Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002648.1 Hibiscus syriacus cultivar Beakdansim tig00005411_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: 636717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:581656 original size:19 final size:19
Alignment explanation
Indices: 581632--581674 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
581622 CTCAGTACTC
581632 CTTACTCCTACTCATGCTT
1 CTTACTCCTACTCATGCTT
581651 CTTACTCCTACTCATGCTT
1 CTTACTCCTACTCATGCTT
581670 CTTAC
1 CTTAC
581675 CTACGCGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.37, G:0.05, T:0.42
Consensus pattern (19 bp):
CTTACTCCTACTCATGCTT
Found at i:584803 original size:24 final size:24
Alignment explanation
Indices: 584753--584804 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
584743 AATCTTTAGA
** *
584753 TCTTCTTTCTTCTCGCAGTCGTTG
1 TCTTCTTTCTTCTCGCAACCGTGG
*
584777 TCTTCTTTCTTCTCTCAACCGTGG
1 TCTTCTTTCTTCTCGCAACCGTGG
584801 TCTT
1 TCTT
584805 TCTCTCTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.31, G:0.13, T:0.50
Consensus pattern (24 bp):
TCTTCTTTCTTCTCGCAACCGTGG
Found at i:588705 original size:17 final size:17
Alignment explanation
Indices: 588675--588719 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
588665 AGAAAAATTG
588675 GTACCGATACTCTAGGA
1 GTACCGATACTCTAGGA
* *
588692 GTATCGATATTCTAGGA
1 GTACCGATACTCTAGGA
588709 GTACCGATACT
1 GTACCGATACT
588720 ACTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (17 bp):
GTACCGATACTCTAGGA
Found at i:589458 original size:11 final size:11
Alignment explanation
Indices: 589442--589480 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
589432 TATTTTTTAA
589442 TTAATTAAATT
1 TTAATTAAATT
*
589453 TTAATTTGAAAGT
1 TTAA-TT-AAATT
589466 TTAATTAAATT
1 TTAATTAAATT
589477 TTAA
1 TTAA
589481 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 12 0.50
12 4 0.17
13 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (11 bp):
TTAATTAAATT
Found at i:590130 original size:30 final size:30
Alignment explanation
Indices: 590094--590153 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
590084 TTATTAAAAA
*
590094 AATATTTCAACTTATTTGATGA-TCTCCTAC
1 AATATTTCAACTTATTTAAT-ACTCTCCTAC
590124 AATATTTCAACTTATTTAATACTCTCCTAC
1 AATATTTCAACTTATTTAATACTCTCCTAC
590154 TTGGACAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AATATTTCAACTTATTTAATACTCTCCTAC
Found at i:593232 original size:27 final size:28
Alignment explanation
Indices: 593197--593267 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 28
593187 TTAAAAGAGA
*
593197 AAAATAAAATAAAATAAGAT-GAAGGAAAT
1 AAAA-AAAATAAAATAAGATAGAA-AAAAT
* * *
593226 ATAAAAACATAAAAAAATATAGAAAAAAT
1 A-AAAAAAATAAAATAAGATAGAAAAAAT
593255 -AAAAAAATAAAAT
1 AAAAAAAATAAAAT
593268 GTATAAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 11 0.32
29 17 0.50
30 6 0.18
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (28 bp):
AAAAAAAATAAAATAAGATAGAAAAAAT
Found at i:593245 original size:18 final size:19
Alignment explanation
Indices: 593222--593263 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
593212 AAGATGAAGG
*
593222 AAATATA-AAAACATAAAA
1 AAATATAGAAAAAATAAAA
593240 AAATATAGAAAAAATAAAA
1 AAATATAGAAAAAATAAAA
593259 AAATA
1 AAATA
593264 AAATGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAATATAGAAAAAATAAAA
Found at i:593295 original size:6 final size:7
Alignment explanation
Indices: 593248--593304 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
593238 AAAAATATAG
593248 AAAAAAT
1 AAAAAAT
593255 AAAAAAAT
1 -AAAAAAT
**
593263 AAAATGT
1 AAAAAAT
**
593270 ATAAATGT
1 A-AAAAAT
*
593278 ATAAAAT
1 AAAAAAT
593285 AAAAAAT
1 AAAAAAT
593292 AAAAAAT
1 AAAAAAT
593299 AAAAAA
1 AAAAAA
593305 AATTAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
7 28 0.67
8 14 0.33
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (7 bp):
AAAAAAT
Found at i:594185 original size:83 final size:84
Alignment explanation
Indices: 594039--594195 Score: 192
Period size: 83 Copynumber: 1.9 Consensus size: 84
594029 GGTTGATACA
* * *
594039 CCCTCGAGCTGAATGGAATCGAACTCGAAAGTCTTCATTGACAGATAGTCCTTCTCGCCTTGAGC
1 CCCTCGAGCTGAATGAAATCGAACTC-AAAGTCTTCATTGACAGATAGACCCTCTCGCCTTGAGC
*
