Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 136 of 226
Found at i:45455190 original size:50 final size:50
Alignment explanation
Indices: 45455048--45455344 Score: 229
Period size: 50 Copynumber: 5.8 Consensus size: 50
45455038 GATAATAACA
* ** * ***
45455048 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAAAT-CGG
* * * * * * **
45455097 TGCCAATGTCATATCCTAGATATGGTCTTACATGAGAGTTCTCAAATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCGG
* * * * ** **
45455147 TTCCCATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCGG
* * **
45455197 TGCCAACACCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCGG
** *
45455247 TGCCAACGCCATGTCTGAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA-AA--TC---GG
* *
45455303 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
45455345 TTACCCAAAT
Statistics
Matches: 195, Mismatches: 45, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
48 1 0.01
49 35 0.18
50 118 0.61
53 2 0.01
56 39 0.20
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCGG
Found at i:45459077 original size:30 final size:31
Alignment explanation
Indices: 45459038--45459095 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
45459028 TTTTTATTTT
45459038 TCCCTCAAAACTTTTACTCCTTCCCACTTTC
1 TCCCTCAAAACTTTTACTCCTTCCCACTTTC
*
45459069 TCCC-CAAAATTTTTACTCCTTCCCACT
1 TCCCTCAAAACTTTTACTCCTTCCCACT
45459096 CCCTCCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (31 bp):
TCCCTCAAAACTTTTACTCCTTCCCACTTTC
Found at i:45459102 original size:30 final size:30
Alignment explanation
Indices: 45459038--45459108 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
45459028 TTTTTATTTT
**
45459038 TCCCTCAAAACTTTTACTCCTTCCCACTTTC
1 TCCC-CAAAACTTTTACTCCTTCCCACTCCC
*
45459069 TCCCCAAAATTTTTACTCCTTCCCACTCCC
1 TCCCCAAAACTTTTACTCCTTCCCACTCCC
*
45459099 TCCCCTAAAC
1 TCCCCAAAAC
45459109 AAAATTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (30 bp):
TCCCCAAAACTTTTACTCCTTCCCACTCCC
Found at i:45459335 original size:21 final size:21
Alignment explanation
Indices: 45459306--45459345 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
45459296 TCCTTCAAAC
45459306 TTTTACTCCCCAAAACTTTTTA
1 TTTTACT-CCCAAAACTTTTTA
*
45459328 TTTT-CTCCCTAAACTTTT
1 TTTTACTCCCAAAACTTTT
45459346 ACTTCTCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTACTCCCAAAACTTTTTA
Found at i:45462890 original size:7 final size:7
Alignment explanation
Indices: 45462878--45462930 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
45462868 TTTCCAGGTC
45462878 TTTTTCA
1 TTTTTCA
45462885 TTTTTCA
1 TTTTTCA
45462892 TTTTTCA
1 TTTTTCA
45462899 TTTTTCA
1 TTTTTCA
45462906 TTTTTCA
1 TTTTTCA
45462913 TTTTTCA
1 TTTTTCA
45462920 TTTTTCA
1 TTTTTCA
45462927 TTTT
1 TTTT
45462931 GAAGAAAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:45463023 original size:58 final size:58
Alignment explanation
Indices: 45462901--45463035 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 58
45462891 ATTTTTCATT
* * * *
45462901 TTTCATTT-TTCATTTTTCATTTTTCATTTTGAAGAAAAACACATTCATTTCCAAATGA
1 TTTCATTTCTCCA-TTTTCATTTTTCATTTTGAAGAAAAACACAGTAATTTCCAAACGA
* * * *
45462959 TTTCATTTCTCCATTTTCATTTTT-ATTTTGCAGAAAACCATAGTAATTTCCAAACGT
1 TTTCATTTCTCCATTTTCATTTTTCATTTTGAAGAAAAACACAGTAATTTCCAAACGA
45463016 TTCTCATTTCTCCATTTTCA
1 TT-TCATTTCTCCATTTTCA
45463036 CTATTTCTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 28 0.42
58 36 0.54
59 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.48
Consensus pattern (58 bp):
TTTCATTTCTCCATTTTCATTTTTCATTTTGAAGAAAAACACAGTAATTTCCAAACGA
Found at i:45469870 original size:7 final size:7
Alignment explanation
Indices: 45469860--45469885 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
45469850 GTAGTTGTTG
45469860 ATTTTAA
1 ATTTTAA
45469867 ATTTTAA
1 ATTTTAA
45469874 ATTTTAA
1 ATTTTAA
45469881 ATTTT
1 ATTTT
45469886 TCGAACCAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:45471209 original size:16 final size:16
Alignment explanation
Indices: 45471175--45471214 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
45471165 AATAGATAAA
* *
45471175 TTATCTAATTAATTTT
1 TTATCTAATTAAATAT
*
45471191 TTATTTAATTAAATAT
1 TTATCTAATTAAATAT
45471207 TTATCTAA
1 TTATCTAA
45471215 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATCTAATTAAATAT
Found at i:45473816 original size:27 final size:27
Alignment explanation
Indices: 45473761--45473848 Score: 94
Period size: 26 Copynumber: 3.3 Consensus size: 27
45473751 ACATGCTTAT
*
45473761 TTAA-ATATATAATTACTT-TAATTTAA
1 TTAATATATATAATTA-TTATTATTTAA
**
45473787 TTAACTATATATTTTTATTA-TATTTAA
1 TTAA-TATATATAATTATTATTATTTAA
*
45473814 TTAATATAAATAATTATTATTATTTAA
1 TTAATATATATAATTATTATTATTTAA
45473841 -TAATATAT
1 TTAATATAT
45473849 CTCTATTTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 23 0.45
27 19 0.37
28 9 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATATATATAATTATTATTATTTAA
Found at i:45473821 original size:13 final size:13
Alignment explanation
Indices: 45473781--45473848 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
45473771 AATTACTTTA
45473781 ATTTAATTAACTAT
1 ATTTAATTAA-TAT
* *
45473795 ATATT-TTTATTAT
1 AT-TTAATTAATAT
45473808 ATTTAATTAATAT
1 ATTTAATTAATAT
** *
45473821 AAATAATTATTATT
1 ATTTAATTAATA-T
45473835 ATTTAA-TAATAT
1 ATTTAATTAATAT
45473847 AT
1 AT
45473849 CTCTATTTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
12 5 0.12
13 24 0.59
14 10 0.24
15 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTAATTAATAT
Found at i:45475368 original size:22 final size:21
Alignment explanation
Indices: 45475343--45475384 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45475333 CCAGCTAGAC
45475343 TTTGACGAATTTAATAAAAAAA
1 TTTGAC-AATTTAATAAAAAAA
* *
45475365 TTTGTCTATTTAATAAAAAA
1 TTTGACAATTTAATAAAAAA
45475385 CCTGCTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTGACAATTTAATAAAAAAA
Found at i:45475449 original size:3 final size:3
Alignment explanation
Indices: 45475441--45475488 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
45475431 TTCAACTTGT
45475441 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45475489 ATAAGATAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45479894 original size:54 final size:55
Alignment explanation
Indices: 45479767--45479896 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 55
45479757 CATCTCATAG
*
45479767 ACTGTGTAACTCACTGACTTGACTCACACAACCGTGTCGCAGGCTGTGTGCTAGT
1 ACTGTGTAACTCACTGACTTGACTCACACAACCATGTCGCAGGCTGTGTGCTAGT
* ** * * *
45479822 AC-GTGTAACCCACTGACTTGGTTCACACAGCCATGTCGTAGGTTGTGTGCTAG-
1 ACTGTGTAACTCACTGACTTGACTCACACAACCATGTCGCAGGCTGTGTGCTAGT
*
45479875 CCTGTGTAACTCA-TGGACTTGA
1 ACTGTGTAACTCACT-GACTTGA
45479897 GACACACGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.03
54 59 0.94
55 2 0.03
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (55 bp):
ACTGTGTAACTCACTGACTTGACTCACACAACCATGTCGCAGGCTGTGTGCTAGT
Found at i:45481760 original size:42 final size:40
Alignment explanation
Indices: 45481650--45481766 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 40
45481640 ATTTATATGC
45481650 CATACGGCTTGGACACTAGCCCATGTCCTTGCCCGTATAGCT
1 CATACGGC-TGGACAC-AGCCCATGTCCTTGCCCGTATAGCT
* * ** *
45481692 CACATGGCCTGGACACATGTACATGTCCTTGCCCGTGTAGCT
1 CATACGG-CTGGACACA-GCCCATGTCCTTGCCCGTATAGCT
*
45481734 CATACGGTCTGGACACACCCCTATGTCCTTGCC
1 CATACGG-CTGGACACAGCCC-ATGTCCTTGCC
45481767 TTTGTGACTT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.03
42 58 0.95
43 1 0.02
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (40 bp):
CATACGGCTGGACACAGCCCATGTCCTTGCCCGTATAGCT
Found at i:45481976 original size:105 final size:105
Alignment explanation
Indices: 45481782--45481979 Score: 256
Period size: 104 Copynumber: 1.9 Consensus size: 105
45481772 GACTTACACG
* * * *
45481782 GCCTGGGCACACGCCCATGTCCTCTGTGCGTGTGGTTCTAAAACATAAGTAGTGAGTTACACGGT
1 GCCTGGGCACACGCCCATGTCCTCTGTGCGTGTGGTACTAAAACACAAATAGTGAGTTACACGGC
* * * *
45481847 CTGGACACACGCCCGTGTCCTTGCCCGTATACCTCACATA
66 CTAGACAAACGCCCATCTCCTTGCCCGTATACCTCACATA
** *
45481887 GCCTGGGCACACGCCCATGTCC-CTG-GCCGTGTGGTACTAAGTCACAAATAGTGAGTTACATGG
1 GCCTGGGCACACGCCCATGTCCTCTGTG-CGTGTGGTACTAAAACACAAATAGTGAGTTACACGG
*
45481950 CCTAGACAAACGCTCATCTCCTTTGCCCGT
65 CCTAGACAAACGCCCATCTCC-TTGCCCGT
45481980 GTGAACCCTA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 1 0.01
104 48 0.61
105 30 0.38
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (105 bp):
GCCTGGGCACACGCCCATGTCCTCTGTGCGTGTGGTACTAAAACACAAATAGTGAGTTACACGGC
CTAGACAAACGCCCATCTCCTTGCCCGTATACCTCACATA
Found at i:45485450 original size:20 final size:20
Alignment explanation
Indices: 45485425--45485472 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
45485415 AAATGATATT
45485425 GATACTTTGTGAAAG-GTATC
1 GATACTTTGT-AAAGAGTATC
*
45485445 GATACTTTGTTAAGAGTATC
1 GATACTTTGTAAAGAGTATC
*
45485465 AATACTTT
1 GATACTTT
45485473 TGATTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (20 bp):
GATACTTTGTAAAGAGTATC
Found at i:45494192 original size:135 final size:135
Alignment explanation
Indices: 45493950--45494219 Score: 540
Period size: 135 Copynumber: 2.0 Consensus size: 135
45493940 TTAAAAAGCT
45493950 AGTTGTGTAGTTAATTAAGTTTTGGTTAAGTGAATTTGCATGAATTAAGAGTAAATAGGTAAAAG
1 AGTTGTGTAGTTAATTAAGTTTTGGTTAAGTGAATTTGCATGAATTAAGAGTAAATAGGTAAAAG
45494015 GACTAAATTGTATATAGGGTAAAAGTTGAATTATAGATTAAAAAAATTAAAGGGACTAAAGAAGT
66 GACTAAATTGTATATAGGGTAAAAGTTGAATTATAGATTAAAAAAATTAAAGGGACTAAAGAAGT
45494080 AATTA
131 AATTA
45494085 AGTTGTGTAGTTAATTAAGTTTTGGTTAAGTGAATTTGCATGAATTAAGAGTAAATAGGTAAAAG
1 AGTTGTGTAGTTAATTAAGTTTTGGTTAAGTGAATTTGCATGAATTAAGAGTAAATAGGTAAAAG
45494150 GACTAAATTGTATATAGGGTAAAAGTTGAATTATAGATTAAAAAAATTAAAGGGACTAAAGAAGT
66 GACTAAATTGTATATAGGGTAAAAGTTGAATTATAGATTAAAAAAATTAAAGGGACTAAAGAAGT
45494215 AATTA
131 AATTA
45494220 TGCCATTTTT
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (135 bp):
AGTTGTGTAGTTAATTAAGTTTTGGTTAAGTGAATTTGCATGAATTAAGAGTAAATAGGTAAAAG
