Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015199.1 Kokia drynarioides strain JFW-HI SEQ_130243, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 887795
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 743 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:348075 original size:23 final size:23
Alignment explanation
Indices: 348049--348107 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
348039 ACTGAACTAA
*
348049 ACCAAATCGAACTGCTAACTTTG
1 ACCAAACCGAACTGCTAACTTTG
348072 ACCAAACCGAACTGCTAACTTTG
1 ACCAAACCGAACTGCTAACTTTG
348095 ACCAAACCGAACT
1 ACCAAACCGAACT
348108 AGACCGTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (23 bp):
ACCAAACCGAACTGCTAACTTTG
Found at i:355165 original size:27 final size:27
Alignment explanation
Indices: 355127--355188 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
355117 CCGACCTAAC
355127 CCATTGACCGAACTAAACCAAACAAAA
1 CCATTGACCGAACTAAACCAAACAAAA
* * ** *
355154 CCATTGATCGAACTGAACTGAACCAAA
1 CCATTGACCGAACTAAACCAAACAAAA
355181 CCATTGAC
1 CCATTGAC
355189 TTTGACCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.29, G:0.11, T:0.16
Consensus pattern (27 bp):
CCATTGACCGAACTAAACCAAACAAAA
Found at i:356811 original size:3 final size:3
Alignment explanation
Indices: 356803--356841 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
356793 TCCAAAACCA
* *
356803 AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
356842 CAAAGTAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:359691 original size:13 final size:13
Alignment explanation
Indices: 359675--359699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
359665 TAACTTCAAT
359675 CATTGACTTTGAC
1 CATTGACTTTGAC
359688 CATTGACTTTGA
1 CATTGACTTTGA
359700 ATTTGATCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
CATTGACTTTGAC
Found at i:364872 original size:514 final size:513
Alignment explanation
Indices: 363855--364868 Score: 1136
Period size: 514 Copynumber: 2.0 Consensus size: 513
363845 TCATCTTGTG
* * *
363855 GTTTTACTTTCTCCTTTTCAATCACCTTTTCCCCCCTCAACCTTAATTGCTAACGACTTCACTTG
1 GTTTTACTTTCTCCCTTTCAATCACC-TTTCCCCCCTCAACCTTAATTGCAAACAACTTCACTTG
* * * * *
363920 GCTAATGGAGAGAATAAATAGCAAGGGGGTCAAATCAAGGCCCCTCTATAGTTGCTCTTGGCTGG
65 GCTAATGGAGAGAATAAATAGCAAAGGAGTCAAATCAAGGCCCATCTATAGTTACTCTTAGCTGG
* *
363985 TGTCAAGCTCAACCACATCATGTTTCCATAGTTGGTAACTCTATTGTTTGCTTTGCCATTACATC
130 TCTCAAGCTCAACCACATCATGTTTCCATAATTGGTAACTCTATTGTTTGCTTTGCCATTACATC
* * * *
364050 TTGAGTCGATGACTCCCCTTTTTGAGTTCATTTGTTGATGTATATTCGTCAAGGTTTAGTATATA
195 TCGAGTCGATGACTCCCCTTTCTGAGTTCATTTGTTGATGTATATTAGTCAAGGTTTAGGATATA
* * * ** * * *
364115 TCTTTTCTTAAATAATGTATTTTATTGATCTTGTCTAAGTTGTTTGTTTGTTTTTTATTGATTAA
260 TCTTTGCTTAAAAAATATATTTTATTGATCCAGTCAAAGTTGTTTGTTTCTTTCTTATTGATTAA
* * * * * * * * * * *
364180 GCTACGAGTTTGAATCGTGTATAAGAATATAGGGCTTTGTGAAGAAGGTGGATTTGTACTGCTTC
325 GCTACCAGATTGAATCGTGTATAAGAACACAAGGCTTCGGGAACAAGGTAGATTTGCAATGCTTC
* * * * ** * * *
364245 TTCATCTTCTTAAGGAAGGTTGCCTCACTACTCCACTAATTAGATCTTTAGGTCAACCATTCCCA
390 TTAATCTTCTTAAGAAAGGCTACCTCACTACTCCAAGAATCAAATATTTAGGTCAACCATTCCCA
* *
364310 TATCCCCTTTAAACTATAGTTGGTTGTTATAGAGCCTTAATTTTTTTTGTTGAGCTATA
455 TATCCCATTTAAACTATAATTGGTTGTTATAGAGCCTTAATTTTTTTTGTTGAGCTATA
*
364369 GTTTTAGC-TTCTCCCTTTCAATCACC-TTCCCCCTCTCAACCTTAATAT-CAAACAATTTCACT
1 GTTTTA-CTTTCTCCCTTTCAATCACCTTTCCCCC-CTCAACCTTAAT-TGCAAACAACTTCACT
* * * *
364431 TGGCTAATGGAGGGAATAAATAGCAAATGAGT-ATATTCAAGTCCTCATCTATAGTTACTCTTAG
63 TGGCTAATGGAGAGAATAAATAGCAAAGGAGTCA-AATCAAGGCC-CATCTATAGTTACTCTTAG
*
364495 CTGGTCTCAAGCTCAA-CAGCCTCATGTTTCCATAATTGGTAACTCTATTGTTTGC-TTGCTCAT
126 CTGGTCTCAAGCTCAACCA-CATCATGTTTCCATAATTGGTAACTCTATTGTTTGCTTTGC-CAT
* * * * *
364558 TGCATCTCGAGTGGATGACTATCCC-TTCTGAGTTCTTTTGTTTATGTATATTAG-CTAAGGTTT
189 TACATCTCGAGTCGATGACT-CCCCTTTCTGAGTTCATTTGTTGATGTATATTAGTC-AAGGTTT
* * * *
364621 AGGCTATATCTTTGCTTAAAAAATATGTTTTGTTGATCCAGTCAAAGTTGTTTTTTTCTTTCTTA
252 AGGATATATCTTTGCTTAAAAAATATATTTTATTGATCCAGTCAAAGTTGTTTGTTTCTTTCTTA
* * *
364686 TT-ATTAAGCTACCAGATTGAATTGTGTATGAGAACACAAGGCTTCGGGACCAAGGTAGATTTGC
317 TTGATTAAGCTACCAGATTGAATCGTGTATAAGAACACAAGGCTTCGGGAACAAGGTAGATTTGC
* * ** * * * *
364750 AATGC-T-TTAATC-TCGTTCAGAAAGGCTACCTCATTGGTTCAAGGATCAAATATTTGGGTCCA
382 AATGCTTCTTAATCTTC-TTAAGAAAGGCTACCTCACTACTCCAAGAATCAAATATTTAGGTCAA
** * * * * *
364812 CCATTCCTTTGTCCTATTTGAGCTATAATT-GTTGTTGTAGAGCCTTAATATTTTTTT
446 CCATTCCCATATCCCATTTAAACTATAATTGGTTGTTATAGAGCCTTAAT-TTTTTTT
364869 TTTGGTCTAA
Statistics
Matches: 412, Mismatches: 77, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
510 20 0.05
511 65 0.16
512 9 0.02
513 119 0.29
514 195 0.47
515 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (513 bp):
GTTTTACTTTCTCCCTTTCAATCACCTTTCCCCCCTCAACCTTAATTGCAAACAACTTCACTTGG
CTAATGGAGAGAATAAATAGCAAAGGAGTCAAATCAAGGCCCATCTATAGTTACTCTTAGCTGGT
CTCAAGCTCAACCACATCATGTTTCCATAATTGGTAACTCTATTGTTTGCTTTGCCATTACATCT
CGAGTCGATGACTCCCCTTTCTGAGTTCATTTGTTGATGTATATTAGTCAAGGTTTAGGATATAT
CTTTGCTTAAAAAATATATTTTATTGATCCAGTCAAAGTTGTTTGTTTCTTTCTTATTGATTAAG
CTACCAGATTGAATCGTGTATAAGAACACAAGGCTTCGGGAACAAGGTAGATTTGCAATGCTTCT
TAATCTTCTTAAGAAAGGCTACCTCACTACTCCAAGAATCAAATATTTAGGTCAACCATTCCCAT
ATCCCATTTAAACTATAATTGGTTGTTATAGAGCCTTAATTTTTTTTGTTGAGCTATA
Found at i:367996 original size:32 final size:32
Alignment explanation
Indices: 367955--368020 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
367945 AGGACAACAT
367955 TGAGTTGTTATTCCAAATTAAATCAATATTAC
1 TGAGTTGTTATTCCAAATTAAATCAATATTAC
* *
367987 TGAGTTGTTATTCCAAATTAACTCAATCTTAC
1 TGAGTTGTTATTCCAAATTAAATCAATATTAC
368019 TG
1 TG
368021 TAACTTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (32 bp):
TGAGTTGTTATTCCAAATTAAATCAATATTAC
Found at i:371067 original size:20 final size:21
Alignment explanation
Indices: 371037--371075 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
371027 AGCTAGTTAC
371037 ATGTATATGCGAACTCTTTAT
1 ATGTATATGCGAACTCTTTAT
371058 ATGT-TATGCGAACTCTTT
1 ATGTATATGCGAACTCTTT
371076 CAATTGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATATGCGAACTCTTTAT
Found at i:372649 original size:59 final size:57
Alignment explanation
Indices: 372515--372654 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 57
372505 GGAAAACTCG
* * * * *
372515 GGGTTAAAAATGGACTTTTTAGACAATTGAGGGTAAAAGGGTAATTTTAAGAGTTTC
1 GGGTCAAAAATGGAATTTTTGGACAATCGAGGGTAAAAGGGTAATTTTAAGAGTTTA
* *
372572 GAGGTCAAAAATGGAATTTTTGGAC-ATCCGAGGGTAAAATGGTAATTATTGGAAG-TTTTA
1 G-GGTCAAAAATGGAATTTTTGGACAAT-CGAGGGTAAAAGGGTAATT-TT--AAGAGTTTA
372632 GGGTCAAAAATGGAATTTTTGGA
1 GGGTCAAAAATGGAATTTTTGGA
372655 AGTTTTTGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
57 3 0.04
58 37 0.52
59 24 0.34
60 4 0.06
61 3 0.04
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (57 bp):
GGGTCAAAAATGGAATTTTTGGACAATCGAGGGTAAAAGGGTAATTTTAAGAGTTTA
Found at i:372708 original size:118 final size:117
Alignment explanation
Indices: 372578--372895 Score: 385
Period size: 118 Copynumber: 2.7 Consensus size: 117
372568 TTTCGAGGTC
* **
372578 AAAAATGGAATTTTTGGACA-TCCGAGGGT-AAAATGGTAATTATTGGAAGTTTTAGGGTCAAAA
1 AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATT-TTGGAAGTTCGAGGGT-AAAA
** * *
372641 ATGGAATTTTTGGAAGTTTTTGGGTTAAAAA-GGGAATTTTAGGAAGTTCATGGGT
62 ATGGAATTTTTGGAAGTTTCGGGGTAAAAAACGGGAATTTTAGGAAGTTCAAGGGT
* * * *
372696 AAAAATGGAATTTTTGGAAGTTTGA-GGTCAAAAATGGAATTTTTTGAAGTTCGGGGGTAAGAAT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT-AAAAATGGAA-TTTTGGAAGTTCGAGGGTAAAAAT
* *
372760 GGAATTTTTGGAAGTTTCGGGGTAAAAAACTGGAATTTTGGGAAGTTCAAGGGT
64 GGAATTTTTGGAAGTTTCGGGGTAAAAAACGGGAATTTTAGGAAGTTCAAGGGT
* *
372814 AAAAATGGAATTTTGGGAAGTTC-AGGGGTAAAAATGGGATTTTGAGAAGTTCGAGGGTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTG-GAAGTTCGAGGGTAAAAAT
372878 GGAATTTTTGGACAGTTT
64 GGAATTTTTGGA-AGTTT
372896 AGGGACCTCC
Statistics
Matches: 172, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
117 40 0.23
118 115 0.67
119 17 0.10
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (117 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTGGAAGTTCGAGGGTAAAAATGG
AATTTTTGGAAGTTTCGGGGTAAAAAACGGGAATTTTAGGAAGTTCAAGGGT
Found at i:372754 original size:58 final size:57
Alignment explanation
Indices: 372578--372895 Score: 327
Period size: 58 Copynumber: 5.4 Consensus size: 57
372568 TTTCGAGGTC
** **
372578 AAAAATGGAATTTTTGGACA-TCCGAGGGT-AAAATGGTAATTATT-GGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGA-AGTTTG-GGGTAAAAATGG-AATT-TTGGGAAGTTCAAGGGT
* * * *
372636 CAAAAATGGAATTTTTGGAAGTTTTTGGGTTAAAAAGGGAATTTTAGGAAGTTCATGGGT
1 -AAAAATGGAATTTTTGGAAG--TTTGGGGTAAAAATGGAATTTTGGGAAGTTCAAGGGT
* ** **
372696 AAAAATGGAATTTTTGGAAGTTTGAGGTCAAAAATGGAATTTTTTGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGT-AAAAATGGAATTTTGGGAAGTTCAAGGGT
*
372754 AAGAATGGAATTTTTGGAAGTTTCGGGGTAAAAAACTGGAATTTTGGGAAGTTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTT-GGGGT-AAAAA-TGGAATTTTGGGAAGTTCAAGGGT
* * * * *
372814 AAAAATGGAATTTTGGGAAGTTCAGGGGTAAAAATGGGATTTTGAGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTT-TGGGGTAAAAATGGAATTTTGGGAAGTTCAAGGGT
372872 AAAAATGGAATTTTTGGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
372896 AGGGACCTCC
Statistics
Matches: 220, Mismatches: 29, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
57 6 0.03
58 85 0.39
59 58 0.26
60 63 0.29
61 8 0.04
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (57 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTGGGAAGTTCAAGGGT
Found at i:372899 original size:29 final size:28
Alignment explanation
Indices: 372578--372899 Score: 283
Period size: 29 Copynumber: 11.0 Consensus size: 28
372568 TTTCGAGGTC
**
372578 AAAAATGGAATTTTTGGACA-TCCGAGGGT
1 AAAAATGGAATTTTTGGA-AGT-TTAGGGT
*
372607 -AAAATGGTAATTATTGGAAGTTTTAGGGT
1 AAAAATGG-AATTTTTGGAAG-TTTAGGGT
*
372636 CAAAAATGGAATTTTTGGAAGTTTTTGGGTT
1 -AAAAATGGAATTTTTGGAAG-TTTAGGG-T
* * *
372667 AAAAAGGGAATTTTAGGAAGTTCATGGGT
1 AAAAATGGAATTTTTGGAAGTTTA-GGGT
372696 AAAAATGGAATTTTTGGAAGTTT-GAGGT
1 AAAAATGGAATTTTTGGAAGTTTAG-GGT
* **
372724 CAAAAATGGAATTTTTTGAAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTT-TAGGGT
* *
372754 AAGAATGGAATTTTTGGAAGTTTCGGGGT
1 AAAAATGGAATTTTTGGAAGTTT-AGGGT
* *
372783 AAAAAACTGGAATTTTGGGAAGTTCAAGGGT
1 -AAAAA-TGGAATTTTTGGAAGTT-TAGGGT
* *
372814 AAAAATGGAATTTTGGGAAGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTA-GGGT
* *
372843 AAAAATGGGA-TTTTGAGAAGTTCGAGGGT
1 AAAAATGGAATTTTTG-GAAGTT-TAGGGT
372872 AAAAATGGAATTTTTGGACAGTTTAGGG
1 AAAAATGGAATTTTTGGA-AGTTTAGGG
372900 ACCTCCAAGG
Statistics
Matches: 246, Mismatches: 27, Indels: 40
0.79 0.09 0.13
Matches are distributed among these distances:
27 1 0.00
28 16 0.07
29 138 0.56
30 62 0.25
31 29 0.12
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGT
Found at i:374466 original size:6 final size:6
Alignment explanation
Indices: 374454--374515 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
374444 TTTGAAAATG
* *