594104 TATGCTGTAAATTTGTTATG
65 TATGATGTAAATTTGTTATG
* * * ** *
594124 CCCTTGAGCTGAATGAAATCGAACTC-AGGTTTTTGTTGACAGATA-ACCCTCATCGCCTTGAGT
1 CCCTCGAGCTGAATGAAATCGAACTCAAAGTCTTCATTGACAGATAGACCCTC-TCGCCTTGAGC
594187 TATGATGTA
65 TATGATGTA
594196 CTAGATTGAG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
82 4 0.07
83 33 0.54
85 24 0.39
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (84 bp):
CCCTCGAGCTGAATGAAATCGAACTCAAAGTCTTCATTGACAGATAGACCCTCTCGCCTTGAGCT
ATGATGTAAATTTGTTATG
Found at i:594735 original size:83 final size:83
Alignment explanation
Indices: 594586--594754 Score: 196
Period size: 83 Copynumber: 2.0 Consensus size: 83
594576 TCGATAGTTT
* * * *
594586 TTTGTTGACAAATAGCCCTTCTCACCTTGAGCTATAATGTAAATTTGATACGCCCTTAAACTGAA
1 TTTGTTGACAAATAACCCTTATCACCTTAAGCTATAATGTAAATTTGATACGCCCTTAAACCGAA
594651 TGT-ATTCGAACTCGAAGG
66 TGTAATT-GAACTCGAAGG
* * * * * * * *
594669 TTTGTTGACATATAACCCTTATCGCCTTAAGCTATACTTTAAATTTGATATGCTCTTGAGCCGAA
1 TTTGTTGACAAATAACCCTTATCACCTTAAGCTATAATGTAAATTTGATACGCCCTTAAACCGAA
**
594734 TGTAATTGAGGTCGAAGG
66 TGTAATTGAACTCGAAGG
594752 TTT
1 TTT
594755 TTATGCTGGT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 68 0.96
84 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (83 bp):
TTTGTTGACAAATAACCCTTATCACCTTAAGCTATAATGTAAATTTGATACGCCCTTAAACCGAA
TGTAATTGAACTCGAAGG
Found at i:599830 original size:25 final size:25
Alignment explanation
Indices: 599785--599837 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
599775 TAAAAAAAAT
599785 AAATATTAAATAAATCAAAGAGAAA
1 AAATATTAAATAAATCAAAGAGAAA
*
599810 AAATATATAAATAAAT-TAAGAGAAA
1 AAATAT-TAAATAAATCAAAGAGAAA
599835 AAA
1 AAA
599838 GGTAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (25 bp):
AAATATTAAATAAATCAAAGAGAAA
Found at i:599853 original size:25 final size:25
Alignment explanation
Indices: 599802--599873 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
599792 AAATAAATCA
* *
599802 AAGAGAAAAAATATATAAATAAATT
1 AAGAGAAAAAAGATATAAAAAAATT
*
599827 AAGAGAAAAAAGGTA-AAAAAAAGTT
1 AAGAGAAAAAAGATATAAAAAAA-TT
* *
599852 AAAAGAGAAAAATGAAATAAAA
1 --AAGAGAAAAAAGATATAAAA
599874 TAAGATGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
24 6 0.16
25 15 0.41
27 12 0.32
28 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (25 bp):
AAGAGAAAAAAGATATAAAAAAATT
Found at i:599904 original size:16 final size:16
Alignment explanation
Indices: 599885--599917 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
599875 AAGATGAAGG
599885 AAATATA-AAAACATAA
1 AAATATAGAAAA-ATAA
599901 AAATATAGAAAAATAA
1 AAATATAGAAAAATAA
599917 A
1 A
599918 CAAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAATATAGAAAAATAA
Found at i:599964 original size:29 final size:30
Alignment explanation
Indices: 599909--599979 Score: 72
Period size: 32 Copynumber: 2.3 Consensus size: 30
599899 AAAAATATAG
* * * **
599909 AAAAATAAACAAAAATAAAATGTATAAATGTT
1 AAAAAGAAAAAAAAATAAAA--TATAAAGGAA
599941 AAAAAGAAAAAAAAATAAAA-ATAAAGGAA
1 AAAAAGAAAAAAAAATAAAATATAAAGGAA
599970 AAAAAGAAAA
1 AAAAAGAAAA
599980 TGTTATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 16 0.47
32 18 0.53
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (30 bp):
AAAAAGAAAAAAAAATAAAATATAAAGGAA
Found at i:601179 original size:22 final size:23
Alignment explanation
Indices: 601154--601202 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
601144 AAAAAACAAA
*
601154 AAAAAGAAGGAA-AAATATTAAT
1 AAAAAGAAGAAATAAATATTAAT
* *
601176 -AAAATAATAAATAAATATTAAT
1 AAAAAGAAGAAATAAATATTAAT
601198 AAAAA
1 AAAAA
601203 ATAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.22
Consensus pattern (23 bp):
AAAAAGAAGAAATAAATATTAAT
Found at i:601209 original size:22 final size:22
Alignment explanation
Indices: 601166--601212 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
601156 AAAGAAGGAA
601166 AAATATTAATAAAATAATAAAT
1 AAATATTAATAAAATAATAAAT
601188 AAATATTAATAAAA-AATAAAAT
1 AAATATTAATAAAATAAT-AAAT
601210 AAA
1 AAA
601213 AAATCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATATTAATAAAATAATAAAT
Found at i:601294 original size:37 final size:37
Alignment explanation
Indices: 601252--601327 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