GACTAAATTGTATATAGGGTAAAAGTTGAATTATAGATTAAAAAAATTAAAGGGACTAAAGAAGT
AATTA
Found at i:45494363 original size:4 final size:4
Alignment explanation
Indices: 45494346--45494399 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
45494336 TAAGTAATAA
*
45494346 AAAG AAAT AAAG AAAG AAAG AATAG AAACG AAACAG AAAG -AAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AA-AG AAA-G -AA-AG AAAG AAAG AAAG
45494393 AAAG AAA
1 AAAG AAA
45494400 TGAGAATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 29 0.67
5 7 0.16
6 3 0.07
7 1 0.02
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:45495374 original size:40 final size:39
Alignment explanation
Indices: 45495253--45495387 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
45495243 GACTTCGAGT
* *
45495253 CGATGAGACACTGGGTGTCAATTTATTATTTCAGATTTATT
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCA-ATTTATC
* * * * ** *
45495294 TGATGAGGCATTGGGTGCCAA-TT-TACTTCGGTTTAAC
1 CGATGAGACACTGGGTGTCAATTTATACTTCAATTTATC
*
45495331 CGATGAGACACTGGGTGTCAATTTACTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCAATTTATC
* *
45495371 CGATGAGGCACTAGGTG
1 CGATGAGACACTGGGTG
45495388 CCAGGCTGGT
Statistics
Matches: 72, Mismatches: 19, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
37 21 0.29
38 7 0.10
40 27 0.38
41 17 0.24
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTTATACTTCAATTTATC
Found at i:45495578 original size:16 final size:16
Alignment explanation
Indices: 45495542--45495596 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
45495532 ATTGAGACAC
45495542 ATGAATTG-TGTAT-T
1 ATGAATTGATGTATGT
45495556 CATGAATTGA-GTATGGT
1 -ATGAATTGATGTAT-GT
*
45495573 ATGAA-TGATGTATTT
1 ATGAATTGATGTATGT
45495588 ATGAATTGA
1 ATGAATTGA
45495597 ATAATTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 21 0.62
16 12 0.35
17 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.42
Consensus pattern (16 bp):
ATGAATTGATGTATGT
Found at i:45498936 original size:9 final size:9
Alignment explanation
Indices: 45498905--45498962 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
45498895 TTAAAACAAT
45498905 AAAGTAAATA
1 AAAG-AAATA
*
45498915 AAATAAA-A
1 AAAGAAATA
45498923 TAAAGAAATA
1 -AAAGAAATA
*
45498933 AAAGAAACA
1 AAAGAAATA
*
45498942 AAAGAAGTA
1 AAAGAAATA
*
45498951 AAAGAAACA
1 AAAGAAATA
45498960 AAA
1 AAA
45498963 AGAACAGGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 1 0.03
9 34 0.87
10 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAGAAATA
Found at i:45498958 original size:18 final size:18
Alignment explanation
Indices: 45498905--45498962 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
45498895 TTAAAACAAT
*
45498905 AAAGTAAATAAAATAAA-A
1 AAAG-AAATAAAAGAAACA
45498923 TAAAGAAATAAAAGAAACA
1 -AAAGAAATAAAAGAAACA
*
45498942 AAAGAAGTAAAAGAAACA
1 AAAGAAATAAAAGAAACA
45498960 AAA
1 AAA
45498963 AGAACAGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 31 0.86
19 5 0.14
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAGAAATAAAAGAAACA
Found at i:45499696 original size:23 final size:23
Alignment explanation
Indices: 45499669--45499802 Score: 143
Period size: 23 Copynumber: 6.0 Consensus size: 23
45499659 GGCTTTGCCG
*
45499669 ATCAGACACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
45499692 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
45499715 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* * **
45499738 TTCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTAT
* ** *
45499759 ATCAGGCACCTCGTGTGTTGT-T
1 ATCAGGCACTTTATGTGTCGTAT
*
45499781 -TCAGGCA-TCTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
45499802 A
1 A
45499803 CTAATTAGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
20 7 0.07
21 27 0.28
22 1 0.01
23 61 0.64
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:45511403 original size:31 final size:31
Alignment explanation
Indices: 45511362--45511733 Score: 219
Period size: 31 Copynumber: 12.2 Consensus size: 31
45511352 CAACAATATA
* *
45511362 TATATTCATATACGAATCAAATTCGGCAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
*
45511393 TATAATCATATACAAATC-AATTTGGCAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
* ** **
45511423 TATAACCATATATGAATCATGTTCGGCAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
* *
45511454 TATAATCATATACAAAT-TAATTCGGTAACT-
1 TATAATCATATACAAATCAAATTCGGCAA-TG
* * ** *
45511484 TAT-ATCCATATACAAATTAATTTTAGCAAAG
1 TATAAT-CATATACAAATCAAATTCGGCAATG
* *
45511515 TATAATCATATACGAATC-AATTCTGCAACT-
1 TATAATCATATACAAATCAAATTCGGCAA-TG
** * **
45511545 TATCTTCATATACAAATCAATTTCGATAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
* ** *
45511576 TATAACCATATACAAAT-AAATTTCAACAATT
1 TATAATCATATACAAATCAAA-TTCGGCAATG
* * * *
45511607 TACAACCATATACAAAT-TAATTCAGCAACT-
1 TATAATCATATACAAATCAAATTCGGCAA-TG
* * **
45511637 TAT-ATCCATATACAATTCAATTTCAACAATG
1 TATAAT-CATATACAAATCAAATTCGGCAATG
* * * *
45511668 TATAA-CTATATACAAATTAATTTCAGCAATT
1 TATAATC-ATATACAAATCAAATTCGGCAATG
* * * *
45511699 TATAATTATATACGAAT-TAATTCGGCAATA
1 TATAATCATATACAAATCAAATTCGGCAATG
45511729 TATAA
1 TATAA
45511734 AACAATCAAA
Statistics
Matches: 263, Mismatches: 61, Indels: 35
0.73 0.17 0.10
Matches are distributed among these distances:
29 3 0.01
30 107 0.41
31 150 0.57
32 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TATAATCATATACAAATCAAATTCGGCAATG
Found at i:45511440 original size:61 final size:60
Alignment explanation
Indices: 45511368--45511733 Score: 267
Period size: 61 Copynumber: 6.0 Consensus size: 60
45511358 TATATATATT
* * *
45511368 CATATACGAATCAAATTCGGCAATGTATAATCATATACAAATCAATTTGGCAATGTATAAC
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAAT-TATAAC
** * * * * *
45511429 CATATATGAATC-ATGTTCGGCAATGTATAATCATATACAAATTAATTCGGTAACTTATATC
1 CATATACAAATCAAT-TTCAGCAATGTATAATCATATACAAATCAATTTGGCAA-TTATAAC
* * * * ***
45511490 CATATACAAATTAATTTTAGCAAAGTATAATCATATACGAATCAATTCT-GCAACTTATCTT
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATT-TGGCAA-TTATAAC
* * * ** *
45511551 CATATACAAATCAATTTC-GATAATGTATAACCATATACAAATAAATTTCAACAATTTACAAC
1 CATATACAAATCAATTTCAG-CAATGTATAATCATATACAAATCAATTT-GGCAA-TTATAAC
* * **
45511613 CATATACAAATTAA-TTCAGCAACT-TAT-ATCCATATACAATTCAATTTCAACAATGTATAAC
1 CATATACAAATCAATTTCAGCAA-TGTATAAT-CATATACAAATCAATTT-GGCAAT-TATAAC
* * * * * * *
45511674 TATATACAAATTAATTTCAGCAATTTATAATTATATACGAATTAATTCGGCAATATATAA
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAAT-TATAA
45511734 AACAATCAAA
Statistics
Matches: 245, Mismatches: 46, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
60 5 0.02
61 191 0.78
62 47 0.19
63 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (60 bp):
CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAATTATAAC
Found at i:45511617 original size:92 final size:92
Alignment explanation
Indices: 45511362--45511726 Score: 369
Period size: 92 Copynumber: 4.0 Consensus size: 92
45511352 CAACAATATA
* * * * * *
45511362 TATATTCATATACGAATCAAATTCGGCAATGTATAATCATATACAAATCAATTT-GGCAATGTAT
1 TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
* *
45511426 AACCATATATGAATCATGTTCGGCAA-T
66 AACCATATACGAATCA-ATTCGGCAACT
* * ** * * *
45511453 GTATAATCATATACAAATTAA-TTCGGTAACT-TATATCCATATACAAATTAATTTTAGCAAAGT
1 -TATATTCATATACAAATCAATTTCGACAA-TGTATAACCATATACAAATTAATTTCAGCAATGT
* *
45511516 ATAATCATATACGAATCAATTCTGCAACT
64 ATAACCATATACGAATCAATTCGGCAACT
* * * * * *
45511545 TATCTTCATATACAAATCAATTTCGATAATGTATAACCATATACAAATAAATTTCAACAATTTAC
1 TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
* * *
45511610 AACCATATACAAATTAATTCAGCAACT
66 AACCATATACGAATCAATTCGGCAACT
* * * * *
45511637 TATATCCATATACAATTCAATTTCAACAATGTATAACTATATACAAATTAATTTCAGCAATTTAT
1 TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
** *
45511702 AATTATATACGAATTAATTCGGCAA
66 AACCATATACGAATCAATTCGGCAA
45511727 TATATAAAAC
Statistics
Matches: 227, Mismatches: 41, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
91 52 0.23
92 175 0.77
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (92 bp):
TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
AACCATATACGAATCAATTCGGCAACT
Found at i:45511671 original size:153 final size:153
Alignment explanation
Indices: 45511342--45511720 Score: 403
Period size: 153 Copynumber: 2.5 Consensus size: 153
45511332 ATCCAATGCT
*
45511342 CAAA-TCAA-TTCAACAATATATATATTCATATACGAATCAAATTCGGCAATGTATAATCATATA
1 CAAATTCAATTTCAACAATGTATA-A-TCATATACGAATC-AATTCGGCAATGTATAATCATATA
* ** * ** * *
45511405 CAAATCAATTTGGCAATGTATAACCATATATGAATCATGTTCGGCAATGTATAATCATATACAAA
63 CAAATCAATTTGACAATGTATAACCATATACAAATAATGTTCAACAATGTACAACCATATACAAA
* *
45511470 TTAATTCGGTAACTTATATCCATATA
128 TTAATTCAGCAACTTATATCCATATA
* * * * **
45511496 CAAATT-AATTTTAGCAAAGTATAATCATATACGAATCAATTCTGCAACT-TATCTTCATATACA
1 CAAATTCAATTTCAACAATGTATAATCATATACGAATCAATTCGGCAA-TGTATAATCATATACA
* *
45511559 AATCAATTTCGATAATGTATAACCATATACAAATAAAT-TTCAACAATTTACAACCATATACAAA
65 AATCAATTT-GACAATGTATAACCATATACAAAT-AATGTTCAACAATGTACAACCATATACAAA
45511623 TTAATTCAGCAACTTATATCCATATA
128 TTAATTCAGCAACTTATATCCATATA
* * * * *
45511649 C-AATTCAATTTCAACAATGTATAA-CTATATACAAATTAATTTCAGCAATTTATAATTATATAC
1 CAAATTCAATTTCAACAATGTATAATC-ATATACGAATCAA-TTCGGCAATGTATAATCATATAC
* *
45511712 GAATTAATT
64 AAATCAATT
45511721 CGGCAATATA
Statistics
Matches: 186, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
152 35 0.19
153 107 0.58
154 33 0.18
155 11 0.06
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (153 bp):
CAAATTCAATTTCAACAATGTATAATCATATACGAATCAATTCGGCAATGTATAATCATATACAA
ATCAATTTGACAATGTATAACCATATACAAATAATGTTCAACAATGTACAACCATATACAAATTA
ATTCAGCAACTTATATCCATATA
Found at i:45516093 original size:33 final size:33
Alignment explanation
Indices: 45516042--45516353 Score: 136
Period size: 33 Copynumber: 8.7 Consensus size: 33
45516032 TTATCCGTTA
*
45516042 TCGGTGGATTCAGCACTTAGCAACCACCAATGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
