Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 54
Found at i:5487079 original size:48 final size:47
Alignment explanation
Indices: 5487017--5487118 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 47
5487007 TTTAAAAACT
*
5487017 TATATATTATATATATATTTCAAAAACGTTTTAAAAATTATATAATA
1 TATATATTATATATATATTTCAAAAACGTTTTAAAAACTATATAATA
* ** *
5487064 TATATATATATATATATGTTTTTAAAATGTTTTAAAAACTATATAATA
1 TATATAT-TATATATATATTTCAAAAACGTTTTAAAAACTATATAATA
5487112 TATATAT
1 TATATAT
5487119 GTTTTCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 7 0.14
48 42 0.86
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (47 bp):
TATATATTATATATATATTTCAAAAACGTTTTAAAAACTATATAATA
Found at i:5488179 original size:81 final size:80
Alignment explanation
Indices: 5488028--5488323 Score: 396
Period size: 80 Copynumber: 3.7 Consensus size: 80
5488018 AATTTATTGA
* * * * *
5488028 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCT-TCGGGCTGAGTGGAATCAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCT-GAGCTGAGTGGAATCAA
*
5488092 ACTCGAAGGTCTTTTG
65 ACTCGAAGGTCTTTGG
* * * *
5488108 TAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGGTGCATTTGAGCTGAGTGGAATCAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT-GTGCCTCTGAGCTGAGTGGAATCAA
5488173 ACTCGAAGGTCTTTGG
65 ACTCGAAGGTCTTTGG
* * * * * *
5488189 CAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGGAATCAAA
5488254 CTCGAAGGTCTTTGG
66 CTCGAAGGTCTTTGG
* *
5488269 CAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATGGTGCCTCTGAGCTGA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT-GTGCCTCTGAGCTGA
5488324 ACGTGGTCAA
Statistics
Matches: 191, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
80 104 0.54
81 86 0.45
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (80 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGGAATCAAA
CTCGAAGGTCTTTGG
Found at i:5488219 original size:161 final size:161
Alignment explanation
Indices: 5488028--5488323 Score: 450
Period size: 161 Copynumber: 1.8 Consensus size: 161
5488018 AATTTATTGA
* * *
5488028 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCT-TCGGGCTGAGTGGAATCAA
1 CAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATAATGTGCCTCT-GAGCTGAGTGGAATCAA
* * * * *
5488092 ACTCGAAGGTCTTTTGTAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGGTGCATTTG
65 ACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGGTGCATCTG
5488157 AGCTGAGTGGAATCAAACTCGAAGGTCTTTGG
130 AGCTGAGTGGAATCAAACTCGAAGGTCTTTGG
* * * *
5488189 CAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATAATGTGCCTCTGAGCTGAGTGGAATCAAA
* *
5488254 CTCGAAGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATACTGCAAATGATGGTGCCTCTGA
66 CTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGGTGCATCTGA
5488319 GCTGA
131 GCTGA
5488324 ACGTGGTCAA
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
161 119 0.99
162 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (161 bp):
CAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATAATGTGCCTCTGAGCTGAGTGGAATCAAA
CTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGGTGCATCTGA
GCTGAGTGGAATCAAACTCGAAGGTCTTTGG
Found at i:5488600 original size:84 final size:84
Alignment explanation
Indices: 5488357--5488914 Score: 484
Period size: 84 Copynumber: 6.7 Consensus size: 84
5488347 TTGTTAGCAT
* * * **
5488357 AACTCGAAGTTATTTGTTGACAGATAACCCTTCTAGCCTTCAGTTATGCTATAAATGATGTGTCC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCC
* * *
5488422 TCAAAGTTGAGTGTAATCG
66 TCGAAGCTGAGCGTAATCG
* * * ** * * * * *
5488441 AACTCGAGGGTCTTTTGATGGTAGATAGCCCTTTTCGACTTAAGCTATGCTGCAAATGATGT-CC
1 AACTCGAAGGT-ATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTC
* *
5488505 CTTTG-AGCTGAGCGTAGTCG
65 C-TCGAAGCTGAGCGTAATCG
* * * * *
5488525 AACTCGAAGGTAATTGTTGACAGATAACCCTTCTAGGCTTGAGTTATGCTGTAAATAATGTGTCC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCC
*
5488590 TCGAAGCTGAGTGTAATCG
66 TCGAAGCTGAGCGTAATCG
* * * * * *
5488609 AACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-C
1 AACTCGAAGGT-ATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTC
* * * *
5488673 ATTTG-AGCTAAGCGTAGTCG
65 -CTCGAAGCTGAGCGTAATCG
* * * * * *
5488693 AACTCGAAGGTGTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGAAAATGATGTGTCC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCC
* * *
5488758 TCGAAGCTAAGTGTAATCA
66 TCGAAGCTGAGCGTAATCG
* * * *
5488777 AACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCC
* * *
5488838 TTGGAGCTGAGCGTAGTCG
66 TCGAAGCTGAGCGTAATCG
* * * * * * *
5488857 AACTTGAAGGTCTTTGGTTGGCAAATAGCCCTTCTCGATTTAAGTTATGCTGCAAATG
1 AACTCGAAGGTATTT-GTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
5488915 TTTCTTTTAA
Statistics
Matches: 373, Mismatches: 89, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
80 28 0.08
81 37 0.10
82 1 0.00
83 82 0.22
84 144 0.39
85 81 0.22
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (84 bp):
AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGTCC
TCGAAGCTGAGCGTAATCG
Found at i:5488637 original size:168 final size:168
Alignment explanation
Indices: 5488357--5488914 Score: 791
Period size: 168 Copynumber: 3.3 Consensus size: 168
5488347 TTGTTAGCAT
* * *
5488357 AACTCGAAGTTATTTGTTGACAGATAACCCTTCTAGCCTTCAGTTATGCTATAAATGATGTGTCC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCC
* * * *
5488422 TCAAAGTTGAGTGTAATCGAACTCGAGGGTCTTTTGATGGTAGATAGCCCTTTTCGACTTAAGCT
66 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAGCT
*
5488487 ATGCTGCAAATGATGTCCCTTTGAGCTGAGCGTAGTCG
131 ATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCG
* * *
5488525 AACTCGAAGGTAATTGTTGACAGATAACCCTTCTAGGCTTGAGTTATGCTGTAAATAATGTGTCC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCC
*
5488590 TCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAGCT
66 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAGCT
* *
5488655 ATGCTGCAAATGATGTGCATTTGAGCTAAGCGTAGTCG
131 ATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCG
* * * *
5488693 AACTCGAAGGTGTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGAAAATGATGTGTCC
1 AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCC
* * *
5488758 TCGAAGCTAAGTGTAATCAAACTCGAGGGTC--TT--TGGCAGATAGCCCTTCTCGACTTAAGTT
66 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAGCT
*
5488819 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
131 ATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCG
* * * * * * ** * *
5488857 AACTTGAAGGTCTTTGGTTGGCAAATAGCCCTTCTCGATTTAAGTTATGCTGCAAATG
1 AACTCGAAGGTATTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
5488915 TTTCTTTTAA
Statistics
Matches: 349, Mismatches: 40, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
164 75 0.21
165 32 0.09
166 2 0.01
168 240 0.69
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (168 bp):
AACTCGAAGGTATTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCC
TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAGCT
ATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCG
Found at i:5490206 original size:90 final size:90
Alignment explanation
Indices: 5490097--5490264 Score: 264
Period size: 90 Copynumber: 1.9 Consensus size: 90
5490087 TTGTATAGAT
* * * *
5490097 ATTATAATCGCCTTTATCAGGCTAGCTGAATATTATCTATAAAACCGGGGCGTTTAACCAATTGC
1 ATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACAGGGGCGTTTAACCAATTGA
5490162 TCTAGAGGGACAAGCTTTATTGTAC
66 TCTAGAGGGACAAGCTTTATTGTAC
* * *
5490187 ATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCAGGGGTGTTTAACCAATTGA
1 ATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACAGGGGCGTTTAACCAATTGA
*
5490252 TTTAGAGGGACAA
66 TCTAGAGGGACAA
5490265 CTCAAGCTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (90 bp):
ATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACAGGGGCGTTTAACCAATTGA
TCTAGAGGGACAAGCTTTATTGTAC
Found at i:5496235 original size:38 final size:38
Alignment explanation
Indices: 5496111--5496240 Score: 170
Period size: 38 Copynumber: 3.4 Consensus size: 38
5496101 CGAGTCAAAT
* * *
5496111 ATATGCACCGTAGTGCTTACACATAAAGTCGTGTCCACC
1 ATATGCACCGAAGTGC-TACACATAAGGTCGTGCCCACC
** *
5496150 ATATGCACAAAAGTGCTATACATAAGGTCGTGCCCACC
1 ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
* *
5496188 ATATGCACCGAAGTGCTACACATAAGGCCATGCCCACC
1 ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
*
5496226 ATATACACCGAAGTG
1 ATATGCACCGAAGTG
5496241 TTTAATTGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 66 0.84
39 13 0.16
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (38 bp):
ATATGCACCGAAGTGCTACACATAAGGTCGTGCCCACC
Found at i:5501551 original size:38 final size:38
Alignment explanation
Indices: 5501482--5501763 Score: 260
Period size: 38 Copynumber: 7.2 Consensus size: 38
5501472 TATACGTCGT
* * * *
5501482 AGTGCTTACAAATAAGGTAGTGCCCAACATATGTACCGA
1 AGTGC-TACACATAAGGTCGTGCCCACCATATGCACCGA
* *
5501521 AGCGCTACACATAAGGTCGTTCCCACCATATGCACCGA
1 AGTGCTACACATAAGGTCGTGCCCACCATATGCACCGA
* * * *
5501559 AGGGCTCCATATAAGGTCGTGCCCGCCATATGCACCGA
1 AGTGCTACACATAAGGTCGTGCCCACCATATGCACCGA
* * *
5501597 AGGGCTCCACATAAGGGCGTGCCCGGCGTGCCCGCCATATGCACCGA
1 AGTGCTACACATAA--G-GT------CGTGCCCACCATATGCACCGA
* * *
5501644 AGTGCTGCACAAAAGGTCGTGCCCACCATATGCATCGA
1 AGTGCTACACATAAGGTCGTGCCCACCATATGCACCGA
* * *
5501682 AGTTCTACACATAAGGTCATGCCCACCATATGCACTGA
1 AGTGCTACACATAAGGTCGTGCCCACCATATGCACCGA
* * *
5501720 AGTACTACACATAAGGTCGTGCCTACCACT-TGCACCAA
1 AGTGCTACACATAAGGTCGTGCCCACCA-TATGCACCGA
5501758 AGTGCT
1 AGTGCT
5501764 TAATTGATAT
Statistics
Matches: 204, Mismatches: 29, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
38 161 0.79
39 5 0.02
40 1 0.00
41 2 0.01
44 2 0.01
45 1 0.00
47 32 0.16
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (38 bp):
AGTGCTACACATAAGGTCGTGCCCACCATATGCACCGA
Found at i:5501631 original size:47 final size:47
Alignment explanation
Indices: 5501576--5501667 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
5501566 CATATAAGGT
*
5501576 CGTGCCCGCCATATGCACCGAAGGGCTCCACATAAGGGCGTGCCCGG
1 CGTGCCCGCCATATGCACCGAAGGGCTCCACAAAAGGGCGTGCCCGG
* * *
5501623 CGTGCCCGCCATATGCACCGAAGTGCTGCACAAAAGGTCGTGCCC
1 CGTGCCCGCCATATGCACCGAAGGGCTCCACAAAAGGGCGTGCCC
5501668 ACCATATGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (47 bp):
CGTGCCCGCCATATGCACCGAAGGGCTCCACAAAAGGGCGTGCCCGG
Found at i:5501705 original size:85 final size:85
Alignment explanation
Indices: 5501546--5501705 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
5501536 GTCGTTCCCA
* * * *
5501546 CCATATGCACCGAAGGGCTCCATATAAGGTCGTGCCCGCCATATGCACCGAAGGGCTCCACATAA
1 CCATATGCACCGAAGGGCTCCACAAAAGGTCGTGCCCACCATATGCACCGAAGGGCTACACATAA
*
5501611 GGGCGTGCCCGGCGTGCCCG
66 GGGCATGCCCGGCGTGCCCG
* * * **
5501631 CCATATGCACCGAAGTGCTGCACAAAAGGTCGTGCCCACCATATGCATCGAAGTTCTACACATAA
1 CCATATGCACCGAAGGGCTCCACAAAAGGTCGTGCCCACCATATGCACCGAAGGGCTACACATAA
*
5501696 GGTCATGCCC
66 GGGCATGCCC
5501706 ACCATATGCA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (85 bp):
CCATATGCACCGAAGGGCTCCACAAAAGGTCGTGCCCACCATATGCACCGAAGGGCTACACATAA
GGGCATGCCCGGCGTGCCCG
Found at i:5501731 original size:123 final size:123
Alignment explanation
