Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 16
Found at i:706213 original size:86 final size:87
Alignment explanation
Indices: 706031--706213 Score: 239
Period size: 86 Copynumber: 2.1 Consensus size: 87
706021 TTGATATTTG
* *
706031 GCGGCA-TTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCACAAACG
1 GCGGCATTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTCCCCACAAACA
* * * *
706095 CCGCAATAGGTGTTGAGATTTA
66 CCGCAAAAGATGCTGAGATATA
* *
706117 TCGGCATTTTTTCC-ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACA
1 GCGGCATTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTCCCCACAAACA
*
706181 CCGTAAAAGAT-CTG-GTATATA
66 CCGCAAAAGATGCTGAG-ATATA
*
706202 GCGGCGTTTTTT
1 GCGGCATTTTTT
706214 AGAGCAAACG
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 16 0.19
86 60 0.71
87 7 0.08
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (87 bp):
GCGGCATTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTCCCCACAAACA
CCGCAAAAGATGCTGAGATATA
Found at i:706408 original size:21 final size:21
Alignment explanation
Indices: 706382--706440 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
706372 ATTTTCCAAT
*
706382 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
706403 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
706424 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
706441 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:708623 original size:36 final size:36
Alignment explanation
Indices: 708581--708669 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 36
708571 CCAGTTGCAG
**
708581 CAGTGGGCATAGATTGATGTGAAAGGGAAGTCATAC
1 CAGTGGGCATAGATTGATGCAAAAGGGAAGTCATAC
708617 CAGTGGGCATAGATTGATGCAAAAGGGAAGTCATAC
1 CAGTGGGCATAGATTGATGCAAAAGGGAAGTCATAC
** *
708653 CAGCAGGCATAGCTTGA
1 CAGTGGGCATAGATTGA
708670 GGTTGACCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (36 bp):
CAGTGGGCATAGATTGATGCAAAAGGGAAGTCATAC
Found at i:711101 original size:52 final size:52
Alignment explanation
Indices: 711045--711203 Score: 291
Period size: 52 Copynumber: 3.1 Consensus size: 52
711035 TAACAACAAA
711045 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
711097 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
* *
711149 ATACATTATAATTTAGAAACATTAAAGTACTTATTCATAAACTGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
711201 ATA
1 ATA
711204 TTGTTCAGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:712324 original size:42 final size:41
Alignment explanation
Indices: 712263--712459 Score: 193
Period size: 42 Copynumber: 4.7 Consensus size: 41
712253 ATGTTTTTTA
* * * * * *
712263 CGGCGTTTATACAAAAAACGCCGCTATTTTACCACTCTATTG
1 CGGCGTTTTTACTATAAACGCCGCTATTGT-CTACTATATTG
** * *
712305 CGGCGTTTTTTGTATAAACGCCGCTAAATGT-TAAATATATTG
1 CGGCGTTTTTACTATAAACGCCGCT-ATTGTCT-ACTATATTG
* * *
712347 CGGC-ATTTTAGCTA-AAACGCCGCTACATGTCTATTATATTG
1 CGGCGTTTTTA-CTATAAACGCCGCTA-TTGTCTACTATATTG
*
712388 CGGCGTTTTTACTATAAACGCCGCTACATGTCTACTATATTG
1 CGGCGTTTTTACTATAAACGCCGCTA-TTGTCTACTATATTG
712430 CGGCGTTTTTACTATAAACGCCGCTATTGT
1 CGGCGTTTTTACTATAAACGCCGCTATTGT
712460 TTAACCTTTC
Statistics
Matches: 131, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 36 0.27
42 91 0.69
43 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (41 bp):
CGGCGTTTTTACTATAAACGCCGCTATTGTCTACTATATTG
Found at i:712367 original size:83 final size:82
Alignment explanation
Indices: 712277--712459 Score: 217
Period size: 83 Copynumber: 2.2 Consensus size: 82
712267 GTTTATACAA
* * **
712277 AAAACGCCGCTATTTTACCACTCTATTGCGGCGTTTTTTGTATAAACGCCGCTAAATGT-TAAAT
1 AAAACGCCGCTATTGT-CCACTATATTGCGGCGTTTTTACTATAAACGCCGCTAAATGTCT-AAT
712341 ATATTGCGGC-ATTTTAGCT
64 ATATTGCGGCGATTTTA-CT
* * * * *
712360 AAAACGCCGCTACATGTCTATTATATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
1 AAAACGCCGCTA-TTGTCCACTATATTGCGGCGTTTTTACTATAAACGCCGCTAAATGTCTAATA
*
712425 TATTGCGGCGTTTTTACT
65 TATTGCGGCGATTTTACT
712443 ATAAACGCCGCTATTGT
1 A-AAACGCCGCTATTGT
712460 TTAACCTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
83 66 0.78
84 19 0.22
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (82 bp):
AAAACGCCGCTATTGTCCACTATATTGCGGCGTTTTTACTATAAACGCCGCTAAATGTCTAATAT
ATTGCGGCGATTTTACT
Found at i:712479 original size:42 final size:42
Alignment explanation
Indices: 712300--712455 Score: 219
Period size: 42 Copynumber: 3.7 Consensus size: 42
712290 TTTACCACTC
** * *
712300 TATTGCGGCGTTTTTTGTATAAACGCCGCTAAATGT-TAAATA
1 TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCT-ACTA
* *
712342 TATTGCGGC-ATTTTAGCTA-AAACGCCGCTACATGTCTATTA
1 TATTGCGGCGTTTTTA-CTATAAACGCCGCTACATGTCTACTA
712383 TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
1 TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
712425 TATTGCGGCGTTTTTACTATAAACGCCGCTA
1 TATTGCGGCGTTTTTACTATAAACGCCGCTA
712456 TTGTTTAACC
Statistics
Matches: 103, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
41 34 0.33
42 69 0.67
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (42 bp):
TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
Found at i:713369 original size:2 final size:2
Alignment explanation
Indices: 713329--713354 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
713319 TTTTAGTGTG
713329 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
713355 CCTATTGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:715515 original size:41 final size:42
Alignment explanation
Indices: 715402--715520 Score: 125
Period size: 44 Copynumber: 2.8 Consensus size: 42
715392 ACTTGTGGCG
* * * *
715402 TTTA-TAATAAAAACGCCACTAATGTACATCACTATTGTAGCA
1 TTTATTAA-AAAAAAGCCACTAAAGTACATGACTATTGCAGCA
* * * *
715444 TTTATTACAAAAAAATGCTACTAAATTACATGATTATTGCGGCA
1 TTTATTA-AAAAAAA-GCCACTAAAGTACATGACTATTGCAGCA
715488 TTTATT-AAAAAAAGCCACTAAAGTACATGACTA
1 TTTATTAAAAAAAAGCCACTAAAGTACATGACTA
715521 GTACGACGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
41 17 0.27
42 11 0.17
43 7 0.11
44 28 0.44
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (42 bp):
TTTATTAAAAAAAAGCCACTAAAGTACATGACTATTGCAGCA
Found at i:715652 original size:41 final size:41
Alignment explanation
Indices: 715565--715667 Score: 102
Period size: 41 Copynumber: 2.6 Consensus size: 41
715555 AAATCTATAA
* ** *
715565 CGGCGTTTGTTTACAAACACCACGAAAGTCTGAGTCTTTCG
1 CGGCGTTTGTATACAAACACCACGAAAGTAAGAGTATTTCG
* * * * *
715606 TGGCGTTTGTATACAAACGCCACTAACGTAAGAGTATTTTG
1 CGGCGTTTGTATACAAACACCACGAAAGTAAGAGTATTTCG
*
715647 CGGCGTTT-TATA-AAAAACCAC
1 CGGCGTTTGTATACAAACACCAC
715668 TAAAAATGAT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
39 7 0.14
40 4 0.08
41 39 0.78
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
CGGCGTTTGTATACAAACACCACGAAAGTAAGAGTATTTCG
Found at i:717039 original size:16 final size:16
Alignment explanation
Indices: 717012--717055 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
717002 AATATTAATC
*
717012 TTAATAACTATAT-TT
1 TTAATAATTATATATT
717027 TTAAATAATTATATATT
1 TT-AATAATTATATATT
*
717044 TTATTAATTATA
1 TTAATAATTATA
717056 CTTATCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 19 0.76
17 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATAATTATATATT
Found at i:718954 original size:23 final size:23
Alignment explanation
Indices: 718934--718986 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
718924 ATAGGAATGT
*
718934 AAGATTACATGTTAAATGAATAA
1 AAGATTACATGTTAAAGGAATAA
718957 AAGATTACATGTTAAAGGAATAA
1 AAGATTACATGTTAAAGGAATAA
718980 AAGATTA
1 AAGATTA
718987 TTGGAACGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (23 bp):
AAGATTACATGTTAAAGGAATAA
Found at i:721770 original size:6 final size:6
Alignment explanation
Indices: 721759--721797 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
721749 CAATTTAACC
721759 CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCT
1 CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCT
721798 AGCCCTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.51, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTCAT
Found at i:729791 original size:20 final size:21
Alignment explanation
Indices: 729745--729805 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
729735 TCCCCTATGG
729745 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
729768 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
729788 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
729806 TGTACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:745063 original size:21 final size:18
Alignment explanation
Indices: 745025--745063 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
745015 CCAATCAATC
745025 CAAAAAATCTTTGAACTT
1 CAAAAAATCTTTGAACTT
745043 CAAAAATATTCTTTGGAACTT
1 CAAAAA-A-TCTTT-GAACTT
