Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 65
Found at i:3043199 original size:14 final size:14
Alignment explanation
Indices: 3043180--3043238 Score: 82
Period size: 14 Copynumber: 4.2 Consensus size: 14
3043170 AGAAAAATTA
* *
3043180 ATACATCTATACAT
1 ATACATATATATAT
3043194 ATACATATATATAT
1 ATACATATATATAT
*
3043208 ATATATATATATAT
1 ATACATATATATAT
*
3043222 ATATATATATATAT
1 ATACATATATATAT
3043236 ATA
1 ATA
3043239 ATGATATAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:3043205 original size:2 final size:2
Alignment explanation
Indices: 3043187--3043257 Score: 92
Period size: 2 Copynumber: 36.0 Consensus size: 2
3043177 TTAATACATC
* *
3043187 TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3043229 TA TA TA TA TA -A TGA TA TA -A GA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
3043258 ATAAAAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
1 2 0.03
2 57 0.93
3 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3043284 original size:9 final size:11
Alignment explanation
Indices: 3043187--3043277 Score: 65
Period size: 12 Copynumber: 7.7 Consensus size: 11
3043177 TTAATACATC
*
3043187 TATACATATACA
1 TATAAATATA-A
*
3043199 TATATATATATA
1 TATAAATATA-A
*
3043211 TATATATATATA
1 TATAAATATA-A
*
3043223 TATATATATATA
1 TATAAATATA-A
3043235 TATAATGATATAA
1 TATAA--ATATAA
* *
3043248 GATATATATAA
1 TATAAATATAA
*
3043259 TAAAAATATAA
1 TATAAATATAA
3043270 TATAAATA
1 TATAAATA
3043278 AATTAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
11 21 0.31
12 38 0.56
13 4 0.06
14 5 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
TATAAATATAA
Found at i:3043326 original size:16 final size:16
Alignment explanation
Indices: 3043302--3043336 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3043292 AATATAGTAA
3043302 ATAAATAAAAAAATAT
1 ATAAATAAAAAAATAT
* *
3043318 ATAATTAAAAATATAT
1 ATAAATAAAAAAATAT
3043334 ATA
1 ATA
3043337 TAGGAGACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATAAAAAAATAT
Found at i:3044497 original size:85 final size:83
Alignment explanation
Indices: 3044377--3044558 Score: 215
Period size: 83 Copynumber: 2.2 Consensus size: 83
3044367 TTTCGTTGAC
* * * * *
3044377 AGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATT-TGATTTACCTCT-GAGTTGAATGTAATC
1 AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATTATG-TGT--CT-TAGAGCTGAACGTAATC
* *
3044440 GATCTCGAAGGTCTTTGATGAT
62 AAACTCGAAGGTCTTTGATGAT
* * *
3044462 AGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTATGTGTCTTAGAGCTGAGCGTAGTCAAAC
1 AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATTATGTGTCTTAGAGCTGAACGTAATCAAAC
*
3044527 TCGAAGGTCTTTGTTGAT
66 TCGAAGGTCTTTGATGAT
3044545 AGATAACCCTTCTT
1 AGATAACCCTTCTT
3044559 TGAGTTGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
82 1 0.01
83 46 0.55
85 35 0.42
86 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (83 bp):
AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATTATGTGTCTTAGAGCTGAACGTAATCAAAC
TCGAAGGTCTTTGATGAT
Found at i:3045811 original size:67 final size:65
Alignment explanation
Indices: 3045679--3046057 Score: 241
Period size: 65 Copynumber: 5.6 Consensus size: 65
3045669 AAGATATCTG
* * * **
3045679 TTGTTTCATGA-AAATCGGTCTCAAGGGAAACAAAATTTTGTTTTAAGG-GAAATAAATTTGAAG
1 TTGTTTCAAGAGAAA-CTGTCTCAAGGGAGACAAAA-TTTGTTTT-AGGAGAAATAAATTCAAAG
3045742 ATT
63 ATT
3045745 TTGTATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGA
1 TTG--TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGA
3045810 TT
64 TT
* * * * * *
3045812 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAA-----T--A-A-AT
* *
3045877 ACAAA-ACT
57 TCAAAGATT
* * * * ** * * * *
3045885 TAGTTCCAAAAGAAATTGTCTCAAGGGAGATGAAATTTGTTTCA-AATAAA-ACATATTCAAATA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATA-A-ATTCAAAGA
*
3045948 AT
64 TT
* ** * *** *
3045950 TTGTTTCAAGGGAAACTGTCTCAAGATAGACAAAATTTGTTTCAAGG-GAAATGTTTTCAATG-T
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-TAGGAGAAATAAATTCAAAGAT
3046013 T
65 T
*
3046014 TATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTT
3046058 CAAGGGAAAC
Statistics
Matches: 245, Mismatches: 49, Indels: 38
0.74 0.15 0.11
Matches are distributed among these distances:
64 9 0.04
65 113 0.46
66 17 0.07
67 27 0.11
68 25 0.10
69 3 0.01
70 1 0.00
72 5 0.02
73 40 0.16
74 5 0.02
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATAAATTCAAAGATT
Found at i:3045863 original size:36 final size:36
Alignment explanation
Indices: 3045811--3045929 Score: 157
Period size: 36 Copynumber: 3.3 Consensus size: 36
3045801 ATTCAAAGAT
*
3045811 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
3045847 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * * *
3045883 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
3045920 TTTGTTTCAA
1 TTTGTTTCAA
3045930 ATAAAACATA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 42 0.59
37 29 0.41
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:3045908 original size:37 final size:36
Alignment explanation
Indices: 3045823--3045914 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
3045813 TGTTTCAAGG
* * * *
3045823 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
3045859 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* *
3045896 GAAATTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
3045915 TGAAATTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 23 0.47
37 26 0.53
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:3046067 original size:37 final size:37
Alignment explanation
Indices: 3046016--3046087 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
3046006 TCAATGTTTA
*
3046016 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
* *
3046053 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
3046088 CTTCTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
Found at i:3047769 original size:21 final size:21
Alignment explanation
Indices: 3047743--3047802 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3047733 TTTTTCTTCA
3047743 ATTTTCCTTTTTTCTCTTTTT
1 ATTTTCCTTTTTTCTCTTTTT
*
3047764 ATTTT-C-TCTTT-TCTTTTT
1 ATTTTCCTTTTTTCTCTTTTT
*
3047782 -TTTTCTTTTTTTTCTCTTTTT
1 ATTTTC-CTTTTTTCTCTTTTT
3047803 GTTCTGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 4 0.12
18 7 0.22
19 4 0.12
20 5 0.16
21 12 0.38
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (21 bp):
ATTTTCCTTTTTTCTCTTTTT
Found at i:3047775 original size:28 final size:26
Alignment explanation
Indices: 3047730--3047801 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 26
3047720 CATATTATCT
**
3047730 TCTTTTTTCTTCAATTTTCCTTTTTTC
