Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 7 of 335
Found at i:2331098 original size:14 final size:14
Alignment explanation
Indices: 2331079--2331107 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2331069 ATGTTGAGAT
2331079 AAGGTTATACCAAG
1 AAGGTTATACCAAG
2331093 AAGGTTATACCAAG
1 AAGGTTATACCAAG
2331107 A
1 A
2331108 CAGCAAGATC
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:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AAGGTTATACCAAG
Found at i:2336795 original size:27 final size:27
Alignment explanation
Indices: 2336765--2336819 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2336755 AAGTAGGATG
2336765 ATGGAATGTGTTGTATCTTGAATTCTA
1 ATGGAATGTGTTGTATCTTGAATTCTA
2336792 ATGGAATGTGTTGTATCTTGAATTCTA
1 ATGGAATGTGTTGTATCTTGAATTCTA
2336819 A
1 A
2336820 CTGATAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (27 bp):
ATGGAATGTGTTGTATCTTGAATTCTA
Found at i:2338009 original size:16 final size:16
Alignment explanation
Indices: 2337981--2338026 Score: 83
Period size: 16 Copynumber: 2.8 Consensus size: 16
2337971 AACAAGGGGC
2337981 AAAATTGGAAATTTTGT
1 AAAATT-GAAATTTTGT
2337998 AAAATTGAAATTTTGT
1 AAAATTGAAATTTTGT
2338014 AAAATTGAAATTT
1 AAAATTGAAATTT
2338027 CATGAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (16 bp):
AAAATTGAAATTTTGT
Found at i:2341844 original size:46 final size:46
Alignment explanation
Indices: 2341777--2342004 Score: 323
Period size: 46 Copynumber: 5.0 Consensus size: 46
2341767 AGTGTGCTCT
2341777 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2341823 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
2341869 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *** *
2341915 GTGACATGAAATGAACAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
2341961 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2342005 TCATGTCAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2354820 original size:38 final size:38
Alignment explanation
Indices: 2354769--2354843 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
2354759 GTATTCGAGT
* * * *
2354769 TAAATCTCGCAGGCTTCGTGTTGGTATTATATCCGGGA
1 TAAATCCCGCAGGCCTAGTGCTGGTATTATATCCGGGA
*
2354807 TAAATCCCGCAGGCCTAGTGCTGGTATTATATTCGGG
1 TAAATCCCGCAGGCCTAGTGCTGGTATTATATCCGGG
2354844 CCTTCGTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (38 bp):
TAAATCCCGCAGGCCTAGTGCTGGTATTATATCCGGGA
Found at i:2354989 original size:43 final size:43
Alignment explanation
Indices: 2354815--2355048 Score: 285
Period size: 43 Copynumber: 5.4 Consensus size: 43
2354805 GATAAATCCC
* * *
2354815 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
2354856 GCAGGCTTAGTGCCGGTGATGTGTATTATTCAGGCCTTCGTGCCTG
1 GCAGGCTTAGTGCCGGTGATGTG---TATTCGGGCCTTCGTGCCTA
*
2354902 GCAGGCTTAGTACCGGTGATGTGTATTC-GGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
2354944 GCAGGCTTCGTGCCGATGATATGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
2354987 GCAGGCTTCGTGCTGGTGATGTGTATTAGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
2355030 ACAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
2355049 AATGGTATGT
Statistics
Matches: 167, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
41 15 0.09
42 39 0.23
43 73 0.44
46 40 0.24
ACGTcount: A:0.15, C:0.23, G:0.32, T:0.30
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:2359603 original size:44 final size:45
Alignment explanation
Indices: 2359513--2359641 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
2359503 GACAGAACGA
*
2359513 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
2359559 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
2359603 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2359642 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:2378524 original size:47 final size:44
Alignment explanation
Indices: 2378469--2378579 Score: 141
Period size: 44 Copynumber: 2.5 Consensus size: 44
2378459 GACAGAACGA
*
2378469 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATT--AAATATGGC-ATTGGAGACAGG
* *
2378516 ATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGG
* **
2378560 AATAATTCATGTAAGTCCAT
1 AATGAGCCATGTAAGTCCAT
2378580 GTCAAAGACA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
44 27 0.47
45 8 0.14
47 22 0.39
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (44 bp):
AATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGG
Found at i:2390728 original size:44 final size:45
Alignment explanation
Indices: 2390638--2390766 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
2390628 GACAGAAGGA
*
2390638 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
2390684 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
2390728 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2390767 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:2393765 original size:22 final size:23
Alignment explanation
Indices: 2393739--2393781 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
2393729 ACCTGATCAG
2393739 AATACGACACAT-AAGTGCCTAA
1 AATACGACACATAAAGTGCCTAA
2393761 AATACGACACATAAAGTGCCT
1 AATACGACACATAAAGTGCCT
2393782 GATCAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTAA
Found at i:2394020 original size:28 final size:28
Alignment explanation
Indices: 2393988--2394067 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
2393978 AACACACCAG
* **
2393988 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGCAAAA
*
2394016 TATAATCCTCCCAAACACACCAGCAAAA
1 TATAATCCTCCAAAACACACCAGCAAAA
*
2394044 TATAATCCATCCAAAACATACCAG
1 TATAATCC-TCCAAAACACACCAG
2394068 AATAGCACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
28 32 0.71
29 13 0.29
ACGTcount: A:0.45, C:0.33, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGCAAAA
Found at i:2408627 original size:42 final size:41
Alignment explanation
Indices: 2408577--2408703 Score: 136
Period size: 42 Copynumber: 3.0 Consensus size: 41
2408567 CTTCATTTTC
* *
2408577 TCGATGCCATAGTTCAACTATGGTCTTACACATC-TTCACATAA
1 TCGATGCCATAG-CCAGCTATGGTCTTACACA-CATTCACAT-A
* *
2408620 T-GATGCCATAGCCCGGCTATGGTCTTACACACATTCATATA
1 TCGATGCCATAG-CCAGCTATGGTCTTACACACATTCACATA
2408661 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCC-AGCTATGGTCTTACAC-ACATTCACATA
2408702 TC
1 TC
2408704 TCACTGATGC
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
41 13 0.18
42 58 0.79
43 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (41 bp):
TCGATGCCATAGCCAGCTATGGTCTTACACACATTCACATA
Found at i:2408763 original size:47 final size:46
Alignment explanation
Indices: 2408662--2408785 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
2408652 ATTCATATAT
* * * * * *
2408662 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
2408708 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
2408755 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
2408786 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:2408838 original size:31 final size:31
Alignment explanation
Indices: 2408803--2408982 Score: 256
Period size: 31 Copynumber: 5.8 Consensus size: 31
2408793 CTTGTCACTT
*
2408803 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
** *
2408834 GTAGCC-AGAGCTACCGTTTTTCAATGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
2408865 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
2408896 GTAGCCAGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
2408927 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2408958 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
2408983 TGTCATTTGT
Statistics
Matches: 133, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.03
31 127 0.95
32 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:2420508 original size:9 final size:9
Alignment explanation
Indices: 2420494--2420535 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