601242 TGTTTTTTTT
*
601252 AAATTGTTTTCAAAACCATATAAAATATATTTTTAAA
1 AAATTGTTTTCAAAACCATATAAAATATATTTTCAAA
* * * *
601289 AAATTGTTTTTAAAACTATATAATATATGTTTTCAAA
1 AAATTGTTTTCAAAACCATATAAAATATATTTTCAAA
601326 AA
1 AA
601328 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (37 bp):
AAATTGTTTTCAAAACCATATAAAATATATTTTCAAA
Found at i:601367 original size:11 final size:11
Alignment explanation
Indices: 601351--601409 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
601341 TATATTATAT
601351 ATATTTTCAAA
1 ATATTTTCAAA
601362 ATATTTTCAAA
1 ATATTTTCAAA
*
601373 ACTATATATT-ATAT
1 A-TAT-T-TTCA-AA
601387 ATATTTTCAAA
1 ATATTTTCAAA
*
601398 ATATTTTTAAA
1 ATATTTTCAAA
601409 A
1 A
601410 ACTATTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 26 0.65
12 5 0.12
13 5 0.12
14 4 0.10
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:601420 original size:37 final size:37
Alignment explanation
Indices: 601300--601655 Score: 422
Period size: 36 Copynumber: 9.6 Consensus size: 37
601290 AATTGTTTTT
*
601300 AAAACTATATA--ATATATGTTTTCAAAAATATTTT-A
1 AAAACTATATATTATATATATTTTC-AAAATATTTTCA
*
601335 AAAAAT-TATATTATATATATTTTCAAAATATTTTC-
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
*
601370 AAAACTATATATTATATATATTTTCAAAATATTTTTA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
* * * *
601407 AAAACTATTTATTATATACATTTTCAAAATGTTTTAA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
* **
601444 AAAACTTTATATTATATAT-TTTAAAAAATATTTTC-
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
*
601479 AAAACTATATAATATATA-AGTTTTCAAAATATTTTCA
1 AAAACTATATATTATATATA-TTTTCAAAATATTTTCA
* *
601516 AAAACTATACATTATATATATATGTTTTCAAAATGTTTTCA
1 AAAACTAT--A-TAT-TATATATATTTTCAAAATATTTTCA
*
601557 AAAACTATATATTATATATATATATTCGAAATATTTTCA
1 AAAACTATATATTATATATAT-T-TTCAAAATATTTTCA
* *
601596 AAAACTATATATTATATATATTTTTTAAAATGTTTTCA
1 AAAACTATATATTATATATA-TTTTCAAAATATTTTCA
601634 AAAACTATATATTATATTATAT
1 AAAACTATATATTATA-TATAT
601656 ATATTTCAAA
Statistics
Matches: 276, Mismatches: 28, Indels: 31
0.82 0.08 0.09
Matches are distributed among these distances:
34 4 0.01
35 36 0.13
36 65 0.24
37 65 0.24
38 33 0.12
39 40 0.14
40 3 0.01
41 30 0.11
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATATTTTCA
Found at i:601488 original size:14 final size:12
Alignment explanation
Indices: 601313--601488 Score: 55
Period size: 12 Copynumber: 14.5 Consensus size: 12
601303 ACTATATAAT
*
601313 ATATGTTTTCAAA
1 ATATATTTT-AAA
601326 A-ATATTTTAAA
1 ATATATTTTAAA
* * *
601337 AAATTATATT-AT
1 ATA-TATTTTAAA
601349 ATATATTTTCAAA
1 ATATATTTT-AAA
*
601362 ATAT-TTTCAAA
1 ATATATTTTAAA
* *
601373 ACTATATATT-AT
1 A-TATATTTTAAA
601385 ATATATTTTCAAA
1 ATATATTTT-AAA
601398 ATAT-TTTTAAA
1 ATATATTTTAAA
* *
601409 A-ACTATTTATTAT
1 ATA-TATTT-TAAA
* *
601422 ATACATTTTCAA
1 ATATATTTTAAA
*
601434 A-ATGTTTTAAA
1 ATATATTTTAAA
**
601445 A-A-ACTTTATATT
1 ATATA-TTT-TAAA
601457 ATATATTTTAAA
1 ATATATTTTAAA
*
601469 AAATATTTTCAAA
1 ATATATTTT-AAA
601482 ACTATAT
1 A-TATAT
601489 AATATATAAG
Statistics
Matches: 118, Mismatches: 27, Indels: 35
0.66 0.15 0.19
Matches are distributed among these distances:
10 1 0.01
11 37 0.31
12 41 0.35
13 33 0.28
14 6 0.05
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.47
Consensus pattern (12 bp):
ATATATTTTAAA
Found at i:602792 original size:259 final size:251
Alignment explanation
Indices: 602247--602824 Score: 793
Period size: 259 Copynumber: 2.3 Consensus size: 251
602237 CATCCGATAC
*
602247 CCGACCCGACCCGAATATATGAATTAGAAATCCGACCC-A----AAATAATAAAAATATTATTTC
1 CCGACCCGACCCGAATATATGAATTAGAAA-CCGACCCGACCCGAAATAATAAAAAAATTATTT-
602307 TATTCAATAAAAACAATGACTTAATTGAAAAAAATTATATATAGAGGGTATTATTGTAATTATTC
64 TATTCAATAAAAACAATGACTTAATTGAAAAAAATTATATATAGAGGGTATTATTGTAATTATTC
* *** * *
602372 CTAAATATATAAGGTAAAATTATATATTTTTTGGGTCGGGTTGGGTATTTTTCACCCTAAACCCG
129 CTAAATATATAAGGTAAAATTATATATTTTTCGAAACGGGTCGGATATTTTTCACCCTAAACCCG
* *
602437 AACCCGACCCAAATATCACACTTAAAAAAACCGACCCGACATGACCAAAATAAAGTTT
194 AACCCGACCCAAATATCACACTTAAAAAAACCAACCCGACACGACCAAAATAAAGTTT
602495 CACCCGACCCGACCCGAATATATGAATTAG-AA---ACCCGACCCGAAATAATAAAAAAATTATT
