Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003566.1 Hibiscus syriacus cultivar Beakdansim tig00007530_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: 113749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8028 original size:27 final size:29
Alignment explanation
Indices: 7976--8041 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
7966 CTATTTATTT
* *
7976 TAATATATTTTTAAAAGTTAAGATAATAA
1 TAATATATTTTTAAAAGTGAAGATAAGAA
*
8005 TAATATATTTTTAATA-TGAA-ATAAGAA
1 TAATATATTTTTAAAAGTGAAGATAAGAA
*
8032 TAAAATATTT
1 TAATATATTT
8042 AAATATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 15 0.45
28 3 0.09
29 15 0.45
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (29 bp):
TAATATATTTTTAAAAGTGAAGATAAGAA
Found at i:8051 original size:10 final size:10
Alignment explanation
Indices: 8032--8061 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
8022 GAAATAAGAA
8032 TAAA-ATATT
1 TAAATATATT
8041 TAAATATATT
1 TAAATATATT
8051 TAAATATATT
1 TAAATATATT
8061 T
1 T
8062 TAAGTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAAATATATT
Found at i:10331 original size:57 final size:57
Alignment explanation
Indices: 10242--10365 Score: 221
Period size: 57 Copynumber: 2.2 Consensus size: 57
10232 ATGATGTTTA
*
10242 CTTTTGTGATTGTTAAGTTGAAAAGGACGATACATCTCAACTCTTTTGCTTTCTTTG
1 CTTTTGTCATTGTTAAGTTGAAAAGGACGATACATCTCAACTCTTTTGCTTTCTTTG
* *
10299 CTTTTGTCATTGTTAAGTTGAAAAGGATGATACGTCTCAACTCTTTTGCTTTCTTTG
1 CTTTTGTCATTGTTAAGTTGAAAAGGACGATACATCTCAACTCTTTTGCTTTCTTTG
10356 CTTTTGTCAT
1 CTTTTGTCAT
10366 GAGGTATTGG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (57 bp):
CTTTTGTCATTGTTAAGTTGAAAAGGACGATACATCTCAACTCTTTTGCTTTCTTTG
Found at i:11227 original size:18 final size:19
Alignment explanation
Indices: 11206--11248 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
11196 ACAAGGGAAA
*
11206 AATAAAATAA-ATAAAAAT
1 AATAAAATAAGAAAAAAAT
*
11224 AATAAGATAAGAAAAAAAT
1 AATAAAATAAGAAAAAAAT
*
11243 AGTAAA
1 AATAAA
11249 GTAATAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
AATAAAATAAGAAAAAAAT
Found at i:11301 original size:2 final size:2
Alignment explanation
Indices: 11288--11335 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
11278 GGAAAAAGAA
*
11288 AT AT AA 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
11330 AT AT AT
1 AT AT AT
11336 CAAAGTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11802 original size:43 final size:45
Alignment explanation
Indices: 11713--11803 Score: 107
Period size: 42 Copynumber: 2.1 Consensus size: 45
11703 AAAGATAATT
* ** * *
11713 ATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGAA
1 ATATATATATAGTAATAATAGAAATATAAGTAAAAAATCAAAGAA
11758 ATATATATATA-TAATAATA-AAATAT-AGTAAAAAATCAAATGAA
1 ATATATATATAGTAATAATAGAAATATAAGTAAAAAATCAAA-GAA
11801 ATA
1 ATA
11804 ATTTAATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 12 0.30
43 10 0.25
44 7 0.17
45 11 0.28
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (45 bp):
ATATATATATAGTAATAATAGAAATATAAGTAAAAAATCAAAGAA
Found at i:12265 original size:37 final size:36
Alignment explanation
Indices: 12215--12352 Score: 163
Period size: 37 Copynumber: 3.8 Consensus size: 36
12205 GTGCTTGTGG
* * * * *
12215 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
** *
12252 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
12289 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
12323 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
12353 GGACGAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
34 28 0.32
35 4 0.05
36 4 0.05
37 52 0.59
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:12326 original size:34 final size:35
Alignment explanation
Indices: 12249--12349 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
12239 TTAGTAGAAC
12249 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
12287 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
12320 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
12350 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:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:13241 original size:105 final size:105
Alignment explanation
Indices: 13053--13502 Score: 703
Period size: 105 Copynumber: 4.3 Consensus size: 105
13043 GCATTGTTCA
* * ** *
13053 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
13113 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
13153 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
13218 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
13258 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
13323 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
13363 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
13428 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
13468 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
13503 CGCGGATGGC
Statistics
Matches: 323, Mismatches: 19, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
100 37 0.11
101 1 0.00
102 1 0.00
104 5 0.02
105 254 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:14197 original size:68 final size:64
Alignment explanation
Indices: 14070--14559 Score: 214
Period size: 73 Copynumber: 7.2 Consensus size: 64
14060 AAAGAGATAG
* * * * *
14070 AATTCGTTTCAAGGGAAATGATCTCAAAGATATATGTTGTTTCATGAGAAACGGTCTCAAGGGAA
1 AATTTGTTTTAAGGGAAATAAT-TCAAAG--AT-T-TTGTTTCAAGAGAAACTGTCTCAAGGGAA
14135 ACAA
61 ACAA
** * *
14139 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAAT-AATTCAAAGA-TTT-TGTTTCAAGAGAAACTGTCTCAAGGGAAA
14204 CAA
62 CAA
* * ** * *
14207 AATTTGTTTTAGGGGAAATAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGATAGACGA
1 AATTTGTTTTAAGGGAAATAATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAAACAA
* * * * * * * *
14271 AATTTATTTCAAGAGAAACT-GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAA
1 AATTTGTTTTAAGGGAAA-TAAT-TC-A-A-AG-----ATTTTGTTTCAAGAGAAACTGTCTCAA
* *
14335 GGGAGACGA
56 GGGAAACAA
* * * * * * * *
14344 AATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTTAAGGGAAATA-ATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAAACAA
* * * * * *
14409 AATTTATTTCAAGAGAAACT-GTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 AATTTGTTTTAAGGGAAA-TAAT-TC-A-A-AG-----ATTTTGTTTCAAGAGAAACTGTCTCAA
* * *
14473 GAGAGACGA
56 GGGAAACAA
* * ** * * *
14482 AATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC-
1 AATTTGTTTTAAGGGAAAT-AATTCAAAGATTT-TGTTTCAAGAGAAACTGTCTCAAGGGAAACA
14545 A
64 A
14546 AATCTTGTTTTAAG
1 AAT-TTGTTTTAAG
14560 AAAAACAATC
Statistics
Matches: 332, Mismatches: 59, Indels: 64
0.73 0.13 0.14
Matches are distributed among these distances:
64 50 0.15
65 87 0.26
66 10 0.03
67 17 0.05
68 37 0.11
69 5 0.02
70 19 0.06
71 4 0.01
72 3 0.01
73 98 0.30
74 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (64 bp):
AATTTGTTTTAAGGGAAATAATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAAACAA
Found at i:14289 original size:36 final size:36
Alignment explanation
