Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 41
Found at i:2940598 original size:21 final size:22
Alignment explanation
Indices: 2940552--2940622 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 22
2940542 GTAATTTAAT
* *
2940552 TTTTTATTTTTATTTTT-ATTGT
1 TTTTTA-TTTTATTTTTAAATGA
2940574 TTTTTATTTTATTTTTAAAT-A
1 TTTTTATTTTATTTTTAAATGA
*
2940595 TTTTTATATTTAACTTTTAAAATGA
1 TTTTTAT-TTT-A-TTTTTAAATGA
2940620 TTT
1 TTT
2940623 AAAAAAGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 17 0.41
22 11 0.27
23 1 0.02
24 8 0.20
25 4 0.10
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTATTTTTAAATGA
Found at i:2940598 original size:22 final size:22
Alignment explanation
Indices: 2940550--2940615 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2940540 TAGTAATTTA
*
2940550 ATTTTTTATTTTTATTTTT-ATT
1 ATTTTTTA-TTTTATTTTTAAAT
*
2940572 GTTTTTTATTTTATTTTTAAAT
1 ATTTTTTATTTTATTTTTAAAT
* *
2940594 ATTTTTATATTTAACTTTTAAA
1 ATTTTT-TATTTTATTTTTAAA
2940616 ATGATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.27
22 14 0.38
23 13 0.35
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
ATTTTTTATTTTATTTTTAAAT
Found at i:2940599 original size:23 final size:23
Alignment explanation
Indices: 2940551--2940615 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
2940541 AGTAATTTAA
2940551 TTTTTTATTTTTATTTTT--ATTG
1 TTTTTTA-TTTTATTTTTAAATTG
2940573 TTTTTTATTTTATTTTTAAATAT-
1 TTTTTTATTTTATTTTTAAAT-TG
* * *
2940596 TTTTATATTTAACTTTTAAA
1 TTTTTTATTTTATTTTTAAA
2940616 ATGATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 10 0.27
22 7 0.19
23 19 0.51
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTTATTTTATTTTTAAATTG
Found at i:2940736 original size:19 final size:19
Alignment explanation
Indices: 2940712--2940748 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2940702 ATGACCAACA
*
2940712 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2940731 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2940749 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2940903 original size:21 final size:21
Alignment explanation
Indices: 2940873--2940934 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
2940863 AGTCCAAATT
* *
2940873 CGTTGCGATAGTCCAAGTTCA
1 CGTTGTGATAGTCGAAGTTCA
2940894 CGTTGTGATAGTCGAAGTTCA
1 CGTTGTGATAGTCGAAGTTCA
2940915 CGTTGTGATAGTCGAAGTTC
1 CGTTGTGATAGTCGAAGTTC
2940935 GCAACGACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (21 bp):
CGTTGTGATAGTCGAAGTTCA
Found at i:2941303 original size:19 final size:19
Alignment explanation
Indices: 2941276--2941317 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2941266 TATTTTGGAT
*
2941276 TTTTCACTATCGCAACACA
1 TTTTAACTATCGCAACACA
2941295 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
2941314 TTTT
1 TTTT
2941318 TCAAAATCGC
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:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:2941326 original size:20 final size:20
Alignment explanation
Indices: 2941274--2941327 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2941264 CTTATTTTGG
*
2941274 ATTTTTCACTATCGCAACAC
1 ATTTTTCAATATCGCAACAC
2941294 A-TTTT-AACTATCGCAACAC
1 ATTTTTCAA-TATCGCAACAC
*
2941313 ATTTTTCAAAATCGC
1 ATTTTTCAATATCGC
2941328 GTTGCGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 10 0.34
21 2 0.07
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (20 bp):
ATTTTTCAATATCGCAACAC
Found at i:2946581 original size:22 final size:21
Alignment explanation
Indices: 2946539--2946594 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2946529 TTCTTATATA
2946539 ATTAAAATATTTTTATATTTT
1 ATTAAAATATTTTTATATTTT
* *
2946560 ATTAATAATATATTT-TGTTTT
1 ATTAA-AATATTTTTATATTTT
2946581 -TT-AAAT-TTTTTATA
1 ATTAAAATATTTTTATA
2946595 AGTTTATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.14
18 4 0.14
19 1 0.03
20 2 0.07
21 10 0.34
22 8 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTAAAATATTTTTATATTTT
Found at i:2951485 original size:24 final size:20
Alignment explanation
Indices: 2951444--2951490 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2951434 AGATAGAGTT
2951444 TTATTTTCTTAAATAATCAA
1 TTATTTTCTTAAATAATCAA
2951464 TTATTTTCTTAAATAATCAA
1 TTATTTTCTTAAATAATCAA
*
2951484 TCATTTT
1 TTATTTT
2951491 TCTGCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTTTCTTAAATAATCAA
Found at i:2955257 original size:12 final size:12
Alignment explanation
Indices: 2955240--2955273 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
2955230 CTAACATTCG
2955240 CAATTCTTCCCC
1 CAATTCTTCCCC
2955252 CAATTCTTCCCC
1 CAATTCTTCCCC
2955264 CAATTCTTCC
1 CAATTCTTCC
2955274 TCGCGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.35
Consensus pattern (12 bp):
CAATTCTTCCCC
Found at i:2960349 original size:12 final size:12
Alignment explanation
Indices: 2960332--2960365 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
2960322 CTAACATTCG
2960332 CAATTCTTCCCC
1 CAATTCTTCCCC
2960344 CAATTCTTCCCC
1 CAATTCTTCCCC
2960356 CAATTCTTCC
1 CAATTCTTCC
2960366 TCGCGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.35
Consensus pattern (12 bp):
CAATTCTTCCCC
Found at i:2964041 original size:20 final size:20
Alignment explanation
Indices: 2964016--2964068 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2964006 GACCAACAAA
2964016 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
2964036 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
2964056 TTCGCAACGCGAA
1 TTCGCAACGCGAA
2964069 TCTGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:2964131 original size:19 final size:19
Alignment explanation
Indices: 2964091--2964162 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
2964081 AACACGATAG
*
2964091 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
2964112 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
2964131 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
2964150 TTAAATTCACAAC
1 TCAAATTCGCAAC
2964163 AGGTTTAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 36 0.75
21 12 0.25
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:2965081 original size:24 final size:24
Alignment explanation
Indices: 2965054--2965107 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2965044 GTATTCGAAA
*
2965054 TTTGATCTTGGTCAATACACGGAC
1 TTTGATCTTGGGCAATACACGGAC
* * *
2965078 TTTGATCTTGGGGAATACTCGGAT
1 TTTGATCTTGGGCAATACACGGAC
2965102 TTTGAT
1 TTTGAT
2965108 GATGTGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGGCAATACACGGAC
Found at i:2968269 original size:24 final size:24
Alignment explanation
Indices: 2968218--2968270 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2968208 TTTCATATGT
* * *
2968218 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
2968242 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTAAATATA
2968266 AATTT
1 AATTT
2968271 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2968617 original size:39 final size:39
Alignment explanation
Indices: 2968574--2968660 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
2968564 TCCGATGCTC
*
2968574 ATCAAAATCCAAAGCTCATATGGTTCCAAGCAAAAAGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
* * *
2968613 ATCAAAATCCAAATCTCATATGGTGCCAAGTAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
2968652 ATCAAAATC
1 ATCAAAATC
2968661 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAAGAA
Found at i:2968924 original size:20 final size:20
Alignment explanation
Indices: 2968899--2968936 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2968889 GCAATGCTTA
2968899 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
2968919 TTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
2968937 TACCTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:2969075 original size:66 final size:64
Alignment explanation
Indices: 2968995--2969138 Score: 225
Period size: 66 Copynumber: 2.2 Consensus size: 64
2968985 TTTTAGAAAC
*
2968995 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAA-CAAAAAAATAAATCTTATTTACACATC-AATT
2969060 A
64 A
* * * *
2969061 AACAAATCAACTTTTACAAATCAATTAATCAATAAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATAAATCTTATTTACACATCAATTA
2969125 AACAAATCAACTTT
1 AACAAATCAACTTT
2969139 CAATGTAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 19 0.26
65 23 0.32
66 31 0.42
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATAAATCTTATTTACACATCAATTA
Found at i:2969724 original size:21 final size:21
Alignment explanation
