Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008465.1 Hibiscus syriacus cultivar Beakdansim tig00111278_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: 924357
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 5
Found at i:419675 original size:45 final size:45
Alignment explanation
Indices: 419626--420004 Score: 459
Period size: 45 Copynumber: 8.6 Consensus size: 45
419616 CATTATGTAT
* * * *
419626 TTTCATTTATGGCATTCTTTCATGCCAATAATGAACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* *
419671 TTTCAATCATGGCATCCTTTCATGTCGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* *
419716 TTTCAATTATGGCATCCTTTCATGTCAATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* *
419761 TTTCAATTATGG----CTTT-ATGTCGATAATGCACCCATGTGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
419801 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* * * * *
419846 TTTAAATTATGGCATCCTTTTATGCTGATAATGCTCCTATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* ** *
419891 TTTCAATTATAGCAT--TTTTTTACCGATAATGCACCCATATGCA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
* * * *
419934 TTTCAATTATGGCATCATTTCATGCCGATAATACA-CTATTATACA
1 TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA-TATGCA
* **
419979 TTTCATTTATAACATCCTTTCATGCC
1 TTTCAATTATGGCATCCTTTCATGCC
420005 TTTTATACAA
Statistics
Matches: 291, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
40 34 0.12
41 4 0.01
43 37 0.13
44 6 0.02
45 210 0.72
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (45 bp):
TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCA
Found at i:419830 original size:130 final size:132
Alignment explanation
Indices: 419653--420003 Score: 476
Period size: 130 Copynumber: 2.7 Consensus size: 132
419643 TTTCATGCCA
* * *
419653 ATAATGAACCCATATGCATTTCAATCATGGCATCCTTTCATGTCGATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCATT
*
419718 TCAATTATGGCATCCTTTCATG-TCAATAATGCACCCATATGCATTTCAATTATGGC-TTTATGT
66 TCAATTATGGCATCCTTTCATGCT-AATAATGCACCCATATGCATTTCAATTATAGCATTTATGT
419781 -CG
130 ACG
*
419783 ATAATGCACCCATGTGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCATT
* * * * * * *
419848 TAAATTATGGCATCCTTTTATGCTGATAATGCTCCTATATGCATTTCAATTATAGCATTTTTTTA
66 TCAATTATGGCATCCTTTCATGCTAATAATGCACCCATATGCATTTCAATTATAGCATTTATGTA
419913 CCG
131 -CG
* * * *
419916 ATAATGCACCCATATGCATTTCAATTATGGCATCATTTCATGCCGATAATACA-CTATTATACAT
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA-TATGCAT
* **
419980 TTCATTTATAACATCCTTTCATGC
65 TTCAATTATGGCATCCTTTCATGC
420004 CTTTTATACA
Statistics
Matches: 194, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
130 109 0.56
131 6 0.03
132 2 0.01
133 77 0.40
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (132 bp):
ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCATATGCATT
TCAATTATGGCATCCTTTCATGCTAATAATGCACCCATATGCATTTCAATTATAGCATTTATGTA
CG
Found at i:420132 original size:81 final size:81
Alignment explanation
Indices: 420039--420195 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
420029 ATACATCTAG
* ***
420039 TCTTTTACTCAAAGGCATTTAACCTTTCATCTATA-TGGCATTATCAACACCTTTTTTTCAAATG
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTA-ACTGGCATAATCAACACCTTTCAGTCAAATG
420103 CACAACTAGGTCATTAA
65 CACAACTAGGTCATTAA
* * ** *
420120 TCTTTTCCTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATCTTTCAGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATCAACACCTTTCAGTCAAATGC
420185 ACAACTAGGTC
66 ACAACTAGGTC
420196 TCAAAGACAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
80 1 0.02
81 65 0.98
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATCAACACCTTTCAGTCAAATGC
ACAACTAGGTCATTAA
Found at i:420327 original size:67 final size:67
Alignment explanation
Indices: 420126--420530 Score: 533
Period size: 67 Copynumber: 6.0 Consensus size: 67
420116 TTAATCTTTT
* * * * * **
420126 CCTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATCTTTCAGTCAAATGCACAACT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATGCACAGTT
420191 AGG
65 AGG
* * * * * *
420194 TCTCAAAGACACTTAGCCTTTCTTCTAACTGGC-TAATTGACACCTTTGTTTCAATGTACAGTTA
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
420258 GG
66 GG
* *
420260 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGTATAATTGATACCTTTCTGTCAATGCACAGTTA
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
420325 GG
66 GG
* * * * * * *
420327 CCTCAAAGACATTTAGCCTTTCATCTAACGGGTATAATTGACACTTTTCTATCAATGCACATTTA
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
**
420392 TT
66 GG
420394 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
420459 GG
66 GG
* * * * *
420461 CATCAAAGGCACTTAGCCTTTCATCTAACTGCCATAATTGACACATTTCTGTCAATGTATAGTTA
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
420526 GG
66 GG
420528 CCT
1 CCT
420531 TAATCTTTTA
Statistics
Matches: 291, Mismatches: 45, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
66 40 0.14
67 224 0.77
68 27 0.09
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (67 bp):
CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTA
GG
Found at i:420862 original size:67 final size:67
Alignment explanation
Indices: 420754--421073 Score: 514
Period size: 67 Copynumber: 4.8 Consensus size: 67
420744 ATAAACAATG
*
420754 CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTGA
1 CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGA
420819 GA
66 GA
* *
420821 CCTAACTGTGTATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGA
1 CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGA
*
420886 GG
66 GA
* *
420888 CCTAATTGTGCATTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGCTAAGTACCTTTGA
1 CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGA
*
420953 GG
66 GA
* *
420955 CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTGA
1 CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGA
421020 GA
66 GA
** * *
421022 CCTAGTTGCGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGG
1 CCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
421074 TCAAATACAT
Statistics
Matches: 235, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
67 197 0.84
68 38 0.16
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (67 bp):
CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGA
GA
Found at i:421299 original size:45 final size:45
Alignment explanation
Indices: 421213--421612 Score: 439
Period size: 45 Copynumber: 8.9 Consensus size: 45
421203 GTATAAAAGA
* * * * * **
421213 CATGAAATGATGCCATAAATGAAATGTATAAT-AGTGTATTATCAT
1 CATGAAAGGATGCCATAATTGAAATGCAT-ATGGGTGCATTATCGG
* * *
421258 CATGAAATGATGCTATAATTGAAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* * * * **
421303 TC-TAAAAGGATGTCATAATTTAAATTCATATGGGT-TTTATATCGG
1 -CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCAT-TATCGG
* ** *
421348 CATGAAATGATATCATAATTGAAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
** * *
421393 CATGAAAGGATGATATAATTTAAATGTATATGGGTGCATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
421438 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* * * *
421483 GATGAAAGGATGCCATAATTGAAATTCATATGGGTGCACTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* *
421528 CATGAAAGGATGCCATGATTGAAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* *
421573 CATGAAAGTATGCCATAAATGAAAATGCATGAT-GGTGCAT
1 CATGAAAGGATGCCATAATTG-AAATGCAT-ATGGGTGCAT
421613 AATAATTATG
Statistics
Matches: 299, Mismatches: 49, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
44 4 0.01
45 276 0.92
46 17 0.06
47 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (45 bp):
CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
Found at i:421834 original size:2 final size:2
Alignment explanation
Indices: 421827--421889 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
421817 CATACTTATG
421827 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
421869 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
421890 TTCTTTACAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:427004 original size:20 final size:20
Alignment explanation
Indices: 426981--427019 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
426971 ATTCCCCAGA
*
426981 AAGTATCGATATTGTTCTTC
1 AAGTACCGATATTGTTCTTC
427001 AAGTACCGATATTGTTCTT
1 AAGTACCGATATTGTTCTT
427020 GCAGCCTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
AAGTACCGATATTGTTCTTC
Found at i:427055 original size:13 final size:13
Alignment explanation
Indices: 427034--427072 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
427024 CCTCGATAGG
*
427034 GTATCGATACCAA
1 GTATTGATACCAA
427047 GTATTGATACCAA
1 GTATTGATACCAA
427060 GTATTGATACCAA
1 GTATTGATACCAA
427073 TCAATTTTAG
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:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (13 bp):
GTATTGATACCAA
Found at i:435083 original size:13 final size:13
Alignment explanation
Indices: 435065--435089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
435055 CCTCGATAGG
435065 GTATCGATACCAA
1 GTATCGATACCAA
435078 GTATCGATACCA
1 GTATCGATACCA
435090 TTCAATTTTA
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:0.24, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACCAA
Found at i:435545 original size:18 final size:17
Alignment explanation
Indices: 435518--435553 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
435508 CAAAAATTTC
435518 ATTAAAATTTTATATATT
1 ATTAAAA-TTTATATATT
*
435536 ATTAATATTTATATATT
1 ATTAAAATTTATATATT
435553 A
1 A
435554 CTATTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAAAATTTATATATT
Found at i:443700 original size:21 final size:21
Alignment explanation
Indices: 443671--443711 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
443661 ATAAATCATA
443671 AAATATTATAATAATGATTCG
1 AAATATTATAATAATGATTCG
*
443692 AAATGTTATAATAATGATTC
1 AAATATTATAATAATGATTC
443712 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (21 bp):
AAATATTATAATAATGATTCG
Found at i:457324 original size:37 final size:37