Indices: 14241--14499 Score: 248
Period size: 36 Copynumber: 7.3 Consensus size: 36
14231 AAAGATTTTG
* * *
14241 TTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
*
14277 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
* * * * *
14313 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 -TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
* * * *
14350 TTTCAA-AGAAAACATAT-TC-----A-A-ATATTTTG
1 TTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTTA
*
14379 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
*
14415 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTA
* * *
14452 TTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
*
14488 TTTCAAGGGAAA
1 TTTCAAGAGAAA
14500 TGTTTTCAAT
Statistics
Matches: 184, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 2 0.01
31 1 0.01
34 1 0.01
35 3 0.02
36 94 0.51
37 64 0.35
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:14393 original size:138 final size:137
Alignment explanation
Indices: 14187--14548 Score: 503
Period size: 138 Copynumber: 2.6 Consensus size: 137
14177 TTTCAAGAGT
* * * *
14187 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATA-ATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTTTGTTTCAAGGGA
*
14251 AACTGTCTCAAGATAGACGAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAGAGAGAC-AAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
14316 CCAAAAGA
130 CCAAAAGA
* * *
14324 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTTTGTTTCAAGGGA
* *
14389 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT
66 AACTGTCTCAAGAGAGAC-AAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
* **
14454 TCAAGGGA
130 CCAAAAGA
* * * * * * *
14462 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AATGTTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT-TGTTTCAAGGG
14526 AAACTGTCTCAAGAGAGACAAAT
65 AAACTGTCTCAAGAGAGACAAAT
14549 CTTGTTTTAA
Statistics
Matches: 199, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
137 44 0.22
138 155 0.78
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTC
CAAAAGA
Found at i:15450 original size:22 final size:22
Alignment explanation
Indices: 15425--15475 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
15415 TTGTGTTTGG
15425 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
15447 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
15469 TCAAAGG
1 TCAAAGG
15476 ATTGATGGGG
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:16161 original size:23 final size:23
Alignment explanation
Indices: 16117--16160 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16107 TTTGTTCTTA
*
16117 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
*
16140 TTTTTTTCTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
16161 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:17929 original size:18 final size:18
Alignment explanation
Indices: 17906--17945 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
17896 ATTAGTCTTT
17906 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
17924 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
17942 CAGA
1 CAGA
17946 CTTGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:20050 original size:37 final size:36
Alignment explanation
Indices: 20000--20071 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
19990 TAAATATATA
*
20000 TATATATATATCAAAGTA-TTAATAAATA-AATAAGTTG
1 TATATATACATCAAA-TACTTAA-AAATAGAA-AAGTTG
*
20037 TATATGTACATCAAATACTTAAAAATAGAAAAGTT
1 TATATATACATCAAATACTTAAAAATAGAAAAGTT
20072 ACCCTCCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (36 bp):
TATATATACATCAAATACTTAAAAATAGAAAAGTTG
Found at i:20543 original size:14 final size:15
Alignment explanation
Indices: 20513--20549 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20503 TATACATATT
*
20513 ATAATAATAACATGA
1 ATAATAATAAAATGA
20528 ATAATAA-AAAATGA
1 ATAATAATAAAATGA
20542 ATAA-AATA
1 ATAATAATA
20550 TCCATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAATAATAAAATGA
Found at i:20956 original size:37 final size:36
Alignment explanation
Indices: 20906--21043 Score: 163
Period size: 37 Copynumber: 3.8 Consensus size: 36
20896 GTGCTTGTGG
* * * * *
20906 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
** *
20943 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
20980 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
21014 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
21044 GGACGAAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
34 28 0.32
35 4 0.05
36 4 0.05
37 52 0.59
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:21017 original size:34 final size:35
Alignment explanation
Indices: 20940--21040 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
20930 TTAGTAGAAC
20940 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
20978 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
21011 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
21041 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:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:26740 original size:13 final size:13
Alignment explanation
Indices: 26722--26746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26712 GTGTAATTCA
26722 GAAACAGGAACAG
1 GAAACAGGAACAG
26735 GAAACAGGAACA
1 GAAACAGGAACA
26747 ACTCCCGAAG
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:0.56, C:0.16, G:0.28, T:0.00
Consensus pattern (13 bp):
GAAACAGGAACAG
Found at i:31941 original size:60 final size:60
Alignment explanation
Indices: 31848--31976 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
31838 AAAAATATTC
* * * * * *
31848 AAAGATTTGGGGACCAATATAGAATGAGGGTCATAGTTTGAGGGTGAAATTATAATGTTCA
1 AAAG-TTTAGGGACCAATATAGAATGAGAGTCATAGTTTAAGGATGAAACTAGAATGTTCA
* * *
31909 AAAGTTTAGGGACCAATTTAGAATGAGAGTCATAGTTTAAGGATGTAACTGGAATGTTCA
1 AAAGTTTAGGGACCAATATAGAATGAGAGTCATAGTTTAAGGATGAAACTAGAATGTTCA
31969 AAAGTTTA
1 AAAGTTTA
31977 AAGACAAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 55 0.93
61 4 0.07
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (60 bp):
AAAGTTTAGGGACCAATATAGAATGAGAGTCATAGTTTAAGGATGAAACTAGAATGTTCA
Found at i:31990 original size:60 final size:60
Alignment explanation
Indices: 31867--32002 Score: 164
Period size: 60 Copynumber: 2.3 Consensus size: 60
31857 GGGACCAATA
* * * * ** * *
31867 TAGAATGAGGGTCATAGTTTGAGGGTGAAATTATAATGTTCAAAAGTTTAGGGACCAATT
1 TAGAATGAGGGTCATAGTTTAAGGATGAAACTAGAATGTTCAAAAGTTTAAAGACAAAAT
* * *
31927 TAGAATGAGAGTCATAGTTTAAGGATGTAACTGGAATGTTCAAAAGTTTAAAGACAAAAT
1 TAGAATGAGGGTCATAGTTTAAGGATGAAACTAGAATGTTCAAAAGTTTAAAGACAAAAT
*
31987 TAGAATAAGGGTCATA
1 TAGAATGAGGGTCATA
32003 AATTGTGAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (60 bp):
TAGAATGAGGGTCATAGTTTAAGGATGAAACTAGAATGTTCAAAAGTTTAAAGACAAAAT
Found at i:37416 original size:2 final size:2
Alignment explanation
Indices: 37409--37442 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
37399 TATTTAACAC
