Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002112.1 Hibiscus syriacus cultivar Beakdansim tig00004321_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: 108539
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4166 original size:21 final size:20
Alignment explanation
Indices: 4126--4167 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4116 CCAACTTACA
*
4126 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
4146 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
4167 A
1 A
4168 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:8640 original size:27 final size:27
Alignment explanation
Indices: 8602--8666 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
8592 GTATTGGAAG
* *
8602 AAAGCTAGAATGTTTTGGGATGGTTTT
1 AAAGCTAGAATGCTTTGGGATGATTTT
8629 AAAGCTAGAATGCTTTGGGATGATTTT
1 AAAGCTAGAATGCTTTGGGATGATTTT
*
8656 GAAGCTA-AATG
1 AAAGCTAGAATG
8667 AGTTAGGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (27 bp):
AAAGCTAGAATGCTTTGGGATGATTTT
Found at i:9969 original size:19 final size:19
Alignment explanation
Indices: 9947--9983 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9937 ATATTCAATT
9947 AAATAAATTAAAATCAAGA
1 AAATAAATTAAAATCAAGA
* *
9966 AAATATATTATAATCAAG
1 AAATAAATTAAAATCAAG
9984 TGATGACACG
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:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATAAATTAAAATCAAGA
Found at i:11950 original size:33 final size:33
Alignment explanation
Indices: 11913--11977 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
11903 TTCTATTTTA
11913 ATTAATATTTTAACAATAAGTGATTAAGGGTTG
1 ATTAATATTTTAACAATAAGTGATTAAGGGTTG
11946 ATTAATATTTTAACAATAAGTGATTAAGGGTT
1 ATTAATATTTTAACAATAAGTGATTAAGGGTT
11978 TATTTGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (33 bp):
ATTAATATTTTAACAATAAGTGATTAAGGGTTG
Found at i:12294 original size:14 final size:13
Alignment explanation
Indices: 12277--12320 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 13
12267 ATTTGTATTG
12277 TTATAATTATATAA
1 TTATAA-TATATAA
12291 TTATAATATATTATA
1 TTATAATATA-TA-A
12306 TTAATAATATATAA
1 TT-ATAATATATAA
12320 T
1 T
12321 AAATAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.15
14 10 0.37
15 5 0.19
16 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATAATATATAA
Found at i:12305 original size:18 final size:17
Alignment explanation
Indices: 12278--12329 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
12268 TTTGTATTGT
12278 TATA-ATTATATAATTA
1 TATATATTATATAATTA
*
12294 TAATATATTATATTAATAA
1 T-ATATATTATA-TAATTA
* *
12313 TATATAATAAATAATTA
1 TATATATTATATAATTA
12330 ATAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 1 0.03
17 8 0.28
18 14 0.48
19 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATTATATAATTA
Found at i:37656 original size:19 final size:19
Alignment explanation
Indices: 37632--37727 Score: 192
Period size: 19 Copynumber: 5.1 Consensus size: 19
37622 TTAGAATGCT
37632 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
37651 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
37670 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
37689 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
37708 AAATTGAGTTAATTTGGGA
1 AAATTGAGTTAATTTGGGA
37727 A
1 A
37728 GTGATGAAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 77 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (19 bp):
AAATTGAGTTAATTTGGGA
Found at i:38469 original size:25 final size:28
Alignment explanation
Indices: 38430--38493 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
38420 ACGTTTTTAT
38430 ATGATATTTTCTTAAAAATG-TATT-AGA
1 ATGAT-TTTTCTTAAAAATGATATTAAGA
*
38457 ATGATTTTT-TTAAAAATGATTTTAAAGA
1 ATGATTTTTCTTAAAAATGATATT-AAGA
38485 ATGATTTTT
1 ATGATTTTT
38494 ATTGTTAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 9 0.27
26 7 0.21
27 5 0.15
28 12 0.36
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (28 bp):
ATGATTTTTCTTAAAAATGATATTAAGA
Found at i:38481 original size:12 final size:13
Alignment explanation
Indices: 38464--38492 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38454 AGAATGATTT
38464 TTTTAAA-AATGA
1 TTTTAAAGAATGA
38476 TTTTAAAGAATGA
1 TTTTAAAGAATGA
38489 TTTT
1 TTTT
38493 TATTGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (13 bp):
TTTTAAAGAATGA
Found at i:41621 original size:23 final size:22
Alignment explanation
Indices: 41557--41622 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
41547 ATTATAGCTA
41557 AAAAATTGC-AAAGATAATTCCT
1 AAAAATTGCAAAAGATAA-TCCT
***
41579 AAAAATCATAAAAGATAATCCT
1 AAAAATTGCAAAAGATAATCCT
41601 AATAAATTGCAAAAGATAATCC
1 AA-AAATTGCAAAAGATAATCC
41623 CCCTAATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 12 0.33
23 24 0.67
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.24
Consensus pattern (22 bp):
AAAAATTGCAAAAGATAATCCT
Found at i:49798 original size:22 final size:22
Alignment explanation
Indices: 49770--49833 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
49760 CAAACGGTTG
49770 GAGATCAAACGTATTTAATTTA
1 GAGATCAAACGTATTTAATTTA
*
49792 GAGATCAAATGTATTTAATTTA
1 GAGATCAAACGTATTTAATTTA
*
49814 GAGATCAAACCTATTTAATT
1 GAGATCAAACGTATTTAATT
49834 AAAAAATCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
GAGATCAAACGTATTTAATTTA
Found at i:51383 original size:44 final size:44
Alignment explanation
Indices: 51334--51422 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
51324 CATTAACCAG
51334 GAACAATGGTAAGTTTCAACACTTGGAAAACATTGAACACAAAA
1 GAACAATGGTAAGTTTCAACACTTGGAAAACATTGAACACAAAA
51378 GAACAATGGTAAGTTTCAACACTTGGAAAACATTGAACACAAAA
1 GAACAATGGTAAGTTTCAACACTTGGAAAACATTGAACACAAAA
51422 G
1 G
51423 TAATGCTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (44 bp):
GAACAATGGTAAGTTTCAACACTTGGAAAACATTGAACACAAAA
Found at i:53426 original size:35 final size:36
Alignment explanation
Indices: 53362--53457 Score: 113
Period size: 35 Copynumber: 2.6 Consensus size: 36
53352 GTGCTTGTGG
* * *
53362 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAAGAGTTTGAATCATAGCAAAATTCT
