Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 15 of 30
Found at i:2457331 original size:20 final size:19
Alignment explanation
Indices: 2457284--2457338 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
2457274 AAAACCCTTG
**
2457284 AAAGTATCGATACACATTC
1 AAAGTATCGATACATGTTC
2457303 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
2457323 AATGTATCGATACATG
1 AAAGTATCGATACATG
2457339 AAAAAGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:2457415 original size:13 final size:13
Alignment explanation
Indices: 2457397--2457422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2457387 TACAGCAAGT
2457397 ATGTATCGATACA
1 ATGTATCGATACA
2457410 ATGTATCGATACA
1 ATGTATCGATACA
2457423 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2459672 original size:21 final size:21
Alignment explanation
Indices: 2459639--2459683 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2459629 TTGCAAGTTG
*
2459639 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2459661 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2459681 AAA
1 AAA
2459684 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2461507 original size:15 final size:15
Alignment explanation
Indices: 2461487--2461517 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2461477 TAAAAATGTC
*
2461487 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2461502 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2461517 C
1 C
2461518 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2463605 original size:20 final size:20
Alignment explanation
Indices: 2463526--2463605 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
2463516 AATGTCCAAA
*
2463526 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
2463546 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
2463571 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
2463591 TTGTATCGATACATT
1 ATGTATCGATACATT
2463606 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:2463609 original size:13 final size:13
Alignment explanation
Indices: 2463591--2463616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2463581 ACATTTTTCT
2463591 TTGTATCGATACA
1 TTGTATCGATACA
2463604 TTGTATCGATACA
1 TTGTATCGATACA
2463617 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2466179 original size:13 final size:13
Alignment explanation
Indices: 2466161--2466186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2466151 TACAGCAAGT
2466161 ATGTATCGATACA
1 ATGTATCGATACA
2466174 ATGTATCGATACA
1 ATGTATCGATACA
2466187 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2467347 original size:14 final size:15
Alignment explanation
Indices: 2467330--2467364 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2467320 TTTCTTTTCC
2467330 TTTTTT-TTATTA-T
1 TTTTTTATTATTACT
2467343 TTTTTTATTATTACT
1 TTTTTTATTATTACT
2467358 TTTTTTA
1 TTTTTTA
2467365 ATTTGATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 6 0.30
15 8 0.40
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTATTATTACT
Found at i:2467727 original size:19 final size:21
Alignment explanation
Indices: 2467688--2467727 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2467678 CTAATTCAAT
2467688 ATGAATTTAATAAAAATATTTG
1 ATGAATTT-ATAAAAATATTTG
2467710 ATGAATTT-TAAAAA-ATTT
1 ATGAATTTATAAAAATATTT
2467728 AAATTGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
ATGAATTTATAAAAATATTTG
Found at i:2467858 original size:152 final size:152
Alignment explanation
Indices: 2467636--2468083 Score: 496
Period size: 153 Copynumber: 2.9 Consensus size: 152
2467626 TTATTATATG
* * * * *
2467636 AAAAAAA-TGTAAAACTTATAAAATAAATTAAA-TTTTCACAAACTAATTCAATATGAATTTAAT
1 AAAAAAATTCTAAAACTTATAAAATAAATTAAATTTTTCA-AAACTGATTTAATATGAATTAAAC
* *
2467699 AAAAATATTTGATGAATTTTAAAAAATT-TAAATTGAGAAAAATCCAATCGGAGAAATTTAAGGA
65 AATAATATTTGAAGAATTTT-AAAAATTATAAATT-AGAAAAATCCAATCGGAGAAATTTAAGGA
* * **
2467763 TTAGAAAACTTCATATCTTGGTGTT
128 GTAGAAAACTCCATATCTTGGTAAT
* * **
2467788 AAAAAAATTCTAAAACTCATAAAAT-AATTAAATTTTTCAAAACTGATTTAACATGGGTTAAACA
1 AAAAAAATTCTAAAACTTATAAAATAAATTAAATTTTTCAAAACTGATTTAATATGAATTAAACA
* * * *
2467852 ATAATATTTGAAGAATTTTGAAAATTATAAACATAGAAAAAT-CACA-CCGAAAAATTTACA-GA
66 ATAATATTTGAAGAATTTTAAAAATTATAAA-TTAGAAAAATCCA-ATCGGAGAAATTTA-AGGA
* * *
2467914 GTAAAAAACTCCGTACCTTGGTAAT
128 GTAGAAAACTCCATATCTTGGTAAT
* * * * *
2467939 AGAAAAAATTTTAAAACTTATAAAATAAATTGAATTTTTCAAAATTGAGTTAATATAAATTAAAC
1 A-AAAAAATTCTAAAACTTATAAAATAAATTAAATTTTTCAAAACTGATTTAATATGAATTAAAC
* * * *
2468004 AATAATATTTGAAGAATTTTAAAAATTATGAATTTAGAAAAATCCTATCGGAGAAATTTACGAAG
65 AATAATATTTGAAGAATTTTAAAAATTAT-AAATTAGAAAAATCCAATCGGAGAAATTTAAGGAG
2468069 TAGAAAACTCCATAT
129 TAGAAAACTCCATAT
2468084 TTTAAAAATA
Statistics
Matches: 242, Mismatches: 42, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
151 39 0.16
152 85 0.35
153 91 0.38
154 27 0.11
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.32
Consensus pattern (152 bp):
AAAAAAATTCTAAAACTTATAAAATAAATTAAATTTTTCAAAACTGATTTAATATGAATTAAACA
ATAATATTTGAAGAATTTTAAAAATTATAAATTAGAAAAATCCAATCGGAGAAATTTAAGGAGTA
GAAAACTCCATATCTTGGTAAT
Found at i:2469342 original size:43 final size:43
Alignment explanation
Indices: 2469295--2469804 Score: 325
Period size: 43 Copynumber: 11.9 Consensus size: 43
2469285 TGGTTGAGAT
* *
2469295 GAAACCATATGAACCAACGAGTTAGAAGGGTGTTGGCTGGGAC
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
* * * ** * * *
2469338 GAAACTATAAGTACCAATGAGTTAGAAGAATGCTGGCTGGGAT
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
* * *
2469381 GAAACCTTACGTACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
* * ** *
2469424 AAAACCATA-CATACCAACAAGTTA-AGAGGATGTTGG-TCAGGAC
1 GAAACCATATGA-ACCAATGAGTTAGA-AGGGTGTTGGCT-AGGAC
* * *
2469467 GAAACCATATGTACCAATGAGTTAGAAGCGTGTTGGC-CGTGAC
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAG-GAC
* * * * **
2469510 AAAACCATGTGAACCAATGAGTTAGAAAGGTGTTGCCCGGGAC
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
* * * * * *
2469553 AAAACCATATGAACCAACGAGTTAGAAAGGTGCTGGCAAGGAT
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
* * * * *
2469596 GAAACTATATGTACCAATAAGTTAGAAGGGTGTTAGCCAGGAC
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
* * * * * * * * * *
2469639 AAAACTATACGAACCGACGAGTTAGAAAGGTGTTAGCCAAGAT
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
** * * * * *
2469682 GAAACCATACAAACCAATGAGTCAAGAA-AGCGTTGG-TCAAGAT
1 GAAACCATATGAACCAATGAGT-TAGAAGGGTGTTGGCT-AGGAC
* * * * *
2469725 GAAACCATA-CATAGCAATGAGTTAGGAA-GGTGTTAGCCAGGAT
1 GAAACCATATGA-ACCAATGAGTTA-GAAGGGTGTTGGCTAGGAC
* * *
2469768 GAAACCATACGTACCAATGAGTTAGGAGGGTGTTGGC
1 GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGC
2469805 CGAGACAAAA
Statistics
Matches: 365, Mismatches: 87, Indels: 30
0.76 0.18 0.06
Matches are distributed among these distances:
42 7 0.02
43 352 0.96
44 6 0.02
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (43 bp):
GAAACCATATGAACCAATGAGTTAGAAGGGTGTTGGCTAGGAC
Found at i:2469494 original size:129 final size:128
Alignment explanation
Indices: 2469307--2469866 Score: 433
Period size: 129 Copynumber: 4.4 Consensus size: 128
2469297 AACCATATGA
* ** * * * *
2469307 ACCAACGAGTT-AGAAGGGTGTTGGCTGGGACGAAACTATAAGTACCAATGAGTTAGAAGAATGC
1 ACCAACGAGTTAAG-AGGATGTTGGCAAGGACGAAACCATATGTACCAATGAGTTAGAAG-GTGT
* ** * * * *
2469371 TGGCTGGGATGAAACCTTACGTACCAATGAGTTAGAAGGGTGTTGGCTAGGACAAAACCATACAT
64 TAGCCAGGATGAAACCATACGAACCAATGAGTTAGAAAGGTGTTGGCCAGGACAAAACCATACAT
*
2469436 ACCAACAAGTTAAGAGGATGTTGGTC-AGGACGAAACCATATGTACCAATGAGTTAGAAGCGTGT
1 ACCAACGAGTTAAGAGGATGTTGG-CAAGGACGAAACCATATGTACCAATGAGTTAGAAG-GTGT
* ** ** * * *
2469500 TGGCC-GTGACAAAACCATGTGAACCAATGAGTTAGAAAGGTGTTGCCCGGGACAAAACCATATG
64 TAGCCAG-GATGAAACCATACGAACCAATGAGTTAGAAAGGTGTTGGCCAGGACAAAACCATA-C
2469564 A-
127 AT
* * * * *
2469565 ACCAACGAGTTAGAAAGG-TGCTGGCAAGGATGAAACTATATGTACCAATAAGTTAGAAGGGTGT
1 ACCAACGAGTTA-AGAGGATGTTGGCAAGGACGAAACCATATGTACCAATGAGTTAGAA-GGTGT
** * * * * * ** *
2469629 TAGCCAGGACAAAACTATACGAACCGACGAGTTAGAAAGGTGTTAGCCAAGATGAAACCATACAA
64 TAGCCAGGATGAAACCATACGAACCAATGAGTTAGAAAGGTGTTGGCCAGGACAAAACCATACAT
* * * * * ** *
2469694 ACCAATGAGTCAAGA-AAGCGTTGGTCAA-GATGAAACCATACATAGCAATGAGTTAGGAAGGTG
1 ACCAACGAGTTAAGAGGA-TGTTGG-CAAGGACGAAACCATATGTACCAATGAGTTA-GAAGGTG
* * * *
2469757 TTAGCCAGGATGAAACCATACGTACCAATGAGTTAGGAGGGTGTTGGCC-GAGACAAAA-CATGC
63 TTAGCCAGGATGAAACCATACGAACCAATGAGTTAGAAAGGTGTTGGCCAG-GACAAAACCATAC
2469820 AT
127 AT
* * * * *
2469822 ACTAACGAGTT-AGAGCA--TTGGCTAGGACAAAACCATATGAACCAA
1 ACCAACGAGTTAAGAGGATGTTGGCAAGGACGAAACCATATGTACCAA
2469867 CAAAGAAAAA
Statistics
Matches: 340, Mismatches: 75, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
124 2 0.01
125 18 0.05
127 3 0.01
128 19 0.06
129 282 0.83
130 16 0.05
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (128 bp):
ACCAACGAGTTAAGAGGATGTTGGCAAGGACGAAACCATATGTACCAATGAGTTAGAAGGTGTTA
GCCAGGATGAAACCATACGAACCAATGAGTTAGAAAGGTGTTGGCCAGGACAAAACCATACAT
Found at i:2469934 original size:41 final size:40
Alignment explanation
Indices: 2469884--2470334 Score: 166
Period size: 41 Copynumber: 11.4 Consensus size: 40
2469874 AAATTGATCG
2469884 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTAGCCA
1 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTT-GCCA
* * ** * * * * *
2469925 AGATGAAACCATGCGAACCAATGAAAAG-AAGTTGAT-CGA
1 GGATGAAACCATACGAGTCAA-CAAAGGAAAGGTGTTGCCA
* **
2469964 -GATAAAACCATACGAGTCAACAAAGGAAAGGTGTTGGCTG
1 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTT-GCCA
* * * * * *
2470004 GGATG-AAGC-TA-GA-TGAACCAATGAAAGGAAGTTGACA
1 GGATGAAACCATACGAGTCAACAAAGGAAAGG-TGTTGCCA
* * *
2470041 GGGATAAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCG
1 -GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTT-GCCA
* * ** * *
2470083 GGATGAAATCATATGAACCAATGAAAGG-AAGTTGATTG---
1 GGATGAAACCATACGAGTCAA-CAAAGGAAAGGTG-TTGCCA
* *
2470121 GGATGAAACCATACGAGTCAACAAAGAAAAGGTGTTAGTCA
1 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTT-GCCA
* * ** * * *
2470162 GGATAAAATCATACGAACCACCAAA--AAA--AGTTGACTA
1 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTG-CCA
* * * * **
2470199 GGATGAAACCATACCAATTAACAAAGGAAAGATGTTGGCTG
1 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTT-GCCA
* * * * * *
2470240 GGACGAAACTATAC-A---AACCAATGAAAGGAAGTTGACTA
1 GGATGAAACCATACGAGTCAACAAAGGAAAGG-TGTTG-CCA
** * *
2470278 GGATGAAACCATATAAGTCAACAAAGGAAAGGTGTTGGCT
1 GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTGCCA
*
2470318 GAAATGAAACCATACGA
1 G-GATGAAACCATACGA
2470335 ACCAATGAAA
Statistics
Matches: 292, Mismatches: 86, Indels: 64
0.66 0.19 0.14
Matches are distributed among these distances:
36 1 0.00
37 57 0.20
38 70 0.24
39 14 0.05
40 8 0.03
41 105 0.36
42 37 0.13
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.17
Consensus pattern (40 bp):
GGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTGCCA
Found at i:2469982 original size:79 final size:79
Alignment explanation
Indices: 2469851--2470369 Score: 492
Period size: 79 Copynumber: 6.6 Consensus size: 79
2469841 GGCTAGGACA
* * * * *
2469851 AAACCATATGAACCAA-CAAAGAAAAATTGATCGGGATGAAACCATACGAGTCAACAAAGGAAAG
1 AAACCATACGAACCAATGAAA-AGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAG
* *
2469915 GTGTTAGCCAAGATG
65 GTGTTGGCCAGGATG
* *
2469930 AAACCATGCGAACCAATGAAAAGAAGTTGATCGAGATAAAACCATACGAGTCAACAAAGGAAAGG
1 AAACCATACGAACCAATGAAAAGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAGG
**
2469995 TGTTGGCTGGGATG
66 TGTTGGCCAGGATG
* * * * * * * *
2470009 AAGCTAGATGAACCAATGAAAGGAAGTTGA-CAGGGATAAAACCATACGAGTTAACAAAGGAAAG
1 AAACCATACGAACCAATGAAAAGAAGTTGATC-GAGATGAAACCATACGAGTCAACAAAGGAAAG
*
2470073 GTGTTGGCCGGGATG
65 GTGTTGGCCAGGATG
* * * * * *
2470088 AAATCATATGAACCAATGAAAGGAAGTTGATTGGGATGAAACCATACGAGTCAACAAAGAAAAGG
1 AAACCATACGAACCAATGAAAAGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAGG
* * *
2470153 TGTTAGTCAGGATA
66 TGTTGGCCAGGATG
* ** * * * * *
2470167 AAATCATACGAACC-ACCAAAAAAAGTTGA-CTAGGATGAAACCATACCAATTAACAAAGGAAAG
1 AAACCATACGAACCAATGAAAAGAAGTTGATCGA-GATGAAACCATACGAGTCAACAAAGGAAAG
* ** *
2470230 ATGTTGGCTGGGACG
65 GTGTTGGCCAGGATG
* * * * **
2470245 AAACTATACAAACCAATGAAAGGAAGTTGA-CTAGGATGAAACCATATAAGTCAACAAAGGAAAG
1 AAACCATACGAACCAATGAAAAGAAGTTGATCGA-GATGAAACCATACGAGTCAACAAAGGAAAG
* *
2470309 GTGTTGG-CTGAAATG
65 GTGTTGGCCAG-GATG
**
2470324 AAACCATACGAACCAATGAAAAGAAGTTGATCGAGACAAAACCATA
1 AAACCATACGAACCAATGAAAAGAAGTTGATCGAGATGAAACCATA
2470370 TGAACCAATG
Statistics
Matches: 360, Mismatches: 73, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
78 58 0.16
79 297 0.82
80 5 0.01
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.17
Consensus pattern (79 bp):
AAACCATACGAACCAATGAAAAGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAGG
TGTTGGCCAGGATG
Found at i:2470058 original size:158 final size:159
Alignment explanation
Indices: 2469883--2470353 Score: 549
Period size: 158 Copynumber: 3.0 Consensus size: 159
2469873 AAAATTGATC
* * ** *
2469883 GGGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTAGCCAAGATGAAACCATGCGAACCAATG
1 GGGATGAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCGGGATGAAACCATACGAACCAATG
* * *
2469948 AAAAGAAGTTGATCGAGATAAAACCATACGAGTCAACAAAGGAAAGGTGTTGGCTGGGATGAAGC
