Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2729738 original size:41 final size:41
Alignment explanation
Indices: 2729693--2729945 Score: 357
Period size: 41 Copynumber: 6.2 Consensus size: 41
2729683 TTAAAAATCG
* *
2729693 CGTTGCGATTTACGGATACGCGTTGCGATTTAACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2729734 CGTTGTGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
2729774 CGTTGCGATTTACAGATAAGTGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2729814 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2729855 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
2729896 CGTTGCGATTTAAGGATACGCGTTACGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2729937 CGTTGCGAT
1 CGTTGCGAT
2729946 AGTCAGAATC
Statistics
Matches: 190, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 70 0.37
41 120 0.63
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2729838 original size:60 final size:61
Alignment explanation
Indices: 2729691--2729945 Score: 245
Period size: 61 Copynumber: 4.2 Consensus size: 61
2729681 CTTTAAAAAT
* *
2729691 CGCGTTGCGATTTACGGATACGCGTTGCGATTTAACGTATTGTCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTAACGTATAGTCGTTGCGATTTACGGATA
* * * * * *
2729752 CGCATTGCGATTTACGTATTCTCGTTGCGATTT-ACAG-ATAAGT-GTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTAAC-GTAT-AGTCGTTGCGATTTACGGATA
* * *
2729812 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTA-TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTAACGTA-TAGTCGTTGCGATTTACGGATA
* * * * *
2729873 CGCGTTGCGATTTTATGTAT-TGTCGTTGCGATTTAA-GGATACG-CGTTACGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATACG-CGTTGCGATTTAACGTATA-GTCGTTGCGA-TTTACGGATA
*
2729935 CTCGTTGCGAT
1 CGCGTTGCGAT
2729946 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 24, Indels: 22
0.78 0.12 0.11
Matches are distributed among these distances:
60 50 0.31
61 70 0.44
62 39 0.25
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTAACGTATAGTCGTTGCGATTTACGGATA
Found at i:2729977 original size:20 final size:20
Alignment explanation
Indices: 2729954--2730026 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
2729944 ATAGTCAGAA
* *
2729954 TCGCGTTGCGATTTAT-ATGT
1 TCGCCTTGCGATTT-TCATAT
*
2729974 TCGCGTTGCGATTTTCATAT
1 TCGCCTTGCGATTTTCATAT
2729994 TCGCCTTGCGATTTTCATAT
1 TCGCCTTGCGATTTTCATAT
2730014 TCGCCTTGCGATT
1 TCGCCTTGCGATT
2730027 CTGGAAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (20 bp):
TCGCCTTGCGATTTTCATAT
Found at i:2730044 original size:21 final size:21
Alignment explanation
Indices: 2730020--2730072 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2730010 ATATTCGCCT
2730020 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
2730041 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
2730062 TGCGATTCTGG
1 TGCGATTCTGG
2730073 GAACTGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:2731036 original size:28 final size:28
Alignment explanation
Indices: 2731004--2731082 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
2730994 TTATAAGGTA
2731004 TATTTTATTCTATTTAATATTTTGTTAG
1 TATTTTATTCTATTTAATATTTTGTTAG
*
2731032 TATTTTATTCCT-TTCTCAA-ATTTTTTTAG
1 TATTTTATT-CTATT-T-AATATTTTGTTAG
* *
2731061 TATTTTATT-TAATTAATTTTTT
1 TATTTTATTCTATTTAATATTTT
2731083 TTGCAGTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
26 2 0.05
27 6 0.14
28 12 0.28
29 21 0.49
30 2 0.05
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.66
Consensus pattern (28 bp):
TATTTTATTCTATTTAATATTTTGTTAG
Found at i:2736922 original size:29 final size:29
Alignment explanation
Indices: 2736865--2736921 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2736855 GATATTTACG
* *
2736865 GGTTGAGAGGATTATTTTTTGATGTTTTA
1 GGTTGAGAGGATTATTGTGTGATGTTTTA
*
2736894 GGTTGAGAGGATTGTTGTGTGAATGTTT
1 GGTTGAGAGGATTATTGTGTG-ATGTTT
2736922 ACGGGGTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47
Consensus pattern (29 bp):
GGTTGAGAGGATTATTGTGTGATGTTTTA
Found at i:2738013 original size:22 final size:22
Alignment explanation
Indices: 2737983--2738025 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2737973 ATATTATTTA
*
2737983 TATTATAAATTATTAGATTTTG
1 TATTATAAATTATTAAATTTTG
* *
2738005 TATTTTAAATTTTTAAATTTT
1 TATTATAAATTATTAAATTTT
2738026 ATGTTCGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTATAAATTATTAAATTTTG
Found at i:2741364 original size:6 final size:6
Alignment explanation
Indices: 2741353--2741381 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2741343 AACATGGCTA