*
53399 ATCCTATTTTAAGAG-TTGAATCATAGCAGAATTCT
1 ATCCTATTTTAAGAGTTTGAATCATAGCAAAATTCT
* *
53434 ATCTTATTTTTGAGAGTTTGAATC
1 ATCCTA-TTTTAAGAGTTTGAATC
53458 CTAGTAGGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
35 22 0.43
36 15 0.29
37 14 0.27
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (36 bp):
ATCCTATTTTAAGAGTTTGAATCATAGCAAAATTCT
Found at i:54323 original size:109 final size:107
Alignment explanation
Indices: 53930--54862 Score: 622
Period size: 109 Copynumber: 9.0 Consensus size: 107
53920 TCCGAGTCCA
* * * * * * **
53930 ATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAGTCAGCC
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCT-GAAATTGAAAATTGTTTGTTGACAACCAGCC
* * * *
53994 GCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-CTA--
64 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-ACG
* * * * * * * *
54036 ATATCCTTCG-CTGTGAAGATGAAATTGACTCTG-AA-CG-AAA-T-CTTGTTGACAATCAGCCG
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCG
*
54095 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * *
54136 ATATCCTTCG-C-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCAGA
1 ATATCCTCCGTCGTG-G-AGTTGAAATCGGCTCTGAAA-TTGAAAATTGTTTGTTGACAACCAGC
* *
54199 TGTCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACG
63 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACG
* ** * *
54245 ATATCCTCCGTCGTGGAGTTAAAATC-GCGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCC
1 ATATCCTCCGTCGTGGAGTTGAAATCGGC-TCTGAAATTGAAAA-TTGTTTGTTGACAACCAGCC
*
54309 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACG
64 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACG
* * *
54354 ATATCCTCTGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCAGCCG
1 ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATT-GAAAATTGTTTGTTGACAACCAGCCG
* *
54419 TCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * * **
54460 ATATCCTTCG-CTGTGAAGTTGAGATTGGCTC------CG-AAATTGCTTGTCGACAGTCAGCCG
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCG
* * * * * * *
54517 CCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * *
54558 ATATCCTTCG-CTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATT-ATTGTTGACAACCAGCC
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAA-TTGAAAATTGTTTGTTGACAACCAGCC
*
54621 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCA--
64 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * **
54663 ATATCCTTCG-CTGTGAAGTTGAGATTGGCTC------CG-AAATTGTTTGTCGACAGTCAGCCG
1 ATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCG
* * * * * * *
54720 CCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-CA
65 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
* * * * * * *
54761 ATATCCTTCAC-T-GTGAAGTTAAAATTGGCCCTGAAACTGGGAAATT-ATTGTTGACAACCAGC
1 ATATCC-TC-CGTCGTGGAGTTGAAATCGGCTCTGAAA-TTGAAAATTGTTTGTTGACAACCAGC
*
54823 CGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCTCGAGT
63 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
54863 CCAATATCCT
Statistics
Matches: 680, Mismatches: 103, Indels: 89
0.78 0.12 0.10
Matches are distributed among these distances:
97 6 0.01
98 156 0.23
99 2 0.00
100 78 0.11
101 3 0.00
102 3 0.00
103 2 0.00
104 4 0.01
105 125 0.18
106 115 0.17
107 1 0.00
108 9 0.01
109 166 0.24
110 8 0.01
111 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (107 bp):
ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATTGAAAATTGTTTGTTGACAACCAGCCGT
CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACG
Found at i:54654 original size:105 final size:104
Alignment explanation
Indices: 53922--54892 Score: 881
Period size: 98 Copynumber: 9.3 Consensus size: 104
53912 AATATTGTTC
* ** * *
53922 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACT-GGAAATT-ATTGTTGACA
** *
53987 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * *
54028 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AAC--GAAA-TCTTGTTGACAAT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGAAATTATTGTTGACAAC
* * *
54089 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
54128 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAA-CTG-GAAAT-TATTGTTGAC
** * * * *
54192 AACCAGATGTCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
63 AACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * ** * *
54234 CGAGTGGCACGATATCCTCCG-TCGTGGAGTT-AAAATCGCGGATGAAACTGAAAAGTTGTTCGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-CCTGAAACTGGAAA-TTATT-GT
* * *
54297 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * * * *
54343 CGGGTAGCACGATATCC-TCTG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGT
1 CGAGT--C-CAATATCCTTC-GCT-GTGAAGTTGAAATTGGCCCTGAAACT-GGAAATT-ATTGT
* *
54406 TGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* ** * *
54452 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC-GAAA-T-----TGCTTGTCGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CCTGAAACTGGAAATTATTGTTGACAA
* *
54510 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* *
54550 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACT-GGAAATTATTGTTGACAA
* * *
54615 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * *
54655 CGAGTTCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC-GAAA-TTG----T-TTGTCGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CCTGAAACTGGAAATTATTGTTGACAA
* *
54713 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
54753 TGGGTCCAATATCCTTCACTGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACT-GGAAATTATTGTTGACAA
* * * *
54818 CCAGCCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCT
65 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
*
54858 CGAGTCCAATATCCTTCGCTGTGAAGTCGAAATTG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
54893 ACTCTAGATA
Statistics
Matches: 721, Mismatches: 105, Indels: 79
0.80 0.12 0.09
Matches are distributed among these distances:
97 4 0.01
98 160 0.22
99 4 0.01
100 83 0.12
101 3 0.00
102 4 0.01
103 1 0.00
104 2 0.00
