
54 194 0.92
55 13 0.06
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (53 bp):
GTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTGAGGGTATTTCG
Found at i:20799436 original size:16 final size:17
Alignment explanation
Indices: 20799415--20799447 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20799405 ATCCGTGTGG
20799415 GGCCCAC-GAGCCCATT
1 GGCCCACAGAGCCCATT
*
20799431 GGCCCACATAGCCCATT
1 GGCCCACAGAGCCCATT
20799448 TCGGCCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.15
Consensus pattern (17 bp):
GGCCCACAGAGCCCATT
Found at i:20801835 original size:2 final size:2
Alignment explanation
Indices: 20801828--20801863 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20801818 CCCCAAAACA
20801828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20801864 GCACGTCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20804602 original size:12 final size:12
Alignment explanation
Indices: 20804587--20804636 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
20804577 TCATATTGTT
20804587 AAATTAATTTTA
1 AAATTAATTTTA
*
20804599 AAATTAATTAT-
1 AAATTAATTTTA
*
20804610 AATTTAA-TTTA
1 AAATTAATTTTA
*
20804621 AAATTATTGTTTA
1 AAATTAAT-TTTA
20804634 AAA
1 AAA
20804637 AAGTTATGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
10 2 0.07
11 11 0.37
12 10 0.33
13 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
AAATTAATTTTA
Found at i:20805765 original size:30 final size:30
Alignment explanation
Indices: 20805695--20805765 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
20805685 CTCTTATTTA
* *
20805695 AACATTTTA-AAAAGTTTAACTTTGATTTG
1 AACATTCTATAAAAGTTTAACTTTGATATG
* ** * *
20805724 AGCATGGTATAAAAGTTTGACTTTTATATG
1 AACATTCTATAAAAGTTTAACTTTGATATG
20805754 AACATTCTATAA
1 AACATTCTATAA
20805766 GATGTAACCC
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (30 bp):
AACATTCTATAAAAGTTTAACTTTGATATG
Found at i:20811930 original size:12 final size:12
Alignment explanation
Indices: 20811913--20811937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20811903 TTAGTTTAGT
20811913 ATTACTTCTCAA
1 ATTACTTCTCAA
20811925 ATTACTTCTCAA
1 ATTACTTCTCAA
20811937 A
1 A
20811938 AGTGTTACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTACTTCTCAA
Found at i:20825059 original size:25 final size:25
Alignment explanation
Indices: 20825010--20825059 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20825000 TTTGCAGTGG
* *
20825010 TTGATTTCTCTTTTGTTAGCTCTGA
1 TTGATTTCTCTTTTGTCAGCGCTGA
20825035 TTGATTTCTCTTTTG-CAGCGGCTGA
1 TTGATTTCTCTTTTGTCAGC-GCTGA
20825060 CAATGCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.50
Consensus pattern (25 bp):
TTGATTTCTCTTTTGTCAGCGCTGA
Found at i:20825640 original size:12 final size:12
Alignment explanation
Indices: 20825623--20825652 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20825613 GCAATGTTTT
*
20825623 AACAATATTATA
1 AACAATATGATA
20825635 AACAATATGATA
1 AACAATATGATA
20825647 AACAAT
1 AACAAT
20825653 CTAAATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (12 bp):
AACAATATGATA
Found at i:20825732 original size:67 final size:67
Alignment explanation
Indices: 20825566--20825777 Score: 309
Period size: 67 Copynumber: 3.1 Consensus size: 67
20825556 AGAAAATTTT
* * * *
20825566 AACAATATGATAAACAATCTAAATAAAGGATAATTATATTATTAGTTG-CAATGTTTTAACAATA
1 AACAATATGATAAACAATCTAAATAAAGGGTAATTATATTATTA-TAGAAAAT-TTGT-ACAATA
*
20825630 TTATA
63 TGATA
*
20825635 AACAATATGATAAACAATCTAAATAAAGGGTAATTGTATTATTATAGAAAATTTGTACAATATGA
1 AACAATATGATAAACAATCTAAATAAAGGGTAATTATATTATTATAGAAAATTTGTACAATATGA
20825700 TA
66 TA
* * *
20825702 AACAATACGATAAACAATCTAAATAAAGGGTAATTATAATATTATAGAAAATTTGTATAATATGA
1 AACAATATGATAAACAATCTAAATAAAGGGTAATTATATTATTATAGAAAATTTGTACAATATGA
20825767 TA
66 TA
20825769 AACAATATG
1 AACAATATG
20825778 TATGATAAAC
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
67 81 0.62
68 5 0.04
69 45 0.34
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (67 bp):
AACAATATGATAAACAATCTAAATAAAGGGTAATTATATTATTATAGAAAATTTGTACAATATGA
TA
Found at i:20825779 original size:21 final size:21
Alignment explanation
Indices: 20825736--20825780 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20825726 AAAGGGTAAT
* *
