Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006146.1 Hibiscus syriacus cultivar Beakdansim tig00014593_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: 96998
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4213 original size:53 final size:51
Alignment explanation
Indices: 4143--4244 Score: 118
Period size: 53 Copynumber: 2.0 Consensus size: 51
4133 GGTAAAAAAG
* * * *
4143 TTTAATGAATAAGTTTTGA-AACTGTTTTATGAAAGAATTTTGAGAAATGTTTA
1 TTTAATGAATAAATTTTGAGAAATGTTTGATG-AAG-ATTTT-AAAAATGTTTA
4196 TTTAATGAA-AGAATTTTGAGAAATGTTTGATGAAGATTTTAAAAATGTT
1 TTTAATGAATA-AATTTTGAGAAATGTTTGATGAAGATTTTAAAAATGTT
4245 GTCCATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
51 8 0.19
52 6 0.14
53 19 0.44
54 10 0.23
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (51 bp):
TTTAATGAATAAATTTTGAGAAATGTTTGATGAAGATTTTAAAAATGTTTA
Found at i:6929 original size:10 final size:10
Alignment explanation
Indices: 6914--6942 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
6904 TACAATTGCA
6914 AATGCAATAC
1 AATGCAATAC
6924 AATGCAATAC
1 AATGCAATAC
6934 AATGCAATA
1 AATGCAATA
6943 AAGGTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (10 bp):
AATGCAATAC
Found at i:7858 original size:14 final size:14
Alignment explanation
Indices: 7839--7879 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
7829 GGTTTCAGAC
7839 CTAGAAAAAAGGTA
1 CTAGAAAAAAGGTA
7853 CTAGAAAAAAGGTA
1 CTAGAAAAAAGGTA
7867 CTAGAAAAAAGGT
1 CTAGAAAAAAGGT
7880 TCACTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (14 bp):
CTAGAAAAAAGGTA
Found at i:8949 original size:45 final size:45
Alignment explanation
Indices: 8770--8948 Score: 222
Period size: 45 Copynumber: 4.1 Consensus size: 45
8760 AATGGATGAA
** *
8770 CACAAATG-AAATGTGTAACTGTGCATT-T--GCATAAAAGGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
* * *
8811 CACAAATGAAAATGCATGACTGTGCATTATCAGCATAAAAGGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
* * *
8856 CACAAATGAAAATGCATAACGGTGCATTTTTGGCATAAAATGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
* * *
8901 CACTAATGAAAATGCATAACGGTGCATTAACGGTATAAAAGGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
8946 CAC
1 CAC
8949 TCATGGTATT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 8 0.07
42 16 0.13
43 1 0.01
45 94 0.79
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (45 bp):
CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
Found at i:18283 original size:25 final size:25
Alignment explanation
Indices: 18251--18300 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
18241 TGTTCGAAGC
18251 GTAAAATATTTTCAAACAATTCATT
1 GTAAAATATTTTCAAACAATTCATT
*
18276 GTAAAATATTTTCAAACTATTCATT
1 GTAAAATATTTTCAAACAATTCATT
18301 TTTAGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (25 bp):
GTAAAATATTTTCAAACAATTCATT
Found at i:25196 original size:3 final size:3
Alignment explanation
Indices: 25190--25238 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
25180 AGTTTTTTTT
*
25190 TTA TTA TT- TATA TTA TTA TTA TTA TTA TTA TTA TGA TATA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
25236 TTA
1 TTA
25239 AATAATAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.90
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:26860 original size:23 final size:22
Alignment explanation
Indices: 26814--26858 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26804 ATATTATAAA
26814 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
26836 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
26859 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:26940 original size:23 final size:26
Alignment explanation
Indices: 26908--26957 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
26898 CATTTTCTGA
*
26908 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
26931 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
26957 T
1 T
26958 TTTCTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:28012 original size:39 final size:38
Alignment explanation
Indices: 27935--28022 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 38
27925 TACAGCTGTT
*
27935 GCTGCTGCTGTTGTGCTTAGGACATGGCTGCGGCTGTG
1 GCTGCTGCTGTTGTGCTTAGGACATGGCTGCGGATGTG
* * *
27973 GCTGCTGCTGTTGTGGCTTAGGAGATGGTTGTGGATGTG
1 GCTGCTGCTGTTGT-GCTTAGGACATGGCTGCGGATGTG
