Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004068.1 Hibiscus syriacus cultivar Beakdansim tig00008908_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: 76180
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3422 original size:21 final size:21
Alignment explanation
Indices: 3398--3438 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3388 AGTTGAGATT
3398 TAAGATTTAAACTTTAGGGTA
1 TAAGATTTAAACTTTAGGGTA
*
3419 TAAGATTTAAATTTTAGGGT
1 TAAGATTTAAACTTTAGGGT
3439 TTATGTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (21 bp):
TAAGATTTAAACTTTAGGGTA
Found at i:3434 original size:28 final size:28
Alignment explanation
Indices: 3376--3432 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3366 TTTTAAAAGG
* *
3376 TTAAAGTTTAGGAGTTGAGATTTAAGAT
1 TTAAACTTTAGGAGTTAAGATTTAAGAT
3404 TTAAACTTTAGG-GTATAAGATTTAA-AT
1 TTAAACTTTAGGAGT-TAAGATTTAAGAT
3431 TT
1 TT
3433 TAGGGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (28 bp):
TTAAACTTTAGGAGTTAAGATTTAAGAT
Found at i:3695 original size:13 final size:13
Alignment explanation
Indices: 3677--3703 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3667 TTTAGATTGA
3677 TATAAAGTAAATT
1 TATAAAGTAAATT
3690 TATAAAGTAAATT
1 TATAAAGTAAATT
3703 T
1 T
3704 CAACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TATAAAGTAAATT
Found at i:25837 original size:11 final size:11
Alignment explanation
Indices: 25806--25839 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
25796 TTAGAGAGTA
* *
25806 TTTCCTTTTCT
1 TTTCTTTTTTT
25817 TTTCTTTTTTT
1 TTTCTTTTTTT
25828 TTTCTTTTTTT
1 TTTCTTTTTTT
25839 T
1 T
25840 GGATATAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:26248 original size:19 final size:19
Alignment explanation
Indices: 26226--26263 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
26216 CAATAAGATT
26226 TGAATTTCTAGATAATTTC
1 TGAATTTCTAGATAATTTC
*
26245 TGAATTTCTAGATTATTTC
1 TGAATTTCTAGATAATTTC
26264 AAGAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TGAATTTCTAGATAATTTC
Found at i:35923 original size:26 final size:26
Alignment explanation
Indices: 35894--35946 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
35884 AGGAAACAGT
35894 CTGCAATAGAGGAGAAAGAAAATAAG
1 CTGCAATAGAGGAGAAAGAAAATAAG
35920 CTGCAATAGAGGAGAAAGAAAATAAG
1 CTGCAATAGAGGAGAAAGAAAATAAG
35946 C
1 C
35947 AGACAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.09, G:0.26, T:0.11
Consensus pattern (26 bp):
CTGCAATAGAGGAGAAAGAAAATAAG
Found at i:39601 original size:16 final size:15
Alignment explanation
Indices: 39575--39604 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39565 CGTTGAGGCC
39575 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
39590 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
39605 TTTCGGCCGA
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:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:39820 original size:3 final size:3
Alignment explanation
Indices: 39788--39847 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
39778 AACGGGAAAA
* *
39788 AAT AA- AAT AA- AAT AAGT GAT AA- AA- AAT AAT AAT AAAT AAT GAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT
39831 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
39848 ATATAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
2 8 0.17
3 35 0.73
4 5 0.10
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:39821 original size:25 final size:24
Alignment explanation
Indices: 39784--39853 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 24
39774 CTGAAACGGG
39784 AAAAAATAA-AATAAAATAAGTGAT
1 AAAAAATAATAATAAAATAA-TGAT
39808 AAAAAATAATAAT-AAATAATGAT
1 AAAAAATAATAATAAAATAATGAT
39831 AATAATAATAATAATAAATATAA
1 AA-AA-AATAATAATAAA-ATAA
39854 AAATTATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.15
24 17 0.41
25 12 0.29
26 2 0.05
27 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAAATAATAATAAAATAATGAT
Found at i:39967 original size:32 final size:32
Alignment explanation
Indices: 39926--39991 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
39916 TAAAAAAACA
*
