Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 72 of 120
Found at i:21255880 original size:26 final size:26
Alignment explanation
Indices: 21255851--21255906 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
21255841 GACCTCCCCT
*
21255851 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
* *
21255877 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
21255903 TTTT
1 TTTT
21255907 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTCTTTGTCTTTTCTTCTTTTTCC
Found at i:21255907 original size:15 final size:14
Alignment explanation
Indices: 21255850--21255909 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
21255840 CGACCTCCCC
21255850 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
*
21255864 TTCTTCTTTTTC--
1 TTTTTCTTTTTCTT
* *
21255876 CTTTTCTTTGTCTT
1 TTTTTCTTTTTCTT
21255890 TTTTTCTTTTTTCTT
1 TTTTTC-TTTTTCTT
21255905 TTTTT
1 TTTTT
21255910 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.24
14 16 0.43
15 12 0.32
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:21255909 original size:8 final size:8
Alignment explanation
Indices: 21255856--21255927 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
21255846 CCCCTTTTTC
21255856 TTTTTCTT
1 TTTTTCTT
*
21255864 TTCTTCTT
1 TTTTTCTT
21255872 TTTCCTT-TT
1 TTT--TTCTT
*
21255881 CTTTGTCTT
1 -TTTTTCTT
21255890 TTTTTC-T
1 TTTTTCTT
21255897 TTTTTCTT
1 TTTTTCTT
*
21255905 TTTTTAATT
1 TTTTT-CTT
21255914 TTTTATCTT
1 TTTT-TCTT
21255923 TTTTT
1 TTTTT
21255928 TTGAAATTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.14
8 22 0.43
9 16 0.31
10 6 0.12
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:21255917 original size:26 final size:25
Alignment explanation
Indices: 21255851--21255926 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
21255841 GACCTCCCCT
* * *
21255851 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTC-TTTACTTTTTTTCTTTTTTC
*
21255877 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTT-ACTTTTTTTCTTTTTTC
*
21255903 TTTT-TTTAATTTTTTATCTTTTTT
1 TTTTCTTTACTTTTTT-TCTTTTTT
21255927 TTTGAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
24 6 0.14
25 14 0.32
26 24 0.55
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (25 bp):
TTTTCTTTACTTTTTTTCTTTTTTC
Found at i:21255923 original size:33 final size:33
Alignment explanation
Indices: 21255856--21255927 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
21255846 CCCCTTTTTC
*
21255856 TTTTTCTTTTCTTCTTTTTCCTTTTCTTTGTCTT
1 TTTTTCTTTTCTTCTTTTT-CTTTTCTTTATCTT
*
21255890 TTTTTCTTTT-TTCTTTTT-TTAATTTTTTATCTT
1 TTTTTCTTTTCTTCTTTTTCTT--TTCTTTATCTT
21255923 TTTTT
1 TTTTT
21255928 TTGAAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
33 22 0.65
34 10 0.29
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (33 bp):
TTTTTCTTTTCTTCTTTTTCTTTTCTTTATCTT
Found at i:21260999 original size:67 final size:70
Alignment explanation
Indices: 21260912--21261077 Score: 225
Period size: 67 Copynumber: 2.4 Consensus size: 70
21260902 TTATTTATTT
* ***
21260912 ATAAT-AATAAATAAATAATAAAGCAAAATTAATATTATTTTACATTTATTTAT-TT-ATATTCA
1 ATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATGTTCATAAAAA
21260974 TAA-A
66 TAATA
* *
21260978 ATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTATATTTATTTATGTTCATAAAAA
1 ATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATGTTCATAAAAA
21261043 TAATA
66 TAATA
*
21261048 ATAATAAATAAATAAA-AATAATAAGAAAAT
1 ATAATAAATAAATAAATAATAA-AACAAAAT
21261078 AGAATTGGGT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
66 5 0.06
67 45 0.51
68 2 0.02
69 12 0.14
70 24 0.27
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (70 bp):
ATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATGTTCATAAAAA
TAATA
Found at i:21261077 original size:17 final size:16
Alignment explanation
Indices: 21261038--21261078 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
21261028 TTATGTTCAT
*
21261038 AAAAATAATAATAATA
1 AAAAATAAAAATAATA
21261054 AATAAATAAAAATAATA
1 AA-AAATAAAAATAATA
21261071 AGAAAATA
1 A-AAAATA
21261079 GAATTGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAATAAAAATAATA
Found at i:21263655 original size:21 final size:20
Alignment explanation
Indices: 21263629--21263671 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
21263619 AAGTTACAAG
* *
21263629 AAACCATAAATAAAATAAAGA
1 AAACCACAAAT-AAAGAAAGA
21263650 AAACCACAAATAAAGAAAGA
1 AAACCACAAATAAAGAAAGA
21263670 AA
1 AA
21263672 CTCAAAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (20 bp):
AAACCACAAATAAAGAAAGA
Found at i:21272084 original size:13 final size:13
Alignment explanation
Indices: 21272062--21272125 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
21272052 TTTAGCATTA
*
21272062 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
21272075 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* * *
21272088 -TGGTGGAAAAGTT
1 CT-TTTGAAAAGTG
21272101 CTTTTGAAAAGTAG
1 CTTTTGAAAAGT-G
*
21272115 -TTTTAAAAAGT
1 CTTTTGAAAAGT
21272126 TTGGTTAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 1 0.03
13 38 0.95
14 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:21272123 original size:26 final size:25
Alignment explanation
Indices: 21272063--21272126 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
21272053 TTAGCATTAC
*
21272063 TTTTAAAAAGTGCTTTTGAAAAGTG
1 TTTTAAAAAGTTCTTTTGAAAAGTG
* **
21272088 TGGTGGAAAAGTTCTTTTGAAAAGTAG
1 T-TTTAAAAAGTTCTTTTGAAAAGT-G
21272115 TTTTAAAAAGTT
1 TTTTAAAAAGTT
21272127 TGGTTAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.03
26 27 0.90
27 2 0.07
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (25 bp):
TTTTAAAAAGTTCTTTTGAAAAGTG
Found at i:21272434 original size:14 final size:14
Alignment explanation
Indices: 21272397--21272438 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
21272387 TTATATTTTA
21272397 AATATTTAAATA-T
1 AATATTTAAATATT
21272410 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
21272424 TATATTTAAATATT
1 AATATTTAAATATT
21272438 A
1 A
21272439 GCACAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:21274240 original size:72 final size:72
Alignment explanation
Indices: 21274137--21274536 Score: 676
Period size: 72 Copynumber: 5.6 Consensus size: 72
21274127 AACAAATTTT
* * * *
21274137 ATATCC-AAAATCAAATATAAACAACTATTGATAAAACTAAAATACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
21274201 AAATTCA
66 AAATTCA
* *
21274208 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAATAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
21274273 AAATTCA
66 AAATTCA
* * *
21274280 ATATCCAAGAACCAAACACAAACAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
21274345 AAATTCA
66 AAATTCA
* *
21274352 ATATCCAAGAACCAAACATAAACAACTATTGATAAAATTAGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
21274417 AAATTCA
66 AAATTCA
* *
21274424 ATATCCAAGAACCAAACATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
21274489 AAATTCA
66 AAATTCA
21274496 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
21274537 TTTAGCATTG
Statistics
Matches: 312, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
71 6 0.02
72 306 0.98
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
AAATTCA
Found at i:21291156 original size:13 final size:13
Alignment explanation
Indices: 21291138--21291171 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21291128 TTACTGGTAA
*
21291138 GAAATTTTGGGAT
1 GAAATTTCGGGAT
21291151 GAAATTTCGGGAT
1 GAAATTTCGGGAT
21291164 GAAATTTC
1 GAAATTTC
21291172 CTTAAGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (13 bp):
GAAATTTCGGGAT
Found at i:21294032 original size:33 final size:33
Alignment explanation
Indices: 21293995--21294068 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
21293985 TCCAATGCCG
*
21293995 CCACAAGATATTAATAATTTACCACCACCGCCT
1 CCACAAGATATTAATAATTTACCACCACCACCT
* * *
21294028 CCACAAGTTATTAATAATTTACCACTATCACCT
1 CCACAAGATATTAATAATTTACCACCACCACCT
21294061 CCACAAGA
1 CCACAAGA
21294069 AGGACAAGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (33 bp):
CCACAAGATATTAATAATTTACCACCACCACCT
Found at i:21298130 original size:20 final size:20
Alignment explanation
Indices: 21298105--21298144 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21298095 GCTGACCACT
21298105 TATCTCAATTGGAAGTTGGA
1 TATCTCAATTGGAAGTTGGA
*
21298125 TATCTCGATTGGAAGTTGGA
1 TATCTCAATTGGAAGTTGGA
21298145 AGTGAAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (20 bp):
TATCTCAATTGGAAGTTGGA
Found at i:21301919 original size:19 final size:19
Alignment explanation
Indices: 21301889--21301941 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
21301879 CTGTAGATAG
21301889 TTTTCA-TGCATTTTTATT
1 TTTTCATTGCATTTTTATT
21301907 TTTTCATTGCATTTTTATT
1 TTTTCATTGCATTTTTATT
* *
21301926 TTGTCATTGCCTTTTT
1 TTTTCATTGCATTTTT
21301942 GTTAAGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 6 0.19
19 26 0.81
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.66
Consensus pattern (19 bp):
TTTTCATTGCATTTTTATT
Found at i:21309505 original size:26 final size:25
Alignment explanation
Indices: 21309469--21309520 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
21309459 GAATTTGATA
21309469 TTTTTTTTAATTTGATACTTAAATT
1 TTTTTTTTAATTTGATACTTAAATT
*
21309494 TTTTTATTTAATTTGGTACTTAAATT
1 TTTTT-TTTAATTTGATACTTAAATT
21309520 T
1 T
21309521 GACACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (25 bp):