745064 TCCAGTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 1 0.06
20 5 0.28
21 6 0.33
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (18 bp):
CAAAAAATCTTTGAACTT
Found at i:748037 original size:13 final size:13
Alignment explanation
Indices: 748019--748043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
748009 TAAAAAGTTA
748019 GTTGCACTCACAT
1 GTTGCACTCACAT
748032 GTTGCACTCACA
1 GTTGCACTCACA
748044 ACTTGATCCC
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:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (13 bp):
GTTGCACTCACAT
Found at i:750303 original size:18 final size:18
Alignment explanation
Indices: 750272--750306 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
750262 TAAAATTATA
750272 ATTAAGTTTTAATAAATG
1 ATTAAGTTTTAATAAATG
750290 ATTAA-TTTTAAATAAAT
1 ATTAAGTTTT-AATAAAT
750307 TCTTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTAAGTTTTAATAAATG
Found at i:756726 original size:31 final size:32
Alignment explanation
Indices: 756691--756754 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
756681 ATAAAAAAAA
*
756691 TAAAATAATAAATTT-AATTTTTTAACTCATT
1 TAAAATAATAAATTTAAAATTTTTAACTCATT
756722 TAAAATAATAAATTTAAAATTTTTAACTCATT
1 TAAAATAATAAATTTAAAATTTTTAACTCATT
756754 T
1 T
756755 TACACTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAAATAATAAATTTAAAATTTTTAACTCATT
Found at i:758365 original size:17 final size:17
Alignment explanation
Indices: 758343--758378 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
758333 ATTACGCGTA
758343 GAAGAAACTAGAAGGCT
1 GAAGAAACTAGAAGGCT
758360 GAAGAAACTAGAAGGCT
1 GAAGAAACTAGAAGGCT
758377 GA
1 GA
758379 TAAGAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.31, T:0.11
Consensus pattern (17 bp):
GAAGAAACTAGAAGGCT
Found at i:759705 original size:28 final size:28
Alignment explanation
Indices: 759665--759733 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
759655 AGGCAATGAA
759665 AACAGTAAAGGGGGGAGGAATTCATTAC
1 AACAGTAAAGGGGGGAGGAATTCATTAC
759693 AACAGTAAAGGGGGGAGGAATTCATTAC
1 AACAGTAAAGGGGGGAGGAATTCATTAC
*
759721 AACAGAAAAGGGG
1 AACAGTAAAGGGG
759734 ACACTTATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.33, T:0.14
Consensus pattern (28 bp):
AACAGTAAAGGGGGGAGGAATTCATTAC
Found at i:760702 original size:17 final size:17
Alignment explanation
Indices: 760677--760710 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
760667 TTGAATGAAG
760677 AGTGACCACTGATGTTT
1 AGTGACCACTGATGTTT
*
760694 AGTGGCCACTGATGTTT
1 AGTGACCACTGATGTTT
760711 GGTGTCCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (17 bp):
AGTGACCACTGATGTTT
Found at i:760990 original size:18 final size:19
Alignment explanation
Indices: 760963--760999 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
760953 TACAAAACAG
*
760963 TTTCTTATTTGTTT-AAAT
1 TTTCTGATTTGTTTCAAAT
760981 TTTCTGATTTGTTTCAAAT
1 TTTCTGATTTGTTTCAAAT
761000 GTCCAAGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTCTGATTTGTTTCAAAT
Found at i:771872 original size:81 final size:80
Alignment explanation
Indices: 771774--772356 Score: 596
Period size: 82 Copynumber: 7.2 Consensus size: 80
771764 AATCAGATCG
* * *
771774 AGTCTTATTTCTCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATATGTCTACCCGAA
1 AGTCTGATTTCCCTGAATGAATAGTGGAGCAGACACGTCTTCCAAA-TTGATATGTCTACCCGAA
* *
771839 GAAGAGGCACAAATCG
65 AAAGAGGCACAAATCA
* * * * * *
771855 AGTCTTATCTCTCTGAATGAATAGTGGAGCAGAGATGTCTTCCAAAGTTGATATGTCTATCCGAA
1 AGTCTGATTTCCCTGAATGAATAGTGGAGCAGACACGTCTTCCAAA-TTGATATGTCTACCCGAA
* * *
771920 GAAGAGGCACAGATCG
65 AAAGAGGCACAAATCA
* * * * *
771936 AGTCTCATTT-ACTAAATGAATAGTGGAGCAGAGATGTCTTCCAAAGTTGATATGTCTA-CCGAA
1 AGTCTGATTTCCCTGAATGAATAGTGGAGCAGACACGTCTTCCAAA-TTGATATGTCTACCCGAA
* *
771999 AAAGAGGCATATATCA
65 AAAGAGGCACAAATCA
* * * ** * *
772015 AGTCTGATTTCCCCCGAATGAATGGTGGAGCAAACTTGTCTTCCAACATTGATTTGCCTACCCGA
1 AGTCTGATTT-CCCTGAATGAATAGTGGAGCAGACACGTCTTCCAA-ATTGATATGTCTACCCGA
*
772080 AAAAGAGGCATAAATCA
64 AAAAGAGGCACAAATCA
* * * * * * *
772097 AGTTTGATTTCCCCTGAAGGAATGGTGGCGCAGACACATCTTTCAACATTGATTTGTCTACCCGA
1 AGTCTGATTT-CCCTGAATGAATAGTGGAGCAGACACGTCTTCCAA-ATTGATATGTCTACCCGA
772162 AAAAGAGGCACAAATCA
64 AAAAGAGGCACAAATCA
* * * * *
772179 AGTCTGATTTCCCTTGAA-GAAATGGTGGAGTAGACACGTCTTTCAACATTGATTTGTCTACCCA
1 AGTCTGATTTCCC-TGAATG-AATAGTGGAGCAGACACGTCTTCCAA-ATTGATATGTCTACCCG
*
772243 AAAAAGAGGAACAAATCA
63 AAAAAGAGGCACAAATCA
** * *
772261 AGTCTGATTTCCCCTGAATGAATAGTGGAGCAGACACGTCTTTTAAAATTGATCTGTCTACTCGA
1 AGTCTGATTT-CCCTGAATGAATAGTGGAGCAGACACGTC-TTCCAAATTGATATGTCTACCCGA
* *
772326 AGAAGGGGCACAAATCA
64 AAAAGAGGCACAAATCA
*
772343 AGTTTGATTTCCCT
1 AGTCTGATTTCCCT
772357 TGAAGTTGTT
Statistics
Matches: 443, Mismatches: 50, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
79 26 0.06
80 46 0.10
81 130 0.29
82 232 0.52
83 9 0.02
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (80 bp):
AGTCTGATTTCCCTGAATGAATAGTGGAGCAGACACGTCTTCCAAATTGATATGTCTACCCGAAA
AAGAGGCACAAATCA
Found at i:772205 original size:164 final size:164
Alignment explanation
Indices: 771786--772360 Score: 660
Period size: 164 Copynumber: 3.5 Consensus size: 164
771776 TCTTATTTCT
* *
771786 CTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATATGTCTACCCGAAGAAGAGGCACAA
1 CTGAATGAATAGTGGAGCAGACACGTCTTCCAAAGTTGATATGTCTACCCGAAAAAGAGGCACAA
* * * * * * *
771851 ATCGAGTCTTATCTCTC-TGAATGAATAGTGGAGCAGAGATGTCTTCCAA-AGTTGATATGTCTA
66 ATCAAGTCTGATTTCCCTTGAATGAATGGTGGAGCAGACATGTCTTCCAACA-TTGATTTGTCTA
* * * * * *
771914 TCCGAAGAAGAGGCACAGATCGAGTCTCATTT--A
130 CCCGAAAAAGAGGCACAAATCAAGTCTGATTTCCC
* * * * *
771947 CTAAATGAATAGTGGAGCAGAGATGTCTTCCAAAGTTGATATGTCTA-CCGAAAAAGAGGCATAT
1 CTGAATGAATAGTGGAGCAGACACGTCTTCCAAAGTTGATATGTCTACCCGAAAAAGAGGCACAA
** * * *
772011 ATCAAGTCTGATTTCCCCCGAATGAATGGTGGAGCAAACTTGTCTTCCAACATTGATTTGCCTAC
66 ATCAAGTCTGATTTCCCTTGAATGAATGGTGGAGCAGACATGTCTTCCAACATTGATTTGTCTAC
* *
772076 CCGAAAAAGAGGCATAAATCAAGTTTGATTTCCC
131 CCGAAAAAGAGGCACAAATCAAGTCTGATTTCCC
* * * * * *
772110 CTGAAGGAATGGTGGCGCAGACACATCTTTCAACA-TTGATTTGTCTACCCGAAAAAGAGGCACA
1 CTGAATGAATAGTGGAGCAGACACGTCTTCCAA-AGTTGATATGTCTACCCGAAAAAGAGGCACA
* * *
772174 AATCAAGTCTGATTTCCCTTGAA-GAAATGGTGGAGTAGACACGTCTTTCAACATTGATTTGTCT
65 AATCAAGTCTGATTTCCCTTGAATG-AATGGTGGAGCAGACATGTCTTCCAACATTGATTTGTCT
* *
772238 ACCCAAAAAAGAGGAACAAATCAAGTCTGATTTCCC
129 ACCCGAAAAAGAGGCACAAATCAAGTCTGATTTCCC
** * * * * *
772274 CTGAATGAATAGTGGAGCAGACACGTCTTTTAAAATTGATCTGTCTACTCGAAGAAGGGGCACAA
1 CTGAATGAATAGTGGAGCAGACACGTCTTCCAAAGTTGATATGTCTACCCGAAAAAGAGGCACAA
*
772339 ATCAAGTTTGATTTCCCTTGAA
66 ATCAAGTCTGATTTCCCTTGAA
772361 GTTGTTTTAG
Statistics
Matches: 349, Mismatches: 57, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
160 27 0.08
161 107 0.31
162 1 0.00
163 38 0.11
164 176 0.50
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (164 bp):
CTGAATGAATAGTGGAGCAGACACGTCTTCCAAAGTTGATATGTCTACCCGAAAAAGAGGCACAA
ATCAAGTCTGATTTCCCTTGAATGAATGGTGGAGCAGACATGTCTTCCAACATTGATTTGTCTAC
CCGAAAAAGAGGCACAAATCAAGTCTGATTTCCC
Found at i:775305 original size:14 final size:14
Alignment explanation
Indices: 775257--775307 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
775247 TTTTATTATT
775257 TATTATTATAATAA
1 TATTATTATAATAA
* *
775271 CATTATTCTAATAA
1 TATTATTATAATAA
* *
775285 GTA-TATTTTAATTA
1 -TATTATTATAATAA
775299 TATTATTAT
1 TATTATTAT
775308 TTGAGAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 2 0.07
14 26 0.90
15 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (14 bp):
TATTATTATAATAA
Found at i:775678 original size:38 final size:38
Alignment explanation
Indices: 775619--775697 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
775609 TTATACTGAA
* *
775619 GATCGAACGGAAACCTATTTAGATACAGGAATAAGAGG
1 GATCGAACGGAAACATATTTAGATACAGGAACAAGAGG
* *
775657 GATCGAACGGAAATATTTTTAGATACAGGAACAAGAGG
1 GATCGAACGGAAACATATTTAGATACAGGAACAAGAGG
775695 GAT
1 GAT
775698 TTGGGAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.20
Consensus pattern (38 bp):
GATCGAACGGAAACATATTTAGATACAGGAACAAGAGG
Found at i:786689 original size:2 final size:2
Alignment explanation
Indices: 786678--786753 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
786668 TAAAGGGGTT
786678 TA TA -A 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
786719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
786754 GCAATAAAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:789671 original size:37 final size:37
Alignment explanation
Indices: 789629--789735 Score: 196
Period size: 37 Copynumber: 2.9 Consensus size: 37
789619 CCTTCGGGCC
789629 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
* *
789666 ATCTTAAGCTTTCACGGAATAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