Alignment explanation
Indices: 457271--457390 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
457261 GAATCCATTT
* *
457271 TAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCATCC
1 TAAGCCTTCACCGAAGAGTAGTGAAGCAAATTCATCA
* * **
457308 TAAGCCTTCACCGAAGAGTAGTGAAACAAATCCATTT
1 TAAGCCTTCACCGAAGAGTAGTGAAGCAAATTCATCA
*
457345 TCAA-CCTTCATCGAAGAGTAGTGAAGCAAATTCATCTA
1 T-AAGCCTTCACCGAAGAGTAGTGAAGCAAATTCATC-A
457383 TAAGCCTT
1 TAAGCCTT
457391 TAGAGCAAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
37 63 0.90
38 7 0.10
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (37 bp):
TAAGCCTTCACCGAAGAGTAGTGAAGCAAATTCATCA
Found at i:457656 original size:133 final size:133
Alignment explanation
Indices: 457418--457693 Score: 480
Period size: 133 Copynumber: 2.1 Consensus size: 133
457408 TACTTTGGGT
*
457418 CATCCATAAGACCTTCGGGTAGGATATTTTGACATGAATTTGAAAAATAAGAAAGTGATGTTTTA
1 CATCCATAAGACCTTCGGGTAGGATATTTTCACATGAATTTGAAAAATAAGAAAGTGATGTTTTA
* *
457483 AGAAGATGAAATCTTTGAAAACTAAGAAGGTGATTTCCAAAATTTTGCACTTAGTGAGTCCTTCA
66 AGAAGATGAAATCTTTGAAAACTAAGAAGGTGATTTCCAAAATTTCGCACTTAGTAAGTCCTTCA
457548 GGC
131 GGC
* * *
457551 CATCCATTAGACCTTCGGGTAGGATGTTTTCACATGAGTTTGAAAAATAAGAAAGTGATGTTTTA
1 CATCCATAAGACCTTCGGGTAGGATATTTTCACATGAATTTGAAAAATAAGAAAGTGATGTTTTA
*
457616 AGAAGATGAAATCTTTGAAAACTAAGAAGGTGATTTCCAAAATTTCGCACTTAGTAAGTCCTTCG
66 AGAAGATGAAATCTTTGAAAACTAAGAAGGTGATTTCCAAAATTTCGCACTTAGTAAGTCCTTCA
457681 GGC
131 GGC
*
457684 CATCAATAAG
1 CATCCATAAG
457694 TCTTTTGAGC
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (133 bp):
CATCCATAAGACCTTCGGGTAGGATATTTTCACATGAATTTGAAAAATAAGAAAGTGATGTTTTA
AGAAGATGAAATCTTTGAAAACTAAGAAGGTGATTTCCAAAATTTCGCACTTAGTAAGTCCTTCA
GGC
Found at i:457948 original size:209 final size:213
Alignment explanation
Indices: 457541--457936 Score: 561
Period size: 209 Copynumber: 1.9 Consensus size: 213
457531 ACTTAGTGAG
* * *
457541 TCCTTCAGGCCATCCATTAGACCTTCGGGTAGGATGTTTTCACATGAGTTTGAAAAATAAGAAAG
1 TCCTTCAGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAATAAGAAAG
* *
457606 TGATGTTTTAAGAAGATGAAATCTTTGAAAACTAAGAAGGTGATTTCCAAAATTTCGCACTTAGT
66 CGATGTTTT---AAGATGAAATCTTTGAAAACTAAGAAGGAGATTTCCAAAATTTCGCACTTAGT
* * * * *
457671 AAGTCCTTCGGGCCATCAATAAGTCTTTTGAGCTTGGTGCTTAAATCCTTCGGGTAATCTGTAAG
128 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGCGTAATCTGTAAG
457736 CCTTTAGAGCAAGATGATAAA
193 CCTTTAGAGCAAGATGATAAA
457757 TCCTTC-GAGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTG-AAAATAAGAAA
1 TCCTTCAG-GCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAATAAGAAA
* * * * *
457820 GCGATGTTTT-A-A-GAAATCTTTGAGAAGTAAGTAGGAGATTTCCAATATTTCTCACTATA-TA
65 GCGATGTTTTAAGATGAAATCTTTGAAAACTAAGAAGGAGATTTCCAAAATTTCGCACT-TAGTA
*
457881 AGTCCTTCGGGCCATCATTAAGTCTTTCGAGCATGATGATTAAATCCTTCGCGTAA
129 AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGCGTAA
457937 GTTTTAAGCC
Statistics
Matches: 162, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
209 90 0.56
210 3 0.02
211 1 0.01
215 21 0.13
216 47 0.29
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (213 bp):
TCCTTCAGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAAATAAGAAAG
CGATGTTTTAAGATGAAATCTTTGAAAACTAAGAAGGAGATTTCCAAAATTTCGCACTTAGTAAG
TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGCGTAATCTGTAAGCCT
TTAGAGCAAGATGATAAA
Found at i:458021 original size:22 final size:22
Alignment explanation
Indices: 457993--458058 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
457983 TGCCATCAAC
457993 AAGTCTTTCGAGCATGATAATT
1 AAGTCTTTCGAGCATGATAATT
* * *
458015 AAGTCTTTC-AGGC--CATCAGT
1 AAGTCTTTCGA-GCATGATAATT
*
458035 AAGTCTTTCGAGCATGATGATT
1 AAGTCTTTCGAGCATGATAATT
458057 AA
1 AA
458059 ATCCTTCAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
20 15 0.44
21 2 0.06
22 17 0.50
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (22 bp):
AAGTCTTTCGAGCATGATAATT
Found at i:458043 original size:42 final size:42
Alignment explanation
Indices: 457984--458068 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
457974 ATCAATAAGT
* *
457984 GCCATCAACAAGTCTTTCGAGCATGATAATTAAGTCTTTCAG
1 GCCATCAACAAGTCTTTCGAGCATGATAATTAAATCCTTCAG
** *
458026 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAG
1 GCCATCAACAAGTCTTTCGAGCATGATAATTAAATCCTTCAG
458068 G
1 G
458069 TAATTTATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (42 bp):
GCCATCAACAAGTCTTTCGAGCATGATAATTAAATCCTTCAG
Found at i:458189 original size:42 final size:42
Alignment explanation
Indices: 458107--458190 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
458097 TGAAGCAAAT
* ** * * *
458107 CCATCAGTAAGTCTTTCGAGTGTGCTGATGAAGTCTTTCGGG
1 CCATCAGTAAGTCTCTCGAGCATGATGATGAAATCCTTCGGG
* *
458149 CCATTAGTAAGTCTCTCGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTCTCGAGCATGATGATGAAATCCTTCGGG
458191 TAATTTGTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
CCATCAGTAAGTCTCTCGAGCATGATGATGAAATCCTTCGGG
Found at i:458202 original size:122 final size:122
Alignment explanation
Indices: 457985--458240 Score: 370
Period size: 122 Copynumber: 2.1 Consensus size: 122
457975 TCAATAAGTG
* ** * * * *
457985 CCATCAACAAGTCTTTCGAGCATGATAATTAAGTCTTTCAGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAATAAGTCTTTCGAGTGTGCTGATGAAGTCTTTCAGGCCATCAGTAAGTCTCTCGAGCAT
458050 GATGATTAAATCCTTCAGGTAATTTATAAGCCTTCACCAAAGAGTCA-TGAAGCAAAT
66 GATGATTAAATCCTTCAGGTAATTTATAAGCCTTCACCAAAGAGT-AGTGAAGCAAAT
* * *
458107 CCATCAGTAAGTCTTTCGAGTGTGCTGATGAAGTCTTTCGGGCCATTAGTAAGTCTCTCGAGCAT
1 CCATCAATAAGTCTTTCGAGTGTGCTGATGAAGTCTTTCAGGCCATCAGTAAGTCTCTCGAGCAT
* * * *
458172 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTGAAGCAAAT
66 GATGATTAAATCCTTCAGGTAATTTATAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
458229 CCATCAATAAGT
1 CCATCAATAAGT
458241 GCCATCGTTA
Statistics
Matches: 118, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
121 1 0.01
122 117 0.99
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (122 bp):
CCATCAATAAGTCTTTCGAGTGTGCTGATGAAGTCTTTCAGGCCATCAGTAAGTCTCTCGAGCAT
GATGATTAAATCCTTCAGGTAATTTATAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
Found at i:458311 original size:93 final size:93
Alignment explanation
Indices: 458156--458426 Score: 461
Period size: 93 Copynumber: 2.9 Consensus size: 93
458146 GGGCCATTAG
*
458156 TAAGTCTCTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTG
* *
458221 AAGCAAATCCATCAATAAGTGCCATCGT
66 AAGCAAATCCATCAATAAGTGACATCAT
* *
458249 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTTGTAAGCCTTCACCGAGAAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTG
*
458314 AAGCAAATCCATCAATAAGTGACATTAT
66 AAGCAAATCCATCAATAAGTGACATCAT
* *
458342 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGAAAGCCTTCACCGAGGAGTAGTG
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTG
*
458407 AAGCAAATCCATCAGTAAGT
66 AAGCAAATCCATCAATAAGT
458427 CTTTCGAGCA
Statistics
Matches: 167, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (93 bp):
TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAGGAGTAGTG
AAGCAAATCCATCAATAAGTGACATCAT
Found at i:458494 original size:42 final size:42
Alignment explanation
Indices: 458415--458852 Score: 263
Period size: 42 Copynumber: 10.0 Consensus size: 42
458405 TGAAGCAAAT
* *
458415 CCATCAGTAAGTCTTTCGAGCATGATAATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *
458457 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * * * *
458499 TAATTTGTAAGCCTTCACTGAAG-A-GTAGTGAAGCAAATTCATCAGTAAGTG
1 CCATCAGTAAGTCTT-TC-G-AGCATG-A-TGATG-AAATCCTTC-G---G-G
* * * * * * *
458550 TCATTAGTAAGTCTTTCAATCATGATGTTAAAATCCTTCGAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * *
458592 TCATCATTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
*
458634 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * *
458676 TAATTTGTAAGCCTTCATCGAAG-A-GTAGTGAAGCAAATCCATCAGTAAGTG
1 CCATCAGTAAGTCTT--TCG-AGCATG-A-TGATG-AAATCCTTC-G---G-G
** *
458727 CCATCAGTAAGTCTTTTAAGCATGATAATGAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* ** * * * *
458769 TCATTTGTAAGTCTTTCGAGCATGATAAAGAAGTCTTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* *
458811 CAATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
458853 TAATTTGTAA
Statistics
Matches: 296, Mismatches: 74, Indels: 52
0.70 0.18 0.12
Matches are distributed among these distances:
42 199 0.67
43 4 0.01
44 8 0.03
45 10 0.03
46 17 0.06
47 16 0.05
48 8 0.03
49 5 0.02
50 5 0.02
51 24 0.08
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:458611 original size:20 final size:19
Alignment explanation
Indices: 458586--458656 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
458576 GTTAAAATCC
458586 TTCGAGTCATCATTAAGTCT
1 TTCGAG-CATCATTAAGTCT
* *
458606 TTCGAGCATGATGATGAAGTCC
1 TTCGAGCATCAT--T-AAGTCT
* *
458628 TTCGGGCCATCAGTAAGTCT
1 TTCGAG-CATCATTAAGTCT
458648 TTCGAGCAT
1 TTCGAGCAT
458657 GATGATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
19 8 0.20
20 16 0.40
21 2 0.05
22 10 0.25
23 4 0.10
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (19 bp):
TTCGAGCATCATTAAGTCT
Found at i:458631 original size:22 final size:21
Alignment explanation
Indices: 458583--458673 Score: 64
Period size: 22 Copynumber: 4.3 Consensus size: 21
458573 GATGTTAAAA
*
458583 TCCTTCGAGTCATCAT--TAAG
1 TCCTTCGAG-CATGATGATAAG
*
458603 TCTTTCGAGCATGATGATGAAG
1 TCCTTCGAGCATGATGAT-AAG
* *
458625 TCCTTCGGGCCATCA-G-TAAG
1 TCCTTCGAG-CATGATGATAAG
* *
458645 TCTTTCGAGCATGATGATTAAA
1 TCCTTCGAGCATGATGA-TAAG
458667 TCCTTCG
1 TCCTTCG
458674 GGTAATTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
19 9 0.17
20 19 0.35
21 2 0.04
22 20 0.37
23 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (21 bp):
TCCTTCGAGCATGATGATAAG
Found at i:458721 original size:177 final size:176
Alignment explanation
Indices: 458416--458940 Score: 793
Period size: 177 Copynumber: 3.0 Consensus size: 176
458406 GAAGCAAATC
*
458416 CATCAGTAAGTCTTTCGAGCATGATAATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