1 TCTTTTTT-TTCTCTTTTCCTTTTTTC
* *
3047757 TCTTTTTATTTTCTCTTTTCTTTTTTTT
1 TC-TTTT-TTTTCTCTTTTCCTTTTTTC
3047785 TCTTTTTTTTCTCTTTT
1 TCTTTTTTTTCTCTTTT
3047802 TGTTCTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 11 0.28
27 6 0.15
28 20 0.51
29 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (26 bp):
TCTTTTTTTTCTCTTTTCCTTTTTTC
Found at i:3047780 original size:26 final size:26
Alignment explanation
Indices: 3047744--3047801 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3047734 TTTTCTTCAA
*
3047744 TTTTCCTTTTTTCTCTTTTTATTTTCTC
1 TTTT-CTTTTTTCT-TCTTTATTTTCTC
* *
3047772 TTTTCTTTTTTTTTCTTTTTTTTCTC
1 TTTTCTTTTTTCTTCTTTATTTTCTC
3047798 TTTT
1 TTTT
3047802 TGTTCTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 15 0.56
27 8 0.30
28 4 0.15
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTCTTTTTTCTTCTTTATTTTCTC
Found at i:3047807 original size:11 final size:10
Alignment explanation
Indices: 3047750--3047807 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
3047740 TCAATTTTCC
3047750 TTTTTTCTCT
1 TTTTTTCTCT
*
3047760 TTTTATTTTC-
1 TTTT-TTCTCT
* *
3047770 TCTTTTCTTT
1 TTTTTTCTCT
3047780 TTTTTTCT-T
1 TTTTTTCTCT
3047789 TTTTTTCTCT
1 TTTTTTCTCT
3047799 TTTTGTTCT
1 TTTT-TTCT
3047808 GATTGAATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 12 0.31
10 19 0.49
11 8 0.21
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:3050946 original size:10 final size:9
Alignment explanation
Indices: 3050933--3050967 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3050923 CAAAACACGT
3050933 AAAAAAATA
1 AAAAAAATA
3050942 AAAAAAATA
1 AAAAAAATA
*
3050951 ATAAAAATA
1 AAAAAAATA
*
3050960 AACAAAAT
1 AAAAAAAT
3050968 GAATAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3050956 original size:18 final size:19
Alignment explanation
Indices: 3050935--3050975 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
3050925 AAACACGTAA
3050935 AAAAATAAAAAAAAT-AAT
1 AAAAATAAAAAAAATGAAT
*
3050953 AAAAATAAACAAAATGAAT
1 AAAAATAAAAAAAATGAAT
3050972 AAAA
1 AAAA
3050976 TGTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAAATAAAAAAAATGAAT
Found at i:3051246 original size:36 final size:39
Alignment explanation
Indices: 3051198--3051284 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
3051188 TATAATATAT
3051198 ATAAATA-A-ATAAAAAC-A-AAAATAGAATATTAAGAA
1 ATAAATATATATAAAAACGATAAAATAGAATATTAAGAA
*
3051233 A-AAATATATATAAAAACGTATAAAATATAATATTAAGAA
1 ATAAATATATATAAAAACG-ATAAAATAGAATATTAAGAA
*
3051272 ATATATATATATA
1 ATAAATATATATA
3051285 CATAGCAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 5 0.11
35 2 0.05
36 8 0.18
38 1 0.02
39 18 0.41
40 10 0.23
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (39 bp):
ATAAATATATATAAAAACGATAAAATAGAATATTAAGAA
Found at i:3051320 original size:8 final size:8
Alignment explanation
Indices: 3051307--3051349 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3051297 AGAAAAATTA
*
3051307 ATACATCT
1 ATACATAT
3051315 ATACATAT
1 ATACATAT
*
3051323 ATATATAT
1 ATACATAT
*
3051331 ATATATAT
1 ATACATAT
*
3051339 ATATATAT
1 ATACATAT
3051347 ATA
1 ATA
3051350 ATGATATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (8 bp):
ATACATAT
Found at i:3051326 original size:2 final size:2
Alignment explanation
Indices: 3051314--3051368 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
3051304 TTAATACATC
*
3051314 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
*
3051356 TA -A GA TA TA TA TA
1 TA TA TA TA TA TA TA
3051369 ATAAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3051381 original size:25 final size:25
Alignment explanation
Indices: 3051333--3051400 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
3051323 ATATATATAT
* *
3051333 ATATATATATATATATAATGATATAAG
1 ATATATATA-ATA-AAAATAATATAAG
*
3051360 ATATATATAATAAAAATAATATAAT
1 ATATATATAATAAAAATAATATAAG
*
3051385 ATAAATA-AATTAAAAA
1 ATATATATAA-TAAAAA
3051401 AGAGGAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.06
25 22 0.61
26 3 0.08
27 9 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (25 bp):
ATATATATAATAAAAATAATATAAG
Found at i:3051392 original size:14 final size:15
Alignment explanation
Indices: 3051319--3051391 Score: 73
Period size: 14 Copynumber: 5.1 Consensus size: 15
3051309 ACATCTATAC
*
3051319 ATATAT-ATATATAT
1 ATATATAATATAAAT
*
3051333 ATATAT-ATATATAT
1 ATATATAATATAAAT
*
3051347 ATA-ATGATATAAGAT
1 ATATATAATATAA-AT
*
3051362 ATATATAATAAAAAT
1 ATATATAATATAAAT
3051377 A-ATATAATATAAAT
1 ATATATAATATAAAT
3051391 A
1 A
3051392 AATTAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
13 2 0.04
14 35 0.67
15 8 0.15
16 7 0.13
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATATATAATATAAAT
Found at i:3053207 original size:31 final size:31
Alignment explanation
Indices: 3053171--3053230 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3053161 AACTTAAAAG
* *
3053171 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
3053202 AGTTTTACAATACTTAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
3053231 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3053807 original size:63 final size:65
Alignment explanation
Indices: 3053723--3053856 Score: 245
Period size: 63 Copynumber: 2.1 Consensus size: 65
3053713 TTATATGATA
*
3053723 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
3053787 TAAAATT-AATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
3053851 TAAAAT
1 TAAAAT
3053857 AAAAATAAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
63 43 0.63
64 25 0.37
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (65 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:3053831 original size:26 final size:26
Alignment explanation
Indices: 3053778--3053852 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 26
3053768 TTTATTTAAA
3053778 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
*
3053803 AATATAATATTAAAAAAGTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
*
3053829 AATTTAT-TTAAAAAATTAATATTA
1 AATTAATATTAAAAAATTAATATTA
3053853 AAATAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
24 15 0.35
25 6 0.14
26 11 0.26
27 1 0.02
28 10 0.23
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:3053867 original size:26 final size:26
Alignment explanation
Indices: 3053837--3053892 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3053827 TTAATTTATT
*
3053837 TAAAAA-ATTAATATTAAAA-TAAAAA
1 TAAAAATAATAATA-TAAAATTAAAAA
*
3053862 TAAAAATAATAATATAAAATTAAATA
1 TAAAAATAATAATATAAAATTAAAAA
3053888 TAAAA
1 TAAAA
3053893 TCTTTTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAAAATAATAATATAAAATTAAAAA
Found at i:3053869 original size:20 final size:20
Alignment explanation
Indices: 3053846--3053890 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3053836 TTAAAAAATT
*
3053846 AATATTAAAATAAAAATAAA
1 AATAATAAAATAAAAATAAA
* *
3053866 AATAATAATATAAAATTAAA
1 AATAATAAAATAAAAATAAA
*
3053886 TATAA
1 AATAA
3053891 AATCTTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAATAAAATAAAAATAAA
Found at i:3053880 original size:63 final size:63
Alignment explanation
Indices: 3053740--3053880 Score: 205
Period size: 63 Copynumber: 2.2 Consensus size: 63
3053730 AAATATCTAT
* * * * *
3053740 AATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATCTAT
1 AATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAATTAATATTAAAATAAAAATCAAA
3053803 AATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATATTAAAATAAAAAT-AAA
1 AATATAATATTAAAAAAGTAATATTTAATTTATTT-AAAAATTAATATTAAAATAAAAATCAAA
3053866 AATAATAATA-TAAAA
1 AAT-ATAATATTAAAA
3053881 TTAAATATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
63 43 0.61
64 28 0.39
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (63 bp):
AATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAATTAATATTAAAATAAAAATCAAA
Found at i:3054719 original size:17 final size:18
Alignment explanation
Indices: 3054687--3054721 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
3054677 GTACGTTATT
3054687 CAAATCTCAAAAATACATC
1 CAAATCTC-AAAATACATC
3054706 CAAATCTC-AAATACAT
1 CAAATCTCAAAATACAT
3054722 ATATGTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
CAAATCTCAAAATACATC
Found at i:3055125 original size:113 final size:112
Alignment explanation
Indices: 3054945--3055163 Score: 325
Period size: 113 Copynumber: 1.9 Consensus size: 112
3054935 TATATATCTC
*
3054945 TTTTGATGTTAATAAGCATGTAACTCTAAAAAAATTATCTTCTATTTTGTTATAGAGTGTTGTCT
1 TTTTGATGTTAATAAGCATGTAACTCTAAAAAAATTATCTTCCATTTTGTTATAGAGTGTTGTCT
*
3055010 TATTAGTATTCATTTAGAAAAATGTATTTTTAGCACTTGCCCTAATTA
66 TATTAGTATTCATATAGAAAAA-GTATTTTTAGCACTTGCCCTAATTA
* ** * *
3055058 TTTTGATGTTGATAAGCATGTAGTTCTCAAAAAATTTATCTTCCATTTTGTTATGGAGCT-TTG-
1 TTTTGATGTTAATAAGCATGTAACTCT-AAAAAAATTATCTTCCATTTTGTTATAGAG-TGTTGT
*
3055121 CTTATTAGTATTCATATATAAAAAGTATTTTTAGCACTTGCCC
64 CTTATTAGTATTCATATAGAAAAAGTATTTTTAGCACTTGCCC
3055164 CAAAAACTGG
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
112 19 0.20
113 46 0.48
114 30 0.31
115 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (112 bp):
TTTTGATGTTAATAAGCATGTAACTCTAAAAAAATTATCTTCCATTTTGTTATAGAGTGTTGTCT
TATTAGTATTCATATAGAAAAAGTATTTTTAGCACTTGCCCTAATTA
Found at i:3063836 original size:2 final size:2
Alignment explanation
Indices: 3063829--3063860 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3063819 ATAATAAGTA
3063829 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
3063861 TATTTTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3065186 original size:21 final size:21
Alignment explanation
Indices: 3065144--3065186 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3065134 TTCAACAAAT
* * *
3065144 CTCTTCATCAAATGGTCTTAA
1 CTCTTCATCAAAAGATCATAA
3065165 CTCTTCATCAAAAGATCATAA
1 CTCTTCATCAAAAGATCATAA
3065186 C
1 C
3065187 CTTTGATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.33
Consensus pattern (21 bp):
CTCTTCATCAAAAGATCATAA
Found at i:3068706 original size:31 final size:31
Alignment explanation
Indices: 3068668--3068737 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
3068658 GTTATGCAAT
3068668 GGTGGACCAGGTCGGATGCACTAAGCCCCTA
1 GGTGGACCAGGTCGGATGCACTAAGCCCCTA
3068699 GGTGGACCAGGTCGGATGCACTAAGCCCCTA
1 GGTGGACCAGGTCGGATGCACTAAGCCCCTA
3068730 GGTGGACC
1 GGTGGACC
3068738 GGCTCGGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (31 bp):
GGTGGACCAGGTCGGATGCACTAAGCCCCTA
Found at i:3085573 original size:4 final size:4
Alignment explanation
Indices: 3085564--3085593 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3085554 CTAACAATTG
3085564 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3085594 CTTATATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:3085676 original size:7 final size:7
Alignment explanation
Indices: 3085664--3085688 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3085654 TCAGACTCTG
3085664 CTAACCA
1 CTAACCA
3085671 CTAACCA
1 CTAACCA
3085678 CTAACCA
1 CTAACCA
3085685 CTAA
1 CTAA
3085689 TTTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCA
Found at i:3085739 original size:34 final size:33
Alignment explanation
Indices: 3085700--3085796 Score: 110
Period size: 34 Copynumber: 2.9 Consensus size: 33
3085690 TTTTTTAATT
3085700 TACTAACATTCTAAC-TTTTATTTTTATTTGTTC
1 TACTAACATTCTAACATTTTATTTTTA-TTGTTC
***
3085733 ATACTAACACAATAACATTTTATTTTTATTGTTC
1 -TACTAACATTCTAACATTTTATTTTTATTGTTC
3085767 TAACTAAC-TTACTAACATTTTA-TTTTATTG
1 T-ACTAACATT-CTAACATTTTATTTTTATTG
3085797 CACAAACTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
33 9 0.17
34 34 0.63
35 11 0.20
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.52
Consensus pattern (33 bp):
TACTAACATTCTAACATTTTATTTTTATTGTTC
Found at i:3086045 original size:16 final size:15
Alignment explanation
Indices: 3086005--3086056 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3085995 TTTCTTCCCC
*
3086005 TTTAATTTCCTGCAT
1 TTTAATTTCCAGCAT
*
3086020 TTT-A-TTCCAGTCCT
1 TTTAATTTCCAG-CAT
3086034 TTTAATTTCCAGCAT
1 TTTAATTTCCAGCAT
3086049 TTTAATTT
1 TTTAATTT
3086057 TTATTATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 14 0.45
16 6 0.19
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTAATTTCCAGCAT
Found at i:3086140 original size:75 final size:75
Alignment explanation
Indices: 3085968--3086140 Score: 201
Period size: 75 Copynumber: 2.3 Consensus size: 75
3085958 TTTATTTTTT
* * *
3085968 CAGCACTTTAAATTTCAGTATTTTATTTTTCTTCCCCTTTAATTTCCTGCATTTTATTCCAGTCC
1 CAGCACTTTAAATTTCAGTATTTCATTTTTCTTCCACTTTAATTTCCTGAATTTTATTCCAGTCC
*
3086033 TTTTAATTTC
66 TTTAAATTTC
* * * * *
3086043 CAGCATTTTAATTTTTATTATTTCATTTTTCTGT-CACTTTAATTT-CT-AATCCTTTAGTT-TA
1 CAGCACTTTAAATTTCAGTATTTCATTTTTCT-TCCACTTTAATTTCCTGAAT--TTTA-TTCCA
3086104 GTCCTTTAAATTTC
62 GTCCTTTAAATTTC
3086118 CAGCACTTTAAATTTCAGTATTT
1 CAGCACTTTAAATTTCAGTATTT
3086141 TGACTTCTGC
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
73 2 0.02
74 2 0.02
75 74 0.91
76 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (75 bp):
CAGCACTTTAAATTTCAGTATTTCATTTTTCTTCCACTTTAATTTCCTGAATTTTATTCCAGTCC
TTTAAATTTC
Found at i:3098912 original size:60 final size:58
Alignment explanation
Indices: 3098770--3098918 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 58
3098760 AACTGATCCT
* * ** *
