Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:277926 original size:25 final size:25
Alignment explanation
Indices: 277888--277944 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
277878 TAAATTACAT
277888 ATAGTTTT-AAAAAATAGTTTTGAAA
1 ATAGTTTTAAAAAAATAGTTTT-AAA
*
277913 ATAGTTTTAGAAAAATAGTTTTAAA
1 ATAGTTTTAAAAAAATAGTTTTAAA
*
277938 AAAGTTT
1 ATAGTTT
277945 ATATATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (25 bp):
ATAGTTTTAAAAAAATAGTTTTAAA
Found at i:277927 original size:14 final size:13
Alignment explanation
Indices: 277888--277940 Score: 81
Period size: 13 Copynumber: 4.1 Consensus size: 13
277878 TAAATTACAT
277888 ATAGTTTTAAAAA
1 ATAGTTTTAAAAA
*
277901 ATAGTTTT-GAAA
1 ATAGTTTTAAAAA
277913 ATAGTTTTAGAAAA
1 ATAGTTTTA-AAAA
277927 ATAGTTTTAAAAA
1 ATAGTTTTAAAAA
277940 A
1 A
277941 GTTTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.31
13 13 0.36
14 12 0.33
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (13 bp):
ATAGTTTTAAAAA
Found at i:278252 original size:57 final size:57
Alignment explanation
Indices: 278160--278274 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
278150 TCAATTAACA
* * * *
278160 AGTCCAAGTGGGATTTAAAAGGTCTAGCAATATACCCCAAGGCATAAGCCCAAGAGT
1 AGTCCAAGTGGGATTTAAAAGGTCCAGCAACATACCCCAACGCATAAGCCAAAGAGT
278217 AGTCCAAGTGGGATTTAAAAGGTCCAGCAACATACCCCAACGCATAAGCCAAAGAGT
1 AGTCCAAGTGGGATTTAAAAGGTCCAGCAACATACCCCAACGCATAAGCCAAAGAGT
278274 A
1 A
278275 CAAACCCGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (57 bp):
AGTCCAAGTGGGATTTAAAAGGTCCAGCAACATACCCCAACGCATAAGCCAAAGAGT
Found at i:282434 original size:19 final size:20
Alignment explanation
Indices: 282378--282434 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
282368 TGTGATATTG
282378 ATACTAAGCCTCTTAGTATCA
1 ATACTAA-CCTCTTAGTATCA
* *
282399 ATATTAACCTTTTAGTATCA
1 ATACTAACCTCTTAGTATCA
*
282419 ATACTCACC-CTTAGTA
1 ATACTAACCTCTTAGTA
282435 CTGATACTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 6 0.19
20 19 0.61
21 6 0.19
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (20 bp):
ATACTAACCTCTTAGTATCA
Found at i:296593 original size:18 final size:17
Alignment explanation
Indices: 296570--296603 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
296560 AAATAACATG
*
296570 ATTATTATAATATTTTAA
1 ATTATTAAAAT-TTTTAA
296588 ATTATTAAAATTTTTA
1 ATTATTAAAATTTTTA
296604 TTTCACACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTAAAATTTTTAA
Found at i:298260 original size:55 final size:56
Alignment explanation
Indices: 298022--298353 Score: 508
Period size: 56 Copynumber: 6.0 Consensus size: 56
298012 TCCACTACCA
* * *
298022 ATACGGAAATTCACAATCTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
* *
298078 ATTCGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
** * *
298134 ATACAAAAATTCATAAACTTATTATGAATTTCATAGTTTTTCCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
** *
298190 ATACATAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGAGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
298245 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
* * *
298300 ATATGGGAATTCATAAACTTATTATGAATTTCTTAG-TTGTGCACACACAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCC
298354 TTTTTAGTAA
Statistics
Matches: 257, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
55 120 0.47
56 137 0.53
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (56 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
Found at i:298687 original size:23 final size:20
Alignment explanation
Indices: 298671--298708 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
298661 TTCTGGCTCA
298671 ATAGTATCGATACTTCTACC
1 ATAGTATCGATACTTCTACC
*
298691 ATGGTATCGATACTTCTA
1 ATAGTATCGATACTTCTA
298709 TACTATGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAGTATCGATACTTCTACC
Found at i:298699 original size:20 final size:21
Alignment explanation
Indices: 298674--298725 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
298664 TGGCTCAATA
298674 GTATCGATACTTC-TACCATG
1 GTATCGATACTTCATACCATG
*
298694 GTATCGATACTTCTATACTATG
1 GTATCGATACTTC-ATACCATG
298716 GTATCGATAC
1 GTATCGATAC
298726 CATTTTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (21 bp):
GTATCGATACTTCATACCATG
Found at i:315867 original size:20 final size:20
Alignment explanation
Indices: 315844--315890 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
315834 ATTCCACCAC
*
315844 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTCCTAA
* * *
315864 ATGCATCTACATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
315884 ATG-AACT
1 ATGCAACT
315891 CTTAGACATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:316176 original size:56 final size:56
Alignment explanation
Indices: 316116--316445 Score: 497
Period size: 56 Copynumber: 5.9 Consensus size: 56
316106 CCCGTTACCA
* * * ** *
316116 ATACGGAAATTTACAATCTTATCCTGAATTTCTTAGTTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
* * * *
316172 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTGTTGCACTCAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
* * *
316228 ATACAGAAATTCATAAAATTATTATGAATTTCTTAGTTTTTGCACACACAGTGCTC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
316284 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
316339 ATACGGAAATTCATAAACTTATTAT-AGATTTCTTAG-TTTTGCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGA-ATTTCTTAGTTTTTGCACACACAGTGCCC
*
316394 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTT-CACGCACAGTG
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTG
316446 TCTTTTTGGT
Statistics
Matches: 252, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
54 1 0.00
55 115 0.46
56 136 0.54
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (56 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCC
Found at i:316796 original size:20 final size:20
Alignment explanation
Indices: 316767--316821 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
316757 TGGCTCAATA
316767 GTATCGATACTCCTACCATG
1 GTATCGATACTCCTACCATG
* * *
316787 GTATCAATACTTCTATACTATG
1 GTATCGATAC-TC-CTACCATG
316809 GTATCGATACTCC
1 GTATCGATACTCC
316822 CTTTCAGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 9 0.32
21 4 0.14
22 15 0.54
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (20 bp):
GTATCGATACTCCTACCATG
Found at i:316912 original size:42 final size:42
Alignment explanation
Indices: 316848--316931 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
316838 CATTTCTACA
316848 TTCTATACCCATGGTATTGATACTCTTCTCCTAGTATCGATAC
1 TTCTATACCCATGGTATTGATACTC-TCTCCTAGTATCGATAC
* **
316891 TTCTATA-CTATGGT-TTCGATACTCTCTTTTAGTATCGATAC
1 TTCTATACCCATGGTATT-GATACTCTCTCCTAGTATCGATAC
316932 CCTTTTGGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 17 0.46
42 13 0.35
43 7 0.19
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (42 bp):
TTCTATACCCATGGTATTGATACTCTCTCCTAGTATCGATAC
Found at i:324138 original size:2 final size:2
Alignment explanation
Indices: 324131--324175 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
324121 TCAATCTACA
324131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324173 AT A
1 AT A
324176 ATTTATGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:324303 original size:13 final size:13
Alignment explanation
Indices: 324255--324311 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
324245 GCAATGAGGA
* *
324255 TCATAAATGAGCG
1 TCATAAATGCGTG
* *
324268 TCATAAATGTGTT
1 TCATAAATGCGTG
324281 TCATAAATGCGTG
1 TCATAAATGCGTG
*
324294 TCATAAATGCGAG
1 TCATAAATGCGTG
324307 TCATA
1 TCATA
324312 TATTTTATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:350033 original size:23 final size:23
Alignment explanation
Indices: 350003--350053 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
349993 TCATTGATCA
*
350003 CTGGCTTGGTCTAATGGCCTCTC
1 CTGGCTTGGTCTAATGGCCTATC
350026 CTGGCTTGGTCTAATGGCCTATC
1 CTGGCTTGGTCTAATGGCCTATC
350049 CTGGC
1 CTGGC
350054 ATCATGAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.10, C:0.29, G:0.27, T:0.33
Consensus pattern (23 bp):
CTGGCTTGGTCTAATGGCCTATC
Found at i:353076 original size:19 final size:21
Alignment explanation
Indices: 353044--353088 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
353034 AATCGGTATT
353044 GATACTGAAAGGGAA-CTATC
1 GATACTGAAAGGGAAGCTATC
*
353064 GATACTG-AAGGGAAGGTATC
1 GATACTGAAAGGGAAGCTATC
353084 GATAC
1 GATAC
353089 CATTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (21 bp):
GATACTGAAAGGGAAGCTATC
Found at i:353138 original size:19 final size:19
Alignment explanation
Indices: 353114--353154 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
353104 TACAAAAATG
353114 GTATCGATACCATAGCATA
1 GTATCGATACCATAGCATA
* *
353133 GTATCGGTACCATAGTATA
1 GTATCGATACCATAGCATA
353152 GTA
1 GTA
353155 GTATCGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATACCATAGCATA
Found at i:354830 original size:20 final size:20
Alignment explanation
Indices: 354789--354833 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
354779 ACCTAAGGGA
354789 GTGAATATCGATACTCTCAG
1 GTGAATATCGATACTCTCAG
* *
354809 GTGAGTATCGATCCTC-CTAG
1 GTGAATATCGATACTCTC-AG
354829 GTGAA
1 GTGAA
354834 ACCTTAGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGAATATCGATACTCTCAG
Found at i:358599 original size:37 final size:36
Alignment explanation
Indices: 358483--358599 Score: 87
Period size: 37 Copynumber: 3.1 Consensus size: 36
358473 AGTGAAACTG
*
358483 TCTCAAGCGAGACAAATCTTTGCTTTGAGAATAATTA
1 TCTCAAGCGAGACAAATCTTTTCTTTGAGAAT-ATTA
* * * * *
358520 TCTCGAGTGAGA-TAAT-TTTTCTATTTCAAGTGAA-ACCTA
1 TCTCAAGCGAGACAAATCTTTTC--TTT---GAGAATA-TTA
358559 TCTCAAGCGAGACAAATCTTTTCTTTGAGAATTATTA
1 TCTCAAGCGAGACAAATCTTTTCTTTGAGAA-TATTA
358596 TCTC
1 TCTC
358600 GAGTGAGATA
Statistics
Matches: 59, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
35 4 0.07
36 7 0.12
37 19 0.32
38 2 0.03
39 15 0.25
40 7 0.12
41 5 0.08