66 AAAGGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTGGCTGGGATGAAAC
* * *
2470013 TAGATGAACCAATGAAAGGAAGTTGAC-A
131 TATACGAACCAATGAAAAGAAGTTGACTA
* * *
2470041 GGGATAAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCGGGATGAAATCATATGAACCAATG
1 GGGATGAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCGGGATGAAACCATACGAACCAATG
* * * * *
2470106 AAAGGAAGTTGATTGGGATGAAACCATACGAGTCAACAAAGAAAAGGTGTTAG-TCAGGAT-AAA
66 AAAGGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTGGCT-GGGATGAAA
* ** *
2470169 ATCATACGAACC-ACCAAAAAAAGTTGACTA
130 CT-ATACGAACCAATGAAAAGAAGTTGACTA
* * * * * * *
2470199 -GGATGAAACCATACCAATTAACAAAGGAAAGATGTTGGCTGGGACGAAACTATACAAACCAATG
1 GGGATGAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCGGGATGAAACCATACGAACCAATG
* ** **
2470263 AAAGGAAGTTGA-CTAGGATGAAACCATATAAGTCAACAAAGGAAAGGTGTTGGCTGAAATGAAA
66 AAAGGAAGTTGATCGA-GATGAAACCATACGAGTCAACAAAGGAAAGGTGTTGGCTGGGATGAAA
*
2470327 CCATACGAACCAATGAAAAGAAGTTGA
130 CTATACGAACCAATGAAAAGAAGTTGA
2470354 TCGAGACAAA
Statistics
Matches: 258, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
157 126 0.49
158 132 0.51
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.17
Consensus pattern (159 bp):
GGGATGAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCGGGATGAAACCATACGAACCAATG
AAAGGAAGTTGATCGAGATGAAACCATACGAGTCAACAAAGGAAAGGTGTTGGCTGGGATGAAAC
TATACGAACCAATGAAAAGAAGTTGACTA
Found at i:2470271 original size:236 final size:237
Alignment explanation
Indices: 2469851--2470356 Score: 651
Period size: 236 Copynumber: 2.1 Consensus size: 237
2469841 GGCTAGGACA
* * * *
2469851 AAACCATATGAACCAA-CAAAGAAAAATTGATCGGGATGAAACCATACGAGTCAACAAAGGAAAG
1 AAACCATATGAACCAATGAAAG-GAAGTTGATCGGGATGAAACCATACGAGTCAACAAAGAAAAG
* * ** * * * *
2469915 GTGTTAGCCAAGATGAAACCATGCGAACCAATGAAAAGAAGTTGATCGAGATAAAACCATACGAG
65 GTGTTAGCCAAGATAAAACCATACGAACCAACCAAAAAAAGTTGATAGAGATAAAACCATACCAA
* * * **
2469980 TCAACAAAGGAAAGGTGTTGGCTGGGATGAAGCTAGATGAACCAATGAAAGGAAGTTGAC-AGGG
130 TCAACAAAGGAAAGATGTTGGCTGGGACGAAACTAGACAAACCAATGAAAGGAAGTTGACTA-GG
* * **
2470044 ATAAAACCATACGAGTTAACAAAGGAAAGGTGTTGGCCGGGATG
194 ATAAAACCATACAAGTCAACAAAGGAAAGGTGTTGGCCGAAATG
* *
2470088 AAATCATATGAACCAATGAAAGGAAGTTGATTGGGATGAAACCATACGAGTCAACAAAGAAAAGG
1 AAACCATATGAACCAATGAAAGGAAGTTGATCGGGATGAAACCATACGAGTCAACAAAGAAAAGG
* * * *
2470153 TGTTAGTCAGGATAAAATCATACGAACC-ACCAAAAAAAGTTGACTAG-GATGAAACCATACCAA
66 TGTTAGCCAAGATAAAACCATACGAACCAACCAAAAAAAGTTGA-TAGAGATAAAACCATACCAA
* *
2470216 TTAACAAAGGAAAGATGTTGGCTGGGACGAAACTATACAAACCAATGAAAGGAAGTTGACTAGGA
130 TCAACAAAGGAAAGATGTTGGCTGGGACGAAACTAGACAAACCAATGAAAGGAAGTTGACTAGGA
* * *
2470281 TGAAACCATATAAGTCAACAAAGGAAAGGTGTTGGCTGAAATG
195 TAAAACCATACAAGTCAACAAAGGAAAGGTGTTGGCCGAAATG
* *
2470324 AAACCATACGAACCAATGAAAAGAAGTTGATCG
1 AAACCATATGAACCAATGAAAGGAAGTTGATCG
2470357 AGACAAAACC
Statistics
Matches: 230, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
236 146 0.63
237 80 0.35
238 4 0.02
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (237 bp):
AAACCATATGAACCAATGAAAGGAAGTTGATCGGGATGAAACCATACGAGTCAACAAAGAAAAGG
TGTTAGCCAAGATAAAACCATACGAACCAACCAAAAAAAGTTGATAGAGATAAAACCATACCAAT
CAACAAAGGAAAGATGTTGGCTGGGACGAAACTAGACAAACCAATGAAAGGAAGTTGACTAGGAT
AAAACCATACAAGTCAACAAAGGAAAGGTGTTGGCCGAAATG
Found at i:2470410 original size:38 final size:38
Alignment explanation
Indices: 2470324--2470402 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
2470314 GGCTGAAATG
* *
2470324 AAACCATACGAACCAATGAAAAGAAGTTGATCGAGACA
1 AAACCATATGAACCAATGAAAAGAAGTTAATCGAGACA
* *
2470362 AAACCATATGAACCAATG-AAAGAAAGTTAATTGGGACA
1 AAACCATATGAACCAATGAAAAG-AAGTTAATCGAGACA
2470400 AAA
1 AAA
2470403 TTATATGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.52, C:0.15, G:0.18, T:0.15
Consensus pattern (38 bp):
AAACCATATGAACCAATGAAAAGAAGTTAATCGAGACA
Found at i:2470501 original size:117 final size:117
Alignment explanation
Indices: 2470288--2470503 Score: 263
Period size: 117 Copynumber: 1.8 Consensus size: 117
2470278 GGATGAAACC
** * *
2470288 ATATAAGTCAACAAAGGAAAGGTGTTGGCTGAAATGAAACCATACGAACCAATGAAAAGAAGTTG
1 ATATAAGTCAACAAAAAAAAGGTGTTGGATGAAATGAAACCATACGAACCAAAGAAAAGAAGTTG
* * *
2470353 ATCGAGACAAAACCATATGAACCAATGAAAGAAAGTTAATTGGGACAAAATT
66 ACCGAGACAAAACCATACGAACCAATAAAAGAAAGTTAATTGGGACAAAATT
* ** ** *
2470405 ATATGAGTCAACAAAAAAAAGGTGTTGGATGGGATGATTCCATACGAACTAAAGAAAA-AACGTT
1 ATATAAGTCAACAAAAAAAAGGTGTTGGATGAAATGAAACCATACGAACCAAAGAAAAGAA-GTT
* * **
2470469 GACCGGGACGAAACCATACGAGTCAATAAAAGAAA
65 GACCGAGACAAAACCATACGAACCAATAAAAGAAA
2470504 TGTGTTGGCT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
116 2 0.02
117 79 0.98
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (117 bp):
ATATAAGTCAACAAAAAAAAGGTGTTGGATGAAATGAAACCATACGAACCAAAGAAAAGAAGTTG
ACCGAGACAAAACCATACGAACCAATAAAAGAAAGTTAATTGGGACAAAATT
Found at i:2470520 original size:158 final size:158
Alignment explanation
Indices: 2470358--2470661 Score: 367
Period size: 158 Copynumber: 1.9 Consensus size: 158
2470348 AGTTGATCGA
* * * **
2470358 GACAAAACCATATGAACCAATGAAAGAAAGTTAATTGGGACAAAATTATATGAGTCAACAAAAAA
1 GACAAAACCATATGAACCAATAAAAGAAAGTTAACTAGGACAAAACCATATGAGTCAACAAAAAA
** * ** *
2470423 AAGGTGTTGGATGGGATGATTCCATACGAACTAAAGAAA-AAACGTTGACCGGGACGAAACCATA
66 AAGGTGTTGGACAGGACGAAACCATACAAACTAAAGAAAGAAA-GTTGACCGGGACGAAACCATA
*
2470487 CGAGTCAATAAAAGAAATGTGTTGGCTCG
130 CGAGTCAACAAAAGAAATGTGTTGGCTCG
* * ** * * * *
2470516 GACAAAACCATATGAACCATTAAAAGAAAGTTGACTAGGATGAAACCATATGAGTTAATATAAGA
1 GACAAAACCATATGAACCAATAAAAGAAAGTTAACTAGGACAAAACCATATGAGTCAACAAAAAA
* * * *
2470581 AAGGTGTTGGCCAGGACGAAACCATACAAACTAATGAAAGAAAGTTGACCGGGATGAAACCATAT
66 AAGGTGTTGGACAGGACGAAACCATACAAACTAAAGAAAGAAAGTTGACCGGGACGAAACCATAC
*
2470646 GAGTCAACAAAGGAAA
131 GAGTCAACAAAAGAAA
2470662 GGCATTAGCT
Statistics
Matches: 120, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
158 117 0.98
159 3 0.03
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (158 bp):
GACAAAACCATATGAACCAATAAAAGAAAGTTAACTAGGACAAAACCATATGAGTCAACAAAAAA
AAGGTGTTGGACAGGACGAAACCATACAAACTAAAGAAAGAAAGTTGACCGGGACGAAACCATAC
GAGTCAACAAAAGAAATGTGTTGGCTCG
Found at i:2470527 original size:41 final size:40
Alignment explanation
Indices: 2470474--2470607 Score: 121
Period size: 41 Copynumber: 3.4 Consensus size: 40
2470464 ACGTTGACCG
2470474 GGACGAAACCATACGAGTCAATAAAAGAAATGTGTTGGCTC
1 GGACGAAACCATACGAGTCAATAAAAGAAA-GTGTTGGCTC
* * ** * * *
2470515 GGACAAAACCATATGAACCATTAAAAGAAA--GTTGACTA
1 GGACGAAACCATACGAGTCAATAAAAGAAAGTGTTGGCTC
* * * *
2470553 GGATGAAACCATATGAGTTAATATAAGAAAGGTGTTGGC-C
1 GGACGAAACCATACGAGTCAATAAAAGAAA-GTGTTGGCTC
2470593 AGGACGAAACCATAC
1 -GGACGAAACCATAC
2470608 AAACTAATGA
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
38 29 0.41
41 42 0.59
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (40 bp):
GGACGAAACCATACGAGTCAATAAAAGAAAGTGTTGGCTC
Found at i:2470581 original size:38 final size:38
Alignment explanation
Indices: 2470538--2470649 Score: 109
Period size: 41 Copynumber: 2.9 Consensus size: 38
2470528 TGAACCATTA
*
2470538 AAAGAAAGTTGACTAGGATGAAACCATATGAGTTAAT-
1 AAAGAAAGTTGACCAGGATGAAACCATATGAGTTAATG
* * ** **
2470575 ATAAGAAAGGTGTTGGCCAGGACGAAACCATACAAACTAATG
1 A-AAGAAA---GTTGACCAGGATGAAACCATATGAGTTAATG
*
2470617 AAAGAAAGTTGACCGGGATGAAACCATATGAGT
1 AAAGAAAGTTGACCAGGATGAAACCATATGAGT
2470650 CAACAAAGGA
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
37 1 0.02
38 25 0.45
41 29 0.52
42 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (38 bp):
AAAGAAAGTTGACCAGGATGAAACCATATGAGTTAATG
Found at i:2470681 original size:79 final size:78
Alignment explanation
Indices: 2470362--2470690 Score: 264
Period size: 79 Copynumber: 4.2 Consensus size: 78
2470352 GATCGAGACA
* * * ** ** ** * *
2470362 AAACCATATGAACCAATGAAAGAAAGTTAATTGGGACAAAATTATATGAGTCAACAAAAAAAAGG
1 AAACCATACGAACTAATGAAAGAAAGTTGACCGGGATGAAACCATATGAGTCAA-TAAAGAAAGG
* * *
2470427 TGTTGGATGGGATG
65 TGTTGGCTAGGACG
** * * * *
2470441 ATTCCATACGAACTAAAGAAA-AAACGTTGACCGGGACGAAACCATACGAGTCAATAAAAGAAAT
1 AAACCATACGAACTAATGAAAGAAA-GTTGACCGGGATGAAACCATATGAGTCAAT-AAAGAAAG
* *
2470505 GTGTTGGCTCGGACA
64 GTGTTGGCTAGGACG
* * * * ** *
2470520 AAACCATATGAACCATTAAAAGAAAGTTGACTAGGATGAAACCATATGAGTTAATATAAGAAAGG
1 AAACCATACGAACTAATGAAAGAAAGTTGACCGGGATGAAACCATATGAGTCAATA-AAGAAAGG
*
2470585 TGTTGGCCAGGACG
65 TGTTGGCTAGGACG
* *
2470599 AAACCATACAAACTAATGAAAGAAAGTTGACCGGGATGAAACCATATGAGTCAACAAAGGAAAGG
1 AAACCATACGAACTAATGAAAGAAAGTTGACCGGGATGAAACCATATGAGTCAATAAA-GAAAGG
** * * *
2470664 CATTAGCTAGAATG
65 TGTTGGCTAGGACG
*
2470678 AAACCATATGAAC
1 AAACCATACGAAC
2470691 CAACGAAAAC
Statistics
Matches: 193, Mismatches: 52, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
78 6 0.03
79 184 0.95
80 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (78 bp):
AAACCATACGAACTAATGAAAGAAAGTTGACCGGGATGAAACCATATGAGTCAATAAAGAAAGGT
GTTGGCTAGGACG
Found at i:2470702 original size:19 final size:19
Alignment explanation
Indices: 2470678--2470717 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2470668 AGCTAGAATG
*
2470678 AAACCATATGAACCAACGA
1 AAACCATACGAACCAACGA
*
2470697 AAACCATACGAACTAACGA
1 AAACCATACGAACCAACGA
2470716 AA
1 AA
2470718 GGAAGTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.25, G:0.10, T:0.10
Consensus pattern (19 bp):
AAACCATACGAACCAACGA
Found at i:2471176 original size:44 final size:41
Alignment explanation
Indices: 2471127--2471225 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
2471117 GAATTGACCG
* *
2471127 AGATGAAACCATACGAGTCAACGAATTAGAAAGAGTGTTGGTCA
1 AGATGAAACCATACG-G--AACGAATGAAAAAGAGTGTTGGTCA
* *
2471171 GGATGAAACCATAC-GAACTAATGAAAAAGAGTGTTGGTCA
1 AGATGAAACCATACGGAACGAATGAAAAAGAGTGTTGGTCA
*
2471211 AGACGAAACCATACG
1 AGATGAAACCATACG
2471226 TATCAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
40 34 0.71
42 1 0.02
44 13 0.27
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (41 bp):
AGATGAAACCATACGGAACGAATGAAAAAGAGTGTTGGTCA
Found at i:2471917 original size:75 final size:74
Alignment explanation
Indices: 2471814--2471961 Score: 242
Period size: 75 Copynumber: 2.0 Consensus size: 74
2471804 TTTTTACGTT
2471814 TTACATTCCCCAGAGAGTCGACAAAATATTAGTGATGCTTCAAAATGACTAAAAACCTCAAACGT
1 TTACATTCCCCAGAGAGTCGACAAAATATTAGTGATGCTTCAAAATGACTAAAAACCTCAAACGT
2471879 TGATTTTTTA
66 TG-TTTTTTA
** * * *
2471889 TTACATTCCTTAGAGAGTCGGCAGAATATTAGTGATGCTTCAAAATGACTAAAACCCTCAAACGT
1 TTACATTCCCCAGAGAGTCGACAAAATATTAGTGATGCTTCAAAATGACTAAAAACCTCAAACGT
2471954 TGTTTTTT
66 TGTTTTTT
2471962 CCTAATAGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 6 0.09
75 62 0.91
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (74 bp):
TTACATTCCCCAGAGAGTCGACAAAATATTAGTGATGCTTCAAAATGACTAAAAACCTCAAACGT
TGTTTTTTA
Found at i:2472600 original size:24 final size:24
Alignment explanation
Indices: 2472564--2472612 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2472554 GTAATGAGCA
2472564 TAAAATAAAAGTATATAGACTACT
1 TAAAATAAAAGTATATAGACTACT
* * *
2472588 TAAAATAATAGTATGTATACTACT
1 TAAAATAAAAGTATATAGACTACT
2472612 T
1 T
2472613 GTCAAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (24 bp):
TAAAATAAAAGTATATAGACTACT
Found at i:2472666 original size:23 final size:23
Alignment explanation
Indices: 2472629--2472681 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2472619 TAGTCATCAG
*
2472629 CATAAT-AATCCTTAGCAATAAC
1 CATAATAAATCATTAGCAATAAC
* *
2472651 CATAATAAATCATTAGCAATGAG
1 CATAATAAATCATTAGCAATAAC
2472674 CATAATAA
1 CATAATAA
2472682 TTGTGGCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.26
Consensus pattern (23 bp):
CATAATAAATCATTAGCAATAAC
Found at i:2476949 original size:87 final size:86
Alignment explanation
Indices: 2476851--2477305 Score: 279
Period size: 87 Copynumber: 5.2 Consensus size: 86
2476841 TCCAGAATAA
* * *
2476851 TAGGGATAGAGTTTCCCCAAAGATAAAATTCCATGAAGGAAAATTT-TATTTTTTTAAGAGCGGG
1 TAGGGATAGAGTTTCCCCAAAGATAAAATTACACGAA-GAAAATTTGAATTTTTTTAA-AGCGGG
* ****
2476915 GTTAGAATGTCCCCTCGGCGGAG
64 GTTAGAATATCCCCTCAAAAGAG
* * * * * * *
2476938 TGGGGATAGAGTTTTCCTAAAGGTAAAATTATACGAAAGAAAATTTGAATTTTGTTAAAGCTGGG
1 TAGGGATAGAGTTTCCCCAAAGATAAAATTACACG-AAGAAAATTTGAATTTTTTTAAAGCGGGG
* * * *
2477003 TTGGAGTATCCCCTTAAAATAG
65 TTAGAATATCCCCTCAAAAGAG
* * *
2477025 TAGGGATAGAGTTTCCCCAAAGATAAAATTTCACGAAGTAAATTTGAATTTTTTTAACA-TGGGG
1 TAGGGATAGAGTTTCCCCAAAGATAAAATTACACGAAGAAAATTTGAATTTTTTTAA-AGCGGGG
* * ** *** *
2477089 TTGGAGTATCCTTTTGTAATAG
65 TTAGAATATCCCCTCAAAAGAG
* * * * * * * * * * * **
2477111 TAGGGATGGA-CTTCTCCAAGGACAAAATTATATGAAGGAAGACTTAAATTTTTGTTAGAGCAAG
1 TAGGGATAGAGTTTCCCCAAAGATAAAATTACACGAA-GAAAATTTGAATTTTT-TTAAAGCGGG
* * * *** *
2477175 GTTGGAGTGTCCCCTTGGAGGAG
64 GTTAGAATATCCCCTCAAAAGAG
* * * * *
2477198 TGGGGATGGAGTTTCCCCAAAGGTAAAATTCCACGAAGTAAATTTGAATTTTTGTTAACA-CGGG
1 TAGGGATAGAGTTTCCCCAAAGATAAAATTACACGAAGAAAATTTGAATTTTT-TTAA-AGCGGG
* *
2477262 GTTAGAATATCCCCTCAAAATAA
64 GTTAGAATATCCCCTCAAAAGAG
* *
2477285 TGGGGATGGAGTTTCCCCAAA
1 TAGGGATAGAGTTTCCCCAAA
2477306 AATTATATGA
Statistics
Matches: 280, Mismatches: 80, Indels: 16
0.74 0.21 0.04
Matches are distributed among these distances:
85 19 0.07
86 63 0.22
87 168 0.60
88 30 0.11
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (86 bp):
TAGGGATAGAGTTTCCCCAAAGATAAAATTACACGAAGAAAATTTGAATTTTTTTAAAGCGGGGT
TAGAATATCCCCTCAAAAGAG