2741353 CTCAGG CTCAGG CTCAGG CTCAGG CTCAG
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAG
2741382 CCAGCTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
CTCAGG
Found at i:2743898 original size:27 final size:27
Alignment explanation
Indices: 2743860--2743919 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
2743850 CTAAGATCCA
* *
2743860 TTCAACGATGATTTTGAAGGTGATTAG
1 TTCAACGATGATTCTGAAAGTGATTAG
2743887 TTCAACGATGATTCTGAAAGTGATTAG
1 TTCAACGATGATTCTGAAAGTGATTAG
2743914 TTCAAC
1 TTCAAC
2743920 TAGAGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (27 bp):
TTCAACGATGATTCTGAAAGTGATTAG
Found at i:2752449 original size:23 final size:23
Alignment explanation
Indices: 2752410--2752497 Score: 87
Period size: 23 Copynumber: 3.9 Consensus size: 23
2752400 TCGGGAAAAT
*
2752410 TATGTAGCACTTT-GGTGCAAACC
1 TATGTGGCA-TTTCGGTGCAAACC
2752433 TATGTGGCATTTCGGTGCAAACC
1 TATGTGGCATTTCGGTGCAAACC
*
2752456 TATGTGGTCA-TTCGG-G-ATAA-T
1 TATGTGG-CATTTCGGTGCA-AACC
*
2752477 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCATTTCGGTGCAAA
2752498 TTATGAGATG
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.04
21 13 0.23
22 9 0.16
23 31 0.54
24 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGCATTTCGGTGCAAACC
Found at i:2777612 original size:20 final size:21
Alignment explanation
Indices: 2777589--2777628 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2777579 CTCTGTATAG
*
2777589 TAGTATTGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
2777609 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
2777629 TCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:2786272 original size:81 final size:81
Alignment explanation
Indices: 2786137--2786294 Score: 280
Period size: 81 Copynumber: 2.0 Consensus size: 81
2786127 GTCTCTTGCA
* *
2786137 CAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
1 CAACTGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
2786202 CGAACCATTCTTGGTG
66 CGAACCATTCTTGGTG
* *
2786218 CAACTGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTTGCTCCGCCATTTCGTGTG
1 CAACTGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
2786283 CGAACCATTCTT
66 CGAACCATTCTT
2786295 TGTAACTCGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.16, C:0.30, G:0.22, T:0.32
Consensus pattern (81 bp):
CAACTGGCTCAGTAACTTCCTGCTCTACACCTCTGTGAGAGCTTGTCGATCCGCCATTTCGTGTG
CGAACCATTCTTGGTG
Found at i:2786596 original size:54 final size:54
Alignment explanation
Indices: 2786410--2786710 Score: 295
Period size: 54 Copynumber: 5.5 Consensus size: 54
2786400 TAGAATTAAC
* *
2786410 GATTGAGCACCTCTGTGCTTCAATCGAGAGATGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAA-T
* **
2786465 GATTGAGCACCTCTGTGCTT-AATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG-----CCAAAAT
* ** * * *
2786523 GACTGAGCACCTCTGTGCTTCAGCCG-GTAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAG-AGCTGACACCTCTGTGCAGCCAAAAT
*
2786577 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCAGCCAATTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAGCCAA-AAT
* * * * * * **
2786632 GACTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TCGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGCAGCCAAAAT
*
2786686 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
2786711 TAAAATCAAG
Statistics
Matches: 204, Mismatches: 30, Indels: 25
0.79 0.12 0.10
Matches are distributed among these distances:
53 1 0.00
54 94 0.46
55 49 0.24
56 15 0.07
58 21 0.10
59 24 0.12
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAAT
Found at i:2786611 original size:113 final size:113
Alignment explanation
Indices: 2786413--2786623 Score: 336
Period size: 113 Copynumber: 1.9 Consensus size: 113
2786403 AATTAACGAT
*
2786413 TGAGCACCTCTGTGCTTCAATCGAGAGATGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGATGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
2786478 TGTGCTTAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
66 TGTGCTTAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
* * * *
2786526 TGAGCACCTCTGTGCTTCAGCCG-GTAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAACCGAG-AGATGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCT
*
2786589 CTGTGCTTCAATCGAGGACTGACACCTCTGTGCAG
65 CTGTGCTT-AATCGAGAACTGACACCTCTGTGCAG
2786624 CCAATTATGA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
112 22 0.24
113 68 0.76
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (113 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGATGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