37409 AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37443 TAATTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40629 original size:19 final size:19
Alignment explanation
Indices: 40602--40638 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40592 AAATGACCAA
*
40602 ATAAATCGCAATGCGATCG
1 ATAAATCGCAACGCGATCG
*
40621 ATAATTCGCAACGCGATC
1 ATAAATCGCAACGCGATC
40639 TCCGGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (19 bp):
ATAAATCGCAACGCGATCG
Found at i:40692 original size:21 final size:21
Alignment explanation
Indices: 40666--40718 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
40656 GTTTCCAGAT
*
40666 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
40687 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
40708 TCGCAATGCGA
1 TCGCAATGCGA
40719 TTTATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:40757 original size:21 final size:21
Alignment explanation
Indices: 40727--40840 Score: 83
Period size: 21 Copynumber: 5.6 Consensus size: 21
40717 GATTTATATA
*
40727 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
40748 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
40769 TT--CGTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
40788 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* * *
40809 AT--CGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
40828 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
40841 TTATTCCAAA
Statistics
Matches: 65, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
19 26 0.40
21 39 0.60
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:40776 original size:19 final size:19
Alignment explanation
Indices: 40752--40857 Score: 59
Period size: 19 Copynumber: 5.3 Consensus size: 19
40742 TCCAAGTTCG
40752 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
* ** * *
40771 CGTTGCAATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
*
40790 CGCATTGCGATTTTCCAAAAT
1 CG--TTGCGATTTTCCAAATT
* ** * *
40811 CGTTGTGATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATT
40830 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
40853 CGTTG
1 CGTTG
40858 GAATCCCACA
Statistics
Matches: 59, Mismatches: 22, Indels: 10
0.65 0.24 0.11
Matches are distributed among these distances:
19 27 0.46
21 25 0.42
22 1 0.02
23 6 0.10
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:40789 original size:40 final size:40
Alignment explanation
Indices: 40733--40857 Score: 187
Period size: 40 Copynumber: 3.1 Consensus size: 40
40723 TATATTCGCA
*
40733 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
* * *
40773 TTGCAATAGTCGAAGTTCGCATTGCGATTTTCCAAAATCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
*
40813 TTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
40855 TTG
1 TTG
40858 GAATCCCACA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
40 60 0.80
41 2 0.03
42 13 0.17
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:41167 original size:40 final size:42
Alignment explanation
Indices: 41089--41183 Score: 158
Period size: 40 Copynumber: 2.3 Consensus size: 42
41079 TACGATTTTG
41089 GACTATCGCAACGAATTTGAAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGAAATAAATCGCAACACGAACTTC
* *
41131 GACTATCGCAACGAATTT-AGA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGAAATAAATCGCAACACGAACTTC
41171 GACTATCGCAACG
1 GACTATCGCAACG
41184 CGAACTTCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 31 0.61
41 2 0.04
42 18 0.35
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGAAATAAATCGCAACACGAACTTC
Found at i:41207 original size:21 final size:21
Alignment explanation
Indices: 41114--41208 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
41104 TTTGAAATAA
*
41114 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
41135 ATCGCAA--CGAATTTAGAAA
1 ATCGCAACGCGAACTTCGACT
41154 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
41175 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
41196 ATCGCAATGCGAA
1 ATCGCAACGCGAA
41209 TATGTAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 15 0.24
21 48 0.76
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:56725 original size:2 final size:2
Alignment explanation
Indices: 56718--56746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56708 AAAAAGATAA
56718 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 A
56747 CCTTTTGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57762 original size:13 final size:13
Alignment explanation
Indices: 57744--57791 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
57734 TATTCTTAAC
57744 TTTTAAAAATATA
1 TTTTAAAAATATA
57757 TTTTAAAAATATA
1 TTTTAAAAATATA
*
57770 TTAATTTCAAAATATA
1 -T--TTTAAAAATATA
57786 TTTTAA
1 TTTTAA
57792 CTTAAGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 17 0.57
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:60612 original size:28 final size:27
Alignment explanation
Indices: 60577--60633 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
60567 TTAAAGTGTG
60577 TTTATATTATAATTATAATTTTATTCATTA
1 TTTAT-TTATAA-TATAATTTTATT-ATTA
* *
60607 TTTATTTGTAATATTATTTTATTATTA
1 TTTATTTATAATATAATTTTATTATTA
60634 CTTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
29 5 0.20
30 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTATTTATAATATAATTTTATTATTA
Found at i:60623 original size:12 final size:11
Alignment explanation
Indices: 60608--60670 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
60598 TATTCATTAT
60608 TTATTTGTAATA
1 TTATTT-TAATA
*
60620 TTATTTTATTA
1 TTATTTTAATA
60631 TTACTTTTAATA
1 TTA-TTTTAATA
60643 -TATTTTAATTA
1 TTATTTTAA-TA
*
60654 TTACTTTAATTA
1 TTATTTTAA-TA
60666 TTATT
1 TTATT
60671 ATTTTCTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
10 6 0.14
11 11 0.25
12 27 0.61
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:60641 original size:23 final size:23
Alignment explanation
Indices: 60615--60670 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
60605 TATTTATTTG
60615 TAATATTATTTT-ATTATTACTTT
1 TAATATTATTTTAATTATTAC-TT
60638 TAATA-TATTTTAATTATTACTT
1 TAATATTATTTTAATTATTACTT
60660 TAATTATTATT
1 TAA-TATTATT
60671 ATTTTCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.37
23 15 0.50
24 4 0.13
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATATTATTTTAATTATTACTT
Found at i:60696 original size:2 final size:2
Alignment explanation
Indices: 60684--60732 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
60674 TTCTTAGTCT
*
60684 TA TA AA TA TA TA TA TA TA TA TA TA TA TGA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
60726 TA TA TA T
1 TA TA TA T
60733 TTGTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:61192 original size:3 final size:3
Alignment explanation
Indices: 61184--61210 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
61174 AACGAATCCT
61184 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
61211 AAAAGAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61554 original size:25 final size:28