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATCTTTTCTTTGAGAATATTA
Found at i:358709 original size:77 final size:76
Alignment explanation
Indices: 358444--358732 Score: 436
Period size: 76 Copynumber: 3.8 Consensus size: 76
358434 ACTTACTTCA
** * * * *
358444 ATCTCGAGTGAGATAAAATTTATGTTTCAAGTGAAA-CTGTCTCAAGCGAGACAAATCTTTGCTT
1 ATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAAATCTTTTCTT
358508 TGAGAATAATT
66 TGAGAATAATT
358519 ATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAAATCTTTTCTT
1 ATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAAATCTTTTCTT
*
358584 TGAGAATTATT
66 TGAGAATAATT
* * * *
358595 ATCTCGAGTGAGATAATTTTTCTGTTTCAAGTGAAACCTGTCTTAAGCGAAACAAATCTTTTCTT
1 ATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAAATCTTTTCTT
*
358660 TGAGAAAAAATT
66 TGAG-AATAATT
* *
358672 ATCTCGAGTAAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGTGAGACAAATCTTT
1 ATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAAATCTTT
358733 CTTCGAAAAT
Statistics
Matches: 193, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
75 32 0.17
76 101 0.52
77 60 0.31
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (76 bp):
ATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAAATCTTTTCTT
TGAGAATAATT
Found at i:358724 original size:153 final size:151
Alignment explanation
Indices: 358444--358732 Score: 479
Period size: 153 Copynumber: 1.9 Consensus size: 151
358434 ACTTACTTCA
*
358444 ATCTCGAGTGAGATAAAATTTATGTTTCAAGTGAAACTGTCTCAAGCGAGACAAATCTTTGCTTT
1 ATCTCGAGTGAGATAAAATTTATGTTTCAAGTGAAACTGTCTCAAGCGAAACAAATCTTTGCTTT
* *
358509 GAGAATAATTATCTCGAGTGAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAA
66 GAGAAAAATTATCTCGAGTAAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAA
358574 ATCTTTTCTTTGAGAATTATT
131 ATCTTTTCTTTGAGAATTATT
** * * *
358595 ATCTCGAGTGAGATAATTTTTCTGTTTCAAGTGAAACCTGTCTTAAGCGAAACAAATCTTTTCTT
1 ATCTCGAGTGAGATAAAATTTATGTTTCAAGTGAAA-CTGTCTCAAGCGAAACAAATCTTTGCTT
*
358660 TGAGAAAAAATTATCTCGAGTAAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGTGAGAC
65 TGAG-AAAAATTATCTCGAGTAAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGAC
358725 AAATCTTT
129 AAATCTTT
358733 CTTCGAAAAT
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 33 0.26
152 29 0.23
153 65 0.51
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (151 bp):
ATCTCGAGTGAGATAAAATTTATGTTTCAAGTGAAACTGTCTCAAGCGAAACAAATCTTTGCTTT
GAGAAAAATTATCTCGAGTAAGATAATTTTTCTATTTCAAGTGAAACCTATCTCAAGCGAGACAA
ATCTTTTCTTTGAGAATTATT
Found at i:359005 original size:6 final size:6
Alignment explanation
Indices: 358988--359017 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
358978 TGCAAAATCA
*
358988 TGTATG TATATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG
359018 CTGATGCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (6 bp):
TGTATG
Found at i:364711 original size:17 final size:15
Alignment explanation
Indices: 364672--364709 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
364662 GGCCTTAATT
364672 CTTCTCATTTTTTTTC
1 CTTCTC-TTTTTTTTC
364688 CTTCTCTTTTTTTTC
1 CTTCTCTTTTTTTTC
364703 CTTCTCT
1 CTTCTCT
364710 CTCTTGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTCTCTTTTTTTTC
Found at i:366868 original size:18 final size:18
Alignment explanation
Indices: 366848--366888 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
366838 AAAAAACCCT
*
366848 AAAATTTTGAAGAACTTTA
1 AAAATTTTCAA-AACTTTA
*
366867 AAAATTTTCAAAACTTTG
1 AAAATTTTCAAAACTTTA
366885 AAAA
1 AAAA
366889 CTCCAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (18 bp):
AAAATTTTCAAAACTTTA
Found at i:368918 original size:31 final size:31
Alignment explanation
Indices: 368882--368940 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
368872 AACTTAAAAG
*
368882 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
368913 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
368941 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:368994 original size:22 final size:22
Alignment explanation
Indices: 368964--369195 Score: 419
Period size: 22 Copynumber: 10.5 Consensus size: 22
368954 ATAATAATTT
* *
368964 TTTTTAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
368986 TTTTAAAATAAATCAATCCATG
1 TTTTAAAATAAATCAATCCATA
369008 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
369030 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
369052 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
369074 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
369096 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
369118 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
369140 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
369162 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
369184 TTTTAAAATAAA
1 TTTTAAAATAAA
369196 ATTTTAAAAT
Statistics
Matches: 202, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 202 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:376291 original size:12 final size:12
Alignment explanation
Indices: 376274--376303 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
376264 TCAGAACTGG
376274 TTAAACTGGTTC
1 TTAAACTGGTTC
376286 TTAAACTGGTTC
1 TTAAACTGGTTC
376298 TTAAAC
1 TTAAAC
376304 AATCTATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (12 bp):
TTAAACTGGTTC
Found at i:378673 original size:21 final size:21
Alignment explanation
Indices: 378647--378701 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
378637 ATTTACCGTG
* *
378647 ATTGCGGCCGTTGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
**
378668 ATTGCGGTTGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
378689 ATTGCGGCCGTCG
1 ATTGCGGCCGTCG
378702 TGGTTAACTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.07, C:0.27, G:0.40, T:0.25
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:379354 original size:13 final size:14
Alignment explanation
Indices: 379327--379358 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
379317 TAATTTATAT
379327 TATATAAAAATTAA
1 TATATAAAAATTAA
379341 TATATAAAAA-TAA
1 TATATAAAAATTAA
379354 TATAT
1 TATAT
379359 TTTTTAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATATAAAAATTAA
Found at i:381300 original size:28 final size:27
Alignment explanation
Indices: 381266--381318 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
381256 ATTTGAATTT
* *
381266 TTTTAAACAAACAATTTTAAAGTTTTTA
1 TTTTAAACAAA-AATTTCAAAATTTTTA
*
381294 TTTTAAATAAAAATTTCAAAATTTT
1 TTTTAAACAAAAATTTCAAAATTTT
381319 ATGAATGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTTAAACAAAAATTTCAAAATTTTTA
Found at i:395575 original size:3 final size:3
Alignment explanation
Indices: 395569--395596 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
395559 TTCCTTTTAT
395569 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
395597 CACTCCTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:399542 original size:32 final size:32
Alignment explanation
Indices: 399506--399574 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
399496 TGTTATGATA
399506 TGCTTAAGCTTCCCGACAGGATTACTGAGTAT
1 TGCTTAAGCTTCCCGACAGGATTACTGAGTAT
*
399538 TGCTTAAGCTTCCCGATAGGATTACTGAGTAT
1 TGCTTAAGCTTCCCGACAGGATTACTGAGTAT
399570 T-CTTA
1 TGCTTA
399575 GATGGTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (32 bp):
TGCTTAAGCTTCCCGACAGGATTACTGAGTAT
Found at i:400765 original size:10 final size:10
Alignment explanation
Indices: 400750--400783 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
400740 CAATTATAAC
*
400750 CTAAATGCAG
1 CTAAATGCAA
400760 CTAAATGCAA
1 CTAAATGCAA
400770 CTAAATGCAA
1 CTAAATGCAA
400780 CTAA
1 CTAA
400784 TATGATGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:405550 original size:21 final size:20
Alignment explanation
Indices: 405487--405553 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
405477 CAATGAGTTT
*
405487 GGGATCGATCATTTGAGAAA
1 GGGATCGATCTTTTGAGAAA
* * *
405507 GGGATCAATCTCTTGCCTG-AA
1 GGGATCGATCTTTTG--AGAAA
405528 GGGATCGATCCTTTTGAGAAA
1 GGGATCGAT-CTTTTGAGAAA
405549 GGGAT
1 GGGAT
405554 TAATACTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
20 13 0.36
21 17 0.47
22 6 0.17
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (20 bp):
GGGATCGATCTTTTGAGAAA
Found at i:411910 original size:51 final size:51
Alignment explanation
Indices: 411769--411913 Score: 163
Period size: 48 Copynumber: 2.9 Consensus size: 51
411759 TAGAAAGAAA
* * * *
411769 TGAGGTAAAAGGGTTAATGGTGAGTTCAATAAAGACAAAAATGCCTAAAGT
1 TGAGGTAAAAGGGGTAATGGTGAGTTCAATAAAGGCGATAATGCCTAAAGT
* * * * * *
411820 TGAGGCAAACA-GGG---TGGTGACTCCAGTAAACGCGATAATGCCTAAGGT
1 TGAGGTAAA-AGGGGTAATGGTGAGTTCAATAAAGGCGATAATGCCTAAAGT
411868 TGAGGTAAAAGGGGTAATGGTGAGTTCAATAAAGGCGATAATGCCT
1 TGAGGTAAAAGGGGTAATGGTGAGTTCAATAAAGGCGATAATGCCT
411914 TAGTGAGGAT
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
47 1 0.01
48 37 0.50
51 35 0.47
52 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.22
Consensus pattern (51 bp):
TGAGGTAAAAGGGGTAATGGTGAGTTCAATAAAGGCGATAATGCCTAAAGT
Found at i:413177 original size:44 final size:44
Alignment explanation
Indices: 413111--413416 Score: 263
Period size: 44 Copynumber: 7.0 Consensus size: 44
413101 TAGAATTACA
* * * * * *
413111 TTCGCTCGATTTCATCGCATAAGGCGATAGATCAAAATCATCAT
1 TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
* *
413155 TTCGCTTGATTCCATCTCATAAGGAGTTGGATCAACATCATCAT
1 TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
* * *
413199 TCCGCTAGATTCCATCACATAAGGAGTTGGATCAACATCACCAT
1 TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
** * * * *
413243 TTCGCTCGATTCTGTCGCATAAGGAGTTGAATTAACATCATTAT
1 TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
** * * * * *
413287 TTCGCTCGATTCTGTCGCATAATGAGTTGAATTAACATCATTAT
1 TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
** ** ** * *
413331 TTCGCTTAATTATATCGTATAAGGAGTTGGATGAGCATCA-CAT