Indices: 5501509--5501742 Score: 315
Period size: 123 Copynumber: 1.9 Consensus size: 123
5501499 TAGTGCCCAA
* * * * *
5501509 CATATGTACCGAAGCGCTACACATAAGGTCGTTCCCACCATATGCACCGAAGGGCTCCATATAAG
1 CATATGCACCGAAGCGCTACACAAAAGGTCGTGCCCACCATATGCACCGAAGGGCTACACATAAG
* * * *
5501574 GTCGTGCCCGCCATATGCACCGAAGGGCTCCACATAAGGGCGTGCCCGGCGTGCCCGC
66 GTCATGCCCACCATATGCACCGAAGGACTACACATAAGGGCGTGCCCGGCGTGCCCGC
* * * **
5501632 CATATGCACCGAAGTGCTGCACAAAAGGTCGTGCCCACCATATGCATCGAAGTTCTACACATAAG
1 CATATGCACCGAAGCGCTACACAAAAGGTCGTGCCCACCATATGCACCGAAGGGCTACACATAAG
* * *
5501697 GTCATGCCCACCATATGCACTGAAGTACTACACATAAGGTCGTGCC
66 GTCATGCCCACCATATGCACCGAAGGACTACACATAAGGGCGTGCC
5501743 TACCACTTGC
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
123 94 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (123 bp):
CATATGCACCGAAGCGCTACACAAAAGGTCGTGCCCACCATATGCACCGAAGGGCTACACATAAG
GTCATGCCCACCATATGCACCGAAGGACTACACATAAGGGCGTGCCCGGCGTGCCCGC
Found at i:5502382 original size:21 final size:21
Alignment explanation
Indices: 5502356--5502395 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5502346 CTTCTTCTAT
5502356 TTAAATTTGTACAATTTATGG
1 TTAAATTTGTACAATTTATGG
5502377 TTAAATTTGTACAATTTAT
1 TTAAATTTGTACAATTTAT
5502396 AGTGAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (21 bp):
TTAAATTTGTACAATTTATGG
Found at i:5504488 original size:31 final size:30
Alignment explanation
Indices: 5504436--5504497 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
5504426 TTTTTCGAAA
* *
5504436 TTATATTTTAGTCTCTAAACTTTTCTAAATT
1 TTATAATTTAGTCTCTAAAC-TTTCAAAATT
*
5504467 TTATAATTTAGTCAT-TTAACTTTCAAAATT
1 TTATAATTTAGTC-TCTAAACTTTCAAAATT
5504497 T
1 T
5504498 ACATTTTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.37
31 16 0.59
32 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.53
Consensus pattern (30 bp):
TTATAATTTAGTCTCTAAACTTTCAAAATT
Found at i:5506629 original size:64 final size:65
Alignment explanation
Indices: 5506497--5506652 Score: 210
Period size: 64 Copynumber: 2.4 Consensus size: 65
5506487 ATAAGACTTA
* ** * *
5506497 GTGCATCGGTACACTAATTATATTCAATGTTTCAAACAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAACAACCCTGGAGTGCATCGATGCATGGTCT
* *
5506562 GTGCATCGGTACACAAAATGCATTCGATGTTTTAATA-AACCCT-GAGTGCATCGATGCATGG-C
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAA-ACAACCCTGGAGTGCATCGATGCATGGTC
5506624 GT
65 -T
5506626 GTGCATCGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
5506653 AATGGGGTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 1 0.01
64 45 0.56
65 34 0.42
66 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAACAACCCTGGAGTGCATCGATGCATGGTCT
Found at i:5507008 original size:13 final size:13
Alignment explanation
Indices: 5506990--5507017 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5506980 TAAGATTTTC
5506990 TTTGAAAATAATT
1 TTTGAAAATAATT
5507003 TTTGAAAATAATT
1 TTTGAAAATAATT
5507016 TT
1 TT
5507018 GTAAAATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTGAAAATAATT
Found at i:5510156 original size:32 final size:31
Alignment explanation
Indices: 5510093--5510157 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5510083 TCCTAGGATT
*
5510093 TGACCCATTTGACCCGACCGTTGACCAGACC
1 TGACCCATTTGACCCGACCGTTAACCAGACC
* *
5510124 TGACCCCTTTGACCCTACCCGTTAACTC-GACC
1 TGACCCATTTGACCCGA-CCGTTAAC-CAGACC
5510156 TG
1 TG
5510158 TTGACCGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 15 0.52
32 13 0.45
33 1 0.03
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (31 bp):
TGACCCATTTGACCCGACCGTTAACCAGACC
Found at i:5511275 original size:27 final size:27
Alignment explanation
Indices: 5511221--5511272 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
5511211 GAAATGATTG
*
5511221 AAATACTCTGGATCTGTCAAATGACCA
1 AAATACTCTGGATATGTCAAATGACCA
5511248 AAATACCTCTGGA-ATG-CAAATGACC
1 AAATA-CTCTGGATATGTCAAATGACC
5511273 CAAGAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 7 0.30
28 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (27 bp):
AAATACTCTGGATATGTCAAATGACCA
Found at i:5512446 original size:23 final size:23
Alignment explanation
Indices: 5512416--5512459 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5512406 ATTTCTATTC
*
5512416 TGATTTCTGATCTGAATTCTACT
1 TGATTTCTGATCAGAATTCTACT
*
5512439 TGATTTCTGATCAGGATTCTA
1 TGATTTCTGATCAGAATTCTA
5512460 TATCTAATCT
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:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (23 bp):
TGATTTCTGATCAGAATTCTACT
Found at i:5514477 original size:13 final size:13
Alignment explanation
Indices: 5514459--5514501 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
5514449 TTGACCCAGT
5514459 TTGACTCGACCCG
1 TTGACTCGACCCG
*
5514472 TTGACTCGACCCA
1 TTGACTCGACCCG
*
5514485 TTGACTCAACCCG
1 TTGACTCGACCCG
5514498 TTGA
1 TTGA
5514502 TCGTTGACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.26
Consensus pattern (13 bp):
TTGACTCGACCCG
Found at i:5521175 original size:25 final size:25
Alignment explanation
Indices: 5521145--5521200 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
5521135 TATAACTGAA
*
5521145 AATAATGACAAGATAACCATATGAT
1 AATAATGACAAGATAACCACATGAT
*
5521170 AATAATGACAAGATAATCACATGAT
1 AATAATGACAAGATAACCACATGAT
*
5521195 AGTAAT
1 AATAAT
5521201 AGTATATGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (25 bp):
AATAATGACAAGATAACCACATGAT
Found at i:5526031 original size:25 final size:25
Alignment explanation
Indices: 5525998--5526058 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
5525988 TGTGTTATAA
*
5525998 ATGAAAATAATGACAAGATAA-CTAC
1 ATGATAATAATGACAAGATAATC-AC
5526023 ATGATAATAATGACAAGATAATCAC
1 ATGATAATAATGACAAGATAATCAC
*
5526048 ATGATAGTAAT
1 ATGATAATAAT
5526059 AGTATATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (25 bp):
ATGATAATAATGACAAGATAATCAC
Found at i:5535282 original size:28 final size:28
Alignment explanation
Indices: 5535250--5535381 Score: 138
Period size: 28 Copynumber: 4.7 Consensus size: 28
5535240 AATGGATCGT
* * *
5535250 GGAACACATCCCATACAAAATAGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
** * *
5535278 GGAACAAATCTTACACAGAATAGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
* ** * *
5535306 GAAATGAATCCCATATAGAACCGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
*
5535334 GGAACAAATCCCATACATAACAGAGCGG
1 GGAACAAATCCCATACAGAACAGAGCGG
*
5535362 GGAACAAATCCCATATAGAA
1 GGAACAAATCCCATACAGAA
5535382 TTAGGATGGG
Statistics
Matches: 82, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 82 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (28 bp):
GGAACAAATCCCATACAGAACAGAGCGG
Found at i:5535440 original size:28 final size:29
Alignment explanation
Indices: 5535408--5535473 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
5535398 GCTCATTTAG
*
5535408 AATCAGTA-CGGGATATAATCCCATGCAA
1 AATCAGGATCGGGATATAATCCCATGCAA
* *
5535436 AATCAGGATGGGGATATAATTCCATGCAA
1 AATCAGGATCGGGATATAATCCCATGCAA
5535465 AATCAGGAT
1 AATCAGGAT
5535474 GAAGGGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (29 bp):
AATCAGGATCGGGATATAATCCCATGCAA
Found at i:5535451 original size:29 final size:29
Alignment explanation
Indices: 5535417--5535474 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5535407 GAATCAGTAC
5535417 GGGATATAATCCCATGCAAAATCAGGATG
1 GGGATATAATCCCATGCAAAATCAGGATG
*
5535446 GGGATATAATTCCATGCAAAATCAGGATG
1 GGGATATAATCCCATGCAAAATCAGGATG
5535475 AAGGGTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (29 bp):
GGGATATAATCCCATGCAAAATCAGGATG
Found at i:5543971 original size:44 final size:44
Alignment explanation
Indices: 5543888--5543983 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
5543878 GGGTTTTATG
* * * *
5543888 TGGGGTTTTTATTTTGGAGTTTAGTTTGGGTCTTTTTTTTGTTT
1 TGGGATTTTTATTTTGGAGTTTAGTTTAGGTCTTGTTTTTATTT
*
5543932 TGGGATTTTTATTTTGGGGTTTAG-TTAGGT-TTAAGTTTTTATTT
1 TGGGATTTTTATTTTGGAGTTTAGTTTAGGTCTT--GTTTTTATTT
5543976 TGGGATTT
1 TGGGATTT
5543984 GGTTTGGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 5 0.11
44 38 0.84
ACGTcount: A:0.11, C:0.01, G:0.27, T:0.60
Consensus pattern (44 bp):
TGGGATTTTTATTTTGGAGTTTAGTTTAGGTCTTGTTTTTATTT
Found at i:5543972 original size:30 final size:30
Alignment explanation
Indices: 5543937--5543993 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5543927 TGTTTTGGGA
*
5543937 TTTTTATTTTGGGGTTTAGTTAGGTTTAAG
1 TTTTTATTTTGGGATTTAGTTAGGTTTAAG
* *
5543967 TTTTTATTTTGGGATTTGGTTTGGTTT
1 TTTTTATTTTGGGATTTAGTTAGGTTT
5543994 GGGCCCATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.61
Consensus pattern (30 bp):
TTTTTATTTTGGGATTTAGTTAGGTTTAAG
Found at i:5553204 original size:12 final size:14
Alignment explanation
Indices: 5553187--5553219 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5553177 TATAAGTTAA
5553187 TTTTTAT-TGAA-G
1 TTTTTATCTGAATG
5553199 TTTTTATCTGAATG
1 TTTTTATCTGAATG
5553213 TTTTTAT
1 TTTTTAT
5553220 ACACCACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 4 0.21
14 8 0.42
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTTTTATCTGAATG
Found at i:5554493 original size:28 final size:28
Alignment explanation
Indices: 5554449--5554594 Score: 121
Period size: 28 Copynumber: 5.2 Consensus size: 28
5554439 GAACCCAAGT
* * *
5554449 CAGAATAGATCGTGGAACACATCCCATA
1 CAGAATAGAGCGGGGAACAAATCCCATA
* * **
5554477 CAAAATAGAGCGGGGAAAAAATCTTATA
1 CAGAATAGAGCGGGGAACAAATCCCATA
* * * **
5554505 CCGAATAGAGCGAGAAATGAATCCCATA
1 CAGAATAGAGCGGGGAACAAATCCCATA
* ** *
5554533 TAGAACCGAGCGGGGAACAAATCTCATA
1 CAGAATAGAGCGGGGAACAAATCCCATA
* *
5554561 CAGAACAGAGTGGGGAACAAATCCCATA
1 CAGAATAGAGCGGGGAACAAATCCCATA
*
5554589 TAGAAT
1 CAGAAT
5554595 TAGGATGGGG
Statistics
Matches: 88, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 88 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (28 bp):
CAGAATAGAGCGGGGAACAAATCCCATA
Found at i:5554544 original size:56 final size:56
Alignment explanation
Indices: 5554484--5554593 Score: 139
Period size: 56 Copynumber: 2.0 Consensus size: 56
5554474 ATACAAAATA
* * * **
5554484 GAGCGGGGAAAAAATCTTATACCGAATAGAGCGAGAAATGAATCCCATATAGAACC
1 GAGCGGGGAAAAAATCTCATACAGAACAGAGCGAGAAACAAATCCCATATAGAACC
* * * *
5554540 GAGCGGGGAACAAATCTCATACAGAACAGAGTGGGGAACAAATCCCATATAGAA
1 GAGCGGGGAAAAAATCTCATACAGAACAGAGCGAGAAACAAATCCCATATAGAA
5554594 TTAGGATGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.15
Consensus pattern (56 bp):
GAGCGGGGAAAAAATCTCATACAGAACAGAGCGAGAAACAAATCCCATATAGAACC
Found at i:5554672 original size:29 final size:29
Alignment explanation
Indices: 5554620--5554689 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
5554610 GCTCATGTAG
*
5554620 AATCAGGACG-GGATATAATCCCATGCAA
1 AATCAGGATGAGGATATAATCCCATGCAA
*
5554648 AATCAGGATGAGGATATAATTCCATGCAA
1 AATCAGGATGAGGATATAATCCCATGCAA
*
5554677 AATCAAGATGAGG
1 AATCAGGATGAGG
5554690 GTTTTTCCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 9 0.24
29 29 0.76
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (29 bp):
AATCAGGATGAGGATATAATCCCATGCAA
Found at i:5557541 original size:20 final size:20
Alignment explanation
Indices: 5557516--5557553 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5557506 TTTGGTTCAC
