Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 84 of 318
Found at i:28605332 original size:46 final size:44
Alignment explanation
Indices: 28605273--28605406 Score: 142
Period size: 46 Copynumber: 3.0 Consensus size: 44
28605263 ACAGGACAGA
* *
28605273 ACAGAAATGAGCCATGTAAGTCTATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCTATATT--AAATATGGCATTGGAG
* * *
28605319 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCTATATTAAATATGGCATTGGAG
* ** * *
28605363 ACAGGAATAATTCATGTAAGTCTATGTCAAAGATATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCTATAT-TAA-ATATGGCATTGG
28605407 CAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 35 0.48
45 1 0.01
46 37 0.51
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCTATATTAAATATGGCATTGGAG
Found at i:28605368 original size:44 final size:45
Alignment explanation
Indices: 28605280--28605406 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 45
28605270 AGAACAGAAA
* *
28605280 TGAGCCATGTAAGTCTATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAT
* *
28605326 TGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAA
1 TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
* ** * * *
28605370 TAATTCATGTAAGTCTATGTCAAAGATATGGCATTGG
1 TGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
28605407 CAGGATATTG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 35 0.51
45 1 0.01
46 32 0.47
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
Found at i:28606987 original size:113 final size:114
Alignment explanation
Indices: 28606857--28607082 Score: 337
Period size: 114 Copynumber: 2.0 Consensus size: 114
28606847 ATGAATTTGA
* * * * *
28606857 CATCATCATAAAATGCAAATTAGTTTAAAAT-TTCAAATGTTTTTACTTTAATATTAAAATCAAA
1 CATCAGCATAAAATGCAAATTAGTTTAAAATATTAAAATATTTTTACTTCAACATTAAAATCAAA
*
28606921 GGCTTTCATGAGTAAAAATTACAAGTCGTGAGCTTATTTAACTACAAAG
66 GGCTTTCAGGAGTAAAAATTACAAGTCGTGAGCTTATTTAACTACAAAG
*
28606970 CATCAGCATAAAATGCAAATTAGTTTAAATTATTAAAATATTTTTACTTCAACATTAAAATCAAA
1 CATCAGCATAAAATGCAAATTAGTTTAAAATATTAAAATATTTTTACTTCAACATTAAAATCAAA
* * * * *
28607035 GGCTTTCAGGAGTAAAAATTATATGTTGTGTGCTTATTTAATTACAAA
66 GGCTTTCAGGAGTAAAAATTACAAGTCGTGAGCTTATTTAACTACAAA
28607083 AATAGCATAA
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
113 29 0.29
114 71 0.71
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (114 bp):
CATCAGCATAAAATGCAAATTAGTTTAAAATATTAAAATATTTTTACTTCAACATTAAAATCAAA
GGCTTTCAGGAGTAAAAATTACAAGTCGTGAGCTTATTTAACTACAAAG
Found at i:28608813 original size:25 final size:25
Alignment explanation
Indices: 28608784--28608840 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
28608774 TAATTAAAAT
*
28608784 TAAAATTAAATAGTAAAATTTAATCA
1 TAAAATTAAATAGCAAAATTTAAT-A
* * *
28608810 -AAAATCAAGTGGCAAAATTTAATA
1 TAAAATTAAATAGCAAAATTTAATA
28608834 TAAAATT
1 TAAAATT
28608841 GAAGTGGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (25 bp):
TAAAATTAAATAGCAAAATTTAATA
Found at i:28610844 original size:29 final size:29
Alignment explanation
Indices: 28610811--28610875 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
28610801 TAATTTTTTA
*
28610811 ATATTAAAATTGTT-AATATATTTTAATTT
1 ATATTAAAATTGTTGAATA-ATATTAATTT
* * *
28610840 ATATTAAATTTTTTGAATAATATTACTTT
1 ATATTAAAATTGTTGAATAATATTAATTT
28610869 ATATTAA
1 ATATTAA
28610876 TCACATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATTAAAATTGTTGAATAATATTAATTT
Found at i:28625960 original size:9 final size:9
Alignment explanation
Indices: 28625948--28625976 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
28625938 TTAATGACAA
28625948 ACCTGCATC
1 ACCTGCATC
28625957 ACCTGCATC
1 ACCTGCATC
28625966 ACCTGCATC
1 ACCTGCATC
28625975 AC
1 AC
28625977 AACCTCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.45, G:0.10, T:0.21
Consensus pattern (9 bp):
ACCTGCATC
Found at i:28630447 original size:21 final size:20
Alignment explanation
Indices: 28630407--28630455 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
28630397 ATAAATAAAA
*
28630407 TCATTCATGTCAATTCCCTG
1 TCATTCATGACAATTCCCTG
*
28630427 TCATTCACTGACAATTTCCTG
1 TCATTCA-TGACAATTCCCTG
28630448 TCATTCAT
1 TCATTCAT
28630456 AACTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (20 bp):
TCATTCATGACAATTCCCTG
Found at i:28630654 original size:21 final size:21
Alignment explanation
Indices: 28630628--28630758 Score: 176
Period size: 21 Copynumber: 6.3 Consensus size: 21
28630618 TGAATACACC
*
28630628 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
28630649 AACAGAAACTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
28630670 AACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
28630689 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
* *
28630710 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
*
28630731 AATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
28630752 AACAGAA
1 AACAGAA
28630759 AGTAGAATAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.17
20 4 0.04
21 74 0.79
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:28630700 original size:61 final size:63
Alignment explanation
Indices: 28630628--28630758 Score: 212
Period size: 61 Copynumber: 2.1 Consensus size: 63
28630618 TGAATACACC
*
28630628 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGCTGAACAGAAGCTCAGAAGAGCTG
* * *
28630689 AACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTGAATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGCTGAACAGAAGCTCAGAAGAGCTG
28630752 AACAGAA
1 AACAGAA
28630759 AGTAGAATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 50 0.78
62 2 0.03
63 12 0.19
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (63 bp):
AACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGCTGAACAGAAGCTCAGAAGAGCTG
Found at i:28634508 original size:22 final size:22
Alignment explanation
Indices: 28634463--28634526 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
28634453 ACTAATGAAT
* * *
28634463 AGAGAGCACTAAAGTGATATAC
1 AGAGAGCACGAAAGTGCTAAAC
* *
28634485 AGCGAGCACGAATGTGCTAAAC
1 AGAGAGCACGAAAGTGCTAAAC
*
28634507 AGAGAGCACTAAAGTGCTAA
1 AGAGAGCACGAAAGTGCTAA
28634527 TAATCGGAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.16
Consensus pattern (22 bp):
AGAGAGCACGAAAGTGCTAAAC
Found at i:28634539 original size:25 final size:25
Alignment explanation
Indices: 28634508--28634598 Score: 121
Period size: 25 Copynumber: 3.6 Consensus size: 25
28634498 GTGCTAAACA
28634508 GAGAGCACTAAAGTGCTAATAATCG
1 GAGAGCACTAAAGTGCTAATAATCG
28634533 GAGAGCACTAACA-TGCTAATAATCG
1 GAGAGCACTAA-AGTGCTAATAATCG
* * *
28634558 AAGAGCACTAACGTGCTAATAATCA
1 GAGAGCACTAAAGTGCTAATAATCG
28634583 GAGACCGCACTAAAGT
1 GAGA--GCACTAAAGT
28634599 TCCTTAATGG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
25 47 0.82
26 1 0.02
27 9 0.16
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.19
Consensus pattern (25 bp):
GAGAGCACTAAAGTGCTAATAATCG
Found at i:28635471 original size:18 final size:18
Alignment explanation
Indices: 28635448--28635485 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28635438 CTTGAAAACC
28635448 TTAGTTTTCCCTTTTTCT
1 TTAGTTTTCCCTTTTTCT
*
28635466 TTAGTTTTTCCTTTTTCT
1 TTAGTTTTCCCTTTTTCT
28635484 TT
1 TT
28635486 CTCTTTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.71
Consensus pattern (18 bp):
TTAGTTTTCCCTTTTTCT
Found at i:28635499 original size:13 final size:12
Alignment explanation
Indices: 28635472--28635512 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
28635462 TTCTTTAGTT
28635472 TTTC-CTTTTTC
1 TTTCTCTTTTTC
28635483 TTTCTCTTTTTC
1 TTTCTCTTTTTC
*
28635495 GTTTCTC-CTTTC
1 -TTTCTCTTTTTC
28635507 TTTCTC
1 TTTCTC
28635513 CCCTGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 10 0.37
12 11 0.41
13 6 0.22
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:28635593 original size:21 final size:18
Alignment explanation
Indices: 28635567--28635607 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
28635557 TTGTTTGTTT
28635567 TTATAATATAATATAATATCA
1 TTATAATAT--TATAATA-CA
28635588 TTATAATATTATAATACA
1 TTATAATATTATAATACA
28635606 TT
1 TT
28635608 TTAACTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
21 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATATTATAATACA
Found at i:28639837 original size:5 final size:5
Alignment explanation
Indices: 28639829--28639877 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
28639819 ATAAAATAAA
*
28639829 GAAAT GAAAT -AAA- GAAAT -AAAT GAAAT -AAAT GAAAT -AAAA GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT
28639874 GAAA
1 GAAA
28639878 AAGAAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 17 0.46
5 20 0.54
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (5 bp):
GAAAT
Found at i:28639840 original size:13 final size:14
Alignment explanation
Indices: 28639822--28639877 Score: 73
Period size: 13 Copynumber: 4.2 Consensus size: 14
28639812 TCTAATAATA
28639822 AAAT-AAAGAAATG
1 AAATAAAAGAAATG
28639835 AAAT-AAAGAAAT-
1 AAATAAAAGAAATG
* *
28639847 AAATGAAATAAATG
1 AAATAAAAGAAATG
28639861 AAATAAAAGAAATG
1 AAATAAAAGAAATG
28639875 AAA
1 AAA