1 ---CCGACCCGACCCGAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATTATT
*
602556 TTATTCAATAAAAACAGTGACTTAATTGAAAAAAAAATTATATATAGAGGGGTATTATTGTAATT
63 TTATTCAATAAAAACAATGACTTAATTG--AAAAAAATTATATATAGA-GGGTATTATTGTAATT
* *
602621 ATTCCTAAATATATGAGGTAAAATTATATATATTTTCGAAACTGGTCGGATATTTTTCACCCTAA
125 ATTCCTAAATATATAAGGTAAAATTATATAT-TTTTCGAAACGGGTCGGATATTTTTCACCCTAA
* * *
602686 ACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACCAACCCGACCCGATCAAAATAAAG
189 ACCCG-A----ACCCGACCCAAATATCACACTTAAAAAAACCAACCCGACACGACCAAAATAAAG
602751 TTT
249 TTT
602754 -C-ACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAA-TATTTT
1 CCGACCCGACCCGAATATATGAATTAGAAA-CCGACCCGACCCGAAATAATAAAAAAATTA-TTT
602816 TATTCAATA
64 TATTCAATA
602825 TATGAATAAG
Statistics
Matches: 292, Mismatches: 15, Indels: 32
0.86 0.04 0.09
Matches are distributed among these distances:
246 4 0.01
247 1 0.00
250 28 0.10
251 46 0.16
252 18 0.06
253 46 0.16
254 55 0.19
255 4 0.01
258 2 0.01
259 88 0.30
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (251 bp):
CCGACCCGACCCGAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATTATTTTA
TTCAATAAAAACAATGACTTAATTGAAAAAAATTATATATAGAGGGTATTATTGTAATTATTCCT
AAATATATAAGGTAAAATTATATATTTTTCGAAACGGGTCGGATATTTTTCACCCTAAACCCGAA
CCCGACCCAAATATCACACTTAAAAAAACCAACCCGACACGACCAAAATAAAGTTT
Found at i:604142 original size:21 final size:21
Alignment explanation
Indices: 604096--604142 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
604086 CTAACAAAAA
*
604096 TCGGATTCAGATCCGGATATT
1 TCGGATTCAGATCCGGAAATT
*
604117 T-GGATATCTGATCC-GAAATT
1 TCGGAT-TCAGATCCGGAAATT
604137 TCGGAT
1 TCGGAT
604143 GTCCGAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGGATTCAGATCCGGAAATT
Found at i:606751 original size:41 final size:41
Alignment explanation
Indices: 606674--606751 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
606664 TATCAGTTTC
* * **
606674 AATTGAAAGATAAGTTGTAATAATATACCTTTAAGCTCAAA
1 AATTGAAAGATAAGTTGCAATAATACACCTCCAAGCTCAAA
* *
606715 AATTGAAAGATAAGTTGCAATACTACGCCTCCAAGCT
1 AATTGAAAGATAAGTTGCAATAATACACCTCCAAGCT
606752 TTGGAATCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (41 bp):
AATTGAAAGATAAGTTGCAATAATACACCTCCAAGCTCAAA
Found at i:607967 original size:29 final size:29
Alignment explanation
Indices: 607925--607980 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
607915 TACCTGTGCA
* *
607925 GTTTGAAGGGTATTTTTCCAATTAATGTC
1 GTTTGAAGGGTATTTGTCCAATAAATGTC
* *
607954 GTTTGGAGGTTATTTGTCCAATAAATG
1 GTTTGAAGGGTATTTGTCCAATAAATG
607981 AATTTTTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (29 bp):
GTTTGAAGGGTATTTGTCCAATAAATGTC
Found at i:608532 original size:24 final size:24
Alignment explanation
Indices: 608483--608530 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
608473 ATATTTTAAA
* *
608483 TATTTTTATATTCTTTTGATAATT
1 TATTGTTATATTCTTTTGAAAATT
*
608507 TATTGTTAT-TTCTTTTTAAAATT
1 TATTGTTATATTCTTTTGAAAATT
608530 T
1 T
608531 TAAAATTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TATTGTTATATTCTTTTGAAAATT
Found at i:608555 original size:28 final size:28
Alignment explanation
Indices: 608523--608588 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
608513 TATTTCTTTT
* * *
608523 TAAAATTTTAAAATTTGGTCTATTAACG
1 TAAAATTCTAAAAATTCGTCTATTAACG
*
608551 TAAAATTCTAAAAATTCGTTTATTAACG
1 TAAAATTCTAAAAATTCGTCTATTAACG
608579 TAAAATTCTA
1 TAAAATTCTA
608589 CATTTGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (28 bp):
TAAAATTCTAAAAATTCGTCTATTAACG
Found at i:612439 original size:8 final size:8
Alignment explanation
Indices: 612426--612455 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
612416 AATGCTAACA
612426 AGGAAATG
1 AGGAAATG
612434 AGGAAATG
1 AGGAAATG
612442 AGGAAATG
1 AGGAAATG
612450 AGGAAA
1 AGGAAA
612456 AAGATTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (8 bp):
AGGAAATG
Found at i:616253 original size:19 final size:20
Alignment explanation
Indices: 616216--616253 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
616206 ATCGCCATTT
*
616216 TTATTACATTTTTTCTCCCA
1 TTATTACATTATTTCTCCCA
*
616236 TTATT-CATTATTTGTCCC
1 TTATTACATTATTTCTCCC
616254 TTTCTTTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTACATTATTTCTCCCA
Found at i:624989 original size:4 final size:4
Alignment explanation
Indices: 624980--625018 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
624970 TCGTCCATAT
* *
624980 TTTA TTTA TTTA TTTA TTTA TTTGT TTTA TTTA TATA TT
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TT
625019 ATATAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:625027 original size:25 final size:25
Alignment explanation
Indices: 624979--625027 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
624969 TTCGTCCATA
* *
624979 TTTTATTTATTTATTTATTTATTTG
1 TTTTATTTATATATTTATTAATTTG
625004 TTTTATTTATATA-TTATATAATTT
1 TTTTATTTATATATTTAT-TAATTT
625028 TGAAAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTATTTATATATTTATTAATTTG
Found at i:625089 original size:12 final size:12
Alignment explanation
Indices: 625026--625103 Score: 56
Period size: 12 Copynumber: 6.7 Consensus size: 12
625016 ATTATATAAT
*
625026 TTTGAAAACAT-
1 TTTGAAAATATA
625037 TTTGAAAATATA
1 TTTGAAAATATA
*
625049 --TG-ATATATA
1 TTTGAAAATATA
* * *
625058 GTTTGCAAATGGTT
1 -TTTGAAAAT-ATA
625072 TTTGAAAATATA
1 TTTGAAAATATA
*
625084 TTTGAAAACATA
1 TTTGAAAATATA
625096 TTTGAAAA
1 TTTGAAAA
625104 CATTTATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 10 0.19
12 22 0.42
13 11 0.21
14 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (12 bp):
TTTGAAAATATA
Found at i:625104 original size:12 final size:12
Alignment explanation
Indices: 625072--625106 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
625062 GCAAATGGTT
*
625072 TTTGAAAATATA
1 TTTGAAAACATA
625084 TTTGAAAACATA
1 TTTGAAAACATA
625096 TTTGAAAACAT
1 TTTGAAAACAT
625107 TTATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (12 bp):
TTTGAAAACATA
Found at i:625132 original size:40 final size:40
Alignment explanation
Indices: 625088--625229 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
625078 AATATATTTG
* * *
625088 AAAACATATTTGAAAACATTTATATATTATATAGTTTTTT
1 AAAACATTTTTGAAAATATATATATATTATATAGTTTTTT
* *
625128 AAAACGTTTTTGAAAATA-A-ATATAATATATAG-TTTTT
1 AAAACATTTTTGAAAATATATATATATTATATAGTTTTTT
* *
625165 AAAACA-TTTTGAAAATATTTATATATTATATAGTTTTGT
1 AAAACATTTTTGAAAATATATATATATTATATAGTTTTTT
*
625204 AAAACGTTTTTGAAAATATATATATA
1 AAAACATTTTTGAAAATATATATATA
625230 GTTTTTAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
36 11 0.13
37 10 0.11
38 24 0.28
39 9 0.10
40 33 0.38
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (40 bp):
AAAACATTTTTGAAAATATATATATATTATATAGTTTTTT
Found at i:625160 original size:38 final size:36
Alignment explanation
Indices: 625109--625257 Score: 157
Period size: 38 Copynumber: 4.1 Consensus size: 36
625099 GAAAACATTT
*
625109 ATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAA
1 ATATAATATATAG-TTTTTAAAAC-TTTTTGAAAATAA
* *
625147 ATATAATATATAGTTTTTAAAACATTTTGAAAATATTT
1 ATATAATATATAGTTTTTAAAACTTTTTGAAAATA--A
*
625185 ATATATTATATAGTTTTGTAAAACGTTTTTG---A-AA
1 ATATAATATATAGTTTT-TAAAAC-TTTTTGAAAATAA
*
625219 ATAT-ATATATAGTTTTTAAAAC-TTTTGAAAATAT
1 ATATAATATATAGTTTTTAAAACTTTTTGAAAATAA
625253 ATATA
1 ATATA
625258 TAGTTTTAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
30 5 0.05
32 6 0.06
33 12 0.13
34 9 0.10
36 12 0.13
37 11 0.12
38 28 0.30
39 6 0.06
40 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACTTTTTGAAAATAA
Found at i:625178 original size:76 final size:71
Alignment explanation
Indices: 625088--625259 Score: 256
Period size: 76 Copynumber: 2.4 Consensus size: 71
625078 AATATATTTG
* *
625088 AAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAATATAA
1 AAAACAT-TTTGAAAATATTTATATATTATATAGTTTTGTAAAACGTTTTTG---A-AAATAT-A
625153 TATATAGTTTTT
60 TATATAGTTTTT
625165 AAAACATTTTGAAAATATTTATATATTATATAGTTTTGTAAAACGTTTTTGAAAATATATATATA
1 AAAACATTTTGAAAATATTTATATATTATATAGTTTTGTAAAACGTTTTTGAAAATATATATATA
625230 GTTTTT
66 GTTTTT
*
625236 AAAAC-TTTTGAAAATATATATATA
1 AAAACATTTTGAAAATATTTATATA
625260 GTTTTAAAAC
Statistics
Matches: 92, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
70 18 0.20
71 18 0.20
72 6 0.07
73 1 0.01
76 42 0.46
77 7 0.08
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (71 bp):
AAAACATTTTGAAAATATTTATATATTATATAGTTTTGTAAAACGTTTTTGAAAATATATATATA
GTTTTT
