Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004462.1 Hibiscus syriacus cultivar Beakdansim tig00009834_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: 80294
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4781 original size:74 final size:73
Alignment explanation
Indices: 4677--4856 Score: 206
Period size: 74 Copynumber: 2.4 Consensus size: 73
4667 GAAGCAAATT
* * *
4677 CTGAAAGCCCATTTCAATC-ATAATCAGGAATATTGACGCATTTTGAATGTTCACGTCA-A-CAA
1 CTGAAAGCCCATTTCAATCAAAAAT-TGGAATATTGACGCATTTTGAACG-TC-CGT-ATAGCAA
**
4739 ATGTTGGGCATG
62 ATACTGGGCATG
* * *
4751 CTGAAAGCACATTTCAATCAAAAATTGGAATATTGGCGCATTTTGAACGTCTGTATTAGCAAATA
1 CTGAAAGCCCATTTCAATCAAAAATTGGAATATTGACGCATTTTGAACGTCCGTA-TAGCAAATA
4816 CTGGGCATG
65 CTGGGCATG
4825 CTGAAAGCCCATTTCAAT-AAGAAATTGGAATA
1 CTGAAAGCCCATTTCAATCAA-AAATTGGAATA
4857 ACATTTGAAC
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
71 1 0.01
72 2 0.02
73 5 0.05
74 80 0.87
75 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (73 bp):
CTGAAAGCCCATTTCAATCAAAAATTGGAATATTGACGCATTTTGAACGTCCGTATAGCAAATAC
TGGGCATG
Found at i:4867 original size:68 final size:70
Alignment explanation
Indices: 4677--4904 Score: 178
Period size: 74 Copynumber: 3.2 Consensus size: 70
4667 GAAGCAAATT
* * * ** *
4677 CTGAAAGCCCATTTCAATC-ATAATCAGGAATATTGACGCATTTTGAATGTTCACGTCAACAAAT
1 CTGAAAGCCCATTTCAATCAAAAAT-TGGAATA--GA--CATTTTGAACGTTCATATCAGCAAAT
**
4741 GTTGGGCATG
61 ACTGGGCATG
* * * *
4751 CTGAAAGCACATTTCAATCAAAAATTGGAATATTGGCGCATTTTGAACG-TCTGTATTAGCAAAT
1 CTGAAAGCCCATTTCAATCAAAAATTGGAATA---G-ACATTTTGAACGTTC-ATATCAGCAAAT
4815 ACTGGGCATG
61 ACTGGGCATG
* *
4825 CTGAAAGCCCATTTCAAT-AAGAAATTGGAATA-ACA-TTTGAACGTTCATATCAGTAAATGCTG
1 CTGAAAGCCCATTTCAATCAA-AAATTGGAATAGACATTTTGAACGTTCATATCAGCAAATACT-
4887 GGGCATG
64 GGGCATG
*
4894 CTGAAGGCCCA
1 CTGAAAGCCCA
4905 CATCATTATG
Statistics
Matches: 127, Mismatches: 20, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
68 19 0.15
69 21 0.17
73 4 0.03
74 77 0.61
75 6 0.05
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (70 bp):
CTGAAAGCCCATTTCAATCAAAAATTGGAATAGACATTTTGAACGTTCATATCAGCAAATACTGG
GCATG
Found at i:6951 original size:45 final size:45
Alignment explanation
Indices: 6897--6995 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
6887 GGAAGCTTTT
* * * *
6897 TGATATTTTTAAAGCCT-TCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCT-GGGTCATCCGTAAGACCTACAGTGCA
6942 TGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCA
1 TGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCA
6987 TGATGTTTT
1 TGATGTTTT
6996 CAAAAAGCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (45 bp):
TGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCA
Found at i:7013 original size:121 final size:121
Alignment explanation
Indices: 6799--7240 Score: 687
Period size: 121 Copynumber: 3.7 Consensus size: 121
6789 CTATTTCCCA
* * * *
6799 CATCTGTAAGCCATTCAGTGCATGATATTTTTAAAGCCTCTAGGTCATCCGTAAGA-CTTACAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAA-ACCCTACAGT
*
6863 GCA-GAATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGT
65 GCATG-ATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGT
6920 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGA-CCTACAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAA-ACCCTACAGT
* *
6984 GCATGATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATATTTTTAAAGCCTCCAGGT
65 GCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGT
*
7041 CATCTGTAA-CCCTTCAGTGCATGATGTTTTTAAAGCCT-TCGGGTCATCTGTAAACCCTACAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCT-GGGTCATCCGTAAACCCTACAGT
*
7104 GCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGT
65 GCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGT
* * ** *
7161 TATTTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCTATAAACCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAACCCTACAGTG
7226 CATGATGTTTTCAAA
66 CATGATGTTTTCAAA
7241 GCCTTTGGGT
Statistics
Matches: 300, Mismatches: 16, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
119 2 0.01
120 110 0.37
121 186 0.62
122 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (121 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAACCCTACAGTG
CATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGT
Found at i:7073 original size:44 final size:45
Alignment explanation
Indices: 7018--7115 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
7008 AGAAGCTTTT
* *
7018 TGATATTTTTAAAGCCTCCAGGTCATCTGT-AACCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCCAGGTCATCTGTAAACCCTACAGTGCA