3098770 TAAACTTTTGAGTATTTCAATTCCATCCCTAAACTATGATTCTCTTTCTAAATTAGCCC
1 TAAACTTTTGAATA-TTCAATTTCATCCCTAAACTATGACACTCTTGCTAAATTAGCCC
* * * *
3098829 TTAAACATTTAAACATTCTAATTTCATCCCTAAACTATGACACTCTTGCTAAATTGGTCTCC
1 -TAAACTTTTGAATATTC-AATTTCATCCCTAAACTATGACACTCTTGCTAAATTAG-C-CC
3098891 -AAACTTTTGAATATTCGAATTTCATCCC
1 TAAACTTTTGAATATTC-AATTTCATCCC
3098919 AAATTCATCC
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 3 0.04
60 67 0.92
61 1 0.01
62 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (58 bp):
TAAACTTTTGAATATTCAATTTCATCCCTAAACTATGACACTCTTGCTAAATTAGCCC
Found at i:3100605 original size:130 final size:130
Alignment explanation
Indices: 3100379--3100824 Score: 813
Period size: 130 Copynumber: 3.4 Consensus size: 130
3100369 TGATATATAG
* *
3100379 TGTGTGGCTTTAAAATGCTGTGTTTTGTGCATGTGGATGAACGGTTTAATCTTAGTTTGGCCAAA
1 TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACAGTTTAATCTTAGTTTGGCCAAA
3100444 GGATGTAGGAAGAGTTTTACCGGTTTGATCTCTTCGTCCCTATTTTGTCTTATGCTTGTATATGT
66 GGATGTAGGAAGAGTTTTACCGGTTTGATCTCTTCGTCCCTATTTTGTCTTATGCTTGTATATGT
*
3100509 TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACGGTTTAATCTTAGTTTGGCCAAA
1 TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACAGTTTAATCTTAGTTTGGCCAAA
*
3100574 GGATGTAGGAAGAGTTTTACCGGTTTGATCTCTTCGTCCCTATTTTGTCTTATGATTGTATATGT
66 GGATGTAGGAAGAGTTTTACCGGTTTGATCTCTTCGTCCCTATTTTGTCTTATGCTTGTATATGT
3100639 TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACAGTTTAATCTTAGTTTGGCCAAA
1 TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACAGTTTAATCTTAGTTTGGCCAAA
* * *
3100704 GGATGTAGGAAGAGTTTTACCGGTTTGATCTGTTCATCCCTATTTTGTCTTATGCTTGTATATAT
66 GGATGTAGGAAGAGTTTTACCGGTTTGATCTCTTCGTCCCTATTTTGTCTTATGCTTGTATATGT
*
3100769 TGTGTGGTTTGAAAATGCTGTGTTTTGTGCATG-GGATGAACAGTTTAATCTTAGTT
1 TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACAGTTTAATCTTAGTT
3100825 AGTACAGATG
Statistics
Matches: 308, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
129 23 0.07
130 285 0.93
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (130 bp):
TGTGTGGCTTGAAAATGCTGTGTTTTGTGCATGTGGATGAACAGTTTAATCTTAGTTTGGCCAAA
GGATGTAGGAAGAGTTTTACCGGTTTGATCTCTTCGTCCCTATTTTGTCTTATGCTTGTATATGT
Found at i:3103985 original size:27 final size:27
Alignment explanation
Indices: 3103953--3104023 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
3103943 ATGTAATGAA
3103953 AATTTTTAATAATTATATT-TTAATTT
1 AATTTTTAATAATTATATTATTAATTT
* *
3103979 AATTTTTAATAACTAT-TTATTCATTT
1 AATTTTTAATAATTATATTATTAATTT
*
3104005 ATATTTTTAAAAATTATAT
1 A-ATTTTTAATAATTATAT
3104024 ACCAAACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 22 0.58
27 13 0.34
28 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
AATTTTTAATAATTATATTATTAATTT
Found at i:3105441 original size:24 final size:22
Alignment explanation
Indices: 3105348--3105451 Score: 90
Period size: 21 Copynumber: 4.8 Consensus size: 22
3105338 AATCAGTTTC
3105348 CAAAATCGCAACGCG-ATTCTT-
1 CAAAATCGCAACGCGAATT-TTA
* * **
3105369 GAAAATCGCAATGCG-ATAGTA
1 CAAAATCGCAACGCGAATTTTA
* **
3105390 CAAATTCGCATTGCG-ATTTTA
1 CAAAATCGCAACGCGAATTTTA
3105411 CAAAATCGCAACGCGAATTTGTA
1 CAAAATCGCAACGCGAATTT-TA
3105434 CTAAAATCGCAACGCGAA
1 C-AAAATCGCAACGCGAA
3105452 CACATAAATC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.01
21 43 0.64
22 4 0.06
23 3 0.04
24 16 0.24
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (22 bp):
CAAAATCGCAACGCGAATTTTA
Found at i:3105462 original size:20 final size:20
Alignment explanation
Indices: 3105437--3105609 Score: 224
Period size: 20 Copynumber: 8.7 Consensus size: 20
3105427 ATTTGTACTA
* *
3105437 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3105457 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3105477 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3105497 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3105517 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3105537 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3105557 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
3105577 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
3105597 AAATCGCAACGCG
1 AAATCGCAACGCG
3105610 ATATTTAAAG
Statistics
Matches: 134, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 131 0.98
21 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3106133 original size:20 final size:20
Alignment explanation
Indices: 3106109--3106183 Score: 98
Period size: 19 Copynumber: 3.8 Consensus size: 20
3106099 TGCAGAAGAG
***
3106109 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
3106129 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
3106150 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
3106169 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
3106184 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:3106224 original size:19 final size:19
Alignment explanation
Indices: 3106202--3106299 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
3106192 GAAACCAAAA
*
3106202 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3106221 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3106235 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3106254 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3106268 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3106287 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3106300 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
16 6 0.09
17 6 0.09
19 32 0.50
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3106243 original size:14 final size:14
Alignment explanation
Indices: 3106224--3106313 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3106214 TTTCATTTCG
3106224 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3106238 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3106257 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3106271 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3106290 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3106304 CGTTGCGATT
1 CGTTGCGATT
3106314 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3106249 original size:33 final size:33
Alignment explanation
Indices: 3106207--3106321 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
3106197 CAAAATCGCA
3106207 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3106240 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3106273 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3106306 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3106322 AACCCAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3108177 original size:93 final size:93
Alignment explanation