1 TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
* * * * *
413374 TTACGATCGAATCTATCACATAAGGACTTGGATCAGCATCATC
1 TT-CGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATC
413417 TTGCTCGAGA
Statistics
Matches: 220, Mismatches: 40, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
43 4 0.02
44 215 0.98
45 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
TTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCATCAT
Found at i:413519 original size:35 final size:36
Alignment explanation
Indices: 413468--413537 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
413458 ATTTTAATCA
* *
413468 AGATTTTATCTTACTTGGGATT-TTTTTCTTAAAAT
1 AGATTTTATCTCACTTGAGATTGTTTTTCTTAAAAT
413503 AGATTTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 AGATTTTATCTCACTTGAGATTGTTTTTCTTAAAA
413538 CAAATATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.51
Consensus pattern (36 bp):
AGATTTTATCTCACTTGAGATTGTTTTTCTTAAAAT
Found at i:415156 original size:229 final size:227
Alignment explanation
Indices: 414751--415199 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 227
414741 GTAAATTATC
* * *
414751 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
414816 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
414881 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAA-TT
414945 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
414979 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
415044 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
*
415108 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
415173 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
415200 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
228 44 0.21
229 164 0.78
230 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:415287 original size:20 final size:19
Alignment explanation
Indices: 415264--415309 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
415254 CGATATACCA
415264 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
415284 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
415304 GGTAAA
1 GGTAAA
415310 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:417814 original size:33 final size:33
Alignment explanation
Indices: 417772--417837 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
417762 AAATAGATGG
*
417772 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
417805 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
417838 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:419672 original size:19 final size:19
Alignment explanation
Indices: 419628--419671 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
419618 AATGTCGAGT
419628 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
419647 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
419666 T-ATTTT
1 TAATTTT
419672 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:420106 original size:200 final size:200
Alignment explanation
Indices: 419754--421175 Score: 2669
Period size: 200 Copynumber: 7.1 Consensus size: 200
419744 TTAAGGGTCA
*
419754 TGTCGATACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
419818 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
419883 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
419948 TAATG
196 TAATG
419953 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420018 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
420083 GTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420148 TAATG
196 TAATG
420153 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420218 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
420282 GTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420347 TAATG
196 TAATG
420352 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420417 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
420482 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420547 TAATG
196 TAATG
*
420552 TGTCGACACTAATATATTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420617 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
420682 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420747 TAATG
196 TAATG
*
420752 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
420817 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
420881 GTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420945 TAATG
196 TAATG
*
420950 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCA-C
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
421014 CATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
421077 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
421142 TAATG
196 TAATG
*
421147 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
421176 CAAATTTAAA
Statistics
Matches: 1202, Mismatches: 18, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
196 82 0.07
197 76 0.06
198 89 0.07
199 309 0.26
200 646 0.54
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (200 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATG
Found at i:420505 original size:399 final size:400
Alignment explanation
Indices: 419754--421175 Score: 2678
Period size: 399 Copynumber: 3.6 Consensus size: 400
419744 TTAAGGGTCA
*
419754 TGTCGATACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
419818 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
419883 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
419948 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
420013 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
261 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
420078 ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
326 ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
420143 CTAAATAATG
391 CTAAATAATG
420153 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420218 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
420282 GTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420347 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
420412 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
261 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
* * *
420477 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
326 ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
420542 CTAAATAATG
391 CTAAATAATG
*
420552 TGTCGACACTAATATATTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420617 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
420682 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
420747 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
* *
420812 GCATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
261 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
420876 ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGT
326 ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
420940 CTAAATAATG
391 CTAAATAATG
*
420950 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCA-C
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
421014 CATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
421077 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
*
421142 TAATGTGTCGACACTAATATATTTTGTGTCGATA
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
421176 CAAATTTAAA
Statistics
Matches: 1002, Mismatches: 19, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
395 137 0.14
397 23 0.02
398 87 0.09
399 503 0.50
400 252 0.25
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (400 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
CTAAATAATG
Found at i:420920 original size:599 final size:598
Alignment explanation
Indices: 419754--421175 Score: 2726
Period size: 599 Copynumber: 2.4 Consensus size: 598
419744 TTAAGGGTCA
*
419754 TGTCGATACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
419818 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
419883 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
*
419948 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATATTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
420013 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
261 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
420078 ATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
326 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
420143 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAAC
391 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAAC
*
420208 AAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
456 AAGGTGCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
420273 AAGTATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
521 AAGTATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAAT
420338 AAGTCTAAATAATG
585 AAGTCTAAATAATG
420352 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
420417 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
420482 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
420547 TAATGTGTCGACACTAATATATTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATATTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
420612 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
261 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
420677 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
326 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
420742 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAAC
391 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAAC
*
420807 AAGGTGCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
456 AAGGTGCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
420872 AAGTATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATA
521 AAGTATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATA
420937 AGTCTAAATAATG
586 AGTCTAAATAATG
*
420950 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCA-C
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
421014 CATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
