Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 90 of 259
Found at i:29417428 original size:40 final size:40
Alignment explanation
Indices: 29417373--29417532 Score: 286
Period size: 40 Copynumber: 4.0 Consensus size: 40
29417363 GGGGTGTTAC
29417373 AACACCAGCACGAATGCTCTTCGAGG-CTTAGCCCGGATAT
1 AACACCAGCACGAATGCTCTTCG-GGACTTAGCCCGGATAT
*
29417413 AACACCAGCACGAATGCTCTTCGAGACTTAGCCCGGATAT
1 AACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
29417453 AACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
1 AACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
*
29417493 AACACCAGCACGAAAGCTCTTCGGGACTTAGCCCGGATAT
1 AACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
29417533 CTAACTCTCA
Statistics
Matches: 116, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 1 0.01
40 115 0.99
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (40 bp):
AACACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
Found at i:29423971 original size:13 final size:13
Alignment explanation
Indices: 29423953--29423978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29423943 CATTATATTA
29423953 TTAAATTCTCATC
1 TTAAATTCTCATC
29423966 TTAAATTCTCATC
1 TTAAATTCTCATC
29423979 AAATTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATTCTCATC
Found at i:29437274 original size:39 final size:39
Alignment explanation
Indices: 29437231--29437358 Score: 184
Period size: 39 Copynumber: 3.3 Consensus size: 39
29437221 AGTTTTTAAC
* *
29437231 CCGGATATTTTTCCAGCATGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
** * * *
29437270 CCGGATATACTTCTAGCATATAGCCTGAGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
29437309 TCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
29437348 CCGGATATTTT
1 CCGGATATTTT
29437359 CAATCTCATA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:29445217 original size:39 final size:39
Alignment explanation
Indices: 29445174--29445301 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
29445164 GGGCTTTAAC
** *
29445174 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * * *
29445213 CCGGATATATTTCTAGCATATAGCTTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
29445252 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
29445291 CCGGATATTTT
1 CCGGATATTTT
29445302 CAATCTCATA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:29448998 original size:33 final size:33
Alignment explanation
Indices: 29448945--29449019 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
29448935 GGCCCTGCCG
* *
29448945 TGGTCTT-TTATTCACATGCCAT-GACTCGGTTA
1 TGGTCTTATTATTCACATGCCATAG-CCCAGTTA
*
29448977 TGGTCTTATTATTCGA-TTGCCATAGCCCAGTTA
1 TGGTCTTATTATTC-ACATGCCATAGCCCAGTTA
29449010 TGGTCTTATT
1 TGGTCTTATT
29449020 CGGCAACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 7 0.19
33 28 0.76
34 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (33 bp):
TGGTCTTATTATTCACATGCCATAGCCCAGTTA
Found at i:29464687 original size:6 final size:6
Alignment explanation
Indices: 29464676--29464700 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29464666 CCATCTATGT
29464676 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
29464701 TGGTTTCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:29465559 original size:20 final size:20
Alignment explanation
Indices: 29465534--29465574 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
29465524 GAATAAAAAA
29465534 TACATATAATGATAATAGAC
1 TACATATAATGATAATAGAC
*
29465554 TACATATGATGATAATAGAC
1 TACATATAATGATAATAGAC
29465574 T
1 T
29465575 TACTCATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (20 bp):
TACATATAATGATAATAGAC
Found at i:29467626 original size:23 final size:24
Alignment explanation
Indices: 29467574--29467635 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
29467564 AATAGGATAA
*
29467574 AATAATTTATTAATTAATAATAGT
1 AATAATTAATTAATTAATAATAGT
*
29467598 AATAATTAATTAATTAA-AATGGT
1 AATAATTAATTAATTAATAATAGT
* *
29467621 AATAATAAAATAATT
1 AATAATTAATTAATT
29467636 GGATCATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (24 bp):
AATAATTAATTAATTAATAATAGT
Found at i:29470547 original size:46 final size:45
Alignment explanation
Indices: 29470480--29470646 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 45
29470470 TGTAACCCGC
* *
29470480 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCAT
* *
29470526 CCATAGGTGAACTCGGACTCAACTCATCGAGTTCGG-ATTC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* * * *
29470572 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCAT
*
29470619 CCATAAGTGAACTCAGACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
29470647 AAGCTCGGAT
Statistics
Matches: 98, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 4 0.04
46 53 0.54
47 28 0.29
48 2 0.02
49 5 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:29470655 original size:93 final size:93
Alignment explanation
Indices: 29470487--29470656 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
29470477 CGCCCATAAG
* * * * *
29470487 CGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
* * *
29470552 TCGAGTTCGGATTCCTAGTTACATTTCA
66 ACAAGCTCGGATTCCTAGTTACATTTCA
29470580 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
29470645 ACAAGCTCGGAT
66 ACAAGCTCGGAT
29470657 GCTCAACCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACAAGCTCGGATTCCTAGTTACATTTCA
Found at i:29488813 original size:47 final size:47
Alignment explanation
Indices: 29488759--29488850 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
29488749 AAGCTCCCGA
*
29488759 TAGCTATGATATCTATAAAACAATTGAAAACACGCGCAAAGTAAGTT
1 TAGCTATGATATCTATAAAACAATTGAAAACACACGCAAAGTAAGTT
* *
29488806 TAGCTATGATATCTATAAAATAATTGAAAACACATGCAAAGTAAG
1 TAGCTATGATATCTATAAAACAATTGAAAACACACGCAAAGTAAG
29488851 CTTTCAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (47 bp):
TAGCTATGATATCTATAAAACAATTGAAAACACACGCAAAGTAAGTT
Found at i:29489260 original size:43 final size:43
Alignment explanation
Indices: 29489199--29489293 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
29489189 AAAGCTTGTA
* * * *
29489199 CAATGCCAATGTCTCAGAT-GTGGTCTTACATGTAATTGAATAT
1 CAATGCCAATCTCCCAGATAG-GGTCTTACATGAAATCGAATAT
* *
29489242 CAATGCCACTCTCCCAGATAGGGTCTTATATGAAATCGAATAT
1 CAATGCCAATCTCCCAGATAGGGTCTTACATGAAATCGAATAT
*
29489285 -GATGCCAAT
1 CAATGCCAAT
29489294 GTCTTAGACA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
42 7 0.16
43 35 0.81
44 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (43 bp):
CAATGCCAATCTCCCAGATAGGGTCTTACATGAAATCGAATAT
Found at i:29492720 original size:6 final size:6
Alignment explanation
Indices: 29492709--29492742 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
29492699 GGAAGCCCTC
29492709 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
29492743 AAGGAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:29493093 original size:50 final size:49
Alignment explanation
Indices: 29492982--29493166 Score: 193
Period size: 49 Copynumber: 3.8 Consensus size: 49
29492972 GAGTTACTGT
* * * *
29492982 GAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCG-TGAAGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATGACG-A
29493029 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-GAAT-ATGCGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCG-ATGA--CGA
* * * *
29493078 GAGCCAATGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATGACGA
* * *
29493127 TAGTCAGTGTAAGACCATGTCTAGGACATGGCATCGGCAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
29493167 TATACCCTAT
Statistics
Matches: 114, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
46 12 0.11
47 14 0.12
48 10 0.09
49 38 0.33
50 38 0.33
51 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (49 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATGACGA
Found at i:29493145 original size:99 final size:96
Alignment explanation
Indices: 29492989--29493166 Score: 277
Period size: 99 Copynumber: 1.8 Consensus size: 96
29492979 TGTGAGCTAG
* *
29492989 TGTAAGACATGTTTGGGACATGCATCGGCCTCGTGAAGTAAGCCAGTGTAAGACCATGTCTGGGA
1 TGTAAGACATGTTTGGGACATGCATCAGCCTCGTGAAGTAAGCCAGTGTAAGACCATGTCTAGGA
29493054 CATGGCATCGGCATGAATATGCGAGAGCCAA
66 CATGGCATCGGCATGAATATGCGAGAGCCAA
* *
29493085 TGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATGACG-ATAGTCAGTGTAAGACCATGTCT
1 TGTAAGA-CATGTTTGGGACAT-GCATCAGCCTCG-TGAAGTA-AGCCAGTGTAAGACCATGTCT
29493149 AGGACATGGCATCGGCAT
62 AGGACATGGCATCGGCAT
29493167 TATACCCTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
96 7 0.09
97 14 0.19
98 12 0.16
99 41 0.55
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (96 bp):
TGTAAGACATGTTTGGGACATGCATCAGCCTCGTGAAGTAAGCCAGTGTAAGACCATGTCTAGGA
CATGGCATCGGCATGAATATGCGAGAGCCAA
Found at i:29493154 original size:49 final size:49
Alignment explanation
Indices: 29492987--29493164 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 49
29492977 ACTGTGAGCT
* *
29492987 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCG-TGAAG-TAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGACGAT-AGCC
* *
29493033 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-GAAT-ATGCGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG-ATGA--CGATAGCC
* * * *
29493083 AATGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATGACGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGACGATAGCC
*
29493132 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
29493165 ATTATACCCT
Statistics
Matches: 109, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
46 9 0.08
47 14 0.13
48 10 0.09
49 36 0.33
50 38 0.35
51 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGACGATAGCC
Found at i:29495803 original size:51 final size:50
Alignment explanation
Indices: 29495680--29495811 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
29495670 GCTATCTGGT