20825736 TATAATATTATAGAAAATTTG
1 TATAATATGATAGAAAATATG
20825757 TATAATATGATA-AACAATATG
1 TATAATATGATAGAA-AATATG
20825778 TAT
1 TAT
20825781 GATAAACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (21 bp):
TATAATATGATAGAAAATATG
Found at i:20827791 original size:32 final size:32
Alignment explanation
Indices: 20827739--20827801 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
20827729 ATTGCAGTTT
*
20827739 AATAATAATAAAGTAGATTATAAATTATAGTG
1 AATAATAATAAAGTAAATTATAAATTATAGTG
* * **
20827771 AATAATAATTATGTAAATTATATTTTATAGT
1 AATAATAATAAAGTAAATTATAAATTATAGT
20827802 ATTATATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (32 bp):
AATAATAATAAAGTAAATTATAAATTATAGTG
Found at i:20827857 original size:44 final size:41
Alignment explanation
Indices: 20827809--20827907 Score: 92
Period size: 44 Copynumber: 2.3 Consensus size: 41
20827799 AGTATTATAT
20827809 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
20827853 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
20827897 ATTATATTTTA
1 ATTATATTTTA
20827908 TAGTATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
41 3 0.06
42 6 0.13
43 1 0.02
44 15 0.32
45 10 0.21
46 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:20827896 original size:26 final size:28
Alignment explanation
Indices: 20827842--20827923 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 28
20827832 TAAGAATAAG
* * *
20827842 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
20827870 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
* *
20827896 AATTATATTTTATAGTATTATATATTAT
1 AATTATATTTAATAATA-TAT-TATTAT
20827924 GATTTTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 18 0.40
27 6 0.13
28 16 0.36
29 4 0.09
30 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:20827919 original size:110 final size:115
Alignment explanation
Indices: 20827755--20828017 Score: 369
Period size: 120 Copynumber: 2.3 Consensus size: 115
20827745 AATAAAGTAG
* * *
20827755 ATTA-TAAATTATAGTGAATAATAATTA-TGTAAATTATATTTTATAGTATTATATATTATGA-T
1 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATT
*
20827817 T-TTAGTAAATTCATATAAG-A-A-TAAGAATTTTATTAAATTATATATT
66 TATTAGTAAATTCATATAAGAATATTAACAATTTTATTAAATTATATATT
20827863 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGA-T
20827928 TTATTAGTAAATTCATATAAGAATATTTATTAACAATTTTATTAAATTATATATT
65 TTATTAGTAAATTCATATAAG-A-A--TATTAACAATTTTATTAAATTATATATT
* * *
20827983 TTTATTAAATTATATTTAATAACAATTATGTTAAA
1 ATTATTAAATTATATTTAATAATAATTATTTTAAA
20828018 ATATGATTAA
Statistics
Matches: 136, Mismatches: 7, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
108 4 0.03
109 21 0.15
110 33 0.24
112 2 0.01
113 18 0.13
116 1 0.01
119 1 0.01
120 56 0.41
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (115 bp):
ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATT
TATTAGTAAATTCATATAAGAATATTAACAATTTTATTAAATTATATATT
Found at i:20828190 original size:39 final size:41
Alignment explanation
Indices: 20828145--20828250 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
20828135 TTTCCTTATG
** *
20828145 CTATTACATCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
20828185 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
20828230 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
20828251 ACAGCGAACC
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 12 0.21
40 2 0.04
41 4 0.07
44 19 0.34
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:20828225 original size:44 final size:46
Alignment explanation
Indices: 20828162--20828253 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
20828152 ATCTCTATTC
*
20828162 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
20828206 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
20828252 CA
1 CA
20828254 GCGAACCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.42
45 4 0.09
46 22 0.49
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:20828261 original size:46 final size:44
Alignment explanation
Indices: 20828166--20828264 Score: 146
Period size: 46 Copynumber: 2.2 Consensus size: 44
20828156 CTATTCCATT
* *
20828166 CAACCAAACACAAGAATACCATTACGCCTCTATTCCATTACATT
1 CAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTACATG
20828210 CAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTACA-G
1 CAACCAAACAAAAGAA-TACC-ATTACGCCTCTATTCCATTACATG
20828255 CGAACCAAAC
1 C-AACCAAAC
20828265 GTGGCCTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 15 0.30
45 5 0.10
46 30 0.60
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.22
Consensus pattern (44 bp):
CAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTACATG
Found at i:20840603 original size:21 final size:21
Alignment explanation
Indices: 20840577--20840630 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
20840567 AACAGCGGTG
*
20840577 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
20840598 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
20840619 GCGGTGAGATTA
1 GCGGTGAGATTA
20840631 AAAACAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.37, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:20846169 original size:20 final size:20
Alignment explanation
Indices: 20846137--20846195 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 20
20846127 TCATATCAAT
*
20846137 AAAT-AATTTAAAATTATAA
1 AAATAAATTCAAAATTATAA
* *
20846156 AAA-ATATTCAAAA-AATAA
1 AAATAAATTCAAAATTATAA
20846174 AAATAAATTCAAAATTATAA
1 AAATAAATTCAAAATTATAA
20846194 AA
1 AA
20846196 CGTTCAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.22
19 19 0.59
20 6 0.19
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAATTCAAAATTATAA
Found at i:20846302 original size:31 final size:32
Alignment explanation
Indices: 20846264--20846325 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
20846254 TTAGTTATTA
*
20846264 TTTTTAAAAA-GTTGATGGACAAATTTAACTC
1 TTTTTAAAAATGTTGATAGACAAATTTAACTC
*
20846295 TTTTTAAAAATGTTGATAGTCAAATTTAACT
1 TTTTTAAAAATGTTGATAGACAAATTTAACT
20846326 TACAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (32 bp):
TTTTTAAAAATGTTGATAGACAAATTTAACTC
Found at i:20871289 original size:50 final size:50
Alignment explanation
Indices: 20871165--20871454 Score: 320
Period size: 50 Copynumber: 5.8 Consensus size: 50
20871155 GATAATAACA
* * ** *
20871165 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TATTTTCT-GTAC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG--G
* * * * ** *
20871214 TGCCAATGCCATATCCCAGATATGGTCTTGCATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
20871264 TG-CACATGCCATGTCCCAGACATGGTCTTAC-GGGAGACCTCTCATCTCGG
1 TGCCA-ACGCCATGTCCCAGACATGGTCTTACATGG-GACCTCTCATCTCGG
* * * * *
20871314 TGCCAACGCAATGTCCCAAACATAGTCTTACATGGGACATCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
20871364 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
20871414 TGCCAACGCCATGTCCCGGACATGGTCTTACATGGGACCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
20871455 GTTACCCAAA
Statistics
Matches: 206, Mismatches: 28, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
49 37 0.18
50 160 0.78
51 8 0.04
52 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:20871454 original size:150 final size:148
Alignment explanation
Indices: 20871165--20871444 Score: 357
Period size: 150 Copynumber: 1.9 Consensus size: 148
20871155 GATAATAACA
* * * * *
20871165 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATATTTTCTGTACTGCCAATGCCATATCC
1 TGCCAAAGCAATGTCCCAAACATAGTCTTACATGGGACATTTTCTG-ACTGCCAACGCCATATCC
* * ** *
20871230 CAGATATGGTCTTGCATGGGAGTTCTCATATCGGTGCACATGCCATGTCCCAGACATGGTCTTAC
65 CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCACACGCCATGTCCCAGACATGGTCTTAC
20871295 GGGAGACCTCTCATCTCGG
130 GGGAGACCTCTCATCTCGG
* * *
20871314 TGCCAACGCAATGTCCCAAACATAGTCTTACATGGGACATCTTATCTCG-GTGCCAACGCCATGT
1 TGCCAAAGCAATGTCCCAAACATAGTCTTACATGGGACAT-TT-TCT-GACTGCCAACGCCATAT
* * *
20871378 CCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGC-CAACGCCATGTCCCGGACATGGTCT
63 CCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCAC-ACGCCATGTCCCAGACATGGTCT
20871442 TAC
127 TAC
20871445 ATGGGACCTC
Statistics
Matches: 111, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
149 36 0.32
150 71 0.64
151 3 0.03
152 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (148 bp):
TGCCAAAGCAATGTCCCAAACATAGTCTTACATGGGACATTTTCTGACTGCCAACGCCATATCCC
AGACATGGTCTTACATGGGACCTCTCATATCGGTGCACACGCCATGTCCCAGACATGGTCTTACG
GGAGACCTCTCATCTCGG
Done.