Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001812.1 Hibiscus syriacus cultivar Beakdansim tig00003667_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: 68883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7879 original size:24 final size:24
Alignment explanation
Indices: 7864--7909 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
7854 TATAATTTGC
7864 ACCGAAGTGCCACATAGAATATGA
1 ACCGAAGTGCCACATAGAATATGA
7888 ACCGAAGTGCCACATAG-ATATG
1 ACCGAAGTGCCACATAGAATATG
7910 TCCAGATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (24 bp):
ACCGAAGTGCCACATAGAATATGA
Found at i:8126 original size:40 final size:40
Alignment explanation
Indices: 8082--8163 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
8072 TATTCTTTAC
* *
8082 TCAAATATAACATATTCACATAGCATATATTCGCGTAGAA
1 TCAAATATAACATATTCACATAGCATATATTCACATAGAA
8122 TCAAATATAACATATTCACATAGCATATATTCACATAGAA
1 TCAAATATAACATATTCACATAGCATATATTCACATAGAA
8162 TC
1 TC
8164 TTTTCATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.30
Consensus pattern (40 bp):
TCAAATATAACATATTCACATAGCATATATTCACATAGAA
Found at i:8169 original size:15 final size:15
Alignment explanation
Indices: 8133--8162 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8123 CAAATATAAC
*
8133 ATATTCACATAGCAT
1 ATATTCACATAGAAT
8148 ATATTCACATAGAAT
1 ATATTCACATAGAAT
8163 CTTTTCATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (15 bp):
ATATTCACATAGAAT
Found at i:8184 original size:15 final size:15
Alignment explanation
Indices: 8166--8219 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
8156 ATAGAATCTT
8166 TTCATATAAAACACA
1 TTCATATAAAACACA
*
8181 TTCACATATATAACACA
1 TT--CATATAAAACACA
** *
8198 TTCGCATAGAACACA
1 TTCATATAAAACACA
8213 TTCATAT
1 TTCATAT
8220 TTTAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 17 0.55
17 14 0.45
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (15 bp):
TTCATATAAAACACA
Found at i:8193 original size:19 final size:17
Alignment explanation
Indices: 8168--8205 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8158 AGAATCTTTT
*
8168 CATATAAAACACATTCA
1 CATATATAACACATTCA
*
8185 CATATATAACACATTCG
1 CATATATAACACATTCA
8202 CATA
1 CATA
8206 GAACACATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (17 bp):
CATATATAACACATTCA
Found at i:14923 original size:24 final size:24
Alignment explanation
Indices: 14896--14966 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
14886 CACATAGATA
*
14896 TGTCCCAAAGGATCGCGTAGAATT
1 TGTCCCGAAGGATCGCGTAGAATT
* *
14920 TGTCCCGAAGGACCACGTAGAAATT
1 TGTCCCGAAGGATCGCGTAG-AATT
* * *
14945 TTTCCCGAATGATCGCATAGAA
1 TGTCCCGAAGGATCGCGTAGAA
14967 CTCTCTACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (24 bp):
TGTCCCGAAGGATCGCGTAGAATT
Found at i:14965 original size:25 final size:25
Alignment explanation
Indices: 14896--14966 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
14886 CACATAGATA
*
14896 TGTCCCAAAGGATCGCGTAG-AATT
1 TGTCCCGAAGGATCGCGTAGAAATT
* *
14920 TGTCCCGAAGGACCACGTAGAAATT
1 TGTCCCGAAGGATCGCGTAGAAATT
* * *
14945 TTTCCCGAATGATCGCATAGAA
1 TGTCCCGAAGGATCGCGTAGAA
14967 CTCTCTACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 17 0.45
25 21 0.55
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (25 bp):
TGTCCCGAAGGATCGCGTAGAAATT
Found at i:18464 original size:2 final size:2
Alignment explanation
Indices: 18459--18500 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
18449 TTTAAATTTA
18459 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
18501 GGGGGATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23560 original size:19 final size:19
Alignment explanation
Indices: 23533--23603 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
23523 ATGCATTTTA
* *
23533 TGCATCGATGCACTCTAAG
1 TGCACCGATGCACTCTTAG
23552 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
23571 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
23590 TGCACCGATGCACT
1 TGCACCGATGCACT
23604 GAGAGTCCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:25867 original size:18 final size:17
Alignment explanation