* *
7062 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAACCCTACAGTGCA
1 TGATGTTTTTAAAGCCTCCAGGTCATCTGTAAACCCTACAGTGCA
*
7107 GGATGTTTT
1 TGATGTTTT
7116 CAAAAAGCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 27 0.56
45 21 0.44
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (45 bp):
TGATGTTTTTAAAGCCTCCAGGTCATCTGTAAACCCTACAGTGCA
Found at i:7112 original size:45 final size:44
Alignment explanation
Indices: 7023--7129 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
7013 CTTTTTGATA
* * * *
7023 TTTTTAAAGCCTCCAGGTCATCTGTAACCCTTCAGTGCATGATG
1 TTTTTAAAGCCTTCGGGTCATCTGTAACCCTACAGTGCAGGATG
7067 TTTTTAAAGCCTTCGGGTCATCTGTAAACCCTACAGTGCAGGATG
1 TTTTTAAAGCCTTCGGGTCATCTGT-AACCCTACAGTGCAGGATG
*
7112 TTTTCAAAAAGCCTTCGG
1 TTTT--TAAAGCCTTCGG
7130 AAGCTTTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 23 0.42
45 21 0.38
47 11 0.20
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTTTAAAGCCTTCGGGTCATCTGTAACCCTACAGTGCAGGATG
Found at i:7192 original size:45 final size:45
Alignment explanation
Indices: 7138--7331 Score: 228
Period size: 45 Copynumber: 4.3 Consensus size: 45
7128 GGAAGCTTTT
* * * * *
7138 TGATATTTTTAAAGCCTCCGGGTTATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTCTGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
7183 TGATGTTTTTAAAGCCTCTGGGTCATCTATAAACCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTCTGGGTCATCTGTAAGCCCTTCAGTGCA
*
7228 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTCTGGGTCATCTGTAAGCCCTTCAGTGCA
* * ** *
7273 TGATGTTTTCAAAGACCTCAGGGCCATCCATAAGACCTAT-AGTGCA
1 TGATGTTTTCAAAG-CCTCTGGGTCATCTGTAAGCCCT-TCAGTGCA
*
7319 GGATGTTTTCAAA
1 TGATGTTTTCAAA
7332 AAGCCTTCGG
Statistics
Matches: 130, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
45 94 0.72
46 35 0.27
47 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTCTGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:7235 original size:241 final size:242
Alignment explanation
Indices: 6799--7240 Score: 721
Period size: 241 Copynumber: 1.8 Consensus size: 242
6789 CTATTTCCCA
*
6799 CATCTGTAAGCCATTCAGTGCATGATATTTTTAAAGCCTCTAGGTCATCCGTAAGACTTACAGTG
1 CATCTGTAAGCCATTCAGTGCATGATATTTTTAAAGCCTCTAGGTCATCCGTAAGACCTACAGTG
*
6864 CAGAATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGTCATCTGTAA
66 CAGAATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGTCATCTGTAA
*
6929 GCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCATGATGTT
131 GCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCATAAGACCTACAGTGCATGATGTT
6994 TTCAAAAAGCCTTCAGAAGCTTTTTGATATTTTTAAAGCCTCCAGGT
196 TTCAAAAAGCCTTCAGAAGCTTTTTGATATTTTTAAAGCCTCCAGGT
* * * *
7041 CATCTGTAA-CCCTTCAGTGCATGATGTTTTTAAAGCCT-TCGGGTCATCTGTAA-ACCCTACAG
1 CATCTGTAAGCCATTCAGTGCATGATATTTTTAAAGCCTCT-AGGTCATCCGTAAGA-CCTACAG
* * *
7103 TGCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGTTATTTGT
64 TGCAGAATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGTCATCTGT
* *
7168 AAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCTATAA-ACCCTTCAGTGCATGAT
129 AAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCATAAGA-CCTACAGTGCATGAT
7232 GTTTTCAAA
193 GTTTTCAAA
7241 GCCTTTGGGT
Statistics
Matches: 185, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
240 3 0.02
241 173 0.94
242 9 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (242 bp):
CATCTGTAAGCCATTCAGTGCATGATATTTTTAAAGCCTCTAGGTCATCCGTAAGACCTACAGTG
CAGAATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTCCGGGTCATCTGTAA
GCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCATAAGACCTACAGTGCATGATGTT
TTCAAAAAGCCTTCAGAAGCTTTTTGATATTTTTAAAGCCTCCAGGT
Found at i:7573 original size:3 final size:3
Alignment explanation
Indices: 7565--7605 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
7555 AATTTTTTCA
*
7565 TAT TAT TAT TAT TAT TGT TAT TAT TA- TAT ATAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TA
7606 AATGAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:7658 original size:22 final size:22
Alignment explanation
Indices: 7631--7672 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7621 TAATAATACA
7631 AACCCACAGCCCA-TTTACAAAG
1 AACCCA-AGCCCAGTTTACAAAG
*
7653 AACCCATGCCCAGTTTACAA
1 AACCCAAGCCCAGTTTACAA
7673 GCCCAACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.17
Consensus pattern (22 bp):
AACCCAAGCCCAGTTTACAAAG
Found at i:8928 original size:20 final size:20
Alignment explanation
Indices: 8905--8944 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8895 TATATATATA