789703 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
789736 GCCATCAGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
Found at i:789878 original size:36 final size:36
Alignment explanation
Indices: 789827--789895 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
789817 AGGCGATTTA
*
789827 TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATC
1 TAAGCCTTCACGGAAGAGTAGTGAAGAAAATCAATC
* *
789863 TAAGCCTTTATGGAAGAGTAGTGAAGAAAATCA
1 TAAGCCTTCACGGAAGAGTAGTGAAGAAAATCA
789896 GATCGAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACGGAAGAGTAGTGAAGAAAATCAATC
Found at i:789885 original size:193 final size:193
Alignment explanation
Indices: 789543--789895 Score: 541
Period size: 193 Copynumber: 1.8 Consensus size: 193
789533 TGTCCTTCGG
* * * * *
789543 GCCATCAAGAAGTCTTCCTAGCATGATGATTAAATCCTTCGGGTCATCTTTCAGGCTTCTGAGTA
1 GCCATCAAGAAGTCTTCCGAGCATGATGATTAAATCCTTCGGGTCATATGTCAAGCTTCTGAGCA
*
789608 AGATGATAAGTCCTTCGGGCCATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAA
66 AGATGATAAGTCCTTCAGGCCATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAA
* *
789673 GCTTTCACGGAATAGTAGTGAAGCAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
131 GCTTTCACGGAAGAGTAGTGAAGAAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
*
789736 GCCATC-AGTAAGTCTTCCGAGCATGATGATTAAATCCTTCGGGTCATATGTCAAGCTTTTGAGC
1 GCCATCAAG-AAGTCTTCCGAGCATGATGATTAAATCCTTCGGGTCATATGTCAAGCTTCTGAGC
* * *
789800 AAGATTATAAGTCCTTCAGGCGATTTATAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATC-T
65 AAGATGATAAGTCCTTCAGGCCATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTT
*
789864 AAGCCTTT-ATGGAAGAGTAGTGAAGAAAATCA
129 AAG-CTTTCACGGAAGAGTAGTGAAGAAAATCA
789896 GATCGAGTTT
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
192 2 0.01
193 102 0.71
194 40 0.28
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (193 bp):
GCCATCAAGAAGTCTTCCGAGCATGATGATTAAATCCTTCGGGTCATATGTCAAGCTTCTGAGCA
AGATGATAAGTCCTTCAGGCCATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCAATCTTAA
GCTTTCACGGAAGAGTAGTGAAGAAAATCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
Found at i:789982 original size:81 final size:81
Alignment explanation
Indices: 789894--790487 Score: 466
Period size: 81 Copynumber: 7.3 Consensus size: 81
789884 TGAAGAAAAT
* * *
789894 CAGATCGAGTTTTATTTCTCTGAATGAATAGTGGAGCAGAGACATCTTCCAAAGTTGATTTGTCT
1 CAGATCAAGTTTTATTTCCCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATTTGTCT
*
789959 ACCAGAAGAAGAGGCA
66 ACCAGAAAAAGAGGCA
* * * * * * *
789975 CAGATCGAGTTTTATCTCCCTAAATGAATAATGGAACAGAGACATCTTCCAAAGTTGATCTGTCT
1 CAGATCAAGTTTTATTTCCCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATTTGTCT
* * *
790040 TCCTGAAGAAGAGGCA
66 ACCAGAAAAAGAGGCA
* * * * *
790056 CATG-TCGAGTCTTATCTCCCAGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATATGTC
1 CA-GATCAAGTTTTATTTCCCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATTTGTC
* *
790120 TACCCA-AAGAAGATGCA
65 TA-CCAGAAAAAGAGGCA
* * * * *
790137 CATATCAAGTCTTATCTCCCTGAATGAATAGTGGAGCAAAGACGTCTTCCAAAGTTGATATGTCT
1 CAGATCAAGTTTTATTTCCCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATTTGTCT
* * *
790202 ACCCGAAAAAAAGGAA
66 ACCAGAAAAAGAGGCA
* * * * * *
790218 CAAATCAAGTTTGATTTCCCTCGAATGAATGGTAGAGTAGACACGTCTTCCAACA-TTGATTTGT
1 CAGATCAAGTTTTATTTCCCT-GAATGAATAGTGGAGCAGAGACGTCTTCCAA-AGTTGATTTGT
*
790282 CTACCCA-ATAAAGAGGCA
64 CTA-CCAGAAAAAGAGGCA
* * * * * * * * * **
790300 CAAAGCAA-TTCTAGTTTCCTCTGAAGGAATGGTGGAACAGACACATATTTTAACA-TTGATTTG
1 CAGATCAAGTTTTA-TTTCC-CTGAATGAATAGTGGAGCAGAGACGTCTTCCAA-AGTTGATTTG
* *
790363 TTTACCCA-AAAAAGAGGGA
63 TCTA-CCAGAAAAAGAGGCA
* * * * * * * *
790382 CAGATCAAGTCTGATTTCTCATGAATTAATGGTGGAACAGACACGTCTTTCAAA-TTGATTTGTC
1 CAGATCAAGTTTTATTTC-CCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATTTGTC
* *
790446 TACCCGAAAAAGAGACA
65 TACCAGAAAAAGAGGCA
* ** *
790463 TATTTCAAGTTTGATTTCCCCTGAA
1 CAGATCAAGTTTTATTT-CCCTGAA
790488 GTTGTAGCAG
Statistics
Matches: 425, Mismatches: 75, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
80 4 0.01
81 266 0.63
82 147 0.35
83 8 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (81 bp):
CAGATCAAGTTTTATTTCCCTGAATGAATAGTGGAGCAGAGACGTCTTCCAAAGTTGATTTGTCT
ACCAGAAAAAGAGGCA
Found at i:794251 original size:2 final size:2
Alignment explanation
Indices: 794244--794272 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
794234 TCAGATCGGA
794244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
794273 CCAGTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:797104 original size:12 final size:13
Alignment explanation
Indices: 797075--797109 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
797065 TAAGATTTTC
*
797075 TTTTTGAAAATAA
1 TTTTTGAAAACAA
797088 TTTTTGAAAACAA
1 TTTTTGAAAACAA
797101 -TTTTGAAAA
1 TTTTTGAAAA
797110 ATTACTCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAACAA
Found at i:797399 original size:23 final size:22
Alignment explanation
Indices: 797366--797431 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
797356 TGTTCAAATT
797366 AAACAT-T-CAAACCATTCAAAC
1 AAACATATCCAAA-CATTCAAAC
* *
797387 AAACATATCCAAAAATCCAAAAC
1 AAACATATCCAAACATTC-AAAC
* *
797410 ACACAAATCCAAAACATTCAAA
1 AAACATATCC-AAACATTCAAA
797432 ATGTTTTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 6 0.17
22 4 0.11
23 19 0.54
24 6 0.17
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACATATCCAAACATTCAAAC
Found at i:798917 original size:18 final size:20
Alignment explanation
Indices: 798875--798919 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
798865 ATGTAGTTTT
798875 CAAAACAACATAATTAAATA
1 CAAAACAACATAATTAAATA
* *
798895 AAAAACAACA-ATTTAAA-A
1 CAAAACAACATAATTAAATA
798913 CAAAACA
1 CAAAACA
798920 TTTTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (20 bp):
CAAAACAACATAATTAAATA
Found at i:799390 original size:21 final size:21
Alignment explanation
Indices: 799341--799391 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
799331 TACACCCGTG
*
799341 AGGGGTATCGATACACATTCA
1 AGGGGTATCGATACACATGCA
* *
799362 AGGTGTATCGATACATA-GCA
1 AGGGGTATCGATACACATGCA
799382 AGGGGGTATC
1 A-GGGGTATC
799392 TAGGTATCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (21 bp):
AGGGGTATCGATACACATGCA
Found at i:810594 original size:19 final size:20
Alignment explanation
Indices: 810570--810621 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
810560 CGGCCAAGAG
*
810570 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
810589 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
810610 CATGTATTTTCA
1 CATGTATTTTCA
810622 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:811023 original size:11 final size:11
Alignment explanation
Indices: 811007--811037 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
810997 TCTTCACTTC
811007 CATCACCATTT
1 CATCACCATTT
811018 CATCACCATTT
1 CATCACCATTT
811029 CATCACCAT
1 CATCACCAT
811038 AAATCCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:814794 original size:20 final size:19
Alignment explanation
Indices: 814756--814792 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
814746 TGACCAAGAG
*
814756 CATGTATTTTCATTAAAAT
1 CATGTAATTTCATTAAAAT
*
814775 CATGTAATTTCTTTAAAA
1 CATGTAATTTCATTAAAA
814793 ATTAATATAT
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:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (19 bp):
CATGTAATTTCATTAAAAT
Found at i:816088 original size:36 final size:36
Alignment explanation
Indices: 816048--816121 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
816038 GTGGCATGTA
816048 TACACTTTTCAATTCAAAACAGACTCAGTTTAGGCC
1 TACACTTTTCAATTCAAAACAGACTCAGTTTAGGCC
816084 TACACTTTTCAATTCAAAACAGACTCAGTTTAGGCC
1 TACACTTTTCAATTCAAAACAGACTCAGTTTAGGCC
816120 TA
1 TA
816122 GAATCGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (36 bp):
TACACTTTTCAATTCAAAACAGACTCAGTTTAGGCC
Found at i:818361 original size:2 final size:2
Alignment explanation
Indices: 818354--818407 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
818344 ATTCCAGCAT
818354 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
818396 TA TA TA TA TA TA
1 TA TA TA TA TA TA
818408 CCTTCACATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:819493 original size:29 final size:30
Alignment explanation
Indices: 819421--819507 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 30
819411 TGGATTGCAT
* * *
819421 AACTTTT-AAAA-TTACACATTAGTCCCTA
1 AACTTTTCAAAATTTACACTTTGGTCACTA
* * *
819449 AACTTTTCAAAGTTTATACTTTGGTTACTA
1 AACTTTTCAAAATTTACACTTTGGTCACTA
*
819479 AAC-TTTCAAAATTTACATTTTGGTCACTA
1 AACTTTTCAAAATTTACACTTTGGTCACTA
819508 GAAAAAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 7 0.15