Indices: 2969700--2969792 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
2969690 GTGGGCAGGA
*
2969700 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
*
2969721 CCTCTTGAACGGTGAGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
2969742 CTTCTTCG-ATGATGAGAGGGA
1 CCTCTT-GAACGATGAGAGGGG
* *
2969763 CCTCTTGAACGATAAGAGGTG
1 CCTCTTGAACGATGAGAGGGG
2969784 CCTCTTGAA
1 CCTCTTGAA
2969793 TAATTATAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.02
21 57 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:2972448 original size:20 final size:20
Alignment explanation
Indices: 2972423--2972570 Score: 144
Period size: 20 Copynumber: 7.5 Consensus size: 20
2972413 GCGTAAAAAC
2972423 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
2972443 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
2972462 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* * *
2972483 A-TTGAATTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2972502 ATTTGACTATT-GCGTTGCGA
1 ATTTGACT-TTCGCGTTGCGA
* *
2972522 ATTTCACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
2972542 ATTTGACTATCACGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2972562 ATTTGACTT
1 ATTTGACTT
2972571 CTGTGTTGCA
Statistics
Matches: 106, Mismatches: 13, Indels: 18
0.77 0.09 0.13
Matches are distributed among these distances:
18 2 0.02
19 19 0.18
20 78 0.74
21 7 0.07
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:2972546 original size:40 final size:40
Alignment explanation
Indices: 2972423--2972601 Score: 185
Period size: 40 Copynumber: 4.5 Consensus size: 40
2972413 GCGTAAAAAC
2972423 ATTTGACT-TTCGCGTTGCGAATTTGACTTCTGTGTTGCG-
1 ATTTGACTATTCGCGTTGCGAATTTGACTTC-GTGTTGCGA
* * *
2972462 ATTT-ACAAATTCGCGTTGCGAA-TTGAATTTTGTGTTGCGA
1 ATTTGAC-TATTCGCGTTGCGAATTTG-ACTTCGTGTTGCGA
* *
2972502 ATTTGACTATT-GCGTTGCGAATTTCACTATCGCGTTGCGA
1 ATTTGACTATTCGCGTTGCGAATTTGACT-TCGTGTTGCGA
*
2972542 ATTTGACTA-TCACGTTGCGAATTTGACTTCTGTGTTGC-A
1 ATTTGACTATTCGCGTTGCGAATTTGACTTC-GTGTTGCGA
*
2972581 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC-TATTCGCGTTGCGA
2972602 TTTACAGATT
Statistics
Matches: 116, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
38 4 0.03
39 36 0.31
40 74 0.64
41 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (40 bp):
ATTTGACTATTCGCGTTGCGAATTTGACTTCGTGTTGCGA
Found at i:2972598 original size:20 final size:20
Alignment explanation
Indices: 2972575--2972625 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2972565 TGACTTCTGT
*
2972575 GTTGCAATTTACAAATTCGC
1 GTTGCAATTTACAAATTAGC
* *
2972595 GTTGCGATTTACAGATTAGC
1 GTTGCAATTTACAAATTAGC
2972615 GTTGCGAATTT
1 GTTGC-AATTT
2972626 GTTGGTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTGCAATTTACAAATTAGC
Found at i:2973828 original size:67 final size:68
Alignment explanation
Indices: 2973729--2973864 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 68
2973719 ATACAAAAAT
2973729 TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
1 TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
2973794 ATA
66 ATA
* *
2973797 TAATTAAATAAAA-TAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
1 TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
2973861 ATA
66 ATA
2973864 T
1 T
2973865 GCATTTATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 53 0.80
68 13 0.20
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (68 bp):
TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
ATA
Found at i:2974215 original size:2 final size:2
Alignment explanation
Indices: 2974210--2974237 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2974200 CACTAATTTA
2974210 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
2974238 CCAACTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2974281 original size:2 final size:2
Alignment explanation
Indices: 2974274--2974303 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2974264 AAAATAATAC
2974274 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
2974304 CCAACTAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2974317 original size:66 final size:66
Alignment explanation
Indices: 2974210--2974335 Score: 243
Period size: 66 Copynumber: 1.9 Consensus size: 66
2974200 CACTAATTTA
2974210 ATATATATATATATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATAATACA
1 ATATATATATATATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATAATACA
2974275 T
66 T
*
2974276 ATATATATATATATATATATATATATATCCAACTAAGCTATACGTTAAACAAATAAAATA
1 ATATATATATATATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATA
2974336 TGGCTATTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.35
Consensus pattern (66 bp):
ATATATATATATATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATAATACA
T
Found at i:2974439 original size:49 final size:47
Alignment explanation
Indices: 2974351--2974448 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 47
2974341 ATTATTCCTC
*
2974351 AGACACGTTAAACAAATATATATATATGAACAAAAAATCAGTTTCCA
1 AGACACGTTAAACAAATATATATATATGAACAAAAAATCAATTTCCA
*
2974398 AGACACGTTAAACGAATATATATATATATGAACAAAGAATCAATTTCCA
1 AGACACGTTAAAC-AA-ATATATATATATGAACAAAAAATCAATTTCCA
2974447 AG
1 AG
2974449 GTATGTGTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 13 0.28
48 2 0.04
49 32 0.68
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (47 bp):
AGACACGTTAAACAAATATATATATATGAACAAAAAATCAATTTCCA
Found at i:2975491 original size:3 final size:3
Alignment explanation
Indices: 2975476--2975533 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
2975466 TAAACACACT
*
2975476 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2975524 T-T TAA TAA TA
1 TAA TAA TAA TA
2975534 TTTTTTAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2975836 original size:105 final size:105
Alignment explanation
Indices: 2975660--2975953 Score: 322
Period size: 105 Copynumber: 2.8 Consensus size: 105
2975650 TCGTTAGATT
* * * *
2975660 GAACAAGTTCTTCTCATTATAAAC-TTCTTCTTTCTCGTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTTC-TCCTT-T--AGGACGAGTTCTTCTCATTATGAACTC
* * * *
2975724 TTTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAAA-
62 TTCTGGAAATGTTGATCCAAATCCATCTGCGGT-GAATTAGAAAG
* *
2975768 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * ** * *
2975833 GGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAAG
66 GGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
* * * *
2975873 GAACAAGTTCTTCTTATTATGAACTTTCTCCTTTATGATGAGTTCTTTTCATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTC-
*
2975938 TTGGAAATGTCGATCC
65 -TGGAAATGTTGATCC
2975954 CTCAAGCGAG
Statistics
Matches: 157, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
104 8 0.05
105 108 0.69
107 13 0.08
108 25 0.16
109 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (105 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
Found at i:2976163 original size:91 final size:90
Alignment explanation
Indices: 2976005--2976172 Score: 284
Period size: 92 Copynumber: 1.9 Consensus size: 90
2975995 TGATAGGTCA
2976005 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
2976070 TCCATTGAAAATGTTGATGCGAAGTTG
66 TCC--TGAAAATGTTGATGCGAAGTTG
* * *
2976097 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTC-GTTGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
2976161 TCCTGAAAATGT
66 TCCTGAAAATGT
2976173 CAATCCCTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
89 9 0.12
91 31 0.42
92 33 0.45
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (90 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
TCCTGAAAATGTTGATGCGAAGTTG
Found at i:2976262 original size:225 final size:223
Alignment explanation
Indices: 2975873--2976310 Score: 693
Period size: 225 Copynumber: 2.0 Consensus size: 223
2975863 AATTTGAAAG
* * *
2975873 GAACAAGTTCTTCTTATTATGAACTTTCTCCTTTATGATGAGTTCTTTTCATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
* * * *
2975938 TTGGAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCAAGTGATAGGT
66 CTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGT
* *
2976003 CAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAAC
131 CAAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTATGAAC
2976068 TCTCCATTGAAAATGTTGATGCGAAGTT
196 TCTCCATTGAAAATGTTGATGCGAAGTT
2976096 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACT
* *
2976160 C-TC-CTGAAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
61 CTTCACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGA
*