8905 TATAGTTTTATTCATATTAT
1 TATAGTTTTATTCATATTAT
* * *
8925 TATATTTTTCTTCATTTTAT
1 TATAGTTTTATTCATATTAT
8945 ATTTCTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (20 bp):
TATAGTTTTATTCATATTAT
Found at i:9011 original size:31 final size:33
Alignment explanation
Indices: 8951--9012 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
8941 TTATATTTCT
*
8951 TTAATTTTAGTCATATTAATATATATTATTTGA
1 TTAATTTTAGTCAAATTAATATATATTATTTGA
8984 TTAATTTTA-T-AAATTAATA-ATATTTATTT
1 TTAATTTTAGTCAAATTAATATATA-TTATTT
9013 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 1 0.04
33 9 0.33
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (33 bp):
TTAATTTTAGTCAAATTAATATATATTATTTGA
Found at i:9275 original size:2 final size:2
Alignment explanation
Indices: 9268--9293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9258 ACAAAAACCC
9268 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
9294 ACTTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10652 original size:57 final size:57
Alignment explanation
Indices: 10583--10707 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
10573 AATGAGCAAA
*
10583 GATGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATTTATATTT
1 GATGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATGTATATTT
* *
10640 GATGTATATTTTGTTGTATGTTACTAAAATGTATCTGGAGTTAATATATGTATATTT
1 GATGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATGTATATTT
10697 GATGTACATTT
1 GATGTACATTT
10708 GATTTTAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (57 bp):
GATGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATGTATATTT
Found at i:26482 original size:55 final size:55
Alignment explanation
Indices: 26421--26703 Score: 335
Period size: 55 Copynumber: 5.1 Consensus size: 55
26411 GCACTTGAAA
* * * *
26421 AATCTTCA-AATAATAAGTTCGCTCCCTATTTCTTCAGGGAGTATAAAACTCGAAC
1 AATCTTCATAA-AATAGGTCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAAC
**
26476 AATCTTCA-ATAAACGGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCATA-AAATAGGTCCGCTCCCTATTCC-TTCAGGGAGTATAGAACTCGAAC
** * ** *
26531 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAAT
1 AATCTTCATAAAATAGGTCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAAC
26586 AATCTTCATAAAAT-GAGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCATAAAATAG-GTCCGCTCCCTATTCC-TTCAGGGAGTATAGAACTCGAAC
* * *
26641 AATCTTCATAAAAT-GGATCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAT
1 AATCTTCATAAAATAGG-TCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAAC
26696 AATCTTCA
1 AATCTTCA
26704 ATATTCAGGC
Statistics
Matches: 202, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
54 7 0.03
55 187 0.93
56 8 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (55 bp):
AATCTTCATAAAATAGGTCCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAAC
Found at i:26614 original size:110 final size:110
Alignment explanation
Indices: 26440--26706 Score: 428
Period size: 110 Copynumber: 2.4 Consensus size: 110
26430 ATAATAAGTT
* * * * * *
26440 CGCTCCCTATTTCTTCAGGGAGTATAAAACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTAT
1 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAATAAACGAGTCCGCTCCCTAT
*
26505 CCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
66 CCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGATC
* *
26550 CGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAATAATCTTC-ATAAAATGAGTCCGCTCCCTA
1 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAAT-AAACGAGTCCGCTCCCTA
*
26614 TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGATC
65 TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGATC
26660 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAATA
1 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAATA
26707 TTCAGGCAGT
Statistics
Matches: 144, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
109 2 0.01
110 140 0.97
111 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (110 bp):
CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAATAAACGAGTCCGCTCCCTAT
CCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGATC
Found at i:26772 original size:89 final size:89
Alignment explanation
Indices: 26618--26795 Score: 270
Period size: 89 Copynumber: 2.0 Consensus size: 89
26608 TCCCTATCCG
* * *
26618 TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGATCCGCTCTCTATTCCTTCAGAGAGT
1 TTCAGGCAGTATAGAACTCGAACAATCTTCATAAAACGGATCCGCTCCCTATTCCTTCAGAGAGT
*
26683 ATAGAACTCGAATAATCTTCAATA
66 ATAGAACTCGAAAAATCTTCAATA
* *
