Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007490.1 Hibiscus syriacus cultivar Beakdansim tig00020682_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: 795028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:333386 original size:21 final size:21
Alignment explanation
Indices: 333360--333406 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
333350 TCGGTAATTA
*
333360 GCGTTGCGAATTTGGAAAATC
1 GCGTTGCGAATTTAGAAAATC
333381 GCGTTGCGAATTTAGAAAATC
1 GCGTTGCGAATTTAGAAAATC
*
333402 ACGTT
1 GCGTT
333407 ACAATAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (21 bp):
GCGTTGCGAATTTAGAAAATC
Found at i:333463 original size:20 final size:20
Alignment explanation
Indices: 333435--333510 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
333425 TATATCGGTA
*
333435 ATTAGCGTTGCGATTTATAT
1 ATTAGCGTTGCGATTTACAT
* *
333455 ATTATCGTTTCGATTTACAT
1 ATTAGCGTTGCGATTTACAT
** * *
333475 ATCCGCTTTGCGATTTACCT
1 ATTAGCGTTGCGATTTACAT
*
333495 ATTCGCGTTGCGATTT
1 ATTAGCGTTGCGATTT
333511 TGGAACATGT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTAGCGTTGCGATTTACAT
Found at i:337297 original size:21 final size:21
Alignment explanation
Indices: 337271--337322 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
337261 GATCCATGTT
337271 TTCACGTGGGCGTTATAGTGC
1 TTCACGTGGGCGTTATAGTGC
*
337292 TTCACGTGGGCGTTGTAGTGC
1 TTCACGTGGGCGTTATAGTGC
*
337313 TTCACATGGG
1 TTCACGTGGG
337323 TAGCTCGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.33
Consensus pattern (21 bp):
TTCACGTGGGCGTTATAGTGC
Found at i:337869 original size:91 final size:91
Alignment explanation
Indices: 337714--338193 Score: 707
Period size: 91 Copynumber: 5.3 Consensus size: 91
337704 AAAGTTGAAC
* * *
337714 GAGTTCTTCTCACTATGAACTC-CCTGCTGGAAATGTTGATGC-AAGGTTGAACAAGTTCTTCTC
1 GAGTTCTTCTCATTATGAACTCTCC-ACTGGAAATCTTGA-GCTAAGGTTGAACAAGTTCTTCTC
*
337777 ATTATGAACTTTTTCTCCCTCGTTGGAT
64 ATTATGAACTTCTTCTCCCTCGTTGGAT
* *
337805 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACTAAGGTTGAAAAAGTTCTTCTCAT
1 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAGCTAAGGTTGAACAAGTTCTTCTCAT
*
337870 TATGAACTTCTTCTCCCTTGTTGGAT
66 TATGAACTTCTTCTCCCTCGTTGGAT
* *
337896 GAGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACTAAGGTTGAACAAGTTCTTCTCAT
1 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAGCTAAGGTTGAACAAGTTCTTCTCAT
* *
337961 TATGAATTTCTTCTCCCTTGTTGGAT
66 TATGAACTTCTTCTCCCTCGTTGGAT
* * ** * ** *
337987 GTGTTCTTATCATTATGAACTCTCCGTTAGAAATGATGAGCTAAGGTTGAACAAGTTCTTCTCTT
1 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAGCTAAGGTTGAACAAGTTCTTCTCAT
* *
338052 TACGAACTTCTTCTCCCTCATTGGAT
66 TATGAACTTCTTCTCCCTCGTTGGAT
*
338078 GAGTTCTTCTCATTATGAACTCTCCACTGGAAATGC-TGAGCCAAGGTTGAACAAGTTCTTCTCA
1 GAGTTCTTCTCATTATGAACTCTCCACTGGAAAT-CTTGAGCTAAGGTTGAACAAGTTCTTCTCA
338142 TTAT-AACTTCTTCTCCCTCGTTGGAT
65 TTATGAACTTCTTCTCCCTCGTTGGAT
338168 GAGTTCTTCTCATTATGAACTCTCCA
1 GAGTTCTTCTCATTATGAACTCTCCA
338194 TTTGAAATTT
Statistics
Matches: 354, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
90 48 0.14
91 304 0.86
92 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (91 bp):
GAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAGCTAAGGTTGAACAAGTTCTTCTCAT
TATGAACTTCTTCTCCCTCGTTGGAT
Found at i:338736 original size:36 final size:36
Alignment explanation
Indices: 338694--339429 Score: 777
Period size: 36 Copynumber: 20.5 Consensus size: 36
338684 AAAAAAACCA
* * *
338694 TCTCAAGTGAGATAGATTTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* *
338730 TCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC-G
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
*
338765 ATCTCAA-AG-G-T----TTGTGTTTCAAGAGAAACTG
1 -TCTCAAGAGAGATAAAATT-TGTTTCAAGGGAAACTG
* * * * *
338796 TCTAAAGGGAGACAAAACTTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* *
338832 TCTCAAGAGAGATAATATTT-TTTCAAGGGAAACAG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
*
338867 AT-TC-A-A-AGAT----TTTGTTTCAAGGGAAACAG
1 -TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
*
338896 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* * *
338932 TATCAAGAAAGACAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
338968 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
*
339004 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
339040 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* * *
339076 TCTCAAGAGAGACAAAAGTTGTTTCAAGTGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* * *
339112 TCTCGATAGAGATAAAATTTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* * *
339148 TCTCGATAGAGACAAAATTTGTTTCAAGGGAAACTG
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* * **
339184 TCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACAA
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* * *
339220 CCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
* *
339256 TCTCAAGCGAGATAAAATCTTCTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGATAAAA--TT-TGTTTCAAGGGAAACTG
* * *
339295 CCTCAAGCGAGATAAAATCTTCTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGATAAAA--TT-TGTTTCAAGGGAAACTG
* * * *
339334 CCTCAAGCGAGATAAAATCTTCTGTTTCAAGTGAAACTA
1 TCTCAAGAGAGATAAAA--TT-TGTTTCAAGGGAAACTG
* * * *
339373 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTA
1 TCTCAAGAGAGATAAAA--TT-TGTTTCAAGGGAAACTG
*
339412 TCTCAAGCGAGATAAAAT
1 TCTCAAGAGAGATAAAAT
339430 CTTCTGTTTC
Statistics
Matches: 621, Mismatches: 56, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.01
29 19 0.03
30 19 0.03
31 3 0.00
32 8 0.01
33 1 0.00
34 2 0.00
35 18 0.03
36 396 0.64
37 2 0.00
38 2 0.00
39 147 0.24
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (36 bp):
TCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTG
Found at i:338820 original size:66 final size:66
Alignment explanation
Indices: 338713--338837 Score: 198
Period size: 66 Copynumber: 1.9 Consensus size: 66
338703 AGATAGATTT
* *
338713 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGGTTT
338778 G
66 G
* *
338779 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTT-GTTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA-TTCGTTTCAAGGGAAACGATCTCAA
338838 GAGAGATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 52 0.96
67 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGGTTT
G
Found at i:339573 original size:76 final size:76
Alignment explanation
Indices: 339476--339698 Score: 324
Period size: 76 Copynumber: 2.9 Consensus size: 76
339466 AATCTTCTTT
339476 AAAAATAATCTTGAGTGAAATGAAATGTTTTCTTTCGAGTAAAAATCGTCTCAAGCGAGACAAAT
1 AAAAATAATCTTGAGTGAAATGAAATGTTTTCTTTCGAGTAAAAATCGTCTCAAGCGAGACAAAT
339541 CTTATTTTAAG
66 CTTATTTTAAG
* * * * *
339552 AAAAACAATCTTAAGTCAAATGAAATGTCTTCTTTCGAGTAAAAATCGTCTTAAGCGAGACAAAT
1 AAAAATAATCTTGAGTGAAATGAAATGTTTTCTTTCGAGTAAAAATCGTCTCAAGCGAGACAAAT
*
339617 CTTGTTTTAAG
66 CTTATTTTAAG
* * *
339628 AAAAATAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAA-CTATCTCAAGCGAGACAA
1 AAAAATAATCTTGAGTGAAATGAAATGTT-TTCTTTCGAGTAAAAATC-GTCTCAAGCGAGAC-A
339691 AATCTTAT
63 AATCTTAT
339699 GTTTCAAGGG
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
75 6 0.05
76 115 0.89
77 8 0.06
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (76 bp):
AAAAATAATCTTGAGTGAAATGAAATGTTTTCTTTCGAGTAAAAATCGTCTCAAGCGAGACAAAT
CTTATTTTAAG
Found at i:339702 original size:40 final size:39
Alignment explanation
Indices: 339649--339745 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 39
339639 TGAGTGAAAT
* * *
339649 AAATCTTCTTGTTTCGAGTAAAAACTATCTCAAGCGAGACA
1 AAATCTT-ATGTTTCAAG-AAAAACTATCTCAAACGAGACA
**
339690 AAATCTTATGTTTCAAGGGAAACTATCTCAAACGAGACA
1 AAATCTTATGTTTCAAGAAAAACTATCTCAAACGAGACA
339729 AAATCTTATGTTTCAAG
1 AAATCTTATGTTTCAAG
339746 CGAAACAACT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 36 0.71
40 8 0.16
41 7 0.14
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (39 bp):
AAATCTTATGTTTCAAGAAAAACTATCTCAAACGAGACA
Found at i:339715 original size:39 final size:39
Alignment explanation
Indices: 339670--339751 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
339660 TTTCGAGTAA
* *
339670 AAACTATCTCAAGCGAGACAAAATCTTATGTTTCAAGGG
1 AAACTATCTCAAACGAGACAAAATCTTATGTTTCAAGCG
339709 AAACTATCTCAAACGAGACAAAATCTTATGTTTCAAGCG
1 AAACTATCTCAAACGAGACAAAATCTTATGTTTCAAGCG
339748 AAAC
1 AAAC
339752 AACTCTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (39 bp):
AAACTATCTCAAACGAGACAAAATCTTATGTTTCAAGCG
Found at i:339802 original size:60 final size:60
Alignment explanation
Indices: 339698--339811 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
339688 CAAAATCTTA
* *
339698 TGTTTCAAGGGAAACTATCTCAAACGAGACAAAATCTTATGTTTCAAGCGAAACAACTCT
1 TGTTTCAAGGGAAACTATCTCAAACGAGACAAAATCTTACGTTTCAAGAGAAACAACTCT
* * * * * * *
339758 TGTTTTAAGTGAAATTATCTCAAGCGAGATAAAATCTTCCGTTTCGAGAGAAAC
1 TGTTTCAAGGGAAACTATCTCAAACGAGACAAAATCTTACGTTTCAAGAGAAAC
339812 CATCTCAAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (60 bp):
TGTTTCAAGGGAAACTATCTCAAACGAGACAAAATCTTACGTTTCAAGAGAAACAACTCT
Found at i:345309 original size:21 final size:21
Alignment explanation
Indices: 345283--345335 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
345273 GATCCATGTT
345283 TTCACGTGGGCGTTGTAGTGC