1 CATCATTAAGTCTTTCGAGCATGATAATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* *
458481 ATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACTGAAGAGTAGTGAAGCAAATTCATCAGTA
66 ATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCAC-GAAGAGTAGTGAAGCAAATCCATCAGTA
* * * **
458546 AGTGTCATTAGTAAGTCTTTCAATCATGATGTTAAAATCCTTCGAGT
130 AGTGCCATCAGTAAGTCTTTCAAGCATGATAATAAAATCCTTCGAGT
*
458593 CATCATTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
1 CATCATTAAGTCTTTCGAGCATGATAATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
458658 ATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCCATCAGTA
66 ATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCA-CGAAGAGTAGTGAAGCAAATCCATCAGTA
* * *
458723 AGTGCCATCAGTAAGTCTTTTAAGCATGATAATGAAATCCTTCGGGT
130 AGTGCCATCAGTAAGTCTTTCAAGCATGATAATAAAATCCTTCGAGT
* * * *
458770 CAT-TTGTAAGTCTTTCGAGCATGATAAAGAAGTCTTTCGGGCAATCAGTAAGTCTTTCGAGCAT
1 CATCAT-TAAGTCTTTCGAGCATGATAATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
458834 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTCCACCGAAGAGTGGTGAAGCAAATCCATTAGT
65 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCA-CGAAGAGTAGTGAAGCAAATCCATCAGT
* * * *
458899 AAGTACCATCAGTAAGTCTTTCGAGCATAATGAT-AAATCCTT
129 AAGTGCCATCAGTAAGTCTTTCAAGCATGATAATAAAATCCTT
458941 TGGTTTTTCA
Statistics
Matches: 320, Mismatches: 26, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
176 9 0.03
177 310 0.97
178 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (176 bp):
CATCATTAAGTCTTTCGAGCATGATAATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGAAGAGTAGTGAAGCAAATCCATCAGTAA
GTGCCATCAGTAAGTCTTTCAAGCATGATAATAAAATCCTTCGAGT
Found at i:458732 original size:13 final size:13
Alignment explanation
Indices: 458714--458738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
458704 TGAAGCAAAT
458714 CCATCAGTAAGTG
1 CCATCAGTAAGTG
458727 CCATCAGTAAGT
1 CCATCAGTAAGT
458739 CTTTTAAGCA
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:458802 original size:22 final size:22
Alignment explanation
Indices: 458775--458836 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
458765 CGGGTCATTT
458775 GTAAGTCTTTCGAGCATGATAAA
1 GTAAGTCTTTCGAGCATGAT-AA
* *
458798 G-AAGTCTTTCGGGCA--ATCA
1 GTAAGTCTTTCGAGCATGATAA
458817 GTAAGTCTTTCGAGCATGAT
1 GTAAGTCTTTCGAGCATGAT
458837 GATTAAATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
22 15 0.45
23 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (22 bp):
GTAAGTCTTTCGAGCATGATAA
Found at i:461914 original size:2 final size:2
Alignment explanation
Indices: 461907--461955 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
461897 AATCTATCTC
461907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
461949 AT AT AT A
1 AT AT AT A
461956 ATTTTATTCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:464402 original size:89 final size:90
Alignment explanation
Indices: 464217--464485 Score: 418
Period size: 89 Copynumber: 3.0 Consensus size: 90
464207 CCAGAACTGC
* * *
464217 GTTCGTAGGGCTTACCCTAAGCACATAGCAAAAGGGAACCAACCTAAGGATATTCCTTGGGACCT
1 GTTCGTAGGG-TTACCCTAAGCACACA-CAAAAGGGAACCAACCTAAGGATATTTCTTGGGGCCT
*
464282 ATGGGCCTACCCAAGGGTATCATTA-A
64 ATGGGCCTACCCAAGGGTATCCTTAGA
* *
464308 GTTCGTAGGGTTACTCTAAGCACACATAAAAGGGAACCAACCTAAGGATATTTCTTGGGGCCTAT
1 GTTCGTAGGGTTACCCTAAGCACACACAAAAGGGAACCAACCTAAGGATATTTCTTGGGGCCTAT
464373 GGGCCTACCCAAGGGTATCCTTAGA
66 GGGCCTACCCAAGGGTATCCTTAGA
*
464398 -TTCGTAGGGTTACCCTAAGCACACAGC-AAAGGGAACCAACCTAAGGATATATCTTGGGGCCTA
1 GTTCGTAGGGTTACCCTAAGCACACA-CAAAAGGGAACCAACCTAAGGATATTTCTTGGGGCCTA
*
464461 TAGGCCTACCCAAGGGTATCCTTAG
65 TGGGCCTACCCAAGGGTATCCTTAG
464486 GTCCGTAAGG
Statistics
Matches: 166, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
89 141 0.85
90 15 0.09
91 10 0.06
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (90 bp):
GTTCGTAGGGTTACCCTAAGCACACACAAAAGGGAACCAACCTAAGGATATTTCTTGGGGCCTAT
GGGCCTACCCAAGGGTATCCTTAGA
Found at i:470775 original size:2 final size:2
Alignment explanation
Indices: 470768--470853 Score: 127
Period size: 2 Copynumber: 42.5 Consensus size: 2
470758 ATGTACATAG
470768 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
* * * *
470810 TA TA TA TA TA TA TA TA CTA TG TA CA TA CA TG 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
470853 T
1 T
470854 GAATTAGTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
2 73 0.97
3 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:473172 original size:25 final size:25
Alignment explanation
Indices: 473138--473191 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
473128 CTTTTTGTTT
473138 TGAAGAAGAAGAAGAAAAGACCACG
1 TGAAGAAGAAGAAGAAAAGACCACG
*
473163 TGAAGAAGAAGAAGAAAAGAGCACG
1 TGAAGAAGAAGAAGAAAAGACCACG
473188 TGAA
1 TGAA
473192 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.56, C:0.09, G:0.30, T:0.06
Consensus pattern (25 bp):
TGAAGAAGAAGAAGAAAAGACCACG
Found at i:475080 original size:23 final size:24
Alignment explanation
Indices: 475052--475115 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
475042 TAAAAGTTAT
*
475052 AAGTTAGAAGTTAGAAAATTAGC-
1 AAGTTAGCAGTTAGAAAATTAGCA
* *
475075 AGGTTAGCGGTTAG-AAATTAGCA
1 AAGTTAGCAGTTAGAAAATTAGCA
475098 AAGTTAGCAGTTA-AAAAT
1 AAGTTAGCAGTTAGAAAAT
475116 AGAATTTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (24 bp):
AAGTTAGCAGTTAGAAAATTAGCA
Found at i:475422 original size:27 final size:27
Alignment explanation
Indices: 475373--475432 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
475363 TAAACAAATG
* * * *
475373 GCAAAGCAAAATAGTGACTAAATTAAA
1 GCAAATCAAAACAGTGACAAAATCAAA
*
475400 GCAAATCAAAACAGTGTCAAAATCAAA
1 GCAAATCAAAACAGTGACAAAATCAAA
*
475427 GAAAAT
1 GCAAAT
475433 AGCAAACAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (27 bp):
GCAAATCAAAACAGTGACAAAATCAAA
Found at i:477757 original size:34 final size:34
Alignment explanation
Indices: 477714--477787 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
477704 AGGATTACCA
477714 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
1 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
477748 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
1 AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
477782 AAAATA
1 AAAATA
477788 TTTTAGCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (34 bp):
AAAATAAAGATCAATGCTGCAACTTAAAATAGAG
Found at i:482665 original size:24 final size:24
Alignment explanation
Indices: 482638--482752 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
482628 CATAGTTCAC
* * *
482638 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
482662 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
482686 GTCAAGTATCAGATCAGAATTCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
482710 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
482734 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
482753 ATCAAATCGA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.03
24 75 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:483898 original size:17 final size:18
Alignment explanation
Indices: 483865--483898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
483855 TTCATTCTGT
*
483865 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
483883 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
483899 GACCTTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:485223 original size:13 final size:13
Alignment explanation
Indices: 485190--485247 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
485180 GGTCAACGTC
*
485190 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
485205 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
485218 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
485231 GGTAAACGGGTCG
1 GGTCAACGGGTCG
485244 GGTC
1 GGTC
485248 GGGTTATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
13 26 0.68
15 12 0.32
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:488302 original size:19 final size:19
Alignment explanation
Indices: 488254--488304 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
488244 TACGAGGTTT
* *
488254 AGGGAGGAAGGAGAAAGTG
1 AGGGAGAAAGAAGAAAGTG
*
488273 AGGGAGGAAGAAGAAAGTG
1 AGGGAGAAAGAAGAAAGTG
488292 AGGG-GAAAAGAAG
1 AGGGAG-AAAGAAG
488305 CCGTTAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.49, T:0.04
Consensus pattern (19 bp):
AGGGAGAAAGAAGAAAGTG
Found at i:488303 original size:16 final size:19
Alignment explanation
Indices: 488254--488295 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
488244 TACGAGGTTT
*
488254 AGGGAGGAAGGAGAAAGTG
1 AGGGAGGAAGAAGAAAGTG
488273 AGGGAGGAAGAAGAAAGTG
1 AGGGAGGAAGAAGAAAGTG
488292 AGGG
1 AGGG
488296 GAAAAGAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.52, T:0.05
Consensus pattern (19 bp):
AGGGAGGAAGAAGAAAGTG
Found at i:495439 original size:53 final size:53
Alignment explanation
Indices: 495355--495571 Score: 264
Period size: 53 Copynumber: 4.2 Consensus size: 53
495345 TTTCTAAGTA
* * *
495355 CTAAGATATTGAGAGATGTATATACTTACACCAGTATAAATATGTGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
* * *
495408 CTACGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTA
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
* * * * * *
495461 CTAAGGTATT-ACGAAATGTACATACTTACACCGGTGCAAGTATATGCTAATTG
1 CTAAGATATTGA-GAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
* *
495514 CTAAGATATTGAGAGATGT--ATA--TACACTAGGGTAAGTATGTGTTAATTG
1 CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
495563 CTAAGATAT
1 CTAAGATAT
495572 GATAATCGTT
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
49 30 0.21
51 3 0.02
52 1 0.01
53 106 0.75
54 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (53 bp):
CTAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATGTGTTAATTG
Found at i:496776 original size:22 final size:22
Alignment explanation
Indices: 496751--496793 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
496741 TAAATATTAT
*