Indices: 25846--25888 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
25836 ATATATACAT
25846 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
25864 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
25881 ATAA-AATA
1 ATAATAATA
25889 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:26287 original size:37 final size:36
Alignment explanation
Indices: 26237--26374 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
26227 GTGCTTGTGG
* * * * *
26237 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
26274 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
26311 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
26345 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
26375 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:26348 original size:34 final size:35
Alignment explanation
Indices: 26271--26371 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
26261 TTAGTAGAAC
26271 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
26309 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
26342 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
26372 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:27396 original size:109 final size:105
Alignment explanation
Indices: 26920--28003 Score: 1123
Period size: 105 Copynumber: 10.4 Consensus size: 105
26910 CATTGTTCCA
* ** * *
26920 AGTCCAATATCCTCCGTCATGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAACTGGAAATTGTTTGTTGACAAC
26985 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * * *
27026 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGACAAC
* * ** *
27090 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * *
27131 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGACAAC
* * * *
27195 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * *
27235 AAGTCCAATATCCTTCGTTGTGAAGATGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 -AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTG-GAAATTGTTTGTTGACAA
27300 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * ** * *
27342 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAA-TCGCGGATGAAACTGAAAAGTTGTTCGTTGA
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAATTGGC-TCTGAAACTGGAAA-TTGTTTGTTGA
27406 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
61 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * ** * * * *
27451 GGTAGCATGATATCCTCCGTCATGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGAC
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGAC
* *
27516 AACCAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCG
62 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* ** * * **
27560 AGTCTAATATCCTTCACTGTGAAGTTGAGATTGGCTC-----C--GAAATT-TCTTGTCGACAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAATTGT-TTGTTGACAAC
* * * * *
27617 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTG
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * *
27658 GGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATT-ATTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGACAAC
27722 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * * ** **
27763 AGTTCAATATCCTTCGCTGTGAAGTTGAGATTGGCTC-----C--GAAATTGTTTGTCAACAGTC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAATTGTTTGTTGACAACC
* * * * * *
27821 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTTG
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-TCG
* * * *
27862 -GTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCCCTGAAACTGGAAAATT-ATTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGG-AAATTGTTTGTTGACAAC
*
27925 CAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
* * *
27966 AGTCCAATATCCTTCGCTGTGAAGTCGAAATTGACTCT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
28004 AGATAAAACG
Statistics
Matches: 825, Mismatches: 120, Indels: 67
0.82 0.12 0.07
Matches are distributed among these distances:
97 7 0.01
98 154 0.19
99 2 0.00
100 1 0.00
103 2 0.00
104 4 0.00
105 345 0.42
106 124 0.15
107 4 0.00
108 6 0.01
109 170 0.21
110 6 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAATTGTTTGTTGACAACC
AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
Found at i:27669 original size:98 final size:100
Alignment explanation
Indices: 27211--27998 Score: 592
Period size: 109 Copynumber: 7.6 Consensus size: 100
27201 TCCTTTCGTC
* * * *
27211 GTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGAAGATGAAATTGGCTCTG
1 GTGAAGTTGAACTTGTGTTGTCTCG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTG
* * * * *
27275 AAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTT
65 AAACT----A-TT-ATTGTCGACAACCAGCCGCCCCTTCGCT
* * * * *
27317 GTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTTGTGGAGTTGAAA-TCGCGG
1 GTGAAGTTGAACTTGTGTTGTCTCGAGT-CCA--ATATCCTTCGCTGTGAAGTTGAAATTGGC-C
* * * * *
27381 ATGAAACTGAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTT
62 CTGAAACT----A-TTATT-GTCGACAACCAGCCGCCCCTTCGCT
* * * *
27426 GTGAAGTTGAACTTGTGTTGTCTCGGGTAGCATGATATCCTCCGTCATG-G-AGTTGAAATCGGC
1 GTGAAGTTGAACTTGTGTTGTCTCGAGT-CCA--ATATCCTTCG-C-TGTGAAGTTGAAATTGGC
* * * * * * *
27489 TCTGGAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGCT
61 CCTGAAACT-----ATT-ATTGTCGACAACCAGCCGCCCCTTCGCT
* * *
27535 GTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCACTGTGAAGTTGAGATTGGCTCC-G
1 GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CCTG
* **
27599 AAA-T-TTCTTGTCGACAGTCAGCCGCCCCTTCGCT
65 AAACTATTATTGTCGACAACCAGCCGCCCCTTCGCT
* * * *
27633 GTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGA
1 GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGA
* * *
27698 AACTAGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTT
66 AACT-----ATTATTGTCGACAACCAGCCGCCCCTTCGCT
* *
27738 GTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC-G
1 GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CCTG
* ** *
27802 AAA-T-TGT-TTGTCAACAGTCAGTCGCCCCTTCGCT
65 AAACTAT-TATTGTCGACAACCAGCCGCCCCTTCGCT
* * * *
27836 GTGAAGTTGAGCTTGTGCTGTCTTTG-GTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCCCTG
1 GTGAAGTTGAACTTGTGTTGTC-TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTG
* * **
27900 AAACTGGAAAATTATTGTTGACAACCAGCCGTCCCTTCATT
65 AAACT-----ATTATTGTCGACAACCAGCCGCCCCTTCGCT
*
27941 GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTCGAAATTG
1 GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
27999 ACTCTAGATA
Statistics
Matches: 562, Mismatches: 85, Indels: 71
0.78 0.12 0.10
Matches are distributed among these distances:
97 4 0.01
98 155 0.28
99 7 0.01
104 6 0.01
105 155 0.28
106 49 0.09
107 5 0.01
108 6 0.01
109 164 0.29
110 9 0.02
111 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (100 bp):
GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGA
AACTATTATTGTCGACAACCAGCCGCCCCTTCGCT
Found at i:27821 original size:203 final size:203
Alignment explanation
Indices: 26966--27998 Score: 1085
Period size: 203 Copynumber: 5.0 Consensus size: 203
26956 CTGGAACCGG
* * * *
26966 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGTTTGTTGACAGCCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGGGTCC
* * * * * *
27031 AATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCG
66 AATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCAGCC
* ** * *
27095 GTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAG-TCTAATATCCTTCGTTGTGAAGTTGA
130 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTC-AATATCCTTCGCTGTGAAGTTGA
*
27159 AATTGGCTCT
194 AATTGGCTCC
* * * *
27169 GAAATTGGGAAGTTGTTTTTGACAAG-CAGCGGTCCTTTCG-TCGTGAAGTTGAACTTGCGTTGT
1 GAAATT-----G-T-TTGTTGAC-AGCCAGCCGTCCCTTCGCT-GTGAAGTTGAACTTGTGTTGT
* * * * * * *
27232 C-TGAAGTCCAATATCCTTCGTTGTGAAGATGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTG
57 CTTG-GGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATT-ATTGTTG
* *
27296 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCG
120 ACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-TCA--ATATCCTTCG
* * * * *
27361 TTGTGGAGTTGAAATCGCGGATGAAACT
182 CTGTGAAGTTGAAAT--TGGCT----CC
* * * *
27389 GAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGT
1 G-AAA-TTGTTTGTTGACAGCCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGGGT
* * * * * *
27454 AGCATGATATCCTCCGTCATG-G-AGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGACA
64 -CCA--ATATCCTTCG-C-TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATT-ATTGTTGACA
* * *
27517 ACCAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAG-TCTAATATCCTTCACTGTG
123 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTC-AATATCCTTCGCTGTG
*
27581 AAGTTGAGATTGGCTCC
187 AAGTTGAAATTGGCTCC
* * * * *
27598 GAAATT-TCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTC
1 GAAATTGT-TTGTTGACAGCCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGGGTC
* *
27662 CAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATTATTGTTGACAACCAGCC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCAGCC
*
27727 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAG
130 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAA
27792 ATTGGCTCC
195 ATTGGCTCC
** * * * * * *
27801 GAAATTGTTTGTCAACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTTGGTCC
1 GAAATTGTTTGTTGACAGCCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGGGTCC
* * *
27866 AATATCCTTCGCTGTGAAGTTAAAATTGGCCCTGAAACTGGAAAATTATTGTTGACAACCAGCCG
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCAGCCG
* * *
27931 TCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTCGAAA
131 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAAA
27996 TTG
196 TTG
27999 ACTCTAGATA
Statistics
Matches: 714, Mismatches: 78, Indels: 76
0.82 0.09 0.09
Matches are distributed among these distances:
202 2 0.00
203 278 0.39
204 37 0.05
206 3 0.00
207 48 0.07
208 4 0.01
209 5 0.01
210 87 0.12
211 50 0.07
212 1 0.00
213 4 0.01
214 24 0.03
215 61 0.09
216 9 0.01
217 2 0.00
218 88 0.12
219 1 0.00
220 5 0.01
221 3 0.00
222 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (203 bp):
GAAATTGTTTGTTGACAGCCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGGGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCAGCCG
TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAAA
TTGGCTCC
Found at i:28326 original size:37 final size:37
Alignment explanation
Indices: 28257--28330 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
28247 CAAAGATATT
** * *
28257 TTTTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAA
1 TTTTGTTTCAAGAAAAACGGTCTCAAGAGAGACAAAA
* *
28294 TTTTGTTTTAAGAAAAACTGTCTCAAGAGAGACAAAA
1 TTTTGTTTCAAGAAAAACGGTCTCAAGAGAGACAAAA
28331 CTTAGTTCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (37 bp):
TTTTGTTTCAAGAAAAACGGTCTCAAGAGAGACAAAA
Found at i:28542 original size:65 final size:65
Alignment explanation
Indices: 28438--28618 Score: 299
Period size: 65 Copynumber: 2.8 Consensus size: 65
28428 GACAAAATTT
28438 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
28503 TGTTTCAAGAGAAACTATCTCAAGAGAGACGGAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
28568 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
28619 CTATCTCAAG
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 93 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:28609 original size:102 final size:102
Alignment explanation
Indices: 28503--28858 Score: 595
Period size: 102 Copynumber: 3.5 Consensus size: 102
28493 TCAATGTTTA
* **
28503 TGTTTCAAGAGAAACTATCTCAAGAGAGACGGAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
28568 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
28605 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
28670 TGTTTCAAGAGAAACTGTCTCAATGGAGACTGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
28707 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
28772 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * **
28809 TGTTTCAAGGGAAACTGTCTCAACAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
28859 CTGTCTCAAG
Statistics
Matches: 237, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 237 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:28619 original size:37 final size:37
Alignment explanation
Indices: 28568--28876 Score: 216
Period size: 37 Copynumber: 8.9 Consensus size: 37
28558 TCAATGTTTA
* *