28639878 AAGAAAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 4 0.11
13 19 0.50
14 15 0.39
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.16
Consensus pattern (14 bp):
AAATAAAAGAAATG
Found at i:28639856 original size:9 final size:9
Alignment explanation
Indices: 28639830--28639873 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
28639820 TAAAATAAAG
28639830 AAATGAAAT
1 AAATGAAAT
28639839 AAA-GAAAT
1 AAATGAAAT
28639847 AAATGAAAT
1 AAATGAAAT
28639856 AAATGAAAT
1 AAATGAAAT
*
28639865 AAAAGAAAT
1 AAATGAAAT
28639874 GAAAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
8 8 0.24
9 25 0.76
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (9 bp):
AAATGAAAT
Found at i:28642661 original size:12 final size:12
Alignment explanation
Indices: 28642646--28642683 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28642636 TTTTCCTTTT
28642646 CTTTTTCTTTCC
1 CTTTTTCTTTCC
28642658 CTTTTTCTTT-C
1 CTTTTTCTTTCC
*
28642669 TTTCTTTCTTTCC
1 CTT-TTTCTTTCC
28642682 CT
1 CT
28642684 GCTCTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 3 0.14
12 17 0.77
13 2 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTTTTCTTTCC
Found at i:28647149 original size:19 final size:20
Alignment explanation
Indices: 28647125--28647167 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
28647115 GGTGATTGTG
*
28647125 TATACATGTGTACA-AATAA
1 TATACATATGTACATAATAA
*
28647144 TATACATATGTATATAATAA
1 TATACATATGTACATAATAA
28647164 TATA
1 TATA
28647168 TGAATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TATACATATGTACATAATAA
Found at i:28647188 original size:5 final size:5
Alignment explanation
Indices: 28647178--28647254 Score: 154
Period size: 5 Copynumber: 15.4 Consensus size: 5
28647168 TGAATAATTA
28647178 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
28647228 ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT AT
28647255 TATAATAACT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 72 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:28648231 original size:41 final size:40
Alignment explanation
Indices: 28648180--28648293 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 40
28648170 CCTCGAGTTA
**
28648180 ATGAGACACTGGGTGTCAATTATTTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGTCAATTA-TTACTTCGGATTAAGCCG
* * *
28648221 ATGA-AGCACTGGGTGCCAACTA--ACTTCGG-TTTAGCCG
1 ATGAGA-CACTGGGTGTCAATTATTACTTCGGATTAAGCCG
*
28648258 ATGAGACACTGGGTGTCAACTTATTACTTCGAATTA
1 ATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
28648294 TCTGATGAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
37 21 0.36
38 10 0.17
40 7 0.12
41 20 0.34
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTATTACTTCGGATTAAGCCG
Found at i:28650667 original size:32 final size:32
Alignment explanation
Indices: 28650622--28650715 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
28650612 TAATTAATAA
**
28650622 TTTTAATAA-TAATAATCATCTAAT-AAATATC
1 TTTTAATAATTAATAAT-AAATAATAAAATATC
*
28650653 TTTTATTAATTAATAATAAATAATAAAATATC
1 TTTTAATAATTAATAATAAATAATAAAATATC
*
28650685 TTTTCACTAATT-ATACATAAATAATACAAAT
1 TTTT-AATAATTAATA-ATAAATAATA-AAAT
28650716 GTGCTTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
31 13 0.24
32 21 0.39
33 16 0.30
34 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTTAATAATTAATAATAAATAATAAAATATC
Found at i:28650705 original size:33 final size:32
Alignment explanation
Indices: 28650642--28650715 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
28650632 AATAATCATC
*
28650642 TAAT-AAATATCTTTTATTAATTAATAATAAA
1 TAATAAAATATCTTTTACTAATTAATAATAAA
28650673 TAATAAAATATCTTTTCACTAATT-ATACATAAA
1 TAATAAAATATCTTTT-ACTAATTAATA-ATAAA
28650706 TAATACAAAT
1 TAATA-AAAT
28650716 GTGCTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 4 0.11
32 14 0.37
33 16 0.42
34 4 0.11
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (32 bp):
TAATAAAATATCTTTTACTAATTAATAATAAA
Found at i:28657010 original size:15 final size:14
Alignment explanation
Indices: 28656992--28657022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
28656982 TTAATTTATT
28656992 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
28657007 TAATAATAATCTAA
1 TAATAATAATCTAA
28657021 TA
1 TA
28657023 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:28657033 original size:21 final size:20
Alignment explanation
Indices: 28657009--28657077 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
28656999 AATGCTAATA
28657009 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
28657030 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
28657049 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
28657070 ATAATAAT
1 ATAATAAT
28657078 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:28658281 original size:19 final size:19
Alignment explanation
Indices: 28658257--28658307 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
28658247 TGTCTCCAAA
*
28658257 ATCTCGATGTGAACTGAGG
1 ATCTCGATGTGAACCGAGG
28658276 ATCTCGATGTGAACCGAGG
1 ATCTCGATGTGAACCGAGG
*
28658295 ATCTCGATCTGAA
1 ATCTCGATGTGAA
28658308 ATTATTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (19 bp):
ATCTCGATGTGAACCGAGG
Found at i:28664219 original size:14 final size:14
Alignment explanation
Indices: 28664195--28664227 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28664185 TCCCTGCTTC
28664195 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
28664210 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
28664223 GTTTC
1 GTTTC
28664228 CTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:28664558 original size:15 final size:14
Alignment explanation
Indices: 28664540--28664570 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
28664530 TTAATTTATT
28664540 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
28664555 TAATAATAATCTAA
1 TAATAATAATCTAA
28664569 TA
1 TA
28664571 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:28667383 original size:25 final size:25
Alignment explanation
Indices: 28667352--28667402 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28667342 TAGCCGAAGT
28667352 AAAGCGGTACCCAGTACCTCATCGA
1 AAAGCGGTACCCAGTACCTCATCGA
28667377 AAAGCGGTACCCAGTACCTCATCGA
1 AAAGCGGTACCCAGTACCTCATCGA
28667402 A
1 A
28667403 TCTATCCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (25 bp):
AAAGCGGTACCCAGTACCTCATCGA
Found at i:28668574 original size:15 final size:16
Alignment explanation
Indices: 28668554--28668587 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28668544 TTTCATATCT
28668554 ATTTGTTTTAT-TTTA
1 ATTTGTTTTATATTTA
*
28668569 ATTTGTTTTCTATTTA
1 ATTTGTTTTATATTTA
28668585 ATT
1 ATT
28668588 AATTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (16 bp):
ATTTGTTTTATATTTA
Found at i:28668764 original size:32 final size:32
Alignment explanation
Indices: 28668724--28668798 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 32
28668714 AATAATCATC
28668724 TAAT-AAATATCTTTT-ACTAATTAATA-ATAAA
1 TAATAAAATAT-TTTTCACTAATT-ATACATAAA
*
28668755 TAATAAAATATTTTTCGCTAATTATACATAAA
1 TAATAAAATATTTTTCACTAATTATACATAAA
28668787 TAATACAAATAT
1 TAATA-AAATAT
28668799 ACTTATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 11 0.28
32 22 0.56
33 6 0.15
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (32 bp):
TAATAAAATATTTTTCACTAATTATACATAAA
Found at i:28673947 original size:21 final size:21
Alignment explanation
Indices: 28673906--28673947 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28673896 TTAACTGCTT
**
28673906 AATTGCATTTTTATATTTTGA
1 AATTGCATTTTTATAAATTGA
28673927 AATTAGCATTTTTA-AAATTGA
1 AATT-GCATTTTTATAAATTGA
28673948 CATATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (21 bp):
AATTGCATTTTTATAAATTGA
Found at i:28679560 original size:17 final size:17
Alignment explanation
Indices: 28679538--28679575 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28679528 TCTAAGTTTA
28679538 ATTTTTTTATATTTTCT
1 ATTTTTTTATATTTTCT
* *
28679555 ATTTTTTTCTTTTTTCT
1 ATTTTTTTATATTTTCT
28679572 -TTTT
1 ATTTT
28679576 GATAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTTTTATATTTTCT
Found at i:28684001 original size:21 final size:22
Alignment explanation
Indices: 28683962--28684010 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
28683952 TACTAGTTAG
* * *
28683962 TATATTTTAAATTCTAATATAC
1 TATATTTAAAATTCGAATAAAC
*
28683984 TATATTTAAAATT-GAATAAAT
1 TATATTTAAAATTCGAATAAAC
28684005 TATATT
1 TATATT
28684011 AGTATCATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATTTAAAATTCGAATAAAC
Found at i:28684354 original size:7 final size:7
Alignment explanation
Indices: 28684342--28684367 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28684332 AACTCGAATA
28684342 TTAAATC
1 TTAAATC
28684349 TTAAATC
1 TTAAATC
28684356 TTAAATC
1 TTAAATC
28684363 TTAAA
1 TTAAA
28684368 CCTTGAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATC
Found at i:28686598 original size:23 final size:23
Alignment explanation
Indices: 28686572--28686619 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28686562 AGGTTTGAAG
28686572 TTGGAACCTATTATTTGCAATCC
1 TTGGAACCTATTATTTGCAATCC