374454 AATTTA AACTTA AA-TTA AATTTA AATTTA AA-ATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
374500 AA-ATA AATTTA AATTT
1 AATTTA AATTTA AATTT
374516 TAAAACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
5 13 0.27
6 35 0.73
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:374476 original size:17 final size:17
Alignment explanation
Indices: 374438--374547 Score: 141
Period size: 17 Copynumber: 6.4 Consensus size: 17
374428 CTTTATTTAT
*
374438 TTTAAATTTGAAAATGAA
1 TTTAAATTT-AAAATAAA
* *
374456 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
374473 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
374490 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
374507 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
*
374525 TTT-AATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
374542 TTTAAA
1 TTTAAA
374548 ATGAGTTTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
16 1 0.01
17 57 0.70
18 23 0.28
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:374477 original size:11 final size:11
Alignment explanation
Indices: 374457--374514 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
374447 GAAAATGAAT
*
374457 TTAAACTTAAA
1 TTAAATTTAAA
374468 TTAAATTTAAA
1 TTAAATTTAAA
*
374479 TTTAAA-ATAAA
1 -TTAAATTTAAA
374490 TTTAAATTTAAA
1 -TTAAATTTAAA
*
374502 ATAAATTTAAA
1 TTAAATTTAAA
374513 TT
1 TT
374515 TTAAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 31 0.77
12 9 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:374477 original size:35 final size:33
Alignment explanation
Indices: 374438--374547 Score: 139
Period size: 35 Copynumber: 3.2 Consensus size: 33
374428 CTTTATTTAT
*
374438 TTTAAATTTGAAAATGAATTTAAACTTAAATTAAA
1 TTTAAATTT-AAAATAAATTTAAACTTAAA-TAAA
*
374473 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAACTT-AAATAAA
* *
374507 TTTAAATTTTAAAACAAATTTAATCTTATAATAAA
1 TTTAAA-TTTAAAATAAATTTAAACTTA-AATAAA
374542 TTTAAA
1 TTTAAA
374548 ATGAGTTTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
34 26 0.39
35 41 0.61
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (33 bp):
TTTAAATTTAAAATAAATTTAAACTTAAATAAA
Found at i:375530 original size:205 final size:205
Alignment explanation
Indices: 374933--375542 Score: 852
Period size: 206 Copynumber: 3.0 Consensus size: 205
374923 TGTTTTGATC
* * * ** ** * *
374933 CACTTCTCTGTGTTTCATCAGGAAGATGGTTTTGGTTTACTTC-CACGTATTTCATCAAGAAGCT
1 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCA-GTATCTCATCAGGAAGCT
*
374997 AACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAG-TCGGGGTTCGAAGATTTG
65 AACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTG
**
375061 CTCACATCGAGCGTGGGTTTGATTTGGTCTTC-TCTTTTGTATCTCATCAGGAAGATGA-TCGCG
129 CTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTC-TCAGTATCTCATCAGGAAGATGACT-GCG
375124 TCGTTTGTTTCAAT
192 TCGTTTGTTTCAAT
* * * *
375138 CTGCTTCTCTGTATCCCAACAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAATCT
1 C-ACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
* * * * *
375203 AACCATTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTTGAGGATTCGC
65 AACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGC
*
375268 TCACATCGAGCGTGGGTTTAATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCG
130 TCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCG
375333 TTTGTTTCAATT
195 TTTGTTTCAA-T
375345 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
1 CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
* * * * *
375410 ATC-TTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTCGAAAATTTGCT
66 ACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCT
* * * *
375474 CACATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCGTCAT
131 CACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGT
375539 TTGT
196 TTGT
375543 GGATAATCGC
Statistics
Matches: 358, Mismatches: 41, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
205 117 0.33
206 233 0.65
207 8 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (205 bp):
CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
ACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCT
CACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGT
TTGTTTCAAT
Found at i:383027 original size:21 final size:22
Alignment explanation
Indices: 382986--383028 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
382976 AATTCCTTGC
382986 ATCGCATTGATTTTCTCCTCTA
1 ATCGCATTGATTTTCTCCTCTA
383008 ATCGC-TTGTATTTT-TCCTCTA
1 ATCGCATTG-ATTTTCTCCTCTA
383029 TTTTTCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.16, C:0.26, G:0.09, T:0.49
Consensus pattern (22 bp):
ATCGCATTGATTTTCTCCTCTA
Found at i:385136 original size:38 final size:38
Alignment explanation
Indices: 385085--385160 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
385075 GGCTGGGGCA
385085 GGTGTCACTCTTTTACTCAATCTATCAAACAAATCTAT
1 GGTGTCACTCTTTTACTCAATCTATCAAACAAATCTAT
*
385123 GGTGTCACTCTTTTACTTAATCTATCAAACAAATCTAT
1 GGTGTCACTCTTTTACTCAATCTATCAAACAAATCTAT
385161 CACCGCGTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (38 bp):
GGTGTCACTCTTTTACTCAATCTATCAAACAAATCTAT
Found at i:387377 original size:29 final size:28
Alignment explanation
Indices: 387344--387777 Score: 231
Period size: 29 Copynumber: 14.9 Consensus size: 28
387334 ATTTTGGGAA
*
387344 AATTCGGGGTTAAAAATGGACTTTTTAG
1 AATTCGGGGTTAAAAATGGAATTTTTAG
* * *
387372 ACATTCGGGGGT-AAAAGGGAAATTTTGAG
1 A-ATTCGGGGTTAAAAATGG-AATTTTTAG
* * * *
387401 AGTTTTGGGGTAAAAAATGGAATTTTTGG
1 A-ATTCGGGGTTAAAAATGGAATTTTTAG
*
387430 ACATTCGGAGG-T-AAAATGGTAATTTTTGG
1 A-ATTCGG-GGTTAAAAATGG-AATTTTTAG
* *
387459 AAGTTTCGTGGTCAAAAATGGAATTTTTAG
1 AA--TTCGGGGTTAAAAATGGAATTTTTAG
*
387489 AAGTTTGGGGGTTAAAAATGGAA-TTTT-G
1 AA--TTCGGGGTTAAAAATGGAATTTTTAG
* * *
387517 AAGTTTAGGGG-TAAGAATGGAATTTTTGG
1 AA--TTCGGGGTTAAAAATGGAATTTTTAG
** * **
387546 AAGTTTTAGGGTTAAAAATGAAATTTTGGG
1 AA--TTCGGGGTTAAAAATGGAATTTTTAG
* *
387576 AAGTTTGTGGG-TAAAAATGGAATTTTTGG
1 AA-TTCG-GGGTTAAAAATGGAATTTTTAG
* *
387605 AAGTACGGGGTTAAAAATGGAATTTTTGG
1 AA-TTCGGGGTTAAAAATGGAATTTTTAG
* *
387634 AAGTACGGGGTTAAAAATGGAATTTTTGG
1 AA-TTCGGGGTTAAAAATGGAATTTTTAG
* * **
387663 AAGTTTCGAGGTAAAAAATGGAATTTTGGG
1 AA--TTCGGGGTTAAAAATGGAATTTTTAG
* * **
387693 AAGTTTGGGGGTAAAAATGGAATTTTGGG
1 AA-TTCGGGGTTAAAAATGGAATTTTTAG
* *
387722 AAGTTCGAGGG-TAAAAAT-AAGATTTTTGG
1 AA-TTCG-GGGTTAAAAATGGA-ATTTTTAG
*
387751 AAGTTCGAGGG-TAAAAATGGATTTTTT
1 AA-TTCG-GGGTTAAAAATGGAATTTTT
387778 GGACAGTTTA
Statistics
Matches: 338, Mismatches: 50, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
27 10 0.03
28 34 0.10
29 199 0.59
30 88 0.26
31 7 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (28 bp):
AATTCGGGGTTAAAAATGGAATTTTTAG
Found at i:387398 original size:59 final size:59
Alignment explanation
Indices: 387333--387718 Score: 232
Period size: 59 Copynumber: 6.6 Consensus size: 59
387323 GTGAAATGAT
** * * *
387333 AATTTTGGGAAAATTCGGGGTTAAAAATGGACTTTTTAGACATTCGGGGGTAAAAGGGA
1 AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTTTAGACATTCGGAGGTAAAAGGGA
* * * * *
387392 AATTTTGAG-AGTTTTGGGGTAAAAAATGGAATTTTTGGACATTCGGAGGTAAAATGGT
1 AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTTTAGACATTCGGAGGTAAAAGGGA
* * * * * *
387450 AATTTTTGGAAGTTTCGTGGTCAAAAATGGAATTTTTAGA-AGTTTGGGGGTTAAAAATGG-
1 AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTTTAGACA-TTCGGAGG-T-AAAAGGGA
* * * * * **
387510 AATTTT--GAAGTTTAGGGGT-AAGAATGGAATTTTTGGA-AGTTTTAGG-GTTAAAAATGA
1 AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTTTAGACA---TTCGGAGGTAAAAGGGA
* * *
387567 AATTTTGGGAAGTTT-GTGGGT-AAAAATGGAATTTTTGGA-AGTACGG-GGTTAAAAATGG-
1 AATTTTGGGAAGTTTCG-GGGTAAAAAATGGAATTTTTAGACA-TTCGGAGG-T-AAAAGGGA
* * * * *
387625 AATTTTTGGAAG-TACGGGGTTAAAAATGGAATTTTTGGA-AGTTTC-GAGGTAAAAAATGG-
1 AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTTTAGACA--TTCGGAGGT--AAAAGGGA
*
387684 AATTTTGGGAAGTTTGGGGGT-AAAAATGGAATTTT
1 AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTT
387719 GGGAAGTTCG
Statistics
Matches: 268, Mismatches: 41, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
56 5 0.02
57 33 0.12
58 95 0.35
59 115 0.43
60 13 0.05
61 7 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (59 bp):
AATTTTGGGAAGTTTCGGGGTAAAAAATGGAATTTTTAGACATTCGGAGGTAAAAGGGA
Found at i:387455 original size:28 final size:27
Alignment explanation
Indices: 387293--387455 Score: 82
Period size: 28 Copynumber: 5.7 Consensus size: 27
387283 CGAATACCTA
*
387293 GGGGCAAAATGGTAATTTT-GA-ATTC
1 GGGGTAAAATGGTAATTTTGGACATTC
* * *
387318 TTGGGGTGAAATGATAATTTTGGGAAAATTC
1 --GGGGTAAAATGGTAATTTT-GG-ACATTC
* *
387349 GGGGTTAAAAATGG-ACTTTTTAGACATTC
1 GGGG-T-AAAATGGTA-ATTTTGGACATTC
* * ** *
387378 GGGGGTAAAAGGGAAATTTTGAGAGTTTT
1 -GGGGTAAAATGGTAATTTTG-GACATTC
387407 GGGGTAAAAAATGG-AATTTTTGGACATTC
1 GGGGT--AAAATGGTAA-TTTTGGACATTC
387436 GGAGGTAAAATGGTAATTTT
1 GG-GGTAAAATGGTAATTTT
387456 TGGAAGTTTC
Statistics
Matches: 103, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
27 16 0.16
28 26 0.25
29 26 0.25
30 22 0.21
31 13 0.13
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (27 bp):
GGGGTAAAATGGTAATTTTGGACATTC
Found at i:387562 original size:117 final size:115
Alignment explanation
Indices: 387326--387790 Score: 432
Period size: 117 Copynumber: 4.0 Consensus size: 115
387316 TCTTGGGGTG
* ** * *
387326 AAATGATAATTTTGGGAAAATTCGGGGTTAAAAATGGACTTTTTAGACA-TTCGGGGGT-AAAAG
1 AAATGGTAATTTTGGGAAGTTTCGGGG-TAAAAATGGAATTTTTAGA-AGTTCGGGGGTAAAAAT
* * *
387389 GGAAATTTT-GAGAGTTTTGGGGTAAAAAATGGAATTTTTGGACA--TTCGGAGGTA
64 GG-AATTTTGGA-AG-TTAGGGGT-AAAAATGGAATTTTTGGACAGTTTAGG-GTTA
* * *
387443 AAATGGTAATTTTTGGAAGTTTCGTGGTCAAAAATGGAATTTTTAGAAGTTTGGGGGTTAAAAAT
1 AAATGGTAATTTTGGGAAGTTTCGGGGT-AAAAATGGAATTTTTAGAAGTTCGGGGG-TAAAAAT
*
387508 GGAATTTT-GAAGTTTAGGGGTAAGAATGGAATTTTTGGA-AGTTTTAGGGTTAA
64 GGAATTTTGGAAG-TTAGGGGTAAAAATGGAATTTTTGGACAG-TTTAGGGTT-A
* * * *
387561 AAAT-GAAATTTTGGGAAGTTT-GTGGGTAAAAATGGAATTTTTGGAAGTACGGGGTTAAAAATG
1 AAATGGTAATTTTGGGAAGTTTCG-GGGTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATG
* *
387624 GAATTTTTGGAAG-TACGGGGTTAAAAATGGAATTTTTGGA-AGTTTCGAGGTAAA
65 GAA-TTTTGGAAGTTA-GGGG-TAAAAATGGAATTTTTGGACAGTTTAG-GGT-TA
* ** * *
387678 AAATGG-AATTTTGGGAAGTTTGGGGGTAAAAATGGAATTTTGGGAAGTTCGAGGGTAAAAATAA
1 AAATGGTAATTTTGGGAAGTTTCGGGGTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAAT-G
* * *
387742 GATTTTTGGAAGTTCGAGGGTAAAAATGGATTTTTTGGACAGTTTAGGG
65 GAATTTTGGAAGTTAG-GGGTAAAAATGGAATTTTTGGACAGTTTAGGG
387791 ACCTTCAGGG
Statistics
Matches: 296, Mismatches: 31, Indels: 42
0.80 0.08 0.11
Matches are distributed among these distances:
115 14 0.05
116 56 0.19
117 188 0.64
118 32 0.11
119 6 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (115 bp):
AAATGGTAATTTTGGGAAGTTTCGGGGTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGG
AATTTTGGAAGTTAGGGGTAAAAATGGAATTTTTGGACAGTTTAGGGTTA
Found at i:387778 original size:29 final size:29
Alignment explanation
