Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007411.1 Hibiscus syriacus cultivar Beakdansim tig00020022_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: 95329
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1116 original size:14 final size:14
Alignment explanation
Indices: 1097--1124 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1087 AGAACACAAT
1097 TATGTTATGGCACA
1 TATGTTATGGCACA
1111 TATGTTATGGCACA
1 TATGTTATGGCACA
1125 GTAGACTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TATGTTATGGCACA
Found at i:11123 original size:6 final size:6
Alignment explanation
Indices: 11071--11119 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
11061 AATTATTCAA
* *
11071 AGAGGG AGAGTG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG ATAGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
11119 A
1 A
11120 TAGGAAACGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.61, T:0.04
Consensus pattern (6 bp):
AGAGGG
Found at i:14797 original size:25 final size:25
Alignment explanation
Indices: 14769--14823 Score: 96
Period size: 23 Copynumber: 2.3 Consensus size: 25
14759 ATATAAAATA
14769 TTAAAAATCTATGAAGTAATATTTT
1 TTAAAAATCTATGAAGTAATATTTT
14794 TT--AAATCTATGAAGTAATATTTT
1 TTAAAAATCTATGAAGTAATATTTT
14817 TTAAAAA
1 TTAAAAA
14824 ATAGGGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 23 0.82
25 5 0.18
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (25 bp):
TTAAAAATCTATGAAGTAATATTTT
Found at i:14801 original size:23 final size:23
Alignment explanation
Indices: 14773--14821 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
14763 AAAATATTAA
14773 AAATCTATGAAGTAATATTTTTT
1 AAATCTATGAAGTAATATTTTTT
14796 AAATCTATGAAGTAATATTTTTT
1 AAATCTATGAAGTAATATTTTTT
14819 AAA
1 AAA
14822 AAATAGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (23 bp):
AAATCTATGAAGTAATATTTTTT
Found at i:15124 original size:23 final size:23
Alignment explanation
Indices: 15098--15144 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
15088 AATATAATAG
15098 TTTGAGTACTAAATGCATTAAAT
1 TTTGAGTACTAAATGCATTAAAT
15121 TTTGAGTACTAAATGCATTAAAT
1 TTTGAGTACTAAATGCATTAAAT
15144 T
1 T
15145 GTTTGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
TTTGAGTACTAAATGCATTAAAT
Found at i:19027 original size:84 final size:84
Alignment explanation
Indices: 18885--19049 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 84
18875 CAAATAAATG
*
18885 TTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTGAACCGGCTCGTATTGCACACTTGAT
1 TTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTGAACCGGCTCGTATCGCACACTTGAT
*
18950 TTTGATTGGTGAATTTATA
66 TTTGATAGGTGAATTTATA
*
18969 TTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTGAATCGGCTCGTATCGCACACTTGAT
1 TTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTGAACCGGCTCGTATCGCACACTTGAT
19034 TTTGATAGGTGAATTT
66 TTTGATAGGTGAATTT
19050 TTTAGGGATT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (84 bp):
TTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTGAACCGGCTCGTATCGCACACTTGAT
TTTGATAGGTGAATTTATA
Found at i:32691 original size:21 final size:21
Alignment explanation
Indices: 32665--32722 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
32655 TTACAAAGGT
*
32665 AGTATCAATACTCATTAAAGA
1 AGTATCGATACTCATTAAAGA
* *
32686 AGTATCGGTACTCATTAAAGG
1 AGTATCGATACTCATTAAAGA
32707 AGTATCGATACTCATT
1 AGTATCGATACTCATT
32723 GTCTTAGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTCATTAAAGA
Found at i:42922 original size:22 final size:23
Alignment explanation
Indices: 42878--42935 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
42868 TGACACGGGA
42878 AAAAATAA-AATAAAATAAGTGAT
1 AAAAATAATAAT-AAATAAGTGAT
42901 AAAAATAATAATAAATAA-TGAT
1 AAAAATAATAATAAATAAGTGAT
* *
42923 GATAATAATAATA
1 AAAAATAATAATA
42936 TATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 15 0.47
23 14 0.44
24 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAATAATAATAAATAAGTGAT
Found at i:42978 original size:27 final size:25
Alignment explanation
Indices: 42933--42982 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