Alignment explanation
Indices: 61526--61577 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
61516 AATTCTTTCT
61526 TTTCA-AA-ATTTATATATAT-TTATTA
1 TTTCATAATATTTATATATATATTATTA
*
61551 TTTCATAATATTTATATGTATATTATT
1 TTTCATAATATTTATATATATATTATT
61578 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 11 0.48
28 5 0.22
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTCATAATATTTATATATATATTATTA
Found at i:62124 original size:46 final size:49
Alignment explanation
Indices: 62048--62140 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 49
62038 AATTTATTTC
* *
62048 ATTTTTTCCTAAATAAATGCATGTGAACTAGAAATCATGCA-GTTAGGTT
1 ATTTTTTCCTAAACAAATGCATGTGAACTAGAAAGCATG-AGGTTAGGTT
*
62097 ATTTTTTTC-AAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 ATTTTTTCCTAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGG
62141 AGTTATACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 1 0.03
46 20 0.50
47 5 0.12
48 6 0.15
49 8 0.20
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (49 bp):
ATTTTTTCCTAAACAAATGCATGTGAACTAGAAAGCATGAGGTTAGGTT
Found at i:64057 original size:14 final size:14
Alignment explanation
Indices: 64040--64070 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64030 TTTGTATTTA
*
64040 CATTTTCATTTTTG
1 CATTTGCATTTTTG
64054 CATTTGCATTTTTG
1 CATTTGCATTTTTG
64068 CAT
1 CAT
64071 AATTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (14 bp):
CATTTGCATTTTTG
Found at i:71352 original size:47 final size:46
Alignment explanation
Indices: 71151--71459 Score: 516
Period size: 45 Copynumber: 6.7 Consensus size: 46
71141 CTATTTCCTA
*
71151 CATCTATAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
71196 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
71241 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
71286 CATATGTAAATCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
*
71333 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGT
* *
71380 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
71426 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAA
71460 CATTTCCATC
Statistics
Matches: 253, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
45 119 0.47
46 47 0.19
47 87 0.34
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:71593 original size:3 final size:3
Alignment explanation
Indices: 71585--71621 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
71575 TCATTTCGTT
71585 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
71622 ATAAAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:73278 original size:23 final size:23
Alignment explanation
Indices: 73248--73332 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
73238 TTATGTTATA
*
73248 ATTTTAATTTTA-TTTATTATTT
1 ATTTTAATATTATTTTATTATTT
73270 ATTTGTAATATTATTTTATTA-TT
1 ATTT-TAATATTATTTTATTATTT
73293 ACTTTTAATA-TATTTTAATTA-TT
1 A-TTTTAATATTATTTT-ATTATTT
*
73316 ACTTTAATTATTATTTT
1 ATTTTAA-TATTATTTT
73333 CTTAATCTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 15 0.27
23 24 0.44
24 16 0.29
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (23 bp):
ATTTTAATATTATTTTATTATTT
Found at i:73283 original size:12 final size:11
Alignment explanation
Indices: 73248--73332 Score: 75
Period size: 12 Copynumber: 7.5 Consensus size: 11
73238 TTATGTTATA
*
73248 ATTTTAATTTT
1 ATTTTAATATT
*
73259 A-TTTATTATTT
1 ATTTTAATA-TT
73270 ATTTGTAATATT
1 ATTT-TAATATT
*
73282 ATTTTATTATT
1 ATTTTAATATT
73293 ACTTTTAATA-T
1 A-TTTTAATATT
73304 ATTTTAATTATT
1 ATTTTAA-TATT
*
73316 ACTTTAATTATT
1 ATTTTAA-TATT
73328 ATTTT
1 ATTTT
73333 CTTAATCTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
10 11 0.18
11 15 0.25
12 31 0.51
13 4 0.07
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (11 bp):
ATTTTAATATT
Found at i:73286 original size:34 final size:34
Alignment explanation
Indices: 73243--73332 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 34
73233 TGTGTTTATG
* * *
73243 TTATAATTTTAATT-TTATTTATTATTTATTTGTAA
1 TTATTATTTTAATTATTATTT-TAATATATTT-TAA
73278 -TATTATTTT-ATTATTACTTTTAATATATTTTAA
1 TTATTATTTTAATTATTA-TTTTAATATATTTTAA
*
73311 TTATTACTTTAATTATTATTTT
1 TTATTATTTTAATTATTATTTT
73333 CTTAATCTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
33 6 0.13
34 31 0.66
35 10 0.21
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (34 bp):
TTATTATTTTAATTATTATTTTAATATATTTTAA
Found at i:73353 original size:2 final size:2
Alignment explanation
Indices: 73341--73379 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
73331 TTCTTAATCT
* *
73341 TA TA AA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73380 TTGTTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:77812 original size:43 final size:43
Alignment explanation
Indices: 77760--78095 Score: 259
Period size: 43 Copynumber: 7.9 Consensus size: 43
77750 TTTGTGAAAA
* * *
77760 AAAATGCCGCAATAGGTCGAAATCTATAGCGACGTTTTTTTAG
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTTTAG
* * **
77803 AAAACGCCGCAAAAGGTCG-GATCTATAGCGGC-ATTTTTCGG
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTTTAG
*
77844 AACAAACGCCGCAATAA-GTCGAGCTCTATAGCGACGTTTTTTTTGGAG
1 -A-AAACGCCGCAA-AAGGTCGAGATCTATAGCGACG-TTTTTTT--AG
* * **
77892 AAAACGCCGTAAAAGGTC-AGATCTATAGCGGCG---TTCCA-
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTTTAG
* * *
77930 AAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTATAG
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTTTAG
* * *
77973 AAAACGCCGTAAAATGTCGA-ATCTATAGCG--GTATTTTTGGAG
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGACGT-TTTTT-TAG
* **
78015 AAAACGCCGCAAATGGTC-AGATCTATAGC-ATCGTTTTTGGA-
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGA-CGTTTTTTTAG
** * *
78056 ACAAACGTTGCAGAAGGTCGAGATATATAGCGACGTTTTT
1 A-AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTT
78096 GGAATAAACG
Statistics
Matches: 235, Mismatches: 35, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
38 16 0.07
39 16 0.07
40 2 0.01
41 14 0.06
42 66 0.28
43 70 0.30
44 16 0.07
45 15 0.06
46 18 0.08
47 1 0.00
48 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
AAAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTTTAG
Found at i:77840 original size:42 final size:42
Alignment explanation
Indices: 77760--78043 Score: 211
Period size: 42 Copynumber: 6.7 Consensus size: 42
77750 TTTGTGAAAA
* * * * *
77760 AAAATGCCGCAATAGGTCGAAATCTATAGCGACGTTTTTTTAG
1 AAAACGCCGCAAAAGGTCG-GATCTATAGCGGCATTTTTTTAG
**
77803 AAAACGCCGCAAAAGGTCGGATCTATAGCGGCA-TTTTTCGG
1 AAAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTTTTAG
* * *
77844 AACAAACGCCGCAATAA-GTCGAGCTCTATAGCGACGTTTTTTTTGGAG
1 -A-AAACGCCGCAA-AAGGTCG-GATCTATAGCGGC-ATTTTTTT--AG
* * * **
77892 AAAACGCCGTAAAAGGTCAGATCTATAGCGGC---GTTCCA-
1 AAAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTTTTAG
* * *
77930 AAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTATAG
1 AAAACGCCGCAAAAGGTCG-GATCTATAGCGGCATTTTTTTAG
* * * * **
