Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008840.1 Hibiscus syriacus cultivar Beakdansim tig00112044_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1122218
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:440935 original size:24 final size:23
Alignment explanation
Indices: 440908--440994 Score: 111
Period size: 24 Copynumber: 3.7 Consensus size: 23
440898 ATTTTCGAAT
*
440908 TGAATTCTGTTCTGATACGTTATC
1 TGAATTCTGTTCTGATAC-TGATC
*
440932 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTGATC
* *
440955 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGATC
*
440979 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
440995 TTCTGATATC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 19 0.35
24 36 0.65
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGATC
Found at i:440945 original size:12 final size:12
Alignment explanation
Indices: 440908--440999 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
440898 ATTTTCGAAT
440908 TGAATTCTGTTC
1 TGAATTCTGTTC
*
440920 TG-ATAC-GTTATC
1 TGAATTCTG-T-TC
440932 TGAATTCTGTTC
1 TGAATTCTGTTC
*
440944 TG-ATTCTGATC
1 TGAATTCTGTTC
*
440955 TGGATTCTGTTC
1 TGAATTCTGTTC
* *
440967 TG-ATATCTGATA
1 TGAAT-TCTGTTC
*
440979 TGAATTCTGTTT
1 TGAATTCTGTTC
*
440991 TGATTTCTG
1 TGAATTCTG
441000 ATATCTCTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
10 1 0.02
11 16 0.25
12 40 0.62
13 6 0.09
14 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:440962 original size:47 final size:48
Alignment explanation
Indices: 440911--441001 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
440901 TTCGAATTGA
* *
440911 ATTCTGTTCTGATA-CGTTATCTGAATTCTGTTCTGA-TTCTGATCTGG
1 ATTCTGTTCTGATATC-TGATATGAATTCTGTTCTGATTTCTGATCTGG
*
440958 ATTCTGTTCTGATATCTGATATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGATATGAATTCTGTTCTGATTTCTGAT
441002 ATCTCTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 31 0.79
48 8 0.21
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGATATGAATTCTGTTCTGATTTCTGATCTGG
Found at i:443099 original size:18 final size:18
Alignment explanation
Indices: 443075--443116 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
443065 GTCATAACCC
*
443075 GACCCGACCTGACCCGTT
1 GACCCGACCCGACCCGTT
*
443093 TACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
443111 GACCCG
1 GACCCG
443117 TTGGCCGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:445541 original size:24 final size:23
Alignment explanation
Indices: 445514--445600 Score: 102
Period size: 24 Copynumber: 3.7 Consensus size: 23
445504 ATTTTCGAAT
* *
445514 TGAATTATGTTCTGATACGTTATC
1 TGAATTCTGTTCTGATAC-TGATC
*
445538 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTGATC
* *
445561 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGATC
*
445585 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
445601 TTCTGATATC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGATC
Found at i:445551 original size:12 final size:12
Alignment explanation
Indices: 445536--445605 Score: 63
Period size: 12 Copynumber: 5.9 Consensus size: 12
445526 TGATACGTTA
445536 TCTGAATTCTGT
1 TCTGAATTCTGT
*
445548 TCTG-ATTCTGA
1 TCTGAATTCTGT
*
445559 TCTGGATTCTGT
1 TCTGAATTCTGT
*
445571 TCTG-ATATCTGA
1 TCTGAAT-TCTGT
*
445583 TATGAATTCTGT
1 TCTGAATTCTGT
* *
445595 TTTGATTTCTG
1 TCTGAATTCTG
445606 ATATCTCTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 12 0.25
12 34 0.71
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
TCTGAATTCTGT
Found at i:445605 original size:24 final size:24
Alignment explanation
Indices: 445538--445609 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
445528 ATACGTTATC
*
445538 TGAATTCTGTTCTGA-TTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
* *
445561 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
*
445585 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
445609 T
1 T
445610 CTCTGTTTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 14 0.33
24 28 0.67
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:448036 original size:18 final size:18
Alignment explanation
Indices: 448013--448049 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
448003 GTTCCTAATG
*
448013 GACAATCTCTTACGAAAT
1 GACAATCTCTTACAAAAT
448031 GACAATCTCTTACAAAAT
1 GACAATCTCTTACAAAAT
448049 G
1 G
448050 TCCCGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (18 bp):
GACAATCTCTTACAAAAT
Found at i:449918 original size:31 final size:31
Alignment explanation
Indices: 449880--449942 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
449870 CCCGAAGGAT
*
449880 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
449911 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
449942 C
1 C
449943 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:450729 original size:64 final size:64
Alignment explanation
Indices: 450661--450798 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 64
450651 TATTACTGGG
* * *
450661 ATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATT-AATGGGATGCATCGATGCACTACT
1 ATGCATCGATGCACGAATTGCATTCGATGTATTCATT-TTAAAAGAG-TGCATCGATGCACTACC
450724 T
64 T
* *
450725 ATGCATCGATGCACGAATTGCATTCGATGTATTTATTTTAAAAGAGTGCATCGATGCACTTCCT
1 ATGCATCGATGCACGAATTGCATTCGATGTATTCATTTTAAAAGAGTGCATCGATGCACTACCT
*
450789 GTGCATCGAT
1 ATGCATCGAT
450799 ACACCTTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 57 0.86
65 9 0.14
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACGAATTGCATTCGATGTATTCATTTTAAAAGAGTGCATCGATGCACTACCT
Found at i:458604 original size:2 final size:2
Alignment explanation
Indices: 458597--458640 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
458587 GGTAATGAAA
458597 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
458639 AG
1 AG
458641 GATACATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:464816 original size:12 final size:12
Alignment explanation
Indices: 464797--464834 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
464787 ATCATTAAGA
464797 AAACATAAATAC
1 AAACATAAATAC
*
464809 ATACATAAATAC
1 AAACATAAATAC
*
464821 AAACATAACTAC
1 AAACATAAATAC
464833 AA
1 AA
464835 GCTTGACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.63, C:0.18, G:0.00, T:0.18
Consensus pattern (12 bp):
AAACATAAATAC
Found at i:473492 original size:26 final size:24
Alignment explanation
Indices: 473463--473534 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
473453 AAAGTCCAAC
473463 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
*
473489 AAA-TGAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
473511 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
473535 ACAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 8 0.22
26 10 0.27
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:475673 original size:17 final size:18
Alignment explanation
Indices: 475632--475670 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
475622 TTTATATTAA
475632 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
475649 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
475667 TAAA
1 TAAA
475671 TACAGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:475954 original size:51 final size:51
Alignment explanation
Indices: 475823--475961 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 51
475813 GCCCCCTGCA
* **
475823 CCGCGCTATACCCTACGTGTCAGATAAAT-AG-GTATAGCGCGGAGCAGGGG
1 CCGCGCTATACCCCACGTGTC-GCCAAATCAGCGTATAGCGCGGAGCAGGGG
** * * *
475873 CCGCGCTATA-CCCACGTGTAACCCAGTCAGCGTATAGCGCGGTGCAGGGG
1 CCGCGCTATACCCCACGTGTCGCCAAATCAGCGTATAGCGCGGAGCAGGGG
* * *
475923 GCGCGCTATACCCCACGTGGCGCCAAATCAGCATATAGC
1 CCGCGCTATACCCCACGTGTCGCCAAATCAGCGTATAGC
475962 ATGGGTCAGG
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
48 2 0.03
49 10 0.14
50 37 0.52
51 22 0.31
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (51 bp):
CCGCGCTATACCCCACGTGTCGCCAAATCAGCGTATAGCGCGGAGCAGGGG
Found at i:476054 original size:30 final size:29
Alignment explanation
Indices: 475992--476054 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
475982 TACTGCTACG
* *
475992 GGTGTTAGATCGGGAAATATAATATGACC