26707 TTCAGGCAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCCCTA-TCCGTTCAGGGA
1 TTCAGGCAGTATAGAACTCGAACAATCTTCATA-AAACGGATCCGCTCCCTATTCC-TTCAGAGA
26770 GTATAGAACTCGAAAAATCTTCAATA
64 GTATAGAACTCGAAAAATCTTCAATA
26796 AACAGGTCCG
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
88 4 0.05
89 77 0.95
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (89 bp):
TTCAGGCAGTATAGAACTCGAACAATCTTCATAAAACGGATCCGCTCCCTATTCCTTCAGAGAGT
ATAGAACTCGAAAAATCTTCAATA
Found at i:26791 original size:55 final size:55
Alignment explanation
Indices: 26714--26902 Score: 308
Period size: 55 Copynumber: 3.4 Consensus size: 55
26704 ATATTCAGGC
* *
26714 AGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATCCGTTCAGGG
1 AGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTCAGAG
* * * *
26769 AGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCTCTATTCC-TTCAAAG
1 AGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTA-TCCGTTCAGAG
26824 AGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTCAGAG
1 AGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTCAGAG
26879 AGTATAGAACTCGAACAATCTTCA
1 AGTATAGAACTCGAACAATCTTCA
26903 TAAAACGAGT
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
54 3 0.02
55 116 0.95
56 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (55 bp):
AGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTCAGAG
Found at i:26830 original size:144 final size:144
Alignment explanation
Indices: 26570--26848 Score: 456
Period size: 144 Copynumber: 1.9 Consensus size: 144
26560 TCCTTCAAAG
* *
26570 AGTATAGAACTCGAATAATCTTCATAAAATGAGTCCGCTCCCTATCCGTTCAGGGAGTATAGAAC
1 AGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCCCTATCCGTTCAGGGAGTATAGAAC
* * *
26635 TCGAACAATCTTCATAAAATGGATCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATC
66 TCGAAAAATCTTCATAAAATGGATCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATC
26700 TTCAATATTCAGGC
131 TTCAATATTCAGGC
*
26714 AGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAA
1 AGTATAGAACTCGAACAATCTTCATA-AAACGAGTCCGCTCCCTATCCGTTCAGGGAGTATAGAA
26778 CTCGAAAAATCTTCAATAAACA-GG-TCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACA
65 CTCGAAAAATCTTC-ATAAA-ATGGATCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACA
26841 ATCTTCAA
128 ATCTTCAA
26849 CAAACAGGTC
Statistics
Matches: 126, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
143 1 0.01
144 117 0.93
145 7 0.06
146 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (144 bp):
AGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCCCTATCCGTTCAGGGAGTATAGAAC
TCGAAAAATCTTCATAAAATGGATCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATC
TTCAATATTCAGGC
Found at i:26863 original size:199 final size:199
Alignment explanation
Indices: 26508--26902 Score: 563
Period size: 199 Copynumber: 2.0 Consensus size: 199
26498 TCCCTATCCG
* *
26508 TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAAAGAGT
1 TTCAGGCAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAAAGAGT
* **
26573 ATAGAACTCGAATAATCTTCATAAAATGAGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCG
66 ATAGAACTCGAAAAATCTTCATAAAATGAGTCCGCTCCCTATCCGTTCAAAGAGTATAGAACTCG
* * *
26638 AACAATCTTCATAAAATGGATCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAATAATCTT
131 AACAATCTTCATAAAAAGGATCCGCTCCCTA-TCCGTTCAGAGAGTATAGAACTCGAACAATCTT
26702 CAATA
195 CAATA
**
26707 TTCAGGCAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCCCTA-TCCGTTCAGGGA
1 TTCAGGCAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCCCTATTCC-TTCAAAGA
*
26770 GTATAGAACTCGAAAAATCTTCAATAAACA-G-GTCCGCTCTCTATTCC-TTCAAAGAGTATAGA
64 GTATAGAACTCGAAAAATCTTC-ATAAA-ATGAGTCCGCTCCCTA-TCCGTTCAAAGAGTATAGA
26832 ACTCGAACAATCTTCA-ACAAACAGG-TCCGCTCCCTATCCGTTCAGAGAGTATAGAACTCGAAC
126 ACTCGAACAATCTTCATA-AAA-AGGATCCGCTCCCTATCCGTTCAGAGAGTATAGAACTCGAAC
26895 AATCTTCA
189 AATCTTCA
26903 TAAAACGAGT
Statistics
Matches: 177, Mismatches: 11, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
198 8 0.05
199 157 0.89
200 11 0.06
201 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (199 bp):
TTCAGGCAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAAAGAGT
ATAGAACTCGAAAAATCTTCATAAAATGAGTCCGCTCCCTATCCGTTCAAAGAGTATAGAACTCG
AACAATCTTCATAAAAAGGATCCGCTCCCTATCCGTTCAGAGAGTATAGAACTCGAACAATCTTC
AATA
Found at i:28224 original size:17 final size:17
Alignment explanation
Indices: 28187--28294 Score: 102
Period size: 14 Copynumber: 6.6 Consensus size: 17
28177 TTTATTTCTT
28187 TTTTTTTTCATTTTTCA
1 TTTTTTTTCATTTTTCA
28204 ---TTTTTCATTTTTCA
1 TTTTTTTTCATTTTTCA
28218 TTTTTTTTCATTTTTTCA