42923 GATAATAATA
42933 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
**
42959 ATATAATATATAAATTTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
42983 TGTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:42988 original size:37 final size:37
Alignment explanation
Indices: 42947--43128 Score: 128
Period size: 38 Copynumber: 5.0 Consensus size: 37
42937 ATATATAAAC
*
42947 GTTTTCAAAAACATATAATATATAAATTTTTTAAAAT
1 GTTTTCAAAAACATATAATATATAAATTTTTCAAAAT
* * *
42984 GTTTTTAAAAAACTATATATTATATATA-TTTTCAAAAT
1 G-TTTTCAAAAAC-ATATAATATATAAATTTTTCAAAAT
* * * *
43022 GGTTTTTAAAAATTATATATTATAT-AATGTTTTCATAAT
1 -GTTTTCAAAAA-CATATAATATATAAAT-TTTTCAAAAT
** * * * *
43061 GTTTTCAAAAGTATCT-AT-TATATA-TTTTAAAAAC
1 GTTTTCAAAAACATATAATATATAAATTTTTCAAAAT
43095 GTTTTCAAAAAC-TAT-ATATATATAA-TTTTCAAAA
1 GTTTTCAAAAACATATAATATATA-AATTTTTCAAAA
43129 ATATATTTTC
Statistics
Matches: 115, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
33 4 0.03
34 21 0.18
35 12 0.10
36 2 0.02
37 6 0.05
38 48 0.42
39 22 0.19
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
GTTTTCAAAAACATATAATATATAAATTTTTCAAAAT
Found at i:43138 original size:14 final size:15
Alignment explanation
Indices: 43114--43142 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43104 AACTATATAT
43114 ATATAATTTTCAAAA
1 ATATAATTTTCAAAA
43129 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
43143 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATAATTTTCAAAA
Found at i:43151 original size:122 final size:125
Alignment explanation
Indices: 43007--43257 Score: 447
Period size: 122 Copynumber: 2.0 Consensus size: 125
42997 TATATATTAT
* *
43007 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAATGTTTTCATAATGTTTTCAAAAG
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAATGTTTTCATAACGTTTTAAAAAG
43072 TA-TC--TATTATATATTTTAAAAACGTTTTCAAAAACTATATA-TATATAATTTTCAAAA
66 TATTCATTA-TATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
43129 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAATGTTTTCATAACGTTTTAAAAAG
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAATGTTTTCATAACGTTTTAAAAAG
43194 TATTCATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
66 TATTCATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
43254 ATAT
1 ATAT
43258 TTTAAAAACT
Statistics
Matches: 123, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
122 65 0.53
123 2 0.02
124 34 0.28
125 22 0.18
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (125 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAATGTTTTCATAACGTTTTAAAAAG
TATTCATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
Found at i:43248 original size:36 final size:37
Alignment explanation
Indices: 42943--43355 Score: 231
Period size: 37 Copynumber: 10.8 Consensus size: 37
42933 ATATATATAT
* * **
42943 AAACGTTTTCAAAAAC-ATATAATATATAAATTTTTTA
1 AAACGTTTT-AAAAACTATATATTATATATATTTTCAA
*
42980 AAATGTTTTTAAAAAACTATATATTATATATATTTTCAA
1 AAACG-TTTT-AAAAACTATATATTATATATATTTTCAA
** * *
43019 AATGGTTTTTAAAAATTATATATTATATAATGTTTTC-A
1 AAACG-TTTTAAAAACTATATATTATAT-ATATTTTCAA
* * * * *
43057 TAATGTTTTCAAAAGTATCTA-T-TATATATTTT-AA
1 AAACGTTTTAAAAACTATATATTATATATATTTTCAA
43091 AAACGTTTTCAAAAACTATATA-TATATA-ATTTTCAAAA
1 AAACGTTTT-AAAAACTATATATTATATATATTTTC--AA
* **
43129 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATA-ATGTTTTCA
1 A-A-A----C------G-TTTTAAAAACTATATATTATATATAT-TTTCAA
* *
43179 TAACGTTTTAAAAAGTAT-TCATTATATATATTTT-AA
1 AAACGTTTTAAAAACTATAT-ATTATATATATTTTCAA
43215 AAACGTTTTCAAAAACTATATATTATATA-ATTTTCAA
1 AAACGTTTT-AAAAACTATATATTATATATATTTTCAA
** * *
43252 AAATATTTTAAAAACTATATAATATACATATTTTCAAA
1 AAACGTTTTAAAAACTATATATTATATATATTTTC-AA
*
43290 AAATGTTTT--AAACTATATATTATATATGTATTTTCAA
1 AAACGTTTTAAAAACTATATATTATATA--TATTTTCAA
** ** *
43327 AAACAATTTGCAAACTATATAATATATAT
1 AAACGTTTTAAAAACTATATATTATATAT
43356 GTGTATATAT
Statistics
Matches: 300, Mismatches: 41, Indels: 70
0.73 0.10 0.17
Matches are distributed among these distances:
34 14 0.05
35 18 0.06
36 52 0.17
37 80 0.27
38 54 0.18
39 49 0.16
40 1 0.00
44 2 0.01
48 1 0.00
49 1 0.00
50 13 0.04