496751 ATTTTAATTAAATTACATTTAG
1 ATTTTAACTAAATTACATTTAG
* *
496773 ATTTTAACTAATTTATATTTA
1 ATTTTAACTAAATTACATTTA
496794 TACGTTTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAACTAAATTACATTTAG
Found at i:496832 original size:23 final size:22
Alignment explanation
Indices: 496781--496838 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
496771 AGATTTTAAC
*
496781 TAATTTATATTTATACGTTTAG
1 TAATTTATATTTAAACGTTTAG
* *
496803 TACTTTATGATTTAAAGCTTTTA-
1 TAATTTAT-ATTTAAA-CGTTTAG
496826 TAATTTA-ATTTAA
1 TAATTTATATTTAA
496839 TGGTGTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 12 0.40
24 5 0.17
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.53
Consensus pattern (22 bp):
TAATTTATATTTAAACGTTTAG
Found at i:499746 original size:32 final size:32
Alignment explanation
Indices: 499700--499767 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
499690 TATGTGAGTG
499700 AAGACTCTGCTTAACCTATGAACAAAAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
* *
499732 AAGACTCTGGTTAACCTATGAACAACAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
499764 AAGA
1 AAGA
499768 GACCATTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (32 bp):
AAGACTCTGCTTAACCTATGAACAAAAATTTA
Found at i:500574 original size:17 final size:17
Alignment explanation
Indices: 500535--500600 Score: 114
Period size: 17 Copynumber: 3.8 Consensus size: 17
500525 TATTTCTGAG
*
500535 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-CA
500553 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
500570 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
500587 GGAATTGGAATCTG
1 GGAATTGGAATCTG
500601 AATCTGAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
17 32 0.68
18 15 0.32
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATCTGTCA
Found at i:504169 original size:19 final size:19
Alignment explanation
Indices: 504145--504186 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
504135 TTTTCAAATA
504145 ATTTATTTA-AAATATATTT
1 ATTTATTTATAAATA-ATTT
504164 ATTTATTTATAAATAATTT
1 ATTTATTTATAAATAATTT
504183 ATTT
1 ATTT
504187 TAAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTATTTATAAATAATTT
Found at i:504182 original size:15 final size:15
Alignment explanation
Indices: 504140--504190 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
504130 AATTGTTTTC
*
504140 AAATAATTTATTTAA
1 AAATAATTTATTTAT
504155 AATATATTTATTTATTTAT
1 AA-ATA---ATTTATTTAT
504174 AAATAATTTATTT-T
1 AAATAATTTATTTAT
504188 AAA
1 AAA
504191 ATATTTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 4 0.13
15 10 0.32
16 3 0.10
18 3 0.10
19 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATAATTTATTTAT
Found at i:504196 original size:14 final size:15
Alignment explanation
Indices: 504135--504193 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
504125 CTTGCAATTG
*
504135 TTTTCAAATAATTTA
1 TTTTAAAATAATTTA
504150 -TTTAAAATATATTTA
1 TTTTAAAATA-ATTTA
504165 TTTATTTATAAATAATTTA
1 --T-TTTA-AAATAATTTA
504184 TTTTAAAATA
1 TTTTAAAATA
504194 TTTCATAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 8 0.22
15 10 0.27
16 4 0.11
17 1 0.03
19 9 0.24
20 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTAAAATAATTTA
Found at i:504805 original size:13 final size:13
Alignment explanation
Indices: 504787--504819 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
504777 ATCGGATAAT
504787 TTGTGATTGTCAC
1 TTGTGATTGTCAC
504800 TTGTGATTGTCAC
1 TTGTGATTGTCAC
504813 TTGTGAT
1 TTGTGAT
504820 ATTGATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.24, T:0.48
Consensus pattern (13 bp):
TTGTGATTGTCAC
Found at i:506739 original size:2 final size:2
Alignment explanation
Indices: 506732--506783 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
506722 ATATTCTCTA
*
506732 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
506772 AT AT AT AT AT AT
1 AT AT AT AT AT AT
506784 TTTGAAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:506748 original size:32 final size:32
Alignment explanation
Indices: 506712--506786 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
506702 TTCATAGAAA
***
506712 ATATAATTTTATATTCTCTAATATATATATAT
1 ATATAATTTTATATTAAATAATATATATATAT
* *
506744 ATAT-ATATATATATTAAATTATATATATATAT
1 ATATAAT-TTTATATTAAATAATATATATATAT
506776 ATATATATTTT
1 ATATA-ATTTT
506787 GAAAATATAG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
31 2 0.06
32 28 0.82
33 2 0.06
34 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATAATTTTATATTAAATAATATATATATAT
Found at i:513583 original size:22 final size:23
Alignment explanation
Indices: 513536--513584 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
513526 CCACCTTATG
*
513536 CAAATATTTACAAAATTAACATC
1 CAAATATTTACAAAATTAACACC
*
513559 CAAAT-TTTACACAAA-TAGCACC
1 CAAATATTTACA-AAATTAACACC
513581 CAAA
1 CAAA
513585 CAGAAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (23 bp):
CAAATATTTACAAAATTAACACC
Found at i:516022 original size:15 final size:15
Alignment explanation
Indices: 516002--516031 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
515992 AATCAATCTG
516002 AAAATTCAAAACATT
1 AAAATTCAAAACATT
516017 AAAATTCAAAACATT
1 AAAATTCAAAACATT
516032 CTGCGACAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATTCAAAACATT
Found at i:516864 original size:32 final size:32
Alignment explanation
Indices: 516818--516885 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
516808 TATGTGAGTG
516818 AAGACTCTGCTTAACCTATGAACAAAAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
* *
516850 AAGACTCTGGTTAACCTATGAACAACAATTTA
1 AAGACTCTGCTTAACCTATGAACAAAAATTTA
516882 AAGA
1 AAGA
516886 GACCATTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (32 bp):
AAGACTCTGCTTAACCTATGAACAAAAATTTA
Found at i:518602 original size:37 final size:37
Alignment explanation
Indices: 518543--518616 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
518533 ATTCCCACCA
*
518543 TGGGAAAGCATGGTGCTGAATATTATGCATTATCCAT
1 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
* * * *
518580 TGGGAAAGTATAGTGTTTAATATTATGTATTATCCAT
1 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
518617 GGTGCTAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (37 bp):
TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
Found at i:520144 original size:24 final size:26
Alignment explanation
Indices: 520114--520161 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
520104 ATATGCATGC
*
520114 TATACTATAA-ATTTAC-AATATAAA
1 TATACTATAAGATATACGAATATAAA
520138 TATACTATAAGATATACGAATATA
1 TATACTATAAGATATACGAATATA
520162 CAAACCCGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (26 bp):
TATACTATAAGATATACGAATATAAA
Found at i:532014 original size:19 final size:19
Alignment explanation
Indices: 531990--532026 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
531980 AAAACGTTAG
531990 ATTAAAAAATAAAATAAAT
1 ATTAAAAAATAAAATAAAT
* *
532009 ATTAAAAATTAAATTAAA
1 ATTAAAAAATAAAATAAA
532027 AAATCAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTAAAAAATAAAATAAAT
Found at i:532057 original size:28 final size:26
Alignment explanation
Indices: 531998--532061 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
531988 AGATTAAAAA
*
531998 ATAAAATAAATATTAAAAATTAAATT
1 ATAAAATAAATATGAAAAATTAAATT
* *
532024 AAAAAATCAAATAATGAAATATTAAATT
1 ATAAAAT-AAAT-ATGAAAAATTAAATT
*
532052 TTAAAA-AAAT
1 ATAAAATAAAT
532062 GTTATATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
26 10 0.32
27 4 0.13
28 17 0.55
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
ATAAAATAAATATGAAAAATTAAATT
Found at i:532178 original size:24 final size:25
Alignment explanation
Indices: 532151--532197 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
532141 AAAAAATGTT
532151 AAACAAAAAAATAA-AAACAAAACA
1 AAACAAAAAAATAATAAACAAAACA
* *
532175 AAACAAAACAATAATAAATAAAA
1 AAACAAAAAAATAATAAACAAAA
532198 GGGAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.09
Consensus pattern (25 bp):
AAACAAAAAAATAATAAACAAAACA
Found at i:532290 original size:18 final size:18
Alignment explanation
Indices: 532269--532311 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
532259 GTTGTTTTTA
532269 AAATAAAA-GATAAGAATT
1 AAATAAAAGGA-AAGAATT
*
532287 AAATAAAAGGAAATAATT
1 AAATAAAAGGAAAGAATT
532305 AAATAAA
1 AAATAAA
532312 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGAAAGAATT
Found at i:533333 original size:33 final size:35
Alignment explanation
Indices: 533266--533339 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
533256 AATTGTATTA
* *
533266 TATATATTTTCGAAAAATGCTTTCAAAACCATATAT
1 TATATATTTTC-AAAAATGCTTTCAAAACAATATAC
* *
533302 TATATATTTTC-AAAATGTTTTTAAAA-AATATAC
1 TATATATTTTCAAAAATGCTTTCAAAACAATATAC
533335 TATAT
1 TATAT
533340 TGATACATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 10 0.29
34 13 0.38
36 11 0.32
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
TATATATTTTCAAAAATGCTTTCAAAACAATATAC
Found at i:534257 original size:2 final size:2
Alignment explanation
Indices: 534250--534274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
534240 TAACTATAAT
534250 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 T
534275 GAAATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:535572 original size:2 final size:2
Alignment explanation
Indices: 535565--535595 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
535555 TAAATAAATA
535565 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
535596 TAAATGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:542886 original size:22 final size:21
Alignment explanation
Indices: 542844--542883 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
542834 GAGTTTATTT
*
542844 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
542865 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
542884 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:545282 original size:30 final size:27
Alignment explanation
Indices: 545214--545289 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 27