TTTTTTTTAATTTGATACTTAAATT
Found at i:21309583 original size:60 final size:59
Alignment explanation
Indices: 21309476--21309638 Score: 213
Period size: 60 Copynumber: 2.7 Consensus size: 59
21309466 ATATTTTTTT
* * *
21309476 TAATTTGATACTTAAATTTTTTT--ATTTAATTTGGTACTTAAATTTGACACTTTTTCC
1 TAATTTGATACCTAAATTTTTTTAGATTCAATTTGGTACTTAAACTTGACACTTTTTCC
* * *
21309533 TAATTTGATACCTAAACTTTTTTTAGATCCAATTTGATACTTAAACTTGACATTTTTTCC
1 TAATTTGATACCTAAA-TTTTTTTAGATTCAATTTGGTACTTAAACTTGACACTTTTTCC
* *
21309593 TAATTTGATATCTAAGTTTTTTTTTAGATTCAATTTGGTACTTAAA
1 TAATTTGATACCTAA--ATTTTTTTAGATTCAATTTGGTACTTAAA
21309639 TTTATTAAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
57 15 0.16
58 7 0.08
60 43 0.47
61 26 0.29
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (59 bp):
TAATTTGATACCTAAATTTTTTTAGATTCAATTTGGTACTTAAACTTGACACTTTTTCC
Found at i:21309601 original size:31 final size:31
Alignment explanation
Indices: 21309502--21309602 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 31
21309492 TTTTTTTATT
* * *
21309502 TAATTTGGTACTTAAATTTGACACTTTTTCC
1 TAATTTGATACTTAAACTTGACATTTTTTCC
*
21309533 TAATTTGATACCTAAACTT----TTTTTAGATCC
1 TAATTTGATACTTAAACTTGACATTTTT---TCC
21309563 -AATTTGATACTTAAACTTGACATTTTTTCC
1 TAATTTGATACTTAAACTTGACATTTTTTCC
21309593 TAATTTGATA
1 TAATTTGATA
21309603 TCTAAGTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
27 4 0.07
29 17 0.30
30 6 0.11
31 25 0.44
33 5 0.09
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
TAATTTGATACTTAAACTTGACATTTTTTCC
Found at i:21310964 original size:17 final size:17
Alignment explanation
Indices: 21310934--21310967 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21310924 TATTTAATTC
**
21310934 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
21310951 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
21310968 AAAATAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:21311090 original size:26 final size:26
Alignment explanation
Indices: 21311033--21311096 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
21311023 ATTATAAAGA
* * *
21311033 TATAAATTATTTAATGTCGAATCGTC
1 TATAATTTTTTTAATGTCAAATCGTC
*
21311059 TATAATTTTTTTAATTTCAAATCGTC
1 TATAATTTTTTTAATGTCAAATCGTC
21311085 TATAATTTTTTT
1 TATAATTTTTTT
21311097 CTAACTTCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (26 bp):
TATAATTTTTTTAATGTCAAATCGTC
Found at i:21320844 original size:16 final size:17
Alignment explanation
Indices: 21320822--21320863 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
21320812 TCGAAAAATG
21320822 AATTTTTAAA-TCTTTTT
1 AATTTTTAAAGT-TTTTT
21320839 -ATTTTTAAAGTTTTTT
1 AATTTTTAAAGTTTTTT
21320855 AATTTTTAA
1 AATTTTTAA
21320864 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
AATTTTTAAAGTTTTTT
Found at i:21320854 original size:17 final size:16
Alignment explanation
Indices: 21320822--21320863 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
21320812 TCGAAAAATG
21320822 AATTTTTAAATCTTTT
1 AATTTTTAAATCTTTT
* *
21320838 TATTTTTAAAGTTTTTT
1 AATTTTTAAA-TCTTTT
21320855 AATTTTTAA
1 AATTTTTAA
21320864 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
AATTTTTAAATCTTTT
Found at i:21331368 original size:49 final size:49
Alignment explanation
Indices: 21331304--21332090 Score: 561
Period size: 49 Copynumber: 16.0 Consensus size: 49
21331294 TTCAATCTGT
* * * *
21331304 TCCCTCTTTGGTTTTAAGGTGTTAGGTCCGTTGTCT-CGCCTTCAACCTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGT-TACGACTTCAACCTA
* * * * * *
21331353 TCCCTCTTCGATTTTAAGGTGTAAGATTCGTCGTTGCAACTTCAACCTT
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * * *
21331402 TCCCT-TGTCGATTTTAGGGTGTTAGGTCCGTCGTTGCGACTTCAAGCTG
1 TCCCTCT-TCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * *
21331451 TCCCTCTTCGATTTTAGGGTGTTAGGTCCGTCATT--GTAGCTTCAACTTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACG-A-CTTCAACCTA
* * * * *
21331500 TCCCTCTT-TAGTTTTAAGGTGTAAGGTCCGCCGTTGA-GGCTTCAACCTT
1 TCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGTCGTT-ACGACTTCAACCTA
* * * * * ** * *
21331549 TTCCTTTTTGGTTTTAGGGTGTTAAATCCGCCGTT--GTAGCTTCAATCTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACG-A-CTTCAACCTA
* * * * *
21331598 TCCCTCTTTGATTTTAAGGTGTTAGGTCCGTCATTATGACTTAAACCAA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * * * ** * *
21331647 TCCCTCTTTGATTTTAAGGTGTAAGATTCGTCGTTGGGACTTCAATCTT
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
** * * *
21331696 TCCCTCTTCGATTTTTTGGGTGTTAGGTCCGCCGTTAGGGCTTCAACCTA
1 TCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * * * * *
21331746 TCCCTCTT-TAGTTTTAAGGTGTAAGGTTCGTCATTACGATTTCAACCTT
1 TCCCTCTTCGA-TTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * * * * * * * *
21331795 TCCCTCTTTGATTTTAGGGTATTAGATTCGCCATTACGACTTTAATCTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * *
21331844 TCTCTCTTCGATTTTAGGGTGTTAGGTCCGTCGTAACGACTTCAACCTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * * * * * * * *
21331893 TCCCTTTTCAATTTTAAGGTGTAAGATCCGTAGTTACGGCTTTAATCTT
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
** *
21331942 TCCCTCTTCGATTTTAAGGTGTTAGGTCCACCGTTGC-AGCTTCAACCTA
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGA-CTTCAACCTA
* * * * * * * *
21331991 TCCTTCTTCAATTTTAAGGTGTAAGGTTCGTTGTTGCGGCTTCAACCTT
1 TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
* * * * *
21332040 TCCCTCATCGATTTT-AGGATGTTAGGTTCGCCGTTGCGACTTTAACCTA
1 TCCCTCTTCGATTTTAAGG-TGTTAGGTCCGTCGTTACGACTTCAACCTA
21332089 TC
1 TC
21332091 TTTCTTCAAA
Statistics
Matches: 575, Mismatches: 145, Indels: 36
0.76 0.19 0.05
Matches are distributed among these distances:
47 2 0.00
48 7 0.01
49 525 0.91
50 39 0.07
51 2 0.00
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.40
Consensus pattern (49 bp):
TCCCTCTTCGATTTTAAGGTGTTAGGTCCGTCGTTACGACTTCAACCTA
Found at i:21345740 original size:201 final size:191
Alignment explanation
Indices: 21345392--21345757 Score: 464
Period size: 201 Copynumber: 1.9 Consensus size: 191
21345382 CTATAAACCA
* * * * *
21345392 TTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAGTATACGTAAAGCATAGTCCCAGCCATTGT
1 TTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATACGTAAAGCATAATCCCAACCATCGT
* * * * *
21345457 AGGGCCTGTAATCCATTTAGGACCCATATTTCTTTTCTGAGTCACGATGCTGCTCACACGAGCTG
66 AGAGCCTGTAATCCATTCAGGACCCATATTTCTTTTCTGACTCACGATGCTACTCACACGAGATG
* *
21345522 TCAAGGACTTGCAACATATGCGGTACCTTAGCCATTGATACGGTATCTATATACATAACTG
131 TCAAGGACTCGCAACATATGCGGCACCTTAGCCATTGATACGGTATCTATATACATAACTG
* * * *
21345583 TTCCCTAACGATGTTGCTCACACGAGCTATCGAGAATATGCAC-TTATGCATAAATCTCAACCAT
1 TTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATAT--ACGTAAAGCAT-AATCCCAACCAT
*
21345647 CGTAGAGCCTGTAATCCATTCAGGATCCATATTTCTTTTCTCATTTCCCGACTCACGATGCTACT
63 CGTAGAGCCTGTAATCCATTCAGGACCCATATTTC-TTT-TC---T---GACTCACGATGCTACT
*
21345712 CGCACGAGATGTCAAGGACTCGCAACATATGCGGCACCTTAGCCAT
120 CACACGAGATGTCAAGGACTCGCAACATATGCGGCACCTTAGCCAT
21345758 CGCGTCGGTT
Statistics
Matches: 146, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
191 36 0.25
192 6 0.04
193 42 0.29
194 3 0.02
195 2 0.01
198 1 0.01
201 56 0.38
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (191 bp):
TTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATACGTAAAGCATAATCCCAACCATCGT
AGAGCCTGTAATCCATTCAGGACCCATATTTCTTTTCTGACTCACGATGCTACTCACACGAGATG
TCAAGGACTCGCAACATATGCGGCACCTTAGCCATTGATACGGTATCTATATACATAACTG
Found at i:21345866 original size:14 final size:14
Alignment explanation
Indices: 21345847--21345875 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21345837 CCATAACATG
21345847 TTCTGTAACAATTA
1 TTCTGTAACAATTA
21345861 TTCTGTAACAATTA
1 TTCTGTAACAATTA
21345875 T
1 T
21345876 AAAGAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (14 bp):
TTCTGTAACAATTA
Found at i:21351653 original size:16 final size:16
Alignment explanation
Indices: 21351629--21351660 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21351619 TCCTTACAAA
*
21351629 TTTATTCCTTTAACAT
1 TTTACTCCTTTAACAT
21351645 TTTACTCCTTTAACAT
1 TTTACTCCTTTAACAT
21351661 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTACTCCTTTAACAT
Found at i:21358050 original size:21 final size:19
Alignment explanation
Indices: 21358024--21358098 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 19
21358014 GGAGTTTTCG
21358024 GTATCGGTAGAAGCATGACTT
1 GTATCGGTAGAA-CA-GACTT
* *
21358045 GTATCGGTAAAAATCACACTT
1 GTATCGGT-AGAA-CAGACTT
* *
21358066 GTATCGATAGAACAAGCACAT
1 GTATCGGTAGAAC-AG-ACTT
21358087 GTATCGGTAGAA
1 GTATCGGTAGAA
21358099 ATCTTTATAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 4 0.09
21 33 0.77
22 5 0.12
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (19 bp):
GTATCGGTAGAACAGACTT
Found at i:21368914 original size:12 final size:12
Alignment explanation
Indices: 21368897--21368966 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 12
21368887 ACAACAATAT
21368897 AAATAAACAAAA
1 AAATAAACAAAA
21368909 AAATAAA-AATAA
1 AAATAAACAA-AA
****
21368921 AAATTAAATGTTA
1 AAA-TAAACAAAA
21368934 AAATAAACAAACA
1 AAATAAACAAA-A
21368947 AATATAAACAATAA
1 AA-ATAAACAA-AA
21368961 AAATAA
1 AAATAA
21368967 TTGAGATTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
11 2 0.04
12 16 0.36
13 15 0.33
14 11 0.24
15 1 0.02
ACGTcount: A:0.74, C:0.06, G:0.01, T:0.19
Consensus pattern (12 bp):
AAATAAACAAAA
Found at i:21368914 original size:16 final size:15