51 12 0.04
52 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAACGTTTTAAAAACTATATATTATATATATTTTCAA
Found at i:43329 original size:38 final size:37
Alignment explanation
Indices: 43226--43357 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 37
43216 AACGTTTTCA
43226 AAAACTATATATTATATA---ATTTTCAAAAATATTTT
1 AAAACTATATATTATATATGTATTTTCAAAAA-ATTTT
**
43261 AAAAACTATATA--ATATACATATTTTCAAAAAATGTTT
1 -AAAACTATATATTATATATGTATTTTCAAAAAAT-TTT
* *
43298 TAAACTATATATTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATATTATATATGTATTTTC-AAAA-AATTTT
* *
43337 CAAACTATATAATATATATGT
1 AAAACTATATATTATATATGT
43358 GTATATATGT
Statistics
Matches: 82, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
34 5 0.06
36 23 0.28
37 14 0.17
38 12 0.15
39 25 0.30
40 3 0.04
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (37 bp):
AAAACTATATATTATATATGTATTTTCAAAAAATTTT
Found at i:44065 original size:84 final size:83
Alignment explanation
Indices: 43969--44420 Score: 509
Period size: 84 Copynumber: 5.4 Consensus size: 83
43959 GAGTCTTTGG
* * *
43969 CAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
44034 ATCGAAGGTCTTTTGGTCA
66 CTCGAAGGTC-TTTGGTCA
* * *
44053 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGA
* * **
44117 ACTCAAAGGTCTTTGTTGG
65 ACTCGAAGGTCTTTGGTCA
* * * ** * *
44136 CAAACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATATGCCTTGGAGCTGAGAGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
**
44201 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGG-TCA
* * * * *
44220 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGTGT-GATCG
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAG-TCG
* **
44284 AACTTGGGGGTCTTTGG---
64 AACTCGAAGGTCTTTGGTCA
* * *
44301 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
44366 CTCGAAGGTCTTTGGTGA
66 CTCGAAGGTCTTTGGTCA
* * *
44384 CAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATG
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
44421 CACACGATAT
Statistics
Matches: 307, Mismatches: 52, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
80 30 0.10
81 40 0.13
82 2 0.01
83 101 0.33
84 102 0.33
85 32 0.10
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (83 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTCA
Found at i:44171 original size:167 final size:164
Alignment explanation
Indices: 43885--44420 Score: 612
Period size: 165 Copynumber: 3.2 Consensus size: 164
43875 ACAATTTTAT
* * * * * * * * * *
43885 TGACAAATAACCTTTCTTGCCATGAGTTATGTTGTAAATGATATGA-CCTCGAAGTTGAGTGTAA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT-ACCCTCGAAGCTGAGCGTGA
** *
43949 TCGAACTC-GTGAGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCC
65 TCGAACTCAAAG-GTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
* *
44013 TTGGAGCTGAGCGGAGTCGAAATCGAAGGTCTTTTGG
129 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* * * * *
44050 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGT-AG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGCGTGA-
* * * * ** *
44113 TCGAACTCAAAGGTCTTTGTTGGCAAACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATATG
65 TCGAACTCAAAGGTC--T-TTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
*
44178 CCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTTTGG
127 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * *
44216 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGTGTGA
1 -TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGCGTGA
**** * *
44281 TCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
65 TCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCT
44346 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
*
44381 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
44421 CACACGATAT
Statistics
Matches: 308, Mismatches: 54, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
163 1 0.00
164 54 0.18
165 115 0.37
166 7 0.02
167 110 0.36
168 20 0.06
169 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (164 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGCGTGAT
CGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:44354 original size:248 final size:249