Indices: 387408--387785 Score: 364
Period size: 29 Copynumber: 12.9 Consensus size: 29
387398 GAGAGTTTTG
387408 GGGTAAAAAATGGAATTTTTGGACA-TTCG-
1 GGGT-AAAAATGGAATTTTTGGA-AGTTCGA
387437 GAGGT-AAAATGGTAATTTTTGGAAGTTTCG-
1 G-GGTAAAAATGG-AATTTTTGGAAG-TTCGA
* * * *
387467 TGGTCAAAAATGGAATTTTTAGAAGTTTGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
387497 GGGTTAAAAATGGAA-TTTT-GAAGTT-TA
1 GGG-TAAAAATGGAATTTTTGGAAGTTCGA
* **
387524 GGGGTAAGAATGGAATTTTTGGAAGTTTTA
1 -GGGTAAAAATGGAATTTTTGGAAGTTCGA
* * * *
387554 GGGTTAAAAATGAAATTTTGGGAAGTTTGT
1 GGG-TAAAAATGGAATTTTTGGAAGTTCGA
*
387584 GGGTAAAAATGGAATTTTTGGAAGTACG-
1 GGGTAAAAATGGAATTTTTGGAAGTTCGA
*
387612 GGGTTAAAAATGGAATTTTTGGAAGTACG-
1 GGG-TAAAAATGGAATTTTTGGAAGTTCGA
387641 GGGTTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGG-TAAAAATGGAATTTTTGGAAG-TTCGA
* * *
387672 -GGTAAAAAATGGAATTTTGGGAAGTTTGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGA
*
387701 GGGTAAAAATGGAATTTTGGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTCGA
*
387730 GGGTAAAAAT-AAGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGA-ATTTTTGGAAGTTCGA
*
387759 GGGTAAAAATGGATTTTTTGGACAGTT
1 GGGTAAAAATGGAATTTTTGGA-AGTT
387786 TAGGGACCTT
Statistics
Matches: 302, Mismatches: 26, Indels: 41
0.82 0.07 0.11
Matches are distributed among these distances:
27 10 0.03
28 25 0.08
29 171 0.57
30 88 0.29
31 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCGA
Found at i:388882 original size:3 final size:3
Alignment explanation
Indices: 388871--388923 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
388861 TATTAAAACA
388871 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
388917 ATT ATT A
1 ATT ATT A
388924 ATGATATCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:389652 original size:17 final size:17
Alignment explanation
Indices: 389634--389726 Score: 132
Period size: 17 Copynumber: 5.4 Consensus size: 17
389624 CTTTATTTAT
* *
389634 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
389651 TTTAAATTTGAAAATGAA
1 TTTAAATTT-AAAATAAA
*
389669 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
389686 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
389703 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
389721 TTTAAA
1 TTTAAA
389727 ATGAGTTTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
17 38 0.56
18 30 0.44
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:389674 original size:35 final size:34
Alignment explanation
Indices: 389634--389726 Score: 132
Period size: 35 Copynumber: 2.7 Consensus size: 34
389624 CTTTATTTAT
* * *
389634 TTTAAATTTATAATAATTTTAAATTTGAAAATGAA
1 TTTAAATTTAAAATAAATTTAAATTT-AAAATAAA
*
389669 TTTAAACTTAAAATAAATTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
389703 TTTAAATTTTAAAATAAATTTAAA
1 TTTAAA-TTTAAAATAAATTTAAA
389727 ATGAGTTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 13 0.25
35 39 0.75
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
Found at i:389713 original size:7 final size:6
Alignment explanation
Indices: 389667--389726 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
389657 TTTGAAAATG
* * *
389667 AATTTA AACTTA AA-ATA AATTTA AATTTA AA-ATA AATTTA AATTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA
*
389714 AA-ATA AATTTA AA
1 AATTTA AATTTA AA
389727 ATGAGTTTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.28
6 25 0.58
7 6 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:389722 original size:12 final size:11
Alignment explanation
Indices: 389688--389728 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
389678 AAAATAAATT
389688 TAAATTTAAAA
1 TAAATTTAAAA
389699 TAAATTT-AAA
1 TAAATTTAAAA
389709 T---TTTAAAA
1 TAAATTTAAAA
389717 TAAATTTAAAA
1 TAAATTTAAAA
389728 T
1 T
389729 GAGTTTGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 3 0.12
8 4 0.15
10 4 0.15
11 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:414185 original size:9 final size:9
Alignment explanation
Indices: 414161--414203 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
414151 GATGATGATT
414161 ATAATTTTAAA
1 ATAATTTT--A
414172 ATAATTTTA
1 ATAATTTTA
414181 ATAATTTTA
1 ATAATTTTA
414190 ATAATTTTA
1 ATAATTTTA
414199 A-AATT
1 ATAATT
414204 AATTGTTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 4 0.12
9 20 0.62
11 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATAATTTTA
Found at i:419540 original size:70 final size:70
Alignment explanation
Indices: 419421--419567 Score: 240
Period size: 70 Copynumber: 2.1 Consensus size: 70
419411 ATATTGAGTG
* *
419421 GTGCCTACCTGTTAAGCGGCACCAATGGTGCCTATTGGGTAGACAGTACTAATGGTGCCACACAG
1 GTGCCTACCTGTCAAGCGGCACCAATGGTGCCTATTGGGTAGACAGTACTAATAGTGCCACACAG
419486 CACCT
66 CACCT
* * * *
419491 GTGCCTACCTGTCAGGCGGCACCAATGGTGCCTATTGGGTAGGCGGTACTAATAGTGCCACATAG
1 GTGCCTACCTGTCAAGCGGCACCAATGGTGCCTATTGGGTAGACAGTACTAATAGTGCCACACAG
419556 CACCT
66 CACCT
419561 GTGCCTA
1 GTGCCTA
419568 TTTAAACACT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.23
Consensus pattern (70 bp):
GTGCCTACCTGTCAAGCGGCACCAATGGTGCCTATTGGGTAGACAGTACTAATAGTGCCACACAG
CACCT
Found at i:422571 original size:22 final size:23
Alignment explanation
Indices: 422534--422576 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
422524 TTGGATCAAG
*
422534 ACTTTTTGAATTTGATATTCTGT
1 ACTTTTTGAATGTGATATTCTGT
422557 ACTTTTT-AATGTGATATTCT
1 ACTTTTTGAATGTGATATTCT
422577 TAATCTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56
Consensus pattern (23 bp):
ACTTTTTGAATGTGATATTCTGT
Found at i:422933 original size:21 final size:21
Alignment explanation
Indices: 422907--422956 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
422897 ATGTTGTAAT
422907 CTAAAACCTAAAACCTAAAAC-
1 CTAAAACCT-AAACCTAAAACA
*
422928 CTAAAACTCTAAACCTCAAACA
1 CTAAAAC-CTAAACCTAAAACA
422950 C-AAAACC
1 CTAAAACC
422957 CTTAACCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (21 bp):
CTAAAACCTAAACCTAAAACA
Found at i:422948 original size:7 final size:7
Alignment explanation
Indices: 422907--422940 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
422897 ATGTTGTAAT
422907 CTAAAAC
1 CTAAAAC
422914 CTAAAAC
1 CTAAAAC
422921 CTAAAAC
1 CTAAAAC
422928 CTAAAAC
1 CTAAAAC
422935 TCTAAA
1 -CTAAA
422941 CCTCAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAAAC
Found at i:422955 original size:14 final size:13
Alignment explanation
Indices: 422909--422956 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
422899 GTTGTAATCT
422909 AAAACCTAAAACC
1 AAAACCTAAAACC
422922 TAAAACCTAAAACTC
1 -AAAACCTAAAAC-C
* *
422937 TAAACCTCAAACAC
1 AAAACCTAAAAC-C
422951 AAAACC
1 AAAACC
422957 CTTAACCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 28 0.97
15 1 0.03
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAACCTAAAACC
Found at i:425371 original size:17 final size:18
Alignment explanation
Indices: 425344--425389 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
425334 ACATGTTGAG
*
425344 AAATAATAAATGATATAA
1 AAATAATAAATGAGATAA
*
425362 ACAT-ATAAATGAGATAA
1 AAATAATAAATGAGATAA
425379 AAATAATAAAT
1 AAATAATAAAT
425390 TACAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (18 bp):
AAATAATAAATGAGATAA
Found at i:426048 original size:6 final size:7
Alignment explanation
Indices: 426031--426057 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
426021 TAAAATAAAT
426031 AAAAAAC
1 AAAAAAC
426038 AAAAAAC
1 AAAAAAC
426045 AAAAAAC
1 AAAAAAC
426052 AAAAAA
1 AAAAAA
426058 TATTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:432461 original size:50 final size:50
Alignment explanation
Indices: 432405--432522 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 50
432395 TGATCCCAAA
* *
432405 AACTTTAGAGATATATGATATACCAATATTAGGTTTAATCCTATCCTTGT
1 AACTTTAGAGATATAGGATATACCAATATTAGGTTTAATCCGATCCTTGT
* * * * * * *
432455 AGCTTTA-AGGATGTAGGATTTACCAATGTTAGTTTTAATTCGATTCTTGT
1 AACTTTAGA-GATATAGGATATACCAATATTAGGTTTAATCCGATCCTTGT
*
432505 AACTTTAGTGATATAGGA
1 AACTTTAGAGATATAGGA
432523 ATTGGTTTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.02
50 53 0.98
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (50 bp):
AACTTTAGAGATATAGGATATACCAATATTAGGTTTAATCCGATCCTTGT
Found at i:432751 original size:196 final size:195
Alignment explanation
Indices: 432471--433166 Score: 917
Period size: 196 Copynumber: 3.5 Consensus size: 195
432461 AAGGATGTAG
* * * * * * *
432471 GATTTACCAATGTTAGTTTTAATTCGATTCTTGTAACTTTAGTGATATAGGAATTGGTTTTGTAG
1 GATTTGCCAATGTTAGTTTTAATCCGATCCTTGTAACTTCAG-GATATAAGATTTGGTGTTGTAG
* * ** * *
432536 CTTCATCTTACTCCATTGTAACTTTAAGGAGATAAAGATTTTCTACTGTTTTAATCCACTTCACT
65 CTTCATCTTGCTCCACTACAACTTTAGGGAGATAAAGATTTGCTACTGTTTTAATCCACTTCACT
* * * *
432601 GTAACTTTAGGAAGATATGATTTGGTCTAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAA
130 GCAACTTTAGGAAGATATGATTTGGTGTGGCTTCATCTTGCTCCACTGTAACTTCAAGGAGATAA
432666 A
195 A
* * * *
432667 GATTTGCCAATGGTAGTTTTAATCCGATCCTTGTAACTTCAGGAATATAAGATTTGATATTGTAA
1 GATTTGCCAATGTTAGTTTTAATCCGATCCTTGTAACTTCAGG-ATATAAGATTTGGTGTTGTAG
* * * ** *
432732 CTTCATCTTGTTACATTGTAACTTTAGGGAGATAAAGATTTGCTACTGTTTTAATCCGCTTCACT
65 CTTCATCTTGCTCCACTACAACTTTAGGGAGATAAAGATTTGCTACTGTTTTAATCCACTTCACT
*
432797 GCAACTTCAGGAAGATATGATTTGGTGTGGCTTCATCTTGCTCCACTGTAACTTCAAGGAGATAA
130 GCAACTTTAGGAAGATATGATTTGGTGTGGCTTCATCTTGCTCCACTGTAACTTCAAGGAGATAA
432862 A
195 A
* * * *
432863 GATTTGTCAATGTTAGTTTTAATCTGATCC-TGCAACTTAAAGGATATAAGATTTGGTGTTGTAG
1 GATTTGCCAATGTTAGTTTTAATCCGATCCTTGTAACTT-CAGGATATAAGATTTGGTGTTGTAG
* * * * *
432927 CTTCATCTTGCTCCACTACAACTTCAGGGAGATAAATATTTGCTACTATTTTAATCCTCTTCAGT
65 CTTCATCTTGCTCCACTACAACTTTAGGGAGATAAAGATTTGCTACTGTTTTAATCCACTTCACT
** * * *
432992 GCAACTTTAGGAAGATAAAAATTTGGTGTGGCTTCATCTTGCTCCATTGCAATTTCAAGGAGATA
130 GCAACTTTAGGAAGAT-ATGATTTGGTGTGGCTTCATCTTGCTCCACTGTAACTTCAAGGAGATA
433057 AA
194 AA
* *
433059 GATTTGCCAATGTTAGTTTTAATCTGATCCCTGTAACTTCAGGGATATAAGATTTGGTGTTGTAG
1 GATTTGCCAATGTTAGTTTTAATCCGATCCTTGTAACTTCA-GGATATAAGATTTGGTGTTGTAG
* * *
433124 CTTTATCTTGCTGCACTACAACTTTATGGAGATAAAGATTTGC
65 CTTCATCTTGCTCCACTACAACTTTAGGGAGATAAAGATTTGC
433167 CAATGTTAGT
Statistics
Matches: 442, Mismatches: 53, Indels: 9
0.88 0.11 0.02
Matches are distributed among these distances:
195 96 0.22
196 278 0.63
197 68 0.15
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (195 bp):
GATTTGCCAATGTTAGTTTTAATCCGATCCTTGTAACTTCAGGATATAAGATTTGGTGTTGTAGC
TTCATCTTGCTCCACTACAACTTTAGGGAGATAAAGATTTGCTACTGTTTTAATCCACTTCACTG
CAACTTTAGGAAGATATGATTTGGTGTGGCTTCATCTTGCTCCACTGTAACTTCAAGGAGATAAA
Found at i:432761 original size:101 final size:100
Alignment explanation
Indices: 432307--433579 Score: 757
Period size: 101 Copynumber: 13.0 Consensus size: 100
432297 GCTTCTCTAC
* * * *
432307 AACTTTAGGAAGATAGGATTTG-G-TGTGGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
1 AACTTCAGGAATATAAGATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
* * ****
432370 AGATTTGCCATTGTTAGTTTTAATCTGATCCCAAA
66 AGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