39926 TTTTAAAAAACTATATAATTTTCAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
* *
39958 TTTTTAAAAACCATATAATTTTTAAAAATGTT
1 TTTTAAAAAACCATATAATTTTCAAAAATGTT
39990 TT
1 TT
39992 AAAAAATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTTAAAAAACCATATAATTTTCAAAAATGTT
Found at i:40088 original size:38 final size:36
Alignment explanation
Indices: 39970--40233 Score: 232
Period size: 38 Copynumber: 7.2 Consensus size: 36
39960 TTTAAAAACC
* * *
39970 ATATA-AT-TTTTAAAAATGTTTTAAAAAATACATA
1 ATATATATATTTTCAAAATGTTTTAAAAACTATATA
* ** *
40004 TTATATATGCTTTCAAAATGTTTTTCAAAATATTATATA
1 ATATATATATTTTCAAAATG-TTTT-AAAA-ACTATATA
*
40043 TTATATATTAATTTTCAAAATGTTTTAAAAACTATATA
1 ATATATA-T-ATTTTCAAAATGTTTTAAAAACTATATA
* *
40081 ATATATATATATTCAAAAAATGTTTTAAAAATTATATA
1 ATATATATATTTTC--AAAATGTTTTAAAAACTATATA
* * * *
40119 TTATATTTCTTTTCAAAAACGTTTT-AAAACTATATA
1 ATATATATATTTTC-AAAATGTTTTAAAAACTATATA
* *
40155 ATATATAAATGTTTTTAAAATGTTTTAAAAACTATAT-
1 ATATAT--ATATTTTCAAAATGTTTTAAAAACTATATA
* * *
40192 AT-CATATATTTTCAAAATGTTTTCAAAATTATATA
1 ATATATATATTTTCAAAATGTTTTAAAAACTATATA
40227 ATATATA
1 ATATATA
40234 AATAAAAAAA
Statistics
Matches: 188, Mismatches: 28, Indels: 26
0.78 0.12 0.11
Matches are distributed among these distances:
34 29 0.15
35 4 0.02
36 34 0.18
37 26 0.14
38 63 0.34
39 17 0.09
40 5 0.03
41 10 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATATATATTTTCAAAATGTTTTAAAAACTATATA
Found at i:40150 original size:74 final size:74
Alignment explanation
Indices: 40018--40237 Score: 266
Period size: 74 Copynumber: 2.9 Consensus size: 74
40008 ATATGCTTTC
40018 AAAATGTTTTTCAAAATATTATATATTATATATTAATTTTCAAAATGTTTTAAAAACTATATAAT
1 AAAATG-TTTT-AAAA-ATTATATATTATAT-TT-ATTTTCAAAATGTTTTAAAAACTATATAAT
*
40083 ATATATATATTCAA
61 ATATAAATATTCAA
* *
40097 AAAATGTTTTAAAAATTATATATTATATTTCTTTTCAAAAACGTTTT-AAAACTATATAATATAT
1 AAAATGTTTTAAAAATTATATATTATATTTATTTTC-AAAATGTTTTAAAAACTATATAATATAT
* ***
40161 AAATGTTTTT
65 AAATATTCAA
* * * *
40171 AAAATGTTTTAAAAACTATATATCATA--TATTTTCAAAATGTTTTCAAAATTATATAATATATA
1 AAAATGTTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAAACTATATAATATATA
40234 AATA
66 AATA
40238 AAAAAATATG
Statistics
Matches: 126, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
71 9 0.07
72 26 0.21
74 52 0.41
75 11 0.09
76 14 0.11
77 4 0.03
78 4 0.03
79 6 0.05
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (74 bp):
AAAATGTTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAAACTATATAATATATA
AATATTCAA
Found at i:41089 original size:165 final size:165
Alignment explanation
Indices: 40745--42024 Score: 1375
Period size: 165 Copynumber: 7.7 Consensus size: 165
40735 GACAGTAGTG
* * * * **
40745 AATGATGTGTCATGGAGCTGATCGTAGTCGAACTCGAATGTCTTT-G-TAACAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
* * * * * * * * ***
40808 CGCCTTGAGTTATACTGTAAATGATGCGCCGTTG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTT
66 CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT
* * * * * *
40872 TGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCA
130 TG---GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * *
40911 AATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
40976 CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
66 CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
*
41041 GGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
131 GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * ** *
41076 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGG-TCACAGATAACCCTCC
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTC
* * * *
41140 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
65 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
*
41205 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCG
130 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* *
41241 AATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTC
1 AATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* *
41305 TCGACTTAAGTTACGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
65 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