Alignment explanation
Indices: 21368877--21368915 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21368867 AAATAGTATG
*
21368877 AAAATAAATAACAAC
1 AAAATAAATAACAAA
*
21368892 AATATAAATAAACAAA
1 AAAATAAAT-AACAAA
21368908 AAAATAAA
1 AAAATAAA
21368916 AATAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:21369005 original size:105 final size:100
Alignment explanation
Indices: 21368877--21369060 Score: 235
Period size: 100 Copynumber: 1.8 Consensus size: 100
21368867 AAATAGTATG
* *
21368877 AAAATAAATAACAACAATATAAATAAACAAAAAAATAAAAATAAAAATTAAATGTTAAAATAAAC
1 AAAATAAATAACAACAAAATAAATAAAC-AAAAAAT--AAAT--AAATTAAATGTCAAAATAAAC
21368942 AAACAAATATAAACAATAAAAATAATTGAGATTAGGCATA
61 AAACAAATATAAACAATAAAAATAATTGAGATTAGGCATA
* * * **
21368982 AAAATAAATGACAA-ATAAATAAATAAACAAAAAATTAATAAATTAAATGTCAAAATAGACAATT
1 AAAATAAATAACAACA-AAATAAATAAACAAAAAATAAATAAATTAAATGTCAAAATAAACAAAC
*
21369046 AAATATAAATAATAA
65 AAATATAAACAATAA
21369061 TAAAAAAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
100 35 0.50
102 3 0.04
104 8 0.11
105 24 0.34
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22
Consensus pattern (100 bp):
AAAATAAATAACAACAAAATAAATAAACAAAAAATAAATAAATTAAATGTCAAAATAAACAAACA
AATATAAACAATAAAAATAATTGAGATTAGGCATA
Found at i:21369016 original size:15 final size:15
Alignment explanation
Indices: 21368981--21369023 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21368971 GATTAGGCAT
*
21368981 AAAAATAAAT-GACA
1 AAAAATAAATAAACA
21368995 AATAAATAAATAAACA
1 AA-AAATAAATAAACA
*
21369011 AAAAATTAATAAA
1 AAAAATAAATAAA
21369024 TTAAATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 18 0.72
16 5 0.20
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAAATAAATAAACA
Found at i:21371347 original size:13 final size:13
Alignment explanation
Indices: 21371329--21371354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21371319 ATTTAATCAC
21371329 ATTAATCTAAGGT
1 ATTAATCTAAGGT
21371342 ATTAATCTAAGGT
1 ATTAATCTAAGGT
21371355 TATGCAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATTAATCTAAGGT
Found at i:21371623 original size:3 final size:3
Alignment explanation
Indices: 21371615--21371685 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
21371605 CAATAAATCT
* * * * *
21371615 AAC AAC AAC AAC AAC AAC AAC AAC GAC AAC GAC AAC GAT AAC GAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
21371663 AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AA
21371686 TAGAATTAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.62, C:0.31, G:0.06, T:0.01
Consensus pattern (3 bp):
AAC
Found at i:21372662 original size:20 final size:20
Alignment explanation
Indices: 21372637--21372679 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
21372627 GTTATCAAAC
21372637 ACTCAAAATTTGCATGAATT
1 ACTCAAAATTTGCATGAATT
21372657 ACTCAAAATTTGCATGAATT
1 ACTCAAAATTTGCATGAATT
21372677 ACT
1 ACT
21372680 AGTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (20 bp):
ACTCAAAATTTGCATGAATT
Found at i:21378857 original size:11 final size:11
Alignment explanation
Indices: 21378834--21378873 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
21378824 CTGCAATGAT
21378834 AAATATTTCAA
1 AAATATTTCAA
21378845 AAAT-TTTCAA
1 AAATATTTCAA
21378855 AAATATTTCAA
1 AAATATTTCAA
21378866 AAATATTT
1 AAATATTT
21378874 TTCAATCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATTTCAA
Found at i:21378943 original size:58 final size:57
Alignment explanation
Indices: 21378880--21378992 Score: 181
Period size: 57 Copynumber: 2.0 Consensus size: 57
21378870 ATTTTTCAAT
** *
21378880 CTCAATGATGAACTAACCCAAATCTTTTTTTTCCGTTTCTTTTCGAAAAAATTATAAC
1 CTCAATGATGAACTAACCCAAATC-TTTTCCTCCATTTCTTTTCGAAAAAATTATAAC
*
21378938 CTCAATGATGAACTAACCCAAGTCTTTTCCTCCATTTCTTTTCGAAAAAATTATA
1 CTCAATGATGAACTAACCCAAATCTTTTCCTCCATTTCTTTTCGAAAAAATTATA
21378993 TATAGAAAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 28 0.55
58 23 0.45
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (57 bp):
CTCAATGATGAACTAACCCAAATCTTTTCCTCCATTTCTTTTCGAAAAAATTATAAC
Found at i:21383229 original size:9 final size:9
Alignment explanation
Indices: 21383195--21383228 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
21383185 TTTTTCTATA
21383195 ATTTTTTAC
1 ATTTTTTAC
21383204 ATTTTTTAC
1 ATTTTTTAC
21383213 ATTTTTTAC
1 ATTTTTTAC
21383222 TATTTTT
1 -ATTTTT
21383229 AGTAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTTTTAC
Found at i:21383425 original size:18 final size:19
Alignment explanation
Indices: 21383404--21383441 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21383394 TATTTACTAA
21383404 ATTTTTATT-TTTTTCTAT
1 ATTTTTATTATTTTTCTAT
21383422 ATTTTTATTATTTTTCTAT
1 ATTTTTATTATTTTTCTAT
21383441 A
1 A
21383442 ATTTCTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTTATTATTTTTCTAT
Found at i:21383477 original size:27 final size:30
Alignment explanation
Indices: 21383415--21383481 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 30
21383405 TTTTTATTTT
21383415 TTTCTAT-AT-TTTTATTATTTTTCTATAA
1 TTTCTATAATATTTTATTATTTTTCTATAA
21383443 TTTCTATAATATTTTATTA-TTTTC-AT-A
1 TTTCTATAATATTTTATTATTTTTCTATAA
*
21383470 TTTTTATAATAT
1 TTTCTATAATAT
21383482 ATTAATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 12 0.33
28 9 0.25
29 7 0.19
30 8 0.22
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTCTATAATATTTTATTATTTTTCTATAA
Found at i:21385217 original size:20 final size:19
Alignment explanation
Indices: 21385187--21385225 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
21385177 TTTAAAAAAA
*
21385187 TTAAAAATATATAAATTAT
1 TTAAAAATATAAAAATTAT
21385206 TTAAAAAGTATAAAAATTAT
1 TTAAAAA-TATAAAAATTAT
21385226 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAAAATATAAAAATTAT
Found at i:21399643 original size:2 final size:2
Alignment explanation
Indices: 21399636--21399660 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21399626 ACAAGTGTAG
21399636 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21399661 TTAAGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21400062 original size:9 final size:9
Alignment explanation
Indices: 21400008--21400165 Score: 70
Period size: 9 Copynumber: 16.6 Consensus size: 9
21399998 ATTTTCTAAG
*
21400008 AAAAATCAT
1 AAAAATTAT
21400017 AAAATATTAT
1 AAAA-ATTAT
21400027 AAAAACTTAT
1 AAAAA-TTAT
* *
21400037 ATATAATTCT
1 A-AAAATTAT
21400047 AATAAATTAT
1 AA-AAATTAT
21400057 AAAAATTTAT
1 AAAAA-TTAT
* *
21400067 AAGAATAAT
1 AAAAATTAT
*
21400076 AAAAAATATT
1 AAAAATTA-T
21400086 AAACATATTA-
1 AAA-A-ATTAT
21400096 AAAATATTA-
1 AAAA-ATTAT
*
21400105 AAAATTTAT
1 AAAAATTAT
*
21400114 AAAAGAACTTGT
1 -AAA-AA-TTAT
** *
21400126 ATTAACTAT
1 AAAAATTAT
21400135 AAAAATTAT
1 AAAAATTAT
*
21400144 AATAA-TAT
1 AAAAATTAT
*
21400152 AATAATTAT
1 AAAAATTAT
21400161 AAAAA
1 AAAAA
21400166 AATCATTTAT
Statistics
Matches: 113, Mismatches: 23, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
8 11 0.10
9 46 0.41
10 44 0.39
11 6 0.05
12 6 0.05
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:21400317 original size:12 final size:12
Alignment explanation
Indices: 21400302--21400336 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
21400292 ATATAAATTT
21400302 TAATATTTTATG
1 TAATATTTTATG
21400314 TAATATTTT-TG
1 TAATATTTTATG
*
21400325 TATTATTTTATG
1 TAATATTTTATG
21400337 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (12 bp):
TAATATTTTATG
Found at i:21400331 original size:11 final size:12
Alignment explanation
Indices: 21400305--21400346 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
21400295 TAAATTTTAA
*
21400305 TATTTTATGTAA
1 TATTTTATGTAT
21400317 TATTTT-TGTAT
1 TATTTTATGTAT
21400328 TATTTTATG-AT
1 TATTTTATGTAT
*
21400339 TTTTTTAT
1 TATTTTAT
21400347 ATATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TATTTTATGTAT
Found at i:21401425 original size:4 final size:4
Alignment explanation
Indices: 21401416--21401447 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
21401406 CAACAAAACA
21401416 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
21401448 CAGATTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:21403063 original size:13 final size:13
Alignment explanation
Indices: 21403041--21403102 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
21403031 TTTAGCATTG
*
21403041 TTTTTAAAAAGTA
1 TTTTTGAAAAGTA
*
21403054 TTTTTGAAAAGTG
1 TTTTTGAAAAGTA
** * *
21403067 TGGTGGAAAAGTT
1 TTTTTGAAAAGTA
21403080 TTTTTGAAAAGTA
1 TTTTTGAAAAGTA
*
21403093 GTTTTGAAAA
1 TTTTTGAAAA
21403103 TTTTGGTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (13 bp):
TTTTTGAAAAGTA
Found at i:21403101 original size:26 final size:25
Alignment explanation
Indices: 21403042--21403106 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
21403032 TTAGCATTGT
* *
21403042 TTTTAAAAAGTATTTTTGAAAAGTG
1 TTTTGAAAAGTTTTTTTGAAAAGTG
* *
21403067 TGGTGGAAAAGTTTTTTTGAAAAGTAG
1 T-TTTGAAAAGTTTTTTTGAAAAGT-G
21403094 TTTTGAAAA-TTTT
1 TTTTGAAAAGTTTT
21403107 GGTTAAAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 5 0.16
26 25 0.78
27 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (25 bp):
TTTTGAAAAGTTTTTTTGAAAAGTG
Found at i:21405239 original size:72 final size:72
Alignment explanation
Indices: 21405120--21405310 Score: 265
Period size: 72 Copynumber: 2.6 Consensus size: 72
21405110 TTTTATATCC
* * * *
21405120 AAAATCAAATATAAACAAATATTGATAAAACTAAAATACACATAAATAAGTAGAACATAAATTCA