1 GGTGTTAGATCGGGAAATATAAGATCACC
* *
476021 GGTGTTAGATCGGTAAATATACCGATCACC
1 GGTGTTAGATCGGGAAATATA-AGATCACC
476051 GGTG
1 GGTG
476055 ATATTTCGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAAGATCACC
Found at i:476119 original size:25 final size:25
Alignment explanation
Indices: 476090--476152 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
476080 TGACGTTGCT
*
476090 TTTTAAAAAGTGAATTTTAAAAGTA
1 TTTTAAAAAGTGAATTTTAAAAATA
* *
476115 TTTTAGAAACG-AAATTTTAAAAATA
1 TTTTA-AAAAGTGAATTTTAAAAATA
*
476140 TTATTTAAAAGTG
1 TT-TTAAAAAGTG
476153 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (25 bp):
TTTTAAAAAGTGAATTTTAAAAATA
Found at i:476944 original size:14 final size:15
Alignment explanation
Indices: 476908--476952 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
476898 TTCCAAAGTA
* *
476908 CTTAACATTTTTAAT
1 CTTAATATTTATAAT
476923 -TT-ATATTTA-AAT
1 CTTAATATTTATAAT
476935 CTTAATATTTATAAT
1 CTTAATATTTATAAT
476950 CTT
1 CTT
476953 TTACACGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 3 0.12
13 7 0.28
14 9 0.36
15 6 0.24
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
CTTAATATTTATAAT
Found at i:477055 original size:3 final size:3
Alignment explanation
Indices: 477039--477071 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
477029 GATAAATACC
477039 GAA GAA -AA -AA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
477072 GTGAGAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:485555 original size:23 final size:23
Alignment explanation
Indices: 485524--485585 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
485514 TATTTGTATT
*
485524 TGTTTATTTATTGTTCTA-GAACA
1 TGTTCATTTATTGTT-TATGAACA
*
485547 TGTTCATTTATATGTTTATTAACA
1 TGTTCATTTAT-TGTTTATGAACA
* *
485571 TGTTCGTTTAGTGTT
1 TGTTCATTTATTGTT
485586 AGTTTATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.55
Consensus pattern (23 bp):
TGTTCATTTATTGTTTATGAACA
Found at i:490029 original size:3 final size:3
Alignment explanation
Indices: 490021--490064 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
490011 TAGATTTAAT
* *
490021 TAA TAA TAA TGA TAA TAA TAA AAA TAA -AA TAA TAA CTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
490065 GTATAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:490070 original size:18 final size:17
Alignment explanation
Indices: 490021--490070 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
490011 TAGATTTAAT
490021 TAATAATAATGATAATAA
1 TAATAATAAT-ATAATAA
* *
490039 TAAAAATAAAATAATAA
1 TAATAATAATATAATAA
*
490056 CTAATAATAGTATAA
1 -TAATAATAATATAA
490071 AAAAAGACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:502961 original size:290 final size:288
Alignment explanation
Indices: 502441--503020 Score: 1067
Period size: 290 Copynumber: 2.0 Consensus size: 288
502431 TCCTCCGCGT
502441 AGATTTTACGCTTACTCGTTGAATTTTATCTTATATCTTATTTCAATAACCGTATTTTTAATTTA
1 AGATTTTACGCTTACTCGTTGAATTTTATCTTATA-CTTATTTCAATAACCGTATTTTTAATTTA
502506 TTTACTTTTTTTAGTTATTAACCGTTATTTTATAGTGTGATTATATGACTTATTTTAATACTATA
65 TTTACTTTTTTTAGTTATTAACCGTTATTTTATAGTGTGATTATATGACTTATTTTAATACTATA
502571 ATATGCAACATAGGATTTAAATATTAATATATTTATTCCATTTTCCCCCACATTACTCCCTTAGT
130 ATATGCAACATAGGATTTAAATATTAATATATTTATTCCATTTTCCCCCACATTACTCCCTTAGT
* *
502636 CGTCTTCTCTCTCCCTCCCCTCCATTTCTCTTATTTCTTTTCAACTAAGACCCACATTGCCTTTC
195 CGTCTTCTCTCTCCCTCCCCCCCATTTCTCTTATTTCTTTTCAAATAAGACCCACATTGCC-TTC
502701 TACTCGTTTCTAGTTGTTTCCGGTTTCCGC
259 TACTCGTTTCTAGTTGTTTCCGGTTTCCGC
502731 AGATTTTACGCTTACTCGTTGAATTTTATCTTATA-TTATTTCAATAACCGTATTTTTAATTTAT
1 AGATTTTACGCTTACTCGTTGAATTTTATCTTATACTTATTTCAATAACCGTATTTTTAATTTAT
502795 TTAC-TTTTTTAGTTATTAACCGTTATTTTATTATAGTGTGATTATATGACTTATTTTAATACTA
66 TTACTTTTTTTAGTTATTAACCGTTA--TT-TTATAGTGTGATTATATGACTTATTTTAATACTA
502859 TAATATGCAACATAGGATTTAAATATTAATATATTTATTCCATTTT-CCCCACATTTACTCCCTT
128 TAATATGCAACATAGGATTTAAATATTAATATATTTATTCCATTTTCCCCCACA-TTACTCCCTT
502923 AGTCGTCTTCTCTCTCCCTCCCCCCCATTTCTCTTATTTCTTTTCAAATAAGACCCACATTGCCT
192 AGTCGTCTTCTCTCTCCCTCCCCCCCATTTCTCTTATTTCTTTTCAAATAAGACCCACATTGCCT
502988 TCTACTCGTTTCTAGTTGTTTCCGGTTTCCGC
257 TCTACTCGTTTCTAGTTGTTTCCGGTTTCCGC
503020 A
1 A
503021 TCTCACTCTC
Statistics
Matches: 284, Mismatches: 2, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
287 21 0.07
288 33 0.12
289 43 0.15
290 187 0.66
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (288 bp):
AGATTTTACGCTTACTCGTTGAATTTTATCTTATACTTATTTCAATAACCGTATTTTTAATTTAT
TTACTTTTTTTAGTTATTAACCGTTATTTTATAGTGTGATTATATGACTTATTTTAATACTATAA
TATGCAACATAGGATTTAAATATTAATATATTTATTCCATTTTCCCCCACATTACTCCCTTAGTC
GTCTTCTCTCTCCCTCCCCCCCATTTCTCTTATTTCTTTTCAAATAAGACCCACATTGCCTTCTA
CTCGTTTCTAGTTGTTTCCGGTTTCCGC
Found at i:505302 original size:82 final size:81
Alignment explanation
Indices: 505207--505369 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 81
505197 TAGATATTAA
505207 TACTCTTAAAGTTGATATTGGTATATTCAG-GACGTAG-CTCTTAGGGCCCAAGGATCCTTCGAT
1 TACTCTTAAAGTTGATA-TGGTATATTCAGCGACGTAGCCTCTTA-GGCCCAAGGAT-CTTCGAT
505270 CCTTATTAAAATTTATATT
63 CCTTATTAAAATTTATATT
505289 TACTCTTAAAGTTGATATGGTATATTCAGCGACGTAGCTCTCTTAGGCCCAAGGATCTTCGATCC
1 TACTCTTAAAGTTGATATGGTATATTCAGCGACGTAGC-CTCTTAGGCCCAAGGATCTTCGATCC
505354 TTATTAAAATTTATAT
65 TTATTAAAATTTATAT
505370 ATTAATATAC
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
81 12 0.15
82 49 0.63
83 11 0.14
84 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (81 bp):
TACTCTTAAAGTTGATATGGTATATTCAGCGACGTAGCCTCTTAGGCCCAAGGATCTTCGATCCT
TATTAAAATTTATATT
Found at i:505452 original size:16 final size:17
Alignment explanation
Indices: 505413--505456 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
505403 CATGTAAAAG
505413 TAAATATTTAAATTTAA
1 TAAATATTTAAATTTAA
* *
505430 AAAATATTTAAA-TTAT
1 TAAATATTTAAATTTAA
505446 TAAATATTTAA
1 TAAATATTTAA
505457 TTAAGTAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATATTTAAATTTAA
Found at i:509135 original size:19 final size:19
Alignment explanation
Indices: 509113--509171 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
509103 TATTATTTTT
509113 AATTTATATATTTTTATAA
1 AATTTATATATTTTTATAA
* *
509132 AA-TT-TAGA--TTCATAA
1 AATTTATATATTTTTATAA
* *
509147 AATTTGTATTTTTTTATAA
1 AATTTATATATTTTTATAA
509166 AATTTA
1 AATTTA
509172 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 5 0.17
18 2 0.07
19 13 0.43
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (19 bp):
AATTTATATATTTTTATAA
Found at i:509180 original size:33 final size:34
Alignment explanation
Indices: 509113--509180 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
509103 TATTATTTTT
***
509113 AATTTATATATTTTTATAAAATTTAGATTCATAA
1 AATTTATATATTTTTATAAAATTTAGAAAAATAA
* *
509147 AATTTGTATTTTTTTATAAAATTTA-AAAAATAA
1 AATTTATATATTTTTATAAAATTTAGAAAAATAA
509180 A
1 A
509181 TGACTATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (34 bp):
AATTTATATATTTTTATAAAATTTAGAAAAATAA
Found at i:509289 original size:29 final size:29
Alignment explanation
Indices: 509218--509302 Score: 79
Period size: 32 Copynumber: 2.9 Consensus size: 29
509208 ATATATCATT
* *
509218 TTAATA-TTAATTAATATT-AATTTTTACA
1 TTAATATTTAAAT-ATATTAAAATTTTACA
*
509246 TCAATTATCTATAAATATATTAAAATTTTACA
1 TTAA-TAT-T-TAAATATATTAAAATTTTACA
509278 TTAATATTTAAATATA--AAAATTTTA
1 TTAATATTTAAATATATTAAAATTTTA
509303 ATAGATGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
27 9 0.19
28 3 0.06
29 10 0.21
30 1 0.02
31 9 0.19
32 16 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TTAATATTTAAATATATTAAAATTTTACA
Found at i:509297 original size:27 final size:31
Alignment explanation
Indices: 509239--509302 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
509229 TAATATTAAT
509239 TTTTACATCAATTATCTATAAATATATTAAAA
1 TTTTACATCAATTATCTATAAATATA-TAAAA
*
509271 TTTTACATTAA-TAT-T-TAAATATA-AAAA
1 TTTTACATCAATTATCTATAAATATATAAAA
509298 TTTTA
1 TTTTA
509303 ATAGATGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 9 0.29
29 8 0.26
30 1 0.03
31 3 0.10
32 10 0.32
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTTACATCAATTATCTATAAATATATAAAA
Found at i:510644 original size:16 final size:16