41370 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
130 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * * * **
41406 AATGATGTGCCTTAGAGCTAAGTGTAGTCGAACTCGAAGGTCTTTTAG-TCACAGATAACCCTTC
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTC
* * * *
41470 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
65 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
*
41535 TGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCA
130 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * *
41571 AATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACATCCCTTC
1 AATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * * * * ** *
41635 TAGA-TTCAAGTTGTGCTGCAAATGATATG-CCTTGGAGTTGAGCGTAGTCGAACTCGAAGATCT
65 TCGACTT-AAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-
* * * * * *
41698 TTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
128 TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * * * * ** *
41739 AATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC--T--TTGGCAGATAGCCCTTC
1 AATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * * * ***
41800 TCGACTTAAGCTATACTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTT
65 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--
* * * * * *
41864 TTGTTGGCAGACAACCCTTCTAGACTTTAAGTTGTGCTACA
128 -T-TTGGCAGATAGCCCTTCTCGAC-TTAAGCTATGCTGCA
*
41905 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
* * * *
41970 CGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCG
66 CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
42025 AAGATCTTTT
Statistics
Matches: 952, Mismatches: 134, Indels: 53
0.84 0.12 0.05
Matches are distributed among these distances:
164 37 0.04
165 636 0.67
166 77 0.08
167 5 0.01
168 89 0.09
169 108 0.11
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
Found at i:41105 original size:249 final size:249
Alignment explanation
Indices: 40794--42024 Score: 1493
Period size: 249 Copynumber: 5.0 Consensus size: 249
40784 GTCTTTGTAA
* * * * * * *
40794 CAGATAACCCTTCTCGCCTTGAGTTATACTGTAAATGATGCGCCGTTGAGCTGAGTGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
*
40859 CTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTT
66 CTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTT
* *
40924 GGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
40989 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
196 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
41043 TAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGA
* * * * * * * * *
41107 ACTCAAAGGACTTTTGGTCA-CAGATAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
65 ACTCAAAGGTCTTTT-GTTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-C
* * * * ** * *
41171 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGC
128 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
* * * * * ***
41232 TATGCTGCGAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGG
193 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC---T-TTGG
* * ** * * * * *
41292 CAGATAACCCTTCTCGACTTAAGTTACGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGA
*** * * * * * *
41357 ACTCGGGGGTC-TTTG---GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
65 ACTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCT
* * * * ** * * *
41418 TAGAGCTAAGTGTAGTCGAACTCGAAGGTCTTTTAG-TCACAGATAACCCTTCTAGCCTTGAGTT
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
*
41482 ATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
194 ATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
41538 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
* * *
41603 CTCAAAGGTCTTTGGTTGGCAGACATCCCTTCTAGA-TTCAAGTTGTGCTGCAAATGATATGCCT
66 CTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTT-AAGTTGTGCTGCAAATGATATGCCT
* * ** * * *
41667 TGGAGTTGAGCGTAGTCGAACTCGAAGATCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTT
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
* *
41731 ATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGG
194 ATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
*