* * * *
29495680 ACGCATAGTAGCCTGTACTTAGTACTACACACGTGACCTCACCATCTAAT
1 ACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCACACCATCGAAG
* * ** **
29495730 ACACATAGTAGCCTGCACTTAGTACTACACACGTGATCACACTTTTCGGGG
1 ACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCACAC-CATCGAAG
29495781 ACGCATAGTAGCCTGCACTTAGTACTACACA
1 ACGCATAGTAGCCTGCACTTAGTACTACACA
29495812 TGCAACCTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
50 38 0.54
51 32 0.46
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (50 bp):
ACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCACACCATCGAAG
Found at i:29499566 original size:50 final size:49
Alignment explanation
Indices: 29499445--29499581 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 49
29499435 AGCCGAAGCT
*
29499445 ATCT-GGTACGCATAGTAGCTGCACTTAGTACTACACACGTGACCTCACC
1 ATCTAGGTACGCATAGTACCTGCACTTAGTACTACACACGTGA-CTCACC
* * *
29499494 ATCTA-ATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TCA-C
1 ATCTAGGTACGCATAGTA-CCTGCACTTAGTACTACACACGTGACTCACC
*
29499541 AGTTTTCAGGTACGCATAGTACCTGCACTTAGTACTACACA
1 A--TCT-AGGTACGCATAGTACCTGCACTTAGTACTACACA
29499582 TGCGACCTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
47 2 0.03
48 3 0.04
49 15 0.20
50 45 0.61
51 9 0.12
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
ATCTAGGTACGCATAGTACCTGCACTTAGTACTACACACGTGACTCACC
Found at i:29501546 original size:51 final size:49
Alignment explanation
Indices: 29501377--29501553 Score: 173
Period size: 50 Copynumber: 3.6 Consensus size: 49
29501367 TCTGGTACGT
* * * *
29501377 ATAGTAGCCTGAACTTAGTACTACACATGTGACCAACAG-TCTGGTACAC
1 ATAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTCAGGTACAC
* * *
29501426 GTAGTTGCCTGCACTTAGTACTACACACGTGACCTCACCA--TCTA-ATACAC
1 ATAGTAGCCTGCACTTAGTACTACACACGTGA--TCA-CAGTTC-AGGTACAC
* * *
29501476 GTAGTAGCCTGCAATTAGTACTACACACGTGATCACAGTTTTCAGGTACGC
1 ATAGTAGCCTGCACTTAGTACTACACACGTGATCACAG--TTCAGGTACAC
29501527 ATAGTAGCCTGCACTTAGTACTACACA
1 ATAGTAGCCTGCACTTAGTACTACACA
29501554 TGCGACCTCA
Statistics
Matches: 106, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
47 2 0.02
48 3 0.03
49 28 0.26
50 39 0.37
51 34 0.32
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
ATAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTCAGGTACAC
Found at i:29501548 original size:101 final size:99
Alignment explanation
Indices: 29501378--29501564 Score: 252
Period size: 101 Copynumber: 1.9 Consensus size: 99
29501368 CTGGTACGTA
* * * *
29501378 TAGTAGCCTGAACTTAGTACTACACATGTGACCAACAGTCTGGTACACGTAGTTGCCTGCACTTA
1 TAGTAGCCTGAACTTAGTACTACACACGTGACCAACAGTCAGGTACACATAGTAGCCTGCACTTA
*
29501443 GTACTACACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* *
29501477 TAGTAGCCTGCAA-TTAGTACTACACACGTGATC-ACAGTTTTCAGGTACGCATAGTAGCCTGCA
1 TAGTAGCCTG-AACTTAGTACTACACACGTGACCAACAG---TCAGGTACACATAGTAGCCTGCA
*
29501540 CTTAGTACTACACATGCGACCTCAC
62 CTTAGTACTACACACGCGACCTCAC
29501565 AATAGATCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
98 4 0.05
99 28 0.37
100 2 0.03
101 42 0.55
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGAACTTAGTACTACACACGTGACCAACAGTCAGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:29505567 original size:13 final size:13
Alignment explanation
Indices: 29505549--29505574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29505539 CTGTGCATTC
29505549 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
29505562 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
29505575 AACAAATACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:29509086 original size:13 final size:13
Alignment explanation
Indices: 29509068--29509092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29509058 AACGAAGTAG
29509068 GACACGGCCGTGC
1 GACACGGCCGTGC
29509081 GACACGGCCGTG
1 GACACGGCCGTG
29509093 TGCACCAACA
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:0.16, C:0.36, G:0.40, T:0.08
Consensus pattern (13 bp):
GACACGGCCGTGC
Found at i:29513979 original size:13 final size:13
Alignment explanation
Indices: 29513961--29513986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29513951 CTGTGCATTC
29513961 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
29513974 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
29513987 AACAAATACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:29518611 original size:43 final size:43
Alignment explanation
Indices: 29518531--29518676 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 43
29518521 AGATATCGTG
* * * *
29518531 TAAGACCGTGTCTGGGACACAGGCCTCG-ATTGAGATTTACGTA
1 TAAGACCATGTCTGGGACACAGGCATCGTATT-TGATTTACATA
** *
29518574 TAAGACCATGTCTGGGACATTGGCATCGTATTTGATTT-CATG
1 TAAGACCATGTCTGGGACACAGGCATCGTATTTGATTTACATA
* * * *
29518616 TAAGACCCTGTCAT-GGACAGAGGTATCAGTA-TTGAATTACATA
1 TAAGACCATGTC-TGGGACACAGGCATC-GTATTTGATTTACATA
*
29518659 TAAGACCACGTCTGGGAC
1 TAAGACCATGTCTGGGAC
29518677 GTCGACATTG
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
42 30 0.36
43 50 0.60
44 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACACAGGCATCGTATTTGATTTACATA
Found at i:29529495 original size:19 final size:18
Alignment explanation
Indices: 29529471--29529563 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
29529461 AATAAATTAC
29529471 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATT-AGT
29529490 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAA-TTAGT
** * *
29529509 TGC-T-GGAATAAATTA-T
1 T-CATCTTAGTTAATTAGT
*
29529525 TCATGTTAGTTAATTAGGT
1 TCATCTTAGTTAATTA-GT
29529544 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAA-TTAGT
29529563 T
1 T
29529564 GCTAGAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.02
16 3 0.05
17 10 0.17
18 4 0.07
19 34 0.59
20 6 0.10
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (18 bp):
TCATCTTAGTTAATTAGT
Found at i:29529522 original size:54 final size:54
Alignment explanation
Indices: 29529445--29529573 Score: 206
Period size: 54 Copynumber: 2.4 Consensus size: 54
29529435 CTTAGTTTAA
*
29529445 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATT-GAGTTCATCTTAG
1 TTAATTTAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAG-GTTCATCTTAG
* *
29529499 TTAATTTAGTTGCTGGAATAAATTATTCATGTTAGTTAATTAGGTTCATCTTAG
1 TTAATTTAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAGGTTCATCTTAG
*
29529553 TTAATTTAGTTGCTAGAATAA
1 TTAATTTAGTTGCTGGAATAA
29529574 TTTAATGATG
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 69 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.44
Consensus pattern (54 bp):
TTAATTTAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAGGTTCATCTTAG
Found at i:29529653 original size:10 final size:9
Alignment explanation
Indices: 29529620--29529660 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
29529610 TTTATTTAAG
29529620 TTAA-GTGT
1 TTAATGTGT
29529628 TTAATGTGT
1 TTAATGTGT
*
29529637 TTTATGTGT
1 TTAATGTGT
29529646 TTAAATGTGT
1 TT-AATGTGT
29529656 TTAAT
1 TTAAT
29529661 TTCAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 17 0.59
10 8 0.28
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (9 bp):
TTAATGTGT
Found at i:29539030 original size:46 final size:46
Alignment explanation
Indices: 29538980--29539155 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
29538970 TGGTTGAGCA
*
29538980 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
29539026 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
29539073 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
29539119 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29539156 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 61 0.56
47 28 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:29539136 original size:93 final size:93
Alignment explanation
Indices: 29538977--29539148 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
29538967 GGATGGTTGA
* *
29538977 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
29539042 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
29539070 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGTCC-GAACTCGTTGAG
29539134 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
29539149 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29546595 original size:46 final size:46
Alignment explanation
Indices: 29546545--29546720 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
29546535 TGGTTGAGCA
29546545 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29546591 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
29546636 CATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
29546684 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29546721 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 60 0.55
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29546701 original size:93 final size:93
Alignment explanation
Indices: 29546542--29546713 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
29546532 GGATGGTTGA
*
29546542 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
29546607 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
29546635 GCATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
29546699 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
29546714 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29552814 original size:49 final size:48
Alignment explanation
Indices: 29552747--29552963 Score: 185
Period size: 49 Copynumber: 4.6 Consensus size: 48
29552737 ATATCTAAGT
* *
29552747 CGATGCCATGTCCAAGACAGGTCTTACACTGACTTTCATATATCGAGGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-TTTCATATATCGAGGC
* * * * * *
29552796 CTATGGCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCG-GTGT
1 CGATGCCATGTCCCAGACAGGTCTTACACT-GATTTCATATATCGAG-GC
* * * * * *
29552845 CGATGCCCTGCCCCAGACAGGTCTTATACTGA---CACATGTC-AAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGATTTCATATATCGAGGC
* * *
29552889 CGATGCCATGTCCCAGATAGGTCTTACACTAGATTTTATATCTCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACT-GATTTCATATATCGAGGC
* *
29552938 CAATG-CATGTCCCAGACATGTCTTAC
1 CGATGCCATGTCCCAGACAGGTCTTAC
29552964 GCTAGCTCTC
Statistics
Matches: 132, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
44 27 0.20
45 7 0.05
48 26 0.20
49 71 0.54
50 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGATTTCATATATCGAGGC
Found at i:29553049 original size:94 final size:95
Alignment explanation
Indices: 29552891--29553063 Score: 242
Period size: 94 Copynumber: 1.8 Consensus size: 95
29552881 TGTCAAGCCG
* * * *
29552891 ATGCCATGTCCCAGATAGGTCTTACACTAGATTTTATATCTCGAGGCCAATGCATGTCCCAGACA
1 ATGCCATGTCACAGATAGGTCTTACACTAGATCTCATATATCGAGGCCAATGCATGTCCCAGACA
*
29552956 TGTCTTACGCTAGCTCTCGTCTTAATGCTA
66 TGTCTTACACTAGCTCTCGTCTTAATGCTA
* * * *
29552986 ATGCCATGTCACAGATATGGTCTTACACTGGCTCTCATA-AT-GTGGCCGATGCATGTCCCAGAC
1 ATGCCATGTCACAGATA-GGTCTTACACTAGATCTCATATATCGAGGCCAATGCATGTCCCAGAC
29553049 ATGTCTTACACTAGC
65 ATGTCTTACACTAGC
29553064 ACAGATCCAT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
94 34 0.50
95 17 0.25
96 17 0.25
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (95 bp):
ATGCCATGTCACAGATAGGTCTTACACTAGATCTCATATATCGAGGCCAATGCATGTCCCAGACA
TGTCTTACACTAGCTCTCGTCTTAATGCTA
Found at i:29553755 original size:20 final size:18
Alignment explanation
Indices: 29553718--29553760 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
29553708 CTATAGCAAC
29553718 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
29553735 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
29553755 TTACAA
1 TCACAA
29553761 ACTTTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 4 0.18
20 9 0.41
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:29555368 original size:8 final size:8
Alignment explanation
Indices: 29555353--29555391 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
29555343 GTATGTATGA
29555353 TATTATTT
1 TATTATTT
*
29555361 TGTTATTT
1 TATTATTT
*
29555369 TGTTATTT
1 TATTATTT
*
29555377 TATCATTT
1 TATTATTT
29555385 TATTATT
1 TATTATT
29555392 ATGGATAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (8 bp):
TATTATTT
Found at i:29555814 original size:17 final size:17
Alignment explanation
Indices: 29555792--29555825 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29555782 ATGCTTTGGG
29555792 GTAAATTTTGTAATTTT
1 GTAAATTTTGTAATTTT
*
29555809 GTAAATTTTTTAATTTT
1 GTAAATTTTGTAATTTT
29555826 TTATGATGGA
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:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
GTAAATTTTGTAATTTT
Found at i:29559643 original size:39 final size:39
Alignment explanation
Indices: 29559588--29559811 Score: 367
Period size: 39 Copynumber: 5.7 Consensus size: 39
29559578 TGTGTGAGAT
*
29559588 TTATATCTGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
*
29559627 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGATA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
* *
29559666 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
* *
29559705 TTATATTCGAGCTAAGTCCCGAAGGCATTCGTGCTGATA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
*
29559744 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
* *
29559783 TTATATCCGAGCTAAGTTCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
29559812 TGGGTTGGAA
Statistics
Matches: 173, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 173 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
Found at i:29560566 original size:1 final size:1
Alignment explanation
Indices: 29560560--29560597 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
29560550 GCTTGTTAAG
29560560 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29560598 ATATTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29566127 original size:15 final size:15
Alignment explanation
Indices: 29566107--29566137 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29566097 AAGTTTGTTA
29566107 AATTGGGCATTCGGC
1 AATTGGGCATTCGGC
29566122 AATTGGGCATTCGGC
1 AATTGGGCATTCGGC
29566137 A
1 A
29566138 TTACTTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (15 bp):
AATTGGGCATTCGGC
Found at i:29567133 original size:38 final size:38
Alignment explanation
Indices: 29567087--29567304 Score: 272
Period size: 38 Copynumber: 5.9 Consensus size: 38
29567077 GCCTTGTGTG
29567087 TGAT-TTATATCCGGGCTAAGTCCGAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGTCCGAAGGCATTCGTGC
* *
29567124 TGATATTATATCCGGGTTAAGTCCCAAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGT-CCGAAGGCATTCGTGC
* *
29567163 TG-TATTATATCTGGGTTAAGTCCGAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGTCCGAAGGCATTCGTGC
*
29567200 TGGTATTATAT-CGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGT-CCGAAGGCATTCGTGC
* *
29567238 TGGTATTATAT-C-GGCTAAGTCC-AA-GCATTTGTGC
1 TGATATTATATCCGGGCTAAGTCCGAAGGCATTCGTGC
**
29567272 TGACGTTATATCCGGGCTAAGTTCCGAA-GCATT
1 TGATATTATATCCGGGCTAAG-TCCGAAGGCATT
29567305 TGGGTTGGAA
Statistics
Matches: 163, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
34 17 0.10
35 3 0.02
36 9 0.06
37 40 0.25
38 77 0.47
39 17 0.10
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (38 bp):
TGATATTATATCCGGGCTAAGTCCGAAGGCATTCGTGC
Found at i:29569044 original size:28 final size:27
Alignment explanation
Indices: 29569012--29569104 Score: 71
Period size: 33 Copynumber: 3.2 Consensus size: 27
29569002 ACAACGCATG
29569012 CAGTAACAGTCTGGGCCTAGGCCCTATT
1 CAGTAACAGTCTGGGCCTA-GCCCTATT
* *
29569040 CAGTATCAGTACAGTCTGGGCCTTAGCCTTATA
1 CAG--T-A--ACAGTCTGGGCC-TAGCCCTATT
* *
29569073 CAGTAACAGTGTGGGCCTAAG-CCAATT
1 CAGTAACAGTCTGGGCCT-AGCCCTATT
29569100 CAGTA
1 CAGTA
29569105 TTAGTACAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
27 9 0.17
28 16 0.31
30 2 0.04
31 2 0.04
33 21 0.40
34 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (27 bp):
CAGTAACAGTCTGGGCCTAGCCCTATT
Found at i:29569077 original size:33 final size:34
Alignment explanation
Indices: 29569012--29569082 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
29569002 ACAACGCATG
* *
29569012 CAGTAACAGTCTGGGCCTAGGCCCTATTCAGTAT
1 CAGTAACAGTCTGGGCCTAGGCCCTATACAGTAA
*
29569046 CAGT-ACAGTCTGGGCCTTA-GCCTTATACAGTAA
1 CAGTAACAGTCTGGGCC-TAGGCCCTATACAGTAA
29569079 CAGT
1 CAGT
29569083 GTGGGCCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (34 bp):
CAGTAACAGTCTGGGCCTAGGCCCTATACAGTAA
Found at i:29569103 original size:27 final size:28
Alignment explanation
Indices: 29569012--29569104 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
29569002 ACAACGCATG
*
29569012 CAGTAACAGTCTGGGCCTAGGCCCT-ATT
1 CAGTAACAGTCTGGGCCTAAG-CCTAATT
* * *
29569040 CAGTATCAGTACAGTCTGGGCCTTAGCCTTATA
1 CAG--T-A--ACAGTCTGGGCCTAAGCCTAATT
*
29569073 CAGTAACAGTGTGGGCCTAAGCC-AATT
1 CAGTAACAGTCTGGGCCTAAGCCTAATT
29569100 CAGTA
1 CAGTA
29569105 TTAGTACAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
27 7 0.13
28 19 0.37
30 2 0.04
31 2 0.04
32 3 0.06
33 19 0.37
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (28 bp):
CAGTAACAGTCTGGGCCTAAGCCTAATT
Found at i:29576297 original size:19 final size:19
Alignment explanation
Indices: 29576273--29576311 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29576263 GGCCGAAGTT
29576273 TTATGTTTTGTTTTAATTA
1 TTATGTTTTGTTTTAATTA
29576292 TTATGTTTTGTTTTAATTA
1 TTATGTTTTGTTTTAATTA
29576311 T
1 T
29576312 AATAACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
TTATGTTTTGTTTTAATTA
Found at i:29584880 original size:15 final size:15
Alignment explanation
Indices: 29584860--29584902 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
29584850 AATCTCTCTC
29584860 TTAGGGTTAGGGTTT
1 TTAGGGTTAGGGTTT
*
29584875 TTAGGGTTAAGG-TT
1 TTAGGGTTAGGGTTT
*
29584889 TT-GGTTTAGGGTTT
1 TTAGGGTTAGGGTTT
29584903 AAGGCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 7 0.29
14 6 0.25
15 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (15 bp):
TTAGGGTTAGGGTTT
Found at i:29587866 original size:13 final size:12
Alignment explanation
Indices: 29587848--29587904 Score: 78
Period size: 13 Copynumber: 4.5 Consensus size: 12
29587838 AGTCACACGC
29587848 CCGTGTGCTACG
1 CCGTGTGCTACG
29587860 TCCGTGTGCTACG
1 -CCGTGTGCTACG
29587873 CCTGTGTGCTACG
1 CC-GTGTGCTACG
*
29587886 CCCGTGTGCTAGG
1 -CCGTGTGCTACG
29587899 CCGTGT
1 CCGTGT
29587905 AGGAAATTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
12 8 0.20
13 31 0.76
14 2 0.05
ACGTcount: A:0.07, C:0.32, G:0.33, T:0.28
Consensus pattern (12 bp):
CCGTGTGCTACG
Found at i:29587880 original size:26 final size:25
Alignment explanation
Indices: 29587848--29587904 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
29587838 AGTCACACGC
*
29587848 CCGTGTGCTACGTCCGTGTGCTACG
1 CCGTGTGCTACGCCCGTGTGCTACG
*
29587873 CCTGTGTGCTACGCCCGTGTGCTAGG
1 CC-GTGTGCTACGCCCGTGTGCTACG
29587899 CCGTGT
1 CCGTGT
29587905 AGGAAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.07, C:0.32, G:0.33, T:0.28
Consensus pattern (25 bp):
CCGTGTGCTACGCCCGTGTGCTACG
Found at i:29603189 original size:28 final size:28
Alignment explanation
Indices: 29603126--29603279 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
29603116 ATATTAAGTC
* * *
29603126 CGCACACTCAGTGCTATACAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29603153 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29603181 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29603209 CGCACACTTAGTGCTACGTAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29603237 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29603265 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29603280 GTACAATTTA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 21 0.17
28 100 0.83