Alignment explanation
Indices: 43965--44420 Score: 614
Period size: 248 Copynumber: 1.8 Consensus size: 249
43955 TCGTGAGTCT
* * * *
43965 TTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTCCCTCGAAGCTGAGCGGAGT
* * * *
44030 CGAAATCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAAATCGAAGGTCTTTTGG--ACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
* *
44095 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAAACAACCCTTCTAGACTTAAGT
129 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAAACAACCCTTCTAGACTTAAGT
*
44160 TGTATTGCAAATGATATGCCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTTTGG
194 TATATTGCAAATGATATGCCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTTTGG
* *
44216 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGTGTGA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT-CCCTCGAAGCTGAGCG-GA
* * ** * *
44281 -TCGAACTTGGGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
64 GTCGAAATCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
* * * * *
44343 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
129 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAAACAACCCTTCTAGACTTAAG
*
44407 TTATGTTGCAAATG
193 TTATATTGCAAATG
44421 CACACGATAT
Statistics
Matches: 177, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
247 2 0.01
248 102 0.58
251 48 0.27
252 23 0.13
253 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTCCCTCGAAGCTGAGCGGAGT
CGAAATCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAAACAACCCTTCTAGACTTAAGTTA
TATTGCAAATGATATGCCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTTTGG
Found at i:44742 original size:105 final size:104
Alignment explanation
Indices: 44440--45116 Score: 1174
Period size: 105 Copynumber: 6.4 Consensus size: 104
44430 TCCTTTGCTA
*
44440 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTG-AATTGAGAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTG
44505 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
**
44546 TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCATG
1 TGAAGTTGAAATTGGCTCTG-AATTGAGAA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTG
44611 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
64 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
44652 TGAAGTTGAGATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGA-GAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
44717 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
44757 TGAAGTTGAAATTGGCTCTGAATTTGAGAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAA-TTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
44822 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
* *
44862 TGAAGTTGAGATTGGCTCTGAATTGACGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAATTGA-GAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
44927 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
44967 TGAAGTTGAAATTGGCTCTGAATTTGAGAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
1 TGAAGTTGAAATTGGCTCTGAA-TTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGA
45032 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
65 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
*
45072 TGAAGTTGAGATTGGCTCTGAATTTGAGAAGTTGTTTGTTGACAA
1 TGAAGTTGAAATTGGCTCTGAA-TTGAGAA-TTGTTTGTTGACAA
45117 ACAACTTTTC
Statistics
Matches: 553, Mismatches: 13, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
104 4 0.01
105 401 0.73
106 148 0.27
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.35
Consensus pattern (104 bp):
TGAAGTTGAAATTGGCTCTGAATTGAGAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAA
GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTG
Found at i:50424 original size:22 final size:23
Alignment explanation
Indices: 50380--50437 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
50370 TGACACGGGA
50380 AAAAATAA-AATAAAATAAGTGAT
1 AAAAATAATAAT-AAATAAGTGAT
50403 AAAAATAATAATAAATAA-TGAT
1 AAAAATAATAATAAATAAGTGAT
* *
50425 GATAATAATAATA
1 AAAAATAATAATA
50438 TATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 15 0.47