Alignment explanation
Indices: 510623--510655 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
510613 TAATAAATAA
510623 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
510639 ACGAACATACACGAAC
1 ACGAACATAAACGAAC
510655 A
1 A
510656 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:510745 original size:16 final size:16
Alignment explanation
Indices: 510720--510767 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
510710 CATTTAATAA
510720 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
* *
510736 ATAAATGAACACGAAC
1 ATAAACGAACACAAAC
*
510752 ATAAACGAACATAAAC
1 ATAAACGAACACAAAC
510768 GTTGGAGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:510751 original size:22 final size:20
Alignment explanation
Indices: 510716--510757 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
510706 CGTTCATTTA
510716 ATAAATAAACGAACACAAAC
1 ATAAATAAACGAACACAAAC
*
510736 ATAAATGAACACGAACATAAAC
1 ATAAAT-AA-ACGAACACAAAC
510758 GAACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.62, C:0.19, G:0.07, T:0.12
Consensus pattern (20 bp):
ATAAATAAACGAACACAAAC
Found at i:510873 original size:31 final size:31
Alignment explanation
Indices: 510823--510907 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
510813 AGTATTGCTG
510823 AGCTCGACTCGAACTCGAAAACTTTCAAAGTC
1 AGCTCGACTCG-ACTCGAAAACTTTCAAAGTC
510855 AGCTCGACTCGACTCGAAAACTTTCAAAGTC
1 AGCTCGACTCGACTCGAAAACTTTCAAAGTC
*
510886 AGTTCGACTCGACTCGAAAACT
1 AGCTCGACTCGACTCGAAAACT
510908 CGCGAGCTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 41 0.79
32 11 0.21
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (31 bp):
AGCTCGACTCGACTCGAAAACTTTCAAAGTC
Found at i:511049 original size:12 final size:11
Alignment explanation
Indices: 511022--511062 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
511012 TCTAGACTCG
511022 AGCTCGATTGA
1 AGCTCGATTGA
*
511033 AGCTCGATTCTA
1 AGCTCGATT-GA
511045 AGCTCGATTGA
1 AGCTCGATTGA
511056 AGCTCGA
1 AGCTCGA
511063 CATTACCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:511315 original size:23 final size:23
Alignment explanation
Indices: 511285--511331 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
511275 CATTAGCTTC
511285 GTGCTATGTAGAAGTTGAAAATT
1 GTGCTATGTAGAAGTTGAAAATT
511308 GTGCTATGTAGAAGTTGAAAATT
1 GTGCTATGTAGAAGTTGAAAATT
511331 G
1 G
511332 GGAGATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (23 bp):
GTGCTATGTAGAAGTTGAAAATT
Found at i:515720 original size:3 final size:3
Alignment explanation
Indices: 515712--515744 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
515702 GGTCGAAAAA
515712 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
515745 ATCATACCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:516469 original size:145 final size:145
Alignment explanation
Indices: 516107--516532 Score: 469
Period size: 145 Copynumber: 2.9 Consensus size: 145
516097 TCAGGATATC
* *
516107 CGATCAACATTTCGAACGGTGAAAAGTTGTGCAAGGCCAACACGAACAACACACTGAAAATTCAG
1 CGATCAACATTCCGAACGGTGAAAAGTTGTGCAAGGCCAACACGAACAACATACTGAAAATTCAG
* * ** * * ** *
516172 GACGATCAGATAGTGGACGGCGGCAGATTGGAGAAAATAAGCCGAACGGTTTTTGG-TTGATTTA
66 GACGATCGGATGGTGGACGATGGCGGATCGGAGAAAATAAATCGAACGGTTTTTGGCCT-ATTTA
* * *
516236 CGACAATCGGGATCTA
130 CGACAACCGAGAACTA
* * * * * * *
516252 CGATTAACATTCCGAACAGTGAAAAGTTGCGCAAGGCCAACACTAACAATATAATGTAAATTCAG
1 CGATCAACATTCCGAACGGTGAAAAGTTGTGCAAGGCCAACACGAACAACATACTGAAAATTCAG
* * * * * *
516317 GACGATCGGACGGTGGAAGTTGGCGGATCGGATAAAATAAATAGAACGCTTTTTGGCCTATTTAC
66 GACGATCGGATGGTGGACGATGGCGGATCGGAGAAAATAAATCGAACGGTTTTTGGCCTATTTAC
*
516382 GACGACCGAGAACT-
131 GACAACCGAGAACTA
* * * *
516396 CTGATCAACGTTCCGAATGGTGAAAAGTTGTGCAAGGCCAACACGAACAACATACTGAAAAATAA
1 C-GATCAACATTCCGAACGGTGAAAAGTTGTGCAAGGCCAACACGAACAACATACTGAAAATTCA
* * * * * *
516461 GAATGATCGGATGTTGGACGATGGAGGATCGGAGAAAATAAATTCGAACGGGTTTTGGCCTTTTT
65 GGACGATCGGATGGTGGACGATGGCGGATCGGAGAAAATAAA-TCGAACGGTTTTTGGCCTATTT
516526 ACGACAA
129 ACGACAA
516533 ATGGAGCCGA
Statistics
Matches: 227, Mismatches: 51, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
144 1 0.00
145 201 0.89
146 25 0.11
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (145 bp):
CGATCAACATTCCGAACGGTGAAAAGTTGTGCAAGGCCAACACGAACAACATACTGAAAATTCAG
GACGATCGGATGGTGGACGATGGCGGATCGGAGAAAATAAATCGAACGGTTTTTGGCCTATTTAC
GACAACCGAGAACTA
Found at i:516845 original size:29 final size:30
Alignment explanation
Indices: 516787--516872 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
516777 TTCTGTTATT
** * * *
516787 TTATTTTAGTCAGTTAAATTTATATTTTTA
1 TTATTTTAGTCCTTTAAATTTCTGTTTTAA
516817 TTA-TTTATGTCCTTTAAATTTCTGTTTTAA
1 TTATTTTA-GTCCTTTAAATTTCTGTTTTAA
* * *
516847 TTGTTTTAGTCTTTTAAGTTTCTGTT
1 TTATTTTAGTCCTTTAAATTTCTGTT
516873 CTTACCATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 4 0.09
30 38 0.83
31 4 0.09
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (30 bp):
TTATTTTAGTCCTTTAAATTTCTGTTTTAA
Found at i:516894 original size:31 final size:31
Alignment explanation
Indices: 516826--516928 Score: 131
Period size: 31 Copynumber: 3.4 Consensus size: 31
516816 ATTATTTATG
* *
516826 TCCTTTAAATTTCTGTT-TTA--ATTGTTTTAG
1 TCCTTTAAGTTTCTGTTCTTACCA-T-TTTTAA
*
516856 TCTTTTAAGTTTCTGTTCTTACCATTTTTAA
1 TCCTTTAAGTTTCTGTTCTTACCATTTTTAA
*
516887 TCCTTTAAGTTCCTGTTCTTACCATTTTTAA
1 TCCTTTAAGTTTCTGTTCTTACCATTTTTAA
516918 TCCTTTAAGTT
1 TCCTTTAAGTT
516929 CATGTTTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.23
31 48 0.74
32 1 0.02
33 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (31 bp):
TCCTTTAAGTTTCTGTTCTTACCATTTTTAA
Found at i:516929 original size:31 final size:31
Alignment explanation
Indices: 516850--516934 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
516840 GTTTTAATTG
* * *
516850 TTTTAGTCTTTTAAGTTTCTGTTCTTACCAT
1 TTTTAATCCTTTAAGTTCCTGTTCTTACCAT
516881 TTTTAATCCTTTAAGTTCCTGTTCTTACCAT
1 TTTTAATCCTTTAAGTTCCTGTTCTTACCAT
*
516912 TTTTAATCCTTTAAGTTCATGTT
1 TTTTAATCCTTTAAGTTCCTGTT
516935 TTTGCTAGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.08, T:0.55
Consensus pattern (31 bp):
TTTTAATCCTTTAAGTTCCTGTTCTTACCAT
Found at i:521520 original size:21 final size:21
Alignment explanation
Indices: 521493--521546 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
521483 GTAAAAGGTA
521493 TACCGATACACTGCTACAGTG
1 TACCGATACACTGCTACAGTG
*
521514 TATCGATACACTGCTACAGTG
1 TACCGATACACTGCTACAGTG
*
521535 TACCAATACACT
1 TACCGATACACT
521547 CAATGTTCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (21 bp):
TACCGATACACTGCTACAGTG
Found at i:523554 original size:30 final size:30
Alignment explanation
Indices: 523518--523618 Score: 113
Period size: 30 Copynumber: 3.5 Consensus size: 30
523508 TTCGAACCGA
523518 ATTAATCAATAACTGAACTTTAAAAAAATT
1 ATTAATCAATAACTGAACTTTAAAAAAATT
* * * **
523548 ATTAATCATTAACTG-A--GTGAACCAA--
1 ATTAATCAATAACTGAACTTTAAAAAAATT
523573 ATTAATCAATAACTGAACTTTAAAAAAATT
1 ATTAATCAATAACTGAACTTTAAAAAAATT
*
523603 ATTAATCATTAACTGA
1 ATTAATCAATAACTGA
523619 GTGAACATAA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
25 14 0.25
26 1 0.02
27 5 0.09
28 5 0.09
29 1 0.02
30 29 0.53
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (30 bp):
ATTAATCAATAACTGAACTTTAAAAAAATT
Found at i:523570 original size:55 final size:55
Alignment explanation
Indices: 523511--523624 Score: 219
Period size: 55 Copynumber: 2.1 Consensus size: 55
523501 AACTGATTTC
*
523511 GAACCGAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGT
1 GAACCAAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGT
523566 GAACCAAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGT
1 GAACCAAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGT
523621 GAAC
1 GAAC
523625 ATAAAATTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (55 bp):
GAACCAAATTAATCAATAACTGAACTTTAAAAAAATTATTAATCATTAACTGAGT
Found at i:523631 original size:30 final size:29
Alignment explanation
Indices: 523541--523633 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 29
523531 TGAACTTTAA
523541 AAAAATTATTAATCATTAACTGAGTGAAC
1 AAAAATTATTAATCATTAACTGAGTGAAC