28012 GCTGCTGCTGT
1 GCTGCTGCTGT
28023 GGTTGTTGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 14 0.31
39 31 0.69
ACGTcount: A:0.08, C:0.17, G:0.41, T:0.34
Consensus pattern (38 bp):
GCTGCTGCTGTTGTGCTTAGGACATGGCTGCGGATGTG
Found at i:29787 original size:3 final size:3
Alignment explanation
Indices: 29781--29851 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
29771 TCATTTAAAT
** * *
29781 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29829 TTA TTA TTA TATA TTA TTTA TTA
1 TTA TTA TTA T-TA TTA -TTA TTA
29852 AATATTATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:29803 original size:12 final size:12
Alignment explanation
Indices: 29786--29859 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
29776 TAAATTTATT
29786 ATTATTATTAAA
1 ATTATTATTAAA
29798 ATTATTATT---
1 ATTATTATTAAA
*
29807 ATTAGTATT---
1 ATTATTATTAAA
*
29816 ATTATTATTATA
1 ATTATTATTAAA
*
29828 ATTATTATTATAT
1 ATTATTATTA-AA
29841 ATTATTTATTAAA
1 ATTA-TTATTAAA
29854 TATTAT
1 -ATTAT
29860 AAAGCCCAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
9 16 0.31
12 19 0.37
13 6 0.12
14 10 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:31207 original size:15 final size:15
Alignment explanation
Indices: 31176--31257 Score: 65
Period size: 15 Copynumber: 5.0 Consensus size: 15
31166 TTTAATACTA
*
31176 TATTTTTATTTCCTTT
1 TATTTTTATTT-ATTT
31192 TATTTTTATTTATTT
1 TATTTTTATTTATTT
* *
31207 TATTATTATTATTTTT
1 TATTTTTATT-TATTT
31223 TATTGTTTTAATTATTATTT
1 TA-T-TTTT-A-T-TTATTT
*
31243 TATTATTATTTATTT
1 TATTTTTATTTATTT
31258 ATAAAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 18 0.33
16 18 0.33
17 2 0.04
18 6 0.11
19 2 0.04
20 7 0.13
21 1 0.02
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.74
Consensus pattern (15 bp):
TATTTTTATTTATTT
Found at i:31214 original size:3 final size:3
Alignment explanation
Indices: 31191--31252 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
31181 TTATTTCCTT
* *
31191 TTA TTT TTA TTTA TT- TTA TTA TTA TTA TT- TT- TTA TTG TT- TTAA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
31234 TTA TTA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
31253 TATTTATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
2 10 0.20
3 35 0.70
4 5 0.10
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:31238 original size:33 final size:34
Alignment explanation
Indices: 31195--31259 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
31185 TTCCTTTTAT
*
31195 TTTTATTTATT-TTATTATTATTATTT-TTTATTG
1 TTTTAATTATTATT-TTATTATTATTTATTTATTG
31228 TTTTAATTATTATTTTATTATTATTTATTTAT
1 TTTTAATTATTATTTTATTATTATTTATTTAT
31260 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (34 bp):
TTTTAATTATTATTTTATTATTATTTATTTATTG
Found at i:31286 original size:20 final size:20
Alignment explanation
Indices: 31257--31299 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
31247 ATTATTTATT
31257 TATAAAAATAAATAAATATA
1 TATAAAAATAAATAAATATA
* *
31277 TATAATAATAAATATATATA
1 TATAAAAATAAATAAATATA
31297 TAT
1 TAT
31300 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAAAATAAATAAATATA
Found at i:31590 original size:16 final size:17
Alignment explanation
Indices: 31560--31596 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
31550 ATATTTTATT
31560 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
31577 TATATTTT-TATATAAT
1 TATATTTTATATATAAA
31593 TATA
1 TATA
31597 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:31595 original size:26 final size:26
Alignment explanation
Indices: 31546--31596 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
31536 TTCTAAATAA
* *
31546 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
31572 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
31597 ACTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:36429 original size:2 final size:2
Alignment explanation
Indices: 36422--36471 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
36412 TTATCCTTTA
36422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36464 AT AT AT AT
1 AT AT AT AT
36472 CATTTGTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38826 original size:114 final size:114
Alignment explanation
Indices: 38626--38848 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 114