28568 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
28605 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
28641 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* **
28669 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACTGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
28707 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
28743 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
28771 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
28809 TGTTTCAAGGGAAACTGTCTCAACAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
28845 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
28877 TGGTGAGCAC
Statistics
Matches: 207, Mismatches: 36, Indels: 58
0.69 0.12 0.19
Matches are distributed among these distances:
28 3 0.01
29 28 0.14
30 6 0.03
32 2 0.01
33 2 0.01
34 2 0.01
35 4 0.02
36 68 0.33
37 86 0.42
38 6 0.03
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:28854 original size:36 final size:36
Alignment explanation
Indices: 28772--28876 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
28762 TCAATGTTTA
* * * *
28772 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAGTT
*
28809 TGTTTCAAGGGAAACTGTCTCAACAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
28845 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
28877 TGGTGAGCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 37 0.60
37 25 0.40
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:29695 original size:22 final size:22
Alignment explanation
Indices: 29670--29720 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
29660 TTGTGTTTGG
29670 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
29692 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
29714 TCAAAGG
1 TCAAAGG
29721 ATTGATGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:30361 original size:21 final size:22
Alignment explanation
Indices: 30337--30385 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
30327 CCTTTTTTTA
30337 TTTTTG-TTCTTGT-TTTTTCC
1 TTTTTGCTTCTTGTCTTTTTCC
* *
30357 TTTTTGCTTCTTTTCTTTTTTC
1 TTTTTGCTTCTTGTCTTTTTCC
30379 TTTTTGC
1 TTTTTGC
30386 CCTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.24
21 6 0.24
22 13 0.52
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTGCTTCTTGTCTTTTTCC
Found at i:30392 original size:22 final size:23
Alignment explanation
Indices: 30349--30391 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
30339 TTTGTTCTTG
*
30349 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
30372 TTTTTT-CTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
30392 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:33599 original size:18 final size:17
Alignment explanation
Indices: 33578--33620 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
33568 ACATATACAT
33578 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
33596 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
33613 ATAA-AATA
1 ATAATAATA
33621 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:34029 original size:37 final size:36
Alignment explanation
Indices: 33979--34116 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
33969 GTGCTTGTGG
* * * * *
33979 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
34016 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
34053 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
34087 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
34117 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:34090 original size:34 final size:35
Alignment explanation
Indices: 34013--34113 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
34003 TTAGTAGAAC
34013 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
34051 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
34084 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
34114 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:34404 original size:21 final size:21
Alignment explanation
Indices: 34369--34410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34359 AAGACTCTAT
*
34369 TTTCAAAATACAAAAATGAAA
1 TTTCAAAATACAAAAACGAAA