* * * *
523570 --CAA--ATTAATCAATAACTGAACTTTAA-
1 AAAAATTATTAATCATTAACTG-A-GTGAAC
523596 AAAAATTATTAATCATTAACTGAGTGAAC
1 AAAAATTATTAATCATTAACTGAGTGAAC
523625 ATAAAATTA
1 A-AAAATTA
523634 ATTGATCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
25 14 0.29
26 1 0.02
27 5 0.10
28 5 0.10
29 2 0.04
30 21 0.44
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAATTATTAATCATTAACTGAGTGAAC
Found at i:524023 original size:14 final size:14
Alignment explanation
Indices: 524001--524049 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
523991 TAAGTAATAT
*
524001 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
524015 GTTCATTTA---T-
1 GTTCATTTATGTTC
*
524025 GTTCATTTGTGTTC
1 GTTCATTTATGTTC
524039 GTTCATTTATG
1 GTTCATTTATG
524050 CGTGTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
10 8 0.29
11 1 0.04
13 1 0.04
14 18 0.64
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:524037 original size:24 final size:24
Alignment explanation
Indices: 523998--524049 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
523988 CGTTAAGTAA
*
523998 TATGTTCGTTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
*
524022 TATGTTCATTTGTGTTCGTTCATT
1 TATGTTCATTTATGTTCGTTCATT
524046 TATG
1 TATG
524050 CGTGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (24 bp):
TATGTTCATTTATGTTCGTTCATT
Found at i:524289 original size:24 final size:24
Alignment explanation
Indices: 524255--524328 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 24
524245 TTTATGCTGA
524255 TTTATTGTGTTCATTTACGTTCT-
1 TTTATTGTGTTCATTTACGTTCTG
* * *
524278 TTTGTTTGTGTTCGTTAACGTT-TG
1 TTT-ATTGTGTTCATTTACGTTCTG
*
524302 TTTATTGTGTTTATTTACGTTC-G
1 TTTATTGTGTTCATTTACGTTCTG
524325 TTTA
1 TTTA
524329 CATCCGTCCG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 23 0.56
24 18 0.44
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (24 bp):
TTTATTGTGTTCATTTACGTTCTG
Found at i:524897 original size:30 final size:29
Alignment explanation
Indices: 524864--525105 Score: 125
Period size: 30 Copynumber: 8.5 Consensus size: 29
524854 TAAAATAAAT
* *
524864 TTAAGATAAGAATAAAATATATTTAATAA
1 TTAAAATAAAAATAAAATATATTTAATAA
* *
524893 TTTAAAATAATAATATAATATATTTAATGAA
1 -TTAAAATAAAAATAAAATATATTTAAT-AA
* * *
524924 TTAAGAT-AAAAT---ATATACTTGAAAAA
1 TTAAAATAAAAATAAAATATA-TTTAATAA
* * *
524950 GTTAAAATAATAGTAAAATATATTTTGAA-AG
1 -TTAAAATAAAAATAAAATATA-TTT-AATAA
* *
524981 TTTAAAT-AAAATAAAAATATATTT-TTAAA
1 TTAAAATAAAAAT-AAAATATATTTAAT-AA
*
525010 TAAAAATAAAAAT--AA-ATATTT-A-AA
1 TTAAAATAAAAATAAAATATATTTAATAA
* *
525034 TAAAAATAAAAATAAAATATTTTTTAA-AA
1 TTAAAATAAAAATAAAATA-TATTTAATAA
** *
525063 -TAAGTTAATAATAAAATATATTTAATAA
1 TTAAAATAAAAATAAAATATATTTAATAA
*
525091 GTTAATATAAAAATA
1 -TTAAAATAAAAATA
525106 TTTTTTAAAG
Statistics
Matches: 162, Mismatches: 30, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
24 15 0.09
26 15 0.09
27 19 0.12
28 23 0.14
29 19 0.12
30 59 0.36
31 10 0.06
32 2 0.01
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
TTAAAATAAAAATAAAATATATTTAATAA
Found at i:524972 original size:57 final size:52
Alignment explanation
Indices: 524845--524974 Score: 136
Period size: 57 Copynumber: 2.4 Consensus size: 52
524835 AATCACACTT
* * *
524845 ATAATAAATTAAAATAAATTTAAGATAAGAATAAAATATATTTAATAATTTAAA
1 ATAAT-AA-TAAAATATATTTAAGATAAGAATAAAATATATTTAAAAAGTTAAA
*
524899 ATAATAATATAATATATTTAATGAATTAAG-ATAAAATATATACTTGAAAAAGTTAAA
1 ATAATAATAAAATATATTTAA-G-A-TAAGAATAAAATATAT--TT-AAAAAGTTAAA
*
524956 ATAATAGTAAAATATATTT
1 ATAATAATAAAATATATTT
524975 TGAAAGTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
52 12 0.19
53 3 0.05
54 17 0.27
55 4 0.06
56 2 0.03
57 26 0.41
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (52 bp):
ATAATAATAAAATATATTTAAGATAAGAATAAAATATATTTAAAAAGTTAAA
Found at i:524990 original size:57 final size:52
Alignment explanation
Indices: 524874--524993 Score: 125
Period size: 57 Copynumber: 2.2 Consensus size: 52
524864 TTAAGATAAG
* * *
524874 AATAAAATATATTTAATAATTTAAAATAATAATATAATATATTTAATGAATTA
1 AATAAAATATATTTAAAAAGTTAAAATAATAATAAAATATATTT-ATGAATTA
*
524927 AGATAAAATATATACTTGAAAAAGTTAAAATAATAGTAAAATATATTT-TGAAAGTTTA
1 A-ATAAAATATAT--TT-AAAAAGTTAAAATAATAATAAAATATATTTATG-AA--TTA
524985 AATAAAATA
1 AATAAAATA
524994 AAAATATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
53 1 0.02
54 11 0.20
55 2 0.04
56 4 0.07
57 34 0.61
58 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.37
Consensus pattern (52 bp):
AATAAAATATATTTAAAAAGTTAAAATAATAATAAAATATATTTATGAATTA
Found at i:525016 original size:6 final size:6
Alignment explanation
Indices: 525007--525050 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
524997 ATATATTTTT
* **
525007 AAATAA AAATAA AAATAA ATATTT AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
525051 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAATAA
Found at i:525062 original size:24 final size:24
Alignment explanation
Indices: 524981--525055 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
524971 ATTTTGAAAG
* *
524981 TTTAAAT-AAAATAAAAATATATT
1 TTTAAATAAAAATAAAAATAAATA
525004 TTTAAATAAAAATAAAAATAAATA
1 TTTAAATAAAAATAAAAATAAATA
525028 TTTAAATAAAAATAAAAATAAAATA
1 TTTAAATAAAAATAAAAAT-AAATA
525053 TTT
1 TTT
525056 TTTAAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.15
24 33 0.69
25 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTAAATAAAAATAAAAATAAATA
Found at i:525072 original size:25 final size:26
Alignment explanation
Indices: 525043--525114 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 26
525033 ATAAAAATAA
525043 AAATAAAATATTTTTTAAAATAAGTT
1 AAATAAAATATTTTTTAAAATAAGTT
*
525069 AATAATAAAATA-TATTT--AATAAGTT
1 -A-AATAAAATATTTTTTAAAATAAGTT
525094 AATATAAAAATATTTTTTAAA
1 AA-AT-AAAATATTTTTTAAA
525115 GTTAATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
23 1 0.03
24 3 0.08
25 14 0.38
26 4 0.11
27 5 0.14
28 10 0.27
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
AAATAAAATATTTTTTAAAATAAGTT
Found at i:525079 original size:16 final size:17
Alignment explanation
Indices: 525058--525090 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
525048 AAATATTTTT
525058 TAAAATA-AGTTAATAA
1 TAAAATATAGTTAATAA
*
525074 TAAAATATATTTAATAA
1 TAAAATATAGTTAATAA
525091 GTTAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAAATATAGTTAATAA
Found at i:525080 original size:53 final size:54
Alignment explanation
Indices: 524984--525114 Score: 130
Period size: 53 Copynumber: 2.5 Consensus size: 54
524974 TTGAAAGTTT
524984 AAATAAAATAAAAATATATTTTTAAATAAAAATAAAAATAAATAT-TTAAATAA
1 AAATAAAATAAAAATATATTTTTAAATAAAAATAAAAATAAATATATTAAATAA
** * *
525037 AAATAAAA-ATAAAATAT-TTTTTAAA-ATAAGTTAATAATAAAATATATTTAAT-A
1 AAATAAAATA-AAAATATATTTTTAAATA-AAAATAAAAAT-AAATATATTAAATAA
** *
525090 AGTTAATATAAAAATAT-TTTTTAAA
1 AAATAAAATAAAAATATATTTTTAAA
525115 GTTAATATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
51 1 0.02
52 17 0.26
53 42 0.64
54 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (54 bp):
AAATAAAATAAAAATATATTTTTAAATAAAAATAAAAATAAATATATTAAATAA
Found at i:525116 original size:24 final size:26
Alignment explanation
Indices: 525061--525134 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 26
525051 TATTTTTTAA
525061 AATAAGTTAATA-ATAAAATATATTT
1 AATAAGTTAATATATAAAATATATTT
*
525086 AATAAGTTAATATA-AAAATATTTTT
1 AATAAGTTAATATATAAAATATATTT
*
525111 TA-AAGTTAATATATATAAA-ATATT
1 AATAAGTTAATATATA-AAATATATT
525135 ATGGATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 11 0.26
25 28 0.65
26 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AATAAGTTAATATATAAAATATATTT
Found at i:525969 original size:29 final size:30
Alignment explanation
Indices: 525937--526005 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
525927 AATGTGCGAT
** * *
525937 CCTTATTTGGTCATTT-TGAAATGTTATGC
1 CCTTATTTGACCATTTGTCAAATGTTAGGC
*
525966 CCTTATTCGACCATTTGTCAAATGTTAGGC
1 CCTTATTTGACCATTTGTCAAATGTTAGGC
525996 CCTTATTTGA
1 CCTTATTTGA
526006 ATAACCTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (30 bp):
CCTTATTTGACCATTTGTCAAATGTTAGGC
Found at i:526928 original size:32 final size:32