41787 CAGATAGCCCTTCTCGACTTAAGCTATACTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
* *
41852 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTTAAGTTGTGCTACAAATGATATGCCT
66 CTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGAC-TTAAGTTGTGCTGCAAATGATATGCCT
41917 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
* * * *
41982 TGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCG
195 TGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
42025 AAGATCTTTT
Statistics
Matches: 836, Mismatches: 122, Indels: 48
0.83 0.12 0.05
Matches are distributed among these distances:
245 70 0.08
246 129 0.15
247 1 0.00
248 8 0.01
249 462 0.55
250 164 0.20
251 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (249 bp):
CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:41283 original size:330 final size:328
Alignment explanation
Indices: 40745--42024 Score: 1516
Period size: 330 Copynumber: 3.9 Consensus size: 328
40735 GACAGTAGTG
* * * * * *
40745 AATGATGTGTCATGGAGCTGATCGTAGTCGAACTCGAATGTCTTT-GTAACAGATAACCCTTCTC
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTA
* * * *
40809 GCCTTGAGTTATACTGTAAATGATGCGCCGTTGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTG
66 GCCTTGAGTTATACTGTAAATGATGTGCCCTCGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
* * * *
40874 TTAGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTTAGCGTAGT
131 ---GCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* *
40939 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATGCTGCAAATGATGTG
193 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
41004 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTA
258 -CCTCGAAGCTGAGCGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTA
41069 TGCTGCA
322 TGCTGCA
* * *
41076 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCACAGATAACCCTCCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCACAGATAACCCTTCT
* ***
41141 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT
65 AGCCTTGAGTTATACTGTAAATGATGTGCCCTCG-AGCTGAGTGTAATCGAACTCAAAGGTCTTT
* * * * *
41205 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATGTGCCGTT-GAGCTGAGCGTAGT
129 TGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGT
* * *
41269 CGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTACGCTACAAATGATGTG
193 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* *
41334 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
258 -CCTCGAAGCTGAGCGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTA
41399 TGCTGCA
322 TGCTGCA
* * * *
41406 AATGATGTGCCTTAGAGCTAAGTGTAGTCGAACTCGAAGGTCTTTTAGTCACAGATAACCCTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCACAGATAACCCTTCT
* ***
41471 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT
65 AGCCTTGAGTTATACTGTAAATGATGTGCCCTCG-AGCTGAGTGTAATCGAACTCAAAGGTCTTT
* * * * *
41535 TGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGT
129 TGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGT
* * * * *
41599 CGAACTCAAAGGTCTTTGGTTGGCAGACATCCCTTCTAGA-TTCAAGTTGTGCTGCAAATGATAT
193 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT-AAGTTATGCTGCAAATGATGT
* * * * ** * * * * *
41663 GCCTTGGAGTTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
257 GCCTCGAAGCTGAGCGTAATCGAACTCGGGGGTC-TTTGGT---AGATAGCCCTTCTCGACTTAA
* *
41728 GTTATGCTGTA
318 GCTATGCTGCA
* * * * * ** *
41739 AATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGG---CAGATAGCCCTTCT
1 AATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCT
* * * * * * * *
41801 CGACTTAAGCTATACTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT
65 AGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAGCTGAGTGTAATCGAACTCAAAGGTC--TT
* * *
41866 GTTGGCAGACAACCCTTCTAGACTTTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAGCGTA
128 -TTGGCAGACAACCCTTCTAGAC-TTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTA
*
41931 GTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
191 GTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * *
41996 TGCCTTGGAGCTGAGCGTAGTCGAACTCG
256 TGCCTCGAAGCTGAGCGTAATCGAACTCG
42025 AAGATCTTTT
Statistics
Matches: 831, Mismatches: 101, Indels: 31