29 25 0.53
30 15 0.32
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (30 bp):
AACTTTTCAAAATTTACACTTTGGTCACTA
Found at i:820991 original size:33 final size:32
Alignment explanation
Indices: 820899--820991 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 32
820889 ACTTTTCTAA
*
820899 CTTACTAGCATTCTAACTTTTATTTTTATTGTT
1 CTTACTAACATTCTAACTTTTA-TTTTATTGTT
820932 CTTACTAACATTCTAACTTTTATTTTATTGTT
1 CTTACTAACATTCTAACTTTTATTTTATTGTT
820964 CTTACTAAC-TTACTAACATTTTATTTTA
1 CTTACTAACATT-CTAAC-TTTTATTTTA
820992 ATGCACAAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
31 2 0.04
32 24 0.42
33 31 0.54
ACGTcount: A:0.26, C:0.16, G:0.03, T:0.55
Consensus pattern (32 bp):
CTTACTAACATTCTAACTTTTATTTTATTGTT
Found at i:822058 original size:24 final size:24
Alignment explanation
Indices: 822031--822078 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
822021 ATAGAAAACG
822031 ATGTGATTTTTCTTATAAAAATAA
1 ATGTGATTTTTCTTATAAAAATAA
822055 ATGTGATTTTTCTTATAAAAATAA
1 ATGTGATTTTTCTTATAAAAATAA
822079 TTATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (24 bp):
ATGTGATTTTTCTTATAAAAATAA
Found at i:822087 original size:24 final size:24
Alignment explanation
Indices: 822036--822090 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
822026 AAACGATGTG
* *
822036 ATTTTTCTTATAAAAATAAATGTG
1 ATTTTTCTTATAAAAATAAATATA
*
822060 ATTTTTCTTATAAAAATAATTATA
1 ATTTTTCTTATAAAAATAAATATA
822084 ATTTTTC
1 ATTTTTC
822091 GGGTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (24 bp):
ATTTTTCTTATAAAAATAAATATA
Found at i:831280 original size:2 final size:2
Alignment explanation
Indices: 831273--831306 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
831263 AATAAAAATG
831273 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
831307 GAAACAGAAA
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:831454 original size:15 final size:17
Alignment explanation
Indices: 831420--831458 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
831410 ATAAATACAG
*
831420 AAACAAAAGATGGAAAA
1 AAACAAAAGAAGGAAAA
831437 AAACAAAA-AAGG-AAA
1 AAACAAAAGAAGGAAAA
831452 AAACAAA
1 AAACAAA
831459 CAAACAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.03
Consensus pattern (17 bp):
AAACAAAAGAAGGAAAA
Found at i:832227 original size:13 final size:13
Alignment explanation
Indices: 832209--832233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
832199 TCTTTGTTGT
832209 GTATTTTTTGTGA
1 GTATTTTTTGTGA
832222 GTATTTTTTGTG
1 GTATTTTTTGTG
832234 GGTTTCTGGT
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:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (13 bp):
GTATTTTTTGTGA
Found at i:832838 original size:15 final size:16
Alignment explanation
Indices: 832820--832856 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
832810 ATATATATAT
832820 TATAAATATGTAAT-A
1 TATAAATATGTAATGA
*
832835 TAT-AATGTGTAATGA
1 TATAAATATGTAATGA
832850 TATAAAT
1 TATAAAT
832857 CACATAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 9 0.47
15 7 0.37
16 3 0.16
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (16 bp):
TATAAATATGTAATGA
Found at i:834555 original size:6 final size:6
Alignment explanation
Indices: 834544--834591 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
834534 ACACACCTTA
834544 TTTTCT TTTTCT TTTTCT TTTTCAATT TTTTCT TTTTC- TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTC---T TTTTCT TTTTCT TTTTCT TTTT
834592 TCAATTTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
9 6 0.16
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:834574 original size:27 final size:27
Alignment explanation
Indices: 834544--834598 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
834534 ACACACCTTA
834544 TTTTCTTTTTCTTTT-TCTTTTTCAATT
1 TTTTCTTTTTCTTTTCT-TTTTTCAATT
834571 TTTTCTTTTTCTTTTCTTTTTTCAATT
1 TTTTCTTTTTCTTTTCTTTTTTCAATT
834598 T
1 T
834599 AGGGCACCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTCTTTTTCTTTTCTTTTTTCAATT
Found at i:834654 original size:14 final size:15
Alignment explanation
Indices: 834630--834658 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
834620 ACCCTAAACG
834630 TTTTTTCTCTTTTTC
1 TTTTTTCTCTTTTTC
834645 TTTTTT-TCTTTTTC
1 TTTTTTCTCTTTTTC
834659 GACTTAGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTCTTTTTC
Found at i:834684 original size:65 final size:62
Alignment explanation
Indices: 834569--834691 Score: 140
Period size: 65 Copynumber: 1.9 Consensus size: 62
834559 TCTTTTTCAA
* * *
834569 TTTTTTCTTTTTCTTTTCTTTTTTCAATTTAGGGCACCCTTTCGGGTTTTCACCCTAAACGT
1 TTTTTTCTTTTTCTTTTCTTTTTTCAACTTAGGACACCCTTTCGGATTTTCACCCTAAACGT
* * * *
834631 TTTTTCTCTTTTTCTTTTTTTCTTTTTCGACTTAGGACTCCCTCTT-GGATTTTCATCCTAA
1 TTTTT-TCTTTTTC-TTTTCT-TTTTTCAACTTAGGACACCCT-TTCGGATTTTCACCCTAA
834692 GCGAAGTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
62 5 0.10
63 8 0.16
64 5 0.10
65 30 0.60
66 2 0.04
ACGTcount: A:0.12, C:0.23, G:0.10, T:0.55
Consensus pattern (62 bp):
TTTTTTCTTTTTCTTTTCTTTTTTCAACTTAGGACACCCTTTCGGATTTTCACCCTAAACGT
Found at i:836754 original size:22 final size:22
Alignment explanation
Indices: 836707--836751 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
836697 TATGTGATAT
*
836707 ATGAACATAAGAGATTAAGTGA
1 ATGAACATAAGAGATTAAATGA
836729 ATGAACAT-AGATGATATAAATGA
1 ATGAACATAAGA-GAT-TAAATGA
836752 TGATATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 11 0.55
23 6 0.30
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.24
Consensus pattern (22 bp):
ATGAACATAAGAGATTAAATGA
Found at i:836783 original size:14 final size:13
Alignment explanation
Indices: 836739--836795 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
836729 ATGAACATAG
836739 ATGATAT-A-AAT
1 ATGATATGAGAAT
*
836750 GATGATATTAGAAT
1 -ATGATATGAGAAT
*
836764 AAGATATGAGTAAT
1 ATGATATGAG-AAT
836778 ATGATATGAGATAT
1 ATGATATGAGA-AT
836792 ATGA
1 ATGA
836796 GAAATATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.18
13 10 0.26
14 21 0.55
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (13 bp):
ATGATATGAGAAT
Found at i:836826 original size:2 final size:2
Alignment explanation
Indices: 836814--836856 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
836804 TGTGAACAAG
836814 AT AT GAT 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
836857 GTTTATGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:838140 original size:78 final size:78
Alignment explanation
Indices: 837999--838151 Score: 229
Period size: 78 Copynumber: 2.0 Consensus size: 78
837989 TGAATTTAAA
* * *
837999 TTTTATTCATTCTCTTAAAGGAAAAATGTTTGAAAAGTCAATGTGACACATCGGACTCGTATCCT
1 TTTTATTCATTCTATTAAAGGAAAAATGTTTGAAAAGTCAATGTGACACATCAGACTCATATCC-
838064 GG-TCGGGTACATG
65 GGATCGGGTACATG
* *
838077 TTTTATTCATTTTATTAAAGGAAAAATGTTTGAAAAGTCAATGTGACACCTCAGACAT-ATATCC
1 TTTTATTCATTCTATTAAAGGAAAAATGTTTGAAAAGTCAATGTGACACATCAGAC-TCATATCC
838141 GGATCGGGTAC
65 GGATCGGGTAC
838152 GGGTTGGGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
77 2 0.03
78 65 0.96
79 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (78 bp):
TTTTATTCATTCTATTAAAGGAAAAATGTTTGAAAAGTCAATGTGACACATCAGACTCATATCCG
GATCGGGTACATG
Found at i:841106 original size:2 final size:2
Alignment explanation
Indices: 841101--841131 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
841091 TATGTGAACA
841101 AT AT AT GAT 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
841132 GTTTATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:841290 original size:31 final size:31
Alignment explanation
Indices: 841247--841329 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
841237 CGATGGTTAC
* *
841247 CTATGTCCTTCGGGACATATGGACAGTTTAA
1 CTATGTCATTCGGGACATATGGACAATTTAA
*
841278 CTATGTCATTCGGGACATATGGACAATTTAC
1 CTATGTCATTCGGGACATATGGACAATTTAA
* * *
841309 CTATGTCTTTAGAGACATATG
1 CTATGTCATTCGGGACATATG
841330 AATAGTGGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
CTATGTCATTCGGGACATATGGACAATTTAA
Found at i:842410 original size:78 final size:78
Alignment explanation
Indices: 842281--842435 Score: 258
Period size: 78 Copynumber: 2.0 Consensus size: 78
842271 TGAATTTGAC
*
842281 TTTTATTCATTATGTGAAAGGGAAAATGTTTGAAAAGTCAATGTGACACCTC-GAACTCGTATCC
1 TTTTATTCATTATGTGAAAGGAAAAATGTTTGAAAAGTCAATGTGACACCTCAG-ACTCGTATCC
842345 GGGTCGGGTACGGA
65 GGGTCGGGTACGGA
* *
842359 TTTTATTCATTCTGTTAAAGGAAAAATGTTTGAAAAGTCAATGTGACACCTCAGACTCGTATCCG
1 TTTTATTCATTATGTGAAAGGAAAAATGTTTGAAAAGTCAATGTGACACCTCAGACTCGTATCCG
*
842424 GGTTGGGTACGG
66 GGTCGGGTACGG
842436 GTTAGGGGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 71 0.99
79 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (78 bp):
TTTTATTCATTATGTGAAAGGAAAAATGTTTGAAAAGTCAATGTGACACCTCAGACTCGTATCCG
