Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 119 of 144
Found at i:27880650 original size:31 final size:31
Alignment explanation
Indices: 27880615--27880676 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
27880605 CAATCGATGG
*
27880615 CTTAAATAAAAACTTTTGAATAGTTCAGTGA
1 CTTAAATAAAAACTTTCGAATAGTTCAGTGA
*
27880646 CTTAAATGAAAACTTTCGAATAGTTCAGTGA
1 CTTAAATAAAAACTTTCGAATAGTTCAGTGA
27880677 TCAAATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (31 bp):
CTTAAATAAAAACTTTCGAATAGTTCAGTGA
Found at i:27881529 original size:26 final size:26
Alignment explanation
Indices: 27881493--27881546 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
27881483 TAGATAGATT
27881493 ATAGATTTAATAAATAATATTATTGA
1 ATAGATTTAATAAATAATATTATTGA
27881519 ATAGATTTAATAAATAATATTATTGA
1 ATAGATTTAATAAATAATATTATTGA
27881545 AT
1 AT
27881547 CCCGTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (26 bp):
ATAGATTTAATAAATAATATTATTGA
Found at i:27881534 original size:13 final size:13
Alignment explanation
Indices: 27881493--27881534 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
27881483 TAGATAGATT
27881493 ATAGATTTAATAA
1 ATAGATTTAATAA
* *
27881506 ATA-ATATTATTGA
1 ATAGAT-TTAATAA
27881519 ATAGATTTAATAA
1 ATAGATTTAATAA
27881532 ATA
1 ATA
27881535 ATATTATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 2 0.09
13 19 0.83
14 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
ATAGATTTAATAA
Found at i:27885990 original size:14 final size:14
Alignment explanation
Indices: 27885971--27886001 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27885961 TATTACCCCA
27885971 CATTTGTAATCTCT
1 CATTTGTAATCTCT
*
27885985 CATTTGTAATCTTT
1 CATTTGTAATCTCT
27885999 CAT
1 CAT
27886002 AATAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (14 bp):
CATTTGTAATCTCT
Found at i:27893480 original size:96 final size:96
Alignment explanation
Indices: 27893364--27893556 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
27893354 AAGTTAAATC
27893364 AGGATTTGGGGTTTTCTATAAAATGTTGAAGTTGAAATATAGTTGGATAGGAAATGGAATACAAA
1 AGGATTTGGGGTTTTCTATAAAATGTTGAAGTTGAAATATAGTTGGATAGGAAATGGAATACAAA
27893429 AAGGGTCAAAACAGAGATATTATAAAATATT
66 AAGGGTCAAAACAGAGATATTATAAAATATT
27893460 AGGATTTGGGGTTTTCTATAAAATGTTGAAGTTGAAATATAGTTGGATAGGAAATGGAATACAAA
1 AGGATTTGGGGTTTTCTATAAAATGTTGAAGTTGAAATATAGTTGGATAGGAAATGGAATACAAA
27893525 AAGGGTCAAAACAGAGATATTATAAAATATT
66 AAGGGTCAAAACAGAGATATTATAAAATATT
27893556 A
1 A
27893557 TATATATTTA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (96 bp):
AGGATTTGGGGTTTTCTATAAAATGTTGAAGTTGAAATATAGTTGGATAGGAAATGGAATACAAA
AAGGGTCAAAACAGAGATATTATAAAATATT
Found at i:27895720 original size:23 final size:23
Alignment explanation
Indices: 27895645--27895758 Score: 106
Period size: 23 Copynumber: 5.0 Consensus size: 23
27895635 AAGTGCTGGG
* *
27895645 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* * ** *
27895668 -AATCAGTAGGCGCACTTAGCGC
1 GAAACAGTAGGCACACAAAGTGC
* *
27895690 -AAGTCAGTAGGCACACGAAGTGC
1 GAA-ACAGTAGGCACACAAAGTGC
27895713 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* *
27895736 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
27895759 TGAACGGTAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.24
23 55 0.73
24 2 0.03
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (23 bp):
GAAACAGTAGGCACACAAAGTGC
Found at i:27895758 original size:46 final size:45
Alignment explanation
Indices: 27895645--27895758 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 45
27895635 AAGTGCTGGG
* * **
27895645 GAAACAGTAAGCACACACAGTGCAATCAGTAGGCGCACTTAGCGC
1 GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
* * *
27895690 -AAGTCAGTAGGCACACGA-AGTGCGAAACAGTAGGCACACAAAGTGC
1 GAA-ACAGTAAGCACAC-ACAGTGC-AAACAGTAGGCACACAAAGCGC
27895736 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGC
27895759 TGAACGGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
44 2 0.04
45 17 0.31
46 34 0.62
47 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (45 bp):
GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
Found at i:27895770 original size:23 final size:23
Alignment explanation
Indices: 27895621--27895758 Score: 102
Period size: 23 Copynumber: 5.9 Consensus size: 23
27895611 CGAAGTACTT
27895621 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
27895647 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * ** *
27895669 ATCAGTAGGCGCACTTAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
27895691 AGTCAGTAGGCACACGAAGTGCGA
1 A-ACAGTAAGCACACAAAGTGCGA
*
27895715 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
27895738 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
27895759 TGAACGGTAA
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
22 18 0.19
23 55 0.59
24 2 0.02
26 14 0.15
27 5 0.05
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:27900093 original size:25 final size:24
Alignment explanation
Indices: 27900037--27900094 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
27900027 AATAAAATAA
*
27900037 ATTATATATTTTTTTAATATTATAT
1 ATTATA-ATTTTTTTAATATCATAT
27900062 ATTATAATTTTTATTAAT-TCATAT
1 ATTATAATTTTT-TTAATATCATAT
*
27900086 TTTAATAAT
1 ATT-ATAAT
27900095 AATTATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATAATTTTTTTAATATCATAT
Found at i:27900206 original size:22 final size:22
Alignment explanation
Indices: 27900178--27900222 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27900168 TATTAAATTT
* **
27900178 ATTTAATAATAATTTTATTAAA
1 ATTTAATAACAATAATATTAAA
27900200 ATTTAATAACAATAATATTAAA
1 ATTTAATAACAATAATATTAAA
27900222 A
1 A
27900223 AAATTATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAATAACAATAATATTAAA
Found at i:27900213 original size:25 final size:25
Alignment explanation
Indices: 27900165--27900215 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
27900155 ATTATTTATT
* *
27900165 TTTTATTAAATTTATTTAATAATAA
1 TTTTATTAAATTTATATAACAATAA
27900190 TTTTATTAAAATTTA-ATAACAATAA
1 TTTTATT-AAATTTATATAACAATAA
27900215 T
1 T
27900216 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTATTAAATTTATATAACAATAA
Found at i:27901600 original size:28 final size:28
Alignment explanation
Indices: 27901550--27901618 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
27901540 TAAAATCAAT
* * **
27901550 AAAAACTAT-AAATATTATTAAATTTTA
1 AAAAAATATAAAATATTATAAAATTAGA
*
27901577 ATAAAATATTAAAATATTA-AAAATTAGA
1 AAAAAATA-TAAAATATTATAAAATTAGA
27901605 AAAAAATATAAAAT
1 AAAAAATATAAAAT
27901619 CATAATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 12 0.35
28 14 0.41
29 8 0.24
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAAAATATAAAATATTATAAAATTAGA
Found at i:27901890 original size:16 final size:16
Alignment explanation
Indices: 27901869--27901902 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
27901859 ATTTTTATAA
*
27901869 ATTTTTACGGTTTTTT
1 ATTTTTACGATTTTTT
27901885 ATTTTTACGATTTTTT
1 ATTTTTACGATTTTTT
27901901 AT
1 AT
27901903 AAAAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.68
Consensus pattern (16 bp):
ATTTTTACGATTTTTT
Found at i:27904840 original size:54 final size:54
Alignment explanation
Indices: 27904776--27904887 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
27904766 TGCAAATGTT
27904776 GTTGGGAGGTTAATGTATGCTATGCTATGTACAATACCTGACATTTCACAAGCA
1 GTTGGGAGGTTAATGTATGCTATGCTATGTACAATACCTGACATTTCACAAGCA
27904830 GTTGGGAGGTTAATGTATGCTATGCTATGTACAATACCTGACATTTCACAAGCA
1 GTTGGGAGGTTAATGTATGCTATGCTATGTACAATACCTGACATTTCACAAGCA
27904884 GTTG
1 GTTG
27904888 CAAGTATATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (54 bp):
GTTGGGAGGTTAATGTATGCTATGCTATGTACAATACCTGACATTTCACAAGCA
Found at i:27906490 original size:17 final size:17
Alignment explanation
Indices: 27906470--27906525 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
27906460 TAGTTTTTAA
*
27906470 TTAAATTTATTATGAAT
1 TTAAATTTATTATAAAT
27906487 TTAAATTTGCA-TA-AAAT
1 TTAAATTT--ATTATAAAT
27906504 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
27906521 TTAAA
1 TTAAA
27906526 CTTAAAACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 1 0.03
16 2 0.06
17 28 0.82
18 2 0.06
19 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:27906542 original size:34 final size:33
Alignment explanation
Indices: 27906468--27906543 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
27906458 TTTAGTTTTT
* * *
27906468 AATTAAATTTATTATGAATTTAAATTTGCATAAA
1 AATTAAATTTATTATAAATTTAAACTT-CAAAAA
*
27906502 ATTTAAATTTATTATAAATTTAAACTT-AAAACTA
1 AATTAAATTTATTATAAATTTAAACTTCAAAA--A
27906536 AATTAAAT
1 AATTAAAT
27906544 GTCCAAAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 3 0.09
34 32 0.91
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (33 bp):
AATTAAATTTATTATAAATTTAAACTTCAAAAA
Found at i:27906613 original size:49 final size:48
Alignment explanation
Indices: 27906553--27906648 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 48
27906543 TGTCCAAAGT
* *
27906553 CCATTTTACAAGCCCGATTGGGCCAAATTTGATTAGCCCAAAGTTCAAC
1 CCATTTTACAAGCCCAATTGGGCCAAATTTGACTAGCCCAAA-TTCAAC
* *
27906602 CCATTTTACAAGCCCAATTGGGCTAAATTTGGCTAGCCCAAATTCAA
1 CCATTTTACAAGCCCAATTGGGCCAAATTTGACTAGCCCAAATTCAA
27906649 TAACAAAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 5 0.12
49 38 0.88
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (48 bp):
CCATTTTACAAGCCCAATTGGGCCAAATTTGACTAGCCCAAATTCAAC
Found at i:27907627 original size:21 final size:21
Alignment explanation
Indices: 27907603--27907642 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27907593 AATAAATGGA
*
27907603 TTTTGAAAGGAAATAATAAAT
1 TTTTGAAAGAAAATAATAAAT
* *
27907624 TTTTTAGAGAAAATAATAA
1 TTTTGAAAGAAAATAATAA
27907643 TAATAATCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (21 bp):
TTTTGAAAGAAAATAATAAAT
Found at i:27908600 original size:59 final size:59
Alignment explanation
Indices: 27908432--27908749 Score: 294
Period size: 59 Copynumber: 5.4 Consensus size: 59
27908422 CCCAAACAGT
* * * * * *
27908432 CCAAAAATTACCATTTTACCCCT-AAAATTTCAGGAAATTACA-TTCTGACCCCGAAACTT--
1 CCAAAAATTACCATTTTACCCCTCGAACTTTCA--AAATTCCATTTTTAACCCCG--ATTTCA
* *
27908491 CCAAAAATTACCATTTTACCCCTCGAACTCTTTAAAATTCCATTTTTAACCCCTATTTCA
1 CCAAAAATTACCATTTTACCCCTCGAACT-TTCAAAATTCCATTTTTAACCCCGATTTCA
* *
27908551 CCAAAAATTACCATTTTACGCC-CGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCTCGAACTTT-CAAAATTCCATTTTTAACCCCGATTTCA
* *
27908610 CC-AAAATTACCATTTTA-CCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTCGAACTTT-CAAAATTCCATTTTTAACCCCGATTTCA
* * * ** * * *
27908668 CTAAAAATTACCGTTTTACCCC-CAAAACACTCAACAATTCTATTTTTTAACCTCGACTTCA
1 CCAAAAATTACCATTTTACCCCTC-GAACTTTCAA-AATTCCA-TTTTTAACCCCGATTTCA
*
27908729 CC-AAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
27908750 CCAAGTATCC
Statistics
Matches: 220, Mismatches: 27, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
57 2 0.01
58 55 0.25
59 80 0.36
60 62 0.28
61 21 0.10
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTCGAACTTTCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:27908644 original size:58 final size:58