2420484 AGAGATTTAA
2420494 TTAAAATAT
1 TTAAAATAT
2420503 TTAAAAT-T
1 TTAAAATAT
*
2420511 TAAGAAATAAT
1 TTA-AAAT-AT
2420522 TTAAAATAT
1 TTAAAATAT
2420531 TTAAA
1 TTAAA
2420536 TTATGTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 3 0.11
9 18 0.64
10 4 0.14
11 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TTAAAATAT
Found at i:2422070 original size:24 final size:24
Alignment explanation
Indices: 2422042--2422101 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2422032 TTAATATATT
*
2422042 TATTT-AGTTTGAATATTAATTTGG
1 TATTTAAGTTT-AATATTAATTTAG
*
2422066 TATTTAAGTTTAATTTTAATTTAG
1 TATTTAAGTTTAATATTAATTTAG
*
2422090 TATTTGAGTTTA
1 TATTTAAGTTTA
2422102 GTATCTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (24 bp):
TATTTAAGTTTAATATTAATTTAG
Found at i:2438515 original size:10 final size:10
Alignment explanation
Indices: 2438500--2438527 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2438490 GTCTCTTTCT
2438500 TCTCTCTCCC
1 TCTCTCTCCC
2438510 TCTCTCTCCC
1 TCTCTCTCCC
2438520 TCTCTCTC
1 TCTCTCTC
2438528 TCTCCCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (10 bp):
TCTCTCTCCC
Found at i:2439740 original size:24 final size:24
Alignment explanation
Indices: 2439695--2439741 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2439685 TTTGTTTGTT
*
2439695 TAATTTTAAAATTCAGATATCAAA
1 TAATTTTAAAATTCAGAAATCAAA
*
2439719 TAATTTTAACAATT-TGAAATCAA
1 TAATTTTAA-AATTCAGAAATCAA
2439742 TCTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAATTTTAAAATTCAGAAATCAAA
Found at i:2439851 original size:21 final size:22
Alignment explanation
Indices: 2439816--2439858 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2439806 ATAACCACCT
*
2439816 AATAATTTGAATAATTTTTTTA
1 AATAATTTGAATAATTATTTTA
2439838 AATAATTT-AATAATTATTTTA
1 AATAATTTGAATAATTATTTTA
2439859 TAACTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATAATTTGAATAATTATTTTA
Found at i:2440333 original size:28 final size:28
Alignment explanation
Indices: 2440275--2440333 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
2440265 ATATGAATCG
* *
2440275 ATTATTTAATTAGTAAACGAAGTATAAA
1 ATTATTTAACTAATAAACGAAGTATAAA
2440303 ATTATTTAACTACATAAAC-AA-TATAATA
1 ATTATTTAACTA-ATAAACGAAGTATAA-A
2440331 ATT
1 ATT
2440334 TTACCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 17 0.63
29 5 0.19
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (28 bp):
ATTATTTAACTAATAAACGAAGTATAAA
Found at i:2441095 original size:16 final size:16
Alignment explanation
Indices: 2441074--2441145 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 16
2441064 TAAAATTAAA
*
2441074 AAATATATATATATTT
1 AAATATATATAAATTT
*
2441090 AAATATATTTAAATTT
1 AAATATATATAAATTT
* *
2441106 -AATAAAT-TAATAATT
1 AAATATATATAA-ATTT
*
2441121 -CATAT-TATAAATTT
1 AAATATATATAAATTT
*
2441135 AAAAATATATA
1 AAATATATATA
2441146 TGTGTAAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
14 7 0.16
15 18 0.42
16 18 0.42
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATATAAATTT
Found at i:2443136 original size:9 final size:9
Alignment explanation
Indices: 2443111--2443140 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2443101 ATCATTAGCC
2443111 TAAGTTAAT
1 TAAGTTAAT
2443120 TAAGGTTAAT
1 TAA-GTTAAT
2443130 TAAGTTAAT
1 TAAGTTAAT
2443139 TA
1 TA
2443141 TGATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:2443150 original size:19 final size:19
Alignment explanation
Indices: 2443111--2443150 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2443101 ATCATTAGCC
*
2443111 TAAGTTAATTAAGGTTAAT
1 TAAGTTAATTAAGATTAAT
* *
2443130 TAAGTTAATTATGATTTAT
1 TAAGTTAATTAAGATTAAT
2443149 TA
1 TA
2443151 TATATTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTAATTAAGATTAAT
Found at i:2443689 original size:24 final size:24
Alignment explanation
Indices: 2443660--2443707 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2443650 AATGAAAAAG
2443660 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
2443684 TTTAAGGAACATTTGAAAATTGAA
1 TTTAAGGAACATTTGAAAATTGAA
2443708 ATTGAACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTAAGGAACATTTGAAAATTGAA
Found at i:2446738 original size:19 final size:17
Alignment explanation
Indices: 2446703--2446744 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
2446693 ATTATTTTAA
2446703 TATTTATATTAGAGTAG
1 TATTTATATTAGAGTAG
*
2446720 TATTATATATTTAGTGTAG
1 TATT-TATA-TTAGAGTAG
2446739 -ATTTAT
1 TATTTAT
2446745 TTTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (17 bp):
TATTTATATTAGAGTAG
Found at i:2450604 original size:6 final size:6
Alignment explanation
Indices: 2450593--2450620 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2450583 TCCCAATATC
2450593 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
1 AGCCTT AGCCTT AGCCTT AGCCTT AGCC
2450621 ATTTCACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.29
Consensus pattern (6 bp):
AGCCTT
Found at i:2452244 original size:38 final size:38
Alignment explanation
Indices: 2452193--2452269 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2452183 CAATTCGACA
* *
2452193 ATCAATATAGTAGATTAATAGTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
2452231 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
1 ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
2452269 A
1 A
2452270 ACATACCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (38 bp):
ATCAATACAGTAGATTAATACTCATTGATAAGTAGAAG
Found at i:2459333 original size:25 final size:24
Alignment explanation
Indices: 2459281--2459339 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
2459271 TAGAATCTAT
*
2459281 TTTTTAA-AATAATTAAATTTAAC
1 TTTTTAATAAAAATTAAATTTAAC
2459304 TTTTTTAATAAAAATTAAACTATTAA-
1 -TTTTTAATAAAAATTAAA-T-TTAAC
2459330 TTTTGTAATA
1 TTTT-TAATA
2459340 CATATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 7 0.23
25 13 0.43
26 6 0.20
27 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTTTAATAAAAATTAAATTTAAC
Found at i:2459333 original size:26 final size:24
Alignment explanation
Indices: 2459279--2459339 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 24
2459269 TTTAGAATCT
*
2459279 ATTTTTTAA-AATAATTAAATTTA
1 ATTTTTTAATAAAAATTAAATTTA
2459302 ACTTTTTTAATAAAAATTAAACTATTA
1 A-TTTTTTAATAAAAATTAAA-T-TTA
*
2459329 ATTTTGTAATA
1 ATTTTTTAATA
2459340 CATATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 1 0.03
24 8 0.25
25 9 0.28
26 10 0.31
27 4 0.12
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTTTAATAAAAATTAAATTTA
Found at i:2462737 original size:2 final size:2
Alignment explanation
Indices: 2462730--2462757 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2462720 CTTATCTAAA
2462730 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2462758 ATGCCATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2465883 original size:15 final size:16
Alignment explanation
Indices: 2465854--2465899 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
2465844 TAATAAAGTC
2465854 TCATTCTTTTCATTTTA
1 TCATT-TTTTCATTTTA
2465871 TCATTTTTT-ATTTTA
1 TCATTTTTTCATTTTA
*
2465886 TTATTTTATTCATT
1 TCATTTT-TTCATT
2465900 CAAAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
16 6 0.23
17 8 0.31
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTTCATTTTA
Found at i:2469949 original size:48 final size:48
Alignment explanation
Indices: 2469888--2470007 Score: 240
Period size: 48 Copynumber: 2.5 Consensus size: 48
2469878 ATTACAAACA
2469888 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
2469936 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
1 TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
2469984 TCAATTATTTACCCTATTAACAAA
1 TCAATTATTTACCCTATTAACAAA
2470008 GCTCGGACTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (48 bp):
TCAATTATTTACCCTATTAACAAATAATCTCATTTTCAAAATTTCATT