105 160 0.22
106 114 0.16
107 11 0.02
108 14 0.02
109 150 0.21
110 11 0.02
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGAAATTATTGTTGACAAC
CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:54709 original size:203 final size:203
Alignment explanation
Indices: 53925--54892 Score: 1104
Period size: 203 Copynumber: 4.7 Consensus size: 203
53915 ATTGTTCCGA
* * * * **
53925 GTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATT-ATTGTTGACAACC
* * * * * *
53990 AGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGA
65 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
* * * *
54055 TGAAATTGACTCTGAACGAAA-T-CTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACT
130 TGAAATTGGCTC----CGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACT
* *
54118 TGTGTTGTCTCGA
191 TGTGCTGTCTCGG
* * **
54131 GTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGACAAC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-CTGGGAAAT-TATTGTTGACAAC
** * * *
54195 CAGATGTCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCG-TCGT
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTTCGCT-GT
* * * * * * * * *
54259 GGAGTTAAAATCGCGGATGAAACTGAAAAGTTG-TTCGTTGACAACCAGCCGTCCCTTCGTTGTG
125 GAAGTTGAAAT--TGGCT----CCG-AAA-TTGCTT-GTCGACAATCAGCCGCCCCTTCGCTGTG
*
54323 AAGTTGAACTTGTGTTGTCTCGG
181 AAGTTGAACTTGTGCTGTCTCGG
* * * * * *
54346 GTAGCACGATATCC-TCTG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGA
1 GT--C-CAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATT-ATTGTTGA
*
54409 CAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGT
60 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGT
* * *
54474 GAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGC
125 GAAGTTGAAATTGGCTCCGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAAC
*
54539 TTGTGCTGTCTTGG
190 TTGTGCTGTCTCGG
* *
54553 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAACTAGGAAATTATTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCA
*
54618 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTT
66 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
* * * *
54683 GAGATTGGCTCCGAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGC
131 GAAATTGGCTCCGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGC
*
54748 TGTCTTGG
196 TGTCTCGG
* * *
54756 GTCCAATATCCTTCACTGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCA
* *
54821 GCCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTC
66 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
54886 GAAATTG
131 GAAATTG
54893 ACTCTAGATA
Statistics
Matches: 661, Mismatches: 73, Indels: 59
0.83 0.09 0.07
Matches are distributed among these distances:
203 278 0.42
204 36 0.05
205 4 0.01
206 83 0.13
207 54 0.08
208 8 0.01
209 21 0.03
211 3 0.00
212 3 0.00
213 3 0.00
214 3 0.00
215 72 0.11
216 3 0.00
217 11 0.02
218 79 0.12
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (203 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCA
GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
GAAATTGGCTCCGAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGC
TGTCTCGG
Found at i:55359 original size:38 final size:37
Alignment explanation
Indices: 55308--55784 Score: 182
Period size: 37 Copynumber: 13.9 Consensus size: 37
55298 TCAAAGATGA
*
55308 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTT
*
55346 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
55382 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTT
* *
55410 ATGTTTCAAGAGAAACTATCTCAAGAGAGACGAAA-TT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
55447 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTT
** *
55475 ATGTTTCAAGAGAAGTTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * *
55513 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
55549 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTT
**
55577 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGAGAAACTGTCTCAA-GAGAGACAAAATTT
* * *
55615 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
55651 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTT
* *
55679 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
55717 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
55753 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
55785 TGGTGAGCAC
Statistics
Matches: 322, Mismatches: 62, Indels: 111
0.65 0.13 0.22
Matches are distributed among these distances:
28 7 0.02
29 55 0.17
30 11 0.03
31 1 0.00
32 4 0.01
33 4 0.01
34 4 0.01
35 9 0.03
36 99 0.31
37 108 0.34
38 20 0.06
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:55395 original size:104 final size:103
Alignment explanation
Indices: 55205--55446 Score: 258
Period size: 103 Copynumber: 2.4 Consensus size: 103
55195 GACAAAATTT
* * * * *
55205 TGTTTTAAGA-AAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCACGGGG
1 TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCACAGAG
*
55269 AGATGAAATTAGTTCCAAGGAAAACATATTCAAAGATGA
66 AGACGAAATTAGTTCCAAGG-AAACATATTCAAAGATGA
* * * *
55308 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCA-AGAG
1 TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCACAGAG
* ** * * * *
55372 AGACGAAATTCA-TTTCAAGGGAAATGTTTTCAATGTTTA
66 AGACGAAATT-AGTTCCAA-GGAAACATATTCAAAGATGA
* *
55411 TGTTTCAAGAG-AAACTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATT
55447 CATTTCAAGG
Statistics
Matches: 116, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
102 22 0.19
103 48 0.41
104 46 0.40
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (103 bp):
TGTTTCAAGAGAAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCACAGAG
AGACGAAATTAGTTCCAAGGAAACATATTCAAAGATGA
Found at i:55450 original size:65 final size:65
Alignment explanation
Indices: 55346--55526 Score: 290
Period size: 65 Copynumber: 2.8 Consensus size: 65
55336 GACAAAATTT
55346 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
55411 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