Found at i:2478985 original size:33 final size:33
Alignment explanation
Indices: 2478943--2479007 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2478933 AAAGAACATC
2478943 AAATCCTAAAACTACCACAAGGAAGGCAACAAT
1 AAATCCTAAAACTACCACAAGGAAGGCAACAAT
* *
2478976 AAATCCTAAAACTACCATAAGGATGGCAACAA
1 AAATCCTAAAACTACCACAAGGAAGGCAACAA
2479008 CAATGCATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (33 bp):
AAATCCTAAAACTACCACAAGGAAGGCAACAAT
Found at i:2485135 original size:3 final size:3
Alignment explanation
Indices: 2485129--2485157 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2485119 GTTATGTTGT
2485129 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2485158 TTGAGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2485523 original size:17 final size:18
Alignment explanation
Indices: 2485478--2485523 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2485468 ATATATATAT
2485478 GTAAAACATT--TATAGA
1 GTAAAACATTGGTATAGA
*
2485494 GTTAAAAAATTGGTATAGA
1 G-TAAAACATTGGTATAGA
2485513 -TAAAACATTGG
1 GTAAAACATTGG
2485524 AAAGTCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 18 0.72
19 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (18 bp):
GTAAAACATTGGTATAGA
Found at i:2491040 original size:153 final size:156
Alignment explanation
Indices: 2490872--2491239 Score: 383
Period size: 152 Copynumber: 2.4 Consensus size: 156
2490862 TACTTGATAC
* * * * *
2490872 CCCTAAAGGATTTAAAAAGGATTATAGATGAGATGAATCTATCCTAAATACTCATCTTCAGCATG
1 CCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATACCCACCTTCAGCATA
* * * *
2490937 AAAGCAGACCCGGTGATAACCTAGGACTTGGTTCTA-AAAATTAC-GAAAATGCCCCTACG-GGC
66 AAAGCAGACCCGATGAAAACCTAAGACTCGGTTCTAGAAAATTACAG-AAATGCCCCTA-GAGGC
* *
2490999 ATACCTTCGATGT-AAA-ATCTCGGCAA
129 ATACCTTCGATGTAAAAGATCCCGACAA
* * * *
2491025 CCCTAAAGGACTTAAAAA-GACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTCAGCATA
1 CCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATACCCACCTTCAGCATA
* * * * *
2491089 AAAGCGGACCTGATGAAAACCTAAGACTCGGTTCTAGGAAATTACAGAAATGTCCCTAGAGGTAT
66 AAAGCAGACCCGATGAAAACCTAAGACTCGGTTCTAGAAAATTACAGAAATGCCCCTAGAGGCAT
* * *
2491154 GCTTTTGATGTAAAAGTATCCCGACAA
131 ACCTTCGATGTAAAAG-ATCCCGACAA
* * * * *
2491181 CCCTAAGGGACTTAAAAAGAATTTTA-ACT-AGGATGAACCTATCCTAAATATCAACCTTC
1 CCCTAAAGGACTTAAAAAGGATTATAGA-TGA-GATGAACCTATCCTAAATACCCACCTTC
2491240 GGCGGACTCG
Statistics
Matches: 174, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
152 69 0.40
153 46 0.26
154 4 0.02
156 26 0.15
157 29 0.17
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (156 bp):
CCCTAAAGGACTTAAAAAGGATTATAGATGAGATGAACCTATCCTAAATACCCACCTTCAGCATA
AAAGCAGACCCGATGAAAACCTAAGACTCGGTTCTAGAAAATTACAGAAATGCCCCTAGAGGCAT
ACCTTCGATGTAAAAGATCCCGACAA
Found at i:2491748 original size:166 final size:165
Alignment explanation
Indices: 2491446--2491755 Score: 473
Period size: 165 Copynumber: 1.9 Consensus size: 165
2491436 CCGTATTCCG
*
2491446 AAAAAAAAGAGAATTTCAAGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTGAAAACTG
1 AAAAAAAAGAAAATTTCAAGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTGAAAACTG
*
2491511 AATTAATATTAAATAAATGATAATATTTGATAAATTTTAAAATTAAAAACCAAGAAAAATCCCCT
66 AATTAATATGAAATAAATGATAATATTTGATAAATTTTAAAATTAAAAACCAAGAAAAATCCCCT
2491576 CGAAAAAATCTACGAAGTAAAAAATATCGTATTTT
131 CGAAAAAATCTACGAAGTAAAAAATATCGTATTTT
* * *
2491611 AAAAAAAAGGAAAATTTTAAG-AAAAAATAAAAAACT-CATGAAAATGAATGAATTTTTGAAAAT
1 AAAAAAAA-GAAAATTTCAAGAAAAAAATAAAAAA-TGAATGAAAATGAATGAATTTTTGAAAAC
** **
2491674 TGAATTAATATGAAATAAATGATAATATTTGATGGATTTTAAAAATTAAAAATTAAGAAAAATCC
64 TGAATTAATATGAAATAAATGATAATATTTGATAAATTTT-AAAATTAAAAACCAAGAAAAATCC
*
2491739 TCC-CGAAAAAATTTACG
128 -CCTCGAAAAAATCTACG
2491756 GAGAAGAAAG
Statistics
Matches: 131, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
165 83 0.63
166 46 0.35
167 2 0.02
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.28
Consensus pattern (165 bp):
AAAAAAAAGAAAATTTCAAGAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTGAAAACTG
AATTAATATGAAATAAATGATAATATTTGATAAATTTTAAAATTAAAAACCAAGAAAAATCCCCT
CGAAAAAATCTACGAAGTAAAAAATATCGTATTTT
Found at i:2492881 original size:42 final size:43
Alignment explanation
Indices: 2492818--2492902 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
2492808 TATCTGAGAA
** *
2492818 TAAATCGACAAGTAGGTAAAAGATACAAAGG-TTGACTTGGGT
1 TAAATCGACAAGTAGACAAAAGATAAAAAGGATTGACTTGGGT
*
2492860 TAAATCGACAAGTCA-ACAAAAGATAAAAAGGATTTACTTGGGT
1 TAAATCGACAAGT-AGACAAAAGATAAAAAGGATTGACTTGGGT
2492903 CTAAGCCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 26 0.70
43 11 0.30
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (43 bp):
TAAATCGACAAGTAGACAAAAGATAAAAAGGATTGACTTGGGT
Found at i:2493258 original size:42 final size:42
Alignment explanation
Indices: 2493151--2493273 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2493141 TTACCCAGGA
* * * * *
2493151 CTAAGCCGACAGGTAAACGATGGATGAAGGAGTCTCCCGGGC
1 CTAAGCCGACAGGCAGACGATTGATAAAGGAATCTCCCGGGC
* * ** * *
2493193 CTGAGTCGACTA-GCAGATAATTGATAAAGGAATCTCTCGGGT
1 CTAAGCCGAC-AGGCAGACGATTGATAAAGGAATCTCCCGGGC
2493235 CTAAGCCGACAGGCAGACGATTGATAAAGGAAGTCTCCC
1 CTAAGCCGACAGGCAGACGATTGATAAAGGAA-TCTCCC
2493274 AGAACTGAGT
Statistics
Matches: 62, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
41 1 0.02
42 55 0.89
43 6 0.10
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (42 bp):
CTAAGCCGACAGGCAGACGATTGATAAAGGAATCTCCCGGGC
Found at i:2493634 original size:42 final size:43
Alignment explanation
Indices: 2493571--2493655 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
2493561 TATCTGAGAA
** *
2493571 TAAATTGACAAGTAGGTAAAAGATACAAAGG-TTGACTTGGGT
1 TAAATTGACAAGTAGACAAAAGATAAAAAGGATTGACTTGGGT
*
2493613 TAAATTGACAAGTCA-ACAAAAGATAAAAAGGATTTACTTGGGT
1 TAAATTGACAAGT-AGACAAAAGATAAAAAGGATTGACTTGGGT
2493656 CTAAGCCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 26 0.70
43 11 0.30
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (43 bp):
TAAATTGACAAGTAGACAAAAGATAAAAAGGATTGACTTGGGT
Found at i:2494224 original size:43 final size:43
Alignment explanation
Indices: 2494135--2494230 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
2494125 CTAGTTGACA
* * * * *
2494135 ATTGATAAAGGAAGTCTCTCGGGTCTGAACCGATGGGAAGATG
1 ATTGATAAAGAAAGTCTCTCGGGTCTGAACCAAAGGCAAGACG
* *
2494178 ATTGATAAAGAAAGTCTCTTGGGTCTGAATCAACAGGCAA-ACG
1 ATTGATAAAGAAAGTCTCTCGGGTCTGAACCAA-AGGCAAGACG
2494221 ATTGATAAAG
1 ATTGATAAAG
2494231 GAGTCTCCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 41 0.91
44 4 0.09
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (43 bp):
ATTGATAAAGAAAGTCTCTCGGGTCTGAACCAAAGGCAAGACG
Found at i:2494337 original size:43 final size:41
Alignment explanation
Indices: 2494213--2494354 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 41
2494203 TGAATCAACA
* *
2494213 GGCAAACGATTGAT-AAAGGAGTCTCCCAGGTCTAGATTGACG
1 GGCAAACGATTGATAAAAGAAGTCTCCCA-GTCTAG-TCGACG
* * * **
2494255 GGCAGACAATTGATAAACGAAGTCTCCCGAAACTGAGTCGACG
1 GGCAAACGATTGATAAAAGAAGTCTCCC-AGTCT-AGTCGACG
* *
2494298 GGCAAACGATTGATAAAAGAAGTCTCCTATGTCTAAGTCGATG
1 GGCAAACGATTGATAAAAGAAGTCTCCCA-GTCT-AGTCGACG
2494341 GGCAAACGATTGAT
1 GGCAAACGATTGAT
2494355 GAAGAATTCT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
42 13 0.16
43 65 0.80
44 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (41 bp):
GGCAAACGATTGATAAAAGAAGTCTCCCAGTCTAGTCGACG
Found at i:2494384 original size:42 final size:42
Alignment explanation
Indices: 2494290--2494402 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
2494280 CCCGAAACTG
* *
2494290 AGTCGACGGGCAAACGATTGATAAAAGAAGTCTCCTATGTCTA
1 AGTCGATGGGCAAACGATTGAT-GAAGAAGTCTCCTATGTCTA
* * *
2494333 AGTCGATGGGCAAACGATTGATGAAGAATTCTCTTGA-GTCTG
1 AGTCGATGGGCAAACGATTGATGAAGAAGTCTCCT-ATGTCTA
* *
2494375 AG-CTGATGGGCAGATGATTGATGAAGAA
1 AGTC-GATGGGCAAACGATTGATGAAGAA
2494403 AGTTTCCCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
41 1 0.02
42 38 0.62
43 22 0.36
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (42 bp):
AGTCGATGGGCAAACGATTGATGAAGAAGTCTCCTATGTCTA
Found at i:2494544 original size:43 final size:43
Alignment explanation
Indices: 2494487--2494580 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
2494477 TTGATAAAAG
* *
2494487 GAAA-TCTCCCAAGACAAAGTCGAC-GGACAGATGATTGATGAA
1 GAAAGTCTCCCAAGACAAAGTCGACAAG-CAGATGATAGATGAA
* ** *
2494529 GAAAGTCTTCCAAGACTGAGTTGACAAGCAGATGATAGATGAA
1 GAAAGTCTCCCAAGACAAAGTCGACAAGCAGATGATAGATGAA
2494572 GAAAGTCTC
1 GAAAGTCTC
2494581 TTGGGACAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 4 0.09
43 38 0.88
44 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.19
Consensus pattern (43 bp):
GAAAGTCTCCCAAGACAAAGTCGACAAGCAGATGATAGATGAA
Found at i:2495241 original size:78 final size:78
Alignment explanation
Indices: 2495101--2495291 Score: 192
Period size: 78 Copynumber: 2.4 Consensus size: 78
2495091 CCTTTATGGA
** * * * *
2495101 CATGTGATGCATTAATACCATTTAGTGTTTGGGAATGAGGGATATGGCTAGGGATGTATGGGAAA
1 CATGTGATGCACCAATATCATCTAGTGTTTGGGAATGAGGGATATGGATAGGGATGGATGGGAAA
*
2495166 --CATCCCTCTTGGC
66 TGC-CCCCT-TTGGC
* * *
2495179 CATGTGATGCACCAATATCATCTAGTATTTGGGAATGAAGGG-TAT-GATTGGGAATGGGTGGGA
1 CATGTGATGCACCAATATCATCTAGTGTTTGGGAATG-AGGGATATGGATAGGG-ATGGATGGGA
*
2495242 AGTGCCCCCTTTGGC
64 AATGCCCCCTTTGGC
* * *
2495257 CTTGTGATGCACCAGTATCATCTAGCGTTTGGGAA
1 CATGTGATGCACCAATATCATCTAGTGTTTGGGAA
2495292 AAAAATAGAA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
77 5 0.05
78 80 0.85
79 8 0.09
80 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (78 bp):
CATGTGATGCACCAATATCATCTAGTGTTTGGGAATGAGGGATATGGATAGGGATGGATGGGAAA
TGCCCCCTTTGGC
Found at i:2497630 original size:13 final size:13
Alignment explanation
Indices: 2497612--2497637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2497602 CAATTTTTTG
2497612 TGTATCGATACAT
1 TGTATCGATACAT
2497625 TGTATCGATACAT
1 TGTATCGATACAT
2497638 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2500199 original size:13 final size:13
Alignment explanation
Indices: 2500181--2500219 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2500171 ATAATCACCC
*
2500181 TGTATCAATACAA
1 TGTATCGATACAA
2500194 TGTATCGATACAA
1 TGTATCGATACAA
2500207 TGTATCGATACAA
1 TGTATCGATACAA
2500220 AGTAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2506133 original size:13 final size:13
Alignment explanation
Indices: 2506115--2506140 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2506105 CAATTTTTTG
2506115 TGTATCGATACAT
1 TGTATCGATACAT
2506128 TGTATCGATACAT
1 TGTATCGATACAT
2506141 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2511677 original size:22 final size:21
Alignment explanation
Indices: 2511642--2511682 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2511632 TAGTTGGTGG
*
2511642 AGGGGGTTTCTTCTTTCTTTTT
1 AGGGGGTATCTTC-TTCTTTTT
*
2511664 AGGGGGTATGTTCTTCTTT
1 AGGGGGTATCTTCTTCTTT
2511683 GCAGATGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.07, C:0.12, G:0.27, T:0.54
Consensus pattern (21 bp):
AGGGGGTATCTTCTTCTTTTT
Found at i:2513730 original size:13 final size:13
Alignment explanation
Indices: 2513712--2513737 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2513702 CAATTTTTTG
2513712 TGTATCGATACAT
1 TGTATCGATACAT
2513725 TGTATCGATACAT
1 TGTATCGATACAT
2513738 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2513821 original size:20 final size:20
Alignment explanation
Indices: 2513776--2513851 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
2513766 CTGCTAAGAA
***
2513776 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
2513797 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
2513817 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
2513837 GTGTATCGATACATT
1 ATGTATCGATACATT
2513852 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:2514477 original size:21 final size:21
Alignment explanation
Indices: 2514436--2514479 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2514426 CTCTCCTTTA
* *
2514436 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2514457 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2514478 TC
1 TC
2514480 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2516303 original size:13 final size:13
Alignment explanation
Indices: 2516285--2516310 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2516275 ATAATCACCC
2516285 TGTATCGATACAA
1 TGTATCGATACAA
2516298 TGTATCGATACAA
1 TGTATCGATACAA
2516311 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2518409 original size:15 final size:15
Alignment explanation
Indices: 2518389--2518419 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2518379 ATTTCGTTTG
*
2518389 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2518404 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2518419 G
1 G
2518420 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2520252 original size:21 final size:21
Alignment explanation
Indices: 2520223--2520267 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2520213 AAGTTTTCAT
*
2520223 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2520243 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2520265 TTT
1 TTT
2520268 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2522590 original size:20 final size:20
Alignment explanation