Found at i:2786688 original size:109 final size:110
Alignment explanation
Indices: 2786413--2786710 Score: 323
Period size: 113 Copynumber: 2.7 Consensus size: 110
2786403 AATTAACGAT
* * * * * *
2786413 TGAGCACCTCTGTGCTTCAATCGAGAGATGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCGAAGA-TGATTGAGCACCTC
2786478 TGTGCTT-AATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
65 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG---AAAAAAAATGAC
* ** * *
2786526 TGAGCACCTCTGTGCTTCAGCCGGTAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCGAAGATGATTGAGCACCTCT
* ** **
2786591 GTGCTTCAATCGAGGACTGACACCTCTGTGCAG-CCAATTATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
* * * * * *
2786635 TGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCATCGGA-ATGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAA-GCTGACACCTCTGTGCAGCGAAGATGATTGAGCACCTC
*
2786699 TGTGCTACAATC
65 TGTGCTTCAATC
2786711 TAAAATCAAG
Statistics
Matches: 159, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
109 54 0.34
110 16 0.10
112 21 0.13
113 68 0.43
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCGAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
Found at i:2793254 original size:130 final size:131
Alignment explanation
Indices: 2793008--2793266 Score: 421
Period size: 130 Copynumber: 2.0 Consensus size: 131
2792998 ATTGTTATAA
2793008 AAACATTTTATAAAACGGAGCTCCATGACACAAGTTTAAATCAAAATATTACAAACTCTCTGAAT
1 AAACATTTTATAAAACGGAGCTCCATGACACAAGTTTAAATCAAAATATTACAAACTCTCTGAAT
* * * **
2793073 ACATTATAAGGGTCCTATGAATACATATGCCCATTAAAGCTAAAACATAGTACTCTGAAGGGGGC
66 ACAATATAAGGGTCCTATGAATACACATGCCCACTAAAAATAAAACATAGTACTCTGAAGGGGGC
2793138 T
131 T
* *
2793139 AAACATTTTATAAAATGGAGCTCCATGACACAATTTTAAATCAAAATATTA-AAACTCTCTGAAT
1 AAACATTTTATAAAACGGAGCTCCATGACACAAGTTTAAATCAAAATATTACAAACTCTCTGAAT
* * *
2793203 ACAATATAAGGGTCTTATGAATACACATGCCCACTAAAAATACAATATAGTACTCTGAAGGGGG
66 ACAATATAAGGGTCCTATGAATACACATGCCCACTAAAAATAAAACATAGTACTCTGAAGGGGG
2793267 TTGTTAGAAG
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
130 69 0.58
131 49 0.42
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (131 bp):
AAACATTTTATAAAACGGAGCTCCATGACACAAGTTTAAATCAAAATATTACAAACTCTCTGAAT
ACAATATAAGGGTCCTATGAATACACATGCCCACTAAAAATAAAACATAGTACTCTGAAGGGGGC
T
Found at i:2795548 original size:2 final size:2
Alignment explanation
Indices: 2795541--2795572 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2795531 TTGTACAAAT
2795541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2795573 AAAGAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2796920 original size:44 final size:42
Alignment explanation
Indices: 2796784--2796994 Score: 140
Period size: 44 Copynumber: 4.9 Consensus size: 42
2796774 ATTTTATGAA
* * *
2796784 ATTGAAAAAACTTAGAGGCTTTAATTATAAATGTGTAAAAT-GAG
1 ATTGAAAAAACTTGGA-GCCTCAATTATAAA-G-GTAAAATCGAG
* * * * * * *
2796828 GTTGAAAAAA-TAGGGGTCTTAGTTATAAAGGTATAATCGAG
1 ATTGAAAAAACTTGGAGCCTCAATTATAAAGGTAAAATCGAG
*
2796869 ATTGAAAAAACTTGGGAGCCTCAATTATAAAGGTAGAAATTGAG
1 ATTGAAAAAACTT-GGAGCCTCAATTATAAAGGTA-AAATCGAG
** * * *
2796913 ATTGAAAACCCTTAAGG-GCATCAATTATAAAGGTAAAAAGCGAA
1 ATTGAAAAAACTT--GGAGCCTCAATTATAAAGGT-AAAATCGAG
* ** *
2796957 ATTGAAGAAACTTAAAGGCCTCAATTATAAAGTTAAAA
1 ATTGAAAAAACTTGGA-GCCTCAATTATAAAGGTAAAA
2796995 AAGTAGGATT
Statistics
Matches: 129, Mismatches: 30, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
40 6 0.05
41 13 0.10
42 12 0.09
43 23 0.18
44 72 0.56
45 3 0.02
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (42 bp):
ATTGAAAAAACTTGGAGCCTCAATTATAAAGGTAAAATCGAG
Found at i:2797078 original size:157 final size:156
Alignment explanation
Indices: 2796889--2797182 Score: 398
Period size: 157 Copynumber: 1.9 Consensus size: 156
2796879 CTTGGGAGCC
* * *
2796889 TCAATTATAAAGGTAGAAATTGAGATTGAAAACCCTTAAGGGCATCAATT-ATAAAGGTA-AAAA
1 TCAAATATAAAGGTAGAAATTGAGATTAAAAACACTTAAGGGCATCAATTGA-AAAGGTATAAAA
* *
2796952 GCGAAATTGAAGAAACTTAAAGGCCTCAATTATAAAGTTAAAAAAGTAGG-ATTACAAAATTAGG
65 -CGAAATTGAAAAAACTTAAAGGCCTCAATTATAAAATT-AAAAAGT-GGAATTA-AAAATTAGG
*
2797016 GG-CTTAATTATCCAAAAAAAATTAGGGGCT
126 GGACTCAATTATCCAAAAAAAATTAGGGGCT
* * * *
2797046 TCAAATATAAAGGTAGAAATTGAGATTAAAAACACTTAGGGGCATTAATTGAAAAGGTATATAAT
1 TCAAATATAAAGGTAGAAATTGAGATTAAAAACACTTAAGGGCATCAATTGAAAAGGTATAAAAC
* * *
2797111 GAGATTGAAAAAACTTAAGGGTCTCAATTATAAAATTAAAAAGTGGAATTAAAAATTAGGGGACT
66 GAAATTGAAAAAACTTAAAGGCCTCAATTATAAAATTAAAAAGTGGAATTAAAAATTAGGGGACT