545204 CTAAAAGCAA
*
545214 TAAAATAAAATAAA-AATAATAAGAAG
1 TAAAATAAAATAAATAATAATAAAAAG
545240 TAAAAACATAAAATAAATAATAATAAAAATG
1 T--AAA-ATAAAATAAATAATAATAAAAA-G
*
545271 CTAAAATTAAAAAAAATAA
1 -TAAAA-TAAAATAAATAA
545290 AACCAACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 1 0.02
28 3 0.07
29 11 0.27
30 24 0.59
31 1 0.02
32 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (27 bp):
TAAAATAAAATAAATAATAATAAAAAG
Found at i:545284 original size:39 final size:38
Alignment explanation
Indices: 545216--545291 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
545206 AAAAGCAATA
*
545216 AAATAAAATAAAAATAATAAGAAGTAAAAACATAAAAT
1 AAATAAAATAAAAATAATAAGAAGTAAAAAAATAAAAT
** *
545254 AAATAATAATAAAAATGCTAA-AATTAAAAAAAATAAAA
1 AAATAA-AATAAAAATAATAAGAAGT-AAAAAAATAAAA
545292 CCAACTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 9 0.28
39 23 0.72
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.20
Consensus pattern (38 bp):
AAATAAAATAAAAATAATAAGAAGTAAAAAAATAAAAT
Found at i:547128 original size:124 final size:124
Alignment explanation
Indices: 546908--547847 Score: 1441
Period size: 124 Copynumber: 7.6 Consensus size: 124
546898 TGACAGATGT
* * * *
546908 CCCTTCGTTGTGAAGTTGAGCTTTGAATTGGATATCATTCATTGTGAAGTTGAAATCCAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* *
546973 AGATGGATGTTGCTGGTGGGCACGATGTCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
* *
547032 CCCTTCGTTGTGAAATTGAGCCTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* * * * *
547097 AGATGAATGTTGCTGGTGGGCATGATATCCTTCATTGTAAAGTTGAAATCATGGATGAC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
* * *
547156 CCATTCGTTATGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* * *
547221 AGATGAATGTTGCTGGTGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTAGATGTC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
*
547280 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATTCAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* * * * * * *
547345 AGATGAATATTGTTGGTAGGCATGATATCCTTCGTCATTAAGTTGAAATCGTGGATGGC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
* * * *
547404 CCTTTTGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTTAAGTTGAAATACAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* *
547469 AGATGAATGTTGCTGGTGCGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
* * *
547528 CCTTTCGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCCAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* *
547593 AGATGAATGTTGCTGGTGGGCATGATATCCTTCGTCATGAAGTTGAAATCGTGGATGAC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
* * * * *
547652 CCCTTCGTTATGAAGTTAAGCCTTGAATTGAATATCATTCATCGTGAAGTTGAAATCCAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
* * * *
547717 ATATGAATGTTGCTGGTGGGCAGGATATCCTTCGCCGTGAAGTTGAAATCGTGGATGGC
66 AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
*
547776 CCCTTCGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAAT-CAATCTAA
1 CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
547840 AGATGAAT
66 AGATGAAT
547848 TTTACTTCGA
Statistics
Matches: 739, Mismatches: 77, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
123 15 0.02
124 724 0.98
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (124 bp):
CCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAA
AGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGAC
Found at i:549235 original size:95 final size:95
Alignment explanation
Indices: 549067--549267 Score: 339
Period size: 95 Copynumber: 2.1 Consensus size: 95
549057 GGGCAACTTA
* * *
549067 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAGACGGGGCATTTAACCAATT
549132 GCTCTAGAGGGACAACTCAAACTTTATTGT
66 GCTCTAGAGGGACAACTCAAACTTTATTGT
*
549162 ATATTATAATCACCTTTATCAGGCAAGCTGAATCTTATCCATAAAGACGGGGCATTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAGACGGGGCATTTAACCAATT
* *
549227 GCTTTAGAGGGACAACTCAAGCTTTATTGT
66 GCTCTAGAGGGACAACTCAAACTTTATTGT
549257 ATATATATAAT
1 ATAT-TATAAT
549268 ATTATAACCT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 93 0.94
96 6 0.06
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (95 bp):
ATATTATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAGACGGGGCATTTAACCAATT
GCTCTAGAGGGACAACTCAAACTTTATTGT
Found at i:551640 original size:32 final size:31
Alignment explanation
Indices: 551565--551640 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
551555 AATGTTAGAT
*
551565 AAGAAATAATAAATAAATATTAAATAAATCAA
1 AAGAAA-AATATATAAATATTAAATAAATCAA
* * * *
551597 AATATATATATATATAATATTAAATGAATCAA
1 AAGAAAAATATATA-AATATTAAATAAATCAA
*
551629 AGGAAAAATATA
1 AAGAAAAATATA
551641 AAAAAATGTT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
31 6 0.18
32 28 0.82
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (31 bp):
AAGAAAAATATATAAATATTAAATAAATCAA
Found at i:552388 original size:9 final size:10
Alignment explanation
Indices: 552376--552427 Score: 72
Period size: 10 Copynumber: 5.2 Consensus size: 10
552366 CTGTAAAAAT
552376 AATAA-AATA
1 AATAATAATA
552385 AATAATAAT-
1 AATAATAATA
552394 AATAATAATAA
1 AATAATAAT-A
552405 TAATAATAATA
1 -AATAATAATA
552416 AATAATAATA
1 AATAATAATA
552426 AA
1 AA
552428 ATATTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.36
10 15 0.38
11 1 0.03
12 9 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:552391 original size:3 final size:3
Alignment explanation
Indices: 552373--552430 Score: 84
Period size: 3 Copynumber: 19.3 Consensus size: 3
552363 GGCCTGTAAA
552373 AAT AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
552419 AAT AAT AA- AAT A
1 AAT AAT AAT AAT A
552431 TTTTTGTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:555821 original size:24 final size:23
Alignment explanation
Indices: 555788--555838 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
555778 GGGATGGAAG
555788 TGAAAAACACTTTCTATTAAGCT
1 TGAAAAACACTTTCTATTAAGCT
*
555811 TGAAAGAACACTTTCTATTGAGCT
1 TGAAA-AACACTTTCTATTAAGCT
555835 TGAA
1 TGAA
555839 GGACACCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (23 bp):
TGAAAAACACTTTCTATTAAGCT
Found at i:561586 original size:16 final size:17
Alignment explanation
Indices: 561550--561594 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
561540 TAGTCATAAT
*
561550 TATTTTTAAAA-TTTAA
1 TATTTTTAAAACATTAA
561566 TATTTTTAAAACATTAA
1 TATTTTTAAAACATTAA
*
561583 -ATTTTAAAAACA
1 TATTTTTAAAACA
561595 ATGATGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTTTAAAACATTAA
Found at i:561852 original size:20 final size:20
Alignment explanation
Indices: 561809--561860 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
561799 GATTTTCCAG
*
561809 AATCGTAACGCG-AATATGA
1 AATCGCAACGCGAAATATGA
561828 AATCGCAACGCGAACATAT-A
1 AATCGCAACGCGAA-ATATGA
561848 AATCGCAACGCGA
1 AATCGCAACGCGA
561861 TTCTTACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.37
20 15 0.50
21 4 0.13
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAATATGA
Found at i:561952 original size:20 final size:20
Alignment explanation
Indices: 561870--562208 Score: 235
Period size: 20 Copynumber: 16.4 Consensus size: 20
561860 ATTCTTACTA
*
561870 CGCAACGAGTATCCGTAAAAT
1 CGCAACGCGTATCCGT-AAAT
561891 CGCAACGCGTATCCGT-AAT
1 CGCAACGCGTATCCGTAAAT
* *
561910 CGCAACGAC-AATACGTAAAAT
1 CGCAACG-CGTATCCGT-AAAT
*
561931 CGCAACGCGTATTCGTAAAT
1 CGCAACGCGTATCCGTAAAT
* *
561951 CGCAACGAC-AATACGTAAACAGAAT
1 CGCAACG-CGTATCCGT----A-AAT
* * ** *
561976 CGTAACGCGAATATGAAAAT
1 CGCAACGCGTATCCGTAAAT
* **
561996 CGCAACGCG-AACATATAAAT
1 CGCAACGCGTATC-CGTAAAT
* * *
562016 CGCAACGCG-ATTCTTACTAT
1 CGCAACGCGTATCCGTA-AAT
*
562036 CGCAACGAGTATCCGTAAAAT
1 CGCAACGCGTATCCGT-AAAT
562057 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
* *
562077 CGCAACGAC-AATACGTAAAAT
1 CGCAACG-CGTATCCGT-AAAT
*
562098 CGCAACGCGTATTCGTAAAT
1 CGCAACGCGTATCCGTAAAT
* *
562118 CGCAACGAC-AATACGTAAAAT
1 CGCAACG-CGTATCCGT-AAAT
562139 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
* *
562159 CGCAACGAC-AATACGTAAAAT
1 CGCAACG-CGTATCCGT-AAAT
562180 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
562200 CGCAACGCG
1 CGCAACGCG
562209 ATTTTTAAAG
Statistics
Matches: 257, Mismatches: 37, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
19 18 0.07
20 118 0.46
21 104 0.40
22 1 0.00
24 2 0.01
25 14 0.05
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
CGCAACGCGTATCCGTAAAT
Found at i:561964 original size:41 final size:41
Alignment explanation
Indices: 561847--562206 Score: 428
Period size: 41 Copynumber: 8.8 Consensus size: 41
561837 GCGAACATAT
* * ** *
561847 AAATCGCAACGCG-ATTC-TTACTACGCAACGAGTATCCGTA
1 AAATCGCAACGCGTATTCGTAAAT-CGCAACGACAATACGTA
*
561887 AAATCGCAACGCGTATCCGT-AATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
561927 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTAAA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGT--A
* * * * *
561970 CAGAATCGTAACGCGAATAT-GAAAATCGCAACG-CGA-ACATA
1 -A-AATCGCAACGCGTAT-TCGTAAATCGCAACGACAATACGTA
* * ** *
562011 TAAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATCCGTA
1 -AAATCGCAACGCGTATTCGTA-AATCGCAACGACAATACGTA
*
562053 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
562094 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
*
562135 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
*
562176 AAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATTCGTAAATCGCAACG
562207 CGATTTTTAA
Statistics
Matches: 279, Mismatches: 28, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
40 66 0.24
41 167 0.60
42 9 0.03
43 4 0.01
44 3 0.01
45 25 0.09
46 1 0.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (41 bp):
AAATCGCAACGCGTATTCGTAAATCGCAACGACAATACGTA
Found at i:562778 original size:21 final size:21
Alignment explanation
Indices: 562748--562822 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
562738 TTTACAGAAG
562748 AATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
* * *
562769 AATCGGAACGCGA-AAATGAC