**
34390 TTTCAAAATTGAAAAACGAAA
1 TTTCAAAATACAAAAACGAAA
34411 ATAGTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.24
Consensus pattern (21 bp):
TTTCAAAATACAAAAACGAAA
Found at i:38077 original size:21 final size:22
Alignment explanation
Indices: 38028--38089 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
38018 ATACCCCCAT
38028 AAGGGAACCGATTCCCCCTTTG
1 AAGGGAACCGATTCCCCCTTTG
38050 AATGGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATTCCC-CCTTTG
* *
38073 -AGGGAATCGATACCCCC
1 AAGGGAACCGATTCCCCC
38090 CATGGGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.06
21 12 0.33
22 3 0.08
23 17 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (22 bp):
AAGGGAACCGATTCCCCCTTTG
Found at i:41641 original size:20 final size:20
Alignment explanation
Indices: 41616--41654 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41606 TTTTCATGGG
41616 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
41636 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
41655 TACTTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:43674 original size:30 final size:30
Alignment explanation
Indices: 43640--43697 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
43630 TGAGGCGTAT
*
43640 TGTTT-GAATTTGTTTTTTTTAACTTTCTAA
1 TGTTTGGAACTTG-TTTTTTTAACTTTCTAA
43670 TGTTTGGAACTTGTTTTTTTAACTTTCT
1 TGTTTGGAACTTGTTTTTTTAACTTTCT
43698 TTGGATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.17, C:0.09, G:0.12, T:0.62
Consensus pattern (30 bp):
TGTTTGGAACTTGTTTTTTTAACTTTCTAA
Found at i:45796 original size:165 final size:167
Alignment explanation
Indices: 45524--46302 Score: 681
Period size: 165 Copynumber: 4.7 Consensus size: 167
45514 CTATTTGCAG
* * *
45524 CATAACTCAAGGCTAGAAGGGTTGTCTG-CTAACAAAAGACCTTCGAGTTCAACTACGCTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCT
* *
45588 CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CC-AAAGACCCTTGAG
65 CCAAGGCACATCAATTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAAGACCCTTGAG
* * * * * * *
45651 TTTGATTACACACAACTTCGAGGGCACGTTACTTACAA
130 TTCGACTACACTCAACTTCGAAGGCACATCATTTACAA
*
45689 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
45754 AAAGGCACATCAATTGGAGTATAACTTAAGTCGAGAAGGGCTATCTGGCAACCAAAAGA-CCTTC
66 CAAGGCACATCAATTGCAGCATAACTTAAGTCGAGAAGGGCTATCT-G--ACCAAAAGACCCTT-
* *** * * ** *
45818 GATTTCGACTATGTTCAGC-TCCAAGGCACATCATTTGTAG
127 GAGTTCGACTACACTCAACTTCGAAGGCACATCATTTACAA
* * * * * * * ** * * * *
45858 TATAGCTTAAGTCGAGAAAGGCTATCT-T--CC-AAAGACCCCCGAGTTTGATTACACTCAGCTT
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * ** * * * * * *
45919 CGAGAGCACATCATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGTCCTTTG
66 CAAG-GCACATCAATTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG--ACCAAAAGACCCTTG
* * * *
45984 AGTTCGACTACGCTCAGCTTC-AAGGCATATCATTTGCATA
128 AGTTCGACTACACTCAACTTCGAAGGCACATCATTTACA-A
* * * * * * * *
46024 -ATAGCTTAAGTCGAGAAGGGTTATCTGCCATCAAAAGACCTTCGAGTTTGACTACGTTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
46088 CAAGGCACATC-ATTCGCAGCATAGCTTAAGTCGAGAAGGGATATCTG-CC-AAAGACCCTTGAG
66 CAAGGCACATCAATT-GCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAAGACCCTTGAG
* *
46150 TTCGATTACACTCAACTTCGAGGGCACATCATTTACAA
130 TTCGACTACACTCAACTTCGAAGGCACATCATTTACAA
* * *
46188 CATAACTCAAGGCTAAAAGGGTTATTTGTCACC-AAATACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * * * **
46252 CAAGGCACATCATTTACAACACAGCTTAAGTCGAGAAAAGCTATCTG-CCAA
66 CAAGGCACATCAATTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAA
46303 CCAAAGACCT
Statistics
Matches: 489, Mismatches: 105, Indels: 40
0.77 0.17 0.06
Matches are distributed among these distances:
164 95 0.19
165 233 0.48
166 43 0.09
167 2 0.00
168 33 0.07
169 67 0.14
170 16 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (167 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGCACATCAATTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAAGACCCTTGAGT
TCGACTACACTCAACTTCGAAGGCACATCATTTACAA
Found at i:45997 original size:250 final size:248
Alignment explanation
Indices: 45556--46385 Score: 1103