421077 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
421142 TAATGTGTCGACACTAATATATTTTGTGTCGATA
196 TAATGTGTCGACACTAATATATTTTGTGTCGATA
421176 CAAATTTAAA
Statistics
Matches: 814, Mismatches: 9, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
595 139 0.17
597 23 0.03
598 117 0.14
599 535 0.66
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (598 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
TAATGTGTCGACACTAATATATTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGT
GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAAC
AAGGTGCACCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
AAGTATAATGTAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATA
AGTCTAAATAATG
Found at i:422654 original size:18 final size:18
Alignment explanation
Indices: 422631--422698 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
422621 ATCGGTCGCA
422631 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
422649 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
422670 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
422691 GAAGATGA
1 GAAGATGA
422699 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:422655 original size:6 final size:6
Alignment explanation
Indices: 422631--422728 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
422621 ATCGGTCGCA
* * * * * *
422631 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
422679 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
422727 GA
1 GA
422729 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:422666 original size:3 final size:3
Alignment explanation
Indices: 422646--422732 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
422636 TGAAGCTGAC
* * * * * ** *
422646 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
422694 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
422733 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:422681 original size:42 final size:42
Alignment explanation
Indices: 422634--422724 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
422624 GGTCGCAGAA
*
422634 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
422676 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
422718 GATGAAG
1 GATGAAG
422725 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:422732 original size:18 final size:18
Alignment explanation
Indices: 422631--422728 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
422621 ATCGGTCGCA
* *
422631 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
422649 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
422667 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
422685 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
422703 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
422721 GAAGATGA
1 GAAGATGA
422729 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:424467 original size:183 final size:183
Alignment explanation
Indices: 424159--424867 Score: 1274
Period size: 183 Copynumber: 3.9 Consensus size: 183
424149 CTTTCAACAT
** * * *
424159 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
424224 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
424289 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* **
424342 ATTATAATGTAATAGATAATTTTGTAATATAACCAGTATAAATATACCAATTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
424407 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
424472 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
424525 ATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATACGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
424590 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
424655 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
424708 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
424773 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
424838 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
424868 GTAATTTTAA
Statistics
Matches: 504, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 504 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:426902 original size:25 final size:25
Alignment explanation
Indices: 426868--426932 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
426858 TTATCATTAA
426868 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
426893 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
426918 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
426933 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:427306 original size:23 final size:23
Alignment explanation
Indices: 427275--427338 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
427265 ATAGGTAAAC
*
427275 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
427298 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
427321 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
427339 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:427345 original size:23 final size:23
Alignment explanation
Indices: 427275--427347 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
427265 ATAGGTAAAC
* **
427275 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
427298 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
427321 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
427344 ATAT
1 ATAT
427348 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:427650 original size:25 final size:25
Alignment explanation
Indices: 427616--427666 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
427606 ACAACAAATC
*
427616 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
427641 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
427666 A
1 A
427667 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:428076 original size:18 final size:18
Alignment explanation
Indices: 428055--428091 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
428045 GTAATTGGAG
428055 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
428073 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
428091 T
1 T
428092 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:428391 original size:39 final size:39
Alignment explanation
Indices: 428348--428434 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
428338 TCCGATGCTC
* *
428348 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATACCAAGCAAAAGGAA
*
428387 ATCAAAATCCAAATCTCATATGATACCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATACCAAGCAAAAGGAA
428426 ATCAAAATC
1 ATCAAAATC
428435 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATACCAAGCAAAAGGAA
Found at i:428852 original size:20 final size:22
Alignment explanation
Indices: 428827--428902 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
428817 ACTTTCAATA
428827 TAATAGGTA-AAC-ATATAATG
1 TAATAGGTAGAACTATATAATG
**
428847 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGAAC-TATATAATG
**
428870 TAATAGGTATCG-TTTATATAATG
1 TAATAGGTA--GAACTATATAATG
428893 TAATAGGTAG
1 TAATAGGTAG
428903 TGTTTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.19
21 2 0.04
23 35 0.74
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (22 bp):
TAATAGGTAGAACTATATAATG
Found at i:428869 original size:23 final size:23
Alignment explanation
Indices: 428839--428911 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
428829 ATAGGTAAAC
*
428839 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGTTT
*
428862 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
428885 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
428908 ATAT
1 ATAT
428912 TATAAAGTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:428936 original size:20 final size:21
Alignment explanation
Indices: 428911--428953 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
428901 AGTGTTTATA
* *
428911 TTAT-AAAGTGTCTATCCTTT
1 TTATAAAAGTGTCCATACTTT
428931 TTATAAAAGTGTCCATACTTT
1 TTATAAAAGTGTCCATACTTT
428952 TT
1 TT
428954 TCACTGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (21 bp):
TTATAAAAGTGTCCATACTTT
Found at i:431904 original size:20 final size:20
Alignment explanation
Indices: 431864--431909 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
431854 CGGTTCACCT
* **
431864 CGGTTTTACCGGTTTTTAGC
1 CGGTTCTACCGGTTTGCAGC
431884 CGGTTCTACCGGTTTGCAGC
1 CGGTTCTACCGGTTTGCAGC
*
431904 CAGTTC
1 CGGTTC
431910 ATTGCCAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.37
Consensus pattern (20 bp):
CGGTTCTACCGGTTTGCAGC
Found at i:434463 original size:288 final size:289
Alignment explanation
Indices: 433946--434539 Score: 1142
Period size: 288 Copynumber: 2.1 Consensus size: 289
433936 TTGTTTCATC
*
433946 TTGTTGGATACTTTCTTCTTTGATTGAGGGCAATCCAAGTTTATATGCTCTCATTTTTTTTGCAC
1 TTGTTGGATACTTTCTTCTTTGATTGAGGGCAATCCAAGTTTATACGCTCTCATTTTTTTTGCAC
434011 TCATAACAAACAACATGATCTTTCTCTTTGGATTCATTTTTGAAGCCCACCTTTTTATGGAACAT
66 TCATAACAAACAACATGATCTTTCTCTTTGGATTCATTTTTGAAGCCCACCTTTTTATGGAACAT
434076 TTTTCCTTTATTGGACCTCATGAATCTCTTGAATTGTTTGAAAAGCATTAGCATATATTCATCTT
131 TTTTCCTTTATTGGACCTCATGAATCTCTTGAATTGTTTGAAAAGCATTAGCATATATTCATCTT
434141 CTTCATTTGAATCACTCTTATCTTTGGTATATTTGAGTGCAATGTCAATATTCTTTCTTCTTCTT
196 CTTCATTTGAATCACTCTTATCTTTGGTATATTTGAGTGCAATGTCAATATTCTTTCTTCTTCTT
434206 CTTCGTTTCTTTCTTTTTTTCATCTTTTT
261 CTTCGTTTCTTTCTTTTTTTCATCTTTTT
434235 TTGTTGGATACTTTCTTCTTTGATTGAGGGCAATCCAAGTTTATACGCTCTCA-TTTTTTTGCAC
1 TTGTTGGATACTTTCTTCTTTGATTGAGGGCAATCCAAGTTTATACGCTCTCATTTTTTTTGCAC
434299 TCATAACAAACAACATGATCTTTCTCTTTGGATTCATTTTTGAAGCCCACCTTTTTATGGAACAT
66 TCATAACAAACAACATGATCTTTCTCTTTGGATTCATTTTTGAAGCCCACCTTTTTATGGAACAT
434364 TTTTCCTTTATTGGACCTCATGAATCTCTTGAATTGTTTGAAAAGCATTAGCATATATTCATCTT
131 TTTTCCTTTATTGGACCTCATGAATCTCTTGAATTGTTTGAAAAGCATTAGCATATATTCATCTT
434429 CTTCATTTGAATCACTCTTATCTTTGGTATATTTGAGTGCAATGTCAATATTCTTTCTTCTTCTT
196 CTTCATTTGAATCACTCTTATCTTTGGTATATTTGAGTGCAATGTCAATATTCTTTCTTCTTCTT
434494 CTTCGTTTCTTTCTTTTTTTCATCTTTTT
261 CTTCGTTTCTTTCTTTTTTTCATCTTTTT
*
434523 TTCTT-GAT-C-TTCTTCTT
1 TTGTTGGATACTTTCTTCTT