**
45516076 TCGGGGAATCAGCACTTAGCAACCCCTTTTCACATTCAAAAAT
1 TCGGGGAATCAGCACTTAGCAA---C----CAC---CAATGAT
* * *
45516119 ACAGTGGAATCAGCACTTAGCAACCACCAATGAA
1 TC-GGGGAATCAGCACTTAGCAACCACCAATGAT
*
45516153 TCGGGGAATCAACACTTAGCAACC-CTTTTCACATTTAAGAT
1 TCGGGGAATCAGCACTTAGCAACCAC----CA-A--T--GAT
* * *
45516194 ACGGTGGGATCAGCACTTAACAACCACCAATGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
45516228 TCGGGGAATCAACACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
* * *
45516255 TGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T--GAT
* *
45516296 ACGGTGGAATCAACACTTAGCAACCACCAATGAAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATG-AT
45516331 T-GGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
45516354 CCTTGGGGGA
Statistics
Matches: 211, Mismatches: 29, Indels: 77
0.67 0.09 0.24
Matches are distributed among these distances:
27 21 0.10
28 2 0.01
29 1 0.00
31 1 0.00
32 3 0.01
33 73 0.35
34 17 0.08
35 2 0.01
36 5 0.02
37 4 0.02
38 2 0.01
39 5 0.02
40 3 0.01
41 12 0.06
42 34 0.16
43 7 0.03
44 19 0.09
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:45516172 original size:77 final size:76
Alignment explanation
Indices: 45516045--45516255 Score: 334
Period size: 75 Copynumber: 2.8 Consensus size: 76
45516035 TCCGTTATCG
* *
45516045 GTGGATTCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCACA
1 GTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTTTCACA
45516110 TTCAAAAATACA
66 TT-AAAAATACA
*
45516122 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAA-CCCTTTTCACA
1 GTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTTTCACA
* * *
45516186 TTTAAGATACG
66 TTAAAAATACA
* *
45516197 GTGGGATCAGCACTTAACAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTT
1 GTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTT
45516256 GGGGGAATCA
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
75 56 0.45
76 18 0.15
77 50 0.40
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (76 bp):
GTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTTTCACA
TTAAAAATACA
Found at i:45516313 original size:102 final size:102
Alignment explanation
Indices: 45516155--45516385 Score: 365
Period size: 102 Copynumber: 2.3 Consensus size: 102
45516145 CCAATGAATC
* ** * * *
45516155 GGGGAATCAACACTTAGCAACCCTTTTCACATTTAAGATACGGTGGGATCAGCACTTAACAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAACAACCA
45516220 CCAATG-ATTCGGGGAATCAACACTTAGCAACCCCTTG
66 CCAATGAATT-GGGGAATCAACACTTAGCAACCCCTTG
*
45516257 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAACAACCA
*
45516322 CCAATGAATTGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATTGGGGAATCAACACTTAGCAACCCCTTG
*
45516359 GGGGAATCAGCATTTAGCAACCCCCTT
1 GGGGAATCAGCACTTAGCAACCCCCTT
45516386 TATATTCAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
102 116 0.97
103 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAACAACCA
CCAATGAATTGGGGAATCAACACTTAGCAACCCCTTG
Found at i:45519156 original size:20 final size:20
Alignment explanation
Indices: 45519103--45519148 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
45519093 CAGTGGTTTT
45519103 CACACGGGCGTGTGCCTATC
1 CACACGGGCGTGTGCCTATC
* *
45519123 CGCACGGGCGTGTGCCTGTC
1 CACACGGGCGTGTGCCTATC
45519143 CACACG
1 CACACG
45519149 AGCATGTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.37, G:0.33, T:0.17
Consensus pattern (20 bp):
CACACGGGCGTGTGCCTATC
Found at i:45522491 original size:22 final size:22
Alignment explanation
Indices: 45522461--45522502 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45522451 ATTTGGAGAT
*
45522461 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
45522483 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
45522503 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:45522529 original size:22 final size:23
Alignment explanation
Indices: 45522504--45522595 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
45522494 ATTTGAGAGT
45522504 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
45522526 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
45522548 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
45522570 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
45522592 TTGA
1 TTGA
45522596 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:45522544 original size:52 final size:51
Alignment explanation
Indices: 45522452--45522554 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
45522442 NNNNNNTGGA
* * *
45522452 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAA-TTGAGAG
*
45522503 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTT-GAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAG-AATTTTGGAAGGGAATTGAGAG
45522555 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
Found at i:45522553 original size:44 final size:44
Alignment explanation
Indices: 45522504--45522595 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
45522494 ATTTGAGAGT
* * * *
45522504 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
45522548 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
45522592 TTGA
1 TTGA
45522596 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:45523265 original size:19 final size:18
Alignment explanation
Indices: 45523224--45523283 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
45523214 ATGAATTTAA
**
45523224 AAAAAATAAAAAATTAGGA
1 AAAAAATAAAAAATT-TTA
*
45523243 AAAAGAATAAAAATCTTTTA
1 AAAA-AATAAAAA-ATTTTA
45523263 AAAAAATAAAAAATTTTA
1 AAAAAATAAAAAATTTTA
45523281 AAA
1 AAA
45523284 TTATAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.23
19 12 0.34
20 13 0.37
21 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAAAATAAAAAATTTTA
Found at i:45523769 original size:12 final size:12
Alignment explanation
Indices: 45523752--45523791 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
45523742 ATTTTTATAT
45523752 TTTAAATTTTTA
1 TTTAAATTTTTA
45523764 TTTAAA--TTTA
1 TTTAAATTTTTA
45523774 TTTAATATTTTT-
1 TTTAA-ATTTTTA
45523786 TTTAAA
1 TTTAAA
45523792 GGCAAACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 11 0.44
13 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAAATTTTTA
Found at i:45533596 original size:61 final size:62
Alignment explanation
Indices: 45533527--45533647 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 62
45533517 TAGTTCACTC
* *
45533527 ATTATCTTCGTATCACTAATACATAGTATAATCTTGTTTTATT-TGACTCCAGAACCTATTT
1 ATTATCTTCGTATCACTAATACATACTATAATCTTATTTTATTGTGACTCCAGAACCTATTT
* ** *
45533588 ATTATCTTCTTATCACTGGTACATACTATAATCTTATTTTATTGTGACTCCATAACCTAT
1 ATTATCTTCGTATCACTAATACATACTATAATCTTATTTTATTGTGACTCCAGAACCTAT
45533648 GTCTATATCC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
61 38 0.72
62 15 0.28
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (62 bp):
ATTATCTTCGTATCACTAATACATACTATAATCTTATTTTATTGTGACTCCAGAACCTATTT
Found at i:45534687 original size:12 final size:13
Alignment explanation
Indices: 45534658--45534695 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
45534648 GATGTATTTA
45534658 TCTTCTTTCTTTCTT
1 TCTTC-TTCTTTC-T
45534673 TCTTCTTC-TTCT
1 TCTTCTTCTTTCT
45534685 TCTTCTTCTTT
1 TCTTCTTCTTT
45534696 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 5 0.23
14 3 0.14
15 5 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTCTTCTTTCT
Found at i:45534699 original size:1 final size:1
Alignment explanation
Indices: 45534693--45534727 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
45534683 CTTCTTCTTC
*
45534693 TTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
45534728 GCGTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:45534734 original size:19 final size:19
Alignment explanation
Indices: 45534697--45534737 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
45534687 TTCTTCTTTT
***
45534697 TTTTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTGCGTTTA
45534716 TTTTTTTTTTTTGCGTTTA
1 TTTTTTTTTTTTGCGTTTA
45534735 TTT
1 TTT
45534738 CCAATTCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTTTGCGTTTA
Found at i:45538965 original size:255 final size:254
Alignment explanation
Indices: 45538473--45538986 Score: 942
Period size: 255 Copynumber: 2.0 Consensus size: 254
45538463 AAAATATTTA
*
45538473 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAATGATTAACTTGGTCT
1 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
45538538 TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTCTATTTTGATACTTGAATTTAGATTC
66 TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTCTATTTTGATACTTGAATTTAGATTC
*
45538603 CATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATGTTTTTAATAATTTATGTATATA
131 CATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATG-ATATA
45538668 TATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
195 TATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
45538728 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
1 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
*
45538793 TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTTTTCTATTTTGATCCTTGAATTTAGA
66 TTGAACTTCTTTATCTCCATTAGCCTTAG---TTTTTTTTTTCTATTTTGATACTTGAATTTAGA
45538858 TTCCATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATG-TA
128 TTCCATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATGATA
*
45538922 TATATATATATATTATTTTTTCAGGTATTAACACAGT-AAAAAAATGTCAAATTTTGAGGCT
193 TATATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
45538983 AATG
1 AATG
45538987 TTAACCAAAA
Statistics
Matches: 252, Mismatches: 4, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
255 120 0.48
256 39 0.15
258 93 0.37
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (254 bp):
AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTCTATTTTGATACTTGAATTTAGATTC
CATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATGATATAT
ATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
Found at i:45544828 original size:43 final size:43
Alignment explanation
Indices: 45544766--45544990 Score: 153