** * * **
55476 TGTTTCAAGAGAAGTTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
55527 ATATCTCAAG
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:55517 original size:102 final size:102
Alignment explanation
Indices: 55411--55766 Score: 586
Period size: 102 Copynumber: 3.5 Consensus size: 102
55401 TCAATGTTTA
* *
55411 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
**
55476 TGTTTCAAGAGAAGTTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
55513 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
55578 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
55615 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
55680 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * **
55717 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
55767 CTGTCTCAAG
Statistics
Matches: 235, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 235 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:55534 original size:37 final size:37
Alignment explanation
Indices: 55476--55784 Score: 198
Period size: 37 Copynumber: 8.9 Consensus size: 37
55466 TCAATGTTTA
* ** *
55476 TGTTTCAAGAGAAGTTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
55513 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
55549 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* **
55577 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
55615 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
55651 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
55679 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
55717 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
55753 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
55785 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 69 0.33
37 85 0.41
38 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:55544 original size:204 final size:202
Alignment explanation
Indices: 55308--55782 Score: 563
Period size: 204 Copynumber: 2.3 Consensus size: 202
55298 TCAAAGATGA
* * *
55308 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TGTTTCAAGGGAAAA-TGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGA
* *
55373 GACGAAATTCATTTCAAGGGAAA-TGTTTTCAAT-G-TTTATGTTTCAAGAGAAACTATCTCAAG
64 GACGAAA-T-ATTTCAAGAGAAACTG-TCTCAATGGATTT-TGTTTCAAGAGAAACTATCTCAAG
* * **
55435 AGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAGTTGTCTCAAG
125 AGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAG
*
55500 GGAGACAAAATTT
190 GGAGAAAAAATTT
* ** * *
55513 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TGTTTTC-A-A-TG
1 TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTG-TCTCAAGAGAG
*** * *
55574 --TTTATGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATCTCA
65 ACGAAATATTTCAAGAGAAACTGTCTCAAT------GG-ATTTTGTTTCAAGAGAAACTATCTCA
55637 AGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCA
123 AGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCA
55702 AGGGAGAAAAAATTT
188 AGGGAGAAAAAATTT
* *
55717 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
55782 C
66 C
55783 AATGGTGAGC
Statistics
Matches: 226, Mismatches: 27, Indels: 30
0.80 0.10 0.11
Matches are distributed among these distances:
196 17 0.08
197 3 0.01
198 1 0.00
200 1 0.00
201 1 0.00
202 3 0.01
203 17 0.08
204 161 0.71
205 20 0.09
206 1 0.00
207 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (202 bp):
TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
CGAAATATTTCAAGAGAAACTGTCTCAATGGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAA
AAAATTT
Found at i:55762 original size:36 final size:36
Alignment explanation
Indices: 55680--55784 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
55670 TCAATGTTTA
* * * *
55680 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAGTT
55717 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
55753 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
55785 TGGTGAGCAC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 38 0.59
37 26 0.41
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:57332 original size:12 final size:11
Alignment explanation
Indices: 57284--57354 Score: 54
Period size: 12 Copynumber: 6.1 Consensus size: 11
57274 TTTTGTTCCC
*
57284 TTTTTTATTTT
1 TTTTTTCTTTT
57295 TGTTCTTTC-TTT
1 T-TT-TTTCTTTT
*
57307 TTTGTTCTTGTT
1 TTTTTTCTT-TT
57319 TTTTTTCCTTTT
1 TTTTTT-CTTTT
**
57331 TTACTTCTTTT
1 TTTTTTCTTTT
57342 CTTTTTTCTTTT
1 -TTTTTTCTTTT
57354 T
1 T
57355 GCCCTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
10 3 0.06
11 10 0.21
12 28 0.60
13 6 0.13
ACGTcount: A:0.03, C:0.13, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:57338 original size:24 final size:22
Alignment explanation
Indices: 57300--57354 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
57290 ATTTTTGTTC
*
57300 TTTCTTTTTTGTTCTTGTT-TTT
1 TTTCTTTTTTCTTCTT-TTCTTT
57322 TTTCCTTTTTTACTTCTTTTCTTT
1 TTT-CTTTTTT-CTTCTTTTCTTT
57346 TTTCTTTTT
1 TTTCTTTTT
57355 GCCCTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.10
23 15 0.52
24 11 0.38
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTTCTTCTTTTCTTT
Found at i:57346 original size:23 final size:23
Alignment explanation
Indices: 57282--57354 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
57272 CTTTTTGTTC
* *
57282 CCTTTTTTATTTTTGTTC--TTT
1 CCTTTTTTCTTCTTGTTCTTTTT
* *
57303 -CTTTTTTGTTCTTGTTTTTTTT
1 CCTTTTTTCTTCTTGTTCTTTTT
57325 CCTTTTTTACTTCTT-TTCTTTTT
1 CCTTTTTT-CTTCTTGTTCTTTTT
*
57348 TCTTTTT
1 CCTTTTT
57355 GCCCTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.33
22 3 0.07
23 20 0.48
24 5 0.12
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (23 bp):
CCTTTTTTCTTCTTGTTCTTTTT
Found at i:60961 original size:11 final size:11
Alignment explanation
Indices: 60883--60962 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
60873 TTATATACGT
*
60883 TAATAGTAAAA
1 TAATATTAAAA
*
60894 TAATAAT-AAA
1 TAATATTAAAA
60904 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
60917 T-ATATATATAA
1 TAATAT-TAAAA
60928 TAACT-TTAAAA
1 TAA-TATTAAAA
*
60939 -AACATTAAAA
1 TAATATTAAAA
*