* * **** * * * * * * *
432405 AACTTTA-GAGATATATGATATACCAATAT-TAGGTTTAATCCT-ATCC-TTGTAGCTTTAAGGA
1 AACTTCAGGA-ATATAAGAT-T-TGTGT-TGTA-GCTTCATCTTGCTCCACTGTAACTTTAGGGA
* * * *
432466 TG-T-AGGATTTACCAATGTTAGTTTTAATTCGATTCTTGT
61 -GATAAAGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
* * * * * * *
432505 AACTTTAGTG-ATATAGGAATTGGTTTTGTAGCTTCATCTTACTCCATTGTAACTTTAAGGAGAT
1 AACTTCAG-GAATATAAG-ATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGAT
* **
432569 AAAGATTT-TC--TACT-GTTTTAATCC-ACTTCAC-TGT
64 AAAGATTTGCCAATGTTAGTTTTAATCCGA--TC-CTTGT
* * * * *
432603 AACTTTAGGAAGATATGATTTG-G-TCTAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAA
1 AACTTCAGGAATATAAGATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
*
432666 AGATTTGCCAATGGTAGTTTTAATCCGATCCTTGT
66 AGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
* * * * *
432701 AACTTCAGGAATATAAGATTTGATATTGTAACTTCATCTTGTTACATTGTAACTTTAGGGAGATA
1 AACTTCAGGAATATAAGATTTG-TGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATA
** * *
432766 AAGATTTG-C--TACT-GTTTTAATCCGCTTCAC-TGC
65 AAGATTTGCCAATGTTAGTTTTAATCCG-ATC-CTTGT
* * * * *
432799 AACTTCAGGAAGATATGATTTG-G-TGTGGCTTCATCTTGCTCCACTGTAACTTCAAGGAGATAA
1 AACTTCAGGAATATAAGATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
* * *
432862 AGATTTGTCAATGTTAGTTTTAATCTGATCC-TGC
66 AGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
* ** *
432896 AACTTAAAGG-ATATAAGATTTGGTGTTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGAT
1 AACTT-CAGGAATATAAGATTT-GTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGAT
* ** ** ** *
432960 AAATATTTG-C--TACTA-TTTTAATCCTCTTCAGTGC
64 AAAGATTTGCCAATGTTAGTTTTAATCC-GATCCTTGT
* * * * * * *
432994 AACTTTAGGAAGATAAAAATTTG-G-TGTGGCTTCATCTTGCTCCATTGCAA-TTTCAAGGAGAT
1 AACTTCAGGAATAT-AAGATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTT-AGGGAGAT
* *
433056 AAAGATTTGCCAATGTTAGTTTTAATCTGATCCCTGT
64 AAAGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
* * * ** *
433093 AACTTCAGGGATATAAGATTTGGTGTTGTAGCTTTATCTTGCTGCACTACAACTTTATGGAGATA
1 AACTTCAGGAATATAAGATTT-GTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATA
*
433158 AAGATTTGCCAATGTTAGTTTTAATTCGAT-CTCTGT
65 AAGATTTGCCAATGTTAGTTTTAATCCGATCCT-TGT
* * * * * * *
433194 AACCTCAGGGATATATGATTTGGTGTTGTAGTTTCATCTTACTCCACTGCAACTTTACGGAGATA
1 AACTTCAGGAATATAAGATTT-GTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATA
** * * *
433259 AAGATTTG-C--TACTA-TTTTAATTCG--CTTTACT
65 AAGATTTGCCAATGTTAGTTTTAATCCGATCCTT-GT
* * * *
433290 ACAACTTCAGGAAAATAGGATTTGATG-TG--GCTTCATCTT-CTTTCATTGTAACTTTAGGGAG
1 --AACTTCAGGAATATAAGATTTG-TGTTGTAGCTTCATCTTGC-TCCACTGTAACTTTAGGGAG
* *
433351 ATAAAGATTTGCTAATGTTAGTTTTAATCTGAT-CTTGT
62 ATAAAGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
* *
433389 CACTTCA-GAGATATAAGATTTGCTGTTATAGC-TCTATCTTGCTCCACTGTAACTTTAGGGAGA
1 AACTTCAGGA-ATATAAGATTTG-TGTTGTAGCTTC-ATCTTGCTCCACTGTAACTTTAGGGAGA
* ** * * *
433452 TAAATATTTG-C--TACTA-TTTTAATCTAC-TTCATTGC
63 TAAAGATTTGCCAATGTTAGTTTTAATC--CGATCCTTGT
** * * * ** * *
433487 AACTTCATAAAGATAGGATTTG-G-TG-GGCTTCATCTTGCTCCACTACAACTTCAAGGAGATAA
1 AACTTCAGGAATATAAGATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
*
433549 AGATTTGCCAATGTTAGTTTTAGTCCGATCC
66 AGATTTGCCAATGTTAGTTTTAATCCGATCC
433580 CTACAGCTTT
Statistics
Matches: 912, Mismatches: 182, Indels: 163
0.73 0.14 0.13
Matches are distributed among these distances:
94 36 0.04
95 124 0.14
96 63 0.07
97 96 0.11
98 171 0.19
99 69 0.08
100 148 0.16
101 188 0.21
102 9 0.01
103 8 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (100 bp):
AACTTCAGGAATATAAGATTTGTGTTGTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
AGATTTGCCAATGTTAGTTTTAATCCGATCCTTGT
Found at i:433064 original size:392 final size:396
Alignment explanation
Indices: 432478--433266 Score: 982
Period size: 392 Copynumber: 2.0 Consensus size: 396
432468 TAGGATTTAC
* * * * *
432478 CAATGTTAGTTTTAATTCGATTCTTGTAACTTTAGTGATATAGGAATTGGTTTTGTAGCTTCATC
1 CAATGTTAGTTTTAATTCGATTCCTGCAACTTAAGTGATATAAGAATTGGTGTTGTAGCTTCATC
* ** * * * *
432543 TTACTCCATTGTAACTTTAAGGAGATAAAGATTTTCTACTGTTTTAATCCACTTCACTGTAACTT
66 TTACTCCACTACAACTTCAAGGAGATAAAGATTTGCTACTATTTTAATCCACTTCACTGCAACTT
** * *
432608 TAGGAAGATATGATTTGGTCTAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTG
131 TAGGAAGATAAAATTTGGTCTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTG
*
432673 CCAATGGTAGTTTTAATCCGATCCTTGTAACTTCAGGAATATAAGATTTGATATTGTAACTTCAT
196 CCAATGGTAGTTTTAATCCGATCCCTGTAACTTCAGGAATATAAGATTTGATATTGTAACTTCAT
* * ** *
432738 CTTGTTACATTGTAACTTTAGGGAGATAAAGATTTG-C-TACT-GTTTTAATCCGCTTCACTGCA
261 CTTGCTACACTACAACTTTAGGGAGATAAAGATTTGCCATACTAGTTTTAATCCG-ATCACTGCA
* * *
432800 ACTTCAGGAAGATATGATTTGGTG-TG-GCTTCATCTTGCTCCACTGTAACTTCAAGGAGATAAA
325 ACCTCAGGAAGATATGATTTGGTGTTGAGCTTCATCTTACTCCACTGCAACTTCAAGGAGATAAA
432863 GATTTGT
390 GATTTGT
*
432870 CAATGTTAGTTTTAA-TCTGA-TCCTGCAACTTAAAG-GATATAAGATTTGGTGTTGTAGCTTCA
1 CAATGTTAGTTTTAATTC-GATTCCTGCAACTT-AAGTGATATAAGAATTGGTGTTGTAGCTTCA
* * * * *
432932 TCTTGCTCCACTACAACTTCAGGGAGATAAATATTTGCTACTATTTTAATCCTCTTCAGTGCAAC
64 TCTTACTCCACTACAACTTCAAGGAGATAAAGATTTGCTACTATTTTAATCCACTTCACTGCAAC
* * * *
432997 TTTAGGAAGATAAAAATTTGGTGTGGCTTCATCTTGCTCCATTGCAATTTCAAGGAGATAAAGAT
129 TTTAGGAAGAT-AAAATTTGGTCTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGAT
* * * * * *
433062 TTGCCAATGTTAGTTTTAATCTGATCCCTGTAACTTCAGGGATATAAGATTTGGTGTTGTAGCTT
193 TTGCCAATGGTAGTTTTAATCCGATCCCTGTAACTTCAGGAATATAAGATTTGATATTGTAACTT
* * * ** * *
433127 TATCTTGCTGCACTACAACTTTATGGAGATAAAGATTTGCCAATGTTAGTTTTAATTCGATCTCT
258 CATCTTGCTACACTACAACTTTAGGGAGATAAAGATTTGCC-ATACTAGTTTTAATCCGATCACT
* * * * * *
433192 GTAACCTCAGGGATATATGATTTGGTGTTGTAGTTTCATCTTACTCCACTGCAACTTTACGGAGA
322 GCAACCTCAGGAAGATATGATTTGGTGTTG-AGCTTCATCTTACTCCACTGCAACTTCAAGGAGA
433257 TAAAGATTTG
386 TAAAGATTTG
433267 CTACTATTTT
Statistics
Matches: 333, Mismatches: 54, Indels: 14
0.83 0.13 0.03
Matches are distributed among these distances:
391 99 0.30
392 154 0.46
393 1 0.00
395 29 0.09
396 12 0.04
398 38 0.11
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (396 bp):
CAATGTTAGTTTTAATTCGATTCCTGCAACTTAAGTGATATAAGAATTGGTGTTGTAGCTTCATC
TTACTCCACTACAACTTCAAGGAGATAAAGATTTGCTACTATTTTAATCCACTTCACTGCAACTT
TAGGAAGATAAAATTTGGTCTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTG
CCAATGGTAGTTTTAATCCGATCCCTGTAACTTCAGGAATATAAGATTTGATATTGTAACTTCAT
CTTGCTACACTACAACTTTAGGGAGATAAAGATTTGCCATACTAGTTTTAATCCGATCACTGCAA
CCTCAGGAAGATATGATTTGGTGTTGAGCTTCATCTTACTCCACTGCAACTTCAAGGAGATAAAG
ATTTGT
Found at i:433297 original size:493 final size:491
Alignment explanation
Indices: 432628--433581 Score: 1328
Period size: 493 Copynumber: 1.9 Consensus size: 491
432618 TGATTTGGTC
**
432628 TAGCTTCATCTTGCTCCACTGTAACTTCAGGGAGATAAAGATTTGCCAATGGTAGTTTTAATCCG
1 TAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAAGATTTGCCAATGGTAGTTTTAATCCG
* ** * *
432693 ATCCTTGTAACTTCAGGAATATAAGATTTGATATTGTAACTTCATCTTGTTACATTGTAACTTTA
66 ATCCTTGTAACCTCAGGAATATAAGATTTGATATTGTAACTTCATCTTACTACACTGCAACTTTA
* * * * * *
432758 GGGAGATAAAGATTTGCTACTGTTTTAATCCGCTTCACTGCAACTTCAGGAAGATATGATTTGGT
131 CGGAGATAAAGATTTGCTACTATTTTAATCCGCTTCACTACAACTTCAGGAAAATAGGATTTGAT
432823 GTGGCTTCATCTTGC-TCCACTGTAACTTCAAGGAGATAAAGATTTG-TCAATGTTAGTTTTAAT
196 GTGGCTTCATCTT-CTTCCACTGTAACTTCAAGGAGATAAAGATTTGCT-AATGTTAGTTTTAAT
* *
432886 CTGATCCTG-CAACTTAA-AGGATATAAGATTTGGTGTTGTAGCT-TCATCTTGCTCCACTACAA
259 CTGATCCTGTC-ACTTAAGA-GATATAAGATTTGCTGTTATAGCTCT-ATCTTGCTCCACTACAA
* *
432948 CTTCAGGGAGATAAATATTTGCTACTATTTTAATCCT-CTTCAGTGCAACTTTAGGAAGATAAAA
321 CTTCAGGGAGATAAATATTTGCTACTATTTTAAT-CTACTTCAGTGCAACTTCAGAAAGAT-AAA
* * *
433012 ATTTGGTGTGGCTTCATCTTGCTCCATTGCAATTTCAAGGAGATAAAGATTTGCCAATGTTAGTT
384 ATTTGGTG-GGCTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATGTTAGTT
*
433077 TTAATCTGATCCCTGTAACTTCAGGGATATAAGATTTGGTGTTG
448 TTAATCCGATCCCTGTAACTTCAGGGATATAAGATTTGGTGTTG
* * * * * *
433121 TAGCTTTATCTTGCTGCACTACAACTTTATGGAGATAAAGATTTGCCAATGTTAGTTTTAATTCG
1 TAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAAGATTTGCCAATGGTAGTTTTAATCCG
* * * * ** *
433186 AT-CTCTGTAACCTCAGGGATATATGATTTGGTGTTGTAGTTTCATCTTACTCCACTGCAACTTT
66 ATCCT-TGTAACCTCAGGAATATAAGATTTGATATTGTAACTTCATCTTACTACACTGCAACTTT
* *
433250 ACGGAGATAAAGATTTGCTACTATTTTAATTCGCTTTACTACAACTTCAGGAAAATAGGATTTGA
130 ACGGAGATAAAGATTTGCTACTATTTTAATCCGCTTCACTACAACTTCAGGAAAATAGGATTTGA
* * * *
433315 TGTGGCTTCATCTTCTTTCATTGTAACTTTAGGGAGATAAAGATTTGCTAATGTTAGTTTTAATC
195 TGTGGCTTCATCTTCTTCCACTGTAACTTCAAGGAGATAAAGATTTGCTAATGTTAGTTTTAATC
* * ** *
433380 TGATCTTGTCACTTCAGAGATATAAGATTTGCTGTTATAGCTCTATCTTGCTCCACTGTAACTTT
260 TGATCCTGTCACTTAAGAGATATAAGATTTGCTGTTATAGCTCTATCTTGCTCCACTACAACTTC
* * **
433445 AGGGAGATAAATATTTGCTACTATTTTAATCTACTTCATTGCAACTTCATAAAGATAGGATTTGG
325 AGGGAGATAAATATTTGCTACTATTTTAATCTACTTCAGTGCAACTTCAGAAAGATAAAATTTGG
*
433510 TGGGCTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATGTTAGTTTTAGTCC
390 TGGGCTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATGTTAGTTTTAATCC
433575 GATCCCT
455 GATCCCT
433582 ACAGCTTTAG
Statistics
Matches: 404, Mismatches: 50, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
491 65 0.16
492 14 0.03
493 321 0.79
494 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (491 bp):
TAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAAGATTTGCCAATGGTAGTTTTAATCCG
ATCCTTGTAACCTCAGGAATATAAGATTTGATATTGTAACTTCATCTTACTACACTGCAACTTTA
CGGAGATAAAGATTTGCTACTATTTTAATCCGCTTCACTACAACTTCAGGAAAATAGGATTTGAT
GTGGCTTCATCTTCTTCCACTGTAACTTCAAGGAGATAAAGATTTGCTAATGTTAGTTTTAATCT
GATCCTGTCACTTAAGAGATATAAGATTTGCTGTTATAGCTCTATCTTGCTCCACTACAACTTCA
GGGAGATAAATATTTGCTACTATTTTAATCTACTTCAGTGCAACTTCAGAAAGATAAAATTTGGT
GGGCTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATGTTAGTTTTAATCCG
ATCCCTGTAACTTCAGGGATATAAGATTTGGTGTTG
Found at i:433492 original size:195 final size:195
Alignment explanation
Indices: 433123--433570 Score: 557
Period size: 195 Copynumber: 2.3 Consensus size: 195
433113 TGGTGTTGTA
* * *
433123 GCTTTATCTTGCTGCACTACAACTTTATGGAGATAAAGATTTGCCAATGTTAGTTTTAATTCGAT
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAAGATTTGCCAATGTTAGTTTTAATTCGAT
* * * * *
433188 CTCTGTAACCTCAGGGATATATGATTTGGTGTTGTAGTTTCATCTTACTCCACTGCAACTTTACG
66 CTCTGTAACCTCAGAGATATAAGATTTGCTGTTATAGTCTCATCTTACTCCACTGCAACTTTACG
* *
433253 GAGATAAAGATTTGCTACTATTTTAATTCGCTTTACTACAACTTCAGGAAA-ATAGGATTTGATG
131 GAGATAAAGATTTGCTACTATTTTAATTCACTTCACTACAACTTCA-GAAAGATAGGATTTGATG
433317 TG
195 -G
* * ** * *
433319 GCTTCATCTT-CTTTCATTGTAACTTTAGGGAGATAAAGATTTGCTAATGTTAGTTTTAA-TCTG
1 GCTTCATCTTGC-TCCACTACAACTTTAAGGAGATAAAGATTTGCCAATGTTAGTTTTAATTC-G
* * * *
433382 ATCT-TGTCACTTCAGAGATATAAGATTTGCTGTTATAG-CTCTATCTTGCTCCACTGTAACTTT
64 ATCTCTGTAACCTCAGAGATATAAGATTTGCTGTTATAGTCTC-ATCTTACTCCACTGCAACTTT
* * * * *
433445 AGGGAGATAAATATTTGCTACTATTTTAA-TCTACTTCATTGCAACTTCATAAAGATAGGATTTG
