Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015272.1 Kokia drynarioides strain JFW-HI SEQ_130317, 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: 880760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 613 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2788 original size:256 final size:256
Alignment explanation
Indices: 2328--2845 Score: 865
Period size: 256 Copynumber: 2.0 Consensus size: 256
2318 TTGTCACTTT
2328 TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
1 TCAA-TTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
* * * * *
2393 GTGTTGAATTTTTCTCAATGACACTACTATGTGAATAACTATTTACTATATTCTTTAGGGATAAT
65 GCGTTGAATCTTTCTCAATAACACTAATATGTGAATAACTATTTAATATATTCTTTAGGGATAAT
* * * **
2458 TATTCATATCCAGTTGGATTTGAAGTAATCATTACCACAATAATGTCTTCAAGTAGTGAATATTG
130 TATTCATATCCAGTTGGATTTGAAGTAATAAATACCACAATAATGTCTTAAAGTACAGAATATTG
*
2523 ATGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCTACTATATTTGCTCAACCCA
195 ATGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACCCA
* *
2585 TCAATTTAAATTGAAACAAAGACTATGGGGCGTAGTTTTATGATAGTTTGCTTAATTAGATTCAG
1 TCAATTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCAG
* *
2650 CGTTGAATCTTTCTCATTAACACTAATATTTGAATAACTATTTAATATATTCTTTAGGGATAATT
66 CGTTGAATCTTTCTCAATAACACTAATATGTGAATAACTATTTAATATATTCTTTAGGGATAATT
* *
2715 ATTCATATCCAGTTGGATTTGTAGTAATAAATACCACAATAATGTGTTAAAGTACAGAATATTGA
131 ATTCATATCCAGTTGGATTTGAAGTAATAAATACCACAATAATGTCTTAAAGTACAGAATATTGA
*
2780 TGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACTCA
196 TGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACCCA
2841 TCAAT
1 TCAAT
2846 GTTTTGCTAT
Statistics
Matches: 243, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
256 239 0.98
257 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (256 bp):
TCAATTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCAG
CGTTGAATCTTTCTCAATAACACTAATATGTGAATAACTATTTAATATATTCTTTAGGGATAATT
ATTCATATCCAGTTGGATTTGAAGTAATAAATACCACAATAATGTCTTAAAGTACAGAATATTGA
TGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCCACTATATTTGCTCAACCCA
Found at i:9220 original size:31 final size:31
Alignment explanation
Indices: 9183--9241 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
9173 CATCAGCTAT
9183 TATTTACTAAATTTCTTATTGGCTTTATAAC
1 TATTTACTAAATTTCTTATTGGCTTTATAAC
9214 TATTTACTAAATTTCTTATTGGCTTTAT
1 TATTTACTAAATTTCTTATTGGCTTTAT
9242 TATTGCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (31 bp):
TATTTACTAAATTTCTTATTGGCTTTATAAC
Found at i:49312 original size:3 final size:3
Alignment explanation
Indices: 49304--49330 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
49294 AATGTCACAT
49304 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
49331 CATTAACAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:51802 original size:27 final size:26
Alignment explanation
Indices: 51749--51802 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
51739 CGAATCAGAC
** **
51749 TCAAATTTAATAATTTTTTATTTTAA
1 TCAAATTTAATAAAATTTTAAATTAA
51775 TCAAATTTAAGTAAAATTTTAAATTAA
1 TCAAATTTAA-TAAAATTTTAAATTAA
51802 T
1 T
51803 TTTAGAAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
TCAAATTTAATAAAATTTTAAATTAA
Found at i:56736 original size:31 final size:31
Alignment explanation
Indices: 56682--56740 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
56672 GTATATGATA
*
56682 AAATTATCTTTTAAAAATTATAAAAATAATT
1 AAATTATCTTTTAAAAATCATAAAAATAATT
***
56713 AAATTATCTTTTAATTCTCATAAAAATA
1 AAATTATCTTTTAAAAATCATAAAAATA
56741 TATAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATTATCTTTTAAAAATCATAAAAATAATT
Found at i:59562 original size:3 final size:3
Alignment explanation
Indices: 59554--59591 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
59544 TTAATTTGTT
59554 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
59592 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:60112 original size:59 final size:60
Alignment explanation
Indices: 60040--60174 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 60
60030 GACAAAATTG
* * * * *
60040 AATAGTTGAGTGACTATTTTGTAAC-TTTCATAGTTGGGTGACCAAAA-AATAAATTTACT
1 AATAATTGGGTGACTATTTTGTAACTTTTCATAATTGAGTGACCAAAATAA-AAATCTACT
* *
60099 AATAATTGGGTGACCATTTTGTAACTTTTTATAATTGAGTGACCAAAATAAAAATCTACT
1 AATAATTGGGTGACTATTTTGTAACTTTTCATAATTGAGTGACCAAAATAAAAATCTACT
*
60159 AATAATTGGGTTACTA
1 AATAATTGGGTGACTA
60175 ATAAAGTAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 22 0.34
60 41 0.63
61 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (60 bp):
AATAATTGGGTGACTATTTTGTAACTTTTCATAATTGAGTGACCAAAATAAAAATCTACT
Found at i:62875 original size:29 final size:27
Alignment explanation
Indices: 62838--62892 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
62828 AATTTTATAG
*
62838 TAATTCAATTTTATTTTATTTTTAATTAT
1 TAATTCAATTTT-TTATA-TTTTAATTAT
62867 TAATTCAATTTTTTATATTTTAATTA
1 TAATTCAATTTTTTATATTTTAATTA
62893 AAGTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.36
28 4 0.16
29 12 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TAATTCAATTTTTTATATTTTAATTAT
Found at i:63202 original size:8 final size:8
Alignment explanation
Indices: 63189--63216 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
63179 GGGTAAAATT
63189 ACTCTTTA
1 ACTCTTTA
63197 ACTCTTTA
1 ACTCTTTA
63205 ACTCTTTA
1 ACTCTTTA
63213 ACTC
1 ACTC
63217 CAAAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.46
Consensus pattern (8 bp):
ACTCTTTA
Found at i:75692 original size:31 final size:30
Alignment explanation
Indices: 75657--75735 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
75647 GAGCCTTTAA
*
75657 AAAATTTTAATTAGAACCTCCAAATTTTTTT
1 AAAATTTTAATTAGAACCTCCAAA-TATTTT
* *
75688 AAAATTCTT-ATTA-ATATTCTCGAAATATTTT
1 AAAATT-TTAATTAGA-A-CCTCCAAATATTTT
75719 AAAATTTTAATT-GAACC
1 AAAATTTTAATTAGAACC
75736 CCCTAAAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
29 1 0.03
30 4 0.10
31 26 0.67
32 8 0.21
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (30 bp):
AAAATTTTAATTAGAACCTCCAAATATTTT
Found at i:78923 original size:19 final size:18
Alignment explanation
Indices: 78901--78945 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
78891 ATATTTTAAT
78901 ATATATAAAAAAATATCAA
1 ATATATAAAAAAATAT-AA
*
78920 ATATTAAAAAAAAAATATAA
1 ATA-T-ATAAAAAAATATAA
78940 ATATAT
1 ATATAT
78946 TTTTGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.05
19 4 0.18
20 6 0.27
21 11 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATATAAAAAAATATAA
Found at i:96681 original size:135 final size:135
Alignment explanation
Indices: 96439--96846 Score: 807
Period size: 135 Copynumber: 3.0 Consensus size: 135
96429 TACTTGTACA
96439 CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACATCCTGCACTTTC
1 CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACATCCTGCACTTTC
96504 TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
66 TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
96569 ACAAG
131 ACAAG
*
96574 CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACGTCCTGCACTTTC
1 CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACATCCTGCACTTTC
96639 TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
66 TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
96704 ACAAG
131 ACAAG
96709 CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACATCCTGCACTTTC
1 CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACATCCTGCACTTTC
96774 TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
66 TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
96839 ACAAG
131 ACAAG
96844 CTG
1 CTG
96847 AGATTGATAT
Statistics
Matches: 271, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 271 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (135 bp):
CTGCAAGCTTTGATTCAGATAGCAATTTGGGTGGCATATGCAGATATTTCACATCCTGCACTTTC
TAAGGTAGATCATGTAAATATATATATTATAATTTGAAAGACTTTACATGTTTTTCTCTGTCCTA
ACAAG
Found at i:102666 original size:16 final size:16
Alignment explanation
Indices: 102645--102677 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
102635 ATAAAATTTT
102645 AGACCATAGTCCAAGC
1 AGACCATAGTCCAAGC
102661 AGACCATAGTCCAAGC
1 AGACCATAGTCCAAGC
102677 A
1 A
102678 TGTCAAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.30, G:0.18, T:0.12
Consensus pattern (16 bp):
AGACCATAGTCCAAGC
Found at i:105349 original size:58 final size:59
Alignment explanation
Indices: 105229--105351 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 59
105219 TGAATATTAC
* *
105229 AATT-TTTCTTATATAGAGGTTTGAATTTTTTTAATTCAAGTTAGGTCCTGAACTAAGA
1 AATTGTTTCTTATATAGAGGTTTGAATTTTTTTAATTCAAATTAGATCCTGAACTAAGA
* * ** *
105287 AATTGTTT-TTATATTGGGGTTTGAATTTTTTTTTTTCCAAATTA-ATCCTTGAACTTAG-
1 AATTGTTTCTTATATAGAGGTTTGAATTTTTTTAATT-CAAATTAGATCC-TGAACTAAGA
105345 AATTGTT
1 AATTGTT
105352 CTCACACTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
58 38 0.69
59 17 0.31
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.50
Consensus pattern (59 bp):
AATTGTTTCTTATATAGAGGTTTGAATTTTTTTAATTCAAATTAGATCCTGAACTAAGA