1 AAAAT-AAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCA
21405185 ATATCCAA
65 ATATCCAA
* * * *
21405193 AAAATAAACATAATCAACTATTGATAAAACTAGATTGCACAGAAATAAGTAGAACATAAATTTAA
1 AAAATAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAA
21405258 TATCCAA
66 TATCCAA
* ** *
21405265 GAACCAAACATAAACAACTATTGATAAAATTAGATTACACATAAAT
1 AAAATAAACATAAACAACTATTGATAAAACTAGATTACACATAAAT
21405311 TAAAGTACAC
Statistics
Matches: 103, Mismatches: 15, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
72 98 0.95
73 5 0.05
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (72 bp):
AAAATAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAA
TATCCAA
Found at i:21405840 original size:18 final size:18
Alignment explanation
Indices: 21405815--21405866 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
21405805 CGTTTCCATC
*
21405815 AATGTTAACATCATTTGA
1 AATGTTAACATCATTTAA
*
21405833 AGTGTTAACATCATTTAA
1 AATGTTAACATCATTTAA
*
21405851 AATATTAACATCATTT
1 AATGTTAACATCATTT
21405867 CTTGCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (18 bp):
AATGTTAACATCATTTAA
Found at i:21411347 original size:24 final size:25
Alignment explanation
Indices: 21411301--21411350 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
21411291 GAGGTCGTTG
21411301 TTGAAGTGTGTCTGTGATGGGAGAA
1 TTGAAGTGTGTCTGTGATGGGAGAA
*
21411326 TTGAATTGTGT-TGTGAAT-GGAGAA
1 TTGAAGTGTGTCTGTG-ATGGGAGAA
21411350 T
1 T
21411351 AATTATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (25 bp):
TTGAAGTGTGTCTGTGATGGGAGAA
Found at i:21411529 original size:30 final size:30
Alignment explanation
Indices: 21411453--21411529 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
21411443 TCTACCTCAA
*
21411453 ATTGGCTTTGCGGAGGCACGATAATGATAT
1 ATTGGCTTTGCGGAGGTACGATAATGATAT
* *
21411483 ATTGGCTTTGTGGAGGTACGGTAATGATAT
1 ATTGGCTTTGCGGAGGTACGATAATGATAT
* *
21411513 ATTGGATTTGCAGAGGT
1 ATTGGCTTTGCGGAGGT
21411530 CATTATATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.34
Consensus pattern (30 bp):
ATTGGCTTTGCGGAGGTACGATAATGATAT
Found at i:21412420 original size:23 final size:21
Alignment explanation
Indices: 21412394--21412446 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
21412384 TTAATATTTT
21412394 ATTTTAATAAAAAATTCAGTTCA
1 ATTTTAAT-AAAAATTCAGTT-A
* * *
21412417 ATTTAAATACAAATTTAGTTA
1 ATTTTAATAAAAATTCAGTTA
21412438 ATATTTAAT
1 AT-TTTAAT
21412447 TTATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 15 0.60
23 7 0.28
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTTTAATAAAAATTCAGTTA
Found at i:21413761 original size:27 final size:27
Alignment explanation
Indices: 21413716--21413767 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
21413706 TAAAGATGAT
*
21413716 TATATAAAAATTTTCAATAATAAAAAA
1 TATATAAAAATTTTAAATAATAAAAAA
*
21413743 TATAT-AAAATTATTAAATATTAAAA
1 TATATAAAAATT-TTAAATAATAAAA
21413768 TAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
TATATAAAAATTTTAAATAATAAAAAA
Found at i:21420703 original size:33 final size:32
Alignment explanation
Indices: 21420657--21420724 Score: 75
Period size: 33 Copynumber: 2.1 Consensus size: 32
21420647 ACCCAAACCC
* *
21420657 ATTTTATTTTTTAAAAAATATT-TAAATTATTTT
1 ATTTTAATATTTAAAAAAT-TTATAAATT-TTTT
* *
21420690 ATTTTAATATTTAATAAATTTATACATTTTTT
1 ATTTTAATATTTAAAAAATTTATAAATTTTTT
21420722 ATT
1 ATT
21420725 CATTGAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTTAATATTTAAAAAATTTATAAATTTTTT
Found at i:21422840 original size:16 final size:16
Alignment explanation
Indices: 21422819--21422849 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21422809 TTCAAAACTC
21422819 ATAAAAATAATATAAA
1 ATAAAAATAATATAAA
*
21422835 ATAAAATTAATATAA
1 ATAAAAATAATATAA
21422850 CTAGTCGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATATAAA
Found at i:21425459 original size:6 final size:6
Alignment explanation
Indices: 21425438--21425471 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
21425428 ATACAAAAAA
*
21425438 AAAGAG AAATGGG AAAGGG AAAGGG AAAGGG AAA
1 AAAGGG AAA-GGG AAAGGG AAAGGG AAAGGG AAA
21425472 CAGAAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (6 bp):
AAAGGG
Found at i:21426019 original size:21 final size:21
Alignment explanation
Indices: 21425981--21426020 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21425971 TATCTTGTAC
* *
21425981 TTCTACCGATACATGTATGAG
1 TTCTACCGAAACAAGTATGAG
*
21426002 TTCTACTGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
21426021 TAGAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAG
Found at i:21426467 original size:12 final size:12
Alignment explanation
Indices: 21426432--21426494 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
21426422 TATTAACTCA
21426432 TTTA-AAGCTCG
1 TTTATAAGCTCG
*
21426443 TTTA-AAGCCCG
1 TTTATAAGCTCG
21426454 TTTATAAGCTCG
1 TTTATAAGCTCG
* *
21426466 TTTATTAGCTCA
1 TTTATAAGCTCG
*
21426478 TTTATAATCTCG
1 TTTATAAGCTCG
21426490 TTTAT
1 TTTAT
21426495 TAGACCCATC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 14 0.32
12 30 0.68
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (12 bp):
TTTATAAGCTCG
Found at i:21426489 original size:24 final size:24
Alignment explanation
Indices: 21426403--21426497 Score: 97
Period size: 23 Copynumber: 4.1 Consensus size: 24
21426393 TTCACGAACA
* * *
21426403 AGCTCATTTAT-GGTTCATTTATT
1 AGCTCATTTATAAGCTCGTTTATT
* *
21426426 AACTCATTTA-AAGCTCGTTTA-A
1 AGCTCATTTATAAGCTCGTTTATT
* *
21426448 AGCCCGTTTATAAGCTCGTTTATT
1 AGCTCATTTATAAGCTCGTTTATT
*
21426472 AGCTCATTTATAATCTCGTTTATT
1 AGCTCATTTATAAGCTCGTTTATT
21426496 AG
1 AG
21426498 ACCCATCAGG
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
22 7 0.12
23 27 0.47
24 23 0.40
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (24 bp):
AGCTCATTTATAAGCTCGTTTATT
Found at i:21427317 original size:23 final size:22
Alignment explanation
Indices: 21427314--21427356 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
21427304 TTATTTGAAA
21427314 TTTAAATTTATTGTAAATTTAAG
1 TTTAAATTTATTG-AAATTTAAG
*
21427337 TTTAAAATTATTGAAATTTA
1 TTTAAATTTATTGAAATTTA
21427357 CTAATGTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTAAATTTATTGAAATTTAAG
Found at i:21427318 original size:40 final size:39
Alignment explanation
Indices: 21427274--21427356 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 39
21427264 TTAAATTCAT
* *
21427274 TTTAAATTTAAATCT-ATTTTAAGTTTAAATTTATTTGAAA
1 TTTAAATTT-AATCTAAATTTAAGTTTAAAATTA-TTGAAA
* *
21427314 TTTAAATTTATTGTAAATTTAAGTTTAAAATTATTGAAA
1 TTTAAATTTAATCTAAATTTAAGTTTAAAATTATTGAAA
21427353 TTTA
1 TTTA
21427357 CTAATGTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 13 0.34
40 25 0.66
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (39 bp):
TTTAAATTTAATCTAAATTTAAGTTTAAAATTATTGAAA
Found at i:21427340 original size:17 final size:17
Alignment explanation
Indices: 21427261--21427340 Score: 106
Period size: 17 Copynumber: 4.7 Consensus size: 17
21427251 ACCCAAACAG
*
21427261 AATTTAAATTCATTTTA
1 AATTTAAATTTATTTTA
*
21427278 AATTTAAATCTATTTTA
1 AATTTAAATTTATTTTA
* *
21427295 AGTTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
21427312 AATTTAAATTTATTGTA
1 AATTTAAATTTATTTTA
*
21427329 AATTTAAGTTTA
1 AATTTAAATTTA
21427341 AAATTATTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:21429214 original size:29 final size:29
Alignment explanation
Indices: 21429116--21429441 Score: 223
Period size: 30 Copynumber: 11.1 Consensus size: 29
21429106 TGAACTGTTT
* * *
21429116 AAAAATTATATTTTGACCGCT-ACACTTTCC
1 AAAAATTACATTTTAACC-CTCAAAC-TTCC
21429146 AAAAATTACATTTTAACCCTCAAACTTTCC
1 AAAAATTACATTTTAACCCTCAAAC-TTCC
*
21429176 AAAAATTACATTTTAACCCTTAAACTTCC
1 AAAAATTACATTTTAACCCTCAAACTTCC
* * *
21429205 TAAAATTACAATTTT-ACCCTTAAATTTTCC
1 AAAAATTAC-ATTTTAACCCTCAAA-CTTCC
* *
21429235 AGAAATCACATTTTAA-CCTCTAAACTTCTC
1 AAAAATTACATTTTAACCCTC-AAACTTC-C
* * * *
21429265 AAATATTCCATTTTTACCCCCAAACTTCC
1 AAAAATTACATTTTAACCCTCAAACTTCC
* * * *
21429294 AAAAATAACATTTT-GCCCTCGAACTTCT
1 AAAAATTACATTTTAACCCTCAAACTTCC
* * * *
21429322 AAAAATTACATTTTTACCCCCGAACATCC
1 AAAAATTACATTTTAACCCTCAAACTTCC
* * *
21429351 AAAAATTACCATTTT-GCCC-CAAGCATCC
1 AAAAATTA-CATTTTAACCCTCAAACTTCC
** ** *
21429379 AAAAATTATTTTTTTTGCCCTCGAACTTCC
1 AAAAATTA-CATTTTAACCCTCAAACTTCC
* ** * *
21429409 AAAAATGACATTTTTGCTCTCGAACTTCC
1 AAAAATTACATTTTAACCCTCAAACTTCC
21429438 AAAA
1 AAAA
21429442 TTTTGATATT
Statistics
Matches: 243, Mismatches: 42, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
28 42 0.17
29 93 0.38
30 105 0.43
31 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTCAAACTTCC
Found at i:21429277 original size:89 final size:88
Alignment explanation
Indices: 21429141--21429365 Score: 215
Period size: 89 Copynumber: 2.6 Consensus size: 88
21429131 ACCGCTACAC
* ** *
21429141 TTTCCAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTCCT
1 TTTCCAAAAATCACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCCCCAAACTTCCA
*
21429206 AAAATTACAATTTTACCCTTAAAT
66 AAAATAAC-ATTTTACCCTTAAAT
* * * *
21429230 TTTCCAGAAATCACATTTTAA-CCTCTAAAC-TTCTCAAATATTCCATTTTTACCCCCAAACTTC
1 TTTCCAAAAATCACATTTTAACCCTC-AAACTTTC-CAAAAATTACATTTTAACCCCCAAACTTC
* **
21429293 CAAAAATAACATTTTGCCCTCGAA-
64 CAAAAATAACATTTTACCCTTAAAT
* * * * * * *
21429317 CTTCTAAAAATTACATTTTTACCCCCGAAC-ATCCAAAAATTACCATTTT
1 TTTCCAAAAATCACATTTTAACCCTCAAACTTTCCAAAAATTA-CATTTT