60949 TAATATTAGAA
1 TAATATTAAAA
60960 TAA
1 TAA
60963 AAATAATTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
10 16 0.30
11 26 0.48
12 7 0.13
13 5 0.09
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:61488 original size:35 final size:37
Alignment explanation
Indices: 61433--61507 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 37
61423 GTTTAAAACA
*
61433 TAGCAAAATTTTATCCTATTTT-AAGAG-TTGAATCC
1 TAGCAAAATTCTATCCTATTTTCAAGAGTTTGAATCC
* * *
61468 TAGCAGAATTCTATCTTATTTTCGAGAGTTTGAATCC
1 TAGCAAAATTCTATCCTATTTTCAAGAGTTTGAATCC
61505 TAG
1 TAG
61508 TAGGACGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 19 0.56
36 4 0.12
37 11 0.32
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
TAGCAAAATTCTATCCTATTTTCAAGAGTTTGAATCC
Found at i:62923 original size:14 final size:15
Alignment explanation
Indices: 62890--62928 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
62880 TACATTTACG
* *
62890 TTTTAATTATTATTA
1 TTTTATTTATTATAA
62905 TTTTATTTATT-TAA
1 TTTTATTTATTATAA
62919 TTTTATTTAT
1 TTTTATTTAT
62929 ATGTACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTATAA
Found at i:63041 original size:2 final size:2
Alignment explanation
Indices: 63036--63091 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
63026 TTTACTTTAG
* * * *
63036 TA TA TA TA TA TT TT TA GA T- TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63077 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
63092 GTTAATTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63159 original size:2 final size:2
Alignment explanation
Indices: 63154--63178 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63144 ATGTTTTTAT
63154 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
63179 CATTTCGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63288 original size:15 final size:17
Alignment explanation
Indices: 63249--63291 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
63239 TGCATTTATT
63249 TATTTATTTACTATGTA
1 TATTTATTTACTATGTA
*
63266 TATATTATTTTCTA-GTA
1 TAT-TTATTTACTATGTA
63283 T-TTTATTTA
1 TATTTATTTA
63292 TTTCATTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.26
16 1 0.04
17 7 0.30
18 9 0.39
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (17 bp):
TATTTATTTACTATGTA
Found at i:63295 original size:18 final size:18
Alignment explanation
Indices: 63245--63295 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
63235 CTCTTGCATT
63245 TATTTATTTATTTACTATG
1 TATTTATTTATTT-CTATG
*
63264 TATATA-TTATTTTCTA-G
1 TATTTATTTA-TTTCTATG
63281 TATTTTATTTATTTC
1 TA-TTTATTTATTTC
63296 ATTTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (18 bp):
TATTTATTTATTTCTATG
Found at i:63372 original size:20 final size:19
Alignment explanation
Indices: 63333--63385 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
63323 ATTTTATGTC
63333 TTTTATTTTATTTATTTAT
1 TTTTATTTTATTTATTTAT
* *
63352 TTTTCTTTTAGTTTCTTTAT
1 TTTTATTTTA-TTTATTTAT
*
63372 TTTTATTTAATTTA
1 TTTTATTTTATTTA
63386 CTTGTTATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTATTTTATTTATTTAT
Found at i:66527 original size:13 final size:14
Alignment explanation
Indices: 66496--66546 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
66486 ATCAGAACAA
*
66496 AAAGAGAAAAAAAGC
1 AAAGAGAAAATAA-C
66511 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
66524 AAAGAGAAAA-AAC
1 AAAGAGAAAATAAC
66537 AAAG-GAAAAT
1 AAAGAGAAAAT
66547 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:66533 original size:26 final size:26
Alignment explanation
Indices: 66494--66546 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
66484 CAATCAGAAC
66494 AAAAAGAGAAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAA-CAAAG-GAAAAT
66522 AAAAAGAG-AAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
66547 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 6 0.24
28 8 0.32
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:66692 original size:69 final size:69
Alignment explanation
Indices: 66599--66736 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
66589 GATTCAAACT
* * *
66599 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATAAAGCA
1 ATGAGATTGATCAAGAACAATCATTTATGAATCACTGAACCACTCCACTCGAAGATCATAAAGCA
66664 TCAA
66 TCAA
* *
66668 ATGAGATTGATCAAGAACAATCATTTATGAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGAACAATCATTTATGAATCACTGAACCACTCCACTCGAAGATCATAAAGCA
66733 TCAA
66 TCAA
66737 GAGAGAGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGAACAATCATTTATGAATCACTGAACCACTCCACTCGAAGATCATAAAGCA
TCAA
Found at i:67720 original size:31 final size:32
Alignment explanation
Indices: 67648--67738 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 32
67638 TGAGGGCATC
*
67648 TTTGAAGATTCAACATCAAATGCTGGGGCATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTT
*
67681 TTTGAGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
* *
67713 TTT-AGATTCAACATCGAATATTGGGG
1 TTTGAGATTCAACATCAAATGTTGGGG
67739 TATCTTTGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 20 0.38
32 29 0.55
33 4 0.08
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:68770 original size:36 final size:36
Alignment explanation
Indices: 68666--68823 Score: 219
Period size: 36 Copynumber: 4.4 Consensus size: 36
68656 ATTTGAATCT
* * *
68666 GTTTCCCTTGAAAAAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * *
68702 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
*
68739 GTTTCTCTTGAAACAAATTTTGTCT-TCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCT-CTTGAGACA
68775 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
68811 GTTTCCCTTGAAA
1 GTTTCCCTTGAAA
68824 TAAAATAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.01
36 75 0.69
37 32 0.30
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:68949 original size:21 final size:21
Alignment explanation
Indices: 68923--68965 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
68913 GTTTCTCTTT
68923 AAACAAATTGTGTATCCCTTG
1 AAACAAATTGTGTATCCCTTG
* *
68944 AAACAAATTTTGTCTCCCTTG