Indices: 2522545--2522620 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
2522535 CTGCCAAGAA
***
2522545 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
2522566 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
2522586 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
2522606 GTGTATCGATACATT
1 ATGTATCGATACATT
2522621 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:2523328 original size:156 final size:157
Alignment explanation
Indices: 2522923--2523582 Score: 447
Period size: 156 Copynumber: 4.2 Consensus size: 157
2522913 TAGATGAGAC
* * * * * ** * * * ***
2522923 AAACCCATCCTAAACACCCACCTTCGGCATGAAAGTGGACCCGGTGACAACCTAGGACTTGGTTC
1 AAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACCTGATGATAACCTAGGACTCAATTC
* * * * *
2522988 T--AAAAAATTACGAAAATGCCCTTACGGGTATACCTTCGACGT---A--ATCCTGACAACCTTA
66 TAAAAAAAATTACGAAAATGTCC-TA-GGGGATACCTTTGACGTAAAAGTATCCTAACAACCCTA
* * * * *
2523046 AAGGACTTAAAAA-GACTAGAGATGGGAT
129 AAGGACATAAAAATGACTATAAAAGGAAT
* * * * ** ** * * **
2523074 GAACTTATCCTAAATGCCCACCTTCAGCATAAAAGTGGACCTTG-TGACAACCTAAGACTTGATT
1 AAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACC-TGATGATAACCTAGGACTCAATT
* * * *
2523138 CT--AGAAAATTACGAAAATATCCCTACGGGTATACCTTTGACGTAAAAGTATCCTAACAACTCT
65 CTAAAAAAAATTACGAAAATGT-CCTA-GGGGATACCTTTGACGTAAAAGTATCCTAACAACCCT
* * *
2523201 AAAGGACATAAAAA-GAATTTTAACTAGG-AT
128 AAAGGACATAAAAATG-ACTATAA-AAGGAAT
* * * * *
2523231 AAACCTA-CTCTAAATA-TCAGCCTTTGGCATAAAAGCGGATC-GGTGATAACCTAGGACTCAAT
1 AAACCTATC-CTAAATACCCA-CATTTGGCATAAAAGCAGACCTGATGATAACCTAGGACTCAAT
* * ** *
2523293 T-TCAAAAAAAATTACGAAAATGTCCTAGGGGATACCTTTGACGTGAAAGTATCTTAGTACCCCT
64 TCT-AAAAAAAATTACGAAAATGTCCTAGGGGATACCTTTGACGTAAAAGTATCCTAACAACCCT
*
2523357 AAAGGACTTAAAAATGACTATAAAAGGAAT
128 AAAGGACATAAAAATGACTATAAAAGGAAT
*
2523387 AAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACCTGATGATAACCTAGGACTCGATTC
1 AAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACCTGATGATAACCTAGGACTCAATTC
* * * * * ** **
2523452 TAAAAAAAGTTATGAAAATG-CCATTTAGGGGATACTTTTGATGTAAAAGTATCTTGGTCCCCCC
66 TAAAAAAAATTACGAAAATGTCC---TAGGGGATACCTTTGACGTAAAAGTATCCT-AACAACCC
* * *
2523516 TAAAGGACTTAAAAAGGACTATAAAAGGGAT
127 TAAAGGACATAAAAATGACTATAAAAGGAAT
* * *
2523547 GAACCTATCCTAAATACCCACATTCGACATAAAAGC
1 AAACCTATCCTAAATACCCACATTTGGCATAAAAGC
2523583 GAACCCAGTG
Statistics
Matches: 415, Mismatches: 69, Indels: 41
0.79 0.13 0.08
Matches are distributed among these distances:
151 88 0.21
152 3 0.01
154 1 0.00
155 5 0.01
156 128 0.31
157 78 0.19
158 19 0.05
159 27 0.07
160 66 0.16
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (157 bp):
AAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACCTGATGATAACCTAGGACTCAATTC
TAAAAAAAATTACGAAAATGTCCTAGGGGATACCTTTGACGTAAAAGTATCCTAACAACCCTAAA
GGACATAAAAATGACTATAAAAGGAAT
Found at i:2523554 original size:160 final size:156
Alignment explanation
Indices: 2523142--2523582 Score: 478
Period size: 156 Copynumber: 2.8 Consensus size: 156
2523132 TTGATTCTAG
* * * ** * *
2523142 AAAATTACGAAAATATCCCTACGGGTATACCTTTGACGTAAAAGTATCCTAACAACTCTAAAGGA
1 AAAATTACGAAAATGT-CCTA-GGGGATACCTTTGACGTAAAAGTATCTTAGTACCCCTAAAGGA
* * * * * * * *
2523207 CATAAAAAGAATTTTAACTAGG-ATAAACCTA-CTCTAAATA-TCAGCCTTTGGCATAAAAGCGG
64 CTTAAAAAGGACTATAA-AAGGAATAAACCTATC-CTAAATACCCA-CATTTGGCATAAAAGCAG
* *
2523269 ATCGGTGATAACCTAGGACTCAATTTCAAAA
126 ACCGATGATAACCTAGGACTCAATTTCAAAA
*
2523300 AAAATTACGAAAATGTCCTAGGGGATACCTTTGACGTGAAAGTATCTTAGTACCCCTAAAGGACT
1 AAAATTACGAAAATGTCCTAGGGGATACCTTTGACGTAAAAGTATCTTAGTACCCCTAAAGGACT
*
2523365 TAAAAATGACTATAAAAGGAATAAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACCTG
66 TAAAAAGGACTATAAAAGGAATAAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACC-G
*
2523430 ATGATAACCTAGGACTCGA-TTCTAAAA
130 ATGATAACCTAGGACTCAATTTC-AAAA
* * * * * *
2523457 AAAGTTATGAAAATG-CCATTTAGGGGATACTTTTGATGTAAAAGTATCTTGGTCCCCCCTAAAG
1 AAAATTACGAAAATGTCC---TAGGGGATACCTTTGACGTAAAAGTATCTTAGT-ACCCCTAAAG
* * * *
2523521 GACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCACATTCGACATAAAAGC
62 GACTTAAAAAGGACTATAAAAGGAATAAACCTATCCTAAATACCCACATTTGGCATAAAAGC
2523583 GAACCCAGTG
Statistics
Matches: 242, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
155 3 0.01
156 87 0.36
157 42 0.17
158 15 0.06
159 29 0.12
160 66 0.27
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (156 bp):
AAAATTACGAAAATGTCCTAGGGGATACCTTTGACGTAAAAGTATCTTAGTACCCCTAAAGGACT
TAAAAAGGACTATAAAAGGAATAAACCTATCCTAAATACCCACATTTGGCATAAAAGCAGACCGA
TGATAACCTAGGACTCAATTTCAAAA
Found at i:2524346 original size:128 final size:127
Alignment explanation
Indices: 2524128--2524366 Score: 345
Period size: 128 Copynumber: 1.9 Consensus size: 127
2524118 AAAAAGTGTC
* **
2524128 ATTTCATACCTTGATGGAAACCCGCCAAGATACGAAAATTTTGAAATCTTTTAATACCCCTACGG
1 ATTTCATACCTTAATGGAAACCCGAAAAGATACGAAAATTTTGAAATCTTTTAATACCCCTACGG
*
2524193 ATACCCATAGGAATATAAAAGATTAAAAACGATTAATATTTATTTATTTTTGGAAAAAAATT
66 ATACCCATAGGAATATAAAAAATTAAAAACGATTAATATTTATTTATTTTTGGAAAAAAATT
* * * *
2524255 ATTTCGTACCTTAATGGATACCCGAAAAGATACGAAAAGTTTTTGAAATCTTTT-ATACTCTTAC
1 ATTTCATACCTTAATGGAAACCCGAAAAGATACGAAAA--TTTTGAAATCTTTTAATACCCCTAC
** * *
2524319 GGATACTTATAGGAATATAAAAAATTAAAAATGATTAATATTTGTTTA
64 GGATACCCATAGGAATATAAAAAATTAAAAACGATTAATATTTATTTA
2524367 AATTAACGGG
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
127 33 0.34
128 51 0.52
129 14 0.14
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (127 bp):
ATTTCATACCTTAATGGAAACCCGAAAAGATACGAAAATTTTGAAATCTTTTAATACCCCTACGG
ATACCCATAGGAATATAAAAAATTAAAAACGATTAATATTTATTTATTTTTGGAAAAAAATT
Found at i:2526009 original size:18 final size:18
Alignment explanation
Indices: 2525988--2526030 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2525978 GAAAAATCTA
*
2525988 TAATTTATGAAACTGAAT
1 TAATTTATAAAACTGAAT
* *
2526006 TAATTTTTTAAAACTGATT
1 TAA-TTTATAAAACTGAAT
2526025 TAATTT
1 TAATTT
2526031 GAATCAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (18 bp):
TAATTTATAAAACTGAAT
Found at i:2526330 original size:18 final size:19
Alignment explanation
Indices: 2526309--2526344 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2526299 AAAAATAAAA
2526309 AATTTATG-AAAATGAATG
1 AATTTATGAAAAATGAATG
*
2526327 AATTTTTGAAAAATGAAT
1 AATTTATGAAAAATGAAT
2526345 TAATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
AATTTATGAAAAATGAATG
Found at i:2526358 original size:164 final size:163
Alignment explanation
Indices: 2525872--2526553 Score: 690
Period size: 164 Copynumber: 4.2 Consensus size: 163
2525862 ATGGGAGTTC
* * * * * * **
2525872 AATGACAATATTAGATGCATTTTAAAAATTTTAGACCAAAGAAAATCTCCCCGAAAATTTTTATG
1 AATGATAATATTTGATGAATTTTAAAAATTATAAACC-AAGAAAATC-CCTCGAAAAAATTTATG
* * * * * * * * *
2525937 GATTAGAAAACTCAGTTTTTCGGAAAAAAG-GAAATTTCAA-AGAAAAATCTATAATTTATGAAA
64 GAGTAGAAAACACCGTATTTC-GAAAAAAGAGGAATTTCAAGAAAAAAAT-AAAAAATTATGAAA
* * * * **
2526000 CTGAATTAATTTTTTAAAACTGATTTAAT-TTGAATCA
127 ATGAATGAATTTTTGAAAACTGAATTAATATAAAAT-A
** * * * * * *
2526037 AACAATGATGTTTGATAAATTTTAAAAATTGA-AAATCGAGAAAATCCC-CCAGAAAAATTTATG
1 AATGATAATATTTGATGAATTTTAAAAATT-ATAAACCAAGAAAATCCCTCGA-AAAAATTTATG
* * *
2526100 GAGTAGAAAACATCGTATTTCAAAAAAAGAGGAATTTCAAG----GAAT--AAAA-TATGAAAAT
64 GAGTAGAAAACACCGTATTTCGAAAAAAGAGGAATTTCAAGAAAAAAATAAAAAATTATGAAAAT
* *
2526158 GAATGAATTTTTGAAAATTGAATTAATATGAAATA
129 GAATGAATTTTTGAAAACTGAATTAATATAAAATA
* *
2526193 AATGATAATATTTGATGAACTTTAAAAATTATAAACCAAGAAAAGTCCACTCGAAAAAATTTATA
1 AATGATAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAA-TCC-CTCGAAAAAATTTATG
2526258 GAGTAGAAAACACCGTATTTCGAAAAAA-A-GAATTTCAAGAAAAAAATAAAAAATTTATGAAAA
64 GAGTAGAAAACACCGTATTTCGAAAAAAGAGGAATTTCAAGAAAAAAATAAAAAA-TTATGAAAA
*
2526321 TGAATGAATTTTTGAAAAATGAATTAATATAAAATA
128 TGAATGAATTTTTGAAAACTGAATTAATATAAAATA
* * * *
2526357 AATGATAATATTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACG
1 AATGATAATATTTGATGAATTTTAAAAATTATAAACCAAG-AAAAT-CCCTCGAAAAAATTTATG
* * * * *
2526422 AAGTAGAAAATATCGTATTTCGAAAAAAGAGGAATTTCAAGTAAAAAATAAAAACATCATGAAAA
64 GAGTAGAAAACACCGTATTTCGAAAAAAGAGGAATTTCAAGAAAAAAATAAAAA-ATTATGAAAA
* *
2526487 TAAATGAATTTTTGAAAACTGAGTTAATATAAAATA
128 TGAATGAATTTTTGAAAACTGAATTAATATAAAATA
*
2526523 AATGATAATATTTAATGAATTTTAAAAATTA
1 AATGATAATATTTGATGAATTTTAAAAATTA
2526554 AAAATTAAAA
Statistics
Matches: 433, Mismatches: 62, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
155 1 0.00
156 76 0.18
157 10 0.02
158 37 0.09
159 2 0.00
160 6 0.01
162 13 0.03
163 36 0.08
164 126 0.29
165 32 0.07
166 93 0.21
167 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.30
Consensus pattern (163 bp):
AATGATAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAATCCCTCGAAAAAATTTATGGA
GTAGAAAACACCGTATTTCGAAAAAAGAGGAATTTCAAGAAAAAAATAAAAAATTATGAAAATGA
ATGAATTTTTGAAAACTGAATTAATATAAAATA
Found at i:2526382 original size:320 final size:327
Alignment explanation
Indices: 2525872--2526553 Score: 819
Period size: 320 Copynumber: 2.1 Consensus size: 327
2525862 ATGGGAGTTC
* * * * * ** *
2525872 AATGACAATATTAGATGCATTTTAAAAATTTTAGACCAAAGAAAATCTCCCCGAAAATTTTTATG
1 AATGATAATATTTGATGAATTTTAAAAATTATAAACCAAAGAAAATCTCCCCGAAAAAATTTATA
* * * * * ** * *
2525937 GATTAGAAAACTCAGTTTTTCGGAAAAAAGGAAATTTCAAAGAAAAATCTATAATTTATGAAACT
66 GAGTAGAAAACACAGTATTTCGGAAAAAAAGAAATTTCAAAAAAAAATAAAAAATTTATGAAAAT
* * * * ** * *
2526002 GAATTAATTTTTTAAAACTGATTTAATTTGAATCAAACAATGATGTTTGATAAATTTTAAAAATT
131 GAATGAATTTTTGAAAAATGAATTAATTAAAATCAAACAATAATATTTGATAAATTTTAAAAATT
* * * * *
2526067 GAAAATCGAG-AAAATCCCC-CAGAAAAATTTATGGAGTAGAAAACATCGTATTTCAAAAAAAGA
196 AAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAACATCGTATTTCAAAAAAAGA
* * * *
2526130 GGAATTTCAAG-GAAT-AAA-AT-ATGAAAATGAATGAATTTTTGAAAATTGAATTAATATGAAA
261 GGAATTTCAAGAAAATAAAACATCATGAAAATAAATGAATTTTTGAAAACTGAATTAATATAAAA
2526191 TA
326 TA
* *
2526193 AATGATAATATTTGATGAACTTTAAAAATTATAAACC-AAGAAAAGTC-CACTCGAAAAAATTTA
1 AATGATAATATTTGATGAATTTTAAAAATTATAAACCAAAGAAAA-TCTC-CCCGAAAAAATTTA
*
2526256 TAGAGTAGAAAACACCGTATTTC-GAAAAAAAG-AATTTCAAGAAAAAAATAAAAAATTTATGAA
64 TAGAGTAGAAAACACAGTATTTCGGAAAAAAAGAAATTTCAA-AAAAAAATAAAAAATTTATGAA
** *
2526319 AATGAATGAATTTTTGAAAAATGAATTAATATAAAAT-AAATGATAATATTTGATGAATTTTAAA
128 AATGAATGAATTTTTGAAAAATGAATTAAT-TAAAATCAAACAATAATATTTGATAAATTTTAAA
* *
2526383 AATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAATATCGTATTTCGAAAA
192 AATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAACATCGTATTTCAAAAA
*
2526448 AAGAGGAATTTCAAGTAAAAAATAAAAACATCATGAAAATAAATGAATTTTTGAAAACTGAGTTA
257 AAGAGGAATTTCAAG---AAAAT-AAAACATCATGAAAATAAATGAATTTTTGAAAACTGAATTA
2526513 ATATAAAATA
318 ATATAAAATA
*
2526523 AATGATAATATTTAATGAATTTTAAAAATTA
1 AATGATAATATTTGATGAATTTTAAAAATTA
2526554 AAAATTAAAA
Statistics
Matches: 302, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
319 8 0.03
320 93 0.31
321 75 0.25
322 50 0.17
326 3 0.01
328 3 0.01
329 2 0.01
330 68 0.23
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.30
Consensus pattern (327 bp):
AATGATAATATTTGATGAATTTTAAAAATTATAAACCAAAGAAAATCTCCCCGAAAAAATTTATA
GAGTAGAAAACACAGTATTTCGGAAAAAAAGAAATTTCAAAAAAAAATAAAAAATTTATGAAAAT
GAATGAATTTTTGAAAAATGAATTAATTAAAATCAAACAATAATATTTGATAAATTTTAAAAATT
AAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAACATCGTATTTCAAAAAAAGA
GGAATTTCAAGAAAATAAAACATCATGAAAATAAATGAATTTTTGAAAACTGAATTAATATAAAA
TA
Found at i:2526543 original size:166 final size:163
Alignment explanation
Indices: 2526047--2526597 Score: 703
Period size: 164 Copynumber: 3.4 Consensus size: 163
2526037 AACAATGATG
* * * * * *
2526047 TTTGATAAATTTTAAAAATTGAAAATCGAG-AAAATCCCC-CAGAAAAATTTATGGAGTAGAAAA
1 TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAA
* *
2526110 CATCGTATTTCAAAAAAAGAGGAATTTCAAG---GAAT--AAAATATGAAAATGAATGAATTTTT
66 CATCGTATTTCGAAAAAAGAGGAATTTCAAGAAAAAATAAAAAATATGAAAATGAATGAATTTTT
* *
2526170 GAAAATTGAATTAATATGAAATAAATGATAATA
131 GAAAAATGAATTAATATAAAATAAATGATAATA
* * * * * * *
2526203 TTTGATGAACTTTAAAAATTATAAACCAAGAAAAGTCCACTCGAAAAAATTTA-TAGAGTAGAAA
1 TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGA-AGTAGAAA
*
2526267 ACACCGTATTTCGAAAAAA-A-GAATTTCAAGAAAAAAATAAAAAATTTATGAAAATGAATGAAT
65 ACATCGTATTTCGAAAAAAGAGGAATTTCAAG-AAAAAATAAAAAA--TATGAAAATGAATGAAT
2526330 TTTTGAAAAATGAATTAATATAAAATAAATGATAATA
127 TTTTGAAAAATGAATTAATATAAAATAAATGATAATA
2526367 TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAA
1 TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAA
* *
2526432 TATCGTATTTCGAAAAAAGAGGAATTTCAAGTAAAAAATAAAAACATCATGAAAATAAATGAATT
66 CATCGTATTTCGAAAAAAGAGGAATTTCAAG-AAAAAATAAAAA-AT-ATGAAAATGAATGAATT
* *
2526497 TTTGAAAACTGAGTTAATATAAAATAAATGATAATA
128 TTTGAAAAATGAATTAATATAAAATAAATGATAATA
* * * * *
2526533 TTTAATGAATTTTAAAAATTAAAAAT-TA-AAAAATCCTCCTGAAAAAAATTTACAAAGAAGAAA
1 TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCC-CCTCAAAAAAATTTACGAAGTAGAAA
2526596 AC
65 AC
2526598 CCTATAATTT
Statistics
Matches: 342, Mismatches: 36, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
156 34 0.10
157 8 0.02
158 35 0.10
160 3 0.01
162 4 0.01
164 132 0.39
165 28 0.08
166 97 0.28
167 1 0.00
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.28
Consensus pattern (163 bp):
TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAAATTTACGAAGTAGAAAA
CATCGTATTTCGAAAAAAGAGGAATTTCAAGAAAAAATAAAAAATATGAAAATGAATGAATTTTT
GAAAAATGAATTAATATAAAATAAATGATAATA
Found at i:2528618 original size:21 final size:21
Alignment explanation
Indices: 2528592--2528664 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
2528582 AACCCTTAAT
2528592 TGTATCAATACAATCTTGTCA
1 TGTATCAATACAATCTTGTCA
*
2528613 TGTATCAATACAATCTTGACA
1 TGTATCAATACAATCTTGTCA
* *
2528634 TGTATCATTACAATCCTGAT-A
1 TGTATCAATACAATCTTG-TCA
2528655 TGTATCAATA
1 TGTATCAATA
2528665 TAAAAGGTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (21 bp):
TGTATCAATACAATCTTGTCA
Found at i:2529163 original size:52 final size:51
Alignment explanation
Indices: 2529089--2529231 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 51
2529079 TTTGGAAAGA
* * *
2529089 AAATGTATCAATATATTTTTCATTGTACTGATACATTCTATGTTTTTGACCC
1 AAATGTATCAATACATTCTTCATTGTA-TGATACATTCTAGGTTTTTGACCC
* * *
2529141 AAATGTATCAATACATTCTTCATTTTATCGATACATTATAGGTTTTTGACCT
1 AAATGTATCAATACATTCTTCATTGTAT-GATACATTCTAGGTTTTTGACCC
** *
2529193 AAATGTATCGGTACATTCTTCAATGTATTGATACATTCT
1 AAATGTATCAATACATTCTTCATTGTA-TGATACATTCT
2529232 TCAATGTATC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 1 0.01
52 76 0.97
53 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.44
Consensus pattern (51 bp):
AAATGTATCAATACATTCTTCATTGTATGATACATTCTAGGTTTTTGACCC
Found at i:2529219 original size:20 final size:20
Alignment explanation
Indices: 2529194--2529241 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2529184 TTTTGACCTA
*
2529194 AATGTATCGGTACATTCTTC
1 AATGTATCGATACATTCTTC
*
2529214 AATGTATTGATACATTCTTC
1 AATGTATCGATACATTCTTC
2529234 AATGTATC
1 AATGTATC
2529242 AATAAATGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:2535146 original size:50 final size:50
Alignment explanation
Indices: 2534984--2535169 Score: 221
Period size: 50 Copynumber: 3.7 Consensus size: 50
2534974 TAACTAGATA
* * *
2534984 TATCGATACATTGAAGAATGTATCGATACATTTGGGTCAAAACCCAGAATG
1 TATCGATACAATAAAAAATGTATCGATACATTT-GGTCAAAACCCAGAATG
* * * * * * *
2535035 TATTGATATAATGAATAATGGATCGATACATTTAGGTCAAAAACTCAAAATG
1 TATCGATACAATAAAAAATGTATCGATACATTT-GGTC-AAAACCCAGAATG
* *
2535087 TATCAATACAATAAAAAATGTATCGATACATTTGGATC-AATCCCAGAATG
1 TATCGATACAATAAAAAATGTATCGATACATTTGG-TCAAAACCCAGAATG
2535137 TATCGATACAATAAAAAATGTATCGATACATTT
1 TATCGATACAATAAAAAATGTATCGATACATTT
2535170 TCTTTCCAGA
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
50 41 0.36
51 34 0.30
52 40 0.35
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (50 bp):
TATCGATACAATAAAAAATGTATCGATACATTTGGTCAAAACCCAGAATG
Found at i:2535259 original size:20 final size:21
Alignment explanation
Indices: 2535234--2535279 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2535224 ACATGCATCG
2535234 ATACATTAAC-TTATGTATCA
1 ATACATTAACTTTATGTATCA
* *
2535254 ATACATTCACTTTTTGTATCA
1 ATACATTAACTTTATGTATCA
2535275 ATACA
1 ATACA
2535280 AATTATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (21 bp):
ATACATTAACTTTATGTATCA
Found at i:2536023 original size:52 final size:52
Alignment explanation
Indices: 2535802--2536451 Score: 386
Period size: 52 Copynumber: 12.4 Consensus size: 52
2535792 CTCAAGTAAT
* * * ** * *
2535802 GTGCCAATGTG-TAGATTCAAAGCTTGCTACATCAGACTTAATGATGATAAAG
1 GTGCCAATGTGCT-GATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* * * *
2535854 GTGCCAATATGCTGATTTAAGGCTAGCAACATTGAACTTAAAGAT-A-AAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* * * *
2535904 TTGCCAATGTGCTGATTCAAGGCCAACGACATAGG-CTTAAAGATAATAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* * * *
2535955 GTGCCAATGTGCTGATTCCAGGCTAGCGACATTGGACTTGAAA-ATGATGAGG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTT-AAAGATAATAAAG
* * **
2536007 GTGCCAATGTGTTGATTCAAGGCTAGCAACATTGGACTTTGGAAAGAAGGTTTTGACAA-
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAC-TT--AAAG-A--TAAT-A-AAG
* * * * * **
2536066 GTGTCAATGTGTTAATTCAAGGCCAGCGACATTGGACTTGAAGATGGTAGAA-
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATA-AAG
* * * * ** * *
2536118 GTGCCAATATACTGATTCAAGGCCAACGACATCAGACTTAAAGTTGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* * * ** * * *
2536170 GTGCCAATATGTTGATTCAAGGCCAATGATATTTGGATTTAAAGAT--GAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACA-TTGGACTTAAAGATAATAAAG
* * * * * * * * * *
2536221 TTGCCAATGTGCTTATTCAGGGCCAACAATATTGGGCTTAAAGATGACAAAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
** * * * * * * * *
2536273 GTGGAAATATGCTAATTCTAGGCCAGCAATATTGGACTTGAAGATGAT-AAG
1 GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* * ** *
2536324 AGTGCTAATGTGCTGATTTAAGGCTAGCGACATTGGACTTAAAGATGGTAAGG
1 -GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* * * * * *
2536377 GTGCCAATATGCT-ATTTCAAGGCTAGCAAAATTAGACTTTAAGATGATAAAG
1 GTGCCAATGTGCTGA-TTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
* *
2536429 GTTCTAATGTGCTGATTCAAGGC
1 GTGCCAATGTGCTGATTCAAGGC
2536452 AAGTGATATT
Statistics
Matches: 472, Mismatches: 105, Indels: 42
0.76 0.17 0.07
Matches are distributed among these distances:
49 9 0.02
50 44 0.09
51 69 0.15
52 282 0.60
53 21 0.04
54 4 0.01
55 1 0.00
56 4 0.01
58 4 0.01
59 33 0.07
60 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAATAAAG
Found at i:2536386 original size:104 final size:104
Alignment explanation
Indices: 2535836--2536451 Score: 485
Period size: 104 Copynumber: 5.9 Consensus size: 104
2535826 TGCTACATCA
* * * * *
2535836 GACTTAATGATGATAAAGGTGCCAATATGCTGATTTAAGGCTAGCAACATTGAACTT-AA-A-GA
1 GACTTAAAGATGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTGAAGATGA
* *
2535898 TAAAAGTTGCCAATGTGCTGATTCAAGGCCAACGACATAG
66 TAAGAG-TGCCAATGTGCTGATTCAAGGCCAACGACATTG
* * * * * * *
2535938 G-CTTAAAGATAATAAAGGTGCCAATGTGCTGATTCCAGGCTAGCGACATTGGACTTGAAAATGA
1 GACTTAAAGATGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTGAAGATGA
* * * * * *
2536002 TGAGGGTGCCAATGTGTTGATTCAAGGCTAGCAACATTG
66 TAAGAGTGCCAATGTGCTGATTCAAGGCCAACGACATTG
** * * * *
2536041 GACTTTGGAAAGAAGGTTTTGACAA-GTGTCAATGTGTTAATTCAAGGCCAGCGACATTGGACTT
1 GAC-TT--AAAG-A--TGAT-A-AAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTT
* * * **
2536105 GAAGATGGT-AGAAGTGCCAATATACTGATTCAAGGCCAACGACATCA
58 GAAGATGATAAG-AGTGCCAATGTGCTGATTCAAGGCCAACGACATTG
* * * *** * * *
2536152 GACTTAAAGTTGATAAAGGTGCCAATATGTTGATTCAAGGCCAATGATATTTGGATTTAAAGATG
1 GACTTAAAGATGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACA-TTGGACTTGAAGATG
* * * * *
2536217 A-AAG-TTGCCAATGTGCTTATTCAGGGCCAACAATATTG
65 ATAAGAGTGCCAATGTGCTGATTCAAGGCCAACGACATTG
* * ** * *
2536255 GGCTTAAAGATGACAAAGGTGGAAATATGCTAATTCTAGGCCAGCAATATTGGACTTGAAGATGA
1 GACTTAAAGATGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTGAAGATGA
* * * *
2536320 TAAGAGTGCTAATGTGCTGATTTAAGGCTAGCGACATTG
66 TAAGAGTGCCAATGTGCTGATTCAAGGCCAACGACATTG
* * * * * * *
2536359 GACTTAAAGATGGTAAGGGTGCCAATATGCTATTTCAAGGCTAGCAAAATTAGACTTTAAGATGA
1 GACTTAAAGATGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTGAAGATGA
* *
2536424 TAA-AGGTTCTAATGTGCTGATTCAAGGC
66 TAAGA-GTGCCAATGTGCTGATTCAAGGC
2536452 AAGTGATATT
Statistics
Matches: 405, Mismatches: 90, Indels: 36
0.76 0.17 0.07
Matches are distributed among these distances:
101 48 0.12
102 17 0.04
103 99 0.24
104 134 0.33
105 19 0.05
107 4 0.01
108 5 0.01
110 6 0.01
111 71 0.18
112 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (104 bp):
GACTTAAAGATGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTGAAGATGA
TAAGAGTGCCAATGTGCTGATTCAAGGCCAACGACATTG
Found at i:2536524 original size:32 final size:32
Alignment explanation
Indices: 2536461--2536636 Score: 142
Period size: 32 Copynumber: 5.5 Consensus size: 32
2536451 CAAGTGATAT
* * *
2536461 TGGGC-TTAG-AAAGAGATGCCACTAACGTGTG
1 TGGGCTTTAGAAAAG-GTTGCCACCAACTTGTG
* * *
2536492 TGGGCTTTTGAGAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAAAGGTTGCCACCAACTTGTG
* * **
2536524 TAGGCTTTAAAAAAAGGTTGCCACTGACTTGTG
1 TGGGCTTT-AGAAAAGGTTGCCACCAACTTGTG
* * *
2536557 TGGGCTTT-GAAAAAGATGCCACCAATTTGTG
1 TGGGCTTTAGAAAAGGTTGCCACCAACTTGTG
* * *
2536588 TGGGCTTAAGAAGAGGTTGCCACCAACTCGTG
1 TGGGCTTTAGAAAAGGTTGCCACCAACTTGTG
* *
2536620 TTGGCTTAAGGAAAAGG
1 TGGGCTTTA-GAAAAGG
2536637 GATTGCTCCA
Statistics
Matches: 112, Mismatches: 28, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
31 29 0.26
32 50 0.45
33 33 0.29
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (32 bp):
TGGGCTTTAGAAAAGGTTGCCACCAACTTGTG
Found at i:2536554 original size:33 final size:33
Alignment explanation
Indices: 2536506--2536626 Score: 122
Period size: 33 Copynumber: 3.8 Consensus size: 33
2536496 CTTTTGAGAG
2536506 GGTTGCCACCAACTTGTGTAGGCTTTAAAAAAA
1 GGTTGCCACCAACTTGTGTAGGCTTTAAAAAAA
** * *
2536539 GGTTGCCACTGACTTGTGTGGGCTTT-GAAAAA
1 GGTTGCCACCAACTTGTGTAGGCTTTAAAAAAA
* * * * *
2536571 -GATGCCACCAATTTGTGTGGGC-TTAAGAAGA
1 GGTTGCCACCAACTTGTGTAGGCTTTAAAAAAA
* *
2536602 GGTTGCCACCAACTCGTGTTGGCTT
1 GGTTGCCACCAACTTGTGTAGGCTT
2536627 AAGGAAAAGG
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
30 2 0.03
31 21 0.30
32 23 0.33
33 24 0.34
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCAACTTGTGTAGGCTTTAAAAAAA
Found at i:2538781 original size:36 final size:34
Alignment explanation
Indices: 2538598--2538788 Score: 234
Period size: 34 Copynumber: 5.8 Consensus size: 34
2538588 CCTTACAACA
*
2538598 CTATCTTTTGA-AGGCTAAGATAGAA-C-C-TCC
1 CTATCTTTTCACAGGCTAAGATAGAACCTCTTCC
* *
2538628 CTATCTTTTCACAGGTTAAGATGGAA---CTTCC
1 CTATCTTTTCACAGGCTAAGATAGAACCTCTTCC
*
2538659 TTATCTTTTCACAGGCTAAGATAGAACCTCTTCC
1 CTATCTTTTCACAGGCTAAGATAGAACCTCTTCC
*
2538693 CTATCTTTTCACAGGCTAAGATTGAACCTCTTCC
1 CTATCTTTTCACAGGCTAAGATAGAACCTCTTCC
* *
2538727 CTATCTTTTCACAGGCTAAGATAGAATCTTTCTCC
1 CTATCTTTTCACAGGCTAAGATAGAACCTCT-TCC
* *
2538762 CTATCTTTTTCAAAAGCTAAGATAGAA
1 CTATC-TTTTCACAGGCTAAGATAGAA
2538789 ACCTTTCAAT
Statistics
Matches: 141, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
30 11 0.08
31 38 0.27
34 65 0.46
35 8 0.06
36 19 0.13
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (34 bp):
CTATCTTTTCACAGGCTAAGATAGAACCTCTTCC
Found at i:2539257 original size:20 final size:19
Alignment explanation
Indices: 2539232--2539273 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
2539222 CGTTGGACTC
*
2539232 AATGTATCGATACAATTCAT
1 AATGTATCCATACAATT-AT
2539252 AATGTATCCATACAATTAT
1 AATGTATCCATACAATTAT
2539271 AAT
1 AAT
2539274 TGTTGGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (19 bp):
AATGTATCCATACAATTAT
Found at i:2543202 original size:20 final size:20
Alignment explanation
Indices: 2543179--2543305 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 20
2543169 AAGTACCCAG
2543179 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
2543199 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
2543219 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
2543239 ATGTATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
2543269 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
2543290 ATGTATCGATACATTT
1 ATGTATCGATACATTT
2543306 AGTGAAAATT
Statistics
Matches: 88, Mismatches: 8, Indels: 22
0.75 0.07 0.19
Matches are distributed among these distances:
20 62 0.70
21 2 0.02
24 5 0.06
27 4 0.05
30 2 0.02
31 13 0.15
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2546914 original size:20 final size:20
Alignment explanation
Indices: 2546885--2546961 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
2546875 TTTTACCCAG
*
2546885 ATGTAACGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
2546905 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
2546925 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
2546945 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
2546962 GTCTTTTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:2547007 original size:91 final size:90
Alignment explanation
Indices: 2546835--2547009 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 90
2546825 TTTTACCCAG
* * * *
2546835 ATGTGTCGATACATTTTTTAATGTATCGATACATTCTATCTTTTACCCAGATGTAACGATACATT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTACCCAGATATAACGATACATT
2546900 CTTCAATGTATCGATACATGTATGA
66 CTTCAATGTATCGATACATGTATGA
* *
2546925 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATATATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATC-TTTTACCCAGATATAACGATACAT
* *
2546990 TTTTCAATGTATTGATACAT
65 TCTTCAATGTATCGATACAT
2547010 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
90 36 0.47
91 40 0.53
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (90 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTACCCAGATATAACGATACATT
CTTCAATGTATCGATACATGTATGA
Found at i:2552660 original size:30 final size:32
Alignment explanation
Indices: 2552625--2552784 Score: 119
Period size: 31 Copynumber: 4.9 Consensus size: 32
2552615 CCTTACAACC
* *
2552625 CTATCTTTTGA-AGGCTAAGATTGAACCTCCT
1 CTATCTTTTCACAGGCTAAGATAGAACCTCCT
* * *
2552656 -TATCTTTTCATAGGTTAAGATAGAA-CTTCT
1 CTATCTTTTCACAGGCTAAGATAGAACCTCCT
* *
2552686 CTATCTTTTCACGGGCTAAGATAGAACCTCTTCC
1 CTATCTTTTCACAGGCTAAGATAGAACCTC--CT
* * * * * *
2552720 CGATCTTTTGACAAGCTAAGATAAAACTTTCCC
1 CTATCTTTTCACAGGCTAAGATAGAAC-CTCCT
* *
2552753 CTTATTTTTTTCAAAGGCTAAGATAGAACCTC
1 C-TA-TCTTTTCACAGGCTAAGATAGAACCTC
2552785 TCAATCACTT
Statistics
Matches: 99, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