2976223 TAGGTCGAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTA
126 TAGGTCAAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTA
*
2976288 TGAACTCTCCATTGGAAATGTTG
191 TGAACTCTCCATTGAAAATGTTG
2976311 GTTCACCTCC
Statistics
Matches: 197, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
223 23 0.12
224 1 0.01
225 141 0.72
226 6 0.03
227 24 0.12
228 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (223 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
CTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATGAATCAAGTGATAGGT
CAAACAAACTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTATGAAC
TCTCCATTGAAAATGTTGATGCGAAGTT
Found at i:2977196 original size:8 final size:8
Alignment explanation
Indices: 2977185--2977279 Score: 89
Period size: 8 Copynumber: 12.5 Consensus size: 8
2977175 CCTTTTTCTC
2977185 TTTTCATT
1 TTTTCATT
2977193 TTTTCA--
1 TTTTCATT
*
2977199 -TTTCTTT
1 TTTTCATT
2977206 TTTTCATT
1 TTTTCATT
2977214 TTTT-A-T
1 TTTTCATT
2977220 TTTTCATTTT
1 TTTTCA--TT
2977230 TTTTCA-T
1 TTTTCATT
2977237 TTTTCA-T
1 TTTTCATT
2977244 TTTTCATT
1 TTTTCATT
2977252 TTTTCATCT
1 TTTTCAT-T
2977261 TTTT-ATT
1 TTTTCATT
*
2977268 TTTTCCTT
1 TTTTCATT
2977276 TTTT
1 TTTT
2977280 TTCAAGCATA
Statistics
Matches: 74, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
5 4 0.05
6 5 0.07
7 21 0.28
8 32 0.43
9 5 0.07
10 7 0.09
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:2977208 original size:14 final size:13
Alignment explanation
Indices: 2977191--2977281 Score: 74
Period size: 13 Copynumber: 6.2 Consensus size: 13
2977181 TCTCTTTTCA
*
2977191 TTTTTTCATTTCT
1 TTTTTTCATTTTT
2977204 TTTTTTCATTTTT
1 TTTTTTCATTTTT
2977217 TATTTTTCATTTTTTT
1 T-TTTTTCA--TTTTT
2977233 TCATTTTTCATTTTT
1 T--TTTTTCATTTTT
2977248 CATTTTTTCATCTTTTT
1 --TTTTTTCA--TTTTT
*
2977265 ATTTTTTCCTTTTT
1 -TTTTTTCATTTTT
2977279 TTT
1 TTT
2977282 CAAGCATAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
13 16 0.24
14 12 0.18
15 12 0.18
16 14 0.21
17 14 0.21
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCATTTTT
Found at i:2977235 original size:24 final size:24
Alignment explanation
Indices: 2977203--2977283 Score: 112
Period size: 24 Copynumber: 3.4 Consensus size: 24
2977193 TTTTCATTTC
2977203 TTTTTTTCATTTTTTATTTTTCAT
1 TTTTTTTCATTTTTTATTTTTCAT
*
2977227 TTTTTTTCATTTTTCATTTTTCA-
1 TTTTTTTCATTTTTTATTTTTCAT
*
2977250 -TTTTTTCATCTTTTTATTTTTTCCT
1 TTTTTTTCAT-TTTTTA-TTTTTCAT
2977275 TTTTTTTCA
1 TTTTTTTCA
2977284 AGCATAGTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 9 0.18
23 5 0.10
24 28 0.56
26 8 0.16
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTTCATTTTTTATTTTTCAT
Found at i:2977243 original size:31 final size:32
Alignment explanation
Indices: 2977177--2977264 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 32
2977167 CAAACCCTCC
*
2977177 TTTTTC-TCTTTTCATTTTTTCA--TTTCTT--
1 TTTTTCAT-TTTTCATTTTTTCATCTTTTTTCA
* *
2977205 TTTTTCATTTTTTA-TTTTTCATTTTTTTTCA
1 TTTTTCATTTTTCATTTTTTCATCTTTTTTCA
2977236 TTTTTCATTTTTCATTTTTTCATCTTTTT
1 TTTTTCATTTTTCATTTTTTCATCTTTTT
2977265 ATTTTTTCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
27 7 0.14
28 11 0.22
29 6 0.12
31 13 0.26
32 13 0.26
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTCATTTTTCATTTTTTCATCTTTTTTCA
Found at i:2977278 original size:7 final size:7
Alignment explanation
Indices: 2977185--2977270 Score: 77
Period size: 7 Copynumber: 11.6 Consensus size: 7
2977175 CCTTTTTCTC
2977185 TTTTCATT
1 TTTTCA-T
2977193 TTTTCAT
1 TTTTCAT
2977200 TTCTT--T
1 TT-TTCAT
2977206 TTTTCAT
1 TTTTCAT
*
2977213 TTTTTAT
1 TTTTCAT
2977220 TTTTCATTTT
1 TTTTCA---T
2977230 TTTTCAT
1 TTTTCAT
2977237 TTTTCAT
1 TTTTCAT
2977244 TTTTCATT
1 TTTTCA-T
2977252 TTTTCAT
1 TTTTCAT
*
2977259 CTTTTTAT
1 -TTTTCAT
2977267 TTTT
1 TTTT
2977271 TCCTTTTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
5 2 0.03
6 3 0.04
7 34 0.51
8 21 0.31
10 7 0.10
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCAT
Found at i:2988788 original size:68 final size:68
Alignment explanation
Indices: 2988702--2988838 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
2988692 ATACAAAAAT
2988702 TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
1 TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
2988767 ATA
66 ATA
* *
2988770 TAATTAAATAAAATAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
1 TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
2988835 ATA
66 ATA
2988838 T
1 T
2988839 GCATTTATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (68 bp):
TAATTAAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACATTCTAATACAAAAATT
ATA
Found at i:2989189 original size:2 final size:2
Alignment explanation
Indices: 2989184--2989221 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2989174 CACTAATTTA
2989184 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
2989222 CCAACTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2989261 original size:45 final size:45
Alignment explanation
Indices: 2989206--2989299 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
2989196 ATATATATAT
2989206 ATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAA
1 ATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAA
*
2989251 ATATATATATATATATCCAACTAAGCTATACGTTAAACAAATAAA
1 ATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAA
2989296 ATAT
1 ATAT
2989300 GGCTATTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (45 bp):
ATATATATATATATATCCAACTAAACTATACGTTAAACAAATAAA
Found at i:2990469 original size:3 final size:3
Alignment explanation
Indices: 2990448--2990520 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
2990438 TAAATACACT
* *
2990448 TAA TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2990496 TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2990521 TTTTTTAACT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 1 0.02
3 62 0.98
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2993321 original size:15 final size:17
Alignment explanation
Indices: 2993288--2993328 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2993278 CTATTTTTAT
*
2993288 TATTTAATAA-AAAATA
1 TATTTAAAAATAAAATA
2993304 TA-TTAAAAATAAAA-A
1 TATTTAAAAATAAAATA
2993319 TATTTAAAAA
1 TATTTAAAAA
2993329 ATATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TATTTAAAAATAAAATA
Found at i:2993337 original size:17 final size:17
Alignment explanation
Indices: 2993297--2993328 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2993287 TTATTTAATA
2993297 AAAAATATATTAAAAAT
1 AAAAATATATTAAAAAT
2993314 AAAAATAT-TTAAAAA
1 AAAAATATATTAAAAA
2993329 ATATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATATATTAAAAAT
Found at i:2996295 original size:39 final size:39
Alignment explanation
Indices: 2996241--2996320 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
2996231 CTAAACGGTT
2996241 ACATATCTTATTCAGAAATTTCTTTTCATATTTAAAACA
1 ACATATCTTATTCAGAAATTTCTTTTCATATTTAAAACA
2996280 ACATATCTTATTCAGAAATTTCTTTTCATATTTAAAACA
1 ACATATCTTATTCAGAAATTTCTTTTCATATTTAAAACA
2996319 AC
1 AC
2996321 GTTAAAATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (39 bp):
ACATATCTTATTCAGAAATTTCTTTTCATATTTAAAACA
Found at i:2997067 original size:30 final size:30
Alignment explanation
Indices: 2997007--2997078 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
2996997 AGAGACATAA
* *
2997007 ATACA-TAAATCAAATATCATATCAGAAAT
1 ATACAGTAAATCAAATATCAGATCAAAAAT
*
2997036 ATACAGTAAATCATATATCAGAT-AAACAAT
1 ATACAGTAAATCAAATATCAGATCAAA-AAT
* *
2997066 ATTCAGGAAATCA
1 ATACAGTAAATCA
2997079 GGTATCATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.19
30 29 0.81
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (30 bp):
ATACAGTAAATCAAATATCAGATCAAAAAT
Found at i:2999139 original size:26 final size:27
Alignment explanation
Indices: 2999090--2999140 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2999080 ATTAAGATAT
2999090 TTTTTTAACGGATGTAATAATTTGAGA
1 TTTTTTAACGGATGTAATAATTTGAGA
* *
2999117 TTTTTTAATGGATGT-ATAGTTTGA
1 TTTTTTAACGGATGTAATAATTTGA
2999141 CGTTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (27 bp):
TTTTTTAACGGATGTAATAATTTGAGA
Found at i:3001046 original size:66 final size:63
Alignment explanation
Indices: 3000975--3001154 Score: 166
Period size: 66 Copynumber: 2.7 Consensus size: 63
3000965 AGTGTCGTGA
*
3000975 ATAAAATATTAGACACAACACGTTAAGTGTCATGGATAAACTTTGGACACGA-GTTAAATGTTGC
1 ATAAAATATT-GACACAACAC-TTAAGTG-C-TGGATAAACTTTGGACACAATGTTAAATGTTGC