23 14 0.44
24 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAATAATAATAAATAAGTGAT
Found at i:50480 original size:27 final size:25
Alignment explanation
Indices: 50435--50484 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
50425 GATAATAATA
50435 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
**
50461 ATATAATATATAAATTTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
50485 TGTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:50523 original size:38 final size:36
Alignment explanation
Indices: 50449--50836 Score: 212
Period size: 38 Copynumber: 10.0 Consensus size: 36
50439 ATATATAAAC
* * *
50449 GTTTTCAAAAAC-ATATAATATATAAATTTTTTAAAAT
1 GTTTT-AAAAACTATATATTATATATA-TTTTCAAAAT
50486 GTTTTTAAAAAACTATATATTATATATATTTTCAAAAT
1 G-TTTT-AAAAACTATATATTATATATATTTTCAAAAT
* * *
50524 GGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAT
1 -G-TTTTAAAAACTATATATTATAT--ATATTTTCAAAAT
* * * * *
50564 GTTTTCAAAAGTATCTATTATATATATTTTAAAAAC
1 GTTTTAAAAACTATATATTATATATATTTTCAAAAT
50600 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAAAATATATT
1 GTTTT-AAAAACTATATATTATATATATTTTC----AA-A-A-T
* * * * * *
50643 TTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAC
1 GT----------TTTAAAAACTATATATTATATATATTTT--CAAAAT
* * *
50691 GTTTTAAAAAGTAT-TCATTATATATATTTTAAAAAC
1 GTTTTAAAAACTATAT-ATTATATATATTTTCAAAAT
50727 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAAAT
1 GTTTT-AAAAACTATATATTATATATATTTTC-AAAAT
* * *
50764 ATTTTAAAAACTATATAATATACATATTTTCAAAAAAT
1 GTTTTAAAAACTATATATTATATATATTTTC--AAAAT
50802 GTTTT--AAACTATATATTATATATGTATTTTCAAAA
1 GTTTTAAAAACTATATATTATATA--TATTTTCAAAA
50837 ACAATTTGCA
Statistics
Matches: 278, Mismatches: 39, Indels: 69
0.72 0.10 0.18
Matches are distributed among these distances:
36 69 0.25
37 48 0.17
38 96 0.35
39 19 0.07
40 13 0.05
41 1 0.00
42 1 0.00
43 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 18 0.06
53 7 0.03
55 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATATATTTTCAAAAT
Found at i:50616 original size:75 final size:77
Alignment explanation
Indices: 50445--50838 Score: 241
Period size: 75 Copynumber: 5.1 Consensus size: 77
50435 ATATATATAT
* *
50445 AAACGTTTTCAAAAAC-ATATAATATATAAATTTTTTAAAATGTTTTTAAAAAACTATATATTAT
1 AAACGTTTTCAAAAACTATATATTATATAAATTTTTCAAAATGTTTTTAAAAAACTATATATTAT
50509 ATATATTTTCAA
66 ATATATTTTCAA
** * * * * * *
50521 AATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATG-TTTT-CAAAAGTATCTATTA
1 AAACGTTTTCAAAAACTATATATTATATAAAT-TTTTCAAAATGTTTTTAAAAAACTATATATTA
50584 TATATATTTT-AA
65 TATATATTTTCAA
*
50596 AAACGTTTTCAAAAACTATATATTATAT-AA-TTTTCAAAAAATATATTTTCAAAATGGTTTTTA
1 AAACGTTTTCAAAAACTATATATTATATAAATTTTTC--AAAATGT-TTTT----A--------A
* *
50659 AAAATTATATATTATATAAATGTTTTC-A
51 AAAACTATATATTATATATAT-TTT-CAA
* * * * * *
50687 TAACGTTTT-AAAAAGTAT-TCATTATATATA-TTTTAAAAACG-TTTTCAAAAACTATATATTA
1 AAACGTTTTCAAAAACTATAT-ATTATATAAATTTTTCAAAATGTTTTTAAAAAACTATATATTA
50748 TATA-ATTTTCAA
65 TATATATTTTCAA
** *
50760 AAATATTTT-AAAAACTATATA--ATATACATATTTTCAAAAAATG-TTTT---AAACTATATAT
1 AAACGTTTTCAAAAACTATATATTATATAAAT-TTTTC--AAAATGTTTTTAAAAAACTATATAT
50818 TATATATGTATTTTCAA
63 TATATA--TATTTTCAA
50835 AAAC
1 AAAC
50839 AATTTGCAAA
Statistics
Matches: 249, Mismatches: 36, Indels: 67
0.71 0.10 0.19
Matches are distributed among these distances:
71 6 0.02
72 23 0.09
73 23 0.09
74 9 0.04
75 64 0.26
76 38 0.15
77 18 0.07
78 9 0.04
87 4 0.02
89 23 0.09
90 18 0.07
91 14 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (77 bp):
AAACGTTTTCAAAAACTATATATTATATAAATTTTTCAAAATGTTTTTAAAAAACTATATATTAT
ATATATTTTCAA
Found at i:50633 original size:25 final size:25
Alignment explanation
Indices: 50601--50677 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
50591 TTTAAAAACG
*
50601 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
50626 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
50653 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
50678 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:50642 original size:127 final size:127
Alignment explanation