28686595 TTGGAACCTATTATTTGCAATCC
1 TTGGAACCTATTATTTGCAATCC
28686618 TT
1 TT
28686620 TTATGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (23 bp):
TTGGAACCTATTATTTGCAATCC
Found at i:28692451 original size:37 final size:41
Alignment explanation
Indices: 28692423--28692505 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 41
28692413 TATTGTTTTA
28692423 ATGAAT-TCA-ATATTAAATTTAATTTAATATTTGTCTAGAT
1 ATGAATATCAGATATTAAATTTAATTTAATA-TTGTCTAGAT
* * *
28692463 ATTAATATGAGATATTAAATTTAATTTAATATTTATCTAGAT
1 ATGAATATCAGATATTAAATTTAATTTAATA-TTGTCTAGAT
28692505 A
1 A
28692506 ATATTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 5 0.13
41 2 0.05
42 31 0.82
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (41 bp):
ATGAATATCAGATATTAAATTTAATTTAATATTGTCTAGAT
Found at i:28692534 original size:16 final size:15
Alignment explanation
Indices: 28692483--28692535 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
28692473 GATATTAAAT
28692483 TTAATTTAATATTTA
1 TTAATTTAATATTTA
28692498 TCTAGA--TAATATTTTA
1 T-TA-ATTTAATA-TTTA
28692514 TTAATTTAATATTTA
1 TTAATTTAATATTTA
28692529 TGTAATT
1 T-TAATT
28692536 AATTCTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.03
15 13 0.41
16 17 0.53
17 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (15 bp):
TTAATTTAATATTTA
Found at i:28692537 original size:15 final size:14
Alignment explanation
Indices: 28692483--28692538 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 14
28692473 GATATTAAAT
28692483 TTAATTTAATATTTA
1 TTAA-TTAATATTTA
28692498 TCTAGA-TAATATTTTA
1 T-TA-ATTAATA-TTTA
28692514 TTAATTTAATATTTA
1 TTAA-TTAATATTTA
28692529 TGTAATTAAT
1 T-TAATTAAT
28692539 TCTAATTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 15 0.43
17 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (14 bp):
TTAATTAATATTTA
Found at i:28700042 original size:16 final size:16
Alignment explanation
Indices: 28700023--28700055 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28700013 TTCATGTTAC
*
28700023 TTTGGTTATCCTTTGT
1 TTTGCTTATCCTTTGT
28700039 TTTGCTTATCCTTTGT
1 TTTGCTTATCCTTTGT
28700055 T
1 T
28700056 ATATTGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.15, T:0.64
Consensus pattern (16 bp):
TTTGCTTATCCTTTGT
Found at i:28702340 original size:33 final size:33
Alignment explanation
Indices: 28702303--28702371 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
28702293 TTTAAATTAT
* * *
28702303 ATTTTATAGTATTATGTATTATGATTTTAGTAA
1 ATTTTATAGTATCATATATTATGATTTGAGTAA
28702336 ATTTTATAGTATCATATATTATGATTTGAGTAA
1 ATTTTATAGTATCATATATTATGATTTGAGTAA
28702369 ATT
1 ATT
28702372 CATATAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (33 bp):
ATTTTATAGTATCATATATTATGATTTGAGTAA
Found at i:28702431 original size:16 final size:16
Alignment explanation
Indices: 28702410--28702451 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28702400 TTATTAAATT
*
28702410 ATATATTTTAATTATA
1 ATATATTTTAATAATA
28702426 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
28702441 AT-TATGTTTAA
1 ATATAT-TTTAA
28702452 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:28702436 original size:15 final size:15
Alignment explanation
Indices: 28702401--28702442 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28702391 TTAAGAATTT
*
28702401 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28702415 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28702429 TATTTAATAATAAT
1 TATTTAATTATAAT
28702443 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28702677 original size:45 final size:44
Alignment explanation
Indices: 28702596--28702686 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
28702586 ACTTCTATTC
*
28702596 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
28702640 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
28702685 CA
1 CA
28702687 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:28702686 original size:16 final size:16
Alignment explanation
Indices: 28702665--28702724 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
28702655 TTGATTTGCT
28702665 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
28702681 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
28702697 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
28702713 ATTACGCCTCTA
1 ATTACACCTCTA
28702725 ATCTAATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:28702706 original size:32 final size:32
Alignment explanation
Indices: 28702665--28702727 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
28702655 TTGATTTGCT
28702665 ATTACACCTCTATTCCATTACACCTCTAATCC
1 ATTACACCTCTATTCCATTACACCTCTAATCC
*
28702697 ATTACACCTCTATTCCATTACGCCTCTAATC
1 ATTACACCTCTATTCCATTACACCTCTAATC
28702728 TAATACAGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.35
Consensus pattern (32 bp):
ATTACACCTCTATTCCATTACACCTCTAATCC
Found at i:28711927 original size:19 final size:20
Alignment explanation
Indices: 28711884--28711928 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28711874 TTGGTCACTT
*
28711884 ATTTTAGTCACTCAATTTCC
1 ATTTTAGTCACTCAATTTAC
28711904 ATTTTAGTCACT-AATTTAC
1 ATTTTAGTCACTCAATTTAC
*
28711923 TTTTTA
1 ATTTTA
28711929 AAGATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTAGTCACTCAATTTAC
Found at i:28718846 original size:167 final size:168
Alignment explanation
Indices: 28718546--28718848 Score: 473
Period size: 167 Copynumber: 1.8 Consensus size: 168
28718536 ATAGATAATC
* * * * *
28718546 AAGAAAAGTTGTTCAGTATTCATCACTGTTTCATTTCAGCTATCTAATGAAGTTCCAGTTCCAAC
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAAGTTCCAATTCCAAC
* * *
28718611 ACAGATGAATGAATGATTGTCTAATTAACAGGTGCTAGTTCAAGAACAATGACTTCCAATTATTA
66 ACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTATTA
28718676 CCCAATATTTAACGTTTCATTTCAGCAATTTGTAAACA
131 CCCAATATTTAACGTTTCATTTCAGCAATTTGTAAACA
* *
28718714 AAGAAAA-CTGTTCAATATTCATCAATGTTTCATTTCAGCAATTTAATGAAGTTCCAATTCCAAT
1 AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAAGTTCCAATTCCAAC
* * * *
28718778 ACAGATCAATGAATGATTGTGTAATTAACAGCTGCTAGTTCAAGAACAATAACTTTCATTTTTTA
66 ACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTATTA
28718843 CCCAAT
131 CCCAAT
28718849 CTTTCAAGCA
Statistics
Matches: 121, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
167 114 0.94
168 7 0.06
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (168 bp):
AAGAAAAGCTGTTCAATATTCATCAATGTTTCATTTCAGCAATCTAATGAAGTTCCAATTCCAAC
ACAGATCAATGAATGATTGTCTAATTAACAGCTGCTAGTTCAAGAACAATAACTTCCAATTATTA
CCCAATATTTAACGTTTCATTTCAGCAATTTGTAAACA
Found at i:28721069 original size:43 final size:42
Alignment explanation
Indices: 28721021--28721109 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 42
28721011 GTCGAATATG
28721021 ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
1 ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
* *
28721063 CATAGGAGAAGACAACTTATGTTAGTAGGTGGTCTAAATAGTT
1 -ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
28721106 ATAG
1 ATAG
28721110 TCTGAAGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (42 bp):
ATAGGAGAAGACAACTTATATTAGTAGGAGGTCTAAATAGTT
Found at i:28722804 original size:5 final size:5
Alignment explanation
Indices: 28722794--28722828 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
28722784 TTACTGTTAT
28722794 TATTA TATTA TATTA TATTA TATATA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT
28722829 AGTAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:28724152 original size:18 final size:18
Alignment explanation
Indices: 28724119--28724177 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28724109 TAAATAAAGG
28724119 TACTGAATAA-TGGACTGC
1 TACTGAATAACT-GACTGC
*
28724137 TACTGAATAACTGACTGT
1 TACTGAATAACTGACTGC
* * * *
28724155 TATTGGATCACTGATTGC
1 TACTGAATAACTGACTGC
28724173 TACTG
1 TACTG
28724178 CGTAAAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 32 0.97
19 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (18 bp):
TACTGAATAACTGACTGC
Found at i:28724234 original size:18 final size:19
Alignment explanation
Indices: 28724190--28724237 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
28724180 TAAAAAATTT
28724190 GTTACTGAATAATTGATTA
1 GTTACTGAATAATTGATTA
*
28724209 -TTACTGAATAATTTA-TA
1 GTTACTGAATAATTGATTA
*
28724226 GTTAATGAATAA
1 GTTACTGAATAA
28724238 CTGACTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (19 bp):
GTTACTGAATAATTGATTA
Found at i:28724248 original size:18 final size:17
Alignment explanation
Indices: 28724195--28724248 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
28724185 AATTTGTTAC
*
28724195 TGAATAATTGATTATTAC
1 TGAATAATTGA-TATTAA
*
28724213 TGAATAATTTATAGTTAA
1 TGAATAATTGATA-TTAA
*
28724231 TGAATAACTGACTATTAA
1 TGAATAATTGA-TATTAA
28724249 AGAGTGACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.41
Consensus pattern (17 bp):
TGAATAATTGATATTAA
Found at i:28735681 original size:68 final size:68
Alignment explanation
Indices: 28735570--28735710 Score: 255
Period size: 68 Copynumber: 2.1 Consensus size: 68
28735560 AGTTAGGCCA
* * *