3001039 AG
62 AG
* *
3001041 ATAAAATATTTGACACAATACACTTAGAAGTG-TGCATAAACTTTGGACACAATGTTAAGTGTTG
1 ATAAAATA-TTGACAC-A-ACACTT--AAGTGCTGGATAAACTTTGGACACAATGTTAAATGTTG
**
3001105 TGG
61 CAG
* * *
3001108 ATAAAATATTGTACACAACACATTGAGAGCGTGGATCAACTTTGGAC
1 ATAAAATATTG-ACACAACAC-TTAAGTGC-TGGATAAACTTTGGAC
3001155 TCGACGTGTT
Statistics
Matches: 95, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
64 3 0.03
65 4 0.04
66 51 0.54
67 28 0.29
68 4 0.04
69 5 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (63 bp):
ATAAAATATTGACACAACACTTAAGTGCTGGATAAACTTTGGACACAATGTTAAATGTTGCAG
Found at i:3005063 original size:60 final size:60
Alignment explanation
Indices: 3004999--3005148 Score: 185
Period size: 59 Copynumber: 2.5 Consensus size: 60
3004989 TATATTGGTT
* * ***
3004999 CTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTCTCATTCTAAATTAGTC
1 CTTAAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACAAACATTCTAAATTAGTC
* * * * *
3005059 CTTAAAATTTTGAACATTCTAATTT-ATCACTAAACTATGACAAACTTTCTAAATTGGTC
1 CTTAAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACAAACATTCTAAATTAGTC
* *
3005118 CCTAAACTTTTGAATATTCCAATTTCATCCC
1 CTTAAACTTTTGAATATTCTAATTTCATCCC
3005149 GAAATTCATC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
59 49 0.66
60 25 0.34
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
CTTAAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACAAACATTCTAAATTAGTC
Found at i:3005395 original size:60 final size:60
Alignment explanation
Indices: 3005274--3005396 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 60
3005264 GTATATATGT
* * *
3005274 ATAGTTTGGGATGAAATTAGAATGTTCACAAAGTTTGAGGACCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATGAAATTAGAATGTTCACAAAGCTTGAGGACCAATTTAAAATGAAAGTC
* *
3005334 ATAGTTTGGGAATGAAATT-GAAATGTTCA-AAAGCTTGATGACTAATTTAAAAT-AATAGTC
1 ATAGTTTGGG-ATGAAATTAG-AATGTTCACAAAGCTTGAGGACCAATTTAAAATGAA-AGTC
3005394 ATA
1 ATA
3005397 AATTAAGGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
59 2 0.04
60 37 0.67
61 16 0.29
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTAGAATGTTCACAAAGCTTGAGGACCAATTTAAAATGAAAGTC
Found at i:3010020 original size:21 final size:20
Alignment explanation
Indices: 3009988--3010071 Score: 105
Period size: 20 Copynumber: 4.0 Consensus size: 20
3009978 ATTGTTAGTA
3009988 TTATTATTTTATTTTTTATTTT
1 TTATT-TTTTA-TTTTTATTTT
3010010 TTATTTTTTATTTTTTATTTT
1 TTATTTTTTA-TTTTTATTTT
*
3010031 TTATTTTTTATTTTTATCTT
1 TTATTTTTTATTTTTATTTT
* * *
3010051 TTATCTTGTATCTTTATTTT
1 TTATTTTTTATTTTTATTTT
3010071 T
1 T
3010072 GTTTTTAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 26 0.46
21 26 0.46
22 5 0.09
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.80
Consensus pattern (20 bp):
TTATTTTTTATTTTTATTTT
Found at i:3010057 original size:7 final size:7
Alignment explanation
Indices: 3009988--3010054 Score: 109
Period size: 7 Copynumber: 9.6 Consensus size: 7
3009978 ATTGTTAGTA
3009988 TTATTATT
1 TTATT-TT
3009996 TTATTTT
1 TTATTTT
3010003 TTATTTT
1 TTATTTT
3010010 TTATTTT
1 TTATTTT
3010017 TTATTTT
1 TTATTTT
3010024 TTATTTT
1 TTATTTT
3010031 TTATTTT
1 TTATTTT
3010038 TTA-TTT
1 TTATTTT
*
3010044 TTATCTT
1 TTATTTT
3010051 TTAT
1 TTAT
3010055 CTTGTATCTT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
6 6 0.11
7 46 0.81
8 5 0.09
ACGTcount: A:0.16, C:0.01, G:0.00, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:3010073 original size:14 final size:13
Alignment explanation
Indices: 3009991--3010071 Score: 67
Period size: 14 Copynumber: 6.1 Consensus size: 13
3009981 GTTAGTATTA
3009991 TTAT-TTTATTTT
1 TTATCTTTATTTT
*
3010003 TTATTTTTTATTTT
1 TTA-TCTTTATTTT
*
3010017 TTATTTTTTATTTT
1 TTA-TCTTTATTTT
*
3010031 TTAT-TTTTTATTT
1 TTATCTTTAT-TTT
*
3010044 TTATCTTTTATCTT
1 TTATC-TTTATTTT
*
3010058 GTATCTTTATTTT
1 TTATCTTTATTTT
3010071 T
1 T
3010072 GTTTTTAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
12 7 0.12
13 16 0.28
14 31 0.53
15 4 0.07
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.80
Consensus pattern (13 bp):
TTATCTTTATTTT
Found at i:3010748 original size:18 final size:18
Alignment explanation
Indices: 3010725--3010774 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
3010715 CGTGGTGGGT
3010725 AGAAGAAATGAAGAAGGA
1 AGAAGAAATGAAGAAGGA
3010743 AGAAGAAATGAAGAAGGA
1 AGAAGAAATGAAGAAGGA
3010761 AGAAGAAA-GAAGAA
1 AGAAGAAATGAAGAA
3010775 AGAAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (18 bp):
AGAAGAAATGAAGAAGGA
Found at i:3019732 original size:60 final size:60
Alignment explanation
Indices: 3019654--3019774 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
3019644 TATGTGTGTG
*
3019654 TGTGTTTGGATGTAATAAACTCTAAAAAATAGTCTGATTTATCTGAAAAAACT-CAAGTTT
1 TGTGTTTGGATATAATAAACTCTAAAAAATAGTCTGATTTATCTGAAAAAA-TGCAAGTTT
3019714 TGTGTTTGGATATAATAAACTCTAAAAAATAGTCTGATTTATCTGAAAAAATGCAAGTTT
1 TGTGTTTGGATATAATAAACTCTAAAAAATAGTCTGATTTATCTGAAAAAATGCAAGTTT
3019774 T
1 T
3019775 CTTTTTCCTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 1 0.02
60 58 0.98
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (60 bp):
TGTGTTTGGATATAATAAACTCTAAAAAATAGTCTGATTTATCTGAAAAAATGCAAGTTT
Found at i:3022507 original size:21 final size:21
Alignment explanation
Indices: 3022483--3022524 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3022473 CTATTGATAG
*
3022483 CATTGACGTGATTGTTCACAA
1 CATTGACATGATTGTTCACAA
*
3022504 CATTGATATGATTGTTCACAA
1 CATTGACATGATTGTTCACAA
3022525 TAAATAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (21 bp):
CATTGACATGATTGTTCACAA
Found at i:3022655 original size:19 final size:20
Alignment explanation
Indices: 3022629--3022669 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3022619 GTTTAATGTT
* *
3022629 TAAAAAATAAATATTTAAAA
1 TAAAAATTAAATATTAAAAA
*
3022649 TAAAAATTAATTATTAAAAA
1 TAAAAATTAAATATTAAAAA
3022669 T
1 T
3022670 TTAAAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATTAAATATTAAAAA
Found at i:3027998 original size:31 final size:31
Alignment explanation
Indices: 3027931--3027990 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3027921 AAATTTAAGG
*
3027931 CAAAATGGTTTTTGGACTTAAATTGAATTTA
1 CAAAATGGTATTTGGACTTAAATTGAATTTA
3027962 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTAAATTGAATTTA
3027991 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTAAATTGAATTTA
Found at i:3028103 original size:20 final size:21
Alignment explanation
Indices: 3028078--3028116 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3028068 ATTTGAACAG
*
3028078 TATG-AAGGGTATCGATTCTC
1 TATGAAAGGGTACCGATTCTC
3028098 TATGAAAGGGTACCGATTC
1 TATGAAAGGGTACCGATTC
3028117 CCCCCATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (21 bp):
TATGAAAGGGTACCGATTCTC
Found at i:3028180 original size:21 final size:21
Alignment explanation
Indices: 3028147--3028186 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3028137 TTTTTGCAAA
*
3028147 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3028169 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3028187 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3030817 original size:21 final size:21
Alignment explanation
Indices: 3030791--3030832 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3030781 ATTTGAATAT
*
3030791 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3030812 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3030833 CCATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3031845 original size:91 final size:91
Alignment explanation
Indices: 3031671--3031845 Score: 235
Period size: 91 Copynumber: 1.9 Consensus size: 91
3031661 CGAGCAAAAA
*
3031671 TGAACAAGTTCTTCTCATTATAAACTTTTTGCCCCTCATCGGATGAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATAAACTTCTTGCCCCTCATCGGATGAGTTCTTCTCATTATGAACT
* * *
3031736 CACCGCTGTAAATGTTGATGCAAGGT
66 CACCACTGGAAATATTGATGCAAGGT
* * * * *
3031762 TGAATAAGTTCTTCTCATTATGAACTTCTT-CTTCCTCGTCGGATGAGTTCTTTTCATTATGAAC
1 TGAACAAGTTCTTCTCATTATAAACTTCTTGC-CCCTCATCGGATGAGTTCTTCTCATTATGAAC
* *
3031826 TCTCCATTGGAAATATTGAT
65 TCACCACTGGAAATATTGAT
3031846 CGGTTTATCT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 1 0.01
91 71 0.99
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (91 bp):
TGAACAAGTTCTTCTCATTATAAACTTCTTGCCCCTCATCGGATGAGTTCTTCTCATTATGAACT
CACCACTGGAAATATTGATGCAAGGT
Found at i:3032248 original size:66 final size:66
Alignment explanation
Indices: 3032141--3032470 Score: 267
Period size: 66 Copynumber: 4.9 Consensus size: 66