Alignment explanation
Indices: 27908494--27908744 Score: 271
Period size: 58 Copynumber: 4.2 Consensus size: 58
27908484 GAAACTTCCA
*
27908494 AAAATTACCATTTTACCCCTCGAACTCTT-TAAAATTCCATTTTTAACCCCT-ATTTCACC
1 AAAATTACCATTTTA-CCCTCGAACT-TTCCAAAATTCCATTTTTAA-CCCTGATTTCACC
27908553 AAAAATTACCATTTTACGCC-CGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC
1 -AAAATTACCATTTTAC-CCTCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC
* *
27908612 AAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTAA-CCTCGATTTCACTA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCT-GATTTCAC-C
* * * ** * *
27908671 AAAATTACCGTTTTACCCCCAAAACACT-CAACAATTCTATTTTTTAA-CCTCGACTTCACC
1 AAAATTACCATTTTACCCTC-GAACTTTCCAA-AATTCCA-TTTTTAACCCT-GATTTCACC
27908731 AAAATTACCATTTT
1 AAAATTACCATTTT
27908745 GCCCCCCAAG
Statistics
Matches: 169, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
57 5 0.03
58 55 0.33
59 51 0.30
60 40 0.24
61 18 0.11
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC
Found at i:27908650 original size:28 final size:28
Alignment explanation
Indices: 27908435--27908653 Score: 111
Period size: 29 Copynumber: 7.5 Consensus size: 28
27908425 AAACAGTCCA
* *
27908435 AAAATTACCATTTTACCCCTAAAATTT-C
1 AAAATTACCATTTTA-CCCTGAACTTTCC
* *
27908463 AGGAAATTA-CATTCTGACCCCGAAAC-TTCC
1 A--AAATTACCATT-TTACCCTG-AACTTTCC
*
27908493 AAAAATTACCATTTTACCCCTCGAACTCTT-T
1 -AAAATTACCATTTTA-CCCT-GAACT-TTCC
27908524 AAAATT-CCATTTTTAACCCCT--A-TTTCACC
1 AAAATTACCA-TTTT-A-CCCTGAACTTT--CC
*
27908553 AAAAATTACCATTTTACGCCCGAACTTTCC
1 -AAAATTACCATTTTAC-CCTGAACTTTCC
27908583 AAAATT-CCATTTTTAACCCTG-A-TTTCACC
1 AAAATTACCA-TTTT-ACCCTGAACTTT--CC
27908612 AAAATTACCATTTTACCCTTGAACTTTCC
1 AAAATTACCATTTTACCC-TGAACTTTCC
27908641 AAAATT-CCATTTT
1 AAAATTACCATTTT
27908654 TAACCTCGAT
Statistics
Matches: 151, Mismatches: 10, Indels: 60
0.68 0.05 0.27
Matches are distributed among these distances:
26 2 0.01
27 4 0.03
28 18 0.12
29 58 0.38
30 49 0.32
31 15 0.10
32 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTGAACTTTCC
Found at i:27908673 original size:29 final size:28
Alignment explanation
Indices: 27908524--27908673 Score: 114
Period size: 29 Copynumber: 5.1 Consensus size: 28
27908514 CGAACTCTTT
*
27908524 AAAATTCCATTTTTAACCCCTATTTCACC
1 AAAATTCCATTTTTAACCCCGATTTCA-C
27908553 AAAAATTACCA-TTTT-ACGCCCGAACTTTC-C
1 -AAAATT-CCATTTTTAAC-CCCG-A-TTTCAC
*
27908583 AAAATTCCATTTTTAACCCTGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTTCA-C
*
27908612 AAAATTACCA-TTTT-ACCCTTGAACTTTC-C
1 AAAATT-CCATTTTTAACCC-CG-A-TTTCAC
*
27908641 AAAATTCCATTTTTAACCTCGATTTCAC
1 AAAATTCCATTTTTAACCCCGATTTCAC
27908669 TAAAA
1 -AAAA
27908674 ATTACCGTTT
Statistics
Matches: 100, Mismatches: 4, Indels: 33
0.73 0.03 0.24
Matches are distributed among these distances:
27 8 0.08
28 13 0.13
29 44 0.44
30 23 0.23
31 8 0.08
32 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTTAACCCCGATTTCAC
Found at i:27910100 original size:28 final size:28
Alignment explanation
Indices: 27910026--27910275 Score: 126
Period size: 28 Copynumber: 8.7 Consensus size: 28
27910016 AAGGGTTCGG
* *
27910026 GGGGTAAAATGATAATTTTTGGTGAAA-TTA
1 GGGGTAAAATGGTAA-TTTT-G-GAAAGTTT
* *
27910056 GGGTTAAAAATGG-AATTTTGAAAAGTTT
1 GGGGT-AAAATGGTAATTTTGGAAAGTTT
*
27910084 GGGGTAAAATGGTAATTTTGGTGAAA--TC
1 GGGGTAAAATGGTAATTTT-G-GAAAGTTT
* * *
27910112 GAGTTAAAAATAG-AATTTTGGAAAGTTT
1 GGGGT-AAAATGGTAATTTTGGAAAGTTT
*
27910140 AGGGGTAAAATGGTAATTTTGGTGAAA--TC
1 -GGGGTAAAATGGTAATTTT-G-GAAAGTTT
* * *
27910169 GAGGTTAAAATGG-AATTTTAGAAAGTTCG
1 G-GGGTAAAATGGTAATTTTGGAAAGTT-T
27910198 GGGGTAAAATGGTAATTTTTGGTGAAA--TT
1 GGGGTAAAATGGTAA-TTTT-G-GAAAGTTT
* * *
27910227 GGGGTTAAAAAT-GAAATTTTAGAAGGTTT
1 GGGG-T-AAAATGGTAATTTTGGAAAGTTT
27910256 GGGGGTAAAATGGTAATTTT
1 -GGGGTAAAATGGTAATTTT
27910276 TTGGAAGTTT
Statistics
Matches: 169, Mismatches: 25, Indels: 53
0.68 0.10 0.21
Matches are distributed among these distances:
26 8 0.05
27 14 0.08
28 53 0.31
29 52 0.31
30 23 0.14
31 15 0.09
32 4 0.02
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.34
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTT
Found at i:27910146 original size:57 final size:58
Alignment explanation
Indices: 27909972--27910275 Score: 377
Period size: 57 Copynumber: 5.2 Consensus size: 58
27909962 CACTGGGGAT
* ** *
27909972 AAATGGTAATTTTGTGTGAAATTGGGGTTAAAAATGGAATTTTTA-AGGGTTCGGGGGGTA
1 AAATGGTAATTTTG-GTGAAATTCGGGTTAAAAATGGAA-TTTTAGAAAGTT-TGGGGGTA
* *
27910032 AAATGATAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTT-GAAAAGTTT-GGGGTA
1 AAATGGTAA-TTTTGGTGAAATTCGGGTTAAAAATGGAATTTTAG-AAAGTTTGGGGGTA
* * * *
27910090 AAATGGTAATTTTGGTGAAA-TCGAGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTA
1 AAATGGTAATTTTGGTGAAATTCGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTA
*
27910147 AAATGGTAATTTTGGTGAAA-TCGAGGTT-AAAATGGAATTTTAGAAAGTTCGGGGGTA
1 AAATGGTAATTTTGGTGAAATTCG-GGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTA
* * *
27910204 AAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGAAATTTTAGAAGGTTTGGGGGTA
1 AAATGGTAA-TTTTGGTGAAATTCGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTA
27910263 AAATGGTAATTTT
1 AAATGGTAATTTT
27910276 TTGGAAGTTT
Statistics
Matches: 217, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
56 25 0.12
57 75 0.35
58 36 0.17
59 41 0.19
60 35 0.16
61 5 0.02
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (58 bp):
AAATGGTAATTTTGGTGAAATTCGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTA
Found at i:27910273 original size:29 final size:29
Alignment explanation
Indices: 27910174--27910275 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
27910164 AAATCGAGGT
* *
27910174 TAAAATGG-AATTTTAGAAAGTTCGGGGG
1 TAAAATGGTAATTTTAGAAGGTTTGGGGG
* ** ** *
27910202 TAAAATGGTAATTTTTGGTGAAATTGGGGT
1 TAAAATGGTAATTTTAGAAG-GTTTGGGGG
*
27910232 TAAAAAT-GAAATTTTAGAAGGTTTGGGGG
1 T-AAAATGGTAATTTTAGAAGGTTTGGGGG
27910261 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
27910276 TTGGAAGTTT
Statistics
Matches: 54, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
28 13 0.24
29 21 0.39
30 15 0.28
31 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.35
Consensus pattern (29 bp):
TAAAATGGTAATTTTAGAAGGTTTGGGGG
Found at i:27911272 original size:75 final size:75
Alignment explanation
Indices: 27911113--27911263 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
27911103 CTTTCATTTT
27911113 TATTGTTTTAGTCCTTTTAAAACCGAACCAGATCTGGAAAATCCAGATCTGGAAGATTTGCTCGA
1 TATTGTTTTAGTCCTTTTAAAACCGAACCAGATCTGGAAAATCCAGATCTGGAAGATTTGCTCGA
27911178 AAATGTCCTC
66 AAATGTCCTC
* *
27911188 TATTGTTTTAGTCCTTTTAAAACCGAACCAGATCTGGAAAATCCATATCTGGAAGATTTGTTCGA
1 TATTGTTTTAGTCCTTTTAAAACCGAACCAGATCTGGAAAATCCAGATCTGGAAGATTTGCTCGA
27911253 AAATGTCCTC
66 AAATGTCCTC
27911263 T
1 T
27911264 TCCTTTTTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (75 bp):
TATTGTTTTAGTCCTTTTAAAACCGAACCAGATCTGGAAAATCCAGATCTGGAAGATTTGCTCGA
AAATGTCCTC
Found at i:27912217 original size:14 final size:13
Alignment explanation
Indices: 27912198--27912242 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
27912188 TTGGGCCTAT
27912198 TTGGGCCATTGTAA
1 TTGGGCC-TTGTAA
27912212 TTGGGCCTT-TAA
1 TTGGGCCTTGTAA
27912224 TTTGGGCCTTTGTAA
1 -TTGGGCC-TTGTAA
27912239 TTGG
1 TTGG
27912243 ACATGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 9 0.32
14 13 0.46
15 3 0.11
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (13 bp):
TTGGGCCTTGTAA
Found at i:27912230 original size:13 final size:13
Alignment explanation
Indices: 27912196--27912234 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
27912186 CATTGGGCCT
27912196 ATTTGGGCCATTGTA
1 ATTTGGGCC-TT-TA
27912211 A-TTGGGCCTTTA
1 ATTTGGGCCTTTA
27912223 ATTTGGGCCTTT
1 ATTTGGGCCTTT
27912235 GTAATTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.13
13 12 0.52
14 7 0.30
15 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (13 bp):
ATTTGGGCCTTTA
Found at i:27912255 original size:27 final size:27
Alignment explanation
Indices: 27912198--27912255 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
27912188 TTGGGCCTAT
* * * *
27912198 TTGGGCCATTGTAATTGGGCCTTTAAT
1 TTGGGCCATTGTAATTGGACATGTAAA
*
27912225 TTGGGCCTTTGTAATTGGACATGTAAA
1 TTGGGCCATTGTAATTGGACATGTAAA
27912252 TTGG
1 TTGG
27912256 ACATTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.40
Consensus pattern (27 bp):
TTGGGCCATTGTAATTGGACATGTAAA
Found at i:27912295 original size:5 final size:5
Alignment explanation
Indices: 27912278--27912361 Score: 80
Period size: 5 Copynumber: 15.6 Consensus size: 5
27912268 TACAAATAAT
27912278 ATTAA ATTTAA ATTAA ATTCAA ACTTAA ATTAA ATTTAA A-TAA ATTTAA
1 ATTAA A-TTAA ATTAA ATT-AA A-TTAA ATTAA A-TTAA ATTAA A-TTAA
* *
27912327 ATTAA ATTAA ATTAAA ATTTAA AATAA ATTTA ATT
1 ATTAA ATTAA ATT-AA A-TTAA ATTAA ATTAA ATT
27912362 TCAAAGTAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
4 4 0.06
5 34 0.50
6 26 0.38
7 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATTAA
Found at i:27912323 original size:10 final size:11
Alignment explanation
Indices: 27912261--27912359 Score: 98
Period size: 11 Copynumber: 8.9 Consensus size: 11
27912251 ATTGGACATT
27912261 TTAAATTTACAA
1 TTAAATTTA-AA
*
27912273 AT-AATATTAAA
1 TTAAAT-TTAAA
27912284 TTTAAA-TTAAA
1 -TTAAATTTAAA
*
27912295 TTCAAACTTAAA
1 TT-AAATTTAAA
27912307 TTAAATTTAAA
1 TTAAATTTAAA
27912318 -TAAATTTAAA
1 TTAAATTTAAA
27912328 TTAAA-TTAAA
1 TTAAATTTAAA
27912338 TTAAAATTTAAA
1 TT-AAATTTAAA
*
27912350 ATAAATTTAA
1 TTAAATTTAA
27912360 TTTCAAAGTA
Statistics
Matches: 75, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
10 19 0.25
11 36 0.48
12 18 0.24
13 2 0.03
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:27912328 original size:16 final size:18
Alignment explanation
Indices: 27912303--27912378 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 18
27912293 AATTCAAACT
27912303 TAAA-TTAAATTT-AAA-
1 TAAATTTAAATTTAAAAG
*
27912318 TAAATTTAAA-TT-AAAT
1 TAAATTTAAATTTAAAAG
*
27912334 TAAATTAAAATTTAAAA-
1 TAAATTTAAATTTAAAAG
*
27912351 TAAATTT-AATTTCAAAG
1 TAAATTTAAATTTAAAAG
27912368 TAAATTCTAAA
1 TAAATT-TAAA
27912379 ACGATTTGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
15 9 0.18
16 22 0.43
17 14 0.27
18 4 0.08
19 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAG
Found at i:27914187 original size:117 final size:112
Alignment explanation
Indices: 27914058--27914307 Score: 274
Period size: 117 Copynumber: 2.2 Consensus size: 112
27914048 TCCCAATACG
*
27914058 CAAAAAAATATTTTTAAATCT-AAAAAATGTGATGTC-AGCCATTTG-GTGCCAAAAACCCAAAA
1 CAAAAAAATATTTTTAAATCTGAAAAAA-GTGATATCGA-CCA-TTGAGTGCCAAAAACCCAAAA
*** * * *
27914120 ATTTATTTTTTTATTCGAATTTTCTTAGGTGTCGACCATTGCTTGTCAAACACT
63 A---AAAATTTTATTCGAAGTTT-TTAGGTGTCAACCATTACTTGTCAAACACT
* * * *
27914174 CAAAAAAAATATTTTTAAATCTGAAAAAAGTGGTATCGACCATTGAGTGCTAAACATCCAAAAAA