Period size: 43 Copynumber: 5.2 Consensus size: 43
45544756 TTTGAAAAAG
*
45544766 CGCCGCTAAAGACCATGACCTATAGCGGCGCTTCTCTAACAAA
1 CGCCGCTAAAGACCATGACCTATAGCGGCGCTTCTCCAACAAA
* * *
45544809 CGCCGCTAAAGA-CATTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGACCA-TGACCTATAGCGGCGCTTCTCCAACAAA
* * * * *
45544852 TGCCGCTATAG-CTCATGAGCTTTAGCGGCGCTTTTTCC-ACAAA
1 CGCCGCTAAAGAC-CATGACCTATAGCGGCGC-TTCTCCAACAAA
* * * * *
45544895 CGTCGCTATAG-CTCTAT-ACCTTTAGCGGTGCATT-TCCCACAAA
1 CGCCGCTAAAGAC-C-ATGACCTATAGCGGCGC-TTCTCCAACAAA
* *
45544938 CGCCGCTATAG-CTCGAT-ACCTTTAGCGGCGCTTCTCACAA-AAA
1 CGCCGCTAAAGAC-C-ATGACCTATAGCGGCGCTTCTC-CAACAAA
*
45544981 CGCCACTAAA
1 CGCCGCTAAA
45544991 AATATAACAT
Statistics
Matches: 156, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
42 7 0.04
43 137 0.88
44 12 0.08
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGACCATGACCTATAGCGGCGCTTCTCCAACAAA
Found at i:45544878 original size:86 final size:86
Alignment explanation
Indices: 45544766--45544990 Score: 237
Period size: 86 Copynumber: 2.6 Consensus size: 86
45544756 TTTGAAAAAG
* *
45544766 CGCCGCTAAAGAC-CATGACCTATAGCGGCGCTTCTCTAACAAACGCCGCTAAAGACAT-T-GAC
1 CGCCGCTATAG-CTCATGACCTTTAGCGGCGCTTCTCTAACAAACGCCGCTAAAG-C-TCTAGAC
*
45544828 CTTTAGCGGCGCTTTTCCCACAAA
63 CTTTAGCGGCGCATTTCCCACAAA
* * * * * * *
45544852 TGCCGCTATAGCTCATGAGCTTTAGCGGCGCTT-TTTCCACAAACGTCGCTATAGCTCTATACCT
1 CGCCGCTATAGCTCATGACCTTTAGCGGCGCTTCTCT-AACAAACGCCGCTAAAGCTCTAGACCT
*
45544916 TTAGCGGTGCATTTCCCACAAA
65 TTAGCGGCGCATTTCCCACAAA
* *
45544938 CGCCGCTATAGCTCGAT-ACCTTTAGCGGCGCTTCTC-ACAAAAACGCCACTAAA
1 CGCCGCTATAGCTC-ATGACCTTTAGCGGCGCTTCTCTA-ACAAACGCCGCTAAA
45544991 AATATAACAT
Statistics
Matches: 113, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
84 1 0.01
85 5 0.04
86 104 0.92
87 3 0.03
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (86 bp):
CGCCGCTATAGCTCATGACCTTTAGCGGCGCTTCTCTAACAAACGCCGCTAAAGCTCTAGACCTT
TAGCGGCGCATTTCCCACAAA
Found at i:45547200 original size:19 final size:20
Alignment explanation
Indices: 45547172--45547214 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
45547162 AAATTATAAA
*
45547172 TTTTAGTTTTTTTATTTCAT
1 TTTTAGTTTTTGTATTTCAT
*
45547192 TTTTA-TTTTTGTATTTTAT
1 TTTTAGTTTTTGTATTTCAT
45547211 TTTT
1 TTTT
45547215 TCTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTTGTATTTCAT
Found at i:45547595 original size:7 final size:7
Alignment explanation
Indices: 45547574--45547626 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
45547564 CCTAATTAAT
*
45547574 CTAACTC
1 CTAACCC
*
45547581 CTAGCCC
1 CTAACCC
45547588 CTAACCC
1 CTAACCC
*
45547595 CTAACTC
1 CTAACCC
45547602 CTAACCC
1 CTAACCC
*
45547609 CTAACTC
1 CTAACCC
45547616 CTAACCC
1 CTAACCC
45547623 CTAA
1 CTAA
45547627 ACCATAATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.28, C:0.49, G:0.02, T:0.21
Consensus pattern (7 bp):
CTAACCC
Found at i:45547597 original size:14 final size:14
Alignment explanation
Indices: 45547587--45547626 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
45547577 ACTCCTAGCC
45547587 CCTAACCCCTAACT
1 CCTAACCCCTAACT
45547601 CCTAACCCCTAACT
1 CCTAACCCCTAACT
45547615 CCTAACCCCTAA
1 CCTAACCCCTAA
45547627 ACCATAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTAACCCCTAACT
Found at i:45547600 original size:21 final size:21
Alignment explanation
Indices: 45547574--45547626 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
45547564 CCTAATTAAT
*
45547574 CTAACTCCTAGCCCCTAACCC
1 CTAACTCCTAACCCCTAACCC
*
45547595 CTAACTCCTAACCCCTAACTC
1 CTAACTCCTAACCCCTAACCC
*
45547616 CTAACCCCTAA
1 CTAACTCCTAA
45547627 ACCATAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.49, G:0.02, T:0.21
Consensus pattern (21 bp):
CTAACTCCTAACCCCTAACCC
Found at i:45548170 original size:15 final size:15
Alignment explanation
Indices: 45548150--45548179 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45548140 CCCTAACCCG
*
45548150 ACCCTAAATCTCTAA
1 ACCCTAAATCACTAA
45548165 ACCCTAAATCACTAA
1 ACCCTAAATCACTAA
45548180 CTCTTAACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
ACCCTAAATCACTAA
Found at i:45548348 original size:82 final size:83
Alignment explanation
Indices: 45548204--45548355 Score: 245
Period size: 82 Copynumber: 1.8 Consensus size: 83
45548194 CCCCTGACAA
* *
45548204 CTAACCCCTAAATCTTATTTAATACATAAATTAAAAAAACACTAATTAATCTAAATCCTAAACCC
1 CTAACCCCTAAATCTTATTTAATACATAAATTAAAAAAACACTAATTAATCTAAACCCTAAACCA
45548269 TAACCCGACCCTGAATCT
66 TAACCCGACCCTGAATCT
* *
45548287 CTAACCCCTAAA-CATTATTTAATATATAAATT-AAAATACACTAATTAATCTAAACCCTAAACC
1 CTAACCCCTAAATC-TTATTTAATACATAAATTAAAAAAACACTAATTAATCTAAACCCTAAACC
45548350 ATAACC
65 ATAACC
45548356 TGTCACTGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
82 35 0.55
83 29 0.45
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.28
Consensus pattern (83 bp):
CTAACCCCTAAATCTTATTTAATACATAAATTAAAAAAACACTAATTAATCTAAACCCTAAACCA
TAACCCGACCCTGAATCT
Found at i:45548466 original size:14 final size:15
Alignment explanation
Indices: 45548449--45548481 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
45548439 CTTAAATCAG
45548449 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
45548463 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
45548478 AATC
1 AATC
45548482 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:45548572 original size:21 final size:22
Alignment explanation
Indices: 45548533--45548575 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
45548523 CTAAATTAAT
*
45548533 CATATATATATATACCCTAAAC
1 CATATATATATAAACCCTAAAC
45548555 CATATATAT-TAAACCCTAAAC
1 CATATATATATAAACCCTAAAC
45548576 TATAATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (22 bp):
CATATATATATAAACCCTAAAC
Found at i:45548878 original size:89 final size:89
Alignment explanation
Indices: 45548778--45548957 Score: 333
Period size: 89 Copynumber: 2.0 Consensus size: 89
45548768 TTATTTCTAC
*
45548778 GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTCAATTAAAAATAAATTGAATTTTAAT
1 GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
45548843 TAATATAAATAAACAAATTAAATA
66 TAATATAAATAAACAAATTAAATA
*
45548867 GTGTCATTATTTCAAATTTATCTATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
1 GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
*
45548932 TAATATAAATAAATAAATTAAATA
66 TAATATAAATAAACAAATTAAATA
45548956 GT
1 GT
45548958 AAATAGACAG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (89 bp):
GTGTCATTATTTCAAATTTATCCATTTTTAACAAATATTAAATTAAAAATAAATTGAATTTTAAT
TAATATAAATAAACAAATTAAATA
Found at i:45549038 original size:41 final size:41
Alignment explanation
Indices: 45548981--45549196 Score: 324
Period size: 41 Copynumber: 5.3 Consensus size: 41
45548971 AAATGTTTTT
*
45548981 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
45549022 GCGGCGCTATTACAAAAACGCCGCTAAAGAACTGAACATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
45549063 GCGGCGCTTTTCCAAAAATGCCGGTAAAGAACTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
45549104 GCGGCGCTTTTACAAAAACGCCGCTAAAGAACTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
45549145 GCGACGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
*
45549186 GCGGTGCTTTT
1 GCGGCGCTTTT
45549197 TTTTAAAAAG
Statistics
Matches: 154, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 154 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
Found at i:45549298 original size:40 final size:39
Alignment explanation
Indices: 45549254--45549390 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
45549244 GGGCTTAGGG
* **
45549254 TTTTTTGCGGCGTTTTTCCAAAAATTGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTT-CAAAAAGCGCCGCTAATGCTCA
* * *
45549294 TTTTTAGCAGCGTTTTTGAAAAAGCGTCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTC-A
* * * ** *
45549334 TCTCTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGC-TCA
45549374 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
45549391 TTGTCTAAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 17 0.22
40 59 0.77
41 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
Found at i:45552144 original size:13 final size:13
Alignment explanation
Indices: 45552126--45552176 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
45552116 AGTTCTTCAT
45552126 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
45552139 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
45552152 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
45552165 TGCTTTTGAAAA
1 TGCTTTTGAAAA
45552177 ATTTGAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:45560805 original size:124 final size:125
Alignment explanation
Indices: 45560587--45560951 Score: 615
Period size: 124 Copynumber: 2.9 Consensus size: 125
45560577 TTTAGGTCTT
*** * *
45560587 GGAAGAAATAATTTCAAGTTGACGTTTGTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
1 GGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
* * *
45560652 ATTTCAGAAGAATTTGTGAAATTGTGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAC
66 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAC
*
45560712 GGAAGAAATAATTT-TTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
1 GGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
*
45560776 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAT
66 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAC
45560836 GGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
1 GGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
* *
45560901 AGTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTGCTACA
66 ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
45560952 ATAGCATGTT
Statistics
Matches: 227, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
124 115 0.51
125 112 0.49
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (125 bp):
GGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
ATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAC
Found at i:45560917 original size:125 final size:125
Alignment explanation