434540 CATTTACCAT
Statistics
Matches: 303, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
285 8 0.03
286 1 0.00
287 3 0.01
288 239 0.79
289 52 0.17
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (289 bp):
TTGTTGGATACTTTCTTCTTTGATTGAGGGCAATCCAAGTTTATACGCTCTCATTTTTTTTGCAC
TCATAACAAACAACATGATCTTTCTCTTTGGATTCATTTTTGAAGCCCACCTTTTTATGGAACAT
TTTTCCTTTATTGGACCTCATGAATCTCTTGAATTGTTTGAAAAGCATTAGCATATATTCATCTT
CTTCATTTGAATCACTCTTATCTTTGGTATATTTGAGTGCAATGTCAATATTCTTTCTTCTTCTT
CTTCGTTTCTTTCTTTTTTTCATCTTTTT
Found at i:438865 original size:21 final size:21
Alignment explanation
Indices: 438839--438889 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
438829 AAGAAAACAC
438839 CGATACTCCTAGACCGAGTAT
1 CGATACTCCTAGACCGAGTAT
*
438860 CGATACTCCTAGTCCGAGTAT
1 CGATACTCCTAGACCGAGTAT
438881 CGATACTCC
1 CGATACTCC
438890 CTATTCTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (21 bp):
CGATACTCCTAGACCGAGTAT
Found at i:443031 original size:15 final size:15
Alignment explanation
Indices: 442980--443036 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
442970 AATCGGGTAT
442980 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
442995 CGGATACCTAC-AAAATC
1 CGGGTACC--CGATTA-C
443012 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
443027 CGGGTACCCG
1 CGGGTACCCG
443037 TAACATCCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 19 0.59
16 4 0.12
17 9 0.28
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:443286 original size:34 final size:34
Alignment explanation
Indices: 443243--443317 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
443233 TTGATTTAGA
443243 AATTTAATAAAGTAATAATTAAACCTTCATTTTT
1 AATTTAATAAAGTAATAATTAAACCTTCATTTTT
443277 AATTTAATAAAGTAATAATTAAACCTTCATTTTT
1 AATTTAATAAAGTAATAATTAAACCTTCATTTTT
443311 AATTTAA
1 AATTTAA
443318 CAAATTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (34 bp):
AATTTAATAAAGTAATAATTAAACCTTCATTTTT
Found at i:443495 original size:34 final size:34
Alignment explanation
Indices: 443468--443601 Score: 133
Period size: 36 Copynumber: 3.7 Consensus size: 34
443458 TTATTCCACC
443468 CTAATATTTTAATTTATTTTTAAATTATTTTACT
1 CTAATATTTTAATTTATTTTTAAATTATTTTACT
* *
443502 ATAATATTTTAAATCATTATTTTTTTCAAATTATTTTATT
1 CTAATATTTT-AAT--TTA--TTTTT-AAATTATTTTACT
* * *
443542 CTAACATTTTAATTTATTTTCAAATTATTTTTCAT
1 CTAATATTTTAATTTATTTTTAAATTATTTTAC-T
* *
443577 CTTAACATTTTAGTTTATTTTTAAA
1 C-TAATATTTTAATTTATTTTTAAA
443602 ATTAATTACA
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
34 19 0.23
35 9 0.11
36 21 0.25
37 6 0.07
39 8 0.10
40 20 0.24
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (34 bp):
CTAATATTTTAATTTATTTTTAAATTATTTTACT
Found at i:443534 original size:14 final size:14
Alignment explanation
Indices: 443517--443573 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
443507 ATTTTAAATC
443517 ATTATTTTTTTCAA
1 ATTATTTTTTTCAA
*
443531 ATTATTTTATTCTAA
1 ATTATTTTTTTC-AA
443546 CATTTTAATTTATTTTCAA
1 -A--TT-ATTT-TTTTCAA
443565 ATTATTTTT
1 ATTATTTTT
443574 CATCTTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
14 13 0.37
15 6 0.17
16 3 0.09
18 3 0.09
19 6 0.17
20 4 0.11
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTTTTTTCAA
Found at i:443726 original size:27 final size:28
Alignment explanation
Indices: 443651--443781 Score: 133
Period size: 27 Copynumber: 4.8 Consensus size: 28
443641 CTTATATTAT
* *
443651 AAATAAGTACTTAAAGTATTTTTTTTC-
1 AAATAAGTACCTAAAGTATTTTTTGTCA
** *
443678 -TTTTAGTTACCTAAAGTATTTTTTGTCA
1 AAATAAG-TACCTAAAGTATTTTTTGTCA
* *
443706 AAATAAGTACCTAAACT-TTTTCTGTCA
1 AAATAAGTACCTAAAGTATTTTTTGTCA
* *
443733 AAATATGTACCTAAAGTATTTTTGGTCA
1 AAATAAGTACCTAAAGTATTTTTTGTCA
* *
443761 AAATAGGTACCTAAAATATTT
1 AAATAAGTACCTAAAGTATTT
443782 AATTTATTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
26 3 0.04
27 42 0.50
28 36 0.43
29 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (28 bp):
AAATAAGTACCTAAAGTATTTTTTGTCA
Found at i:443934 original size:29 final size:27
Alignment explanation
Indices: 443861--443935 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 27
443851 TGAAAAAATG
*
443861 AATACTTTAGGTACTTTTTTGACCAAAA
1 AATACTTTAGGTA-TTTATTGACCAAAA
* *
443889 AGATAAGTTTAGATATTTGATTGACCAAGAA
1 A-AT-ACTTTAGGTATTT-ATTGACCAA-AA
443920 AATACTTTAGGTATTT
1 AATACTTTAGGTATTT
443936 CAATATTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 16 0.42
30 18 0.47
31 3 0.08
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (27 bp):
AATACTTTAGGTATTTATTGACCAAAA
Found at i:453032 original size:81 final size:81
Alignment explanation
Indices: 452895--453304 Score: 588
Period size: 81 Copynumber: 5.1 Consensus size: 81
452885 AAAATGAAAT
* * * *
452895 ATTAAATGTCTGACTGTGCATTTGGCAAAAAGGTGCCAATCATGCAAGTTAGATGAAAGGATAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
452960 TGCCTTTGGGTAAAAG
66 TGCCTTTGGGTAAAAG
* * * * **
452976 AATAAATGCCTAACTGTGCATTTGGCAAAAATGTGCCAATCGTGCAAGTTAGATGAAATTTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* *
453041 TGTCTTTGGGCAAAAG
66 TGCCTTTGGGTAAAAG
* *
453057 ATTAAATGTCTAACTGTGCATTTGGCATAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
453122 TGCCTTTGGGT-AAAG
66 TGCCTTTGGGTAAAAG
* * *
453137 ATTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGAAGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* *
453202 TGCGTTTGGATAAAAG
66 TGCCTTTGGGTAAAAG
* * *
453218 ATTAAATGCCTAATTGTGTATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* *
453283 TGCGTTTGGATAAAAG
66 TGCCTTTGGGTAAAAG
*
453299 ACTAAA
1 ATTAAA
453305 CCTTAACAGT
Statistics
Matches: 299, Mismatches: 29, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
80 74 0.25
81 225 0.75
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (81 bp):
ATTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
TGCCTTTGGGTAAAAG
Found at i:453243 original size:161 final size:161
Alignment explanation
Indices: 452895--453296 Score: 590
Period size: 161 Copynumber: 2.5 Consensus size: 161
452885 AAAATGAAAT
* * *
452895 ATTAAATGTCTGACTGTGCATTTGGCAAAAAGGTGCCAATCATGCAAGTTAGATGAAAGGATAAA
1 ATTAAATGTCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* * *
452960 TGCCTTTGGGTAAAAGAATAAATGCCTAACTGTGCATTTGGCAAAAATGTGCCAATCGTGCAAGT
66 TGCCTTTGGGT-AAAGAATAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGT
* ** *
453025 TAGATGAAATTTTAAATGTCTTTGGGCAAAAG
130 TAGAAGAAAGGTTAAATGTCTTTGGACAAAAG
*
453057 ATTAAATGTCTAACTGTGCATTTGGCATAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGTCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* * *
453122 TGCCTTTGGGTAAAGATTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTT
66 TGCCTTTGGGTAAAGAATAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTT
*
453187 AGAAGAAAGGTTAAATG-CGTTTGGATAAAAG
131 AGAAGAAAGGTTAAATGTC-TTTGGACAAAAG
* * * *
453218 ATTAAATGCCTAATTGTGTATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGTCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* *
453283 TGCGTTTGGATAAA
66 TGCCTTTGGGTAAA
453297 AGACTAAACC
Statistics
Matches: 218, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
160 1 0.00
161 145 0.67
162 72 0.33
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (161 bp):
ATTAAATGTCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
TGCCTTTGGGTAAAGAATAAATGCCTAACTGTGCATTTGGCAAAAAGGTGACAATCATGCAAGTT
AGAAGAAAGGTTAAATGTCTTTGGACAAAAG
Found at i:460317 original size:161 final size:162
Alignment explanation
Indices: 459960--460371 Score: 612
Period size: 161 Copynumber: 2.5 Consensus size: 162
459950 AAAATGAAAT
* * * *
459960 ATTAAATGGCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTATATGAAATGCTAAA
1 ATTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAAGTTAAA
* * * *
460025 TGCCTTTAGGTAAAAGAATAAATGCCTAACTGTGCATTTGGCAGAAATGTGTCAATCATGCAAGT
66 TGTCTTTGGGTAAAAGAATAAATGCCTAACTGTGCATTTGGCAGAAATGGGACAATCATGCAAGT
* *
460090 TAGATGAAAGGGTAAATGTCTTTGGGTAAAAG
131 TAGATGAAAGGGTAAATGACTTTGGATAAAAG
* *
460122 ATTAAATGCCTAACTGTGCATTTTGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAAGTTAAA
1 ATTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAAGTTAAA
* *
460187 TGTCTTTGGGTAAAAGATTAAATGCCTAACTGTGCATTTGGTAGAAA-GGGACAATCATGCAAGT
66 TGTCTTTGGGTAAAAGAATAAATGCCTAACTGTGCATTTGGCAGAAATGGGACAATCATGCAAGT
*
460251 TAGATGAAAGGTTAAAT-ACATTTGGATAAAAG
131 TAGATGAAAGGGTAAATGAC-TTTGGATAAAAG
* *
460283 ATTAAATGCCTAATTGTGCATTTGGCATAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAAGTTAAA
* * * *
460348 TGTGTTTGGATAAATGACTAAATG
66 TGTCTTTGGGTAAAAGAATAAATG
460372 TTTAACAATG
Statistics
Matches: 226, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
160 1 0.00
161 123 0.54
162 102 0.45
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (162 bp):
ATTAAATGCCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAAGTTAAA
TGTCTTTGGGTAAAAGAATAAATGCCTAACTGTGCATTTGGCAGAAATGGGACAATCATGCAAGT
TAGATGAAAGGGTAAATGACTTTGGATAAAAG
Found at i:460356 original size:81 final size:81
Alignment explanation
Indices: 459960--460371 Score: 596
Period size: 81 Copynumber: 5.1 Consensus size: 81
459950 AAAATGAAAT
* * * * *
459960 ATTAAATGGCTAATTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTATATGAAATGCTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
*
460025 TGCCTTTAGG-TAAAAG
66 TGTCTTT-GGATAAAAG
* * * *
460041 AATAAATGCCTAACTGTGCATTTGGCAGAAATGTGTCAATCATGCAAGTTAGATGAAAGGGTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
*
460106 TGTCTTTGGGTAAAAG
66 TGTCTTTGGATAAAAG
* *
460122 ATTAAATGCCTAACTGTGCATTTTGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAAGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
*
460187 TGTCTTTGGGTAAAAG
66 TGTCTTTGGATAAAAG
*
460203 ATTAAATGCCTAACTGTGCATTTGGTAGAAAGG-GACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
*
460267 T-ACATTTGGATAAAAG
66 TGTC-TTTGGATAAAAG
* *
460283 ATTAAATGCCTAATTGTGCATTTGGCATAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* *