30 13 0.13
31 34 0.34
32 2 0.02
33 3 0.03
34 26 0.26
35 21 0.21
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (32 bp):
CTATCTTTTCACAGGCTAAGATAGAACCTCCT
Found at i:2553395 original size:13 final size:13
Alignment explanation
Indices: 2553377--2553401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2553367 TACAAAAAAC
2553377 ATGTATCGATACA
1 ATGTATCGATACA
2553390 ATGTATCGATAC
1 ATGTATCGATAC
2553402 TAAGTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2553419 original size:33 final size:32
Alignment explanation
Indices: 2553359--2553422 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
2553349 CATTTTATGG
2553359 TGTATCGATACAAAAAACATGTATCGATACAA
1 TGTATCGATACAAAAAACATGTATCGATACAA
** *
2553391 TGTATCGATACTAAGTAATATGTATCGATACA
1 TGTATCGATAC-AAAAAACATGTATCGATACA
2553423 TTTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAAAAACATGTATCGATACAA
Found at i:2553748 original size:15 final size:14
Alignment explanation
Indices: 2553729--2553763 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2553719 TTTGTTCACC
*
2553729 TTTTTTTTATTTTT
1 TTTTTTTTACTTTT
2553743 TGTTTTTTTACTTTT
1 T-TTTTTTTACTTTT
2553758 TTTTTT
1 TTTTTT
2553764 AAATTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.89
Consensus pattern (14 bp):
TTTTTTTTACTTTT
Found at i:2553750 original size:16 final size:16
Alignment explanation
Indices: 2553729--2553763 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2553719 TTTGTTCACC
2553729 TTTTTTTTA-TTTTTT
1 TTTTTTTTACTTTTTT
*
2553744 GTTTTTTTACTTTTTT
1 TTTTTTTTACTTTTTT
2553760 TTTT
1 TTTT
2553764 AAATTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTTTTTACTTTTTT
Found at i:2565080 original size:19 final size:20
Alignment explanation
Indices: 2565038--2565089 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2565028 AAGCCCAGAA
* *
2565038 GTATCGATACATATTACTTT
1 GTATCGATACATGTTACATT
2565058 GTATCGATACATGTT-CATT
1 GTATCGATACATGTTACATT
2565077 GTATCGATACATG
1 GTATCGATACATG
2565090 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
GTATCGATACATGTTACATT
Found at i:2565157 original size:13 final size:13
Alignment explanation
Indices: 2565141--2565168 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2565131 TGGGACATTA
2565141 TATTGATACATAG
1 TATTGATACATAG
2565154 TATTGATACATAG
1 TATTGATACATAG
2565167 TA
1 TA
2565169 AAATGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
TATTGATACATAG
Found at i:2566707 original size:26 final size:26
Alignment explanation
Indices: 2566630--2566709 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 26
2566620 TTTCCAACAA
2566630 CTGTTTCTCTTATTTCTTCATTGCAG
1 CTGTTTCTCTTATTTCTTCATTGCAG
* *
2566656 CTATCAGTT-TC-TA-AT-TTCATTGCAG
1 CTGT---TTCTCTTATTTCTTCATTGCAG
2566681 CTGTTTCTCTTATTTCTTCATTGCAG
1 CTGTTTCTCTTATTTCTTCATTGCAG
2566707 CTG
1 CTG
2566710 CTATTACTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 2 0.05
25 14 0.33
26 17 0.40
27 2 0.05
28 2 0.05
29 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (26 bp):
CTGTTTCTCTTATTTCTTCATTGCAG
Found at i:2566727 original size:27 final size:26
Alignment explanation
Indices: 2566671--2566730 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
2566661 AGTTTCTAAT
* *
2566671 TTCATTGCAGCTGTTTCTCTTATTTC
1 TTCATTGCAGCTGTTTCACTTATTGC
2566697 TTCATTGCAGCTGCTATT-ACTTATTGC
1 TTCATTGCAGCTG-T-TTCACTTATTGC
2566724 TTCATTG
1 TTCATTG
2566731 GTTTCAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 13 0.43
27 15 0.50
28 2 0.07
ACGTcount: A:0.15, C:0.22, G:0.13, T:0.50
Consensus pattern (26 bp):
TTCATTGCAGCTGTTTCACTTATTGC
Found at i:2567238 original size:57 final size:57
Alignment explanation
Indices: 2567155--2567307 Score: 210
Period size: 57 Copynumber: 2.8 Consensus size: 57
2567145 TGAAGTTTTC
2567155 ATGCAATGCAATGCCACCTAGAAAGCTTATGTGGCAACAAATTAAGCATGAAATGCA
1 ATGCAATGCAATGCCACCTAGAAAGCTTATGTGGCAACAAATTAAGCATGAAATGCA
* * *
2567212 ATGTAATGTAATGCCACCTA-ACAAGCTTTTGTGGCAACAAATTAAGCATG-AA-G--
1 ATGCAATGCAATGCCACCTAGA-AAGCTTATGTGGCAACAAATTAAGCATGAAATGCA
* *
2567265 -TGCAATGCAATGCCACCTAGAAAGCTTAAGTGGCAATAAATTA
1 ATGCAATGCAATGCCACCTAGAAAGCTTATGTGGCAACAAATTA
2567308 TGTAGAAATC
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
52 36 0.42
53 1 0.01
55 1 0.01
56 3 0.03
57 45 0.52
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (57 bp):
ATGCAATGCAATGCCACCTAGAAAGCTTATGTGGCAACAAATTAAGCATGAAATGCA
Found at i:2567418 original size:22 final size:22
Alignment explanation
Indices: 2567393--2567439 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2567383 AATAATTAAC
2567393 TAAATTTTAATT-TTGTTATTTT
1 TAAATTTT-ATTATTGTTATTTT
* *
2567415 TAAATTTTTTTATTTTTATTTT
1 TAAATTTTATTATTGTTATTTT
2567437 TAA
1 TAA
2567440 TAAATTGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TAAATTTTATTATTGTTATTTT
Found at i:2567422 original size:16 final size:16
Alignment explanation
Indices: 2567397--2567432 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2567387 ATTAACTAAA
2567397 TTTT-AATTTTGTTAT
1 TTTTAAATTTTGTTAT
*
2567412 TTTTAAATTTTTTTAT
1 TTTTAAATTTTGTTAT
2567428 TTTTA
1 TTTTA
2567433 TTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTAAATTTTGTTAT
Found at i:2568437 original size:42 final size:42
Alignment explanation
Indices: 2567968--2568463 Score: 294
Period size: 42 Copynumber: 11.7 Consensus size: 42
2567958 TCTCGGACCT
* * *
2567968 AAGCCGA-AGGGCAGAC-AAAGGGTAAAAAAGTCTCTAAGGTCG
1 AAGCCGACA-GGCAGACTAAA-GGTAAAGAAGTCTCTAGGGTCA
** * * *
2568010 AAGTTGACAAGTAGACTAAAGGTAAAGAATTCTC-ATGGGTCA
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTA-GGGTCA
* * *
2568052 AAGCCGACAAGCAGACTAAAGATAAAGAAGTTTCTAGGGTCA
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTAGGGTCA
*** * * *
2568094 AAATTGACAAGCAGACTAAAGGTAAAGAACTCT-TCAAGGTCA
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCT-AGGGTCA
* *
2568136 AAGCCGATAGGTAGAC-AAGAGGTGAAA-AAGTCTCTAGGGTCA
1 AAGCCGACAGGCAGACTAA-AGGT-AAAGAAGTCTCTAGGGTCA
* ** * * *
2568178 AAGCTGATGGGCAGACTAAAGGTAAAGAAGTTTTTAGGGTTA
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTAGGGTCA
* * * * * *
2568220 AAGCCAACGGGCAAAC-AAGAGGTGAAA-AAGTTTCCAAGGTCA
1 AAGCCGACAGGCAGACTAA-AGGT-AAAGAAGTCTCTAGGGTCA
** * *
2568262 AAGCTAACAAGCAGAGC-AAAGGTAAAGAAGTCTCTAAGGTCA
1 AAGCCGACAGGCAGA-CTAAAGGTAAAGAAGTCTCTAGGGTCA
* * * * * * *
2568304 AAGCCAATAAGTAGACTAAATGTAGAGAAATCTCCTA-GGTCA
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT-CTAGGGTCA
* * * **
2568346 AAGCCGATAGGCA-AATAAAAGGTAAAAAAAAAGTCTCTAAAGTCA
1 AAGCCGACAGGCAGACT-AAAGGT---AAAGAAGTCTCTAGGGTCA
* * *
2568391 AAGCCGACCGGAAAACTAAAGGTAAAGAAGTCTCTAGGGTCA
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTAGGGTCA
* * * * *
2568433 AAGCCAATAGGCAGTCTAAAAGTAAAAAAGT
1 AAGCCGACAGGCAGACTAAAGGTAAAGAAGT
2568464 TAGAAGGGTT
Statistics
Matches: 353, Mismatches: 79, Indels: 44
0.74 0.17 0.09
Matches are distributed among these distances:
41 15 0.04
42 286 0.81
43 20 0.06
44 3 0.01
45 27 0.08
46 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.17
Consensus pattern (42 bp):
AAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTAGGGTCA
Found at i:2568626 original size:101 final size:100
Alignment explanation
Indices: 2568517--2568718 Score: 287
Period size: 101 Copynumber: 2.0 Consensus size: 100
2568507 ATGGGTTGAC
* * * ** *
2568517 TTTGGCAAAACCAATGAAGTCAATCAGTTAAAAGGTTAGTCAAGGGGTTAAAAAGGTTTGACCAT
1 TTTGGCAAAACCAATGAAGTCAATCAATTAAAAAGTCAGTCAAAAGGTTAAAAAGATTTGACCAT
*
2568582 GGTGGTAACCATACATCAAATCAAAATGAAAAGAA
66 GGTGGTAACCATACATCAAATCAAAATAAAAAGAA
* * *
2568617 TTTGAGCAAAACTAATGAAGTTAATCAATTAAAAAGTCAGTCAAAAGGTTAGAAAGATTTGACCA
1 TTTG-GCAAAACCAATGAAGTCAATCAATTAAAAAGTCAGTCAAAAGGTTAAAAAGATTTGACCA
* *
2568682 TGGTGGTAACCATACGTCAAATCAGAATAAAAAGAA
65 TGGTGGTAACCATACATCAAATCAAAATAAAAAGAA
2568718 T
1 T
2568719 CTGACTAGGG
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
100 4 0.04
101 85 0.96
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (100 bp):
TTTGGCAAAACCAATGAAGTCAATCAATTAAAAAGTCAGTCAAAAGGTTAAAAAGATTTGACCAT
GGTGGTAACCATACATCAAATCAAAATAAAAAGAA
Found at i:2568732 original size:44 final size:43
Alignment explanation
Indices: 2568669--2569444 Score: 488
Period size: 44 Copynumber: 17.7 Consensus size: 43
2568659 AAAAGGTTAG
*
2568669 AAAG-ATTTGACCATGGTGGTAACCATACGTCAAATCAGAATAA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * * *
2568712 AAAGAATCTGACTAGGGTGGTAACCATACGTCAGACAGGAA-AG
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACA-GAATAA
** * *
2568755 AGGGGATTTGACCAGAGTGGTAACCATACGTCAAATCAGAATAA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * * * * * * *
2568799 GAAGAATCTAACTAGGGCGGTAACCATATGTCAGACTAAAATGAGA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAAC-AGAAT-A-A
** *
2568845 AAAG--TTTGACCAAAGTGGTAGCCATACGTCAAACA-AA-AA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAGAATAA
** * * * *
2568884 GGAAGAGGCTTTGACTAGGGAGGTAAACATATGTCAAATCAGAATAA
1 --AA-AGAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * * * * * *
2568931 GAAGAATTTGACTAAGGAGGTAACCATACGTGAGACTAAAATAA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAAC-AGAATAA
* * * *
2568975 GAAA-AGTTTGACCAAGGTGGTAACTATACATCAAACAGAA-AGA
1 -AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAGAATA-A
* * *
2569018 AAAGGGATTTGACTAGGGTGTTAACCATACGTCAAATCAGAATAA
1 AAA-GAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * * * * * * *** *
2569063 GAAGAATCTAACTAGGCTGGTAACTATACCTTTGACTGAAATGAGA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAG-AAT-A-A
*
2569109 AAAG--TTTGACCAGGGTGGTAACTATACGTCAAACAGAA-AGGA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAGAATA--A
2569151 AAATG-ATTTGACCAGGGTGGTAACCATACGTCAAATCAGAATAA
1 AAA-GAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * *
2569195 GAAGAA-TTGACCAAGGTGGTAACCATATGTCAAACAGAA-AGGA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAGAATA--A
* * * **
2569238 AAGGGATTTGACCAGGGTGGTAGCCATATTTCAAATCAGAATAA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * * *
2569282 GAAGAATCTGACCAGGGTAGTAACCATACGTCAAACTGAAATGAGA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAG-AAT-A-A
* * * * *
2569328 AAAG--TTTGACTAGGGTGGTAGCCATATGTTAAACA-AAAAGA
1 AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAGAATA-A
* *
2569369 AAAGGGATTTGACCAGGGTGGTAACCATGCGTCAAATCAGAATAA
1 AAA-GAATTTGACCAGGGTGGTAACCATACGTCAAA-CAGAATAA
* * *
2569414 GAAGAATCTGACCACGGTGGTAACCATACGT
1 AAAGAATTTGACCAGGGTGGTAACCATACGT
2569445 TAGACAAGAG
Statistics
Matches: 561, Mismatches: 128, Indels: 87
0.72 0.16 0.11
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 10 0.02
42 21 0.04
43 83 0.15
44 392 0.70
45 31 0.06
46 20 0.04
47 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (43 bp):
AAAGAATTTGACCAGGGTGGTAACCATACGTCAAACAGAATAA
Found at i:2569278 original size:132 final size:128
Alignment explanation
Indices: 2568720--2569444 Score: 645
Period size: 132 Copynumber: 5.5 Consensus size: 128
2568710 AAAAAGAATC
* * * * * *
2568720 TGACTAGGGTGGTAACCATACGTCAGACAGGAAAGAGGGGATTTGACCAGAGTGGTAACCATACG
1 TGACCAGGGTGGTAACCATACGTCAAACAGAAAAGAAGAGATTTGACCAGGGTGGTAACCATACG
* * * *
2568785 TCAAATCAGAATAAGAAGAATCTAACTAGGGCGGTAACCATATGTCAGACTAAAATGAGAAAAGT
66 TCAAATCAGAATAAGAAGAAT-TGACTAAGGTGGTAACCATATGTCAGAC-AAAAAG-GAAAAGT
2568850 T
128 T
** * * * * *
2568851 TGACCAAAGTGGTAGCCATACGTCAAACA-AAAAGGAAGAGGCTTTGACTAGGGAGGTAAACATA
1 TGACCAGGGTGGTAACCATACGTCAAACAGAAAA-GAAGA-GATTTGACCAGGGTGGTAACCATA
* * * * *
2568915 TGTCAAATCAGAATAAGAAGAATTTGACTAAGGAGGTAACCATACGTGAGACTAAAATAAGAAAA
64 CGTCAAATCAGAATAAGAAGAA-TTGACTAAGGTGGTAACCATATGTCAGAC-AAAA-AGGAAAA
2568980 GTT
126 GTT
* * * * * * *
2568983 TGACCAAGGTGGTAACTATACATCAAACAGAAAGAAAAGGGATTTGACTAGGGTGTTAACCATAC
1 TGACCAGGGTGGTAACCATACGTCAAACAGAAA-AGAAGAGATTTGACCAGGGTGGTAACCATAC
* * ** ** * *
2569048 GTCAAATCAGAATAAGAAGAATCTAACT-AGGCTGGTAACTATACCTTTGACTGAAATGAGAAAA
65 GTCAAATCAGAATAAGAAGAAT-TGACTAAGG-TGGTAACCATATGTCAGAC-AAAAAG-GAAAA
2569112 GTT
126 GTT
* * *
2569115 TGACCAGGGTGGTAACTATACGTCAAACAGAAAGGAAAATGATTTGACCAGGGTGGTAACCATAC
1 TGACCAGGGTGGTAACCATACGTCAAACAGAAAAGAAGA-GATTTGACCAGGGTGGTAACCATAC
* * * *
2569180 GTCAAATCAGAATAAGAAGAATTGACCAAGGTGGTAACCATATGTCAAACAGAAAGGAAAGGGAT
65 GTCAAATCAGAATAAGAAGAATTGACTAAGGTGGTAACCATATGTCAGACAAAAAGGAAA-AG-T
2569245 T
128 T
* ** * *
2569246 TGACCAGGGTGGTAGCCATATTTCAAATCAGAATAAGAAGA-ATCTGACCAGGGTAGTAACCATA
1 TGACCAGGGTGGTAACCATACGTCAAA-CAGAA-AAGAAGAGATTTGACCAGGGTGGTAACCATA
* * * * * *
2569310 CGTCAAA-CTGAAATGAGAA-AAGTTTGACTAGGGTGGTAGCCATATGTTAAACAAAAA-GAAAA
64 CGTCAAATCAG-AATAAGAAGAA--TTGACTAAGGTGGTAACCATATGTCAGACAAAAAGGAAAA
2569372 GGGATT
126 --G-TT
* * *
2569378 TGACCAGGGTGGTAACCATGCGTCAAATCAGAATAAGAAGA-ATCTGACCACGGTGGTAACCATA
1 TGACCAGGGTGGTAACCATACGTCAAA-CAGAA-AAGAAGAGATTTGACCAGGGTGGTAACCATA
2569442 CGT
64 CGT
2569445 TAGACAAGAG
Statistics
Matches: 491, Mismatches: 83, Indels: 39
0.80 0.14 0.06
Matches are distributed among these distances:
129 4 0.01
130 11 0.02
131 113 0.23
132 350 0.71
133 12 0.02
134 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (128 bp):
TGACCAGGGTGGTAACCATACGTCAAACAGAAAAGAAGAGATTTGACCAGGGTGGTAACCATACG
TCAAATCAGAATAAGAAGAATTGACTAAGGTGGTAACCATATGTCAGACAAAAAGGAAAAGTT
Found at i:2569322 original size:219 final size:219