1 TTTTTTTTCA-TTTTTCA
*
28236 TTTTTTTATTATTTTTC-
1 TTTTTTT-TCATTTTTCA
* * *
28253 -CTTTTTT-ATTTCTCT
1 TTTTTTTTCATTTTTCA
*
28268 TTTTTTTTCTTTTTTCA
1 TTTTTTTTCATTTTTCA
*
28285 TTTCTTTTCA
1 TTTTTTTTCA
28295 GGAGAAATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
14 20 0.27
15 1 0.01
16 11 0.15
17 20 0.27
18 20 0.27
19 2 0.03
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTTCATTTTTCA
Found at i:28240 original size:7 final size:7
Alignment explanation
Indices: 28190--28222 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28180 ATTTCTTTTT
28190 TTTTTCA
1 TTTTTCA
28197 TTTTTCA
1 TTTTTCA
28204 TTTTTCA
1 TTTTTCA
28211 TTTTTCA
1 TTTTTCA
28218 TTTTT
1 TTTTT
28223 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:28252 original size:50 final size:50
Alignment explanation
Indices: 28181--28292 Score: 147
Period size: 50 Copynumber: 2.2 Consensus size: 50
28171 CCTCCTTTTA
* *
28181 TTTC-TTTTTTTTTTCATTTTTCATTTTTCATTTTTCATTTTTTTTCATTT
1 TTTCATTTTTTTATTCATTTTTCATTTTTCATTTCTCATTTTTTTTC-TTT
* * *
28231 TTTCATTTTTTTATT-ATTTTTCCTTTTTTATTTCTCTTTTTTTTTCTTT
1 TTTCATTTTTTTATTCATTTTTCATTTTTCATTTCTCATTTTTTTTCTTT
28280 TTTCATTTCTTTT
1 TTTCATTT-TTTT
28293 CAGGAGAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
49 11 0.20
50 35 0.64
51 9 0.16
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (50 bp):
TTTCATTTTTTTATTCATTTTTCATTTTTCATTTCTCATTTTTTTTCTTT
Found at i:28263 original size:14 final size:13
Alignment explanation
Indices: 28189--28289 Score: 52
Period size: 12 Copynumber: 7.9 Consensus size: 13
28179 TATTTCTTTT
*
28189 TTTTTTCATTTTTC
1 TTTTTT-ATTTCTC
* *
28203 ATTTTTCATTTTTC
1 -TTTTTTATTTCTC
*
28217 ATTTTT-TTTCAT-
1 TTTTTTATTTC-TC
*
28229 TTTTTCATTT-T-
1 TTTTTTATTTCTC
* *
28240 TTTATTATTTTTCC
1 TTTTTTATTTCT-C
28254 TTTTTTATTTCTC
1 TTTTTTATTTCTC
28267 TTTTTT-TTTCT-
1 TTTTTTATTTCTC
*
28278 TTTTTCATTTCT
1 TTTTTTATTTCT
28290 TTTCAGGAGA
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
11 14 0.20
12 18 0.26
13 15 0.22
14 17 0.25
15 5 0.07
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTCTC
Found at i:28288 original size:24 final size:24
Alignment explanation
Indices: 28197--28289 Score: 100
Period size: 24 Copynumber: 3.8 Consensus size: 24
28187 TTTTTTTTCA
* * *
28197 TTTTTCATTTTTCATTTTTCATTT
1 TTTTTCTTTTTTCATTTCTCTTTT
*
28221 TTTTTCATTTTTTCATTT-TTTTATT
1 TTTTTC-TTTTTTCATTTCTCTT-TT
28246 ATTTTTCCTTTTTT-ATTTCTCTTTT
1 -TTTTT-CTTTTTTCATTTCTCTTTT
28271 TTTTTCTTTTTTCATTTCT
1 TTTTTCTTTTTTCATTTCT
28290 TTTCAGGAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
23 7 0.12
24 19 0.32
25 18 0.31
26 14 0.24
27 1 0.02
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTCTTTTTTCATTTCTCTTTT
Found at i:37988 original size:45 final size:45
Alignment explanation
Indices: 37921--38057 Score: 238
Period size: 45 Copynumber: 3.0 Consensus size: 45
37911 CCATGCTTTG
*
37921 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTTGCATGC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTTGCATGC
37968 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
*
38013 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
38058 ATTTACTCGA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
45 72 0.82
46 9 0.10
47 7 0.08
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
Found at i:44046 original size:3 final size:3
Alignment explanation
Indices: 44040--44140 Score: 141
Period size: 3 Copynumber: 34.0 Consensus size: 3
44030 TTTATCCATT
* * *
44040 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
44088 TTA TCA TTA TTA ATA TTA TTT TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44135 TTA TTA
1 TTA TTA
44141 AATATATTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44055 original size:21 final size:21
Alignment explanation
Indices: 44040--44149 Score: 161
Period size: 21 Copynumber: 5.3 Consensus size: 21
44030 TTTATCCATT
44040 TTATTATTATTATTATTAATA
1 TTATTATTATTATTATTAATA
*
44061 TTATTATTATCATTATTAATA
1 TTATTATTATTATTATTAATA
*
44082 TTATTATTATCATTATTAATA
1 TTATTATTATTATTATTAATA
* *
44103 TTATTTTTATTATTATTATTA
1 TTATTATTATTATTATTAATA
44124 TTATTATT-TTATTATTAA-A
1 TTATTATTATTATTATTAATA
44143 TATATTA
1 T-TATTA
44150 AATACATATA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
19 2 0.02
20 14 0.17
21 66 0.80
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATTATTATTATTAATA
Found at i:44598 original size:1 final size:1
Alignment explanation
Indices: 44592--44624 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
44582 CCCACCTGCG