1 TTCACGTGGGCGTTGTAGTGC
*
345304 TTCACGTGGGTGTTGTAGTGC
1 TTCACGTGGGCGTTGTAGTGC
*
345325 TTCACATGGGC
1 TTCACGTGGGC
345336 AGCTCGATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.19, G:0.36, T:0.34
Consensus pattern (21 bp):
TTCACGTGGGCGTTGTAGTGC
Found at i:353396 original size:19 final size:20
Alignment explanation
Indices: 353372--353416 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
353362 CTTTTAATAT
*
353372 TTTATTTTGA-AAATAAAAA
1 TTTATTTTCATAAATAAAAA
*
353391 TTTATTTTCATAGATAAAAA
1 TTTATTTTCATAAATAAAAA
353411 TTTATT
1 TTTATT
353417 AAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTATTTTCATAAATAAAAA
Found at i:353965 original size:16 final size:17
Alignment explanation
Indices: 353938--353973 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
353928 GATATGAGAA
353938 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
353955 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
353971 AAA
1 AAA
353974 ATAACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:369198 original size:9 final size:9
Alignment explanation
Indices: 369186--369211 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
369176 TTGCAAATCA
369186 AAAAAATAT
1 AAAAAATAT
369195 AAAAAATAT
1 AAAAAATAT
369204 AAAAAATA
1 AAAAAATA
369212 AAATAAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAATAT
Found at i:373026 original size:17 final size:17
Alignment explanation
Indices: 373006--373038 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
372996 TTTAGGGAAG
373006 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
373023 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
373039 TTAACTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:382171 original size:17 final size:16
Alignment explanation
Indices: 382120--382169 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 16
382110 GGTTCTATAC
382120 AATATTATTTAAAATT
1 AATATTATTTAAAATT
*
382136 AAATAGATAATTTTAAAATT
1 -AAT--ATTA-TTTAAAATT
382156 AATATTATTTAAAA
1 AATATTATTTAAAA
382170 ATAAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 7 0.25
17 6 0.21
19 6 0.21
20 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATATTATTTAAAATT
Found at i:382176 original size:17 final size:17
Alignment explanation
Indices: 382120--382176 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
382110 GGTTCTATAC
*
382120 AATATTATTTAAAATTA
1 AATATTATTTAAAAATA
* * *
382137 AATAGATAATTTTAAAATT
1 AAT--ATTATTTAAAAATA
382156 AATATTATTTAAAAATA
1 AATATTATTTAAAAATA
382173 AATA
1 AATA
382177 ATTAATATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 18 0.58
19 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATTATTTAAAAATA
Found at i:382193 original size:22 final size:24
Alignment explanation
Indices: 382152--382226 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 24
382142 ATAATTTTAA
382152 AATTAATATTATTTAAAAATAAAT
1 AATTAATATTATTTAAAAATAAAT
*
382176 AATTAATATTA-TT-CAAATAAAT
1 AATTAATATTATTTAAAAATAAAT
*
382198 AATT--TGTT-TTTAAAAATTAAAT
1 AATTAATATTATTTAAAAA-TAAAT
*
382220 AAATAAT
1 AATTAAT
382227 TTCATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 5 0.12
21 3 0.07
22 20 0.48
23 2 0.05
24 12 0.29
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
AATTAATATTATTTAAAAATAAAT
Found at i:382703 original size:30 final size:31
Alignment explanation
Indices: 382663--382722 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
382653 TAAATGGTTT
* *
382663 TGAAAAAAAAA-TAAAGTTTAGGTACTAAAA
1 TGAAAAAAAAATTAAAGTATAGATACTAAAA
* *
382693 TGAAATAAAAATTATAGTATAGATACTAAA
1 TGAAAAAAAAATTAAAGTATAGATACTAAA
382723 TGTGTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.58, C:0.03, G:0.12, T:0.27
Consensus pattern (31 bp):
TGAAAAAAAAATTAAAGTATAGATACTAAAA
Found at i:383181 original size:25 final size:26
Alignment explanation
Indices: 383136--383187 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
383126 AATATTCGCC
* *
383136 TCCTTGAAATTTATAAGTTCATTCAT
1 TCCTTGAAATTTATAAATTCATCCAT
383162 TCCTT-AAATTT-TAAAATTCATCCAT
1 TCCTTGAAATTTAT-AAATTCATCCAT
383187 T
1 T
383188 TAACATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 1 0.04
25 17 0.74
26 5 0.22
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (26 bp):
TCCTTGAAATTTATAAATTCATCCAT
Found at i:386359 original size:19 final size:20
Alignment explanation
Indices: 386312--386359 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
386302 TTTAGTCTGC
386312 TTTATTT-TTAATGATTTTA
1 TTTATTTATTAATGATTTTA
* * *
386331 TATATATATTGAT-ATTTTA
1 TTTATTTATTAATGATTTTA
386350 TTTATTTATT
1 TTTATTTATT
386360 TATTCTCACC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATTTATTAATGATTTTA
Found at i:388882 original size:41 final size:42
Alignment explanation
Indices: 388837--388931 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 42
388827 TACATATATC
* *
388837 GTGGCGTTTT-CAAATAAACGCCGCTAGAA-CCTAGTACTTTA
1 GTGGCGTTTTACAAAAAAACGCCGCTA-AATACTAGTACTTTA
* *
388878 GTGGCGTTTTAAGCAAAAAAACGTCGCTAAATACTCGTACTTTA
1 GTGGCGTTTT-A-CAAAAAAACGCCGCTAAATACTAGTACTTTA
*
388922 GTGGCATTTT
1 GTGGCGTTTT
388932 TATATAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 10 0.22
43 2 0.04
44 33 0.73
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (42 bp):
GTGGCGTTTTACAAAAAAACGCCGCTAAATACTAGTACTTTA
Found at i:388906 original size:44 final size:44
Alignment explanation
Indices: 388847--388931 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
388837 GTGGCGTTTT
* * *
388847 CAAATAAACGCCGCTAGAA-CCTAGTACTTTAGTGGCGTTTTAAG
1 CAAAAAAACGCCGCTA-AATACTAGTACTTTAGTGGCATTTTAAG
* *
388891 CAAAAAAACGTCGCTAAATACTCGTACTTTAGTGGCATTTT
1 CAAAAAAACGCCGCTAAATACTAGTACTTTAGTGGCATTTT
388932 TATATAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (44 bp):
CAAAAAAACGCCGCTAAATACTAGTACTTTAGTGGCATTTTAAG
Found at i:389013 original size:41 final size:41
Alignment explanation
Indices: 388904--389020 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 41
388894 AAAAACGTCG
* * **
388904 CTAAATACTCGTACTTTAGTGGCATTTTTATATAAATGCCT
1 CTAAAGACTCGTACTTTAGTGGCATTTTTATACAAATGCAA
*
388945 CTAAAGACT-GTACTTTCGTGGCATTTTTATACAAATGCAA
1 CTAAAGACTCGTACTTTAGTGGCATTTTTATACAAATGCAA
* * **
388985 CTATAGACTCATACTTTAGTGGTGTTTTTATACAAA
1 CTAAAGACTCGTACTTTAGTGGCATTTTTATACAAA
389021 CGCCATAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 35 0.54
41 30 0.46
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (41 bp):
CTAAAGACTCGTACTTTAGTGGCATTTTTATACAAATGCAA
Found at i:392584 original size:44 final size:41
Alignment explanation
Indices: 392536--392631 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 41
392526 TTTTACATTC
* *
392536 ACAAACGCCACTATATGACATAACATTTAGCGGCGTTTTTGGG
1 ACAAACGCCACTATATGACACAACATTTAGCGGC--TTTTGAG
* * * * *
392579 AACAAATGACATTATATGTCACAACATTTAGTGGCTTTTGAG
1 -ACAAACGCCACTATATGACACAACATTTAGCGGCTTTTGAG
392621 ACAAACGCCAC
1 ACAAACGCCAC
392632 AGAAGAAAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
41 8 0.19
42 6 0.14
44 28 0.67
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (41 bp):
ACAAACGCCACTATATGACACAACATTTAGCGGCTTTTGAG
Found at i:394522 original size:31 final size:31
Alignment explanation
Indices: 394482--394546 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
394472 TTGCAATACA
*
394482 GTCCCCCAACATTTAGTCTGTTTGCAAAATG
1 GTCCACCAACATTTAGTCTGTTTGCAAAATG
*
394513 GTCCACCAACATTTAGTCTGTTTGCAATATG
1 GTCCACCAACATTTAGTCTGTTTGCAAAATG
394544 GTC
1 GTC
394547 TCCGATCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (31 bp):
GTCCACCAACATTTAGTCTGTTTGCAAAATG
Found at i:396531 original size:31 final size:31
Alignment explanation
Indices: 396483--396568 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
396473 TAACGGCGTC
*
396483 AAATGGTTGGA-GTCCATATTGCAAACAGACT
1 AAAT-GTTGGAGGACCATATTGCAAACAGACT
* *
396514 AAATGTTGGGGGACCATATTGCAAACTGACT
1 AAATGTTGGAGGACCATATTGCAAACAGACT
*
396545 AAATGTTGGAGGACTATATTGCAA
1 AAATGTTGGAGGACCATATTGCAA
396569 GTTTTAAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (31 bp):
AAATGTTGGAGGACCATATTGCAAACAGACT
Found at i:401122 original size:23 final size:25
Alignment explanation
Indices: 401093--401139 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
401083 TAGTCATTTT
401093 ATGATT-ATTTTTACTATT-TTATA
1 ATGATTAATTTTTACTATTATTATA
*
401116 ATGATTAATTTTTATTATTATTAT
1 ATGATTAATTTTTACTATTATTAT
401140 TTTCTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
ATGATTAATTTTTACTATTATTATA
Found at i:401345 original size:5 final size:5
Alignment explanation
Indices: 401331--401430 Score: 61
Period size: 5 Copynumber: 20.4 Consensus size: 5
401321 GTTTTATTAT
*
401331 TTTTC TTTT- TCTTT- TTTTC TTTT- TTCTT- TTTTC TTTT- TGTTTA
1 TTTTC TTTTC T-TTTC TTTTC TTTTC TT-TTC TTTTC TTTTC T-TTTC
* * * *
401374 TGTTTC TTTTC TATTC TTTT- TTTTG TTTTG TTTTC ATTTC TTTTC TATTT-
1 T-TTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC
401424 TTTTC TT
1 TTTTC TT
401431 ATTTTTATCA
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
4 16 0.20
5 55 0.69
6 9 0.11
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:401346 original size:7 final size:7
Alignment explanation
Indices: 401330--401368 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
401320 TGTTTTATTA