Alignment explanation
Indices: 2568982--2569442 Score: 654
Period size: 219 Copynumber: 2.1 Consensus size: 219
2568972 TAAGAAAAGT
* * *
2568982 TTGACCAAGGTGGTAACTATACATCAAACAGAAAGAAAAGGGATTTGACTAGGGTGTTAACCATA
1 TTGACCAAGGTGGTAACCATACATCAAACAGAAAGAAAAGGGATTTGACCAGGGTGGTAACCATA
* * * ***
2569047 CGTCAAATCAGAATAAGAAGAATCTAACTAGGCTGGTAACTATACCTTTGACTGAAATGAGAAAA
66 CGTCAAATCAGAATAAGAAGAATCTAACCAGGCTAGTAACCATACCTCAAACTGAAATGAGAAAA
* * *
2569112 GTTTGACCAGGGTGGTAACTATACGTCAAACAGAAAGGAAAA-TGATTTGACCAGGGTGGTAACC
131 GTTTGACCAGGGTGGTAACCATACGTCAAACA-AAAAGAAAAGGGATTTGACCAGGGTGGTAACC
2569176 ATACGTCAAATCAGAATAAGAAGAA
195 ATACGTCAAATCAGAATAAGAAGAA
** * *
2569201 TTGACCAAGGTGGTAACCATATGTCAAACAGAAAGGAAAGGGATTTGACCAGGGTGGTAGCCATA
1 TTGACCAAGGTGGTAACCATACATCAAACAGAAAGAAAAGGGATTTGACCAGGGTGGTAACCATA
** * * *
2569266 TTTCAAATCAGAATAAGAAGAATCTGACCAGGGTAGTAACCATACGTCAAACTGAAATGAGAAAA
66 CGTCAAATCAGAATAAGAAGAATCTAACCAGGCTAGTAACCATACCTCAAACTGAAATGAGAAAA
* * * *
2569331 GTTTGACTAGGGTGGTAGCCATATGTTAAACAAAAAGAAAAGGGATTTGACCAGGGTGGTAACCA
131 GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAGAAAAGGGATTTGACCAGGGTGGTAACCA
*
2569396 TGCGTCAAATCAGAATAAGAAGAA
196 TACGTCAAATCAGAATAAGAAGAA
*
2569420 TCTGACCACGGTGGTAACCATAC
1 T-TGACCAAGGTGGTAACCATAC
2569443 GTTAGACAAG
Statistics
Matches: 212, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
218 8 0.04
219 185 0.87
220 19 0.09
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (219 bp):
TTGACCAAGGTGGTAACCATACATCAAACAGAAAGAAAAGGGATTTGACCAGGGTGGTAACCATA
CGTCAAATCAGAATAAGAAGAATCTAACCAGGCTAGTAACCATACCTCAAACTGAAATGAGAAAA
GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAGAAAAGGGATTTGACCAGGGTGGTAACCA
TACGTCAAATCAGAATAAGAAGAA
Found at i:2569769 original size:43 final size:43
Alignment explanation
Indices: 2569721--2569808 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
2569711 ATATCACTTT
2569721 AACACACAATTCATTCATGACATCAACTCCAAATCAGCGTGGG
1 AACACACAATTCATTCATGACATCAACTCCAAATCAGCGTGGG
* *
2569764 AACACACAATTCATTCATGACATCAACTCCTAATTAGCGTGGG
1 AACACACAATTCATTCATGACATCAACTCCAAATCAGCGTGGG
2569807 AA
1 AA
2569809 TCATGAGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (43 bp):
AACACACAATTCATTCATGACATCAACTCCAAATCAGCGTGGG
Found at i:2571570 original size:47 final size:44
Alignment explanation
Indices: 2571506--2571611 Score: 140
Period size: 47 Copynumber: 2.3 Consensus size: 44
2571496 TTTAAGTTTT
*
2571506 CATGCAATGCAATGCCACCTAGAAAGCTTATGTGGCAACAAATTAAG
1 CATGAAATGCAATGCCACCTAGAAAGCTTATGTGGCAA-AAA--AAG
* * *
2571553 CATGAAATGCAATGCCACCTAGCAAGCTTTTGTGGCAATAAAAG
1 CATGAAATGCAATGCCACCTAGAAAGCTTATGTGGCAAAAAAAG
*
2571597 CTTGAAATGCAATGC
1 CATGAAATGCAATGC
2571612 AATGCAATGC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 17 0.31
46 2 0.04
47 35 0.65
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (44 bp):
CATGAAATGCAATGCCACCTAGAAAGCTTATGTGGCAAAAAAAG
Found at i:2571612 original size:5 final size:5
Alignment explanation
Indices: 2571602--2571631 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2571592 AAAAGCTTGA
*
2571602 AATGC AATGC AATGC AATGC AATGT AATGC
1 AATGC AATGC AATGC AATGC AATGC AATGC
2571632 CACCTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (5 bp):
AATGC
Found at i:2573315 original size:65 final size:65
Alignment explanation
Indices: 2573192--2573652 Score: 447
Period size: 65 Copynumber: 7.2 Consensus size: 65
2573182 TAAGTCTTCG
* * *
2573192 AAGAGCAGGACGCCTTTCTTTTTCCTTTTAAAGCTCACACAAGCTAGTGGCACCTTTTAGTCCTT
1 AAGAGCAGGACGCTTTTCTTTTT-CTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTT
2573257 A
65 A
* * * * * *
2573258 AAGAGCAGGCCGCTTTTCTTTTTCTTCTAAAGCCCATATAAGTTGGTGGCACCTTTTAGTCTTTA
1 AAGAGCAGGACGCTTTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTTA
* ** *
2573323 AAGAGCATGACGCCCTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACTTTTTAGTCCTTA
1 AAGAGCAGGACGCTTTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTTA
* * * * *
2573388 AAGAGCTA-AATGCTTTTCTTTTTCTTCTAAAGCCCACATATGCTGGTGGCACCTTTTA-TCCTT
1 AAGAGC-AGGACGCTTTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTT
2573451 A
65 A
* * * * * *
2573452 AAGAGTAAGACGCCTTTTC--TTT-TTTTAAAGCCCACACAA-TTAGGTTGCATCTTTTAGTCTT
1 AAGAGCAGGACG-CTTTTCTTTTTCTTTTAAAGCCCACACAAGCT-GGTGGCACCTTTTAGTCCT
2573513 TA
64 TA
* ** * * *
2573515 AAGAGTAGGACATTTTTCTTTTTCTTTTAAAGCCCACACAAGTTGGTCGCACCTTTTAGTCCTCA
1 AAGAGCAGGACGCTTTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTTA
* * * * * * * *
2573580 AAGAGTAGAATAC-CTTTT-TGTTT-TTTGAAA-CCCATATAAGCTGGTGGCACTTTTTAGTCAT
1 AAGAGCAG--GACGCTTTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCT
*
2573641 CA
64 TA
2573643 AAGAGCAGGA
1 AAGAGCAGGA
2573653 TGTCTTTAAA
Statistics
Matches: 328, Mismatches: 56, Indels: 27
0.80 0.14 0.07
Matches are distributed among these distances:
61 2 0.01
62 31 0.09
63 53 0.16
64 22 0.07
65 190 0.58
66 28 0.09
67 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (65 bp):
AAGAGCAGGACGCTTTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTTA
Found at i:2573418 original size:130 final size:128
Alignment explanation
Indices: 2573177--2573810 Score: 466
Period size: 130 Copynumber: 5.0 Consensus size: 128
2573167 AACATTTTAT
* * * * *
2573177 CCTTTTAAGTCTTCGAAGAGCAGGACGCCTTTCTTTTTCCTTTTAAAGCTCACACAAGCTAGTGG
1 CCTTTT-AGTCCTCAAAGAGCA-GACGCCCTT-TTTTT--TTTTAAAGCCCACACAAGCTGGTGG
* *** *
2573242 CACCTTTTAGTCCTTAAAGAGC-AGGCCGCTTTTCTTTTTCTTCTAAAGCCCATATAAGTTGGTG
61 CACTTTTTAGTCCTTAAAGAGCTAGAATGCTTTTCTTTTTCTTCTAAAGCCCACATAAGTTGGTG
2573306 GCA
126 GCA
* *
2573309 CCTTTTAGTCTTTAAAGAGCATGACGCCCTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCA-GACGCCCTT-TTTTT-TTTTAAAGCCCACACAAGCTGGTGGCA
* *
2573374 CTTTTTAGTCCTTAAAGAGCTA-AATGCTTTTCTTTTTCTTCTAAAGCCCACATATGCTGGTGGC
63 CTTTTTAGTCCTTAAAGAGCTAGAATGCTTTTCTTTTTCTTCTAAAGCCCACATAAGTTGGTGGC
2573438 A
128 A
* * * *
2573439 CCTTTTA-TCCTTAAAGAGTAAGACG-CCTTTTCTTTTTTTAAAGCCCACACAA-TTAGGTTGCA
1 CCTTTTAGTCCTCAAAGAG-CAGACGCCCTTTT-TTTTTTTAAAGCCCACACAAGCT-GGTGGCA
* * *
2573501 -TCTTTTAGTCTTTAAAGAG-TAGGACAT--TTTTCTTTTTCTTTTAAAGCCCACACAAGTTGGT
63 CT-TTTTAGTCCTTAAAGAGCTA-GA-ATGCTTTTCTTTTTCTTCTAAAGCCCACATAAGTTGGT
*
2573562 CGCA
125 GGCA
* *** * *
2573566 CCTTTTAGTCCTCAAAGAGTAGAATACCTTTTTGTTTTTTGAAA-CCCATATAAGCTGGTGGCAC
1 CCTTTTAGTCCTCAAAGAGCAGACGCCCTTTTT-TTTTTT-AAAGCCCACACAAGCTGGTGGCAC
* * * * *
2573630 TTTTTAGTCATCAAAGAGC-AGGATG----------TCTT-TAAAGCCCACACAATTTGGTGGCA
64 TTTTTAGTCCTTAAAGAGCTAGAATGCTTTTCTTTTTCTTCTAAAGCCCACATAAGTTGGTGGC-
2573683 A
128 A
* * * ** *
2573684 TCTTTTTTAGTCCTCAAAAAGTAGGACG-CC-TTTTCCTTTTAAAGCCCATACAAGCTGGTGGCA
1 -C-CTTTTAGTCCTCAAAGAGCA-GACGCCCTTTTTTTTTTTAAAGCCCACACAAGCTGGTGGCA
* * * *
2573747 CCTTTT-GTCCTCAAAGA-ATATG-A-CCTTTT-TTCTTTC-TC-AAAGCCCACATAAGTTGGTG
63 CTTTTTAGTCCTTAAAGAGCTA-GAATGCTTTTCTT-TTTCTTCTAAAGCCCACATAAGTTGGTG
2573805 GCA
126 GCA
2573808 CCT
1 CCT
2573811 ATCTACTTCA
Statistics
Matches: 418, Mismatches: 50, Indels: 78
0.77 0.09 0.14
Matches are distributed among these distances:
117 36 0.09
118 33 0.08
119 5 0.01
120 20 0.05
121 2 0.00
122 1 0.00
123 1 0.00
124 1 0.00
125 21 0.05
126 8 0.02
127 86 0.21
128 59 0.14
129 21 0.05
130 90 0.22
131 28 0.07
132 6 0.01
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (128 bp):
CCTTTTAGTCCTCAAAGAGCAGACGCCCTTTTTTTTTTTAAAGCCCACACAAGCTGGTGGCACTT
TTTAGTCCTTAAAGAGCTAGAATGCTTTTCTTTTTCTTCTAAAGCCCACATAAGTTGGTGGCA
Found at i:2573574 original size:192 final size:196
Alignment explanation
Indices: 2573206--2573584 Score: 500
Period size: 192 Copynumber: 2.0 Consensus size: 196
2573196 GCAGGACGCC
* * * *
2573206 TTTCTTTTTCCTTTTAAAGCTCACACAAGCTAGTGGCACCTTTTAGTCCTTAAAGAGCAGGCCGC
1 TTTCTTTTTCCTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTTAAAGAGCAAGACGC
* * * *
2573271 TTTTCTTTTTCTTCTAAAGCCCATATAAGTTGGTGGCACCTTTTAGTCTTTAAAGAGCATGACGC
66 TTTTCTTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTTAAAGAGCAGGACAC
* * *
2573336 CCTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACTTTTTAGTCCTTAAAGAGCTAAATGC
131 CCTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTCGCACCTTTTAGTCCTCAAAGAGCTAAATGC
2573401 T
196 T
* * * *
2573402 TTTCTTTTT-CTTCTAAAGCCCACATATGCTGGTGGCACCTTTTA-TCCTTAAAGAGTAAGACGC
1 TTTCTTTTTCCTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTTAAAGAGCAAGACG-
* * *
2573465 CTTTTC-TTTT-TT-TAAAGCCCACACAA-TTAGGTTGCATCTTTTAGTCTTTAAAGAGTAGGAC
65 CTTTTCTTTTTCTTCTAAAGCCCACACAAGTT-GGTGGCACCTTTTAGTCTTTAAAGAGCAGGAC
*** *
2573526 ATTTTTCTTTTTCTTTTAAAGCCCACACAAGTTGGTCGCACCTTTTAGTCCTCAAAGAG
129 ACCCTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTCGCACCTTTTAGTCCTCAAAGAG
2573585 TAGAATACCT
Statistics
Matches: 159, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
191 2 0.01
192 91 0.57
193 2 0.01
194 19 0.12
195 36 0.23
196 9 0.06
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (196 bp):
TTTCTTTTTCCTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTTAAAGAGCAAGACGC
TTTTCTTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTTTAAAGAGCAGGACAC
CCTTCTTTTTCTTTTAAAGCCCACACAAGCTGGTCGCACCTTTTAGTCCTCAAAGAGCTAAATGC
T
Found at i:2573745 original size:118 final size:116
Alignment explanation
Indices: 2573540--2573763 Score: 274
Period size: 117 Copynumber: 1.9 Consensus size: 116
2573530 TTCTTTTTCT
* * **
2573540 TTTAAAGCCCACACAAGTTGGTCGCACCTTTTAGTCCTCAAAGAGTAGAATACCTTTTTGTTTTT
1 TTTAAAGCCCACACAAGTTGGTCGCACCTTTTAGTCCTCAAAAAGTAGAACACCTTTTTGCCTTT
* *
2573605 TGAAACCCATATAAGCTGGTGGCACTTTTTAGTCATCAAAGAGCAGGATGTC
66 TGAAACCCATACAAGCTGGTGGCACCTTTT-GTCATCAAAGAGCAGGATGTC
* * * * *
2573657 TTTAAAGCCCACACAATTTGGTGGCAATCTTTTTTAGTCCTCAAAAAGTAGGACGCC-TTTT-CC
1 TTTAAAGCCCACACAAGTTGGTCGC-A-C-CTTTTAGTCCTCAAAAAGTAGAACACCTTTTTGCC
*
2573720 TTTT-AAAGCCCATACAAGCTGGTGGCACCTTTTGTCCTCAAAGA
63 TTTTGAAA-CCCATACAAGCTGGTGGCACCTTTTGTCATCAAAGA
2573764 ATATGACCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
117 36 0.40
118 28 0.31
119 5 0.05
120 22 0.24
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (116 bp):
TTTAAAGCCCACACAAGTTGGTCGCACCTTTTAGTCCTCAAAAAGTAGAACACCTTTTTGCCTTT
TGAAACCCATACAAGCTGGTGGCACCTTTTGTCATCAAAGAGCAGGATGTC
Found at i:2580649 original size:17 final size:17
Alignment explanation
Indices: 2580627--2580659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2580617 GTCACCATGA
2580627 AGTCACCAAAA-TTTTGG
1 AGTCA-CAAAAGTTTTGG
2580644 AGTCACAAAAGTTTTG
1 AGTCACAAAAGTTTTG
2580660 ATATAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
AGTCACAAAAGTTTTGG
Found at i:2580968 original size:13 final size:13
Alignment explanation
Indices: 2580950--2580974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2580940 CATATTGCTT
2580950 TGTATCGATACAA
1 TGTATCGATACAA
2580963 TGTATCGATACA
1 TGTATCGATACA
2580975 TGTTCTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2580993 original size:32 final size:33
Alignment explanation
Indices: 2580931--2580993 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2580921 AAGCCCATAA
*
2580931 GTATCGATACATATTGCTTTGTATCGATACAAT
1 GTATCGATACATATTGCTTTATATCGATACAAT
*
2580964 GTATCGATACATGTT-CTTTATATCGATACA
1 GTATCGATACATATTGCTTTATATCGATACA
2580994 TGAAGAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (33 bp):
GTATCGATACATATTGCTTTATATCGATACAAT
Found at i:2581089 original size:33 final size:33
Alignment explanation
Indices: 2581045--2581109 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2581035 TATTACTGTT
* *
2581045 TGTATCGATACATGGGACATTGCATCGATACAA
1 TGTATCCATACATAGGACATTGCATCGATACAA
*
2581078 TGTATCCATACATAGGACATTGTATCGATACA
1 TGTATCCATACATAGGACATTGCATCGATACA
2581110 TAGTAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (33 bp):
TGTATCCATACATAGGACATTGCATCGATACAA
Found at i:2581121 original size:20 final size:20
Alignment explanation
Indices: 2581076--2581127 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2581066 GCATCGATAC
* *
2581076 AATGTATCCATACATAGGAC
1 AATGTATCGATACATAGGAA
* *
2581096 ATTGTATCGATACATAGTAA
1 AATGTATCGATACATAGGAA
2581116 AATGTATCGATA
1 AATGTATCGATA
2581128 AATTGTGCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATAGGAA
Found at i:2587264 original size:13 final size:13
Alignment explanation
Indices: 2587246--2587307 Score: 106
Period size: 13 Copynumber: 4.8 Consensus size: 13
2587236 AGGATCTTTG
2587246 TATCGATACATTA
1 TATCGATACATTA
*
2587259 TATCGATACATTG
1 TATCGATACATTA
2587272 TATCGATACATTA
1 TATCGATACATTA
*
2587285 TATCGATACATTG
1 TATCGATACATTA
2587298 TATCGATACA
1 TATCGATACA
2587308 AGGGTTACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:2587279 original size:26 final size:26
Alignment explanation
Indices: 2587243--2587307 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
2587233 ACAAGGATCT
2587243 TTGTATCGATACATTATATCGATACA
1 TTGTATCGATACATTATATCGATACA
2587269 TTGTATCGATACATTATATCGATACA
1 TTGTATCGATACATTATATCGATACA
2587295 TTGTATCGATACA
1 TTGTATCGATACA
2587308 AGGGTTACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (26 bp):
TTGTATCGATACATTATATCGATACA
Found at i:2588978 original size:205 final size:206
Alignment explanation
Indices: 2588616--2589241 Score: 975
Period size: 206 Copynumber: 3.0 Consensus size: 206
2588606 TCCACAACGG
* * * * *
2588616 GACGACGAAGAACAAGCAATGGAAGCCGATGTGCCTCCTCCTCTACCTTTGGCACTTTCGGCAAC