Indices: 45560579--45560951 Score: 622
Period size: 125 Copynumber: 3.0 Consensus size: 125
45560569 TTAGGGTTTT
* *** * *
45560579 TAGGTCTTGGAAGAAATAATTTCAAGTTGACGTTTGTGATCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
45560644 AGGATGCTATTTCAGAAGAATTTGTGAAATTGTGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
45560704 TAGGTCACGGAAGAAATAATTT-TTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
45560768 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
45560828 TAGGTCATGGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
45560893 AGGATGCTAGTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTGCTACA
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
45560952 ATAGCATGTT
Statistics
Matches: 233, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
124 115 0.49
125 118 0.51
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTCTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:45564610 original size:18 final size:18
Alignment explanation
Indices: 45564572--45564611 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
45564562 GACTCGGAAA
* *
45564572 AGGATACATATAAGGGTT
1 AGGATACATATAAGAGCT
45564590 AGGATACATATAAGAGCT
1 AGGATACATATAAGAGCT
45564608 AGGA
1 AGGA
45564612 AACGCACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGAGCT
Found at i:45566215 original size:25 final size:23
Alignment explanation
Indices: 45566187--45566241 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 23
45566177 CTTTTATAAC
*
45566187 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAA-TAAAAATTAT-TAA
*
45566212 AAATGCATAAATAAAAATTATTAA
1 AAAT-AATAAATAAAAATTATTAA
45566236 ATAATA
1 A-AATA
45566242 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 4 0.16
25 16 0.64
26 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAATAAATAAAAATTATTAA
Found at i:45578730 original size:32 final size:28
Alignment explanation
Indices: 45578673--45578727 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
45578663 TAATAAAAAT
*
45578673 TATTTAAAAATTATAAGAAATTATTAAC
1 TATTTAAAAATTATAAAAAATTATTAAC
45578701 TATTTAAAAATTAATTAAAAAA-TATTA
1 TATTTAAAAATT-A-TAAAAAATTATTA
45578728 TTATGAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 6 0.25
30 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TATTTAAAAATTATAAAAAATTATTAAC
Found at i:45579120 original size:19 final size:19
Alignment explanation
Indices: 45579088--45579126 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
45579078 TCATTCTGGA
45579088 TGTTATTTTAAATAAATTT
1 TGTTATTTTAAATAAATTT
45579107 TGTTAATTTT-AATAAATTT
1 TGTT-ATTTTAAATAAATTT
45579126 T
1 T
45579127 ATAATTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TGTTATTTTAAATAAATTT
Found at i:45579140 original size:19 final size:19
Alignment explanation
Indices: 45579092--45579133 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
45579082 TCTGGATGTT
*
45579092 ATTTTAAATAAATTTTGTTA
1 ATTTT-AATAAATTTTGATA
45579112 ATTTTAATAAATTTT-ATA
1 ATTTTAATAAATTTTGATA
45579130 ATTT
1 ATTT
45579134 CTTATAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTAATAAATTTTGATA
Found at i:45581802 original size:49 final size:50
Alignment explanation
Indices: 45581682--45581803 Score: 228
Period size: 50 Copynumber: 2.5 Consensus size: 50
45581672 TAAGAATATT
45581682 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAAATA
*
45581732 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTC-AAATTA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAAATA
45581781 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
45581804 TAATATAAAC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
49 28 0.39
50 43 0.61
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (50 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAAATA
Found at i:45582250 original size:18 final size:18
Alignment explanation
Indices: 45582224--45582265 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45582214 GACTAGAAAA
* * *
45582224 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
45582242 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
45582260 AGGATA
1 AGGATA
45582266 TGCACCTGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:45584133 original size:51 final size:51
Alignment explanation
Indices: 45584072--45584171 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
45584062 AAATAATTAA
45584072 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAGTTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAGTTGAGAGCAAATTGAGATT
* * * *
45584123 AAATATGGATTTGAGAGAAATTTGGAAGGAAGTTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAGTTGAGAGCAAATTGAGA
45584172 GGAAATTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.29, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAGTTGAGAGCAAATTGAGATT
Found at i:45584174 original size:22 final size:22
Alignment explanation
Indices: 45584133--45584180 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
45584123 AAATATGGAT
*
45584133 TTGAGAGAAATTTGGAAGGAAG
1 TTGAGAGAAATTTGGAAGGAAA
*
45584155 TTGAGAGCAATTT-GAGAGGAAA
1 TTGAGAGAAATTTGGA-AGGAAA
45584177 TTGA
1 TTGA
45584181 TAAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.25
Consensus pattern (22 bp):
TTGAGAGAAATTTGGAAGGAAA
Found at i:45584655 original size:19 final size:20
Alignment explanation
Indices: 45584613--45584655 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
45584603 AACTGACATG
*
45584613 TTTTATGAATTTTTTTATAG
1 TTTTATGAATTTTTTTATAA
*
45584633 TTTTATTAA-TTTTTTATAA
1 TTTTATGAATTTTTTTATAA
45584652 TTTT
1 TTTT
45584656 TATATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTATGAATTTTTTTATAA
Found at i:45589704 original size:20 final size:21
Alignment explanation
Indices: 45589656--45589704 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
45589646 AAAAATAATA
45589656 AAATCTAATTAGTTATAAAATT
1 AAAT-TAATTAGTTATAAAATT
** *
45589678 ATTTTAATTA-TTATTAAATT
1 AAATTAATTAGTTATAAAATT
45589698 AAATTAA
1 AAATTAA
45589705 AAGTCACATC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.64
21 6 0.27
22 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTAATTAGTTATAAAATT
Found at i:45590115 original size:28 final size:25
Alignment explanation
Indices: 45590082--45590141 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
45590072 ATTAAAATTG
*
45590082 ATATAAACTTATAAATATTATAAAAAT
1 ATATAAACTAAT-AA-ATTATAAAAAT
*
45590109 ATGATAATCTAATAAATTATAAAAAT
1 AT-ATAAACTAATAAATTATAAAAAT
45590135 ATATAAA
1 ATATAAA
45590142 ATTAAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 4 0.14
26 13 0.45
27 4 0.14
28 8 0.28
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATAAACTAATAAATTATAAAAAT
Found at i:45590135 original size:37 final size:38
Alignment explanation
Indices: 45590045--45590142 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 38
45590035 ATATTTTCTC
* * *
45590045 ATAAAATATTAAAAATATCATAAAAATATTAAAATTGAT
1 ATAAATTA-TAAAAATATTATAAAAATATGAAAATTGAT
*
45590084 ATAAACTTAT--AAATATTATAAAAATATGATAATCT-A-
1 ATAAA-TTATAAAAATATTATAAAAATATGAAAAT-TGAT
45590120 ATAAATTATAAAAATA-TATAAAA
1 ATAAATTATAAAAATATTATAAAA
45590143 TTAAAAAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
35 4 0.08
36 12 0.24
37 26 0.51
38 1 0.02
39 6 0.12
40 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (38 bp):
ATAAATTATAAAAATATTATAAAAATATGAAAATTGAT
Found at i:45590471 original size:15 final size:16
Alignment explanation
Indices: 45590451--45590485 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
45590441 CAGTTCAATT
*
45590451 AAATAAAATAT-TAAA
1 AAATAAAAAATATAAA
45590466 AAATAAAAAATATAAA
1 AAATAAAAAATATAAA
45590482 AAAT
1 AAAT
45590486 GTATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAAAATATAAA
Found at i:45590693 original size:21 final size:22
Alignment explanation
Indices: 45590663--45590714 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
45590653 AATACTTTTT
*
45590663 TATGATTTTTATAGAA-TTTAAA
1 TATG-TTTTTATAAAATTTTAAA
*
45590685 TTTGTTTTTATAAAATTTTAAA
1 TATGTTTTTATAAAATTTTAAA
45590707 TATGTTTT
1 TATGTTTT
45590715 GGTAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (22 bp):
TATGTTTTTATAAAATTTTAAA
Found at i:45590704 original size:22 final size:22
Alignment explanation
Indices: 45590668--45590738 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
45590658 TTTTTTATGA
*
45590668 TTTTTATAGAA-TTTAAATTTG
1 TTTTTATAAAATTTTAAATTTG
*
45590689 TTTTTATAAAATTTTAAATATG
1 TTTTTATAAAATTTTAAATTTG
** *
45590711 TTTTGGT--AATTTTATATTT-
1 TTTTTATAAAATTTTAAATTTG
45590730 TTTTTATAA
1 TTTTTATAA
45590739 TTTATTAGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.13
20 10 0.26
21 10 0.26
22 14 0.36
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTTATAAAATTTTAAATTTG
Found at i:45590764 original size:9 final size:9
Alignment explanation
Indices: 45590750--45590853 Score: 63
Period size: 9 Copynumber: 11.3 Consensus size: 9
45590740 TTATTAGAGT
45590750 TTTATAATA
1 TTTATAATA
45590759 TTTATAATA
1 TTTATAATA
45590768 TTTAATAATAA
1 TTT-ATAAT-A
*
45590779 TTTTATTATA
1 -TTTATAATA
*
45590789 TTTATAATC
1 TTTATAATA
45590798 TTATATCAAT-
1 TT-TAT-AATA
* * *
45590808 TTT-CACTT
1 TTTATAATA
45590816 TTTA-AATA
1 TTTATAATA
*
45590824 TTTTTAATA
1 TTTATAATA
*
45590833 TTTAATAATT
1 TTT-ATAATA
45590843 TTTAT-ATA
1 TTTATAATA
45590851 TTT
1 TTT
45590854 TTGATAACTT
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
7 2 0.03
8 13 0.17
9 31 0.41
10 18 0.24
11 8 0.11
12 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTATAATA
Found at i:45590836 original size:17 final size:18
Alignment explanation
Indices: 45590823--45590886 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
45590813 CTTTTTAAAT
45590823 ATTTTTA-ATATTTAATA
1 ATTTTTATATATTTAATA
*
45590840 ATTTTTATATATTTTTGATA
1 ATTTTTATATA--TTTAATA
* * *
45590860 ACTTTTCTGATTTTTAATA
1 ATTTTTAT-ATATTTAATA
45590879 ATTTTTAT
1 ATTTTTAT
45590887 GGGAAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 7 0.19
18 3 0.08
19 12 0.33