GGTCGGGTACGGA
Found at i:846267 original size:78 final size:79
Alignment explanation
Indices: 846138--846294 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 79
846128 TTATTATGGT
846138 AACAATAGTGGTTACCATCTCTATTCCTTGATGTATTCGAATGTGGTGCGAGAAGCCATGCTTTC
1 AACAATAGTGGTTACCATCTCTATTCCTTGATGTATTCGAATGTGGTGCGAGAAGCCATGCTTTC
846203 ACTA-TTGGCTCCA
66 ACTATTTGGCTCCA
846216 AACAATAGTGGTTACCATCTCTATTCCTTGATGTATTCGAATGTGGTGCGAGAAGCCATGCTTTC
1 AACAATAGTGGTTACCATCTCTATTCCTTGATGTATTCGAATGTGGTGCGAGAAGCCATGCTTTC
846281 ACTATTTGGCTCCA
66 ACTATTTGGCTCCA
846295 TACCCAAGCT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 69 0.88
79 9 0.12
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (79 bp):
AACAATAGTGGTTACCATCTCTATTCCTTGATGTATTCGAATGTGGTGCGAGAAGCCATGCTTTC
ACTATTTGGCTCCA
Found at i:847977 original size:21 final size:20
Alignment explanation
Indices: 847951--847991 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
847941 ATGAATGTAA
847951 AAACATGGAAAATAGAAAAAT
1 AAACATGGAAAA-AGAAAAAT
*
847972 AAACATGGAAAAATAAAAAT
1 AAACATGGAAAAAGAAAAAT
847992 GCAAAGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (20 bp):
AAACATGGAAAAAGAAAAAT
Found at i:851414 original size:23 final size:22
Alignment explanation
Indices: 851358--851430 Score: 53
Period size: 23 Copynumber: 3.2 Consensus size: 22
851348 AAAGAGAAAG
851358 AAAATATATAATAAAAGAATAAAA
1 AAAAT-TA-AATAAAAGAATAAAA
*
851382 AATAACTAAATAAAA-AATTAAATA
1 AA-AATTAAATAAAAGAA-TAAA-A
*
851406 AAAATTAAA-AGAA-AATAAAA
1 AAAATTAAATAAAAGAATAAAA
*
851426 GAAAT
1 AAAAT
851431 AAAAAATAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 5 0.12
21 4 0.10
22 7 0.17
23 17 0.40
24 7 0.17
25 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (22 bp):
AAAATTAAATAAAAGAATAAAA
Found at i:851481 original size:2 final size:2
Alignment explanation
Indices: 851474--851503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
851464 TAATAAAAGG
851474 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
851504 GAAACAGAAC
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:851543 original size:13 final size:15
Alignment explanation
Indices: 851527--851555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
851517 AAGAAAAAAG
851527 AAAA-AAAAATATAA
1 AAAATAAAAATATAA
851541 AAAATAAAAATATAA
1 AAAATAAAAATATAA
851556 GAATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAAAATATAA
Found at i:851563 original size:2 final size:2
Alignment explanation
Indices: 851558--851584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
851548 AAATATAAGA
851558 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
851585 ATGTTAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:851651 original size:2 final size:2
Alignment explanation
Indices: 851644--851669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
851634 AAATAAATAA
851644 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
851670 TAGATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:854589 original size:23 final size:23
Alignment explanation
Indices: 854562--854615 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
854552 AAAAAACAGA
* *
854562 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
854585 AAAGAAAAATCTAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
854609 -AAGAAAA
1 AAAGAAAA
854616 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.13, G:0.17, T:0.09
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:859183 original size:17 final size:17
Alignment explanation
Indices: 859141--859183 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
859131 CATGCTTGCT
*
859141 AGCTAGCTCCACACTCA
1 AGCTAGCTTCACACTCA
859158 AGCTAGCTTCACACTCA
1 AGCTAGCTTCACACTCA
*
859175 AGTTAGCTT
1 AGCTAGCTT
859184 GGAATGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.26
Consensus pattern (17 bp):
AGCTAGCTTCACACTCA
Found at i:860160 original size:23 final size:23
Alignment explanation
Indices: 860132--860185 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
860122 AAAAATCAGA
* *
860132 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
860155 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
860179 -AAGAAAA
1 AAAGAAAA
860186 AATAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:862974 original size:11 final size:13
Alignment explanation
Indices: 862944--862976 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
862934 GCCAAAGATA
862944 AAAAGGTATGTTG
1 AAAAGGTATGTTG
862957 AAAAGGTATG-TG
1 AAAAGGTATGTTG
862969 -AAAGGTAT
1 AAAAGGTAT
862977 TTAGTATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 2 0.10
13 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
AAAAGGTATGTTG
Found at i:864725 original size:17 final size:17
Alignment explanation
Indices: 864683--864725 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
864673 CATGCTTGCT
*
864683 AGCTAGCTCCACACTCA
1 AGCTAGCTTCACACTCA
*
864700 AGCTAGCTTCACAGTCA
1 AGCTAGCTTCACACTCA
*
864717 AGTTAGCTT
1 AGCTAGCTT
864726 GGAAGGAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (17 bp):
AGCTAGCTTCACACTCA
Found at i:865736 original size:2 final size:2
Alignment explanation
Indices: 865711--865794 Score: 129
Period size: 2 Copynumber: 43.0 Consensus size: 2
865701 AGAAACATAA
*
865711 AT AT A- AT AT AT A- ACT AT AC A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
865751 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
865793 AT
1 AT
865795 GTGTAATGAT
Statistics
Matches: 77, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
1 3 0.04
2 73 0.95
3 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:866065 original size:13 final size:13
Alignment explanation
Indices: 866047--866071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
866037 TCCAATTCCG
866047 TTTACTTGCTCCA
1 TTTACTTGCTCCA
866060 TTTACTTGCTCC
1 TTTACTTGCTCC
866072 CACTTGCCAC
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:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTACTTGCTCCA
Found at i:866551 original size:15 final size:15
Alignment explanation
Indices: 866531--866563 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
866521 TTGAAATATA
866531 ATTTTTATCTAAAAT
1 ATTTTTATCTAAAAT
*
866546 ATTTTTATTTAAAAT
1 ATTTTTATCTAAAAT
866561 ATT
1 ATT
866564 AAAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTATCTAAAAT
Found at i:874413 original size:132 final size:131
Alignment explanation
Indices: 874013--875027 Score: 715
Period size: 132 Copynumber: 7.7 Consensus size: 131
874003 AGGGAGGTTA
* * * ** * **** * *
874013 AATCGAGGTTGACTTGCTTCATTGCTCCTCAGGGAAGATCAAAT-TTGCTAAAAGGGATATGCTT
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAAAAAAAAGGGATCTGCTC
** * * * * *
874077 TGTTGCGTTCTGAGGTGGATCAGATCTTGAGACTTTGATTCACTTCACTACTCTTCAGGGAATAT
66 TACTGCGTTCAG-GGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGAT
874142 TG
130 TG
* * * * * * *
874144 AATCAAGGTAGGTTTGCTCCACTATTCTTCAGCGAAGATCAAATAT-AGAAAAATGGATATGCTC
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAAAAAAAAGGGATCTGCTC
* ** * * * * * * * *
874208 TGCTGTTTTTCAGGGAATATCAGATCTGGA-AATGTTGATTAATTTCATTGTTC-TCTAAGGAAG
66 TACTG-CGTTCAGGGTAGATCAGATCTGGAGACT-TTGATTCACTTCACTGCTCTTC-AGGGAAG
*
874271 CTTG
128 ATTG
* * * ** * *
874275 AGTCAAGGTAGATTTACTTCACTGCTCTTCAGGGAAGATCAAATCTAAAAAAAAGGGATCTTCTC
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAAAAAAAAGGGATCTGCTC
* * * * *
874340 TGCTGCGCTTCAGGGTAAATCAGATCTGGAGACTTTGATTCACTTCACTGTTATTCAGTGAAGAT
66 TACTGCG-TTCAGGGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGAT
874405 TG
130 TG
* * ** * *
874407 GATCAAGGTTGATTTACTTCACTATTCTTCAGGGAAGAGAAAATATGAAAAAAAA-GGATATGTT
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATAT-AAAAAAAAGGGATCTGCT
* * * *
874471 CCT-TTGCGTTCTAGGGTAGGTCAGATCTGGAGACTTTGATTCACTTTACTGCTCTTCAAGGAAG
65 -CTACTGCGTTC-AGGGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAG
874535 ATTG
128 ATTG
*** * * * ** *
874539 AATTGGGGTTGATTTGCTTCACTGTTCTTCAGGGAA-AGTCAAATATGAGGAAAATA-TAATTTG
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGA-TCAAATAT-A-AAAAAAAGGGATCTG
* * * * * * * * *
874602 CTCCACTACGTCCCAGGGTAGGTTAGATGTGGAGACTTTGATTCACTTCACTTCTATTAAGGGAA
63 CTCTACTGCGT-TCAGGGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAA
* *
874667 AATTT
127 GATTG
* * * * * * *
874672 AATCAAGGTTGATTTGTTTCACTATTATTCAAGGAAGA-CTATTCT-TAAAAAAGGGATCTGCTC
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAAAAAAAAGGGATCTGCT-
* * *
874735 CT-CTACGTTCCAAGGTAGGTCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGA
65 CTACTGCGTT-CAGGGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGA
874799 TTG
129 TTG
** * * * * * ** ** *
874802 AATCGGGGTTGATTTGTTTCATTGTTCTTCAGGGAAGATTAAATATGAGGAAAATAGATATGCTC