Found at i:2471618 original size:5 final size:5
Alignment explanation
Indices: 2471608--2471635 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2471598 TATATATATA
2471608 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
2471636 CTTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:2474330 original size:31 final size:31
Alignment explanation
Indices: 2474256--2474316 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2474246 GTTAACACTC
2474256 TTAAAATTATTTTATCAAATTCAGGTTCATA
1 TTAAAATTATTTTATCAAATTCAGGTTCATA
2474287 TTAAAATTATTTTATCAAATTCAGGTTCAT
1 TTAAAATTATTTTATCAAATTCAGGTTCAT
2474317 TATAGCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (31 bp):
TTAAAATTATTTTATCAAATTCAGGTTCATA
Found at i:2476179 original size:20 final size:20
Alignment explanation
Indices: 2476154--2476195 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2476144 TACTATTAAT
2476154 ATTATTTTAATATTAATA-TA
1 ATTATTTTAA-ATTAATACTA
*
2476174 ATTATTTTTAATTAATACTA
1 ATTATTTTAAATTAATACTA
2476194 AT
1 AT
2476196 ATAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTTTAAATTAATACTA
Found at i:2476188 original size:25 final size:25
Alignment explanation
Indices: 2476160--2476218 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 25
2476150 TAATATTATT
2476160 TTAATATTAATATAAT-TATTTTTAA
1 TTAATATTAATATAATAT-TTTTTAA
*
2476185 TTAATACTAATATAATATTTTTTAA
1 TTAATATTAATATAATATTTTTTAA
2476210 TTATATATT
1 TTA-ATATT
2476219 GATTATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATATTAATATAATATTTTTTAA
Found at i:2477596 original size:150 final size:152
Alignment explanation
Indices: 2477417--2477723 Score: 476
Period size: 159 Copynumber: 2.0 Consensus size: 152
2477407 ACACATAGAT
**
2477417 TGTCACATGGATAACATGTCATCACTTAATTAATTTTTTAAATTTTAAAAAATTCAAAAAATTC-
1 TGTCACATAAATAACATGTCATCACTTAATTAATTTTTTAAATTTTAAAAAATTC-AAAAATTCA
2477481 A-AAAAA-ATATTTTTTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATGCCATCC
65 ATAAAAATATATTTTTTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATGCCATCC
2477544 ACCAAAAAATCCACATGTAAGAC
130 ACCAAAAAATCCACATGTAAGAC
2477567 TGTCACATAAATAACATGTCATCACTTAATTAATTTTTTAAATTTTAAAAAATTCAAAAATTCAA
1 TGTCACATAAATAACATGTCATCACTTAATTAATTTTTTAAATTTTAAAAAATTCAAAAATTC--
2477632 AAAAATATAAAAATATATTTTTTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATG
64 ----A-ATAAAAATATATTTTTTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATG
* * *
2477697 CCATCCACCCAACAATTCACATGTAAG
124 CCATCCACCAAAAAATCCACATGTAAG
2477724 CCACATCAAC
Statistics
Matches: 142, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
149 8 0.06
150 53 0.37
157 1 0.01
158 5 0.04
159 75 0.53
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (152 bp):
TGTCACATAAATAACATGTCATCACTTAATTAATTTTTTAAATTTTAAAAAATTCAAAAATTCAA
TAAAAATATATTTTTTATATTTTTAATATTTTAAAAGAATTAATTAAATATTAAAATGCCATCCA
CCAAAAAATCCACATGTAAGAC
Found at i:2489721 original size:14 final size:15
Alignment explanation
Indices: 2489694--2489737 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
2489684 TAATAAATTG
2489694 AAAAATAAAGTATTA
1 AAAAATAAAGTATTA
2489709 AAAAATAAA-TATTA
1 AAAAATAAAGTATTA
* *
2489723 AAAATTTAAGTATTA
1 AAAAATAAAGTATTA
2489738 GATTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AAAAATAAAGTATTA
Found at i:2493578 original size:35 final size:35
Alignment explanation
Indices: 2493551--2493716 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
2493541 CATGGCAAAG
*
2493551 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
2493586 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
2493621 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
2493661 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
2493696 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
2493717 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:2493670 original size:75 final size:75
Alignment explanation
Indices: 2493551--2493721 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
2493541 CATGGCAAAG
** *
2493551 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
2493610 CCATACTGAGC
65 CCATACCGAGC
2493621 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
2493686 CATACCGAGT
66 CATACCGAGC
**
2493696 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
2493722 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:2501069 original size:35 final size:35
Alignment explanation
Indices: 2501042--2501207 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
2501032 CATGGCAAAG
*
2501042 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
2501077 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
2501112 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
2501152 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
2501187 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
2501208 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:2501161 original size:75 final size:75
Alignment explanation
Indices: 2501042--2501212 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
2501032 CATGGCAAAG
** *
2501042 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
2501101 CCATACTGAGC
65 CCATACCGAGC
2501112 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
2501177 CATACCGAGT
66 CATACCGAGC
**
2501187 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
2501213 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:2511632 original size:46 final size:45
Alignment explanation
Indices: 2511572--2511837 Score: 339
Period size: 46 Copynumber: 6.0 Consensus size: 45
2511562 TTTGACATGA
* * * * * *
2511572 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** *
2511618 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
2511664 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
2511710 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
2511756 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
2511794 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
2511838 ATAGCACACT
Statistics
Matches: 197, Mismatches: 13, Indels: 20
0.86 0.06 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
43 1 0.01
44 3 0.02
45 4 0.02
46 149 0.76
47 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:2511801 original size:38 final size:38
Alignment explanation
Indices: 2511750--2511825 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2511740 ACATTTTATA
2511750 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2511788 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2511826 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:2513980 original size:11 final size:11
Alignment explanation
Indices: 2513964--2514015 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
2513954 TATACTAAAT
2513964 AAATAATAATA
1 AAATAATAATA
*
2513975 AAATAAT-ATT
1 AAATAATAATA
* *
2513985 AAATATCTCATA
1 AAATA-ATAATA
*
2513997 AAATATTAATA
1 AAATAATAATA
2514008 AAATAATA
1 AAATAATA
2514016 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:2518445 original size:2 final size:2
Alignment explanation
Indices: 2518440--2518471 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2518430 GTGAAAGTCG
2518440 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2518472 TCTGAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2518965 original size:39 final size:39
Alignment explanation
Indices: 2518911--2519021 Score: 186
Period size: 39 Copynumber: 2.8 Consensus size: 39
2518901 TTCAGTGATG
*
2518911 TATCCGGACTTAGGGTCCGCAGGCTATGTGTTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
*
2518950 TATCCGGACTTAGGGTCCGCAAGCTATGTGCTGGAATTA
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
* *
2518989 TATCCGGACTTAAGGTCCGCAGGCTACGTGCTG
1 TATCCGGACTTAGGGTCCGCAGGCTATGTGCTG
2519022 AAAATATGTC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (39 bp):
TATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:2519034 original size:39 final size:39
Alignment explanation
Indices: 2518911--2519099 Score: 179
Period size: 39 Copynumber: 4.9 Consensus size: 39
2518901 TTCAGTGATG
* *
2518911 TATCCGGACTTAGGGTCCGCAGGCTATGTGTTGGAATTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* *
2518950 TATCCGGACTTAGGGTCCGCAAGCTATGTGCTGGAATTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* * *
2518989 TATCCGGACTTAAGGTCCGCAGGCTACGTGCTGAAAATA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
* * * * *
2519028 TGTCCGGGC-TAAAGTCCCGCAGGCT-TCGAGCTGGTATTA
1 TATCCGGACTTAAGGT-CCGCAGGCTAT-GTGCTGGAATTA
** **
2519067 TA-CCGGGTTTAAATTTCCGCAGGCT-TGTGCTGG
1 TATCCGGACTT-AAGGTCCGCAGGCTATGTGCTGG
2519100 TATTTGGATT
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
38 16 0.13
39 107 0.85
40 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (39 bp):
TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTA
Found at i:2522069 original size:23 final size:23
Alignment explanation
Indices: 2522039--2522189 Score: 115
Period size: 21 Copynumber: 7.0 Consensus size: 23
2522029 ACTTTACTGA
*
2522039 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTGTGTGTCGTATT
* *
2522062 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTTGTGTGTCGTATT
*
2522083 TCAGGTACTTTGTGTGTC--ATT
1 TCAGGCACTTTGTGTGTCGTATT
* * *
2522104 TTAGGCATTTTATGTGTCGTATT
1 TCAGGCACTTTGTGTGTCGTATT
2522127 TCAGGCA-TCTTGTGTGTCGTA--
1 TCAGGCACT-TTGTGTGTCGTATT
* * *
2522148 TCAGGCACCTCGTGTTTCG--TT
1 TCAGGCACTTTGTGTGTCGTATT
* *
2522169 TCAAGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTGTGTGTCGTAT
2522190 ACTGATCAGG
Statistics
Matches: 99, Mismatches: 19, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 7 0.07
21 51 0.52
22 2 0.02
23 38 0.38
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTGTGTGTCGTATT
Found at i:2524795 original size:7 final size:7
Alignment explanation
Indices: 2524783--2524861 Score: 54
Period size: 7 Copynumber: 10.6 Consensus size: 7
2524773 TATATAAAAA
2524783 TATATAT
1 TATATAT
2524790 TATATAT
1 TATATAT
2524797 TATATTAACT
1 TATA-T-A-T
2524807 TA-ATAT
1 TATATAT
2524813 T-TAAGTAT
1 TAT-A-TAT
2524821 TAATATAT
1 T-ATATAT
*
2524829 AATATAT
1 TATATAT
2524836 TATATTAT
1 TATA-TAT
2524844 TATATAT
1 TATATAT
* *
2524851 AATATAA
1 TATATAT
2524858 TATA
1 TATA
2524862 ATATATAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.03
7 33 0.57
8 16 0.28
9 3 0.05
10 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:2524855 original size:20 final size:20
Alignment explanation
Indices: 2524784--2524869 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
2524774 ATATAAAAAT
* *
2524784 ATATATTATATATTATATTA
1 ATATATAATATATAATATTA
* *
2524804 A-CT-TAATATTTAAGTATTA
1 ATATATAATATATAA-TATTA
*
2524823 ATATATAATATATTATATTA
1 ATATATAATATATAATATTA
*
2524843 TTATAT-ATAATATAATA-TA
1 ATATATAAT-ATATAATATTA
2524862 ATATATAA
1 ATATATAA
2524870 AACATAAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
18 7 0.14
19 16 0.31
20 20 0.39
21 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
ATATATAATATATAATATTA
Found at i:2526070 original size:22 final size:22
Alignment explanation
Indices: 2526041--2526097 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2526031 TAGCACGTTA
2526041 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCA-ATCT
* * *
2526064 -GTGCTCTCTGTATAGCATTTT
1 AGTGCTCTCTGTTTAGCAATCT
2526085 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
2526098 CGTTTGTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCAATCT
Found at i:2528206 original size:50 final size:50
Alignment explanation
Indices: 2528131--2528456 Score: 537
Period size: 50 Copynumber: 6.5 Consensus size: 50
2528121 CCATGGCAAC
* *
2528131 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
2528181 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
2528231 AA-TGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
2528280 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
2528330 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
2528380 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
2528431 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
2528457 CTGATCAATG
Statistics
Matches: 258, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
49 48 0.19
50 187 0.72
51 23 0.09
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:2528335 original size:149 final size:151
Alignment explanation
Indices: 2528131--2528456 Score: 557
Period size: 149 Copynumber: 2.2 Consensus size: 151
2528121 CCATGGCAAC
*
2528131 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGAAAGTGATAAGTGATA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAAAGTGATAAGTGATA
*
2528196 GCTTCGGCTACACTTATCTGATCAAGGACAAATGAAA-TGATAAGTGATAGCTTCGGCTACACTT
66 GCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATAGCTTCAGCTACACTT
2528260 ATCTGATCAAAGACAAAT-GA
131 ATCTGATCAAAGACAAATGGA
* *
2528280 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGAAAGTGATAAGTGATA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAAAGTGATAAGTGATA
2528345 GCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATAGCTTCAGCTACACTT
66 GCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATAGCTTCAGCTACACTT
* *
2528410 ATCTGATCAAGGACAAATGGC
131 ATCTGATCAAAGACAAATGGA
* * *
2528431 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
2528457 CTGATCAATG
Statistics
Matches: 166, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
149 99 0.60
150 43 0.26
151 24 0.14
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (151 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAAAGTGATAAGTGATA
GCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATAGCTTCAGCTACACTT
ATCTGATCAAAGACAAATGGA
Found at i:2528474 original size:31 final size:31
Alignment explanation
Indices: 2528436--2528494 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
2528426 ATGGCAAGTA
2528436 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
2528467 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
2528495 TCGGCTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:2528502 original size:46 final size:46
Alignment explanation
Indices: 2528449--2528540 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
2528439 AGTGGTAGCT
* * *
2528449 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCAGCTACCTGATCA
* * *
2528495 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCAGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCAGCTACCTGATCA
2528541 GTGAATAGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCAGCTACCTGATCA
Found at i:2528564 original size:31 final size:31
Alignment explanation
Indices: 2528495--2528564 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
2528485 TACCTGATCA
* * *
2528495 TCGGCTACTTGATTAGTGAAAAATGGTAGCT
1 TCGGCTACCTGATCAGTGAAAAATGATAGCT
* * * *
2528526 CCAGCTACCTGATCAGTGAATAGTGATAGCT
1 TCGGCTACCTGATCAGTGAAAAATGATAGCT
2528557 TCGGCTAC
1 TCGGCTAC
2528565 AAGTGACAAG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (31 bp):
TCGGCTACCTGATCAGTGAAAAATGATAGCT
Found at i:2531953 original size:47 final size:46
Alignment explanation
Indices: 2531843--2531972 Score: 163
Period size: 46 Copynumber: 2.8 Consensus size: 46
2531833 ATAATCTCAC
* * **
2531843 CCATAATGAACTCGGAACGCAACTCAATGAGCTCGGGTGTTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAAGTTCGCAT
* * *
2531889 TCATAATGAACTTGGAACACAACTCAACGAGTTCGGAAGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAAG-TTCGCAT
*
2531935 CCATAGGTGAACTCGGAACGCAACTCAACGAGTTCGGA
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGA
2531973 TGCCTCATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
46 40 0.56
47 31 0.44
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAAGTTCGCAT
Found at i:2543191 original size:2 final size:2
Alignment explanation
Indices: 2543184--2543208 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2543174 GAAAGAACTT
2543184 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
2543209 GAAACAAATA
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:2547019 original size:7 final size:7
Alignment explanation
Indices: 2547007--2547038 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2546997 TGCTGATAGT
2547007 AAAAAAC
1 AAAAAAC
2547014 -AAAAA-
1 AAAAAAC
2547019 AAAAAAC
1 AAAAAAC
2547026 AAAAAAC
1 AAAAAAC
2547033 AAAAAA
1 AAAAAA
2547039 TTAAGACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 10 0.43
7 13 0.57
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:2547024 original size:12 final size:12
Alignment explanation
Indices: 2547007--2547037 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
2546997 TGCTGATAGT
2547007 AAAAAACAAAAA
1 AAAAAACAAAAA
2547019 AAAAAACAAAAA
1 AAAAAACAAAAA
2547031 ACAAAAA
1 A-AAAAA
2547038 ATTAAGACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:2547891 original size:18 final size:18
Alignment explanation
Indices: 2547870--2547911 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2547860 CATGCATGAC
2547870 ATGCAAAACATAATAAAA
1 ATGCAAAACATAATAAAA
* *
2547888 ATGCAGAACATAATAGAA
1 ATGCAAAACATAATAAAA
2547906 ATGCAA
1 ATGCAA
2547912 CAATTGAAGT
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:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (18 bp):
ATGCAAAACATAATAAAA
Found at i:2562149 original size:28 final size:29
Alignment explanation
Indices: 2562088--2562159 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
2562078 AAAGTATTTG
2562088 AAATTTTTTATTTAAATAATTGAACTATT
1 AAATTTTTTATTTAAATAATTGAACTATT
* *
2562117 AAATTTTTTATTTAAGTCATT-AAGCTATT
1 AAATTTTTTATTTAAATAATTGAA-CTATT
2562146 -AATTTTTT-TTTAAA
1 AAATTTTTTATTTAAA
2562160 AAAAAATCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 5 0.13
28 10 0.26
29 24 0.62
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
AAATTTTTTATTTAAATAATTGAACTATT
Found at i:2563406 original size:2 final size:2
Alignment explanation
Indices: 2563399--2563427 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2563389 TGATTCATTC
2563399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2563428 AGGTACGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2575322 original size:5 final size:5
Alignment explanation
Indices: 2575312--2575349 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
2575302 ATAGAAGATA
*
2575312 TTATT TTATT TTGTT TTA-- TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
2575350 ATTTTAGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
5 26 0.90
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:2575333 original size:18 final size:18
Alignment explanation
Indices: 2575310--2575355 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2575300 AAATAGAAGA
*
2575310 TATTATTTTATTTTGTTT
1 TATTATTTTATTTTATTT
2575328 TATTATTTTATTTTATTT
1 TATTATTTTATTTTATTT
2575346 TATTATTTTA
1 TATTATTTTA
2575356 GGATTTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
TATTATTTTATTTTATTT
Found at i:2575335 original size:13 final size:13
Alignment explanation
Indices: 2575317--2575355 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2575307 AGATATTATT
*
2575317 TTATTTTGTTTTA
1 TTATTTTATTTTA
2575330 TTATTTTATTTTA
1 TTATTTTATTTTA
2575343 TT-TTATTATTTTA
1 TTATT-TTATTTTA
2575356 GGATTTAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 2 0.08
13 22 0.92
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:2594413 original size:59 final size:59
Alignment explanation
Indices: 2594344--2594462 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
2594334 AAACGCAACA
*
2594344 TATACTTATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
*
2594403 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTGCCTTTCAATTTTTCTATAGT
1 TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
2594462 T
1 T
2594463 TTACTCTCAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.54
Consensus pattern (59 bp):
TATACATATTCCATTACTTCAATTCCTTTATTTTATCTACCTTTCAATTTTTCTATAGT
Found at i:2610902 original size:39 final size:39
Alignment explanation
Indices: 2610848--2610922 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
2610838 GGCATGTTCA
2610848 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
*
2610887 TTCAAGGTCAACATTTTTACTCTCTTCTCAATTTAA
1 TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAA
2610923 CATTCTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (39 bp):
TTCAAGGTCAACATTTTTACTCTCCTCTCAATTTAATAT
Found at i:2616766 original size:12 final size:13
Alignment explanation
Indices: 2616749--2616778 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2616739 AAGATGTAAT
2616749 AAAATA-TTAAAA
1 AAAATATTTAAAA
2616761 AAAATATTTAAAA
1 AAAATATTTAAAA
2616774 AAAAT
1 AAAAT
2616779 TGTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATATTTAAAA
Found at i:2635197 original size:2 final size:2
Alignment explanation
Indices: 2635181--2635218 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2635171 TATGAATAAA
*
2635181 AT AT A- AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2635219 AAAGAATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2636447 original size:17 final size:17
Alignment explanation
Indices: 2636407--2636450 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2636397 ATTATGAGCC
*
2636407 TAAAAAAAACTAAATAG
1 TAAAAAATACTAAATAG
* *
2636424 TATAAAAATACTTATTAG
1 TA-AAAAATACTAAATAG
2636442 TAAAAAATA
1 TAAAAAATA
2636451 ATAATATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
TAAAAAATACTAAATAG
Found at i:2638676 original size:2 final size:2
Alignment explanation
Indices: 2638669--2638697 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2638659 GAGACTAGTC
2638669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2638698 CATGTCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2641823 original size:135 final size:134
Alignment explanation
Indices: 2641601--2641844 Score: 353
Period size: 135 Copynumber: 1.8 Consensus size: 134
2641591 TGTCGATCCA
* * * * * *
2641601 TGGAGATAAGATTCACCGAAATTTGGTCGCTCCGCTCCTGCTCAGCGAAGATAAGACCTGGTATA
1 TGGAGATAAGATTCACCAAAATTTGATCGCTCCACTCCTACTCAACGAAGATAAGACCGGGTATA
*
2641666 TTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAACTGATGATTGGAATCTGTTTAATCGCCGG
66 TTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAAACTGATGATTGGAATCTGTTTAATCGCCGG
2641731 TACG
131 TACG
* * * *
2641735 TGGAGATAAGATTCTCCAAAATTTGATCTGCTTCACTCCTACTCAATGAAGATAAGATCGGGTAT
1 TGGAGATAAGATTCACCAAAATTTGATC-GCTCCACTCCTACTCAACGAAGATAAGACCGGGTAT
* **
2641800 GTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
65 ATTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAAACTGATGAT
2641845 ATCTGTCTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
134 25 0.26
135 70 0.74
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (134 bp):
TGGAGATAAGATTCACCAAAATTTGATCGCTCCACTCCTACTCAACGAAGATAAGACCGGGTATA
TTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAAACTGATGATTGGAATCTGTTTAATCGCCGG
TACG
Found at i:2646330 original size:35 final size:35
Alignment explanation
Indices: 2646286--2646452 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
2646276 TCCTCATTGA
** *
2646286 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
2646321 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2646361 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2646396 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2646431 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2646453 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2646369 original size:75 final size:73
Alignment explanation