1 AAACAAATTGTGTATCCCTTG
68965 A
1 A
68966 GACGGTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (21 bp):
AAACAAATTGTGTATCCCTTG
Found at i:68977 original size:36 final size:36
Alignment explanation
Indices: 68937--69022 Score: 154
Period size: 36 Copynumber: 2.4 Consensus size: 36
68927 AAATTGTGTA
*
68937 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACGGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
*
68973 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
69009 TCCCTTGAAACAAA
1 TCCCTTGAAACAAA
69023 ATAATTGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
Found at i:68977 original size:195 final size:195
Alignment explanation
Indices: 68745--69122 Score: 657
Period size: 195 Copynumber: 1.9 Consensus size: 195
68735 GACAGTTTCT
*
68745 CTTGAAACAAATTTTGTCTTCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
* *
68810 AGTTTCCCTTGAAATAAAATAATTGAATATGTTTTCCTTGAAACTAATTTCGTCTCCATTGAGAT
66 AGTTTCCCTTGAAACAAAATAATTGAATATGTTTTCCTTGAAACTAATTTCGTCTCCATTGAGAC
* * * * *
68875 AATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTTAAACAAATTGTGTATCC
131 AATTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACAAATTGTGTATCC
*
68940 CTTGAAACAAATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
* *
69005 AGTTTCCCTTGAAACAAAATAATTGAATCTGTTTTCCTTGAAACTAATTTCGTCTCCCTTGAGAC
66 AGTTTCCCTTGAAACAAAATAATTGAATATGTTTTCCTTGAAACTAATTTCGTCTCCATTGAGAC
69070 AATTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACA
131 AATTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACA
69123 TAAACATTGA
Statistics
Matches: 172, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
195 172 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (195 bp):
CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATAATTGAATATGTTTTCCTTGAAACTAATTTCGTCTCCATTGAGAC
AATTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACAAATTGTGTATCC
Found at i:69121 original size:102 final size:101
Alignment explanation
Indices: 68937--69189 Score: 298
Period size: 102 Copynumber: 2.5 Consensus size: 101
68927 AAATTGTGTA
* * * *
68937 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCTCTTGA
1 TCCCTTGAAACTAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGA
* * *
69002 GACAGTTTCCCTTGAAACA-AAATAATTG-AATCTGTT
66 GACAGTTTACCTTGAAACATAAA-AATTGAAAAC-ATT
* * * *
69038 TTCCTTGAAACTAATTTCGTCTCCCTTGAGACAATTTCT-TTTAGAACTAAATTTTGTCTCCCTT
1 TCCCTTGAAACTAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA-AAC-AAATTTTGTCTCCCTT
* *
69102 GAGACAGTTTATCTTGAAACATAAACATTGAAAACATT
64 GAGACAGTTTACCTTGAAACATAAAAATTGAAAACATT
**
69140 TCCCTTGAAA-TGAATTTTGTCTCCCTTGAGACAGTTTCTCTAAAAACAAA
1 TCCCTTGAAACT-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA
69190 ATCTTTGAAT
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
100 3 0.02
101 40 0.31
102 77 0.60
103 8 0.06
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (101 bp):
TCCCTTGAAACTAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGA
GACAGTTTACCTTGAAACATAAAAATTGAAAACATT
Found at i:69170 original size:167 final size:166
Alignment explanation
Indices: 68971--69357 Score: 560
Period size: 166 Copynumber: 2.3 Consensus size: 166
68961 CTTGAGACGG
**
68971 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTG
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTG
*
69036 TTTTCC-TTGAAACTAATTTCGTCTCCCTTGAGACAATTTCTTTTAGAACTAAATTTTGTCTCCC
66 -TTTCCTTTGAAACAAATTTCGTCTCCCTTGAGAC-ATTTCTTTTAGAACTAAATTTTGTCTCCC
*
69100 TTGAGACAGTTTATCTTGAAACATAAACATTGAAAACA
129 TTGAGACAGTTTATCTTGAAACATAAACATTAAAAACA
* * ** ** *
69138 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCTCTAAAAACAAAATCTTTGAATTTG
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTG
* * * *
69203 TTTCCTTTGAAACAAATTTCGTCTCCCTTGAGACATTTTTTTTTGAACTAAGTTTTGTCTCTCTT
66 TTTCCTTTGAAACAAATTTCGTCTCCCTTGAGACATTTCTTTTAGAACTAAATTTTGTCTCCCTT
* * *
69268 GATATAGTTTCTCTTGAAACATAAACATTAAAAACA
131 GAGACAGTTTATCTTGAAACATAAACATTAAAAACA
* * *
69304 TTTCCCTTGAAATGAATTTTGTATCTCTTGAGATAGGTTCCCTTGAAACAAAAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
69358 TTTGTCTCCC
Statistics
Matches: 194, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
166 111 0.57
167 83 0.43
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (166 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATAATTGAATCTG
TTTCCTTTGAAACAAATTTCGTCTCCCTTGAGACATTTCTTTTAGAACTAAATTTTGTCTCCCTT
GAGACAGTTTATCTTGAAACATAAACATTAAAAACA
Found at i:69198 original size:65 final size:65
Alignment explanation
Indices: 69086--69237 Score: 180
Period size: 65 Copynumber: 2.3 Consensus size: 65
69076 TTTTAGAACT
** *
69086 AAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTATCTAAAAACATAAACATTGAAAACATTTCCCTTGAAAC
* * * **** *
69151 GAATTTTGTCTCCCTTGAGACAGTTTCTCTAAAAACA-AAATCTTTGAATTTGTTTCCTTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTATCTAAAAACATAAA-CATTGAAAACATTTCCCTTGAAA
69215 C
65 C
*
69216 AAATTTCGTCTCCCTTGAGACA
1 AAATTTTGTCTCCCTTGAGACA
69238 TTTTTTTTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 3 0.04
65 70 0.96
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (65 bp):
AAATTTTGTCTCCCTTGAGACAGTTTATCTAAAAACATAAACATTGAAAACATTTCCCTTGAAAC
Found at i:69314 original size:268 final size:268
Alignment explanation
Indices: 68941--69438 Score: 682
Period size: 268 Copynumber: 1.9 Consensus size: 268
68931 TGTGTATCCC
* *
68941 TTGAAACAAATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * * *
69006 GTTTCCCTTGAAACAAAATAATTGAATCTGTTTTCCTTGAAACT-AATTTCGTCTCCCTTGAGAC
66 GTTTCCCTTGAAACAAAATAATTAAAACTATTTCCCTTGAAA-TGAATTTCGTATCCCTTGAGAC
* * * *
69070 AA-TTTCTTTTAGAACTAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAA
130 AAGTTCCCTTGA-AACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAA
69134 AACATTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCTCTAAAAACAAAATCTTTGAA
194 AACATTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCTCTAAAAACAAAATCTTTGAA
69199 TTTGTTTCCT
259 TTTGTTTCCT
* *** * * *