460348 TGTGTTTGGATAAATG
66 TGTCTTTGGATAAAAG
*
460364 ACTAAATG
1 ATTAAATG
460372 TTTAACAATG
Statistics
Matches: 300, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
79 1 0.00
80 74 0.25
81 225 0.75
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (81 bp):
ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
TGTCTTTGGATAAAAG
Found at i:466531 original size:22 final size:20
Alignment explanation
Indices: 466506--466550 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
466496 GGAGTATCAG
466506 TACCATAGTATAAAAGTATCGA
1 TACCATAGTAT--AAGTATCGA
* *
466528 TACCATGGTATGAGTATCGA
1 TACCATAGTATAAGTATCGA
466548 TAC
1 TAC
466551 TATTGAGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (20 bp):
TACCATAGTATAAGTATCGA
Found at i:467087 original size:81 final size:81
Alignment explanation
Indices: 466952--467202 Score: 403
Period size: 81 Copynumber: 3.1 Consensus size: 81
466942 AAAATGAAAT
* * *
466952 ATTAAATGCCTAATTGTGCATTTGGTAGAAATGTGTCAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAATGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
* *
467017 TGCCTTTGGGTAAAAG
66 TGCGTTTGGATAAAAG
* *
467033 ATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAATGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
467098 TGCGTTTGGATAAAAG
66 TGCGTTTGGATAAAAG
* *
467114 ATTAAATACCTAACTGTGCATTTGGCATAAATGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
1 ATTAAATGCCTAACTGTGCATTTGGCAGAAATGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
*
467179 TGTGTTTGGATAAAAG
66 TGCGTTTGGATAAAAG
*
467195 ACTAAATG
1 ATTAAATG
467203 TTTAACAGTG
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 156 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (81 bp):
ATTAAATGCCTAACTGTGCATTTGGCAGAAATGTGACAATCATGCAAGTTAGATGAAAGGTTAAA
TGCGTTTGGATAAAAG
Found at i:473954 original size:24 final size:25
Alignment explanation
Indices: 473913--473959 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
473903 GTACTCAAAA
473913 AAAATTAGAAGCTCGATTGAAGCCT
1 AAAATTAGAAGCTCGATTGAAGCCT
* *
473938 AAAATTCG-AGCTTGATTGAAGC
1 AAAATTAGAAGCTCGATTGAAGC
473960 AAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGCCT
Found at i:485525 original size:17 final size:17
Alignment explanation
Indices: 485484--485529 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
485474 TGAATTTATG
485484 TTAAATATTATATAACT
1 TTAAATATTATATAACT
** * *
485501 TTGGATATTATATGATT
1 TTAAATATTATATAACT
485518 TTAAATATTATA
1 TTAAATATTATA
485530 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
TTAAATATTATATAACT
Found at i:487320 original size:3 final size:3
Alignment explanation
Indices: 487307--487343 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
487297 CGAACATTTC
*
487307 ATT AAT ATT ATT ATT ATT ATT ATT AATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
487344 TTGATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:488758 original size:2 final size:2
Alignment explanation
Indices: 488716--488743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
488706 TTTATTTAAG
488716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
488744 TTGTGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:497719 original size:2 final size:2
Alignment explanation
Indices: 497707--497746 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
497697 CTGTATATGC
*
497707 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
497747 CATCTCGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:501237 original size:8 final size:8
Alignment explanation
Indices: 501202--501274 Score: 75
Period size: 8 Copynumber: 9.6 Consensus size: 8
501192 ATACTTCGCC
501202 TAAAG-AA
1 TAAAGAAA
501209 TAAA-AAA
1 TAAAGAAA
*
501216 CAAAGAAA
1 TAAAGAAA
501224 -AAAGAAA
1 TAAAGAAA
501231 TAAAGAAA
1 TAAAGAAA
*
501239 TAAAAAAAA
1 T-AAAGAAA
501248 TAAA-AAA
1 TAAAGAAA
501255 -AAAGAAA
1 TAAAGAAA
*
501262 TAAATAAA
1 TAAAGAAA
501270 TAAAG
1 TAAAG
501275 GGGGTTCAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
6 3 0.05
7 22 0.39
8 24 0.43
9 7 0.12
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.11
Consensus pattern (8 bp):
TAAAGAAA
Found at i:501256 original size:31 final size:30
Alignment explanation
Indices: 501202--501273 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
501192 ATACTTCGCC
* *
501202 TAAAG-AATAAAAAACAAAGAAAAAAGAAA
1 TAAAGAAATAAAAAAAAAAAAAAAAAGAAA
501231 TAAAGAAATAAAAAAAATAAAAAAAAAGAAA
1 TAAAGAAATAAAAAAAA-AAAAAAAAAGAAA
*
501262 TAAATAAATAAA
1 TAAAGAAATAAA
501274 GGGGGTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 5 0.13
30 10 0.26
31 23 0.61
ACGTcount: A:0.81, C:0.01, G:0.07, T:0.11
Consensus pattern (30 bp):
TAAAGAAATAAAAAAAAAAAAAAAAAGAAA
Found at i:503072 original size:125 final size:127
Alignment explanation
Indices: 502714--503090 Score: 402
Period size: 134 Copynumber: 2.9 Consensus size: 127
502704 GCAGATCCAT
* * * * * *
502714 TTTTTCCATATTTGATCTTCCCTGAATAGTATTGGAACAAATCTACCTCGATTCAATCTTCCCTG
1 TTTTTCCAAATTTGATCTTCCCTGAAGAGCAATGGAACAAATATACCTCGATTCAATCTTCTCTG
* * *
502779 AAGAACAGTGGAATGAATCAATGTTCCCATATCTGATCTATCCTGAAGAACAGCAGAGCAGATCC
66 AAGAATAGTGGAATGAATCAATGTTACCATATCTGATCTACCCTGAAG---AGC--AG-AGATCC
502844 CCC
125 CCC
* * * *
502847 TGTTTTCCAAATTTGATCTTCCCTGAGGATCAGTGAAACAAATATACCTCGATTCAATCTTCAT-
1 T-TTTTCCAAATTTGATCTTCCCTGAAGAGCAATGGAACAAATATACCTCGATTCAATCTTC-TC
* *
502911 TGAAGAATAGTGGAATGAATCAGTGTTTCCATATCTGATCTACCCTGAAGAGCAG-GAT-CCCC
64 TGAAGAATAGTGGAATGAATCAATGTTACCATATCTGATCTACCCTGAAGAGCAGAGATCCCCC
* * * * * * *
502973 TTTTTCTAGATTTGATCTTCCATGAAGAGCAATGGAACAAGCT-TGCCTCGATTCAATATACTCT
1 TTTTTCCAAATTTGATCTTCCCTGAAGAGCAATGGAACAA-ATATACCTCGATTCAATCTTCTCT
* * * * *
503037 GAAGAGTAGTGGAGTGAATCAAAGTTACCAGATCTGATCTACCCTAAAGAGCAG
65 GAAGAATAGTGGAATGAATCAATGTTACCATATCTGATCTACCCTGAAGAGCAG
503091 CGGAGCAAAT
Statistics
Matches: 209, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
124 1 0.00
125 95 0.45
126 6 0.03
127 3 0.01
129 2 0.01
131 3 0.01
133 1 0.00
134 98 0.47
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (127 bp):
TTTTTCCAAATTTGATCTTCCCTGAAGAGCAATGGAACAAATATACCTCGATTCAATCTTCTCTG
AAGAATAGTGGAATGAATCAATGTTACCATATCTGATCTACCCTGAAGAGCAGAGATCCCCC
Found at i:503322 original size:6 final size:6
Alignment explanation
Indices: 503313--503355 Score: 77
Period size: 6 Copynumber: 7.0 Consensus size: 6
503303 AATATTAATA
503313 TTATTT TTATTTT TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTA-TTT TTATTT TTATTT TTATTT TTATTT TTATTT
503356 ACTTTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:503362 original size:18 final size:17
Alignment explanation
Indices: 503318--503363 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
503308 TAATATTATT
503318 TTTATTTTTTATTTTTA
1 TTTATTTTTTATTTTTA
*
503335 TTTTTATTTTTATTTTTA
1 TTTAT-TTTTTATTTTTA
503353 TTTACTTTTTT
1 TTTA-TTTTTT
503364 TGCATGCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 20 0.80
19 1 0.04
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTATTTTTTATTTTTA
Found at i:504148 original size:16 final size:16
Alignment explanation
Indices: 504123--504155 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
504113 CGATGATTAA
*
504123 AAAAAGAAAAAAAATG
1 AAAAACAAAAAAAATG
504139 AAAAACAAAAAAAATG
1 AAAAACAAAAAAAATG
504155 A
1 A
504156 GAGGGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAACAAAAAAAATG
Found at i:525460 original size:22 final size:23
Alignment explanation
Indices: 525435--525483 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 23
525425 TTTTTTATCA
525435 AAAAGA-TGAGGGATTT-TAAAAG
1 AAAAGAGT-AGGGATTTATAAAAG
525457 AAAAGAGTAGGGATTTCATAAAAG
1 AAAAGAGTAGGGATTT-ATAAAAG
525481 AAA
1 AAA
525484 TTCGTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 14 0.58
23 1 0.04
24 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.20
Consensus pattern (23 bp):
AAAAGAGTAGGGATTTATAAAAG
Found at i:532490 original size:24 final size:24
Alignment explanation
Indices: 532463--532517 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
532453 CACCATAGCT
*
532463 CGTATAAATTGCATCGAAGTGCCA
1 CGTAGAAATTGCATCGAAGTGCCA
532487 CGTAGAAATTGCATCGAAGTGCCA
1 CGTAGAAATTGCATCGAAGTGCCA
*
532511 CATAGAA
1 CGTAGAA
532518 TGTCTCGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
CGTAGAAATTGCATCGAAGTGCCA
Found at i:532567 original size:23 final size:23
Alignment explanation
Indices: 532541--532605 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
532531 TTCATTGTAT
532541 TGTCCCGAAGGACCACGTAGAAA
1 TGTCCCGAAGGACCACGTAGAAA
* * *
532564 TGTCTCGAAGAACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAA
*
532587 TGTCCCGAAGGACCGCGTA
1 TGTCCCGAAGGACCACGTA
532606 AAGCCTCGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAA
Found at i:541776 original size:41 final size:42
Alignment explanation
Indices: 541693--541776 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
541683 TTAAAATTCT
* *
541693 TAAAGAGTAAAATGTAAAATTCTGAAAAATGAAAACAGATTA
1 TAAAGAGTAAAATCTAAAATTCTGAAAAATGAAAACAAATTA
*
541735 TAAAGAGTAAATTCTAAAATTCT-AAAAA-GTAAAACAAATTA
1 TAAAGAGTAAAATCTAAAATTCTGAAAAATG-AAAACAAATTA
541776 T
1 T
541777 TAATAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 1 0.03
41 16 0.42
42 21 0.55
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (42 bp):
TAAAGAGTAAAATCTAAAATTCTGAAAAATGAAAACAAATTA
Found at i:541788 original size:41 final size:42
Alignment explanation
Indices: 541707--541788 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 42
541697 GAGTAAAATG
* **
541707 TAAAATTCTGAAAAATGAAAACAGATTATAAAGAGTAAATTC
1 TAAAATTCTGAAAAATGAAAACAAATTATAAAGAAAAAATTC
* *
541749 TAAAATTCT-AAAAA-GTAAAACAAATTATTAATAAAAAATT
1 TAAAATTCTGAAAAATG-AAAACAAATTATAAAGAAAAAATT
541789 ACAATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.03
41 24 0.71
42 9 0.26
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (42 bp):
TAAAATTCTGAAAAATGAAAACAAATTATAAAGAAAAAATTC