1 C-AAAAAAATATTTTTAAATCTGAAAAAAGTGATATCGACCATTGAGTGCCAAAAACCCAAAAAA
* * *
27914239 AAATTTTATTCGTAGTTTTTGGGTGTCAATCATTACTTGTCAAACACT
65 AAATTTTATTCGAAGTTTTTAGGTGTCAACCATTACTTGTCAAACACT
27914287 C-AAAAAATATTTTTAAATCTG
1 CAAAAAAATATTTTTAAATCTG
27914308 GGAAATATGG
Statistics
Matches: 116, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
111 20 0.17
113 27 0.23
114 14 0.12
116 4 0.03
117 44 0.38
118 7 0.06
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (112 bp):
CAAAAAAATATTTTTAAATCTGAAAAAAGTGATATCGACCATTGAGTGCCAAAAACCCAAAAAAA
AATTTTATTCGAAGTTTTTAGGTGTCAACCATTACTTGTCAAACACT
Found at i:27916728 original size:21 final size:24
Alignment explanation
Indices: 27916679--27916730 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
27916669 ACAGAGTTAA
27916679 ATTTAATAAAATAATATGGATGTG
1 ATTTAATAAAATAATATGGATGTG
* *
27916703 TTTTAATAAAAT-ATAT-TATGT-
1 ATTTAATAAAATAATATGGATGTG
27916724 ATTTAAT
1 ATTTAAT
27916731 TCCGTAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 4 0.16
23 4 0.16
24 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (24 bp):
ATTTAATAAAATAATATGGATGTG
Found at i:27919524 original size:17 final size:19
Alignment explanation
Indices: 27919497--27919535 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
27919487 ATACGAGACC
*
27919497 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
27919515 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
27919533 AAA
1 AAA
27919536 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:27922045 original size:18 final size:18
Alignment explanation
Indices: 27922022--27922060 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27922012 AAAAATCAAA
*
27922022 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
27922040 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
27922058 TTT
1 TTT
27922061 ATCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:27922168 original size:23 final size:20
Alignment explanation
Indices: 27922141--27922183 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
27922131 AATGTTTTCT
27922141 TACTCAAGCATTCAAAATCATAA
1 TACTCAAGC--TCAAAAT-ATAA
27922164 TACTCAAGCTCAAAATATAA
1 TACTCAAGCTCAAAATATAA
27922184 CCATGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
23 9 0.45
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (20 bp):
TACTCAAGCTCAAAATATAA
Found at i:27923093 original size:16 final size:18
Alignment explanation
Indices: 27923062--27923099 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
27923052 TTTCCTTCTT
27923062 TTATATTTATTAATATTA
1 TTATATTTATTAATATTA
27923080 TTATA-TTA-TAATATTA
1 TTATATTTATTAATATTA
27923096 TTAT
1 TTAT
27923100 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATTAATATTA
Found at i:27929103 original size:17 final size:19
Alignment explanation
Indices: 27929076--27929114 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
27929066 ATACGAGACC
*
27929076 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
27929094 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
27929112 AAA
1 AAA
27929115 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:27930564 original size:3 final size:3
Alignment explanation
Indices: 27930487--27930553 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
27930477 ATGTTTTAGC
* *
27930487 TAA TAA TAA TAA CAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27930535 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
27930554 GTTGATAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:27932736 original size:7 final size:7
Alignment explanation
Indices: 27932724--27932761 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
27932714 GTTTCTCTGT
*
27932724 ATTTTAA
1 ATTTTCA
*
27932731 ATTTTAA
1 ATTTTCA
27932738 ATTTTCA
1 ATTTTCA
27932745 ATTTTCA
1 ATTTTCA
27932752 ATTTTCA
1 ATTTTCA
27932759 ATT
1 ATT
27932762 ATAATCGGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTTCA
Found at i:27947822 original size:22 final size:24
Alignment explanation
Indices: 27947797--27947857 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
27947787 TAAAAATGAT
*
27947797 AAAATTTTAATTTAATCT-TT-TA
1 AAAATTATAATTTAATCTATTGTA
* *
27947819 AAAATTATATTTTTA-CTATTGTA
1 AAAATTATAATTTAATCTATTGTA
27947842 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
27947858 TTCGGTCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 14 0.45
23 15 0.48
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (24 bp):
AAAATTATAATTTAATCTATTGTA
Found at i:27948376 original size:20 final size:18
Alignment explanation
Indices: 27948351--27948387 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
27948341 GTATTATTTA
27948351 ATAAATTATTAAATAATAGG
1 ATAAATTA-TAAA-AATAGG
27948371 ATAAATTATAAAAATAG
1 ATAAATTATAAAAATAG
27948388 TCATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
ATAAATTATAAAAATAGG
Found at i:27949084 original size:32 final size:32
Alignment explanation
Indices: 27949042--27949102 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
27949032 TTAAAAATAG
27949042 TTTTAACATGTTGTCTATATACTTTTAAGTTT
1 TTTTAACATGTTGTCTATATACTTTTAAGTTT
* *
27949074 TTTTAGCATGTTGTCTATATATTTTTAAG
1 TTTTAACATGTTGTCTATATACTTTTAAG
27949103 GTAAAATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (32 bp):
TTTTAACATGTTGTCTATATACTTTTAAGTTT
Found at i:27959393 original size:54 final size:51
Alignment explanation
Indices: 27959311--27959497 Score: 225
Period size: 51 Copynumber: 3.6 Consensus size: 51
27959301 ATTTCCTTTG
* ** * *
27959311 ATACTCACGATGACA-TATGGTCATCGGACCTCTTGTGTTCATATAGGAATTCAT
1 ATACTCACGATGACACT-TAGTCATCGGACCTC-T-AATCCATAAAGG-ATTCAT
27959365 ATACTCACGATGACACTTAGTCATCGGACCTCTAATCCATAAAGGATTCACT
1 ATACTCACGATGACACTTAGTCATCGGACCTCTAATCCATAAAGGATTCA-T
* * *
27959417 -TACTCATGATGACACTTAGTCATCGGACCTCTAATCCGTAAAGGATTTAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCTAATCCATAAAGGATTCAT
* *
27959467 TTACTCACGATAACACTTAGTCATCGGACCT
1 ATACTCACGATGACACTTAGTCATCGGACCT
27959498 TTTCGTTATA
Statistics
Matches: 120, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
50 1 0.01
51 79 0.66
52 9 0.08
53 1 0.01
54 29 0.24
55 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (51 bp):
ATACTCACGATGACACTTAGTCATCGGACCTCTAATCCATAAAGGATTCAT
Found at i:27972684 original size:42 final size:37
Alignment explanation
Indices: 27972650--27972724 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
27972640 AAATACAATA
* * *
27972650 CTAATTTCACTATTATTTCAATTAAAGAATCAAAATT
1 CTAATTTAACTATTATTTCAATTAAAAAAACAAAATT
**
27972687 CTAATTTAACTATTATTTCAAAAAAAAAAATCAAAATT
1 CTAATTTAACTATTATTTCAATTAAAAAAA-CAAAATT
27972725 AAATACTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.37
Consensus pattern (37 bp):
CTAATTTAACTATTATTTCAATTAAAAAAACAAAATT
Found at i:27976816 original size:23 final size:21
Alignment explanation
Indices: 27976772--27976816 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
27976762 ATTATGTAGC
*
27976772 ATATCTTGATCTCCAAAATTA
1 ATATCTTGATCGCCAAAATTA
*
27976793 ATATCTTGATTCCGCCAAATTTA
1 ATATCTTGA-T-CGCCAAAATTA
27976816 A
1 A
27976817 ACATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
ATATCTTGATCGCCAAAATTA
Found at i:27983139 original size:26 final size:25
Alignment explanation
Indices: 27983080--27983149 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
27983070 GTCTACATTA
* *
27983080 TCATGATTTTATTTTATTCACAGTT
1 TCATGGTTTTATTTTGTTCACAGTT
* *
27983105 TCATGGTTTTATTTTGTTCATATTTT
1 TCATGGTTTTATTTTGTTCACA-GTT
*
27983131 TCGTGGTTTTAATTTTGTT
1 TCATGGTTTT-ATTTTGTT
27983150 TACTCTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 19 0.50
26 11 0.29
27 8 0.21
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (25 bp):
TCATGGTTTTATTTTGTTCACAGTT
Found at i:27988985 original size:5 final size:5
Alignment explanation
Indices: 27988975--27989009 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
27988965 AAAGTAAAAT
27988975 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
1 GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG GGAAG
27989010 AAGTGGTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
GGAAG
Found at i:28003209 original size:16 final size:17
Alignment explanation
Indices: 28003179--28003212 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28003169 ATATATTTAT
*
28003179 ATAAATTTTATAAAAAA
1 ATAAATTTTAGAAAAAA
28003196 ATAAA-TTTAGAAAAAA
1 ATAAATTTTAGAAAAAA
28003212 A
1 A
28003213 AATACAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAATTTTAGAAAAAA
Found at i:28003873 original size:25 final size:24
Alignment explanation
Indices: 28003844--28003892 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28003834 AAGTGACGGT
*
28003844 TGACGTGACAATAATAATGACGTGA
1 TGACGTGA-AAAAATAATGACGTGA
*
28003869 TGACGTGAAAAAATATTGACGTGA
1 TGACGTGAAAAAATAATGACGTGA
28003893 AAACAATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (24 bp):
TGACGTGAAAAAATAATGACGTGA
Found at i:28003890 original size:16 final size:17
Alignment explanation
Indices: 28003869--28003900 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28003859 AATGACGTGA
28003869 TGACGTGAAAA-AATAT
1 TGACGTGAAAACAATAT
28003885 TGACGTGAAAACAATA
1 TGACGTGAAAACAATA
28003901 CTATAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (17 bp):
TGACGTGAAAACAATAT
Found at i:28011246 original size:151 final size:144
Alignment explanation
Indices: 28011074--28011372 Score: 350
Period size: 144 Copynumber: 2.0 Consensus size: 144
28011064 AAGTCAATTT
* * * * * * *
28011074 TTAAAAAAAATTAATCCATAAATTGATACGTAAATTATGTCATTTTT-TCATTTTGGTACCTAAT
1 TTAAAAAAAATTAACCCATAAA-TGATACCTAAACTATATCATTTTTCCCATTTTGATACCTAAC
* *
28011138 ATTTTTTTAGTCACAAATGATATTTATTATCTAAACTATTTTTTTCCCAAATTA-ATACTTTTAT
65 ATTTTTTTAGTCACAAATG-------GTATCTAAACTATTTTTTTCCCAAATTAGA-ACCTTTAT
*
28011202 TAGTTCAATCGTTAATCAAACTC
122 TAGTTCAATCGTTAATCAAACAC
** * *
28011225 TTAAAAAGGATTAACCCATAAATGGTACCTAAACTATATCATTTTTCCCATTTTGATATCTAACA
1 TTAAAAAAAATTAACCCATAAATGATACCTAAACTATATCATTTTTCCCATTTTGATACCTAACA
* * *
28011290 TTTTTTTGGTTACAAATGGTATCTAAACTATTTTTTTCCCAAATTAGAACCTTTGTTAGTTCAAT
66 TTTTTTTAGTCACAAATGGTATCTAAACTATTTTTTTCCCAAATTAGAACCTTTATTAGTTCAAT
28011355 CGTTAATCAAACAC
131 CGTTAATCAAACAC
28011369 TTAA
1 TTAA
28011373 GTTTATTTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
144 59 0.46
145 1 0.01
150 20 0.16
151 49 0.38
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (144 bp):
TTAAAAAAAATTAACCCATAAATGATACCTAAACTATATCATTTTTCCCATTTTGATACCTAACA
TTTTTTTAGTCACAAATGGTATCTAAACTATTTTTTTCCCAAATTAGAACCTTTATTAGTTCAAT
CGTTAATCAAACAC
Found at i:28011517 original size:19 final size:19
Alignment explanation
Indices: 28011481--28011518 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28011471 ATATATATAT
*
28011481 TTAAAAATATTAAAATTTA
1 TTAAAAATATAAAAATTTA
28011500 TTAAAAATA-AAAATATTTA
1 TTAAAAATATAAAA-ATTTA
28011519 AACATTACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAATATAAAAATTTA
Found at i:28012292 original size:29 final size:30
Alignment explanation
Indices: 28012259--28012328 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 30