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAAAAAAAAGGGATCTGCTC
* * * * * *
874867 CACTACGTTCCAGTGTAGATCAGATATAGAGACTTTGATTCACTTCACTGCTCTTCCGGGAAGAT
66 TACTGCGTT-CAGGGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGAT
874932 TG
130 TG
** * * * * * * *
874934 AATCTGGGTTGATTTGCTTCATTATTCTTCAAGGAAGACCAAATCTAAGAAAATA--TATCTACT
1 AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAA-AAAAAAGGGATCTGCT
* *
874997 CCACTGCGTTCCAGGGTAAATCAGATCTGGA
65 CTACTGCGTT-CAGGGTAGATCAGATCTGGA
875028 AAGTTTGTAT
Statistics
Matches: 692, Mismatches: 169, Indels: 46
0.76 0.19 0.05
Matches are distributed among these distances:
129 5 0.01
130 97 0.14
131 164 0.24
132 317 0.46
133 107 0.15
134 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (131 bp):
AATCAAGGTTGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATAAAAAAAAGGGATCTGCTC
TACTGCGTTCAGGGTAGATCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATT
G
Found at i:874802 original size:263 final size:263
Alignment explanation
Indices: 874094--874977 Score: 832
Period size: 263 Copynumber: 3.4 Consensus size: 263
874084 TTCTGAGGTG
* * * * * * *
874094 GATCAGATCTTGAGACTTTGATTCACTTCACTACTCTTCAGGGAATATTGAATCAAGGTAGGTTT
1 GATCAGATATGGAGACTTTGATTCACTTCACTTCTATTCAGGGAAGATTGAATCAAGGTTGATTT
* * * *** * *
874159 GCTCCACTATTCTTC-AGCGAAGATCAAATAT-AGAAAAATGGATATGCT-CTGCTGTTTTTCAG
66 GCTTCACTATTCTTCAAG-GAAGA-CAAATATGAAAAAAAAGGATATGCTCCT-CTACGTTCCAA
* ** * * * * * * * **
874221 GGAATATCAGATCTGGA-AATGTTGATTAATTTCATTGTTC-TCTAAGGAAGCTTGAGTCAAGGT
128 GGTAGGTCAGATCTGGAGACT-TTGATTCACTTCACTGCTCTTC-AAGGAAGATTGAATCGGGGT
* * * * * ** *** * * ** *
874284 AGATTTACTTCACTGCTCTTCAGGGAAGATCAAATCTAAAAAAAAGGGATCTTCTCTGCTGCG-C
191 TGATTTGCTTCACTGTTCTTCAGGGAAGATCAAATATGAGGAAAATAAATATGCTCCACTACGTC
*
874348 TTCAGGGTA
256 -CCAGGGTA
* * * *
874357 AATCAGATCTGGAGACTTTGATTCACTTCACTGT-TATTCAGTGAAGATTGGATCAAGGTTGATT
1 GATCAGATATGGAGACTTTGATTCACTTCACT-TCTATTCAGGGAAGATTGAATCAAGGTTGATT
* * * * * * * *
874421 TACTTCACTATTCTTCAGGGAAGAGAAAATATGAAAAAAAAGGATATGTTCCTTTGCGTTCTAGG
65 TGCTTCACTATTCTTCAAGGAAGA-CAAATATGAAAAAAAAGGATATGCTCCTCTACGTTCCAAG
* *
874486 GTAGGTCAGATCTGGAGACTTTGATTCACTTTACTGCTCTTCAAGGAAGATTGAATTGGGGTTGA
129 GTAGGTCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGTTGA
*
874551 TTTGCTTCACTGTTCTTCAGGGAA-AGTCAAATATGAGGAAAATATAATTTGCTCCACTACGTCC
194 TTTGCTTCACTGTTCTTCAGGGAAGA-TCAAATATGAGGAAAATA-AATATGCTCCACTACGTCC
874615 CAGGGTA
257 CAGGGTA
* * * * * *
874622 GGTTAGATGTGGAGACTTTGATTCACTTCACTTCTATTAAGGGAAAATTTAATCAAGGTTGATTT
1 GATCAGATATGGAGACTTTGATTCACTTCACTTCTATTCAGGGAAGATTGAATCAAGGTTGATTT
* * * * * * * *
874687 GTTTCACTATTATTCAAGGAAGACTATTCT-TAAAAAAGGGATCTGCTCCTCTACGTTCCAAGGT
66 GCTTCACTATTCTTCAAGGAAGACAAATATGAAAAAAAAGGATATGCTCCTCTACGTTCCAAGGT
*
874751 AGGTCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGGGTTGATT
131 AGGTCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGTTGATT
* * * * * *
874816 TGTTTCATTGTTCTTCAGGGAAGATTAAATATGAGGAAAATAGATATGCTCCACTACGTTCCAGT
196 TGCTTCACTGTTCTTCAGGGAAGATCAAATATGAGGAAAATAAATATGCTCCACTACGTCCCAGG
874881 GTA
261 GTA
* * * * **
874884 GATCAGATATAGAGACTTTGATTCACTTCACTGCTCTTCCGGGAAGATTGAATCTGGGTTGATTT
1 GATCAGATATGGAGACTTTGATTCACTTCACTTCTATTCAGGGAAGATTGAATCAAGGTTGATTT
*
874949 GCTTCATTATTCTTCAAGGAAGACCAAAT
66 GCTTCACTATTCTTCAAGGAAGA-CAAAT
874978 CTAAGAAAAT
Statistics
Matches: 505, Mismatches: 104, Indels: 24
0.80 0.16 0.04
Matches are distributed among these distances:
262 95 0.19
263 208 0.41
264 105 0.21
265 96 0.19
266 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (263 bp):
GATCAGATATGGAGACTTTGATTCACTTCACTTCTATTCAGGGAAGATTGAATCAAGGTTGATTT
GCTTCACTATTCTTCAAGGAAGACAAATATGAAAAAAAAGGATATGCTCCTCTACGTTCCAAGGT
AGGTCAGATCTGGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGTTGATT
TGCTTCACTGTTCTTCAGGGAAGATCAAATATGAGGAAAATAAATATGCTCCACTACGTCCCAGG
GTA
Found at i:876225 original size:32 final size:32
Alignment explanation
Indices: 876189--876251 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
876179 TATCTTTCCA
876189 TTTTTTCTTTTT-TTCATTTCTTTTTTT-TCTTG
1 TTTTTTCTTTTTGTT--TTTCTTTTTTTATCTTG
876221 TTTTTTCTTTTTGTTTTTCTTTTTTTATCTT
1 TTTTTTCTTTTTGTTTTTCTTTTTTTATCTT
876252 CAGGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 11 0.38
32 16 0.55
33 2 0.07
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (32 bp):
TTTTTTCTTTTTGTTTTTCTTTTTTTATCTTG
Found at i:876227 original size:19 final size:19
Alignment explanation
Indices: 876205--876245 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
876195 CTTTTTTTCA
*
876205 TTTCTTTTT-TTTCTTGTTT
1 TTTCTTTTTGTTT-TTCTTT
876224 TTTCTTTTTGTTTTTCTTT
1 TTTCTTTTTGTTTTTCTTT
876243 TTT
1 TTT
876246 TATCTTCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (19 bp):
TTTCTTTTTGTTTTTCTTT
Found at i:876244 original size:13 final size:12
Alignment explanation
Indices: 876189--876245 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
876179 TATCTTTCCA
*
876189 TTTTTTCTTTTT
1 TTTTTTGTTTTT
* *
876201 TTCATTTCTTTTT
1 TT-TTTTGTTTTT
*
876214 TTTCTTGTTTTT
1 TTTTTTGTTTTT
876226 TCTTTTTGTTTTT
1 T-TTTTTGTTTTT
876239 CTTTTTT
1 -TTTTTT
876246 TATCTTCAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
12 10 0.27
13 26 0.70
14 1 0.03
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.84
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:876251 original size:22 final size:22
Alignment explanation
Indices: 876170--876252 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 22
876160 CTTGAACCTC
**
876170 TCTTTTATTTATCTTTCCATTTTT
1 TCTTTT-TTTATC-TTCTTTTTTT
876194 TCTTTTTTTCAT-TTCTTTTTTT
1 TCTTTTTTT-ATCTTCTTTTTTT
876216 TCTTGTTTTT-TCTT-TTTGTTTT
1 TCTT-TTTTTATCTTCTTT-TTTT
876238 TCTTTTTTTATCTTC
1 TCTTTTTTTATCTTC
876253 AGGTAAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
21 9 0.18
22 26 0.51
23 8 0.16
24 8 0.16
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.77
Consensus pattern (22 bp):
TCTTTTTTTATCTTCTTTTTTT
Found at i:886347 original size:2 final size:2
Alignment explanation
Indices: 886342--886396 Score: 71
Period size: 2 Copynumber: 28.5 Consensus size: 2
886332 AATACAATTA
*
886342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
886383 -T AT ACT AT AT -T AT A
1 AT AT A-T AT AT AT AT A
886397 CTTAATATGC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:886783 original size:28 final size:29
Alignment explanation
Indices: 886752--886823 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 29
886742 TACAAAAGTA
886752 AAATAATATAATAATG-TA-TACT-TGAAAT
1 AAATAATATAAT-ATGCTATTACTAT-AAAT
*
886780 AAAT-ATATGATATGCTATTACTATAAAT
1 AAATAATATAATATGCTATTACTATAAAT
886808 AAAT-ATATATATATGC
1 AAATAATATA-ATATGC
886824 ATTCTTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.08
27 8 0.21
28 20 0.53
29 7 0.18
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.38
Consensus pattern (29 bp):
AAATAATATAATATGCTATTACTATAAAT
Found at i:890327 original size:26 final size:26
Alignment explanation
Indices: 890296--890359 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
890286 CAAATATATA
*
890296 TATATATATAATATTTTTTATTAAATTT
1 TATAAATAT-ATATTTTTTATT-AATTT
*
890324 TATAAATATGTATTTTTTATTAATTT
1 TATAAATATATATTTTTTATTAATTT
890350 TATAAATATA
1 TATAAATATA
890360 AATATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 14 0.42
27 11 0.33
28 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TATAAATATATATTTTTTATTAATTT
Found at i:890345 original size:27 final size:26
Alignment explanation
Indices: 890307--890358 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
890297 ATATATATAA
890307 TATTTTTTATTAAATTTTATAAATATG
1 TATTTTTTATT-AATTTTATAAATATG
890334 TATTTTTTATTAATTTTATAAATAT
1 TATTTTTTATTAATTTTATAAATAT
890359 AAATATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTTTTATTAATTTTATAAATATG
Found at i:897736 original size:2 final size:2
Alignment explanation
Indices: 897731--897755 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
897721 GATATATATA
897731 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
897756 TTATCGTATG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:902643 original size:2 final size:2
Alignment explanation
Indices: 902636--902682 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
902626 TTTAAGGTTA
*
902636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
902678 AT AT A
1 AT AT A
902683 ATAATAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:902698 original size:3 final size:3
Alignment explanation
Indices: 902692--902744 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
902682 AATAATAATA
*
902692 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