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:29605755 original size:29 final size:28
Alignment explanation
Indices: 29605713--29605773 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
29605703 GTGAGCATGA
*
29605713 ATATAAGGTGATTTGGGCCTAACGGGCC
1 ATATAAGGTGATTTGGGCCTAACAGGCC
*
29605741 ATATAAAGGTGATTTGGGCCTAATAGGCC
1 ATAT-AAGGTGATTTGGGCCTAACAGGCC
29605770 ATAT
1 ATAT
29605774 GAATATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (28 bp):
ATATAAGGTGATTTGGGCCTAACAGGCC
Found at i:29605836 original size:29 final size:29
Alignment explanation
Indices: 29605720--29605836 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
29605710 TGAATATAAG
* * * * *
29605720 GTGATTTGGGCCTAACGGGCCATATAAAG
1 GTGAATTGAGCCTAATGGGCCATATGAAT
* * *
29605749 GTGATTTGGGCCTAATAGGCCATATGAAT
1 GTGAATTGAGCCTAATGGGCCATATGAAT
* * *
29605778 ATGAATT-AGGCTTGATGGGCCATATGAAT
1 GTGAATTGA-GCCTAATGGGCCATATGAAT
*
29605807 GTGAATTGAGCCTAATGGGCAATATGAAT
1 GTGAATTGAGCCTAATGGGCCATATGAAT
29605836 G
1 G
29605837 AGATGGGCGA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
29 71 0.99
30 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (29 bp):
GTGAATTGAGCCTAATGGGCCATATGAAT
Found at i:29612842 original size:54 final size:53
Alignment explanation
Indices: 29612773--29613034 Score: 293
Period size: 54 Copynumber: 4.9 Consensus size: 53
29612763 TGACCAGGGC
* ** *
29612773 AACAAGTGATGAGTGATACCCGTATAAGACCATAGCTGGGCTATGGCATCAGAA
1 AACAAGTGATAAGTGATTTCCGTATAAGACCATAGCAGGGCTATGGCATC-GAA
*
29612827 AACAAGTGATAAGTGATTTCTGTATAAGACCATAGCAGGGCTATGGCATCAGAA
1 AACAAGTGATAAGTGATTTCCGTATAAGACCATAGCAGGGCTATGGCATC-GAA
* *
29612881 AACAAGTGATAAGTGATTTCTGTATAAGACCATAGCAGGGCTATGGCTTCGAA
1 AACAAGTGATAAGTGATTTCCGTATAAGACCATAGCAGGGCTATGGCATCGAA
29612934 ATA-AAGTGATACAAGTGA--TCCGTATAAGACCATAGCTA-GGCTATGGCATCGAA
1 A-ACAAGTGAT--AAGTGATTTCCGTATAAGACCATAGC-AGGGCTATGGCATCGAA
* * * * * * *
29612987 GAA-ATGTGATAAGTG-TTTTCATGTAAGACCATATCCGGGATATGGCAT
1 -AACAAGTGATAAGTGATTTCCGTATAAGACCATAGCAGGGCTATGGCAT
29613035 TGGTATGATA
Statistics
Matches: 185, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
51 5 0.03
52 24 0.13
53 49 0.26
54 101 0.55
55 6 0.03
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (53 bp):
AACAAGTGATAAGTGATTTCCGTATAAGACCATAGCAGGGCTATGGCATCGAA
Found at i:29622880 original size:50 final size:50
Alignment explanation
Indices: 29622705--29622934 Score: 234
Period size: 50 Copynumber: 4.6 Consensus size: 50
29622695 ATTGTGAATA
* * * *
29622705 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTG-TTAAGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCA-AATGATGAGGT
* * * * * ** *
29622755 CGCATGTGTAGTACTAAGTGCAGGCTGCTATGCGTACTC-AATGACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAAATGA-TGAGGT
*
29622806 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAAATGATGAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGATGAGGT
* *
29622856 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGAATTGTTGA--T
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AAATGATGAGGT
* * *
29622905 CGCATGTGTAGTACTAAGTGCATGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
29622935 TGCATATCAG
Statistics
Matches: 150, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
49 31 0.21
50 72 0.48
51 47 0.31
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGATGAGGT
Found at i:29622880 original size:101 final size:99
Alignment explanation
Indices: 29622705--29622934 Score: 277
Period size: 101 Copynumber: 2.3 Consensus size: 99
29622695 ATTGTGAATA
* * * * *
29622705 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATGTGTAGTACT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCATAATGTGAAGTCACATGTGTAGTACT
* *
29622770 AAGTGCAGGCTGCTATGCGTACTC-AA-TGACTTCGAT
66 AAGTGCAGGCTACTACGCGTA-TCGAATTG--TT-GAT
* *
29622806 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCA-AATGATGAGGTCACGTGTGTAGTAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCATAATG-TGAAGTCACATGTGTAGTAC
*
29622870 TAAGTGCAGGCTACTACGTGTATCGAATTGTTGAT
65 TAAGTGCAGGCTACTACGCGTATCGAATTGTTGAT
* * *
29622905 CGCATGTGTAGTACTAAGTGCATGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
29622935 TGCATATCAG
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
99 30 0.27
100 7 0.06
101 74 0.65
102 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (99 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCATAATGTGAAGTCACATGTGTAGTACT
AAGTGCAGGCTACTACGCGTATCGAATTGTTGAT
Found at i:29623063 original size:27 final size:26
Alignment explanation
Indices: 29623033--29623084 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
29623023 ACGAAAATCG
29623033 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGT-G-AATATGTGCAAAGTTATT
* *
29623060 ATAAGGTGAATATGTGCAAATTTAT
1 ATAAAGTGAATATGTGCAAAGTTAT
29623085 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 8 0.36
26 8 0.36
27 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (26 bp):
ATAAAGTGAATATGTGCAAAGTTATT
Found at i:29624311 original size:9 final size:9
Alignment explanation
Indices: 29624297--29624338 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
29624287 TTCTTATATT
29624297 TTTTTTTAC
1 TTTTTTTAC
29624306 TTTTTTTAC
1 TTTTTTTAC
29624315 TTTTTTTAC
1 TTTTTTTAC
*
29624324 -TTTTTAAC
1 TTTTTTTAC
29624332 TTTTTTT
1 TTTTTTT
29624339 TCTTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:29624320 original size:17 final size:18
Alignment explanation
Indices: 29624297--29624338 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
29624287 TTCTTATATT
*
29624297 TTTTTTTACTTTTTTTAC
1 TTTTTTTACTTTTTTAAC
29624315 TTTTTTTAC-TTTTTAAC
1 TTTTTTTACTTTTTTAAC
29624332 TTTTTTT
1 TTTTTTT
29624339 TCTTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTACTTTTTTAAC
Found at i:29624424 original size:36 final size:36
Alignment explanation
Indices: 29624355--29624428 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
29624345 ATTTTGTCTC
*
29624355 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
29624392 TTTCTTA-ATTTATTTTGCTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
29624428 T
1 T
29624429 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 15 0.44
37 11 0.32
38 8 0.24
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:29624433 original size:18 final size:17
Alignment explanation
Indices: 29624382--29624429 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
29624372 TTTTTTAAGT
*
29624382 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
* *
29624400 TTTATTTTGCTTATTTAA
1 TTTATATT-ATTATTTAA
29624418 TTTATATTATTA
1 TTTATATTATTA
29624430 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:29624442 original size:23 final size:22
Alignment explanation
Indices: 29624416--29624507 Score: 64
Period size: 23 Copynumber: 4.1 Consensus size: 22
29624406 TTGCTTATTT
*
29624416 AATTTATATTATTAATTTTAAAA
1 AATTTATAATATT-ATTTTAAAA
*
29624439 AATTTGTAATA-TATATTTAAAA
1 AATTTATAATATTAT-TTTAAAA
** * *
29624461 TGTTTTATAATATTGTTTT-TAA
1 -AATTTATAATATTATTTTAAAA
*
29624483 AATTT-TAATTATTATTTTTAAA
1 AATTTATAA-TATTATTTTAAAA
29624505 AAT
1 AAT
29624508 ATTTTTTAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
20 3 0.06
21 13 0.25
22 15 0.28
23 20 0.38
24 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
AATTTATAATATTATTTTAAAA
Found at i:29624500 original size:21 final size:22
Alignment explanation
Indices: 29624418--29624505 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 22
29624408 GCTTATTTAA
* *
29624418 TTTATATTATTAATTTTAAAAAA
1 TTTATATTATT-ATTTTTAAAAT
* * *
29624441 TTTGTAATA-TATATTTAAAATGT
1 TTTATATTATTATTTTTAAAA--T
* *
29624464 TTTATAATATTGTTTTTAAAAT
1 TTTATATTATTATTTTTAAAAT
29624486 TTTA-ATTATTATTTTTAAAA
1 TTTATATTATTATTTTTAAAA
29624506 ATATTTTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
21 22 0.42
22 6 0.12
23 15 0.29
24 9 0.17
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTATATTATTATTTTTAAAAT
Found at i:29625000 original size:27 final size:26
Alignment explanation
Indices: 29624970--29625035 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
29624960 TTTTAAATAC
* *
29624970 AATTTTTAAATACATTTAAAAAATTAT
1 AATTTTTAAATA-ATATAAAAAATCAT
* *
29624997 AATTTTTTAATAATATAAGAAATCAT
1 AATTTTTAAATAATATAAAAAATCAT
29625023 AATATTTTAAATA
1 AAT-TTTTAAATA
29625036 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (26 bp):
AATTTTTAAATAATATAAAAAATCAT
Found at i:29625019 original size:26 final size:27
Alignment explanation
Indices: 29624970--29625032 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
29624960 TTTTAAATAC
* * *
29624970 AATTTTTAAATACATTTAAAAAATTAT
1 AATTTTTTAATACATATAAAAAATCAT
*
29624997 AATTTTTTAATA-ATATAAGAAATCAT
1 AATTTTTTAATACATATAAAAAATCAT
*
29625023 AATATTTTAA
1 AATTTTTTAA
29625033 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTTTTTAATACATATAAAAAATCAT
Found at i:29625092 original size:34 final size:33
Alignment explanation
Indices: 29625034--29625106 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 33
29625024 ATATTTTAAA
* *
29625034 TATTTTTTTAAAATTTTGTCTTTTTCCTTTTTT
1 TATTTTTTGAAAATTTTGTCTTTTTCCTTATTT
* *
29625067 TACTTTTTTGAAATTTTATGT-TTTTTTCTTATTT
1 TA-TTTTTTGAAAATTT-TGTCTTTTTCCTTATTT
29625101 TATTTT
1 TATTTT
29625107 GTTTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 6 0.18
34 25 0.74
35 3 0.09
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (33 bp):
TATTTTTTGAAAATTTTGTCTTTTTCCTTATTT
Found at i:29625199 original size:21 final size:21
Alignment explanation
Indices: 29625160--29625203 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29625150 ATTTAAAATG
29625160 TTTTATAATATATTTTTTACAA
1 TTTTATAATATATTTTTTA-AA
29625182 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATAT-TTTTTAAA
29625202 TT
1 TT