5557516 GGAATATAAA-ATTACCAGTG
1 GGAATA-AAAGATTACCAGTG
5557536 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
5557554 AGAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:5557779 original size:36 final size:36
Alignment explanation
Indices: 5557709--5557779 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
5557699 GTTAGAAAAT
* *
5557709 ATTTATATATTTTCTTTAAAAATTTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAATATATAAA
5557745 ATTTATATAATTTT-TTTACAAAATTGAAA-ATATAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAATATATAA
5557780 TTTATGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAATATATAAA
Found at i:5561120 original size:20 final size:19
Alignment explanation
Indices: 5561097--5561156 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
5561087 CTTAAACCCA
5561097 TGTTACTGGTTTTAATAATG
1 TGTTACT-GTTTTAATAATG
*
5561117 TGTTCCT-TTTTAATAA--
1 TGTTACTGTTTTAATAATG
5561133 TGTTACTGATTTTAATAATG
1 TGTTACTG-TTTTAATAATG
5561153 TGTT
1 TGTT
5561157 CCTTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 6 0.18
18 18 0.53
20 10 0.29
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (19 bp):
TGTTACTGTTTTAATAATG
Found at i:5561127 original size:18 final size:18
Alignment explanation
Indices: 5561106--5561164 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
5561096 ATGTTACTGG
5561106 TTTTAATAATGTGTTCCT
1 TTTTAATAATGTGTTCCT
*
5561124 TTTTAATAA--TGTTACT
1 TTTTAATAATGTGTTCCT
5561140 GATTTTAATAATGTGTTCCT
1 --TTTTAATAATGTGTTCCT
5561160 TTTTA
1 TTTTA
5561165 TTACCTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 6 0.17
18 23 0.66
20 6 0.17
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.56
Consensus pattern (18 bp):
TTTTAATAATGTGTTCCT
Found at i:5561146 original size:36 final size:36
Alignment explanation
Indices: 5561096--5561164 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
5561086 GCTTAAACCC
*
5561096 ATGTTACTGGTTTTAATAATGTGTTCCTTTTTAATA
1 ATGTTACTGATTTTAATAATGTGTTCCTTTTTAATA
5561132 ATGTTACTGATTTTAATAATGTGTTCCTTTTTA
1 ATGTTACTGATTTTAATAATGTGTTCCTTTTTA
5561165 TTACCTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.54
Consensus pattern (36 bp):
ATGTTACTGATTTTAATAATGTGTTCCTTTTTAATA
Found at i:5567378 original size:20 final size:20
Alignment explanation
Indices: 5567324--5567379 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
5567314 ATGCTCTATG
*
5567324 GGTACCGATACCCCCACAGA
1 GGTACCGATACCCCTACAGA
* *
5567344 GGTATCGATACCCCTATAGA
1 GGTACCGATACCCCTACAGA
5567364 GGTACCGATACCCCTA
1 GGTACCGATACCCCTA
5567380 GTCAATTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.18
Consensus pattern (20 bp):
GGTACCGATACCCCTACAGA
Found at i:5573208 original size:19 final size:20
Alignment explanation
Indices: 5573166--5573203 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5573156 CCCTTTGAAT
5573166 GGGTACCGATACCCCCATGA
1 GGGTACCGATACCCCCATGA
5573186 GGGTACCGATACCCCCAT
1 GGGTACCGATACCCCCAT
5573204 CGGGTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.16
Consensus pattern (20 bp):
GGGTACCGATACCCCCATGA
Found at i:5573638 original size:19 final size:21
Alignment explanation
Indices: 5573609--5573651 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5573599 AAAAAAATTG
5573609 TTTTGATTTTAAAT-TGTAGT
1 TTTTGATTTTAAATATGTAGT
*
5573629 TTTTGA-TTTAAATATGTTGT
1 TTTTGATTTTAAATATGTAGT
5573649 TTT
1 TTT
5573652 GAAAACTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (21 bp):
TTTTGATTTTAAATATGTAGT
Found at i:5573652 original size:19 final size:19
Alignment explanation
Indices: 5573606--5573653 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5573596 ATAAAAAAAA
5573606 TTGTTTTGATTTTAAATTG
1 TTGTTTTGATTTTAAATTG
*
5573625 TAGTTTTTGA-TTTAAATATG
1 TTG-TTTTGATTTTAAAT-TG
5573645 TTGTTTTGA
1 TTGTTTTGA
5573654 AAACTACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (19 bp):
TTGTTTTGATTTTAAATTG
Found at i:5596529 original size:17 final size:17
Alignment explanation
Indices: 5596468--5596520 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
5596458 ACCAAAATAC
5596468 CCCTGGAATATAAATGA
1 CCCTGGAATATAAATGA
*
5596485 CCCTGGAATGTAAATGA
1 CCCTGGAATATAAATGA
5596502 CCCTGGAATATAAATGA
1 CCCTGGAATATAAATGA
5596519 CC
1 CC
5596521 TAAGAATATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (17 bp):
CCCTGGAATATAAATGA
Found at i:5598656 original size:27 final size:27
Alignment explanation
Indices: 5598626--5598706 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
5598616 AATGCATCAT
*
5598626 TTCATGCATTTTCAATTATGGCATTCG
1 TTCATGCATTTTCAATTATGGCATCCG
* *
5598653 TTCATGC-----C-TTTAT-GCATCCT
1 TTCATGCATTTTCAATTATGGCATCCG
*
5598673 TTCATGGATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTATGGCATCCG
5598700 TTCATGC
1 TTCATGC
5598707 CTTAATGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
20 11 0.28
21 4 0.10
22 1 0.03
25 1 0.03
26 4 0.10
27 19 0.47
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (27 bp):
TTCATGCATTTTCAATTATGGCATCCG
Found at i:5598738 original size:48 final size:47
Alignment explanation
Indices: 5598571--5598740 Score: 243
Period size: 47 Copynumber: 3.6 Consensus size: 47
5598561 CATATTAACA
* *
5598571 CATCCATTT-ATGCATTTTAATATATATGGCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCA-AT-TATGGCATCCGTTCATGCCTTAATG
* * *
5598620 CATCATTTCATGCATTTTCAATTATGGCATTCGTTCATGCCTTTATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
*
5598667 CATCCTTTCATGGATTTTCAATTATGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
5598714 TCATCCTTTCATGCATTTTCAATTATG
1 -CATCCTTTCATGCATTTTCAATTATG
5598741 AATTTGATTT
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
47 65 0.60
48 30 0.28
49 14 0.13
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
Found at i:5599303 original size:94 final size:95
Alignment explanation
Indices: 5599107--5599304 Score: 303
Period size: 94 Copynumber: 2.1 Consensus size: 95
5599097 GCCCTAGTAA
* * * *
5599107 CGATACTTCTATACTATGGTACCGATACCCCCTTTCGGTATCGATACCAAATTTAGCTTCGATGT
1 CGATACTACTATACTATGGTACCGATACCCCCTTTCAGTATCGATACCAAAATTAGATTCGATGT
5599172 TGCCTGGTATTGATACCCTTACCATGGTAT
66 TGCCTGGTATTGATACCCTTACCATGGTAT
* *
5599202 CGATACTACTATACTATGGTACCGATA-CCCGTTTCTAGTATCGATACCAAAATTATATT-GATG
1 CGATACTACTATACTATGGTACCGATACCCCCTTTC-AGTATCGATACCAAAATTAGATTCGATG
5599265 TT-CACTGGTATTGATACCCTTACCATGGTAT
65 TTGC-CTGGTATTGATACCCTTACCATGGTAT
5599296 CGATACTAC
1 CGATACTAC
5599305 ATCTTCAATA
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
93 1 0.01
94 49 0.52
95 45 0.47
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (95 bp):
CGATACTACTATACTATGGTACCGATACCCCCTTTCAGTATCGATACCAAAATTAGATTCGATGT
TGCCTGGTATTGATACCCTTACCATGGTAT
Found at i:5605444 original size:27 final size:27
Alignment explanation
Indices: 5605405--5605552 Score: 144
Period size: 27 Copynumber: 6.0 Consensus size: 27
5605395 ATGTCTTAAT
*
5605405 GCATCCTTTCATGCATTTTCATTTATG
1 GCATCCTTTCATGCATTTTCAATTATG
* * *
5605432 ACATCCATTCATGC--CTT--A--AT-
1 GCATCCTTTCATGCATTTTCAATTATG
5605452 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
5605479 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
* *
5605506 GCATCCGTTCATGC---CT-AA--AT-
1 GCATCCTTTCATGCATTTTCAATTATG
5605526 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
5605553 AATTTGATTT
Statistics
Matches: 96, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
20 25 0.26
21 4 0.04
22 2 0.02
23 3 0.03
24 4 0.04
25 2 0.02
26 4 0.04
27 52 0.54
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTCAATTATG
Found at i:5605454 original size:47 final size:46
Alignment explanation
Indices: 5605357--5605492 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 46
5605347 CGTATTAGCA
* *
5605357 CATCCATTT-ATGCATTTTAATATATATGGCATCCTTCCATGTCTTAATG
1 CATCC-TTTCATGCATTTTCAT-T-TATGGCATCCTT-CATGCCTTAATG
*
5605406 CATCCTTTCATGCATTTTCATTTATGACATCCATTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCATTTATGGCATCC-TTCATGCCTTAATG
*
5605453 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGC
1 CATCCTTTCATGCATTTTCATTTATGGCATCC-TTCATGC
5605493 ATTTTCAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
47 57 0.72
48 6 0.08
49 16 0.20
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTCATTTATGGCATCCTTCATGCCTTAATG
Found at i:5605462 original size:20 final size:20
Alignment explanation
Indices: 5605385--5605465 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 20
5605375 AATATATATG
* *
5605385 GCATCCTTCCATGTCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
5605405 GCATCCTTTCATGCATTTTCATTTAT
1 GCATCCTTTCATGC-----C-TTAAT
*
5605431 GACATCCATTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
5605452 GCATCCTTTCATGC
1 GCATCCTTTCATGC
5605466 ATTTTCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
20 24 0.50
21 5 0.10
22 1 0.02
25 1 0.02
26 5 0.10
27 12 0.25
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:5605490 original size:74 final size:74
Alignment explanation
Indices: 5605405--5605552 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
5605395 ATGTCTTAAT
* *
5605405 GCATCCTTTCATGCATTTTCATTTATGACATCCATTCATGCCTTAATGCATCCTTTCATGCATTT
1 GCATCCTTTCATGCATTTTCAATTATGACATCCATTCATGCCTAAATGCATCCTTTCATGCATTT
5605470 TCAATTATG
66 TCAATTATG
* *
5605479 GCATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTAAATGCATCCTTTCATGCATTT
1 GCATCCTTTCATGCATTTTCAATTATGACATCCATTCATGCCTAAATGCATCCTTTCATGCATTT
5605544 TCAATTATG
66 TCAATTATG
5605553 AATTTGATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (74 bp):
GCATCCTTTCATGCATTTTCAATTATGACATCCATTCATGCCTAAATGCATCCTTTCATGCATTT
TCAATTATG
Found at i:5606011 original size:20 final size:21
Alignment explanation
Indices: 5605986--5606041 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
5605976 CGATGTTTCC
5605986 TGGTATTGATACCCT-TACCA
1 TGGTATTGATACCCTATACCA
* ** *
5606006 TGGTATCGATACTATTATACTA
1 TGGTATTGATAC-CCTATACCA
5606028 TGGTATTGATACCC
1 TGGTATTGATACCC
5606042 CTTTCTGGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 15 0.56
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (21 bp):
TGGTATTGATACCCTATACCA
Found at i:5606092 original size:95 final size:95
Alignment explanation
Indices: 5605907--5606114 Score: 303
Period size: 95 Copynumber: 2.2 Consensus size: 95
5605897 TCGATACTAC
* * * *
5605907 TACCCTGGTACCGATACT-TCTATACTATGGTACTGATACCCCTTCTGGTATCGATACCGAATTT
1 TACCATGGTATCGATACTATCTATACTATGGTACTGATACCCCTTCTGGTATCGATACCAAAATT
* * *
5605971 AGCTTCGATGTTTCCTGGTATTGATACCCT
66 AGATTCGATGTTTACTGGTATAGATACCCT
*
5606001 TACCATGGTATCGATACTAT-TATACTATGGTATTGATACCCCTTTCTGGTATCGATACCAAAAT
1 TACCATGGTATCGATACTATCTATACTATGGTACTGATACCCC-TTCTGGTATCGATACCAAAAT
* *
5606065 TATATTCGATGTTTACTGGTATAGATACCTT
65 TAGATTCGATGTTTACTGGTATAGATACCCT
5606096 TACCATGGTATCGATACTA
1 TACCATGGTATCGATACTA
5606115 CATCTTCGGT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
94 37 0.36
95 65 0.64
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (95 bp):
TACCATGGTATCGATACTATCTATACTATGGTACTGATACCCCTTCTGGTATCGATACCAAAATT
AGATTCGATGTTTACTGGTATAGATACCCT
Found at i:5612893 original size:25 final size:25