77973 AAAACGCCGTAAAATGTCGAATCTATAGCGGTATTTTTGGAG
1 AAAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTTTTAG
* *
78015 AAAACGCCGCAAATGGTCAGATCTATAGC
1 AAAACGCCGCAAAAGGTCGGATCTATAGC
78044 ATCGTTTTTG
Statistics
Matches: 189, Mismatches: 38, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
38 16 0.08
39 14 0.07
41 8 0.04
42 57 0.30
43 48 0.25
44 13 0.07
45 13 0.07
46 18 0.10
47 1 0.01
48 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (42 bp):
AAAACGCCGCAAAAGGTCGGATCTATAGCGGCATTTTTTTAG
Found at i:77947 original size:38 final size:39
Alignment explanation
Indices: 77892--77965 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
77882 TTTTTTGGAG
*
77892 AAAACGCCGTAAAAGGTC-AGATCTATAGCGGCGTTCCA
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTCCA
*
77930 AAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTT
1 AAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTT
77966 TTTATAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 16 0.48
39 17 0.52
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (39 bp):
AAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTCCA
Found at i:78052 original size:42 final size:42
Alignment explanation
Indices: 77781--78152 Score: 200
Period size: 42 Copynumber: 8.8 Consensus size: 42
77771 ATAGGTCGAA
** * *
77781 ATCTATAGC-GACGTTTTTTTAGAAAACGCCGCAAAAGGTCGG
1 ATCTATAGCAG-CGTTTTTGGAGAAAACGCCGCAAATGGTCAG
* * *
77823 ATCTATAGCGGCATTTTTCGGA-ACAAACGCCGC-AATAAGTCGAG
1 ATCTATAGCAGCGTTTTT-GGAGA-AAACGCCGCAAAT-GGTC-AG
* * *
77867 CTCTATAGC-GACGTTTTTTTTGGAGAAAACGCCGTAAAAGGTCAG
1 ATCTATAGCAG-CG---TTTTTGGAGAAAACGCCGCAAATGGTCAG
* **
77912 ATCTATAGCGGCG---TTCCA-AAAACGCCGC-AATAGGTCGAG
1 ATCTATAGCAGCGTTTTTGGAGAAAACGCCGCAAAT-GGTC-AG
* ** *
77951 ATCTATAGCGGCGTTTTTATAGAAAACGCCGTAAAAT-GTC-G
1 ATCTATAGCAGCGTTTTTGGAGAAAACGCCG-CAAATGGTCAG
* **
77992 AATCTATAGCGGTATTTTTGGAGAAAACGCCGCAAATGGTCAG
1 -ATCTATAGCAGCGTTTTTGGAGAAAACGCCGCAAATGGTCAG
* **
78035 ATCTATAGCATCGTTTTTGGA-ACAAACGTTGCAGAA-GGTCGAG
1 ATCTATAGCAGCGTTTTTGGAGA-AAACGCCGCA-AATGGTC-AG
* * *
78078 ATATATAGC-GACGTTTTTGGA-ATAAACGCCGTAAAAT-TTCAG
1 ATCTATAGCAG-CGTTTTTGGAGA-AAACGCCG-CAAATGGTCAG
* *
78120 ATATATAGCAGCGTTTTTGGATGCAAACGCCGC
1 ATCTATAGCAGCGTTTTTGGA-GAAAACGCCGC
78153 TAATTATCGT
Statistics
Matches: 259, Mismatches: 39, Indels: 64
0.72 0.11 0.18
Matches are distributed among these distances:
37 2 0.01
38 13 0.05
39 18 0.07
41 6 0.02
42 101 0.39
43 70 0.27
44 11 0.04
45 15 0.06
46 15 0.06
47 8 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (42 bp):
ATCTATAGCAGCGTTTTTGGAGAAAACGCCGCAAATGGTCAG
Found at i:78062 original size:127 final size:125
Alignment explanation
Indices: 77803--78128 Score: 308
Period size: 127 Copynumber: 2.6 Consensus size: 125
77793 GTTTTTTTAG
* * *
77803 AAAACGCCGCAAAAGGTCG-GATCTATAGCGGCATTTTTCGGAACAAACGCCGCAATAA-GTCGA
1 AAAACGCCGC-AAAGGTCGAGATCTATAGCGGCGTTTTTCAG-ACAAACGCCGTAA-AATGTCGA
* * * *
77866 GCTCTATAGCGACGTTTTTTTTGGAGAAAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTCCA
63 GATCTATAGCGA-GTTATTTTTGGAGAAAACGCCGCAAAAGGTCAGATCTATAGCAGCGTTCCA
*
77930 AAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTATAGA-AAACGCCGTAAAATGTCGA-
1 AAAACGCCGCAA-AGGTCGAGATCTATAGCGGCGTTTTT-CAGACAAACGCCGTAAAATGTCGAG
* * **
77993 ATCTATAGCG-G-TATTTTTGGAGAAAACGCCGCAAATGGTCAGATCTATAGCATCGTTTTTGGA
64 ATCTATAGCGAGTTATTTTTGGAGAAAACGCCGCAAAAGGTCAGATCTATAGCAGCG---TTCCA
** * * * * *
78056 ACAAACGTTGCAGAAGGTCGAGATATATAGCGACGTTTTT-GGAATAAACGCCGTAAAATTTC-A
1 A-AAACGCCGCA-AAGGTCGAGATCTATAGCGGCGTTTTTCAG-ACAAACGCCGTAAAATGTCGA
*
78119 GATATATAGC
63 GATCTATAGC
78129 AGCGTTTTTG
Statistics
Matches: 168, Mismatches: 19, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
123 39 0.23
124 1 0.01
125 1 0.01
126 19 0.11
127 87 0.52
128 20 0.12
129 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (125 bp):
AAAACGCCGCAAAGGTCGAGATCTATAGCGGCGTTTTTCAGACAAACGCCGTAAAATGTCGAGAT
CTATAGCGAGTTATTTTTGGAGAAAACGCCGCAAAAGGTCAGATCTATAGCAGCGTTCCA
Found at i:78108 original size:170 final size:168
Alignment explanation
Indices: 77759--78092 Score: 412
Period size: 170 Copynumber: 2.0 Consensus size: 168
77749 GTTTGTGAAA
* * *
77759 AAAAATGCCGCAATAGGTCGAAATCTATAGCGACGTTTTTTTAGAAAACGCCGCAAAAGGTCGGA
1 AAAAACGCCGCAATAGGTCGAAATCTATAGCGACGTTTTTATAGAAAACGCCGCAAAAGGTCGAA
*
77824 TCTATAGCGGCATTTTTCGGAACAAACGCCGCAATAAGTCGAGCTCTATAGCGACGTTTTTTTTG
66 TCTATAGCGGCATTTTTCGGAACAAACGCCGCAATAAGTCGAGATCTATAGCGACG--TTTTTTG
* * *
77889 GAGAAAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTCC
129 GAGAAAACGCCGCAAAAGGTCAGATATATAGCGACGTTCC
* * * *
77929 AAAAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTATAGAAAACGCCGTAAAATGTCGAA
1 AAAAACGCCGCAATAGGTCGAAATCTATAGCGACGTTTTTATAGAAAACGCCGCAAAAGGTCGAA
* *
77994 TCTATAGCGGTATTTTT-GGAGA-AAACGCCGCAA-ATGGTC-AGATCTATAGC-ATCG-TTTTT
66 TCTATAGCGGCATTTTTCGGA-ACAAACGCCGCAATA-AGTCGAGATCTATAGCGA-CGTTTTTT
** *
78053 GGA-ACAAACGTTGCAGAAGGTCGAGATATATAGCGACGTT
128 GGAGA-AAACGCCGCAAAAGGTC-AGATATATAGCGACGTT
78093 TTTGGAATAA
Statistics
Matches: 143, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
164 1 0.01
165 21 0.15
166 15 0.10
167 1 0.01
168 13 0.09
169 17 0.12
170 75 0.52
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (168 bp):
AAAAACGCCGCAATAGGTCGAAATCTATAGCGACGTTTTTATAGAAAACGCCGCAAAAGGTCGAA
TCTATAGCGGCATTTTTCGGAACAAACGCCGCAATAAGTCGAGATCTATAGCGACGTTTTTTGGA
GAAAACGCCGCAAAAGGTCAGATATATAGCGACGTTCC
Found at i:81901 original size:41 final size:41
Alignment explanation
Indices: 81848--82226 Score: 253
Period size: 41 Copynumber: 9.4 Consensus size: 41
81838 TTGTAAACAC
* *
81848 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACGACTCTATAGCGGCGTTTGTATAA
* * *
81889 AAACGCCGCTAAAGAACGTA-TTTATAGCGGCGTTTGAATAA
1 AAACGCCGCTAAAGTACG-ACTCTATAGCGGCGTTTGTATAA
* * ** *
81930 AAATGCCACTAAAGTACGTGTCTATAGTGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACGACTCTATAGCGGCGTTTGTATAA
** * * *
81971 AAACGCCGCTAAAGTAATACTCTTTTGCGGTGTTTGTATAAA
1 AAACGCCGCTAAAGTACGACTCTATAGCGGCGTTTGTAT-AA
* * *
82013 AAACGCCGCTAAAGTACTACTATATTGCGGCGTTTGT-TAA
1 AAACGCCGCTAAAGTACGACTCTATAGCGGCGTTTGTATAA
* * * * *
82053 AAACGCC-TTAATA-TATGAACCCTATTGCGGC-ATT-T-T--
1 AAACGCCGCTAA-AGTACG-ACTCTATAGCGGCGTTTGTATAA
* * * * *
82089 -AACGCCGCTAAAGTACTACTATGTCA-CGGCGTTTATTTAAA
1 AAACGCCGCTAAAGTACGACTCTAT-AGCGGCGTTTGTAT-AA
* * * * *
82130 AAATGCCACTATAG-ATGAAC-CTATTGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACG-ACTCTATAGCGGCGTTTGTATAA
* * * *
82170 AAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGTATAA
1 AAACGCCGCTAAAGTACGACTCTATAGCGGCG-TTTGTATAA
*
82212 AAACGCTGCTAAAGT
1 AAACGCCGCTAAAGT
82227 TACTATTTTA
Statistics
Matches: 262, Mismatches: 56, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
35 15 0.06
36 7 0.03
37 1 0.00
38 3 0.01
39 7 0.03
40 37 0.14
41 122 0.47
42 70 0.27
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (41 bp):
AAACGCCGCTAAAGTACGACTCTATAGCGGCGTTTGTATAA