29625204 CTTTTGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATAATATATTTTTTAAA
Found at i:29628388 original size:30 final size:30
Alignment explanation
Indices: 29628352--29628474 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
29628342 GTCCCAGAGC
* *
29628352 AGTTCATATAACCCGGACATAGGTAGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
29628382 AGTTCATATCACCCGGACATGGGTGGTTCA
1 AGTTCATATCACCCGGACATAGGTGGTTCG
*
29628412 AGTTCATATCACCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* * *
29628442 AGTTCATATCACCTGGATATAGGCGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
29628472 AGT
1 AGT
29628475 CTATTTGACC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:29631980 original size:20 final size:21
Alignment explanation
Indices: 29631955--29631993 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
29631945 AACTATTAAA
29631955 AATATATTTTTAA-ATTATTT
1 AATATATTTTTAATATTATTT
29631975 AATATATTTTTAATATTAT
1 AATATATTTTTAATATTAT
29631994 AAAACATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATATATTTTTAATATTATTT
Found at i:29632014 original size:10 final size:9
Alignment explanation
Indices: 29631963--29632021 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
29631953 AAAATATATT
*
29631963 TTTAAATTA
1 TTTAAAATA
*
29631972 TTTAATATA
1 TTTAAAATA
**
29631981 TTTTTAATA
1 TTTAAAATA
*
29631990 TTATAAAACA
1 TT-TAAAATA
29632000 TTTAAAATGA
1 TTTAAAAT-A
29632010 TTTAAAATA
1 TTTAAAATA
29632019 TTT
1 TTT
29632022 TTTAATATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 24 0.62
10 15 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (9 bp):
TTTAAAATA
Found at i:29632035 original size:20 final size:21
Alignment explanation
Indices: 29631953--29632035 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 21
29631943 ATAACTATTA
29631953 AAAATATATTTTTAA-ATTATT
1 AAAATATATTTTTAATATT-TT
* *
29631974 -TAATATATTTTTAATATTAT
1 AAAATATATTTTTAATATTTT
* **
29631994 -AAA-ACATTTAAAATGA-TTT
1 AAAATATATTTTTAAT-ATTTT
29632013 AAAATAT-TTTTTAATATTTT
1 AAAATATATTTTTAATATTTT
29632033 AAA
1 AAA
29632036 TGACTTTAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
19 11 0.23
20 32 0.68
21 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
AAAATATATTTTTAATATTTT
Found at i:29632044 original size:30 final size:27
Alignment explanation
Indices: 29631999--29632061 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 27
29631989 ATTATAAAAC
*
29631999 ATTTAAAATGATTTAAAATATTTTTTAA
1 ATTTTAAATGATTT-AAATATTTTTTAA
29632027 TATTTTAAATGACTTTAAATATTTTTTAA
1 -ATTTTAAATGA-TTTAAATATTTTTTAA
29632056 ATTTTA
1 ATTTTA
29632062 CATAGAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 6 0.19
29 23 0.72
30 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTTTAAATGATTTAAATATTTTTTAA
Found at i:29632592 original size:20 final size:20
Alignment explanation
Indices: 29632556--29632602 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29632546 AAAATACAAT
* *
29632556 AAGAAAATAATATAAAACTTA
1 AAGAAAATAA-AAAAAAATTA
29632577 AA-AAAATAAAAAAAAATTA
1 AAGAAAATAAAAAAAAATTA
29632596 AAGAAAA
1 AAGAAAA
29632603 AGACAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.43
20 11 0.48
21 2 0.09
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (20 bp):
AAGAAAATAAAAAAAAATTA
Found at i:29632807 original size:37 final size:36
Alignment explanation
Indices: 29632737--29632807 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
29632727 AATAATTATT
*
29632737 TTTTTAAAATTTTAAAAAATTAATTTGAAAAATACA
1 TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
* *
29632773 TTTTTAAAATTTATAAATAATTAATTTCACAAATA
1 TTTTTAAAATTT-TAAAAAATTAATTTCAAAAATA
29632808 TATATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
Found at i:29632877 original size:22 final size:22
Alignment explanation
Indices: 29632823--29632896 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 22
29632813 ATAAAGTTAA
*
29632823 AAAATATTTTAAAAAATAATAATT
1 AAAA-ATTTTAAAAAAT-ATTATT
29632847 AAAAA-TTTAAAAAATATTA-T
1 AAAAATTTTAAAAAATATTATT
*
29632867 AAAACATTTT-AAATATA-TATT
1 AAAA-ATTTTAAAAAATATTATT
*
29632888 ACAAATTTT
1 AAAAATTTT
29632897 TTAAAATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
20 12 0.27
21 14 0.32
22 13 0.30
23 1 0.02
24 4 0.09
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATTTTAAAAAATATTATT
Found at i:29632950 original size:18 final size:18
Alignment explanation
Indices: 29632900--29632951 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
29632890 AAATTTTTTA
* *
29632900 AAATTAATAATATATATT
1 AAATAAATAATATAAATT
* *
29632918 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
29632936 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
29632952 ACTTAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:29633032 original size:56 final size:54
Alignment explanation
Indices: 29632931--29633034 Score: 138
Period size: 56 Copynumber: 1.9 Consensus size: 54
29632921 TAAGTAAAAT
* *
29632931 AAATTAAGAAAATAATATAAAACTTAAAAAAGAAAAAAATCTAAAAAAGAGACA
1 AAATTAAGAAAAAAATAAAAAACTTAAAAAAGAAAAAAATCTAAAAAAGAGACA
* *
29632985 AAATATAAGAAAAAAAGTAAAAAAGTTAAAAAAGTAAAAAAA-GTAAAAAA
1 AAAT-TAAGAAAAAAA-TAAAAAACTTAAAAAAG-AAAAAAATCTAAAAAA
29633035 AAAATATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
54 4 0.09
55 10 0.23
56 22 0.51
57 7 0.16
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (54 bp):
AAATTAAGAAAAAAATAAAAAACTTAAAAAAGAAAAAAATCTAAAAAAGAGACA
Found at i:29633037 original size:39 final size:39
Alignment explanation
Indices: 29632937--29633038 Score: 93
Period size: 39 Copynumber: 2.5 Consensus size: 39
29632927 AAATAAATTA
29632937 AGAAAATAATATAAAACTTAAAAAAGAAAAAAATCTAAAAAAG
1 AGAAAA-AATATAAAA---AAAAAAGAAAAAAATCTAAAAAAG
* * *
29632980 AGACAAAATATAAGAAAAAAAGTAAAAAAGT-TAAAAAAG
1 AGAAAAAATATAAAAAAAAAAG-AAAAAAATCTAAAAAAG
*
29633019 TA-AAAAAA-GTAAAAAAAAAA
1 -AGAAAAAATATAAAAAAAAAA
29633039 TATATGAACC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
38 10 0.20
39 20 0.39
40 8 0.16
42 8 0.16
43 5 0.10
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.14
Consensus pattern (39 bp):
AGAAAAAATATAAAAAAAAAAGAAAAAAATCTAAAAAAG
Found at i:29639749 original size:50 final size:50
Alignment explanation
Indices: 29639578--29639752 Score: 192
Period size: 50 Copynumber: 3.5 Consensus size: 50
29639568 TGAATACACA
* * * * * * *
29639578 TGTGTAGTACTAAGTGTAGGCTACTACGTTTATGATACTG-TTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCA-AATGATTAGGTCACG
* * * *
29639628 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-AATGACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAAATGA-TTAGGTCACG
* *
29639679 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCAAATGATGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGATTAGGTCACG
29639729 TGTGTAGTACTAAGTGCAGGCTAC
1 TGTGTAGTACTAAGTGCAGGCTAC
29639753 CATGCATATT
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.03
50 61 0.59
51 40 0.38
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGATTAGGTCACG
Found at i:29639773 original size:101 final size:101
Alignment explanation
Indices: 29639578--29639760 Score: 251
Period size: 101 Copynumber: 1.8 Consensus size: 101
29639568 TGAATACACA
* * * * * * *
29639578 TGTGTAGTACTAAGTGTAGGCTACTACGTTTATGATACTGTTAAGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCATAATGTGAAGTCACATGTGTAGTACTAAGT
* *
29639643 GCAGGCTACTATGCGTACTCAATGACTTCGATCACG
66 GCAGGCTACCATGCATACTCAATGACTTCGATCACG
* *
29639679 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCA-AATGATGAGGTCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCATAATG-TGAAGTCACATGTGTAGTACTAAG
29639743 TGCAGGCTACCATGCATA
65 TGCAGGCTACCATGCATA
29639761 TTAGATTGCT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
100 3 0.04
101 67 0.96
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (101 bp):
TGTGTAGTACTAAGTGCAGGCTACTACATGTATCATAATGTGAAGTCACATGTGTAGTACTAAGT
GCAGGCTACCATGCATACTCAATGACTTCGATCACG
Found at i:29641205 original size:17 final size:17
Alignment explanation
Indices: 29641183--29641227 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
29641173 AATTTTGGCA
29641183 CTTTACAAATCAATCCT
1 CTTTACAAATCAATCCT
* *
29641200 CTTTACAAATTAGTCCT
1 CTTTACAAATCAATCCT
29641217 CTTTACTAAAT
1 CTTTAC-AAAT
29641228 TGAAGACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.40
Consensus pattern (17 bp):
CTTTACAAATCAATCCT
Found at i:29645834 original size:46 final size:46
Alignment explanation
Indices: 29645656--29646018 Score: 190
Period size: 46 Copynumber: 7.7 Consensus size: 46
29645646 TTCGTGCGCT
* * *
29645656 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGAGAGCC
* * * * ** *
29645702 AGTATAAGACCATGTTTGGGACATGGCATCTGC-ATTGAGACAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGATGAGAGCC
* * *
29645750 AGTGTAAGTCATGTCAGGGACATGCATCGGCCT-TGAGATGCA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATG-AGAGCC
* * *
29645796 AGTGTAAGACATGTCTGGGACATGCATTGGCTACGAGAT--GTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAGAGCC
* * *
29645840 AGTGTAAGACCATGTCTGGAACATGGCATCGGC-ACGGAAATGTGGGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC-GAGA--TGAGAGCC
* * * * ** * *
29645890 AGTGTAAGACCATGTTTAGGACATGGCGTCGGCCT-TGATTTCGATAGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGAT-GAGAGCC
* * *
29645939 AGTGTAAGACCATGTCTGGGACATGGGATCGACT-TGATGGAT-A-AGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGA--GATGAGAGCC
29645986 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
29646019 ATTACACCCT
Statistics
Matches: 249, Mismatches: 47, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
44 11 0.04
45 17 0.07
46 64 0.26
47 62 0.25
48 28 0.11
49 32 0.13
50 34 0.14
51 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAGAGCC
Found at i:29646002 original size:47 final size:47
Alignment explanation