20 12 0.33
21 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTTATATATTTAATA
Found at i:45593450 original size:11 final size:11
Alignment explanation
Indices: 45593436--45593480 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
45593426 AAAAAATCAT
45593436 AAAAATTATAA
1 AAAAATTATAA
45593447 AAAAATTATTAA
1 AAAAATTA-TAA
45593459 AAAAGA-TATAA
1 AAAA-ATTATAA
*
45593470 AAAATTTATAA
1 AAAAATTATAA
45593481 TTTATAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 20 0.67
12 9 0.30
13 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:45594228 original size:23 final size:23
Alignment explanation
Indices: 45594202--45594255 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
45594192 TGATTGTTAA
* * *
45594202 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTAATTAGTAATAAT
45594225 ATTTAGAATTAATTAGTAATAAT
1 ATTTAGAATTAATTAGTAATAAT
45594248 ATTTAGAA
1 ATTTAGAA
45594256 AAAATCTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (23 bp):
ATTTAGAATTAATTAGTAATAAT
Found at i:45596466 original size:43 final size:43
Alignment explanation
Indices: 45596402--45596695 Score: 398
Period size: 43 Copynumber: 6.8 Consensus size: 43
45596392 TTTTCTTTAC
* * *
45596402 AACGACGCTATAAACCATGGTCTTTAGCGGCGCTTACCCATCA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* *
45596445 AACGCCGCTATAGACCTTGGTCTTTAGCGGCGCTTACCAAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
45596488 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* * *
45596531 AATGCCGCTATAGACCATGGTCTTTCGCGGCACTTACCCAACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
* *
45596574 AACGCCGCTATAGACCATGGTCTTTAGCTGCGCTTA-CCATGAAA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCA--ACA
45596618 AACGCCGCTATAGACCATGGTCTTTAGCGGCGCCTT-CACC-ACA
1 AACGCCGCTATAGACCATGGTCTTTAGCGGCG-CTTAC-CCAACA
* * *
45596661 AACGCCGCTAAAG-CTTATGGTTTTTAGCGGCGCTT
1 AACGCCGCTATAGAC-CATGGTCTTTAGCGGCGCTT
45596696 TTAGAAAAAC
Statistics
Matches: 225, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
42 7 0.03
43 180 0.80
44 33 0.15
45 3 0.01
46 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (43 bp):
AACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACA
Found at i:45597036 original size:21 final size:21
Alignment explanation
Indices: 45597010--45597058 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
45597000 TTTAAGCTGT
* *
45597010 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCACTGCAGCA
* *
45597031 TCTGCTTCTCTCACTGCCGCA
1 TCTGCTTCCCTCACTGCAGCA
45597052 TCTGCTT
1 TCTGCTT
45597059 TAAGCTACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.43, G:0.16, T:0.35
Consensus pattern (21 bp):
TCTGCTTCCCTCACTGCAGCA
Found at i:45597119 original size:87 final size:88
Alignment explanation
Indices: 45597013--45597175 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 88
45597003 AAGCTGTTCT
45597013 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACT-GCTGGAGTT
1 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAG-TACTAGCTGGAGTT
45597077 CTTCATA-CTTTCGTTGAAATTCA
65 CTTCATATCTTTCGTTGAAATTCA
* * * * ** **
45597100 GCTTCTCTTGCTGCTGCCTCTGCTTCTCTCGCTTTCGCATCTGCTTTAAGTTGTAGCTGGAGTTC
1 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTC
45597165 TTCATATCTTT
66 TTCATATCTTT
45597176 TTTGGACCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 2 0.03
87 60 0.91
88 4 0.06
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (88 bp):
GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGTACTAGCTGGAGTTC
TTCATATCTTTCGTTGAAATTCA
Found at i:45597188 original size:87 final size:87
Alignment explanation
Indices: 45597013--45597196 Score: 228
Period size: 87 Copynumber: 2.1 Consensus size: 87
45597003 AAGCTGTTCT
*
45597013 GCTTCCCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTC
1 GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTC
*
45597078 TTCATACTTTCGTTGAAATTCA
66 TTCATACTTTCGTTGAAACTCA
* * * ** **
45597100 GCTTCTCTTGCTGCTGCCTCTGCTTCTCTCGCTTTCGCATCTGCTTTAAG-TTGTAGCTGGAGTT
1 GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACT-GCTGGAGTT
* * *
45597164 CTTCATATCTTT-TTTGGACCTCA
65 CTTCATA-CTTTCGTTGAAACTCA
45597187 GCTTCTCTCG
1 GCTTCTCTCG
45597197 ATGTTGCCTC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 2 0.02
87 76 0.93
88 4 0.05
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (87 bp):
GCTTCTCTCGCTGCAGCCTCTGCTTCTCTCACTGCCGCATCTGCTTTAAGCTACTGCTGGAGTTC
TTCATACTTTCGTTGAAACTCA
Found at i:45602745 original size:15 final size:15
Alignment explanation
Indices: 45602706--45602747 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
45602696 TCGTATTATG
45602706 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
*
45602721 AAATGTTATGTATTAA
1 TAA-GTTATGTATTAA
45602737 TAAGTTATGTA
1 TAAGTTATGTA
45602748 AGTTATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
TAAGTTATGTATTAA
Found at i:45602849 original size:76 final size:77
Alignment explanation
Indices: 45602725--45602889 Score: 260
Period size: 76 Copynumber: 2.2 Consensus size: 77
45602715 TATTAAAAAT
* * * * *
45602725 GTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAAAAAATATATATTAATAAGTTATGT
1 GTTATGTATTAATAAGGTAGGAAAGATATGTATCATTTTAAAAAATATATATTAACAAGTTATGT
45602790 CGTATTATATAA
66 CGTATTATATAA
*
45602802 GTTATGTATTAATAAGGT-GGAAAGATATGTATCATTTTAAAATATATATATTAACAAGTTATGT
1 GTTATGTATTAATAAGGTAGGAAAGATATGTATCATTTTAAAAAATATATATTAACAAGTTATGT
*
45602866 CGTATTATGTAA
66 CGTATTATATAA
45602878 GTTATGTATTAA
1 GTTATGTATTAA
45602890 AAATGTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 64 0.79
77 17 0.21
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44
Consensus pattern (77 bp):
GTTATGTATTAATAAGGTAGGAAAGATATGTATCATTTTAAAAAATATATATTAACAAGTTATGT
CGTATTATATAA
Found at i:45602884 original size:53 final size:53
Alignment explanation
Indices: 45602827--45602979 Score: 163
Period size: 53 Copynumber: 3.1 Consensus size: 53
45602817 GGTGGAAAGA
*
45602827 TATGTATCATTTTAAAATATATATATTAACAAGTTATGTCGTATTATGTAAGT
1 TATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATGTAAGT
* * *
45602880 TATG--T-A--TTAAAA-ATGT-TATGTATTAA--TA---AG--TTATGTAAGT
1 TATGTATCATTTTAAAATATATATAT-TAATAAGTTATGTCGTATTATGTAAGT
45602920 TATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATGTAAGT
1 TATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATGTAAGT
45602973 TATGTAT
1 TATGTAT
45602980 TATATAANNN
Statistics
Matches: 78, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
40 14 0.18
42 2 0.03
43 1 0.01
45 8 0.10
46 11 0.14
47 10 0.13
48 8 0.10
50 1 0.01
51 2 0.03
53 21 0.27
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.46
Consensus pattern (53 bp):
TATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTATTATGTAAGT
Found at i:45602914 original size:15 final size:15
Alignment explanation
Indices: 45602875--45602916 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
45602865 TCGTATTATG
45602875 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
*
45602890 AAATGTTATGTATTAA
1 TAA-GTTATGTATTAA
45602906 TAAGTTATGTA
1 TAAGTTATGTA
45602917 AGTTATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
TAAGTTATGTATTAA
Found at i:45602941 original size:93 final size:92
Alignment explanation
Indices: 45602802--45602981 Score: 306
Period size: 93 Copynumber: 1.9 Consensus size: 92
45602792 TATTATATAA
45602802 GTTATGTATTAATAAGGTGGAAAGATATGTATCATTTTAAAATATATATATTAACAAGTTATGTC
1 GTTATGTATTAATAAGGTGGAAAGATATGTATCATTTTAAAATATATATATTAACAAGTTATGTC
45602867 GTATTATGTAAGTTATGTATTAAAAAT
66 GTATTATGTAAGTTATGTATTAAAAAT
* * * * *
45602894 GTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGT
1 GTTATGTATTAATAAGGT-GGAAAGATATGTATCATTTTAAAATATATATATTAACAAGTTATGT
45602959 CGTATTATGTAAGTTATGTATTA
65 CGTATTATGTAAGTTATGTATTA
45602982 TATAANNNNN
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 17 0.21
93 65 0.79
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.44
Consensus pattern (92 bp):
GTTATGTATTAATAAGGTGGAAAGATATGTATCATTTTAAAATATATATATTAACAAGTTATGTC
GTATTATGTAAGTTATGTATTAAAAAT
Found at i:45603259 original size:16 final size:15
Alignment explanation
Indices: 45603246--45603473 Score: 104
Period size: 16 Copynumber: 14.7 Consensus size: 15
45603236 TCGTATTATG
45603246 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
*
45603261 AAATGTTATGTATTAA
1 TAA-GTTATGTATTAA
45603277 TAAGTTATGTAAGTT-A
1 TAAGTTATGT-A-TTAA
45603293 T--GTATCAT-T-TTAA
1 TAAGT-T-ATGTATTAA
* *
45603306 -AA-TATATATATCAA
1 TAAGT-TATGTATTAA
*
45603320 TAAGTTATGTCGTATTATG
1 TAAGTTA--T-GTATTA-A
45603339 TAAGTTATGTATTATA
1 TAAGTTATGTATTA-A
*
45603355 CAAGTTATGTATTAA
1 TAAGTTATGTATTAA
45603370 TAAGTTATGTA--AGA
1 TAAGTTATGTATTA-A
*
45603384 TATGTATCAT-T-TTAA
1 TAAGT-T-ATGTATTAA
*
45603399 -AA-TATATATATTAA
1 TAAGT-TATGTATTAA
45603413 TAAGTTATGTCGTATTATA
1 TAAGTTA--T-GTATTA-A
45603432 TAAGTTATGTATTAA
1 TAAGTTATGTATTAA
* *
45603447 AAATGTTATGTATGAA
1 TAA-GTTATGTATTAA
45603463 TAAGTTATGTA
1 TAAGTTATGTA
45603474 AGTTATGTAT
Statistics
Matches: 168, Mismatches: 15, Indels: 60
0.69 0.06 0.25
Matches are distributed among these distances:
12 6 0.04
13 10 0.06
14 15 0.09
15 44 0.26
16 63 0.38
17 6 0.04
18 9 0.05
19 15 0.09
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (15 bp):
TAAGTTATGTATTAA
Found at i:45603342 original size:53 final size:53
Alignment explanation
Indices: 45603281--45603515 Score: 177
Period size: 43 Copynumber: 4.9 Consensus size: 53
45603271 TATTAATAAG
*
45603281 TTATGTAAGTTATGTATCATTTTAAAATATATATATCAATAAGTTATGTCGTA
1 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTA
* * *
45603334 TTATGTAAGTTATG--T-ATTATACAAGT-TATGTATTAATAAGTTA--T-GTA
1 TTATGTAAGTTATGTATCATTTTA-AAATATATATATTAATAAGTTATGTCGTA
45603381 --A-G--A--TATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTA
1 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTA
* * *
45603427 TTATATAAGTTATG--T-A--TTAAAA-ATGT-TATGT-ATGAA--TA---AG--
1 TTATGTAAGTTATGTATCATTTTAAAATATATATAT-TAAT-AAGTTATGTCGTA