1 AATCGCAACGAGAGAAATGAA
*
562789 TATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
562810 AATCGCAACGAGA
1 AATCGCAACGAGA
562823 AACCAAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (21 bp):
AATCGCAACGAGAGAAATGAA
Found at i:562878 original size:33 final size:33
Alignment explanation
Indices: 562836--562957 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
562826 CAAAATCGCA
562836 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
562869 TTGCGATTTTCATTTCGCAG-TGCGATTCTATCG
1 TTGCGATTTTCATTTCGC-GTTGCGATTCTCTCG
*
562902 TTGCGATTTTTATTTCCGCGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGC----G--ATTCTCTCG
562942 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
562958 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
33 45 0.59
34 7 0.09
38 1 0.01
39 1 0.01
40 22 0.29
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:562954 original size:20 final size:20
Alignment explanation
Indices: 562893--562955 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
562883 TCGCAGTGCG
* *
562893 ATTCTATCGTTGCGATTTTT
1 ATTCTCTCGTTGCGATTTTC
* **
562913 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATTTTC
562933 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
562953 ATT
1 ATT
562956 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:564858 original size:93 final size:94
Alignment explanation
Indices: 564645--564868 Score: 371
Period size: 94 Copynumber: 2.4 Consensus size: 94
564635 TAGATTGCTT
* * *
564645 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
564710 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
* *
564739 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTTAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
564803 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
*
564832 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
564869 AATACCCTGA
Statistics
Matches: 123, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 20 0.16
93 48 0.39
94 55 0.45
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
Found at i:564991 original size:20 final size:19
Alignment explanation
Indices: 564966--565094 Score: 91
Period size: 19 Copynumber: 7.3 Consensus size: 19
564956 TAGTTTACTT
564966 TCGCAACACGAAACAT-AAAA
1 TCGCAACACG-AA-ATGAAAA
*
564986 TCGCAACGCGAAATGAAAA
1 TCGCAACACGAAATGAAAA
*
565005 TCGCAA-A-G--A-GAGAA
1 TCGCAACACGAAATGAAAA
*
565019 TCGCAACGCGAAATGAAAA
1 TCGCAACACGAAATGAAAA
565038 TCGC-A-ACG--A-GAAAA
1 TCGCAACACGAAATGAAAA
**
565052 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATGAAAA
* **
565071 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAATGAAAA
565090 TCGCA
1 TCGCA
565095 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.22
15 3 0.03
16 3 0.03
17 3 0.03
18 5 0.06
19 46 0.52
20 9 0.10
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACACGAAATGAAAA
Found at i:565006 original size:19 final size:19
Alignment explanation
Indices: 564982--565094 Score: 111
Period size: 19 Copynumber: 6.5 Consensus size: 19
564972 CACGAAACAT
564982 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
565001 AAAATCGCAA----AGA-G
1 AAAATCGCAACGCGAAATG
*
565015 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
565034 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
565048 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
**
565067 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
565086 AAAATCGCA
1 AAAATCGCA
565095 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 21 0.27
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 46 0.60
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:565064 original size:14 final size:14
Alignment explanation
Indices: 565000--565057 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
564990 AACGCGAAAT
*
565000 GAAAATCGCAAAGA
1 GAAAATCGCAACGA
*
565014 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
565032 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
565047 GAAAATCGCAA
1 GAAAATCGCAA
565058 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:565077 original size:33 final size:33
Alignment explanation
Indices: 564982--565083 Score: 168
Period size: 33 Copynumber: 3.1 Consensus size: 33
564972 CACGAAACAT
*
564982 AAAATCGCAACGCGAAATGAAAATCGCAAAGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
*
565015 AGAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
* *
565048 AAAATCGCAATGCGAAATGAAAATCGCAACGCG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAG
565081 AAA
1 AAA
565084 CCAAAATCGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.10
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAG
Found at i:565100 original size:19 final size:19
Alignment explanation
Indices: 565048--565100 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
565038 TCGCAACGAG
**
565048 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAACC
*
565067 AAAATCGCAACGCGAAACC
1 AAAATCGCAATGCGAAACC
*
565086 AAAATCGCATTGCGA
1 AAAATCGCAATGCGA
565101 TTTTCATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAACC
Found at i:565112 original size:19 final size:19
Alignment explanation
Indices: 565090--565290 Score: 127
Period size: 19 Copynumber: 11.6 Consensus size: 19
565080 GAAACCAAAA
*
565090 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
565109 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
565123 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
565142 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
565156 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
565175 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* **
565194 TCGTGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
565213 TCGCGTTGCCA--TTC---
1 TCGCGTTGCGATTTTCATT
*
565227 TCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
565241 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
565260 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
565280 TCGTGTTGCGA
1 TCGCGTTGCGA
565291 AAGTAAACTA
Statistics
Matches: 150, Mismatches: 16, Indels: 31
0.76 0.08 0.16
Matches are distributed among these distances:
14 42 0.28
16 9 0.06
17 8 0.05
19 79 0.53
20 12 0.08
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:565133 original size:14 final size:14
Alignment explanation
Indices: 565114--565168 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
565104 TCATTTCGCA
565114 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
565128 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
565147 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
565161 TTGCGATT
1 TTGCGATT
565169 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:565137 original size:33 final size:33
Alignment explanation
Indices: 565095--565239 Score: 191
Period size: 33 Copynumber: 4.2 Consensus size: 33
565085 CAAAATCGCA
*
565095 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
565128 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
565161 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGTG
1 TTGCGATTTTCATTTCGCGTTGCGA--TT-CTCTC--G
** *
565199 TTGCGATTTTGGTTTCGCGTTGCCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
565232 TTGCGATT
1 TTGCGATT
565240 CTCTCGTTGC
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
33 66 0.67
35 5 0.05
36 5 0.05
38 23 0.23
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:565234 original size:52 final size:52
Alignment explanation
Indices: 565090--565268 Score: 158
Period size: 52 Copynumber: 3.5 Consensus size: 52
565080 GAAACCAAAA
* * * *
565090 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCGTTTCGCGTTGCCATTCTCTCGTTGCGATTTTCATT
** * **
565142 TCGCGTTGCGATTCTCTCG-TT-GCGATTTTCATT-TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATT-T-TCGTTTCGCG-TTGCCATTCTCTCGTTGCGATTTTCATT
* *
565194 TCGTGTTGCGATTTTGGTTTCGCGTTGCCATTCTCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCGTTTCGCGTTGCCATTCTCTCGTTGCGATTTTCATT
* *
565241 TCTCGTTGCGATTTTCATTTCGCGTTGC
1 TCGCGTTGCGATTTTCGTTTCGCGTTGC
565269 GATTTTAAGT
Statistics
Matches: 102, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
47 24 0.24
50 4 0.04
51 9 0.09
52 55 0.54
53 8 0.08
54 2 0.02
ACGTcount: A:0.09, C:0.23, G:0.22, T:0.46
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCGTTTCGCGTTGCCATTCTCTCGTTGCGATTTTCATT
Found at i:565250 original size:14 final size:14
Alignment explanation
Indices: 565216--565253 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
565206 TTTGGTTTCG
*
565216 CGTTGCCATTCTCT
1 CGTTGCGATTCTCT
565230 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
565244 CGTTGCGATT
1 CGTTGCGATT
565254 TTCATTTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.29, G:0.21, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:567175 original size:14 final size:14
Alignment explanation
Indices: 567156--567188 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
567146 ATTGTTTAAT
567156 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
567170 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
567184 TGATT
1 TGATT
567189 CAATAGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:567298 original size:81 final size:83
Alignment explanation
Indices: 567097--567268 Score: 244
Period size: 84 Copynumber: 2.1 Consensus size: 83
567087 TGGCTGCAAT
* *
567097 AGTTGATACAATAGTAGATGAGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTAATTGATTT
1 AGTTGATTCAATAATAGAT-AGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTAATTGATTT
567162 GTAAAAGATGATTTGTAAA
65 GTAAAAGATGATTTGTAAA
* ***
567181 AGTTGATTCAATAGTAGATAAGGAAATAAGAATTATTGCTTA-TTTTTGATTG-TTAATTGA-TT
1 AGTTGATTCAATAATAGAT-AGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTAATTGATTT
567243 GTAAAAGATGATTTGT-AA
65 GTAAAAGATGATTTGTAAA
567261 AGTTGATT
1 AGTTGATT
567269 TGTTTAATTG
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
80 10 0.12
81 18 0.22
82 8 0.10
83 10 0.12
84 37 0.45
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.43
Consensus pattern (83 bp):
AGTTGATTCAATAATAGATAGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTAATTGATTTG
TAAAAGATGATTTGTAAA
Found at i:567415 original size:14 final size:14
Alignment explanation
Indices: 567396--567450 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
567386 GCGAAATGAA
567396 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
567410 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
567429 AATCGCAACGAGAG
1 AATCGCAACGAGAG
567443 AATCGCAA
1 AATCGCAA
567451 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:567420 original size:33 final size:33
Alignment explanation
Indices: 567378--567509 Score: 192
Period size: 33 Copynumber: 3.8 Consensus size: 33
567368 AAAAATGACT
567378 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
567411 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
567444 ATCGCAATGCGAAATGAAAATCGCAATCCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAGA
567483 ATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGC-GAAATGAAAATCGCAA
567510 TGCGAAATGA
Statistics
Matches: 91, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
33 59 0.65
35 1 0.01
36 1 0.01
38 1 0.01
39 13 0.14
40 16 0.18
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:567479 original size:20 final size:19
Alignment explanation
Indices: 567378--567561 Score: 200
Period size: 19 Copynumber: 10.4 Consensus size: 19
567368 AAAAATGACT
567378 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
567397 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
567411 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
567430 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
567444 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
567463 ATCGCAATCCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
567483 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
567503 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
567522 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
567536 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
567555 ATCGCAA
1 ATCGCAA
567562 CGAGAGAATC
Statistics
Matches: 140, Mismatches: 9, Indels: 32
0.77 0.05 0.18
Matches are distributed among these distances:
14 30 0.21
15 3 0.02
16 6 0.04
17 6 0.04
18 3 0.02
19 54 0.39
20 38 0.27
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:567593 original size:33 final size:33
Alignment explanation
Indices: 567502--567580 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
567492 CGGAAATGAA
*
567502 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATAAAAATCGCAACGAGAG
567535 AATCGCAATGCGAAATAAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATAAAAATCGCAACGAGAG
567568 AATCGCAATGCGA
1 AATCGCAATGCGA
567581 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATAAAAATCGCAACGAGAG
Found at i:567653 original size:20 final size:19
Alignment explanation
Indices: 567570--567766 Score: 225
Period size: 20 Copynumber: 10.7 Consensus size: 19
567560 AACGAGAGAA
*
567570 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
567589 TCGCATTGGGATTCTCA--
1 TCGCATTGCGATTTTCATT
567606 -CG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
567622 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
567641 TCCACATTACGATTTTCATT
1 T-CGCATTGCGATTTTCATT
567661 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
567681 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
567700 TCCGCGTTGCGATTTTCATAT
1 T-CGCATTGCGATTTTCAT-T
567721 TCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATT
*
567738 T-G--TTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATT
567754 TCGCATTGCGATT
1 TCGCATTGCGATT
567767 CTCTCGTTGC
Statistics
Matches: 152, Mismatches: 13, Indels: 26
0.80 0.07 0.14
Matches are distributed among these distances:
14 21 0.14
16 4 0.03
17 4 0.03
19 55 0.36
20 66 0.43
21 2 0.01
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:567693 original size:39 final size:38
Alignment explanation
Indices: 567570--567766 Score: 225
Period size: 39 Copynumber: 5.3 Consensus size: 38
567560 AACGAGAGAA
* * *
567570 TCGCAATGCGATTTTCATTTCGCATTGGGATTCTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
567606 -CG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
567641 TCCACATTACGATTTTCATTTCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATT
*
567681 TCGCATTGCGATTTTCATTTCCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCAT-T
*
567721 TCGCATTGCGATTTTCA--T-G--TTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
567754 TCGCATTGCGATT
1 TCGCATTGCGATT
567767 CTCTCGTTGC
Statistics
Matches: 144, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
33 42 0.29
34 12 0.08
35 2 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 48 0.33
40 37 0.26
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (38 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:567700 original size:59 final size:59
Alignment explanation
Indices: 567608--567738 Score: 219
Period size: 59 Copynumber: 2.2 Consensus size: 59
567598 GATTCTCACG
567608 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCAT-TTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCATATT-CGCA
* * *
567667 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCGTTGCGATTTTCATATTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCATATTCGCA
567726 TTGCGATTTTCAT
1 TTGCGATTTTCAT
567739 GTTGCGGTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 66 0.97
60 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.47
Consensus pattern (59 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACATTACGATTTTCATATTCGCA
Found at i:567788 original size:33 final size:34
Alignment explanation
Indices: 567667--567799 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 34
567657 CATTTCCGCA
*
567667 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCA--T---CG
*
567706 TTGCGATTTTCATATTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCAT-TTCGCATTGCGATTCTCATCG
*
567740 TTGCGGTTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCATCG
* * *
567773 TTGCGATTGTAATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
567800 AGTCATTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
32 1 0.01
33 29 0.34
34 23 0.27
38 1 0.01
39 13 0.15
40 18 0.21
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATCG
Found at i:567845 original size:20 final size:20
Alignment explanation
Indices: 567772--567845 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
567762 CGATTCTCTC
* * *
567772 GTTGCGATTGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
**
567792 GTTGCGATAGTCA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
567812 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
567833 GTTGCGATAGTCA
1 GTTGCGATAGTCA
567846 AATGCATGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.55
21 13 0.31
22 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:569610 original size:33 final size:34
Alignment explanation
Indices: 569568--569635 Score: 129
Period size: 33 Copynumber: 2.0 Consensus size: 34
569558 GAATATGATT
569568 ACTAATCTTGAACTGAGCATTCATGTCAG-CATA
1 ACTAATCTTGAACTGAGCATTCATGTCAGTCATA
569601 ACTAATCTTGAACTGAGCATTCATGTCAGTCATA
1 ACTAATCTTGAACTGAGCATTCATGTCAGTCATA
569635 A
1 A
569636 TTTCATGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (34 bp):
ACTAATCTTGAACTGAGCATTCATGTCAGTCATA
Found at i:570313 original size:24 final size:24
Alignment explanation
Indices: 570279--570331 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
570269 CTGAAACATC
*
570279 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
570303 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
570327 ATCAA
1 ATCAA
570332 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:571038 original size:20 final size:20
Alignment explanation
Indices: 571013--571284 Score: 312
Period size: 20 Copynumber: 13.4 Consensus size: 20
571003 AAATTTCAGT
*
571013 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
571033 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
571053 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCTC
*
571073 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
571093 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
571113 GTTGCGATTTACGGATACAT-
1 GTTGCGATTTACGGATTC-TC
* *
571133 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATTCTC
* *
571154 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
571174 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATTCTC
* *
571195 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
571215 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATTCTC
* *
571236 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
571256 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATTCTC
571277 GTTGCGAT
1 GTTGCGAT
571285 AGTAAGAATC
Statistics
Matches: 214, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
20 147 0.69
21 67 0.31
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:571157 original size:41 final size:41
Alignment explanation
Indices: 571011--571284 Score: 330
Period size: 41 Copynumber: 6.8 Consensus size: 41
571001 CAAAATTTCA
*
571011 GTGTTGCGA-TTTACAG-ATTCTCGTTGCGATTTACGGATTA-
1 GTGTTGCGATTTTAC-GTATTGTCGTTGCGATTTACGGA-TAC
* * *
571051 -TCGTTGCGA-TTTACAG-ATTATCGTTGCGATTTACAGATTC
1 GT-GTTGCGATTTTAC-GTATTGTCGTTGCGATTTACGGATAC
* *
571091 -TCGTTGCGA-TTTACGGATTATCGTTGCGATTTACGGATAC
1 GT-GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
571131 ATGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
571172 GCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
*
571213 GCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
* * **
571254 GCGTTGCGATTTTACGGATACTCGTTGCGAT
1 GTGTTGCGATTTTACGTATTGTCGTTGCGAT
571285 AGTAAGAATC
Statistics
Matches: 217, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.01
40 76 0.35
41 138 0.64
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (41 bp):
GTGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