2797176 CAATTAT
131 CAATTAT
2797183 AAAGGTAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
155 13 0.11
156 19 0.16
157 84 0.70
158 4 0.03
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (156 bp):
TCAAATATAAAGGTAGAAATTGAGATTAAAAACACTTAAGGGCATCAATTGAAAAGGTATAAAAC
GAAATTGAAAAAACTTAAAGGCCTCAATTATAAAATTAAAAAGTGGAATTAAAAATTAGGGGACT
CAATTATCCAAAAAAAATTAGGGGCT
Found at i:2797178 original size:41 final size:39
Alignment explanation
Indices: 2797113--2797269 Score: 122
Period size: 41 Copynumber: 3.8 Consensus size: 39
2797103 TATATAATGA
*
2797113 GATTGAAAAAACTTAAGGGTCTCAATTATAAAATTAAAAAGTG
1 GATTG-AAAAA-TT-AGGGACTCAATTATAAAA-TAAAAAGTG
* **
2797156 GAATT-AAAAATTAGGGGACTCAATTATAAAGGTAAAAAAAG
1 G-ATTGAAAAATTA-GGGACTCAATTATAAA-ATAAAAAGTG
*
2797197 GATTGAAAAA-TAGAGACTTCAATTATAAAGATAAAAAGTG
1 GATTGAAAAATTAGGGAC-TCAATTATAAA-ATAAAAAGTG
*
2797237 AGATTGAATAAAATTA-GGACCTCAATTAAAAAA
1 -GATTG-A-AAAATTAGGGA-CTCAATTATAAAA
2797270 ATTAAAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
39 4 0.04
40 25 0.27
41 35 0.37
42 7 0.07
43 17 0.18
44 6 0.06
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (39 bp):
GATTGAAAAATTAGGGACTCAATTATAAAATAAAAAGTG
Found at i:2797351 original size:28 final size:28
Alignment explanation
Indices: 2797297--2797352 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
2797287 TAAAAAATTA
*
2797297 GGGGCCTAATTATAAATATGAAGAAATG
1 GGGGCCTAATTATAAAGATGAAGAAATG
2797325 GGGGCCCTAATTA-AAAGGATGAA-AAATG
1 GGGG-CCTAATTATAAA-GATGAAGAAATG
2797353 CTCAGGGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.21
Consensus pattern (28 bp):
GGGGCCTAATTATAAAGATGAAGAAATG
Found at i:2806882 original size:31 final size:30
Alignment explanation
Indices: 2806847--2806904 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2806837 TAGCAGTTGT
2806847 TAACGACGAGTGA-TCATTTTGTAACAAAAAA
1 TAACG-CGAGTGACT-ATTTTGTAACAAAAAA
**
2806878 TAACGTTAGTGACTATTTTGTAACAAA
1 TAACGCGAGTGACTATTTTGTAACAAA
2806905 TGATAACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (30 bp):
TAACGCGAGTGACTATTTTGTAACAAAAAA
Found at i:2806889 original size:30 final size:30
Alignment explanation
Indices: 2806862--2806920 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2806852 ACGAGTGATC
2806862 ATTTTGTAACAAAAAATAACGTTAGTGACT
1 ATTTTGTAACAAAAAATAACGTTAGTGACT
**
2806892 ATTTTGTAACAAATGATAACGTTAGTGAC
1 ATTTTGTAACAAAAAATAACGTTAGTGAC
2806921 CGATTTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (30 bp):
ATTTTGTAACAAAAAATAACGTTAGTGACT
Found at i:2807336 original size:70 final size:70
Alignment explanation
Indices: 2807218--2807348 Score: 226
Period size: 70 Copynumber: 1.9 Consensus size: 70
2807208 TTTATTGTGG
*
2807218 TAATGATTTAGCACTTAAAAGAAAGAATCATTGCAAAGAGTTTCATCATACATAATTTGATCAAG
1 TAATGATTTAGCACTTAAAAGAAAGAATCATTGAAAAGAGTTTCATCATACATAATTTGATCAAG
2807283 CCGAC
66 CCGAC
* * *
2807288 TAATGATTTAGCACTTAAAATAAATAATCATTGAAAAGAGTTTTATCATACATAATTTGAT
1 TAATGATTTAGCACTTAAAAGAAAGAATCATTGAAAAGAGTTTCATCATACATAATTTGAT
2807349 TTAGCACATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 57 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (70 bp):
TAATGATTTAGCACTTAAAAGAAAGAATCATTGAAAAGAGTTTCATCATACATAATTTGATCAAG
CCGAC
Found at i:2811941 original size:29 final size:29
Alignment explanation
Indices: 2811852--2811941 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
2811842 AGGCCAAAAT
* * *
2811852 ATTAAACTTCTAAAAATTACATGTTTGATC
1 ATTAAACTTTTAAAACTTACATTTTTG-TC
* * * * *
2811882 CTTAAACTTTTCAAATCTTATACTTTGGTC
1 ATTAAACTTTT-AAAACTTACATTTTTGTC
*
2811912 ATTAAAATTTTAAAACTTACATTTTTGTC
1 ATTAAACTTTTAAAACTTACATTTTTGTC
2811941 A
1 A
2811942 CTACTAAAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
29 15 0.33
30 20 0.44
31 10 0.22
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (29 bp):
ATTAAACTTTTAAAACTTACATTTTTGTC
Found at i:2813164 original size:16 final size:17
Alignment explanation
Indices: 2813143--2813174 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2813133 AATCACGATG
2813143 ACCAAA-ATTTGATCAA
1 ACCAAATATTTGATCAA
2813159 ACCAAATATTTGATCA
1 ACCAAATATTTGATCA
2813175 CTCCAAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (17 bp):
ACCAAATATTTGATCAA
Found at i:2816353 original size:201 final size:199
Alignment explanation
Indices: 2815954--2816420 Score: 497
Period size: 201 Copynumber: 2.3 Consensus size: 199
2815944 TTGAGAATAA
* * *
2815954 CTATCTGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAGCTCGAGAGCACATTGAATGCATGGT