Found at i:625247 original size:30 final size:31
Alignment explanation
Indices: 625185--625286 Score: 136
Period size: 30 Copynumber: 3.2 Consensus size: 31
625175 GAAAATATTT
*
625185 ATATATTATATAGTTTTGTAAAACGTTTTTGAAA
1 ATATA-TATATAGTTTT-TAAAAC-ATTTTGAAA
625219 ATATATATATAGTTTTTAAAAC-TTTTGAAA
1 ATATATATATAGTTTTTAAAACATTTTGAAA
*
625249 ATATATATATAG-TTTTAAAACATTTAGAAA
1 ATATATATATAGTTTTTAAAACATTTTGAAA
625279 ACTATATA
1 A-TATATA
625287 ATTTGAAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
29 9 0.14
30 28 0.43
31 6 0.09
32 6 0.09
33 11 0.17
34 5 0.08
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (31 bp):
ATATATATATAGTTTTTAAAACATTTTGAAA
Found at i:625295 original size:27 final size:26
Alignment explanation
Indices: 625253--625314 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
625243 TTGAAAATAT
* *
625253 ATATATAGTTTTAAAACATTTAGAAA
1 ATATATAATTTGAAAACATTTAGAAA
* **
625279 ACTATATAATTTGAAAATATTTTTAAA
1 A-TATATAATTTGAAAACATTTAGAAA
625306 ATATATAAT
1 ATATATAAT
625315 ATATAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (26 bp):
ATATATAATTTGAAAACATTTAGAAA
Found at i:625361 original size:36 final size:33
Alignment explanation
Indices: 625281--625359 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 33
625271 TTTAGAAAAC
*
625281 TATATAATTTGAAAATATTTTTAAAATATATAA
1 TATATAATTTTAAAATATTTTTAAAATATATAA
* *
625314 TATATAATTTTAAAATGTTTTTAAAAATATATAT
1 TATATAATTTTAAAATATTTTT-AAAATATATAA
625348 TATATAGATTTT
1 TATATA-ATTTT
625360 TAGAAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 20 0.49
34 16 0.39
35 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (33 bp):
TATATAATTTTAAAATATTTTTAAAATATATAA
Found at i:631860 original size:165 final size:165
Alignment explanation
Indices: 631623--632663 Score: 1503
Period size: 165 Copynumber: 6.3 Consensus size: 165
631613 TATCTGCCAA
* * * * * * * * *
631623 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGAATATCATTTGCAGCACAACTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAGT
*
631687 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
631752 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * *
631787 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCACAACTTAAGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAGT
* * **
631852 CTAGAAGGGTTGTCTGCCAACAAAAGATCTTTGAGTTCGACTACGCTCAGCTCAGCGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
* *
631917 TTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTA
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
*
631952 CCAAAGACCC-CTGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAA-
1 CCAAAGACCCTC-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAG
** * * *
632015 TACTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATAT
65 T-CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACAT
* *
632080 CATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTG
129 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * * *
632117 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCACAACTTATGT
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAGT
* * **
632182 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTTAGCTCAGCGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
*
632247 TTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * *
632282 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAGT
** * * *
632347 CTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
632412 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * * * *
632447 CCAAAGACCCCCGGGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGG
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAGT
** * * *
632512 CTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
*
632577 TTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* * * * *
632612 CCAAAGACCCCCGGGTTCGATTACACTCAACTTCGAGGTCATATCATTTACA
1 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
632664 ACATAGCTCA
Statistics
Matches: 804, Mismatches: 68, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
164 31 0.04
165 771 0.96
166 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (165 bp):
CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCACAACTCAAGT
CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
Found at i:632594 original size:495 final size:495
Alignment explanation
Indices: 631623--632660 Score: 1693
Period size: 495 Copynumber: 2.1 Consensus size: 495
631613 TATCTGCCAA
* * * * *
631623 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGAATATCATTTGCAGCACAACTTAAGT
1 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCACAACTTAAGT
631687 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
66 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
*
631752 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAG
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
* * * * *
631817 CTTCGAGGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGATCT
196 CTTCGAGGGCACATCATTTACAGCACAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
* * *
631882 TTGAGTTCGACTACGCTCAGCTCAGCGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCT
261 TCGAGTTCGACTACGCTCAGCTCAGAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
* *
631947 ATCTACCAAAGACCCCTGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
326 ATCTACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACT
* *
632012 CAATACTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
391 CAAGACTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* *
632077 TATCATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTG
456 CATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
* *
632117 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCACAACTTATGT
1 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCACAACTTAAGT
* **
632182 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTTAGCTCAGCGGCACATCA
66 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
*
632247 TTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
131 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
* * ** *
632312 CTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCT
196 CTTCGAGGGCACATCATTTACAGCACAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
632377 TCGAGTTCGACTACGCTCAGCTCTA-AGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
261 TCGAGTTCGACTACGCTCAGCTC-AGAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
* *
632441 TATCTGCCAAAGACCCCCGGGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAAC
325 TATCTACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAAC
* *
632506 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
390 TCAAGACTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
632571 ACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
455 ACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
** * * *
632612 CCAAAGACCCCCGGGTTCGATTACACTCAACTTCGAGGTCATATCATTT
1 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTT
632661 ACAACATAGC
Statistics
Matches: 501, Mismatches: 41, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
494 29 0.06
495 471 0.94
496 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (495 bp):
CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTGCAGCACAACTTAAGT
CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCA
TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAG
CTTCGAGGGCACATCATTTACAGCACAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCT
TCGAGTTCGACTACGCTCAGCTCAGAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
ATCTACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACT
CAAGACTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
CATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG
Found at i:633279 original size:21 final size:21
Alignment explanation
Indices: 633233--633279 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
633223 TTTCGTCCAT
* *
633233 ATTTTATTTATTTATTTATTT
1 ATTTTATTTATATATTTATTA
*
633254 GTTTTATTTATATA-TTATATA
1 ATTTTATTTATATATTTAT-TA
633275 ATTTT
1 ATTTT
633280 GAAAACATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTATTTATATATTTATTA
Found at i:633340 original size:12 final size:12
Alignment explanation
Indices: 633277--633354 Score: 56
Period size: 12 Copynumber: 6.7 Consensus size: 12
633267 ATTATATAAT
*
633277 TTTGAAAACAT-
1 TTTGAAAATATA
633288 TTTGAAAATATA
1 TTTGAAAATATA
*
633300 --TG-ATATATA
1 TTTGAAAATATA
* * *