Found at i:571219 original size:82 final size:82
Alignment explanation
Indices: 571013--571345 Score: 387
Period size: 82 Copynumber: 4.1 Consensus size: 82
571003 AAATTTCAGT
* * *
571013 GTTGCGA-TTTACAGATTCTCGTTGCGATTTACGGATTA-TCGTTGCGA-TTTACAG-ATTATCG
1 GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGA-TACGCGTTGCGATTTTAC-GTATTGTCG
* *
571074 TTGCGATTTACAGATTCTC
64 TTGCGATTTACAGATACGC
* **
571093 GTTGCGA-TTTACGGATTATCGTTGCGATTTACGGATACATGTTGCGATTTTACGTATTGTCGTT
1 GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
*
571157 GCGATTTACGGATACGC
66 GCGATTTACAGATACGC
* *
571174 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
1 GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
*
571239 GCGATTTACGGATACGC
66 GCGATTTACAGATACGC
* * * *
571256 GTTGCGATTTTACGGATACTCGTTGCGATAGTAAGAAT-CGCGTTGCGATTTATA--TATTCG-C
1 GTTGCGATTTTACGGATTCTCGTTGCGAT-TTACGGATACGCGTTGCGATTT-TACGTATT-GTC
* * *
571317 GTTGCGATTTTCATATTCGC
63 GTTGCGATTTACAGATACGC
571337 GTTGCGATT
1 GTTGCGATT
571346 CTGGAAACTG
Statistics
Matches: 224, Mismatches: 22, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
79 2 0.01
80 41 0.18
81 64 0.29
82 110 0.49
83 7 0.03
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (82 bp):
GTTGCGATTTTACGGATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTT
GCGATTTACAGATACGC
Found at i:571316 original size:20 final size:20
Alignment explanation
Indices: 571293--571345 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
571283 ATAGTAAGAA
571293 TCGCGTTGCGATTTAT-ATAT
1 TCGCGTTGCGATTT-TCATAT
571313 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
571333 TCGCGTTGCGATT
1 TCGCGTTGCGATT
571346 CTGGAAACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:572875 original size:27 final size:27
Alignment explanation
Indices: 572845--572907 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
572835 TTATAACCAC
572845 TCTAATATAAT-AAAAATATT-TAGATTT
1 TCTAATATAATGAAAAA-ATTATA-ATTT
*
572872 TCT-ATATTATGAAAAAATTATAATTT
1 TCTAATATAATGAAAAAATTATAATTT
*
572898 TGTAAT-TAAT
1 TCTAATATAAT
572908 TTAGAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (27 bp):
TCTAATATAATGAAAAAATTATAATTT
Found at i:580104 original size:108 final size:107
Alignment explanation
Indices: 579958--580173 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 107
579948 CCTTATAAGC
579958 TATGTTTCTCTGACTATTCATTTTCTTATCCGACACTCGTGTCCTACACATATCTAGCTATGGGT
1 TATGTTTCTCTGACTATTCATTTTCTTATCCGACACTCGTGTCCTACACATATCTAGCTATGGGT
580023 ATGTGGATATAACCCCTCTCGCATTGAAAAACTTTGGAAGAG
66 ATGTGGATATAACCCCTCTCGCATTGAAAAACTTTGGAAGAG
580065 TATGTTTCTCTGACTATTCATTTTTCTTATCCGACACTCGTGTCCTACACATATCTAGCTATGGG
1 TATGTTTCTCTGACTATTCA-TTTTCTTATCCGACACTCGTGTCCTACACATATCTAGCTATGGG
580130 TATGTGGATATAACCCCTCTCGCATTGAAAAACTTTGGAAGAG
65 TATGTGGATATAACCCCTCTCGCATTGAAAAACTTTGGAAGAG
580173 T
1 T
580174 TGAATATATG
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 20 0.19
108 88 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (107 bp):
TATGTTTCTCTGACTATTCATTTTCTTATCCGACACTCGTGTCCTACACATATCTAGCTATGGGT
ATGTGGATATAACCCCTCTCGCATTGAAAAACTTTGGAAGAG
Found at i:583426 original size:21 final size:22
Alignment explanation
Indices: 583383--583480 Score: 76
Period size: 23 Copynumber: 4.4 Consensus size: 22
583373 GAAATTTGAA
583383 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATAGAATGTC
*
583405 CCGAAGGACCACATA-TATGTC
1 CCGAAGGACCACATAGAATGTC
* *
583426 CCGAAGGACTGA-GTAGAAATGTC
1 CCGAAGGAC-CACATAG-AATGTC
* ** *
583449 CCAAAATACCACGTAGAATTGTC
1 CCGAAGGACCACATAGAA-TGTC
583472 CCGAAGGAC
1 CCGAAGGAC
583481 TGCGTAGAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
21 17 0.29
22 17 0.29
23 25 0.42
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATGTC
Found at i:583486 original size:23 final size:23
Alignment explanation
Indices: 583421--583489 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
583411 GACCACATAT
*
583421 ATGTCCCGAAGGACTGAGTAGAA
1 ATGTCCCGAAGGACTGCGTAGAA
* ** **
583444 ATGTCCCAAAATACCACGTAGAA
1 ATGTCCCGAAGGACTGCGTAGAA
*
583467 TTGTCCCGAAGGACTGCGTAGAA
1 ATGTCCCGAAGGACTGCGTAGAA
583490 CCTCGACTCT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
ATGTCCCGAAGGACTGCGTAGAA
Found at i:585007 original size:23 final size:23
Alignment explanation
Indices: 584973--585045 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
584963 CAAGTGAGGG
*
584973 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
*
584996 TTCTACGTGGTCCTTCGAGAC-A
1 TTCTACGTGGTCCTTCGGGACAA
* * *
585018 TT-T-CGTGATCATTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
585039 TTCTACG
1 TTCTACG
585046 CGATCATTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 13 0.32
21 3 0.07
22 4 0.10
23 21 0.51
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:585054 original size:23 final size:23
Alignment explanation
Indices: 584973--585065 Score: 77
Period size: 23 Copynumber: 4.2 Consensus size: 23
584963 CAAGTGAGGG
* * * *
584973 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGATCATTCGAGACAT
* * *
584996 TTCTACGTGGTCCTTCGAGACA-
1 TTCTACGCGATCATTCGAGACAT
* *
585018 TT-T-CGTGATCATTCGGGACAT
1 TTCTACGCGATCATTCGAGACAT
585039 TTCTACGCGATCATTCGAGAC-T
1 TTCTACGCGATCATTCGAGACAT
585061 TTCTA
1 TTCTA
585066 TACGGTCTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
20 14 0.23
21 3 0.05
22 9 0.15
23 34 0.57
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (23 bp):
TTCTACGCGATCATTCGAGACAT
Found at i:592956 original size:2 final size:2
Alignment explanation
Indices: 592949--592978 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
592939 ATAATAAAAC
592949 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
592979 ATTTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:595684 original size:14 final size:15
Alignment explanation
Indices: 595665--595693 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
595655 AATCTATCTG
595665 AAAATTC-AAACATT
1 AAAATTCAAAACATT
595679 AAAATTCAAAACATT
1 AAAATTCAAAACATT
595694 CTGCAACAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATTCAAAACATT
Found at i:596803 original size:15 final size:16
Alignment explanation
Indices: 596775--596805 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
596765 AATCTATCTG
596775 AAAATTCAAAAACATT
1 AAAATTCAAAAACATT
596791 AAAATTC-AAAACATT
1 AAAATTCAAAAACATT
596806 CTGCAACAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATTCAAAAACATT
Found at i:597610 original size:30 final size:30
Alignment explanation
Indices: 597574--597635 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
597564 TATGTGAGTG
597574 AAGACTCT-GCTAACCTATGAACAAAAATTT
1 AAGACTCTGGCTAACCTATG-ACAAAAATTT
* *
597604 AAGACTCTGGTTAACCTATGACAACAATTT
1 AAGACTCTGGCTAACCTATGACAAAAATTT
597634 AA
1 AA
597636 AGAGACCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.27
Consensus pattern (30 bp):
AAGACTCTGGCTAACCTATGACAAAAATTT
Found at i:599344 original size:37 final size:37
Alignment explanation
Indices: 599291--599364 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
599281 ATTCCCACCA
*
599291 TGGGAAAGCATGGTGCTGAATATTATGCATTATCCAT
1 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
599328 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
1 TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
599365 GGTACTGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (37 bp):
TGGGAAAGCATAGTGCTGAATATTATGCATTATCCAT
Found at i:600953 original size:13 final size:13
Alignment explanation
Indices: 600935--600969 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
600925 TGCTATACTA
600935 TAAATATACAATG
1 TAAATATACAATG
600948 TAAATATACAATG
1 TAAATATACAATG
600961 TAAATATAC
1 TAAATATAC
600970 TATAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (13 bp):
TAAATATACAATG
Found at i:601658 original size:115 final size:116
Alignment explanation
Indices: 601456--601687 Score: 353
Period size: 115 Copynumber: 2.0 Consensus size: 116
601446 TCCTTCGTTG
*
601456 TGAAGTTGAAATCCTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTT
1 TGAAGTTGAAATCCTAGGTGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTT
*
601521 GTGAAGTTGAAATCCAATCTTGTAAATTGAATCGCTTT-GAGATT-AATATC
66 GTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTCGAG-TTCAATATC
**
601571 TGAAGTTGAAATTGT-GGATGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGT
1 TGAAGTTGAAATCCTAGG-TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGT
* * * *
601635 TGTGAAGTTGAAATTCACTCTTGTGAATTGTATCACTTTCGAGTTCAATATC
65 TGTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTCGAGTTCAATATC
601687 T
1 T
601688 TTCGCTGTGA
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
114 2 0.02
115 94 0.89
116 10 0.09
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (116 bp):
TGAAGTTGAAATCCTAGGTGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTT
GTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTCGAGTTCAATATC
Found at i:610720 original size:23 final size:23
Alignment explanation
Indices: 610689--610739 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
610679 GGAATCGTTA
610689 CCCCC-TTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
610711 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCGATT
610734 CCCCCT
1 CCCCCT
610740 GTAAGGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.20
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCGATT
Found at i:616351 original size:22 final size:22
Alignment explanation
Indices: 616325--616410 Score: 86
Period size: 21 Copynumber: 3.9 Consensus size: 22
616315 TTGGTACAGA
*
616325 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
616347 GGGAACCGATTCCCCCCTTTGAAG
1 GGGAACCGA-TACCCCC-TTGAAG
*
616371 GGGAACCGATTCCCCC-TGTAA-
1 GGGAACCGATACCCCCTTG-AAG
* *
616392 GGGAATCGATACCTCCTTG
1 GGGAACCGATACCCCCTTG
616411 GGGTTCTGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 15 0.28
22 12 0.22
23 12 0.22
24 15 0.28
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Done.