401330 TTTTTC-
1 TTTTTCT
401336 TTTTTCTT
1 TTTTTC-T
401344 TTTTTCT
1 TTTTTCT
401351 TTTTTCT
1 TTTTTCT
401358 TTTTTCT
1 TTTTTCT
401365 TTTT
1 TTTT
401369 GTTTATGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.19
7 19 0.61
8 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTCT
Found at i:401347 original size:14 final size:13
Alignment explanation
Indices: 401330--401383 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
401320 TGTTTTATTA
401330 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TT
401344 TTTTTCTTTTTTCT
1 TTTTTCTTTTTT-T
401358 TTTTTCTTTTTGTT
1 TTTTTCTTTTT-TT
401372 TATGTTTCTTTT
1 T-T-TTTCTTTT
401384 CTATTCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.03
14 25 0.69
15 2 0.06
16 8 0.22
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:401403 original size:34 final size:33
Alignment explanation
Indices: 401330--401443 Score: 102
Period size: 34 Copynumber: 3.6 Consensus size: 33
401320 TGTTTTATTA
*
401330 TTTTTCTTTTTCTTTT--TTTC-TTT-T-TTCT
1 TTTTTCTTTTTGTTTTCATTTCTTTTCTATTCT
*
401358 TTTTTCTTTTTGTTTAT-GTTTCTTTTCTATTCT
1 TTTTTCTTTTTGTTT-TCATTTCTTTTCTATTCT
*
401391 TTTTTTTGTTTTGTTTTCATTTCTTTTCTA-T-T
1 TTTTTCT-TTTTGTTTTCATTTCTTTTCTATTCT
*
401423 TTTTTCTTATTT-TTATCATTT
1 TTTTTCTT-TTTGTTTTCATTT
401444 TATTCATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
28 14 0.19
29 1 0.01
30 4 0.05
31 12 0.16
32 11 0.15
33 12 0.16
34 19 0.26
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.79
Consensus pattern (33 bp):
TTTTTCTTTTTGTTTTCATTTCTTTTCTATTCT
Found at i:401408 original size:29 final size:30
Alignment explanation
Indices: 401345--401427 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
401335 CTTTTTCTTT
* * *
401345 TTTTCTTTTTTCTTTTTTCTTTTTGTTTATG
1 TTTTCTTTTCTATTCTTT-TTTTTGTTTATG
401376 -TTTCTTTTCTATTCTTTTTTTTGTTT-TG
1 TTTTCTTTTCTATTCTTTTTTTTGTTTATG
* *
401404 TTTTCATTTCTTTTCTATTTTTTT
1 TTTTCTTTTCTATTCT-TTTTTTT
401428 CTTATTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.04
29 22 0.49
30 21 0.47
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.80
Consensus pattern (30 bp):
TTTTCTTTTCTATTCTTTTTTTTGTTTATG
Found at i:401436 original size:29 final size:28
Alignment explanation
Indices: 401336--401436 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 28
401326 ATTATTTTTC
* *
401336 TTTTTCTTTTTTTCTTTTTTCTTTT-TTCT
1 TTTTTCTTATTTT-TCTTTTCTTTTCTT-T
* *
401365 TTTTGT-TTATGTTTCTTTTCTATTCTTT
1 TTTT-TCTTATTTTTCTTTTCTTTTCTTT
* * *
401393 TTTTTGTTTTGTTTTCATTTCTTTTCTATT
1 TTTTTCTTAT-TTTTCTTTTCTTTTCT-TT
401423 TTTTTCTTATTTTT
1 TTTTTCTTATTTTT
401437 ATCATTTTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.02
28 17 0.30
29 28 0.49
30 11 0.19
ACGTcount: A:0.05, C:0.11, G:0.04, T:0.80
Consensus pattern (28 bp):
TTTTTCTTATTTTTCTTTTCTTTTCTTT
Found at i:401460 original size:28 final size:28
Alignment explanation
Indices: 401420--401490 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
401410 TTTCTTTTCT
*
401420 ATTTTTTTCTTATTTTTA-TCATTTTATTC
1 ATTTTATT-TTATTTTTATTCATTTTA-TC
* **
401449 ATTTTATTTTATGTTTATTTGTTTTATC
1 ATTTTATTTTATTTTTATTCATTTTATC
401477 ATTTTATTTTATTT
1 ATTTTATTTTATTT
401491 CCTTATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (28 bp):
ATTTTATTTTATTTTTATTCATTTTATC
Found at i:401503 original size:23 final size:22
Alignment explanation
Indices: 401452--401511 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
401442 TTTATTCATT
* *
401452 TTATTTTATGTTTATTTGTTTTA
1 TTATTTTAT-TTTATTTCTTATA
*
401475 TCATTTTATTTTATTTCCTTATA
1 TTATTTTATTTTATTT-CTTATA
401498 TTA-TTTATTTTATT
1 TTATTTTATTTTATT
401512 ATCATTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (22 bp):
TTATTTTATTTTATTTCTTATA
Found at i:407688 original size:45 final size:49
Alignment explanation
Indices: 407614--407712 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 49
407604 TTTATTTTCG
*
407614 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTTA
* *
407662 TTTTTT-GAAT-AA-GCATGCGAATTAGATATCATGAGGTTAGGATTTC
1 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTTA
407708 TTTTT
1 TTTTT
407713 GTGGATAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
45 27 0.57
46 10 0.21
47 4 0.09
48 6 0.13
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (49 bp):
TTTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTTA
Found at i:417444 original size:20 final size:21
Alignment explanation
Indices: 417414--417458 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
417404 AATAAAAATG
417414 AGAAGAAGAAAAAGAGGAAAAAA
1 AGAAGAA-AAAAAGA-GAAAAAA
*
417437 AGAGGAAAAAAAGAGAAAAAA
1 AGAAGAAAAAAAGAGAAAAAA
417458 A
1 A
417459 TGGAAAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 7 0.33
23 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAAGAGAAAAAA
Found at i:417509 original size:14 final size:14
Alignment explanation
Indices: 417470--417509 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
417460 GGAAAATGGA
417470 AGAAAAATG-AAAG
1 AGAAAAATGAAAAG
**
417483 AGAAAAACAAAAAG
1 AGAAAAATGAAAAG
417497 AGAAAAATGAAAA
1 AGAAAAATGAAAA
417510 AAAATAGAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (14 bp):
AGAAAAATGAAAAG
Found at i:419136 original size:55 final size:52
Alignment explanation
Indices: 418835--419249 Score: 457
Period size: 51 Copynumber: 7.9 Consensus size: 52
418825 GAAGCAAACT
* *
418835 CGTTTGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTATTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
418886 AGTTCATTGAAGATT-GAGT-TCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTATTGAAGATTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACA
* ** *
418937 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTATTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* ** *
418988 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTATTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
*
419039 CGTTTATTGAAGA-TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTATTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
419090 CGTTTTTTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTATTGAAGA---TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * *
419145 GGTTTACTGAAGATTATTCGAGTTTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTTATTGAAG---ATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
419200 CGTTTACTGAAGATTGTTCGAGTCTTATACTC-CATGAAAGAATAGGGAGC
1 CGTTTATTGAAGA---TTCGAGTCTTATACTCTC-TGAAGGAATAGGGAGC
419250 AGACCCGCCA
Statistics
Matches: 326, Mismatches: 24, Indels: 24
0.87 0.06 0.06
Matches are distributed among these distances:
50 1 0.00
51 201 0.62
52 1 0.00
54 1 0.00
55 121 0.37
58 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (52 bp):
CGTTTATTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:419269 original size:55 final size:54
Alignment explanation
Indices: 419003--419256 Score: 291
Period size: 55 Copynumber: 4.7 Consensus size: 54
418993 GTTGAAGATT
* * * * *
419003 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA----TC
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCCGTTTA-TGAAGATTGTTC
* * * *
419054 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTTTGAAGATTGTTC
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCCG-TTTATGAAGATTGTTC
* ** *
419109 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACAGGTTTACTGAAGATTATTC
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCCGTTTA-TGAAGATTGTTC
* * *
419164 GAGTTTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTGAAGATTGTTC
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCCGTTTA-TGAAGATTGTTC
*
419219 GAGTCTTATACTCCATGAAAGAATAGGGAGCAGACCCG
1 GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCCG
419257 CCATTTGAAG
Statistics
Matches: 179, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
51 42 0.23
52 3 0.02
54 3 0.02
55 131 0.73
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (54 bp):
GAGTCTTATACTCCCTGAAAGAATAGGGAGCAGACCCGTTTATGAAGATTGTTC
Found at i:419269 original size:110 final size:109
Alignment explanation
Indices: 418952--419253 Score: 300
Period size: 110 Copynumber: 2.8 Consensus size: 109
418942 GTTGAAGATT
* * * * *** *
418952 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTATA
1 GAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTATA
* * *
419013 CTCTC-TGAAGGAATAGGGAGCGGACA-CGTTTATTGAAG---A-TC
66 CTC-CATGAAAGAATAGGGAGCAGACAGC-ATTA-TGAAGATTATTC
* * * **
419054 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTTTGAAGATTGTTCGAGTCTTATA
1 GAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTATA
* * **
419119 CTCCCTGAACGAATAGGGAGCAGACAGGTTTACTGAAGATTATTC
66 CTCCATGAAAGAATAGGGAGCAGACAGCATTA-TGAAGATTATTC
* *
419164 GAGTTTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTATA
1 GAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTATA
419229 CTCCATGAAAGAATAGGGAGCAGAC
66 CTCCATGAAAGAATAGGGAGCAGAC
419254 CCGCCATTTG
Statistics
Matches: 171, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
102 44 0.26
105 3 0.02
106 40 0.23
109 1 0.01
110 83 0.49
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (109 bp):
GAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTACTGAAGATTGTTCGAGTCTTATA
CTCCATGAAAGAATAGGGAGCAGACAGCATTATGAAGATTATTC