0.86 0.10 0.03
Matches are distributed among these distances:
329 49 0.06
330 464 0.56
331 38 0.05
332 4 0.00
333 109 0.13
334 165 0.20
335 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (328 bp):
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGATAACCCTTCTA
GCCTTGAGTTATACTGTAAATGATGTGCCCTCGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
GCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
ACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
CGAAGCTGAGCGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCT
GCA
Found at i:45152 original size:19 final size:19
Alignment explanation
Indices: 45125--45170 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
45115 AGTTAATGTG
*
45125 AATGTAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
45144 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
45163 AATGCAAA
1 AATGCAAA
45171 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:45951 original size:16 final size:16
Alignment explanation
Indices: 45930--45973 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
45920 ACAAAAAATC
45930 CTACCCCACATGATAT
1 CTACCCCACATGATAT
45946 CTACCCCACATGATAT
1 CTACCCCACATGATAT
*
45962 CTACCGCACATG
1 CTACCCCACATG
45974 CTTTACTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.30, C:0.39, G:0.09, T:0.23
Consensus pattern (16 bp):
CTACCCCACATGATAT
Found at i:46888 original size:12 final size:12
Alignment explanation
Indices: 46871--46895 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46861 CGAAAATTAG
46871 AAAATTTAAATT
1 AAAATTTAAATT
46883 AAAATTTAAATT
1 AAAATTTAAATT
46895 A
1 A
46896 CTCGATTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:48373 original size:16 final size:15
Alignment explanation
Indices: 48347--48376 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48337 CGTTGAGTCC
48347 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
48362 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
48377 TTTCGGCCTG
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:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:48592 original size:3 final size:3
Alignment explanation
Indices: 48560--48625 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
48550 AACGGGAAAA
* *
48560 AAT AA- AAT AA- AAT AAGT GAT AA- AA- AAT AAT AAT AAAT AAT GAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT -AAT AAT AAT
48603 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
48626 ATATAAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 8 0.15
3 41 0.76
4 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:48731 original size:31 final size:32
Alignment explanation
Indices: 48684--48763 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 32
48674 CTATATATTA
*
48684 TATATAAATTTAAAAAA-ACATTTTTAAAAAC
1 TATATAATTTTAAAAAATACATTTTTAAAAAC
* *** *
48715 TATATAATTTTCAAAAATGTTTTTTTAAAAGC
1 TATATAATTTTAAAAAATACATTTTTAAAAAC
*
48747 -ATATAATTTTTAAAAAT
1 TATATAATTTTAAAAAAT
48764 GTTTTAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 31 0.76
32 10 0.24
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
TATATAATTTTAAAAAATACATTTTTAAAAAC
Found at i:48764 original size:31 final size:32
Alignment explanation
Indices: 48704--48768 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
48694 TAAAAAAACA
48704 TTTTTAAAAACTATATAATTTTCAAAAATGTT
1 TTTTTAAAAACTATATAATTTTCAAAAATGTT
* *
48736 TTTTTAAAAGC-ATATAATTTTTAAAAATGTT
1 TTTTTAAAAACTATATAATTTTCAAAAATGTT
48767 TT
1 TT
48769 AAAAATTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (32 bp):
TTTTTAAAAACTATATAATTTTCAAAAATGTT
Found at i:48799 original size:36 final size:36
Alignment explanation
Indices: 48754--49012 Score: 268
Period size: 38 Copynumber: 6.9 Consensus size: 36
48744 AGCATATAAT
* * *
48754 TTTTAAAAATGTTTTAAAAATTACATATTATATATG
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATA
*
48790 CTTTCAAAATGTTTTTCAAAATATTATATATTATATATTAA
1 TTTTCAAAATG-TTTT-AAAA-ATTATATATTATATA-T-A
* * *
48831 TTTTCAAAACGTTTTAAAAACTATATAATATATATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATA
* *
48867 TTTTCAAAAAATGTTTTAAAAATTATATATTATATTTT