3032131 TAAAATTTCT
* * * * * *
3032141 TGTTTCAAGGGAAATTTGTCTCAAGCGAGACAAA-TTTGTTTCGAGGGAAACAATCTCAAAG-GT
1 TGTTTCAAGAGAAA-CTGTCTCAAGAGAGA-AAACTATGTTTCAAGGGAAACAATCTCAAAGATT
*
3032204 TGG
64 TTG
* *
3032207 TGTTTCAAGAGAAACTGTCTCAGGAGAGATAAAAC-ATGTTTCAAGGGAAACAAACTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCA--AGAGAGAAAACTATGTTTCAAGGGAAACAATCTCAAAGATT
3032271 TTG
64 TTG
* * *
3032274 TGTTTCAAGAGAAACTATCTCAAGAGAGACAACTTTGTTTCAAGGGAAACAGAT-TCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAACTATGTTTCAAGGGAAACA-ATCTCAAAGATTT
*
3032338 TA
65 TG
* * * * **
3032340 TGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAACTATGTTTCAAGGGAAACAATCTCAA---AG-
**
3032405 CAAAATT-
61 --ATTTTG
* * * *
3032412 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCTAGGGAAACTATCTCAA
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGA-AAACTATGTTTCAAGGGAAACAATCTCAA
3032471 GGGAGACAAA
Statistics
Matches: 221, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
65 16 0.07
66 94 0.43
67 52 0.24
70 2 0.01
71 1 0.00
72 53 0.24
73 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAACTATGTTTCAAGGGAAACAATCTCAAAGATTTT
G
Found at i:3032281 original size:31 final size:30
Alignment explanation
Indices: 3032243--3032354 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 30
3032233 AGATAAAACA
*
3032243 TGTTTCAAGGGAAACAAACTCAAAGATTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATTTT
* * **
3032273 GTGTTTCAAGAGAAACTATCTCAAGAGAGACAACTT
1 -TGTTTCAAGAGAAACAAACTC-A-A-AG--ATTTT
* * *
3032309 TGTTTCAAGGGAAACAGATTCAAAGATTTT
1 TGTTTCAAGAGAAACAAACTCAAAGATTTT
3032339 ATGTTTCAAGAGAAAC
1 -TGTTTCAAGAGAAAC
3032355 TGTCTCAATA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
30 3 0.05
31 32 0.52
32 3 0.05
33 2 0.03
34 3 0.05
35 16 0.26
36 3 0.05
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAAACTCAAAGATTTT
Found at i:3032301 original size:67 final size:66
Alignment explanation
Indices: 3032141--3032390 Score: 279
Period size: 66 Copynumber: 3.8 Consensus size: 66
3032131 TAAAATTTCT
* * * * * * * *
3032141 TGTTTCAAGGGAAATTTGTCTCAAGCGAGACAAATTTGTTTCGAGGGAAACAATCTCAAAG-GTT
1 TGTTTCAAGAGAAA-CTGTCTCAAGAGAGAAAAACTTGTTTCAAGGGAAACAAACTCAAAGATTT
*
3032205 GG
65 TG
* *
3032207 TGTTTCAAGAGAAACTGTCTCAGGAGAGATAAAACATGTTTCAAGGGAAACAAACTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAACTTGTTTCAAGGGAAACAAACTCAAAGATTT
3032272 TG
65 TG
* * * *
3032274 TGTTTCAAGAGAAACTATCTCAAGAGAG-ACAACTTTGTTTCAAGGGAAACAGATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAC-TTGTTTCAAGGGAAACAAACTCAAAGATTT
*
3032338 TA
65 TG
* * *
3032340 TGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATTTGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAACTTGTTTCAAGGGAAAC
3032391 TGTCTCAAGG
Statistics
Matches: 156, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
65 16 0.10
66 93 0.60
67 44 0.28
68 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAACTTGTTTCAAGGGAAACAAACTCAAAGATTTT
G
Found at i:3032387 original size:36 final size:36
Alignment explanation
Indices: 3032340--3032613 Score: 241
Period size: 36 Copynumber: 7.8 Consensus size: 36
3032330 AAAGATTTTA
*
3032340 TGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
3032376 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
3032412 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
* * * *
3032448 TGTTTCTAGGGAAACTATCTCAAGGGAGAC-AAATCT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-T
* ** *
3032484 TGTTTCAAGGGAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
3032513 TGTTTCAAGGGAAACAGTCTCAAGGGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
3032550 TGTTTGAAGCGAAATTGTCTCAAGAAAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
3032584 TATTTCAATG-GAAACTGTCTCAAGCGAGAC
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGAC
3032614 GAAGTTTGAT
Statistics
Matches: 199, Mismatches: 25, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 3 0.02
32 2 0.01
33 2 0.01
34 25 0.13
35 9 0.05
36 110 0.55
37 28 0.14
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:3032398 original size:133 final size:133
Alignment explanation
Indices: 3032141--3032390 Score: 333
Period size: 133 Copynumber: 1.9 Consensus size: 133
3032131 TAAAATTTCT
* * * * *
3032141 TGTTTCAAGGGAAATTTGTCTCAAGCGAGACAAATTTGTTTCGAGGGAAACAATCTCAAAGGTTG
1 TGTTTCAAGAGAAATCTATCTCAAGAGAGACAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTG
* * * *
3032206 GTGTTTCAAGAGAAACTGTCTCAGGAGAGATAAAACATGTTTCAAGGGAAACAAACTCAAAGATT
66 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATGTTTCAAGAGAAACAAACTCAAAGATT
3032271 TTG
131 TTG
* *
3032274 TGTTTCAAGAGAAA-CTATCTCAAGAGAGACAACTTTGTTTCAAGGGAAACAGAT-TCAAAGATT
1 TGTTTCAAGAGAAATCTATCTCAAGAGAGACAAATTTGTTTCAAGGGAAACA-ATCTCAAAG-GT
* * **
3032337 TTATGTTTCAAGAGAAACTGTCTCAATAGAGACAAAATTTGTTTCAAGAGAAAC
64 TGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATGTTTCAAGAGAAAC
3032391 TGTCTCAAGG
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
132 38 0.38
133 62 0.62
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (133 bp):
TGTTTCAAGAGAAATCTATCTCAAGAGAGACAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTG
ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACATGTTTCAAGAGAAACAAACTCAAAGATT
TTG
Found at i:3032580 original size:37 final size:37
Alignment explanation
Indices: 3032511--3032581 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
3032501 ATTCAAAGAT
* **
3032511 TTTGTTTCAAGGGAAACAGTCTCAAGGGAGACAAAAC
1 TTTGTTTCAAGCGAAACAGTCTCAAGAAAGACAAAAC
* **
3032548 TTTGTTTGAAGCGAAATTGTCTCAAGAAAGACAA
1 TTTGTTTCAAGCGAAACAGTCTCAAGAAAGACAA
3032582 TTTATTTCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (37 bp):
TTTGTTTCAAGCGAAACAGTCTCAAGAAAGACAAAAC
Found at i:3033919 original size:2 final size:2
Alignment explanation
Indices: 3033903--3033939 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3033893 TCAACATTAT
* *
3033903 TA TA TA CA TA CA 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 TA TA TA T
3033940 TGGGTATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3035277 original size:149 final size:149
Alignment explanation
Indices: 3035007--3035447 Score: 542
Period size: 149 Copynumber: 3.0 Consensus size: 149
3034997 TTCAAAATTT
* * ** *
3035007 CTACTTCATCTCCTACTTTCAAAAATCTTTCGAGCTGGTTCGCAATCTTCAATTGTTGACTTCGG
1 CTACTTCATTTCCTACTTCCAAAAATCTTTCGAGCTGGTTCGTGATCTTCAATTGTTGGCTTCGG
* * * * *
3035072 TGTTGAATCTTCTCGAGTCTAACTTGTTACCTCAATAGGAAAATATATGGATCGTCTCCTTGGTA
66 AGTTGAATCGTCTCGAGTCTAACTTGTTACCTCAGTAGGCAAATGTATGGATCGTCTCCTTGGTA
*
3035137 GATAGACTCTCTCTA-TCTC
131 GATAGACTCCCTCTAGT-TC
* * * * *
3035156 CTACTTCCTTTCTTACTTCCAAAAATCTTTCGAGTTGGTTTGTGATCTTCAAATGTTGGCTTCGG
1 CTACTTCATTTCCTACTTCCAAAAATCTTTCGAGCTGGTTCGTGATCTTCAATTGTTGGCTTCGG
* *
3035221 AGTTGAATCGTCTCAAGTCTAACTTGTTACCTCAGTAGGCAAATGTCTGGATCGTCTCCTTGGTA
66 AGTTGAATCGTCTCGAGTCTAACTTGTTACCTCAGTAGGCAAATGTATGGATCGTCTCCTTGGTA
*
3035286 GATAGACTCCCTCTAGTTT
131 GATAGACTCCCTCTAGTTC
* * ** *
3035305 CTACTTCATTTCCTACTTCTAGAAATCTTTCGAGCTAATTCGTGATCTTCAATTGTTGGCTTCAG
1 CTACTTCATTTCCTACTTCCAAAAATCTTTCGAGCTGGTTCGTGATCTTCAATTGTTGGCTTCGG
* * * * * * * * * *
3035370 CGTCGAATTGTCTCGAGTCCAACTTGTTAGCTCAGCAGGCAGATGTATGGCTTGTCTCATTGGTA
66 AGTTGAATCGTCTCGAGTCTAACTTGTTACCTCAGTAGGCAAATGTATGGATCGTCTCCTTGGTA
* *
3035435 GGTAGACTTCCTC
131 GATAGACTCCCTC
3035448 CTGACGTTAC
Statistics
Matches: 248, Mismatches: 43, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
149 247 1.00
150 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (149 bp):
CTACTTCATTTCCTACTTCCAAAAATCTTTCGAGCTGGTTCGTGATCTTCAATTGTTGGCTTCGG
AGTTGAATCGTCTCGAGTCTAACTTGTTACCTCAGTAGGCAAATGTATGGATCGTCTCCTTGGTA
GATAGACTCCCTCTAGTTC
Found at i:3043637 original size:28 final size:28
Alignment explanation
Indices: 3043589--3043642 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3043579 TCCGTCTATG
**
3043589 TTATGTCGTCGAGCATGTGCTTGAAACA
1 TTATGTCGTCGAGCAAATGCTTGAAACA
*
3043617 TTATGTCGTCGAGTAAATGCTTGAAA
1 TTATGTCGTCGAGCAAATGCTTGAAA
3043643 GCAACGGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (28 bp):
TTATGTCGTCGAGCAAATGCTTGAAACA
Found at i:3045763 original size:25 final size:25
Alignment explanation
Indices: 3045734--3045783 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3045724 TATTGGTCCC
* * *
3045734 CCCGTCCCCGTCCCCGTTTAAAAAA
1 CCCGTACCCATCCCCGCTTAAAAAA
3045759 CCCGTACCCATCCCCGCTTAAAAAA
1 CCCGTACCCATCCCCGCTTAAAAAA