69209 TTGAAACAAATTTCGTCTCCCTTGAGACATTTTTTTTTG-AACTAAGTTTTGTCTCTCTTGATAT
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGAC
* * * *
69273 AGTTTCTCTTGAAACATAAA-CATTAAAAAC-ATTTCCCTTGAAATGAATTTTGTATCTCTTGAG
65 AGTTTCCCTTGAAACA-AAATAATT-AAAACTATTTCCCTTGAAATGAATTTCGTATCCCTTGAG
* * *
69336 ATAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
128 ACAAGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGA
*
69401 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
193 AAACATTTCCCTTGAAATGAATTTTGTCTCCCTTGAGA
69439 TAGGTTCCCT
Statistics
Matches: 199, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
267 4 0.02
268 183 0.92
269 12 0.06
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (268 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
GTTTCCCTTGAAACAAAATAATTAAAACTATTTCCCTTGAAATGAATTTCGTATCCCTTGAGACA
AGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTATCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCTCTAAAAACAAAATCTTTGAATT
TGTTTCCT
Found at i:69371 original size:37 final size:37
Alignment explanation
Indices: 69305--69390 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 37
69295 TTAAAAACAT
** * *
69305 TTCCCTTGAAA-TGAATTTTGTATCTCTTGAGATAGG
1 TTCCCTTGAAACAAAATTTTGTATCCCTTGAGACAGG
* *
69341 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTTGTATCCCTTGAGACAGG
*
69378 TTCTCTTGAAACA
1 TTCCCTTGAAACA
69391 TAAACATTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTATCCCTTGAGACAGG
Found at i:69389 original size:102 final size:102
Alignment explanation
Indices: 69255--69512 Score: 417
Period size: 102 Copynumber: 2.5 Consensus size: 102
69245 TTGAACTAAG
* * * *
69255 TTTTGTCTCTCTTGATATAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
69320 TTTTGTATCTCTTGAGATAGGTTCCCTTGAAACAAAA
66 TTTTGTATCTCTTGAGATAGGTTCCCTTGAAACAAAA
69357 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
*
69422 TTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAA
66 TTTTGTATCTCTTGAGATAGGTTCCCTTGAAACAAAA
* * ** *
69459 TTTTGTCTCCATTGAGACAATTTCTCTTGAGGCATAAACTTTGAAAACAGTTTC
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA-TTTC
69513 ATTTGAAACA
Statistics
Matches: 145, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 141 0.97
103 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (102 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
TTTTGTATCTCTTGAGATAGGTTCCCTTGAAACAAAA
Found at i:69596 original size:34 final size:34
Alignment explanation
Indices: 69549--69653 Score: 113
Period size: 36 Copynumber: 3.0 Consensus size: 34
69539 TCTACGTTAA
* * * * *
69549 ACAAATTTCGTCTCCCTTGAAACAGTTTCTTTTG
1 ACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
69583 -GAAGTTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 ACAAG-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
69617 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 --ACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
69653 A
1 A
69654 AACTTCAACC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
33 2 0.03
34 26 0.44
36 28 0.47
37 3 0.05
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (34 bp):
ACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:69609 original size:21 final size:20
Alignment explanation
Indices: 69588--69646 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 20
69578 TTTTGGAAGT
69588 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAGACAG
*
69608 ---T-T-TCTCTTGAAACAAG
1 TTTTGTCTCTCTTGAGAC-AG
69624 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAGACAG
69644 TTT
1 TTT
69647 CCCTTGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 1 0.03
19 1 0.03
20 6 0.19
21 10 0.32
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (20 bp):
TTTTGTCTCTCTTGAGACAG
Found at i:69635 original size:36 final size:36
Alignment explanation
Indices: 69588--69656 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
69578 TTTTGGAAGT
*
69588 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAG
69624 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
69657 TTCAACCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAG
Found at i:69897 original size:84 final size:82
Alignment explanation
Indices: 69732--69977 Score: 224
Period size: 84 Copynumber: 2.9 Consensus size: 82
69722 AACCAAACCC
* * * * * * * * * * *
69732 TCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAACATAACTCAAGGCTAGAAGAGT
1 TCGAGTTCAACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAGCTCAAGGC-AAAAGGGC
*
69797 TATCTGCCACCA-AAAGACCT
64 TATCTGTCA--ATAAAGACCT
* * * * * * *
69817 TCGAGTTCAACTATGCTCAGCTCTAAGGGACATCATTTGCAGCGTAGCTTAAGTCAATAAGGGCT
1 TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAA-AAGGGCT
69882 ATCTGTCAACTAAAGACCT
65 ATCTGTCAA-TAAAGACCT
* * * *
69901 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTATAGCATAGCTCAAGGCAAAAGGGTTA
1 TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAAAGGGCTA
69966 TCTGTCAATAAA
66 TCTGTCAATAAA
69978 ATTGTCGAGT
Statistics
Matches: 129, Mismatches: 29, Indels: 9
0.77 0.17 0.05
Matches are distributed among these distances:
82 5 0.04
83 16 0.12
84 91 0.71
85 17 0.13
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (82 bp):
TCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAAAGGGCTA
TCTGTCAATAAAGACCT
Found at i:71181 original size:5 final size:5
Alignment explanation
Indices: 71166--71236 Score: 53
Period size: 5 Copynumber: 15.2 Consensus size: 5
71156 TATTTTTTAG
* * * *
71166 TATTT TA-TT TATTT TATTT GATTT TA-TG GACTT TA-TT TA-TT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
* *
71212 TA-TG TCTTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
71237 TCTTTTCGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
4 16 0.31
5 36 0.69
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:71189 original size:10 final size:9
Alignment explanation
Indices: 71166--71236 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
71156 TATTTTTTAG
71166 TATTTTATT
1 TATTTTATT
71175 TATTTTATT
1 TATTTTATT
*