Found at i:105886 original size:14 final size:14
Alignment explanation
Indices: 105867--105894 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
105857 TGAAGCGTAC
105867 GTAACACGTCAAGT
1 GTAACACGTCAAGT
105881 GTAACACGTCAAGT
1 GTAACACGTCAAGT
105895 TATTCCGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
GTAACACGTCAAGT
Found at i:113281 original size:21 final size:21
Alignment explanation
Indices: 113243--113370 Score: 80
Period size: 23 Copynumber: 5.6 Consensus size: 21
113233 ATACGGAACA
* *
113243 AACAGAGAGTACCAAAGTACT
1 AACAGAGAGCACAAAAGTACT
*
113264 AACAGAGAGCACATAAGTGTTGGA-T
1 AACAGAGAGCACA-AA-AG-T--ACT
*
113289 AACAGAGAGCACACACAA-TGCT
1 AACAGAGAGCACA-A-AAGTACT
113311 AAACAGAGAGCACACAAAGTACT
1 -AACAGAGAGCACA-AAAGTACT
* *
113334 AATCAGAAAGCACACAAAGTGCT
1 AA-CAGAGAGCACA-AAAGTACT
113357 AATCAGAGAGCACA
1 AA-CAGAGAGCACA
113371 CACAGTGCTA
Statistics
Matches: 87, Mismatches: 10, Indels: 18
0.76 0.09 0.16
Matches are distributed among these distances:
21 11 0.13
22 7 0.08
23 51 0.59
24 1 0.01
25 15 0.17
26 2 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (21 bp):
AACAGAGAGCACAAAAGTACT
Found at i:113315 original size:23 final size:23
Alignment explanation
Indices: 113289--113414 Score: 123
Period size: 23 Copynumber: 5.4 Consensus size: 23
113279 AGTGTTGGAT
113289 AACAGAGAGCACACACAATGCTA
1 AACAGAGAGCACACACAATGCTA
*
113312 AACAGAGAGCACACA-AAGTACTA
1 AACAGAGAGCACACACAA-TGCTA
* *
113335 ATCAGAAAGCACACA-AAGTGCTA
1 AACAGAGAGCACACACAA-TGCTA
* *
113358 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAATGCT-A
* *
113382 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAATGCTA
113406 AACAGAGAG
1 AACAGAGAG
113415 AGCGCTAGTG
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
22 2 0.02
23 66 0.73
24 3 0.03
25 16 0.18
26 3 0.03
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAATGCTA
Found at i:113320 original size:48 final size:45
Alignment explanation
Indices: 113264--113414 Score: 137
Period size: 48 Copynumber: 3.2 Consensus size: 45
113254 CCAAAGTACT
*
113264 AACAGAGAGCACATAAGTGTTGGATAACAGAGAGCACACACAATGCTA
1 AACAGAGAGCACACAAGTG-T--ATAACAGAGAGCACACACAATGCTA
* *
113312 AACAGAGAGCACACAA-AGTACTAATCAGAAAGCACACA-AAGTGCTA
1 AACAGAGAGCACACAAGTGTA-TAA-CAGAGAGCACACACAA-TGCTA
* * *
113358 ATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGAC-GTGCTA
1 AACAGAGAGCACACA-AGTG-T-ATAACAGAGAGCAC-ACACAATGCTA
113406 AACAGAGAG
1 AACAGAGAG
113415 AGCGCTAGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
44 1 0.01
45 5 0.06
46 32 0.38
47 2 0.02
48 38 0.45
49 6 0.07
50 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (45 bp):
AACAGAGAGCACACAAGTGTATAACAGAGAGCACACACAATGCTA
Found at i:113357 original size:46 final size:47
Alignment explanation
Indices: 113290--113414 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 47
113280 GTGTTGGATA
113290 ACAGAGAGCACACACAA-TGCTAAACAGAGAGCACACAAAGTACTAAT
1 ACAGAGAGCACACA-AAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * *
113337 -CAGAAAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* *
113383 AACAGAGAGCACGA-GACGTGCTAAACAGAGAG
1 -ACAGAGAGCAC-ACAAAGTGCTAAACAGAGAG
113415 AGCGCTAGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.03
46 39 0.59
48 24 0.36
49 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (47 bp):
ACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:113364 original size:69 final size:69
Alignment explanation
Indices: 113242--113394 Score: 186
Period size: 69 Copynumber: 2.2 Consensus size: 69
113232 TATACGGAAC
* * * *
113242 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGTTGGATAACAGAGAGCACACACAA
1 AAACAGAGAGCACCAAAGTACTAACAGAAAGCACAAAAGTGCT-GATAACAGAGAGCACACACAA
113307 TGCT-
65 TGCTA
*
113311 AAACAGAGAGCACACAAAGTACTAATCAGAAAGCACACAAAGTGCT-A-ATCAGAGAGCACACAC
1 AAACAGAGAGCAC-CAAAGTACTAA-CAGAAAGCACA-AAAGTGCTGATAACAGAGAGCACACAC
*
113374 AGTGCTA
63 AATGCTA
113381 ATAACAGAGAGCAC
1 A-AACAGAGAGCAC
113395 GAGACGTGCT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
69 32 0.44
70 13 0.18
71 22 0.30
72 6 0.08
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (69 bp):
AAACAGAGAGCACCAAAGTACTAACAGAAAGCACAAAAGTGCTGATAACAGAGAGCACACACAAT
GCTA
Found at i:116527 original size:29 final size:29
Alignment explanation
Indices: 116440--116528 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
116430 TTGAGTTCCT
116440 TAAAAATTGGTAAAAAAATATTTAACCTA
1 TAAAAATTGGTAAAAAAATATTTAACCTA
* *
116469 T-AAAA--GTTAAAAAAAT-TTTGAGCCCT-
1 TAAAAATTGGTAAAAAAATATTT-A-ACCTA
*
116495 TAAAAATTGGTAAAAAAATATTTAACATA
1 TAAAAATTGGTAAAAAAATATTTAACCTA
116524 TAAAA
1 TAAAA
116529 GTTAAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
25 3 0.06
26 12 0.25
27 7 0.15
28 6 0.12
29 17 0.35
30 3 0.06
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (29 bp):
TAAAAATTGGTAAAAAAATATTTAACCTA
Found at i:116575 original size:57 final size:57
Alignment explanation
Indices: 116420--116559 Score: 232
Period size: 55 Copynumber: 2.5 Consensus size: 57
116410 AAAAACTTTA
* *
116420 AAAAAAAATTTTGAGTTCCTTAAAAATTGGTAAAAAAATATTTAACCTATAAAAGTT
1 AAAAAAAATTTTGAGCTCCTTAAAAATTGGTAAAAAAATATTTAACATATAAAAGTT
116477 -AAAAAAATTTTGAGC-CCTTAAAAATTGGTAAAAAAATATTTAACATATAAAAGTT
1 AAAAAAAATTTTGAGCTCCTTAAAAATTGGTAAAAAAATATTTAACATATAAAAGTT
116532 AAAAAAAATTTTG-GACTCCTTAAAAATT
1 AAAAAAAATTTTGAG-CTCCTTAAAAATT
116560 AAAAAAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
55 40 0.51
56 27 0.35
57 11 0.14
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (57 bp):
AAAAAAAATTTTGAGCTCCTTAAAAATTGGTAAAAAAATATTTAACATATAAAAGTT
Found at i:136139 original size:29 final size:26
Alignment explanation
Indices: 136064--136143 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
136054 AAATTTGTTT
* *
136064 TCAACGTCTATTCATTTAACCAGTGG
1 TCAATGTCTATCCATTTAACCAGTGG
* *
136090 TCGATGTCTA-CCAATTCAACCAGTGG
1 TCAATGTCTATCC-ATTTAACCAGTGG
136116 TCAAAAATGTCTATCCATTTAACCAGTG
1 TC---AATGTCTATCCATTTAACCAGTG
136144 ATCGCCGTCG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
25 1 0.02
26 22 0.51
29 18 0.42
30 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (26 bp):
TCAATGTCTATCCATTTAACCAGTGG
Found at i:138271 original size:19 final size:20
Alignment explanation
Indices: 138242--138279 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
138232 CTTTTAATTT
138242 TTTTATAATTTCTTAATATG
1 TTTTATAATTTCTTAATATG
*
138262 TTTTAT-ATTTTTTAATAT
1 TTTTATAATTTCTTAATAT
138280 TTTATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTATAATTTCTTAATATG
Found at i:138281 original size:10 final size:10
Alignment explanation
Indices: 138233--138294 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
138223 CCTGAAAATC
138233 TTTTAAT-TT
1 TTTTAATATT
138242 TTTT-ATAATT
1 TTTTAAT-ATT
* *
138252 TCTTAATATG
1 TTTTAATATT
138262 TTTT-ATATT
1 TTTTAATATT
138271 TTTTAATATT
1 TTTTAATATT
138281 TTATGTAATATT
1 TT-T-TAATATT
138293 TT
1 TT
138295 AATTTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 2 0.05
9 12 0.28
10 17 0.40
11 3 0.07
12 9 0.21
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTAATATT
Found at i:138303 original size:29 final size:28
Alignment explanation
Indices: 138233--138304 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
138223 CCTGAAAATC
*
138233 TTTTAATTTTTTT-ATAATTTCTTAATA
1 TTTTAATTTTTTTAATAATTTATTAATA
* *
138260 TGTTTTATATTTTTTAATATTTTATGTAATA
1 T-TTTAAT-TTTTTTAATAATTTAT-TAATA
138291 TTTTAATTTTTTTA
1 TTTTAATTTTTTTA
138305 GATGATAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 1 0.03
28 5 0.14
29 13 0.35
30 12 0.32
31 6 0.16
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTAATTTTTTTAATAATTTATTAATA
Found at i:139730 original size:2 final size:2
Alignment explanation
Indices: 139723--139760 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
139713 NNNNNNNNNN
139723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
139761 TAATGACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148006 original size:22 final size:20
Alignment explanation
Indices: 147955--148008 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
147945 GAGAAAATTT
*
147955 AGAAGGTTTGAGAGAGTTTA
1 AGAAGGTTTGAGAGAGTTGA
147975 A-AAGTGTTTGAGAGAGTTGA
1 AGAAG-GTTTGAGAGAGTTGA
147995 GAGAAGGATTTGAG
1 -AGAAGG-TTTGAG
148009 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
21 2 0.07
22 9 0.31
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (20 bp):
AGAAGGTTTGAGAGAGTTGA
Found at i:150631 original size:13 final size:13
Alignment explanation
Indices: 150606--150647 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
150596 TTAAATAATT
150606 AATTAAT-AGAATC
1 AATTAATCA-AATC
*
150619 AATTGATCAAATC
1 AATTAATCAAATC
150632 AATTAATCAAATC
1 AATTAATCAAATC
150645 AAT
1 AAT
150648 CATTATAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 25 0.96
14 1 0.04
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (13 bp):
AATTAATCAAATC
Found at i:152303 original size:26 final size:25
Alignment explanation