Found at i:82798 original size:15 final size:14
Alignment explanation
Indices: 82774--82807 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
82764 AAGAAAAGAG
*
82774 TATTTTTTTTATTT
1 TATTTATTTTATTT
82788 CTATTTATTTTATTT
1 -TATTTATTTTATTT
82803 TATTT
1 TATTT
82808 TTAAGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTATTTTATTT
Found at i:83747 original size:20 final size:20
Alignment explanation
Indices: 83722--83791 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
83712 TCACAATTCT
83722 CAATGCGAATAAGTAAATCG
1 CAATGCGAATAAGTAAATCG
83742 CAATGCGAATAAGTAAATCG
1 CAATGCGAATAAGTAAATCG
83762 CAATGCGAATAAGTAAATCG
1 CAATGCGAATAAGTAAATCG
83782 CAATGCGAAT
1 CAATGCGAAT
83792 CTGACTATCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
CAATGCGAATAAGTAAATCG
Found at i:84401 original size:19 final size:19
Alignment explanation
Indices: 84335--84394 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
84325 TAGTTTCGAG
84335 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
84355 AATGACTATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
84374 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
84393 AA
1 AA
84395 CCAAAATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:84446 original size:14 final size:14
Alignment explanation
Indices: 84423--84511 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
84413 TTTCATTTCG
*
84423 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
84437 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
84456 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
84470 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
84489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
84503 CGTTGCGAT
1 CGTTGCGAT
84512 AGTCATTTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 29 0.48
16 5 0.08
17 5 0.08
19 21 0.35
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:84448 original size:33 final size:33
Alignment explanation
Indices: 84406--84560 Score: 202
Period size: 33 Copynumber: 4.5 Consensus size: 33
84396 CAAAATTGCA
*
84406 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
84439 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
84472 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
84505 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGA--TTC----TCTCG
84545 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
84561 AACCAAAAGA
Statistics
Matches: 110, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
33 78 0.71
34 10 0.09
36 3 0.03
39 1 0.01
40 18 0.16
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:84537 original size:20 final size:20
Alignment explanation
Indices: 84503--84560 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
84493 GCGATTCTCT
**
84503 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
84523 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
84543 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
84561 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:86385 original size:94 final size:94
Alignment explanation
Indices: 86224--86478 Score: 458
Period size: 94 Copynumber: 2.7 Consensus size: 94
86214 TCACTTAGAT
*
86224 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTGTTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
*
86289 TAAATTTGTTCGGTTGTTGCCAATTCTGC
66 TAAATTTGTTCGGTTGCTGCCAATTCTGC
86318 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
*
86383 TAAATTTGTTCGTTTGCTGCCAATTCTGC
66 TAAATTTGTTCGGTTGCTGCCAATTCTGC
* *
86412 TAAACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-AAG
1 TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
86476 TAA
66 TAA
86479 TGCAATCCAT
Statistics
Matches: 156, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 6 0.04
94 150 0.96
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (94 bp):
TAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAG
TAAATTTGTTCGGTTGCTGCCAATTCTGC
Found at i:86566 original size:12 final size:12
Alignment explanation
Indices: 86549--86575 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
86539 TTTAGTAACA
86549 TTGTTTTGTCTT
1 TTGTTTTGTCTT
86561 TTGTTTTGTCTT
1 TTGTTTTGTCTT
86573 TTG
1 TTG
86576 GTTTCGCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.19, T:0.74
Consensus pattern (12 bp):
TTGTTTTGTCTT
Found at i:86615 original size:19 final size:19
Alignment explanation
Indices: 86577--86617 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
86567 TGTCTTTTGG
**
86577 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
86596 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
86615 TTT
1 TTT
86618 TTCACGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:87110 original size:42 final size:42
Alignment explanation
Indices: 87059--87152 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
87049 CCACTCCTAT
* * *
87059 CGTTGAAGAGGCCCCTATCATTCATTGAA-A-GTCCCCTTCCAC
1 CGTTCAAGAGGCCACTATCA-TCATTGAAGAGGT-CCCTCCCAC
* *
87101 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCATTGAAGAGGTCCCTCCCAC
*
87143 CATTCAAGAG
1 CGTTCAAGAG
87153 CTCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 7 0.16
42 35 0.80
43 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCATTGAAGAGGTCCCTCCCAC
Found at i:88522 original size:14 final size:14
Alignment explanation
Indices: 88503--88538 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
88493 ATTGTTTAAT
88503 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
88517 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
88531 TGATTTGT
1 TGATTTGT
88539 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:88661 original size:19 final size:19
Alignment explanation
Indices: 88645--88794 Score: 132
Period size: 19 Copynumber: 8.7 Consensus size: 19
88635 AAAAATGACT
88645 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
88664 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
88683 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
88697 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
88716 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
88730 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
88749 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
88763 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
88782 ATCGCAATGCGAA
1 ATCGCAATGCGAA
88795 TTTAGTTTCG
Statistics
Matches: 106, Mismatches: 10, Indels: 30
0.73 0.07 0.21
Matches are distributed among these distances:
14 29 0.27
15 3 0.03
16 6 0.06
17 6 0.06
18 3 0.03
19 59 0.56
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:88701 original size:14 final size:14
Alignment explanation
Indices: 88682--88738 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
88672 GCGAAATGAA
88682 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
88696 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
88715 AATCGCAACGAGAG
1 AATCGCAACGAGAG
88729 AATCGCAACG
1 AATCGCAACG
88739 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:88709 original size:33 final size:33