Alignment explanation
Indices: 5612864--5612919 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
5612854 TATAACTGAA
5612864 AATAATGACAAGATAA-CTACATGAT
1 AATAATGACAAGATAATC-ACATGAT
5612889 AATAATGACAAGATAATCACATGAT
1 AATAATGACAAGATAATCACATGAT
*
5612914 AGTAAT
1 AATAAT
5612920 AGTATATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (25 bp):
AATAATGACAAGATAATCACATGAT
Found at i:5613649 original size:14 final size:14
Alignment explanation
Indices: 5613630--5613662 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5613620 CAACGTTTGG
5613630 ATGTTTCCTTTCGT
1 ATGTTTCCTTTCGT
5613644 ATGTTTCCTTTCGT
1 ATGTTTCCTTTCGT
5613658 ATGTT
1 ATGTT
5613663 AGTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.15, T:0.58
Consensus pattern (14 bp):
ATGTTTCCTTTCGT
Found at i:5627713 original size:158 final size:157
Alignment explanation
Indices: 5627517--5627831 Score: 621
Period size: 158 Copynumber: 2.0 Consensus size: 157
5627507 TACCACTTGC
5627517 TATGTTGTAAATCGAGTAATGATTAGGCCTATTTTAAAGAAAACTCCATATAAAATTTTCAAAAA
1 TATGTTGTAAATCGAGTAATGATTAGGCCTATTTTAAAGAAAACTCCATATAAAATTTTCAAAAA
5627582 TAAAAAGCCTAACATTAGCTATTTTCATCCTTTTGGATGTAAATGTTTTGTTTTAAACAACAGTA
66 TAAAAAGCCTAACATTAGCTATTTTCATCCTTTTGGATGTAAATGTTTT-TTTTAAACAACAGTA
5627647 AAGAAAATCTTGGCAAATTTGGTGCTAA
130 AAGAAAATCTTGGCAAATTTGGTGCTAA
5627675 TATGTTGTAAATCGAGTAATGATTAGGCCTATTTTAAAGAAAACTCCATATAAAATTTTCAAAAA
1 TATGTTGTAAATCGAGTAATGATTAGGCCTATTTTAAAGAAAACTCCATATAAAATTTTCAAAAA
5627740 TAAAAAGCCTAACATTAGCTATTTTCATCCTTTTGGATGTAAATGTTTTTTTTAAACAACAGTAA
66 TAAAAAGCCTAACATTAGCTATTTTCATCCTTTTGGATGTAAATGTTTTTTTTAAACAACAGTAA
5627805 AGAAAATCTTGGCAAATTTGGTGCTAA
131 AGAAAATCTTGGCAAATTTGGTGCTAA
5627832 AAGTGATGAA
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 43 0.27
158 114 0.73
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (157 bp):
TATGTTGTAAATCGAGTAATGATTAGGCCTATTTTAAAGAAAACTCCATATAAAATTTTCAAAAA
TAAAAAGCCTAACATTAGCTATTTTCATCCTTTTGGATGTAAATGTTTTTTTTAAACAACAGTAA
AGAAAATCTTGGCAAATTTGGTGCTAA
Found at i:5630026 original size:20 final size:20
Alignment explanation
Indices: 5630001--5630061 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
5629991 TTTTGGTGCA
*
5630001 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
5630021 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
5630042 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
5630062 TTTTCCCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:5632709 original size:20 final size:19
Alignment explanation
Indices: 5632672--5632708 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5632662 AATTTTACAC
5632672 TTAGGGAACCGATTCCCCA
1 TTAGGGAACCGATTCCCCA
*
5632691 TTAGGGGACCGATTCCCC
1 TTAGGGAACCGATTCCCC
5632709 CCACGCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (19 bp):
TTAGGGAACCGATTCCCCA
Found at i:5635670 original size:191 final size:193
Alignment explanation
Indices: 5635286--5635717 Score: 473
Period size: 191 Copynumber: 2.3 Consensus size: 193
5635276 GCAATACATG
* * * * * * *
5635286 GTTACCTATTAGCAATATAAATGATGTTTATACATAACGTCACTTTATAATTAATACTCAATGAC
1 GTTACCTAATAGTATTATGAATGAAGATTATGCATAACGTCACTTTATAATTAATACTCAATGAC
* * *
5635351 AACTAGTTACGTCATTAAATTATATAAAATTTTGTTATTAATAATTCACATCTTCACGAATAATA
66 AACTAGTTACGTCACTAAATTATATAAAATCTTGTTATTAATAATTCACATCGTCACGAATAATA
* * * * *
5635416 CATTAAAACCAATATATATGTGACAAAATAGATATTGTCACATTTTCAGTGACCTAATATAAT
131 CAATAAAACCAACATATATGTGACAAAAGAGATATTGTCAAATTTTCAGTGACATAATATAAT
* *
5635479 GTTACCTAATAGTATTATGAATGACAG-TTATGCATAACGTCATTTTATAACTT-ATATTGC-AT
1 GTTACCTAATAGTATTATGAATGA-AGATTATGCATAACGTCACTTTATAA-TTAATACT-CAAT
** * * * *
5635541 GACAGTTAGTTA-GATCACTAAATTATATAATA-CTT-TTATTAATAATTTATATCGTCACGCAT
63 GACAACTAGTTACG-TCACTAAATTATATAAAATCTTGTTATTAATAATTCACATCGTCACGAAT
* * * * * *
5635603 ACTACAATAAAATCAACATATATGTTACGAAAGAGATATTTTCAAATTTTTAGTGACATAATATA
127 AATACAATAAAACCAACATATATGTGACAAAAGAGATATTGTCAAATTTTCAGTGACATAATATA
5635668 AT
192 AT
** * * *
5635670 GTTATGTAATAGTATTTTGAATGATGATTATGCAT-ACGTCACCTTATA
1 GTTACCTAATAGTATTATGAATGAAGATTATGCATAACGTCACTTTATA
5635718 CAATTTTCTC
Statistics
Matches: 200, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
190 12 0.06
191 108 0.54
192 3 0.01
193 73 0.37
194 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (193 bp):
GTTACCTAATAGTATTATGAATGAAGATTATGCATAACGTCACTTTATAATTAATACTCAATGAC
AACTAGTTACGTCACTAAATTATATAAAATCTTGTTATTAATAATTCACATCGTCACGAATAATA
CAATAAAACCAACATATATGTGACAAAAGAGATATTGTCAAATTTTCAGTGACATAATATAAT
Found at i:5647041 original size:54 final size:52
Alignment explanation
Indices: 5646967--5647089 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 52
5646957 ATTTCTGATT
* * *
5646967 TTTTGTTAAACGCTGCTATTTTTTACAAAATAATTGTCA-TTTTTTTATTTTAAA
1 TTTTGCTAAACGATGCTATTTTTTACAAAATAATTGTCAGTTTTTTCA---TAAA
*
5647021 TTTTGCTAAACGATGCTATTTTTTACAAAATAATTGTTAGTTTTTTCATAAA
1 TTTTGCTAAACGATGCTATTTTTTACAAAATAATTGTCAGTTTTTTCATAAA
*
5647073 TTTTGCTAAACGTTGCT
1 TTTTGCTAAACGATGCT
5647090 GCTTTTATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
52 20 0.32
54 36 0.57
55 7 0.11
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (52 bp):
TTTTGCTAAACGATGCTATTTTTTACAAAATAATTGTCAGTTTTTTCATAAA
Found at i:5649394 original size:18 final size:18
Alignment explanation
Indices: 5649371--5649408 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5649361 TTTTAAGATT
5649371 TTATATTCAATTTAAATA
1 TTATATTCAATTTAAATA
* *
5649389 TTATATTCGATTTAATTA
1 TTATATTCAATTTAAATA
5649407 TT
1 TT
5649409 CAAATATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (18 bp):
TTATATTCAATTTAAATA
Found at i:5657052 original size:18 final size:17
Alignment explanation
Indices: 5657015--5657049 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5657005 AATATTTGGA
*
5657015 TGTTTGTTTTGAATATT
1 TGTTTGGTTTGAATATT
*
5657032 TGTTTGGTTTGGATATT
1 TGTTTGGTTTGAATATT
5657049 T
1 T
5657050 TGTGTCTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (17 bp):
TGTTTGGTTTGAATATT
Found at i:5657245 original size:2 final size:2
Alignment explanation
Indices: 5657238--5657264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5657228 TAGCAGCTAT
5657238 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
5657265 TATATACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5662033 original size:45 final size:45
Alignment explanation
Indices: 5661937--5662042 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
5661927 GGTGCACTAA
* *
5661937 GAGTGCATCAATGCATAAAATGCATTCGATGTTTCAAAATAGCTT
1 GAGTGCATCAATGCATAAAATGCATTCGATGTTTCAAAATACCAT
* * * *
5661982 GAGTGCATCGATGCATCAAATGCATTCGATG-TTCAATTTATTCCAT
1 GAGTGCATCAATGCATAAAATGCATTCGATGTTTCAA--AATACCAT
5662028 G-GTGCATCAATGCAT
1 GAGTGCATCAATGCAT
5662043 GGATTGGTGC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 5 0.10
45 42 0.81
46 5 0.10
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (45 bp):
GAGTGCATCAATGCATAAAATGCATTCGATGTTTCAAAATACCAT
Found at i:5668156 original size:21 final size:19
Alignment explanation
Indices: 5668123--5668164 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
5668113 AGTTTATTTT
5668123 CATTTTTCAATTTTGAAATAA
1 CATTTTTCAATTTT-AAA-AA
5668144 CATTTTT-ATATTTTAAAAA
1 CATTTTTCA-ATTTTAAAAA
5668163 CA
1 CA
5668165 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (19 bp):
CATTTTTCAATTTTAAAAA
Found at i:5670088 original size:17 final size:18
Alignment explanation
Indices: 5670066--5670100 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5670056 GCACTAAGAG
5670066 TGTATT-GATGTATAAAA
1 TGTATTCGATGTATAAAA
*
5670083 TGTATTCGATGTTTAAAA
1 TGTATTCGATGTATAAAA
5670101 ATAGCCTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (18 bp):
TGTATTCGATGTATAAAA
Found at i:5670186 original size:65 final size:65
Alignment explanation
Indices: 5670080--5670224 Score: 170
Period size: 65 Copynumber: 2.2 Consensus size: 65
5670070 TTGATGTATA
* * *
5670080 AAATGTATTCGATG-TTTAAAAATAGCCTGAGTGAATCGATGCATGGCT-GGTGCATCGATGCAT
1 AAATGCATTCGATGTTTTAAAAATACCCTGAGTGAATCGATGCAT-GATAGGTGCATCGATGCAT
5670143 C
65 C
* * * * *
5670144 AAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGATATGTTCATCGATTCAT
1 AAATGCATTCGATGTTTT-AAAAATACCCTGAGTGAATCGATGCATGATAGGTGCATCGATGCAT
*
5670208 G
65 C
5670209 AAATGCATTCGATGTT
1 AAATGCATTCGATGTT
5670225 CAATTTATTC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 15 0.22
65 50 0.72
66 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (65 bp):
AAATGCATTCGATGTTTTAAAAATACCCTGAGTGAATCGATGCATGATAGGTGCATCGATGCATC
Found at i:5672010 original size:65 final size:65
Alignment explanation
Indices: 5671877--5672036 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
5671867 TGCACTAAGA
* *
5671877 GTGCAACGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
* * *
5671941 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATAGC
5672004 AT-
64 -TG
* *
5672006 GTGCATCGATTCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
5672037 CAATTTATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 27 0.32
65 53 0.63
66 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
Found at i:5674722 original size:23 final size:23
Alignment explanation
Indices: 5674692--5674773 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
5674682 GCATGGCCTT
5674692 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
* * *
5674715 GTGCATCGGTGCACCTTCATGGC
1 GTGCATCGATGCACATTCAAGGC
*
5674738 GT--ATTGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGC
5674759 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
5674774 CGTTAAGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 12 0.26
22 4 0.09
23 22 0.47
24 9 0.19
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGC
Found at i:5677549 original size:16 final size:15
Alignment explanation
Indices: 5677523--5677552 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5677513 TTAGCACAAG
5677523 CATCACAAATTTTAT
1 CATCACAAATTTTAT
5677538 CATCATCAAATTTTA
1 CATCA-CAAATTTTA
5677553 GTTTAGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
CATCACAAATTTTAT
Found at i:5683358 original size:17 final size:17
Alignment explanation
Indices: 5683333--5683366 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5683323 CCGGTTTCGG
5683333 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
5683350 TTTTTAAAAAACTGGTT
1 TTTTAAAAAAACCGGTT
5683367 ATAAAAAACC
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:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:5684058 original size:13 final size:13
Alignment explanation
Indices: 5684037--5684091 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
5684027 AAGTTCGATA
*
5684037 AATTCAAATACTT
1 AATTGAAATACTT
5684050 AATTGAAATACTT
1 AATTGAAATACTT
* *
5684063 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
5684077 AATTGAAATACTT
1 AATTGAAATACTT
5684090 AA
1 AA
5684092 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:5684122 original size:33 final size:33
Alignment explanation
Indices: 5684077--5684169 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
5684067 AACTCAACAT
* *
5684077 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