Indices: 2646281--2646452 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
2646271 GGTTTTCCTC
** * * **
2646281 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
2646345 TCAGTATGG
65 TCAGTATGG
*
2646354 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2646419 CTCAGTATGG
64 CTCAGTATGG
2646429 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2646453 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2650733 original size:46 final size:46
Alignment explanation
Indices: 2650666--2650838 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
2650656 TGTAACCCGC
*
2650666 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
2650712 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
2650762 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC--TCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
2650803 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
2650839 ATGCCCAAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 29 0.26
46 35 0.32
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:2650831 original size:91 final size:92
Alignment explanation
Indices: 2650674--2650843 Score: 306
Period size: 91 Copynumber: 1.8 Consensus size: 92
2650664 GCCCATAAGT
*
2650674 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACG-TCGCATCCATAAGTGAACTCGGACTCAACTCAA
2650739 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
*
2650767 GAACTCGGACTCAACTCAACGAGTTCGGAC-TCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
2650831 GAGTTCGGATGCC
66 GAGTTCGGATGCC
2650844 CAAATATCCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 47 0.63
93 28 0.37
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2653266 original size:30 final size:30
Alignment explanation
Indices: 2653222--2653310 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
2653212 CAAAGATAAC
2653222 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
2653251 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
2653281 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
2653311 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:2653270 original size:15 final size:15
Alignment explanation
Indices: 2653222--2653301 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
2653212 CAAAGATAAC
*
2653222 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
2653236 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
2653251 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
2653266 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
2653281 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
2653296 AAGAAA
1 AAGAAA
2653302 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:2653310 original size:15 final size:15
Alignment explanation
Indices: 2653233--2653310 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
2653223 AGAAAACCGA
2653233 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
2653248 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
2653262 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
2653277 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
2653293 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
2653308 ATA
1 ATA
2653311 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:2656372 original size:93 final size:93
Alignment explanation
Indices: 2656260--2656431 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
2656250 GCCCATAAGT
* *
2656260 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2656325 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
2656353 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2656418 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
2656432 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2656427 original size:46 final size:46
Alignment explanation
Indices: 2656252--2656427 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
2656242 TGTAACCCGC
* * *
2656252 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
2656298 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
2656348 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
2656391 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2656428 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:2662197 original size:35 final size:35
Alignment explanation
Indices: 2662153--2662319 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
2662143 TCCTCATTGA
** *
2662153 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
2662188 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2662228 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2662263 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2662298 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2662320 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2662236 original size:75 final size:73
Alignment explanation
Indices: 2662148--2662319 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
2662138 GGTTTTCCTC
** * * **
2662148 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
2662212 TCAGTATGG
65 TCAGTATGG
*
2662221 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2662286 CTCAGTATGG
64 CTCAGTATGG
2662296 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2662320 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2668157 original size:21 final size:21
Alignment explanation
Indices: 2668133--2668177 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2668123 GCTGGCTCAT
*
2668133 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
* *
2668154 CATGTTTTTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCCAG
2668175 CAT
1 CAT
2668178 TTGATCATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:2682514 original size:113 final size:113
Alignment explanation
Indices: 2682311--2682536 Score: 434
Period size: 113 Copynumber: 2.0 Consensus size: 113
2682301 CGGAACGCCC
2682311 CACTTTTTACTTAAGAGTTAACTTTTTTTATTTTCTTTAATTTTTTTATTTACTAATCCTTACTA
1 CACTTTTTACTTAAGAGTTAACTTTTTTTATTTTCTTTAATTTTTTTATTTACTAATCCTTACTA
* *
2682376 ATGCCATAAAATATAAGCTATTGAAACGAGAACATTTCGTTAGGGTTT
66 ATGCCATAAAATATAAGCCACTGAAACGAGAACATTTCGTTAGGGTTT
2682424 CACTTTTTACTTAAGAGTTAACTTTTTTTATTTTCTTTAATTTTTTTATTTACTAATCCTTACTA
1 CACTTTTTACTTAAGAGTTAACTTTTTTTATTTTCTTTAATTTTTTTATTTACTAATCCTTACTA
2682489 ATGCCATAAAATATAAGCCACTGAAACGAGAACATTTCGTTAGGGTTT
66 ATGCCATAAAATATAAGCCACTGAAACGAGAACATTTCGTTAGGGTTT
2682537 AGCCGTGGCT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (113 bp):
CACTTTTTACTTAAGAGTTAACTTTTTTTATTTTCTTTAATTTTTTTATTTACTAATCCTTACTA
ATGCCATAAAATATAAGCCACTGAAACGAGAACATTTCGTTAGGGTTT
Found at i:2689248 original size:27 final size:28
Alignment explanation
Indices: 2689218--2689284 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
2689208 AATTCACATA
*
2689218 TTCA-CCATATTCATAATTT-AATTTATT
1 TTCATCCA-ATTCATAATTTCAATTCATT
* *
2689245 TTCATTCAATTCATATTTTCAATTCATTT
1 TTCATCCAATTCATAATTTCAATTCA-TT
*
2689274 TTCAACCAATT
1 TTCATCCAATT
2689285 TCAAATCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 14 0.44
28 7 0.22
29 11 0.34
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (28 bp):
TTCATCCAATTCATAATTTCAATTCATT
Found at i:2689277 original size:12 final size:13
Alignment explanation
Indices: 2689249--2689278 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2689239 TTTATTTTCA
2689249 TTCAATTCATATT
1 TTCAATTCATATT
2689262 TTCAATTCAT-TT
1 TTCAATTCATATT
2689274 TTCAA
1 TTCAA
2689279 CCAATTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
TTCAATTCATATT
Found at i:2690220 original size:3 final size:3
Alignment explanation
Indices: 2690212--2690256 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2690202 TTATATATAT
2690212 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2690257 TTTAATTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2690403 original size:3 final size:3
Alignment explanation