*
902738 ACT ATT A
1 ATT ATT A
902745 ACGTATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:902885 original size:29 final size:29
Alignment explanation
Indices: 902853--902918 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
902843 TTTTTCTCTT
902853 TGTTTT-TATTTATTTATTTATTTAGTATA
1 TGTTTTATATTTATTTATTTATTT-GTATA
* * *
902882 TGTTTTATTTTTATTTCTTTGTTTGTATA
1 TGTTTTATATTTATTTATTTATTTGTATA
*
902911 TATTTTAT
1 TGTTTTAT
902919 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (29 bp):
TGTTTTATATTTATTTATTTATTTGTATA
Found at i:902919 original size:29 final size:30
Alignment explanation
Indices: 902861--902967 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
902851 TTTGTTTTTA
*
902861 TTTATTTATTTATTTAGTATATGTTTTATT
1 TTTATTTATTTATTTAGTATATATTTTATT
* *
902891 TTTATTTCTTTGTTT-GTATATATTTTATT
1 TTTATTTATTTATTTAGTATATATTTTATT
* * * * * ** *
902920 ATATATATATATATATATTACCTTTTTTATAT
1 -TTTATTTATTTATTTAGTATATATTTTAT-T
902952 TTTATTTATTTATTTA
1 TTTATTTATTTATTTA
902968 TTTTTTCCTT
Statistics
Matches: 57, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
29 13 0.23
30 22 0.39
31 21 0.37
32 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (30 bp):
TTTATTTATTTATTTAGTATATATTTTATT
Found at i:903134 original size:19 final size:21
Alignment explanation
Indices: 903110--903157 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
903100 TATTTTGATC
903110 TTCTTTATTTC-TT-ATTATT
1 TTCTTTATTTCATTCATTATT
*
903129 TTCTTTA-TTCATTCATTTTT
1 TTCTTTATTTCATTCATTATT
903149 TTCTTTATT
1 TTCTTTATT
903158 ATTTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 9 0.36
20 12 0.48
21 1 0.04
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTTTATTTCATTCATTATT
Found at i:903165 original size:19 final size:19
Alignment explanation
Indices: 903110--903166 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
903100 TATTTTGATC
*
903110 TTCTTTATT-TCTTATTATT
1 TTCTTTATTAT-TTATTTTT
*
903129 TTCTTTATTCATTCATTTTT
1 TTCTTTATT-ATTTATTTTT
903149 TTCTTTATTATTTATTTT
1 TTCTTTATTATTTATTTT
903167 CCTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 17 0.52
20 15 0.45
21 1 0.03
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (19 bp):
TTCTTTATTATTTATTTTT
Found at i:906846 original size:95 final size:94
Alignment explanation
Indices: 906691--906877 Score: 286
Period size: 95 Copynumber: 2.0 Consensus size: 94
906681 TTATAATATT
* **
906691 TTATATATTCAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACACCCTGGCTTTATGG
1 TTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACACCCAAGCTTTATGG
* *
906756 ATAATATTCAGCTACCCTGATAAAGGTTA
66 ATAAGATTCAGCTAACCTGATAAAGGTTA
* *
906785 TTATACTATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCAAGCTTTAT
1 TTATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GAAATTGGTTAAACACCCAAGCTTTAT
906849 GGATAAGATTCAGCTAACCTGATAAAGGT
64 GGATAAGATTCAGCTAACCTGATAAAGGT
906878 GTTTACATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
94 6 0.07
95 78 0.93
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
TTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGAAATTGGTTAAACACCCAAGCTTTATGG
ATAAGATTCAGCTAACCTGATAAAGGTTA
Found at i:907860 original size:41 final size:41
Alignment explanation
Indices: 907747--907848 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
907737 TAGGCCATCA
*
907747 ACGATTTCAACTCCATGATGAGGATATCGTACCCACGAATCC
1 ACGATTTCAACTCCACGATGAGGATATCGTACCCAC-AATCC
* *
907789 ATGATTTCAACTCCACGATGGAGGATATCGTACCCA-TATCC
1 ACGATTTCAACTCCACGAT-GAGGATATCGTACCCACAATCC
*
907830 ACGATTTCAACTTCACGAT
1 ACGATTTCAACTCCACGAT
907849 AAAAGATATC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 21 0.39
42 17 0.31
43 16 0.30
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (41 bp):
ACGATTTCAACTCCACGATGAGGATATCGTACCCACAATCC
Found at i:908156 original size:124 final size:124
Alignment explanation
Indices: 908005--908284 Score: 384
Period size: 124 Copynumber: 2.3 Consensus size: 124
907995 AATACAAGCA
** *
908005 TGGATTTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAAC
1 TGGATTTCAACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAAC
* * * * ** *
908070 CACGGTTTCAACTTCACGA-AGGAGGGAATCGTGCTCACCAGCAGCATTTATCATC-ATAT
66 CACGGTTTCAACTTCACGACA-AAGGGAATCGTCCACACAAGCAGCATCAATC-TCTAGAT
* * * * *
908129 TGGATTTCAACTTCATGACAAAGGATATCCAATTCAAGGCTCAACTTCACGACGGAGGGGCCATC
1 TGGATTTCAACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAAC
908194 CACGGTTTCAACTTCACGACAAAGGGAATCGTCCACACAAGCAGCATCAATCTCTAGAT
66 CACGGTTTCAACTTCACGACAAAGGGAATCGTCCACACAAGCAGCATCAATCTCTAGAT
*
908253 TGGATTTCAACTTCACGACAAAAGATATCCAA
1 TGGATTTCAACTTCACGACAAAGGATATCCAA
908285 CTCGAAGAAG
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
123 2 0.01
124 134 0.98
125 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (124 bp):
TGGATTTCAACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCAAC
CACGGTTTCAACTTCACGACAAAGGGAATCGTCCACACAAGCAGCATCAATCTCTAGAT
Found at i:908676 original size:37 final size:36
Alignment explanation
Indices: 908635--908727 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
908625 ACAAGGGCTC
*
908635 GTCTCGCTTGAGACTAATTT-ACTCAAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTTCACTCAAAACAAA-TTTT
* * **
908672 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCACTCAAAACAAATTTT
*
908708 GTCTCTCTTGAGACAGTTTC
1 GTCTCTCTTGAGACAATTTC
908728 CCTTGAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 28 0.56
37 22 0.44
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
GTCTCTCTTGAGACAATTTCACTCAAAACAAATTTT
Found at i:908715 original size:36 final size:37
Alignment explanation
Indices: 908660--908739 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 37
908650 AATTTACTCA
908660 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
908697 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
908733 AAACAAA
1 AAACAAA
908740 ATCTTTGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.84
37 7 0.16
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:908822 original size:37 final size:36
Alignment explanation
Indices: 908759--908874 Score: 137
Period size: 36 Copynumber: 3.2 Consensus size: 36
908749 TATGTTTTCC
* *
908759 TTGAAA-AAATTTCGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
* * *
908794 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
*
908831 TTGAAACAAATTTTGTCT-TCCTTAAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCT-CTTGAGACAGTTTCTT
*
908867 CTGAAACA
1 TTGAAACA
908875 TAAACTTTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 6 0.09
36 31 0.46
37 31 0.46
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:911233 original size:12 final size:14
Alignment explanation
Indices: 911216--911253 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
911206 ACTTTGTTTG
911216 TATATAT-TTTAT-
1 TATATATATTTATA
*
911228 TATATATATATATA
1 TATATATATTTATA
911242 TATATATATTTA
1 TATATATATTTA
911254 CCTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATATATTTATA
Found at i:911273 original size:21 final size:20
Alignment explanation
Indices: 911248--911300 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
911238 TATATATATA
911248 TATTTACCTTTTTTTATATTT
1 TATTTACCTTTTTTTAT-TTT
*
911269 TATTTA-TTTATTTTTATTTT
1 TATTTACCTT-TTTTTATTTT
911289 TATTT-CCTTTTT
1 TATTTACCTTTTT
911301 ACTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 13 0.46
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTTACCTTTTTTTATTTT
Found at i:911418 original size:28 final size:24
Alignment explanation
Indices: 911387--911445 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
911377 TGTTTAGAGG
911387 TTTTCTATGCATATATTTTTATTATTAT
1 TTTTCT-T-CATATA-TTTTATT-TTAT
*
911415 TTTTCTTCATTTATTTTATTTTAT
1 TTTTCTTCATATATTTTATTTTAT
*
911439 TTATCTT
1 TTTTCTT
911446 ATTCATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.34
25 7 0.24
26 5 0.17
27 1 0.03
28 6 0.21
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTCTTCATATATTTTATTTTAT
Found at i:911502 original size:19 final size:20
Alignment explanation
Indices: 911404--911525 Score: 78
Period size: 19 Copynumber: 6.1 Consensus size: 20
911394 TGCATATATT
*
911404 TTTATT-ATTATTTTTCTTCA
1 TTTATTCATTA-TTTTCTTTA
*
911424 TTTATT--TTATTTTATTTA
1 TTTATTCATTATTTTCTTTA
*
911442 TCTTATTCATTTTTTTATCTCTGT-
1 T-TTATTCA-TTATTT-TCT-T-TA
*
911466 TTTATT--TTGATCTTCTTTA
1 TTTATTCATT-ATTTTCTTTA
*
911485 TTTCTT-ATTATTTTCTTTA
1 TTTATTCATTATTTTCTTTA
*
911504 TTTATTCATTTTTTTCTTTA
1 TTTATTCATTATTTTCTTTA
911524 TT
1 TT
911526 ATTTATTTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
18 9 0.11
19 28 0.35
20 27 0.33
21 2 0.02
22 5 0.06
23 7 0.09
24 2 0.02
25 1 0.01