1 CTATCTGTCAACCAAAGCTTTCGAGTTTGATTCCACTCAGTTCGAGAGCACATTGACTGCATGGT
* ** ** * ** *
2816019 AACAACAAAGAGTTACTTTCAATCAAAATTCAAACCAAGGTCCTTCAGCCACTAAGAAGACCTAG
66 AGCAACAAAGAACTACTTTCAATCAAAATTCAAACCAAGAACCTTAAGCCAAGAAGAAGACCCAG
* * * ***
2816084 GTTGACTATGATTTGGTAATAAGGAACCACTTCCTAGCCAAATTTCAACATAGCTTAAGGTTAGA
131 GTTAACTATGATTTGGCAATAAGGAACCACTTCCTAGCCAAATATCAACATAGCTTAAGACGAGA
2816149 AGAG
196 AGAG
* * * *
2816153 CTATCTGTCGACCAAAGCTTTTGAGTTTTATTACACTCAGTTTCGAGAGCACATTGACTGCATGG
1 CTATCTGTCAACCAAAGCTTTCGAGTTTGATTCCACTCAG-TTCGAGAGCACATTGACTGCATGG
* ** * * * *
2816218 TAGCAGCAAAGAACTACATTTCGGTCAAATTTCAAATCGAGAACTTTAAGCCAAGAAGAAGACCC
65 TAGCAACAAAGAACTAC-TTTCAATCAAAATTCAAACCAAGAACCTTAAGCCAAGAAGAAGACCC
* * * * * * **
2816283 AGGTTAACTGTGATTTTGCAATAAAGG-ACCACTTTCTAGTCAGATATCGATGTAGCTTAAGACG
129 AGGTTAACTATGATTTGGCAAT-AAGGAACCACTTCCTAGCCAAATATCAACATAGCTTAAGACG
2816347 AGAAGAG
193 AGAAGAG
* * * * **
2816354 CTATGTGTCAACCAAAGCTTTCGAGTTCGATTCCACTCAGCTT-GAGAGCGCATCGACCACATGG
1 CTATCTGTCAACCAAAGCTTTCGAGTTTGATTCCACTCAG-TTCGAGAGCACATTGACTGCATGG
2816418 TAG
65 TAG
2816421 TAGTGGGGAA
Statistics
Matches: 217, Mismatches: 48, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
199 35 0.16
200 55 0.25
201 123 0.57
202 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (199 bp):
CTATCTGTCAACCAAAGCTTTCGAGTTTGATTCCACTCAGTTCGAGAGCACATTGACTGCATGGT
AGCAACAAAGAACTACTTTCAATCAAAATTCAAACCAAGAACCTTAAGCCAAGAAGAAGACCCAG
GTTAACTATGATTTGGCAATAAGGAACCACTTCCTAGCCAAATATCAACATAGCTTAAGACGAGA
AGAG
Found at i:2817026 original size:200 final size:199
Alignment explanation
Indices: 2815954--2817029 Score: 773
Period size: 200 Copynumber: 5.4 Consensus size: 199
2815944 TTGAGAATAA
* * ** * * ***
2815954 CTATCTGTCAACCAAAGCTTTCAAGTTTGATTCCACTCAGCTCGAGAGCACATTGAATGCATGGT
1 CTATCTGTCGACCAAAGCTTT-TAGTTCAATTCCACTCAGCTCGAGAGGACATCGACCACATGGT
* * * ** * *** * * * **
2816019 AACAACAAAGAGTTA-CTTTCAATCAAAATTCAAACCAAGGTCCTTCAGCCACTAAGAAGACCTA
65 AGCAGCAAGGAACTACCTTTCAGTCAAAATTCAAAATGAGATCTTTAAGCCAAGAAGAAGACCTA
* * * * ** **
2816083 GGTTGACTATGATTTGGTAATAAGGAACCACTTCCTAGCCAAATTTCAACATAGCTTAAGGTTAG
130 GGTTGACTGTGATTTGGCAACAAGGAACCACTTCCTAGTCAAATTTTGACATAGCTTAAGGAGAG
2816148 AAGAG
195 AAGAG
** * * * * **
2816153 CTATCTGTCGACCAAAGCTTTTGAGTTTTATTACACTCAGTTTCGAGAGCACATTGACTGCATGG
1 CTATCTGTCGACCAAAGCTTTT-AGTTCAATTCCACTCAG-CTCGAGAGGACATCGACCACATGG
* * * * *
2816218 TAGCAGCAAAGAACTACATTTCGGTCAAATTTC-AAATCGAGAACTTTAAGCCAAGAAGAAGACC
64 TAGCAGCAAGGAACTACCTTTCAGTCAAAATTCAAAAT-GAGATCTTTAAGCCAAGAAGAAGACC
* * * * * * * * **
2816282 CAGGTTAACTGTGATTTTGCAATAAAGG-ACCACTTTCTAGTCAGATATCGATGTAGCTTAA-GA
128 TAGGTTGACTGTGATTTGGCAA-CAAGGAACCACTTCCTAGTCAAATTTTGACATAGCTTAAGGA
2816345 CGAGAAGAG
192 -GAGAAGAG
* * * * *
2816354 CTATGTGTCAACCAAAGCTTTCGAGTTCGATTCCACTCAGCTTGAGAGCG-CATCGACCACATGG
1 CTATCTGTCGACCAAAGCTTT-TAGTTCAATTCCACTCAGCTCGAGAG-GACATCGACCACATGG
* *** * * * * * * *
2816418 TAGTAGTGGGGAACTAAC-TTCTGGTTAAAATTCAAACTAAGGTCTTTAAGCCAAGAAGAATACC
64 TAGCAGCAAGGAACTACCTTTC-AGTCAAAATTCAAAATGAGATCTTTAAGCCAAGAAGAAGACC
* * * * ** * ** * * *
2816482 TCGGTTGGCTTTGATTTGGCAATAAAAAACCATTTTTTAGTCAAAATTTGACATAGATTAAGGTG
128 TAGGTTGACTGTGATTTGGCAACAAGGAACCACTTCCTAGTCAAATTTTGACATAGCTTAAGGAG
2816547 AGAAGAG
193 AGAAGAG
* * ** * ** * **
2816554 CTA------G-CCAAAGATTTCGAGTTTGATTCCACACAGCTCGAGAACACATCAACCGTATGGT
1 CTATCTGTCGACCAAAGCTTT-TAGTTCAATTCCACTCAGCTCGAGAGGACATCGACCACATGGT
* * * * * * *
2816612 ACCAGCGAGGAACTACCTTCCAGTCAAAATTCAAAAAGAGTTCTTTAAGCCAA-AAAAAAACCTA
65 AGCAGCAAGGAACTACCTTTCAGTCAAAATTCAAAATGAGATCTTTAAGCCAAGAAGAAGACCTA
* * * *
2816676 GGTTGACTGTGATTTGGTAACAATGAACCACTTCCCAGTCAAATTTTGACGA-AGCTTAAGGCGA
130 GGTTGACTGTGATTTGGCAACAAGGAACCACTTCCTAGTCAAATTTTGAC-ATAGCTTAAGGAGA
* *
2816740 GAAAAA
194 GAAGAG
* * * * **
2816746 CTATATGTCGACCAAAGATTTTAAGTTCAATTCCAATCAACTTAAGAGCG-CATCGACCACATGG
1 CTATCTGTCGACCAAAGCTTTT-AGTTCAATTCCACTCAGCTCGAGAG-GACATCGACCACATGG
* * * *
2816810 TAGCAGTATGGAACTACCTTTCAGTCAAATTTTAAAATGATG-TCTTTAAGCCAAGAAGAAGACC
64 TAGCAGCAAGGAACTACCTTTCAGTCAAAATTCAAAATGA-GATCTTTAAGCCAAGAAGAAGACC
* *
2816874 TAGGTTGACTGCGATTTGGCAACAAGGAACCACTTCCTAGTCAAATTTTGACATAGCTTAAGGAA
128 TAGGTTGACTGTGATTTGGCAACAAGGAACCACTTCCTAGTCAAATTTTGACATAGCTTAAGGAG
*
2816939 ATAAGAG
193 AGAAGAG
* * * * * **
2816946 TTATCTATCGACTAAAGCTTTTATGTTCAATTTCACTTAGCTCGAGAGGACATTAACCACATGGT
1 CTATCTGTCGACCAAAGCTTTTA-GTTCAATTCCACTCAGCTCGAGAGGACATCGACCACATGGT
2817011 AGCAGCAAGGAACTACCTT
65 AGCAGCAAGGAACTACCTT