28012249 AAATTAAAAT
28012259 TTCATGTATACAATTGCACA-AAATCA-AA
1 TTCATGTATACAATTGCACACAAATCATAA
28012287 GTTCATGTATACAATTGCACACTAAATCATAA
1 -TTCATGTATACAATTGCACAC-AAATCATAA
28012319 TTCATGTATA
1 TTCATGTATA
28012329 GTTTTGGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 20 0.53
31 16 0.42
32 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (30 bp):
TTCATGTATACAATTGCACACAAATCATAA
Found at i:28019158 original size:15 final size:14
Alignment explanation
Indices: 28019131--28019157 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28019121 TTGTTTTATT
28019131 GAAAATGATTTTTG
1 GAAAATGATTTTTG
28019145 GAAAATGATTTTT
1 GAAAATGATTTTT
28019158 TTTTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (14 bp):
GAAAATGATTTTTG
Found at i:28022431 original size:25 final size:25
Alignment explanation
Indices: 28022381--28022431 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28022371 AACAATTTTG
*
28022381 ACATTTTGAAAATGTTATAATGTTA
1 ACATTTTGAAAATGTTATAATATTA
*
28022406 ACATTTTGAAAATGTTATTATATTA
1 ACATTTTGAAAATGTTATAATATTA
28022431 A
1 A
28022432 AAGAAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (25 bp):
ACATTTTGAAAATGTTATAATATTA
Found at i:28022524 original size:6 final size:6
Alignment explanation
Indices: 28022513--28022538 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28022503 TTCTGCAACT
28022513 CGACAC CGACAC CGACAC CGACAC CG
1 CGACAC CGACAC CGACAC CGACAC CG
28022539 TCAACGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
CGACAC
Found at i:28030626 original size:71 final size:70
Alignment explanation
Indices: 28030511--28030798 Score: 522
Period size: 70 Copynumber: 4.1 Consensus size: 70
28030501 AAAGTCAACC
*
28030511 ATACTTTTTTATTTAATTTATTATATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
28030576 ATCAA
66 ATCAA
* *
28030581 ATACTTTTTTTGTTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAATC
1 ATAC-TTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACC
28030646 AATCAA
65 AATCAA
*
28030652 ATACTTCTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
28030717 ATCAA
66 ATCAA
28030722 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTTACCACATGTGGAACC
1 ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTG-TTTACCACATGTGGAACC
28030787 AATCAA
65 AATCAA
28030793 ATACTT
1 ATACTT
28030799 CATGACGCTG
Statistics
Matches: 209, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
70 112 0.54
71 97 0.46
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (70 bp):
ATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
ATCAA
Found at i:28030706 original size:141 final size:141
Alignment explanation
Indices: 28030511--28030799 Score: 526
Period size: 141 Copynumber: 2.0 Consensus size: 141
28030501 AAAGTCAACC
* *
28030511 ATACTTTTTTATTTAATTTATTATATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
1 ATACTTCTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
*
28030576 ATCAAATACTTTTTTTGTTTAATTTATTAAATGAAATTTATTAATTACCTTG-TTTACCACATGT
66 ATCAAATAC-TTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTTACCACATGT
*
28030640 GGAATCAATCAA
130 GGAACCAATCAA
28030652 ATACTTCTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
1 ATACTTCTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
28030717 ATCAAATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTTACCACATGTG
66 ATCAAATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTTACCACATGTG
28030782 GAACCAATCAA
131 GAACCAATCAA
28030793 ATACTTC
1 ATACTTC
28030800 ATGACGCTGA
Statistics
Matches: 143, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
140 41 0.29
141 102 0.71
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (141 bp):
ATACTTCTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTACCACATGTGGAACCA
ATCAAATACTTTTTTATTTAATTTATTAAATGAAATTTATTAATTACCTTGTTTTACCACATGTG
GAACCAATCAA
Found at i:28031232 original size:26 final size:25
Alignment explanation
Indices: 28031203--28031260 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
28031193 CCACCACCGT
*
28031203 ACTTCAACA-TCCATCTTTCCATGCAA
1 ACTTCAACATTCCATC-GTCC-TGCAA
28031229 ACTTCAA-ATTCCATCGTCCTGCAA
1 ACTTCAACATTCCATCGTCCTGCAA
*
28031253 ATTTCAAC
1 ACTTCAAC
28031261 CTCCCATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 11 0.39
25 4 0.14
26 13 0.46
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (25 bp):
ACTTCAACATTCCATCGTCCTGCAA
Found at i:28032293 original size:2 final size:2
Alignment explanation
Indices: 28032286--28032321 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28032276 TTAATAAATA
28032286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28032322 TGCATGAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28038080 original size:16 final size:16
Alignment explanation
Indices: 28038067--28038120 Score: 74
Period size: 15 Copynumber: 3.4 Consensus size: 16
28038057 TCAAAATAAA
28038067 TATTTTTTAAAATATT
1 TATTTTTTAAAATATT
*
28038083 TA-TTTTTACAATATT
1 TATTTTTTAAAATATT
*
28038098 TATTTTTTTAAAATTTT
1 TA-TTTTTTAAAATATT
28038115 TATTTT
1 TATTTT
28038121 AAATAATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 14 0.42
16 6 0.18
17 13 0.39
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTTAAAATATT
Found at i:28038105 original size:17 final size:17
Alignment explanation
Indices: 28038069--28038120 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
28038059 AAAATAAATA
28038069 TTTTTTAAAATATTTA-
1 TTTTTTAAAATATTTAT
*
28038085 -TTTTTACAATATTTAT
1 TTTTTTAAAATATTTAT
*
28038101 TTTTTTAAAATTTTTAT
1 TTTTTTAAAATATTTAT
28038118 TTT
1 TTT
28038121 AAATAATATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.45
17 17 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTAAAATATTTAT
Found at i:28044508 original size:63 final size:63
Alignment explanation
Indices: 28044433--28044560 Score: 148
Period size: 63 Copynumber: 2.0 Consensus size: 63
28044423 TCTTCAATCT
* ** * * *
28044433 AAAAAATTCAATAAAATTAGGCATCAATGTTTACAAAAATTATCATTTTAGTTTTAATTCTAA
1 AAAAAACTCAATAAAATTAACCATCAATATTTACAAAAATTATCAATTTAGTTCTAATTCTAA
* * * * * *
28044496 AAAAAACTCAATAAATTTAACCTTCAATATTTACAAAATTTGTGAATTTAGTTCTAATTTTAA
1 AAAAAACTCAATAAAATTAACCATCAATATTTACAAAAATTATCAATTTAGTTCTAATTCTAA
28044559 AA
1 AA
28044561 GTTTAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (63 bp):
AAAAAACTCAATAAAATTAACCATCAATATTTACAAAAATTATCAATTTAGTTCTAATTCTAA
Found at i:28049090 original size:31 final size:29
Alignment explanation
Indices: 28049052--28049121 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
28049042 TTAAAATTTT
*
28049052 AATAATAAAA-TTGTACTTTGATTTTTTTAAA
1 AATAATAAAATTTG-A-TTT-AATTTTTTAAA
28049083 AATAATAAAAATTTGATTTAATTTTTTAAA
1 AATAAT-AAAATTTGATTTAATTTTTTAAA
*
28049113 AATTATAAA
1 AATAATAAA
28049122 GATATATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 3 0.09
30 15 0.43
31 9 0.26
32 5 0.14
33 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (29 bp):
AATAATAAAATTTGATTTAATTTTTTAAA
Found at i:28052474 original size:15 final size:15
Alignment explanation
Indices: 28052399--28052474 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
28052389 TAATTTAATA
28052399 TAATAATAATTATAT
1 TAATAATAATTATAT
* *
28052414 TAAGAAT-GTTAT-T
1 TAATAATAATTATAT
* *
28052427 AAATTATATATTAT-T
1 TAATAATA-ATTATAT
* *
28052442 TTATTA-AATTATATT
1 TAATAATAATTATA-T
28052457 TAATAATAATTATAT
1 TAATAATAATTATAT
28052472 TAA
1 TAA
28052475 AATTTAATAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
13 10 0.22
14 5 0.11
15 24 0.52
16 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAATAATAATTATAT
Found at i:28055891 original size:6 final size:6
Alignment explanation
Indices: 28055882--28055948 Score: 75
Period size: 6 Copynumber: 11.2 Consensus size: 6
28055872 TTTTAATTTT
*
28055882 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
28055930 CTTTGA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
28055949 CAAAAGTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 38 0.73
8 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:28055903 original size:17 final size:16
Alignment explanation
Indices: 28055873--28055946 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
28055863 TAAATTGATT
*
28055873 TTTAATTTTATTTAAA
1 TTTAAATTTATTTAAA
28055889 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
28055906 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
28055920 TTTAAATTTACTTTGAA
1 TTTAAATTTA-TTTAAA
28055937 TTTAAATTTA
1 TTTAAATTTA
28055947 AACAAAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.22
15 2 0.04
16 11 0.22
17 27 0.53
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:28056931 original size:12 final size:12
Alignment explanation
Indices: 28056916--28056941 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28056906 GAAAAAAGAT
28056916 AATATAAAAATA
1 AATATAAAAATA
28056928 AATATAAAAATA
1 AATATAAAAATA
28056940 AA
1 AA
28056942 CAAAGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATATAAAAATA
Found at i:28057701 original size:30 final size:30
Alignment explanation
Indices: 28057662--28057962 Score: 313
Period size: 30 Copynumber: 9.9 Consensus size: 30
28057652 CCCCAAACAA
* *
28057662 TCCAGAAATTATATTTTGACCCCGAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
28057693 TCCAAAATTACATTTTGACCCTAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
28057722 TCCAAAATTGCATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28057752 TCCAAAATTACATTTTAACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * * * *
28057781 TCAAAAATTGCATTTTAACCCTAAAAATTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28057811 TCCAAAATTACATTTTGACCCCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * **
28057841 TCCAAAATTATATTTTAATTTTAACCTTAAAAC-TT
1 TCCAAAA-T-TA----CATTTTGACCCCAAAACTTT
28057876 TCCAAAAATTACATTTTGACCCCCAAAACTTT
1 TCC-AAAATTACATTTTGA-CCCCAAAACTTT
*
28057908 TCCAAAATTACATTTTGACCCTAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
28057937 TCAAAAATTACATTTTGCCCCCAAAA
1 TCCAAAATTACATTTTGACCCCAAAA
28057963 ATTTCCTAAA
Statistics
Matches: 229, Mismatches: 30, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
29 77 0.34
30 94 0.41
31 27 0.12
32 7 0.03
34 2 0.01
35 6 0.03
36 16 0.07
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:28057759 original size:59 final size:59
Alignment explanation
Indices: 28057686--28057987 Score: 347
Period size: 59 Copynumber: 5.0 Consensus size: 59
28057676 TTTGACCCCG
*
28057686 AAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTCCAAAATTGCATTTTAACCCTA
1 AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCCAAAATTGCATTTTAACCCTA
* *
28057745 AAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTCAAAAATTGCATTTTAACCCTA
1 AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCCAAAATTGCATTTTAACCCTA
* * ** *
28057804 AAAATTTTCCAAAATTACATTTTGACCCCGAAACTTTTCCAAAATTATATTTTAATTTTAACCTT
1 AAACTTTTCCAAAATTACATTTTGACCCCAAAAC-TTTCC--AA--A-A-TTGCATTTTAACCCT
28057869 A
59 A
* *
28057870 AAAC-TTTCCAAAAATTACATTTTGACCCCCAAAACTTTTCCAAAATTACATTTTGACCCTA