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTCATTATTTTCTTTA
Found at i:911523 original size:16 final size:15
Alignment explanation
Indices: 911485--911535 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
911475 ATCTTCTTTA
911485 TTTC-TTATTATTTT
1 TTTCTTTATTATTTT
*
911499 CTTTATTTATTCATTTT
1 -TTTCTTTATT-ATTTT
911516 TTTCTTTATTATTTAT
1 TTTCTTTATTATTT-T
911532 TTTC
1 TTTC
911536 CTTTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.23
16 19 0.61
17 5 0.16
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCTTTATTATTTT
Found at i:911546 original size:61 final size:62
Alignment explanation
Indices: 911417--911535 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 62
911407 ATTATTATTT
* * * *
911417 TTCTTCATTTATT-TTATTTTATTTATCTTATTCATTTTTTTATCTCTGTTTTATTTTGATC
1 TTCTTTATTTCTTATTATTTTATTTATCTTATTCATTTTTTTATCTATGTTTTATTTTCATC
* * *
911478 TTCTTTATTTCTTATTATTTTCTTTAT-TTATTCATTTTTTTCTTTAT-TATTTATTTTC
1 TTCTTTATTTCTTATTATTTTATTTATCTTATTCATTTTTTTATCTATGT-TTTATTTTC
911536 CTTTTTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
60 1 0.02
61 36 0.73
62 12 0.24
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (62 bp):
TTCTTTATTTCTTATTATTTTATTTATCTTATTCATTTTTTTATCTATGTTTTATTTTCATC
Found at i:912572 original size:3 final size:3
Alignment explanation
Indices: 912566--912601 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
912556 ATAATAATAA
*
912566 TAT TAT TAT TAT TAT TAT AAAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
912602 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 28 0.93
4 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:912591 original size:16 final size:17
Alignment explanation
Indices: 912570--912604 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
912560 TAATAATATT
912570 ATTATTATTATTA-TAA
1 ATTATTATTATTATTAA
912586 ATTATTATTATTATTAA
1 ATTATTATTATTATTAA
912603 AT
1 AT
912605 AAAAAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTATTATTATTAA
Found at i:912591 original size:19 final size:20
Alignment explanation
Indices: 912562--912605 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
912552 AATAATAATA
912562 ATAATATTATTATTATTATT
1 ATAATATTATTATTATTATT
912582 ATAA-ATTATTATTATTATT
1 ATAATATTATTATTATTATT
912601 A-AATA
1 ATAATA
912606 AAAAATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATATTATTATTATTATT
Found at i:912873 original size:22 final size:22
Alignment explanation
Indices: 912848--912891 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
912838 GCAGCCCACG
* *
912848 ACCATCCCTATGGTGAGTCACC
1 ACCATACCTATGGTGACTCACC
*
912870 ACCATAGCTATGGTGACTCACC
1 ACCATACCTATGGTGACTCACC
912892 TAGGCAACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (22 bp):
ACCATACCTATGGTGACTCACC
Found at i:913953 original size:15 final size:15
Alignment explanation
Indices: 913897--913961 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
913887 TATTATTTTG
913897 TTATTACTTTTATATT-
1 TTATTA-TTTT-TATTA
*
913913 TTAATTATTTCTT-TAA
1 TT-ATTATTT-TTATTA
913929 TTATTA-TTTTATTA
1 TTATTATTTTTATTA
*
913943 TTATTATTTTTATTG
1 TTATTATTTTTATTA
913958 TTAT
1 TTAT
913962 CTTAGTCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.05
14 10 0.24
15 16 0.39
16 8 0.20
17 5 0.12
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTATTTTTATTA
Found at i:913956 original size:12 final size:12
Alignment explanation
Indices: 913909--913947 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
913899 ATTACTTTTA
913909 TATTTTAATTAT
1 TATTTTAATTAT
913921 T-TCTTTAATTAT
1 TAT-TTTAATTAT
913933 TATTTT-ATTAT
1 TATTTTAATTAT
913944 TATT
1 TATT
913948 ATTTTTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 14 0.56
13 1 0.04
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:915490 original size:46 final size:49
Alignment explanation
Indices: 915416--915506 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
915406 TTTTCTTTTC
* *
915416 TTTTTCCTTAATAAACGCATGCGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCTAAATAAACGCATGCGAACTAGAAAGCATG-AGGTTAGGTTAA
915465 TTTTTCC-AAATAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCTAAATAAACGCATGCGAACTAGAAAGCATGAGGTTAGG
915507 ATTTATACCT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 1 0.03
46 20 0.51
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (49 bp):
TTTTTCCTAAATAAACGCATGCGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:919568 original size:11 final size:11
Alignment explanation
Indices: 919546--919577 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
919536 ATTATACTTG
919546 AAGAAGAAAAAA
1 AAGAA-AAAAAA
919558 AAGAAAAAAAA
1 AAGAAAAAAAA
919569 AAGAAAAAA
1 AAGAAAAAA
919578 TGAATCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:928198 original size:23 final size:23
Alignment explanation
Indices: 928180--928240 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
928170 CTCGTATAAA
*
928180 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
* *
928203 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
928226 TGCACCAAAGTGCCA
1 TGCACCAAAGTGCCA
928241 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:934077 original size:2 final size:2
Alignment explanation
Indices: 934070--934126 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
934060 TTATTTTAAA
934070 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
934112 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
934127 CACCCACATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:934275 original size:12 final size:12
Alignment explanation
Indices: 934260--934319 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
934250 AAGAAATCAA
934260 AACAGAATTCAG
1 AACAGAATTCAG
934272 AACAG-ATATCAG
1 AACAGAAT-TCAG
* *
934284 AACAAAATCCAG
1 AACAGAATTCAG
** *
934296 ATTAGAAATCAG
1 AACAGAATTCAG
934308 AACAGAATTCAG
1 AACAGAATTCAG
934320 GTCATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:934282 original size:24 final size:24
Alignment explanation
Indices: 934255--934342 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
934245 GATATAAGAA
*
934255 ATCAAAACAGAATTCAGAACAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * * *
934279 ATCAGAACAAAATCCAGATTAGAA
1 ATCAAAACAGAATTCAGATCAGAT
* *
934303 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAAAACAGAATTCAGATCA-GAT
934327 ATCAAAACAGAATTCA
1 ATCAAAACAGAATTCA
934343 AGTCAGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 50 0.98
25 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:934351 original size:48 final size:48
Alignment explanation
Indices: 934251--934356 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
934241 CGGAGATATA
* * * *
934251 AGAAATCAAAACAGAATTCAGAACAGATATCAGAACAAAATCCAGATT
1 AGAAATCAGAACAGAATTCAGAACAGATATCAAAACAAAATCAAGATC
** *
934299 AGAAATCAGAACAGAATTCAGGTCATG-TATCAAAACAGAATTCAAG-TC
1 AGAAATCAGAACAGAATTCAGAACA-GATATCAAAACA-AAATCAAGATC
934347 AGAAATCAGA
1 AGAAATCAGA
934357 TAAAATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
48 42 0.86
49 7 0.14
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGAACAGATATCAAAACAAAATCAAGATC
Found at i:934354 original size:24 final size:25
Alignment explanation
Indices: 934251--934354 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 25
934241 CGGAGATATA
*
934251 AGAAATCAAAACAGAATTC-AGAAC
1 AGAAATCAAAACAGAATTCAAGATC
* * * * *
934275 AGATATCAGAACA-AAATCCAGATT
1 AGAAATCAAAACAGAATTCAAGATC
* *
934299 AGAAATCAGAACAGAATTC-AGGTC
1 AGAAATCAAAACAGAATTCAAGATC
*
934323 ATG-TATCAAAACAGAATTCAAG-TC
1 A-GAAATCAAAACAGAATTCAAGATC
934347 AGAAATCA
1 AGAAATCA
934355 GATAAAATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
23 5 0.08
24 51 0.81
25 7 0.11
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.18
Consensus pattern (25 bp):
AGAAATCAAAACAGAATTCAAGATC
Found at i:936144 original size:36 final size:36
Alignment explanation
Indices: 936104--936176 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
936094 GATAAATTAT
*
936104 AATCTACATATCCATGGTTAATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTAATTCTTTTATCACTTA
* *
936140 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTAATTCTTTTATCACTTA
936176 A
1 A
936177 TTCCATAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTAATTCTTTTATCACTTA
Found at i:937491 original size:24 final size:24
Alignment explanation
Indices: 937459--937530 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
937449 AAATGGTCAA
937459 ATCATGAGTTTAGCCATTGAACTT
1 ATCATGAGTTTAGCCATTGAACTT
937483 ATCATGAGTTTAGCCATTGAACTT
1 ATCATGAGTTTAGCCATTGAACTT
937507 ATCATGAGTTTAGCCATTGAACTT
1 ATCATGAGTTTAGCCATTGAACTT
937531 CCTACATTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
ATCATGAGTTTAGCCATTGAACTT
Done.