Alignment explanation
Indices: 526892--526952 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
526882 TAGGCAGTCC
*
526892 TTTATCCCATTGTTGGGATAATTTTTGTATCT
1 TTTATCCCATTGCTGGGATAATTTTTGTATCT
*
526924 TTTATCCCATTGCTGGGATTATTTTTGTA
1 TTTATCCCATTGCTGGGATAATTTTTGTA
526953 GAAGAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.52
Consensus pattern (32 bp):
TTTATCCCATTGCTGGGATAATTTTTGTATCT
Found at i:529683 original size:15 final size:15
Alignment explanation
Indices: 529663--529807 Score: 227
Period size: 15 Copynumber: 9.7 Consensus size: 15
529653 TGTTTTGCTT
* *
529663 AATCATTCAACACTG
1 AATCATTCAGCTCTG
529678 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
*
529693 AATCATTCAGCTCTA
1 AATCATTCAGCTCTG
* *
529708 AATCATTCAACACTG
1 AATCATTCAGCTCTG
*
529723 AATCATTCAGCACTG
1 AATCATTCAGCTCTG
529738 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
529753 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
*
529768 AATCATTCAGCTTTG
1 AATCATTCAGCTCTG
529783 AATCATTCAGCTCTG
1 AATCATTCAGCTCTG
529798 AATCATTCAG
1 AATCATTCAG
529808 AGGTGAGAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 120 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (15 bp):
AATCATTCAGCTCTG
Found at i:530545 original size:23 final size:20
Alignment explanation
Indices: 530504--530544 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
530494 CGTCAACGAG
*
530504 TAATAATTCTGGCAATCTTC
1 TAATAATTATGGCAATCTTC
530524 TAATAATTATGGCAATCTTC
1 TAATAATTATGGCAATCTTC
530544 T
1 T
530545 TATATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
TAATAATTATGGCAATCTTC
Found at i:534150 original size:3 final size:3
Alignment explanation
Indices: 534144--534187 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
534134 GTCATCATCA
* * * *
534144 TCG TCG TCG TCA CCA TCG TCA TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
534188 CTGAGCAGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.07, C:0.36, G:0.25, T:0.32
Consensus pattern (3 bp):
TCG
Found at i:534160 original size:18 final size:18
Alignment explanation
Indices: 534134--534172 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
534124 ACTCCTCGCT
* *
534134 GTCATCATCATCGTCGTC
1 GTCACCATCATCATCGTC
*
534152 GTCACCATCGTCATCGTC
1 GTCACCATCATCATCGTC
534170 GTC
1 GTC
534173 GTCGTCGTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.31
Consensus pattern (18 bp):
GTCACCATCATCATCGTC
Found at i:534165 original size:21 final size:21
Alignment explanation
Indices: 534136--534175 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
534126 TCCTCGCTGT
534136 CATCATCATCGTCGTCGTCAC
1 CATCATCATCGTCGTCGTCAC
*
534157 CATCGTCATCGTCGTCGTC
1 CATCATCATCGTCGTCGTC
534176 GTCGTCGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.17, T:0.30
Consensus pattern (21 bp):
CATCATCATCGTCGTCGTCAC
Found at i:534320 original size:33 final size:33
Alignment explanation
Indices: 534278--534351 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
534268 CGAAAACTGG
534278 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
1 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
534311 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
1 GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
534344 GAAAACTG
1 GAAAACTG
534352 TACAGGAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (33 bp):
GAAAACTGGGAAAACCCAGACATCGCTGAGTGT
Found at i:536206 original size:111 final size:111
Alignment explanation
Indices: 536074--536295 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
536064 ATTACAAAAA
* *
536074 TTAATTCTTAATCTAATAATCATGCATTAAATAAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
536139 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
536185 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
536250 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
536296 ATGATTTTCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTAGAGATAT
Found at i:536445 original size:10 final size:11
Alignment explanation
Indices: 536427--536462 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
536417 AAGATAGAGT
536427 ATTTGAGAGAA
1 ATTTGAGAGAA
536438 ATTT-AGAG-A
1 ATTTGAGAGAA
536447 ATTTGAGAG-A
1 ATTTGAGAGAA
536457 ATTTGA
1 ATTTGA
536463 TGTGATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.21
10 15 0.62
11 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:537705 original size:23 final size:23
Alignment explanation
Indices: 537653--537698 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
537643 ACAATCCAAA
537653 AGATTGATGAGTTTAATTAAATT
1 AGATTGATGAGTTTAATTAAATT
537676 AGATTGATGAGTTTAATTAAATT
1 AGATTGATGAGTTTAATTAAATT
537699 TAATTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.43
Consensus pattern (23 bp):
AGATTGATGAGTTTAATTAAATT
Found at i:539333 original size:7 final size:8
Alignment explanation
Indices: 539307--539343 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
539297 TCTCAATCTA
539307 ATTTTCAG
1 ATTTTCAG
539315 ATTTTCAG
1 ATTTTCAG
539323 ATTTT-AG
1 ATTTTCAG
*
539330 A-TTTCAA
1 ATTTTCAG
539337 ATTTTCA
1 ATTTTCA
539344 AAGCAACAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 3 0.12
7 5 0.19
8 18 0.69
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (8 bp):
ATTTTCAG
Found at i:543247 original size:16 final size:16
Alignment explanation
Indices: 543215--543274 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
543205 TAACAGACTT
543215 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
543229 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
*
543245 GTCTATTTTCTACACA
1 GTCTGTTTTCTACACA
*
543261 GTTTGTTTTCTACA
1 GTCTGTTTTCTACA
543275 TGAACTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.27
16 30 0.73
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:547278 original size:24 final size:24
Alignment explanation
Indices: 547251--547299 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
547241 TGCATCCAAT
547251 TGTAAGGTCATTTATTGTAGTAAC
1 TGTAAGGTCATTTATTGTAGTAAC
547275 TGTAAGGTCATTTATTGTAGTAAC
1 TGTAAGGTCATTTATTGTAGTAAC
547299 T
1 T
547300 TTTCTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (24 bp):
TGTAAGGTCATTTATTGTAGTAAC
Found at i:555085 original size:722 final size:722
Alignment explanation
Indices: 553700--555130 Score: 2844
Period size: 722 Copynumber: 2.0 Consensus size: 722
553690 TAAATTGAAA
553700 AAAAATATTTGTGTTGAATCAAGTTGAGTCAAACATGTTTTTATCTAAAATTTGAGTCAAATAAA
1 AAAAATATTTGTGTTGAATCAAGTTGAGTCAAACATGTTTTTATCTAAAATTTGAGTCAAATAAA
553765 AACTAGTCAAATATCGAGTTAAATTGAAATCAGATAAAATTTAAATTTTTGTATGGAATTTGAGA
66 AACTAGTCAAATATCGAGTTAAATTGAAATCAGATAAAATTTAAATTTTTGTATGGAATTTGAGA
553830 CTAACAAAATTTAACTCATCGTGCGTATGTATATATATATATTGCTCATTGAACTTTACAACATT
131 CTAACAAAATTTAACTCATCGTGCGTATGTATATATATATATTGCTCATTGAACTTTACAACATT
553895 TTACTCACTTTGCAGTTAACTTTTTAACGGTGTCATGACATGGAACAAGCATAAAAATGACGTCG
196 TTACTCACTTTGCAGTTAACTTTTTAACGGTGTCATGACATGGAACAAGCATAAAAATGACGTCG
553960 TTTTGAAAAACTCAAATATACACAAAAATGACGTCGTTTCGAGTCCTCTTCTTCCCCCATTGCCA
261 TTTTGAAAAACTCAAATATACACAAAAATGACGTCGTTTCGAGTCCTCTTCTTCCCCCATTGCCA
554025 CTGCCGACCACCATGTCATTTTTCATTCCGGCTATCGTCGATGTCATTGATGGTGGCCGTTCGGT
326 CTGCCGACCACCATGTCATTTTTCATTCCGGCTATCGTCGATGTCATTGATGGTGGCCGTTCGGT
554090 CCCAAAATTCATGGGTCGATTCGTCTCGACCCCTGAGTCTGAATCTAGTGGTTGTTTCATTGGAA
391 CCCAAAATTCATGGGTCGATTCGTCTCGACCCCTGAGTCTGAATCTAGTGGTTGTTTCATTGGAA
554155 AATATCCCAAAATCCGTGAATCTCAACTGAAACCTTTCGATTTCCTCATTTTCAATCCCCTATAC
456 AATATCCCAAAATCCGTGAATCTCAACTGAAACCTTTCGATTTCCTCATTTTCAATCCCCTATAC
554220 GTAGACTTCGGAGTAAGTTCTAACAAAATGGAAGTCGGATTCAGACTCTAGGTGTCTAGATGAAA
521 GTAGACTTCGGAGTAAGTTCTAACAAAATGGAAGTCGGATTCAGACTCTAGGTGTCTAGATGAAA
*
554285 TGACCCATGAAATTTGGGACTGAACACCCACCATCAACGATGGTCTACGGTGGCCGGTGGTGGCA
586 TGACACATGAAATTTGGGACTGAACACCCACCATCAACGATGGTCTACGGTGGCCGGTGGTGGCA
554350 TCTAACCACCTTATGTTTTTCTTTATAGTGAGCAAAATAGGAGAGAGTGTAAAGTTTAGGAGAGA
651 TCTAACCACCTTATGTTTTTCTTTATAGTGAGCAAAATAGGAGAGAGTGTAAAGTTTAGGAGAGA
554415 GTGGTTC
716 GTGGTTC
554422 AAAAATATTTGTGTTGAATCAAGTTGAGTCAAACATGTTTTTATCTAAAATTTGAGTCAAATAAA