Found at i:542107 original size:13 final size:13
Alignment explanation
Indices: 542098--542134 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
542088 TGGTTTGATT
542098 AGTTGATTTGAGA
1 AGTTGATTTGAGA
542111 AGTTGATTTGAGA
1 AGTTGATTTGAGA
*
542124 AATTGATTTGA
1 AGTTGATTTGA
542135 TTAACTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (13 bp):
AGTTGATTTGAGA
Found at i:547616 original size:27 final size:27
Alignment explanation
Indices: 547572--547684 Score: 201
Period size: 27 Copynumber: 4.2 Consensus size: 27
547562 CCTTAGCCCC
*
547572 TAAGCCCAGC-AACCCTGTCTTTCAAAT
1 TAAGCCCAGCTAA-TCTGTCTTTCAAAT
547599 TAAGCCCAGCTAATCTGTCTTTCAAAT
1 TAAGCCCAGCTAATCTGTCTTTCAAAT
547626 TAAGCCCAGCTAATCTGTCTTTCAAAT
1 TAAGCCCAGCTAATCTGTCTTTCAAAT
547653 TAAGCCCAGCTAATCTGTCTTTCAAAT
1 TAAGCCCAGCTAATCTGTCTTTCAAAT
547680 TAAGC
1 TAAGC
547685 TTAGGAAGGT
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
27 82 0.98
28 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (27 bp):
TAAGCCCAGCTAATCTGTCTTTCAAAT
Found at i:548735 original size:18 final size:16
Alignment explanation
Indices: 548710--548759 Score: 68
Period size: 15 Copynumber: 3.1 Consensus size: 16
548700 TATGTGATAT
548710 AAATATTAATAAAATA
1 AAATATTAATAAAATA
548726 AGATATATT-ATAAAA-A
1 A-A-ATATTAATAAAATA
548742 AAATATTAATAAAATA
1 AAATATTAATAAAATA
548758 AA
1 AA
548760 TTATGTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 6 0.20
17 7 0.23
18 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATATTAATAAAATA
Found at i:553176 original size:23 final size:23
Alignment explanation
Indices: 553111--553178 Score: 127
Period size: 23 Copynumber: 3.0 Consensus size: 23
553101 GTCGAACCGA
*
553111 TTCGACCGGTTGAACCAGTAAAG
1 TTCGACCGGTTGAACCAGTGAAG
553134 TTCGACCGGTTGAACCAGTGAAG
1 TTCGACCGGTTGAACCAGTGAAG
553157 TTCGACCGGTTGAACCAGTGAA
1 TTCGACCGGTTGAACCAGTGAA
553179 CCGATAGCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (23 bp):
TTCGACCGGTTGAACCAGTGAAG
Found at i:553396 original size:15 final size:16
Alignment explanation
Indices: 553378--553418 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
553368 TAAATCAAGT
553378 ATAAATAAATTTAAA-
1 ATAAATAAATTTAAAC
*
553393 AT-AATAAAAATTAAAC
1 ATAAAT-AAATTTAAAC
553409 ATAAATAAAT
1 ATAAATAAAT
553419 ATTTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 3 0.14
15 10 0.48
16 5 0.24
17 3 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATAAATTTAAAC
Found at i:563996 original size:20 final size:21
Alignment explanation
Indices: 563950--564000 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
563940 ATCATTCAAA
563950 GAGTATCGATACCAACAGGTG
1 GAGTATCGATACCAACAGGTG
* *
563971 GA-TATCGATACCCA-AGGTT
1 GAGTATCGATACCAACAGGTG
*
563990 TAGTATCGATA
1 GAGTATCGATA
564001 TTGAACGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 19 0.73
21 2 0.08
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (21 bp):
GAGTATCGATACCAACAGGTG
Found at i:566349 original size:23 final size:23
Alignment explanation
Indices: 566300--566350 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
566290 TACGCGATCA
*
566300 TTCGGGACAATACTATGTGGTCT
1 TTCGGGACAATACTATGTGGTCC
* *
566323 TTCGGGACATTATTATGTGG-CAC
1 TTCGGGACAATACTATGTGGTC-C
566346 TTCGG
1 TTCGG
566351 TGCAATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (23 bp):
TTCGGGACAATACTATGTGGTCC
Found at i:566369 original size:24 final size:24
Alignment explanation
Indices: 566341--566387 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
566331 ATTATTATGT
* *
566341 GGCACTTCGGTGCAATTTCTACGC
1 GGCACTTCGATGCAATTTATACGC
566365 GGCACTTCGATGCAATTTATACG
1 GGCACTTCGATGCAATTTATACG
566388 AGTTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (24 bp):
GGCACTTCGATGCAATTTATACGC
Found at i:566525 original size:6 final size:6
Alignment explanation
Indices: 566494--566523 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
566484 ATGAACAGTG
*
566494 AATGAT AATGAT AATGAT AATGAT GATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT
566524 GAGGATATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (6 bp):
AATGAT
Found at i:567769 original size:18 final size:20
Alignment explanation
Indices: 567729--567773 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
567719 TTTGGGTGAA
*
567729 TATCGATACTCTACCCTGGG
1 TATCGATACTCTACCCTGAG
567749 TATCGATACTC-A-CCTGAG
1 TATCGATACTCTACCCTGAG
567767 TATCGAT
1 TATCGAT
567774 GCCAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 1 0.04
20 11 0.46
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACTCTACCCTGAG
Found at i:569848 original size:10 final size:10
Alignment explanation
Indices: 569833--569998 Score: 82
Period size: 10 Copynumber: 15.9 Consensus size: 10
569823 TATTAAAATG
*
569833 ATAAACGAAC
1 ATAAACAAAC
*
569843 ATAAACAAAA
1 ATAAACAAAC
* *
569853 AAAAACGAAC
1 ATAAACAAAC
*
569863 ATAAACAAAG
1 ATAAACAAAC
569873 ATAAACAAACAC
1 ATAAAC-AA-AC
569885 AATAAACAAAC
1 -ATAAACAAAC
* *
569896 GTAAATAAAC
1 ATAAACAAAC
569906 ATAAACAAAC
1 ATAAACAAAC
* *
569916 ACAAATGAACAC
1 ATAAA-CAA-AC
569928 A-AATGAGCAAAC
1 ATAA--A-CAAAC
* *
569940 GTAAACGAAC
1 ATAAACAAAC
*
569950 ATAAACAAGC
1 ATAAACAAAC
* *
569960 GTAAACGAAC
1 ATAAACAAAC
* *
569970 ACAAACAAGC
1 ATAAACAAAC
* *
569980 GTAAACGAAC
1 ATAAACAAAC
*
569990 ACAAACAAA
1 ATAAACAAA
569999 TCTGCACAAA
Statistics
Matches: 112, Mismatches: 36, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
10 84 0.75
11 9 0.08
12 8 0.07
13 11 0.10
ACGTcount: A:0.63, C:0.19, G:0.09, T:0.08
Consensus pattern (10 bp):
ATAAACAAAC
Found at i:569915 original size:33 final size:32
Alignment explanation
Indices: 569833--569920 Score: 108
Period size: 33 Copynumber: 2.8 Consensus size: 32
569823 TATTAAAATG
* *
569833 ATAAACGAACATAAACAAA-A-AAAAACGAAC
1 ATAAACAAACATAAACAAACACAAAAACAAAC
*
569863 ATAAACAAAGATAAACAAACACAATAAACAAAC
1 ATAAACAAACATAAACAAACACAA-AAACAAAC
* *
569896 GTAAATAAACATAAACAAACACAAA
1 ATAAACAAACATAAACAAACACAAA
569921 TGAACACAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.35
31 1 0.02
32 3 0.06
33 28 0.57
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (32 bp):
ATAAACAAACATAAACAAACACAAAAACAAAC
Found at i:569954 original size:44 final size:41
Alignment explanation
Indices: 569833--569998 Score: 147
Period size: 44 Copynumber: 4.0 Consensus size: 41
569823 TATTAAAATG
* *** *
569833 ATAAACGAACATAA-ACAAAAAAAAACGAACATAAACAAAG
1 ATAAACGAACACAATACAAACGTAAACGAACATAAACAAAC
* **
569873 ATAAACAAACACAATAAACAAACGTAAATAAACATAAACAAAC
1 ATAAACGAACACAAT--ACAAACGTAAACGAACATAAACAAAC
* * *
569916 ACAAATGAACACAAATGAGCAAACGTAAACGAACATAAACAAGC
1 ATAAACGAACAC-AAT-A-CAAACGTAAACGAACATAAACAAAC
* * *
569960 GTAAACGAACACAA-ACAAGCGTAAACGAACACAAACAAA
1 ATAAACGAACACAATACAAACGTAAACGAACATAAACAAA
569999 TCTGCACAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
40 33 0.33
41 1 0.01
43 32 0.32
44 34 0.34
ACGTcount: A:0.63, C:0.19, G:0.09, T:0.08
Consensus pattern (41 bp):
ATAAACGAACACAATACAAACGTAAACGAACATAAACAAAC
Found at i:571974 original size:12 final size:12
Alignment explanation
Indices: 571959--571983 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
571949 TAAAATGATC
571959 ATTAAGATAAAT
1 ATTAAGATAAAT
571971 ATTAAGATAAAT
1 ATTAAGATAAAT
571983 A
1 A
571984 ATAGGGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTAAGATAAAT
Found at i:572466 original size:37 final size:37
Alignment explanation
Indices: 572425--572604 Score: 134
Period size: 37 Copynumber: 5.2 Consensus size: 37
572415 GAAAATATAT
*
572425 AAGTGGCCAAATAGGTAGTTTACCCTAAATAATAATC
1 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
* ** **
572462 AAGTGACCAAA-AGATAAATTA--GAAAAT-AT-AT-
1 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
572493 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
1 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
** ** **
572530 GAA-TGACCAAA-ACATAAATTA-GAT-AAT-AT-AT-
1 -AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
*
572561 AAGTGACCAAATAGGTAGTTTATCCTAAATAATAATC
1 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
*
572598 GAGTGAC
1 AAGTGAC
572605 TAAAATATAA
Statistics
Matches: 105, Mismatches: 24, Indels: 28
0.67 0.15 0.18
Matches are distributed among these distances:
30 2 0.02
31 19 0.18
32 17 0.16
33 5 0.05
34 14 0.13
35 5 0.05
36 17 0.16
37 24 0.23
38 2 0.02
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (37 bp):
AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATC
Found at i:572492 original size:68 final size:68
Alignment explanation
Indices: 572383--572653 Score: 409
Period size: 68 Copynumber: 4.0 Consensus size: 68
572373 AATTTTGAAA
* * *
572383 AAATAATAATCGAGTGATCAAAAGATAAATTAGAAAATATATAAGTGGCCAAATAGGTAGTTTAC
1 AAATAATAATCAAGTGACCAAAAGATAAATTAGAAAATATATAAGTGACCAAATAGGTAGTTTAC
572448 CCT
66 CCT
572451 AAATAATAATCAAGTGACCAAAAGATAAATTAGAAAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCAAGTGACCAAAAGATAAATTAGAAAATATATAAGTGACCAAATAGGTAGTTTAC
572516 CCT
66 CCT
* *
572519 AAATAATAATCGAA-TGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
1 AAATAATAATC-AAGTGACCAAAAGATAAATTAGAAAATATATAAGTGACCAAATAGGTAGTTTA
*
572583 TCCT
65 CCCT
* * * * * * *
572587 AAATAATAATCGAGTGACTAAAATATAAATTAGATAATATATAAATAACCAAATATGTAGTTTAC
1 AAATAATAATCAAGTGACCAAAAGATAAATTAGAAAATATATAAGTGACCAAATAGGTAGTTTAC
572652 CC
66 CC
572654 AAAAAATTTA
Statistics
Matches: 188, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
67 1 0.01
68 185 0.98
69 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (68 bp):
AAATAATAATCAAGTGACCAAAAGATAAATTAGAAAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:572497 original size:31 final size:31
Alignment explanation
Indices: 572395--572571 Score: 104
Period size: 31 Copynumber: 5.3 Consensus size: 31
572385 ATAATAATCG
*
572395 AGTGATCAAAAGATAAATTAGAAAATATATA
1 AGTGACCAAAAGATAAATTAGAAAATATATA
* * ** **
572426 AGTGGCCAAATAGGTAGTTTACCCTAAATAATAATCA