3045784 TCGCGGGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.44, G:0.10, T:0.18
Consensus pattern (25 bp):
CCCGTACCCATCCCCGCTTAAAAAA
Found at i:3046525 original size:27 final size:27
Alignment explanation
Indices: 3046487--3046546 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
3046477 GACTGAAATA
3046487 AATACAACATACAAATTAGAAACCAAT
1 AATACAACATACAAATTAGAAACCAAT
* *
3046514 AATACAAGATACAAATTAGAAACCGAT
1 AATACAACATACAAATTAGAAACCAAT
3046541 AA-ACAA
1 AATACAA
3046547 ATAAACATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (27 bp):
AATACAACATACAAATTAGAAACCAAT
Found at i:3048382 original size:12 final size:12
Alignment explanation
Indices: 3048359--3048407 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
3048349 TTTTAATATT
*
3048359 TATCGGGCCGGG
1 TATCGGGTCGGG
*
3048371 TATCAGGTCGGG
1 TATCGGGTCGGG
*
3048383 TATCGGGGCGGG
1 TATCGGGTCGGG
3048395 TAATCGGGTCGGG
1 T-ATCGGGTCGGG
3048408 GATTACCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.12, C:0.18, G:0.49, T:0.20
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:3048394 original size:24 final size:25
Alignment explanation
Indices: 3048359--3048407 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
3048349 TTTTAATATT
3048359 TATCGGGCCGGGT-ATCAGGTCGGG
1 TATCGGGCCGGGTAATCAGGTCGGG
* *
3048383 TATCGGGGCGGGTAATCGGGTCGGG
1 TATCGGGCCGGGTAATCAGGTCGGG
3048408 GATTACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.12, C:0.18, G:0.49, T:0.20
Consensus pattern (25 bp):
TATCGGGCCGGGTAATCAGGTCGGG
Found at i:3048429 original size:6 final size:6
Alignment explanation
Indices: 3048418--3048452 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3048408 GATTACCAAA
*
3048418 CCCGTC CCCGTC CCCGTC CCCGTC CCCGTC TCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
3048453 TTAGCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.63, G:0.17, T:0.20
Consensus pattern (6 bp):
CCCGTC
Found at i:3049775 original size:19 final size:20
Alignment explanation
Indices: 3049741--3049785 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
3049731 ATATTAATTT
3049741 TTTTTTTGTAATTTTTCTG-
1 TTTTTTTGTAATTTTTCTGA
*
3049760 TTTTTTTGT-ATGTTTTTTGA
1 TTTTTTTGTAAT-TTTTCTGA
3049780 TTTTTT
1 TTTTTT
3049786 AAATTCAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 15 0.65
20 6 0.26
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTTGTAATTTTTCTGA
Found at i:3049820 original size:115 final size:112
Alignment explanation
Indices: 3049664--3049878 Score: 288
Period size: 115 Copynumber: 1.9 Consensus size: 112
3049654 CTATAATTTA
* * * * *
3049664 ATTTTTTTAATTCAAATATATTAAATTATAATATAGATAAAAATATATTGAAATTAGATAAATAA
1 ATTTTTTAAATTCAAATATATTAAATTACAAGATAGATAAAAATACATTAAAATTAGATAAATAA
*
3049729 ACATATTAATTTTTTTTTTGTAATTTTTCTG-TTTTTTTGTATGTTTTTTG
66 ACATACT-A---TTTTTTTGTAATTTTTCTGATTTTTTTGTATGTTTTTTG
* * * **
3049779 ATTTTTTAAATTCAAGTATATTAATTTGCAAGATAGATAAAAATACATTAAAATTAGATACGTAA
1 ATTTTTTAAATTCAAATATATTAAATTACAAGATAGATAAAAATACATTAAAATTAGATAAATAA
3049844 ACATACTATTTTTTTGTAATTTTTCTGATTTTTTT
66 ACATACTATTTTTTTGTAATTTTTCTGATTTTTTT
3049879 AAATTCAAGT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
111 19 0.22
112 7 0.08
114 1 0.01
115 61 0.69
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (112 bp):
ATTTTTTAAATTCAAATATATTAAATTACAAGATAGATAAAAATACATTAAAATTAGATAAATAA
ACATACTATTTTTTTGTAATTTTTCTGATTTTTTTGTATGTTTTTTG
Found at i:3051165 original size:20 final size:21
Alignment explanation
Indices: 3051140--3051191 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3051130 TTTTCCCAAT
*
3051140 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3051160 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3051181 TCGCAATGCGA
1 TCGCAATGCGA
3051192 TACTGAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3051205 original size:20 final size:20
Alignment explanation
Indices: 3051180--3051233 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3051170 AATTGGGAAA
3051180 ATCGCAATGCGATACTGAAT
1 ATCGCAATGCGATACTGAAT
* *
3051200 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGAAT
3051220 ATCGCAATGCGATA
1 ATCGCAATGCGATA
3051234 ATACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGAAT
Found at i:3051265 original size:40 final size:40
Alignment explanation
Indices: 3051180--3051272 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
3051170 AATTGGGAAA
* * * * * *
3051180 ATCGCAATGCGATACTGAATATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAATCAAAATCGCAACGAGATACTGACT
3051220 ATCGCAATGCGATAATACAAAATCGCAACGAGATA-TGACT
1 ATCGCAATGCGATAAT-CAAAATCGCAACGAGATACTGACT
* *
3051260 TTCGCAACGCGAT
1 ATCGCAATGCGAT
3051273 TTACAGCGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 30 0.68
41 14 0.32
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
ATCGCAATGCGATAATCAAAATCGCAACGAGATACTGACT
Found at i:3051857 original size:20 final size:20
Alignment explanation
Indices: 3051812--3051857 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3051802 GCAACGAGAG
* *
3051812 AATCGCAACGTGAAATAAAA
1 AATCGCAACGCGAAACAAAA
3051832 AA-CGCAACGCGAAACAAAA
1 AATCGCAACGCGAAACAAAA
3051851 AATCGCA
1 AATCGCA
3051858 TGCGATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.54, C:0.22, G:0.15, T:0.09
Consensus pattern (20 bp):
AATCGCAACGCGAAACAAAA
Found at i:3051881 original size:18 final size:18
Alignment explanation
Indices: 3051858--3051920 Score: 99
Period size: 18 Copynumber: 3.4 Consensus size: 18
3051848 AAAAATCGCA
3051858 TGCGATTTCATTTCGCGT
1 TGCGATTTCATTTCGCGT
*
3051876 TGCGATTTTATTTCGCGGT
1 TGCGATTTCATTTCGC-GT
3051895 TGCGATTTTCATTTCGCGT
1 TGCGA-TTTCATTTCGCGT
3051914 TGCGATT
1 TGCGATT
3051921 GCTGGTCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.41
19 14 0.34
20 10 0.24
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (18 bp):
TGCGATTTCATTTCGCGT
Found at i:3051898 original size:19 final size:18
Alignment explanation
Indices: 3051858--3051920 Score: 99
Period size: 19 Copynumber: 3.4 Consensus size: 18
3051848 AAAAATCGCA
*
3051858 TGCGATTTCATTTCGCGT
1 TGCGATTTTATTTCGCGT
3051876 TGCGATTTTATTTCGCGGT
1 TGCGATTTTATTTCGC-GT
3051895 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-ATTTCGCGT
3051914 TGCGATT
1 TGCGATT
3051921 GCTGGTCGCG
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 15 0.36
19 20 0.48
20 7 0.17
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:3051930 original size:38 final size:37
Alignment explanation
Indices: 3051858--3051930 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
3051848 AAAAATCGCA
* **
3051858 TGCGATTTCATTTCGCGTTGCGATTTTATTTCGCGGT
1 TGCGATTTCATTTCGCGTTGCGATTCTAGGTCGCGGT
3051895 TGCGATTTTCATTTCGCGTTGCGATTGCT-GGTCGCG
1 TGCGA-TTTCATTTCGCGTTGCGATT-CTAGGTCGCG
3051931 ATAGTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.16
38 25 0.81
39 1 0.03
ACGTcount: A:0.10, C:0.21, G:0.27, T:0.42
Consensus pattern (37 bp):
TGCGATTTCATTTCGCGTTGCGATTCTAGGTCGCGGT
Found at i:3051960 original size:14 final size:14
Alignment explanation
Indices: 3051943--3051979 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3051933 AGTCATTTCG
*
3051943 CGTTGCGATTCTCT
1 CGTTGCGATTCTAT
3051957 CGTTGCGATTCTAT
1 CGTTGCGATTCTAT
*
3051971 TGTTGCGAT
1 CGTTGCGAT
3051980 AGTCATTCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTAT
Found at i:3052004 original size:19 final size:20
Alignment explanation
Indices: 3051972--3052025 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
3051962 CGATTCTATT
**
3051972 GTTGCGATAGTCATT-CCGC
1 GTTGCGATTCTCATTACCGC
* *
3051991 GTTGCGATTCTCATTATCTC
1 GTTGCGATTCTCATTACCGC
*
3052011 GTTGCGATTTTCATT
1 GTTGCGATTCTCATT
3052026 TCAACCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (20 bp):
GTTGCGATTCTCATTACCGC
Found at i:3053973 original size:21 final size:21
Alignment explanation
Indices: 3053949--3054013 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
3053939 TCATTCCTCG
3053949 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3053970 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3053991 AGA-T-CCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCGTTCA
3054010 AGAG
1 AGAG
3054014 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 13, Indels: 3
0.65 0.28 0.07
Matches are distributed among these distances:
19 12 0.40
21 18 0.60
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3053973 original size:42 final size:42
Alignment explanation
Indices: 3053897--3054013 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