38616 TGCCATGTGA
* * *
38626 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * *
38691 TTTGGTATGAACCCTAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGC
* *
38740 TCATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
38805 TTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
38849 CTGCATAATC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTGC
Found at i:41245 original size:22 final size:22
Alignment explanation
Indices: 41220--41294 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
41210 ATCTACATTC
41220 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
41242 TTCAAAGATGAAAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
41264 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
41286 TTCAAAGAT
1 TTCAAAGAT
41295 AAAAGCTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:42570 original size:76 final size:76
Alignment explanation
Indices: 42146--43008 Score: 1441
Period size: 75 Copynumber: 11.4 Consensus size: 76
42136 CTATTTCCCA
*
42146 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42210 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
42221 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42285 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
42296 CATCTGTAAGTCCTGCAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42360 AGCCTTCGGGT
66 AGCCTTCGGGT
*
42371 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
42436 AAACCTTAGGGT
65 AAGCCTTCGGGT
42448 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42513 AGCCTTCGGGT
66 AGCCTTCGGGT
*
42524 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
42589 AGCCTTCAGGT
66 AGCCTTCGGGT
42600 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42664 AGCCTTCGGGT
66 AGCCTTCGGGT
*
42675 CATCTGTAAGTCATTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42740 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
42751 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGAGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
42816 AGCCTTAGGGT
66 AGCCTTCGGGT
* *
42827 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42891 A-CCTTCGGGT
66 AGCCTTCGGGT
* * * *
42901 TATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGTTGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
*
42966 AAAACCTTCGGGT
64 AAAGCCTTCGGGT
* *
42979 CATCTGTAAGCCCTTCAGTGCCTGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
43009 TCAACATTTC
Statistics
Matches: 745, Mismatches: 36, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
74 61 0.08
75 291 0.39
76 283 0.38
77 75 0.10
78 35 0.05
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:42677 original size:227 final size:227
Alignment explanation
Indices: 42146--43008 Score: 1437
Period size: 227 Copynumber: 3.8 Consensus size: 227
42136 CTATTTCCCA
*
42146 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
* *
42211 GCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
* *
42276 ATGTTTTC-AAGCCTTCGGGTCATCTGTAAGTCCTGCAGTACATGATGTTTCCAAAAAGCCTTCG
131 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
* *
42340 GGAGCTTTTTGATGTTTTC-AAGCCTTCGGGT
196 GGAGTTTTTTGATGTTTTCAAAGCCTTCAGGT
* *
42371 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT--A
* *
42436 AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
64 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
42501 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
129 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
42566 CGGGAGTTTTTTGATGTTTTCAAAGCCTTCAGGT
194 CGGGAGTTTTTTGATGTTTTCAAAGCCTTCAGGT
*
42600 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
*
42665 GCCTTCGGGTCATCTGTAAGTCATTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
*
42730 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCG
131 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
*
42795 AGAGTTTTTTGATGTTTTCAAAGCCTT-AGGGT
196 GGAGTTTTTTGATGTTTTCAAAGCCTTCA-GGT
* *
42827 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
* * *
42892 -CCTTCGGGTTATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTG
66 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
* * * *
42956 TTGTTTTCAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCCTGATGTTT
131 ATGTTTTC--AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