128 ACGGAGATAAAGATTTGCTACTATTTTAATTC-ACTTCACTACAACTTCAGAAAGATAGGATTTG
*
433509 GTGG
192 ATGG
*
433513 GCTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATGTTAGTTTTA
1 GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAAGATTTGCCAATGTTAGTTTTA
433571 GTCCGATCCC
Statistics
Matches: 215, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
194 57 0.27
195 103 0.48
196 55 0.26
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (195 bp):
GCTTCATCTTGCTCCACTACAACTTTAAGGAGATAAAGATTTGCCAATGTTAGTTTTAATTCGAT
CTCTGTAACCTCAGAGATATAAGATTTGCTGTTATAGTCTCATCTTACTCCACTGCAACTTTACG
GAGATAAAGATTTGCTACTATTTTAATTCACTTCACTACAACTTCAGAAAGATAGGATTTGATGG
Found at i:438615 original size:26 final size:26
Alignment explanation
Indices: 438579--438630 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
438569 CAATGCACCC
438579 TTTACAACGGGTGATGATATGTAATG
1 TTTACAACGGGTGATGATATGTAATG
438605 TTTACAACGGGTGATGATATGTAATG
1 TTTACAACGGGTGATGATATGTAATG
438631 CCTTTGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.35
Consensus pattern (26 bp):
TTTACAACGGGTGATGATATGTAATG
Found at i:443704 original size:29 final size:29
Alignment explanation
Indices: 443672--443962 Score: 215
Period size: 30 Copynumber: 9.9 Consensus size: 29
443662 GCACGGGGGC
* *
443672 AAAATGGTAGTTTTGGAGGGTTCGGAGTCA
1 AAAATGGTATTTTTGGA-GGTTCGGGGTCA
*
443702 AAAATGAG-ATTTTTGGAAGTTCGAGGGT--
1 AAAATG-GTATTTTTGGAGGTTCG-GGGTCA
*
443730 AAAATGGTAATTTTTAGAAGGTTC-GGGTCA
1 AAAATGGT-ATTTTT-GGAGGTTCGGGGTCA
* *
443760 AAAATGGGATTTTTGGAAGTTCAGGGGT--
1 AAAATGGTATTTTTGGAGGTTC-GGGGTCA
* *
443788 AAAATGGTAATTTTTAGAAGGTTCGGGGTCT
1 AAAATGGT-ATTTTT-GGAGGTTCGGGGTCA
* * *
443819 AAAATGGGATTTTTAGAAGTTCGGGGGT--
1 AAAATGGTATTTTTGGAGGTTC-GGGGTCA
* * *
443847 AAAATGGTAATTTTTAGAAGGCTCGGGATCA
1 AAAATGGT-ATTTTT-GGAGGTTCGGGGTCA
* *
443878 AAAATGGGATTTTTGGAAGTTCGGGGGT--
1 AAAATGGTATTTTTGGAGGTTC-GGGGTCA
*
443906 AAAATGGTAATTTTTAGAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTT-GGAGGTTCGGGGTCA
* *
443937 AAAATGGGATTTTTGGAAGTTCGGGG
1 AAAATGGTATTTTTGGAGGTTCGGGG
443963 GTAAATGGTA
Statistics
Matches: 206, Mismatches: 32, Indels: 47
0.72 0.11 0.16
Matches are distributed among these distances:
27 1 0.00
28 37 0.18
29 69 0.33
30 77 0.37
31 22 0.11
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (29 bp):
AAAATGGTATTTTTGGAGGTTCGGGGTCA
Found at i:443762 original size:58 final size:58
Alignment explanation
Indices: 443665--443982 Score: 496
Period size: 59 Copynumber: 5.4 Consensus size: 58
443655 TTCGGATGCA
* * * * *
443665 CGGGGGCAAAATGGT-AGTTTTGGAGGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGG-GTCAAAAATGGGATTTTTGGAAGTT
*
443723 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTT
* * *
443781 CAGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCTAAAATGGGATTTTTAGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTT
*
443840 CGGGGGTAAAATGGTAATTTTTAGAAGGCTCGGGATCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGG-TCAAAAATGGGATTTTTGGAAGTT
443899 CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTAGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTT
443958 CGGGGGT-AAATGGTAATTTTTAGAA
1 CGGGGGTAAAATGGTAATTTTTAGAA
443983 AGTTTAGGGA
Statistics
Matches: 241, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
58 87 0.36
59 151 0.63
60 3 0.01
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.32
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:443978 original size:29 final size:29
Alignment explanation
Indices: 443710--443982 Score: 272
Period size: 29 Copynumber: 9.3 Consensus size: 29
443700 CAAAAATGAG
* *
443710 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTAGAAGTTCGGGGGTAAAATGGTA
*** *
443739 ATTTTTAGAAGGTTCGGGTCAAAAATGG-G
1 ATTTTTAGAA-GTTCGGGGGTAAAATGGTA
* *
443768 ATTTTTGGAAGTTCAGGGGTAAAATGGTA
1 ATTTTTAGAAGTTCGGGGGTAAAATGGTA
* *
443797 ATTTTTAGAAGGTTCGGGGTCTAAAATGG-G
1 ATTTTTAGAA-GTTCGGGG-GTAAAATGGTA
443827 ATTTTTAGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTAGAAGTTCGGGGGTAAAATGGTA
* * *
443856 ATTTTTAGAAGGCTC-GGGATCAAAAATGG-G
1 ATTTTTAGAA-GTTCGGGGGT--AAAATGGTA
*
443886 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTAGAAGTTCGGGGGTAAAATGGTA
*
443915 ATTTTTAGAAGGTTC-GGGGTCAAAAATGG-G
1 ATTTTTAGAA-GTTCGGGGGT--AAAATGGTA
*
443945 ATTTTTGGAAGTTCGGGGGT-AAATGGTA
1 ATTTTTAGAAGTTCGGGGGTAAAATGGTA
443973 ATTTTTAGAA
1 ATTTTTAGAA
443983 AGTTTAGGGA
Statistics
Matches: 199, Mismatches: 30, Indels: 31
0.77 0.12 0.12
Matches are distributed among these distances:
27 6 0.03
28 37 0.19
29 70 0.35
30 64 0.32
31 22 0.11
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
ATTTTTAGAAGTTCGGGGGTAAAATGGTA
Found at i:450848 original size:21 final size:23
Alignment explanation
Indices: 450815--450856 Score: 54
Period size: 21 Copynumber: 1.9 Consensus size: 23
450805 TTATTAAAAT
450815 AAGACTGATTCAAATGA-AAATAA
1 AAGACTGATTC-AATGATAAATAA
450838 AAGAC-GA-TCAATGATAAAT
1 AAGACTGATTCAATGATAAAT
450857 GAATAGTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 2 0.11
23 5 0.28
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.21
Consensus pattern (23 bp):
AAGACTGATTCAATGATAAATAA
Found at i:460371 original size:53 final size:53
Alignment explanation
Indices: 460314--460429 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
460304 AACTAGAAGT
460314 CTAATATA-CAATATAGTGTAATTAATGCAATGCAACATTATTTAAAATAGTAA
1 CTAAT-TAGCAATATAGTGTAATTAATGCAATGCAACATTATTTAAAATAGTAA
460367 CTAATTAGCAATATAGTGTAATTAATGCAATGCAACATTATTTAAAATAGTAA
1 CTAATTAGCAATATAGTGTAATTAATGCAATGCAACATTATTTAAAATAGTAA
460420 CTAATTAGCA
1 CTAATTAGCA
460430 TAGATAACAT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 2 0.03
53 60 0.97
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (53 bp):
CTAATTAGCAATATAGTGTAATTAATGCAATGCAACATTATTTAAAATAGTAA
Found at i:462948 original size:23 final size:23
Alignment explanation
Indices: 462922--462965 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
462912 CAAGGTCCAC
*
462922 CGATTTCGATCGTCGGCGATCGG
1 CGATTGCGATCGTCGGCGATCGG
*
462945 CGATTGGGATCGTCGGCGATC
1 CGATTGCGATCGTCGGCGATC
462966 AAGCGGGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (23 bp):
CGATTGCGATCGTCGGCGATCGG
Found at i:465868 original size:16 final size:16
Alignment explanation
Indices: 465849--465897 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
465839 CATATGCCAT
465849 TGTTTGATTATTTGCA
1 TGTTTGATTATTTGCA
* *
465865 TGTTTTA-TATAT---
1 TGTTTGATTATTTGCA
465877 TGTTTGATTATTTGCA
1 TGTTTGATTATTTGCA
465893 TGTTT
1 TGTTT
465898 TATAGGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 6 0.24
13 4 0.16
15 4 0.16
16 11 0.44
ACGTcount: A:0.18, C:0.04, G:0.16, T:0.61
Consensus pattern (16 bp):
TGTTTGATTATTTGCA
Found at i:465879 original size:28 final size:28
Alignment explanation
Indices: 465847--465901 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
465837 ATCATATGCC
465847 ATTGTTTGATTATTTGCATGTTTTATAT
1 ATTGTTTGATTATTTGCATGTTTTATAT
465875 ATTGTTTGATTATTTGCATGTTTTATA
1 ATTGTTTGATTATTTGCATGTTTTATA
465902 GGAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.04, G:0.15, T:0.60
Consensus pattern (28 bp):
ATTGTTTGATTATTTGCATGTTTTATAT
Found at i:479879 original size:30 final size:30
Alignment explanation
Indices: 479843--479929 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
479833 GGGTAATCTC
* **
479843 GATATAATGTTAGCTTGTGTGAGCAATTCT
1 GATATAATGTCAGCTTGTGTGAGCAACCCT
* *
479873 -ATTATAATGTCAACTTGTGTGAACAACCCT
1 GA-TATAATGTCAGCTTGTGTGAGCAACCCT
*
479903 GATATACTGTCAGCTTGTGTGAGCAAC
1 GATATAATGTCAGCTTGTGTGAGCAAC
479930 TTATTCTCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (30 bp):
GATATAATGTCAGCTTGTGTGAGCAACCCT
Found at i:501365 original size:16 final size:16
Alignment explanation
Indices: 501320--501365 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
501310 AAAGCACCAA
501320 CCTTTCTTTTCTT-TT
1 CCTTTCTTTTCTTATT
*
501335 CCTTTCTTTTTTTATT
1 CCTTTCTTTTCTTATT
*
501351 CCTTTCTTCTCTTAT
1 CCTTTCTTTTCTTAT
501366 GCTCGGAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (16 bp):
CCTTTCTTTTCTTATT
Found at i:502699 original size:14 final size:14
Alignment explanation
Indices: 502680--502707 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
502670 TTCTCTTCAG
502680 GAGTCTCAATGATA
1 GAGTCTCAATGATA
502694 GAGTCTCAATGATA
1 GAGTCTCAATGATA
502708 TTTAAGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
GAGTCTCAATGATA
Found at i:506918 original size:17 final size:17
Alignment explanation
Indices: 506896--506929 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
506886 TTAAAATTGG
506896 ATTGGGAACATT-ATTTA
1 ATTGGGAA-ATTAATTTA
506913 ATTGGGAAATTAATTTA
1 ATTGGGAAATTAATTTA
506930 TTATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
ATTGGGAAATTAATTTA
Found at i:510428 original size:23 final size:23
Alignment explanation
Indices: 510402--510528 Score: 200
Period size: 23 Copynumber: 5.4 Consensus size: 23
510392 TGCTGGGCAA
* *
510402 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTACTAAT
510425 CAGAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTACTAAT
*
510448 CAAAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTACTAAT
510471 CAGAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTACTAAT
510494 CAGAGAGCACACACAAAGTACTAAT
1 CAGAGAG--CACACAAAGTACTAAT
*
510519 TAGAGAGCAC
1 CAGAGAGCAC
510529 GCAATGTGCT
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
23 75 0.77
25 22 0.23
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTACTAAT
Found at i:510569 original size:71 final size:70
Alignment explanation
Indices: 510405--510572 Score: 189
Period size: 71 Copynumber: 2.4 Consensus size: 70
510395 TGGGCAACAG
*
510405 AGAGCACACACAGTGCTAATCAGAGAG-CACACAAAGTACTAATCAAAGAGCACACAAAGTACTA
1 AGAGCACACAAAGTGCTAATCAGAGAGCCACACAAAGTACTAATCAAAGAGCACACAAAGTACTA
*
510469 ATCAG
66 ATCAA
* * * * * *
510474 AGAGCACACAAAGTACTAATCAGAGAGCACACACAAAGTACTAATTAGAGAGCACGCAATGTGCT
1 AGAGCACACAAAGTGCTAATCAGAGAGC-CACACAAAGTACTAATCAAAGAGCACACAAAGTACT
*
510539 GATCAA
65 AATCAA
* *
510545 ATG-GCACGA-AACGTGCTAAACAGAGAGC
1 A-GAGCAC-ACAAAGTGCTAATCAGAGAGC
510573 GCGCTAGTGT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
69 25 0.30
71 56 0.67
72 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (70 bp):
AGAGCACACAAAGTGCTAATCAGAGAGCCACACAAAGTACTAATCAAAGAGCACACAAAGTACTA
ATCAA
Found at i:513325 original size:30 final size:30
Alignment explanation
Indices: 513285--513360 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 30
513275 CTACTTTTCT
513285 ATAATATAATTAATATAAATAC-ATTTCCCC
1 ATAATATAATTAATATAAA-ACAATTTCCCC
* *
513315 ATAATGTAATTAATATAAAACTAATTTCTCC
1 ATAATATAATTAATATAAAAC-AATTTCCCC
513346 -TAATATAATTAATAT
1 ATAATATAATTAATAT
513361 GAGCATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 2 0.05
30 32 0.78
31 7 0.17
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (30 bp):
ATAATATAATTAATATAAAACAATTTCCCC
Found at i:513889 original size:18 final size:16
Alignment explanation