1 AGTGACCAAA-AGATAAATTA--GAAAAT-AT-AT-A
572463 AGTGACCAAAAGATAAATTAGAAAATATATA
1 AGTGACCAAAAGATAAATTAGAAAATATATA
* ** **
572494 AGTGACCAAATAGGTAGTTTACCCTAAATA-ATA
1 AGTGACCAAA-AGATAAATTA--GAAAATATATA
* *
572527 ATCGAATGACCAAAACATAAATTAGATAATATATA
1 A--G--TGACCAAAAGATAAATTAGAAAATATATA
572562 AGTGACCAAA
1 AGTGACCAAA
572572 TAGGTAGTTT
Statistics
Matches: 107, Mismatches: 25, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
31 27 0.25
32 16 0.15
33 7 0.07
34 17 0.16
35 7 0.07
36 15 0.14
37 18 0.17
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (31 bp):
AGTGACCAAAAGATAAATTAGAAAATATATA
Found at i:575592 original size:13 final size:14
Alignment explanation
Indices: 575576--575669 Score: 72
Period size: 13 Copynumber: 7.1 Consensus size: 14
575566 TTGTTTTTTG
*
575576 TGTTTGTGTT-GTT
1 TGTTTATGTTCGTT
575589 TGTTTATGTTCGTT
1 TGTTTATGTTCGTT
* * *
575603 T-ATTGTGTTCATT
1 TGTTTATGTTCGTT
*
575616 T-ATTATGTTCGTT
1 TGTTTATGTTCGTT
* *
575629 CGTTTGTGTTCGTT
1 TGTTTATGTTCGTT
*
575643 T-ATTATGTTCGTT
1 TGTTTATGTTCGTT
*
575656 T-ATTATGTTCGTT
1 TGTTTATGTTCGTT
575669 T
1 T
575670 ATCATTTAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
13 53 0.79
14 14 0.21
ACGTcount: A:0.10, C:0.07, G:0.20, T:0.63
Consensus pattern (14 bp):
TGTTTATGTTCGTT
Found at i:575640 original size:40 final size:40
Alignment explanation
Indices: 575582--575668 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
575572 TTTGTGTTTG
* *
575582 TGTT-GTTTGTTTATGTTCGTTTATTGTGTTCATTTATTA
1 TGTTCGTTCGTTTATGTTCGTTTATTATGTTCATTTATTA
* *
575621 TGTTCGTTCGTTTGTGTTCGTTTATTATGTTCGTTTATTA
1 TGTTCGTTCGTTTATGTTCGTTTATTATGTTCATTTATTA
575661 TGTTCGTT
1 TGTTCGTT
575669 TATCATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.10, C:0.08, G:0.20, T:0.62
Consensus pattern (40 bp):
TGTTCGTTCGTTTATGTTCGTTTATTATGTTCATTTATTA
Found at i:575670 original size:13 final size:13
Alignment explanation
Indices: 575592--575671 Score: 108
Period size: 13 Copynumber: 6.1 Consensus size: 13
575582 TGTTGTTTGT
575592 TTATGTTCGTTTA
1 TTATGTTCGTTTA
* *
575605 TTGTGTTCATTTA
1 TTATGTTCGTTTA
575618 TTATGTTCGTTCGT-
1 TTATGTTCGTT--TA
*
575632 TTGTGTTCGTTTA
1 TTATGTTCGTTTA
575645 TTATGTTCGTTTA
1 TTATGTTCGTTTA
575658 TTATGTTCGTTTA
1 TTATGTTCGTTTA
575671 T
1 T
575672 CATTTAAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
12 1 0.02
13 46 0.79
14 10 0.17
15 1 0.02
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.61
Consensus pattern (13 bp):
TTATGTTCGTTTA
Found at i:577501 original size:2 final size:2
Alignment explanation
Indices: 577494--577538 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
577484 TATAAATTTA
577494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
577536 AT A
1 AT A
577539 AAGATTTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:581507 original size:21 final size:21
Alignment explanation
Indices: 581465--581520 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
581455 TTGTCTACAA
581465 TCATTGAATTATTA-TTCTTAGC
1 TCATT-AA-TATTAGTTCTTAGC
*
581487 TCATTAATATTAGTTTTTAGC
1 TCATTAATATTAGTTCTTAGC
581508 T--TTAATACTTAGT
1 TCATTAATA-TTAGT
581521 AGGATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 6 0.19
20 10 0.32
21 10 0.32
22 5 0.16
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.52
Consensus pattern (21 bp):
TCATTAATATTAGTTCTTAGC
Found at i:582634 original size:19 final size:20
Alignment explanation
Indices: 582600--582638 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
582590 AATCAGTAAA
582600 CAGAGATATCAGAAATCAGAG
1 CAGAGATA-CAGAAATCAGAG
582621 CAGAGATA-AGAAATCAGA
1 CAGAGATACAGAAATCAGA
582639 ACATAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.51, C:0.13, G:0.23, T:0.13
Consensus pattern (20 bp):
CAGAGATACAGAAATCAGAG
Found at i:583583 original size:45 final size:45
Alignment explanation
Indices: 583515--583611 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
583505 TCCCAGTAAT
* * *
583515 TTTAATGTACCATTATGCATTTCATTTATGGCCTCCTTTCATGCC
1 TTTAATGCACCATTATGCATTTCATTTATGGCATCATTTCATGCC
* * *
583560 TTTAATGCACCGTTATGCTTTTCATTTATGTCATCATTTCATGCC
1 TTTAATGCACCATTATGCATTTCATTTATGGCATCATTTCATGCC
583605 TTTAATG
1 TTTAATG
583612 TACAATTAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (45 bp):
TTTAATGCACCATTATGCATTTCATTTATGGCATCATTTCATGCC
Found at i:583779 original size:54 final size:55
Alignment explanation
Indices: 583710--583815 Score: 169
Period size: 54 Copynumber: 1.9 Consensus size: 55
583700 AACTCTATAG
**
583710 TTTGCACACGTAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
1 TTTGCACACG-AGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTT
*
583766 TTTGCACAC-AGTGCCCATACAAAAATTTATAAACTTATTATGAATTTCTT
1 TTTGCACACGAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTT
583816 GGTTCGCACA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 38 0.81
56 9 0.19
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (55 bp):
TTTGCACACGAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTT
Found at i:583833 original size:54 final size:55
Alignment explanation
Indices: 583713--583834 Score: 160
Period size: 54 Copynumber: 2.2 Consensus size: 55
583703 TCTATAGTTT
** * *
583713 GCACACGTAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTT
1 GCACACG-AGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTGTTC
*
583769 GCACAC-AGTGCCCATACAAAAATTTATAAACTTATTATGAATTTCTT-G-GTTC
1 GCACACGAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTGTTC
583821 GCACACAGAGTGCC
1 GCACAC-GAGTGCC
583835 TATATAGTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
52 8 0.14
53 1 0.02
54 44 0.75
56 6 0.10
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (55 bp):
GCACACGAGTGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTGTTC
Found at i:583863 original size:54 final size:53
Alignment explanation
Indices: 583797--584212 Score: 448
Period size: 54 Copynumber: 7.7 Consensus size: 53
583787 AAAATTTATA
* ** *
583797 AACTTATTATGAATTTCTTGGTTCGCACACAGAGTGCCT-ATATAGTTGTTCATC
1 AACTTATGATGAATTTCTTGGTT-GCACACTTAGTGCCTGA-ACAGTTGTTCATC
* * * *
583851 AA-TATATGATGAATTCCATGGGTTGCACACTTAGTGCCTAAATAGTTGTTCATC
1 AACT-TATGATGAATTTC-TTGGTTGCACACTTAGTGCCTGAACAGTTGTTCATC
*
583905 AACTTATGATGAA-TTCTGTGGGTTGCACACTTAGTGCCTGAAC-GATTTTTCATC
1 AACTTATGATGAATTTCT-T-GGTTGCACACTTAGTGCCTGAACAG-TTGTTCATC
* *
583959 AACTTATGATGAATTTCATGGGTTGCACACTTAGTGCCTGAACGGTTGTTCATC
1 AACTTATGATGAATTTC-TTGGTTGCACACTTAGTGCCTGAACAGTTGTTCATC
* * * * *
584013 AATTTATGATGAATTCCGTGGTTGCACACTTAGTGCCTGAACAATTTTTCATC
1 AACTTATGATGAATTTCTTGGTTGCACACTTAGTGCCTGAACAGTTGTTCATC
* * * *
584066 AACTTATGATGAATTCCGTGGGTTGCACACTTAGTGCCTGAACGGTTGTTCGTC
1 AACTTATGATGAATTTC-TTGGTTGCACACTTAGTGCCTGAACAGTTGTTCATC
* *
584120 AACTTATGATGAA-TTCTGTGGGTTGCACACATAGTGTCTGAAC-GATTGTTCATC
1 AACTTATGATGAATTTCT-T-GGTTGCACACTTAGTGCCTGAACAG-TTGTTCATC
* * *
584174 AACTTGTGATGAATTCCGTGGGTTGCACACTTAGTGCCT
1 AACTTATGATGAATTTC-TTGGTTGCACACTTAGTGCCT
584213 ATTTGGTAAT
Statistics
Matches: 310, Mismatches: 36, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
52 2 0.01
53 54 0.17
54 239 0.77
55 13 0.04
56 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (53 bp):
AACTTATGATGAATTTCTTGGTTGCACACTTAGTGCCTGAACAGTTGTTCATC
Found at i:583919 original size:162 final size:161
Alignment explanation
Indices: 583767--584213 Score: 448
Period size: 161 Copynumber: 2.8 Consensus size: 161
583757 TTCTTAGTTT
* *
583767 TTGCACAC-AGTGCC-CATACAAAAATTT-ATAAACTTATTATGAATTTC-TTGGTTCGCACACA
1 TTGCACACTAGTGCCTCA-AC-AAAATTTCATAAACTTATGATGAATTTCATGGGTT-GCACACA
*
583828 GAGTGCCT-ATATAGTTGTTCATCAATATATGATGAATTCCATGGGTTGCACACTTAGTGCCTAA
63 GAGTGCCTGA-ACAGTTGTTCATCAATATATGATGAATTCCAT-GGTTGCACACTTAGTGCCTAA
* *
583892 ATAGTTGTTCATCAACTTATGATGAA-TTCTGTGGG
126 ACAATTGTTCATCAACTTATGATGAATTTCTGTGGG
* * ** * **
583927 TTGCACACTTAGTGCCTGAACGATTTTTCATCAACTTATGATGAATTTCATGGGTTGCACACTTA
1 TTGCACAC-TAGTGCCTCAACAAAATTTCATAAACTTATGATGAATTTCATGGGTTGCACACAGA
* * * *
583992 GTGCCTGAACGGTTGTTCATCAATTTATGATGAATTCCGTGGTTGCACACTTAGTGCCTGAACAA
65 GTGCCTGAACAGTTGTTCATCAATATATGATGAATTCCATGGTTGCACACTTAGTGCCTAAACAA
* *
584057 TTTTTCATCAACTTATGATGAA-TTCCGTGGG
130 TTGTTCATCAACTTATGATGAATTTCTGTGGG
* *** * * *
584088 TTGCACACTTAGTGCCTGAAC-GGTTGTTCGTCAACTTATGATGAA-TTCTGTGGGTTGCACACA
1 TTGCACAC-TAGTGCCTCAACAAAAT-TTCATAAACTTATGATGAATTTC-ATGGGTTGCACACA
* * * *
584151 TAGTGTCTGAAC-GATTGTTCATCAACT-TGTGATGAATTCCGTGGGTTGCACACTTAGTGCCTA
63 GAGTGCCTGAACAG-TTGTTCATCAA-TATATGATGAATTCCAT-GGTTGCACACTTAGTGCCTA
584214 TTTGGTAATC
Statistics
Matches: 250, Mismatches: 26, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
160 14 0.06
161 142 0.57
162 87 0.35
163 7 0.03
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (161 bp):
TTGCACACTAGTGCCTCAACAAAATTTCATAAACTTATGATGAATTTCATGGGTTGCACACAGAG
TGCCTGAACAGTTGTTCATCAATATATGATGAATTCCATGGTTGCACACTTAGTGCCTAAACAAT
TGTTCATCAACTTATGATGAATTTCTGTGGG
Found at i:584097 original size:27 final size:27
Alignment explanation
Indices: 584067--584149 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
584057 TTTTTCATCA
584067 ACTTATGATGAATTCCGTGGGTTGCAC
1 ACTTATGATGAATTCCGTGGGTTGCAC
* * *
584094 ACTTAGTGCCTGAA--CGGT-TGTTCGTCA-
1 ACTTA-TG-ATGAATTCCGTGGGTT-G-CAC
*
584121 ACTTATGATGAATTCTGTGGGTTGCAC
1 ACTTATGATGAATTCCGTGGGTTGCAC
584148 AC
1 AC
584150 ATAGTGTCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
25 4 0.10
26 7 0.17
27 20 0.48
28 7 0.17
29 4 0.10
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (27 bp):
ACTTATGATGAATTCCGTGGGTTGCAC
Found at i:591676 original size:12 final size:12
Alignment explanation
Indices: 591659--591686 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
591649 AGGGGGAGTA
591659 ATTTCAAAATTG
1 ATTTCAAAATTG
591671 ATTTCAAAATTG
1 ATTTCAAAATTG
591683 ATTT
1 ATTT
591687 TCTTAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (12 bp):
ATTTCAAAATTG
Done.