Indices: 3108018--3108300 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
3108008 TAGATTGCTT
*
3108018 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3108083 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3108111 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3108176 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3108204 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
3108269 TTTGTCTTTGTTTTGTCTATTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3108296 AGTAA
1 AGTAA
3108301 TGCAATCCAT
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 182 0.97
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3108388 original size:19 final size:19
Alignment explanation
Indices: 3108348--3108476 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3108338 TAGTTTACTT
* *
3108348 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3108368 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3108387 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3108406 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3108420 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3108439 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3108453 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3108472 TCGCA
1 TCGCA
3108477 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3108427 original size:33 final size:32
Alignment explanation
Indices: 3108384--3108476 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3108374 CGCGAAACCA
**
3108384 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3108416 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3108449 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3108477 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3108474 original size:52 final size:52
Alignment explanation
Indices: 3108348--3108476 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3108338 TAGTTTACTT
**
3108348 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3108400 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3108453 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
3108477 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3108494 original size:19 final size:19
Alignment explanation
Indices: 3108472--3108605 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
3108462 GAAACCAAAA
*
3108472 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3108491 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
**
3108507 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
3108524 TCGCGTTGCGATTTT-A--
1 TCGCGTTGCGATTTTCATT
*
3108540 ---AGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3108556 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3108575 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3108595 TCGTGTTGCGA
1 TCGCGTTGCGA
3108606 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 11 0.12
14 9 0.10
16 5 0.05
17 6 0.06
19 50 0.54
20 12 0.13
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3108550 original size:32 final size:32
Alignment explanation
Indices: 3108477--3108570 Score: 143
Period size: 32 Copynumber: 2.9 Consensus size: 32
3108467 CAAAATCGCA
**
3108477 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TTAAG
**
3108510 TTGCGATTTTGGTTTCGCGTTGCGATTTTAAG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTAAG
3108542 TTGCGATTTTCATTTCGCGTTGCGATTTT
1 TTGCGATTTTCATTTCGCGTTGCGATTTT
3108571 GGTTTCGCGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTAAG
Found at i:3110677 original size:19 final size:19
Alignment explanation
Indices: 3110661--3110758 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
3110651 AAAAATGACT
3110661 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3110680 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3110699 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
3110713 ATCGCAATGCGAAATGAAT
1 ATCGCAATGCGAAATGAAA
3110732 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3110752 ATCGCAA
1 ATCGCAA
3110759 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.55
20 15 0.22
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3110790 original size:53 final size:53
Alignment explanation
Indices: 3110661--3110777 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
3110651 AAAAATGACT
*
3110661 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3110713 ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
3110766 ATCGCAATGCGA
1 ATCGCAATGCGA
3110778 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 28 0.44
53 35 0.56
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:3110795 original size:19 final size:19
Alignment explanation
Indices: 3110767--3110987 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
3110757 AACGAGAGAA
*
3110767 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3110786 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3110805 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
3110821 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3110838 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3110857 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3110873 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3110890 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3110909 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
3110925 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
3110942 TCCGCATTGCGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
3110959 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
3110975 TCGCATTGCGATT
1 TCGCATTGCGATT
3110988 CTCTCGTTGC
Statistics
Matches: 171, Mismatches: 9, Indels: 44
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.03
14 27 0.16
15 1 0.01
16 18 0.11
17 17 0.10
18 2 0.01
19 95 0.56
20 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3110833 original size:33 final size:32
Alignment explanation
Indices: 3110791--3111001 Score: 212
Period size: 33 Copynumber: 6.2 Consensus size: 32
3110781 TCATTTCGCA
3110791 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-TCTCG
3110824 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTTC---TCG
* * * * *
3110860 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATTTCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTTCTCG
3110895 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCTCG
*
3110928 TTGCGATTTTTATTTCCGCATTGCGATTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTTC-TCG
*
3110961 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATT-TCTCG
3110994 TTGCGATT
1 TTGCGATT
3111002 GTAATTTCCG
Statistics
Matches: 148, Mismatches: 14, Indels: 32