28735570 TGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCTTAAAATTGAGCACGCGGGCAGAGACAC
1 TGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACAC
28735635 GGG
66 GGG
28735638 TGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACAC
1 TGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACAC
28735703 GGG
66 GGG
28735706 TGTGT
1 TGTGT
28735711 GTCTCAACCG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (68 bp):
TGTGTCCCCTGCACCTTAATTTTGAGAAATAGAATGCTCAAAATTGAGCACACAGGCAGAGACAC
GGG
Found at i:28737664 original size:36 final size:36
Alignment explanation
Indices: 28737595--28737665 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
28737585 TGTCGGGGAG
* *
28737595 TGTTGGGCACACCCATTTGTCGATTGTATCGACCAA
1 TGTTGGGCACACCCATTTGTCGATTATACCGACCAA
* * *
28737631 TGTTGGGCACATCTATTTGTCGGTTATACCGACCA
1 TGTTGGGCACACCCATTTGTCGATTATACCGACCA
28737666 GTGTAGGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (36 bp):
TGTTGGGCACACCCATTTGTCGATTATACCGACCAA
Found at i:28749118 original size:21 final size:21
Alignment explanation
Indices: 28749094--28749146 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28749084 CGCTGTTTCT
*
28749094 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
28749115 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
28749136 AATCTCACCGC
1 AATCTCACCGC
28749147 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:28750611 original size:21 final size:22
Alignment explanation
Indices: 28750584--28750639 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
28750574 ATAGTGCTGA
* *
28750584 CGGTGAGATTAG-TTACTGTAG
1 CGGTGAGATTAGAATACTATAG
*
28750605 TGGTGAGATT-GAATACTATAG
1 CGGTGAGATTAGAATACTATAG
28750626 CGGTGAGATTAGAA
1 CGGTGAGATTAGAA
28750640 ACAATGGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 25 0.86
22 3 0.10
ACGTcount: A:0.30, C:0.07, G:0.32, T:0.30
Consensus pattern (22 bp):
CGGTGAGATTAGAATACTATAG
Found at i:28752619 original size:15 final size:16
Alignment explanation
Indices: 28752601--28752634 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28752591 AAAAGCATAG
28752601 CATAAAAAA-ACCAAA
1 CATAAAAAATACCAAA
*
28752616 CATAAAAAATACCATA
1 CATAAAAAATACCAAA
28752632 CAT
1 CAT
28752635 TAGTTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.21, G:0.00, T:0.15
Consensus pattern (16 bp):
CATAAAAAATACCAAA
Found at i:28765595 original size:32 final size:32
Alignment explanation
Indices: 28765559--28765717 Score: 239
Period size: 32 Copynumber: 5.0 Consensus size: 32
28765549 TATAACTATG
28765559 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
28765591 CTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
28765623 CTACTTTTTTATATGTGAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
28765655 ATACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
28765687 CTAC-TTTTTATAGGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
28765718 ATTTTTTATG
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 24 0.21
32 89 0.79
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:28765660 original size:64 final size:64
Alignment explanation
Indices: 28765559--28765719 Score: 270
Period size: 64 Copynumber: 2.5 Consensus size: 64
28765549 TATAACTATG
* *
28765559 CTACTTTTTTATATGTAAAACTAATGTATGATCTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGAT
* *
28765623 CTACTTTTTTATATGTGAACCTAATGTATGATATACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGAT
*
28765687 CTAC-TTTTTATAGGTAAACCTAATGTATGATAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATAT
28765720 TTTTTATGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 27 0.30
64 64 0.70
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (64 bp):
CTACTTTTTTATATGTAAACCTAATGTATGATATACTTTTTCATATGCAAAACTAATGTATGAT
Found at i:28767750 original size:21 final size:21
Alignment explanation
Indices: 28767725--28767798 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
28767715 CGTTGTTTCT
*
28767725 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
28767746 AATCTCACCGCTACAATAACC
1 AATCTCACCGCTACAGTAACC
*
28767767 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
28767788 AATCTCACCGC
1 AATCTCACCGC
28767799 CACCGCTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.32, C:0.38, G:0.08, T:0.22
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:28768885 original size:25 final size:25
Alignment explanation
Indices: 28768856--28768906 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
28768846 CAAAGAAAAA
** *
28768856 TCCTAATCTAATTCCTAGTTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
28768881 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
28768906 T
1 T
28768907 TTATAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:28799919 original size:25 final size:25
Alignment explanation
Indices: 28799872--28799921 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
28799862 TTCCTTATAA
**
28799872 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
28799897 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
28799922 TTTTCCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:28816395 original size:27 final size:27
Alignment explanation
Indices: 28816333--28816402 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
28816323 TTGTATTCAA
* * *
28816333 TTTTTATACTTTAATTTTTAACATAAT
1 TTTTTATATTTTTATATTTAACATAAT
28816360 TTTTTATATTTTTATATTTAACATAAT
1 TTTTTATATTTTTATATTTAACATAAT
28816387 TTTTTATATTTTTATA
1 TTTTTATATTTTTATA
28816403 ATATTGTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTATATTTTTATATTTAACATAAT
Found at i:28817654 original size:31 final size:32
Alignment explanation
Indices: 28817617--28817688 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
28817607 CAAGTTAATC
* * *
28817617 CCTAAACTTTG-CAGTTGTTCCCACGTTGAGG
1 CCTAAACTTTGACAATTATTCCCACATTGAGG
* *
28817648 CCTAAAC-TTGACAATTATTCCTACATTGGGG
1 CCTAAACTTTGACAATTATTCCCACATTGAGG
28817679 CCTAAACTTT
1 CCTAAACTTT
28817689 ATGGTTTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 3 0.09
31 29 0.85
32 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (32 bp):
CCTAAACTTTGACAATTATTCCCACATTGAGG
Found at i:28826297 original size:30 final size:30
Alignment explanation
Indices: 28826262--28826341 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 30
28826252 TTGAGATATT
*
28826262 AAAATATTATTTTATTATTTTTGAAGAGAC
1 AAAATATTATTTTATTATTTTTAAAGAGAC
* *
28826292 TAAATATACTTATTTT-TTATTTTTAAAGGGTC
1 -AAA-ATA-TTATTTTATTATTTTTAAAGAGAC
* *
28826324 AAAGTATAATTTTATTAT
1 AAAATATTATTTTATTAT
28826342 ATGTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 6 0.15
30 6 0.15
31 6 0.15
32 16 0.39
33 7 0.17
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (30 bp):
AAAATATTATTTTATTATTTTTAAAGAGAC
Found at i:28827244 original size:24 final size:24
Alignment explanation
Indices: 28827217--28827273 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
28827207 TTTTCAAAAA
* *
28827217 TAAAAAATTTTAATAAATCTTTTT
1 TAAAAAATATTAATAAATATTTTT
*
28827241 TAAAAAAAATTAATAAATATTTTT
1 TAAAAAATATTAATAAATATTTTT
28827265 TAAAAAATA
1 TAAAAAATA
28827274 ATGAAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAAAATATTAATAAATATTTTT
Found at i:28828707 original size:15 final size:15
Alignment explanation
Indices: 28828687--28828794 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
28828677 TTTATGGAAA
28828687 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
28828702 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
28828716 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
28828732 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
28828746 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
28828762 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
28828776 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
28828792 ATC
1 ATC
28828795 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:28828724 original size:30 final size:30
Alignment explanation
Indices: 28828681--28828804 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
28828671 TCCATATTTA
* *
28828681 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
28828711 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
28828741 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
28828771 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
28828802 TGG
1 TGG
28828805 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:28833400 original size:15 final size:15
Alignment explanation
Indices: 28833380--28833460 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
28833370 TTTATGGAAA
28833380 ATCAAAGATATAGGT
1 ATCAAAGATATAGGT
* **
28833395 ATCAAATA-ATAGAA
1 ATCAAAGATATAGGT
28833409 AGTCAAAGATATAGGT
1 A-TCAAAGATATAGGT
* *
28833425 ATC-AA-ATATTGGAA
1 ATCAAAGATATAGG-T
*
28833439 AGTCAAAGATATGGGT
1 A-TCAAAGATATAGGT
28833455 ATCAAA
1 ATCAAA
28833461 TATTGGAAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
13 6 0.12
14 8 0.16
15 22 0.44
16 8 0.16
17 6 0.12
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATAGGT
Found at i:28833417 original size:30 final size:30
Alignment explanation