5684110 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
5684143 AATTCAAATACTTAAAAACTT-CAAGTT
1 AATTCAAATACTTAAAAACTTCCAAGTT
5684170 CGACAATTGA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 6 0.10
33 52 0.90
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.34
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTGATA
Found at i:5688977 original size:19 final size:19
Alignment explanation
Indices: 5688953--5688995 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
5688943 TAGCAACCTC
5688953 AATGATTGAGGATTAAGTA
1 AATGATTGAGGATTAAGTA
5688972 AATGATTGAGGATTAAGTA
1 AATGATTGAGGATTAAGTA
5688991 AATGA
1 AATGA
5688996 GTTTGATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (19 bp):
AATGATTGAGGATTAAGTA
Found at i:5692363 original size:12 final size:12
Alignment explanation
Indices: 5692346--5692385 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5692336 GAGATAATCC
5692346 ACTGAGCCGTTG
1 ACTGAGCCGTTG
5692358 ACTGAGCCGTT-
1 ACTGAGCCGTTG
*
5692369 AGCCGAGCCGTTG
1 A-CTGAGCCGTTG
5692382 ACTG
1 ACTG
5692386 TTAACCGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (12 bp):
ACTGAGCCGTTG
Found at i:5695391 original size:47 final size:47
Alignment explanation
Indices: 5695316--5695496 Score: 240
Period size: 47 Copynumber: 3.8 Consensus size: 47
5695306 TAATAACACA
* * *
5695316 ATCATTT-ATGCATTTTAATATATATGGCATCCTTTAATTCTTTAATGC
1 ATCATTTCATGCATTTTCA-AT-TATGGCATCCTTTCATTCCTTAATGC
* *
5695364 ATCATTTCAAT-CATTTTCAATTATGGCATCCATTCATGCCTTAATGC
1 ATCATTTC-ATGCATTTTCAATTATGGCATCCTTTCATTCCTTAATGC
* *
5695411 ATCATTTCATGCATTTTCAATTATGACATCCTTTTATTCCTTAATGC
1 ATCATTTCATGCATTTTCAATTATGGCATCCTTTCATTCCTTAATGC
* *
5695458 ATCCTTTCATGCATTTTCAACTATGGCATCCTTTCATTC
1 ATCATTTCATGCATTTTCAATTATGGCATCCTTTCATTC
5695497 ATTTTCAATT
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
46 2 0.02
47 97 0.83
48 9 0.08
49 7 0.06
50 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (47 bp):
ATCATTTCATGCATTTTCAATTATGGCATCCTTTCATTCCTTAATGC
Found at i:5695440 original size:27 final size:26
Alignment explanation
Indices: 5695360--5695556 Score: 112
Period size: 27 Copynumber: 8.1 Consensus size: 26
5695350 TAATTCTTTA
*
5695360 ATGCATCATTTCAAT-CATTTTCAATT
1 ATGCATCCTTTC-ATGCATTTTCAATT
* *
5695386 ATGGCATCCATTCATGC--CTT--A--
1 AT-GCATCCTTTCATGCATTTTCAATT
*
5695407 ATGCATCATTTCATGCATTTTCAATT
1 ATGCATCCTTTCATGCATTTTCAATT
*
5695433 ATGACATCCTTT--T--A--TTC-CTT
1 ATG-CATCCTTTCATGCATTTTCAATT
*
5695453 AATGCATCCTTTCATGCATTTTCAACT
1 -ATGCATCCTTTCATGCATTTTCAATT
*
5695480 ATGGCATCCTTTCATTCATTTTCAATT
1 AT-GCATCCTTTCATGCATTTTCAATT
*
5695507 ATGGCAT-CTGTTCATGC--CTT--A--
1 AT-GCATCCT-TTCATGCATTTTCAATT
5695528 ATGCATCCTTTCATGCATTTTCAATT
1 ATGCATCCTTTCATGCATTTTCAATT
5695554 ATG
1 ATG
5695557 AATTTGATTT
Statistics
Matches: 130, Mismatches: 15, Indels: 52
0.66 0.08 0.26
Matches are distributed among these distances:
20 33 0.25
21 12 0.09
22 5 0.04
23 3 0.02
24 3 0.02
25 5 0.04
26 17 0.13
27 52 0.40
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (26 bp):
ATGCATCCTTTCATGCATTTTCAATT
Found at i:5695530 original size:74 final size:74
Alignment explanation
Indices: 5695409--5695556 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 74
5695399 ATGCCTTAAT
* *
5695409 GCATCATTTCATGCATTTTCAATTATGACATCCTTTTATTCCTTAATGCATCCTTTCATGCATTT
1 GCATCATTTCATGCATTTTCAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
5695474 TCAACTATG
66 TCAACTATG
* * *
5695483 GCATCCTTTCATTCATTTTCAATTATGGCAT-CTGTTCATGCCTTAATGCATCCTTTCATGCATT
1 GCATCATTTCATGCATTTTCAATTATGACATCCT-TTCATGCCTTAATGCATCCTTTCATGCATT
*
5695547 TTCAATTATG
65 TTCAACTATG
5695557 AATTTGATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 2 0.03
74 65 0.97
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (74 bp):
GCATCATTTCATGCATTTTCAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT
TCAACTATG
Found at i:5696082 original size:95 final size:95
Alignment explanation
Indices: 5695919--5696119 Score: 278
Period size: 95 Copynumber: 2.1 Consensus size: 95
5695909 TACTACCCTA
* * * *
5695919 GTATCGATACTTCTATACTATGGTACCGATACCCCCTTCCGGTATCGATACCGAATTTAGTTTTG
1 GTATCGATACTACTATACTATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGTTTCG
* * *
5695984 ATGTTGCCTGGTATTGATACCCTTATCATG
66 ATGTTGACTGGTATCGATACCCTTACCATG
* * * *
5696014 GTATCAATACTACTATATTATGGTACCGATACCCCTTTCTGGTATCGATACCAAAATTA-TATTC
1 GTATCGATACTACTATACTATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGT-TTC
*
5696078 GATGTTTACTGGTATCGATACCCTTACCATG
65 GATGTTGACTGGTATCGATACCCTTACCATG
5696109 GTATCGATACT
1 GTATCGATACT
5696120 GCATCTTCGG
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 1 0.01
95 91 0.99
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (95 bp):
GTATCGATACTACTATACTATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGTTTCG
ATGTTGACTGGTATCGATACCCTTACCATG
Found at i:5701475 original size:15 final size:16
Alignment explanation
Indices: 5701450--5701480 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5701440 GAAGATTTTG
5701450 ACATCAATAATAACAT
1 ACATCAATAATAACAT
5701466 ACAT-AATAATAACAT
1 ACATCAATAATAACAT
5701481 TTCAATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (16 bp):
ACATCAATAATAACAT
Found at i:5702294 original size:27 final size:27
Alignment explanation
Indices: 5702262--5702417 Score: 142
Period size: 27 Copynumber: 6.3 Consensus size: 27
5702252 TAATGTATCA
5702262 TTTCATGCATTTTCAATTATGGCATCC
1 TTTCATGCATTTTCAATTATGGCATCC
* *
5702289 CTTCATGC--CTT--A--AT-GCATCC
1 TTTCATGCATTTTCAATTATGGCATCC
*
5702309 TTTCATGCATTTTCAATTATGGCATCT
1 TTTCATGCATTTTCAATTATGGCATCC
*
5702336 TTTCATGC--CTT--A--AT-GCATCC
1 TTTCATGCATTTTCAATTATGGCATCC
*
5702356 TTTCATGAATTTTCAATTATGGCATCC
1 TTTCATGCATTTTCAATTATGGCATCC
* *
5702383 CTTCATGTATTTTCAATTATGGCATCC
1 TTTCATGCATTTTCAATTATGGCATCC
*
5702410 GTTCATGC
1 TTTCATGC
5702418 CTTAATGCAT
Statistics
Matches: 102, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
20 25 0.25
21 4 0.04
22 4 0.04
23 2 0.02
24 2 0.02
25 4 0.04
26 4 0.04
27 57 0.56
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.43
Consensus pattern (27 bp):
TTTCATGCATTTTCAATTATGGCATCC
Found at i:5702298 original size:47 final size:47
Alignment explanation
Indices: 5702212--5702389 Score: 241
Period size: 47 Copynumber: 3.8 Consensus size: 47
5702202 TTAACACATC
* ** * *
5702212 CATTT-ATGCATTTTAATATATATGGCATCTTTTCTTGCCTTAATGTAT
1 CATTTCATGCATTTTCA-AT-TATGGCATCCCTTCATGCCTTAATGCAT
5702260 CATTTCATGCATTTTCAATTATGGCATCCCTTCATGCCTTAATGCAT
1 CATTTCATGCATTTTCAATTATGGCATCCCTTCATGCCTTAATGCAT
* **
5702307 CCTTTCATGCATTTTCAATTATGGCATCTTTTCATGCCTTAATGCAT
1 CATTTCATGCATTTTCAATTATGGCATCCCTTCATGCCTTAATGCAT
* *
5702354 CCTTTCATGAATTTTCAATTATGGCATCCCTTCATG
1 CATTTCATGCATTTTCAATTATGGCATCCCTTCATG
5702390 TATTTTCAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
47 101 0.86
48 7 0.06
49 10 0.08
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (47 bp):
CATTTCATGCATTTTCAATTATGGCATCCCTTCATGCCTTAATGCAT
Found at i:5702339 original size:94 final size:96
Alignment explanation
Indices: 5702208--5702389 Score: 289
Period size: 94 Copynumber: 1.9 Consensus size: 96
5702198 CATATTAACA
* * *
5702208 CATCCATTTATGCATTTTAATATATATGGCATCTTTTCTTGCCTTAATGTATCATTTCATGCATT
1 CATCCATTTATGCATTTTAATATATATGGCATCTTTTCATGCCTTAATGCATCATTTCATGAATT
5702273 TTCAATTATGGCATCCCTTCATGCCTTAATG
66 TTCAATTATGGCATCCCTTCATGCCTTAATG
* *
5702304 CATCC-TTTCATGCATTTTCA-AT-TATGGCATCTTTTCATGCCTTAATGCATCCTTTCATGAAT
1 CATCCATTT-ATGCATTTTAATATATATGGCATCTTTTCATGCCTTAATGCATCATTTCATGAAT
5702366 TTTCAATTATGGCATCCCTTCATG
65 TTTCAATTATGGCATCCCTTCATG
5702390 TATTTTCAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
94 60 0.75
95 5 0.06
96 15 0.19
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (96 bp):
CATCCATTTATGCATTTTAATATATATGGCATCTTTTCATGCCTTAATGCATCATTTCATGAATT
TTCAATTATGGCATCCCTTCATGCCTTAATG
Found at i:5702359 original size:20 final size:20
Alignment explanation
Indices: 5702283--5702362 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 20
5702273 TTCAATTATG
*
5702283 GCATCCCTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
5702303 GCATCCTTTCATGCATTTTCAATTAT
1 GCATCCTTTCATGC--CTT--A--AT
*
5702329 GGCATCTTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
5702350 GCATCCTTTCATG
1 GCATCCTTTCATG
5702363 AATTTTCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 25 0.52
21 2 0.04
22 2 0.04
23 1 0.02
24 1 0.02
25 2 0.04
26 2 0.04
27 13 0.27
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:5702429 original size:20 final size:20
Alignment explanation
Indices: 5702404--5702457 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
5702394 TTCAATTATG
*
5702404 GCATCCGTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
5702424 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
5702444 GCATCCTTTCATGC
1 GCATCCTTTCATGC
5702458 ATTTTCACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:5703032 original size:20 final size:20
Alignment explanation
Indices: 5703007--5703056 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
5702997 ATGTTTACCA
5703007 GTATCGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
5703027 GTATCGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
5703047 GTATCGATAC
1 GTATCGATAC
5703057 TACATCTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCTTACCATG
Found at i:5709216 original size:47 final size:47
Alignment explanation
Indices: 5709147--5709264 Score: 157
Period size: 47 Copynumber: 2.5 Consensus size: 47
5709137 TATATGGCAA
*
5709147 CCTTTTATGCATTTTCAATTATGACATTC-GTTCATGCCATAATGCAT
1 CCTTTAATGCATTTTCAATTATGACA-TCAGTTCATGCCATAATGCAT
* * * *
5709194 CCTTTAATACATTTTCAATTATGGCATCATTTCATGCCTTAATGCAT
1 CCTTTAATGCATTTTCAATTATGACATCAGTTCATGCCATAATGCAT
* *
5709241 CATTTCATGCATTTTCAATTATGA
1 CCTTTAATGCATTTTCAATTATGA
5709265 ATTTGGTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 2 0.03
47 59 0.97
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.43
Consensus pattern (47 bp):
CCTTTAATGCATTTTCAATTATGACATCAGTTCATGCCATAATGCAT
Found at i:5711638 original size:11 final size:11
Alignment explanation
Indices: 5711622--5711649 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5711612 GATTGTATAA
5711622 TTTTTATTATT
1 TTTTTATTATT
5711633 TTTTTATTATT
1 TTTTTATTATT
5711644 TTTTTA
1 TTTTTA
5711650 ATTTCCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:5714167 original size:21 final size:20
Alignment explanation
Indices: 5714121--5714174 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
5714111 GATTCTAACT
5714121 ATCGCATTGCGATTTTCCAA
1 ATCGCATTGCGATTTTCCAA
* *
5714141 ATTCGCGTTGCGATTTTCGTAA
1 A-TCGCATTGCGATTTTC-CAA
*
5714163 ATCGCAATGCGA
1 ATCGCATTGCGA
5714175 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCCAA
Found at i:5714183 original size:20 final size:20
Alignment explanation
Indices: 5714158--5714196 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5714148 TTGCGATTTT
*
5714158 CGTAAATCGCAATGCGAATA
1 CGTAAATCGCAACGCGAATA
5714178 CGTAAATCGCAACGCGAAT
1 CGTAAATCGCAACGCGAAT
5714197 CTGACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