Indices: 513855--513886 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
513845 AAATATTATG
513855 TTAAAAAAGCAGATGT
1 TTAAAAAAGCAGATGT
513871 TTAAAAAAGCAGATGT
1 TTAAAAAAGCAGATGT
513887 GTTACCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
TTAAAAAAGCAGATGT
Found at i:516474 original size:9 final size:9
Alignment explanation
Indices: 516460--516711 Score: 85
Period size: 10 Copynumber: 26.6 Consensus size: 9
516450 ATATTTAGAA
516460 AAAAATTAT
1 AAAAATTAT
516469 AAAAA-TA-
1 AAAAATTAT
516476 AAAAATTATTT
1 AAAAATTA--T
516487 AAAAAATTAAAT
1 -AAAAATT--AT
516499 ATTAAAATTAT
1 A--AAAATTAT
*
516510 ATAAACTTAT
1 A-AAAATTAT
*
516520 AATAATTAT
1 AAAAATTAT
*
516529 AAAAA-CA-
1 AAAAATTAT
*
516536 AAAACTTAT
1 AAAAATTAT
*
516545 AAATATTAT
1 AAAAATTAT
516554 -AAAA-TAT
1 AAAAATTAT
516561 AAAAATT-T
1 AAAAATTAT
*
516569 AATAAATTCT
1 AA-AAATTAT
516579 AATAAATTAT
1 AA-AAATTAT
516589 -AAAATTAT
1 AAAAATTAT
*
516597 -AAAGTTAAT
1 AAAAATT-AT
*
516606 AAAACATATTT
1 AAAA-AT-TAT
516617 AAAATATT-T
1 AAAA-ATTAT
**
516626 AGAACTTTAT
1 A-AAAATTAT
*
516636 AAAAACATAT
1 AAAAA-TTAT
*
516646 AAAAATTCTTT
1 AAAAA-T-TAT
516657 AAAAATTAT
1 AAAAATTAT
516666 -AAAATTATT
1 AAAAATTA-T
516675 AAAATATTACAT
1 AAAA-ATT--AT
*
516687 ATAAACTTAT
1 A-AAAATTAT
*
516697 AAAAAATCAT
1 -AAAAATTAT
516707 AAAAA
1 AAAAA
516712 CTTGAATTGG
Statistics
Matches: 186, Mismatches: 27, Indels: 60
0.68 0.10 0.22
Matches are distributed among these distances:
7 12 0.06
8 35 0.19
9 45 0.24
10 47 0.25
11 23 0.12
12 13 0.07
13 10 0.05
14 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:516540 original size:25 final size:26
Alignment explanation
Indices: 516512--516573 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
516502 AAAATTATAT
516512 AAACTTATAATAATTATAAAA-ACAA
1 AAACTTATAATAATTATAAAATACAA
*
516537 AAACTTATAA-ATATTATAAAATATAA
1 AAACTTATAATA-ATTATAAAATACAA
516563 AAA-TT-TAATAA
1 AAACTTATAATAA
516574 ATTCTAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 5 0.15
25 22 0.67
26 6 0.18
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
AAACTTATAATAATTATAAAATACAA
Found at i:516566 original size:18 final size:18
Alignment explanation
Indices: 516545--516599 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
516535 AAAAACTTAT
516545 AAATATTATAAAATATAA
1 AAATATTATAAAATATAA
* *
516563 AAAT-TTAATAAATTCTAA
1 AAATATT-ATAAAATATAA
*
516581 TAA-ATTATAAAATTATAA
1 AAATATTATAAAA-TATAA
516599 A
1 A
516600 GTTAATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATTATAAAATATAA
Found at i:516595 original size:8 final size:8
Alignment explanation
Indices: 516461--516609 Score: 65
Period size: 8 Copynumber: 17.5 Consensus size: 8
516451 TATTTAGAAA
516461 AAAATTAT
1 AAAATTAT
* *
516469 AAAAATAA
1 AAAATTAT
516477 AAAATTATTT
1 AAAATTA--T
*
516487 AAAA-AAT
1 AAAATTAT
*
516494 TAAA-TATT
1 AAAATTA-T
516502 AAAATTAT
1 AAAATTAT
516510 ATAAACTTAT
1 A-AAA-TTAT
516520 AATAATTAT
1 AA-AATTAT
**
516529 AAAAACA-
1 AAAATTAT
516536 AAAACTTAT
1 AAAA-TTAT
516545 AAATATTAT
1 AAA-ATTAT
516554 AAAA-TAT
1 AAAATTAT
516561 AAAAATT-T
1 -AAAATTAT
*
516569 AATAAATTCT
1 -A-AAATTAT
516579 AATAAATTAT
1 -A-AAATTAT
516589 AAAATTAT
1 AAAATTAT
*
516597 AAAGTTAAT
1 AAAATT-AT
516606 AAAA
1 AAAA
516610 CATATTTAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 29
0.72 0.10 0.19
Matches are distributed among these distances:
7 12 0.11
8 42 0.38
9 35 0.32
10 22 0.20
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:517791 original size:21 final size:20
Alignment explanation
Indices: 517767--517806 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
517757 AAATTTTAAA
*
517767 TAATTTAAATATATTTTTTAT
1 TAATTT-AATATAGTTTTTAT
*
517788 TAATTTTATATAGTTTTTA
1 TAATTTAATATAGTTTTTA
517807 AATAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATTTAATATAGTTTTTAT
Found at i:517860 original size:9 final size:9
Alignment explanation
Indices: 517834--518153 Score: 103
Period size: 9 Copynumber: 35.0 Consensus size: 9
517824 CTATTAGATT
517834 TTTTTATAA
1 TTTTTATAA
517843 TTTTATATAA
1 TTTT-TATAA
*
517853 TATTTATAA
1 TTTTTATAA
* *
517862 GTTTTATGA
1 TTTTTATAA
*
517871 TTTTTATAG
1 TTTTTATAA
517880 TTTTTATAA
1 TTTTTATAA
*
517889 GTTTATATGAA
1 -TTTTTAT-AA
*
517900 -TTTTATAG
1 TTTTTATAA
517908 TTTTTATAA
1 TTTTTATAA
*
517917 GTTTATATGAA
1 -TTTTTAT-AA
**
517928 -TTTTAGCA
1 TTTTTATAA
*
517936 TTTTAAT-A
1 TTTTTATAA
**
517944 TTTAAAT-A
1 TTTTTATAA
517952 TTTTTAT-A
1 TTTTTATAA
*
517960 TTTTTATGA
1 TTTTTATAA
*
517969 TTTTTAATGA
1 TTTTT-ATAA
*
517979 TTTGTAATAA
1 TTT-TTATAA
*
517989 TTTTTATAG
1 TTTTTATAA
*
517998 GTTTT-T--
1 TTTTTATAA
518004 TTTTTATAA
1 TTTTTATAA
* *
518013 CTTTTATACG
1 TTTTTATA-A
518023 TTTTTATAAAA
1 TTTTTAT--AA
**
518034 AGTTTA-AA
1 TTTTTATAA
*
518042 TATTTTAAACA
1 T-TTTTATA-A
518053 TGTTTTTATTAA
1 --TTTTTA-TAA
518065 TTTTGTAT--
1 TTTT-TATAA
*
518073 TTTTTATCA
1 TTTTTATAA
* * *
518082 TTGATTAGAT
1 TT-TTTATAA
518092 TTTTTAT-A
1 TTTTTATAA
518100 TTTTTA-AA
1 TTTTTATAA
*
518108 TATTTATAA
1 TTTTTATAA
518117 GTTTTTAT--
1 -TTTTTATAA
*
518125 TTATTTATTA
1 TT-TTTATAA
518135 TTTGTTATAA
1 TTT-TTATAA
518145 TTTTTATAA
1 TTTTTATAA
518154 GTCTATATAA
Statistics
Matches: 232, Mismatches: 46, Indels: 66
0.67 0.13 0.19
Matches are distributed among these distances:
6 4 0.02
7 6 0.03
8 47 0.20
9 88 0.38
10 66 0.28
11 12 0.05
12 7 0.03
13 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:517866 original size:28 final size:28
Alignment explanation
Indices: 517841--517932 Score: 118
Period size: 28 Copynumber: 3.2 Consensus size: 28
517831 ATTTTTTTAT
517841 AATTTTATATAATATTTATAAGTTT-TATG
1 AATTTTATAT-AT-TTTATAAGTTTATATG
*
517870 ATTTTTATAGT-TTTTATAAGTTTATATG
1 AATTTTATA-TATTTTATAAGTTTATATG
517898 AATTTTATAGT-TTTTATAAGTTTATATG
1 AATTTTATA-TATTTTATAAGTTTATATG
517926 AATTTTA
1 AATTTTA
517933 GCATTTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
27 11 0.19
28 39 0.66
29 8 0.14
30 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.58
Consensus pattern (28 bp):
AATTTTATATATTTTATAAGTTTATATG
Found at i:517939 original size:28 final size:28
Alignment explanation
Indices: 517855--517932 Score: 140
Period size: 28 Copynumber: 2.8 Consensus size: 28
517845 TTATATAATA
*
517855 TTTATAAGTTT-TATGATTTTTATAGTT
1 TTTATAAGTTTATATGAATTTTATAGTT
517882 TTTATAAGTTTATATGAATTTTATAGTT
1 TTTATAAGTTTATATGAATTTTATAGTT
517910 TTTATAAGTTTATATGAATTTTA
1 TTTATAAGTTTATATGAATTTTA
517933 GCATTTTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 11 0.22
28 38 0.78
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (28 bp):
TTTATAAGTTTATATGAATTTTATAGTT
Found at i:518123 original size:18 final size:17
Alignment explanation
Indices: 518094--518194 Score: 55
Period size: 18 Copynumber: 5.8 Consensus size: 17
518084 GATTAGATTT
518094 TTTAT-ATTTTTAAATA
1 TTTATAATTTTTAAATA
**
518110 TTTATAAGTTTTTATTTA
1 TTTATAA-TTTTTAAATA
* *
518128 TTTATTATTTGTTATAATT
1 TTTATAATTT-TTA-AATA
* *
518147 TTTATAAGTCTATATAA-A
1 TTTATAA-TTTTTA-AATA
*
518165 TTT-TAATATTTAAATA
1 TTTATAATTTTTAAATA
*
518181 TTTAATAATATTTA
1 TTT-ATAATTTTTA
518195 TATTTTATCT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
15 2 0.03
16 13 0.20
17 7 0.11
18 29 0.45
19 12 0.18
20 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATAATTTTTAAATA
Found at i:518142 original size:10 final size:9
Alignment explanation
Indices: 518092--518153 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 9
518082 TTGATTAGAT
518092 TTTTTAT-A
1 TTTTTATAA
518100 TTTTTA-AA
1 TTTTTATAA
*
518108 TATTTATAA
1 TTTTTATAA
518117 GTTTTTAT--
1 -TTTTTATAA
*
518125 TTATTTATTA
1 TT-TTTATAA
518135 TTTGTTATAA
1 TTT-TTATAA
518145 TTTTTATAA
1 TTTTTATAA
518154 GTCTATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.05
8 17 0.39
9 9 0.20
10 16 0.36
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:518437 original size:24 final size:23
Alignment explanation
Indices: 518410--518460 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
518400 CAAATTTAAT
*
518410 ACATGAGCTTAATTGATTTTTTTG
1 ACATGAGCTTAAGTG-TTTTTTTG
***
518434 ACATTTTCTTAAGTGTTTTTTTG
1 ACATGAGCTTAAGTGTTTTTTTG
518457 ACAT
1 ACAT
518461 ATAAGCCTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (23 bp):
ACATGAGCTTAAGTGTTTTTTTG
Found at i:518742 original size:20 final size:20
Alignment explanation
Indices: 518719--518761 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
518709 AAAAATGATT
*
518719 AAAAAATATGAGAA-ATTATA
1 AAAAAATA-GAAAATATTATA
518739 AAAAAATAGAAAATATTATA
1 AAAAAATAGAAAATATTATA
518759 AAA
1 AAA
518762 TTATTACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAAAATAGAAAATATTATA
Found at i:518887 original size:21 final size:22
Alignment explanation
Indices: 518838--518887 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
518828 TAAAATCAAT
* *
518838 AAACATATTTAAAATTTTATTT
1 AAACATATTTAAAATTCTATTA
518860 AAACATA-TTAAAATTCTA-TA
1 AAACATATTTAAAATTCTATTA
518880 AAATCATA
1 AAA-CATA
518888 AAAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 14 0.56
22 7 0.28
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
AAACATATTTAAAATTCTATTA
Found at i:518897 original size:28 final size:27
Alignment explanation
Indices: 518864--518948 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
518854 TTATTTAAAC
* *
518864 ATATTAAAATTCTATAAAATCATAAAAA
1 ATATTAAAACT-TATAAAATTATAAAAA
*
518892 ATATTAAAACTTATAAAACTTATTAAAA
1 ATATTAAAACTTATAAAA-TTATAAAAA
*
518920 TTA-TATAAACTTATAAAATTATAAAAA
1 ATATTA-AAACTTATAAAATTATAAAAA
518947 AT
1 AT
518949 CATAAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.37
28 31 0.63
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATTAAAACTTATAAAATTATAAAAA
Found at i:518918 original size:10 final size:9
Alignment explanation
Indices: 518896--518945 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
518886 TAAAAAATAT
518896 TAAAACTTA
1 TAAAACTTA
518905 TAAAACTTA
1 TAAAACTTA
518914 TTAAAA-TTA
1 -TAAAACTTA
518923 TATAAACTTA
1 TA-AAACTTA
518933 TAAAA-TTA
1 TAAAACTTA
518941 TAAAA
1 TAAAA
518946 AATCATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 10 0.26
9 18 0.47
10 10 0.26
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAACTTA
Found at i:518947 original size:10 final size:10
Alignment explanation
Indices: 518869--518956 Score: 51
Period size: 10 Copynumber: 9.3 Consensus size: 10
518859 TAAACATATT
* *
518869 AAAATTCTAT
1 AAAATTATAA
*
518879 AAAATCATAA
1 AAAATTATAA
*
518889 AAAA-TATTA
1 AAAATTATAA
*
518898 AAACTTAT-A
1 AAAATTATAA
* *
518907 AAACTTAT-T
1 AAAATTATAA
*
518916 AAAATTATAT
1 AAAATTATAA
*
518926 AAACTTAT--
1 AAAATTATAA
518934 AAAATTATAA
1 AAAATTATAA
*
518944 AAAATCATAA
1 AAAATTATAA
518954 AAA
1 AAA
518957 TTGAAATTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
8 7 0.11
9 22 0.35
10 34 0.54
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATTATAA
Found at i:518953 original size:18 final size:18
Alignment explanation
Indices: 518876--518955 Score: 74
Period size: 18 Copynumber: 4.4 Consensus size: 18