1 GACGATGAAGAACAAGCAATGGAAGCCGACGCGCCTCCTCCTCCACC-TTGGCACTTTCGACAAC
* * * * *
2588681 TCCATCAGTACGAGAGATGATCATGTCACTTTCTCAGTGCACTGATCAGCACTTCAGCTCCTTAA
65 TCCATCAGTACGAGAGATGATCACGTCACTTTCTCAGTGCATTGATCAACACTTCAACTACTTAA
* * *
2588746 ACCAGCGCGTTGATTCGATAAATGCTCGGCTCACTAAAATCGT-CATCACTTTTCCTTTACTCCG
130 ACTAGCGCGTTGATTCGATAGATGCTCGGCTCACCAAAATCGTGCATCACTTTTCCTTTACTCCG
*
2588810 ACTAACTTTAGT
195 ACTAACTCTAGT
*
2588822 GACGATGAAGAACAAGCAATGGAAGCCGACGCACCTCCTCCTCCACCTTGGCACTTTCGACAACT
1 GACGATGAAGAACAAGCAATGGAAGCCGACGCGCCTCCTCCTCCACCTTGGCACTTTCGACAACT
* * * *
2588887 CCATCAATACGAGAGATGATCACGTCACTTTCTCAGCGCATTGATCAACACTTCAACTTCTTGAA
66 CCATCAGTACGAGAGATGATCACGTCACTTTCTCAGTGCATTGATCAACACTTCAACTACTTAAA
* *
2588952 CTAGCGCGTTGATTCGATAGATGCTCGGCTTACCAAAATCGTGCATCATTTTTCCTTTACTCCGA
131 CTAGCGCGTTGATTCGATAGATGCTCGGCTCACCAAAATCGTGCATCACTTTTCCTTTACTCCGA
2589017 CTAACTCTAGT
196 CTAACTCTAGT
* * * *
2589028 GATGATGAAGAATAAGCAATGGAAACCTACGCGCCTCCTCCTCCACCTTGGCACTTTCGACAACT
1 GACGATGAAGAACAAGCAATGGAAGCCGACGCGCCTCCTCCTCCACCTTGGCACTTTCGACAACT
*
2589093 CCATCAGTACGAGAGATGATCACGTCACTTTCTCAGTGCATTGATCACCACTTCAACTACTTAAA
66 CCATCAGTACGAGAGATGATCACGTCACTTTCTCAGTGCATTGATCAACACTTCAACTACTTAAA
* *
2589158 CTAGCACGTTGATTCGATAGATGCTCGGTTCACCAAAATCGTGCATCACTTTTCCTTTACTCCGA
131 CTAGCGCGTTGATTCGATAGATGCTCGGCTCACCAAAATCGTGCATCACTTTTCCTTTACTCCGA
*
2589223 CTAAGTCTAGT
196 CTAACTCTAGT
2589234 GACGATGA
1 GACGATGA
2589242 GTCATAGGAT
Statistics
Matches: 383, Mismatches: 36, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
205 112 0.29
206 271 0.71
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (206 bp):
GACGATGAAGAACAAGCAATGGAAGCCGACGCGCCTCCTCCTCCACCTTGGCACTTTCGACAACT
CCATCAGTACGAGAGATGATCACGTCACTTTCTCAGTGCATTGATCAACACTTCAACTACTTAAA
CTAGCGCGTTGATTCGATAGATGCTCGGCTCACCAAAATCGTGCATCACTTTTCCTTTACTCCGA
CTAACTCTAGT
Found at i:2589790 original size:171 final size:171
Alignment explanation
Indices: 2589501--2589835 Score: 525
Period size: 171 Copynumber: 2.0 Consensus size: 171
2589491 TTTTGAAAAT
* * * *
2589501 AAATTTGATAAAAGGGAGAAATTATTTTATAGATAGTAAGTTTTGTTTTAGATAACAAAAGGGGG
1 AAATTTGATAAAAGGGAGAAATTATTTTATAGAAAGTAAGTTTTGTTTTAGATAACAAAAAGAGA
2589566 GAGAAAATCATTTTAACAAAAAAAAGCATTAAATATTTTATCAAGGAGGAGAGAAATTTTATTAA
66 GAGAAAATCATTTTAACAAAAAAAAGCATTAAATATTTTATCAAGGAGGAGAGAAATTTTATTAA
2589631 -GAGAGAGTTTTATTGAAAATTTACTTTAGTATCTCTTAGGA
131 GGAG-GAGTTTTATTGAAAATTTACTTTAGTATCTCTTAGGA
*
2589672 AAATTTGA-AAAAGGGGGAGAAATTGTTTTATAGAAAGTAAGTTTT-TTTTAGATAACAAAAAGA
1 AAATTTGATAAAA--GGGAGAAATTATTTTATAGAAAGTAAGTTTTGTTTTAGATAACAAAAAGA
* * * *
2589735 GAGAGAAAATCGTTTTAACAAAAGAAAGCTTTAAATATTTTATCAAATG-GGAGAGAAATTTTAT
64 GAGAGAAAATCATTTTAACAAAAAAAAGCATTAAATATTTTATC-AAGGAGGAGAGAAATTTTAT
2589799 TAAGGAGGAGTTTTATTGAAAATTTACTTTAGTATCT
128 TAAGGAGGAGTTTTATTGAAAATTTACTTTAGTATCT
2589836 TTTAATAAAA
Statistics
Matches: 151, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
170 4 0.03
171 112 0.74
172 35 0.23
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (171 bp):
AAATTTGATAAAAGGGAGAAATTATTTTATAGAAAGTAAGTTTTGTTTTAGATAACAAAAAGAGA
GAGAAAATCATTTTAACAAAAAAAAGCATTAAATATTTTATCAAGGAGGAGAGAAATTTTATTAA
GGAGGAGTTTTATTGAAAATTTACTTTAGTATCTCTTAGGA
Found at i:2590541 original size:39 final size:39
Alignment explanation
Indices: 2590487--2590909 Score: 261
Period size: 39 Copynumber: 9.8 Consensus size: 39
2590477 TGTGGGGACG
2590487 AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
*
2590526 AATATCGCTGGCCTTGAATCAGCACATTGGCACAAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
* * *
2590565 AATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACC
1 AATATCGCTGGCCTTGAATCAGCACATTGG------CA----TAAGCCC
* * *
2590614 GATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTGAGTCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA----T---A-----AGCCC
* *
2590665 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA---------TAAGCCC
* * * * *
2590713 AATGTCACTGGCCTTAAATTAGCACATTGGCACAAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
* * * * *
2590752 AATATCTCTGGCCTTGAATCCGCATATTTGCACCTTGTCTTTAAGACC
1 AATATCGCTGGCCTTGAAT---C--A---GCACATTGGC-ATAAGCCC
* *
2590800 AATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
* *
2590839 AATGTCGCTGGCCTTGAATCAGCACATTGGCATGAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
* *
2590878 AATATCGCTGGCCTTGAATCATCATATTGGCA
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA
2590910 CCTTCATCTT
Statistics
Matches: 312, Mismatches: 40, Indels: 64
0.75 0.10 0.15
Matches are distributed among these distances:
39 158 0.51
40 8 0.03
43 7 0.02
44 1 0.00
45 3 0.01
46 1 0.00
47 8 0.03
48 53 0.17
49 33 0.11
51 35 0.11
53 1 0.00
56 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (39 bp):
AATATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
Found at i:2590742 original size:48 final size:47
Alignment explanation
Indices: 2590563--2591106 Score: 310
Period size: 39 Copynumber: 11.7 Consensus size: 47
2590553 TGGCACAAGC
*
2590563 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--TCTTTAAGA
* * *
2590612 CCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTGAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT--C-T-TTAAGA
2590663 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TCTTTAAGA
* * * * * *
2590711 CCAATGTCACTGGCCTTAAATTAGCACATTGGCA-----C---AAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCTTTAAGA
* * *
2590750 CCAATATCTCTGGCCTTGAATCCGCATATTTGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TCTTTAAGA
* * *
2590798 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-----C---AAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCTTTAAGA
* * * *
2590837 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--------TGAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCTTTAAGA
* * *
2590876 CCAATATCGCTGGCCTTGAATCATCATATTGGCACCTTCATCTTGAAAA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--TCTTTAAGA
* * * * * * *
2590925 TCGATGTCGTTGGCCTTGAATCAGCATATCGGCACCTCAACCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-----TTCTTTAAGA
* * * *
2590977 CCGATATCGTTGGCCTTGAATCATCATATTGGCACCTTTAACATTCCTAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT--C-TT--TAAGA
* ** * * * **
2591029 CCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA-TTCTTCTTCAATT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TTCTTTAAGA
* * * *
2591076 CTAATGTCACTGGCCTTGAATCAGCACATTG
1 CCAATATCGCTGGCCTTGAATCAGCATATTG
2591107 TTATTCTTCG
Statistics
Matches: 393, Mismatches: 66, Indels: 74
0.74 0.12 0.14
Matches are distributed among these distances:
39 101 0.26
42 2 0.01
45 1 0.00
47 31 0.08
48 65 0.17
49 73 0.19
50 5 0.01
51 42 0.11
52 73 0.19
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (47 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCTTTAAGA
Found at i:2590811 original size:87 final size:87
Alignment explanation
Indices: 2590663--2590870 Score: 344
Period size: 87 Copynumber: 2.4 Consensus size: 87
2590653 CATCTTGAGT
2590663 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
*
2590728 AAATTAGCACATTGGCACAAGC
66 AAATCAGCACATTGGCACAAGC
* * * *
2590750 CCAATATCTCTGGCCTTGAATCCGCATATTTGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
*
2590815 GAATCAGCACATTGGCACAAGC
66 AAATCAGCACATTGGCACAAGC
* *
2590837 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA
2590871 TGAGCCCAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 110 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT
AAATCAGCACATTGGCACAAGC
Found at i:2590992 original size:52 final size:49
Alignment explanation
Indices: 2590879--2591013 Score: 164
Period size: 52 Copynumber: 2.7 Consensus size: 49
2590869 CATGAGCCCA
* *
2590879 ATATCGCTGGCCTTGAATCATCATATTGGCACCTTCATCTTGAAAATCG
1 ATATCGTTGGCCTTGAATCATCATATTGGCACCTCCATCTTGAAAATCG
* * * * *
2590928 ATGTCGTTGGCCTTGAATCAGCATATCGGCACCTCAACCATCTT-TAAGTCCG
1 ATATCGTTGGCCTTGAATCATCATATTGGCACCT---CCATCTTGAAAAT-CG
2590980 ATATCGTTGGCCTTGAATCATCATATTGGCACCT
1 ATATCGTTGGCCTTGAATCATCATATTGGCACCT
2591014 TTAACATTCC
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
49 30 0.42
51 3 0.04
52 39 0.54
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
ATATCGTTGGCCTTGAATCATCATATTGGCACCTCCATCTTGAAAATCG
Found at i:2591043 original size:52 final size:50
Alignment explanation
Indices: 2590873--2591046 Score: 163
Period size: 52 Copynumber: 3.4 Consensus size: 50
2590863 CATTGGCATG
2590873 AGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTT--CATCTTGA
1 AGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTTAACATCTT-A
*** * * * * * *
2590922 AAATCGATGTCGTTGGCCTTGAATCAGCATATCGGCACCTCAACCATCTTTA
1 AGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTTAA-CATC-TTA
* * * *
2590974 AGTCCGATATCGTTGGCCTTGAATCATCATATTGGCACCTTTAACATTCCTA
1 AGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACC-TTAACA-TCTTA
*
2591026 AGCCCAATGTCGCTGGCCTTG
1 AGCCCAATATCGCTGGCCTTG
2591047 TCTCAGCACA
Statistics
Matches: 98, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
49 32 0.33
52 59 0.60
53 7 0.07
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (50 bp):
AGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTTAACATCTTA
Found at i:2591695 original size:39 final size:40
Alignment explanation
Indices: 2591641--2591759 Score: 141
Period size: 48 Copynumber: 2.8 Consensus size: 40
2591631 TGTGGGGATG
*
2591641 AATATCGCTGGCCTTGAATCAGCACATTGGCA-TAAGCCC
1 AATATCGCTGGCCTTGAATCAGCACATTGGCATTAAGACC
*
2591680 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACC
1 AATATCGCTGGCCTTGAATCAGCACATTGG---C--A---TTAAGACC
2591728 AATATCGCTGGCCTTGAATCAGCACATTGGCA
1 AATATCGCTGGCCTTGAATCAGCACATTGGCA
2591760 CATTGGCCTT
Statistics
Matches: 68, Mismatches: 3, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
39 29 0.43
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
48 35 0.51
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (40 bp):
AATATCGCTGGCCTTGAATCAGCACATTGGCATTAAGACC
Found at i:2592062 original size:13 final size:13
Alignment explanation
Indices: 2592044--2592104 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
2592034 GCCAAGGAAA
2592044 TGTATCGATACAT
1 TGTATCGATACAT
2592057 TGTATCGATACAT
1 TGTATCGATACAT
2592070 TG-ATC--T---T
1 TGTATCGATACAT
*
2592077 TGTATCGATACAC
1 TGTATCGATACAT
2592090 TGTATCGATACAT
1 TGTATCGATACAT
2592103 TG
1 TG
2592105 ATCTTTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
10 2 0.05
12 3 0.08
13 29 0.73
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2592081 original size:20 final size:20
Alignment explanation
Indices: 2592056--2592122 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
2592046 TATCGATACA
2592056 TTGTATCGATACATTGATCT
1 TTGTATCGATACATTGATCT
2592076 TTGTATCGATAC----A-C-
1 TTGTATCGATACATTGATCT
2592090 -TGTATCGATACATTGATCT
1 TTGTATCGATACATTGATCT
2592109 TTGTATCGATACAT
1 TTGTATCGATACAT
2592123 CTGGGAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 25 0.62
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGATCT
Found at i:2592086 original size:33 final size:33
Alignment explanation
Indices: 2592044--2592122 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
2592034 GCCAAGGAAA
2592044 TGTATCGATACATTGTATCGATACATTGATCTT
1 TGTATCGATACATTGTATCGATACATTGATCTT
*
2592077 TGTATCGATACACTGTATCGATACATTGATCTT
1 TGTATCGATACATTGTATCGATACATTGATCTT
2592110 TGTATCGATACAT
1 TGTATCGATACAT
2592123 CTGGGAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACATTGATCTT
Found at i:2595336 original size:20 final size:21
Alignment explanation
Indices: 2595301--2595339 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2595291 AGGTCAAAAC
2595301 CCTAGAAAGTAACGATACAAG
1 CCTAGAAAGTAACGATACAAG
*
2595322 CCTAG-AAGTATCGATACA
1 CCTAGAAAGTAACGATACA
2595340 TATTACTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (21 bp):
CCTAGAAAGTAACGATACAAG
Found at i:2595388 original size:32 final size:33
Alignment explanation
Indices: 2595331--2595392 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2595321 GCCTAGAAGT
*
2595331 ATCGATACATATTACTTTGTATCGATACATTGC
1 ATCGATACATATTACATTGTATCGATACATTGC
*
2595364 ATCGATACATGTT-CATTGTATCGATACAT
1 ATCGATACATATTACATTGTATCGATACAT
2595393 GAAGAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (33 bp):
ATCGATACATATTACATTGTATCGATACATTGC
Found at i:2595403 original size:20 final size:20
Alignment explanation
Indices: 2595378--2595415 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2595368 ATACATGTTC
2595378 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
*
2595398 ATTGTATTGATACATGAA
1 ATTGTATCGATACATGAA
2595416 ACTGGTAGTA
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:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:2597974 original size:26 final size:27
Alignment explanation
Indices: 2597945--2598009 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 27
2597935 TTGGCTATTT
2597945 AAATGACA-ACATGCTCATAACAAAAG
1 AAATGACAGACATGCTCATAACAAAAG
*
2597971 AAATGACACAAGGACATGCTCATAATAAAAG
1 AAATG--AC-A-GACATGCTCATAACAAAAG
2598002 AAATGACA
1 AAATGACA
2598010 CAAGGACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 5 0.15
28 3 0.09
29 3 0.09
31 22 0.67
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.15
Consensus pattern (27 bp):
AAATGACAGACATGCTCATAACAAAAG
Done.