45603467 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGT
1 TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGT
45603516 AATGTATGTA
Statistics
Matches: 140, Mismatches: 12, Indels: 62
0.65 0.06 0.29
Matches are distributed among these distances:
40 17 0.12
42 7 0.05
43 22 0.16
44 1 0.01
45 10 0.07
46 14 0.10
47 14 0.10
48 10 0.07
50 21 0.15
51 6 0.04
53 18 0.13
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (53 bp):
TTATGTAAGTTATGTATCATTTTAAAATATATATATTAATAAGTTATGTCGTA
Found at i:45603394 original size:93 final size:93
Alignment explanation
Indices: 45603235--45603515 Score: 501
Period size: 93 Copynumber: 3.0 Consensus size: 93
45603225 NNNNNNNNNN
45603235 GTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCA
1 GTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCA
*
45603300 TTTTAAAATATATATATCAATAAGTTAT
66 TTTTAAAATATATATATTAATAAGTTAT
* *
45603328 GTCGTATTATGTAAGTTATGTATTATACAA-GTTATGTATTAATAAGTTATGTAAGATATGTATC
1 GTCGTATTATGTAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATC
45603392 ATTTTAAAATATATATATTAATAAGTTAT
65 ATTTTAAAATATATATATTAATAAGTTAT
* *
45603421 GTCGTATTATATAAGTTATGTATTAAAAATGTTATGTATGAATAAGTTATGTAAGTTATGTATCA
1 GTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCA
45603486 TTTTAAAATATATATATTAATAAGTTAT
66 TTTTAAAATATATATATTAATAAGTTAT
45603514 GT
1 GT
45603516 AATGTATGTA
Statistics
Matches: 179, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
92 3 0.02
93 173 0.97
94 3 0.02
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (93 bp):
GTCGTATTATGTAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCA
TTTTAAAATATATATATTAATAAGTTAT
Found at i:45604158 original size:15 final size:15
Alignment explanation
Indices: 45604130--45604165 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
45604120 GTAATAAAAG
*
45604130 GAAAA-AGTAGAAAT
1 GAAAACAGTACAAAT
45604144 GAAAACAGTACAAAT
1 GAAAACAGTACAAAT
45604159 GAAAACA
1 GAAAACA
45604166 AATTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (15 bp):
GAAAACAGTACAAAT
Found at i:45608425 original size:41 final size:41
Alignment explanation
Indices: 45608314--45608425 Score: 102
Period size: 41 Copynumber: 2.7 Consensus size: 41
45608304 GATTTTATTA
* * *
45608314 TTAGCGGCGCTATCTACA-AAACGCCACTAATGCTCCGGTCT
1 TTAGCGGCGTTTTCTA-AGAAACGCCGCTAATGCTCCGGTCT
* ** * *
45608355 TTAGCGGCGTTTTCTAATATGCGCCGCTAATGCTGCGGTTT
1 TTAGCGGCGTTTTCTAAGAAACGCCGCTAATGCTCCGGTCT
* *
45608396 TTAGCGGTGCTTTT-TAAGAAACGCTGCTAA
1 TTAGCGGCG-TTTTCTAAGAAACGCCGCTAA
45608426 AGACCTAAGC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
40 1 0.02
41 52 0.91
42 4 0.07
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (41 bp):
TTAGCGGCGTTTTCTAAGAAACGCCGCTAATGCTCCGGTCT
Found at i:45608441 original size:41 final size:40
Alignment explanation
Indices: 45608396--45608670 Score: 313
Period size: 41 Copynumber: 6.8 Consensus size: 40
45608386 GCTGCGGTTT
* * * *
45608396 TTAGCGGTGCTTTTTAAGAAACGCTGCTAAAGACCTAAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCT-AGCA
* * *
45608437 TTAGCGGCGCTTCGTAAAAAACGCCGTTAAAGACTGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGAC-CTAGCA
*
45608478 TTAGTGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACC-TAGCA
45608519 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCGTAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACC-TAGCA
45608560 TTAGCGGCGCTTTGT-AAAAACGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCT-AGCA
* * * * *
45608600 TTAGCGGTGCATAT-TAGAAAACGCCGCGAAAGACCGCAGCA
1 TTAGCGGCGC-TTTGTAAAAAACGCCGCTAAAGACC-TAGCA
* * *
45608641 TTAGCGACGATTATGT-AAAAGCGCCGCTAA
1 TTAGCGGCGCTT-TGTAAAAAACGCCGCTAA
45608671 GGGCCCCAAA
Statistics
Matches: 202, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.00
40 34 0.17
41 165 0.82
42 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTTGTAAAAAACGCCGCTAAAGACCTAGCA
Found at i:45608600 original size:81 final size:81
Alignment explanation
Indices: 45608396--45608670 Score: 347
Period size: 82 Copynumber: 3.4 Consensus size: 81
45608386 GCTGCGGTTT
* * * * *
45608396 TTAGCGGTGCTTTTTAAGAAACGCTGCTAAAGACCTAAGCATTAGCGGCGCTTCGTAAAAAACGC
1 TTAGCGGCGCTTTGTAA-AAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTGTAAAAAACGC
* *
45608461 CGTTAAAGACTGTAGCA
65 CGCTAAAGACCGTAGCA
*
45608478 TTAGTGGCGCTTTGTAAAAAACGCCGCTAAAGACC-GTAGCATTAGCGGCGCTTTGTAAAAAACG
1 TTAGCGGCGCTTTGT-AAAAACGCCGCTAAAGACCTG-AGCATTAGCGGCGCTTTGTAAAAAACG
45608542 CCGCTAAAGACCGTAGCA
64 CCGCTAAAGACCGTAGCA
* * *
45608560 TTAGCGGCGCTTTGTAAAAACGCCGCTAAAGACCTGAGCATTAGCGGTGCATAT-TAGAAAACGC
1 TTAGCGGCGCTTTGTAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGC-TTTGTAAAAAACGC
* *
45608624 CGCGAAAGACCGCAGCA
65 CGCTAAAGACCGTAGCA
* * *
45608641 TTAGCGACGATTATGTAAAAGCGCCGCTAA
1 TTAGCGGCGCTT-TGTAAAAACGCCGCTAA
45608671 GGGCCCCAAA
Statistics
Matches: 171, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
81 66 0.39
82 103 0.60
83 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (81 bp):
TTAGCGGCGCTTTGTAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTGTAAAAAACGCC
GCTAAAGACCGTAGCA
Found at i:45608864 original size:41 final size:41
Alignment explanation
Indices: 45608778--45608864 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
45608768 ATATATCGCC
*
45608778 GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAGCGCC
1 GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAGCGCA
* * * *
45608819 GCTAATGCTCG-ATTTTTTGTGGCGTTTTTTGTCCAAA-CGCA
1 GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGT--AAAGCGCA
45608860 GCTAA
1 GCTAA
45608865 AAGCCTGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 17 0.44
41 19 0.49
42 3 0.08
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (41 bp):
GCTAATGCTCGTATCTTTGGCGGCGTTTTTCGTAAAGCGCA
Found at i:45609960 original size:51 final size:51
Alignment explanation
Indices: 45609900--45609998 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
45609890 TAAATTCGGT
* *
45609900 GATAATGCTCATTTTCTTGTAGTGTTGATGATTGGAAAATTACTTATAGAA
1 GATAATGCTCATTTTCTTATAGTGTTGATGAATGGAAAATTACTTATAGAA
* *
45609951 GATAATGCTCATTTTCTTATAGTGTTGATTAATGGAAATTTACTTATA
1 GATAATGCTCATTTTCTTATAGTGTTGATGAATGGAAAATTACTTATA
45609999 TAGGTGAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.43
Consensus pattern (51 bp):
GATAATGCTCATTTTCTTATAGTGTTGATGAATGGAAAATTACTTATAGAA
Found at i:45610188 original size:17 final size:18
Alignment explanation
Indices: 45610155--45610188 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45610145 ATAAATTTTT
*
45610155 AATTTTTTAATAGTTAAA
1 AATTTTTAAATAGTTAAA
45610173 AATTTTTAAATA-TTAA
1 AATTTTTAAATAGTTAA
45610189 TATAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTTTAAATAGTTAAA
Found at i:45612540 original size:17 final size:17
Alignment explanation
Indices: 45612518--45612577 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
45612508 TTTAATATAA
45612518 TTAATACTATCTATTAT
1 TTAATACTATCTATTAT
** * *
45612535 TTAATAAAATTTTAATATAA
1 TTAATACTA-TCT-AT-TAT
45612555 TTAATACTATCTATTAT
1 TTAATACTATCTATTAT
45612572 TTAATA
1 TTAATA
45612578 AAATTTTATT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 4 0.12
20 9 0.28
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATACTATCTATTAT
Found at i:45612545 original size:37 final size:37
Alignment explanation
Indices: 45612504--45612585 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
45612494 AATAATTAGT
45612504 AAATTTTAATATAATTAATACTATCTATTATTTAATA
1 AAATTTTAATATAATTAATACTATCTATTATTTAATA
45612541 AAATTTTAATATAATTAATACTATCTATTATTTAATA
1 AAATTTTAATATAATTAATACTATCTATTATTTAATA
45612578 AAATTTTA
1 AAATTTTA
45612586 TTATTTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (37 bp):
AAATTTTAATATAATTAATACTATCTATTATTTAATA
Found at i:45612905 original size:16 final size:18
Alignment explanation
Indices: 45612867--45612912 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
45612857 TATTTCAAAT
45612867 ATTAATTTTTTAATGATA
1 ATTAATTTTTTAATGATA
45612885 A--AATTTTTTAA-G-TA
1 ATTAATTTTTTAATGATA
*
45612899 ATTAATTTATTAAT
1 ATTAATTTTTTAAT
45612913 ATTTATCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
14 3 0.12
15 1 0.04
16 19 0.79
18 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
ATTAATTTTTTAATGATA
Found at i:45613735 original size:22 final size:20
Alignment explanation
Indices: 45613688--45613735 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
45613678 ACATGGACTA
*
45613688 AAAAATTGATGACATGAATT
1 AAAAATTGATAACATGAATT
* *
45613708 GAAAATTGCTAACATGGAAGTT
1 AAAAATTGATAACAT-GAA-TT
45613730 AAAAAT
1 AAAAAT
45613736 CTTTTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.55
21 3 0.14
22 7 0.32
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (20 bp):
AAAAATTGATAACATGAATT
Found at i:45615979 original size:17 final size:16
Alignment explanation
Indices: 45615953--45615984 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
45615943 AATCCCCTTC
45615953 TTATTATATATAAATA
1 TTATTATATATAAATA
45615969 TTATCTATATATAAAT
1 TTAT-TATATATAAAT
45615985 GTACCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTATATATAAATA
Found at i:45617559 original size:17 final size:17
Alignment explanation
Indices: 45617537--45617569 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45617527 TTAATTAATT
45617537 AATT-AATTAATTTTCTC
1 AATTAAATT-ATTTTCTC
45617554 AATTAAATTATTTTCT
1 AATTAAATTATTTTCT
45617570 TAACCCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTAAATTATTTTCTC
Found at i:45620091 original size:6 final size:6
Alignment explanation
Indices: 45620080--45620149 Score: 88
Period size: 6 Copynumber: 11.3 Consensus size: 6
45620070 GGTTTTCTCC
*
45620080 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAGATG AAAAATA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAA-ATG -AAAATG
*
45620130 AAAATG -ACATG AAAAATG AA
1 AAAATG AAAATG -AAAATG AA
45620150 TATACGCTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.07