518866 ATTAAAATTC
*
518876 TATAAAATCATAAAAAA-
1 TATAAAATTATAAAAAAT
*
518893 TATTAAAACTTAT-AAAACT
1 TA-TAAAA-TTATAAAAAAT
* *
518912 TATTAAAATTATATAAACT
1 TA-TAAAATTATAAAAAAT
518931 TATAAAATTATAAAAAAT
1 TATAAAATTATAAAAAAT
*
518949 CATAAAA
1 TATAAAA
518956 ATTGAAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.04
18 33 0.62
19 18 0.34
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAAATTATAAAAAAT
Found at i:518958 original size:19 final size:19
Alignment explanation
Indices: 518869--518958 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 19
518859 TAAACATATT
* *
518869 AAAATTCTATAAAATCATAA
1 AAAATTATA-AAAATTATAA
*
518889 AAAA-TATTAAAACTTAT-A
1 AAAATTA-TAAAAATTATAA
* * *
518907 AAACTTATTAAAATTATAT
1 AAAATTATAAAAATTATAA
*
518926 AAACTTAT-AAAATTATAA
1 AAAATTATAAAAATTATAA
*
518944 AAAATCATAAAAATT
1 AAAATTATAAAAATT
518959 GAAATTTACC
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
18 27 0.48
19 23 0.41
20 6 0.11
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAAATTATAA
Found at i:519155 original size:27 final size:27
Alignment explanation
Indices: 519125--519178 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
519115 GTCACTAATG
*
519125 TTTTAGATCATTTCTATTTTGGTCACT
1 TTTTAGATAATTTCTATTTTGGTCACT
519152 TTTTAGATAATTTCTATTTTGGTCACT
1 TTTTAGATAATTTCTATTTTGGTCACT
519179 CTCAGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (27 bp):
TTTTAGATAATTTCTATTTTGGTCACT
Found at i:523271 original size:4 final size:4
Alignment explanation
Indices: 523262--523288 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
523252 TGGTAGTAAT
523262 CAGG CAGG CAGG CAGG CAGG CAGG CAG
1 CAGG CAGG CAGG CAGG CAGG CAGG CAG
523289 ACCAAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.48, T:0.00
Consensus pattern (4 bp):
CAGG
Found at i:532235 original size:17 final size:18
Alignment explanation
Indices: 532196--532240 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
532186 AATTTAAATT
532196 AAAAATATTAATAACTAC
1 AAAAATATTAATAACTAC
* *
532214 AAAAATATTAATTACTAT
1 AAAAATATTAATAACTAC
532232 AAAAA-ATTA
1 AAAAATATTA
532241 TCAATACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATTAATAACTAC
Found at i:532809 original size:76 final size:75
Alignment explanation
Indices: 532580--532809 Score: 174
Period size: 76 Copynumber: 3.1 Consensus size: 75
532570 ATAGTTTGCA
532580 TTATTTTTTATCCAAATGAATAAATTAAAATAAAGTATTATCTAACTTCGAAATTTTAATATAAT
1 TTATTTTTTATCCAAATGAATAAATTAAAATAAAGT-TTATCTAACTTCGAAATTTTAATATAAT
532645 TT-ACTTTTTGT
65 TTAAC-TTTTGT
* ** ** * * * * * * *
532656 TTA---TTTAT--AATATAAAT-TTTTGTAAT-AACTTTAT-AAAATACATGTAATTATAGTTAT
1 TTATTTTTTATCCAA-ATGAATAAATTAAAATAAAGTTTATCTAACTTC--GAAATTTTA-ATAT
* *
532713 AATCTATAGTTTAT-T
62 AATTTA-ACTTT-TGT
*
532728 TTATTTTTTATCCAAATGAATAAATTAAAATAAAGTGTTATCTAACTTCGAAATTTTAATACAAT
1 TTATTTTTTATCCAAATGAATAAATTAAAATAAAGT-TTATCTAACTTCGAAATTTTAATATAAT
532793 TTAACTTTTGT
65 TTAACTTTTGT
532804 TTATTT
1 TTATTT
532810 ATGATATAAT
Statistics
Matches: 108, Mismatches: 29, Indels: 34
0.63 0.17 0.20
Matches are distributed among these distances:
68 4 0.04
69 4 0.04
70 10 0.09
71 14 0.13
72 12 0.11
73 7 0.06
75 6 0.06
76 19 0.18
77 14 0.13
78 10 0.09
79 4 0.04
80 4 0.04
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (75 bp):
TTATTTTTTATCCAAATGAATAAATTAAAATAAAGTTTATCTAACTTCGAAATTTTAATATAATT
TAACTTTTGT
Found at i:533003 original size:14 final size:14
Alignment explanation
Indices: 532986--533030 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
532976 TTTTTTTTTT
532986 TGAACCTTGAGTGA
1 TGAACCTTGAGTGA
533000 TGAACC-T-A-TGA
1 TGAACCTTGAGTGA
533011 -GAACCTTGAGTGA
1 TGAACCTTGAGTGA
533024 TGAACCT
1 TGAACCT
533031 ATGACTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 2 0.07
13 4 0.15
14 12 0.44
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (14 bp):
TGAACCTTGAGTGA
Found at i:533019 original size:24 final size:24
Alignment explanation
Indices: 532987--533034 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
532977 TTTTTTTTTT
532987 GAACCTTGAGTGATGAACCTATGA
1 GAACCTTGAGTGATGAACCTATGA
533011 GAACCTTGAGTGATGAACCTATGA
1 GAACCTTGAGTGATGAACCTATGA
533035 CTGCCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (24 bp):
GAACCTTGAGTGATGAACCTATGA
Found at i:534154 original size:39 final size:39
Alignment explanation
Indices: 534093--534306 Score: 160
Period size: 39 Copynumber: 5.5 Consensus size: 39
534083 ATTGAAAATG
* * *
534093 CAGTGACACTGTAAGCAGTGCAATACTATATTGAACTGG
1 CAGTGACACTGTAAACACTGCAATACTATATTGAACTGA
** ** *
534132 CAGTGACACTACAAACACTGCAATGGTACATTGAACTGA
1 CAGTGACACTGTAAACACTGCAATACTATATTGAACTGA
* * * * * * *
534171 TAATGACATTGTAAACACTTCGATGCTATACTGAACTGA
1 CAGTGACACTGTAAACACTGCAATACTATATTGAACTGA
* *
534210 CAGTGACACTGTAAACACTGCAATA-TAGCATCGAACTGA
1 CAGTGACACTGTAAACACTGCAATACTA-TATTGAACTGA
* * * * * ** * * *
534249 CAATGACATTGTAAATACCGTAATGTTATACTGAGCTGG
1 CAGTGACACTGTAAACACTGCAATACTATATTGAACTGA
*
534288 TAGTGACACTGTAAACACT
1 CAGTGACACTGTAAACACT
534307 ACTAGGTCGA
Statistics
Matches: 130, Mismatches: 43, Indels: 4
0.73 0.24 0.02
Matches are distributed among these distances:
38 2 0.02
39 126 0.97
40 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (39 bp):
CAGTGACACTGTAAACACTGCAATACTATATTGAACTGA
Found at i:534279 original size:78 final size:77
Alignment explanation
Indices: 534118--534306 Score: 229
Period size: 78 Copynumber: 2.4 Consensus size: 77
534108 CAGTGCAATA
* ** * * *
534118 CTATATTGAACTGGCAGTGACACTACAAACACTGCAATGGTACATTGAACTGATAATGACATTGT
1 CTATACTGAACTGGCAGTGACACTGTAAACACTGCAATGATACATCGAACTGACAATGACATTGT
534183 AAACACTTCGATG
66 AAACAC-TCGATG
*
534196 CTATACTGAACTGACAGTGACACTGTAAACACTGCAAT-ATAGCATCGAACTGACAATGACATTG
1 CTATACTGAACTGGCAGTGACACTGTAAACACTGCAATGATA-CATCGAACTGACAATGACATTG
*
534260 TAAATAC-CGTAATG
65 TAAACACTCG--ATG
* * *
534274 TTATACTGAGCTGGTAGTGACACTGTAAACACT
1 CTATACTGAACTGGCAGTGACACTGTAAACACT
534307 ACTAGGTCGA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
76 2 0.02
77 2 0.02
78 92 0.96
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (77 bp):
CTATACTGAACTGGCAGTGACACTGTAAACACTGCAATGATACATCGAACTGACAATGACATTGT
AAACACTCGATG
Found at i:534839 original size:70 final size:67
Alignment explanation
Indices: 534713--534845 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
534703 ATAAACAATA
* * * * * *
534713 TAATGGTTTTGCCTTTTAACTTAATAAGTAAACATTTATTAAAATGACGTAATTTTGCTTTTTAA
1 TAATGGTTTCGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAATTTTGCCTTTTAA
534778 CT
66 CT
* *
534780 TAATGGTTTCGACTTTTAACTTTAGAAAAGGTGAACATTTATCAAAACGACGTAGTTTTGCCTTT
1 TAATGGTTTCGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACGACGTAATTTTGCCTTT
534845 T
63 T
534846 CTTATTCGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 18 0.33
68 3 0.05
69 3 0.05
70 31 0.56
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (67 bp):
TAATGGTTTCGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAATTTTGCCTTTTAA
CT
Found at i:538054 original size:52 final size:52
Alignment explanation
Indices: 537966--538146 Score: 281
Period size: 52 Copynumber: 3.5 Consensus size: 52
537956 TTCTCATTTA
* * * *
537966 ATACTCACGATGACACATTGTCATCGGACCTCATAATCTGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
* *
538018 ATACTCACGATGACACATAGTTATCAAACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
*
538070 ATACTCACGATGACACATAGTCATCAGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
**
538122 ATACTCATAATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
538147 GGATCTTTTG
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
Found at i:543716 original size:6 final size:6
Alignment explanation
Indices: 543705--543733 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
543695 ACACCTGAAT
543705 GGAAAA GGAAAA GGAAAA GGAAAA GGAAA
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAA
543734 TCATTGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:552854 original size:28 final size:29
Alignment explanation
Indices: 552800--552857 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
552790 GTTTTTTTTA
*
552800 ATTTAATATTAAATAAATAAATAATATTT
1 ATTTAATATTAAATAAATAAAAAATATTT
552829 ATTTAATATTAAA-AAATAAAAAATATTT
1 ATTTAATATTAAATAAATAAAAAATATTT
552857 A
1 A
552858 AATAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATTTAATATTAAATAAATAAAAAATATTT
Found at i:552863 original size:28 final size:29
Alignment explanation
Indices: 552803--552864 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
552793 TTTTTTAATT
* **
552803 TAATATTAAATAAATAAATAATATTTATT
1 TAATATTAAATAAATAAAAAATATTTAAA
552832 TAATATTAAA-AAATAAAAAATATTTAAA
1 TAATATTAAATAAATAAAAAATATTTAAA
552860 TAATA
1 TAATA
552865 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TAATATTAAATAAATAAAAAATATTTAAA
Found at i:552881 original size:17 final size:17
Alignment explanation
Indices: 552833--552878 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
552823 ATATTTATTT
552833 AATA-TTAAAAAATAAAA
1 AATATTTAAAAAAT-AAA
*
552850 AATATTTAAATAATAAA
1 AATATTTAAAAAATAAA
552867 AAT-TTTAAAAAA
1 AATATTTAAAAAA
552879 ATATTGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 8 0.31
17 10 0.38
18 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATTTAAAAAATAAA
Found at i:553005 original size:26 final size:27
Alignment explanation
Indices: 552953--553019 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
552943 TGACAGACGG
*
552953 CACCAAATGTGCCTACCTCACAGGCGA
1 CACCAAAGGTGCCTACCTCACAGGCGA
* * *
552980 CACTAGAGGTGCCTA-CTGACAGGCGA
1 CACCAAAGGTGCCTACCTCACAGGCGA
553006 CACCAAAGGTGCCT
1 CACCAAAGGTGCCT
553020 TCTTGGCAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 22 0.65
27 12 0.35
ACGTcount: A:0.28, C:0.33, G:0.24, T:0.15
Consensus pattern (27 bp):
CACCAAAGGTGCCTACCTCACAGGCGA
Found at i:553188 original size:9 final size:9
Alignment explanation
Indices: 553167--553198 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
553157 ATATCCATTC
553167 AAATTATAAA
1 AAATTA-AAA
553177 AAATTAAAA
1 AAATTAAAA
553186 AAATTAAAA
1 AAATTAAAA
553195 AAAT
1 AAAT
553199 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAATTAAAA
Found at i:557579 original size:28 final size:28
Alignment explanation
Indices: 557526--557590 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
557516 CATTTTTCAC
*
557526 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTGAAT
**
557554 TTGGAATTAATTCTGTTTA-AATTTGAAT
1 TTGGAATTAATTAAGTTTATAA-TTGAAT
557582 TT--AATTAAT
1 TTGGAATTAAT
557591 AATTTTTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.21
27 1 0.03
28 25 0.76
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTGAAT
Found at i:557668 original size:16 final size:14
Alignment explanation
Indices: 557641--557676 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
557631 AAGGTGATTA
557641 GTTTAAGATTTAAG
1 GTTTAAGATTTAAG
557655 GTCTTAAGGATTTAAG
1 GT-TTAA-GATTTAAG
557671 GTTTAA
1 GTTTAA