Indices: 50509--50762 Score: 474
Period size: 127 Copynumber: 2.0 Consensus size: 127
50499 TATATATTAT
* *
50509 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTAAAAA
50574 GTA-TCTATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATTC-ATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
50636 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTAAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTAAAAA
50701 GTATTCATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATTCATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
50763 TATTTTAAAA
Statistics
Matches: 124, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
127 122 0.98
128 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTAAAAA
GTATTCATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:50645 original size:15 final size:16
Alignment explanation
Indices: 50620--50649 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50610 ACTATATATT
50620 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
50636 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
50650 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:50729 original size:36 final size:37
Alignment explanation
Indices: 50636--50863 Score: 198
Period size: 36 Copynumber: 6.1 Consensus size: 37
50626 TTTTCAAAAA
** *
50636 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTAT
1 ATATATTTTCAAAAACG-TTTTAAAAACTATATATTAT
* * *
50674 ATAAATGTTTTC-ATAACGTTTTAAAAAGTAT-TCATTAT
1 AT--ATATTTTCAAAAACGTTTTAAAAACTATAT-ATTAT
50712 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACGTTTT-AAAAACTATATATTAT
** *
50749 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
* *
50785 ACATATTTTCAAAAAATGTTTT--AAACTATATATTAT
1 ATATATTTTC-AAAAACGTTTTAAAAACTATATATTAT
** ** *
50821 ATATGTATTTTCAAAAACAATTTGCAAACTATATAATAT
1 ATA--TATTTTCAAAAACGTTTTAAAAACTATATATTAT
50860 ATAT
1 ATAT
50864 GTGTATATAT
Statistics
Matches: 158, Mismatches: 19, Indels: 27
0.77 0.09 0.13
Matches are distributed among these distances:
36 52 0.33
37 41 0.26
38 39 0.25
39 19 0.12
40 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
Found at i:50837 original size:38 final size:37
Alignment explanation
Indices: 50734--50865 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 37
50724 AACGTTTTCA
50734 AAAACTATATATTATATA---ATTTTCAAAAATATTTT
1 AAAACTATATATTATATATGTATTTTCAAAAA-ATTTT
**
50769 AAAAACTATATA--ATATACATATTTTCAAAAAATGTTT
1 -AAAACTATATATTATATATGTATTTTCAAAAAAT-TTT
* *
50806 TAAACTATATATTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATATTATATATGTATTTTC-AAAA-AATTTT
* *
50845 CAAACTATATAATATATATGT
1 AAAACTATATATTATATATGT
50866 GTATATATGT
Statistics
Matches: 82, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
34 5 0.06
36 23 0.28
37 14 0.17
38 12 0.15
39 25 0.30
40 3 0.04
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (37 bp):
AAAACTATATATTATATATGTATTTTCAAAAAATTTT
Found at i:54520 original size:31 final size:31
Alignment explanation
Indices: 54463--54530 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
54453 TTATCAATTG
* ** *
54463 AAGGACTAAAATCAAACATATTGATAATGTT
1 AAGGACTAAAATCAAACAGAACGATAATATT
* *
54494 AGGGACTAAAATCATACAGAACGATAATATT
1 AAGGACTAAAATCAAACAGAACGATAATATT
54525 AAGGAC
1 AAGGAC
54531 CATTCCCCCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (31 bp):
AAGGACTAAAATCAAACAGAACGATAATATT
Found at i:64808 original size:31 final size:32
Alignment explanation
Indices: 64751--64816 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
64741 TAGAGTAACC
* **
64751 ATTTTATTACAAATCGATTATGTTAGTGA-CG
1 ATTTTATTACAAATCGATAACATTAGTGATCG
64782 ATTTTATTACAAATCGATAACATTAGTGATCG
1 ATTTTATTACAAATCGATAACATTAGTGATCG
64814 ATT
1 ATT
64817 GTTACTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (32 bp):
ATTTTATTACAAATCGATAACATTAGTGATCG
Found at i:64899 original size:78 final size:78
Alignment explanation
Indices: 64770--64916 Score: 240
Period size: 78 Copynumber: 1.9 Consensus size: 78
64760 CAAATCGATT
* * *
64770 ATGTTAGTGACGATTTTATTACAAATCGATAACATTAGTGATCGATTGTTACTTTTGAAGTTTCA
1 ATGTTAGTGACGATTTTATTACAAATCGATAACATTAATGATCGATTGTTACTTTTGAAGCTGCA