0.76 0.07 0.16
Matches are distributed among these distances:
31 9 0.06
32 16 0.11
33 82 0.55
34 13 0.09
35 1 0.01
36 3 0.02
38 12 0.08
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCTCG
Found at i:3110987 original size:52 final size:52
Alignment explanation
Indices: 3110773--3110956 Score: 332
Period size: 52 Copynumber: 3.5 Consensus size: 52
3110763 AGAATCGCAA
3110773 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
3110825 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
3110877 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
3110929 TGCGATTTTTATTTCCGCATTGCGATTT
1 TGCGATTTTCATTT-CGCATTGCGATTT
3110957 CATGTTGGGA
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 115 0.90
53 13 0.10
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:3113321 original size:12 final size:12
Alignment explanation
Indices: 3113304--3113328 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3113294 TCTTCGGGGA
3113304 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3113316 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3113328 C
1 C
3113329 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3113537 original size:24 final size:24
Alignment explanation
Indices: 3113503--3113549 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3113493 CTGAAACATC
3113503 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3113527 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3113550 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3114285 original size:20 final size:20
Alignment explanation
Indices: 3114260--3114484 Score: 245
Period size: 20 Copynumber: 11.2 Consensus size: 20
3114250 TGCCCTACCG
* *
3114260 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
3114280 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
**
3114300 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
3114320 GATTTACGGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
*
3114340 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* * *
3114360 GATATACGGATACGCATTGC
1 GATTTACGGATTCGCGTTGC
** *
3114380 GATTTACCCATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* *
3114400 GATTTACGGATACACGTTGC
1 GATTTACGGATTCGCGTTGC
*
3114420 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
*
3114440 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATTCGCGTTGC
* **
3114460 GATTTTCATATTCGCGTTGC
1 GATTTACGGATTCGCGTTGC
3114480 GATTT
1 GATTT
3114485 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GATTTACGGATTCGCGTTGC
Found at i:3114501 original size:21 final size:21
Alignment explanation
Indices: 3114471--3114553 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3114461 ATTTTCATAT
*
3114471 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3114492 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3114513 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3114534 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3114554 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3114544 original size:42 final size:43
Alignment explanation
Indices: 3114451--3114549 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3114441 ATTTATGTGT
* *
3114451 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3114492 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3114534 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3114550 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3114598 original size:19 final size:18
Alignment explanation
Indices: 3114574--3114610 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3114564 ATTCTGGGGA
3114574 TCGCGTTGCGATTTGTATT
1 TCGCGTTGCGATTT-TATT
3114593 TCGCGTTGCGATTTTATT
1 TCGCGTTGCGATTTTATT
3114611 GGTCATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (18 bp):
TCGCGTTGCGATTTTATT
Found at i:3115800 original size:23 final size:22
Alignment explanation
Indices: 3115752--3115819 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
3115742 AGTGTATATT
**
3115752 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
* *
3115774 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
* *
3115797 ATATTATTAGATTATTATATTAA
1 ATATT-TTAAAATATTA-ATTAA
3115820 TATTAAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 10 0.29
23 16 0.46
24 9 0.26
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:3115813 original size:19 final size:19
Alignment explanation
Indices: 3115789--3115859 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
3115779 TTAAATATCT
*
3115789 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
3115808 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
3115827 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
3115847 TTATTAAATATAT
1 TTATTAAA-ATAT
3115860 AAAACAATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:3115840 original size:24 final size:26
Alignment explanation
Indices: 3115813--3115990 Score: 79
Period size: 30 Copynumber: 6.6 Consensus size: 26
3115803 TTAGATTATT
3115813 ATATTA-A-TATTAAATATATAAATA
1 ATATTATATTATTAAATATATAAATA
*
3115837 ATATTATTCATTATTAAATATATAAAACA
1 ATATTA-T-ATTATTAAATATAT-AAATA
*
3115866 ATTATTATATATTTATTAAA-ATAAAAATATA
1 A-TA-T-TATA-TTATTAAATAT-ATAA-ATA
*
3115897 ATATCTTATATTATTATA-ATAT-AAT-
1 ATA--TTATATTATTAAATATATAAATA
*
3115922 -TGATTATTTTATTATAATATTATAAATATA
1 AT-ATTATATTATTA-AATA-TAT-AA-ATA
*
3115952 ATATTATATTATTATAA-ATATTAATA
1 ATATTATATTATTA-AATATATAAATA
*
3115978 A-A-TATATTTTTAA
1 ATATTATATTATTAA
3115991 TATTTTAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 43
0.69 0.06 0.24
Matches are distributed among these distances:
23 11 0.09
24 17 0.14
25 3 0.02
26 9 0.07
27 3 0.02
28 17 0.14
29 17 0.14
30 27 0.22
31 16 0.13
32 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATTATATTATTAAATATATAAATA
Found at i:3115913 original size:8 final size:8
Alignment explanation
Indices: 3115902--3115967 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
3115892 ATATAATATC
3115902 TTATATTA
1 TTATATTA
*
3115910 TTATAATA
1 TTATATTA
3115918 -TA-ATTGA
1 TTATATT-A
*
3115925 TTATTTTA
1 TTATATTA
*
3115933 TTATAATA
1 TTATATTA
3115941 TTATA--A
1 TTATATTA
* *
3115947 ATATAATA
1 TTATATTA
3115955 TTATATTA
1 TTATATTA
3115963 TTATA
1 TTATA
3115968 AATATTAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 7 0.16
7 3 0.07
8 33 0.73
9 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (8 bp):
TTATATTA
Found at i:3115953 original size:14 final size:14
Alignment explanation
Indices: 3115934--3115983 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
3115924 ATTATTTTAT
3115934 TATAATATTATAAA
1 TATAATATTATAAA
*
3115948 TATAATATTATATTAT