3053887 GACTCGCCTG
* * *
3053897 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
3053939 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
** * *
3053981 TCATCGTTGAAGA-TCC-CTCCCACCATTCAAGAG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAG
3054014 CCCGATTCAC
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 16 0.26
41 3 0.05
42 42 0.69
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:3055371 original size:14 final size:14
Alignment explanation
Indices: 3055352--3055387 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3055342 ATTGTTTAAT
3055352 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3055366 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3055380 TGATTTGT
1 TGATTTGT
3055388 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3055513 original size:19 final size:19
Alignment explanation
Indices: 3055489--3055538 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
3055479 AGGCAAAACT
3055489 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
* *
3055508 ATCGCAACGCGAAATTAAA
1 ATCGCAATGCGAAATAAAA
* *
3055527 TTCGCATTGCGA
1 ATCGCAATGCGA
3055539 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:3055549 original size:19 final size:19
Alignment explanation
Indices: 3055527--3055657 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
3055517 CGAAATTAAA
3055527 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
3055546 TTCGCGTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
3055562 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
3055579 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
3055593 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3055612 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
3055628 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3055645 TTCGCATTGCGAT
1 TTCGCATTGCGAT
3055658 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 23 0.27
16 13 0.15
17 13 0.15
19 35 0.42
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3055575 original size:33 final size:32
Alignment explanation
Indices: 3055533--3055657 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 32
3055523 TAAATTCGCA
*
3055533 TTGCGATTTTCATTTCGCGTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-CCTCG
**
3055566 TTGCGATTTTCATTTCGCATTGCGAAATT-AGCG
1 TTGCGATTTTCATTTCGCATTGCG--ATTCCTCG
3055599 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTC-CTCG
3055632 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3055658 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCTCG
Found at i:3055612 original size:66 final size:66
Alignment explanation
Indices: 3055524--3055656 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
3055514 ACGCGAAATT
* *
3055524 AAATTCGCATTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3055589 G
66 G
* *
3055590 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
3055655 G
66 G
3055656 A
1 A
3055657 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:3057921 original size:12 final size:12
Alignment explanation
Indices: 3057904--3057928 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3057894 TCTTCGGGGA
3057904 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3057916 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3057928 C
1 C
3057929 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3059206 original size:20 final size:20
Alignment explanation
Indices: 3059181--3059237 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3059171 TTCATTTGAC
3059181 TATCGCAACGCGAAAATGGA
1 TATCGCAACGCGAAAATGGA
*
3059201 TATCGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGA
*
3059221 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
3059238 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGA
Found at i:3059424 original size:14 final size:14
Alignment explanation
Indices: 3059405--3059441 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3059395 CATCAATTAA
3059405 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3059419 ACAAATCATCTTTT
1 ACAAATCAACATTT
3059433 ACAAATCAA
1 ACAAATCAA
3059442 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3061264 original size:20 final size:19
Alignment explanation
Indices: 3061229--3061295 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3061219 GAAACTTAAA
3061229 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3061248 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3061268 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3061287 ATCGCAACG
1 ATCGCAACG
3061296 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3061303 original size:14 final size:14
Alignment explanation
Indices: 3061284--3061341 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
3061274 ATGCGAAATG
3061284 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3061298 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
3061314 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
3061330 AAAATCGCAACG
1 AAAATCGCAACG
3061342 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3061331 original size:32 final size:33
Alignment explanation
Indices: 3061268--3061346 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
3061258 GGAAATGGCT
*
3061268 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
3061301 ATCGCAACGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3061333 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3061347 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3061379 original size:18 final size:18
Alignment explanation
Indices: 3061353--3061486 Score: 86
Period size: 18 Copynumber: 7.6 Consensus size: 18
3061343 GAAACACAAA
* *
3061353 TCGCATTGCTATTTCATT
1 TCGCGTTGCGATTTCATT
*
3061371 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
3061387 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
3061403 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
3061419 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
* **
3061436 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGAT-TTCATT
*
3061455 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGAT-TTCA-TT
*
3061476 TCGTGTTGCGA
1 TCGCGTTGCGA
3061487 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 12, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.21
15 3 0.03
16 6 0.07
17 2 0.02
18 24 0.26
19 12 0.13
20 23 0.25
21 3 0.03
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:3061393 original size:14 final size:14
Alignment explanation
Indices: 3061374--3061431 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3061364 TTTCATTTCG
3061374 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3061388 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3061404 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3061420 CGTTGCGATTTT
1 CGTTGCGATTTT
3061432 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3061404 original size:32 final size:32
Alignment explanation
Indices: 3061358--3061447 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
3061348 ACAAATCGCA
*
3061358 TTGCTATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
3061390 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
*
3061422 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGA-TTTCATTTCGCGTTGCGAT
3061448 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 37 0.67
33 18 0.33
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:3061466 original size:20 final size:19
Alignment explanation
Indices: 3061432--3061486 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3061422 TTGCGATTTT
*
3061432 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3061451 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3061471 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3061487 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3061982 original size:18 final size:18
Alignment explanation
Indices: 3061956--3062000 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3061946 GTCGATCAGA
*
3061956 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
3061974 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
3061992 TGATGGCTC
1 TGATGGCTC
3062001 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:3063353 original size:20 final size:20
Alignment explanation
Indices: 3063305--3063363 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3063295 AATAGTTTCT
** *
3063305 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
3063325 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