1 AAAAATATTTGTGTTGAATCAAGTTGAGTCAAACATGTTTTTATCTAAAATTTGAGTCAAATAAA
554487 AACTAGTCAAATATCGAGTTAAATTGAAATCAGATAAAATTTAAATTTTTGTATGGAATTTGAGA
66 AACTAGTCAAATATCGAGTTAAATTGAAATCAGATAAAATTTAAATTTTTGTATGGAATTTGAGA
554552 CTAACAAAATTTAACTCATCGTGCGTATGTATATATATATATTGCTCATTGAACTTTACAACATT
131 CTAACAAAATTTAACTCATCGTGCGTATGTATATATATATATTGCTCATTGAACTTTACAACATT
554617 TTACTCACTTTGCAGTTAACTTTTTAACGGTGTCATGACATGGAACAAGCATAAAAATGACGTCG
196 TTACTCACTTTGCAGTTAACTTTTTAACGGTGTCATGACATGGAACAAGCATAAAAATGACGTCG
554682 TTTTGAAAAACTCAAATATACACAAAAATGACGTCGTTTCGAGTCCTCTTCTTCCCCCATTGCCA
261 TTTTGAAAAACTCAAATATACACAAAAATGACGTCGTTTCGAGTCCTCTTCTTCCCCCATTGCCA
554747 CTGCCGACCACCATGTCATTTTTCATTCCGGCTATCGTCGATGTCATTGATGGTGGCCGTTCGGT
326 CTGCCGACCACCATGTCATTTTTCATTCCGGCTATCGTCGATGTCATTGATGGTGGCCGTTCGGT
554812 CCCAAAATTCATGGGTCGATTCGTCTCGACCCCTGAGTCTGAATCTAGTGGTTGTTTCATTGGAA
391 CCCAAAATTCATGGGTCGATTCGTCTCGACCCCTGAGTCTGAATCTAGTGGTTGTTTCATTGGAA
554877 AATATCCCAAAATCCGTGAATCTCAACTGAAACCTTTCGATTTCCTCATTTTCAATCCCCTATAC
456 AATATCCCAAAATCCGTGAATCTCAACTGAAACCTTTCGATTTCCTCATTTTCAATCCCCTATAC
*
554942 GTGGACTTCGGAGTAAGTTCTAACAAAATGGAAGTCGGATTCAGACTCTAGGTGTCTAGATGAAA
521 GTAGACTTCGGAGTAAGTTCTAACAAAATGGAAGTCGGATTCAGACTCTAGGTGTCTAGATGAAA
555007 TGACACATGAAATTTGGGACTGAACACCCACCATCAACGATGGTCTACGGTGGCCGGTGGTGGCA
586 TGACACATGAAATTTGGGACTGAACACCCACCATCAACGATGGTCTACGGTGGCCGGTGGTGGCA
555072 TCTAACCACCTTATGTTTTTCTTTATAGTGAGCAAAATAGGAGAGAGTGTAAAGTTTAG
651 TCTAACCACCTTATGTTTTTCTTTATAGTGAGCAAAATAGGAGAGAGTGTAAAGTTTAG
555131 TGATAAGCGA
Statistics
Matches: 707, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
722 707 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (722 bp):
AAAAATATTTGTGTTGAATCAAGTTGAGTCAAACATGTTTTTATCTAAAATTTGAGTCAAATAAA
AACTAGTCAAATATCGAGTTAAATTGAAATCAGATAAAATTTAAATTTTTGTATGGAATTTGAGA
CTAACAAAATTTAACTCATCGTGCGTATGTATATATATATATTGCTCATTGAACTTTACAACATT
TTACTCACTTTGCAGTTAACTTTTTAACGGTGTCATGACATGGAACAAGCATAAAAATGACGTCG
TTTTGAAAAACTCAAATATACACAAAAATGACGTCGTTTCGAGTCCTCTTCTTCCCCCATTGCCA
CTGCCGACCACCATGTCATTTTTCATTCCGGCTATCGTCGATGTCATTGATGGTGGCCGTTCGGT
CCCAAAATTCATGGGTCGATTCGTCTCGACCCCTGAGTCTGAATCTAGTGGTTGTTTCATTGGAA
AATATCCCAAAATCCGTGAATCTCAACTGAAACCTTTCGATTTCCTCATTTTCAATCCCCTATAC
GTAGACTTCGGAGTAAGTTCTAACAAAATGGAAGTCGGATTCAGACTCTAGGTGTCTAGATGAAA
TGACACATGAAATTTGGGACTGAACACCCACCATCAACGATGGTCTACGGTGGCCGGTGGTGGCA
TCTAACCACCTTATGTTTTTCTTTATAGTGAGCAAAATAGGAGAGAGTGTAAAGTTTAGGAGAGA
GTGGTTC
Found at i:555607 original size:30 final size:30
Alignment explanation
Indices: 555532--555599 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
555522 CTTTTAAAAC
* * * *
555532 TTGCAATAAAATCCCTAACATTTAGTTCGT
1 TTGCAATACAGTCCCCAACATTTAGTCCGT
555562 TTGCAATACAGTCCCCAACATTTAGTCCGT
1 TTGCAATACAGTCCCCAACATTTAGTCCGT
555592 TTGCAATA
1 TTGCAATA
555600 TGGTCCCCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (30 bp):
TTGCAATACAGTCCCCAACATTTAGTCCGT
Found at i:557141 original size:25 final size:25
Alignment explanation
Indices: 557107--557157 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
557097 CAACATGATA
557107 CTTAGTTCATCTTAGTAGTATTTGT
1 CTTAGTTCATCTTAGTAGTATTTGT
557132 CTTAGTTCATCTTAGTAGTATTTGT
1 CTTAGTTCATCTTAGTAGTATTTGT
557157 C
1 C
557158 AACTCTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.51
Consensus pattern (25 bp):
CTTAGTTCATCTTAGTAGTATTTGT
Found at i:558030 original size:18 final size:18
Alignment explanation
Indices: 558007--558061 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
557997 ATTATCCCTC
558007 TATATATAGAGACAACAT
1 TATATATAGAGACAACAT
558025 TATATATAGAGACAACAT
1 TATATATAGAGACAACAT
558043 TATATATAGAGACAACAT
1 TATATATAGAGACAACAT
558061 T
1 T
558062 TTTCTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
TATATATAGAGACAACAT
Found at i:558220 original size:21 final size:21
Alignment explanation
Indices: 558183--558223 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
558173 ATTATATATT
558183 ATAAAAAGAAAGAAAGAAAAA
1 ATAAAAAGAAAGAAAGAAAAA
*
558204 ATAAAGAGAGAAG-AAGAAAA
1 ATAAAAAGA-AAGAAAGAAAA
558224 GGTCTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (21 bp):
ATAAAAAGAAAGAAAGAAAAA
Found at i:560604 original size:17 final size:17
Alignment explanation
Indices: 560582--560617 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
560572 TAATTTTAAT
*
560582 TACTCATCGATTAAGGG
1 TACTCATAGATTAAGGG
560599 TACTCATAGATTAAGGG
1 TACTCATAGATTAAGGG
560616 TA
1 TA
560618 GTTATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (17 bp):
TACTCATAGATTAAGGG
Found at i:562194 original size:2 final size:2
Alignment explanation
Indices: 562187--562281 Score: 163
Period size: 2 Copynumber: 47.5 Consensus size: 2
562177 ATAATTTATT
* *
562187 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
562229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
562271 TA TA TA TA TA T
1 TA TA TA TA TA T
562282 GCATATGCTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:571866 original size:12 final size:13
Alignment explanation
Indices: 571849--571878 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
571839 TCGACCGGGT
571849 AAAATTAAAAA-A
1 AAAATTAAAAAGA
571861 AAAATTAAAAAGA
1 AAAATTAAAAAGA
571874 AAAAT
1 AAAAT
571879 CAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAATTAAAAAGA
Found at i:574125 original size:2 final size:2
Alignment explanation
Indices: 574118--574148 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
574108 TATATTTTTG
574118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
574149 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:597474 original size:22 final size:21
Alignment explanation
Indices: 597429--597474 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
597419 TAACTTTTTC
*
597429 TTTTCTCTTTCATTATTAATT
1 TTTTCTCTTTCATTATTAACT
*
597450 TTTTCTCTTTCATTTTTTAACT
1 TTTTCTCTTTCA-TTATTAACT
597472 TTT
1 TTT
597475 ACTTTTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:599168 original size:45 final size:46
Alignment explanation
Indices: 599060--599173 Score: 158
Period size: 47 Copynumber: 2.5 Consensus size: 46
599050 ACCTTTTATC
599060 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTAAATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATT-AATT
* ** * *
599107 CCATAAGCTCGTAAGCTTATTTTTTTCAATATACTTGCCATT-ATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTAATT
*
599152 CCGTAAGCTCATAAGCTTATTT
1 CCATAAGCTCATAAGCTTATTT
599174 GCATGGTTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 23 0.38
47 37 0.62
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (46 bp):
CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTAATT
Found at i:599333 original size:40 final size:40
Alignment explanation
Indices: 599278--599399 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
599268 ACCATAGTGC
599278 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
599318 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
599358 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
599398 TA
1 TA
599400 TAAACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:602901 original size:22 final size:22
Alignment explanation
Indices: 602869--602945 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
602859 GAAGGACCAT
602869 TACGTCCCGAATGACCACTGGA
1 TACGTCCCGAATGACCACTGGA
* *
602891 TACATCCCGAAGGACCACTGGA
1 TACGTCCCGAATGACCACTGGA
* *
602913 TACGTTCCGAATGACCATTGGA
1 TACGTCCCGAATGACCACTGGA
*
602935 TATGTCCCGAA
1 TACGTCCCGAA
602946 GGATCACTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (22 bp):
TACGTCCCGAATGACCACTGGA
Found at i:602923 original size:44 final size:44
Alignment explanation
Indices: 602869--602953 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
602859 GAAGGACCAT
602869 TACGTCCCGAATGACCACTGGATACATCCCGAAGGACCACTGGA
1 TACGTCCCGAATGACCACTGGATACATCCCGAAGGACCACTGGA
* * ** *
602913 TACGTTCCGAATGACCATTGGATATGTCCCGAAGGATCACT
1 TACGTCCCGAATGACCACTGGATACATCCCGAAGGACCACT
602954 AAAAACCCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (44 bp):
TACGTCCCGAATGACCACTGGATACATCCCGAAGGACCACTGGA
Found at i:609473 original size:20 final size:21
Alignment explanation