Indices: 29645886--29646016 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 47
29645876 GAAATGTGGG
* * *
29645886 AGCCAGTGTAAGACCATGTTTAGGACATGGCG-TCGGCCTTGATTTCGAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGG-GATC-GACTTGA-TTCGAT
* *
29645935 AGTCAGTGTAAGACCATGTCTGGGACATGGGATCGACTTGA-TGGAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGGATCGACTTGATTCGAT
*
29645981 AAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGGATCG
29646017 GCATTACACC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
46 4 0.05
47 33 0.45
48 7 0.10
49 29 0.40
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGGATCGACTTGATTCGAT
Found at i:29656827 original size:40 final size:40
Alignment explanation
Indices: 29656589--29656813 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
29656579 TTGAATGATG
* * * *
29656589 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29656629 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29656669 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29656708 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* **
29656748 TCCGGGTTAAGTCCCGAAGGCATTTGTGTTAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29656789 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29656814 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29665082 original size:40 final size:40
Alignment explanation
Indices: 29664844--29665068 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
29664834 TTGAATGATG
* * * *
29664844 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29664884 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29664924 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29664963 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29665003 TCCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29665044 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29665069 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29672044 original size:49 final size:50
Alignment explanation
Indices: 29671972--29672114 Score: 157
Period size: 51 Copynumber: 2.9 Consensus size: 50
29671962 GCCGAAGCTA
*
29671972 TCTGGTA-AGCATAGTATCCTGCACTTAGTACTACACATGCGA-C-CAATAG
1 TCTGGTACA-CATAGTAGCCTGCACTTAGTACTACACATGCGATCACAAT-G
* * * *
29672021 TCTGGTACACATAGTAGCCTGCACTTAGTATTACACATGTGATCACAGTT
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGATCACAATG
* * * *
29672071 TTTGGGAACGCATAGTAGCCTACACTTAGTACTACACATGCGAT
1 TCT-GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGAT
29672115 GTGACAGCCC
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
49 37 0.47
50 4 0.05
51 38 0.48
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGATCACAATG
Found at i:29673696 original size:40 final size:40
Alignment explanation
Indices: 29673613--29673915 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
29673603 TTGAATGCTG
* * * * * *
29673613 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
29673653 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
29673693 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
29673733 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
29673773 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
29673813 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29673853 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29673892 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29673916 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:29681735 original size:80 final size:80
Alignment explanation
Indices: 29681598--29681780 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
29681588 TTGAATGCTG
* * *
29681598 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGG-CAT
29681662 TGTGCGAGATACTAAA
65 TGTGCGAGATACTAAA
* * * * * *
29681678 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCAT
* *
29681741 TGTGTGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
29681757 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29681781 TGAACGAGGA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 38 0.44
80 43 0.49
81 6 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
GTGCGAGATACTAAA
Found at i:29681762 original size:39 final size:39
Alignment explanation
Indices: 29681598--29681780 Score: 179
Period size: 40 Copynumber: 4.6 Consensus size: 39
29681588 TTGAATGCTG
* * * * * * *
29681598 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
29681638 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
29681678 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
29681718 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
29681757 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
29681781 TGAACGAGGA
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 39 0.32
40 75 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:29687653 original size:43 final size:43
Alignment explanation
Indices: 29687598--29687752 Score: 206
Period size: 43 Copynumber: 3.7 Consensus size: 43
29687588 ATATCGTACA
*
29687598 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * *
29687641 ATGCCACCGTCCCAGATAGGGTCTTACATG-AATCAAATA-CG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * * *
29687682 ATGTCGATGTCCCAGACATGGTCTTACACGTAATCACATATTG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATATCG
29687725 ATGCCAACGTCCCAGACATGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
29687753 CGAGAACACA
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
41 25 0.27
42 16 0.17
43 52 0.56
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:29691690 original size:23 final size:22
Alignment explanation
Indices: 29691639--29691690 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
29691629 CCTCGTCTTT
*
29691639 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
29691661 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
29691684 TTCTTTT
1 TTCTTTT
29691691 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:29700944 original size:40 final size:40
Alignment explanation
Indices: 29700796--29701007 Score: 223
Period size: 40 Copynumber: 5.3 Consensus size: 40
29700786 CATTTGAATG
* * *
29700796 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* * * *
29700836 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* *
29700876 TTACCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * *
29700916 ATATCCAGGCTAAGACCCGAAGGCATTTGTACGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * * ** *
29700956 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
29700996 ATATCC-GGCTAA
1 ATATCCGGGCTAA
29701008 ATTTCGAAGA
Statistics
Matches: 150, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 7 0.05
40 140 0.93
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:29702988 original size:21 final size:21
Alignment explanation
Indices: 29702964--29703005 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29702954 CATTAAATGA
29702964 GCACAAAATACAACCCATTGT
1 GCACAAAATACAACCCATTGT
*
29702985 GCACAGAATACAACCCATTGT
1 GCACAAAATACAACCCATTGT
29703006 ACACCTTATT
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:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (21 bp):
GCACAAAATACAACCCATTGT
Found at i:29704566 original size:56 final size:56
Alignment explanation
Indices: 29704479--29704585 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
29704469 CATGGCATCA
*
29704479 ATATATGTGTGCGAGTAAGACCCTATTTGGGACAGTGGCATCGATATGTGACTCTG
1 ATATATGTGTGCGAGTAAGACCCTATCTGGGACAGTGGCATCGATATGTGACTCTG
*
29704535 ATATATGTGTGCGAGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGA
1 ATATATGTGTGCGAGTAAGACCCTATCTGGGACAGTGGCATCGATATGTGA
29704586 TTACATGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (56 bp):
ATATATGTGTGCGAGTAAGACCCTATCTGGGACAGTGGCATCGATATGTGACTCTG
Found at i:29706721 original size:17 final size:18
Alignment explanation
Indices: 29706699--29706732 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29706689 CACATTGAAG
29706699 TGTTTT-ATCGAAAACCT
1 TGTTTTCATCGAAAACCT
*
29706716 TGTTTTCATTGAAAACC
1 TGTTTTCATCGAAAACC
29706733 CTTCCTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TGTTTTCATCGAAAACCT
Found at i:29709106 original size:29 final size:29
Alignment explanation
Indices: 29709045--29709133 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
29709035 ACATACATGT
* * **
29709045 ATATGGCCCACTAGGCCC-AATCTTATTC
1 ATATGGCCTATTAGGCCCAAATCACATTC
*
29709073 ATATGGTCC-ATTGGGCCCAAATCACATTC
1 ATATGG-CCTATTAGGCCCAAATCACATTC
* *
29709102 GTATGGCCTATTAGGCCCAAATCACATAC
1 ATATGGCCTATTAGGCCCAAATCACATTC
29709131 ATA
1 ATA
29709134 GTCATGCTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 15 0.30
29 35 0.70
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (29 bp):
ATATGGCCTATTAGGCCCAAATCACATTC
Found at i:29716427 original size:44 final size:44
Alignment explanation
Indices: 29716362--29716445 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
29716352 TTGATATCTC
* *
29716362 AAAGTCCATGGTTGTACCATGGCAATTAAGGAAGAATTGAAGGA
1 AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGAAGGA
* *
29716406 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGA
1 AAAGTCCATGGTT-ATAACATGGCAATTAAGGAAGAATTGA
29716446 CGGTTAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.09
44 32 0.91
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGAAGGA
Found at i:29716645 original size:47 final size:47
Alignment explanation
Indices: 29716585--29716706 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
29716575 GCATTGGCAC
* *
29716585 TAAGACAAGGATACCATGTAAGACCATGTTTGGAATATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
*
29716632 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
* *
29716679 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
29716707 CCAAGGCATG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