CGTAAATCGCAACGCGAATA
Found at i:5714407 original size:22 final size:22
Alignment explanation
Indices: 5714382--5714457 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
5714372 CACTCTCTAA
* *
5714382 GACGACATCCGTCCCCATCTCT
1 GACGAAATCAGTCCCCATCTCT
*
5714404 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCT
* * * *
5714426 GATGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCT
*
5714448 GGCGAAATCA
1 GACGAAATCA
5714458 TTCACGGTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCT
Found at i:5714882 original size:20 final size:20
Alignment explanation
Indices: 5714829--5714883 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
5714819 CGGTAGTTAA
* **
5714829 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
5714849 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
5714869 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
5714884 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:5714891 original size:20 final size:20
Alignment explanation
Indices: 5714848--5714891 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5714838 CGATAGTCAT
** *
5714848 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
5714868 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
5714888 TTTC
1 TTTC
5714892 AGAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:5716793 original size:20 final size:20
Alignment explanation
Indices: 5716768--5717023 Score: 283
Period size: 20 Copynumber: 13.5 Consensus size: 20
5716758 GAGATAGTTT
5716768 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
5716788 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
5716808 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
5716824 A--ATTGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
5716841 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
5716857 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
5716875 ACTATCGCAATGAGAAAATG
1 ACTATCGCAATGCGAAAATG
5716895 ACTATCGCAA-GCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
5716914 ACTACCGC-ATGCGAAAAATG
1 ACTATCGCAATGCG-AAAATG
5716934 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
5716954 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
5716974 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
**
5716994 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
5717014 ACTATCGCAA
1 ACTATCGCAA
5717024 CGAAAGAATC
Statistics
Matches: 204, Mismatches: 15, Indels: 34
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.06
16 10 0.05
17 8 0.04
18 5 0.02
19 24 0.12
20 139 0.68
21 5 0.02
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:5716972 original size:40 final size:40
Alignment explanation
Indices: 5716768--5717061 Score: 283
Period size: 40 Copynumber: 7.9 Consensus size: 40
5716758 GAGATAGTTT
*
5716768 ACTATCGCAATGCGAAAATGACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
* *
5716808 ACTATCGCAA--CG-AGA-GA--ATTGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
5716841 AAAATCGCAA--C-AACAA--A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAA-AATGACTATCGCAATGCGAAAATG
*
5716875 ACTATCGCAATGAGAAAATGACTATCGCAA-GCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
*
5716914 ACTACCGC-ATGCGAAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCG-AAAATGACTATCGCAATGCGAAAATG
*
5716954 ACTATCGCAATGCGAAAATGACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
5716994 ACTATCGCAATGCGAATTTGACTATCGCAA--CG-AAA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
5717030 A--ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGA
5717062 TTCTTGTTGC
Statistics
Matches: 215, Mismatches: 23, Indels: 36
0.78 0.08 0.13
Matches are distributed among these distances:
33 35 0.16
34 34 0.16
35 2 0.01
36 6 0.03
37 7 0.03
38 8 0.04
39 32 0.15
40 86 0.40
41 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.18
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:5717091 original size:20 final size:20
Alignment explanation
Indices: 5717067--5717154 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
5717057 TGCGATTCTT
**
5717067 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
* *
5717087 ATTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGC
*
5717107 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGC
5717127 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
5717147 GTTGCGAT
1 GTTGCGAT
5717155 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:5717738 original size:41 final size:40
Alignment explanation
Indices: 5717661--5717751 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 40
5717651 CCTCCCCTAT
*
5717661 CGTTCAAGAGGCCCTATCATCCCTCAAGAGTCCCCTCCCA
1 CGTTCAAGAGGCCCTATCATCACTCAAGAGTCCCCTCCCA
* * *
5717701 CGTTCAAGAGGCCACTGTCATCATTGAAGAGGT-CCCTCCCA
1 CGTTCAAGAGGCC-CTATCATCACTCAAGA-GTCCCCTCCCA
* *
5717742 CATTCTAGAG
1 CGTTCAAGAG
5717752 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
40 13 0.30
41 28 0.65
42 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (40 bp):
CGTTCAAGAGGCCCTATCATCACTCAAGAGTCCCCTCCCA
Found at i:5720712 original size:20 final size:20
Alignment explanation
Indices: 5720687--5720740 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
5720677 AAATTCAGTA
5720687 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
5720707 TTGCGATAGTCAAAATCTCG
1 TTGCGATAGTCAGAATCTCG
5720727 TTGCGATAGTCAGA
1 TTGCGATAGTCAGA
5720741 TTCGCATTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:5720750 original size:20 final size:20
Alignment explanation
Indices: 5720686--5720753 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
5720676 GAAATTCAGT
5720686 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCTC
* *
5720706 GTTGCGATAGTCAAAATCTC
1 ATTGCGATAGTCAGAATCTC
* * *
5720726 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCTC
5720746 ATTGCGAT
1 ATTGCGAT
5720754 TTACGTATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCTC
Found at i:5720763 original size:20 final size:20
Alignment explanation
Indices: 5720740--5720872 Score: 230
Period size: 20 Copynumber: 6.7 Consensus size: 20
5720730 CGATAGTCAG
5720740 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5720760 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
5720780 CTTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
5720800 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
5720820 ATTCTCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5720840 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5720860 ATTCGCATTGCGA
1 ATTCGCATTGCGA
5720873 ATTAGGAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:5720771 original size:40 final size:40
Alignment explanation
Indices: 5720727--5720853 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
5720717 CAAAATCTCG
5720727 TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCA
*
5720767 TTGCGATTTACGTC---TTCGTATTGCGATTTACGTATTCGCA
1 TTGCGA--TA-GTCAGATTCGCATTGCGATTTACGTATTCGCA
* * *
5720807 TTACGAT--TTACGTATTCTCATTGCGATTTACGTATTCGCA
1 TTGCGATAGTCA-G-ATTCGCATTGCGATTTACGTATTCGCA
5720847 TTGCGAT
1 TTGCGAT
5720854 TTACGTATTC
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
35 1 0.01
38 1 0.01
40 66 0.90
42 2 0.03
43 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCA
Found at i:5720892 original size:21 final size:21
Alignment explanation
Indices: 5720862--5720914 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5720852 ATTTACGTAT
*
5720862 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
5720883 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
5720904 TCGCAATGCGA
1 TCGCAATGCGA
5720915 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:5725790 original size:25 final size:25
Alignment explanation
Indices: 5725761--5725816 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
5725751 TATAACTGAA
5725761 AATAATGACAAGATAACCACATGAT
1 AATAATGACAAGATAACCACATGAT
*
5725786 AATAATGACAAGATAATCACATGAT
1 AATAATGACAAGATAACCACATGAT
*
5725811 AGTAAT
1 AATAAT
5725817 AGTGTATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (25 bp):
AATAATGACAAGATAACCACATGAT
Found at i:5728517 original size:80 final size:82
Alignment explanation
Indices: 5728426--5728656 Score: 234
Period size: 80 Copynumber: 2.9 Consensus size: 82
5728416 TTTAGCAGCA
* ** *
5728426 TTTTAGAACAAACGTCATTAAATACTTTTACTTTAGTAGTGTTTTT-ATACAAACGCCGCT-AAG
1 TTTTAGAACAAACGTCACTAAATACTCGTACTTTAGTAGTGTTTTTAATACAAACGCCGATAAAG
5728489 ACTGTACTTAGCAGTGC
66 ACTGTACTTAGCAGTGC
* *
5728506 TTTTAGAACAAACGTCGCTAAATACTCGTACTTTAGTGGTGTTTTTAATACAAACGCCGATAAAG
1 TTTTAGAACAAACGTCACTAAATACTCGTACTTTAGTAGTGTTTTTAATACAAACGCCGATAAAG
*
5728571 ATTGTACTTTAGC-G-GC
66 ACTGTAC-TTAGCAGTGC
* * * *
5728587 GTTTTA-TA-AAACG-C-CGT--AGACTCGTACTTTAGT-G-GCTTTTTTATACAAACGCCGCTA
1 -TTTTAGAACAAACGTCAC-TAAATACTCGTACTTTAGTAGTG-TTTTTAATACAAACGCCGATA
5728644 AAGACTTGTACTT
63 AAGAC-TGTACTT
5728657 TAGTGGCGTT
Statistics
Matches: 132, Mismatches: 12, Indels: 18
0.81 0.07 0.11
Matches are distributed among these distances:
75 1 0.01
76 26 0.20
77 20 0.15
78 1 0.01
79 2 0.02
80 46 0.35
81 16 0.12
82 15 0.11
83 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (82 bp):
TTTTAGAACAAACGTCACTAAATACTCGTACTTTAGTAGTGTTTTTAATACAAACGCCGATAAAG
ACTGTACTTAGCAGTGC
Found at i:5728718 original size:82 final size:82
Alignment explanation
Indices: 5728454--5728965 Score: 587
Period size: 81 Copynumber: 6.3 Consensus size: 82
5728444 TAAATACTTT
* * ** * * *
5728454 TACTTTAGTAGTGTTTTTATACAAACGCCGCT-AAGACT-GTAC-TTAGCAGTGCTTTTAGAACA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA-TACA
* * *
5728516 AACGTCGCTAAATACTCG
65 AACGCCGCTAAAGACTCA
* * * *
5728534 TACTTTAGTGGTGTTTTTAATACAAACGCCGATAAAGA-TTGTACTTTAGCGGCG-TTTTATA-A
1 TACTTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACA
*
5728596 AACGCCG-T--AGACTCG
65 AACGCCGCTAAAGACTCA
* * *
5728611 TACTTTAGTGGCTTTTTTATACAAACGCCGCTAAAGACTTGTACTTTAGTGGCGTTTTTATTCAA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
5728676 ACGCCGCTAAAGACTCA
66 ACGCCGCTAAAGACTCA
* * * *
5728693 TTC-TTAGTGGCGTTTTTAATACAAACGACGCTATAGACTCGTATTTTAGTGGCGTTTTTTATAC
1 TACTTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCG-TTTTTATAC
*
5728757 AAACGCCGCTAGAGACTCA
64 AAACGCCGCTAAAGACTCA
* * * *
5728776 TACTTTAGTGGCGTTTTAATACAAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTAATACA
1 TACTTTAGTGGCGTTTTTATAC-AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACA
* *
5728841 AACGCCGCTATAGACTCG
65 AACGCCGCTAAAGACTCA
* * * *
5728859 TACTTTATTGGCGTTTTTATACAAACGCCACTATAGACTCGTAC-TTAGTGGAGTTTTTATACAA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
*
5728923 ACGCCGCTATAGACTCA
66 ACGCCGCTAAAGACTCA
*
5728940 TACTTTAGTGGCGTTTTTTTACAAAC
1 TACTTTAGTGGCGTTTTTATACAAAC
5728966 TCCGATGTAG
Statistics
Matches: 380, Mismatches: 38, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
76 18 0.05
77 37 0.10
78 6 0.02
79 9 0.02
80 25 0.07
81 85 0.22
82 74 0.19
83 84 0.22
84 42 0.11
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (82 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
ACGCCGCTAAAGACTCA
Found at i:5728849 original size:207 final size:200
Alignment explanation