Alignment explanation
Indices: 88663--88788 Score: 225
Period size: 33 Copynumber: 3.8 Consensus size: 33
88653 GCGAAATGAA
88663 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
88696 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
88729 AATCGCAACGCGAAATGAAAATCGCAACGAGGG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
88762 AATCGCAAAGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
88789 TGCGAATTTA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:88837 original size:33 final size:33
Alignment explanation
Indices: 88800--88879 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
88790 GCGAATTTAG
* * *
88800 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
88833 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
88866 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
88880 AGTCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:88845 original size:19 final size:19
Alignment explanation
Indices: 88821--88899 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
88811 GATTTTGTCG
88821 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
88840 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
88854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
88873 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
88893 TTGCGAT
1 TTGCGAT
88900 AGACATTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 7 0.14
19 19 0.39
20 10 0.20
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:88898 original size:20 final size:20
Alignment explanation
Indices: 88852--88945 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
88842 GCGATTCTCT
**
88852 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
88871 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
88891 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
88910 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
88932 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
88946 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:91225 original size:12 final size:12
Alignment explanation
Indices: 91208--91232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
91198 TCTTGGGGGA
91208 CTTTTTCTTCTT
1 CTTTTTCTTCTT
91220 CTTTTTCTTCTT
1 CTTTTTCTTCTT
91232 C
1 C
91233 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:91434 original size:24 final size:24
Alignment explanation
Indices: 91407--91460 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
91397 TTGAAACATC
*
91407 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
91431 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
91455 ATCAAA
1 ATCAAA
91461 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:92254 original size:20 final size:20
Alignment explanation
Indices: 92190--92304 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
92180 GATTCTGTAT
*
92190 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
92210 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
92230 AATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGATAGTCAG
* * *
92250 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
92271 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
92291 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
92305 TTTCCAAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:92282 original size:41 final size:41
Alignment explanation
Indices: 92170--92307 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
92160 AACTTTGAAA
* * *
92170 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
* * ** ** * *
92211 ATCTCGTTGCGA--AAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGT
92251 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
92292 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
92308 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 2 0.03
40 27 0.36
41 45 0.59
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
Found at i:92323 original size:41 final size:40
Alignment explanation
Indices: 92232--92385 Score: 116
Period size: 41 Copynumber: 3.8 Consensus size: 40
92222 AAAGTCAGAA
* * * * *
92232 TCGCGTTGCGAAAGTTAGTATCGCATTGCGATTTTGTATT
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGAAAT
* *
92272 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATAGTCAGTATCGCATTGCGATTTT-GAAAT
* * ** *
92314 TCGCATTGCGAT--TTACTTATTCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGATAGTCA-GTA-TCGCATTGCG-ATTTTGAAAT
*
92355 TCGCATTGCGATAGTCA-TAATCGCGTTGCGA
1 TCGCATTGCGATAGTCAGT-ATCGCATTGCGA
92386 ATCTGGAAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 79 0.86
42 6 0.07
43 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGAAAT
Found at i:92378 original size:20 final size:20
Alignment explanation
Indices: 92197--92385 Score: 82
Period size: 20 Copynumber: 9.3 Consensus size: 20
92187 TATTATCTCG
* * *
92197 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCATAATCGCA
* * *
92217 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
* *
92237 TTGCGAAAGTTAGT-ATCGCA
1 TTGCGATAGTCA-TAATCGCA
* * *
92257 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCATAATCGCA
92278 TTGCGATAGTCAGT-ATCGCA
1 TTGCGATAGTCA-TAATCGCA
**
92298 TTGCGATTTTCCA-AATTCGCA
1 TTGCGATAGT-CATAA-TCGCA
* * *
92319 TTGCGAT-TTACTTATTCGCA
1 TTGCGATAGT-CATAATCGCA
* ** *
92339 TTGCGAATTGGGAAAATCGCA
1 TTGCG-ATAGTCATAATCGCA
*
92360 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCATAATCGCA
92380 TTGCGA
1 TTGCGA
92386 ATCTGGAAAC
Statistics
Matches: 131, Mismatches: 26, Indels: 24
0.72 0.14 0.13
Matches are distributed among these distances:
19 3 0.02
20 85 0.65
21 41 0.31
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:93007 original size:15 final size:15
Alignment explanation
Indices: 92989--93054 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
92979 TATTAAAGTC
*
92989 AATAATAATTTTAAT
1 AATAATAATATTAAT
* * *
93004 AATAAAAATACTAAA
1 AATAATAATATTAAT
* * *
93019 AATAGTAATAATAAC
1 AATAATAATATTAAT
* *
93034 AATAATAATGTAAAT
1 AATAATAATATTAAT
93049 AATAAT
1 AATAAT
93055 TGTAATTGTA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
AATAATAATATTAAT
Found at i:95627 original size:28 final size:28
Alignment explanation
Indices: 95571--95629 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
95561 TATGTGGGGA
* * *
95571 AAAATATAAAAATAATTAATTTAGTTTT
1 AAAATATAAAAATAAATAATTAAGATTT
95599 AAAATATAAAATATAAAT-ATTAAGATTT
1 AAAATATAAAA-ATAAATAATTAAGATTT
95627 AAA
1 AAA
95630 TCTAAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATATAAAAATAAATAATTAAGATTT
Found at i:97629 original size:2 final size:2
Alignment explanation
Indices: 97622--97646 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97612 TAAGAAAATA
97622 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 A
97647 AAGTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100520 original size:6 final size:5
Alignment explanation
Indices: 100493--100611 Score: 50
Period size: 5 Copynumber: 22.8 Consensus size: 5