Found at i:424604 original size:10 final size:10
Alignment explanation
Indices: 424589--424623 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
424579 TTTATGATTA
424589 TTTTTACTAT
1 TTTTTACTAT
424599 TTTTTACTAT
1 TTTTTACTAT
**
424609 TTTTTTTTAT
1 TTTTTACTAT
424619 TTTTT
1 TTTTT
424624 TATTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTACTAT
Found at i:424772 original size:10 final size:10
Alignment explanation
Indices: 424718--424773 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
424708 TCCTAATGTT
424718 TATTTATATA
1 TATTTATATA
* *
424728 TGTATATATA
1 TATTTATATA
*
424738 TATTTATTTA
1 TATTTATATA
* *
424748 TTTTTACATA
1 TATTTATATA
424758 -ATTTATATA
1 TATTTATATA
*
424767 TCTTTAT
1 TATTTAT
424774 TATTTTTCTT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
9 7 0.21
10 27 0.79
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (10 bp):
TATTTATATA
Found at i:424800 original size:16 final size:15
Alignment explanation
Indices: 424770--424804 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
424760 TTATATATCT
424770 TTATTATTTTTCTTA
1 TTATTATTTTTCTTA
*
424785 TTATTGTTTTTACTTA
1 TTATTATTTTT-CTTA
424801 TTAT
1 TTAT
424805 ACTAAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (15 bp):
TTATTATTTTTCTTA
Found at i:424875 original size:6 final size:6
Alignment explanation
Indices: 424832--424978 Score: 64
Period size: 6 Copynumber: 25.0 Consensus size: 6
424822 ACTATATATA
* * *
424832 TTATTT ATATTCT TT-TTT ATTATTT TT-CTT TTACTTT TTA-TT TT-TGT
1 TTATTT TTATT-T TTATTT -TTATTT TTATTT TTA-TTT TTATTT TTATTT
* * *
424879 TTATTT TTCTTT TATATTT TT-TTCT TT-TTT TTACTT TTGTTT TCT-TTT
1 TTATTT TTATTT T-TATTT TTATT-T TTATTT TTATTT TTATTT T-TATTT
* * *
424927 CATT-TTT TTATTT TTATTT TTATTT TT-TTA TCA-TT TTA-TT TTATGT
1 --TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
424973 TTATTT
1 TTATTT
424979 ATTTTATCAT
Statistics
Matches: 108, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
5 30 0.28
6 57 0.53
7 20 0.19
8 1 0.01
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:424913 original size:47 final size:47
Alignment explanation
Indices: 424851--424978 Score: 129
Period size: 47 Copynumber: 2.7 Consensus size: 47
424841 TTCTTTTTTA
424851 TTATTTTTCTTTTACTTTTTATTTTTGTTTATTTTTCT-TTTATATTT
1 TTATTTTT-TTTTACTTTTTATTTTTGTTTATTTTTCTATTTATATTT
* * * *
424898 TTTTCTTTTTTTTACTTTTGT-TTTCTT-TTCATTTTTTTATTTTTATTT
1 TTAT-TTTTTTTTACTTTT-TATTT-TTGTTTATTTTTCTATTTATATTT
* *
424946 TTATTTTTTTAT-CATTTTATTTTATGTTTATTT
1 TTATTTTTTTTTACTTTTTATTTT-TGTTTATTT
424979 ATTTTATCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
45 2 0.03
46 8 0.12
47 38 0.58
48 18 0.27
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (47 bp):
TTATTTTTTTTTACTTTTTATTTTTGTTTATTTTTCTATTTATATTT
Found at i:424947 original size:40 final size:40
Alignment explanation
Indices: 424866--424947 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 40
424856 TTTCTTTTAC
* *
424866 TTTTTATTTTTGTTTATTTTTCTTTTATATTTTTTTCTTT
1 TTTTTACTTTTGTTTATTTTTCTTTTATATTTTTTTATTT
424906 TTTTTACTTTTGTTT-TCTTTTCATTTT-T-TTATTTTTATTT
1 TTTTTACTTTTGTTTAT-TTTTC-TTTTATATT-TTTTTATTT
424946 TT
1 TT
424948 ATTTTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
39 3 0.08
40 30 0.81
41 4 0.11
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.82
Consensus pattern (40 bp):
TTTTTACTTTTGTTTATTTTTCTTTTATATTTTTTTATTT
Found at i:424983 original size:28 final size:27
Alignment explanation
Indices: 424932--424995 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
424922 CTTTTCATTT
*
424932 TTTTATTTTTATTTTTATTTTTTTATCA
1 TTTTA-TTTTATGTTTATTTTTTTATCA
424960 TTTTATTTTATGTTTATTTATTTTATCA
1 TTTTATTTTATGTTTATTT-TTTTATCA
424988 TTTTATTT
1 TTTTATTT
424996 GCTTTCCCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 13 0.38
28 21 0.62
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTATTTTATGTTTATTTTTTTATCA
Found at i:424994 original size:13 final size:13
Alignment explanation
Indices: 424952--424995 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
424942 ATTTTTATTT
424952 TTTTATCATTTTA
1 TTTTATCATTTTA
**
424965 TTTTATGTTTATTTA
1 TTTTAT-CAT-TTTA
424980 TTTTATCATTTTA
1 TTTTATCATTTTA
424993 TTT
1 TTT
424996 GCTTTCCCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 13 0.52
14 2 0.08
15 10 0.40
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTATCATTTTA
Found at i:435893 original size:13 final size:13
Alignment explanation
Indices: 435875--435902 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
435865 CAGAGTTAAT
435875 CATTGACTTTGAC
1 CATTGACTTTGAC
435888 CATTGACTTTGAC
1 CATTGACTTTGAC
435901 CA
1 CA
435903 AAAAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGACTTTGAC
Found at i:438318 original size:64 final size:64
Alignment explanation
Indices: 438203--438342 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 64
438193 TTCAAGGTGT
* * * *
438203 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCACAAG-TAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCA-AAGATAGTGC
* * * *
438267 ATCGATGCACCCCCTTAAAATACAAACATCGAATGAGATTTA-TGTACCGATGCATAGATAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCAGTGTACCGATGCAAAGATAGTGC
*
438331 ATTGATGCACCC
1 ATCGATGCACCC
438343 GTCAAGGGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.03
64 61 0.94
65 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCAAAGATAGTGC
Found at i:439134 original size:8 final size:8
Alignment explanation
Indices: 439121--439147 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
439111 AATGCATTGT
439121 TATATTTA
1 TATATTTA
439129 TATATTTA
1 TATATTTA
439137 TATATTTA
1 TATATTTA
439145 TAT
1 TAT
439148 TATGCCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATTTA
Found at i:452002 original size:24 final size:23
Alignment explanation
Indices: 451970--452042 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
451960 TTCCTCATAG
451970 ATTTGTCCCGAATGACCGCGTAGA
1 ATTTGTCCCGAA-GACCGCGTAGA
* * * *
451994 ATTTGTCCCGGAGAACCACATAAA
1 ATTTGTCCCGAAG-ACCGCGTAGA
*
452018 ATTTGTCCCAAAAGACCGCGTAGA
1 ATTTGTCCC-GAAGACCGCGTAGA
452042 A
1 A
452043 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
23 1 0.03
24 35 0.92
25 2 0.05
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
ATTTGTCCCGAAGACCGCGTAGA
Found at i:463009 original size:27 final size:27
Alignment explanation
Indices: 462968--463022 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
462958 TTTATTTTGA
* *
462968 TCTTTTGTTTTGTATGAAACAAGTTGG
1 TCTTTTGTTTAGTATGAAACAAGCTGG
*
462995 TCTTTTGTTTAGTATGCAACAAGCTGG
1 TCTTTTGTTTAGTATGAAACAAGCTGG
463022 T
1 T
463023 TGATGAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (27 bp):
TCTTTTGTTTAGTATGAAACAAGCTGG
Found at i:466301 original size:21 final size:23
Alignment explanation
Indices: 466252--466301 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
466242 CGAGGGGTAT
* *
466252 CGATACACATTCAAAGAGGGTAT
1 CGATACACATTCAAAGAGAGTAC
*
466275 CGATACACATT-GAAG-GAGTAC
1 CGATACACATTCAAAGAGAGTAC
466296 CGATAC
1 CGATAC
466302 CTAGCAAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (23 bp):
CGATACACATTCAAAGAGAGTAC
Found at i:471483 original size:116 final size:117
Alignment explanation
Indices: 471277--471497 Score: 268
Period size: 116 Copynumber: 1.9 Consensus size: 117
471267 CTTTTAAATC
* * *
471277 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTGTTCAATATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTGTTCAACATTT
* *
471342 CATTTTAATTTTCAAAATCCATTTTAG-TTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTAATTTTCAAAATACATTTTAGCTTTC-AAAAGAAGTTTGTTTAATTT
* * * * *
471394 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTCA-TTTTAAAAGCTCTAACTCTTTTTTCAACATT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTGTTCAACATT
* * * **
471457 TCATTTTGATTTTCCAATTATGTTTTAGCTTTCAAAAGAAG
65 TCATTTTAATTTTCAAAATACATTTTAGCTTTCAAAAGAAG
471498 ATCATTTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
116 56 0.64
117 31 0.36
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTAAAAGCTCTAAATCCTTGTTCAACATTT
CATTTTAATTTTCAAAATACATTTTAGCTTTCAAAAGAAGTTTGTTTAATTT
Found at i:472867 original size:74 final size:74
Alignment explanation
Indices: 472787--472973 Score: 259
Period size: 74 Copynumber: 2.5 Consensus size: 74
472777 GTTAAATGAC
* * * *
472787 TAGGGGTATCAGTACCTCTAAG-GGGGTATCGGTACCTATTGGGCATTTTGTTTTTCTCGAAGCC
1 TAGGGGTATCGGTACC-CTATGAGGGGTATCGGTACCTATTGGACATTCTGTTTTTCTCGAAGCC
472851 AAAATTGGCA
65 AAAATTGGCA
* * * *
472861 TAGGGGTATCGGTACCCTATGAGGGGTATCGATACCCATTTGACATTCTGTTTTTCTCGGAGCCA
1 TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCTATTGGACATTCTGTTTTTCTCGAAGCCA
*
472926 AATTTGGCA
66 AAATTGGCA
472935 TAGGGGTATCGGTACACCCTATGAGGGGTATCGGTACCT
1 TAGGGGTATCGGT--ACCCTATGAGGGGTATCGGTACCT
472974 CCCTATTTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
73 4 0.04
74 73 0.74
76 22 0.22
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (74 bp):
TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCTATTGGACATTCTGTTTTTCTCGAAGCCA
AAATTGGCA
Found at i:473518 original size:28 final size:28
Alignment explanation
Indices: 473487--473566 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