Indices: 28833374--28833497 Score: 185
Period size: 30 Copynumber: 4.1 Consensus size: 30
28833364 TCCATATTTA
* *
28833374 TGGAAAATCAAAGATATAGGTATCAAATAA
1 TGGAAAGTCAAAGATATAGGTATCAAATAT
*
28833404 TAGAAAGTCAAAGATATAGGTATCAAATAT
1 TGGAAAGTCAAAGATATAGGTATCAAATAT
*
28833434 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATAGGTATCAAATAT
* *
28833464 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATAGGTATC-AAATAT
28833495 TGG
1 TGG
28833498 CATAATAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 79 0.91
31 8 0.09
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATAGGTATCAAATAT
Found at i:28833474 original size:15 final size:15
Alignment explanation
Indices: 28833426--28833475 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
28833416 GATATAGGTA
28833426 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
* **
28833441 TCAAAGATATGGGTA-
1 TCAAATAT-TGGAAAG
28833456 TCAAATATTGGAAAG
1 TCAAATATTGGAAAG
28833471 TCAAA
1 TCAAA
28833476 GATATGGGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 19 0.70
16 4 0.15
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (15 bp):
TCAAATATTGGAAAG
Found at i:28834525 original size:11 final size:12
Alignment explanation
Indices: 28834506--28834537 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28834496 TAATTTTTAA
28834506 ATAATATATTTT
1 ATAATATATTTT
28834518 ATAA-ATATTTT
1 ATAATATATTTT
28834529 A-AATATATT
1 ATAATATATT
28834538 ATTTACTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 13 0.68
12 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATAATATATTTT
Found at i:28844033 original size:120 final size:120
Alignment explanation
Indices: 28843836--28844459 Score: 1160
Period size: 120 Copynumber: 5.2 Consensus size: 120
28843826 TTTTCAAGTT
28843836 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28843901 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
28843956 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28844021 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
28844076 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
28844141 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
*
28844196 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* ** *
28844261 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
28844317 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
28844382 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
28844437 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
28844460 TAAATATGAT
Statistics
Matches: 491, Mismatches: 10, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
119 2 0.00
120 373 0.76
121 114 0.23
122 2 0.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
Found at i:28844195 original size:18 final size:17
Alignment explanation
Indices: 28844167--28844201 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28844157 ATTATTAAGA
*
28844167 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28844184 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28844202 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28844712 original size:17 final size:16
Alignment explanation
Indices: 28844678--28844746 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
28844668 GATTAGCTAT
*
28844678 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
28844694 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
28844711 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28844727 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
28844743 TACA
1 TACA
28844747 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
16 33 0.67
17 16 0.33
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28844721 original size:33 final size:32
Alignment explanation
Indices: 28844678--28844746 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
28844668 GATTAGCTAT
*
28844678 TACACTTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
28844711 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
28844743 TACA
1 TACA
28844747 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:28847079 original size:17 final size:18
Alignment explanation
Indices: 28847044--28847081 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28847034 AATTTAAAAA
*
28847044 TGAGTTCAGTTTTAATTT
1 TGAGTTCAGTTCTAATTT
*
28847062 TGAGTT-AGTTCTACTTT
1 TGAGTTCAGTTCTAATTT
28847079 TGA
1 TGA
28847082 AATACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.53
Consensus pattern (18 bp):
TGAGTTCAGTTCTAATTT
Found at i:28854239 original size:21 final size:21
Alignment explanation
Indices: 28854213--28854253 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28854203 ATCAGCTCAA
* *
28854213 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
28854234 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
28854254 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:28862378 original size:21 final size:22
Alignment explanation
Indices: 28862345--28862385 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28862335 TGGGTAGTTG
*
28862345 TTATTAAACTGAGCAGAATACT
1 TTATGAAACTGAGCAGAATACT
*
28862367 TTATGAAA-TGAGCGGAATA
1 TTATGAAACTGAGCAGAATA
28862386 GCCGAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (22 bp):
TTATGAAACTGAGCAGAATACT
Found at i:28887010 original size:46 final size:46
Alignment explanation
Indices: 28886943--28887117 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
28886933 TGTAACCCGC
28886943 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
28886989 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACG--T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTT-CGCAT
* * * * * *
28887039 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
28887082 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
28887118 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 1 0.01
44 2 0.02
45 2 0.02
46 63 0.58
47 26 0.24
48 3 0.03
49 2 0.02
50 1 0.01
51 3 0.03
52 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:28887063 original size:93 final size:93
Alignment explanation
Indices: 28886951--28887121 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
28886941 GCCCATAAGT
* * *
28886951 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28887016 CGAGCTCGGATGCCTAGTTACGTCTCAC
66 CGAGCTCGGATGCCTAGTTACGTCTCAC
*
28887044 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28887109 CGAGTTCGGATGC
66 CGAGCTCGGATGC
28887122 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACGTCTCAC
Found at i:28891480 original size:5 final size:5
Alignment explanation
Indices: 28891470--28891538 Score: 75
Period size: 5 Copynumber: 12.8 Consensus size: 5
28891460 TTAGTCTTAT
* *
28891470 TTTTA TTTTA TTTTA TTTTA TTTTC TTTTAA TTTTTA TTTTCA TTTCAA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA TTTT-A TTT-TA
28891519 TTTTA TTATTA TTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTT
28891539 GAAAGATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
5 37 0.67
6 14 0.25
7 4 0.07
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:28891480 original size:11 final size:11
Alignment explanation
Indices: 28891466--28891538 Score: 78
Period size: 11 Copynumber: 6.6 Consensus size: 11
28891456 TTATTTAGTC
28891466 TTATTTTTATT
1 TTATTTTTATT
28891477 TTA-TTTTATT
1 TTATTTTTATT
28891487 TTATTTTCT-TT
1 TTATTTT-TATT
*
28891498 TAATTTTTATT
1 TTATTTTTATT
**
28891509 TTCATTTCAATT
1 TT-ATTTTTATT
*
28891521 TTATTATTATT
1 TTATTTTTATT
28891532 TTATTTT
1 TTATTTT
28891539 GAAAGATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
10 11 0.22
11 29 0.58
12 10 0.20
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:28891523 original size:17 final size:16
Alignment explanation
Indices: 28891470--28891538 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
28891460 TTAGTCTTAT
*
28891470 TTTTATTTT-ATTTTA
1 TTTTATTTTCATTTAA
*
28891485 TTTTATTTTCTTTTAA
1 TTTTATTTTCATTTAA
28891501 TTTTTATTTTCATTTCAA
1 -TTTTATTTTCATTT-AA
*
28891519 TTTTATTATT-ATTTTA
1 TTTTATT-TTCATTTAA
28891535 TTTT
1 TTTT
28891539 GAAAGATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
15 9 0.20
16 9 0.20
17 24 0.52
18 4 0.09
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTTTCATTTAA
Found at i:28897069 original size:17 final size:19
Alignment explanation
Indices: 28897047--28897093 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
28897037 AACGATAATG
28897047 ATAAAA-GAA-AAAAGAAA
1 ATAAAACGAATAAAAGAAA
28897064 ATAAAACGAATAAAAG--A
1 ATAAAACGAATAAAAGAAA
28897081 ATAAAACGAATAA
1 ATAAAACGAATAA
28897094 GCTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 20 0.71
18 3 0.11
19 5 0.18
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (19 bp):
ATAAAACGAATAAAAGAAA
Found at i:28897077 original size:9 final size:9
Alignment explanation
Indices: 28897063--28897093 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28897053 GAAAAAAGAA
28897063 AATAAAACG
1 AATAAAACG
28897072 AATAAAA-G
1 AATAAAACG
28897080 AATAAAACG
1 AATAAAACG
28897089 AATAA
1 AATAA
28897094 GCTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (9 bp):
AATAAAACG