557677 AATGACGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 8 0.40
16 10 0.50
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (14 bp):
GTTTAAGATTTAAG
Found at i:557729 original size:52 final size:53
Alignment explanation
Indices: 557641--557757 Score: 125
Period size: 52 Copynumber: 2.3 Consensus size: 53
557631 AAGGTGATTA
*
557641 GTTTAA-GA-TTTAAGGTCTTAAGGATTTAAGGTTTAAAATGACGAGTTTAAC
1 GTTTAATGATTTTTAGGTCTTAAGGATTTAAGGTTTAAAATGACGAGTTTAAC
* * * * ** * *
557692 GTTTAATGATTTTTAGGTTTTAAGGGTTTGA-GTTTAAAGTGATTATTTTAAG
1 GTTTAATGATTTTTAGGTCTTAAGGATTTAAGGTTTAAAATGACGAGTTTAAC
557744 GTTT-ATGATTTTTA
1 GTTTAATGATTTTTA
557758 ATGGTTTAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 16 0.29
52 22 0.40
53 17 0.31
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (53 bp):
GTTTAATGATTTTTAGGTCTTAAGGATTTAAGGTTTAAAATGACGAGTTTAAC
Found at i:565726 original size:18 final size:18
Alignment explanation
Indices: 565703--565770 Score: 127
Period size: 18 Copynumber: 3.8 Consensus size: 18
565693 ATACATGATT
565703 ATGTATATGTGATGAAAA
1 ATGTATATGTGATGAAAA
565721 ATGTATATGTGATGAAAA
1 ATGTATATGTGATGAAAA
565739 ATGTATATGTGATGAAAA
1 ATGTATATGTGATGAAAA
*
565757 ATGTATATATGATG
1 ATGTATATGTGATG
565771 TATAAGTTGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
ATGTATATGTGATGAAAA
Found at i:565822 original size:12 final size:12
Alignment explanation
Indices: 565801--565839 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
565791 TGATCAAAAT
*
565801 TGAAAGTGAAAG
1 TGAAATTGAAAG
*
565813 TGAAATTGAAAT
1 TGAAATTGAAAG
*
565825 TGGAATTGAAAG
1 TGAAATTGAAAG
565837 TGA
1 TGA
565840 TATGAATTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (12 bp):
TGAAATTGAAAG
Found at i:565834 original size:18 final size:17
Alignment explanation
Indices: 565797--565858 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
565787 TTTGTGATCA
* *
565797 AAATTGAAAGTGAAAGTG
1 AAATTGAAA-TGGAATTG
565815 AAATTGAAATTGGAATTG
1 AAATTGAAA-TGGAATTG
* *
565833 AAAGTGATAT-GAATTG
1 AAATTGAAATGGAATTG
565849 TAAATTGAAA
1 -AAATTGAAA
565859 ATCCCTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 6 0.17
17 8 0.22
18 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (17 bp):
AAATTGAAATGGAATTG
Found at i:565989 original size:41 final size:40
Alignment explanation
Indices: 565941--566041 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
565931 TCGACCTCGA
** *
565941 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
565981 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
566019 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
566042 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:573555 original size:13 final size:13
Alignment explanation
Indices: 573537--573562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
573527 CGAATCTATA
573537 TTGAACTCGCATG
1 TTGAACTCGCATG
573550 TTGAACTCGCATG
1 TTGAACTCGCATG
573563 ATGCTAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TTGAACTCGCATG
Found at i:577279 original size:18 final size:19
Alignment explanation
Indices: 577244--577280 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
577234 TGTCAATTTG
577244 AAAAAAAAAAAATCAATAT
1 AAAAAAAAAAAATCAATAT
*
577263 AAAAACAAAAAAT-AATAT
1 AAAAAAAAAAAATCAATAT
577281 TATTTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAAAAAAATCAATAT
Found at i:580369 original size:22 final size:22
Alignment explanation
Indices: 580318--580396 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
580308 GCTGGGGAAA
* *
580318 CAGTAAGCACGCACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
580340 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
** * *
580363 CAGTAGGCGTACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
580386 CAGTAGGCACA
1 CAGTAGGCACA
580397 TGAGGTGCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.32
23 32 0.68
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:580412 original size:23 final size:23
Alignment explanation
Indices: 580386--580443 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
580376 TAGCGCAAAT
* * *
580386 CAGTAGGCACATGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
580409 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
580432 CAGCAAGCACAC
1 CAGTAAGCACAC
580444 ACAGTGTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.24, G:0.28, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:580563 original size:24 final size:26
Alignment explanation
Indices: 580525--580572 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
580515 TCTACATGGG
580525 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
580551 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
580573 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:590799 original size:3 final size:3
Alignment explanation
Indices: 590791--590831 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
590781 ACTAAATTTG
590791 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
590832 AACAAAACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:590813 original size:17 final size:17
Alignment explanation
Indices: 590791--590823 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
590781 ACTAAATTTG
590791 AATAATAATAATAATAT
1 AATAATAATAATAATAT
590808 AATAATAATAATAATA
1 AATAATAATAATAATA
590824 ATATATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:590816 original size:20 final size:20
Alignment explanation
Indices: 590791--590828 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
590781 ACTAAATTTG
590791 AATAATAATAATAATATAAT
1 AATAATAATAATAATATAAT
590811 AATAATAATAATAATATA
1 AATAATAATAATAATATA
590829 TAAAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAATAATAATAATATAAT
Found at i:590924 original size:9 final size:9
Alignment explanation
Indices: 590910--590944 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
590900 TTCACTCATC
*
590910 TTTTATTTG
1 TTTTATTTT
590919 TTTTATTTT
1 TTTTATTTT
590928 TTTTATTTT
1 TTTTATTTT
590937 TTTTATTT
1 TTTTATTT
590945 CTCCCTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTATTTT
Found at i:591364 original size:2 final size:2
Alignment explanation
Indices: 591357--591387 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
591347 ACTAATCAGC
*
591357 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
591388 AATGCGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:592564 original size:18 final size:18
Alignment explanation
Indices: 592523--592564 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
592513 AATTAAAATC
* *
592523 AATTTAATTATTTTTCTT
1 AATTAAATTATTGTTCTT
592541 AATTAAATTATTGTT-TT
1 AATTAAATTATTGTTCTT
592558 AACTTAA
1 AA-TTAA
592565 TTTTAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTAAATTATTGTTCTT
Found at i:597559 original size:22 final size:22
Alignment explanation
Indices: 597518--597559 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
597508 TTTTGTTTAA
* *
597518 ATTTATTTTGATTTAGAATCGG
1 ATTTATTTTAATTTACAATCGG
*
597540 ATTTATTTTAATTTTCAATC
1 ATTTATTTTAATTTACAATC
597560 CGATAATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.55
Consensus pattern (22 bp):
ATTTATTTTAATTTACAATCGG
Found at i:600919 original size:7 final size:7
Alignment explanation
Indices: 600907--600940 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
600897 TGGACCTCTT
600907 AAAAATA
1 AAAAATA
600914 AAAAATA
1 AAAAATA
600921 AAAAATA
1 AAAAATA
600928 AAAAATA
1 AAAAATA
600935 AAAAAT
1 AAAAAT
600941 TAGACCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:607139 original size:29 final size:29
Alignment explanation
Indices: 607106--607194 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 29
607096 TTGATTTAAC
607106 GTGCAATTGTATACATGAACTCTAATTTG
1 GTGCAATTGTATACATGAACTCTAATTTG
* * * *
607135 GTGCAATTATACACGTAAAACTCTAATTGTG
1 GTGCAATTGTATACAT-GAACTCTAATT-TG
* * * *
607166 GTTCAAATGTATACTTGAAACTTTAATTT
1 GTGCAATTGTATACATG-AACTCTAATTT
607195 TGATTTAATC
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
29 13 0.28
30 11 0.24
31 22 0.48
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (29 bp):
GTGCAATTGTATACATGAACTCTAATTTG
Found at i:607368 original size:29 final size:29
Alignment explanation
Indices: 607337--607393 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
607327 GAATTGGATC
607337 AAATCAAAATATCATGTATAAAATTGCACA
1 AAATCAAAAT-TCATGTATAAAATTGCACA
* *
607367 AAATCAAAGTTCATGTATATAATTGCA
1 AAATCAAAATTCATGTATAAAATTGCA
607394 TATTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (29 bp):
AAATCAAAATTCATGTATAAAATTGCACA
Found at i:618215 original size:59 final size:59
Alignment explanation
Indices: 618123--618234 Score: 197
Period size: 59 Copynumber: 1.9 Consensus size: 59
618113 ATAGTTTTTT
* *
618123 TTTTTTTTTTAAATAAGAGAAAGGTGTAGGAATTATCCGGACATTAAATCCGAACATAG
1 TTTTTTTTTTAAATAAGAGAAAGGAGTAGGAATTATCCAGACATTAAATCCGAACATAG
*
618182 TTTTTTTTTTAAGTAAGAGAAAGGAGTAGGAATTATCCAGACATTAAATCCGA
1 TTTTTTTTTTAAATAAGAGAAAGGAGTAGGAATTATCCAGACATTAAATCCGA
618235 GACTTCTTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.34
Consensus pattern (59 bp):
TTTTTTTTTTAAATAAGAGAAAGGAGTAGGAATTATCCAGACATTAAATCCGAACATAG
Found at i:618873 original size:6 final size:6
Alignment explanation
Indices: 618862--618914 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
618852 TCAAATTTGT
* * **
618862 TTTAAA TTTAAA TTTAAA TTT-AA TTTGAG TTTAAA TTTATT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
618909 TTTAAA
1 TTTAAA
618915 ATTATTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:618878 original size:29 final size:28
Alignment explanation
Indices: 618830--618909 Score: 65
Period size: 29 Copynumber: 2.8 Consensus size: 28
618820 GGACTAAACC
618830 TGTTTTAAAATTT-ATCTTAAGATCAAATT
1 TGTTTT-AAATTTAATCTTAA-ATCAAATT
**
618859 TGTTTTAAATTTAAAT-TTAAATTTAATT
1 TGTTTTAAATTT-AATCTTAAATCAAATT
* * *
618887 TGAGTTTAAATTTATTTTTAAAT
1 TG-TTTTAAATTTAATCTTAAAT
618910 TTAAAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 16 0.37
29 25 0.58
30 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (28 bp):
TGTTTTAAATTTAATCTTAAATCAAATT
Found at i:618880 original size:23 final size:23
Alignment explanation
Indices: 618862--618914 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
618852 TCAAATTTGT
618862 TTTAAATTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAAATTTAA
* * **
618885 TTTGAGTTTAAATTTATTTTTAAA
1 TTTAAATTTAAATTTAAATTT-AA
618909 TTTAAA
1 TTTAAA
618915 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATTTAAATTTAA
Found at i:618886 original size:17 final size:17
Alignment explanation
Indices: 618866--618926 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
618856 ATTTGTTTTA
618866 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
* *
618883 AATTTGAGTTTAAATTT
1 AATTTAAATTTAAATTT
* *
618900 ATTTTTAAATTTAAAATT
1 A-ATTTAAATTTAAATTT
*
618918 ATTTTAAAT
1 AATTTAAAT
618927 AAAGTCCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
17 24 0.65
18 13 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Done.