1 AAACTTTTCC-AAAATTACATTTTGA-CCCCAAAAC-TTTCCAAAATTGCATTTTAACCCTA
* * * * **
28057931 AAAC-TTTCAAAAATTACATTTTGCCCCCAAAAATTTCCTAAATCCCATTTTTAACCC
1 AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCCAAAATTGCA-TTTTAACCC
28057988 CGATTTCACC
Statistics
Matches: 210, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
58 11 0.05
59 103 0.49
60 18 0.09
61 20 0.10
62 3 0.01
63 1 0.00
64 1 0.00
65 8 0.04
66 31 0.15
67 14 0.07
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTCCAAAATTGCATTTTAACCCTA
Found at i:28057884 original size:66 final size:67
Alignment explanation
Indices: 28057792--28057962 Score: 209
Period size: 66 Copynumber: 2.7 Consensus size: 67
28057782 CAAAAATTGC
* * *
28057792 ATTTTAACCCTAAAAATTTTCCAAAATTACATTTTGA-CCCCGAAACTTTTCCAAAATTATATTT
1 ATTTTAACCCTAAAAACTTTCCAAAATTACATTTTGACCCCCAAAACTTTTCCAAAATTACATTT
28057856 TA
66 TA
*
28057858 ATTTTAA-CCTTAAAACTTTCCAAAAATTACATTTTGACCCCCAAAACTTTTCCAAAATTAC---
1 ATTTTAACCCTAAAAACTTTCC-AAAATTACATTTTGACCCCCAAAACTTTTCCAAAATTACATT
28057919 ---
65 TTA
* *
28057919 ATTTTGACCCT-AAAACTTTCAAAAATTACATTTTG-CCCCCAAAA
1 ATTTTAACCCTAAAAACTTTCCAAAATTACATTTTGACCCCCAAAA
28057963 ATTTCCTAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 13
0.83 0.05 0.11
Matches are distributed among these distances:
59 9 0.09
60 14 0.15
61 15 0.16
62 3 0.03
65 12 0.12
66 22 0.23
67 21 0.22
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (67 bp):
ATTTTAACCCTAAAAACTTTCCAAAATTACATTTTGACCCCCAAAACTTTTCCAAAATTACATTT
TA
Found at i:28057981 original size:29 final size:29
Alignment explanation
Indices: 28057662--28057973 Score: 183
Period size: 29 Copynumber: 10.3 Consensus size: 29
28057652 CCCCAAACAA
* * **
28057662 TCCAGAAATTATATTTTGACCCCGAAACTTT
1 TCCA-AAATTACATTTTG-CCCCCAAAAATT
* * *
28057693 TCCAAAATTACATTTTGACCCTAAAACTT
1 TCCAAAATTACATTTTGCCCCCAAAAATT
* ** * *
28057722 TCCAAAATTGCATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGCCCCCAAAA-ATT
** *
28057752 TCCAAAATTACATTTTAACCCCAAAACTT
1 TCCAAAATTACATTTTGCCCCCAAAAATT
* * ** *
28057781 TCAAAAATTGCATTTTAACCCTAAAAATTT
1 TCCAAAATTACATTTTGCCCCCAAAAA-TT
* **
28057811 TCCAAAATTACATTTTGACCCCGAAACTTT
1 TCCAAAATTACATTTTG-CCCCCAAAAATT
* ** ** *
28057841 TCCAAAATTATATTTTAATTTTAACCTTAAAACTT
1 TCCAAAA-T-TA----CATTTTGCCCCCAAAAATT
*
28057876 TCCAAAAATTACATTTTGACCCCCAAAACTTT
1 TCC-AAAATTACATTTTG-CCCCCAAAA-ATT
* * *
28057908 TCCAAAATTACATTTTGACCCTAAAACTT
1 TCCAAAATTACATTTTGCCCCCAAAAATT
*
28057937 TCAAAAATTACATTTTGCCCCCAAAAATT
1 TCCAAAATTACATTTTGCCCCCAAAAATT
*
28057966 TCCTAAAT
1 TCCAAAAT
28057974 CCCATTTTTA
Statistics
Matches: 225, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
29 90 0.40
30 75 0.33
31 31 0.14
32 7 0.03
34 2 0.01
35 11 0.05
36 9 0.04
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAATTACATTTTGCCCCCAAAAATT
Found at i:28058119 original size:59 final size:58
Alignment explanation
Indices: 28057970--28058135 Score: 228
Period size: 58 Copynumber: 2.9 Consensus size: 58
28057960 AAAATTTCCT
*
28057970 AAATCCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCTCGAACTTTAA
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCTCGAACTTTAA
* * *
28058028 AAATTTCATTTTTATCCCCGATTTCACTAAAATTTACCATTTTACCCTCGAAGCTTCT-A
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCTCGAA-CTT-TAA
* * * *
28058087 AAATTCCGTTTTCAACCTCGATTTCACCAAAA-TTACCATTTTGCCCTCG
1 AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCTCG
28058136 GGTATCCATA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
58 64 0.67
59 30 0.32
60 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (58 bp):
AAATTCCATTTTTAACCCCGATTTCACCAAAATTTACCATTTTACCCTCGAACTTTAA
Found at i:28058134 original size:29 final size:29
Alignment explanation
Indices: 28057979--28058135 Score: 98
Period size: 29 Copynumber: 5.4 Consensus size: 29
28057969 TAAATCCCAT
28057979 TTTTAACCC-CGATTTCACCAAAATTTACCA
1 TTTT-ACCCTCGATTTCACCAAAA-TTACCA
*
28058009 TTTTACCCTCGAACTTT-A--AAAATT-TCA
1 TTTTACCCTCG-A-TTTCACCAAAATTACCA
*
28058036 TTTTTATCCC-CGATTTCACTAAAATTTACCA
1 -TTTTA-CCCTCGATTTCACCAAAA-TTACCA
* * *
28058067 TTTTACCCTCGAAGCTT--CTAAAATT-CCG
1 TTTTACCCTCG-A-TTTCACCAAAATTACCA
*
28058095 TTTTCAACCTCGATTTCACCAAAATTACCA
1 TTTT-ACCCTCGATTTCACCAAAATTACCA
*
28058125 TTTTGCCCTCG
1 TTTTACCCTCG
28058136 GGTATCCATA
Statistics
Matches: 100, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
26 3 0.03
27 6 0.06
28 16 0.16
29 38 0.38
30 27 0.27
31 5 0.05
32 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTTACCCTCGATTTCACCAAAATTACCA
Found at i:28070152 original size:68 final size:68
Alignment explanation
Indices: 28070040--28070509 Score: 849
Period size: 68 Copynumber: 6.9 Consensus size: 68
28070030 TTGCAGGTCT
*
28070040 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
28070105 GAG
66 GAG
*
28070108 TAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
28070173 GAG
66 GAG
28070176 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
28070241 GAG
66 GAG
28070244 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
28070309 GAG
66 GAG
28070312 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
28070377 GAG
66 GAG
*
28070380 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT-A
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
28070444 GAG
66 GAG
* *
28070447 CAACGTCAT-CCCTTGAAATTGAAGTAGAGTGGATAACGCT-TC-TCATCCCTTGAAATTGAAGT
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAAC-ATGTCTTCATCTC-TGAAATTGAAGT
28070509 A
64 A
28070510 GAGTGGATAA
Statistics
Matches: 392, Mismatches: 7, Indels: 7
0.97 0.02 0.02
Matches are distributed among these distances:
65 6 0.02
66 42 0.11
67 13 0.03
68 331 0.84
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
GAG
Found at i:28070610 original size:103 final size:98
Alignment explanation
Indices: 28070400--28070587 Score: 277
Period size: 103 Copynumber: 1.8 Consensus size: 98
28070390 CCCTTGAAAT
28070400 TGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAGAGCAACGTCATCCCTTGAAA
1 TGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAGAGCAACGTCATCCCTTGAAA
* * *
28070465 TTGAAGTAGAGTGGATAACGCTTCTCATCCCTTGAAAT
66 TTGAAGTAAAGTGGATAAAGCTTCTCATCCC-----AC
28070503 TGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGA
1 TGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT-AGAGCAACGTCATCC-CTTGA
28070568 AATTGAAGTAAAGTTGGATA
64 AATTGAAGTAAAG-TGGATA
28070588 GCAAAGTCTT
Statistics
Matches: 81, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
103 43 0.53
104 15 0.19
105 17 0.21
106 6 0.07
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (98 bp):
TGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAGAGCAACGTCATCCCTTGAAA
TTGAAGTAAAGTGGATAAAGCTTCTCATCCCAC
Found at i:28070891 original size:22 final size:22
Alignment explanation
Indices: 28070866--28070932 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
28070856 CTTTTGAGAT
* *
28070866 AATTGATTTTTAATTTTATTTA
1 AATTGATTTTAAATTTAATTTA
*
28070888 AATTTATTTTAAATTTAATTT-
1 AATTGATTTTAAATTTAATTTA
* *
28070909 AATT-A-TTTAAATTTACTTTG
1 AATTGATTTTAAATTTAATTTA
28070929 AATT
1 AATT
28070933 TAAATTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.32
20 5 0.12
21 4 0.10
22 18 0.45
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (22 bp):
AATTGATTTTAAATTTAATTTA
Found at i:28070892 original size:6 final size:6
Alignment explanation
Indices: 28070883--28070943 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
28070873 TTTTAATTTT
* * *
28070883 ATTTAA ATTT-A TTTTAA ATTT-A ATTTAA TTATTTAA ATTT-A CTTTGA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA
28070930 ATTTAA ATTTAA AT
1 ATTTAA ATTTAA AT
28070944 AAAAGTTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
5 13 0.29
6 26 0.58
8 6 0.13
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (6 bp):
ATTTAA
Found at i:28070917 original size:30 final size:31
Alignment explanation
Indices: 28070881--28070941 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
28070871 ATTTTTAATT
*
28070881 TTATTTAAATTTATTTTAAATTT-AATTTAA
1 TTATTTAAATTTACTTTAAATTTAAATTTAA
*
28070911 TTATTTAAATTTACTTTGAATTTAAATTTAA
1 TTATTTAAATTTACTTTAAATTTAAATTTAA
28070942 ATAAAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
TTATTTAAATTTACTTTAAATTTAAATTTAA
Found at i:28070934 original size:11 final size:10
Alignment explanation
Indices: 28070874--28070934 Score: 63
Period size: 11 Copynumber: 6.0 Consensus size: 10
28070864 ATAATTGATT
*
28070874 TTTAATTTTA
1 TTTAAATTTA
28070884 TTTAAATTTA
1 TTTAAATTTA
28070894 TTTTAAATTTAA
1 -TTTAAATTT-A
28070906 TTT-AA-TTA
1 TTTAAATTTA
28070914 TTTAAATTTA
1 TTTAAATTTA
*
28070924 CTTTGAATTTA
1 -TTTAAATTTA
28070935 AATTTAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 14 0.32
11 21 0.48
12 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:28071907 original size:13 final size:13
Alignment explanation
Indices: 28071891--28071917 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28071881 GAAAAAAGAT
28071891 AATATAAAAATAA
1 AATATAAAAATAA
28071904 AATATAAAAATAA
1 AATATAAAAATAA
28071917 A
1 A
28071918 CAAAGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATATAAAAATAA
Found at i:28072715 original size:30 final size:29
Alignment explanation
Indices: 28072646--28072831 Score: 237
Period size: 30 Copynumber: 6.3 Consensus size: 29
28072636 CCCTAAACAA
* *
28072646 TCCAGAAATTGCATTTTAACCCCAAAACTT
1 TCCA-AAATTACATTTTGACCCCAAAACTT
*
28072676 TCTAAAATTACATTTTGACCCCAAAACTCT
1 TCCAAAATTACATTTTGACCCCAAAACT-T
*
28072706 TCCAAAATTACATTTTGACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAAC-TT
*
28072736 TCCAAAATTACATTTTGACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAAC-TT
**
28072766 TCCAAAATTACATTTTGACCTTAAAACTT
1 TCCAAAATTACATTTTGACCCCAAAACTT
* * *
28072795 TCAAAAATTACATTTTGCCCCCAAAAATT
1 TCCAAAATTACATTTTGACCCCAAAACTT
*
28072824 TCCTAAAT
1 TCCAAAAT
28072832 CCCATTTTTA
Statistics
Matches: 139, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
29 54 0.39
30 84 0.60
31 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAATTACATTTTGACCCCAAAACTT
Found at i:28072859 original size:59 final size:59
Alignment explanation
Indices: 28072796--28073051 Score: 250
Period size: 59 Copynumber: 4.4 Consensus size: 59
28072786 TTAAAACTTT
* * * * *
28072796 CAAAAATTA-CATTTTGCCCCCAAAAATTTCCTAAATCCCATTTTTAACCCCGATTTTAC
1 CAAAAATTACCATTTTACCCCCAAAACTTT-CAAAATTCCATTTTTAACCCCGATTTCAC
* * * * * *
28072855 CAAAATTTACCATTTTACCCCCGAACCTTTAAAAATTTCATTTTTAACCCTGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAAACTTTCAAAATTCCATTTTTAACCCCGATTTCAC
* * * * ** *
28072914 TAAAATTTACCATTTTACCCCCGAAGC-TTCTAAAATTCTGTTTTTAACCCCGATTTCAT
1 CAAAAATTACCATTTTACCCCCAAAACTTTC-AAAATTCCATTTTTAACCCCGATTTCAC
** * * *
28072973 TGAAAATTACCATTTTACCCCCAAACCTTT-AAAATTCCATTTTCAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAAACTTTCAAAATTCCATTTTTAACCCCGATTTCAC
*
28073031 C-AAAATTACCATTTTGCCCCC
1 CAAAAATTACCATTTTACCCCC
28073052 GGGTATCCAT