1 TATAATATTATA--AA
3115964 TATAAATATTAATAAA
1 TAT-AATATT-ATAAA
3115980 TATA
1 TATA
3115984 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 12 0.40
15 1 0.03
16 8 0.27
17 6 0.20
18 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATAATATTATAAA
Found at i:3115959 original size:22 final size:23
Alignment explanation
Indices: 3115931--3115977 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
3115921 TTGATTATTT
3115931 TATTATAATATTATAAATA-TAA
1 TATTATAATATTATAAATATTAA
*
3115953 TATTATATTATTATAAATATTAA
1 TATTATAATATTATAAATATTAA
3115976 TA
1 TA
3115978 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTATAATATTATAAATATTAA
Found at i:3115982 original size:22 final size:22
Alignment explanation
Indices: 3115939--3115982 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3115929 TTTATTATAA
*
3115939 TATTATAAATATAATATTATAT
1 TATTATAAATATAATATAATAT
3115961 TATTATAAATATTAATA-AATAT
1 TATTATAAATA-TAATATAATAT
3115983 ATTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATAAATATAATATAATAT
Found at i:3116263 original size:42 final size:42
Alignment explanation
Indices: 3116207--3116299 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
3116197 TTCCTCTAAC
* * * **
3116207 CAAACACTGGAAAACATTTTTCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTACAGAAAACGAATTAAATGAAA
3116249 CAAACACGGGAAAACATTTTACAGAAAACGAATTAAATGAAA
1 CAAACACGGGAAAACATTTTACAGAAAACGAATTAAATGAAA
3116291 CAAACACGG
1 CAAACACGG
3116300 AATTTTGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.17
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTACAGAAAACGAATTAAATGAAA
Found at i:3116575 original size:31 final size:31
Alignment explanation
Indices: 3116540--3116628 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 31
3116530 ACTTAAAGTT
*
3116540 TTTTAGCACCTAAACTATTAATTTTGATATG
1 TTTTAGCACCTAAACTATTAATTTTGATATA
3116571 TTTTAGTACACCTAAACTATTAATTTTGATATA
1 TTTTAG--CACCTAAACTATTAATTTTGATATA
* *
3116604 TTTTAGTACTTAAACT-TTCAATTTT
1 TTTTAGCACCTAAACTATT-AATTTT
3116629 TTCAAAACTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 2 0.04
31 20 0.38
33 30 0.58
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (31 bp):
TTTTAGCACCTAAACTATTAATTTTGATATA
Found at i:3116583 original size:33 final size:33
Alignment explanation
Indices: 3116546--3116612 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3116536 AGTTTTTTAG
*
3116546 CACCTAAACTATTAATTTTGATATGTTTTAGTA
1 CACCTAAACTATTAATTTTGATATATTTTAGTA
3116579 CACCTAAACTATTAATTTTGATATATTTTAGTA
1 CACCTAAACTATTAATTTTGATATATTTTAGTA
3116612 C
1 C
3116613 TTAAACTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.45
Consensus pattern (33 bp):
CACCTAAACTATTAATTTTGATATATTTTAGTA
Found at i:3118879 original size:3 final size:3
Alignment explanation
Indices: 3118871--3119142 Score: 411
Period size: 3 Copynumber: 91.0 Consensus size: 3
3118861 AGCTGACCGG
*
3118871 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3118919 GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3118967 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
3119014 TAT GAT TAT GAT TAT GAT TAT GAT TAT TAT TAT TAT GAT GAT GAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3119062 TAT TAT TAT TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3119110 TAT GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3119143 CATCGTGGTC
Statistics
Matches: 246, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
2 2 0.01
3 244 0.99
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3120057 original size:19 final size:19
Alignment explanation
Indices: 3120033--3120078 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3120023 TTGATACGTA
3120033 AATTTTAAAATTGAT-CATT
1 AATTTTAAAATTGATGC-TT
**
3120052 AATTTTAATTTTGATGCTT
1 AATTTTAAAATTGATGCTT
3120071 AATTTTAA
1 AATTTTAA
3120079 CTTGCTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTTTAAAATTGATGCTT
Found at i:3121864 original size:12 final size:11
Alignment explanation
Indices: 3121846--3121879 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3121836 TTATACAAAA
3121846 TTTAATTTAAT
1 TTTAATTTAAT
*
3121857 TATTAATTAAAT
1 T-TTAATTTAAT
3121869 TTTAATTTAAT
1 TTTAATTTAAT
3121880 ACACAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:3127839 original size:23 final size:24
Alignment explanation
Indices: 3127809--3127868 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
3127799 CATATCAAAT
*
3127809 ATCAGAACAGAATCCAGATCA-GA
1 ATCAGAACAGAATCCAGATAATGA
* * *
3127832 ATCAGAACAGAATTCAGGTAATGT
1 ATCAGAACAGAATCCAGATAATGA
3127856 ATCAGAACAGAAT
1 ATCAGAACAGAAT
3127869 TCAATTCGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATAATGA
Found at i:3127842 original size:11 final size:11
Alignment explanation
Indices: 3127809--3127844 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3127799 CATATCAAAT
3127809 ATCAGAACAGA
1 ATCAGAACAGA
*
3127820 ATCCAGATCAGA
1 AT-CAGAACAGA
3127832 ATCAGAACAGA
1 ATCAGAACAGA
3127843 AT
1 AT
3127845 TCAGGTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (11 bp):
ATCAGAACAGA
Found at i:3127848 original size:12 final size:12
Alignment explanation
Indices: 3127810--3127848 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3127800 ATATCAAATA
3127810 TCAGAACAGAAT
1 TCAGAACAGAAT
* *
3127822 CCAGATCAGAA-
1 TCAGAACAGAAT
3127833 TCAGAACAGAAT
1 TCAGAACAGAAT
3127845 TCAG
1 TCAG
3127849 GTAATGTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (12 bp):
TCAGAACAGAAT
Found at i:3127869 original size:24 final size:23
Alignment explanation
Indices: 3127785--3127871 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
3127775 GATATCAGAA
* * * *
3127785 ATCAAAACATAATTCATATCAAAT
1 ATCAGAACAGAATTCAGAT-AAGT
* * *
3127809 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATAAGT
*
3127832 ATCAGAACAGAATTCAGGTAATGT
1 ATCAGAACAGAATTCAGATAA-GT
3127856 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
3127872 ATTCGGAAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 19 0.37
24 32 0.63
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATAAGT
Found at i:3130337 original size:13 final size:13
Alignment explanation
Indices: 3130319--3130361 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3130309 GCCGGTCAAC
*
3130319 GGTCAATGGGTCG
1 GGTCAACGGGTCG
*
3130332 GGTCAACGGGTTG
1 GGTCAACGGGTCG
*
3130345 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3130358 GGTC
1 GGTC
3130362 GGGTCGGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.47, T:0.21
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3132529 original size:24 final size:23
Alignment explanation