43009 TCAACATTTC
Statistics
Matches: 603, Mismatches: 28, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
225 60 0.10
226 68 0.11
227 291 0.48
228 112 0.19
229 72 0.12
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (227 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCG
GGAGTTTTTTGATGTTTTCAAAGCCTTCAGGT
Found at i:43146 original size:3 final size:3
Alignment explanation
Indices: 43140--43207 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
43130 TCATTTAAAT
** * *
43140 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43188 TTA TTA TTTA TTA TTTA TTA
1 TTA TTA -TTA TTA -TTA TTA
43208 AATATTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:43160 original size:15 final size:14
Alignment explanation
Indices: 43142--43215 Score: 70
Period size: 15 Copynumber: 5.6 Consensus size: 14
43132 ATTTAAATTT
43142 ATTATTATTATTAAA
1 ATTATTATTATT-AA
43157 ATTATTATTATT--
1 ATTATTATTATTAA
*
43169 AGTATTATTATTATA
1 ATTATTATTATTA-A
*
43184 ATTATTATTATT-T
1 ATTATTATTATTAA
43197 ATTA-T-TTATTAA
1 ATTATTATTATTAA
43209 A-TATTAT
1 ATTATTAT
43216 AAAGCCCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 7 0.14
12 14 0.29
13 5 0.10
15 23 0.47
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:43161 original size:18 final size:18
Alignment explanation
Indices: 43134--43215 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
43124 TTTTTTTCAT
*
43134 TTAAATTTATTATTATTA
1 TTAAAATTATTATTATTA
43152 TTAAAATTATTATTATTA
1 TTAAAATTATTATTATTA
* *
43170 GT---ATTATTATTATAA
1 TTAAAATTATTATTATTA
**
43185 TTATTATTATTTATTATTTA
1 TTAAAATTA-TTATTA-TTA
43205 TTAAATATTAT
1 TTAAA-ATTAT
43216 AAAGCCCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 13 0.25
18 22 0.43
19 6 0.12
20 6 0.12
21 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TTAAAATTATTATTATTA
Found at i:44464 original size:15 final size:15
Alignment explanation
Indices: 44445--44528 Score: 57
Period size: 16 Copynumber: 5.5 Consensus size: 15
44435 AATACTATAT
*
44445 TTTTTATTTCCTTTTA
1 TTTTTATTT-ATTTTA
44461 TTTTTATTTATTTTA
1 TTTTTATTTATTTTA
* *
44476 TTATTATTATTTTTTA
1 TTTTTATT-TATTTTA
* *
44492 TTGTT-TTAATTATTA
1 TTTTTATTTATT-TTA
44507 -TTTTA-TTATTATTA
1 TTTTTATTTATT-TTA
44521 TTATTTAT
1 TT-TTTAT
44529 AAAAATAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
14 13 0.24
15 18 0.33
16 23 0.43
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:44481 original size:3 final size:3
Alignment explanation
Indices: 44458--44525 Score: 65
Period size: 3 Copynumber: 23.7 Consensus size: 3
44448 TTATTTCCTT
* *
44458 TTA TTT TTA TTTA TT- TTA TTA TTA TTA TT- TT- TTA TTG TT- TTAA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
44501 TTA TTA TT- TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
44526 TATAAAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
2 10 0.18
3 41 0.73
4 5 0.09
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:44558 original size:18 final size:19
Alignment explanation
Indices: 44533--44575 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
44523 ATTTATAAAA
44533 ATAAATAAATATATATATAT
1 ATAAATAAATA-ATATATAT
44553 ATATAATAAATAATATATAT
1 ATA-AATAAATAATATATAT
44573 ATA
1 ATA
44576 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATAAATAATATATAT
Found at i:44867 original size:16 final size:17
Alignment explanation
Indices: 44837--44873 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
44827 ATATTTTATT
44837 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
44854 TATATTTT-TATATAAT
1 TATATTTTATATATAAA
44870 TATA
1 TATA
44874 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:44872 original size:26 final size:26
Alignment explanation
Indices: 44823--44873 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
44813 TTCTAAATAA
* *
44823 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
44849 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
44874 ACTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:50138 original size:13 final size:13
Alignment explanation
Indices: 50120--50144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50110 TATTCTCTGT
50120 TTGTTGTTGTTTG
1 TTGTTGTTGTTTG
50133 TTGTTGTTGTTT
1 TTGTTGTTGTTT
50145 CTGATTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (13 bp):