100483 ATTATATACT
*
100493 TTTTC TTTTA -TTTA TTTTA TTTTCA TTTTTA TTCTTA -TTTA TTATT-
1 TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA TT-TTA TTTTA TT-TTA
*** * *
100539 TTTTAA CTAACA TTTT- TTATA TTTTTA TTTTA CTTTA TTTTA TTATTA
1 TTTT-A -TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TT-TTA
*
100587 TTTTA TTATT- TTCTA TTATTA TTTT
1 TTTTA TT-TTA TTTTA TT-TTA TTTT
100612 TAGTAACTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
4 13 0.15
5 45 0.52
6 23 0.27
7 5 0.06
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:100579 original size:16 final size:17
Alignment explanation
Indices: 100558--100613 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 17
100548 ACATTTTTTA
100558 TATTTTTATT-TTACTT
1 TATTTTTATTATTACTT
*
100574 TA-TTTTATTATTATTT
1 TATTTTTATTATTACTT
100590 TATTATTT-TCTATTA--T
1 TATT-TTTAT-TATTACTT
100606 TATTTTTA
1 TATTTTTA
100614 GTAACTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 10 0.29
16 14 0.41
17 2 0.06
18 8 0.24
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTTATTATTACTT
Found at i:100582 original size:21 final size:20
Alignment explanation
Indices: 100498--100598 Score: 66
Period size: 21 Copynumber: 4.9 Consensus size: 20
100488 ATACTTTTTC
100498 TTTTA-TTTATTTTATTTTCAT
1 TTTTATTTTA-TTTATTTT-AT
100519 TTTTATTCTTATTTATTATT-T
1 TTTTATT-TTATTTATT-TTAT
* ***
100540 TTTAACTAACATTT-TTTATAT
1 TTTTA-TTTTATTTATTT-TAT
100561 TTTTATTTTACTTTATTTTAT
1 TTTTATTTTA-TTTATTTTAT
*
100582 TATTATTTTA-TTATTTT
1 TTTTATTTTATTTATTTT
100599 CTATTATTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
19 8 0.13
20 5 0.08
21 34 0.54
22 11 0.17
23 5 0.08
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTTATTTATTTTAT
Found at i:100585 original size:24 final size:24
Alignment explanation
Indices: 100553--100613 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
100543 AACTAACATT
*
100553 TTTTA-TATTTTTATTTTACTTTA
1 TTTTATTATTTTTATATTACTTTA
* *
100576 TTTTATTATTATTT-TATTATTTTC
1 TTTTATTATT-TTTATATTACTTTA
*
100600 TATTATTATTTTTA
1 TTTTATTATTTTTA
100614 GTAACTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 8 0.26
24 20 0.65
25 3 0.10
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTATTATTTTTATATTACTTTA
Found at i:100603 original size:21 final size:20
Alignment explanation
Indices: 100551--100611 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 20
100541 TTAACTAACA
*
100551 TTTTTTATATTTTTATTTTAC
1 TTTTTT-TATTATTATTTTAC
100572 TTTATTTTATTATTATTTTA-
1 TTT-TTTTATTATTATTTTAC
100592 TTATTTTCTATTATTATTTT
1 TT-TTTT-TATTATTATTTT
100612 TAGTAACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 5 0.14
21 28 0.78
22 3 0.08
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTTATTATTATTTTAC
Found at i:100604 original size:68 final size:69
Alignment explanation
Indices: 100487--100632 Score: 169
Period size: 68 Copynumber: 2.1 Consensus size: 69
100477 CTTACTATTA
* *
100487 TATACTTTTTCTTTTATTTATTTTATTTTCATTTTTATTCTTATTTATTATT-TTTTAACTAACA
1 TATA-TTTTTATTTTATTTATTTTATTTTCATTTTTATTATTATTTATTATTATTTTAACTAAC-
100551 TTTT-T
64 TTTTGT
* *
100556 TATATTTTTATTTTACTTTATTTTATTATT-A-TTTTATTATT-TTCTATTATTATTTTTAGTAA
1 TATATTTTTATTTTA-TTTATTTTATT-TTCATTTTTATTATTATT-TATTATTATTTTAACTAA
100618 CTTTTGT
63 CTTTTGT
100625 T-TATTTTT
1 TATATTTTT
100633 GTCGTATATT
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
67 2 0.03
68 37 0.54
69 27 0.40
70 2 0.03
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (69 bp):
TATATTTTTATTTTATTTATTTTATTTTCATTTTTATTATTATTTATTATTATTTTAACTAACTT
TTGT
Found at i:100797 original size:13 final size:13
Alignment explanation
Indices: 100779--100808 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
100769 CGAACCGAAT
100779 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
100792 TTTTAATTTTTAA
1 TTTTAAATTTTAA
100805 TTTT
1 TTTT
100809 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:102583 original size:16 final size:15
Alignment explanation
Indices: 102562--102591 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
102552 AACACCCGCT
102562 TTAAAAATAATAAAAG
1 TTAAAAATAA-AAAAG
102578 TTAAAAATAAAAAA
1 TTAAAAATAAAAAA
102592 CTTCTTGCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TTAAAAATAAAAAAG
Found at i:102684 original size:17 final size:17
Alignment explanation
Indices: 102662--102694 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
102652 ATAATGTCTC
102662 TATTACTTAAACCTCTA
1 TATTACTTAAACCTCTA
102679 TATTACTTAAACCTCT
1 TATTACTTAAACCTCT
102695 CTTTACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTACTTAAACCTCTA
Found at i:103972 original size:73 final size:72
Alignment explanation
Indices: 103842--104014 Score: 220
Period size: 73 Copynumber: 2.3 Consensus size: 72
103832 TAAATAAGGA
* *
103842 GGTACCGATACCCCTCCTAGAGGTACCGTACCCATATGCCAATTTTGGCTCCAAGAAAAATAGAA
1 GGTACCGATA-CCC-CCTAGAGGTACCGTACCCATATGCCAATTTTAGCTCCAAGAAAAACAGAA
103907 TGCCCAATG
64 TGCCCAATG
* * * * ** *
103916 GGTACCGATACCCCCTAGAGGTACTGATTCCCTTGTGTTAATTTTAGCTCCGAGAAAAACAGAAT
1 GGTACCGATACCCCCTAGAGGTACCG-TACCCATATGCCAATTTTAGCTCCAAGAAAAACAGAAT
*
103981 GTCCAATG
65 GCCCAATG
103989 GGTACCGATACCCCCATAGAGGTACC
1 GGTACCGATACCCCC-TAGAGGTACC
104015 AATACCCGTA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 12 0.14
73 55 0.64
74 19 0.22
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (72 bp):
GGTACCGATACCCCCTAGAGGTACCGTACCCATATGCCAATTTTAGCTCCAAGAAAAACAGAATG
CCCAATG
Found at i:111488 original size:46 final size:46
Alignment explanation
Indices: 111416--111523 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 46
111406 GGTACACTGA
* *
111416 GGGTGCATCGATGTATAAAATACATTCGATGTTTCAAACA-AGCCT
1 GGGTGCATCGATGCATAAAATACATTCGATGTTTCAAAAATAGCCT
* * *
111461 GGAGTGCATCGATGCATAAAATGCATTCGATGTTTTAAAAATAGCTT
1 GG-GTGCATCGATGCATAAAATACATTCGATGTTTCAAAAATAGCCT
*
111508 GGGTGCATTGATGCAT
1 GGGTGCATCGATGCAT
111524 GGCTTATGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.04
46 47 0.85
47 6 0.11
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (46 bp):
GGGTGCATCGATGCATAAAATACATTCGATGTTTCAAAAATAGCCT
Found at i:111924 original size:12 final size:12
Alignment explanation
Indices: 111904--111935 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
111894 TAAGATTTTC
111904 TTTGAAAACAAT
1 TTTGAAAACAAT
*
111916 TTTGTAAACAAT
1 TTTGAAAACAAT
111928 TTTGAAAA
1 TTTGAAAA
111936 TTTACTCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (12 bp):
TTTGAAAACAAT
Found at i:112631 original size:27 final size:27
Alignment explanation
Indices: 112592--112646 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
112582 TGTGGGTGCC
* * *
112592 GGTGGAGGTGGAGCACGAGAGGAGCTA
1 GGTGCAGGAGGAGCACGAGAAGAGCTA
* *
112619 GGTGCAGGAGGAGCTCGTGAAGAGCTA
1 GGTGCAGGAGGAGCACGAGAAGAGCTA
112646 G
1 G
112647 CTCCCGGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.13, G:0.49, T:0.13
Consensus pattern (27 bp):
GGTGCAGGAGGAGCACGAGAAGAGCTA
Done.