Statistics
Matches: 164, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
57 19 0.12
58 25 0.15
59 102 0.62
60 18 0.11
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAAACTTTCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:28072877 original size:30 final size:29
Alignment explanation
Indices: 28072837--28072937 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
28072827 TAAATCCCAT
28072837 TTTTAACCCCGATTTTACCAAAATTTACCA
1 TTTTAACCCCGATTTTA-CAAAATTTACCA
* *
28072867 TTTTACCCCCGAACCTTTA-AAAATTT--CA
1 TTTTAACCCCG-A-TTTTACAAAATTTACCA
* *
28072895 TTTTTAACCCTGATTTCACTAAAATTTACCA
1 -TTTTAACCCCGATTTTAC-AAAATTTACCA
*
28072926 TTTTACCCCCGA
1 TTTTAACCCCGA
28072938 AGCTTCTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 16 0.29
30 27 0.48
31 3 0.05
32 4 0.07
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTTAACCCCGATTTTACAAAATTTACCA
Found at i:28072947 original size:30 final size:29
Alignment explanation
Indices: 28072856--28072950 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
28072846 CGATTTTACC
28072856 AAAATTTACCATTTTACCCCCGAACCTT-T
1 AAAATTTACCATTTTACCCCCGAA-CTTCT
* * *
28072885 AAAAATTT--CATTTTTAACCCTG-ATTTCACT
1 -AAAATTTACCA-TTTTACCCCCGAACTT--CT
28072915 AAAATTTACCATTTTACCCCCGAAGCTTCT
1 AAAATTTACCATTTTACCCCCGAA-CTTCT
28072945 AAAATT
1 AAAATT
28072951 CTGTTTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
29 16 0.31
30 25 0.49
31 3 0.06
32 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAATTTACCATTTTACCCCCGAACTTCT
Found at i:28077110 original size:36 final size:36
Alignment explanation
Indices: 28077067--28077135 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
28077057 TATTGAGGTA
28077067 GAGGAGGTCGATGGAAGCA-ATGTTGAGATATTAATG
1 GAGGAGGTCGATGGAAG-AGATGTTGAGATATTAATG
*
28077103 GAGGAGGTGGATGGAAGAGATGTTGAGATATTA
1 GAGGAGGTCGATGGAAGAGATGTTGAGATATTA
28077136 TAGTTATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.33, C:0.03, G:0.39, T:0.25
Consensus pattern (36 bp):
GAGGAGGTCGATGGAAGAGATGTTGAGATATTAATG
Found at i:28080449 original size:38 final size:39
Alignment explanation
Indices: 28080371--28080471 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
28080361 TCTAATATTA
**
28080371 TATATTATGATTTTTATT-AATTCATATTTTAATAATAAT
1 TATATTAAAATTTTTATTAAATT-ATATTTTAATAATAAT
28080410 TATATTAAAATTTTTATTAAATTATA-TTTAATAATAAT
1 TATATTAAAATTTTTATTAAATTATATTTTAATAATAAT
* * *
28080448 TATGTTAAAA-TATAATTAAATTAT
1 TATATTAAAATTTTTATTAAATTAT
28080472 TTATTATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 12 0.21
38 21 0.38
39 19 0.34
40 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (39 bp):
TATATTAAAATTTTTATTAAATTATATTTTAATAATAAT
Found at i:28080511 original size:32 final size:31
Alignment explanation
Indices: 28080419--28080511 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 31
28080409 TTATATTAAA
28080419 ATTTTTATTAAATTATATTTAATAATAA-TT
1 ATTTTTATTAAATTATATTTAATAATAATTT
* * * *
28080449 A-TGTTA--AAA-TATAATTAA-ATTATTTATT
1 ATTTTTATTAAATTATATTTAATAATA-AT-TT
28080477 ATTTTTATTAAATTATATTTAATAATAATCTT
1 ATTTTTATTAAATTATATTTAATAATAAT-TT
28080509 ATT
1 ATT
28080512 AAAATTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 3 0.07
26 8 0.17
27 3 0.07
28 3 0.07
29 8 0.17
30 1 0.02
31 3 0.07
32 14 0.30
33 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
ATTTTTATTAAATTATATTTAATAATAATTT
Found at i:28081574 original size:39 final size:38
Alignment explanation
Indices: 28081531--28081610 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
28081521 TTGATTCAAG
*
28081531 TCGTTTTTCAACCGGTTTCATAATCGTT-ATTAGAAACGT
1 TCGTTTTTCAACCAGTTTCATAAT--TTCATTAGAAACGT
*
28081570 TCGTTTTTCAACTAGTTTCATAATTTCCATTAGAAACGT
1 TCGTTTTTCAACCAGTTTCATAATTT-CATTAGAAACGT
28081609 TC
1 TC
28081611 TTAATCATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 2 0.05
39 35 0.95
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (38 bp):
TCGTTTTTCAACCAGTTTCATAATTTCATTAGAAACGT
Found at i:28084477 original size:19 final size:20
Alignment explanation
Indices: 28084402--28084478 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
28084392 TTATAATAAA
28084402 AAATAAAAATCATTAAAATT
1 AAATAAAAATCATTAAAATT
*
28084422 ATAA-AAAAA--ATTAACATT
1 A-AATAAAAATCATTAAAATT
* * *
28084440 TAA-CAAAATTATTAGAAATT
1 AAATAAAAATCATTA-AAATT
28084460 AAATAAAAATCA-TAAAATT
1 AAATAAAAATCATTAAAATT
28084479 TCTAATAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
17 6 0.13
18 8 0.18
19 9 0.20
20 14 0.31
21 8 0.18
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (20 bp):
AAATAAAAATCATTAAAATT
Found at i:28090237 original size:206 final size:206
Alignment explanation
Indices: 28089477--28090494 Score: 1219
Period size: 207 Copynumber: 4.9 Consensus size: 206
28089467 TATAGCTTGC
* * * *
28089477 GACAATTCTTCAATCATATGCCTCATCTCTGACAATTCTATTTCTTGGATTTGATTTTCTCTT-C
1 GACAATTCTTCTATCATA-GCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCTTCC
* *
28089541 TTGACCTCTTATATGT-CAATTCATGGCTTAAAAGTGATTTCTAATATAAGTCTTAAGATCTAAT
65 TTGACCTCTTGTATGTCCAA-TCATGGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAAT
* * * *
28089605 TAAGCTCTGATACTAAAACTGATGTGGTAAATTATTAGGTTAAGTGAAAAATCTAAATAGC-TAA
129 TAAGCTCTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCAAAA
28089669 AAAA-T-AAATGT
194 AAAATTAAAATGT
* * * * *
28089680 GACAATTCTTCTATCATAGTCTCATCTCTGACAACTCTATTTGTTGGCTTTTATTTTTTCTTCCT
1 GACAATTCTTCTATCATAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCTTCCT
* ** *
28089745 TGACCTCTTGTATGTCCAGTCATGCGTCATGCTTTAAAAGTGATTTTTAATATAAGTCTTAATAT
66 TGACCTCTTGTATGTCCAATCAT--G----GC-TTAAAAGTGATTTCCAATATAAGTCTTAAGAT
* * *
28089810 CTAATT-AGACTCTAATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTAAAAAATCTAAATA
124 CTAATTAAG-CTCTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATA
* *
28089874 GCTAAAAAAATTAAAATGC
188 GCAAAAAAAATTAAAATGT
* *
28089893 GACAATTCTTCTATCATAAGCCTCATCTCAAACAATTCTATTTGTTGGCTTTGATATTT-TCTTA
1 GACAATTCTTCTATCAT-AGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGAT-TTTCTCTTC
* * * * *
28089957 CTTGACCTCTTATATGTCCAATTATGACTTAAAAGTGACTTCCAATATAAGTCCTAAGATCTAAT
64 CTTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAAT
* * *
28090022 TATGCTTTGATACCAAAAATGATGTGGTAAAGTATTAGGTTGAGTGAAAAATCTAAATAGCAAAA
129 TAAGCTCTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCAAAA
* *
28090087 AAAATTTAGATGT
194 AAAATTAAAATGT
* * *
28090100 TACAATTCTTCTATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATTTTCTCTTCCT
1 GACAATTCTTCTATCATAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCTTCCT
* * * * ** * * *
28090165 TGACCTCTTGTGTGTCTAGTCATGGCTTAAAGGCAATTTCCACTATAAATCCTAAGATCTAATTA
66 TGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAATTA
* * * * *
28090230 AGCTTTGATAGCAAAATTTATGTGGTAAATTATTAGGTTTGAGTGGAAAATCTAAATAGCTAAAA
131 AGCTCTGATACCAAAAATGATGTGGTAAATTATTAGG-TTGAGTGAAAAATCTAAATAGC-AAAA
28090295 AAAATTAAAATGT
194 AAAATTAAAATGT
* * *
28090308 -ACAATT-TTTTATCATACGCCTCATCTCTAACAATTTTATTTGTTGGCTTTGATTTTCCCTTCC
1 GACAATTCTTCTATCATA-GCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCTTCC
* * * * *
28090371 TTGACTTCTTGTTTGTCCAATCATAGCTTAAAAGTGATTTTCAATATAAGTCTTTAGATCTAATT
65 TTGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAATT
* * * * * *
28090436 -AGACTCTAATACCAAAAATAATGTGATAAAATGTTAGGTTGAGTGGAAAATCTAAATAG
130 AAG-CTCTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAG
28090495 TTAAAAAATT
Statistics
Matches: 700, Mismatches: 94, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
202 38 0.05
203 37 0.05
204 2 0.00
205 4 0.01
206 157 0.22
207 262 0.37
208 17 0.02
209 4 0.01
210 88 0.13
211 6 0.01
212 2 0.00
213 22 0.03
214 58 0.08
215 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (206 bp):
GACAATTCTTCTATCATAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCTTCCT
TGACCTCTTGTATGTCCAATCATGGCTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAATTA
AGCTCTGATACCAAAAATGATGTGGTAAATTATTAGGTTGAGTGAAAAATCTAAATAGCAAAAAA
AATTAAAATGT
Found at i:28090391 original size:413 final size:411
Alignment explanation
Indices: 28089474--28090503 Score: 1322
Period size: 413 Copynumber: 2.5 Consensus size: 411
28089464 TAATATAGCT
* * * * *
28089474 TGCGACAATTCTTCAATCATATGCCTCATCTCTGACAATTCTATTTCTTGGATTTGATTTTCTCT
1 TGCGACAATTCTTCTATCATAAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCT
* *
28089539 TCTTGACCTCTTATATGT-CAATTCATGGCTTAAAAGTGATTTCTAATATAAGTCTTAAGATCTA
66 TCTTGACCTCTTATATGTCCAATT-ATGACTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTA
* * * * *
28089603 ATTAAGCTCTGATACTAAAACTGATGTGGTAAATTATTAGGTTAAGTGAAAAATCTAAATAGCTA
130 ATT-AGCTCTGATACCAAAAATGATGTGGTAAAATATTAGGTTGAGTGAAAAATCTAAATAGCAA
* *
28089668 AAAAATAAATGTGACAATTCTTCTATCATAGTCTCATCTCTGACAACTCTATTTGTTGGCTTTTA
194 AAAAATAAATGTGACAATTCTTCTATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGA
* ** **
28089733 TTTTTTCTTCCTTGACCTCTTGTATGTCCAGTCATGCGTCATGCTTTAAAAGTGATTTTTAATAT
259 TTTTCTCTTCCTTGACCTCTTGTATGTCCAGTCAT-CG---TGCTTTAAAAGCAATTTCCAATAT
* * *
28089798 AAGTCTTAATATCTAATTAGACTCTAATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTAAA
320 AAATCCTAAGATCTAATTAGACTCTAATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTAAA
28089863 AAATCTAAATAGCTAAAAAAATTAAAA
385 AAATCTAAATAGCTAAAAAAATTAAAA
*
28089890 TGCGACAATTCTTCTATCATAAGCCTCATCTCAAACAATTCTATTTGTTGGCTTTGATATTT-TC
1 TGCGACAATTCTTCTATCATAAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGAT-TTTCTC
* *
28089954 TTACTTGACCTCTTATATGTCCAATTATGACTTAAAAGTGACTTCCAATATAAGTCCTAAGATCT
65 TT-CTTGACCTCTTATATGTCCAATTATGACTTAAAAGTGATTTCCAATATAAGTCTTAAGATCT
* *
28090019 AATTATGCTTTGATACCAAAAATGATGTGGTAAAGTATTAGGTTGAGTGAAAAATCTAAATAGCA
129 AATTA-GCTCTGATACCAAAAATGATGTGGTAAAATATTAGGTTGAGTGAAAAATCTAAATAGC-
* *
28090084 AAAAAAATTTAGATGTTACAATTCTTCTATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCT
192 AAAAAAA--TAAATGTGACAATTCTTCTATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCT
* * * *
28090149 TTGATTTTCTCTTCCTTGACCTCTTGTGTGTCTAGTCAT-G-GC-TTAAAGGCAATTTCCACTAT
255 TTGATTTTCTCTTCCTTGACCTCTTGTATGTCCAGTCATCGTGCTTTAAAAGCAATTTCCAATAT
* * * * *
28090211 AAATCCTAAGATCTAATTA-AGCTTTGATAGCAAAATTTATGTGGTAAATTATTAGGTTTGAGTG
320 AAATCCTAAGATCTAATTAGA-CTCTAATACCAAAATTGATGTGGTAAATTATTAGG-TTGAGTA
*
28090275 GAAAATCTAAATAGCTAAAAAAAATTAAAA
383 AAAAATCTAAATAGCT-AAAAAAATTAAAA
* * * * *
28090305 TG-TACAATT-TTTTATCATACGCCTCATCTCTAACAATTTTATTTGTTGGCTTTGATTTTCCCT
1 TGCGACAATTCTTCTATCATAAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCT
* * * * * *
28090368 TCCTTGACTTCTTGTTTGTCCAATCAT-AGCTTAAAAGTGATTTTCAATATAAGTCTTTAGATCT
66 T-CTTGACCTCTTATATGTCCAATTATGA-CTTAAAAGTGATTTCCAATATAAGTCTTAAGATCT
* * * * * **
28090432 AATTAGACTCTAATACCAAAAATAATGTGATAAAATGTTAGGTTGAGTGGAAAATCTAAATAGTT
129 AATTAG-CTCTGATACCAAAAATGATGTGGTAAAATATTAGGTTGAGTGAAAAATCTAAATAGCA
28090497 AAAAAAT
193 AAAAAAT
28090504 TAGGAGATAC
Statistics
Matches: 539, Mismatches: 62, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
410 1 0.00