TTGTTGTTGTTTG
Found at i:58441 original size:10 final size:10
Alignment explanation
Indices: 58428--58457 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
58418 TATGTAAAAT
58428 TTAATATTAA
1 TTAATATTAA
58438 TTAATATTAA
1 TTAATATTAA
*
58448 TTAAAATTAA
1 TTAATATTAA
58458 AATAATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTAATATTAA
Found at i:65568 original size:2 final size:2
Alignment explanation
Indices: 65561--65638 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
65551 TGCACATAAG
65561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65603 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65639 AAAGTGATGA
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65899 original size:20 final size:21
Alignment explanation
Indices: 65846--65900 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
65836 AGGTAACGAT
*
65846 TTTGACAAAATCGATTGGAAA
1 TTTGACAAAATCGGTTGGAAA
65867 -TTGACAAAATCGGTT-GAAA
1 TTTGACAAAATCGGTTGGAAA
65886 TTTGACAAAATCGGT
1 TTTGACAAAATCGGT
65901 AAAGAGCTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (21 bp):
TTTGACAAAATCGGTTGGAAA
Found at i:67016 original size:3 final size:3
Alignment explanation
Indices: 67008--67032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
66998 TCTATAGTTC
67008 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
67033 TCTCTTCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:76832 original size:18 final size:17
Alignment explanation
Indices: 76791--76842 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
76781 AGATGTAAGC
*
76791 TAAATTTTGTATTTGAA
1 TAAATTTTGTATGTGAA
76808 TAGAATTTTGTATGTGAA
1 TA-AATTTTGTATGTGAA
*
76826 TGAAATTATGTATGTGA
1 T-AAATTTTGTATGTGA
76843 TGAGCAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.06
18 28 0.90
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (17 bp):
TAAATTTTGTATGTGAA
Found at i:78585 original size:20 final size:21
Alignment explanation
Indices: 78536--78577 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
78526 AGGCATAAAC
78536 ATAATGTATCGATACTTATTAT
1 ATAA-GTATCGATACTTATTAT
78558 ATAAGTATCGATACTT-TTAT
1 ATAAGTATCGATACTTATTAT
78578 TCCAGTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (21 bp):
ATAAGTATCGATACTTATTAT
Found at i:78763 original size:21 final size:20
Alignment explanation
Indices: 78739--78777 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
78729 CGTAAACATA
78739 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTT-TTATAT
*
78760 AAGTATCGATGCTTTTAT
1 AAGTATCGATACTTTTAT
78778 TCCAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (20 bp):
AAGTATCGATACTTTTATAT
Found at i:79104 original size:199 final size:199
Alignment explanation
Indices: 78460--79548 Score: 1393
Period size: 199 Copynumber: 5.5 Consensus size: 199
78450 TTTTGAAATG
* * *
78460 TATTACTTTAAAGTAATATGTAAATTTACAATGTAAACGGTAAAAATCTATCGATTTAATGATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * * * * * *
78525 TAGGCATAAACAT-AATGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCA
66 TAGGCGTAAACATCAA-GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCT
* **
78589 TCTCAAGCAATTTG-AACGCACAAAGTATCGATACACCTGTATAAAGTATCGATAC-AAAGAATT
130 TCTCAA-CAATTTGCAA-GCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGA-AATT
* *
78652 TTGAAACT
192 TCGAAACC
*
78660 TATTTCTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACTC-GTTTAATGATA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTAC-CGGTTTAATGATA
* * * * * *
78724 ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAGTATCGATGCTTTTATTCCAATATG-T
65 ATAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCT
* * * ** *
78788 ATCTCAAACAATTTGCATGCAAAAAAGAATCGATACACATGTATAAAGTATCGATACTTGTAATT
130 -TCTC-AACAATTTGCAAGC-ACAAAGTATCGATACACATGTATAAAGTATCGATACGCGAAATT
*
78853 TCAAAACC
192 TCGAAACC
* * * *
78861 TATTACTATAAAGTAATACGTAAATTTACAATGTATACGGTAAAAATCTACCGGTTTAATTATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * * *
78926 TAGACGTAAACATCATGTATTGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGTTT
66 TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
* * * *
78991 ATCAACAATTTCCAAGAACAAAGTATCGATACACATGTATACAA-TATCGATACGCGAAATTTCA
131 CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATA-AAGTATCGATACGCGAAATTTCG