1 TTTTC--AAAATGTTTTAAAAATTATATATTATATATA
* * *
48905 TTTTCAAAAACGTTTT-AAAACTATATAATATATAAATA
1 TTTTC-AAAATGTTTTAAAAATTATAT-AT-TATATATA
* * *
48943 TTTTTAAAATGTTTTAAAAACTATATATCATATATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATATA
* *
48979 TTTTCAAAATGTTTTCAAAATTATATAATATATA
1 TTTTCAAAATGTTTTAAAAATTATATATTATATA
49013 AATAAAAAAA
Statistics
Matches: 186, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
36 59 0.32
37 28 0.15
38 67 0.36
39 18 0.10
40 5 0.03
41 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTCAAAATGTTTTAAAAATTATATATTATATATA
Found at i:48925 original size:74 final size:72
Alignment explanation
Indices: 48754--49012 Score: 286
Period size: 74 Copynumber: 3.5 Consensus size: 72
48744 AGCATATAAT
* * * * * **
48754 TTTTAAAAATGTTTTAAAAATTACATATTATATATGCTTTCAAAATGTTTTTCAAAATATTATAT
1 TTTTCAAAACGTTTTAAAAACTATATAATATATATATTTTCAAAATG-TTTT-AAAA-ATTATAT
48819 ATTATATATTAA
63 ATTATAT-TT-A
48831 TTTTCAAAACGTTTTAAAAACTATATAATATATATATTTTCAAAAAATGTTTTAAAAATTATATA
1 TTTTCAAAACGTTTTAAAAACTATATAATATATATATTTTC--AAAATGTTTTAAAAATTATATA
*
48896 TTATATTTT
64 TTATATTTA
* *
48905 TTTTCAAAAACGTTTT-AAAACTATATAATATATAAATATTTTTAAAATGTTTTAAAAACTATAT
1 TTTTC-AAAACGTTTTAAAAACTATATAATATAT--ATATTTTCAAAATGTTTTAAAAATTATAT
* *
48969 ATCATATATA
63 ATTATATTTA
* * *
48979 TTTTCAAAATGTTTTCAAAATTATATAATATATA
1 TTTTCAAAACGTTTTAAAAACTATATAATATATA
49013 AATAAAAAAA
Statistics
Matches: 161, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
72 1 0.01
73 9 0.06
74 70 0.43
75 12 0.07
76 21 0.13
77 38 0.24
78 4 0.02
79 6 0.04
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (72 bp):
TTTTCAAAACGTTTTAAAAACTATATAATATATATATTTTCAAAATGTTTTAAAAATTATATATT
ATATTTA
Found at i:50321 original size:29 final size:31
Alignment explanation
Indices: 50287--50366 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
50277 ATCTTTTAAT
*
50287 TTTAGATAGAATAT-AATTTGA-CCCTAAAC
1 TTTAGATAAAATATCAATTTGACCCCTAAAC
*
50316 TTTAGATAAAATATCATTTTGACCCCTAAAC
1 TTTAGATAAAATATCAATTTGACCCCTAAAC
50347 TTT-GTATAAAATATCAATTT
1 TTTAG-ATAAAATATCAATTT
50367 AACACATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 13 0.29
30 7 0.16
31 25 0.56
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTAGATAAAATATCAATTTGACCCCTAAAC
Found at i:52651 original size:27 final size:28
Alignment explanation
Indices: 52603--52656 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
52593 CTAAAAAATT
*
52603 CGGGTTGGATGGAATGTATAT-ATTTTC
1 CGGGTCGGATGGAATGTATATAATTTTC
*
52630 CGGGTCGGATGGAA-GATTTATAATTTT
1 CGGGTCGGATGGAATG-TATATAATTTT
52657 GGGTCTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.04
27 17 0.74
28 5 0.22
ACGTcount: A:0.24, C:0.07, G:0.30, T:0.39
Consensus pattern (28 bp):
CGGGTCGGATGGAATGTATATAATTTTC
Found at i:62624 original size:16 final size:16
Alignment explanation
Indices: 62600--62636 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
62590 AATACGACAT
*
62600 GTGTCATTTAATATTA
1 GTGTTATTTAATATTA
62616 GTGTTATTTAATATTA
1 GTGTTATTTAATATTA
62632 GTGTT
1 GTGTT
62637 TGAGCACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (16 bp):
GTGTTATTTAATATTA
Found at i:65537 original size:41 final size:41
Alignment explanation
Indices: 65492--65605 Score: 210
Period size: 41 Copynumber: 2.8 Consensus size: 41
65482 TAAATAAAGT
*
65492 TTTATCGAAAGTATTAAAAACAATAACATTTTCGATAATAC
1 TTTATCGAAAATATTAAAAACAATAACATTTTCGATAATAC
65533 TTTATCGAAAATATTAAAAACAATAACATTTTCGATAATAC
1 TTTATCGAAAATATTAAAAACAATAACATTTTCGATAATAC
*
65574 TTTATCGAAAATATTAAAAACAATAATATTTT
1 TTTATCGAAAATATTAAAAACAATAACATTTT
65606 TTATAGCACA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (41 bp):
TTTATCGAAAATATTAAAAACAATAACATTTTCGATAATAC
Found at i:68131 original size:21 final size:21
Alignment explanation
Indices: 68107--68148 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
68097 TATTGTCCTG
*
68107 AATCTGATAGGAAGTGCATGA
1 AATCTGACAGGAAGTGCATGA
68128 AATCTGACAGGAAGTGCATGA
1 AATCTGACAGGAAGTGCATGA
68149 TAGCAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (21 bp):
AATCTGACAGGAAGTGCATGA
Done.