21429366 GCCCCAAGCA
Statistics
Matches: 110, Mismatches: 22, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
86 7 0.06
87 27 0.25
88 21 0.19
89 55 0.50
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (88 bp):
TTTCCAAAAATCACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCCCCAAACTTCCA
AAAATAACATTTTACCCTTAAAT
Found at i:21429424 original size:58 final size:57
Alignment explanation
Indices: 21429143--21429441 Score: 197
Period size: 59 Copynumber: 5.1 Consensus size: 57
21429133 CGCTACACTT
* * * * * ** *
21429143 TCCAAAAATTACATTTTAACCCTCAAACTTTCCAAAAATTACATTTTAACCCTTAAACT
1 TCCAAAAATTACATTTTTACCCCCGAAC-TTCCAAAAATAACATTTT-GCCCTCGAACA
* * *** * * * ** * *
21429202 TCCTAAAATTACAATTTTACCCTTAAATTTTCCAGAAATCACATTTTAACCTCTAAACT
1 TCCAAAAATTACATTTTTACCCCCGAA-CTTCCAAAAATAACATTTTGCCCTC-GAACA
* * * *
21429261 TCTCAAATATTCCATTTTTACCCCCAAACTTCCAAAAATAACATTTTGCCCTCGAACT
1 TC-CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATAACATTTTGCCCTCGAACA
* * *
21429319 TCTAAAAATTACATTTTTACCCCCGAACATCCAAAAATTACCATTTTGCCC-C-AAGCA
1 TCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAA-TAACATTTTGCCCTCGAA-CA
** * * * * *
21429376 TCCAAAAATTATTTTTTTTGCCCTCGAACTTCCAAAAATGACATTTTTGCTCTCGAACT
1 TCCAAAAATTA-CATTTTTACCCCCGAACTTCCAAAAATAACA-TTTTGCCCTCGAACA
21429435 TCCAAAA
1 TCCAAAA
21429442 TTTTGATATT
Statistics
Matches: 193, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
56 2 0.01
57 45 0.23
58 50 0.26
59 75 0.39
60 21 0.11
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (57 bp):
TCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATAACATTTTGCCCTCGAACA
Found at i:21441115 original size:39 final size:39
Alignment explanation
Indices: 21441067--21441198 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 39
21441057 CAGGCATTTG
* *
21441067 ATCTTTTACCCCGAGCTTGGGGTAGATCATTATCAACAA
1 ATCTCTTACCCCGAGCATGGGGTAGATCATTATCAACAA
* * * * *
21441106 ATCTGTTACCCTGATCATGGGGCAGATTTCAGTTATC--C-G
1 ATCTCTTACCCCGAGCATGGGGTAGA--TCA-TTATCAACAA
* * * *
21441145 ATCTCTTACCTCGAGCCTGGGGTAGATTATCAT-AAGCAA
1 ATCTCTTACCCCGAGCATGGGGTAGATCATTATCAA-CAA
21441184 ATCTCTTACCCCGAG
1 ATCTCTTACCCCGAG
21441199 TCTAGGGCAG
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
36 3 0.04
37 2 0.03
38 1 0.01
39 55 0.79
40 1 0.01
41 3 0.04
42 5 0.07
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCATGGGGTAGATCATTATCAACAA
Found at i:21441161 original size:156 final size:155
Alignment explanation
Indices: 21440843--21441271 Score: 504
Period size: 156 Copynumber: 2.8 Consensus size: 155
21440833 GATTTTTTAC
* * * * * ** * *
21440843 CCCGAGCTTGGGGCAGATCACCATCAGCCAATCTTTTACCCTAAGCTTAGGGCAGATTGCAACCA
1 CCCGAGCCTGGGGTAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCA
* * * *
21440908 TTTGATCTTTTCCCCCGAGCCT-AGACAGATCATCATCAGCAAATCTCTTACCCCAATCATGGGG
66 TTTGATCTTTTACCCCGAGCTTGGGATAGATCATCATCAGCAAATCTCTTACCCCAATCATGGGG
*
21440972 CAAATTACAGTTATCTGATCTCTTA
131 CAAATTACAGTTATCCGATCTCTTA
* * *
21440997 CCCTGAGCCTGGAGTAGATCATCATCAGCAAATCTCTTACCCCGAGCCT-GTGGCAAATTGCAGG
1 CCC-GAGCCTGGGGTAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAG-GGCAGATTGCAGC
* * * * **
21441061 CATTTGATCTTTTACCCCGAGCTTGGGGTAGATCATTATCAACAAATCTGTTACCCTGATCATGG
64 CATTTGATCTTTTACCCCGAGCTTGGGATAGATCATCATCAGCAAATCTCTTACCCCAATCATGG
* *
21441126 GGCAGATTTCAGTTATCCGATCTCTTA
129 GGCAAATTACAGTTATCCGATCTCTTA
* * *
21441153 CCTCGAGCCTGGGGTAGATTATCATAAGCAAATCTCTTACCCCGAGTCTAGGGCAGATTGCAGCC
1 CC-CGAGCCTGGGGTAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCC
** * * *
21441218 ATCCGATCTTTTATCCCGAGCTTAGGGCT-GATCATCATCAGTAAATCTCTTACC
65 ATTTGATCTTTTACCCCGAGCTT-GGGATAGATCATCATCAGCAAATCTCTTACC
21441272 TTGAGCTTAG
Statistics
Matches: 230, Mismatches: 39, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
154 4 0.02
155 68 0.30
156 152 0.66
157 6 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (155 bp):
CCCGAGCCTGGGGTAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCA
TTTGATCTTTTACCCCGAGCTTGGGATAGATCATCATCAGCAAATCTCTTACCCCAATCATGGGG
CAAATTACAGTTATCCGATCTCTTA
Found at i:21441278 original size:39 final size:39
Alignment explanation
Indices: 21441235--21441310 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
21441225 CTTTTATCCC
*
21441235 GAGCTTAGGGCT-GATCATCATCAGTAAATCTCTTACCTT
1 GAGCTTAGGG-TAGATCATCATCAGCAAATCTCTTACCTT
*
21441274 GAGCTTAGGGTAGATCATCATCAGCCAATCTCTTACC
1 GAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACC
21441311 CCGATCATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (39 bp):
GAGCTTAGGGTAGATCATCATCAGCAAATCTCTTACCTT
Found at i:21441283 original size:78 final size:78
Alignment explanation
Indices: 21440832--21441288 Score: 368
Period size: 78 Copynumber: 5.9 Consensus size: 78
21440822 ATTGAAGATT
* * * * * **
21440832 TGATTTTTTACCCCGAGCTTGGGGC-AGATCACCATCAGCCAATCTTTTACCCTAAGCTTAGGGC
1 TGATCTTTTACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCTTACCCCGAGCTTAGGGC
* *
21440896 AGATTGCAACCATT
65 AGATTGCAGCCATC
* * * * * * *
21440910 TGATCTTTTCCCCCGAGCCTAGAC-AGATCATCATCAGCAAATCTCTTACCCCAATCATGGGGCA
1 TGATCTTTTACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCTTACCCCGAGCTTAGGGCA
* * **
21440974 AATTACAGTTATC
66 GATTGCAGCCATC
* * *
21440987 TGATCTCTTACCCTGAGCCTGGAG-TAGATCATCATCAGCAAATCTCTTACCCCGAGCCT-GTGG
1 TGATCTTTTACCCCGAGCCTGG-GCTAGATCATCATCAGCAAATCTCTTACCCCGAGCTTAG-GG
* * *
21441050 CAAATTGCAGGCATT
64 CAGATTGCAGCCATC
* * * * * * * * *
21441065 TGATCTTTTACCCCGAGCTTGGGGTAGATCATTATCAACAAATCTGTTACCCTGATCATGGGGCA
1 TGATCTTTTACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCTTACCCCGAGCTTAGGGCA
* **
21441130 GATTTCAGTTATC
66 GATTGCAGCCATC
* * * * * *
21441143 CGATCTCTTACCTCGAGCCTGGGGTAGATTATCATAAGCAAATCTCTTACCCCGAG-TCTAGGGC
1 TGATCTTTTACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCTTACCCCGAGCT-TAGGGC
21441207 AGATTGCAGCCATC
65 AGATTGCAGCCATC
* * * * ** *
21441221 CGATCTTTTATCCCGAGCTTAGGGCT-GATCATCATCAGTAAATCTCTTACCTTGAGCTTAGGGT
1 TGATCTTTTACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCTTACCCCGAGCTTAGGGC
21441285 AGAT
65 AGAT
21441289 CATCATCAGC
Statistics
Matches: 300, Mismatches: 71, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
77 62 0.21
78 232 0.77
79 6 0.02
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (78 bp):
TGATCTTTTACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCTTACCCCGAGCTTAGGGCA
GATTGCAGCCATC
Found at i:21441777 original size:17 final size:17
Alignment explanation
Indices: 21441755--21441817 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
21441745 ACCCAAACAG
*
21441755 AATTTAAATTCATTTTA
1 AATTTAAATTTATTTTA
*
21441772 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
21441789 AATTTAAATTTATTGTA
1 AATTTAAATTTATTTTA
*
21441806 AATTTAAGTTTA
1 AATTTAAATTTA
21441818 AAATTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:21441791 original size:11 final size:10
Alignment explanation
Indices: 21441773--21441833 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
21441763 TTCATTTTAA
21441773 ATTTAAATTT
1 ATTTAAATTT
*
21441783 ATTTGAA---
1 ATTTAAATTT
21441790 ATTTAAATTT
1 ATTTAAATTT
21441800 ATTGTAAATTT
1 ATT-TAAATTT
*
21441811 AAGTTTAAAATT
1 -A-TTTAAATTT
21441823 ATTTAAATTT
1 ATTTAAATTT
21441833 A
1 A
21441834 CTAATTTCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
7 6 0.15
10 18 0.44
11 8 0.20
12 7 0.17
13 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:21441793 original size:7 final size:6
Alignment explanation
Indices: 21441755--21441833 Score: 55
Period size: 6 Copynumber: 14.0 Consensus size: 6
21441745 ACCCAAACAG
* *
21441755 AATTTA AA-TTC ATTTTA AATTTA AATTT- -ATTTGA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* *
21441800 -ATTGTA AATTTA AGTTTA AAATT- -ATTTA AATTTA
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA
21441834 CTAATTTCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
4 10 0.18
5 4 0.07
6 35 0.62
7 7 0.12
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:21441817 original size:23 final size:22
Alignment explanation
Indices: 21441791--21441833 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
21441781 TTATTTGAAA
*
21441791 TTTAAATTTATTGTAAATTTAAG
1 TTTAAAATTATT-TAAATTTAAG
21441814 TTTAAAATTATTTAAATTTA
1 TTTAAAATTATTTAAATTTA
21441834 CTAATTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTAAAATTATTTAAATTTAAG
Found at i:21442150 original size:31 final size:31
Alignment explanation
Indices: 21442112--21442172 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
21442102 CCTTAAGTTG
21442112 CAAAAGACAGAATAGAATCATTGTAAAATAT
1 CAAAAGACAGAATAGAATCATTGTAAAATAT
*
21442143 CAAAAGACATAATAGAATCATTGTAAAATA
1 CAAAAGACAGAATAGAATCATTGTAAAATA
21442173 GGTTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.23
Consensus pattern (31 bp):
CAAAAGACAGAATAGAATCATTGTAAAATAT
Found at i:21446759 original size:24 final size:25
Alignment explanation
Indices: 21446730--21446792 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
21446720 GGTTAGTTAA
*
21446730 CATAAACGAACATGTTT-GCGAATG
1 CATAAACGAACATGTTTCGCGAACG
*
21446754 CATAAACGAACAT-TTTCGTGAACG
1 CATAAACGAACATGTTTCGCGAACG
*
21446778 -TTAAACGAACATGTT
1 CATAAACGAACATGTT
21446793 CATGAACATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.41
24 20 0.59
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (25 bp):
CATAAACGAACATGTTTCGCGAACG