Indices: 152274--152324 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
152264 TAAAAGATAT
152274 TTAAAT-AATTTTAGCAATTCCTAAAA
1 TTAAATCAATTTTAG-AATT-CTAAAA
* *
152300 TTAATTCTATTTTAGAATTCTAAAA
1 TTAAATCAATTTTAGAATTCTAAAA
152325 AAAAAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 9 0.41
27 7 0.32
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (25 bp):
TTAAATCAATTTTAGAATTCTAAAA
Found at i:153085 original size:16 final size:16
Alignment explanation
Indices: 153046--153087 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
153036 TAAAAAACAA
153046 AAACAT-AAATATAAAT
1 AAACATGAAA-ATAAAT
*
153062 AGACATGAAAATAAAT
1 AAACATGAAAATAAAT
*
153078 AAAGATGAAA
1 AAACATGAAA
153088 TAAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (16 bp):
AAACATGAAAATAAAT
Found at i:153782 original size:21 final size:21
Alignment explanation
Indices: 153753--153821 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
153743 AAAAACATAT
153753 TTTTATTTTTAAAAATTTAAAC
1 TTTT-TTTTTAAAAATTTAAAC
** *
153775 TTTTTTTTTTTAAATTCAAAAC
1 TTTTTTTTTAAAAATT-TAAAC
* *
153797 -TTTGTTTAAAAAATTTAAAC
1 TTTTTTTTTAAAAATTTAAAC
153817 TTTTT
1 TTTTT
153822 CCTTCAAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (21 bp):
TTTTTTTTTAAAAATTTAAAC
Found at i:153850 original size:95 final size:93
Alignment explanation
Indices: 153703--153886 Score: 257
Period size: 95 Copynumber: 2.0 Consensus size: 93
153693 AAGAAAAATC
*
153703 AAACTTGGTTTAAAAATTTAAACTTTTTTTAAATGACTAAAAAAACATATTTTTATTTTTAAAAA
1 AAACTTGGTTTAAAAATTTAAACTTTTTTTAAATGACTAAAAAAACAAATTTTTATTTTTAAAAA
**
153768 TTTAAACTTT-T-TTTTT-TTAAATTCA
66 CCTAAACTTTCTGTTTTTATTAAATTCA
* *
153793 AAACTTTGTTTAAAAAATTTAAACTTTTTCCTTCAAAATGACTAAAAAAATAAATTTTTATTTTT
1 AAACTTGGTTT-AAAAATTTAAACTTTTT--TT--AAATGACTAAAAAAACAAATTTTTATTTTT
153858 AAAAACCTAAACTTTCTGTTTTTATTAAA
61 AAAAACCTAAACTTTCTGTTTTTATTAAA
153887 GAAAATCACT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
90 10 0.12
91 17 0.21
93 2 0.02
95 41 0.51
96 1 0.01
97 5 0.06
98 5 0.06
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (93 bp):
AAACTTGGTTTAAAAATTTAAACTTTTTTTAAATGACTAAAAAAACAAATTTTTATTTTTAAAAA
CCTAAACTTTCTGTTTTTATTAAATTCA
Found at i:153919 original size:19 final size:20
Alignment explanation
Indices: 153877--153921 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
153867 AACTTTCTGT
**
153877 TTTTATTAAAGAAAATCACTA
1 TTTT-TTAAAGAAAATCAAAA
153898 TTTTTTAAA-AAAATCAAAA
1 TTTTTTAAAGAAAATCAAAA
153917 TTTTT
1 TTTTT
153922 ATTTCTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 5 0.23
21 4 0.18
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTTTTAAAGAAAATCAAAA
Found at i:153921 original size:20 final size:22
Alignment explanation
Indices: 153876--153924 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
153866 AAACTTTCTG
**
153876 TTTTTATTAAAGAAAATCACTA
1 TTTTTATTAAAGAAAATCAAAA
153898 -TTTT-TTAAA-AAAATCAAAA
1 TTTTTATTAAAGAAAATCAAAA
153917 TTTTTATT
1 TTTTTATT
153925 TCTAAATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 8 0.35
20 9 0.39
21 6 0.26
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTTATTAAAGAAAATCAAAA
Found at i:157590 original size:20 final size:21
Alignment explanation
Indices: 157565--157604 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
157555 AAGCAAAAGT
157565 AAAAC-AAAAACAATGAAAAC
1 AAAACAAAAAACAATGAAAAC
*
157585 AAAACAAAAAATAATGAAAA
1 AAAACAAAAAACAATGAAAA
157605 ATTCCTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.78, C:0.10, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAACAAAAAACAATGAAAAC
Found at i:165571 original size:18 final size:18
Alignment explanation
Indices: 165548--165584 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
165538 TTTGTGATCA
165548 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
165566 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
165584 A
1 A
165585 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:169145 original size:15 final size:16
Alignment explanation
Indices: 169125--169159 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
169115 ATAACATATA
169125 TTTCTCTTT-TCTTCT
1 TTTCTCTTTCTCTTCT
169140 TTTCTCTTTCCTCTTCT
1 TTTCTCTTT-CTCTTCT
169157 TTT
1 TTT
169160 TTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTCTTTCTCTTCT
Found at i:169762 original size:17 final size:17
Alignment explanation
Indices: 169742--169795 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
169732 ACTACAATGC
*
169742 AAATGTAATAACAAATA
1 AAATGCAATAACAAATA
* *
169759 AAATGCAGTGACAAATAA
1 AAATGCAATAACAAAT-A
* *
169777 AAATGCAATGACAACTA
1 AAATGCAATAACAAATA
169794 AA
1 AA
169796 TGCTATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (17 bp):
AAATGCAATAACAAATA
Found at i:169781 original size:18 final size:18
Alignment explanation
Indices: 169742--169795 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
169732 ACTACAATGC
* *
169742 AAATGTAATAACAAAT-A
1 AAATGCAATGACAAATAA
*
169759 AAATGCAGTGACAAATAA
1 AAATGCAATGACAAATAA
*
169777 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
169795 A
1 A
169796 TGCTATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:180456 original size:17 final size:17
Alignment explanation
Indices: 180417--180470 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
180407 ATGCATAGCA
* *
180417 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
180435 TTTATTTGTCACTGCAT
1 TTTATTTGTCACTGCAT
* *
180452 TTTATTTGTTACTACAT
1 TTTATTTGTCACTGCAT
180469 TT
1 TT
180471 GCATTGTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:190514 original size:18 final size:18
Alignment explanation
Indices: 190450--190517 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
190440 TGTCACCACA
*
190450 TTCCCTTTGTCATTGCAT
1 TTCCATTTGTCATTGCAT
** * *
190468 TTTTAATTGTCACTGCAT
1 TTCCATTTGTCATTGCAT
* *
190486 GTGCA-TTGTCATTGCAT
1 TTCCATTTGTCATTGCAT
190503 TTCCATTTGTCATTG
1 TTCCATTTGTCATTG
190518 TAAATTAATG
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
17 14 0.37
18 24 0.63
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.49
Consensus pattern (18 bp):
TTCCATTTGTCATTGCAT
Found at i:193800 original size:24 final size:24
Alignment explanation
Indices: 193767--193826 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
193757 CAAGTAAATA
* *
193767 AACTATCGATACTTTTAAGTGTAG
1 AACTAACGATACTTTTAAGTGCAG
*
193791 AACTACCGATACTTTTAAGTGCAG
1 AACTAACGATACTTTTAAGTGCAG
193815 AACTAACGATAC
1 AACTAACGATAC
193827 CTACTATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (24 bp):
AACTAACGATACTTTTAAGTGCAG
Found at i:194410 original size:25 final size:25
Alignment explanation
Indices: 194382--194451 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
194372 CTCTAGAATT
194382 TTAGCTCTTACGAGCCCAGACAGAA
1 TTAGCTCTTACGAGCCCAGACAGAA
194407 TTAGCTCTTACGAGCCCAGACAGAA
1 TTAGCTCTTACGAGCCCAGACAGAA
*
194432 TTAGCTCTTATGAGCCCAGA
1 TTAGCTCTTACGAGCCCAGA
194452 ATTAGCTCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (25 bp):
TTAGCTCTTACGAGCCCAGACAGAA
Found at i:194453 original size:21 final size:23
Alignment explanation
Indices: 194382--194463 Score: 105
Period size: 25 Copynumber: 3.5 Consensus size: 23
194372 CTCTAGAATT
194382 TTAGCTCTTACGAGCCCAGACAGAA
1 TTAGCTCTTACGAGCCC--ACAGAA
194407 TTAGCTCTTACGAGCCCAGACAGAA
1 TTAGCTCTTACGAGCCC--ACAGAA
*
194432 TTAGCTCTTATGAG-CC-CAGAA
1 TTAGCTCTTACGAGCCCACAGAA
194453 TTAGCTCTTAC
1 TTAGCTCTTAC
194464 AAGTCCAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 15 0.27
24 2 0.04
25 38 0.69
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (23 bp):
TTAGCTCTTACGAGCCCACAGAA
Found at i:198746 original size:21 final size:21
Alignment explanation
Indices: 198722--198775 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
198712 TGAGGCAGTA
198722 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* * *
198743 CTACTGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
198764 CTACCGATACAA
1 CTACCGATACAA
198776 AAAAATCTGG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:202721 original size:36 final size:36
Alignment explanation
Indices: 202681--202874 Score: 255
Period size: 36 Copynumber: 5.4 Consensus size: 36
202671 TGATGATTAT
* * **
202681 TGTGAAAGTAAATATGTGGGCATGTTATTCATGTCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATACCA
*
202717 TGTGACAGTAAATGTGTGGGTATGTTATTCATACCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATACCA
* * *
202753 TGAGACAGTATATATGTGGATATGTTATTCATACCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATACCA
* * **
202789 TGTGACAATAAATATGTGGGCATGTTATTCATGTCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATACCA
*
202825 TG-GACAGTAAAAATGTGGGTATGTTATTCATACCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATACCA
*
202860 TGTGACAGTGAATAT
1 TGTGACAGTAAATAT
202875 ATTGTGTTGA
Statistics
Matches: 134, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
35 30 0.22
36 104 0.78
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (36 bp):
TGTGACAGTAAATATGTGGGTATGTTATTCATACCA
Found at i:203365 original size:59 final size:59