Found at i:29716749 original size:54 final size:54
Alignment explanation
Indices: 29716685--29717090 Score: 397
Period size: 54 Copynumber: 7.6 Consensus size: 54
29716675 TTGGTAAGAT
* * *
29716685 AAGGATATCATGTAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* * * *
29716739 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTATAAGGC
* * * *
29716794 AAAGG-TCCCATGTAAGACTATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGAC
1 -AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* *** **
29716847 AAGGATACCATGTTAGACCATG-TTTGGAACATGGCATT--TG-G-----TAAGAT
1 AAGGATACCATGTAAGACCATGCCAAGG--CATGGCATTGATGAGTTCTATAAGGC
* *
29716894 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* * * * *
29716948 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATTAGGC
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTATAAGGC
* *
29717003 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* * * *
29717056 AAGGATACCACGTAAGACCACGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCA
29717091 ATGGTAAGTT
Statistics
Matches: 290, Mismatches: 45, Indels: 35
0.78 0.12 0.09
Matches are distributed among these distances:
46 9 0.03
47 25 0.09
48 3 0.01
49 1 0.00
51 1 0.00
52 12 0.04
53 51 0.18
54 96 0.33
55 84 0.29
56 8 0.03
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
Found at i:29716884 original size:109 final size:109
Alignment explanation
Indices: 29716693--29717090 Score: 521
Period size: 109 Copynumber: 3.7 Consensus size: 109
29716683 ATAAGGATAT
* *
29716693 CATGTAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
29716758 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
66 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
* * * * * *
29716802 CATGTAAGACTATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGACAAGGATACCATGTTAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
*** ** *
29716866 ATGTTTGGAACATGGCATT--TG-G-TAAGATAAGG-ATA--T--
66 ATGTCAAG-ACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
*
29716902 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
*
29716967 ATGTCAAGACATGGCATTGATGAGTTACTATTAGGCAAAGGTCC
66 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
* * * *
29717011 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
*
29717075 ACGTCAAGACATGGCA
66 ATGTCAAGACATGGCA
29717091 ATGGTAAGTT
Statistics
Matches: 244, Mismatches: 34, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
100 45 0.18
101 27 0.11
102 3 0.01
103 1 0.00
104 9 0.04
105 10 0.04
106 1 0.00
107 3 0.01
108 65 0.27
109 80 0.33
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCATGTAAGACC
ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
Found at i:29716979 original size:100 final size:102
Alignment explanation
Indices: 29716632--29717098 Score: 462
Period size: 109 Copynumber: 4.5 Consensus size: 102
29716622 TGGCATTTGG
* * *** * *
29716632 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAAGATAAGG-ATA-T-C
1 TAAGGCAAGGATACCATGTAAGACCATGTCAAG-ACATGGCATTTGGTAAGATAAGGCAAAGTCC
* * *
29716694 ATGTAAGACCATGCCAAGGCATGACATTGATAAGTTCTA
65 ATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-A
* * **
29716733 TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAG
1 TAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATT--TG-G-TAAGATAAGGCAAA-
*
29716798 GTCCCATGTAAGACTATGCCAAGGCATGGCATTGGTGAGTTCA
61 GT-CCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
* * *** *
29716841 TAAGACAAGGATACCATGTTAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGG-ATA-T-C
1 TAAGGCAAGGATACCATGTAAGACCATGTCAAG-ACATGGCATTTGGTAAGATAAGGCAAAGTCC
* *
29716903 ATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
65 ATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-A
* * ** *
29716942 TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATTAGGCAAAG
1 TAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATT--TG-G-TAAGATAAGGCAAA-
29717007 GTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
61 GT-CCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
* * *
29717050 TAAGGCAAGGATACCACGTAAGACCACGTCAAGACATGGCA-ATGGTAAG
1 TAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTTGGTAAG
29717099 TTCAAAAAGG
Statistics
Matches: 298, Mismatches: 48, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
100 54 0.18
101 53 0.18
102 5 0.02
103 4 0.01
104 18 0.06
105 14 0.05
106 1 0.00
107 4 0.01
108 65 0.22
109 80 0.27
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (102 bp):
TAAGGCAAGGATACCATGTAAGACCATGTCAAGACATGGCATTTGGTAAGATAAGGCAAAGTCCA
TGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCA
Found at i:29716992 original size:209 final size:209
Alignment explanation
Indices: 29716632--29717075 Score: 816
Period size: 209 Copynumber: 2.1 Consensus size: 209
29716622 TGGCATTTGG
*
29716632 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAAGATAAGGATATCATG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAAGATAAGGATATCATG
29716697 TAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
66 TAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
*
29716762 CAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACTATGCCAAGGCATGG
131 CAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGG
29716827 CATTGGTGAGTTCA
196 CATTGGTGAGTTCA
* *
29716841 TAAGACAAGGATACCATGTTAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAAGATAAGGATATCATG
*
29716906 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
66 TAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
*
29716971 CAAGACATGGCATTGATGAGTTACTATTAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGG
131 CAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGG
29717036 CATTGGTGAGTTCA
196 CATTGGTGAGTTCA
* *
29717050 TAAGGCAAGGATACCACGTAAGACCA
1 TAAGACAAGGATACCATGTAAGACCA
29717076 CGTCAAGACA
Statistics
Matches: 226, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
209 226 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (209 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAAGATAAGGATATCATG
TAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGT
CAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGG
CATTGGTGAGTTCA
Found at i:29717035 original size:155 final size:154
Alignment explanation
Indices: 29716739--29717039 Score: 358
Period size: 155 Copynumber: 1.9 Consensus size: 154
29716729 TCTATAAGGC
* * **
29716739 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCA
1 AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGAACCA
* * * *
29716804 TGTAAGACTATGCCAAGGCATGGCATTGGTGAGTTCATAAGACAAGGATACCATGTTAGACCATG
66 TGTAAGACCATGCCAAGACATGGCATTGATGAGTTCATAAGACAAGGATACCATGTAAGACCATG
***
29716869 TTTGGAACATGGCATTTGGTAAGAT
131 CAAGG-ACATGGCATTTGGTAAGAT
* * *
29716894 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGGC-AAGGAAATC
1 AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGG-AACC
* * * *
29716957 ATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATTAGGCAAAGG-TCCCATGTAAGAC
65 ATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-C-ATAAGAC-AAGGATACCATGTAAGAC
29717021 CATGCCAAGG-CATGGCATT
127 CATG-CAAGGACATGGCATT
29717040 GGTGAGTTCA
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
153 4 0.03
154 42 0.34
155 51 0.41
156 20 0.16
157 6 0.05
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (154 bp):
AAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGAACCA
TGTAAGACCATGCCAAGACATGGCATTGATGAGTTCATAAGACAAGGATACCATGTAAGACCATG
CAAGGACATGGCATTTGGTAAGAT
Found at i:29717237 original size:17 final size:16
Alignment explanation
Indices: 29717204--29717237 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29717194 CTTATTTAAT
*
29717204 ATTGAGATTGTAAGTA
1 ATTGAGATTATAAGTA
29717220 ATTGAGATTATCAAGTA
1 ATTGAGATTAT-AAGTA
29717237 A
1 A
29717238 GTGATAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATTGAGATTATAAGTA
Found at i:29721685 original size:43 final size:43
Alignment explanation
Indices: 29721638--29721797 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 43
29721628 AATGCCAACG
* * *
29721638 TCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTT
1 TCCCAGAAGTGGTCTTACACGTAATCACATATCGATGCCACTA
* * *
29721681 TCCCAGATAG-GGTCTTACACG-AATCAAATAT-GATGTCGA-TG
1 TCCCAGA-AGTGGTCTTACACGTAATCACATATCGATG-CCACTA
* *
29721722 TCTCAGAAATGGTCTTACACGTAATCACATATCGATGCCAAC-A
1 TCCCAGAAGTGGTCTTACACGTAATCACATATCGATGCC-ACTA
* * *
29721765 TCCTAGACGTGGTCTTACATGTAATCACATATC
1 TCCCAGAAGTGGTCTTACACGTAATCACATATC
29721798 AGAAATCCTA
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
40 1 0.01
41 22 0.23
42 21 0.22
43 50 0.53
44 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
TCCCAGAAGTGGTCTTACACGTAATCACATATCGATGCCACTA
Found at i:29729186 original size:16 final size:16
Alignment explanation
Indices: 29729151--29729200 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
29729141 GTAGATTGAC
* *
29729151 AAATCCCGAAAAGCCA
1 AAATACCGAAAAGCCG
*
29729167 AAATACCGAAAAGCTG
1 AAATACCGAAAAGCCG
*
29729183 AAATGCC-AAAAGCCG
1 AAATACCGAAAAGCCG
29729198 AAA
1 AAA
29729201 GGTTGGCCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.52, C:0.24, G:0.16, T:0.08
Consensus pattern (16 bp):
AAATACCGAAAAGCCG
Found at i:29729455 original size:28 final size:29
Alignment explanation
Indices: 29729415--29729526 Score: 113
Period size: 28 Copynumber: 4.0 Consensus size: 29
29729405 CATGACTGTA
* *
29729415 AATGTGATTTGGGTCTAGT-GGCCATATG
1 AATGTGATTTGGGCCTAATAGGCCATATG
* * *
29729443 AATGTGATTTGGGCCTAATGGGCCACATA
1 AATGTGATTTGGGCCTAATAGGCCATATG
* *
29729472 AATGTCAATT-GGCCTAATAGGCCATATG
1 AATGTGATTTGGGCCTAATAGGCCATATG
* * *
29729500 AAAGAGA-TTGGGCCTAGTAGGCCATAT
1 AATGTGATTTGGGCCTAATAGGCCATAT
29729527 ATATATAGGT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
27 2 0.03
28 52 0.75
29 15 0.22