3063345 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
3063364 AGATAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:3063653 original size:22 final size:22
Alignment explanation
Indices: 3063626--3063669 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3063616 GATGGAGATA
3063626 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3063648 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3063670 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3063883 original size:20 final size:20
Alignment explanation
Indices: 3063857--3063929 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
3063847 GATTATGTAT
3063857 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3063877 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3063897 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
3063917 TATCTCGTTGCGA
1 TATCGCGTTGCGA
3063930 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3063984 original size:20 final size:20
Alignment explanation
Indices: 3063940--3064032 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3063930 TTTTGTATTA
* **
3063940 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
3063961 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
3063981 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
3064002 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
3064022 TCGCATTGCGA
1 TCGCATTGCGA
3064033 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:3063985 original size:41 final size:41
Alignment explanation
Indices: 3063940--3064032 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3063930 TTTTGTATTA
3063940 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3063981 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3064022 TCGCATTGCGA
1 TCGCATTGCGA
3064033 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3065487 original size:17 final size:17
Alignment explanation
Indices: 3065465--3065501 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3065455 ACTCCAACTC
3065465 CAAATTGCTTCAATCTT
1 CAAATTGCTTCAATCTT
3065482 CAAATTGCTTCAATCTT
1 CAAATTGCTTCAATCTT
3065499 CAA
1 CAA
3065502 GCTTGACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (17 bp):
CAAATTGCTTCAATCTT
Found at i:3066355 original size:30 final size:30
Alignment explanation
Indices: 3066297--3066392 Score: 167
Period size: 30 Copynumber: 3.2 Consensus size: 30
3066287 AATTGTGTTG
*
3066297 AAGACGCCGAGAGTTCCAACCT-CCATGCA
1 AAGACGCCGAGAGTTCCAAGCTGCCATGCA
3066326 AAGACGCCGAGAGTTCCAAGCTGCCATGCA
1 AAGACGCCGAGAGTTCCAAGCTGCCATGCA
*
3066356 AAGAAGCCGAGAGTTCCAAGCTGCCATGCA
1 AAGACGCCGAGAGTTCCAAGCTGCCATGCA
3066386 AAGACGC
1 AAGACGC
3066393 ATCTATTGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 21 0.33
30 42 0.67
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.12
Consensus pattern (30 bp):
AAGACGCCGAGAGTTCCAAGCTGCCATGCA
Found at i:3066836 original size:22 final size:22
Alignment explanation
Indices: 3066811--3066861 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3066801 ACGTGAGAAT
*
3066811 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
*
3066833 CACGGGTTCTGCAAGGAGAAAT
1 CACGGGTTCTGCAAGGAGAAAG
3066855 CACGGGT
1 CACGGGT
3066862 CCTGGGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:3066904 original size:23 final size:23
Alignment explanation
Indices: 3066878--3066921 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3066868 TCCTGCAAGG
3066878 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
3066901 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
3066922 GGGCATGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:3067642 original size:169 final size:170
Alignment explanation
Indices: 3067360--3067712 Score: 532
Period size: 169 Copynumber: 2.1 Consensus size: 170
3067350 ATTATAAAGT
* * * * *
3067360 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
3067425 ACTATGCTGGAATTTAGTATTAGTATGCTAATGGTTAAATTAGAAAGAATTTA-AAATTTA-TGG
66 ACTATGCTGGAATTTAGTATTAGTATGCTAATGGTTAAATTAGAAAGAATTTATAAATTTAGT-G
* *
3067488 ATTAAATTGCTAACTTTGAAAATATTGAGAACCAATAGTAA
130 ATTAAATTGCAAACTTTGAAAATATTGAGAACCAAAAGTAA
* * *
3067529 TTAGGGATCATTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
3067594 ACTATGCTTGAATTTAGTATTA-TATGCTTAATGGTTAAATTTGAAAGAATTTATAAATTTAGTG
66 ACTATGCTGGAATTTAGTATTAGTATGC-TAATGGTTAAATTAGAAAGAATTTATAAATTTAGTG
* * *
3067658 ATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAAAGTAA
130 ATTAAATTGCAAACTTTGAAAATATTGAGAACCAAAAGTAA
3067699 TTAGGGATCATTTT
1 TTAGGGATCATTTT
3067713 ATTTGATGTT
Statistics
Matches: 166, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
168 5 0.03
169 102 0.61
170 58 0.35
171 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (170 bp):
TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAGTATGCTAATGGTTAAATTAGAAAGAATTTATAAATTTAGTGA
TTAAATTGCAAACTTTGAAAATATTGAGAACCAAAAGTAA
Found at i:3068893 original size:15 final size:15
Alignment explanation
Indices: 3068873--3068906 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3068863 AATTAATAAG
*
3068873 TGAATACGGCCGTTA
1 TGAATACGACCGTTA
3068888 TGAATACGACCGTTA
1 TGAATACGACCGTTA
3068903 TGAA
1 TGAA
3068907 ACTTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (15 bp):
TGAATACGACCGTTA
Found at i:3071210 original size:18 final size:18
Alignment explanation
Indices: 3071187--3071233 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
3071177 AAATTATTAG
3071187 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
3071205 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
3071223 TCTCACGCTTC
1 TCTCACGCTTC
3071234 GGACACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:3071629 original size:112 final size:106
Alignment explanation
Indices: 3071493--3071713 Score: 302
Period size: 112 Copynumber: 2.0 Consensus size: 106
3071483 AGATTCCCGC
3071493 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCC-T-ATGCAGAAGACGCCGAGAG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTAATGCAGAAGACGCCGAGAG
3071556 ATCCCACTCCGAGAGATCCCAATTGCTTGAAGACGCCGAGCATTCCCAT
66 ATCCCA---C-----ATCCCAATTGCTTGAAGACGCCGAGCATTCCCAT
3071605 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCC-T-TA--ATGCAGAAGACGCCG
* *
3071670 AGATATCCCACATGCCAATTGCTTGAAGACGCCGAGCATTCCCA
62 AGAGATCCCACATCCCAATTGCTTGAAGACGCCGAGCATTCCCA
3071714 GAGTGTCATA
Statistics
Matches: 101, Mismatches: 2, Indels: 14
0.86 0.02 0.12
Matches are distributed among these distances:
110 32 0.32
112 43 0.43
115 2 0.02
118 24 0.24
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.17
Consensus pattern (106 bp):
CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTAATGCAGAAGACGCCGAGAG
ATCCCACATCCCAATTGCTTGAAGACGCCGAGCATTCCCAT
Found at i:3073357 original size:2 final size:2
Alignment explanation
Indices: 3073352--3073385 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3073342 ATATGAAGAA
3073352 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
3073386 TGTATATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3074150 original size:17 final size:16
Alignment explanation
Indices: 3074128--3074195 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
3074118 TGTTTAAGGT
*
3074128 ATATTTTATTATATTTA
1 ATATTTAATT-TATTTA
3074145 ATATTTAATTTATTTA
1 ATATTTAATTTATTTA
*
3074161 AGTATTTAAATTATTTA
1 A-TATTTAATTTATTTA
*
3074178 ATA-TTATATTTAATTA
1 ATATTTA-ATTTATTTA
3074194 AT
1 AT
3074196 TTCTTTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
15 3 0.07
16 18 0.40
17 24 0.53
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
ATATTTAATTTATTTA
Found at i:3075449 original size:33 final size:33
Alignment explanation
Indices: 3075412--3075479 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
3075402 TTACCCAATG
* *
3075412 CCACCACCGCCACTGTCACCTG-GTTTTATGACC
1 CCACCACCGCCACCGTCA-CAGAGTTTTATGACC
* *
3075445 CCACCGCCGTCACCGTCACAGAGTTTTATGACC
1 CCACCACCGCCACCGTCACAGAGTTTTATGACC
3075478 CC
1 CC
3075480 TCCTAGAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.19, C:0.43, G:0.16, T:0.22
Consensus pattern (33 bp):
CCACCACCGCCACCGTCACAGAGTTTTATGACC
Found at i:3077508 original size:2 final size:2
Alignment explanation
Indices: 3077501--3077561 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
3077491 ATTATGCATG
3077501 AT AT AT AT A- AT AT -T A- 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
3077540 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3077562 CACACAAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.