Alignment explanation
Indices: 203298--203598 Score: 406
Period size: 59 Copynumber: 5.1 Consensus size: 59
203288 TGTGATTATA
* * * *
203298 TGATTAAATGTGACTAAATGTGATTAATATGTGATGCGATAAATACTGAAATATTCATA
1 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATG
* * * *
203357 TGATTAAATATAACTAGATGTGATTAATATGTGATGTGATAAATGTTGAAATATTAATG
1 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATG
* *
203416 TGATTATATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTAATG
1 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATG
* * *
203475 TGATTATATGTGACTAAATGTGATTAATATGTGATGTAATAAATGCTGAAATATTCATG
1 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATG
* * * * * * * *
203534 TGACT-AATGTGATTAAATGTGATTAATATGTGTTGTGTTAAATGCTTAAGTACTCATG
1 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATG
203592 TGATTAA
1 TGATTAA
203599 TGCGATTAAT
Statistics
Matches: 216, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
58 49 0.23
59 167 0.77
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (59 bp):
TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTAATG
Found at i:203428 original size:10 final size:10
Alignment explanation
Indices: 203409--203509 Score: 60
Period size: 10 Copynumber: 9.2 Consensus size: 10
203399 ATGTTGAAAT
203409 ATTA-ATGTG
1 ATTATATGTG
203418 ATTATATGTG
1 ATTATATGTG
* *
203428 ACTAAATGTG
1 ATTATATGTG
203438 ATTAATATGTG
1 ATT-ATATGTG
203449 ATGTGATAAATGTTG
1 AT-T-AT--ATG-TG
*
203464 AAATATTAATGTG
1 -ATTA-T-ATGTG
203477 ATTATATGTG
1 ATTATATGTG
* *
203487 ACTAAATGTG
1 ATTATATGTG
203497 ATTAATATGTG
1 ATT-ATATGTG
203508 AT
1 AT
203510 GTAATAAATG
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
9 4 0.06
10 30 0.42
11 17 0.24
12 6 0.08
13 2 0.03
14 8 0.11
15 4 0.06
16 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.42
Consensus pattern (10 bp):
ATTATATGTG
Found at i:203428 original size:33 final size:34
Alignment explanation
Indices: 203390--203495 Score: 124
Period size: 33 Copynumber: 3.4 Consensus size: 34
203380 TTAATATGTG
203390 ATGTGA-TAAATGTTGAAATATTAATGTGATTAT
1 ATGTGACTAAATGTTGAAATATTAATGTGATTAT
* *
203423 ATGTGACTAAATG-TG----ATTAATATG--T-G
1 ATGTGACTAAATGTTGAAATATTAATGTGATTAT
203449 ATGTGA-TAAATGTTGAAATATTAATGTGATTAT
1 ATGTGACTAAATGTTGAAATATTAATGTGATTAT
203482 ATGTGACTAAATGT
1 ATGTGACTAAATGT
203496 GATTAATATG
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
25 6 0.10
26 8 0.14
27 1 0.02
29 8 0.14
30 8 0.14
32 1 0.02
33 14 0.24
34 13 0.22
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.41
Consensus pattern (34 bp):
ATGTGACTAAATGTTGAAATATTAATGTGATTAT
Found at i:203452 original size:26 final size:24
Alignment explanation
Indices: 203423--203498 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
203413 ATGTGATTAT
203423 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGA-TAAATGTGA-TAATATGTG
*
203449 ATGTGATAAATGTTGA-AATAT-TA
1 ATGTGATAAATG-TGATAATATGTG
*
203472 ATGTGATTATATGTGACTAA-ATGTG
1 ATGTGA-TAAATGTGA-TAATATGTG
203497 AT
1 AT
203499 TAATATGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
23 10 0.24
24 12 0.29
25 11 0.26
26 9 0.21
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (24 bp):
ATGTGATAAATGTGATAATATGTG
Found at i:203478 original size:23 final size:23
Alignment explanation
Indices: 203418--203487 Score: 61
Period size: 26 Copynumber: 2.8 Consensus size: 23
203408 TATTAATGTG
203418 ATTATATGTGACTAAATGTGATTAAT
1 ATTA-ATGTGA-TAAATGTGA-TAAT
*
203444 ATGTGATGTGATAAATGTTGA-AAT
1 AT-TAATGTGATAAATG-TGATAAT
*
203468 ATTAATGTGATTATATGTGA
1 ATTAATGTGA-TAAATGTGA
203488 CTAAATGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 10 0.26
24 10 0.26
25 6 0.16
26 11 0.29
27 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.41
Consensus pattern (23 bp):
ATTAATGTGATAAATGTGATAAT
Found at i:207734 original size:3 final size:3
Alignment explanation
Indices: 207726--207779 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
207716 CCTAGTTGCT
* *
207726 AGA AGA AGA AGA AGCA A-A AG- AGA AGA A-A AAA AAA AGA AGA AGA
1 AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
207769 AAA AGA AGA AG
1 AGA AGA AGA AG
207780 TATAAAAGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.14
3 36 0.82
4 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:207751 original size:17 final size:15
Alignment explanation
Indices: 207728--207779 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
207718 TAGTTGCTAG
**
207728 AAGAAGAAGAAGCAA
1 AAGAAGAAGAAAAAA
207743 AAG-AGAAGAAAAAA
1 AAGAAGAAGAAAAAA
*
207757 AA-AAGAAGAAGAAA
1 AAGAAGAAGAAAAAA
207771 AAGAAGAAG
1 AAGAAGAAG
207780 TATAAAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 23 0.72
15 9 0.28
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAAAA
Found at i:208757 original size:31 final size:31
Alignment explanation
Indices: 208706--208765 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
208696 CCCCCATTTT
*
208706 TTTATTATTTTCCCTCCAAAATTTTACTCTC
1 TTTATTACTTTCCCTCCAAAATTTTACTCTC
208737 TTTATTTACTTTCCCT-CAAAATTTTACTC
1 TTTA-TTACTTTCCCTCCAAAATTTTACTC
208766 CCCAAAACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTATTACTTTCCCTCCAAAATTTTACTCTC
Found at i:208912 original size:31 final size:34
Alignment explanation
Indices: 208884--208949 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
208874 TAATAAATTT
208884 ATTT-ATA-TCTACTATTTATATTATTAAATTAA
1 ATTTCATATTCTACTATTTATATTATTAAATTAA
*
208916 ATTTCATATTTTGTACTATTTATATTATTAAATT
1 ATTTCATA--TTCTACTATTTATATTATTAAATT
208950 GTTTAATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 4 0.14
33 3 0.10
36 22 0.76
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (34 bp):
ATTTCATATTCTACTATTTATATTATTAAATTAA
Found at i:214283 original size:41 final size:42
Alignment explanation
Indices: 214209--214287 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 42
214199 ATTATTCACA
* *
214209 CAAAATAAATGAAGCTTCAAAGTATGAGTTTAAACTGCTCAT
1 CAAAATAAATGAAGCTCCAAAGTATGAGCTTAAACTGCTCAT
* * *
214251 CAAAA-AAATGATGCTCCTAAGTGTGAGCTTAAACTGC
1 CAAAATAAATGAAGCTCCAAAGTATGAGCTTAAACTGC
214288 AAATCCAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 27 0.84
42 5 0.16
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (42 bp):
CAAAATAAATGAAGCTCCAAAGTATGAGCTTAAACTGCTCAT
Found at i:214888 original size:33 final size:31
Alignment explanation
Indices: 214851--214914 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
214841 CTGTAATTAG
* *
214851 TGTAAAAATAATAATGACGATAAAATTAAATAT
1 TGTAAAAATAAT-ATAACG-TAAAATAAAATAT
* *
214884 TGTAACAATACTATAACGTAAAATAAAATAT
1 TGTAAAAATAATATAACGTAAAATAAAATAT
214915 AAACTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 12 0.44
32 5 0.19
33 10 0.37
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (31 bp):
TGTAAAAATAATATAACGTAAAATAAAATAT
Found at i:235818 original size:19 final size:19
Alignment explanation
Indices: 235794--235832 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
235784 ACATGGAGTT
235794 AGAAAAATGGAACGCTTTC
1 AGAAAAATGGAACGCTTTC
235813 AGAAAAATGGAACGCTTTC
1 AGAAAAATGGAACGCTTTC
235832 A
1 A
235833 CATTTGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (19 bp):
AGAAAAATGGAACGCTTTC
Found at i:246906 original size:15 final size:15
Alignment explanation
Indices: 246883--246916 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
246873 ACATTTTCAA
* *
246883 TTTTTCTTTTATTTG
1 TTTTACTTTTACTTG
246898 TTTTACTTTTACTTG
1 TTTTACTTTTACTTG
246913 TTTT
1 TTTT
246917 GTTTCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTACTTTTACTTG
Found at i:256537 original size:111 final size:111
Alignment explanation
Indices: 256343--256565 Score: 410
Period size: 111 Copynumber: 2.0 Consensus size: 111
256333 TAAGACTATA
256343 TAGAGTTTAAATTCATCAGAACTCTATCTTATAAATAATCTTGATTATGAGCCATTGATGTAATT
1 TAGAGTTTAAATTCATCAGAACTCTATCTTATAAATAATCTTGATTATGAGCCATTGATGTAATT
* *
256408 CATTTTGTACCTTGAATGTAGAGGAGCTCAATTATAGATAGAGGCC
66 CATTCTGTACCTTGAATGTAGAAGAGCTCAATTATAGATAGAGGCC
* *
256454 TAGAGTTTAAATTCATTAGAACTCTATCTTGTAAATAATCTTGATTATGAGCCATTGATGTAATT
1 TAGAGTTTAAATTCATCAGAACTCTATCTTATAAATAATCTTGATTATGAGCCATTGATGTAATT
256519 CATTCTGTACCTTGAATGTAGAAGAGCTCAATTATAGATAGAGGCC
66 CATTCTGTACCTTGAATGTAGAAGAGCTCAATTATAGATAGAGGCC
256565 T
1 T
256566 TTCCCATCTC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (111 bp):
TAGAGTTTAAATTCATCAGAACTCTATCTTATAAATAATCTTGATTATGAGCCATTGATGTAATT
CATTCTGTACCTTGAATGTAGAAGAGCTCAATTATAGATAGAGGCC
Found at i:259954 original size:28 final size:28
Alignment explanation
Indices: 259871--259956 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
259861 TACTAGTAAC
* * *
259871 AAGCATGACTTTTGGGTCAACAGGGAGC
1 AAGCATGACCTTTGGGTCAACAAGGAGT
259899 AAGCATGACCTTTGGGTCAACAAGGAGT
1 AAGCATGACCTTTGGGTCAACAAGGAGT
259927 AAGCATGACCTTTGGGTCAACAAGGAGT
1 AAGCATGACCTTTGGGTCAACAAGGAGT
259955 AA
1 AA
259957 ATCGGATGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (28 bp):
AAGCATGACCTTTGGGTCAACAAGGAGT
Found at i:262071 original size:11 final size:11