412 12 0.02
413 213 0.40
414 29 0.05
415 15 0.03
416 57 0.11
417 112 0.21
418 12 0.02
420 88 0.16
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (411 bp):
TGCGACAATTCTTCTATCATAAGCCTCATCTCTAACAATTCTATTTGTTGGCTTTGATTTTCTCT
TCTTGACCTCTTATATGTCCAATTATGACTTAAAAGTGATTTCCAATATAAGTCTTAAGATCTAA
TTAGCTCTGATACCAAAAATGATGTGGTAAAATATTAGGTTGAGTGAAAAATCTAAATAGCAAAA
AAATAAATGTGACAATTCTTCTATCATAGTCTCATCTCTAACAACTCTATTTGTTGGCTTTGATT
TTCTCTTCCTTGACCTCTTGTATGTCCAGTCATCGTGCTTTAAAAGCAATTTCCAATATAAATCC
TAAGATCTAATTAGACTCTAATACCAAAATTGATGTGGTAAATTATTAGGTTGAGTAAAAAATCT
AAATAGCTAAAAAAATTAAAA
Found at i:28094555 original size:3 final size:3
Alignment explanation
Indices: 28094547--28094575 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28094537 GAATTTTAAT
28094547 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28094576 CTTAGATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28096437 original size:20 final size:20
Alignment explanation
Indices: 28096408--28096446 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28096398 TATTAAATTA
*
28096408 AATTTGATATTAAAATAATC
1 AATTTAATATTAAAATAATC
*
28096428 AATTTAATATTAAATTAAT
1 AATTTAATATTAAAATAAT
28096447 AAAATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTTAATATTAAAATAATC
Found at i:28101217 original size:14 final size:13
Alignment explanation
Indices: 28101192--28101216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28101182 CTTGAATACT
28101192 TTGCTTTTTTTTG
1 TTGCTTTTTTTTG
28101205 TTGCTTTTTTTT
1 TTGCTTTTTTTT
28101217 TTTATATAAA
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:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (13 bp):
TTGCTTTTTTTTG
Found at i:28101929 original size:3 final size:3
Alignment explanation
Indices: 28101921--28101954 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28101911 AATCTTTTAG
28101921 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28101955 ACTCTTGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28104972 original size:594 final size:593
Alignment explanation
Indices: 28103845--28105034 Score: 2290
Period size: 594 Copynumber: 2.0 Consensus size: 593
28103835 GAAAAATACG
28103845 AGACACACCCCTCACAAAGGAATAGATATCTTAAAACACATATAAGCAACTTAGATATAGGGATG
1 AGACACACCCCTCACAAAGGAATAGATATCTTAAAACACATATAAGCAACTTAGATATAGGGATG
*
28103910 AAGAATAGTGAGAAGAGATCACATAATTTTTTTTTATAAAATCGAAGCTTCATTAAAAGAGAAAA
66 AAGAATAGTAAGAAGAGATCACATAATTTTTTTTTATAAAATCGAAGCTTCATTAAAAGAGAAAA
28103975 AGGGGAATATCCAAAAGACCGGTGGAAAACAAATAGTCCTAACAAAAGAAAAGAGAATAGTGAAT
131 AGGGGAATATCCAAAAGACCGGTGGAAAACAAATAGTCCTAACAAAAGAAAAGAGAATAGTGAAT
28104040 AAAGAAAGGGTAAACTATCAAAATACTCACTTTTATTTGTCTTAGGTTACATTGTAGTCACTTAC
196 AAAGAAAGGGTAAACTATCAAAATACTCACTTTTATTTGTCTTAGGTTACATTGTAGTCACTTAC
28104105 GTTATTGTGTTGTAATATTTTAGTCACTGAGCCATCGGTGTAACGGTAAGCTGACGTAACACATT
261 GTTATTGTGTTGTAATATTTTAGTCACTGAGCCATCGGTGTAACGGTAAGCTGACGTAACACATT
28104170 AAATCATCATTTAAAATGAAAATTTTAGGTTAAAGTATATAATTTCTCCCTATATTTTTTCATTT
326 AAATCATCATTTAAAATGAAAATTTTAGGTTAAAGTATATAATTTCTCCCTATATTTTTTCATTT
* *
28104235 TGAGCTTTTTCGTTCGATTTAGGATTCGAATTTGGTAACAGTTCTAGTACATTGAGCCTTGCAAT
391 TGAGCTTTTCCGTTCGATTTAGGATTCGAATTTGGTAACAGTTCTAGCACATTGAGCCTTGCAAT
28104300 TACTTTTGGTGACCGTCGTTGTTTATCATTATCGTCCACCTCATCTTTGCATTGGTTCACAGATA
456 TACTTTTGGTGACCGTCGTTGTTTATCATTATCGTCCACCTCATCTTTGCATTGGTTCACAGATA
28104365 ATATAGAGGCATTCGTACAGATCTTCCGGGGCTTAAGGCTTCATTTGGCATCAACGACAACTTTG
521 ATATAGAGGCATTCGTACAGATCTTCCGGGGCTTAAGGCTTCATTTGGCATCAACGACAACTTTG
28104430 CTATCCAA
586 CTATCCAA
28104438 AGACACACCCCTCACAAAGGAATAGATATCTTAAAACACATATAAGCAACTTAGATATAGGGATG
1 AGACACACCCCTCACAAAGGAATAGATATCTTAAAACACATATAAGCAACTTAGATATAGGGATG
*
28104503 AAGAATAGTAAGAAGAGATCGCATAATTTTTTTTTTATAAAATCGAAGCTTCATTAAAAGAGAAA
66 AAGAATAGTAAGAAGAGATCACATAA-TTTTTTTTTATAAAATCGAAGCTTCATTAAAAGAGAAA
28104568 AAGGGGAATATCCAAAAGACCGGTGGAAAACAAATAGTCCTAACAAAAGAAAAGAGAATAGTGAA
130 AAGGGGAATATCCAAAAGACCGGTGGAAAACAAATAGTCCTAACAAAAGAAAAGAGAATAGTGAA
28104633 TAAAGAAAGGGTAAACTATCAAAATACTCACTTTTATTTGTCTTAGGTTACATTGTAGTCACTTA
195 TAAAGAAAGGGTAAACTATCAAAATACTCACTTTTATTTGTCTTAGGTTACATTGTAGTCACTTA
* *
28104698 CGTTATTGTGTTGTAATATTTTAGTCACTGAGCCATCGGTGTAACGGTAAGCTGACGTGACATAT
260 CGTTATTGTGTTGTAATATTTTAGTCACTGAGCCATCGGTGTAACGGTAAGCTGACGTAACACAT
*
28104763 TAAATCATCATTTAAAATGAAAATTTTAGGTTTAAGTATATAATTTCTCCCTATATTTTTTCATT
325 TAAATCATCATTTAAAATGAAAATTTTAGGTTAAAGTATATAATTTCTCCCTATATTTTTTCATT
28104828 TTGAGCTTTTCCGTTCGATTTAGGATTCGAATTTGGTAACAGTTCTAGCACATTGAGCCTTGCAA
390 TTGAGCTTTTCCGTTCGATTTAGGATTCGAATTTGGTAACAGTTCTAGCACATTGAGCCTTGCAA
28104893 TTACTTTTGGTGACCGTCGTTGTTTATCATTATCGTCCACCTCATCTTTGCATTGGTTCACAGAT
455 TTACTTTTGGTGACCGTCGTTGTTTATCATTATCGTCCACCTCATCTTTGCATTGGTTCACAGAT
* *
28104958 AATATAGAGGCATTCGTACAGATCTTCCGGGGCTTAAGGCTTTATTTGGCATCAACGACAGCTTT
520 AATATAGAGGCATTCGTACAGATCTTCCGGGGCTTAAGGCTTCATTTGGCATCAACGACAACTTT
28105023 GCTATCCAA
585 GCTATCCAA
28105032 AGA
1 AGA
28105035 GGGCCTTAGA
Statistics
Matches: 587, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
593 89 0.15
594 498 0.85
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (593 bp):
AGACACACCCCTCACAAAGGAATAGATATCTTAAAACACATATAAGCAACTTAGATATAGGGATG
AAGAATAGTAAGAAGAGATCACATAATTTTTTTTTATAAAATCGAAGCTTCATTAAAAGAGAAAA
AGGGGAATATCCAAAAGACCGGTGGAAAACAAATAGTCCTAACAAAAGAAAAGAGAATAGTGAAT
AAAGAAAGGGTAAACTATCAAAATACTCACTTTTATTTGTCTTAGGTTACATTGTAGTCACTTAC
GTTATTGTGTTGTAATATTTTAGTCACTGAGCCATCGGTGTAACGGTAAGCTGACGTAACACATT
AAATCATCATTTAAAATGAAAATTTTAGGTTAAAGTATATAATTTCTCCCTATATTTTTTCATTT
TGAGCTTTTCCGTTCGATTTAGGATTCGAATTTGGTAACAGTTCTAGCACATTGAGCCTTGCAAT
TACTTTTGGTGACCGTCGTTGTTTATCATTATCGTCCACCTCATCTTTGCATTGGTTCACAGATA
ATATAGAGGCATTCGTACAGATCTTCCGGGGCTTAAGGCTTCATTTGGCATCAACGACAACTTTG
CTATCCAA
Found at i:28112378 original size:38 final size:39
Alignment explanation
Indices: 28112327--28112402 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
28112317 TTAATAGGGG
28112327 TATTTTAAGAGTAT-AAAAATTAATAGGAATATTTTAAA
1 TATTTTAAGAGTATAAAAAATTAATAGGAATATTTTAAA
* * *
28112365 TATTTTAGGAGTATAAAAAAATTACTAGGAGTATTTTA
1 TATTTTAAGAGTAT-AAAAAATTAATAGGAATATTTTA
28112403 GGTAGAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 13 0.39
40 20 0.61
ACGTcount: A:0.46, C:0.01, G:0.13, T:0.39
Consensus pattern (39 bp):
TATTTTAAGAGTATAAAAAATTAATAGGAATATTTTAAA
Found at i:28112559 original size:158 final size:169
Alignment explanation
Indices: 28112368--28112754 Score: 426
Period size: 181 Copynumber: 2.3 Consensus size: 169
28112358 TTTTAAATAT
* *
28112368 TTTAGGAGTATAAAAAAATTACTA-GGAGTATTTTAGGTAGAATAAAAAATCAAT-AGATAA-T-
1 TTTAAGAGTAT-AAAAAATTAATAGGGA-TATTTTAGGTAGAATAAAAAATCAATAAGATAATTA
*
28112429 A-A-TA-AGGA-TAAT-TTAGGTA-TTTGCAAACAAAGTTAATTTATTTATTTATAAATTTT-AA
64 ACATTACA-AATTAATATTAGGTATTTTGCAAACAAAGTTAATTTATTTATTTATAAATTTTAAA
**
28112487 TTCTTATTATT-A-ATTTTTTATTTAATATAAATAAAGGTGG
128 TTCTTATTATTAATATTTTTTATTTAATATAAATAAAGGTAC
28112527 TTTAAGAGTATAAAAAATTAATAGGGATATTTTAGGTAGAA-AAGAAAATCAATAGAGATAATTT
1 TTTAAGAGTATAAAAAATTAATAGGGATATTTTAGGTAGAATAA-AAAATCAATA-AGATAA-TT
*
28112591 AAGCATTACAAATTAATAAGAAAAAATTAGGTATTTTGTAAACAAAGTTAATTTATTTATTTATA
63 AA-CATTACAAATTAAT--------ATTAGGTATTTTGCAAACAAAGTTAATTTATTTATTTATA
*
28112656 AATTTTAAATTCTTATTATTAATTATTTTTTATTTAATATAAATAAGGGTAC
119 AATTTTAAATTCTTATTATTAA-TATTTTTTATTTAATATAAATAAAGGTAC
* * *
28112708 TTTAACAATATAAAAAAATAATAGAGG-TATTTTAGGTAGAATAAAAA
1 TTTAAGAGTATAAAAAATTAATAG-GGATATTTTAGGTAGAATAAAAA
28112755 GGCAATAGGA
Statistics
Matches: 190, Mismatches: 10, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
157 2 0.01
158 34 0.18
159 13 0.07
160 6 0.03
162 1 0.01
163 1 0.01
165 1 0.01
166 3 0.02
167 5 0.03
176 7 0.04
177 36 0.19
178 13 0.07
179 1 0.01
181 63 0.33
182 4 0.02
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (169 bp):
TTTAAGAGTATAAAAAATTAATAGGGATATTTTAGGTAGAATAAAAAATCAATAAGATAATTAAC
ATTACAAATTAATATTAGGTATTTTGCAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTC
TTATTATTAATATTTTTTATTTAATATAAATAAAGGTAC
Found at i:28112741 original size:181 final size:176
Alignment explanation
Indices: 28112441--28112779 Score: 495
Period size: 181 Copynumber: 1.9 Consensus size: 176
28112431 TAAGGATAAT
28112441 TTAGGTATTTGCAAACAAAGTTAATTTATTTATTTATAAATTTTAATTCTTATTATTAATTTTTT
1 TTAGGTATTTGCAAACAAAGTTAATTTATTTATTTATAAATTTTAATTCTTATTATTAATTTTTT
** * * *
28112506 ATTTAATATAAATAAAGGTGGTTTAAGAGTATAAAAAATTAATAGGGATATTTTAGGTAGAA-AA
66 ATTTAATATAAATAAAGGTACTTTAACAATATAAAAAAATAATAGGGATATTTTAGGTAGAATAA
*
28112570 GAAAATCAATA-GAGATAATTTAAGCATTACAAATTAATAAGAAAAAA
131 -AAAAGCAATAGGA-ATAATTTAAGCATTACAAATTAATAAGAAAAAA
*
28112617 TTAGGTATTTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTAT
1 TTAGGTA-TTTGCAAACAAAGTTAATTTATTTATTTATAAATTTT-AATTCTTATTATT-A--AT
*
28112682 TTTTTATTTAATATAAATAAGGGTACTTTAACAATATAAAAAAATAATAGAGG-TATTTTAGGTA
61 TTTTTATTTAATATAAATAAAGGTACTTTAACAATATAAAAAAATAATAG-GGATATTTTAGGTA
* *
28112746 GAATAAAAAGGCAATAGGAATAATTTAGGCATTA
125 GAATAAAAAAGCAATAGGAATAATTTAAGCATTA
28112780 GAAGGCATTT
Statistics
Matches: 145, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
176 7 0.05
177 36 0.25
178 13 0.09
179 1 0.01
181 82 0.57
182 6 0.04
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.40
Consensus pattern (176 bp):
TTAGGTATTTGCAAACAAAGTTAATTTATTTATTTATAAATTTTAATTCTTATTATTAATTTTTT
ATTTAATATAAATAAAGGTACTTTAACAATATAAAAAAATAATAGGGATATTTTAGGTAGAATAA
AAAAGCAATAGGAATAATTTAAGCATTACAAATTAATAAGAAAAAA
Found at i:28112813 original size:177 final size:177
Alignment explanation
Indices: 28112448--28112871 Score: 483
Period size: 181 Copynumber: 2.4 Consensus size: 177
28112438 AATTTAGGTA
*
28112448 TTTGCAAACAAAGTTAATTTATTTATTTATAAATTTT-AATTCTTATTATT-A--ATTTTTTATT
1 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
** * * *
28112509 TAATATAAATAAAGGTGGTTTAAGAGTATAAAAAATTAATAGGGATATTTTAGGTAGAAAAGAAA
66 TAATATAAATAAAGGTACTTTAACAATATAAAAAAATAATAGGGATATTTTAGGTAGAAAAGAAA
*
28112574 ATCAATAGAGATAATTTAAGCATTACAAATTAATAAGAAAAAATTAGGTAT
131 AGCAATAGAGATAATTTAAGCATTACAAATT-ATAAG--AAAATTA-GTAT
28112625 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
1 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
*
28112690 TAATATAAATAAGGGTACTTTAACAATATAAAAAAATAATAGAGG-TATTTTAGGTAGAATAA-A
66 TAATATAAATAAAGGTACTTTAACAATATAAAAAAATAATAG-GGATATTTTAGGTAGAA-AAGA
* * * * ** *
28112753 AAGGCAATAG-GAATAATTTAGGCATTAGAAGGCATT-TTAG-GTATT-TTAT
129 AAAGCAATAGAG-ATAATTTAAGCATTACAA---ATTATAAGAAAATTAGTAT
* * * * *
28112802 TTTGTAAACAAACTTAATTTTTTTATTTATAAATTTTAAACTTTATTATGATTAGTTA-TTTTTA
1 TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAA--TTCTTATTATTAATTATTTTTTA
28112866 TTTAAT
64 TTTAAT
28112872 CTATATCTAT
Statistics
Matches: 215, Mismatches: 20, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
177 77 0.36
178 25 0.12
179 17 0.08
180 1 0.00
181 85 0.40
182 7 0.03
184 3 0.01
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (177 bp):
TTTGTAAACAAAGTTAATTTATTTATTTATAAATTTTAAATTCTTATTATTAATTATTTTTTATT