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATAGGCCATATG
Found at i:29736675 original size:27 final size:27
Alignment explanation
Indices: 29736645--29736822 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
29736635 ATATTGAGTC
* * * *
29736645 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29736672 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29736699 CTCACACTTAGTGCTATATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29736727 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29736754 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29736781 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29736808 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29736823 GTACAATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.83
28 22 0.17
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29736787 original size:82 final size:81
Alignment explanation
Indices: 29736666--29736821 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
29736656 TGCTATATAA
* * * *
29736666 TCAACTCGCACACTTAGTGCTACGTAATCAAATCTCACACTTAGTGCTATATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29736731 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29736748 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29736812 CACTTAGTGC
65 CACTTAGTGC
29736822 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 16 0.25
82 49 0.75
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29736805 original size:54 final size:54
Alignment explanation
Indices: 29736645--29736822 Score: 214
Period size: 54 Copynumber: 3.3 Consensus size: 54
29736635 ATATTGAGTC
* * * *
29736645 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* * ** * *
29736699 CTCACACTTAGTGCTATATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
29736754 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTAT-ATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
29736808 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29736823 GTACAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 61 0.59
55 43 0.41
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:29744851 original size:27 final size:27
Alignment explanation
Indices: 29744821--29744998 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
29744811 ATATTGAGTC
* * *
29744821 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
29744848 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* * *
29744875 CTCACACTTAGTGCTATATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** * *
29744903 CGCACACTTAGTGCCGCATGATCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
29744930 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
29744957 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
29744984 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29744999 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 104 0.83
28 21 0.17
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:29744963 original size:82 final size:81
Alignment explanation
Indices: 29744841--29744997 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
29744831 GTGCTATATA
* * * *
29744841 ATCAACTCGCACACTTAGTGCTACGTAATCAAATCTCACACTTAGTGCTATATAGTCAAACTCGC
1 ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
29744906 ACACTTAGTGCCGCATG
65 ACACTTAGTGCCGCATG
* * **
29744923 ATCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 ATCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGC
29744987 ACACTTAGTGC
65 ACACTTAGTGC
29744998 TGTACAATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (81 bp):
ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATG
Found at i:29744987 original size:54 final size:54
Alignment explanation
Indices: 29744821--29744998 Score: 207
Period size: 54 Copynumber: 3.3 Consensus size: 54
29744811 ATATTGAGTC
* * * *
29744821 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* * ** *
29744875 CTCACACTTAGTGCTATATAGTCAAACTCGCACACTTAGTGCCGCAT-GATCAATT
1 CGCACACTTAGTGCTATATAATC-AACTCGCACACTTAGTGCAACATAG-TCAAAT
* **
29744930 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTAT-ATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
29744984 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29744999 GTACAATTTA
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
54 60 0.58
55 44 0.42
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:29757803 original size:40 final size:40
Alignment explanation
Indices: 29757619--29757800 Score: 249
Period size: 40 Copynumber: 4.5 Consensus size: 40
29757609 ACTTGAATTC
* * *
29757619 TCGCACACTGAGTGCCAATACTTAGCCGAAGCTATTTC-AA
1 TCGCACACTAAGTGCC-ATACATAGCCGAAGCTATCTCGAA
* *
29757659 TCTCGCACATTAAGTGCCATACATAGCCGAAGCTATCTCAAA
1 --TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
* *
29757701 TCGCACAGTAAGTGCCATACATAGCCAAAGCTATCTCGAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
* *
29757741 TCGTACACTAAGTGCCATACGTAGCCGAAGCTATCTCGAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
29757781 TCGCACACTAAGTGCCATAC
1 TCGCACACTAAGTGCCATAC
29757801 GTAACCAAAT
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 92 0.72
41 19 0.15
42 16 0.13
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
Found at i:29761628 original size:24 final size:23
Alignment explanation
Indices: 29761584--29761628 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
29761574 GTTTATCTAC
*
29761584 AATATAAACATTAAATTTAATTT
1 AATATAAACATTAAATATAATTT
29761607 AATATTAAACTATTAAA-ATAAT
1 AATA-TAAAC-ATTAAATATAAT
29761629 ATTATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 9 0.47
25 6 0.32
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAAACATTAAATATAATTT
Found at i:29767290 original size:24 final size:24
Alignment explanation
Indices: 29767258--29767330 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
29767248 ATCAACACCC
29767258 ATCATGAACATACTTTCATTTGTG
1 ATCATGAACATACTTTCATTTGTG
29767282 ATCATGAACATACTTTCATTTGTG
1 ATCATGAACATACTTTCATTTGTG
*
29767306 ATCATGAACATAATTTCATTTGTG
1 ATCATGAACATACTTTCATTTGTG
29767330 A
1 A
29767331 GTTATCTTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (24 bp):
ATCATGAACATACTTTCATTTGTG
Found at i:29771618 original size:18 final size:19
Alignment explanation
Indices: 29771589--29771627 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29771579 CTAAAAAATG
29771589 ATAAATAATATTTCAAAAA
1 ATAAATAATATTTCAAAAA
*
29771608 ATAAA-AATATTTTAAAAA
1 ATAAATAATATTTCAAAAA
29771626 AT
1 AT
29771628 TTAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATAATATTTCAAAAA
Found at i:29772599 original size:17 final size:19
Alignment explanation
Indices: 29772577--29772616 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29772567 GATGTCTCGT
*
29772577 TCATTTT-C-AAAATTTAA
1 TCATTTTGCAAAAAGTTAA
29772594 TCATTTTGCAAAAAGTTAA
1 TCATTTTGCAAAAAGTTAA
29772613 TCAT
1 TCAT
29772617 ATTAAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (19 bp):
TCATTTTGCAAAAAGTTAA
Found at i:29797129 original size:40 final size:40
Alignment explanation
Indices: 29797045--29797228 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
29797035 TTGAATGCTG
* * * *
29797045 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
29797084 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
29797125 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
29797165 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
29797205 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29797229 GTATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:29797182 original size:80 final size:81
Alignment explanation
Indices: 29797045--29797225 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
29797035 TTGAATGCTG
* *
29797045 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
29797109 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
29797125 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
29797186 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
29797205 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
29797226 ATTGTATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:29801003 original size:16 final size:15
Alignment explanation
Indices: 29800978--29801025 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29800968 TGTTTTTGGA
*
29800978 TTGATTTGAATGAAT
1 TTGATTTGAATAAAT
29800993 TTGAGTTTGAATAAAT
1 TTGA-TTTGAATAAAT
** *
29801009 TAAATTTGAATTAAT
1 TTGATTTGAATAAAT
29801024 TT
1 TT
29801026 AGATCAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (15 bp):
TTGATTTGAATAAAT
Found at i:29801387 original size:44 final size:42
Alignment explanation
Indices: 29801309--29801408 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 42
29801299 CAATATGTTT
* ** **
29801309 TTTCTTGTAAGACCACGTCTGGGACGTTGTCATCG-ACTTATGA
1 TTTCGTGTAAGACCACGTCTGGGAAATTAACATCGTA-TT-TGA
*
29801352 TTTACGTGTAAGACCATGTCTGGGAAATTAACATCGTATTTGA
1 TTT-CGTGTAAGACCACGTCTGGGAAATTAACATCGTATTTGA
29801395 TTTCGTGTAAGACC
1 TTTCGTGTAAGACC
29801409 CTATTTGGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 11 0.22
43 9 0.18
44 28 0.57
45 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (42 bp):
TTTCGTGTAAGACCACGTCTGGGAAATTAACATCGTATTTGA
Found at i:29801418 original size:42 final size:43
Alignment explanation
Indices: 29801349--29801452 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 43
29801339 CATCGACTTA
* *
29801349 TGATTTACGTGTAAGACCATGTCTGGGAAATTAACATCG-TATT
1 TGATTT-CGTGTAAGACCATATCTGGGAAAGTAACATCGATATT
* * * **
29801392 TGATTTCGTGTAAGACCCTATTTGGGACAGTGTCATCGATATT
1 TGATTTCGTGTAAGACCATATCTGGGAAAGTAACATCGATATT
* *
29801435 TGATTACATGTAAGACCA
1 TGATTTCGTGTAAGACCA
29801453 CTCCAAGACG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 25 0.50
43 25 0.50
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATATCTGGGAAAGTAACATCGATATT
Done.