Alignment explanation
Indices: 262055--262123 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
262045 GACGATGATT
262055 ATAATTTTAAA
1 ATAATTTTAAA
262066 ATAATTTT---
1 ATAATTTTAAA
262074 AT-ATTTTAAAAA
1 ATAATTTT--AAA
262086 ATAATTTTAAA
1 ATAATTTTAAA
*
262097 TTAATTTT--A
1 ATAATTTTAAA
262106 ATAATTTTAAA
1 ATAATTTTAAA
*
262117 ATCATTT
1 ATAATTT
262124 GTTGATGTGG
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
7 5 0.11
8 2 0.04
9 8 0.17
11 25 0.53
12 2 0.04
13 5 0.11
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:262085 original size:19 final size:20
Alignment explanation
Indices: 262053--262098 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
262043 ATGACGATGA
262053 TTATAATTTT-AAAATAATT
1 TTATAATTTTAAAAATAATT
262072 TTAT-ATTTTAAAAAATAATT
1 TTATAATTTT-AAAAATAATT
262092 TTA-AATT
1 TTATAATT
262099 AATTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATAATTTTAAAAATAATT
Found at i:262093 original size:31 final size:33
Alignment explanation
Indices: 262055--262117 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 33
262045 GACGATGATT
262055 ATAATTTTAAAATAATTTT-AT-ATTTTAAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTAAAAA
*
262086 ATAATTTTAAATTAATTTTAATAATTTTAAAA
1 ATAATTTTAAAATAATTTTAATAATTTTAAAA
262118 TCATTTGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 18 0.62
32 2 0.07
33 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATAATTTTAAAATAATTTTAATAATTTTAAAAA
Found at i:262123 original size:20 final size:20
Alignment explanation
Indices: 262085--262123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
262075 TATTTTAAAA
*
262085 AATAATTTTAAATTAATTTT
1 AATAATTTTAAAATAATTTT
*
262105 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
262124 GTTGATGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:268742 original size:28 final size:28
Alignment explanation
Indices: 268702--268757 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
268692 CTGGTAATAG
* *
268702 GCATGACTTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGGTCAACAAGGAGTAA
268730 GCATGACCTTTGGGTCAACAAGGAGTAA
1 GCATGACCTTTGGGTCAACAAGGAGTAA
268758 ATTGGATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (28 bp):
GCATGACCTTTGGGTCAACAAGGAGTAA
Found at i:270582 original size:20 final size:20
Alignment explanation
Indices: 270557--270606 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
270547 TCATTAAGCT
*
270557 TTAATTAACCCTTTTTAGT-C
1 TTAATTAACCCTATTTA-TAC
*
270577 TTAATTAAACCTATTTATAC
1 TTAATTAACCCTATTTATAC
270597 TTAATATAAC
1 TTAAT-TAAC
270607 TCATGCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.46
Consensus pattern (20 bp):
TTAATTAACCCTATTTATAC
Found at i:272965 original size:52 final size:52
Alignment explanation
Indices: 272826--273014 Score: 229
Period size: 52 Copynumber: 3.7 Consensus size: 52
272816 TCATTCACAA
* * * * * *
272826 ACTCACGATAACACATAGCCACCAGACCTCATAATCCGCAAGGGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTCTTAATCCGTAAAGGATTCATAT
** *
272878 ACTCATAAT-A-ACACAGTCATCAGACCTCTTAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTCTTAATCCGTAAAGGATTCATAT
* *
272928 ACTCACGATGACACAGAGTCATCAAACCTCTTAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTCTTAATCCGTAAAGGATTCATAT
* * * *
272980 ACTCGCGATGATACATAGTCATCGGACCTTTTAAT
1 ACTCACGATGACACATAGTCATCAGACCTCTTAAT
273015 TTGTTTATGG
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
50 41 0.35
51 2 0.02
52 74 0.63
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCAGACCTCTTAATCCGTAAAGGATTCATAT
Found at i:280131 original size:17 final size:17
Alignment explanation
Indices: 280095--280127 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
280085 TCTGGTATAG
280095 GTTTCTTATTTGCTTTT
1 GTTTCTTATTTGCTTTT
*
280112 GTTTCTT-TTTTCTTTT
1 GTTTCTTATTTGCTTTT
280128 TGTTCCCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.76
Consensus pattern (17 bp):
GTTTCTTATTTGCTTTT
Found at i:282889 original size:28 final size:28
Alignment explanation
Indices: 282840--282895 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
282830 TCAATTAAGT
*
282840 GGTAAATTTACGGTAATAAAAATGTATA
1 GGTAAATTTAAGGTAATAAAAATGTATA
* *
282868 GGTAAATTTAAGGTGATTAAAATGTATA
1 GGTAAATTTAAGGTAATAAAAATGTATA
282896 AAAAAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.34
Consensus pattern (28 bp):
GGTAAATTTAAGGTAATAAAAATGTATA
Found at i:282902 original size:28 final size:28
Alignment explanation
Indices: 282843--282902 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
282833 ATTAAGTGGT
* ***
282843 AAATTTACGGTAATAAAAATGTATAGGT
1 AAATTTAAGGTAATAAAAATGTATAAAA
* *
282871 AAATTTAAGGTGATTAAAATGTATAAAA
1 AAATTTAAGGTAATAAAAATGTATAAAA
282899 AAAT
1 AAAT
282903 ATGGTAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.32
Consensus pattern (28 bp):
AAATTTAAGGTAATAAAAATGTATAAAA
Found at i:293356 original size:2 final size:2
Alignment explanation
Indices: 293349--293375 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
293339 CTTACATTAA
293349 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
293376 TTTTGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:298744 original size:29 final size:29
Alignment explanation
Indices: 298659--298847 Score: 115
Period size: 27 Copynumber: 6.7 Consensus size: 29
298649 CGTCCTTTCC
* **
298659 AACCTTTTCATTTATTATCCTTTTAGATAT
1 AACCTTTTCAATTA-TATCCTTTCGGATAT
* * *
298689 AACCTTTTCAA--ATATCGTCTCGAATAT
1 AACCTTTTCAATTATATCCTTTCGGATAT
298716 AACCTTTTCAATTATATCCTTTCGGATAT
1 AACCTTTTCAATTATATCCTTTCGGATAT
* ** *
298745 --CCCTTTC-CGTAGTATCCTTACGGATAT
1 AACCTTTTCAATTA-TATCCTTTCGGATAT
* * * * *
298772 AACATTTTCAATAATATACATACGGATAT
1 AACCTTTTCAATTATATCCTTTCGGATAT
* * *
298801 -TCCTTTTC-ATTGATTTCCTTGCGGATAT
1 AACCTTTTCAATT-ATATCCTTTCGGATAT
* *
298829 -CCCTTTTCAATAATATCCT
1 AACCTTTTCAATTATATCCT
298848 AATTGATATT
Statistics
Matches: 121, Mismatches: 30, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
26 2 0.02
27 43 0.36
28 32 0.26
29 33 0.27
30 11 0.09
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.43
Consensus pattern (29 bp):
AACCTTTTCAATTATATCCTTTCGGATAT
Found at i:298772 original size:56 final size:57
Alignment explanation
Indices: 298712--298955 Score: 174
Period size: 56 Copynumber: 4.3 Consensus size: 57
298702 ATCGTCTCGA
* * *
298712 ATATAACCTTTTCAATTATATCCTTTCGGATATCCCTTTCCGTAG-TATCCTTACGG
1 ATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTCCATAGATATCCTTACGG
* * * * * * * *
298768 ATATAACATTTTCAATAATATACATACGGATATTCCTTTTCATTGATTTCCTTGCGG
1 ATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTCCATAGATATCCTTACGG
* * ** * * * * *
298825 ATAT-CCCTTTTCAATAATATCCTAATTGATATTCCTTTTCATTGATATCATTGC-G
1 ATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTCCATAGATATCCTTACGG
* * * * * * * *
298880 A-ATATCCTTTTTCAATAATATCCTAACGAATATTCCTTTTCATTGATATCCTTGCGA
1 ATATAACC-TTTTCAATAATATCCTTACGGATATCCCTTTCCATAGATATCCTTACGG
*
298937 ATAT-CCCTTTTCACATAAT
1 ATATAACCTTTTCA-ATAAT
298956 TTTAGATCAA
Statistics
Matches: 155, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
54 2 0.01
55 4 0.03
56 126 0.81
57 21 0.14
58 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (57 bp):
ATATAACCTTTTCAATAATATCCTTACGGATATCCCTTTCCATAGATATCCTTACGG
Found at i:298825 original size:28 final size:28
Alignment explanation
Indices: 298797--298949 Score: 150
Period size: 28 Copynumber: 5.5 Consensus size: 28
298787 ATACATACGG
* *
298797 ATATTCCTTTTCATTGATTTCCTTGCGG
1 ATATTCCTTTTCATTGATATCCTTGCGA
* * * *
298825 ATATCCCTTTTCAATAATATCCTAAT-TG-
1 ATATTCCTTTTCATTGATATCCT--TGCGA
*
298853 ATATTCCTTTTCATTGATATCATTGCGA
1 ATATTCCTTTTCATTGATATCCTTGCGA
* * **
298881 ATA-TCCTTTTTCAATAATATCCTAACGA
1 ATATTCC-TTTTCATTGATATCCTTGCGA
298909 ATATTCCTTTTCATTGATATCCTTGCGA
1 ATATTCCTTTTCATTGATATCCTTGCGA
*
298937 ATATCCCTTTTCA
1 ATATTCCTTTTCA
298950 CATAATTTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 89 0.90
29 4 0.04
30 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (28 bp):
ATATTCCTTTTCATTGATATCCTTGCGA
Found at i:298834 original size:112 final size:111
Alignment explanation
Indices: 298709--298955 Score: 275
Period size: 112 Copynumber: 2.2 Consensus size: 111
298699 AATATCGTCT
* * * * *
298709 CGAATATAACCTTTTCAATTATATCCT-TTCGGATATCCCTTTCCGTAG-TATCCTTACGGATAT
1 CGAATAT-CCCTTTTCAATAATATCCTATT--GATATCCCTTTCCATAGATATCATTACGAATAT
* *
298772 AACATTTTCAATAATATACAT-ACGGATATTCCTTTTCATTGATTTCCTTG
63 -ACATTTTCAATAATAT-CATAACGAATATTCCTTTTCATTGATATCCTTG
* * * * * *
298822 CGGATATCCCTTTTCAATAATATCCTAATTGATATTCCTTTTCATTGATATCATTGCGAATATCC
1 CGAATATCCCTTTTCAATAATATCCT-ATTGATATCCCTTTCCATAGATATCATTACGAATATAC
* *
298887 TTTTTCAATAATATCCTAACGAATATTCCTTTTCATTGATATCCTTG
65 ATTTTCAATAATATCATAACGAATATTCCTTTTCATTGATATCCTTG
298934 CGAATATCCCTTTTCACATAAT
1 CGAATATCCCTTTTCA-ATAAT
298956 TTTAGATCAA
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
111 2 0.02
112 86 0.76
113 23 0.20
114 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (111 bp):