Found at i:28897363 original size:3 final size:3
Alignment explanation
Indices: 28897357--28897471 Score: 78
Period size: 3 Copynumber: 40.0 Consensus size: 3
28897347 GTAAAAAAAC
* * * *
28897357 ATA ATA ATA AT- ATA ATA GTA ATA ATA AT- ATA ATA AAA ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** * * * * *
28897403 ATA GCA ATA A-A ATA ATA GTT ATA A-A ATA ATA CTA ATA GTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
28897449 ATA ATA AT- ACA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
28897472 GTAGTAGTAA
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
2 9 0.11
3 76 0.89
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28897380 original size:20 final size:20
Alignment explanation
Indices: 28897357--28897471 Score: 88
Period size: 23 Copynumber: 5.3 Consensus size: 20
28897347 GTAAAAAAAC
28897357 ATAATAATAATATAATAGTA
1 ATAATAATAATATAATAGTA
*
28897377 ATAATAATATAATAAAAATAGTA
1 ATAAT-A-ATAAT-ATAATAGTA
* * *
28897400 GTAATAGCAATAAAATAATAGTT
1 ATAAT---AATAATATAATAGTA
28897423 ATAA-AATAATACTAATAGTAGTA
1 ATAATAATAATA-T-A-A-TAGTA
*
28897446 ATAATAATAATACAATAGTA
1 ATAATAATAATATAATAGTA
28897466 ATAATA
1 ATAATA
28897472 GTAGTAGTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
19 6 0.08
20 17 0.23
21 3 0.04
22 7 0.09
23 30 0.40
24 11 0.15
25 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (20 bp):
ATAATAATAATATAATAGTA
Found at i:28897412 original size:46 final size:46
Alignment explanation
Indices: 28897357--28897471 Score: 137
Period size: 43 Copynumber: 2.6 Consensus size: 46
28897347 GTAAAAAAAC
* *
28897357 ATAATAATAATATAATAGTAATAATAATATAATAAAAATAGTAGTA
1 ATAACAATAATATAATAGTAATAATAAAATAATAAAAATAGTAGTA
* * **
28897403 ATAGCAATAAAATAATAGT--T-ATAAAATAATACTAATAGTAGTA
1 ATAACAATAATATAATAGTAATAATAAAATAATAAAAATAGTAGTA
* *
28897446 ATAATAATAATACAATAGTAATAATA
1 ATAACAATAATATAATAGTAATAATA
28897472 GTAGTAGTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 35 0.62
44 1 0.02
45 1 0.02
46 19 0.34
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (46 bp):
ATAACAATAATATAATAGTAATAATAAAATAATAAAAATAGTAGTA
Found at i:28898218 original size:20 final size:19
Alignment explanation
Indices: 28898187--28898234 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
28898177 AAATAGATTC
*
28898187 GAAAAGAAAAGAAAGAAAA
1 GAAAAAAAAAGAAAGAAAA
*
28898206 TAAAATAAAAAGAAAGAAAA
1 GAAAA-AAAAAGAAAGAAAA
28898226 GAAAAAAAA
1 GAAAAAAAA
28898235 TAAATAACAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (19 bp):
GAAAAAAAAAGAAAGAAAA
Found at i:28899008 original size:93 final size:92
Alignment explanation
Indices: 28898903--28899389 Score: 314
Period size: 93 Copynumber: 5.3 Consensus size: 92
28898893 TTCATCCTGC
* * * *
28898903 TCCACTGCAACTTTAGGAAGATAAAGTTTGTTATGATCTGCTCTATAGCAACTTTAGAGAGATAA
1 TCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGATCTGCTCTAT-GCAACTTCAGAGAGATAA
*
28898968 GGTCTGTTTATTTATGGCTTCAATCTGT
65 GATCTGTTTATTTATGGCTTCAATCTGT
* * *
28898996 TCCACTGCAACTTCAGGGAA-ATAAGGTTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
1 TCCACTGCAACTTCA-GGAAGATAAGGTTTG-T-T-TTGA-TCTGCTCTA-TGCAACTTCAGAGA
* * * * *
28899060 GATAA-AAC----TA---GTGACTTCAACCTGC
60 GATAAGATCTGTTTATTTATGGCTTCAATCTGT
* *
28899085 TCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTATTGCAACTTCAGAGAGATAA
1 TCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGATCTGCTCTA-TGCAACTTCAGAGAGATAA
* * *
28899150 GATTTGTTTATTTATAGCTTCAATCTAT
65 GATCTGTTTATTTATGGCTTCAATCTGT
* * * * * * *
28899178 TCTACTGCAACTTTAGGGAA-ATAAGATTTGCTGTCTTCAGTCTGCTCCACTGCATCTTCAGGGA
1 TCCACTGCAACTTCA-GGAAGATAAGGTTTG-T-T-TTGA-TCTGCTCTA-TGCAACTTCAGAGA
** * *
28899242 GATAAGA-C----TA---GCGACTTCAA-CTGC
60 GATAAGATCTGTTTATTTATGGCTTCAATCTGT
* * * *
28899266 TCCTCTGTAACTTCA-GAGAGGTAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGATAGATA
1 TCCACTGCAACTTCAGGA-AGATAAGGTTTGTTTTGATCTGCTCTA-TGCAACTTCAGAGAGATA
* * * *
28899330 AGATCTGTTTATTCATAGCTTTAATATGT
64 AGATCTGTTTATTTATGGCTTCAATCTGT
** *
28899359 TCCACTAAAACTTCAGGGAA-ATAAGATTTGT
1 TCCACTGCAACTTCA-GGAAGATAAGGTTTGT
28899390 AATCTCCAGC
Statistics
Matches: 294, Mismatches: 67, Indels: 66
0.69 0.16 0.15
Matches are distributed among these distances:
84 27 0.09
85 30 0.10
86 7 0.02
87 3 0.01
88 25 0.09
89 43 0.15
90 2 0.01
92 9 0.03
93 76 0.26
94 10 0.03
95 4 0.01
96 6 0.02
97 51 0.17
98 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (92 bp):
TCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGATCTGCTCTATGCAACTTCAGAGAGATAAG
ATCTGTTTATTTATGGCTTCAATCTGT
Found at i:28899049 original size:45 final size:43
Alignment explanation
Indices: 28898985--28899331 Score: 193
Period size: 45 Copynumber: 7.8 Consensus size: 43
28898975 TTATTTATGG
* *
28898985 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGGTTTGCTAT
1 CTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TAT
*** *
28899030 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGA-
1 CTTCA-TCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT-AT
* *
28899074 CTTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGT-T
1 CTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAT
* * * * *
28899117 -TTGATCTGCTCTATTGCAACTTCAGAGAGATAAGATTTGTTTATTTAT
1 CTTCATCTGCTCCACTGCAACTTCAGGGAGATAAG----G-TT-TGTAT
** * * * * *
28899165 AGCTTCAATCTATTCTACTGCAACTTTAGGGAAATAAGATTTGCTGT
1 --CTTC-ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TAT
* ** * *
28899212 CTTCAGTCTGCTCCACTGCATCTTCAGGGAGATAAGACTAGCGA-
1 CTTCA-TCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TAT
* * * * *
28899256 CTTCAACTGCTCCTCTGTAACTTCAGAGAGGTAAGGTTTGT-T
1 CTTCATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAT
* * **
28899298 -TTGATCTGCTCTACTGCAACTTCAGATAGATAAG
1 CTTCATCTGCTCCACTGCAACTTCAGGGAGATAAG
28899332 ATCTGTTTAT
Statistics
Matches: 228, Mismatches: 56, Indels: 40
0.70 0.17 0.12
Matches are distributed among these distances:
41 53 0.23
42 2 0.01
43 26 0.11
44 42 0.18
45 68 0.30
46 3 0.01
47 6 0.03
48 1 0.00
51 2 0.01
52 25 0.11
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (43 bp):
CTTCATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAT
Found at i:28899217 original size:182 final size:182
Alignment explanation
Indices: 28898893--28899388 Score: 724
Period size: 182 Copynumber: 2.7 Consensus size: 182
28898883 GTTTGTAGTT
* * * * * * * *
28898893 TTCATCCTGCTCCACTGCAACTTTAGGAAGATAAAGTTTGTTATGATCTGCTCTATAGCAACTTT
1 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTATTGCAACTTC
* * *
28898958 AGAGAGATAAGGTCTGTTTATTTATGGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGGT
66 AGAGAGATAAGATCTGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
*
28899023 TTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGTGAC
131 TTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGCGAC
28899075 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTATTGCAACTTC
1 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTATTGCAACTTC
* * * *
28899140 AGAGAGATAAGATTTGTTTATTTATAGCTTCAATCTATTCTACTGCAACTTTAGGGAAATAAGAT
66 AGAGAGATAAGATCTGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
* * *
28899205 TTGCTGTCTTCAGTCTGCTCCACTGCATCTTCAGGGAGATAAGACTAGCGAC
131 TTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGCGAC
* * * *
28899257 TTCAA-CTGCTCCTCTGTAACTTCAGAGAGGTAAGGTTTGTTTTGATCTGCTCTACTGCAACTTC
1 TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTATTGCAACTTC
* * * * **
28899321 AGATAGATAAGATCTGTTTATTCATAGCTTTAATATGTTCCACTAAAACTTCAGGGAAATAAGAT
66 AGAGAGATAAGATCTGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
28899386 TTG
131 TTG
28899389 TAATCTCCAG
Statistics
Matches: 281, Mismatches: 33, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
181 113 0.40
182 168 0.60
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (182 bp):
TTCAACCTGCTCCTCTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTATTGCAACTTC
AGAGAGATAAGATCTGTTTATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGAT
TTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTAGCGAC
Found at i:28899502 original size:44 final size:44
Alignment explanation
Indices: 28899373--28899508 Score: 120
Period size: 44 Copynumber: 3.1 Consensus size: 44
28899363 CTAAAACTTC
* * *
28899373 AGGGAAATAAGATTTGTAATCTCCAGCCTGTTGCCCTACTGCTT
1 AGGGAGATAAGATTTGTAATTTCCAGCCTATTGCCCTACTGCTT
* * * * *
28899417 AGGG-GATTAAGACTCATTGT--CTTCGA-TCTACT-CCACAACTGCTT
1 AGGGAGA-TAAGA-T--TTGTAATTTCCAGCCTATTGCC-CTACTGCTT
28899461 AGGGAGATAAGATTTGTAATTTCCAGCCTATTGCCCTACTGCTT
1 AGGGAGATAAGATTTGTAATTTCCAGCCTATTGCCCTACTGCTT
28899505 AGGG
1 AGGG
28899509 GGTTAAGGCT
Statistics
Matches: 69, Mismatches: 13, Indels: 20
0.68 0.13 0.20
Matches are distributed among these distances:
41 4 0.06
43 8 0.12
44 45 0.65
45 8 0.12
47 4 0.06
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (44 bp):
AGGGAGATAAGATTTGTAATTTCCAGCCTATTGCCCTACTGCTT
Found at i:28899531 original size:88 final size:88
Alignment explanation
Indices: 28899373--28900172 Score: 1016
Period size: 88 Copynumber: 9.1 Consensus size: 88
28899363 CTAAAACTTC