64835 GTGGTAGGGGATA
66 GTGGTAGGGGATA
* * *
64848 ATGTTAGTGACGATTTTATTATAAATTGATAACATTAATGGTCGATTGTTACTTTTGAAGCTGCA
1 ATGTTAGTGACGATTTTATTACAAATCGATAACATTAATGATCGATTGTTACTTTTGAAGCTGCA
64913 GTGG
66 GTGG
64917 AAGAGTGATT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.39
Consensus pattern (78 bp):
ATGTTAGTGACGATTTTATTACAAATCGATAACATTAATGATCGATTGTTACTTTTGAAGCTGCA
GTGGTAGGGGATA
Found at i:67935 original size:17 final size:19
Alignment explanation
Indices: 67898--67942 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
67888 ACCCTTAGTT
*
67898 CATCGGTGCACTAAGAGTG
1 CATCGATGCACTAAGAGTG
67917 CATCGATGCA-TAA-AGTG
1 CATCGATGCACTAAGAGTG
67934 CATTCGATG
1 CA-TCGATG
67943 TTTCAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 9 0.38
19 9 0.38
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (19 bp):
CATCGATGCACTAAGAGTG
Found at i:68047 original size:65 final size:64
Alignment explanation
Indices: 67914--68073 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 64
67904 TGCACTAAGA
*
67914 GTGCATCGATGCATAAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTACATCGATGCATGGCTG
1 GTGCATCGATGCATAAA-TGCATTCGATGTTTTCAAAATAGCCACAGTACATCGATGCATGGCTG
* * * *
67978 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTTCA-AAATAGCCACAGTACATCGATGCATGGCT
*
68041 AT
64 -G
68043 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCAT-AAATGCATTCGATGTT
68074 CAATTTAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 26 0.31
65 56 0.66
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAGCCACAGTACATCGATGCATGGCTG
Found at i:68926 original size:30 final size:31
Alignment explanation
Indices: 68875--68932 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
68865 GATACTAAAA
68875 TGAAACAAAAACTAAACTTTAGGCATTATTT
1 TGAAACAAAAACTAAACTTTAGGCATTATTT
* * *
68906 TGAAA-AAAAATTAAAGTTTAGGTATTA
1 TGAAACAAAAACTAAACTTTAGGCATTA
68933 AAATTGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (31 bp):
TGAAACAAAAACTAAACTTTAGGCATTATTT
Found at i:73506 original size:28 final size:27
Alignment explanation
Indices: 73453--73506 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
73443 CTATGACTTA
* *
73453 AAAAAAATAAAGTTTGATTATAAAATT
1 AAAAAAATAAAGTTTAAGTATAAAATT
*
73480 AAAAAAATAATAGTTTAAGTATTAAAT
1 AAAAAAATAA-AGTTTAAGTATAAAAT
73507 ATGTAGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (27 bp):
AAAAAAATAAAGTTTAAGTATAAAATT
Found at i:81859 original size:31 final size:31
Alignment explanation
Indices: 81811--81875 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
81801 AAAAATTAAG
* **
81811 GTCCATAACATTATTGATTCGTTTGATTTTA
1 GTCCATAACATTATTGATCCGTTCAATTTTA
* *
81842 GTCCCTAACGTTATTGATCCGTTCAATTTTA
1 GTCCATAACATTATTGATCCGTTCAATTTTA
81873 GTC
1 GTC
81876 TCTCAGTCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (31 bp):
GTCCATAACATTATTGATCCGTTCAATTTTA
Found at i:82073 original size:2 final size:2
Alignment explanation
Indices: 82068--82108 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
82058 ACACACACAC
82068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
82109 ATTTGATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:91896 original size:21 final size:21
Alignment explanation
Indices: 91841--91898 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
91831 TCGCCATTAA
*
91841 AAACTTAACATATTTAGTACAT
1 AAACTTAATAT-TTTAGTACAT
*
91863 AAAC-T-ATCGATTTTGGTACAT
1 AAACTTAAT--ATTTTAGTACAT
91884 AAACTTAATATTTTA
1 AAACTTAATATTTTA
91899 AAAAAACGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
20 1 0.03
21 19 0.66
22 7 0.24
23 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
AAACTTAATATTTTAGTACAT
Found at i:93547 original size:19 final size:19
Alignment explanation
Indices: 93503--93548 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
93493 TGACAGAGTT
*
93503 CAGAAGCCTTGCACCTCTC
1 CAGAAGTCTTGCACCTCTC
93522 CAGAAGTCTTGCACCTCTC
1 CAGAAGTCTTGCACCTCTC
93541 CAGAAGTC
1 CAGAAGTC
93549 GTTATCCTTT
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:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (19 bp):
CAGAAGTCTTGCACCTCTC
Done.