CGAATATCCCTTTTCAATAATATCCTATTGATATCCCTTTCCATAGATATCATTACGAATATACA
TTTTCAATAATATCATAACGAATATTCCTTTTCATTGATATCCTTG
Found at i:299183 original size:17 final size:19
Alignment explanation
Indices: 299157--299194 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
299147 TGATTTAAAT
*
299157 AATAATTTCATTTAA-TTA
1 AATAATTTCATATAACTTA
299175 AATAA-TTCATATAACTTA
1 AATAATTTCATATAACTTA
299193 AA
1 AA
299195 ATAGTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATTTCATATAACTTA
Found at i:299484 original size:20 final size:21
Alignment explanation
Indices: 299459--299497 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
299449 TTTCATAGCT
*
299459 TCAAAA-TCTAACAATTTCTA
1 TCAAAACTCAAACAATTTCTA
299479 TCAAAACTCAAACAATTTC
1 TCAAAACTCAAACAATTTC
299498 ACTCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
TCAAAACTCAAACAATTTCTA
Found at i:302066 original size:36 final size:36
Alignment explanation
Indices: 302026--302165 Score: 185
Period size: 36 Copynumber: 3.9 Consensus size: 36
302016 CAGTAACAAG
*
302026 CATGACCTTTGAGTCAATAGAGAGTAAAACAAGCAT
1 CATGACCTTTGAGTCAATAGAGAGTAAAACGAGCAT
* *
302062 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGAGTCAATAGAGAGTAAAACGAGCAT
* *
302098 CATGACCTCT-AGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGA-GTCAATAGAGAGTAAAACGAGCAT
* *
302134 TATGACCTTCG-GATCAATAGAGAGTAAAACGA
1 CATGACCTTTGAG-TCAATAGAGAGTAAAACGA
302166 ATAACGAATG
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.01
36 91 0.99
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (36 bp):
CATGACCTTTGAGTCAATAGAGAGTAAAACGAGCAT
Found at i:302890 original size:21 final size:21
Alignment explanation
Indices: 302828--302901 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
302818 GAAGTTTTTG
* *
302828 GTATCGGTAGAATTAAGACTT
1 GTATCGGTAGAACTGAGACTT
*
302849 GTATCGGTAGAAGTGAGACTT
1 GTATCGGTAGAACTGAGACTT
* *
302870 GTTTCGGTAGAACTGACACTT
1 GTATCGGTAGAACTGAGACTT
*
302891 GTGTC-GTAGAA
1 GTATCGGTAGAA
302902 AACTGTACCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 6 0.13
21 41 0.87
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAACTGAGACTT
Found at i:304370 original size:18 final size:18
Alignment explanation
Indices: 304347--304385 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
304337 ATTAAATATT
* *
304347 TTAAATTTATTGGAATGA
1 TTAAATTGATGGGAATGA
*
304365 TTAAATTGATGGGAATTA
1 TTAAATTGATGGGAATGA
304383 TTA
1 TTA
304386 TCTAGATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
TTAAATTGATGGGAATGA
Found at i:304989 original size:24 final size:24
Alignment explanation
Indices: 304962--305031 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
304952 AACGTGTATA
*
304962 TATATAAGCTGACGAGCGTAAACG
1 TATATAAGCTAACGAGCGTAAACG
*
304986 TATATAAGCTAACGAGCGTAAACA
1 TATATAAGCTAACGAGCGTAAACG
* ** *
305010 TGTGCAAGTTAACGAGCGTAAA
1 TATATAAGCTAACGAGCGTAAA
305032 TGAAATGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (24 bp):
TATATAAGCTAACGAGCGTAAACG
Found at i:307020 original size:17 final size:17
Alignment explanation
Indices: 306969--307018 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
306959 ACCCATTTTT
306969 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
306986 TTTATTTTAAGTTTAAA
1 TTTATTTTAAATTTAAA
*
307003 TTTA-TTTAAATCTAAA
1 TTTATTTTAAATTTAAA
307019 ATAAATAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:308761 original size:29 final size:29
Alignment explanation
Indices: 308728--309212 Score: 399
Period size: 29 Copynumber: 16.7 Consensus size: 29
308718 CTATTTTCTT
308728 TAAAAATCACATTTTTACCCTCGAACTTC
1 TAAAAATCACATTTTTACCCTCGAACTTC
* *
308757 TAAAAAATTACATTTTTGCCCTCGAACTTC
1 T-AAAAATCACATTTTTACCCTCGAACTTC
*
308787 CAAAAATCACATTTTTA-CCTCGAACTTC
1 TAAAAATCACATTTTTACCCTCGAACTTC
*
308815 TCAAAAATTACATTTTTACCCT--AAGCTT-
1 T-AAAAATCACATTTTTACCCTCGAA-CTTC
*
308843 TCAAAAA-CAACATTTTTACCC-CTAAACTTCC
1 T-AAAAATC-ACATTTTTACCCTC-GAACTT-C
* * *
308874 AAAAAATCACATTTTTACCCTTGAACTTT
1 TAAAAATCACATTTTTACCCTCGAACTTC
* *
308903 TCAAAAATTACATTTTT-CTCCT-GAGCTTC
1 T-AAAAATCACATTTTTAC-CCTCGAACTTC
* * *
308932 CAAAAATCACATTTTTATCCAT-GGACTT-
1 TAAAAATCACATTTTTA-CCCTCGAACTTC
*
308960 TCAAAAATAACATTTTTACCCTCGAACTTC
1 T-AAAAATCACATTTTTACCCTCGAACTTC
* * * * *
308990 TTAAAAATTACATATTTGCCGTCGAGCTTC
1 -TAAAAATCACATTTTTACCCTCGAACTTC
* *
309020 CAAAAATCATATTTTTACCCTCGAACTTC
1 TAAAAATCACATTTTTACCCTCGAACTTC
*
309049 CAAAAATCACATTTTTACCC-CGGAACTTC
1 TAAAAATCACATTTTTACCCTC-GAACTTC
* * * *
309078 CAAAAATCACGTCTTT-CTCCT-AAACTTC
1 TAAAAATCACATTTTTAC-CCTCGAACTTC
* *
309106 TCAAAAATTATATTTTT-CCCTCGAACTTCC
1 T-AAAAATCACATTTTTACCCTCGAACTT-C
*
309136 AAAAAAT-ACATTTTTACCCTCGAACTTC
1 TAAAAATCACATTTTTACCCTCGAACTTC
* * *
309164 CAAAAATTACATTTTTGCCCT-GAACTTC
1 TAAAAATCACATTTTTACCCTCGAACTTC
* *
309192 TCAAAAATCATATCTTTACCC
1 T-AAAAATCACATTTTTACCC
309213 CGACTTTTCC
Statistics
Matches: 371, Mismatches: 56, Indels: 58
0.76 0.12 0.12
Matches are distributed among these distances:
28 81 0.22
29 193 0.52
30 95 0.26
31 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
TAAAAATCACATTTTTACCCTCGAACTTC
Found at i:308901 original size:88 final size:87
Alignment explanation
Indices: 308729--309212 Score: 460
Period size: 88 Copynumber: 5.5 Consensus size: 87
308719 TATTTTCTTT
* * * *
308729 AAAAATCACATTTTTACCCTCGAA-CTTCTAAAAAATTACATTTTTGCCCTCGAACTTCCAAAAA
1 AAAAATTACATTTTT-CCCTC-AAGCTTCTCAAAAA-CACATTTTTACCCTCGAACTTCCAAAAA
308793 TCACATTTTTA-CCTCGAACTTCTC
63 TCACATTTTTACCCTCGAACTTCTC
*
308817 AAAAATTACATTTTTACCCT-AAGCTT-TCAAAAACAACATTTTTACCC-CTAAACTTCCAAAAA
1 AAAAATTACATTTTT-CCCTCAAGCTTCTCAAAAAC-ACATTTTTACCCTC-GAACTTCC-AAAA
* *
308879 ATCACATTTTTACCCTTGAACTTTTC
62 ATCACATTTTTACCCTCGAACTTCTC
* * * *
308905 AAAAATTACATTTTTCTCCT-GAGCTTC-CAAAAATCACATTTTTATCCAT-GGACTTTCAAAAA
1 AAAAATTACATTTTTC-CCTCAAGCTTCTCAAAAA-CACATTTTTA-CCCTCGAACTTCCAAAAA
* *
308967 TAACATTTTTACCCTCGAACTTCTT
63 TCACATTTTTACCCTCGAACTTCTC
* * * *
308992 AAAAATTACATATTTGCCGTCGAGCTTC-CAAAAATCATATTTTTACCCTCGAACTTCCAAAAAT
1 AAAAATTACAT-TTTTCCCTCAAGCTTCTCAAAAA-CACATTTTTACCCTCGAACTTCCAAAAAT
309056 CACATTTTTACCC-CGGAACTTC-C
64 CACATTTTTACCCTC-GAACTTCTC
* * * * * *
309079 AAAAATCACGTCTTTCTCCT-AAACTTCTCAAAAATTATATTTTT-CCCTCGAACTTCCAAAAAA
1 AAAAATTACATTTTTC-CCTCAAGCTTCTCAAAAA-CACATTTTTACCCTCGAACTTCC-AAAAA
309142 T-ACATTTTTACCCTCGAACTTC-C
63 TCACATTTTTACCCTCGAACTTCTC
* * *
309165 AAAAATTACATTTTTGCCCTGAA-CTTCTCAAAAATCATATCTTTACCC
1 AAAAATTACATTTTT-CCCTCAAGCTTCTCAAAAA-CACATTTTTACCC
309213 CGACTTTTCC
Statistics
Matches: 338, Mismatches: 37, Indels: 43
0.81 0.09 0.10
Matches are distributed among these distances:
85 1 0.00
86 101 0.30
87 102 0.30
88 131 0.39
89 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (87 bp):
AAAAATTACATTTTTCCCTCAAGCTTCTCAAAAACACATTTTTACCCTCGAACTTCCAAAAATCA
CATTTTTACCCTCGAACTTCTC
Found at i:311397 original size:30 final size:30
Alignment explanation
Indices: 311361--311422 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
311351 TAATTAGTCC
311361 AAAACACTTTTTTTTGTTTATTGGCAACAT
1 AAAACACTTTTTTTTGTTTATTGGCAACAT
*
311391 AAAACACTTTTTTTTGTTTATTTGCAACAT
1 AAAACACTTTTTTTTGTTTATTGGCAACAT
311421 AA
1 AA
311423 GACTAAAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (30 bp):
AAAACACTTTTTTTTGTTTATTGGCAACAT
Found at i:318856 original size:16 final size:18
Alignment explanation
Indices: 318817--318850 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
318807 TAATTTTATA
318817 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
318834 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
318851 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:320446 original size:35 final size:34
Alignment explanation
Indices: 320380--320446 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
320370 ATTTTAATAT
**
320380 ATAAAAAATTCATATAAAATTCTTAAAAATAAAA
1 ATAAAAAATTCATATAAAATTAATAAAAATAAAA
*
320414 ATAAAAAA-TCATATAAACTATTAATAATAATAA
1 ATAAAAAATTCATATAAA--ATTAATAAAAATAA
320447 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 9 0.32
34 8 0.29
35 11 0.39
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAAATTCATATAAAATTAATAAAAATAAAA
Found at i:320672 original size:16 final size:17
Alignment explanation
Indices: 320642--320674 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
320632 TGGTGTATTT
*
320642 AAAAATAATATACAATA
1 AAAAAAAATATACAATA
320659 AAAAAAAATA-ACAATA
1 AAAAAAAATATACAATA
320675 CTAAATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAAAAATATACAATA
Found at i:324870 original size:53 final size:53
Alignment explanation
Indices: 324809--324914 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
324799 TGTTGAAATG
*
324809 AATAGTATTATAGCCAGGTTTTTGTGGCAAAAAGGACATGGAAAAAGGGGAAT
1 AATAGTATTATAACCAGGTTTTTGTGGCAAAAAGGACATGGAAAAAGGGGAAT
324862 AATAGTATTATAACCAGGTTTTTGTGGCAAAAAGGACATGGAAAAAGGGGAAT
1 AATAGTATTATAACCAGGTTTTTGTGGCAAAAAGGACATGGAAAAAGGGGAAT
324915 GCACTGGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.25
Consensus pattern (53 bp):