473477 CAGAAAACAG
*
473487 TAAACCTAAAAGCTTAAACATTAACTTA
1 TAAACCCAAAAGCTTAAACATTAACTTA
*
473515 TAAACCCAAATGCTTAAACATTAACTTA
1 TAAACCCAAAAGCTTAAACATTAACTTA
473543 TAAACCCAAATA-CTTAAACATTAA
1 TAAACCCAAA-AGCTTAAACATTAA
473567 AACCATAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.28
Consensus pattern (28 bp):
TAAACCCAAAAGCTTAAACATTAACTTA
Found at i:475666 original size:16 final size:16
Alignment explanation
Indices: 475642--475672 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
475632 CTTATACATG
475642 TTCACTCTCTTTTTTA
1 TTCACTCTCTTTTTTA
*
475658 TTCATTCTCTTTTTT
1 TTCACTCTCTTTTTT
475673 TTTTTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCACTCTCTTTTTTA
Found at i:477236 original size:4 final size:4
Alignment explanation
Indices: 477227--477257 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
477217 TTTTTTCCCG
*
477227 TTCT TTCT TTCT TCCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
477258 AATGGATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:484111 original size:20 final size:21
Alignment explanation
Indices: 484086--484141 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
484076 GGCATTCATG
*
484086 AGGTATCGATACCAAT-GTGT
1 AGGTATCGATACCAATAGTAT
*
484106 AGGTATCGGTACC-ATAGTAT
1 AGGTATCGATACCAATAGTAT
484126 AGTAGTATCGATACCA
1 AG--GTATCGATACCA
484142 GGTTAAGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.07
20 17 0.59
22 10 0.34
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (21 bp):
AGGTATCGATACCAATAGTAT
Found at i:484837 original size:18 final size:18
Alignment explanation
Indices: 484813--484886 Score: 112
Period size: 18 Copynumber: 4.1 Consensus size: 18
484803 TGAGGGTTAT
*
484813 AAGTGGTCATTCGGGATA
1 AAGTGGTCATTCGGGACA
*
484831 TAGTGGTCATTCGGGACA
1 AAGTGGTCATTCGGGACA
*
484849 AAGTGGTCCTTCGGGACA
1 AAGTGGTCATTCGGGACA
*
484867 AAGTGGTCATTCGAGACA
1 AAGTGGTCATTCGGGACA
484885 AA
1 AA
484887 TTTTAAGTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.24
Consensus pattern (18 bp):
AAGTGGTCATTCGGGACA
Found at i:487159 original size:55 final size:55
Alignment explanation
Indices: 487075--487182 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
487065 AAAAACTAAA
* *
487075 ATTTACTAGCATATGTCAAAATTGCCTTACCACCATTCCTTCTATCAAGCTTTAC
1 ATTTACTAGCATAGGTCAAAATTGCCTTACCACCACTCCTTCTATCAAGCTTTAC
487130 ATTTACTAGCATAGGTCAAAATTGCCTTACCACCACTCCTTCTATCAAGCTTT
1 ATTTACTAGCATAGGTCAAAATTGCCTTACCACCACTCCTTCTATCAAGCTTT
487183 CCCTTATTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (55 bp):
ATTTACTAGCATAGGTCAAAATTGCCTTACCACCACTCCTTCTATCAAGCTTTAC
Found at i:491110 original size:54 final size:54
Alignment explanation
Indices: 491005--491110 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 54
490995 GGTTTCATGC
* * **
491005 CTAGATTGCATTGGGTAATTATTTGTGCCATGCTTTTATACTGTTGGCTCTTAT
1 CTAGATTGCATTGGGTAATTATTTGTACAATGCTTTTATACTGTTAACTCTTAT
* * * **
491059 CTAGATTGCGTTGGGTGATTATTTTTACAATGCTTTTATTTTGTTAACTCTT
1 CTAGATTGCATTGGGTAATTATTTGTACAATGCTTTTATACTGTTAACTCTT
491111 TAGTTGAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (54 bp):
CTAGATTGCATTGGGTAATTATTTGTACAATGCTTTTATACTGTTAACTCTTAT
Found at i:492859 original size:31 final size:31
Alignment explanation
Indices: 492822--492881 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
492812 CTTTTATAAA
492822 TTTTTTTCATGTATGAACTGATAAAATACTT
1 TTTTTTTCATGTATGAACTGATAAAATACTT
492853 TTTTTTTCATGTATGAACTGATAAAATAC
1 TTTTTTTCATGTATGAACTGATAAAATAC
492882 AGTGATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTTTTTCATGTATGAACTGATAAAATACTT
Found at i:496261 original size:3 final size:3
Alignment explanation
Indices: 496246--496277 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
496236 TATTTTATAT
*
496246 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
496278 TTAAAAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:496622 original size:47 final size:47
Alignment explanation
Indices: 496557--496944 Score: 259
Period size: 47 Copynumber: 8.7 Consensus size: 47
496547 TGCCATATTT
*
496557 AGGGATAATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
* **
496604 AGGGATGATAACATGGTTCCTACGTGATGAGGACGACAGGTTATCTA
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
*
496651 AGGGTTGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
*
496698 AGGG-TG---ACACGGATCCTACGTGATGA-GA----AGG---TCT-
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
* * * * * * ** *
496732 AGTCGATGGATGACACGGTTCCTACATGATGAGAATGGCAGGCCATCTTT
1 AG-GGAT-GATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATC-TA
* * * * *
496782 AGGGATGATAACATGGTTCCTACGTAATGAGGATGTTAGGTTATCAA
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
** * * *
496829 AGGG-TG---ACACGACTCCTACGTGATGAAGA-GGT---TTGGTC-G
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTT-ATCTA
* ** **
496868 ATGGATG---ACACGACTCCTACGTGATGAGGACGAAAGGTTATCTA
1 AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
* * * *
496912 AGGGTTGATAATACGATTCCTACGTGACGAGGA
1 AGGGATGATAACACGGTTCCTACGTGATGAGGA
496945 TAACACGTTA
Statistics
Matches: 271, Mismatches: 44, Indels: 52
0.74 0.12 0.14
Matches are distributed among these distances:
34 2 0.01
35 4 0.01
36 1 0.00
37 1 0.00
38 3 0.01
39 5 0.02
40 44 0.16
41 2 0.01
42 4 0.01
43 39 0.14
44 7 0.03
45 3 0.01
46 4 0.01
47 114 0.42
48 32 0.12
49 4 0.01
50 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (47 bp):
AGGGATGATAACACGGTTCCTACGTGATGAGGACGGTAGGTTATCTA
Found at i:496812 original size:131 final size:131
Alignment explanation
Indices: 496618--497446 Score: 706
Period size: 131 Copynumber: 6.3 Consensus size: 131
496608 ATGATAACAT
* ** * *
496618 GGTTCCTACGTGATGAGGACGACAGGTTATC-TAAGGGTTGATAACACGGTTCCTACGTGATGAG
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAG
*
496682 GACGGTAGGTTATCTAAGGGTGACACGGA-TCCTACGTGATGAGAAGGTCTAGTCGATGGATGAC
66 GACGGTAGGTTATCTAAGGGTGACAC-GACTCCTACGTGATGAGAAGGTCTGGTCGATGGATGAC
496746 AC
130 AC
* * * * *
496748 GGTTCCTACATGATGAGAATGGCAGGCCATCTTTAGGGATGATAACATGGTTCCTACGTAATGAG
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAG
* * * *
496813 GATGTTAGGTTATCAAAGGGTGACACGACTCCTACGTGATGA-AGAGGTTTGGTCGATGGATGAC
66 GACGGTAGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGA-AGGTCTGGTCGATGGATGAC
496877 AC
130 AC
** ** ** * * * * *
496879 GACTCCTACGTGATGAGGACGAAAGGTTATC-TAAGGGTTGATAATACGATTCCTACGTGACGAG
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAG
**** * * * * * * * *
496943 GATAACACGTTATCTAAGGGTGACATGGAC-CCTTCGTGATAAGGAGATCTAGTCGGTGGATGAC
66 GACGGTAGGTTATCTAAGGGTGACA-CGACTCCTACGTGATGAGAAGGTCTGGTCGATGGATGAC
497007 AC
130 AC
* * * * * * * *
497009 GGTTCTTACGTGATGATGACGGGAAGCCATCTTTAAGGATGATAACACAGTTTCTACGTGACGAG
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAG
* ** * * *
497074 GACGGAAAATTATCTAAGGGTGATACGGCTCCTACGTGATGA-AGAGGTCTGGTCGGTGGATGAC
66 GACGGTAGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGA-AGGTCTGGTCGATGGATGAC
*
497138 AT
130 AC
* * * ** ** * * *
497140 GATTCTTACGTGATGAGGATGGTTGATCATATTTAGGGAATGGTGATAACATGGTTCCTACGCGA
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGG-A---TGATAACACGGTTCCTACGTGA
* * * * * * * *
497205 TGTGGACGGCT-GATTATCTAGGGGTGATACGACCCCTACGTGATAAGGAGGTCTGGTC-AGGGG
62 TGAGGACGG-TAGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGAAGGTCTGGTCGA-TGG
* *
497268 ATGGCAT
125 ATGACAC
* * * * * *
497275 GGTTCATATGCGATGAGGACGGCATGCCATCTTTA-GGATGATAACACGGTTCCTATGTGATGAT
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAG
** * **
497339 GACGGCT-GGTTATCTAAGGGTTGACACGACTCCTAAATGATGAGAAGGTCTGGCCGGGGGGATG
66 GACGG-TAGGTTATCTAAGGG-TGACACGACTCCTACGTGATGAGAAGGTCTGGTC-GATGGATG
497403 ACAC
128 ACAC
*
497407 GGTTCCTACGTGATGAGGACGGTAGGCCATCTTTAGGGAT
1 GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGAT
497447 AATGTCTCAA
Statistics
Matches: 546, Mismatches: 134, Indels: 35
0.76 0.19 0.05
Matches are distributed among these distances:
130 165 0.30
131 238 0.44
132 39 0.07
133 5 0.01
134 2 0.00
135 97 0.18
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (131 bp):
GGTTCCTACGTGATGAGGACGGCAGGCCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAG
GACGGTAGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGAAGGTCTGGTCGATGGATGACA
C
Found at i:497095 original size:261 final size:261
Alignment explanation
Indices: 496621--497158 Score: 700
Period size: 261 Copynumber: 2.1 Consensus size: 261
496611 ATAACATGGT
* * * *
496621 TCCTACGTGATGAGGACGACAGGTTATCTAAGGGTTGATAACACGGTTCCTACGTGATGAGGACG
1 TCCTACGTGATGAGGACGAAAGGTTATCTAAGGGTTGATAACACGATTCCTACGTGACGAGGACA
** * * * *
496686 GTAGGTTATCTAAGGGTGACACGGATCCTACGTGATGAGAAGGTCTAGTCGATGGATGACACGGT
66 ACACGTTATCTAAGGGTGACACGGACCCTACGTGATAAGAAGATCTAGTCGATGGATGACACGGT
* * * ** * *
496751 TCCTACATGATGAGAATGGCAGGCCATCTTTAGGGATGATAACATGGTTCCTACGTAATGAGGAT
131 TCCTACATGATGAGAACGGCAAGCCATCTTTAAGGATGATAACACAGTTCCTACGTAACGAGGAC
** ** *
496816 GTTAGGTTATCAAAGGGTGACACGACTCCTACGTGATGAAGAGGTTTGGTCGATGGATGACACGA
196 GGAAAATTATCAAAGGGTGACACGACTCCTACGTGATGAAGAGGTCTGGTCGATGGATGACACGA
496881 C
261 C
* *
496882 TCCTACGTGATGAGGACGAAAGGTTATCTAAGGGTTGATAATACGATTCCTACGTGACGAGGATA
1 TCCTACGTGATGAGGACGAAAGGTTATCTAAGGGTTGATAACACGATTCCTACGTGACGAGGACA
* * * *