2817030 GCTGTTAAAC
Statistics
Matches: 678, Mismatches: 170, Indels: 57
0.75 0.19 0.06
Matches are distributed among these distances:
192 64 0.09
193 83 0.12
194 2 0.00
198 1 0.00
199 125 0.18
200 281 0.41
201 118 0.17
202 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (199 bp):
CTATCTGTCGACCAAAGCTTTTAGTTCAATTCCACTCAGCTCGAGAGGACATCGACCACATGGTA
GCAGCAAGGAACTACCTTTCAGTCAAAATTCAAAATGAGATCTTTAAGCCAAGAAGAAGACCTAG
GTTGACTGTGATTTGGCAACAAGGAACCACTTCCTAGTCAAATTTTGACATAGCTTAAGGAGAGA
AGAG
Found at i:2819580 original size:41 final size:40
Alignment explanation
Indices: 2819523--2819616 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 40
2819513 GTTCTTTGTT
* * * * * *
2819523 AACGCTGCAACAGATTAGTACTTTAGCTGCACTTTTATACA
1 AACGCCGCAATAGATTAGAAATTTAGCGGC-CTTTTAAACA
* *
2819564 AACGCCTCAATAGATTAGAAATTTAGCGGCGTTTTAAACA
1 AACGCCGCAATAGATTAGAAATTTAGCGGCCTTTTAAACA
*
2819604 AAGGCCGCAATAG
1 AACGCCGCAATAG
2819617 TATTTACCTA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
40 19 0.44
41 24 0.56
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (40 bp):
AACGCCGCAATAGATTAGAAATTTAGCGGCCTTTTAAACA
Found at i:2820380 original size:20 final size:22
Alignment explanation
Indices: 2820348--2820390 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2820338 TAGGGTTTTT
2820348 ACCTTTAAAAATG-TTAATTTG
1 ACCTTTAAAAATGTTTAATTTG
2820369 ACCTTT-AAAATGTTTAATTTG
1 ACCTTTAAAAATGTTTAATTTG
2820390 A
1 A
2820391 ATTGAAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
ACCTTTAAAAATGTTTAATTTG
Found at i:2824628 original size:43 final size:43
Alignment explanation
Indices: 2824498--2824662 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 43
2824488 TTTGTATCTC
* * * *
2824498 AAAATGCCGCTATAGAT-TTGATCTTTTGTGGTGTTTGTTTCA
1 AAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTTCCA
* * *
2824540 AAAACGCCGTTATAGATC-TGACCTTTTGCGG-GTTTGTTCTAA
1 AAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTTC-CA
* * *
2824582 AAAATGTCGCTATAGATCTTGACCTTTTACGACGTTTGTTCCA
1 AAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTTCCA
* *
2824625 AAAATGACGCTATAGATCTCGACCTTTTGCGGCGTTTG
1 AAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTG
2824663 GCGTTTGTTC
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
41 7 0.07
42 42 0.41
43 46 0.45
44 8 0.08
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (43 bp):
AAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTTCCA
Found at i:2824639 original size:85 final size:86
Alignment explanation
Indices: 2824498--2824662 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 86
2824488 TTTGTATCTC
* ** ** * * *
2824498 AAAATGCCGCTATAGATTTGATCTTTTGTGGTGTTTGTTTCAAAAACGCCGTTATAGATCT-GAC
1 AAAATGCCGCTATAGATTTGACCTTTTACGACGTTTGTTCCAAAAACGACGCTATAGATCTCGAC
2824562 CTTTTGCGG-GTTTGTTCTAA
66 CTTTTGCGGCGTTTGTTCTAA
* *
2824582 AAAATGTCGCTATAGATCTTGACCTTTTACGACGTTTGTTCCAAAAATGACGCTATAGATCTCGA
1 AAAATGCCGCTATAGAT-TTGACCTTTTACGACGTTTGTTCCAAAAACGACGCTATAGATCTCGA
2824647 CCTTTTGCGGCGTTTG
65 CCTTTTGCGGCGTTTG
2824663 GCGTTTGTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 16 0.24
85 35 0.51
86 12 0.18
87 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (86 bp):
AAAATGCCGCTATAGATTTGACCTTTTACGACGTTTGTTCCAAAAACGACGCTATAGATCTCGAC
CTTTTGCGGCGTTTGTTCTAA
Found at i:2829653 original size:321 final size:321
Alignment explanation
Indices: 2829071--2829713 Score: 1277
Period size: 321 Copynumber: 2.0 Consensus size: 321
2829061 AATTGCTGGT
2829071 CACTCCTAGAAGCTTGAAATTATCAGGGCCCCTTGATAGGAAATTGCAGGAGAGCTTGATGCTCA
1 CACTCCTAGAAGCTTGAAATTATCAGGGCCCCTTGATAGGAAATTGCAGGAGAGCTTGATGCTCA
2829136 ATGATAGGAGCCCAAAGGTTCATGGTGACAACAGCAGGAAGAAGGCAAGTGGGGACTTCGTTGAA
66 ATGATAGGAGCCCAAAGGTTCATGGTGACAACAGCAGGAAGAAGGCAAGTGGGGACTTCGTTGAA
*
2829201 CATACATTTTGGGAAGCACTGTTTCAGGACATGAAACCTACTTGACTTCACCATGGCCTTACAGA
131 CATACATTTTGCGAAGCACTGTTTCAGGACATGAAACCTACTTGACTTCACCATGGCCTTACAGA
2829266 TTATTCTTTTACAGTTTTATCAATATGCATGCAATTGTTGTTTCCATTCTTTTCGAGTTCATGTA
196 TTATTCTTTTACAGTTTTATCAATATGCATGCAATTGTTGTTTCCATTCTTTTCGAGTTCATGTA
2829331 ATCTAAATCTTCAAGAATTATATATACTTTTAAGTTTCATGGTTTGCTTGAGATGTTTGGG
261 ATCTAAATCTTCAAGAATTATATATACTTTTAAGTTTCATGGTTTGCTTGAGATGTTTGGG
2829392 CACTCCTAGAAGCTTGAAATTATCAGGGCCCCTTGATAGGAAATTGCAGGAGAGCTTGATGCTCA
1 CACTCCTAGAAGCTTGAAATTATCAGGGCCCCTTGATAGGAAATTGCAGGAGAGCTTGATGCTCA
2829457 ATGATAGGAGCCCAAAGGTTCATGGTGACAACAGCAGGAAGAAGGCAAGTGGGGACTTCGTTGAA
66 ATGATAGGAGCCCAAAGGTTCATGGTGACAACAGCAGGAAGAAGGCAAGTGGGGACTTCGTTGAA