* * * * * * *
28899373 AGGGAAATAAGATTTGTAATCTCCAGCCTGTTGCCCTACTGCTTAGGGGATTAAGACTCATTGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
*
28899438 TTCGATCTACTCCACAACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * *
28899461 AGGGAGATAAGATTTGTAAT-TTCCAGCCTATTGCCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 AGGGAGATAAGATCTGTAATCTT-CAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGT
*
28899525 -TGTCGATCTACCCCACTACTGCTT
65 CT-TCGATCTACTCCACTACTGCTT
* * * *
28899549 AGGGAGATAAGATATGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGATTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
28899614 TTCGAT-T-CGTTCCACTACTGCTT
66 TTCGATCTAC--TCCACTACTGCTT
* * *
28899637 AGGGAGATAAGATCTGTAATCTGCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCATT
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
*
28899702 TTCGATCTACTCCACTACTACTT
66 TTCGATCTACTCCACTACTGCTT
* * * *
28899725 AAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTATTGCTTAGGGGGTTAAGGTTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
**
28899790 TTCGATCCGCTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * * *
28899813 AGGGAGATAAGATCTGTAATCTTTACCCTGTTTCCCTACTACTTAGGGGGTTAAAGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
*
28899878 TTTGATCT-CTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
* * * *
28899900 ATGGAGATAAGATCCGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGTGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* * *
28899965 TTTGATCTACTCCATTACTACTT
66 TTCGATCTACTCCACTACTGCTT
* * * * ** * *
28899988 AGAGAGATGAGATCTGTAATCTTTAGCTTGTTTCCCTACTATTTAAGGGGTTAAGGCTCGTCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* * *
28900053 TTCGATCTGCTGCACTACTGTTT
66 TTCGATCTACTCCACTACTGCTT
** * * * *
28900076 AGGGAGATAAGGCCTGTAATCTTCAGTCTGTTTCCCAACTGCTTAGGAGGTTAAGGCTCACCGTC
1 AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
28900141 TTCGATCTACTCCACTACTGCTT
66 TTCGATCTACTCCACTACTGCTT
28900164 AGGGAGATA
1 AGGGAGATA
28900173 GGATGGTGGC
Statistics
Matches: 613, Mismatches: 90, Indels: 18
0.85 0.12 0.02
Matches are distributed among these distances:
86 1 0.00
87 81 0.13
88 526 0.86
89 4 0.01
90 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (88 bp):
AGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
TTCGATCTACTCCACTACTGCTT
Found at i:28899588 original size:44 final size:44
Alignment explanation
Indices: 28899540--28899946 Score: 246
Period size: 44 Copynumber: 9.3 Consensus size: 44
28899530 ATCTACCCCA
*
28899540 CTACTGCTTAGGGAGATAAGATATGTAATCTTCAGCCTGTTTCC
1 CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
* * ** **
28899584 CTACTACTTAGGG-GATTAAG-GCTCGTCGTCTTC-GATTCG-TTCC
1 CTACTGCTTAGGGAGA-TAAGATCT-GTAATCTTCAGCCT-GTTTCC
*
28899627 ACTACTGCTTAGGGAGATAAGATCTGTAATCTGCAGCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
* * * * * * * **
28899672 CTACTGCTTAGGGGGTTAAG-GCTCATCATTTTC-GATCT-ACTCC
1 CTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAG-CCTGTTTCC
* *
28899715 ACTACTACTTAAGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
* * * * ** * *
28899760 CTATTGCTTAGGGGGTTAAGGT-TCGTCGTCTTCGATCC-G-CTCC
1 CTACTGCTTAGGGAGATAAGATCT-GTAATCTTC-AGCCTGTTTCC
* *
28899803 ACTACTGCTTAGGGAGATAAGATCTGTAATCTTTACCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
* * * * ** * * * *
28899848 CTACTACTTAGGGGGTTAA-AGCTCGTCGTCTT-TG-ATCTCTCC
1 CTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAGCCTGTTTCC
* *
28899890 ACTACTGCTTATGGAGATAAGATCCGTAATCTTCAGCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
28899935 CTACTGCTTAGG
1 CTACTGCTTAGG
28899947 TGGTTAAGGC
Statistics
Matches: 260, Mismatches: 78, Indels: 50
0.67 0.20 0.13
Matches are distributed among these distances:
42 5 0.02
43 46 0.18
44 181 0.70
45 28 0.11
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTTCC
Found at i:28902520 original size:38 final size:38
Alignment explanation
Indices: 28902469--28902541 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
28902459 ATATCTAGGG
28902469 ACCTGTTGAAGGCAGATTCCAAAGAATAAATGATTTTA
1 ACCTGTTGAAGGCAGATTCCAAAGAATAAATGATTTTA
28902507 ACCTGTTGAAGGCAGATTCCAAAGAATAAATGATT
1 ACCTGTTGAAGGCAGATTCCAAAGAATAAATGATT
28902542 CTAAGGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (38 bp):
ACCTGTTGAAGGCAGATTCCAAAGAATAAATGATTTTA
Found at i:28906054 original size:20 final size:20
Alignment explanation
Indices: 28906031--28906068 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28906021 CAAAGCAGTA
28906031 ACGAAAATAGGAACAAAATG
1 ACGAAAATAGGAACAAAATG
* *
28906051 ACGAAAATCGTAACAAAA
1 ACGAAAATAGGAACAAAA
28906069 ACGGATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.11
Consensus pattern (20 bp):
ACGAAAATAGGAACAAAATG
Found at i:28907234 original size:15 final size:15
Alignment explanation
Indices: 28907194--28907236 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
28907184 ATTTTAAAAA
*
28907194 AATGATAGTAATAGT
1 AATGATAATAATAGT
* *
28907209 AATGATCATAATATT
1 AATGATAATAATAGT
*
28907224 AATGGTAATAATA
1 AATGATAATAATA
28907237 CAAGTAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (15 bp):
AATGATAATAATAGT
Found at i:28907369 original size:3 final size:3
Alignment explanation
Indices: 28907356--28907494 Score: 97
Period size: 3 Copynumber: 47.3 Consensus size: 3
28907346 AATAGGTAAA
*
28907356 AAT ATAT AAT AAT AAT AAT -AT AAT AGT AAT AAT AAT -AT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * * * *
28907400 AAT AGC AGT AAC AGT AAT AA- AAT AAT AGT TAT AAA AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
28907447 AGT AGT AAT AAT AAT AAT -AC AAT AGT AAT AAT AAT AGT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28907494 A
1 A
28907495 TTGAATTAAT
Statistics
Matches: 105, Mismatches: 26, Indels: 10
0.74 0.18 0.07
Matches are distributed among these distances:
2 7 0.07
3 95 0.90
4 3 0.03
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28907387 original size:23 final size:23
Alignment explanation
Indices: 28907361--28907482 Score: 126
Period size: 23 Copynumber: 5.4 Consensus size: 23
28907351 GTAAAAATAT
28907361 ATAATAATAATAATATAATAGTA
1 ATAATAATAATAATATAATAGTA
*
28907384 ATAATAAT-ATAATAATAATAGCA
1 ATAATAATAATAAT-ATAATAGTA
* * * *
28907407 GTAACAGTAATAAAATAATAGT-
1 ATAATAATAATAATATAATAGTA
*
28907429 -T-ATAAAAATAATACTAATAGTA
1 ATAATAATAATAATA-TAATAGTA
* *
28907451 GTAATAATAATAATACAATAGTA
1 ATAATAATAATAATATAATAGTA
28907474 ATAATAATA
1 ATAATAATA
28907483 GTAGTAATAA
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
20 8 0.10
21 8 0.10
22 5 0.06
23 44 0.55
24 15 0.19
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (23 bp):
ATAATAATAATAATATAATAGTA
Found at i:28907454 original size:44 final size:44
Alignment explanation
Indices: 28907366--28907491 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 44
28907356 AATATATAAT
28907366 AATAATAATATAATAGTAATAATAATATAATAATAATAGCAGTAAC
1 AATAATAATATAATAGTAATAA-AA-ATAATAATAATAGCAGTAAC
* * * * * *
28907412 AGTAATAAAATAATAGTTATAAAAATAATACTAATAGTAGTAAT
1 AATAATAATATAATAGTAATAAAAATAATAATAATAGCAGTAAC
* * * *
28907456 AATAATAATACAATAGTAATAATAATAGTAGTAATA
1 AATAATAATATAATAGTAATAAAAATAATAATAATA
28907492 ATATTGAATT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 46 0.69
45 2 0.03
46 19 0.28
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (44 bp):
AATAATAATATAATAGTAATAAAAATAATAATAATAGCAGTAAC
Found at i:28908290 original size:20 final size:20
Alignment explanation
Indices: 28908265--28908302 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28908255 ATTAGAAAAG
*
28908265 AAAAGAAAGAAAATAAAATA
1 AAAAGAAAGAAAAGAAAATA
28908285 AAAAGAAAGAAAAGAAAA
1 AAAAGAAAGAAAAGAAAA
28908303 AAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAGAAAGAAAAGAAAATA
Found at i:28912818 original size:26 final size:24
Alignment explanation
Indices: 28912789--28912843 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 24
28912779 GGACTCACCA
*
28912789 CAGCTTGTATGAGCTTACTGATATAT
1 CAGCTTGTAAGAGCTTACTG-T-TAT
28912815 CAGCTTGTAAGAGCTTACTGTTAT
1 CAGCTTGTAAGAGCTTACTGTTAT
28912839 CAGCT
1 CAGCT
28912844 CAATAGAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 8 0.29
25 1 0.04
26 19 0.68
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (24 bp):
CAGCTTGTAAGAGCTTACTGTTAT
Found at i:28912851 original size:24 final size:24
Alignment explanation
Indices: 28912824--28912893 Score: 97
Period size: 23 Copynumber: 2.9 Consensus size: 24
28912814 TCAGCTTGTA
*
28912824 AGAGCTTACTGTTATCAGCTCAAT
1 AGAGCTTACTGTTATCAACTCAAT
*
28912848 AGAGCTTACCGTT-TCAACTCAAT
1 AGAGCTTACTGTTATCAACTCAAT
*
28912871 AGAGCTTATTGTTTATCAACTCA
1 AGAGCTTACTG-TTATCAACTCA
28912894 GGAGGAGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 18 0.45
24 14 0.35
25 8 0.20
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (24 bp):
AGAGCTTACTGTTATCAACTCAAT
Found at i:28913461 original size:18 final size:18
Alignment explanation
Indices: 28913438--28913474 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28913428 TTATGCTTTT
28913438 GGTATATCTTGTGTATTA