496947 ACACGTTATCTAAGGGTGACATGGACCCTTCGTGATAAGGAGATCTAGTCGGTGGATGACACGGT
66 ACACGTTATCTAAGGGTGACACGGACCCTACGTGATAAGAAGATCTAGTCGATGGATGACACGGT
* * * * *
497012 TCTTACGTGATGATG-ACGGGAAGCCATCTTTAAGGATGATAACACAGTTTCTACGTGACGAGGA
131 TCCTACATGATGA-GAACGGCAAGCCATCTTTAAGGATGATAACACAGTTCCTACGTAACGAGGA
* * * * *
497076 CGGAAAATTATCTAAGGGTGATACGGCTCCTACGTGATGAAGAGGTCTGGTCGGTGGATGACATG
195 CGGAAAATTATCAAAGGGTGACACGACTCCTACGTGATGAAGAGGTCTGGTCGATGGATGACACG
*
497141 AT
260 AC
*
497143 TCTTACGTGATGAGGA
1 TCCTACGTGATGAGGA
497159 TGGTTGATCA
Statistics
Matches: 236, Mismatches: 40, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
261 235 1.00
262 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (261 bp):
TCCTACGTGATGAGGACGAAAGGTTATCTAAGGGTTGATAACACGATTCCTACGTGACGAGGACA
ACACGTTATCTAAGGGTGACACGGACCCTACGTGATAAGAAGATCTAGTCGATGGATGACACGGT
TCCTACATGATGAGAACGGCAAGCCATCTTTAAGGATGATAACACAGTTCCTACGTAACGAGGAC
GGAAAATTATCAAAGGGTGACACGACTCCTACGTGATGAAGAGGTCTGGTCGATGGATGACACGA
C
Found at i:497656 original size:69 final size:66
Alignment explanation
Indices: 497449--497687 Score: 207
Period size: 66 Copynumber: 3.6 Consensus size: 66
497439 TTAGGGATAA
* * * * *
497449 TGTCTCAAGAGATACAAAGTTTTG-TTCAAGGGAAACAGACTCAAGGATGATTG--TTTCAAGAG
1 TGTCTCAAAAGACACAAA-TTTTGTTTTAAGGGAAACAAACTCAAAGAT--TTGTATTTCAAGAG
497511 AAAC
63 AAAC
* * * * * * * *
497515 TATCTCAAGAGATAAAAATTTTTGTTTTAAGAGAAA-AGACTCAAAGATTTGTCTTTCAATAGAA
1 TGTCTCAAAAGACACAAA-TTTTGTTTTAAGGGAAACAAACTCAAAGATTTGTATTTCAAGAGAA
497579 AC
65 AC
* * *
497581 TGTCTCAAAGGACACACAATTTTGTTTCAAGGGAAACAAACTCAAAGATTTTTTTATTTCAAGAG
1 TGTCTCAAAAGACACA-AATTTTGTTTTAAGGGAAACAAACTCAAAGA--TTTGTATTTCAAGAG
*
497646 AAAT
63 AAAC
* **
497650 TGTCTCAAAAGAGACAAAACTTGTTTTAAGGGAAACAA
1 TGTCTCAAAAGACACAAATTTTGTTTTAAGGGAAACAA
497688 TTTCAATGTT
Statistics
Matches: 142, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
64 3 0.02
66 70 0.49
67 21 0.15
68 19 0.13
69 29 0.20
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (66 bp):
TGTCTCAAAAGACACAAATTTTGTTTTAAGGGAAACAAACTCAAAGATTTGTATTTCAAGAGAAA
C
Found at i:497999 original size:35 final size:36
Alignment explanation
Indices: 497916--498010 Score: 147
Period size: 36 Copynumber: 2.7 Consensus size: 36
497906 AGGAAAAATG
**
497916 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATTA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACCA
*
497952 TCTCAAGCGAGACAAAATTTGTTTTTATA-AAACCA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACCA
*
497987 TCTCAAGTGAGACAAAATTTGTTT
1 TCTCAAGCGAGACAAAATTTGTTT
498011 CTAAAATTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
35 27 0.49
36 28 0.51
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACCA
Found at i:498430 original size:10 final size:10
Alignment explanation
Indices: 498401--498431 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
498391 ATGTAACATG
*
498401 TATGTATGTA
1 TATGTATGTT
498411 TATGTATGTT
1 TATGTATGTT
498421 TATGTATGTT
1 TATGTATGTT
498431 T
1 T
498432 TCTAGATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (10 bp):
TATGTATGTT
Found at i:499443 original size:2 final size:2
Alignment explanation
Indices: 499436--499466 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
499426 TCAGCTTTAT
499436 TA TA TA 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 T
499467 TGGGTATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:504677 original size:59 final size:59
Alignment explanation
Indices: 504578--504714 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
504568 CAGCAGTCTG
** *
504578 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
* ** *
504637 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
504696 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
504715 CGGTGCTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
58 1 0.02
59 65 0.98
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
Found at i:504924 original size:51 final size:47
Alignment explanation
Indices: 504815--504979 Score: 201
Period size: 44 Copynumber: 3.5 Consensus size: 47
504805 GTAAGCATAC
* * *
504815 AAATAAGCTTACGAGCTTTTGGAA--T-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGTA
*
504859 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAAAAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGG---TA
* * *
504909 AATATAAGCTTACGAGCTTATGGAATTTTAAACGATAAGTATTTTGGTA
1 AA-ATAAGCTTACGAGCTTATGGAA-TTTAAATGGTAAGTATATTGGTA
504958 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
504980 GATAAATAGT
Statistics
Matches: 105, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
44 23 0.22
46 1 0.01
47 15 0.14
48 20 0.19
49 3 0.03
50 3 0.03
51 22 0.21
52 18 0.17
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGTA
Found at i:508074 original size:3 final size:3
Alignment explanation
Indices: 508066--508100 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
508056 TATTTTATAT
508066 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
508101 TATTAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:508601 original size:2 final size:2
Alignment explanation
Indices: 508589--508656 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
508579 TAATATCAAA
508589 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
508630 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
508657 CACACCAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:508864 original size:15 final size:15
Alignment explanation
Indices: 508844--508872 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
508834 ATAAATACTT
508844 TTGAATAATTAAAAC
1 TTGAATAATTAAAAC
508859 TTGAATAATTAAAA
1 TTGAATAATTAAAA
508873 TCTATAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (15 bp):
TTGAATAATTAAAAC
Found at i:514416 original size:24 final size:25
Alignment explanation
Indices: 514381--514438 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
514371 TATTCACGAA
* **
514381 CAAGCTCGTTTATGAGTTTGTTTAT
1 CAAGCTCATTTATGAACTTGTTTAT
514406 -AAGCTCATTTATGAACTTGTTTAT
1 CAAGCTCATTTATGAACTTGTTTAT
514430 CAA-CTCATT
1 CAAGCTCATT
514439 CATTTATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (25 bp):
CAAGCTCATTTATGAACTTGTTTAT
Found at i:514669 original size:11 final size:11
Alignment explanation
Indices: 514655--514703 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
514645 AAAAGAATGA
514655 TAAACAAACAC
1 TAAACAAACAC
*
514666 TAAA-ACAACGC
1 TAAACA-AACAC
514677 TAAACAAACAC
1 TAAACAAACAC
**
514688 TAAATGAACAC
1 TAAACAAACAC
514699 TAAAC
1 TAAAC
514704 GAATTGTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 1 0.03
11 29 0.94
12 1 0.03
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.12
Consensus pattern (11 bp):
TAAACAAACAC
Found at i:514669 original size:22 final size:22
Alignment explanation
Indices: 514644--514691 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
514634 ATCGAATATA
* *
514644 TAAAAGAATGATAAACAAACAC
1 TAAAACAACGATAAACAAACAC
*
514666 TAAAACAACGCTAAACAAACAC
1 TAAAACAACGATAAACAAACAC
514688 TAAA
1 TAAA
514692 TGAACACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.19, G:0.06, T:0.12
Consensus pattern (22 bp):
TAAAACAACGATAAACAAACAC
Found at i:514701 original size:22 final size:22
Alignment explanation
Indices: 514655--514703 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
514645 AAAAGAATGA
*
514655 TAAACAAACACTAAAACAACGC
1 TAAACAAACACTAAAACAACAC
**
514677 TAAACAAACACTAAATGAACAC
1 TAAACAAACACTAAAACAACAC
514699 TAAAC
1 TAAAC
514704 GAATTGTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.12
Consensus pattern (22 bp):
TAAACAAACACTAAAACAACAC
Found at i:519943 original size:21 final size:21
Alignment explanation
Indices: 519918--519977 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
519908 CGTTGGGGCA
*
519918 GCTCATGATATTGGATCTAGT
1 GCTCATGATATTGGAGCTAGT
519939 GCTCATGATATTGGAGCTAGT
1 GCTCATGATATTGGAGCTAGT
* *
519960 GCGCATGATAGTGGAGCT
1 GCTCATGATATTGGAGCT
519978 CGTGATAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (21 bp):
GCTCATGATATTGGAGCTAGT
Found at i:520111 original size:24 final size:24
Alignment explanation
Indices: 520081--520126 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
520071 ATATTGGGAG
* *
520081 CCACACCACTTGGACTTGGAGCAA
1 CCACACCACTTGAACTGGGAGCAA
*
520105 CCACACCGCTTGAACTGGGAGC
1 CCACACCACTTGAACTGGGAGC
520127 TATGTCTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (24 bp):
CCACACCACTTGAACTGGGAGCAA
Found at i:521518 original size:30 final size:30
Alignment explanation
Indices: 521452--521510 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
521442 CGAGCAGATG
521452 AGGCAGAATTGTCTGTGTCAGATTTTGCAA
1 AGGCAGAATTGTCTGTGTCAGATTTTGCAA
*
521482 AGGCAGAATTGTCTGTGTCAGCTTTTGCA
1 AGGCAGAATTGTCTGTGTCAGATTTTGCA
521511 TATGCAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (30 bp):
AGGCAGAATTGTCTGTGTCAGATTTTGCAA
Found at i:523257 original size:212 final size:212
Alignment explanation
Indices: 522890--523301 Score: 797
Period size: 212 Copynumber: 1.9 Consensus size: 212
522880 CATTTACCCG
522890 ATTCTCCTTTTCCTTTTATTTTTTACATTTTAAATATTGGTGAAGATAAGGATTAAATAGAAACA
1 ATTCTCCTTTTCCTTTTATTTTTTACATTTTAAATATTGGTGAAGATAAGGATTAAATAGAAACA
*
522955 CATGATAAAAGTTACATTTTAAACTATGAATTTTAAGAAGTTTAAGCACTAGTGGCGTAATTTTA