TAATATAAATAAAGGTACTTTAACAATATAAAAAAATAATAGGGATATTTTAGGTAGAAAAGAAA
AGCAATAGAGATAATTTAAGCATTACAAATTATAAGAAAATTAGTAT
Found at i:28116210 original size:22 final size:22
Alignment explanation
Indices: 28116168--28116210 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28116158 CTTGGATGAC
* * *
28116168 AAAAACATAAATTACAGAAAAT
1 AAAAACAAAAATTAAAAAAAAT
28116190 AAAAACAAAAATTAAAAAAAA
1 AAAAACAAAAATTAAAAAAAA
28116211 GGGGAGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAACAAAAATTAAAAAAAAT
Found at i:28117143 original size:26 final size:26
Alignment explanation
Indices: 28117081--28117149 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
28117071 TCTAATTTCC
*
28117081 ATTTAATATTTTATA--TAATTATAA
1 ATTTAAAATTTTATATTTAATTATAA
*
28117105 ATATAAAGTATTTTATATTGTAATTA-AA
1 ATTTAAA--ATTTTATATT-TAATTATAA
28117133 ATTTAAAATTTTATATT
1 ATTTAAAATTTTATATT
28117150 CATAAGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.14
26 18 0.49
28 8 0.22
29 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTTAAAATTTTATATTTAATTATAA
Found at i:28123829 original size:6 final size:6
Alignment explanation
Indices: 28123797--28123828 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
28123787 AGGAAAAAAA
*
28123797 AACAAT AACAAT AACAAT AACAAT AATAAT AA
1 AACAAT AACAAT AACAAT AACAAT AACAAT AA
28123829 TGAGCTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (6 bp):
AACAAT
Found at i:28139815 original size:31 final size:26
Alignment explanation
Indices: 28139755--28139807 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28139745 AACCAAACAA
28139755 ACTTATACGAATTATATCATATTCTC
1 ACTTATACGAATTATATCATATTCTC
28139781 ACTTATACGAATTATATCATATTCTC
1 ACTTATACGAATTATATCATATTCTC
28139807 A
1 A
28139808 GGTCACTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.42
Consensus pattern (26 bp):
ACTTATACGAATTATATCATATTCTC
Found at i:28158853 original size:18 final size:21
Alignment explanation
Indices: 28158822--28158861 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
28158812 CAACTTAACT
28158822 TATATATTATAAAATA-TAAA
1 TATATATTATAAAATATTAAA
28158842 TATA-ATTA-AAAATATTAAA
1 TATATATTATAAAATATTAAA
28158861 T
1 T
28158862 TTTAAGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATATTATAAAATATTAAA
Found at i:28171078 original size:15 final size:16
Alignment explanation
Indices: 28171058--28171091 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28171048 GAATTTTTTA
28171058 ATTTAAAT-AAATATT
1 ATTTAAATAAAATATT
28171073 ATTTAAATAAAATATT
1 ATTTAAATAAAATATT
28171089 ATT
1 ATT
28171092 CTGTGCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAAATAAAATATT
Found at i:28172498 original size:42 final size:41
Alignment explanation
Indices: 28172432--28172537 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 41
28172422 ATAAAGAAAG
*
28172432 TTAAAAATCAAAATACAATACTAATTTCA-CTATTATTTCAA
1 TTAAAAATCAAAATACAATACTAATTT-AGCTACTATTTCAA
* * *
28172473 TTAAAGAATCGAAATATAATTCTAATTTAGCTACTATTTCAAA
1 TTAAA-AATCAAAATACAATACTAATTTAGCTACTATTTC-AA
**
28172516 AAAAAAATCAAAATACAATACT
1 TTAAAAATCAAAATACAATACT
28172538 TTTTTAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
41 6 0.11
42 42 0.79
43 5 0.09
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (41 bp):
TTAAAAATCAAAATACAATACTAATTTAGCTACTATTTCAA
Found at i:28176091 original size:244 final size:244
Alignment explanation
Indices: 28175662--28176145 Score: 860
Period size: 244 Copynumber: 2.0 Consensus size: 244
28175652 ATCAGTCCTG
* *
28175662 CACCCAAAGAATAGACAAGTGAAGCAGTGAGTCTACAAATCCATGATATATAACCTGAGTTCCAA
1 CACCCAAAGAATAAACAAGTGAAACAGTGAGTCTACAAATCCATGATATATAACCTGAGTTCCAA
*
28175727 AACATTAACCCTCAAGAGTAATTGATAAGCATAGCTCCAGAATAAAGAAAACCCTAACGACTATC
66 AACATTAACCCTCAAGAGTAATTGATAAGCATAGCTCCAGAATAAAGAAAACCCTAACGACTACC
28175792 GTTTACATGACAATTCTAAAAGAAAGTTGGTTTGAATATTAATAAAAAAGTAACTGCTTTCTATT
131 GTTTACATGACAATTCTAAAAGAAAGTTGGTTTGAATATTAATAAAAAAGTAACTGCTTTCTATT
*
28175857 TATTTTCTAAGTAGTCACAATTAGAAGGAAAAAACCCTAAACCCTCCGA
196 TATTCTCTAAGTAGTCACAATTAGAAGGAAAAAACCCTAAACCCTCCGA
* *
28175906 CACCCAAAGAATAAACAAGTGAAACAGTGAGTCTATAAATCCATGATATATAACCTGAGTTCCTA
1 CACCCAAAGAATAAACAAGTGAAACAGTGAGTCTACAAATCCATGATATATAACCTGAGTTCCAA
*
28175971 AACATTAACCCTCAAGAGTAATTGATAAGCATAGCTCCAGAATAAAGAAAACCCTAATGACTACC
66 AACATTAACCCTCAAGAGTAATTGATAAGCATAGCTCCAGAATAAAGAAAACCCTAACGACTACC
** *
28176036 GTTTGTATGACAATTCTAACAGAAAGTTGGTTTGAATATTAATAAAAAAGTAACTGCTTTCTATT
131 GTTTACATGACAATTCTAAAAGAAAGTTGGTTTGAATATTAATAAAAAAGTAACTGCTTTCTATT
* *
28176101 TATTCTCTAAGTAGTCACAATTAGAATGAACAAACCCTAAACCCT
196 TATTCTCTAAGTAGTCACAATTAGAAGGAAAAAACCCTAAACCCT
28176146 AAACCCGTAA
Statistics
Matches: 228, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
244 228 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (244 bp):
CACCCAAAGAATAAACAAGTGAAACAGTGAGTCTACAAATCCATGATATATAACCTGAGTTCCAA
AACATTAACCCTCAAGAGTAATTGATAAGCATAGCTCCAGAATAAAGAAAACCCTAACGACTACC
GTTTACATGACAATTCTAAAAGAAAGTTGGTTTGAATATTAATAAAAAAGTAACTGCTTTCTATT
TATTCTCTAAGTAGTCACAATTAGAAGGAAAAAACCCTAAACCCTCCGA
Found at i:28181905 original size:20 final size:20
Alignment explanation
Indices: 28181869--28181918 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
28181859 ATAATTAGGT
28181869 TTATTTCTTTAAATTAA-G-A
1 TTATTT-TTTAAATTAATGTA
28181888 GTTATTTTTTAAATTTAATGTA
1 -TTATTTTTTAAA-TTAATGTA
28181910 TTATTTTTT
1 TTATTTTTT
28181919 TTGTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.22
20 10 0.37
21 10 0.37
22 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
TTATTTTTTAAATTAATGTA
Found at i:28189282 original size:18 final size:19
Alignment explanation
Indices: 28189242--28189283 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
28189232 CCGTCGGGCG
* *
28189242 TAGGTATAGCCGCATTGGGA
1 TAGGTATAG-CGCATAGGCA
28189262 TAGGTATAG-GCATAGGCA
1 TAGGTATAGCGCATAGGCA
28189280 TAGG
1 TAGG
28189284 GATTCAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.24
Consensus pattern (19 bp):
TAGGTATAGCGCATAGGCA
Found at i:28189516 original size:13 final size:13
Alignment explanation
Indices: 28189498--28189523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28189488 AATAAGTTAT
28189498 TAATTTGTAAAAA
1 TAATTTGTAAAAA
28189511 TAATTTGTAAAAA
1 TAATTTGTAAAAA
28189524 GGAAAACACA
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TAATTTGTAAAAA
Found at i:28190066 original size:5 final size:5
Alignment explanation
Indices: 28190056--28190088 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
28190046 CCTGCTTTAA
28190056 GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGG
1 GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGG
28190089 TGCCCTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.64, T:0.18
Consensus pattern (5 bp):
GGGAT
Found at i:28207352 original size:169 final size:170
Alignment explanation
Indices: 28207073--28207410 Score: 570
Period size: 169 Copynumber: 2.0 Consensus size: 170
28207063 GGACTGTGAC
*
28207073 TCTGAGCATGTCACAAGATCACAAGCATGCCCAAGTTCGATTATACTACACTTTTAGTGGATTAT
1 TCTGAGCATGTCACAAGATCACAAGCATGCCCAAGTTCAATTATACTACACTTTTAGTGGATTAT
* * * *
28207138 TTTTCCTTGTTTTCTGGTTTAACAGATGGCTTGCCTGTTCTGCTGTTTTAAATCAAGAC-AAATT
66 TTTTCCCTGTTTTCTGGTTTAACAGATGGATGGCCTGTTCTGCTGTTGTAAATCAAGACAAAATT
*
28207202 AATTTTGAATAATTGGCTTGTGAAATATGAATCCTTCTTT
131 AATTTTGAATAATTGGCTTCTGAAATATGAATCCTTCTTT
* * *
28207242 TCTGAGCATTTCACAATATCAGAAGCATGCCCAAGTTCAATTATACTACACTTTTAGTGGATTAT
1 TCTGAGCATGTCACAAGATCACAAGCATGCCCAAGTTCAATTATACTACACTTTTAGTGGATTAT
28207307 TTTTCCCTGTTTTCTGGTTTAACAGATGGATGGCCTGTTCTGCTGTTGTAAATCAAGACAAAATT
66 TTTTCCCTGTTTTCTGGTTTAACAGATGGATGGCCTGTTCTGCTGTTGTAAATCAAGACAAAATT
* *
28207372 AATTTTGAATAATTGGCTTCTGAAATCTGAATCTTTCTT
131 AATTTTGAATAATTGGCTTCTGAAATATGAATCCTTCTT
28207411 CTAAACTGCC
Statistics
Matches: 157, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
169 116 0.74
170 41 0.26
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (170 bp):
TCTGAGCATGTCACAAGATCACAAGCATGCCCAAGTTCAATTATACTACACTTTTAGTGGATTAT
TTTTCCCTGTTTTCTGGTTTAACAGATGGATGGCCTGTTCTGCTGTTGTAAATCAAGACAAAATT
AATTTTGAATAATTGGCTTCTGAAATATGAATCCTTCTTT
Found at i:28207693 original size:219 final size:219
Alignment explanation
Indices: 28207314--28207752 Score: 824
Period size: 219 Copynumber: 2.0 Consensus size: 219
28207304 TATTTTTCCC
*
28207314 TGTTTTCTGGTTTAACAGATGGATGGCCTGTTCTGCTGTTGTAAATCAAGACAAAATTAATTTTG
1 TGTTTTCTGGTTTAACAGATGGATGACCTGTTCTGCTGTTGTAAATCAAGACAAAATTAATTTTG
28207379 AATAATTGGCTTCTGAAATCTGAATCTTTCTTCTAAACTGCCACTAATATAGATAATTTTCTCAA
66 AATAATTGGCTTCTGAAATCTGAATCTTTCTTCTAAACTGCCACTAATATAGATAATTTTCTCAA
28207444 TTGCATATTCAATGCTTTTGTATTAAATGTATTAGCCATGATGCATGGTGTTACCGGTGCATTAC
131 TTGCATATTCAATGCTTTTGTATTAAATGTATTAGCCATGATGCATGGTGTTACCGGTGCATTAC
28207509 ATATTCTTTATTCTGCTCTATTGT
196 ATATTCTTTATTCTGCTCTATTGT
*
28207533 TGTTTTCTGGTTTAACAGATGGCTGACCTGTTCTGCTGTTGTAAATCAAGACAAAATTAATTTTG
1 TGTTTTCTGGTTTAACAGATGGATGACCTGTTCTGCTGTTGTAAATCAAGACAAAATTAATTTTG
* * *
28207598 AATAATTGGCTTCTGAAATCTGAATCTTTCTTCTAGACTGCCACTAATATGGATAATTTTTTCAA
66 AATAATTGGCTTCTGAAATCTGAATCTTTCTTCTAAACTGCCACTAATATAGATAATTTTCTCAA
*
28207663 TTGCATATTCGATGCTTTTGTATTAAATGTATTAGCCATGATGCATGGTGTTACCGGTGCATTAC
131 TTGCATATTCAATGCTTTTGTATTAAATGTATTAGCCATGATGCATGGTGTTACCGGTGCATTAC
28207728 ATATTCTTTATTCTGCTCTATTGT
196 ATATTCTTTATTCTGCTCTATTGT
28207752 T
1 T
28207753 TATATACTTT
Statistics
Matches: 214, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
219 214 1.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (219 bp):
TGTTTTCTGGTTTAACAGATGGATGACCTGTTCTGCTGTTGTAAATCAAGACAAAATTAATTTTG
AATAATTGGCTTCTGAAATCTGAATCTTTCTTCTAAACTGCCACTAATATAGATAATTTTCTCAA
TTGCATATTCAATGCTTTTGTATTAAATGTATTAGCCATGATGCATGGTGTTACCGGTGCATTAC
ATATTCTTTATTCTGCTCTATTGT
Found at i:28214807 original size:18 final size:19
Alignment explanation
Indices: 28214786--28214827 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28214776 TAAATAATTC
28214786 AAATATTATAAAAAT-A-AA
1 AAATATTA-AAAAATCATAA
28214804 AAATATTAAAAAATCATAA
1 AAATATTAAAAAATCATAA
28214823 AAATA
1 AAATA
28214828 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 9 0.41
19 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATATTAAAAAATCATAA
Found at i:28214901 original size:12 final size:12
Alignment explanation
Indices: 28214884--28214916 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28214874 ATTTAAAAAT
28214884 TTAATATT-TTA
1 TTAATATTCTTA
28214895 GTTAATATTCTTA
1 -TTAATATTCTTA
28214908 TTAATATTC
1 TTAATATTC
28214917 ATTTTGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (12 bp):
TTAATATTCTTA
Found at i:28216647 original size:22 final size:22
Alignment explanation
Indices: 28216619--28216663 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28216609 AACACAATGA
*
28216619 AAAAAGAGTTGATAAAAATAGT
1 AAAAAGAGTTGAAAAAAATAGT
28216641 AAAAAGAGTTGAAAAAAATAGT
1 AAAAAGAGTTGAAAAAAATAGT
28216663 A
1 A
28216664 GATCATGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (22 bp):
AAAAAGAGTTGAAAAAAATAGT
Done.