AATAGTATTATAACCAGGTTTTTGTGGCAAAAAGGACATGGAAAAAGGGGAAT
Found at i:324991 original size:21 final size:21
Alignment explanation
Indices: 324965--325006 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
324955 GAAGGAGGGT
324965 TAGGTTTTCGTGACTTAGTAA
1 TAGGTTTTCGTGACTTAGTAA
324986 TAGGTTTTCGTGACTTAGTAA
1 TAGGTTTTCGTGACTTAGTAA
325007 AATTTAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
TAGGTTTTCGTGACTTAGTAA
Found at i:342541 original size:7 final size:7
Alignment explanation
Indices: 342531--342555 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
342521 GCCAAAATAA
342531 AAAAAAT
1 AAAAAAT
342538 AAAAAAT
1 AAAAAAT
342545 AAAAAAT
1 AAAAAAT
342552 AAAA
1 AAAA
342556 CTCAGTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:358024 original size:32 final size:32
Alignment explanation
Indices: 357988--358084 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 32
357978 ATGATCAATG
357988 GTATTATGATACTCATATAGTATGTGTGGTTA
1 GTATTATGATACTCATATAGTATGTGTGGTTA
*** * * ** *
358020 GTA-T-TGA-AAAAATATAAATATG-ATGAATG
1 GTATTATGATACTCATAT-AGTATGTGTGGTTA
358049 GTATTATGATACTCATATAGTATGTGTGGTTA
1 GTATTATGATACTCATATAGTATGTGTGGTTA
358081 GTAT
1 GTAT
358085 ATTGATTCAT
Statistics
Matches: 44, Mismatches: 16, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
29 11 0.25
30 9 0.20
31 9 0.20
32 15 0.34
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (32 bp):
GTATTATGATACTCATATAGTATGTGTGGTTA
Found at i:358039 original size:61 final size:60
Alignment explanation
Indices: 357960--358084 Score: 232
Period size: 61 Copynumber: 2.1 Consensus size: 60
357950 AATGAAATTT
357960 GTATTGAAAAAAATAAATATGATCAATGGTATTATGATACTCATATAGTATGTGTGGTTA
1 GTATTGAAAAAAATAAATATGATCAATGGTATTATGATACTCATATAGTATGTGTGGTTA
*
358020 GTATTGAAAAAATATAAATATGATGAATGGTATTATGATACTCATATAGTATGTGTGGTTA
1 GTATTGAAAAAA-ATAAATATGATCAATGGTATTATGATACTCATATAGTATGTGTGGTTA
358081 GTAT
1 GTAT
358085 ATTGATTCAT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 12 0.19
61 51 0.81
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (60 bp):
GTATTGAAAAAAATAAATATGATCAATGGTATTATGATACTCATATAGTATGTGTGGTTA
Found at i:361348 original size:10 final size:10
Alignment explanation
Indices: 361327--361357 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
361317 AGGTGAACCA
361327 TTCTTC-TTC
1 TTCTTCTTTC
361336 TTCTTCTTTC
1 TTCTTCTTTC
361346 TTCTTCTTTC
1 TTCTTCTTTC
361356 TT
1 TT
361358 AATGATAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:367786 original size:71 final size:71
Alignment explanation
Indices: 367658--367955 Score: 225
Period size: 69 Copynumber: 4.3 Consensus size: 71
367648 CTTCAATGTC
* * * * *
367658 CAACGCAGTTAGCAAGAGCTACAAACTCTTAGCTGTCATATTAAGGCTCATAGGTGAAGAGCCGC
1 CAACACAGTTAGCGAGAGCTACAAACTCTTAGCTATCATATTAAGGCTCACAAGTGAAGAGCCGC
367723 AGTC-TT
66 AG-CATT
* *
367729 CAACATAGTTAGCGAGAGTTACAAACT-TCTAGCTATCATATTAAGGCTCACAAGTGAAGAGCCG
1 CAACACAGTTAGCGAGAGCTACAAACTCT-TAGCTATCATATTAAGGCTCACAAGTGAAGAGCCG
*
367793 TAGCATT
65 CAGCATT
* * ** * * * ** * * *
367800 CAACACAGTTAGAGAGAGC-A-AAGCTCCCAACTGTCACATTAAGGCTCTTAGGTTAAGAGTCGC
1 CAACACAGTTAGCGAGAGCTACAAACTCTTAGCTATCATATTAAGGCTCACAAGTGAAGAGCCGC
*
367863 AGC-CT
66 AGCATT
* * * * * *
367868 CTAACACAGTTAGCGAGAGC-A-AAGCTCCTAGTTGTCACATTAAGGCTCGA-AAGTGAAGTGCC
1 C-AACACAGTTAGCGAGAGCTACAAACTCTTAGCTATCATATTAAGGCTC-ACAAGTGAAGAGCC
* * *
367930 ACAGCCTC
64 GCAGCATT
*
367938 CAACACAGTTAGTGAGAG
1 CAACACAGTTAGCGAGAG
367956 AAGAGCTCCT
Statistics
Matches: 184, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
68 2 0.01
69 103 0.56
70 4 0.02
71 75 0.41
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (71 bp):
CAACACAGTTAGCGAGAGCTACAAACTCTTAGCTATCATATTAAGGCTCACAAGTGAAGAGCCGC
AGCATT
Found at i:367874 original size:69 final size:69
Alignment explanation
Indices: 367801--368082 Score: 273
Period size: 69 Copynumber: 4.1 Consensus size: 69
367791 CGTAGCATTC
** * * *
367801 AACACAGTTAGAGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCTTAGGTTAAGAGTCGCAGC
1 AACACAGTTAGAGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCGAAGGTGAAGAGCCACAGC
367866 CTCT
66 CTCT
* * ** * *
367870 AACACAGTTAGCGAGAGCAAAGCTCCTAGTTGTCACATTAAGGCTCGAAAGTGAAGTGCCACAGC
1 AACACAGTTAGAGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCGAAGGTGAAGAGCCACAGC
*
367935 CTCC
66 CTCT
* * * * * *
367939 AACACAGTTAGTGAGAG-AAGAGCTCCTAGA-TGTCACACTAAGGCTCGCAGGTGAAGAACCATA
1 AACACAGTTAGAGAGAGCAA-AGCTCCCA-ACTGTCACATTAAGGCTCGAAGGTGAAGAGCCACA
*
368002 GCCTTT
64 GCCTCT
* * * ** *
368008 AACACATTTAGCA-AGAGCAAAGCTCCCAACTATCACATTAAGGCTTGTCGGTGAAGAGCCGCAG
1 AACACAGTTAG-AGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCGAAGGTGAAGAGCCACAG
* *
368072 ACTCC
65 CCTCT
368077 AACACA
1 AACACA
368083 ATTCTTGACT
Statistics
Matches: 172, Mismatches: 36, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
68 3 0.02
69 167 0.97
70 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (69 bp):
AACACAGTTAGAGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCGAAGGTGAAGAGCCACAGC
CTCT
Found at i:367975 original size:138 final size:137
Alignment explanation
Indices: 367690--368052 Score: 374
Period size: 138 Copynumber: 2.6 Consensus size: 137
367680 AAACTCTTAG
* * *
367690 CTGTCATATTAAGGCTCATAGGTGAAGAGCCGCAGTCTTCAACATAGTTAGCGAGAGTTACAAA-
1 CTGTCACATTAAGGCTCATAGGTGAAGAGCCGCAGCCTT-AACACAGTTAGCGAGAG---CAAAG
* * ** *
367754 CTTCTAGCTATCATATTAAGGCTCACAAGTGAAGAGCCGTAGCATTCAACACAGTTAGAGAGAGC
62 CTCCTAGCTATCACATTAAGGCTCACAAGTGAAGAGCCACAGCATCCAACACAGTTAGAGAGAGC
367819 AAAGCTCCCAA
127 AAAGCTCCCAA
* * *
367830 CTGTCACATTAAGGCTCTTAGGTTAAGAGTCGCAGCCTCTAACACAGTTAGCGAGAGCAAAGCTC
1 CTGTCACATTAAGGCTCATAGGTGAAGAGCCGCAGCCT-TAACACAGTTAGCGAGAGCAAAGCTC
* * * * *
367895 CTAGTTGTCACATTAAGGCTCGA-AAGTGAAGTGCCACAGCCTCCAACACAGTTAGTGAGAG-AA
65 CTAGCTATCACATTAAGGCTC-ACAAGTGAAGAGCCACAGCATCCAACACAGTTAGAGAGAGCAA
*
367958 GAGCTCCTAGA
129 -AGCTCCCA-A
* ** * ** * *
367969 -TGTCACACTAAGGCTCGCAGGTGAAGAACCATAGCCTTTAACACATTTAGCAAGAGCAAAGCTC
1 CTGTCACATTAAGGCTCATAGGTGAAGAGCCGCAGCC-TTAACACAGTTAGCGAGAGCAAAGCTC
* *
368033 CCAACTATCACATTAAGGCT
65 CTAGCTATCACATTAAGGCT
368053 TGTCGGTGAA
Statistics
Matches: 186, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
137 6 0.03
138 127 0.68
139 3 0.02
140 49 0.26
141 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (137 bp):
CTGTCACATTAAGGCTCATAGGTGAAGAGCCGCAGCCTTAACACAGTTAGCGAGAGCAAAGCTCC
TAGCTATCACATTAAGGCTCACAAGTGAAGAGCCACAGCATCCAACACAGTTAGAGAGAGCAAAG
CTCCCAA
Found at i:373529 original size:17 final size:17
Alignment explanation
Indices: 373490--373554 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
373480 ATATATATGG
**
373490 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
373507 AGATGCAACGACAATAA
1 AAATGCAATGACAATAA
* *
373524 AAATGCAGTGACGATAA
1 AAATGCAATGACAATAA
*
373541 AAATGCAGTGACAA
1 AAATGCAATGACAA
373555 AATACTAAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:375863 original size:24 final size:24
Alignment explanation
Indices: 375813--375863 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
375803 TAAAAGAATT
*
375813 AATTGTCAATGCAAATATAAAATA
1 AATTGTCAATGCAAATATAAAAAA
375837 AATTGTCAGA-GCAAAT-TAAGAAAA
1 AATTGTCA-ATGCAAATATAA-AAAA
375861 AAT
1 AAT
375864 GAATAGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
24 20 0.83
25 1 0.04
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
AATTGTCAATGCAAATATAAAAAA
Found at i:378833 original size:2 final size:2
Alignment explanation
Indices: 378816--378853 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
378806 CAACATTTAT
*
378816 TA TA TA -A TA TA CA 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 TA TA TA TA TA TA TA T
378854 TCTTTTCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:379963 original size:18 final size:18
Alignment explanation
Indices: 379922--379978 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
379912 CGAGGCAACA
* *
379922 TCTTCTTCTTTTTCCTCC
1 TCTTTTTCTTTTTCTTCC
379940 TCTTTTTCTTTTTCTT-C
1 TCTTTTTCTTTTTCTTCC
* *
379957 TTTTTTTCCTTCTTCTTCC
1 TCTTTTT-CTTTTTCTTCC
379976 TCT
1 TCT
379979 GACTCAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 7 0.22
18 22 0.69
19 3 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTTTTCTTTTTCTTCC
Found at i:395550 original size:34 final size:34
Alignment explanation
Indices: 395512--395584 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
395502 TGACTAGTGT
* *
395512 TGGGCACACAT-TCATCGGTTTATCCGACTAGCA-C
1 TGGGCACA-ATATCATCGGTTAATCCAACTAG-AGC
* *
395546 TGGGCGCAATATCATTGGTTAATCCAACTAGAGC
1 TGGGCACAATATCATCGGTTAATCCAACTAGAGC
395580 TGGGC
1 TGGGC
395585 TCACTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 3 0.09
34 30 0.91
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (34 bp):
TGGGCACAATATCATCGGTTAATCCAACTAGAGC
Found at i:395577 original size:108 final size:108
Alignment explanation
Indices: 395383--395586 Score: 318
Period size: 108 Copynumber: 1.9 Consensus size: 108
395373 TGCAACTTTC
* * * **