6 40 0.71
7 9 0.16
8 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:45620349 original size:22 final size:24
Alignment explanation
Indices: 45620306--45620349 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
45620296 GTTGAGAAAA
*
45620306 TTATTTTATTGGAAATATGAAAGT
1 TTATTTTATGGGAAATATGAAAGT
45620330 TTATTTT-TGGGAAATA-GAAA
1 TTATTTTATGGGAAATATGAAA
45620350 AAAAATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (24 bp):
TTATTTTATGGGAAATATGAAAGT
Found at i:45621600 original size:24 final size:24
Alignment explanation
Indices: 45621555--45621600 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
45621545 AAATATGCTT
* *
45621555 TAGGATGAATTTTGTAATCTTTTC
1 TAGGATGAATTTTGGAAACTTTTC
45621579 TAGGATGGAA-TTTGGAAACTTT
1 TAGGAT-GAATTTTGGAAACTTT
45621601 GGCTGGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (24 bp):
TAGGATGAATTTTGGAAACTTTTC
Found at i:45640832 original size:14 final size:14
Alignment explanation
Indices: 45640813--45640839 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45640803 ATTTATTAAA
45640813 AAAATTACAAATAT
1 AAAATTACAAATAT
45640827 AAAATTACAAATA
1 AAAATTACAAATA
45640840 CACTACACTT
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:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTACAAATAT
Found at i:45642194 original size:63 final size:57
Alignment explanation
Indices: 45642069--45642181 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
45642059 AAAAATGGTG
* *
45642069 AAATGGAGAAATAGGAAACATTTGGAAATGATTAAGGTTTTCTCCAAAATGAAAATAA
1 AAATGGAGAAATA-GAAACATTTGGAAATGAATAAGATTTTCTCCAAAATGAAAATAA
*
45642127 AAATGGAGAAAT-GAAATCATTTGGAAATGAATATGATTTTCTCCAAAATGAAAAT
1 AAATGGAGAAATAGAAA-CATTTGGAAATGAATAAGATTTTCTCCAAAATGAAAAT
45642182 GACATGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 4 0.08
57 35 0.69
58 12 0.24
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAATAGAAACATTTGGAAATGAATAAGATTTTCTCCAAAATGAAAATAA
Found at i:45650403 original size:23 final size:23
Alignment explanation
Indices: 45650317--45650396 Score: 135
Period size: 23 Copynumber: 3.5 Consensus size: 23
45650307 TTTATACATT
45650317 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
45650340 AATCACATTAATATTTAAGCATA
1 AATCACATTAATATTTAAGCATA
*
45650363 AAGCACATTAACT-TTTAAGCATA
1 AATCACATTAA-TATTTAAGCATA
45650386 AATCACATTAA
1 AATCACATTAA
45650397 CTTTTAACAC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
23 53 0.98
24 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:45653762 original size:20 final size:20
Alignment explanation
Indices: 45653739--45653777 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45653729 AGTTAGTGAT
45653739 AAACACATAACTTAACTAAA
1 AAACACATAACTTAACTAAA
*
45653759 AAACACATAACTTAGCTAA
1 AAACACATAACTTAACTAA
45653778 TCCATCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (20 bp):
AAACACATAACTTAACTAAA
Found at i:45655551 original size:16 final size:17
Alignment explanation
Indices: 45655522--45655554 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
45655512 ATAGACCTTG
45655522 AAACTATAGAATTGTGA
1 AAACTATAGAATTGTGA
45655539 AAACTATAG-ATTGTGA
1 AAACTATAGAATTGTGA
45655555 GACTATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (17 bp):
AAACTATAGAATTGTGA
Found at i:45661903 original size:51 final size:51
Alignment explanation
Indices: 45661771--45662065 Score: 307
Period size: 51 Copynumber: 5.8 Consensus size: 51
45661761 ACTTTTATCA
* ** *
45661771 TTCGATACACGTAGTAGCCTTCACATAGTACTAAACACATGATC-AAG-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * *
45661820 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * *
45661872 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGC-TT
* *
45661922 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACATGTGACCAAAGCTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
* * * * *
45661974 CTC-AGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TT
1 TTCGA-TACACGTAGTAGCCTTCACATAGTACTACACATGTGACCA-AAGCTT
* *
45662024 TATCGATACACGTAGTAGCCTTCACACAATACTACACATGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACATGTG
45662066 TTCATCGATA
Statistics
Matches: 206, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
49 4 0.02
50 43 0.21
51 149 0.72
52 8 0.04
53 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
Found at i:45661954 original size:102 final size:102
Alignment explanation
Indices: 45661771--45662061 Score: 404
Period size: 102 Copynumber: 2.9 Consensus size: 102
45661761 ACTTTTATCA
* * * * ** * *** *
45661771 TTCGATACACGTAGTAGCCTTCACATAGTACTAAACACATGATCAAGTTTTA-CGGTTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
45661835 TAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
45661872 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
45661937 TAGCCTTCACACAGTACTACACATGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
* * * * *
45661974 CTCAGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
45662039 TAGCCTTCACACAATACTACACA
66 TAGCCTTCACACAGTACTACACA
45662062 TGTGTTCATC
Statistics
Matches: 170, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 42 0.25
102 128 0.75
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (102 bp):
TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
Found at i:45662040 original size:153 final size:151
Alignment explanation
Indices: 45661772--45662065 Score: 358
Period size: 153 Copynumber: 1.9 Consensus size: 151
45661762 CTTTTATCAT
* * * * * *
45661772 TCGATACACGTAGTAGCCTTCACATAGTACTAAACACATGATCAAGTTTTACGGTTCACGTAGTA
1 TCGATACACGTAGTAGCCTTCACACAGTACTAAACACATGACCAAGTTCTACAGTACACATAGTA
* ** *
45661837 GCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAATA
45661902 CTACACATGTGACCATCATTTA
130 CTACACATGTGACCATCATTTA
* * ** *
45661924 TCGATTCACGTAGTAGCCTTCACACAGTACTACACATGTGACCAAAGCTTCT-CAGTACACATTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTAAACACATGACC-AAG-TTCTACAGTACACATAG
* * * *
45661988 TAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCACACA
64 TAGCCTTCACATAGTACTACACACGTGACCA-AACTTT-TCGATACACATAGTAGCCTTCACACA
45662052 ATACTACACATGTG
127 ATACTACACATGTG
45662066 TTCATCGATA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
152 40 0.34
153 75 0.63
154 4 0.03
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (151 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTAAACACATGACCAAGTTCTACAGTACACATAGTA
GCCTTCACATAGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTCACACAATAC
TACACATGTGACCATCATTTA
Found at i:45665031 original size:41 final size:40
Alignment explanation
Indices: 45664892--45665023 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 40
45664882 AAAAATTATG
*
45664892 AATTGCACATACGTGACCTTATTTGTACTTCGGTACCCCTA
1 AATTGCACATACGTGCCCTTATTTGTACTTCGGTA-CCCTA
* * * *
45664933 AATTGCACAAACGTGCCCTTGTCTATACTTCGGTACCCTTA
1 AATTGCACATACGTGCCCTTATTTGTACTTCGGTACCC-TA
* * * * *
45664974 AATTGCAAATATGTGCCCCTATTTGTACTTCGGTACGACTG
1 AATTGCACATACGTGCCCTTATTTGTACTTCGGTAC-CCTA
45665015 AATTGCACA
1 AATTGCACA
45665024 CATGTGCCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 70 0.95
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (40 bp):
AATTGCACATACGTGCCCTTATTTGTACTTCGGTACCCTA
Found at i:45665332 original size:16 final size:16
Alignment explanation
Indices: 45665311--45665346 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
45665301 TATAATGGTG
45665311 TTTGATGTAGGTGTGT
1 TTTGATGTAGGTGTGT
45665327 TTTGATGTAGGTGTGT
1 TTTGATGTAGGTGTGT
45665343 TTTG
1 TTTG
45665347 GTATCTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.53
Consensus pattern (16 bp):
TTTGATGTAGGTGTGT
Found at i:45672164 original size:41 final size:40
Alignment explanation
Indices: 45672111--45672229 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 40
45672101 TTCACATGTA
45672111 TGCCCCTATTTGTACTTCGGTACCCCTAAATTGCACATATG
1 TGCCCCT-TTTGTACTTCGGTACCCCTAAATTGCACATATG
** * *
45672152 TGCCCCTGTTTGTACTTTAGTACTCCTGAATTGCACATATG
1 TGCCCCT-TTTGTACTTCGGTACCCCTAAATTGCACATATG
*
45672193 TGCCCCTTCTTGTACTTCGATACCCCTAAATTGCACA
1 TGCCCCTT-TTGTACTTCGGTACCCCTAAATTGCACA
45672230 CACCCCTGCC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 1 0.01
41 66 0.99
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.35
Consensus pattern (40 bp):
TGCCCCTTTTGTACTTCGGTACCCCTAAATTGCACATATG
Found at i:45679445 original size:27 final size:25
Alignment explanation
Indices: 45679415--45679483 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
45679405 CGTTCTGTCC
* *
45679415 CACAGCTCGTGTGAGCAGACCTATTTT
1 CACAGCTCGTGTGAGCAAACCGA--TT
* *
45679442 CACAGCTCATGTAAGCAAACCGATT
1 CACAGCTCGTGTGAGCAAACCGATT
45679467 CACAGCTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
45679484 TACATGTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 17 0.47
27 19 0.53
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCAAACCGATT
Found at i:45684570 original size:17 final size:17
Alignment explanation
Indices: 45684548--45684581 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45684538 CACTAACATT
45684548 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
45684565 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
45684582 TTTACTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:45692145 original size:31 final size:32
Alignment explanation
Indices: 45692060--45692156 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 32
45692050 GTCAAAGTAT
* *
45692060 AATTTTAGGAAAA-TTTGGGGGCC-AAATGTG
1 AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
** *
45692090 AA---TAGGAAAAGTTAAAGGGTCAAAATGT-
1 AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
* *
45692118 AATTTTAGGAAAAGTTGGGGGGCCAAAATATA
1 AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
45692150 AATTTTA
1 AATTTTA
45692157 AATTTTTTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
27 8 0.15
28 8 0.15
29 6 0.12
30 2 0.04
31 21 0.40
32 7 0.13
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (32 bp):
AATTTTAGGAAAAGTTAGGGGGCCAAAATGTA
Done.