1 GGTATATCTTGTGTATTA
28913456 GGTATATCTTGTGTATTA
1 GGTATATCTTGTGTATTA
28913474 G
1 G
28913475 CTAAGCCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (18 bp):
GGTATATCTTGTGTATTA
Found at i:28917243 original size:41 final size:41
Alignment explanation
Indices: 28917130--28917298 Score: 225
Period size: 41 Copynumber: 4.1 Consensus size: 41
28917120 GCAAAAATTG
* * ***
28917130 TAAAACACAGAGCAATAGCGGCG-TTTTACCAAAAACGCCGC
1 TAAAAGACAGAGCATTAGCGGCGCTTTT-GGTAAAACGCCGC
* * *
28917171 TAAAA-ACTGAGCAATAACGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
* *
28917211 TAAAAGACAGAGCTTTAGCGGCGCTTTTGGTAAAACGTCGC
1 TAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
28917252 TAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
28917293 TAAAAG
1 TAAAAG
28917299 TCATATAACT
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 30 0.26
41 84 0.74
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (41 bp):
TAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:28917941 original size:24 final size:24
Alignment explanation
Indices: 28917914--28917962 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
28917904 CGTATATTTA
*
28917914 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
28917938 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
28917962 T
1 T
28917963 GTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:28918303 original size:7 final size:7
Alignment explanation
Indices: 28918244--28918396 Score: 67
Period size: 7 Copynumber: 21.6 Consensus size: 7
28918234 GAGTTACTAT
*
28918244 TTTAAGG
1 TTTATGG
28918251 TTTATGG
1 TTTATGG
*
28918258 ATTATGG
1 TTTATGG
*
28918265 ATTATGGG
1 TTTAT-GG
28918273 TTTATGG
1 TTTATGG
*
28918280 ATTATGG
1 TTTATGG
**
28918287 TTTACAG
1 TTTATGG
28918294 TTTATGG
1 TTTATGG
*
28918301 TTTAAGG
1 TTTATGG
* **
28918308 GTTGGGG
1 TTTATGG
*
28918315 TTTAAGG
1 TTTATGG
28918322 TTTA-GG
1 TTTATGG
*
28918328 TGTTAGGG
1 T-TTATGG
*
28918336 GTTATGG
1 TTTATGG
* *
28918343 GTTAGGG
1 TTTATGG
*
28918350 GTTATGG
1 TTTATGG
*
28918357 GTTATGG
1 TTTATGG
*
28918364 ATTTAAGG
1 -TTTATGG
*
28918372 GTTAT-G
1 TTTATGG
*
28918378 TTGTATGA
1 TT-TATGG
*
28918386 TTTAGGG
1 TTTATGG
28918393 TTTA
1 TTTA
28918397 GGGGATAAAA
Statistics
Matches: 112, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
6 5 0.04
7 92 0.82
8 15 0.13
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.44
Consensus pattern (7 bp):
TTTATGG
Found at i:28918317 original size:21 final size:21
Alignment explanation
Indices: 28918295--28918375 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
28918285 GGTTTACAGT
28918295 TTATGGTTTAAGGGTT-GGGG
1 TTATGGTTTAAGGGTTAGGGG
*
28918315 TTTAAGGTTT-AGGTGTTAGGGG
1 -TTATGGTTTAAGG-GTTAGGGG
* * *
28918337 TTATGGGTTAGGGGTTATGGG
1 TTATGGTTTAAGGGTTAGGGG
28918358 TTATGGATTTAAGGGTTA
1 TTATGG-TTTAAGGGTTA
28918376 TGTTGTATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.06
21 31 0.63
22 15 0.31
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.41
Consensus pattern (21 bp):
TTATGGTTTAAGGGTTAGGGG
Found at i:28918537 original size:14 final size:14
Alignment explanation
Indices: 28918518--28918584 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
28918508 GTTTGCAGGT
*
28918518 AAAATGTTTTCTGG
1 AAAATGATTTCTGG
28918532 AAAATGATTTCTGG
1 AAAATGATTTCTGG
* *
28918546 AAAATAATTTCTTGA
1 AAAATGATTTC-TGG
*
28918561 AAAATGATTTATGG
1 AAAATGATTTCTGG
28918575 AAAATGATTT
1 AAAATGATTT
28918585 ACTTTTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 35 0.76
15 11 0.24
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.39
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:28918769 original size:13 final size:13
Alignment explanation
Indices: 28918729--28918779 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
28918719 TTGAGTTTAC
*
28918729 TTTATATA-TATA
1 TTTATATATTAAA
* *
28918741 TATATATTAATAAA
1 TTTATA-TATTAAA
*
28918755 TTTATATTTTAAA
1 TTTATATATTAAA
28918768 TTTATATATTAA
1 TTTATATATTAA
28918780 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 5 0.16
13 18 0.58
14 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTATATATTAAA
Found at i:28919185 original size:22 final size:21
Alignment explanation
Indices: 28919143--28919200 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
28919133 ATTTTTTAAA
*
28919143 AAAAATTATTTAAAATTAATAT
1 AAAAATTA-TAAAAATTAATAT
28919165 AAAAGA-TATAAAAATTCAATAT
1 AAAA-ATTATAAAAATT-AATAT
28919187 AAAAATTATAAAAA
1 AAAAATTATAAAAA
28919201 AGTCAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.25
22 23 0.72
23 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAATTATAAAAATTAATAT
Found at i:28919279 original size:38 final size:40
Alignment explanation
Indices: 28919211--28919319 Score: 186
Period size: 38 Copynumber: 2.8 Consensus size: 40
28919201 AGTCAAAAAT
28919211 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
* *
28919251 TAGCGGCGTTTAT-AT-AAAACACCGCAAAAGGCAAGCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
28919289 TAGCGGCGTTTATGATAAAAACGCCGCAAAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAA
28919320 AGTAATTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
38 34 0.53
39 4 0.06
40 26 0.41
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (40 bp):
TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
Found at i:28919626 original size:35 final size:34
Alignment explanation
Indices: 28919544--28919627 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 34
28919534 TGACTAAGCC
* *
28919544 ATTTGCCTAAATCATAGTTCCCCCGAAACCCTCA
1 ATTTCCCTAAATCATAGTTCCCCCAAAACCCTCA
* * *
28919578 TTTTCTCCCAAATCATAGTTCCCTCAAAACCC-CAAA
1 ATTTC-CCTAAATCATAGTTCCCCCAAAACCCTC--A
28919614 ATTTCCCTAAATCA
1 ATTTCCCTAAATCA
28919628 AACCCATTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
34 4 0.10
35 31 0.77
36 5 0.12
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.29
Consensus pattern (34 bp):
ATTTCCCTAAATCATAGTTCCCCCAAAACCCTCA
Found at i:28922325 original size:241 final size:242
Alignment explanation
Indices: 28921896--28922331 Score: 856
Period size: 241 Copynumber: 1.8 Consensus size: 242
28921886 GTATGAATTA
28921896 ATTTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACC
1 ATTTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACC
28921961 TTTTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCG
66 TTTTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCG
28922026 AGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
131 AGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
28922091 TCAAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAAT
196 TCAAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAAT
28922138 ATTTT-TTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACC
1 ATTTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACC
28922202 TTTTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCG
66 TTTTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCG
*
28922267 AGCTGTAAGATATAATGGATCTTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
131 AGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
28922332 AACTTACATA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
241 188 0.97
242 5 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (242 bp):
ATTTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACC
TTTTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCG
AGCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAAT
TCAAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAAT
Found at i:28922344 original size:9 final size:9
Alignment explanation
Indices: 28922330--28922388 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
28922320 ATCTTAAAAA
28922330 ATAACTTAC
1 ATAACTTAC
*
28922339 ATAACTCAC
1 ATAACTTAC
28922348 ATAACTTAC
1 ATAACTTAC
*
28922357 ATAATTTAC
1 ATAACTTAC
*
28922366 ATAACTCAC
1 ATAACTTAC
*
28922375 ATAACGTAC
1 ATAACTTAC
28922384 ATAAC
1 ATAAC
28922389 AACTTACAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.29
Consensus pattern (9 bp):
ATAACTTAC
Found at i:28922368 original size:27 final size:27
Alignment explanation
Indices: 28922330--28922388 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
28922320 ATCTTAAAAA
*
28922330 ATAACTTACATAACTCACATAACTTAC
1 ATAACTTACATAACTCACATAACGTAC
*
28922357 ATAATTTACATAACTCACATAACGTAC
1 ATAACTTACATAACTCACATAACGTAC
28922384 ATAAC
1 ATAAC
28922389 AACTTACAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.29
Consensus pattern (27 bp):
ATAACTTACATAACTCACATAACGTAC
Found at i:28927591 original size:46 final size:46
Alignment explanation
Indices: 28927524--28927618 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
28927514 ACTTAATAAT
*
28927524 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTTTTTA
1 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
*
28927570 ATTTGATTTATTCTAAATATTTATAATCTTTAATTATAATTGTTTA
1 ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
28927616 ATT
1 ATT
28927619 CAATTCATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (46 bp):
ATTTGATTTATTCTAAATATTTATAATCTTTAATGATAATTGTTTA
Done.