66 CATGATAAAAGTTACATTTTAAACTATGAATTTTAAGAAGCTTAAGCACTAGTGGCGTAATTTTA
523020 TCATTTTTCTTTAACTTGTAAATGAAATTAAAAATCAAATATATAAACGAACAATAAACAAACAC
131 TCATTTTTCTTTAACTTGTAAATGAAATTAAAAATCAAATATATAAACGAACAATAAACAAACAC
523085 TAAAACAACGCTAAACA
196 TAAAACAACGCTAAACA
*
523102 ATTCTCCTTTTCCTTTTATTTTTTATATTTTAAATATTGGTGAAGATAAGGATTAAATAGAAACA
1 ATTCTCCTTTTCCTTTTATTTTTTACATTTTAAATATTGGTGAAGATAAGGATTAAATAGAAACA
523167 CATGATAAAAGTTACATTTTAAACTATGAATTTTAAGAAGCTTAAGCACTAGTGGCGTAATTTTA
66 CATGATAAAAGTTACATTTTAAACTATGAATTTTAAGAAGCTTAAGCACTAGTGGCGTAATTTTA
*
523232 TCATTTTTCTTTAACTTGTAAATGAAATTAAAAATCGAATATATAAACGAACAATAAACAAACAC
131 TCATTTTTCTTTAACTTGTAAATGAAATTAAAAATCAAATATATAAACGAACAATAAACAAACAC
523297 TAAAA
196 TAAAA
523302 AACAAACTGT
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 197 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (212 bp):
ATTCTCCTTTTCCTTTTATTTTTTACATTTTAAATATTGGTGAAGATAAGGATTAAATAGAAACA
CATGATAAAAGTTACATTTTAAACTATGAATTTTAAGAAGCTTAAGCACTAGTGGCGTAATTTTA
TCATTTTTCTTTAACTTGTAAATGAAATTAAAAATCAAATATATAAACGAACAATAAACAAACAC
TAAAACAACGCTAAACA
Found at i:523343 original size:24 final size:23
Alignment explanation
Indices: 523316--523378 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
523306 AACTGTTCAT
523316 GAACATGTTCGTGAACATATAAAC
1 GAACATGTTCGTGAACAT-TAAAC
* * * *
523340 GAACACGTTTGCGAACATTAAAT
1 GAACATGTTCGTGAACATTAAAC
*
523363 GAAC-TGTTCATGAACA
1 GAACATGTTCGTGAACA
523379 CGTTCATGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 8 0.26
23 8 0.26
24 15 0.48
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (23 bp):
GAACATGTTCGTGAACATTAAAC
Found at i:523376 original size:58 final size:58
Alignment explanation
Indices: 523306--523424 Score: 202
Period size: 58 Copynumber: 2.1 Consensus size: 58
523296 CTAAAAAACA
* *
523306 AACTGTTCATGAACATGTTCGTGAACATATAAACGAACACGTTTGCGAACATTAAATG
1 AACTGTTCATGAACACGTTCATGAACATATAAACGAACACGTTTGCGAACATTAAATG
* *
523364 AACTGTTCATGAACACGTTCATGAACATATAAATGAACATGTTTGCGAACATTAAATG
1 AACTGTTCATGAACACGTTCATGAACATATAAACGAACACGTTTGCGAACATTAAATG
523422 AAC
1 AAC
523425 ATGTACGTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (58 bp):
AACTGTTCATGAACACGTTCATGAACATATAAACGAACACGTTTGCGAACATTAAATG
Found at i:523379 original size:34 final size:36
Alignment explanation
Indices: 523340--523406 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
523330 ACATATAAAC
**
523340 GAACACGTTTGCGAACAT-TAAATGAAC-TGTTCAT
1 GAACACGTTCACGAACATATAAATGAACATGTTCAT
*
523374 GAACACGTTCATGAACATATAAATGAACATGTT
1 GAACACGTTCACGAACATATAAATGAACATGTT
523407 TGCGAACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.54
35 9 0.32
36 4 0.14
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (36 bp):
GAACACGTTCACGAACATATAAATGAACATGTTCAT
Found at i:523401 original size:24 final size:24
Alignment explanation
Indices: 523372--523454 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 24
523362 TGAACTGTTC
*
523372 ATGAACACGTTCATGAACATATAA
1 ATGAACACGTTCGTGAACATATAA
* * *
523396 ATGAACATGTTTGCGAACAT-TAA
1 ATGAACACGTTCGTGAACATATAA
* *
523419 ATGAACATGTACGTGAACAATAAATAA
1 ATGAACACGTTCGTGAAC-AT--ATAA
523446 ATGAACACG
1 ATGAACACG
523455 AATACATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
23 18 0.38
24 18 0.38
27 11 0.23
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (24 bp):
ATGAACACGTTCGTGAACATATAA
Found at i:535939 original size:24 final size:24
Alignment explanation
Indices: 535909--535990 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
535899 AATGATGTGA
535909 TAATAATGATTTAATAATGATTAC
1 TAATAATGATTTAATAATGATTAC
*
535933 TAATAAT--TTTAATGAT--TTGGAC
1 TAATAATGATTTAATAATGATT--AC
* *
535955 T-TTAATGATTTAATAATGATTAG
1 TAATAATGATTTAATAATGATTAC
*
535978 TAATAATGTTTTA
1 TAATAATGATTTA
535991 TTATTAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.04
21 4 0.09
22 11 0.24
23 10 0.22
24 16 0.36
25 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.46
Consensus pattern (24 bp):
TAATAATGATTTAATAATGATTAC
Found at i:535983 original size:13 final size:11
Alignment explanation
Indices: 535909--536079 Score: 55
Period size: 11 Copynumber: 14.5 Consensus size: 11
535899 AATGATGTGA
535909 TAATAATGATT
1 TAATAATGATT
535920 TAATAATGA-T
1 TAATAATGATT
* *
535930 TACTAATAATT
1 TAATAATGATT
535941 T--TAATGATT
1 TAATAATGATT
*
535950 TGGACTTTAATGATT
1 T--A--ATAATGATT
535965 TAATAATGATT
1 TAATAATGATT
*
535976 AGTAATAATGTTT
1 --TAATAATGATT
* * *
535989 TATTATTAATAT
1 TAATAATGAT-T
536001 T--TAATGATT
1 TAATAATGATT
* *
536010 TGATACAAATAATT
1 T-A-A-TAATGATT
*
536024 TAGTAATGATT
1 TAATAATGATT
536035 ACTAATAATGAAATT
1 --TAATAATG--ATT
*
536050 ATAATAATTATT
1 -TAATAATGATT
536062 ACTAATAATGATT
1 --TAATAATGATT
536075 TAATA
1 TAATA
536080 GTAAAAAACT
Statistics
Matches: 119, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
9 10 0.08
10 13 0.11
11 36 0.30
12 5 0.04
13 29 0.24
14 14 0.12
15 12 0.10
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:536004 original size:45 final size:45
Alignment explanation
Indices: 535912--536010 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
535902 GATGTGATAA
**
535912 TAATGATTTAATAATGATTACTAATAATTTTAATGATTTGGACTT
1 TAATGATTTAATAATGATTACTAATAATTTTAATGATTAAGACTT
* * * *
535957 TAATGATTTAATAATGATTAGTAATAATGTTTTATTATTAATA-TT
1 TAATGATTTAATAATGATTACTAATAAT-TTTAATGATTAAGACTT
536002 TAATGATTT
1 TAATGATTT
536011 GATACAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 38 0.81
46 9 0.19
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.49
Consensus pattern (45 bp):
TAATGATTTAATAATGATTACTAATAATTTTAATGATTAAGACTT
Found at i:536078 original size:24 final size:25
Alignment explanation
Indices: 536020--536079 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
536010 TGATACAAAT
*
536020 AATTTAGTAATGATTACTAATAATG
1 AATTTAATAATGATTACTAATAATG
*
536045 AAATTATAATAATTATTACTAATAATG
1 -AATT-TAATAATGATTACTAATAATG
536072 -ATTTAATA
1 AATTTAATA
536080 GTAAAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 5 0.16
25 3 0.10
26 4 0.13
27 19 0.61
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (25 bp):
AATTTAATAATGATTACTAATAATG
Found at i:536844 original size:7 final size:7
Alignment explanation
Indices: 536832--536865 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
536822 TATTTAAAAT
536832 ACCCTAA
1 ACCCTAA
536839 ACCCTAA
1 ACCCTAA
536846 ACCCTAA
1 ACCCTAA
536853 ACCCTAA
1 ACCCTAA
536860 ACCCTA
1 ACCCTA
536866 TGGTAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:537737 original size:30 final size:29
Alignment explanation
Indices: 537703--537768 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
537693 AATTATTAAA
537703 TATTAATAATAAAAAATTACTACTAATCAT
1 TATTAATAAT-AAAAATTACTACTAATCAT
* * * *
537733 TATTAAATCATTAAAATTATTAGTAATCAT
1 TATT-AATAATAAAAATTACTACTAATCAT
537763 TATTAA
1 TATTAA
537769 ATTATTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 2 0.06
30 24 0.77
31 5 0.16
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (29 bp):
TATTAATAATAAAAATTACTACTAATCAT
Found at i:537743 original size:11 final size:11
Alignment explanation
Indices: 537727--537803 Score: 70
Period size: 11 Copynumber: 7.0 Consensus size: 11
537717 AATTACTACT
537727 AATCATTATTA
1 AATCATTATTA
537738 AATCATTA--A
1 AATCATTATTA
* *
537747 AATTATTAGT-
1 AATCATTATTA
537757 AATCATTATTAA
1 AATCATTATT-A
*
537769 ATTATTATTATTA
1 A--ATCATTATTA
537782 AATCATTATTA
1 AATCATTATTA
*
537793 AATCAATATTA
1 AATCATTATTA
537804 TTATTAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
9 8 0.15
10 8 0.15
11 27 0.50
12 1 0.02
13 2 0.04
14 8 0.15
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.45
Consensus pattern (11 bp):
AATCATTATTA
Found at i:537780 original size:14 final size:14
Alignment explanation
Indices: 537761--537831 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
537751 ATTAGTAATC
*
537761 ATTATTAAATTATT
1 ATTATTAAATCATT
537775 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
537789 ATTAAATCAAT-ATT
1 ATT-ATTAAATCATT
*
537803 ATTATTAAATAATT
1 ATTATTAAATCATT
* *
537817 AGTAGTAAATCATT
1 ATTATTAAATCATT
537831 A
1 A
537832 AATCGTTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
13 5 0.11
14 37 0.79
15 5 0.11
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:537791 original size:25 final size:26
Alignment explanation
Indices: 537727--537817 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 26
537717 AATTACTACT
**
537727 AATCATTATTAAATCATTAAAATTATTA
1 AATCATTATTAAAT-A-TATTATTATTA
537755 GTAATCATTATTAAAT-TATTATTATTA
1 --AATCATTATTAAATATATTATTATTA
537782 AATCATTATTAAATCAATATTATTATTA
1 AATCATTATTAAAT--ATATTATTATTA
*
537810 AATAATTA
1 AATCATTA
537818 GTAGTAAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
25 14 0.25
27 9 0.16
28 18 0.33
30 14 0.25
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (26 bp):
AATCATTATTAAATATATTATTATTA
Found at i:548518 original size:17 final size:16
Alignment explanation
Indices: 548492--548567 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 16
548482 ATGATTATTA
*
548492 TTTTTCTATTTCACTTT
1 TTTTTTTATTTCA-TTT
548509 TTTTTTTATTTCATTT
1 TTTTTTTATTTCATTT
* * *
548525 TTTTATT-TTCCCTTT
1 TTTTTTTATTTCATTT
*
548540 TATTTTTTTTCTTCATTT