Indices: 2690395--2690465 Score: 62
Period size: 3 Copynumber: 25.0 Consensus size: 3
2690385 TAATTTATTT
* * *
2690395 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA T-T TAA TAA T-T TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2690440 TAA -AA CT-A TAA TAA TAA TTA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA
2690466 ATATCTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
2 7 0.13
3 47 0.87
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2691393 original size:51 final size:51
Alignment explanation
Indices: 2691329--2691464 Score: 155
Period size: 51 Copynumber: 2.7 Consensus size: 51
2691319 TGGAAACATG
*
2691329 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * ** * * ** *
2691380 ATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGTA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* *
2691431 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAATCTTAGAGAT
2691465 TTGATGGTAG
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:2693435 original size:96 final size:96
Alignment explanation
Indices: 2693147--2693436 Score: 463
Period size: 96 Copynumber: 3.0 Consensus size: 96
2693137 GTGTCCGAGG
* * * * * *
2693147 AAGTCTGTTATCGATGGGAATGATCGAGCAGATACGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
* * *
2693212 AAAAGCCGAAGCCAAGAGGGCAAAAAGGAAC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
2693243 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
2693308 TAAAGCCGAAGCCAAGAGGGCAAAGAAGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
* *
2693339 AAGTCTGTCATCGAAGGGAACAATGGAGCAGACAAGGAGCCCAAAAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
2693404 TAAAGCCGAAGCCAAGAGGGCTAAGAGGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
2693435 AA
1 AA
2693437 AAAGAAGCGA
Statistics
Matches: 180, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 180 1.00
ACGTcount: A:0.37, C:0.18, G:0.33, T:0.12
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
Found at i:2694407 original size:51 final size:51
Alignment explanation
Indices: 2694343--2694478 Score: 155
Period size: 51 Copynumber: 2.7 Consensus size: 51
2694333 TGGAAACATG
*
2694343 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * ** * * ** *
2694394 ATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGTA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* *
2694445 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAATCTTAGAGAT
2694479 TTGATGGTAG
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:2695171 original size:27 final size:27
Alignment explanation
Indices: 2695133--2695186 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2695123 GTACTAAATG
2695133 TTAGCCATCTATTTGAAGGGATTTGAT
1 TTAGCCATCTATTTGAAGGGATTTGAT
2695160 TTAGCCATCTATTTGAAGGGATTTGAT
1 TTAGCCATCTATTTGAAGGGATTTGAT
2695187 CTATAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (27 bp):
TTAGCCATCTATTTGAAGGGATTTGAT
Found at i:2701518 original size:19 final size:20
Alignment explanation
Indices: 2701478--2701527 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2701468 CTTTATGTAA
2701478 TTAAAATAAATTATATTATT
1 TTAAAATAAATTATATTATT
*
2701498 TTAAAATAATTTAATATT-TT
1 TTAAAATAAATT-ATATTATT
*
2701518 TAAAAATAAA
1 TTAAAATAAA
2701528 ATTTGAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAATAAATTATATTATT
Found at i:2701651 original size:38 final size:38
Alignment explanation
Indices: 2701609--2701686 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
2701599 TATTTTTTAT
2701609 TTTTTATTGTAATATATATAATTTATTATCTTTATCAA
1 TTTTTATTGTAATATATATAATTTATTATCTTTATCAA
* * * *
2701647 TTTTTATTGTATTATGTATAATTTATTGTCTTTATTAA
1 TTTTTATTGTAATATATATAATTTATTATCTTTATCAA
2701685 TT
1 TT
2701687 GTAGATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (38 bp):
TTTTTATTGTAATATATATAATTTATTATCTTTATCAA
Found at i:2702458 original size:29 final size:28
Alignment explanation
Indices: 2702393--2702460 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
2702383 CTTTTCACAA
2702393 ATTTAAAATTTAATATTTGTACTTTTAT
1 ATTTAAAATTTAATATTTGTACTTTTAT
* *
2702421 -TTATAAAAATTTAATATTTTTATTTTTAT
1 ATT-T-AAAATTTAATATTTGTACTTTTAT
2702450 ATTTCAAAATT
1 ATTT-AAAATT
2702461 CATATTCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 29 0.85
30 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTAAAATTTAATATTTGTACTTTTAT
Found at i:2702667 original size:12 final size:12
Alignment explanation
Indices: 2702652--2702678 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2702642 CTTAAATTTC
2702652 TAAATATATATA
1 TAAATATATATA
2702664 TAAATATATATA
1 TAAATATATATA
2702676 TAA
1 TAA
2702679 GAACTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATATATATA
Found at i:2704136 original size:193 final size:193
Alignment explanation
Indices: 2703885--2704261 Score: 567
Period size: 193 Copynumber: 2.0 Consensus size: 193
2703875 CCGAATAAAA
* * ** *
2703885 AAAGAGAAAACTACATCGTTTTGATAAATTTTTGCTTTTTCTAAAGTTAAAAGTCAAAATCATTA
1 AAAGACAAAACTACATCATTTTGATAAATTTTAACTTTTTCTAAAGTTAAAAGTCAAAACCATTA
* * * *
2703950 AGTTAAAAGATAAAATTATATTGTTTTGATAAATATTTACTCATTAAATTAAAAAATAAAATAAT
66 AGTTAAAAGACAAAATTACATCGTTTTAATAAATATTTACTCATTAAATTAAAAAATAAAATAAT
* * * *
2704015 TATATTATTTATATAGTTAAATAATCTTATACTTTGTTTACTAATTAAATAATCGATCTATGT
131 TATATTATTTATATAGTTAAACAATATTAGACTTCGTTTACTAATTAAATAATCGATCTATGT
* * *
2704078 AAAGACAAAAGTACGTCATTTTGATAAATATTTAAC-TTTTCTAATGTTAAAAGTCAAAACCATT
1 AAAGACAAAACTACATCATTTTGATAAAT-TTTAACTTTTTCTAAAGTTAAAAGTCAAAACCATT
*
2704142 AAGTTAAAAGACAAAATTACATCGTTTTAATAAATATTTACTCATTAAATTAAAAGATAAAATAA
65 AAGTTAAAAGACAAAATTACATCGTTTTAATAAATATTTACTCATTAAATTAAAAAATAAAATAA
* *
2704207 TTATATTATTTATGTAGTTAAACAATATTGGACTTCGTTTACTAATTAAATAATC
130 TTATATTATTTATATAGTTAAACAATATTAGACTTCGTTTACTAATTAAATAATC
2704262 AGTCCATGTA
Statistics
Matches: 164, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
193 160 0.98
194 4 0.02
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (193 bp):
AAAGACAAAACTACATCATTTTGATAAATTTTAACTTTTTCTAAAGTTAAAAGTCAAAACCATTA
AGTTAAAAGACAAAATTACATCGTTTTAATAAATATTTACTCATTAAATTAAAAAATAAAATAAT
TATATTATTTATATAGTTAAACAATATTAGACTTCGTTTACTAATTAAATAATCGATCTATGT
Found at i:2709043 original size:21 final size:19
Alignment explanation
Indices: 2709002--2709039 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2708992 TTTTGATAAA
*
2709002 TTTTTTATGTGATAGTTAT
1 TTTTTTAAGTGATAGTTAT
*
2709021 TTTTTTAAGTGATATTTAT
1 TTTTTTAAGTGATAGTTAT
2709040 ATTTAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (19 bp):
TTTTTTAAGTGATAGTTAT
Found at i:2709225 original size:21 final size:22
Alignment explanation
Indices: 2709182--2709227 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2709172 ATTAAAATAC
2709182 ATTTAATGTTGGTTATGAATTT
1 ATTTAATGTTGGTTATGAATTT
*
2709204 ATTTAATTTTGTGTT-T-AATTT
1 ATTTAATGTTG-GTTATGAATTT
2709225 ATT
1 ATT
2709228 AAATATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (22 bp):
ATTTAATGTTGGTTATGAATTT
Found at i:2711150 original size:17 final size:18
Alignment explanation
Indices: 2711128--2711165 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2711118 ATTTTATACC
2711128 AAATTTAAAT-TAT-AAAT
1 AAATTT-AATCTATAAAAT
2711145 AAATTTAATCTATAAAAT
1 AAATTTAATCTATAAAAT
2711163 AAA
1 AAA
2711166 AGATATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTAATCTATAAAAT
Found at i:2719346 original size:2 final size:2
Alignment explanation
Indices: 2719339--2719369 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2719329 ATTCATCTAC
2719339 TA TA TA 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 TA TA TA T
2719370 TCATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2720727 original size:23 final size:23
Alignment explanation
Indices: 2720695--2720738 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2720685 AATACTATTT