Found at i:21446786 original size:23 final size:24
Alignment explanation
Indices: 21446755--21446814 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
21446745 TTGCGAATGC
* *
21446755 ATAAACGAACATTTTCGTGAACGT
1 ATAAACGAACATTTTCATGAACAT
*
21446779 -TAAACGAACATGTTCATGAACAT
1 ATAAACGAACATTTTCATGAACAT
21446802 ATAAACGAACATT
1 ATAAACGAACATT
21446815 AAACAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (24 bp):
ATAAACGAACATTTTCATGAACAT
Found at i:21446811 original size:12 final size:12
Alignment explanation
Indices: 21446796--21446848 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
21446786 ACATGTTCAT
21446796 GAACATATAAAC
1 GAACATATAAAC
21446808 GAACAT-TAAAC
1 GAACATATAAAC
* * **
21446819 AAACATGTTCAC
1 GAACATATAAAC
*
21446831 GTACATATAAAC
1 GAACATATAAAC
21446843 GAACAT
1 GAACAT
21446849 GTTCACTAAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (12 bp):
GAACATATAAAC
Found at i:21446817 original size:35 final size:35
Alignment explanation
Indices: 21446773--21446903 Score: 122
Period size: 35 Copynumber: 3.7 Consensus size: 35
21446763 ACATTTTCGT
*
21446773 GAACGTTAAACGAACATGTTCATGAACATATAAAC
1 GAACATTAAACGAACATGTTCATGAACATATAAAC
* * *
21446808 GAACATTAAACAAACATGTTCACGTACATATAAAC
1 GAACATTAAACGAACATGTTCATGAACATATAAAC
** * * * **
21446843 GAACATGTTCACTAAC--GTTAAATGAACATGTTCAC
1 GAACAT-TAAACGAACATGTT-CATGAACATATAAAC
*
21446878 GAACATTAAACGAACATGTTCGTGAA
1 GAACATTAAACGAACATGTTCATGAA
21446904 TGATAAACAA
Statistics
Matches: 74, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
34 9 0.12
35 56 0.76
36 9 0.12
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (35 bp):
GAACATTAAACGAACATGTTCATGAACATATAAAC
Found at i:21446836 original size:23 final size:23
Alignment explanation
Indices: 21446810--21446898 Score: 117
Period size: 23 Copynumber: 3.8 Consensus size: 23
21446800 ATATAAACGA
*
21446810 ACATTAAACAAACATGTTCACGT
1 ACATTAAACGAACATGTTCACGT
21446833 ACATATAAACGAACATGTTCAC-T
1 ACAT-TAAACGAACATGTTCACGT
* * *
21446856 AACGTTAAATGAACATGTTCACGA
1 -ACATTAAACGAACATGTTCACGT
21446880 ACATTAAACGAACATGTTC
1 ACATTAAACGAACATGTTC
21446899 GTGAATGATA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
23 38 0.67
24 19 0.33
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (23 bp):
ACATTAAACGAACATGTTCACGT
Found at i:21446847 original size:47 final size:46
Alignment explanation
Indices: 21446796--21446894 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 46
21446786 ACATGTTCAT
*
21446796 GAACATATAAACGAACATTAAACAAACATGTTCACGTACATATAAAC
1 GAACATATAAACGAACATTAAACAAACATGTTCACGAACAT-TAAAC
* ** * * **
21446843 GAACATGTTCACTAACGTTAAATGAACATGTTCACGAACATTAAAC
1 GAACATATAAACGAACATTAAACAAACATGTTCACGAACATTAAAC
21446889 GAACAT
1 GAACAT
21446895 GTTCGTGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 11 0.25
47 33 0.75
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.23
Consensus pattern (46 bp):
GAACATATAAACGAACATTAAACAAACATGTTCACGAACATTAAAC
Found at i:21448384 original size:20 final size:20
Alignment explanation
Indices: 21448348--21448385 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21448338 TCATTAAGCT
*
21448348 TTAATTAACCTTTTTTAATC
1 TTAATTAACCTTATTTAATC
21448368 TTAATTAAACC-TATTTAA
1 TTAATT-AACCTTATTTAA
21448386 AATTAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATTAACCTTATTTAATC
Found at i:21448788 original size:69 final size:69
Alignment explanation
Indices: 21448676--21448811 Score: 263
Period size: 69 Copynumber: 2.0 Consensus size: 69
21448666 TAAAGCTAGA
21448676 CTTGTAGGGAAATGTTACACACATAAAAAAGGCATCAAATACGATGAGACCTTCTTTTCGATAGT
1 CTTGTAGGGAAATGTTACACACATAAAAAAGGCATCAAATACGATGAGACCTTCTTTTCGATAGT
21448741 CATG
66 CATG
*
21448745 CTTGTAGGGAAATGTTACACACATAAAAAAGGCATCAATTACGATGAGACCTTCTTTTCGATAGT
1 CTTGTAGGGAAATGTTACACACATAAAAAAGGCATCAAATACGATGAGACCTTCTTTTCGATAGT
21448810 CA
66 CA
21448812 CGCTCAAGTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (69 bp):
CTTGTAGGGAAATGTTACACACATAAAAAAGGCATCAAATACGATGAGACCTTCTTTTCGATAGT
CATG
Found at i:21449754 original size:27 final size:28
Alignment explanation
Indices: 21449706--21449762 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
21449696 ACTCCTCAAG
* *
21449706 CCCAAAGCCCAAAGCCACCCTATTTCCC
1 CCCAAAGCCAAAACCCACCCTATTTCCC
21449734 CCCAAAGCCAAAACCCA-CCTATTTCCC
1 CCCAAAGCCAAAACCCACCCTATTTCCC
21449761 CC
1 CC
21449763 TCCCTCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.30, C:0.51, G:0.05, T:0.14
Consensus pattern (28 bp):
CCCAAAGCCAAAACCCACCCTATTTCCC
Found at i:21450045 original size:27 final size:27
Alignment explanation
Indices: 21450000--21450054 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
21449990 CTTAATTCTT
21450000 CTTCTTCTTCTTCAATTCATTCGAACC
1 CTTCTTCTTCTTCAATTCATTCGAACC
*
21450027 CTTCTTCTTCATT-AGTTCATTCGAACC
1 CTTCTTCTTC-TTCAATTCATTCGAACC
21450054 C
1 C
21450055 CCAAAATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.18, C:0.33, G:0.05, T:0.44
Consensus pattern (27 bp):
CTTCTTCTTCTTCAATTCATTCGAACC
Found at i:21452296 original size:5 final size:5
Alignment explanation
Indices: 21452286--21452314 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
21452276 TGCACCCTTT
21452286 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
21452315 CTTCTCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:21460347 original size:59 final size:58
Alignment explanation
Indices: 21460271--21460384 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 58
21460261 ATACATTCGG
21460271 GGGTAAAACGGTAATTTTTAAGAA-AATCGGGATCAAAAATGGAATTTTTGGACATCCGA
1 GGGTAAAACGGTAATTTTT-AGAATAATCGGG-TCAAAAATGGAATTTTTGGACATCCGA
* * ** *
21460330 GGGTAAAATGGTAATTTTTGGAATTTTCGGGTCAAAAATGGAGTTTTTGGACATC
1 GGGTAAAACGGTAATTTTTAGAATAATCGGGTCAAAAATGGAATTTTTGGACATC
21460385 TTGGGGCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 26 0.53
59 23 0.47
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (58 bp):
GGGTAAAACGGTAATTTTTAGAATAATCGGGTCAAAAATGGAATTTTTGGACATCCGA
Found at i:21460367 original size:58 final size:58
Alignment explanation
Indices: 21460297--21460601 Score: 255
Period size: 58 Copynumber: 5.2 Consensus size: 58
21460287 TTTAAGAAAA
21460297 TCGGGATCAAAAATGGAATTTTTGGACA-TCCGAGGGTAAAATGGTAATTTTTGGAATTT
1 TCGGG-TCAAAAATGGAATTTTTGGACAGTCCGAGGGTAAAAT-GTAATTTTTGGAATTT
* * * * * * *
21460356 TCGGGTCAAAAATGGAGTTTTTGGACA-TCTTG-GGGCAAAATATAATGTTTGAAAGTT
1 TCGGGTCAAAAATGGAATTTTTGGACAGTC-CGAGGGTAAAATGTAATTTTTGGAATTT
* * * *
21460413 TCGAGGTCAAAAATTGAATTTTTGGA-AGTTCGAGGGCAAAATATAATTTTTGGAAGTTT
1 TCG-GGTCAAAAATGGAATTTTTGGACAGTCCGAGGGTAAAATGTAATTTTTGGAA-TTT
** * * *
21460472 TAAGGTCAAAAATAGAATTTTT-GAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTT
1 TCGGGTCAAAAATGGAATTTTTGGACAGTCCGAGGGT-AAAATGTAATTTTTGGAA-TTT
* * * ** *
21460531 TGGGGTTAAAAATGGATTTTTTTGGA-AGT-TTAGGGGTAAAAATGTAATTTTTGGAAGTT
1 TCGGGTCAAAAATGGA-ATTTTTGGACAGTCCGA-GGGT-AAAATGTAATTTTTGGAATTT
*
21460590 TCAAGGTCAAAA
1 TC-GGGTCAAAA
21460602 TATAATTTTT
Statistics
Matches: 205, Mismatches: 30, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
57 19 0.09
58 100 0.49
59 46 0.22
60 38 0.19
61 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (58 bp):
TCGGGTCAAAAATGGAATTTTTGGACAGTCCGAGGGTAAAATGTAATTTTTGGAATTT
Found at i:21460394 original size:29 final size:29
Alignment explanation
Indices: 21460304--21460395 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
21460294 AAATCGGGAT
*
21460304 CAAAAATGGAATTTTTGGACATC-CGAGGG
1 CAAAAATGGAATTTTTGGACATCTTG-GGG
* * *
21460333 -TAAAATGGTAATTTTTGGA-ATTTTCGGGT
1 CAAAAATGG-AATTTTTGGACATCTT-GGGG
*
21460362 CAAAAATGGAGTTTTTGGACATCTTGGGG
1 CAAAAATGGAATTTTTGGACATCTTGGGG
21460391 CAAAA
1 CAAAA
21460396 TATAATGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
28 9 0.18
29 29 0.58
30 12 0.24
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.32
Consensus pattern (29 bp):
CAAAAATGGAATTTTTGGACATCTTGGGG
Found at i:21460423 original size:29 final size:29
Alignment explanation
Indices: 21460341--21460620 Score: 191
Period size: 29 Copynumber: 9.6 Consensus size: 29
21460331 GGTAAAATGG
*
21460341 TAATTTTTGGAATTTTCG-GGTCAAAA-A
1 TAATTTTTGGAAGTTTCGAGGTCAAAATA
* *
21460368 TGGAGTTTTTGGACA-TCTT-G-GGGCAAAATA
1 T--AATTTTTGGA-AGT-TTCGAGGTCAAAATA
* *
21460398 TAATGTTTGAAAGTTTCGAGGTCAAAA-A
1 TAATTTTTGGAAGTTTCGAGGTCAAAATA
*
21460426 TTGAATTTTTGGAAG-TTCGAGGGCAAAATA
1 -T-AATTTTTGGAAGTTTCGAGGTCAAAATA
**
21460456 TAATTTTTGGAAGTTTTAAGGTCAAAAATA
1 TAATTTTTGGAAGTTTCGAGGTC-AAAATA
* * * *
21460486 GAATTTTTGAAAG-TTCGAGGGTAAAAATG
1 TAATTTTTGGAAGTTTCGA-GGTCAAAATA
* * *
21460515 TAATTTTTGGAAGTTTTGGGGTTAAAA-A
1 TAATTTTTGGAAGTTTCGAGGTCAAAATA
* * * * *
21460543 TGGATTTTTTTGGAAGTTTAGGGGTAAAAATG
1 T--A-ATTTTTGGAAGTTTCGAGGTCAAAATA
*
21460575 TAATTTTTGGAAGTTTCAAGGTCAAAATA
1 TAATTTTTGGAAGTTTCGAGGTCAAAATA
*
21460604 TAATTTTTTGATAGTTT
1 TAATTTTTGGA-AGTTT
21460621 AGGGACCTCT
Statistics
Matches: 198, Mismatches: 35, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
27 4 0.02
28 23 0.12
29 102 0.52
30 46 0.23
31 22 0.11
32 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTCGAGGTCAAAATA
Found at i:21461654 original size:3 final size:3
Alignment explanation
Indices: 21461648--21461691 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
21461638 AATTATTAAC
* * *
21461648 ATT ATT ATT AGT ATT ATT AATT AAT ATT ATC ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT A