Period size: 250 Copynumber: 3.3 Consensus size: 248
45546 TGTCTGCTAA
** *
45556 CAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * * *
45621 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACACAACTTCGAGGGCACGTTACTTA
66 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAACTTCGAGGGCACATCATTTA
*
45686 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAG
131 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGTCCTTTGAGTTCGACTACGCTCAG
* * *
45751 CTCAAAGGCACATCAATTGGAGTATAACTTAAGTCGAGAAGGGCTATCTGGCAAC
196 CTC-AAGGCACATCATTTGCA-TATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
* * *
45806 CAAAAGACCTTCGA-TTTCGACTATGTTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGT
1 CAAAAGACCTTCGAGTTT-GACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
* * ** * *
45870 CGAGAAAGGCTATCTTCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGAGCACATCATTT
65 CGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAACTTCGAGGGCACATCATTT
*
45935 ACAATATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGTCCTTTGAGTTCGACTACGCTCA
130 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGTCCTTTGAGTTCGACTACGCTCA
* * * *
46000 GCTTCAAGGCATATCATTTGCATAATAGCTTAAGTCGAGAAGGGTTATCT-GCCAT
195 GC-TCAAGGCACATCATTTGCAT-ATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
*
46055 CAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTC
1 CAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* *
46120 GAGAAGGGATATCTGCCAAAGACCCTTGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTA
66 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAACTTCGAGGGCACATCATTTA
* * *
46185 CAACATAACTCAAGGCTAAAAGGGTTATTTGTCACC-AAA-TACCTTCGAGTTCGACTACGCTCA
131 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGT-CCTTTGAGTTCGACTACGCTCA
* * * ** *
46248 GCTCCAAGGCACATCATTTACAACACAGCTTAAGTCGAGAAAAGCTATCTGCCAAC
195 GCT-CAAGGCACATCATTTGC-ATATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
* ** * * * * *
46304 C-AAAGACCTTCGAGTTTGATTATATTCAGCTCAAAGGCATATCAAATTTTACAGCATAGCTCAG
1 CAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATC--A-TTTGCAGCATAGCTTAA
* *
46368 GGCAAGAAGGGCTATCTG
63 GTCGAGAAGGGCTATCTG
46386 TCAATAAAGT
Statistics
Matches: 506, Mismatches: 63, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
247 2 0.00
248 100 0.20
249 157 0.31
250 217 0.43
251 30 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (248 bp):
CAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAACTTCGAGGGCACATCATTTA
CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGTCCTTTGAGTTCGACTACGCTCAG
CTCAAGGCACATCATTTGCATATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
Found at i:46306 original size:84 final size:84
Alignment explanation
Indices: 45538--46319 Score: 592
Period size: 84 Copynumber: 9.4 Consensus size: 84
45528 ACTCAAGGCT
* * * * *
45538 AGAAGGGTTGTCTGCTAACAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
45603 TGCAGCATAGCTTAAGTCG
66 TGCAACATAGCTTAAGTCG
* * * * * * * * *
45622 AGAAGGGCTATCTG----CCAAAGACCCTT-GAGTTTGATTACACACAACTTCGAGGGCACGTTA
1 AGAAGGGCTATCTGCCAACCAAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
* * * * * *
45682 CTTACAACATAACTCAAGGCT
64 TTTGCAACATAGCTTAAGTCG
* * * * *
45703 AGAAGGGTTATCTGTC-ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCAA
1 AGAAGGGCTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* ** *
45767 TTGGAGTATAACTTAAGTCG
65 TTGCAACATAGCTTAAGTCG
* * * *
45787 AGAAGGGCTATCTGGCAACCAAAAGACCTTCGATTTCGACTATGTTCAGCTCCAAGGCACATCAT
1 AGAAGGGCTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* **
45852 TTGTAGTATAGCTTAAGTCG
65 TTGCAACATAGCTTAAGTCG
* * ** * * * * *
45872 AGAAAGGCTATCT----TCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGAGCACATCAT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCAT
* * * * * *
45933 TTACAATATAACTCAAGGCT
65 TTGCAACATAGCTTAAGTCG
* * * * * *
45953 AGAAGGGTTATCTGTC-ACCAAAAGTCCTTTGAGTTCGACTACGCTCAGCTTCAAGGCATATCAT
1 AGAAGGGCTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
46017 TTGCATA-ATAGCTTAAGTCG
65 TTGCA-ACATAGCTTAAGTCG
* * * * *
46037 AGAAGGGTTATCTGCCATCAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
46102 CGCAGCATAGCTTAAGTCG
66 TGCAACATAGCTTAAGTCG
* * * * * *
46121 AGAAGGGATATCTG----CCAAAGACCCTT-GAGTTCGATTACACTCAACTTCGAGGGCACATCA
1 AGAAGGGCTATCTGCCAACCAAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
* * * * *
46181 TTTACAACATAACTCAAGGCT
64 TTTGCAACATAGCTTAAGTCG
* * * * *
46202 AAAAGGGTTATTTGTC-ACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
46266 TACAACACAGCTTAAGTCG
66 TGCAACATAGCTTAAGTCG
**
46285 AGAAAAGCTATCTGCCAACCAAAGACCTTCGAGTT
1 AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTT
46320 TGATTATATT
Statistics
Matches: 543, Mismatches: 132, Indels: 46
0.75 0.18 0.06
Matches are distributed among these distances:
80 64 0.12
81 117 0.22
83 42 0.08
84 200 0.37
85 120 0.22
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
AGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAACATAGCTTAAGTCG
Found at i:53053 original size:81 final size:80
Alignment explanation
Indices: 52862--53121 Score: 299
Period size: 84 Copynumber: 3.1 Consensus size: 80
52852 TAAAGAAACT
* * * *
52862 ATTTGCAGCATAAATCAAGGCTAGAAGGGTTGTCTGCTAACAAAAGACCTTCGAGTTCAACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGC---C-AAAGACCTTCGAGTTCGACTACA
*
52927 TTCAGCTCCAAGGCACATC
62 CTCAGCTCCAAGGCACATC
* * * *
52946 ATTTGCAGCATAGCTTAA-GTTGAGAAGGGTTATCTGCCAAAGACCCTT-GAGTTCGATTACACT
1 ATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAAAGA-CCTTCGAGTTCGACTACACT
* *
53009 CAGCTTCGAGGGCACATC
64 CAGC-TCCAAGGCACATC
*
53027 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG---CCAAAGACCTTCGAGTTCGACTACAC
53092 TCAGCTCCAAGGCACATC
63 TCAGCTCCAAGGCACATC
*
53110 ATTTGCAACATA
1 ATTTGCAGCATA
53122 GCTTAAGTCG
Statistics
Matches: 148, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
80 20 0.14
81 45 0.30
82 2 0.01
83 27 0.18
84 54 0.36
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (80 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGACTACACTCA
GCTCCAAGGCACATC
Found at i:53157 original size:84 final size:85
Alignment explanation
Indices: 52905--53194 Score: 299
Period size: 84 Copynumber: 3.5 Consensus size: 85
52895 CTGCTAACAA
* ** *
52905 AAGACCTTCGAGTTCAACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
52970 AAGGGTTATCTGCCAAA--G
66 AAGGGTTATCTGCCAAACCG
* * * * * * * * *
52988 -A-CCCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* *
53050 GAAGGGTTATCTGTC--ACCA
65 GAAGGGTTATCTGCCAAACCG
*
53069 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
** *
53134 AAAAGCTATCTG-CAAACCG
66 AAGGGTTATCTGCCAAACCG
* * * * *
53153 AAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATCA
1 AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCA
53195 AATTTTATAG
Statistics
Matches: 165, Mismatches: 34, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
79 1 0.01
80 15 0.09
81 46 0.28
82 3 0.02
83 42 0.25
84 58 0.35
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (85 bp):
AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGTTATCTGCCAAACCG
Found at i:57500 original size:20 final size:19
Alignment explanation
Indices: 57472--57510 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
57462 GTAAGGTAAT
57472 TTTTAATAT-ATTATATTGA
1 TTTTAATATAATTAT-TTGA
57491 TTTTATATATAATTATTTGA
1 TTTTA-ATATAATTATTTGA
57511 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTAATATAATTATTTGA
Found at i:59692 original size:14 final size:14
Alignment explanation
Indices: 59673--59701 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59663 CCCTATGTCC
59673 AACATAGGTACTGT
1 AACATAGGTACTGT
59687 AACATAGGTACTGT
1 AACATAGGTACTGT
59701 A
1 A
59702 TCAGACAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (14 bp):
AACATAGGTACTGT
Found at i:62967 original size:15 final size:14
Alignment explanation
Indices: 62949--62978 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
62939 TCGAAATATC
62949 AAAAATAAAAATAAA
1 AAAAATAAAAA-AAA
62964 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
62978 A
1 A
62979 TTGAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAATAAAAAAAA
Done.