2720695 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2720718 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2720739 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2720731 original size:13 final size:11
Alignment explanation
Indices: 2720699--2720741 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2720689 CTATTTTCTA
*
2720699 AATAAAATAAT
1 AATAAAATATT
2720710 AAT-AAATATCT
1 AATAAAATAT-T
2720721 AAGTAAAATATT
1 AA-TAAAATATT
2720733 AATAAAATA
1 AATAAAATA
2720742 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2724235 original size:2 final size:2
Alignment explanation
Indices: 2724228--2724262 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2724218 AAATTTCTTC
2724228 TA TA TA TA TA 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 TA TA TA TA TA T
2724263 CGTTACTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2728321 original size:26 final size:26
Alignment explanation
Indices: 2728284--2728343 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 26
2728274 TTTTGTAGTG
2728284 TAATAAATAATTTTTCTAT-TTAA-ATT
1 TAAT-AATAATTTTT-TATATTAATATT
2728310 TAATAATGAATTTTTTATATTAATATT
1 TAATAAT-AATTTTTTATATTAATATT
2728337 TATATAA
1 TA-ATAA
2728344 CTTTTGAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.20
26 15 0.50
27 5 0.17
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
TAATAATAATTTTTTATATTAATATT
Found at i:2735979 original size:18 final size:17
Alignment explanation
Indices: 2735956--2736037 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
2735946 CATTATTTTT
2735956 AAATTTAAATAATTAAAA
1 AAATTTAAATAA-TAAAA
2735974 AAATTTAAA-AATTTAGAAA
1 AAATTTAAATAA--TA-AAA
* *
2735993 ATATTTAATTAATAAAA
1 AAATTTAAATAATAAAA
* *
2736010 ATAA-TTAGATAATAATA
1 A-AATTTAAATAATAAAA
*
2736027 AATTTTAAATA
1 AAATTTAAATA
2736038 TATATATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
16 1 0.02
17 23 0.45
18 15 0.29
19 10 0.20
20 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTAAATAATAAAA
Found at i:2736126 original size:17 final size:18
Alignment explanation
Indices: 2736106--2736140 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2736096 ATCATAAATC
2736106 AATCATAATTA-TCTTTT
1 AATCATAATTACTCTTTT
2736123 AATCATAATTACTCTTTT
1 AATCATAATTACTCTTTT
2736141 GTAACTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
AATCATAATTACTCTTTT
Found at i:2739767 original size:5 final size:5
Alignment explanation
Indices: 2739757--2739781 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2739747 TAGTAAATTA
2739757 CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CCTTC CCTTC CCTTC
2739782 GCACAACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTTC
Found at i:2739817 original size:5 final size:5
Alignment explanation
Indices: 2739809--2739836 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2739799 TTTATACTGT
2739809 ACCAA ACCAA ACCAA ACCAA ACCAA ACC
1 ACCAA ACCAA ACCAA ACCAA ACCAA ACC
2739837 GAAGGGGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCAA
Found at i:2745244 original size:15 final size:15
Alignment explanation
Indices: 2745224--2745264 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
2745214 CGTGACATAA
2745224 TTTAAAAATAAAAAT
1 TTTAAAAATAAAAAT
*
2745239 TTTAAAAAATAAATAT
1 TTT-AAAAATAAAAAT
*
2745255 TGTAAAAATA
1 TTTAAAAATA
2745265 GATTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
TTTAAAAATAAAAAT
Found at i:2745300 original size:16 final size:16
Alignment explanation
Indices: 2745267--2745310 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2745257 TAAAAATAGA
2745267 TTTAAAAATCTTGATTT
1 TTTAAAAAT-TTGATTT
**
2745284 TTTAAAAATTTTTTTT
1 TTTAAAAATTTGATTT
2745300 TTTAAAGAATT
1 TTTAAA-AATT
2745311 CATAAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTAAAAATTTGATTT
Found at i:2750565 original size:21 final size:21
Alignment explanation
Indices: 2750539--2750579 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2750529 ATCTGCTCAA
* *
2750539 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2750560 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2750580 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2753477 original size:15 final size:15
Alignment explanation
Indices: 2753429--2753482 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2753419 AAAGTAAAAC
2753429 AAAAGAAAAAGAAATG
1 AAAAGAAAAAG-AATG
*
2753445 AAAAAAAAAAG-ATAG
1 AAAAGAAAAAGAAT-G
*
2753460 AAAAGAAACAGAATG
1 AAAAGAAAAAGAATG
*
2753475 AAACGAAA
1 AAAAGAAA
2753483 CAGAGAGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 2 0.06
15 18 0.56
16 12 0.38
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (15 bp):
AAAAGAAAAAGAATG
Found at i:2755308 original size:18 final size:18
Alignment explanation
Indices: 2755287--2755471 Score: 162
Period size: 18 Copynumber: 10.3 Consensus size: 18
2755277 TAACTGATTA
*
2755287 TTACTGAATAATTAACTG
1 TTACTGAATAATTGACTG
*
2755305 TTACCGAATAATTGACTG
1 TTACTGAATAATTGACTG
2755323 TTACTGAAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * * * *
2755341 TTATTGAATAACTAAATA
1 TTACTGAATAATTGACTG
*
2755359 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
2755377 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
2755395 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
2755413 TTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
** *
2755432 TTACTGAATACCTGA-TT
1 TTACTGAATAATTGACTG
2755449 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
2755467 TTACT
1 TTACT
2755472 AGATAACCGA
Statistics
Matches: 134, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
17 20 0.15
18 95 0.71
19 19 0.14
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:2755520 original size:18 final size:18
Alignment explanation
Indices: 2755497--2755557 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
2755487 TGATCGAGAC
*
2755497 TGAATAACTGGTTATTAT
1 TGAATAACTGATTATTAT
* *
2755515 TGAATAATTGATTGTTAT
1 TGAATAACTGATTATTAT
* * * *
2755533 CGAATAACTGACTGTTAC
1 TGAATAACTGATTATTAT
2755551 TGAATAA
1 TGAATAA
2755558 ATAATTATTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (18 bp):
TGAATAACTGATTATTAT
Found at i:2755555 original size:36 final size:36
Alignment explanation
Indices: 2755275--2755557 Score: 187
Period size: 36 Copynumber: 7.6 Consensus size: 36
2755265 AAAGGTATAA
* * * *
2755275 AATAACTGATTATTACTGAATAATTAACTGTTACCG
1 AATAACTGATTGTTACTGAATAATTGATTGTTACTG
* * * *
2755311 AATAATTGACTGTTACTGAAT-ATTAGACTGTTATTG
1 AATAACTGATTGTTACTGAATAATT-GATTGTTACTG
* * * **
2755347 AATAACTAAATATTACTGAATAATTGATCATTACTG
1 AATAACTGATTGTTACTGAATAATTGATTGTTACTG
* *
2755383 AATAACTGATTGTCACTGAATGAA-TGACTGTTACTG
1 AATAACTGATTGTTACTGAAT-AATTGATTGTTACTG
* **
2755419 AATAACTTAATTGTTACTGAATACCTGATT-TTACTG
1 AATAAC-TGATTGTTACTGAATAATTGATTGTTACTG
* * * **
2755455 AATAATTGACTGTTACTAGATAACCGATCAATTGATCGAGACTG
1 AATAACTGATTGTTACT-G---A---AT-AATTGATTGTTACTG
* * *
2755499 AATAACTGGTTATTATTGAATAATTGATTGTTA-TCG
1 AATAACTGATTGTTACTGAATAATTGATTGTTACT-G
*
2755535 AATAACTGACTGTTACTGAATAA
1 AATAACTGATTGTTACTGAATAA
2755558 ATAATTATTC
Statistics
Matches: 187, Mismatches: 45, Indels: 30
0.71 0.17 0.11
Matches are distributed among these distances:
35 13 0.07
36 124 0.66
37 24 0.13
39 1 0.01
40 1 0.01
42 2 0.01
43 6 0.03
44 16 0.09
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (36 bp):
AATAACTGATTGTTACTGAATAATTGATTGTTACTG
Found at i:2757442 original size:21 final size:21
Alignment explanation
Indices: 2757396--2757442 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2757386 ATTTAATATT
* *
2757396 TATAATATATTATTATAATAA
1 TATAATATAATATTAAAATAA
2757417 TATAATATAATATTTAAAATAA
1 TATAATATAATA-TTAAAATAA
2757439 -ATAA
1 TATAA
2757443 AAGAAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAATATAATATTAAAATAA
Done.