21461692 AATATTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:21461656 original size:12 final size:12
Alignment explanation
Indices: 21461639--21461699 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
21461629 ATTAATTAAA
*
21461639 ATTATTAACATT
1 ATTATTAATATT
*
21461651 ATTATTAGTATT
1 ATTATTAATATT
21461663 ATTAATTAATATT
1 ATT-ATTAATATT
* *
21461676 ATCATTATTATT
1 ATTATTAATATT
21461688 ATTA--AATATT
1 ATTATTAATATT
21461698 AT
1 AT
21461700 AATAAACTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 7 0.17
12 24 0.59
13 10 0.24
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (12 bp):
ATTATTAATATT
Found at i:21461670 original size:25 final size:25
Alignment explanation
Indices: 21461642--21461692 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
21461632 AATTAAAATT
*
21461642 ATTAACATTATTATTAGTATTATTA
1 ATTAACATTATCATTAGTATTATTA
* *
21461667 ATTAATATTATCATTATTATTATTA
1 ATTAACATTATCATTAGTATTATTA
21461692 A
1 A
21461693 ATATTATAAT
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:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (25 bp):
ATTAACATTATCATTAGTATTATTA
Found at i:21461675 original size:22 final size:22
Alignment explanation
Indices: 21461639--21461699 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
21461629 ATTAATTAAA
*
21461639 ATTATTAACATTATTATTAGTATT
1 ATTATTAA-A-TATTATCAGTATT
*
21461663 ATTAATT-AATATTATCATTATT
1 ATT-ATTAAATATTATCAGTATT
21461685 ATTATTAAATATTAT
1 ATTATTAAATATTAT
21461700 AATAAACTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 3 0.09
22 22 0.67
23 1 0.03
24 4 0.12
25 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTATTAAATATTATCAGTATT
Found at i:21462392 original size:17 final size:16
Alignment explanation
Indices: 21462372--21462481 Score: 96
Period size: 17 Copynumber: 6.4 Consensus size: 16
21462362 CTTTGTTTAT
*
21462372 TTTAAATTTATAATAAT
1 TTTAAATTTA-AATAAA
21462389 TTTAAATTTGAAGATAAA
1 TTTAAATTT-AA-ATAAA
*
21462407 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
21462424 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
*
21462441 TTTAAATTTTTAAACAAA
1 TTTAAA--TTTAAATAAA
*
21462459 TTT-AATCTTAAAACAAA
1 TTTAAAT-TT-AAATAAA
21462476 TTTAAA
1 TTTAAA
21462482 ATGAGTTTGG
Statistics
Matches: 80, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
15 1 0.01
16 3 0.04
17 46 0.57
18 27 0.34
19 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:21462417 original size:6 final size:6
Alignment explanation
Indices: 21462372--21462449 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
21462362 CTTTGTTTAT
* * ** *
21462372 TTTAAA TTTATAA --TAAT TTTAAA TTTGAA GATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
21462419 -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
21462450 TTAAACAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
4 1 0.02
5 11 0.20
6 42 0.75
7 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:21462428 original size:11 final size:12
Alignment explanation
Indices: 21462403--21462446 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
21462393 AATTTGAAGA
21462403 TAAATTTAAACT
1 TAAATTTAAACT
*
21462415 TAAA-TTAAATT
1 TAAATTTAAACT
*
21462426 TAAATTTAAA-A
1 TAAATTTAAACT
21462437 TAAATTTAAA
1 TAAATTTAAA
21462447 TTTTTAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:21462439 original size:52 final size:52
Alignment explanation
Indices: 21462372--21462481 Score: 141
Period size: 52 Copynumber: 2.1 Consensus size: 52
21462362 CTTTGTTTAT
* * * **
21462372 TTTAAATTTATAATAATTTTAAA-TTTGAAGATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAATTTAAATTTTGAA-ACAAATTTAAACTTAAAACAAA
* *
21462424 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAATTTAATCTTAAAACAAA
1 TTTAAATTTAAAATAAATTTAAATTTTGAAACAAATTTAAACTTAAAACAAA
21462476 TTTAAA
1 TTTAAA
21462482 ATGAGTTTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 45 0.90
53 5 0.10
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTTGAAACAAATTTAAACTTAAAACAAA
Found at i:21462460 original size:35 final size:35
Alignment explanation
Indices: 21462372--21462481 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
21462362 CTTTGTTTAT
* * *
21462372 TTTAAATTTAT-AATAATTTTAAATTTGAAGATAAA
1 TTTAAATTTTTAAATAAATTTAAATTT-AAAATAAA
*
21462407 TTTAAA--CTTAAATTAAATTTAAATTTAAAATAAA
1 TTTAAATTTTTAAA-TAAATTTAAATTTAAAATAAA
* *
21462441 TTTAAATTTTTAAACAAATTT-AATCTTAAAACAAA
1 TTTAAATTTTTAAATAAATTTAAAT-TTAAAATAAA
21462476 TTTAAA
1 TTTAAA
21462482 ATGAGTTTGG
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
33 1 0.02
34 18 0.29
35 39 0.62
36 5 0.08
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (35 bp):
TTTAAATTTTTAAATAAATTTAAATTTAAAATAAA
Found at i:21463199 original size:207 final size:202
Alignment explanation
Indices: 21462827--21463567 Score: 1083
Period size: 207 Copynumber: 3.6 Consensus size: 202
21462817 TCTATATCCT
* *
21462827 ATCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTT
1 ATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTT
* ** * * * * *
21462892 CGAAGAGTTGCTCGCATCGAGCG-TCGAGTTCGTATACTTCTCTGTATCTCATTAGGAAGATGAG
66 CGAAGACTTGCTCATATCGAGCGTTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATGAC
* ** *
21462956 CGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCA
131 CGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCA
21463021 GTATCTC
196 GTATCTC
*
21463028 ATCAAGAACCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGGT
1 ATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGT
* * *
21463093 TCGAAGACTTGCTTATATCGAGCGTGGGTTTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAG
65 TCGAAGACTTGCTCATATCGAGC----GTTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAG
*
21463158 ATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC-AGATTTAGTCCAC
126 ATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGA-ATTTGGTCCAC
*
21463222 TTCTCAGTATCAC
190 TTCTCAGTATCTC
21463235 ATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGGT
1 ATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGT
* * *
21463300 TCGAAGACTTGCTCATATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
65 TCGAAGACTTGCTCATATCGAGC----GTTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAG
*
21463365 ATGACCGCATCGTTTGTTTCAATCCGATTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACT
126 ATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACT
*
21463430 TCTCAGTATTTC
191 TCTCAGTATCTC
* * *
21463442 ATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTTAGTATCTCATCAAGAAGCTGGGGTT
1 ATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTT
* * *
21463507 CGAAGATTTGCTCATATCAAGC-CTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGAT
66 CGAAGACTTGCTCATATCGAGCGTTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGAT
21463568 AATCGCCTCA
Statistics
Matches: 495, Mismatches: 37, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
201 91 0.18
202 24 0.05
206 28 0.06
207 351 0.71
208 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (202 bp):
ATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTT
CGAAGACTTGCTCATATCGAGCGTTTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATGAC
CGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCA
GTATCTC
Found at i:21470271 original size:21 final size:21
Alignment explanation
Indices: 21470245--21470284 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21470235 AGTGGAGACC
21470245 TAATTTCTTCAAC-ATTTCTCT
1 TAATTT-TTCAACTATTTCTCT
*
21470266 TAATTTTTGAACTATTTCT
1 TAATTTTTCAACTATTTCT
21470285 TCCAACAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (21 bp):
TAATTTTTCAACTATTTCTCT
Found at i:21471236 original size:59 final size:60
Alignment explanation
Indices: 21471171--21471491 Score: 295
Period size: 59 Copynumber: 5.4 Consensus size: 60
21471161 AAAATCAGAA
* * *
21471171 TAAAAAATAGAATTTTTGGACA-TCCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGGGG
1 TAAAAAATGGAATTTTTGGACAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGG
* * * * *
21471230 TGAAAAATGGAGTTTTTGGACA-TTTGAGGGTAAAATGGTAATTTTTAAAAGTTTCGGGA
1 TAAAAAATGGAATTTTTGGACAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGG
* * * ***
21471289 TAAAAAATGTAATTTTT-GAAAGTTCGAGGGTTAAAAT-ATAATTTTTGAAAGTTTTAAGG
1 TAAAAAATGGAATTTTTGGACAGTTCGAGGG-TAAAATGGTAATTTTTGAAAGTTTCGGGG
* * *
21471348 TCAAAAATGGAATTTTT-GAAAGTTCGAGGGTCAAAAATGG-AATTTTTGAAAGTTTTGGGG
1 TAAAAAATGGAATTTTTGGACAGTTCGAGGGT--AAAATGGTAATTTTTGAAAGTTTCGGGG
* * * * *
21471408 TTAAAAAATGGATTTTTTAGA-AGTT-TAGGGGTAAAAAT-GTAATTTTTGGAAGTTTCAGGG
1 -TAAAAAATGGAATTTTTGGACAGTTCGA-GGGT-AAAATGGTAATTTTTGAAAGTTTCGGGG
*
21471468 TCAAAATAT--AATTTTTGGACAGTT
1 T-AAAAAATGGAATTTTTGGACAGTT
21471492 TAGGGACCTC
Statistics
Matches: 218, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
58 12 0.06
59 122 0.56
60 59 0.27
61 23 0.11
62 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (60 bp):
TAAAAAATGGAATTTTTGGACAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGG
Found at i:21471396 original size:30 final size:29
Alignment explanation
Indices: 21471173--21471484 Score: 194
Period size: 30 Copynumber: 10.6 Consensus size: 29
21471163 AATCAGAATA
* * *
21471173 AAAAATAGAATTTTTGGACA-TCCGAGGGT
1 AAAAATGGAATTTTT-GAAAGTTCGAGGGT
*
21471202 -AAAATGGTAATTTTTGGAAGTTTCG-GGGT
1 AAAAATGG-AATTTTTGAAAG-TTCGAGGGT
* * *
21471231 GAAAAATGGAGTTTTTGGACA-TTTGAGGGT
1 -AAAAATGGAATTTTT-GAAAGTTCGAGGGT