Indices: 609448--609487 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
609438 TGATCATGAC
609448 ATTTCAATATG-CATATATAT
1 ATTTCAATATGACATATATAT
*
609468 ATTTCACTATGACATATATA
1 ATTTCAATATGACATATATA
609488 ATCATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTTCAATATGACATATATAT
Found at i:609709 original size:22 final size:22
Alignment explanation
Indices: 609675--609734 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
609665 GGACCATTAT
609675 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
* * *
609697 GTCCCAAAAGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAC
609719 GTCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
609735 ATAAACTCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.32, G:0.23, T:0.15
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:610292 original size:20 final size:20
Alignment explanation
Indices: 610264--610340 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
610254 CTAACTGAGA
* *
610264 TATATATACCTTGTCTATGG
1 TATAGATACCTTGCCTATGG
610284 TATAGATACCCTT-CCTATGG
1 TATAGATA-CCTTGCCTATGG
* *
610304 TGTAGATACCCTGCCTATGG
1 TATAGATACCTTGCCTATGG
*
610324 TATAGATACCCTGCCTA
1 TATAGATACCTTGCCTA
610341 CATTCTGGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 3 0.06
20 43 0.86
21 4 0.08
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (20 bp):
TATAGATACCTTGCCTATGG
Found at i:614467 original size:19 final size:19
Alignment explanation
Indices: 614431--614481 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
614421 ATTTTATTGA
* *
614431 AAATAAAAAAATTA-AATT
1 AAATCAAAAATTTATAATT
*
614449 ACAAT-AAAGATTTATAATT
1 A-AATCAAAAATTTATAATT
614468 AAATCAAAAATTTA
1 AAATCAAAAATTTA
614482 AAATATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATCAAAAATTTATAATT
Found at i:615334 original size:15 final size:15
Alignment explanation
Indices: 615314--615370 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
615304 AACCATACAG
615314 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
**
615329 GGGGAATCAATACCCC
1 GGGGAATCTGTA-CCC
*
615345 TGGAGGGAATCTGTTCCC
1 --G-GGGAATCTGTACCC
615363 GGGGAATC
1 GGGGAATC
615371 GATACCCCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 4 0.12
18 4 0.12
19 8 0.24
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:615388 original size:35 final size:34
Alignment explanation
Indices: 615313--615397 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
615303 AAACCATACA
*
615313 GGGGGAATCTGTACCCGGGGAATCAATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCAATACCCCTG
* *
615347 GAGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCAATA-CCCCTG
615382 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
615398 CCTGGGGGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 25 0.54
35 21 0.46
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCAATACCCCTG
Found at i:615405 original size:21 final size:21
Alignment explanation
Indices: 615363--615423 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
615353 ATCTGTTCCC
615363 GGGGAATC-GATACCCCCT-GG
1 GGGGAATCTG-TACCCCCTGGG
*
615383 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
615404 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
615424 ACAATCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.15, C:0.30, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:618909 original size:15 final size:15
Alignment explanation
Indices: 618889--618945 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
618879 AACCATGCAG
618889 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
618904 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
618920 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
618938 GGGGAATC
1 GGGGAATC
618946 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:618968 original size:36 final size:34
Alignment explanation
Indices: 618888--618973 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
618878 AAACCATGCA
*
618888 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
618922 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTGG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCT-G
618958 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
618974 CCTGGGGGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 27 0.55
35 5 0.10
36 17 0.35
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:618974 original size:20 final size:20
Alignment explanation
Indices: 618904--618994 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
618894 ATCTGTACCC
618904 GGGGAATC-GATA-CCCCTGG
1 GGGGAATCTG-TACCCCCTGG
*
618923 GGGGAATCTGT--TCCC---
1 GGGGAATCTGTACCCCCTGG
618938 GGGGAATC-GATACCCCCTGGG
1 GGGGAATCTG-TACCCCCT-GG
*
618959 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
618979 GGGGAATCTGTACCCC
1 GGGGAATCTGTACCCC
618995 TTGGACAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
17 3 0.05
18 3 0.05
19 9 0.15
20 18 0.31
21 15 0.25
22 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:620996 original size:29 final size:29
Alignment explanation
Indices: 620959--621023 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
620949 GTAATGTTAG
*
620959 ACACCTAAATGGGTCAAAAAATAGTTTAA
1 ACACCTAAATGAGTCAAAAAATAGTTTAA
620988 ACACCTAAATGAGTCAAAAAATAGTTTAA
1 ACACCTAAATGAGTCAAAAAATAGTTTAA
621017 ACACCTA
1 ACACCTA
621024 TTCGAGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (29 bp):
ACACCTAAATGAGTCAAAAAATAGTTTAA
Found at i:621653 original size:21 final size:21
Alignment explanation
Indices: 621627--621668 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
621617 TCCATTTTCC
621627 TTGCATTGAAAATATAAATAA
1 TTGCATTGAAAATATAAATAA
621648 TTGCATTGAAAATATAAATAA
1 TTGCATTGAAAATATAAATAA
621669 GATCGTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
TTGCATTGAAAATATAAATAA
Found at i:622194 original size:20 final size:20
Alignment explanation
Indices: 622148--622186 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
622138 TATAAATATT
*
622148 AAATTTAAAAAATATATTCA
1 AAATTTTAAAAATATATTCA
622168 AAATTTTAAAAA-ATATTCA
1 AAATTTTAAAAATATATTCA
622187 CTAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTTAAAAATATATTCA
Found at i:622658 original size:6 final size:6
Alignment explanation
Indices: 622644--622719 Score: 71
Period size: 6 Copynumber: 12.7 Consensus size: 6
622634 CATTTGATTA
* * * * * * *
622644 TATATG TATACG TATATA TATACG TATATA TATACG TATATA TATACG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
**
622692 TATATG TATACA TATATG TATATG TATA
1 TATATG TATATG TATATG TATATG TATA
622720 CACAAACGTA
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (6 bp):
TATATG
Found at i:622665 original size:12 final size:12
Alignment explanation
Indices: 622644--622719 Score: 107
Period size: 12 Copynumber: 6.3 Consensus size: 12
622634 CATTTGATTA
*
622644 TATATGTATACG
1 TATATATATACG
622656 TATATATATACG
1 TATATATATACG
622668 TATATATATACG
1 TATATATATACG
622680 TATATATATACG
1 TATATATATACG
* *
622692 TATATGTATACA
1 TATATATATACG
* *
622704 TATATGTATATG
1 TATATATATACG
622716 TATA
1 TATA
622720 CACAAACGTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (12 bp):
TATATATATACG
Found at i:622721 original size:18 final size:18
Alignment explanation
Indices: 622650--622731 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
622640 ATTATATATG
* *
622650 TATACGTATATATATACG
1 TATACGTATATGTATACA
** * *
622668 TATATATATACGTATATA
1 TATACGTATATGTATACA
622686 TATACGTATATGTATACA
1 TATACGTATATGTATACA
*
622704 TATATGTATATGTATACA
1 TATACGTATATGTATACA
* *
622722 CAAACGTATA
1 TATACGTATA
622732 ATCTATAGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (18 bp):
TATACGTATATGTATACA
Found at i:622856 original size:2 final size:2
Alignment explanation
Indices: 622851--622879 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
622841 ACACACACAC
622851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
622880 CATAGCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:623024 original size:29 final size:29
Alignment explanation
Indices: 622982--623067 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