71184 TGATTTTATG
1 T-ATTTTATT
* *
71194 GACTTTATT
1 TATTTTATT
71203 TA-TTTATTT
1 TATTTTA-TT
*
71212 TATGTCT-TT
1 TAT-TTTATT
71221 TATTTTATTT
1 TATTTTA-TT
71231 TATTTT
1 TATTTT
71237 TCTTTTCGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
8 6 0.12
9 26 0.53
10 15 0.31
11 2 0.04
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.72
Consensus pattern (9 bp):
TATTTTATT
Found at i:73021 original size:19 final size:17
Alignment explanation
Indices: 72982--73034 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
72972 GATAGTAAAT
* *
72982 ATTTTTTTTTATTTTAT
1 ATTTTTTTTTATATTAC
72999 ATTTATTTTCTTATATTAC
1 ATTT-TTTT-TTATATTAC
73018 ATTTTTATATTTATATT
1 ATTTTT-T-TTTATATT
73035 TTTTGTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.20
19 19 0.63
20 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTTTTATATTAC
Found at i:73037 original size:14 final size:14
Alignment explanation
Indices: 72993--73037 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
72983 TTTTTTTTTA
72993 TTTTATATTTAT-T
1 TTTTATATTTATAT
*
73006 TTCTTATA-TTACAT
1 TT-TTATATTTATAT
73020 TTTTATATTTATAT
1 TTTTATATTTATAT
73034 TTTT
1 TTTT
73038 TGTTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATATTTATAT
Found at i:73575 original size:2 final size:2
Alignment explanation
Indices: 73570--73599 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
73560 TATTCAAAAA
73570 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73600 AATTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73616 original size:10 final size:11
Alignment explanation
Indices: 73570--73616 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
73560 TATTCAAAAA
*
73570 ATATATATATAT
1 ATATATAAAT-T
*
73582 ATATATATATT
1 ATATATAAATT
73593 ATATATAAATT
1 ATATATAAATT
73604 -TATAATAAATT
1 ATAT-ATAAATT
73615 AT
1 AT
73617 TTTCCTTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 3 0.09
11 18 0.56
12 11 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATATAAATT
Found at i:79462 original size:15 final size:16
Alignment explanation
Indices: 79423--79463 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
79413 TTAACATTAC
*
79423 ATATATAAAATTAAAT
1 ATATATAAATTTAAAT
*
79439 ATATTTAAATTTAAAT
1 ATATATAAATTTAAAT
79455 A-ATATAAAT
1 ATATATAAAT
79464 ATCATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATAAATTTAAAT
Found at i:87049 original size:22 final size:21
Alignment explanation
Indices: 87007--87046 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
86997 GAGCTTATTT
*
87007 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
87028 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
87047 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:93036 original size:2 final size:2
Alignment explanation
Indices: 93029--93068 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
93019 TTTCTACTTG
93029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93069 CCAACAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96550 original size:23 final size:24
Alignment explanation
Indices: 96519--96566 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
96509 TAAATTTATA
*
96519 TTTATATTAGTT-TTCATGTTATGT
1 TTTATATTAGTTATT-ATATTATGT
96543 TTTA-ATTAGTTATTATATTATGT
1 TTTATATTAGTTATTATATTATGT
96566 T
1 T
96567 CATGTCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.62
Consensus pattern (24 bp):
TTTATATTAGTTATTATATTATGT
Found at i:99841 original size:20 final size:20
Alignment explanation
Indices: 99803--99842 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
99793 TATATTATTG
* *
99803 AAAAATCAAATTAATATTTT
1 AAAAAACAAATTAACATTTT
*
99823 AAAAAACAAATTTACATTTT
1 AAAAAACAAATTAACATTTT
99843 TAATATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAACAAATTAACATTTT
Found at i:105115 original size:24 final size:23
Alignment explanation
Indices: 105083--105128 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
105073 AGAAACTGCC
*
105083 CAACTAACCAGGAACAGTTACAA
1 CAACTAACCAGAAACAGTTACAA
105106 CAACTTAACCAGAAACAGTTACA
1 CAAC-TAACCAGAAACAGTTACA
105129 GCTAATCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.48, C:0.26, G:0.11, T:0.15
Consensus pattern (23 bp):
CAACTAACCAGAAACAGTTACAA
Found at i:106904 original size:18 final size:18
Alignment explanation
Indices: 106883--106938 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
106873 ATGATGATGA
*
106883 TGATGGTGAAGGTAGTGG
1 TGATGGTGAAGGTAGTAG
106901 TGATGGTGAAGGTAGTAG
1 TGATGGTGAAGGTAGTAG
*
106919 TGATGGTGAAGGTGGTAG
1 TGATGGTGAAGGTAGTAG
106937 TG
1 TG
106939 GCGATGGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.23, C:0.00, G:0.48, T:0.29
Consensus pattern (18 bp):
TGATGGTGAAGGTAGTAG
Found at i:106918 original size:21 final size:20
Alignment explanation
Indices: 106883--106948 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 20
106873 ATGATGATGA
106883 TGATGGTGAA-G-GTAGTGG
1 TGATGGTGAAGGTGTAGTGG
*
106901 TGATGGTGAA-G-GTAGTAG
1 TGATGGTGAAGGTGTAGTGG
106919 TGATGGTGAAGGTGGTAGTGG
1 TGATGGTGAAGGT-GTAGTGG
*
106940 CGATGGTGA
1 TGATGGTGA
106949 TGAATTAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.64
19 1 0.02
21 14 0.33
ACGTcount: A:0.23, C:0.02, G:0.48, T:0.27
Consensus pattern (20 bp):
TGATGGTGAAGGTGTAGTGG
Found at i:107063 original size:21 final size:21
Alignment explanation
Indices: 107024--107064 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
107014 AAGGTAGTGG
* *
107024 TGATGGTGAAGATGGTGATGT
1 TGATGGTGAAGAAGATGATGT
*
107045 TGATGGTGTAGAAGATGATG
1 TGATGGTGAAGAAGATGATG
107065 AATTTGAACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (21 bp):
TGATGGTGAAGAAGATGATGT
Found at i:108241 original size:21 final size:22
Alignment explanation
Indices: 108200--108241 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
108190 TAGAATTATT
*
108200 AACATGCATTTCATCATCAGTA
1 AACATGCAATTCATCATCAGTA
*
108222 AACATGCAATT-ATTATCAGT
1 AACATGCAATTCATCATCAGT
108242 GTTATTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
AACATGCAATTCATCATCAGTA
Done.