Indices: 5728444--5728971 Score: 652
Period size: 207 Copynumber: 2.6 Consensus size: 200
5728434 CAAACGTCAT
* * * * ** * *
5728444 TAAATACTTTTACTTTAGTAGTGTTTTTATACAAACGCCGCT-AAGACT-GTACTTAGCAGTGCT
1 TAAAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTAGTGGAGTT
* * * * *
5728507 TTTAGA-ACAAACGTCGCTAAATACTCGTACTTTAGTGGTGTTTTTAATACAAACGCCGATAAAG
66 TTTA-ATACAAACGACGCTATAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGATAAAG
** * *
5728571 ATTGTACTTTAGCGGCGTTTTATAAAACGCCGTAGACTCGTACTTTAGTGGCTTTTTTATACAAA
130 ATCATACTTTAGCGGCGTTTTATAAAACGCCGTAGACTCGTACTTTAGTGGCATTTTAATACAAA
5728636 CGCCGC
195 CGCCGC
* * * *
5728642 TAAAGACTTGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTAAAGACTCATTCTTAGTGGCGTT
1 TAAAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTAGTGGAGTT
* * *
5728707 TTTAATACAAACGACGCTATAGACTCGTATTTTAGTGGCGTTTTTTATACAAACGCCGCTAGAGA
66 TTTAATACAAACGACGCTATAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGATAAAGA
*
5728772 CTCATACTTTAGTGGCGTTTTAATACAAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTAA
131 -TCATACTTTAGCGGCGTTTT-AT--AAAACGCCG---TAGACTCGTACTTTAGTGGCATTTTAA
5728837 TACAAACGCCGC
189 TACAAACGCCGC
* * * * *
5728849 TATAGACTCGTACTTTATTGGCGTTTTTATACAAACGCCACTATAGACTCGTACTTAGTGGAGTT
1 TAAAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTAGTGGAGTT
* * *
5728914 TTT-ATACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTT-TACAAACTCCGAT
66 TTTAATACAAACGACGCTATAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGAT
5728972 GTAGACTCGT
Statistics
Matches: 282, Mismatches: 38, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
198 37 0.13
199 7 0.02
200 64 0.23
201 17 0.06
202 2 0.01
204 9 0.03
205 11 0.04
206 39 0.14
207 96 0.34
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (200 bp):
TAAAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTAGTGGAGTT
TTTAATACAAACGACGCTATAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCGATAAAGA
TCATACTTTAGCGGCGTTTTATAAAACGCCGTAGACTCGTACTTTAGTGGCATTTTAATACAAAC
GCCGC
Found at i:5728989 original size:41 final size:41
Alignment explanation
Indices: 5728454--5728981 Score: 601
Period size: 41 Copynumber: 13.0 Consensus size: 41
5728444 TAAATACTTT
* *
5728454 TACTTTAGTAGTGTTTTTATACAAACGCCGCTA-AGACT-G
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
** * * * * * *
5728493 TAC-TTAGCAGTGCTTTTAGAACAAACGTCGCTAAATACTCG
1 TACTTTAGTGGCGTTTTTA-TACAAACGCCGCTATAGACTCG
* * * *
5728534 TACTTTAGTGGTGTTTTTAATACAAACGCCGATAAAGA-TTG
1 TACTTTAGTGGCGTTTTT-ATACAAACGCCGCTATAGACTCG
*
5728575 TACTTTAGCGGCG-TTTTATA-AAACGCCG---TAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
* * *
5728611 TACTTTAGTGGCTTTTTTATACAAACGCCGCTAAAGACTTG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
* * *
5728652 TACTTTAGTGGCGTTTTTATTCAAACGCCGCTAAAGACTCA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
* *
5728693 TTC-TTAGTGGCGTTTTTAATACAAACGACGCTATAGACTCG
1 TACTTTAGTGGCGTTTTT-ATACAAACGCCGCTATAGACTCG
* * *
5728734 TATTTTAGTGGCGTTTTTTATACAAACGCCGCTAGAGACTCA
1 TACTTTAGTGGCG-TTTTTATACAAACGCCGCTATAGACTCG
*
5728776 TACTTTAGTGGCGTTTTAATACAAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATAC-AAACGCCGCTATAGACTCG
* *
5728818 TACTTTAGTGGCATTTTAATACAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
* *
5728859 TACTTTATTGGCGTTTTTATACAAACGCCACTATAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
* *
5728900 TAC-TTAGTGGAGTTTTTATACAAACGCCGCTATAGACTCA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
* * * *
5728940 TACTTTAGTGGCGTTTTTTTACAAACTCCGATGTAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
5728981 T
1 T
5728982 GCCTTAGTTG
Statistics
Matches: 419, Mismatches: 54, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.01
36 13 0.03
37 7 0.02
38 29 0.07
39 18 0.04
40 58 0.14
41 181 0.43
42 104 0.25
43 6 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCG
Found at i:5729332 original size:108 final size:110
Alignment explanation
Indices: 5729121--5729341 Score: 369
Period size: 110 Copynumber: 2.0 Consensus size: 110
5729111 TGTTTGTTGA
5729121 TTAATTTGTTCATCTCATATAATATAAGACATATATAAATATTAAAAAAATTATACATTATTATT
1 TTAATTTGTTCATCTCA-ATAATATAAGACATATATAAATATTAAAAAAATTATA-ATTATTATT
*
5729186 TTTTGAACACAAGGAAAAGCCAACGGTTTTATTGAATTAAATAAATG
64 TTTTGAACAAAAGGAAAAGCCAACGGTTTTATTGAATTAAATAAATG
5729233 TTAATTTGTTCATCTC-ATAATATAAGACATATATAAATATTAAAAAAATTACT-ATTA-TATTT
1 TTAATTTGTTCATCTCAATAATATAAGACATATATAAATATTAAAAAAATTA-TAATTATTATTT
5729295 TTTGAACAAAAAGGAAAAGCCAACGG-TTTATTGAATTAAATAAATG
65 TTTGAAC-AAAAGGAAAAGCCAACGGTTTTATTGAATTAAATAAATG
5729341 T
1 T
5729342 GATCCAGCTG
Statistics
Matches: 106, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
108 33 0.31
109 21 0.20
110 35 0.33
111 1 0.01
112 16 0.15
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (110 bp):
TTAATTTGTTCATCTCAATAATATAAGACATATATAAATATTAAAAAAATTATAATTATTATTTT
TTGAACAAAAGGAAAAGCCAACGGTTTTATTGAATTAAATAAATG
Found at i:5730431 original size:43 final size:43
Alignment explanation
Indices: 5730381--5730628 Score: 295
Period size: 43 Copynumber: 5.8 Consensus size: 43
5730371 CGTTTTTACT
* * * *
5730381 AAAAACGCCGCTATAGATATGACTTTTTGCGACGTTTTTATCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCC
* * *
5730424 AAAAACGCCACTATAGTTCTAACCTTTTGCGGCGTTTGTATCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCC
* * * *
5730467 AAAAATGCCACTATATATCTGACCTTTTGCGGCGTTTCTATCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCC
*
5730510 AAAAACGCCGCTATAGATCTCGACATTTTGCGGCGTTTGT-TCC
1 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTATCC
* *
5730553 -AAAATGCCGCTATAGATATCGACCTTTTGCGGCGTTTGT-TCC
1 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTATCC
* * *
5730595 AGAAACGCCGCGATAGATCTTGACCTATTGCGGC
1 AAAAACGCCGCTATAGATC-TGACCTTTTGCGGC
5730629 ATTTTTTTGT
Statistics
Matches: 177, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 39 0.22
43 120 0.68
44 18 0.10
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCC
Found at i:5731471 original size:16 final size:17
Alignment explanation
Indices: 5731434--5731479 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5731424 TTTTATGGGA
5731434 AAAAAATAGTATTATTG
1 AAAAAATAGTATTATTG
*
5731451 TAAAAAT-GTAATTATT-
1 AAAAAATAGT-ATTATTG
*
5731467 AAAAAATAATATT
1 AAAAAATAGTATT
5731480 TTACTACCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (17 bp):
AAAAAATAGTATTATTG
Found at i:5744127 original size:134 final size:134
Alignment explanation
Indices: 5743958--5744225 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 134
5743948 AATTTACAAT
5743958 GTAAGTGGTAAAAATAAATTTTTATAATGAGAAAATTAATAAACATAAAGTTTCGAACATTTTTG
1 GTAAGTGGTAAAAATAAATTTTTATAATGAGAAAATTAATAAACATAAAGTTTCGAACATTTTTG
5744023 TCCAGTATGCTTCCCAAACTTGAGGTATCGATACATGTATTATAAGTATTGATCCCAAAAACATT
66 TCCAGTATGCTTCCCAAACTTGAGGTATCGATACATGTATTATAAGTATTGATCCCAAAAACATT
5744088 GAAA
131 GAAA
5744092 GTAAGTGGTAAAAATAAATTTTTATAATGAGAAAATTAATAAACATAAAGTTTCGAACATTTTTG
1 GTAAGTGGTAAAAATAAATTTTTATAATGAGAAAATTAATAAACATAAAGTTTCGAACATTTTTG
5744157 TCCAGTATGCTTCCCAAACTTGAGGTATCGATACATGTATTATAAGTATTGATCCCAAAAACATT
66 TCCAGTATGCTTCCCAAACTTGAGGTATCGATACATGTATTATAAGTATTGATCCCAAAAACATT
5744222 GAAA
131 GAAA
5744226 CCGATAATTA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (134 bp):
GTAAGTGGTAAAAATAAATTTTTATAATGAGAAAATTAATAAACATAAAGTTTCGAACATTTTTG
TCCAGTATGCTTCCCAAACTTGAGGTATCGATACATGTATTATAAGTATTGATCCCAAAAACATT
GAAA
Found at i:5744645 original size:199 final size:200
Alignment explanation
Indices: 5744184--5745145 Score: 1491
Period size: 199 Copynumber: 4.8 Consensus size: 200
5744174 ACTTGAGGTA
* * * *
5744184 TCGATACATGTATTATAAGTATTGATCC-CAAAAACATTGAAACCGATAATTATAAAGTAATAGG
1 TCGATACATTTATTATAAGTATCGATCCTC-AAAACATCGAAACCGATTATTATAAAGTAATAGG
* * *
5744248 AAAATTTACAATGTAACCCGTAAAAATATAACGGTTTAATGAGAGAATAGGTAAACATAATGTAT
65 TAAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTAT
* * *
5744313 CGATACTTTTTTTAAATTGTATCGATACTTTTTATCCAGAATGAATGTCAAACGAGATGCACGCA
130 CGATAC-TTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACA
5744378 TAAAGTG
194 TAAAGTG
* *
5744385 TCGATACATTTATTATAAGTATCGATCGTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAACCGATTATTATAAAGTAATAGGT
* * * * *
5744450 AAATTTACGATGTAATCGGTAAAAATATACCAGTTTAATGAGATAATAGATAAACATAATGTATC
66 AAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* *
5744515 GATACTTTTTTAAATTTTA-CTGATACTTTTT-TCCAGAATTAATGCCAAACGAGATGCACACAT
131 GATACTTTTTTAAATTGTATC-GATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
*
5744578 GAAGTG
195 AAAGTG
* * *
5744584 TCGATACATTTATTATAAGTATCGATCCTTAAAATATCGAAACTGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAACCGATTATTATAAAGTAATAGGT
* *
5744649 AAATTTACAATGTAACCGGTAAAAATATACTGGTTTAATGAGAGAATAGGTAAACATAATATATC
66 AAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * * *
5744714 GATACTTTTTTAAATTGTATCAACACTTTTTGTCCATAATGAATGCCAAACGAGATGCACGCATA
131 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
5744779 AAGTG
196 AAGTG
5744784 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAA-CGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAACCGATTATTATAAAGTAATAGGT
* * *
5744848 AAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGATAATAGGTAAAAATAATATATC
66 AAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
*
5744913 GATTCTTTTTTAAATTGTATCGATACTTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
131 GATACTTTTTTAAATTGTATCGATAC-TTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
5744978 AAAGTG
195 AAAGTG
* *
5744984 TCGATACATTTATTATAAGTATCGGTCCTCAAAACATCGAAACTGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAACCGATTATTATAAAGTAATAGGT
* * *
5745049 AAATTTACAATGTAATCGGTAAAAATATACCGATTTAATGAGAGAATAGGTAGACATAATGTATC
66 AAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* *
5745114 AATACTTTTTCAAATTGTATCGATACGTTTTT
131 GATACTTTTTTAAATTGTATCGATAC-TTTTT
5745146 TAAATTACGC
Statistics
Matches: 694, Mismatches: 61, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
199 285 0.41
200 181 0.26
201 227 0.33
202 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (200 bp):
TCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAACCGATTATTATAAAGTAATAGGT
AAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
AAGTG
Found at i:5744952 original size:400 final size:398
Alignment explanation
Indices: 5744184--5745134 Score: 1510
Period size: 400 Copynumber: 2.4 Consensus size: 398
5744174 ACTTGAGGTA
* * * * * * *
5744184 TCGATACATGTATTATAAGTATTGATCCCAAAAACATTGAAACCGATAATTATAAAGTAATAGGA
1 TCGATACATTTATTATAAGTATCGATCCTAAAAACATCGAAACTGATTATTATAAAGTAATAGGT
*
5744249 AAATTTACAATGTAACCCGTAAAAATATAACGGTTTAATGAGAGAATAGGTAAACATAATGTATC
66 AAATTTACAATGTAACCGGTAAAAATAT-ACGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * *
5744314 GATACTTTTTTTAAATTGTATCGATACTTTTTATCCAGAATGAATGTCAAACGAGATGCACGCAT
130 GATAC-TTTTTTAAATTGTATCAACACTTTTTATCCAGAATGAATGCCAAACGAGATGCACGCAT
*
5744379 AAAGTGTCGATACATTTATTATAAGTATCGATCGTCAAAACATCAAAACCGATTATTATAAAGTA
194 AAAGTGTCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTA
* * *