622972 AATGTTGGCC
*
622982 GTAGGTCGTCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
623011 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
623040 GTAGGTCACCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
623068 ACCCTCACGT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 53 0.98
30 1 0.02
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:623162 original size:33 final size:34
Alignment explanation
Indices: 623125--623210 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 34
623115 CCCTCGCTCA
* *
623125 GCTGCCCTAGGATTCTCTCG-CATAGCTCGTTCG
1 GCTGCCCTCGGATGCTCTCGACATAGCTCGTTCG
*
623158 GCTGCCCTCGGATGCCCT-GACATAGCTCGTTCG
1 GCTGCCCTCGGATGCTCTCGACATAGCTCGTTCG
* *
623191 GATGGCCTCGGATGCTCTCG
1 GCTGCCCTCGGATGCTCTCG
623211 GATGGCATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 43 0.96
34 1 0.02
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.27
Consensus pattern (34 bp):
GCTGCCCTCGGATGCTCTCGACATAGCTCGTTCG
Found at i:623213 original size:20 final size:20
Alignment explanation
Indices: 623188--623241 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
623178 CATAGCTCGT
623188 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
* *
623208 TCGGATGGCATCTGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
623228 TCGGATAGCCTCGG
1 TCGGATGGCCTCGG
623242 TCGGATGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.28, G:0.33, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:623335 original size:29 final size:29
Alignment explanation
Indices: 623298--623355 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
623288 GCTATCTCTT
*
623298 GTAGCTCGCAGGGAAGACATGACGACCTA
1 GTAGCTCGCACGGAAGACATGACGACCTA
* * * *
623327 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCACGGAAGACATGACGACCTA
623356 CGGCCAACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCACGGAAGACATGACGACCTA
Found at i:623463 original size:2 final size:2
Alignment explanation
Indices: 623456--623504 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
623446 AAAGTTTTAT
623456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
623498 TA TA TA T
1 TA TA TA T
623505 TAGGAAGGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:638312 original size:22 final size:24
Alignment explanation
Indices: 638287--638332 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
638277 ATTTATCTTT
*
638287 TAAA-ATTA-TAAAAAATTATATA
1 TAAATATTATTAAAAAAATATATA
*
638309 TAAATTTTATTAAAAAAATATATA
1 TAAATATTATTAAAAAAATATATA
638333 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATTATTAAAAAAATATATA
Found at i:638383 original size:25 final size:25
Alignment explanation
Indices: 638354--638411 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
638344 ATAAAGTAAT
638354 ATATTTTCGATGATTTTTTATATAA
1 ATATTTTCGATGATTTTTTATATAA
638379 ATATTTTCGATGATTTTTTATATAA
1 ATATTTTCGATGATTTTTTATATAA
638404 ATATTTTC
1 ATATTTTC
638412 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (25 bp):
ATATTTTCGATGATTTTTTATATAA
Found at i:638590 original size:29 final size:28
Alignment explanation
Indices: 638548--638627 Score: 124
Period size: 28 Copynumber: 2.8 Consensus size: 28
638538 ACCAAACACA
*
638548 GTAATGTAACATTCCCAATAATGTATTAG
1 GTAATGTTACATT-CCAATAATGTATTAG
* *
638577 GTAATGTTACATTCCAATAATATTTTAG
1 GTAATGTTACATTCCAATAATGTATTAG
638605 GTAATGTTACATTCCAATAATGT
1 GTAATGTTACATTCCAATAATGT
638628 TATTCCCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 35 0.74
29 12 0.26
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (28 bp):
GTAATGTTACATTCCAATAATGTATTAG
Found at i:646074 original size:2 final size:2
Alignment explanation
Indices: 646067--646095 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
646057 TAATTTAAAT
646067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
646096 TAATATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:646883 original size:16 final size:16
Alignment explanation
Indices: 646850--646883 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
646840 TCGGATCGAA
* *
646850 TTAAATTCGGTTCGGG
1 TTAAATTCGATTCAGG
646866 TTAAATTCGATTCAGG
1 TTAAATTCGATTCAGG
646882 TT
1 TT
646884 GCTTTCGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (16 bp):
TTAAATTCGATTCAGG
Found at i:647174 original size:37 final size:37
Alignment explanation
Indices: 647131--647207 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
647121 TAATCGGTTT
647131 ACAGATATTTACCATTGCGTCTCAGTTTACGATTCTG
1 ACAGATATTTACCATTGCGTCTCAGTTTACGATTCTG
647168 ACAGATATTTACCATTGCGTCTCAGTTTACGATTCTG
1 ACAGATATTTACCATTGCGTCTCAGTTTACGATTCTG
647205 ACA
1 ACA
647208 TGGGCTCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
ACAGATATTTACCATTGCGTCTCAGTTTACGATTCTG
Found at i:651146 original size:3 final size:3
Alignment explanation
Indices: 651140--651179 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
651130 ATGGCTGCTG
*
651140 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT
651180 CCACATGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:658709 original size:20 final size:20
Alignment explanation
Indices: 658633--658717 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
658623 AACAGAACCC
*
658633 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
**
658654 GTGGGGGGAATC-AGTTCCCCTT
1 CAGGGGGGAATCGA-TT-CCC-T
* *
658676 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
658697 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
658717 C
1 C
658718 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
20 18 0.36
21 17 0.34
22 4 0.08
23 11 0.22
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:662469 original size:22 final size:21
Alignment explanation
Indices: 662427--662466 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
662417 GAGTTTGTTT
*
662427 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
662448 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
662467 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:666564 original size:18 final size:20
Alignment explanation
Indices: 666528--666569 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
666518 AATTTGATTT
*
666528 TTTTTTTTAAATTATAAT-A
1 TTTTTTTTAAATTAAAATAA
666547 TTTTTTTTAAA-TAAAATAA
1 TTTTTTTTAAATTAAAATAA
666566 TTTT
1 TTTT
666570 GTGACATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTTAAATTAAAATAA
Found at i:675426 original size:30 final size:32
Alignment explanation
Indices: 675362--675432 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 32
675352 ATCAAAAGTA
675362 TTTAATTATAATAGTTTTAATTTAAAATATTAT
1 TTTAA-TATAATAGTTTTAATTTAAAATATTAT
*
675395 TTTAATATAATA--TTTATATTTTAAA-ATTAT
1 TTTAATATAATAGTTTTA-ATTTAAAATATTAT
675425 TTTAATAT
1 TTTAATAT
675433 GACATTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 17 0.47
31 7 0.19
32 7 0.19
33 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TTTAATATAATAGTTTTAATTTAAAATATTAT
Found at i:676056 original size:12 final size:12
Alignment explanation
Indices: 676039--676090 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
676029 TAAACAAGTC
676039 TTAATTATATAT
1 TTAATTATATAT
676051 TTAATT-TATAAT
1 TTAATTATAT-AT
*
676063 TGTAATTATAAAT
1 T-TAATTATATAT
*
676076 TTTATTATAATAT
1 TTAATTAT-ATAT
676089 TT
1 TT
676091 TATGTTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 3 0.09
12 15 0.45
13 13 0.39
14 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTAATTATATAT
Found at i:676068 original size:25 final size:24
Alignment explanation
Indices: 676040--676086 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
676030 AAACAAGTCT
*
676040 TAATTATATATTTAATTTATAATTG
1 TAATTATAAATTTAA-TTATAATTG
*
676065 TAATTATAAATTTTATTATAAT
1 TAATTATAAATTTAATTATAAT
676087 ATTTTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TAATTATAAATTTAATTATAATTG
Found at i:682810 original size:14 final size:14
Alignment explanation
Indices: 682791--682818 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
682781 AAGTTAAAGA
682791 ATAGTTATATAATT
1 ATAGTTATATAATT
682805 ATAGTTATATAATT
1 ATAGTTATATAATT
682819 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Done.