44592 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44625 GAAGACAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44688 original size:25 final size:24
Alignment explanation
Indices: 44643--44689 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
44633 AAAACCAGAG
* * *
44643 AGAAAAAACAGAGAACGGAAAAGA
1 AGAAAAAACAAACAACAGAAAAGA
44667 AGAAAAAACAAACACACAGAAAA
1 AGAAAAAACAAACA-ACAGAAAA
44690 AATACTAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (24 bp):
AGAAAAAACAAACAACAGAAAAGA
Found at i:45611 original size:20 final size:21
Alignment explanation
Indices: 45565--45611 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
45555 CCACTTTTAA
45565 ATATATTGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
45586 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
45605 ATATATT
1 ATATATT
45612 TAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:45704 original size:13 final size:12
Alignment explanation
Indices: 45661--45704 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
45651 GAATAATAAA
45661 TAATATTTTTTT
1 TAATATTTTTTT
* *
45673 TAATAAATTATTT
1 TAAT-ATTTTTTT
45686 TAATATTTTTTT
1 TAATATTTTTTT
45698 TATATAT
1 TA-ATAT
45705 ATCGAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TAATATTTTTTT
Found at i:57040 original size:14 final size:14
Alignment explanation
Indices: 57021--57047 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57011 TGCTTGAAGA
57021 AAAGAAAGAAAAAG
1 AAAGAAAGAAAAAG
57035 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
57048 AAAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAAAG
Found at i:58699 original size:52 final size:52
Alignment explanation
Indices: 58237--58692 Score: 767
Period size: 52 Copynumber: 8.8 Consensus size: 52
58227 TGAATGTGCT
58237 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
58289 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
58341 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* *
58393 CATAGCATCTTCTGGAAGCGTTCTTTGAGTTATCTGATCTGGTT-GATCATAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
58445 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
58497 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
* * *
58549 CATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTT-GATCATAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
58601 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* *
58653 CATAGCATTTTCTGGAAGTGTTCTTTGAGATATCTGATCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
58693 AATTGGATAG
Statistics
Matches: 384, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
51 6 0.02
52 372 0.97
53 6 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (52 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:59539 original size:114 final size:113
Alignment explanation
Indices: 59330--59992 Score: 1040
Period size: 114 Copynumber: 5.8 Consensus size: 113
59320 ATTCAAATCT
* *
59330 ATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATTCGTCATCTGAAGA
1 ATCACTTGATGGATCATCTTTTCCAG-AGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* *
59395 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTC
61 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
*
59448 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
59513 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *
59562 ATCAAATTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
59627 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* *
59676 ATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
59741 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
*
59789 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
59854 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
* * * *
59903 ATCAGTTGATGGATCAACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
59967 AGAAAAAGTTCATAATGAGAAGAACT
65 AGAAGAAGTTCATAATGAGAAGAACT
59993 CATCAAGAGC
Statistics
Matches: 507, Mismatches: 34, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
112 1 0.00
113 181 0.36
114 267 0.53
115 13 0.03
117 17 0.03
118 19 0.04
119 9 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATCACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
Found at i:59753 original size:227 final size:226
Alignment explanation
Indices: 59330--59992 Score: 1049
Period size: 227 Copynumber: 2.9 Consensus size: 226
59320 ATTCAAATCT
*
59330 ATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATTCGTCATCTGAAGA
1 ATCAATTGATGGATCATCATTTCCAG-AGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * *
59395 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
61 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGG
*
59460 ATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
126 ATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
59525 TAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTC
190 TAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTC
*
59562 ATCAAATTGATGGATCATCGTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
59627 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCA
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCA
59692 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
130 TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
59757 AGAAGAACTTGTTCAACCTTTTGTTTAAATTC
195 AGAAGAACTTGTTCAACCTTTTGCTTAAATTC
* * *
59789 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAATTGATGGATCA-TCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
59854 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAGTTGATGGATCA
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCA
* * * *
59919 ACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAAT
130 TCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
59983 GAGAAGAACT
194 GAGAAGAACT
59993 CATCAAGAGC
Statistics
Matches: 403, Mismatches: 25, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
226 13 0.03
227 271 0.67
228 72 0.18
229 1 0.00
231 18 0.04
232 7 0.02
233 21 0.05
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (226 bp):
ATCAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAT
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTTAAATTC
Found at i:59776 original size:341 final size:344
Alignment explanation
Indices: 59325--59990 Score: 1189
Period size: 341 Copynumber: 1.9 Consensus size: 344
59315 CAAAGATTCA
*
59325 AATCTATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATTCGTCATCT
1 AATCCATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAA-TCGTCATCT
59390 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTT
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTT
59455 GATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
130 GATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* * *
59520 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATCATCGTTT
195 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-AATTGATGGATCAACATTA
*
59585 CCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
259 CCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAG
59649 AATTTGTTCAACCTTTTACCTG
323 AATTTGTTCAACCTTTTACCTG
* *
59671 AATCCATCATTTGGTGGATCATCTTTTCCAG-AGAA-AGTTCATAATGAGAAGAA-C-TCATCTG
1 AATCCATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATCGTCATCTG
59732 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTG
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTG
59797 ATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
131 ATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
59862 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAGTTGATGGATCAACATTACC
196 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTGATGGATCAACATTACC
59927 AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
261 AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
59991 CTCATCAAGA
Statistics
Matches: 310, Mismatches: 9, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
339 1 0.00
340 78 0.25
341 180 0.58
342 1 0.00
344 18 0.06
345 4 0.01
346 28 0.09
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (344 bp):
AATCCATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAATCGTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTG
ATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTGATGGATCAACATTACC
AGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTACCTG
Found at i:60247 original size:3 final size:3
Alignment explanation
Indices: 60241--60341 Score: 141
Period size: 3 Copynumber: 34.0 Consensus size: 3
60231 TTTATCCATT
* * *
60241 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
60289 TTA TCA TTA TTA ATA TTA TTT TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60336 TTA TTA
1 TTA TTA
60342 AATATATTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:60256 original size:21 final size:21
Alignment explanation
Indices: 60241--60350 Score: 161
Period size: 21 Copynumber: 5.3 Consensus size: 21
60231 TTTATCCATT
60241 TTATTATTATTATTATTAATA
1 TTATTATTATTATTATTAATA
*
60262 TTATTATTATCATTATTAATA
1 TTATTATTATTATTATTAATA
*
60283 TTATTATTATCATTATTAATA
1 TTATTATTATTATTATTAATA
* *
60304 TTATTTTTATTATTATTATTA
1 TTATTATTATTATTATTAATA