2829522 CATACATTTTGCGAAGCACTGTTTCAGGACATGAAACCTACTTGACTTCACCATGGCCTTACAGA
131 CATACATTTTGCGAAGCACTGTTTCAGGACATGAAACCTACTTGACTTCACCATGGCCTTACAGA
2829587 TTATTCTTTTACAGTTTTATCAATATGCATGCAATTGTTGTTTCCATTCTTTTCGAGTTCATGTA
196 TTATTCTTTTACAGTTTTATCAATATGCATGCAATTGTTGTTTCCATTCTTTTCGAGTTCATGTA
2829652 ATCTAAATCTTCAAGAATTATATATACTTTTAAGTTTCATGGTTTGCTTGAGATGTTTGGG
261 ATCTAAATCTTCAAGAATTATATATACTTTTAAGTTTCATGGTTTGCTTGAGATGTTTGGG
2829713 C
1 C
2829714 TACTTATCTT
Statistics
Matches: 321, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
321 321 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (321 bp):
CACTCCTAGAAGCTTGAAATTATCAGGGCCCCTTGATAGGAAATTGCAGGAGAGCTTGATGCTCA
ATGATAGGAGCCCAAAGGTTCATGGTGACAACAGCAGGAAGAAGGCAAGTGGGGACTTCGTTGAA
CATACATTTTGCGAAGCACTGTTTCAGGACATGAAACCTACTTGACTTCACCATGGCCTTACAGA
TTATTCTTTTACAGTTTTATCAATATGCATGCAATTGTTGTTTCCATTCTTTTCGAGTTCATGTA
ATCTAAATCTTCAAGAATTATATATACTTTTAAGTTTCATGGTTTGCTTGAGATGTTTGGG
Found at i:2832654 original size:22 final size:23
Alignment explanation
Indices: 2832624--2832675 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
2832614 AGATTTTTTA
* *
2832624 TGAATAGTGATGAACAGTACC-G
1 TGAACAGTGATGAACAATACCTG
2832646 TGAACAGTGATGAACAATACCTG
1 TGAACAGTGATGAACAATACCTG
2832669 TGAACAG
1 TGAACAG
2832676 CACATAGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (23 bp):
TGAACAGTGATGAACAATACCTG
Found at i:2833203 original size:45 final size:45
Alignment explanation
Indices: 2833137--2833287 Score: 196
Period size: 45 Copynumber: 3.3 Consensus size: 45
2833127 CAATATTTTT
* * *
2833137 CCATTTATTAACCATAAGCTCGTAAGCTTATTTTATCAAAATACTTA
1 CCATTTATT--CCATAAGCTCGTAAACTTATTTTACCAATATACTTA
* * *
2833184 CCATTTATCCCATAAGCTCGTAAACTTATCTTACCATTATACTTA
1 CCATTTATTCCATAAGCTCGTAAACTTATTTTACCAATATACTTA
* * *
2833229 CCATTTGTTCCATAAGCTCGTAAACTTATTTTACCAATACACTTG
1 CCATTTATTCCATAAGCTCGTAAACTTATTTTACCAATATACTTA
2833274 CCA-TTATTCCATAA
1 CCATTTATTCCATAA
2833288 CCATATACCA
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 10 0.11
45 73 0.80
47 8 0.09
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (45 bp):
CCATTTATTCCATAAGCTCGTAAACTTATTTTACCAATATACTTA
Found at i:2833465 original size:57 final size:56
Alignment explanation
Indices: 2833366--2833489 Score: 158
Period size: 57 Copynumber: 2.2 Consensus size: 56
2833356 ACCGTAGTGC
** * **
2833366 TATCCCGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTA
1 TATCCCGTATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTTAAGTA
* * * *
2833422 TAGTCCCGTATGGCACATAAGGTCGTACCCACTATATACACTAGGTATCCTTTAGTG
1 TA-TCCCGTATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTTAAGTA
2833479 TATCCCGTATG
1 TATCCCGTATG
2833490 CAGCCTGTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 11 0.19
57 47 0.81
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (56 bp):
TATCCCGTATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTTAAGTA
Found at i:2838887 original size:22 final size:23
Alignment explanation
Indices: 2838857--2838908 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
2838847 GATTTTTTTA
*
2838857 TGAATAGTGATGAACAGTACC-G
1 TGAACAGTGATGAACAGTACCTG
2838879 TGAACAGTGATGAACAGTACCTG
1 TGAACAGTGATGAACAGTACCTG
2838902 TGAACAG
1 TGAACAG
2838909 CACATAGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (23 bp):
TGAACAGTGATGAACAGTACCTG
Found at i:2839436 original size:45 final size:45
Alignment explanation
Indices: 2839367--2839520 Score: 202
Period size: 45 Copynumber: 3.4 Consensus size: 45
2839357 ATTCAATATT
* *
2839367 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTATCAAAATAC
1 TTACCATTTATT--CCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
2839414 TTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
2839459 TTACCATTTGTTCCATAAGCTCGTAAACTTATTTTACCAATACAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
2839504 TTGCCA-TTATTCCATAA
1 TTACCATTTATTCCATAA
2839521 CCATATACCA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 10 0.11
45 73 0.78
47 11 0.12
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.38
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:2840636 original size:30 final size:30
Alignment explanation
Indices: 2840587--2840651 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2840577 ATTTTGGTCC
* *
2840587 CTAAACTTTCCAATTTTTATACTTTGATCA
1 CTAAACTTTCCAATATTTATAATTTGATCA
*
2840617 CTAAACTTTACCAA-ATTTATAATTTGTTCA
1 CTAAACTTT-CCAATATTTATAATTTGATCA
*
2840647 TTAAA
1 CTAAA
2840652 TAAATCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (30 bp):