5744444 ATAGGTAAATTTACGATGTAATCGGTAAAAATATACCAGTTTAATGAGATAATAGATAAACATAA
259 ATAGGTAAATTTACAATGTAACCGGTAAAAATATACCAGTTTAATGAGATAATAGATAAAAATAA
* * *
5744509 TGTATCGATACTTTTTTAAATTTTACTGATACTTTTTTCCAGAATTAATGCCAAACGAGATGCAC
324 TATATCGATACTTTTTTAAATTGTACTGATACTTTTTTCCAGAATGAATGCCAAACGAGATGCAC
*
5744574 ACATGAAGTG
389 ACATAAAGTG
* *
5744584 TCGATACATTTATTATAAGTATCGATCCTTAAAATATCGAAACTGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTAAAAACATCGAAACTGATTATTATAAAGTAATAGGT
*
5744649 AAATTTACAATGTAACCGGTAAAAATATACTGGTTTAATGAGAGAATAGGTAAACATAATATATC
66 AAATTTACAATGTAACCGGTAAAAATATAC-GGTTTAATGAGAGAATAGGTAAACATAATGTATC
* *
5744714 GATACTTTTTTAAATTGTATCAACACTTTTTGTCCATAATGAATGCCAAACGAGATGCACGCATA
130 GATACTTTTTTAAATTGTATCAACACTTTTTATCCAGAATGAATGCCAAACGAGATGCACGCATA
*
5744779 AAGTGTCGATACATTTATTATAAGTATCGATCCTCAAAACATCGAAA-CGATTATTATAAAGTAA
195 AAGTGTCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAA
* *
5744843 TAGGTAAATTTACAATGTAACCGGTAAAAATATACCGGTTTAATGAGATAATAGGTAAAAATAAT
260 TAGGTAAATTTACAATGTAACCGGTAAAAATATACCAGTTTAATGAGATAATAGATAAAAATAAT
*
5744908 ATATCGATTCTTTTTTAAATTGTA-TCGATACTTTTTTGTCCAGAATGAATGCCAAACGAGATGC
325 ATATCGATACTTTTTTAAATTGTACT-GATAC-TTTTT-TCCAGAATGAATGCCAAACGAGATGC
5744972 ACACATAAAGTG
387 ACACATAAAGTG
* *
5744984 TCGATACATTTATTATAAGTATCGGTCCTCAAAACATCGAAACTGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTAAAAACATCGAAACTGATTATTATAAAGTAATAGGT
* * *
5745049 AAATTTACAATGTAATCGGTAAAAATATACCGATTTAATGAGAGAATAGGTAGACATAATGTATC
66 AAATTTACAATGTAACCGGTAAAAATATA-CGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* *
5745114 AATACTTTTTCAAATTGTATC
130 GATACTTTTTTAAATTGTATC
5745135 GATACGTTTT
Statistics
Matches: 509, Mismatches: 37, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
397 1 0.00
398 103 0.20
399 107 0.21
400 297 0.58
401 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (398 bp):
TCGATACATTTATTATAAGTATCGATCCTAAAAACATCGAAACTGATTATTATAAAGTAATAGGT
AAATTTACAATGTAACCGGTAAAAATATACGGTTTAATGAGAGAATAGGTAAACATAATGTATCG
ATACTTTTTTAAATTGTATCAACACTTTTTATCCAGAATGAATGCCAAACGAGATGCACGCATAA
AGTGTCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAAT
AGGTAAATTTACAATGTAACCGGTAAAAATATACCAGTTTAATGAGATAATAGATAAAAATAATA
TATCGATACTTTTTTAAATTGTACTGATACTTTTTTCCAGAATGAATGCCAAACGAGATGCACAC
ATAAAGTG
Found at i:5745132 original size:21 final size:22
Alignment explanation
Indices: 5745108--5745151 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5745098 GTAGACATAA
5745108 TGTATCAATAC-TTTTTCAAAT
1 TGTATCAATACGTTTTTCAAAT
* *
5745129 TGTATCGATACGTTTTTTAAAT
1 TGTATCAATACGTTTTTCAAAT
5745151 T
1 T
5745152 ACGCATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (22 bp):
TGTATCAATACGTTTTTCAAAT
Found at i:5745498 original size:36 final size:36
Alignment explanation
Indices: 5745437--5745507 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
5745427 GGGTCTTTTA
* *
5745437 AACGACAACATTCTTCTTAACCAAGCTCTTATTCTC
1 AACGACAACATTCTTCTCAAACAAGCTCTTATTCTC
* * *
5745473 AACGACAACCTTTTTCTCAAACAAGCTCTTCTTCT
1 AACGACAACATTCTTCTCAAACAAGCTCTTATTCT
5745508 GACCAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.30, C:0.31, G:0.06, T:0.34
Consensus pattern (36 bp):
AACGACAACATTCTTCTCAAACAAGCTCTTATTCTC
Found at i:5745507 original size:18 final size:18
Alignment explanation
Indices: 5745447--5745507 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
5745437 AACGACAACA
* *
5745447 TTCTTCTTAACCAAGCTC
1 TTCTTCTCAAACAAGCTC
*
5745465 TTATTCTCAACGACAA-C-C
1 TTCTTCTCAA--ACAAGCTC
*
5745483 TTTTTCTCAAACAAGCTC
1 TTCTTCTCAAACAAGCTC
5745501 TTCTTCT
1 TTCTTCT
5745508 GACCAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 1 0.03
18 25 0.74
19 1 0.03
20 3 0.09
ACGTcount: A:0.25, C:0.31, G:0.05, T:0.39
Consensus pattern (18 bp):
TTCTTCTCAAACAAGCTC
Found at i:5749356 original size:93 final size:93
Alignment explanation
Indices: 5749248--5749433 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
5749238 CTAGTGTTAG
5749248 GAGTGATCATGGCACTGAATTTGAAAATCTTAGATTTGCTGAGTTTTGTAATTCTAATGGTATTA
1 GAGTGATCATGGCACTGAATTTGAAAATCTTAGATTTGCTGAGTTTTGTAATTCTAATGGTATTA
5749313 GTCACAAATTTTTAGCACCTAGAACCCC
66 GTCACAAATTTTTAGCACCTAGAACCCC
5749341 GAGTGATCATGGCACTGAATTTGAAAATCTTAGATTTGCTGAGTTTTGTAATTCTAATGGTATTA
1 GAGTGATCATGGCACTGAATTTGAAAATCTTAGATTTGCTGAGTTTTGTAATTCTAATGGTATTA
5749406 GTCACAAATTTTTAGCACCTAGAACCCC
66 GTCACAAATTTTTAGCACCTAGAACCCC
5749434 TCAACAAAAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (93 bp):
GAGTGATCATGGCACTGAATTTGAAAATCTTAGATTTGCTGAGTTTTGTAATTCTAATGGTATTA
GTCACAAATTTTTAGCACCTAGAACCCC
Found at i:5754700 original size:21 final size:22
Alignment explanation
Indices: 5754676--5754719 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5754666 GTAAATATAA
5754676 TGTATCAATAC-TTTTTTAAAT
1 TGTATCAATACGTTTTTTAAAT
*
5754697 TGTATCGATACGTTTTTTAAAT
1 TGTATCAATACGTTTTTTAAAT
5754719 T
1 T
5754720 ACGCATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (22 bp):
TGTATCAATACGTTTTTTAAAT
Found at i:5758792 original size:24 final size:24
Alignment explanation
Indices: 5758741--5758793 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5758731 TTTCGTTTTT
* * * *
5758741 AATTGGAGTTTGAATTTAAATTTT
1 AATTTGAGTTTAAATTTAAATATA
*
5758765 AATTTGAGTTTAAATTTCAATATA
1 AATTTGAGTTTAAATTTAAATATA
5758789 AATTT
1 AATTT
5758794 CGGCTCCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTAAATTTAAATATA
Found at i:5762409 original size:16 final size:16
Alignment explanation
Indices: 5762388--5762419 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5762378 ACAGATGTAC
*
5762388 TAAATAATAATTAATA
1 TAAATAATAAATAATA
5762404 TAAATAATAAATAATA
1 TAAATAATAAATAATA
5762420 AAGTGTACGA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAATAATAAATAATA
Found at i:5767679 original size:3 final size:3
Alignment explanation
Indices: 5767671--5767699 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5767661 AGGTTAATAA
5767671 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5767700 AGATTATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5769095 original size:36 final size:36
Alignment explanation
Indices: 5769055--5769624 Score: 119
Period size: 36 Copynumber: 15.3 Consensus size: 36
5769045 ATAAATTTTA
* *
5769055 TCTCAGTTGATATTGTTTTTCTTAAAACAAACTTCG
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
** * * * **
5769091 TCTCACTTGAGACATT-TTTCACTCGAAATAGAAATTTTA
1 TCTCACTT--GACATTGTTTTTCT-TAAA-ACAAACTTCG
*
5769130 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCG
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
** * ** * * * **
5769166 TCTTGCTTGAGACA-GGTTTCACTCGAAACATAAATTTTA
1 TCTCACTT--GACATTGTTTTTCT-TAAA-ACAAACTTCG
* * *
5769205 TCTCACTCGAGATTGTTTTTCTTAAAACAAACTTCT
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
** * ** * * * **
5769241 TCTTGCTTGAGACAGTTTTCACTTGAAACATAAATTTTA
1 TCTCACTTGACATTGTTTT-TCTT-AAA-ACAAACTTCG
* * **
5769280 TCTCACTTAAGATTGTTTTTCTTAAAACAAACTTTA
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
* * ** * *
5769316 TATCACTTGAGACAAT-TTTCAC-TAGAAACAAAAATT-T
1 TCTCACTT--GACATTGTTTTTCTTA-AAAC-AAACTTCG
* * *
5769353 TATCACATTCAAGATTGTTTTTCTTAAAACAAACTTCG
1 TCTCAC-TT-GACATTGTTTTTCTTAAAACAAACTTCG
* * ** * * * * **
5769391 TCTCGCTTGAGACAGTTTTCACTCGAAATAGAAATTTTA
1 TCTCACTTGACATTGTTTT-TCT-TAAA-ACAAACTTCG
* *
5769430 TCTCACTTGAGATTGTTTTTCTTAAAATAAACTTCG
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
* ** ** ** * **
5769466 TCTCACTTGAGACAGTTCTCACTCGAAACATAAATTTA
1 TCTCACTTGACATTGTT-TTTCTTAAAACA-AACTTCG
* *
5769504 TCTCACTTGAGATTGTTTTTCTTAAAATAAACTTCG
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
** * * * * **
5769540 TCTGGCTTAAGACA--GTTTTCACTCGAAACAGAAATTTTA
1 TCTCACTT--GACATTGTTTT-TCT-TAAA-ACAAACTTCG
* *
5769579 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
*
5769615 TCTCGCTTGA
1 TCTCACTTGA
5769625 GATAATTTTT
Statistics
Matches: 369, Mismatches: 132, Indels: 66
0.65 0.23 0.12
Matches are distributed among these distances:
36 116 0.31
37 82 0.22
38 85 0.23
39 86 0.23
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
TCTCACTTGACATTGTTTTTCTTAAAACAAACTTCG
Found at i:5769101 original size:75 final size:75
Alignment explanation
Indices: 5768974--5769708 Score: 990
Period size: 75 Copynumber: 9.8 Consensus size: 75
5768964 AATATTAGAT
* * *
5768974 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAATAAACTTCGTCTTGTTTGAGACAGTTTTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
*
5769039 CGAAACATAA
66 CGAAACAGAA
* * * *
5769049 ATTTTATCTCAGTTGATATTGTTTTTCTTAAAACAAACTTCGTCTCACTTGAGACATTTTTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
*
5769114 CGAAATAGAA
66 CGAAACAGAA
* *
5769124 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTTGCTTGAGACAGGTTTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
*
5769189 CGAAACATAA
66 CGAAACAGAA
* * *
5769199 ATTTTATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTCTTCTTGCTTGAGACAGTTTTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
* *
5769264 TGAAACATAA
66 CGAAACAGAA
* ** * * *
5769274 ATTTTATCTCACTTAAGATTGTTTTTCTTAAAACAAACTTTATATCACTTGAGACAATTTTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
* *
5769339 AGAAACAAAA
66 CGAAACAGAA
* *
5769349 ATTTTATCACA-TTCAAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCAC
1 ATTTTATCTCACTT-GAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCAC
*
5769413 TCGAAATAGAA
65 TCGAAACAGAA
* * *
5769424 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAATAAACTTCGTCTCACTTGAGACAGTTCTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
*
5769489 CGAAACATAA
66 CGAAACAGAA
* * *
5769499 A-TTTATCTCACTTGAGATTGTTTTTCTTAAAATAAACTTCGTCTGGCTTAAGACAGTTTTCACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
5769563 CGAAACAGAA
66 CGAAACAGAA
* * * *
5769573 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCTTGAGATAATTTTTACT
1 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
*
5769638 CGAAGCAAGAA
66 CGAAAC-AGAA
* * * * * * * *
5769649 ATTTCATTTCAATCGAGATT-TTGTTTCTTAAAACAAATTTCATCTCGCTTTAGAAAGTTT
1 ATTTTATCTCACTTGAGATTGTT-TTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTT
5769709 CCCTCAAATA
Statistics
Matches: 585, Mismatches: 70, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
74 71 0.12
75 461 0.79
76 53 0.09
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (75 bp):
ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTCACT
CGAAACAGAA
Found at i:5769357 original size:37 final size:37
Alignment explanation
Indices: 5769246--5769358 Score: 88
Period size: 37 Copynumber: 3.0 Consensus size: 37
5769236 CTTCTTCTTG
* * *
5769246 CTTGAGACAGTTTTCACTTGAAACATAAATTTTATCTCA
1 CTTGAGACAATTTTCACTAGAAACAAAAATTTTA--TCA
* *** * *
5769285 CTTAAGATTGTTTTTC-TTA-AAAC-AAACTTTATATCA
1 CTTGAGA-CAATTTTCACTAGAAACAAAAATTT-TATCA
5769321 CTTGAGACAATTTTCACTAGAAACAAAAATTTTATCA
1 CTTGAGACAATTTTCACTAGAAACAAAAATTTTATCA
5769358 C
1 C
5769359 ATTCAAGATT
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
35 5 0.09
36 11 0.20
37 15 0.27
38 12 0.22
39 7 0.13
40 5 0.09
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
CTTGAGACAATTTTCACTAGAAACAAAAATTTTATCA
Done.