* *
21471261 -AAAATGGTAATTTTTAAAAGTTTCG-GGAT
1 AAAAATGG-AATTTTTGAAAG-TTCGAGGGT
*
21471290 AAAAAATGTAATTTTTGAAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGAAAGTTCGAGGGT
* ** ** *
21471320 TAAAATATAATTTTTGAAAGTTTTAAGGT
1 AAAAATGGAATTTTTGAAAGTTCGAGGGT
21471349 CAAAAATGGAATTTTTGAAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGAAAGTTCGAGGGT
*
21471379 CAAAAATGGAATTTTTGAAAGTTTTG-GGGTT
1 -AAAAATGGAATTTTTGAAAG-TTCGAGGG-T
* *
21471410 AAAAAATGG-ATTTTTTAGAAGTT-TAGGGGT
1 -AAAAATGGAATTTTTGA-AAGTTCGA-GGGT
* *
21471440 AAAAATGTAATTTTTGGAAGTTTC-AGGGT
1 AAAAATGGAATTTTTGAAAG-TTCGAGGGT
* **
21471469 CAAAATATAATTTTTG
1 AAAAATGGAATTTTTG
21471485 GACAGTTTAG
Statistics
Matches: 225, Mismatches: 36, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
28 17 0.08
29 79 0.35
30 96 0.43
31 33 0.15
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGAAAGTTCGAGGGT
Found at i:21472558 original size:3 final size:3
Alignment explanation
Indices: 21472550--21472601 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
21472540 TATTACTAAC
* * *
21472550 ATT ATT ATT AGT ATT ATT AATT AAT ATT ATC ATT ATT ATT ATT AATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT -ATT
21472597 ATT AT
1 ATT AT
21472602 AATAAACTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:21472570 original size:34 final size:32
Alignment explanation
Indices: 21472530--21472600 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
21472520 TTTATCATTA
21472530 TATTAATTAATATTACTAACATTATTATTAGT-AT
1 TATTAATTAATATTA-T--CATTATTATTAGTAAT
*
21472564 TATTAATTAATATTATCATTATTATTATTAAT
1 TATTAATTAATATTATCATTATTATTAGTAAT
21472596 TATTA
1 TATTA
21472601 TAATAAACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 12 0.34
32 7 0.20
33 1 0.03
34 15 0.43
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (32 bp):
TATTAATTAATATTATCATTATTATTAGTAAT
Found at i:21472577 original size:22 final size:22
Alignment explanation
Indices: 21472550--21472601 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21472540 TATTACTAAC
*
21472550 ATTATTATTAGTATTATTAATTA
1 ATTATTATCAGTATTATT-ATTA
*
21472573 A-TATTATCATTATTATTATTA
1 ATTATTATCAGTATTATTATTA
21472594 ATTATTAT
1 ATTATTAT
21472602 AATAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.19
22 20 0.77
23 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTATTATCAGTATTATTATTA
Found at i:21472578 original size:25 final size:25
Alignment explanation
Indices: 21472550--21472597 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21472540 TATTACTAAC
*
21472550 ATTATTATTAGTATTATTAATTAAT
1 ATTATCATTAGTATTATTAATTAAT
*
21472575 ATTATCATTATTATTATTAATTA
1 ATTATCATTAGTATTATTAATTA
21472598 TTATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTATCATTAGTATTATTAATTAAT
Found at i:21475248 original size:28 final size:28
Alignment explanation
Indices: 21475188--21475251 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
21475178 AAGTCAAGTA
*
21475188 TTTTTTTTCTTATTTTTAAAAATATATG
1 TTTTTTTTCTTATTTTTAAAAATAGATG
* **
21475216 ATTTTTTTCTTATTTATTATTAATAGAT-
1 TTTTTTTTCTTATTT-TTAAAAATAGATG
21475244 TTTTTTTT
1 TTTTTTTT
21475252 AATTTCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTTTCTTATTTTTAAAAATAGATG
Found at i:21475452 original size:14 final size:14
Alignment explanation
Indices: 21475435--21475474 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
21475425 TAATTATTTT
21475435 AATTTTCAAATAAA
1 AATTTTCAAATAAA
**
21475449 AATTTAAAAATAAA
1 AATTTTCAAATAAA
*
21475463 AAATTTCAAATA
1 AATTTTCAAATA
21475475 TAGATTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTTTCAAATAAA
Found at i:21478874 original size:31 final size:32
Alignment explanation
Indices: 21478821--21478880 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
21478811 TCTTTTGTTC
**
21478821 CTTGTTTTTCCTCTTTCTTCTCATCTTTTTAT
1 CTTGTTTTTCCTCCATCTTCTCATCTTTTTAT
21478853 CTTGTTTTTCC-CCATCTTCTCATCTTTT
1 CTTGTTTTTCCTCCATCTTCTCATCTTTT
21478881 GCTTATCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.07, C:0.28, G:0.03, T:0.62
Consensus pattern (32 bp):
CTTGTTTTTCCTCCATCTTCTCATCTTTTTAT
Found at i:21488120 original size:16 final size:17
Alignment explanation
Indices: 21488089--21488122 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21488079 ATGAGATAGA
*
21488089 ATAATGTTTAAGTATTT
1 ATAATGGTTAAGTATTT
21488106 ATAATGGTT-AGTATTT
1 ATAATGGTTAAGTATTT
21488122 A
1 A
21488123 GGGTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAAGTATTT
Found at i:21494194 original size:15 final size:15
Alignment explanation
Indices: 21494167--21494203 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21494157 CAAAAATAAA
21494167 AATAAAATAAAATTC
1 AATAAAATAAAATTC
21494182 AATAATAAT-AAATTC
1 AATAA-AATAAAATTC
21494197 AATAAAA
1 AATAAAA
21494204 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAATAAAATTC
Found at i:21494209 original size:16 final size:16
Alignment explanation
Indices: 21494170--21494209 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
21494160 AAATAAAAAT
*
21494170 AAAATAAAATTCAATA
1 AAAATTAAATTCAATA
*
21494186 ATAA-TAAATTCAATA
1 AAAATTAAATTCAATA
21494201 AAAATTAAA
1 AAAATTAAA
21494210 AAATTTCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAAATTCAATA
Found at i:21501993 original size:11 final size:12
Alignment explanation
Indices: 21501943--21501993 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 12
21501933 TCATAAACCA
21501943 AAAATAAATAA-
1 AAAATAAATAAT
*
21501954 ATAATAAATAAT
1 AAAATAAATAAT
21501966 AAAGTATAAA-AAT
1 AAA--ATAAATAAT
21501979 AAAATAAA-AAT
1 AAAATAAATAAT
21501990 AAAA
1 AAAA
21501994 ACTCGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 22 0.63
12 2 0.06
13 6 0.17
14 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:21504686 original size:32 final size:31
Alignment explanation
Indices: 21504650--21504734 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 31
21504640 TTAGTTTTAA
*
21504650 AAAATAAAAAATAATAGAAAAAATGTGAAAAG
1 AAAATAAAAAATAAAAGAAAAAAT-TGAAAAG
* *
21504682 AAAATAATAAATAAAAGAGAAAATTG-AAA-
1 AAAATAAAAAATAAAAGAAAAAATTGAAAAG
* *
21504711 AAAAGAAGAAA-AAAAGAAAAAATT
1 AAAATAAAAAATAAAAGAAAAAATT
21504735 CAATGGTCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.26
29 9 0.19
30 3 0.06
31 2 0.04
32 21 0.45
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (31 bp):
AAAATAAAAAATAAAAGAAAAAATTGAAAAG
Found at i:21505742 original size:32 final size:30
Alignment explanation
Indices: 21505684--21505744 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
21505674 AACAATAGTA
* *
21505684 AAAACGCATAAAAATAACATCCAAACAACC
1 AAAACGCATAAAAATAACAGCAAAACAACC
*
21505714 AAAACAGCAGTAAAAATAACCGCAAAACAAC
1 AAAAC-GCA-TAAAAATAACAGCAAAACAAC
21505745 AACAGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 3 0.12
32 18 0.69
ACGTcount: A:0.61, C:0.25, G:0.07, T:0.08
Consensus pattern (30 bp):
AAAACGCATAAAAATAACAGCAAAACAACC
Found at i:21505786 original size:24 final size:24
Alignment explanation
Indices: 21505725--21505799 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
21505715 AAACAGCAGT
*
21505725 AAAAATAACCGC-AAAACAACAAC
1 AAAAATAACAGCAAAAACAACAAC
* * * *
21505748 AGAAATAGCAACAAAAACAGCAAC
1 AAAAATAACAGCAAAAACAACAAC
* *
21505772 AAAAATAATAGCAAAAACAACACC
1 AAAAATAACAGCAAAAACAACAAC
21505796 AAAA
1 AAAA
21505800 CAGTAAAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 8 0.20
24 32 0.80
ACGTcount: A:0.67, C:0.21, G:0.07, T:0.05
Consensus pattern (24 bp):
AAAAATAACAGCAAAAACAACAAC
Found at i:21505798 original size:12 final size:12
Alignment explanation
Indices: 21505737--21505799 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
21505727 AAATAACCGC
21505737 AAAACAACAACA
1 AAAACAACAACA
* * *
21505749 GAAATAGCAACA
1 AAAACAACAACA
*
21505761 AAAACAGCAACA
1 AAAACAACAACA
* * *
21505773 AAAATAATAGCA
1 AAAACAACAACA
*
21505785 AAAACAACACCA
1 AAAACAACAACA
21505797 AAA
1 AAA
21505800 CAGTAAAAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.68, C:0.21, G:0.06, T:0.05
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:21505839 original size:21 final size:21
Alignment explanation
Indices: 21505815--21505931 Score: 89
Period size: 23 Copynumber: 5.4 Consensus size: 21
21505805 AAAAAGCACC
21505815 AAAACAACAATCAAAATAGT-
1 AAAACAACAATCAAAATAGTA
* * *
21505835 AAAA-AA-AATTAAAACAGCAA
1 AAAACAACAATCAAAATAG-TA
* *
21505855 AAAATAACAACCAAAATAGTA
1 AAAACAACAATCAAAATAGTA
21505876 AAAACAACAACATCAAAATAGTAA
1 AAAACAAC-A-ATCAAAATAGT-A
*
21505900 AAAACAAC-ATCCAAAACAGTGAA
1 AAAACAACAAT-CAAAATAGT--A
21505923 AAAACAACA
1 AAAACAACA
21505932 CCAAAACAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
18 9 0.12
19 2 0.03
20 8 0.10
21 12 0.16
22 17 0.22
23 20 0.26
24 9 0.12
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (21 bp):
AAAACAACAATCAAAATAGTA
Found at i:21505892 original size:23 final size:22
Alignment explanation
Indices: 21505867--21505937 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
21505857 AATAACAACC
21505867 AAAATAGTAAAAACAACAACATC
1 AAAATAGTAAAAA-AACAACATC
21505890 AAAATAGT-AAAAAACAACATCC
1 AAAATAGTAAAAAAACAACAT-C
* * *
21505912 AAAACAGTGAAAAAACAACACC
1 AAAATAGTAAAAAAACAACATC
21505934 AAAA
1 AAAA
21505938 CAACAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 8 0.18
22 17 0.39
23 19 0.43
ACGTcount: A:0.66, C:0.18, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAATAGTAAAAAAACAACATC
Done.