79055 AAACC
195 AAACC
* * ** *
79060 GATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGCCTACTGGTTTAATGATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* **
79125 TAGGTGTAAACATCAAGTATCGATACACTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
66 TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
* *
79190 CTCAATAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGACACGC-AGAATTTCG
131 CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGA-AATTTCG
79254 AAACC
195 AAACC
* * * * * *
79259 GATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAATTCTATCAGTTTAATGAAAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * *
79324 TAGGCGTAAACATCAAGTATCAATACGTTTTGTATAGGTATCGATACTTTTAGTCCAATATGATT
66 TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
* * *
79389 CTCAACAATTTGCATGCACAGAGTATCGATACACATGTATAAAGTATCGATACGCGGAATTTCGA
131 CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGAAATTTCGA
79454 AACC
196 AACC
* * * * *
79458 TATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACAGGTATATTGATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * *
79523 TAGGCATAAATA-CAAGTATTGATACT
66 TAGGCGTAAACATCAAGTATCGATACT
79549 GTCTATATAG
Statistics
Matches: 784, Mismatches: 92, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
198 14 0.02
199 465 0.59
200 142 0.18
201 162 0.21
202 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (199 bp):
TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGAAATTTCGA
AACC
Found at i:79617 original size:20 final size:20
Alignment explanation
Indices: 79585--79661 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
79575 ATAGTTAACG
*
79585 AATTTGACTAAACCGATTAA
1 AATTTGACAAAACCGATTAA
* * * *
79605 AAATTGACAAAACTGGTTGA
1 AATTTGACAAAACCGATTAA
**
79625 AATTTGACAAAACCGATTTT
1 AATTTGACAAAACCGATTAA
*
79645 AATTTGAGAAAACCGAT
1 AATTTGACAAAACCGAT
79662 AAAGAGATAC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (20 bp):
AATTTGACAAAACCGATTAA
Found at i:79851 original size:20 final size:20
Alignment explanation
Indices: 79822--79876 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
79812 CATGTTGAAG
* *
79822 TTTGAAAAAACTGGTTTCAA
1 TTTGACAAAACCGGTTTCAA
79842 TTTGACAAAACCGGTTTCAA
1 TTTGACAAAACCGGTTTCAA
79862 TTTGACAAAACCGGT
1 TTTGACAAAACCGGT
79877 AAAGAGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
TTTGACAAAACCGGTTTCAA
Found at i:82682 original size:180 final size:178
Alignment explanation
Indices: 82198--82741 Score: 626
Period size: 180 Copynumber: 3.0 Consensus size: 178
82188 AAGTATCGAT
* *
82198 ATACTTAGAATTTCGAAACCTATTATTTTAAAGTAATATGTAAATTTACAATGTAAACGGTAAAA
1 ATACTTAGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA
** * * **
82263 ATCTATTGGTTTAATGATAATAGGT-GTAAATATAATGTATCAATACTTTTTTTTATAGGTATCG
66 ATCTACCGGTTTAATGATAATA-GTCGTAAATATAAAGTATCGATAC--TTTAATATAGGTATCG
* * * * *
82327 GTACTTTTATTCCAATGTGTTTCTCAAACAATTTGCACGCAAAAAAAGTATTG
128 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCACGC--AAAATGTATCG
* ** * * * * *
82380 ATATTTTTAATTCCGAAACCTATTACTATAAAGTAATAGTTAAATTAACAATGTAAAGGGTAAAA
1 ATACTTAGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA
* * * * * * * ** *
82445 GTTTACCAGTATAATGATCATAGGCGTATATACCAAGTATCGATACTTTATATATAGGTATCAAT
66 ATCTACCGGTTTAATGATAATAGTCGTAAATATAAAGTATCGATACTTTA-ATATAGGTATCGAT
* * *
82510 ACTTTTAGTT-CAGTATGCATCTCAAACAATTTGCACGCAAAATGCATCG
130 ACTTTTA-TTCCAATATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
* *
82559 ATACTCAGAATTTCTGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
1 ATACTTAGAATTTC-GAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * * *
82624 AATCTACCGGTTTAATGGTAATAGTCATAAACATAAAGTATCGATACATTTAATATAGGTTTCGA
65 AATCTACCGGTTTAATGATAATAGTCGTAAATATAAAGTATCGATAC-TTTAATATAGGTATCGA
82689 TACTTTT-TTCCAATATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
129 TACTTTTATTCCAATATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
82738 ATAC
1 ATAC
82742 ACATATATAA
Statistics
Matches: 295, Mismatches: 61, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
178 2 0.01
179 57 0.19
180 101 0.34
181 47 0.16
182 88 0.30
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (178 bp):
ATACTTAGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA
ATCTACCGGTTTAATGATAATAGTCGTAAATATAAAGTATCGATACTTTAATATAGGTATCGATA
CTTTTATTCCAATATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
Found at i:83061 original size:127 final size:125
Alignment explanation
Indices: 82758--83076 Score: 374
Period size: 128 Copynumber: 2.5 Consensus size: 125
82748 ATAAATTTTT
* * * * * *
82758 TATATTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTTAATTTACAATGAAAATGATAAA
1 TATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTAAA
* *
82823 AGTCAATCAGTATAATGATAATAGGCGTAAATATCAAGTATCGATAAACATGTATAAAGTA
66 AGTCAACCAGTATAATGAAAATAGGCGTAAATATCAAGTATCGAT-AACATGTATAAAGTA
* ** *
82884 TCGATACGTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTA
1 T--ATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTA
** * * *
82949 AACTTTTCTACCGGTATAATGAAAATAGTCGTAAATATACAAGTATCGAT-AC-TGTCATATAAG
64 AA--AGTCAACCAGTATAATGAAAATAGGCGTAAATAT-CAAGTATCGATAACATGT-ATA-AAG
83012 TA
124 TA
* *
83014 T-TTCTTATAATTTCGAAACCTATTACTATAAAGTAATAGGTAAATTAACAATGTACATGGTAA
1 TATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTAA
83077 TATGTTGATA
Statistics
Matches: 163, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
126 1 0.01
127 56 0.34
128 57 0.35
129 5 0.03
130 33 0.20
131 11 0.07
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (125 bp):
TATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTAAA
AGTCAACCAGTATAATGAAAATAGGCGTAAATATCAAGTATCGATAACATGTATAAAGTA
Found at i:83468 original size:226 final size:226
Alignment explanation
Indices: 83074--83679 Score: 952
Period size: 226 Copynumber: 2.7 Consensus size: 226
83064 ATGTACATGG
* *
83074 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAATCTATTTTGTTATCGTCGTATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
* * * * **
83139 AGACCCCATCAGCTTTAAACAAGCGCTGCCTATTAAATTAAATAATCTTTACTTGTTATGTTATT
66 AGGCCCCATCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTATT
* *
83204 ATGGTTGATAATGTGTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
131 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
83269 CTTAAAATTTGGTAACATTTTAGGCGCTACC
196 CTTAAAATTTGGTAACATTTTAGGCGCTACC
*
83300 TAATATGTTGATAATACTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
* * *
83365 AGGCCCCATCAGCTTTAAACAGGCACTACCTATTGCATTAAATAAACGCTACTTGTTATGTTATT
66 AGGCCCCATCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTATT
83430 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
131 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
83495 CTTAAAATTTGGTAACATTTTAGGCGCTACC
196 CTTAAAATTTGGTAACATTTTAGGCGCTACC
* *
83526 TAATATGTTGATAATATTGATAACAAATCAAGTAACTAACCTATTTTGTTATTGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
* * * * *
83591 AGG-CCCA-CAACTTTAAA-AATGCGCTACCTATTACGTTACATAAGCGCTA-TCT-ATATGTTA
66 AGGCCCCATCAGCTTTAAACAA-GCGCTACCTATTACATTAAATAAACGCTACT-TGTTATGTTA
* *
83651 TTATGGTTAATAATATTTCCAGTAATTAA
129 TTATGGTTGATAATGTTTCCAGTAATTAA
83680 TCGATTATGT
Statistics
Matches: 351, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
223 36 0.10
224 34 0.10
225 4 0.01
226 277 0.79
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (226 bp):
TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
AGGCCCCATCAGCTTTAAACAAGCGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTATT
ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
CTTAAAATTTGGTAACATTTTAGGCGCTACC
Found at i:86873 original size:22 final size:21
Alignment explanation
Indices: 86848--86889 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
86838 AAAAAAGTAC
86848 AAAATAAATGTAAAAAT-TTACT
1 AAAA-AAA-GTAAAAATATTACT
*
86870 AAAAAAAGTTAAAATATTAC
1 AAAAAAAGTAAAAATATTAC
86890 CTTCTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAAAGTAAAAATATTACT
Found at i:91397 original size:37 final size:34
Alignment explanation
Indices: 91348--91416 Score: 111
Period size: 37 Copynumber: 1.9 Consensus size: 34
91338 CCTTTAATTA
91348 GTACTAATTTTCTTTTGGGGACATAGTCTCTCTCTC
1 GTACTAATTTTCTTTTGGGGAC--AGTCTCTCTCTC
91384 GTACTAAATTTTCTTTTGGGGACAGTCTCTCTC
1 GTACT-AATTTTCTTTTGGGGACAGTCTCTCTC
91417 GTCTATCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 10 0.31
36 5 0.16
37 17 0.53
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (34 bp):
GTACTAATTTTCTTTTGGGGACAGTCTCTCTCTC
Done.