395383 GTCAGTTTAACTGACTAGTGTTGGGTACACTTTCGTCGGTTTATCCGACTAGTGCTAGGCGCAAT
1 GTCAGTTTAACTGACTAGTGTTGGGCACACATTCATCGGTTTATCCGACTAGCACTAGGCGCAAT
* *
395448 ACCGTTGGTTAATCCATCTAGAGCTGAGCTCCTTATTTATATT
66 ACCATTGGTTAATCCAACTAGAGCTGAGCTCCTTATTTATATT
*
395491 GTCAGTTTAACTGACTAGTGTTGGGCACACATTCATCGGTTTATCCGACTAGCACTGGGCGCAAT
1 GTCAGTTTAACTGACTAGTGTTGGGCACACATTCATCGGTTTATCCGACTAGCACTAGGCGCAAT
* *
395556 ATCATTGGTTAATCCAACTAGAGCTGGGCTC
66 ACCATTGGTTAATCCAACTAGAGCTGAGCTC
395587 ACTTTTAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 86 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (108 bp):
GTCAGTTTAACTGACTAGTGTTGGGCACACATTCATCGGTTTATCCGACTAGCACTAGGCGCAAT
ACCATTGGTTAATCCAACTAGAGCTGAGCTCCTTATTTATATT
Found at i:400743 original size:9 final size:9
Alignment explanation
Indices: 400729--400753 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
400719 AGTAACAAAT
400729 AAATAATTA
1 AAATAATTA
400738 AAATAATTA
1 AAATAATTA
400747 AAATAAT
1 AAATAAT
400754 GCCAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATAATTA
Found at i:402659 original size:13 final size:13
Alignment explanation
Indices: 402623--402671 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
402613 TAAAATACAC
402623 ATATAAAA--ATA
1 ATATAAAATTATA
402634 AT-TAAAA-TATA
1 ATATAAAATTATA
*
402645 ATATAATATTATA
1 ATATAAAATTATA
402658 ATATAAAATTATA
1 ATATAAAATTATA
402671 A
1 A
402672 AAAAACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 4 0.12
13 17 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAAAATTATA
Found at i:402684 original size:26 final size:26
Alignment explanation
Indices: 402630--402693 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
402620 CACATATAAA
* * *
402630 AATAAT-TAAAA-TATAATATAATAT
1 AATAATATAAAATTATAAAAAAACAT
*
402654 TATAATATAAAATTATAAAAAAACAT
1 AATAATATAAAATTATAAAAAAACAT
402680 AATAA-ATCAAAATT
1 AATAATAT-AAAATT
402694 CGTATAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 5 0.16
25 7 0.22
26 20 0.62
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAATATAAAATTATAAAAAAACAT
Found at i:402746 original size:57 final size:55
Alignment explanation
Indices: 402641--402749 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 55
402631 ATAATTAAAA
*
402641 TATAATATAATATTATAATATAAAATTATAAAAAAACATAATAAATCAAAATTCG
1 TATAATATAATATTATAATATAAAATTATAAAAAAACATAACAAATCAAAATTCG
* * * * *
402696 TATAATATAAATTATTATCATATAAAAATT-TATAACAATATAACACATCAAAAT
1 TATAATAT-AA-TATTATAATAT-AAAATTATAAAAAAACATAACAAATCAAAAT
402750 CAATTACAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 8 0.18
56 2 0.04
57 29 0.64
58 6 0.13
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (55 bp):
TATAATATAATATTATAATATAAAATTATAAAAAAACATAACAAATCAAAATTCG
Found at i:403168 original size:28 final size:27
Alignment explanation
Indices: 403137--403195 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
403127 TTCTGAATTC
*
403137 TTTT-AATAAATATGTACTTAATTTGAAG
1 TTTTCAAT-AATATGTACGTAATTTG-AG
* *
403165 TTTTCACTAATATTTACGTAATTTGAG
1 TTTTCAATAATATGTACGTAATTTGAG
403192 TTTT
1 TTTT
403196 TAACCAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 19 0.70
29 2 0.07
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTTCAATAATATGTACGTAATTTGAG
Found at i:403196 original size:28 final size:28
Alignment explanation
Indices: 403145--403208 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
403135 TCTTTTAATA
* * * *
403145 AATATGTACTTAATTTGAAGTTTTCACT
1 AATATTTACGTAATTTGAAGTTTTAACC
403173 AATATTTACGTAATTTG-AGTTTTTAACC
1 AATATTTACGTAATTTGAAG-TTTTAACC
403201 AATATTTA
1 AATATTTA
403209 AATAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (28 bp):
AATATTTACGTAATTTGAAGTTTTAACC
Found at i:403214 original size:28 final size:28
Alignment explanation
Indices: 403155--403225 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
403145 AATATGTACT
* * **
403155 TAATTTGAAGTTTTCACTAATATTTACG
1 TAATTTGAAGTTTTAACCAATATTTAAA
403183 TAATTTG-AGTTTTTAACCAATATTTAAA
1 TAATTTGAAG-TTTTAACCAATATTTAAA
* *
403211 TAATTTAAAATTTTA
1 TAATTTGAAGTTTTA
403226 TGAGCATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.06
28 32 0.91
29 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (28 bp):
TAATTTGAAGTTTTAACCAATATTTAAA
Found at i:405386 original size:24 final size:24
Alignment explanation
Indices: 405350--405424 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
405340 ATATTGGTTA
405350 AACTCTATCTGGGCTCGAATGAGCT
1 AACT-TATCTGGGCTCGAATGAGCT
* *
405375 AACTTATTTGGGCTC-ATAAGAGCT
1 AACTTATCTGGGCTCGA-ATGAGCT
* *
405399 AACCTATCTGGGCTCGTATGAGCT
1 AACTTATCTGGGCTCGAATGAGCT
405423 AA
1 AA
405425 TTTTGTCTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
23 1 0.02
24 37 0.88
25 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (24 bp):
AACTTATCTGGGCTCGAATGAGCT
Found at i:410918 original size:116 final size:116
Alignment explanation
Indices: 410714--410945 Score: 385
Period size: 116 Copynumber: 2.0 Consensus size: 116
410704 AGAATGTGAG
*
410714 ATATTATGTGATGTTTTTATAAGGGGGAGTAAATACGCGTTGTACTCTTTTTCCTTTAATGAGGT
1 ATATTATGTGATGTTTTTATAAGGGGGAGTAAATACGCGTTGTACTCTTTTTCCCTTAATGAGGT
* **
410779 TTTGTCCCATTGGGTTTTCCTGGTAAGCTTTTTAATGAGGTAACATGTTAT
66 TTTGTCCCATTGAGTTTTCCTGGTAAGCTTTTTAATGAGACAACATGTTAT
*
410830 ATATTATGTGATGTTTTTATGA-GGGGAGTAAATACGCGTTGTACTCTTTTTCCCTTAATCGAGG
1 ATATTATGTGATGTTTTTATAAGGGGGAGTAAATACGCGTTGTACTCTTTTTCCCTTAAT-GAGG
* *
410894 TTTTGTCCCATTGAGTTTTCCTGGTAAGGTTTTTAATTAGACAACATGTTAT
65 TTTTGTCCCATTGAGTTTTCCTGGTAAGCTTTTTAATGAGACAACATGTTAT
410946 GCGTATTATA
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 36 0.33
116 72 0.67
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.44
Consensus pattern (116 bp):
ATATTATGTGATGTTTTTATAAGGGGGAGTAAATACGCGTTGTACTCTTTTTCCCTTAATGAGGT
TTTGTCCCATTGAGTTTTCCTGGTAAGCTTTTTAATGAGACAACATGTTAT
Found at i:411455 original size:24 final size:24
Alignment explanation
Indices: 411392--411456 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
411382 AAAATTACTG
* *
411392 TAATATATTTTTTAAAA-ATTCCA
1 TAATATGTTTTTTAAAATAATCCA
* ** * *
411415 TAATTTGAATTTAAAAATAATCCT
1 TAATATGTTTTTTAAAATAATCCA
411439 TAATATGTTTTTTAAAAT
1 TAATATGTTTTTTAAAAT
411457 TTTAAAAGTA
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (24 bp):
TAATATGTTTTTTAAAATAATCCA
Found at i:416733 original size:55 final size:55
Alignment explanation
Indices: 416667--416786 Score: 177
Period size: 55 Copynumber: 2.2 Consensus size: 55
416657 TTTGGTTCGC
* * **
416667 TTATAGCTCGGGTAGAGCTTTGGACTACTTACGTCTAGGTTAGAGTGTAAAACTA
1 TTATAGCTCGGGTAGAGCTTTGGACTACATACATCTAGGTTAGAGCATAAAACTA
* *
416722 TTATAGCTCGGGTAGAGCTTTGGACTACATACATCTCGGTTAGAGCATAAGACTA
1 TTATAGCTCGGGTAGAGCTTTGGACTACATACATCTAGGTTAGAGCATAAAACTA
*
416777 TTTTAGCTCG
1 TTATAGCTCG
416787 AAAAGAGCGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (55 bp):
TTATAGCTCGGGTAGAGCTTTGGACTACATACATCTAGGTTAGAGCATAAAACTA
Found at i:416748 original size:27 final size:28
Alignment explanation
Indices: 416666--416767 Score: 75
Period size: 28 Copynumber: 3.7 Consensus size: 28
416656 CTTTGGTTCG
416666 CTTATAGCTCGGGTAGAGCTTTGGACTA
1 CTTATAGCTCGGGTAGAGCTTTGGACTA
* * * ***
416694 CTTA-CGTCTAGGTTAGAG-TGTAAAACTA
1 CTTATAG-CTCGGGTAGAGCT-TTGGACTA
416722 -TTATAGCTCGGGTAGAGCTTTGGACTA
1 CTTATAGCTCGGGTAGAGCTTTGGACTA
* * * *
416749 CATACATCTCGGTTAGAGC
1 CTTATAGCTCGGGTAGAGC
416768 ATAAGACTAT
Statistics
Matches: 53, Mismatches: 16, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
27 19 0.36
28 34 0.64
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (28 bp):
CTTATAGCTCGGGTAGAGCTTTGGACTA
Found at i:417867 original size:21 final size:20
Alignment explanation
Indices: 417842--417880 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
417832 TTGTGTTTAT
*
417842 GTTTTGAGGGTTTTTTTTTGG
1 GTTTT-AGGGTTTATTTTTGG
*
417863 GTTTTCGGGTTTATTTTT
1 GTTTTAGGGTTTATTTTT
417881 ATCTCCATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.05, C:0.03, G:0.28, T:0.64
Consensus pattern (20 bp):
GTTTTAGGGTTTATTTTTGG
Found at i:419336 original size:19 final size:20
Alignment explanation
Indices: 419298--419341 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
419288 ACAATTACTA
* *
419298 TAATGATTCAAGATTAAATT
1 TAATAATTCAAGACTAAATT
419318 TAATAATTC-AGACTAAATT
1 TAATAATTCAAGACTAAATT
*
419337 GAATA
1 TAATA
419342 GACGGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (20 bp):
TAATAATTCAAGACTAAATT
Found at i:425533 original size:29 final size:29
Alignment explanation
Indices: 425469--425565 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 29
425459 AAAACTTTAG
* * * *
425469 GGGTCAAATTGGAATTTTTGGAAAATTCGA
1 GGGTCAAATTTGAATTTTTAGAAAGTT-AA
*
425499 TGGTCAAATTTGAATTTTTAGAAAGTTAA
1 GGGTCAAATTTGAATTTTTAGAAAGTTAA
* *
425528 GGGTCAAATTT-AGATTTTTAAAAAGTTCA
1 GGGTCAAATTTGA-ATTTTTAGAAAGTTAA
425557 GGTGTCAAA
1 GG-GTCAAA
425566 AAAATAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
28 1 0.02
29 27 0.47
30 29 0.51
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTAGAAAGTTAA
Done.