CTAAACTTTCCAATATTTATAATTTGATCA
Found at i:2848048 original size:3 final size:3
Alignment explanation
Indices: 2848042--2848097 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
2848032 TTACCCATAA
*
2848042 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2848090 TAT TAT TA
1 TAT TAT TA
2848098 AATATATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2848609 original size:16 final size:16
Alignment explanation
Indices: 2848590--2848620 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2848580 GACAGAGCCG
*
2848590 GAGAAAGAAAAAAACA
1 GAGAAAAAAAAAAACA
2848606 GAGAAAAAAAAAAAC
1 GAGAAAAAAAAAAAC
2848621 TACTACCAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
GAGAAAAAAAAAAACA
Found at i:2849544 original size:16 final size:16
Alignment explanation
Indices: 2849520--2849550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2849510 TAAATATTTT
*
2849520 TATAGTAATAAATATA
1 TATAATAATAAATATA
2849536 TATAATAATAAATAT
1 TATAATAATAAATAT
2849551 TTATTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAATAATAAATATA
Found at i:2860898 original size:1 final size:1
Alignment explanation
Indices: 2860892--2860939 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
2860882 ATGCTTTAAG
* * * * *
2860892 AAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAGAAGAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2860940 GGAGGGTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:2860910 original size:10 final size:10
Alignment explanation
Indices: 2860895--2860939 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
2860885 CTTTAAGAAA
2860895 AAAAAAAAAG
1 AAAAAAAAAG
2860905 AAAAAAAAAG
1 AAAAAAAAAG
2860915 -AAAAAAAAG
1 AAAAAAAAAG
2860924 AAGAAAAAAAG
1 AA-AAAAAAAG
2860935 AAAAA
1 AAAAA
2860940 GGAGGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.27
10 14 0.42
11 10 0.30
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2860920 original size:19 final size:20
Alignment explanation
Indices: 2860892--2860939 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2860882 ATGCTTTAAG
2860892 AAAA-AAAAAAAAGAA-AAA
1 AAAAGAAAAAAAAGAAGAAA
2860910 AAAAGAAAAAAAAGAAGAAA
1 AAAAGAAAAAAAAGAAGAAA
2860930 AAAAGAAAAA
1 AAAAGAAAAA
2860940 GGAGGGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 13 0.46
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAAGAAA
Found at i:2860920 original size:20 final size:21
Alignment explanation
Indices: 2860897--2860936 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2860887 TTAAGAAAAA
2860897 AAAAAAAGAAAAAAAAAG-A-
1 AAAAAAAGAAAAAAAAAGAAG
2860916 AAAAAAAGAAGAAAAAAAGAA
1 AAAAAAAGAA-AAAAAAAGAA
2860937 AAAGGAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 8 0.42
21 1 0.05
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAGAAG
Found at i:2860934 original size:11 final size:11
Alignment explanation
Indices: 2860889--2860936 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
2860879 ATTATGCTTT
2860889 AAGAA-AAAAA
1 AAGAAGAAAAA
*
2860899 AAAAAGAAAAA
1 AAGAAGAAAAA
2860910 AA-AAGAAAAAA
1 AAGAAG-AAAAA
2860921 AAGAAGAAAAA
1 AAGAAGAAAAA
2860932 AAGAA
1 AAGAA
2860937 AAAGGAGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 7 0.21
11 24 0.71
12 3 0.09
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:2862297 original size:82 final size:83
Alignment explanation
Indices: 2862066--2862446 Score: 681
Period size: 82 Copynumber: 4.7 Consensus size: 83
2862056 CATTAAATGA
2862066 AAGATGAA-TTGCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTA--TGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2862127 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
2862145 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2862210 A-CAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
2862227 AAGATGAATTTG-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2862291 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
2862309 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC-GA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2862373 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
2862391 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTG-G-TATTTGATCTGGTT
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2862447 TGGTAGAACT
Statistics
Matches: 293, Mismatches: 3, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
79 8 0.03
80 18 0.06
81 84 0.29
82 117 0.40
83 66 0.23
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACCAATCATTGAATTTAG
Done.