633309 GTTTGCAAATGGTT
1 -TTTGAAAAT-ATA
633323 TTTGAAAATATA
1 TTTGAAAATATA
*
633335 TTTGAAAACATA
1 TTTGAAAATATA
633347 TTTGAAAA
1 TTTGAAAA
633355 CATTTATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 10 0.19
12 22 0.42
13 11 0.21
14 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.40
Consensus pattern (12 bp):
TTTGAAAATATA
Found at i:633355 original size:12 final size:12
Alignment explanation
Indices: 633323--633357 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
633313 GCAAATGGTT
*
633323 TTTGAAAATATA
1 TTTGAAAACATA
633335 TTTGAAAACATA
1 TTTGAAAACATA
633347 TTTGAAAACAT
1 TTTGAAAACAT
633358 TTATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (12 bp):
TTTGAAAACATA
Found at i:633383 original size:40 final size:40
Alignment explanation
Indices: 633339--633470 Score: 182
Period size: 38 Copynumber: 3.4 Consensus size: 40
633329 AATATATTTG
*
633339 AAAACATATTTGAAAACATTTATATATTATATAGTTTTTT
1 AAAACATTTTTGAAAACATTTATATATTATATAGTTTTTT
* ** *
633379 AAAACGTTTTTG-AAA-ATAAATATAATATATAG-TTTTT
1 AAAACATTTTTGAAAACATTTATATATTATATAGTTTTTT
633416 AAAACA-TTTTGAAAACATTTATATATTATATAGTTTTTT
1 AAAACATTTTTGAAAACATTTATATATTATATAGTTTTTT
*
633455 AAAACGTTTTTGAAAA
1 AAAACATTTTTGAAAA
633471 TAAAATATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
36 5 0.06
37 13 0.17
38 28 0.36
39 13 0.17
40 19 0.24
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (40 bp):
AAAACATTTTTGAAAACATTTATATATTATATAGTTTTTT
Found at i:633411 original size:38 final size:36
Alignment explanation
Indices: 633360--633513 Score: 168
Period size: 38 Copynumber: 4.1 Consensus size: 36
633350 GAAAACATTT
*
633360 ATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAA
1 ATATAATATATAG-TTTTTAAAAC-TTTTTGAAAATAA
* **
633398 ATATAATATATAGTTTTTAAAACATTTTGAAAACATTT
1 ATATAATATATAGTTTTTAAAACTTTTTG-AAA-ATAA
*
633436 ATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAA
1 ATATAATATATAG-TTTTTAAAAC-TTTTTGAAAAT-AA
* *
633475 ATATAATATATAGTCTTT-AAA-TTTTTGAAAATAT
1 ATATAATATATAGTTTTTAAAACTTTTTGAAAATAA
633509 ATATA
1 ATATA
633514 TAGTTTTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
34 6 0.06
35 11 0.11
36 5 0.05
37 16 0.16
38 32 0.32
39 25 0.25
40 5 0.05
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACTTTTTGAAAATAA
Found at i:633429 original size:76 final size:78
Alignment explanation
Indices: 633339--633495 Score: 291
Period size: 76 Copynumber: 2.0 Consensus size: 78
633329 AATATATTTG
633339 AAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAAT-AAATATA
1 AAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAAATATA
*
633403 ATATATAGTTTTT
66 ATATATAGTCTTT
633416 AAAACAT-TTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAAATATA
1 AAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAAATATA
633480 ATATATAGTCTTT
66 ATATATAGTCTTT
633493 AAA
1 AAA
633496 TTTTTGAAAA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
76 49 0.63
77 29 0.37
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (78 bp):
AAAACATATTTGAAAACATTTATATATTATATAGTTTTTTAAAACGTTTTTGAAAATAAAATATA
ATATATAGTCTTT
Found at i:633516 original size:29 final size:31
Alignment explanation
Indices: 633472--633543 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 31
633462 TTTTGAAAAT
*
633472 AAAATATAATATATAGTCTTT-AA-ATTTTTG
1 AAAATAT-ATATATAGTCTTTAAACATTTTAG
*
633502 AAAATATATATATAGTTTTTAAACATTTTAG
1 AAAATATATATATAGTCTTTAAACATTTTAG
633533 AAAACTATATA
1 AAAA-TATATA
633544 ATTTTGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 12 0.32
30 9 0.24
31 10 0.27
32 6 0.16
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (31 bp):
AAAATATATATATAGTCTTTAAACATTTTAG
Found at i:633593 original size:30 final size:31
Alignment explanation
Indices: 633538--633610 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
633528 TTTAGAAAAC
*
633538 TATATAATTTTGAAAATATTTTTTAAAAATA
1 TATATAATTTTGAAAATAGTTTTTAAAAATA
633569 TAATATAATTTT-AAAAT-GTTTTTAAAAATA
1 T-ATATAATTTTGAAAATAGTTTTTAAAAATA
633599 TATATAGATTTT
1 TATATA-ATTTT
633611 TAGAAAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 5 0.13
30 18 0.46
31 6 0.15
32 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
TATATAATTTTGAAAATAGTTTTTAAAAATA
Done.