1 T-TTTTTTAT-TTCATTT
*
548558 TTTATTTATT
1 TTTTTTTATT
548568 CATATTCATT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
15 7 0.15
16 15 0.32
17 19 0.40
18 6 0.13
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTTATTTCATTT
Found at i:548540 original size:31 final size:33
Alignment explanation
Indices: 548491--548564 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
548481 TATGATTATT
*
548491 ATTTTTCTA-TTTCACTTTT-TTTTTTAT-TTC
1 ATTTTTTTATTTTCACTTTTATTTTTTATCTTC
* *
548521 ATTTTTTTATTTTCCCTTTTATTTTTTTTCTTC
1 ATTTTTTTATTTTCACTTTTATTTTTTATCTTC
548554 A-TTTTTTATTT
1 ATTTTTTTATTT
548565 ATTCATATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 8 0.21
31 9 0.24
32 17 0.45
33 4 0.11
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (33 bp):
ATTTTTTTATTTTCACTTTTATTTTTTATCTTC
Found at i:560278 original size:2 final size:2
Alignment explanation
Indices: 560267--560298 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
560257 TACTACATCT
560267 TA TA -A TA 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 T
560299 CATTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:563277 original size:18 final size:18
Alignment explanation
Indices: 563227--563279 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 18
563217 AAATTTTAAG
563227 GAAAGTTTCGAAACTCTT
1 GAAAGTTTCGAAACTCTT
563245 GAGATAGTTTCGAAACTCTT
1 GA-A-AGTTTCGAAACTCTT
*
563265 GAAAGTATCGAAACT
1 GAAAGTTTCGAAACT
563280 TTTTGGACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 13 0.41
19 2 0.06
20 17 0.53
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (18 bp):
GAAAGTTTCGAAACTCTT
Found at i:571657 original size:20 final size:20
Alignment explanation
Indices: 571634--571672 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
571624 TAAAAATAAA
571634 AAATATTTAAAATTA-AAATG
1 AAAT-TTTAAAATTATAAATG
*
571654 AAATTTTATAATTATAAAT
1 AAATTTTAAAATTATAAAT
571673 TAAAATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATTTTAAAATTATAAATG
Found at i:575849 original size:22 final size:22
Alignment explanation
Indices: 575824--575878 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
575814 TCAGGAGTTA
* *
575824 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
575846 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
575868 CGGGAGTTATA
1 CAGGAGTTATA
575879 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:581426 original size:5 final size:5
Alignment explanation
Indices: 581407--581465 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
581397 GTCTGTCCGT
* * * * * *
581407 CTCGT CTCGT CTCGG CTCGG CACAG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
581457 CTCGG CTCG
1 CTCGG CTCG
581466 TGGTCGTGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 49 1.00
ACGTcount: A:0.07, C:0.41, G:0.34, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:581474 original size:6 final size:6
Alignment explanation
Indices: 581463--581535 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
581453 TCGGCTCGGC
*
581463 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
581511 TCGGGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
581536 AATACGTGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.01, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:581839 original size:22 final size:22
Alignment explanation
Indices: 581814--581868 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
581804 TCAGGAGTTA
* *
581814 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
581836 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
581858 CGGGAGTTATA
1 CAGGAGTTATA
581869 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:584918 original size:3 final size:3
Alignment explanation
Indices: 584912--584954 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
584902 GGGTTTTTTT
*
584912 TTA TTA TTA TTAA TTA TTA TTAA CTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TTA TTA TTA TT
584955 TTTAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:584928 original size:13 final size:12
Alignment explanation
Indices: 584912--584954 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
584902 GGGTTTTTTT
584912 TTATTATTATTAA
1 TTATTATTATT-A
*
584925 TTATTATTAACTA
1 TTATTATT-ATTA
584938 TTATTATTATTA
1 TTATTATTATTA
584950 TTATT
1 TTATT
584955 TTTAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 8 0.30
13 17 0.63
14 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATTATTATTA
Found at i:584929 original size:10 final size:10
Alignment explanation
Indices: 584914--584952 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
584904 GTTTTTTTTT
584914 ATTATTATTA
1 ATTATTATTA
584924 ATTATTATTA
1 ATTATTATTA
*
584934 ACTATTATT-
1 ATTATTATTA
584943 ATTATTATTA
1 ATTATTATTA
584953 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATTATTA
Found at i:585559 original size:6 final size:6
Alignment explanation
Indices: 585551--585590 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
585541 AGAGCTCAAG
* *
585551 AAAAAG AAAAAC AAAAAG AAAAAC AAAAA- AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
585591 AAAGGAGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:585593 original size:11 final size:12
Alignment explanation
Indices: 585551--585590 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
585541 AGAGCTCAAG
585551 AAAAAGAAAAAC
1 AAAAAGAAAAAC
585563 AAAAAGAAAAAC
1 AAAAAGAAAAAC
585575 AAAAA-AAAAAC
1 AAAAAGAAAAAC
585586 AAAAA
1 AAAAA
585591 AAAGGAGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:598806 original size:8 final size:8
Alignment explanation
Indices: 598795--598865 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
598785 AAAAAAGGGA
598795 AAAAAATG
1 AAAAAATG
598803 AAAATATGATG
1 AAAA-A--ATG
*
598814 GAAAAATG
1 AAAAAATG
598822 -AAAAATG
1 AAAAAATG
598829 AAAAAA-G
1 AAAAAATG
598836 AAGAAAA--
1 AA-AAAATG
*
598843 AGAAAATG
1 AAAAAATG
*
598851 AAAAAAAG
1 AAAAAATG
598859 AAAAAAT
1 AAAAAAT
598866 TAAATAAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
6 4 0.08
7 11 0.22
8 28 0.55
9 1 0.02
10 1 0.02
11 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:598870 original size:21 final size:22
Alignment explanation
Indices: 598814--598864 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 22
598804 AAATATGATG
598814 GAAAAATGAAAAATGAAAAAAGAA
1 GAAAAA-G-AAAATGAAAAAAGAA
598838 GAAAAAGAAAATGAAAAAAAGAA
1 GAAAAAGAAAATG-AAAAAAGAA
598861 -AAAA
1 GAAAA
598865 TTAAATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.38
23 10 0.38
24 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (22 bp):
GAAAAAGAAAATGAAAAAAGAA
Found at i:600018 original size:134 final size:135
Alignment explanation
Indices: 599804--600070 Score: 414
Period size: 134 Copynumber: 2.0 Consensus size: 135
599794 AACATCAGCG
* * * *
599804 GACCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCCTAGATAACCAGCTGTCCTCATCGCGT
1 GACCAAATCTCCTCATCACGTAGGAGTCGTGTCACACCATAGATAACCAGCTGTCCTCATCACGT
* * * *
599869 AGGAACCAAGTTATCACCTTTTCTAAAGATGTCCA-AGAACTCTTCATCACGTATGAGTCGTGTC
66 AGGAACCAAGTTATCACCCTTCCAAAAGATGGCCAGA-AACTCTTCATCACGTATGAGTCGTGTC
599933 ATCCCC
130 ATCCCC
599939 GACCAAATCTCCTCATCACGTAGGAGTCGTGTCA-ACCATAGATAACCAG-TCGTCCTCATCACG
1 GACCAAATCTCCTCATCACGTAGGAGTCGTGTCACACCATAGATAACCAGCT-GTCCTCATCACG
*
600002 TAGGAACCGAGTTATCACCCTTCCAAAAGATGGCCAGAAACTCTTCATCACGTATGAGTCGTGTC
65 TAGGAACCAAGTTATCACCCTTCCAAAAGATGGCCAGAAACTCTTCATCACGTATGAGTCGTGTC
600067 ATCC
130 ATCC
600071 ACCCTTAGAC
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
133 1 0.01
134 86 0.71
135 34 0.28
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (135 bp):
GACCAAATCTCCTCATCACGTAGGAGTCGTGTCACACCATAGATAACCAGCTGTCCTCATCACGT
AGGAACCAAGTTATCACCCTTCCAAAAGATGGCCAGAAACTCTTCATCACGTATGAGTCGTGTCA
TCCCC
Found at i:600271 original size:3 final size:3
Alignment explanation
Indices: 600263--600330 Score: 109
Period size: 3 Copynumber: 21.7 Consensus size: 3
600253 ATCCGGGTCT
600263 TTA TTA TTA TTA TTA TTA TTTA TTTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA
600311 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
600331 TACAATATAC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.83
4 11 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:600281 original size:27 final size:27
Alignment explanation
Indices: 600251--600330 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
600241 ACACCCGTTT
* *
600251 TTATCCGGGTCTTTATTATTATTATTA
1 TTATCCAGGTATTTATTATTATTATTA
** **
600278 TTATTTATTTATTTATTATTATTATTA
1 TTATCCAGGTATTTATTATTATTATTA
* *
600305 TTAT-TA-TTA-TTATTATTATTATTA
1 TTATCCAGGTATTTATTATTATTATTA
600329 TT
1 TT
600331 TACAATATAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 17 0.36
25 3 0.06
26 2 0.04
27 25 0.53
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (27 bp):
TTATCCAGGTATTTATTATTATTATTA
Found at i:605552 original size:30 final size:32
Alignment explanation
Indices: 605518--605585 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
605508 ATAGTTTTTA
605518 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
605548 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
605581 TATTT
1 TATTT
605586 ATTTAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Done.