60325 TTATTATT-TTATTATTAA-A
1 TTATTATTATTATTATTAATA
60344 TATATTA
1 T-TATTA
60351 AATACATATA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
19 2 0.02
20 14 0.17
21 66 0.80
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATTATTATTATTAATA
Found at i:60799 original size:1 final size:1
Alignment explanation
Indices: 60793--60826 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
60783 CCCACCTGCG
*
60793 AAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60827 GAAGACAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:60831 original size:14 final size:13
Alignment explanation
Indices: 60793--60831 Score: 62
Period size: 12 Copynumber: 3.0 Consensus size: 13
60783 CCCACCTGCG
60793 AAAAAAAAAAA-A
1 AAAAAAAAAAAGA
60805 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
60818 AAAAAAAAAGAAGA
1 AAAAAAAAA-AAGA
60832 CAGAAAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.44
13 10 0.40
14 4 0.16
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:60838 original size:14 final size:14
Alignment explanation
Indices: 60793--60831 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
60783 CCCACCTGCG
60793 AAAAAAAAAA-AAA
1 AAAAAAAAAAGAAA
60806 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
*
60820 AAAAAAAGAAGA
1 AAAAAAAAAAGA
60832 CAGAAAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:60890 original size:25 final size:24
Alignment explanation
Indices: 60845--60891 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
60835 AAAACCAGAG
* * *
60845 AGAAAAAACAGAGAACGGAAAAGA
1 AGAAAAAACAAACAACAGAAAAGA
60869 AGAAAAAACAAACACACAGAAAA
1 AGAAAAAACAAACA-ACAGAAAA
60892 AATACTAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (24 bp):
AGAAAAAACAAACAACAGAAAAGA
Found at i:61811 original size:20 final size:21
Alignment explanation
Indices: 61765--61811 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
61755 CCACTTTTAA
61765 ATATATTGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
61786 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
61805 ATATATT
1 ATATATT
61812 TAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:61905 original size:13 final size:12
Alignment explanation
Indices: 61862--61905 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
61852 GAATAATAAA
61862 TAATATTTTTTT
1 TAATATTTTTTT
* *
61874 TAATAAATTATTT
1 TAAT-ATTTTTTT
61887 TAATATTTTTTT
1 TAATATTTTTTT
61899 TATATAT
1 TA-ATAT
61906 ATCGAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TAATATTTTTTT
Found at i:63707 original size:35 final size:35
Alignment explanation
Indices: 63661--63730 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
63651 CAGTAAAACC
*
63661 AGAATTGGAATTATTTTACAAAAGAGTAGAAAAAA
1 AGAATAGGAATTATTTTACAAAAGAGTAGAAAAAA
63696 AGAATAGGAATTATTTTACAAAAGAGTAGAAAAAA
1 AGAATAGGAATTATTTTACAAAAGAGTAGAAAAAA
63731 CACCATGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.56, C:0.03, G:0.17, T:0.24
Consensus pattern (35 bp):
AGAATAGGAATTATTTTACAAAAGAGTAGAAAAAA
Found at i:71294 original size:18 final size:18
Alignment explanation
Indices: 71271--71341 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
71261 TGAATATTTA
*
71271 TCCCGAATGACCACTATG
1 TCCCGAAGGACCACTATG
71289 TCCCGAAGGACCACTAATTG
1 TCCCGAAGGACCACT-A-TG
* * * *
71309 TTCCAAAGAACCACTATA
1 TCCCGAAGGACCACTATG
71327 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
71342 GATAATCCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 27 0.63
19 2 0.05
20 14 0.33
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:78139 original size:18 final size:18
Alignment explanation
Indices: 78113--78183 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
78103 TGAATATTTA
78113 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
78131 TCCCAAAGGACCACTAACTG
1 TCCCGAAGGACCACT-A-TG
* *
78151 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
78169 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
78184 GATAATCCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 29 0.64
19 2 0.04
20 14 0.31
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:80065 original size:31 final size:31
Alignment explanation
Indices: 80030--80096 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
80020 TTTTGACCAG
*
80030 ATTCAATGATCAAATTGA-TATTTTATCTAAA
1 ATTCAAGGATCAAATT-ACTATTTTATCTAAA
* *
80061 ATTCAAGGATGAAATTACTATTTTATCTAAC
1 ATTCAAGGATCAAATTACTATTTTATCTAAA
80092 ATTCA
1 ATTCA
80097 GGTCAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (31 bp):
ATTCAAGGATCAAATTACTATTTTATCTAAA
Done.