Indices: 3132502--3132573 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
3132492 GTAAACGGAG
*
3132502 ATATCATAAATCAAAACAGAATTC
1 ATATCA-AAATCAGAACAGAATTC
* *
3132526 ATATCAGATATCAGAACAGAATCC
1 ATATCA-AAATCAGAACAGAATTC
*
3132550 AGATCAAAATCAGAACAGAATTC
1 ATATCAAAATCAGAACAGAATTC
3132573 A
1 A
3132574 GGTAACGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 16 0.39
24 25 0.61
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (23 bp):
ATATCAAAATCAGAACAGAATTC
Found at i:3132574 original size:12 final size:12
Alignment explanation
Indices: 3132516--3132574 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
3132506 CATAAATCAA
*
3132516 AACAGAATTCAT
1 AACAGAATTCAG
*
3132528 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
3132540 AACAGAATCCAG
1 AACAGAATTCAG
* *
3132552 ATCA-AAATCAG
1 AACAGAATTCAG
3132563 AACAGAATTCAG
1 AACAGAATTCAG
3132575 GTAACGTATC
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
11 10 0.29
12 23 0.66
13 2 0.06
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.19
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:3135053 original size:13 final size:13
Alignment explanation
Indices: 3135035--3135064 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3135025 GCCGGTCAAC
*
3135035 GGTCAACGGGTTG
1 GGTCAACGGGTCG
3135048 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3135061 GGTC
1 GGTC
3135065 GGGTCTGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3139141 original size:4 final size:4
Alignment explanation
Indices: 3139132--3140057 Score: 1651
Period size: 4 Copynumber: 234.5 Consensus size: 4
3139122 CCAATAACCC
*
3139132 ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139180 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139228 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139276 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139324 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139370 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139416 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139464 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139512 A--T ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
3139557 ATGT ATGT CTGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139604 ATGT A-GT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
3139649 ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
3139697 ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGC ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
3139745 ATGT ATGC ATGC ATGT ATGT ATGC ATGC ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139793 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139841 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139889 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139937 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3139985 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3140033 ATGT ATGT ATGT ATGT ATGT A-GT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
3140058 TCTTATCAAT
Statistics
Matches: 890, Mismatches: 20, Indels: 24
0.95 0.02 0.03
Matches are distributed among these distances:
2 8 0.01
3 12 0.01
4 870 0.98
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:3142100 original size:95 final size:93
Alignment explanation
Indices: 3141930--3142111 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 93
3141920 TTTGCTCAAT
* *
3141930 TTAGGGTATGTTTGTTTCATGTAAAACATTTTTTTGAATTTTTTTCTCACTTTCTAGTGTTTGAT
1 TTAGGGTATGTTTGTTTCATGTAAAACATTTTTCTGAATGTTTTTCTCACTTTCTAGTGTTTGAT
3141995 TGACAAAAAACGGTTGATTATTATATAC
66 TGACAAAAAACGGTTGATTATTATATAC
3142023 TTAGGGTATGTTTGTTTCATGTAAAACA-TTTTCTGAAAAATGTTTTTCTCACTTTCTAGTGTTT
1 TTAGGGTATGTTTGTTTCATGTAAAACATTTTTCTG---AATGTTTTTCTCACTTTCTAGTGTTT
* * *
3142087 GATTTACGAAAAACGGTTGGTTATT
63 GATTGACAAAAAACGGTTGATTATT
3142112 GTACAATATT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
92 6 0.07
93 28 0.35
95 47 0.58
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.47
Consensus pattern (93 bp):
TTAGGGTATGTTTGTTTCATGTAAAACATTTTTCTGAATGTTTTTCTCACTTTCTAGTGTTTGAT
TGACAAAAAACGGTTGATTATTATATAC
Found at i:3142375 original size:21 final size:21
Alignment explanation
Indices: 3142340--3142396 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
3142330 TTTTTAATAC
*
3142340 TATAA-AATATTTAATTATAT
1 TATAATAATATATAATTATAT
*
3142360 TATAATAATATATAATTTTAT
1 TATAATAATATATAATTATAT
* *
3142381 TCTACTAATATATAAT
1 TATAATAATATATAAT
3142397 AAATTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAATAATATATAATTATAT
Found at i:3142520 original size:23 final size:23
Alignment explanation
Indices: 3142493--3142552 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
3142483 ATAATATAGT
*
3142493 AATATTTTAATAA-AAATACTTAA
1 AATATATTAATAATAAAT-CTTAA
* *
3142516 AATATATTATTAATAAATTTTAA
1 AATATATTAATAATAAATCTTAA
*
3142539 AATATAAT-ATAATA
1 AATATATTAATAATA
3142553 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 22 0.71
24 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AATATATTAATAATAAATCTTAA
Found at i:3142582 original size:31 final size:30
Alignment explanation
Indices: 3142542--3142647 Score: 80
Period size: 34 Copynumber: 3.5 Consensus size: 30
3142532 ATTTTAAAAT
3142542 ATAAT-ATAATATTTTTATTTTAATACTATA
1 ATAATAATAATATTTTTATTTTAATA-TATA
* *
3142572 ATAATAATAATCTTATTTA-TATAAGTA-ATTAA
1 ATAATAATAATATT-TTTATTTTAA-TATA-T-A
3142604 TATAATTAATAATATTTATTATTTTAATA-ATA
1 -ATAA-TAATAATATTT-TTATTTTAATATATA
3142636 AT-ATAA-AATATT
1 ATAATAATAATATT
3142648 CATTATACCC
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
28 6 0.10
29 3 0.05
30 7 0.11
31 14 0.22
32 8 0.13
33 6 0.10
34 15 0.24
35 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (30 bp):
ATAATAATAATATTTTTATTTTAATATATA
Found at i:3144343 original size:61 final size:61
Alignment explanation
Indices: 3144248--3144376 Score: 213
Period size: 61 Copynumber: 2.1 Consensus size: 61
3144238 ATTTTATGTT
* *
3144248 AGGGGACGAACTTAAACTTAAAGGGATGAACAAAAGTTTTAGAGGGCAAACTAAAATTCTA
1 AGGGGACGAACTTAAACTTAAAGGGATGAACAAAAATTTCAGAGGGCAAACTAAAATTCTA
* * *
3144309 AGGGGACGAATTTAAACTTAAGGGGATGAACAAAAATTTCAGAGGTCAAACTAAAATTCTA
1 AGGGGACGAACTTAAACTTAAAGGGATGAACAAAAATTTCAGAGGGCAAACTAAAATTCTA
3144370 AGGGGAC
1 AGGGGAC
3144377 AGATTTCCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (61 bp):
AGGGGACGAACTTAAACTTAAAGGGATGAACAAAAATTTCAGAGGGCAAACTAAAATTCTA
Found at i:3150192 original size:10 final size:10
Alignment explanation
Indices: 3150179--3150220 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
3150169 GCCAATTTAT
3150179 TTTTTATCTA
1 TTTTTATCTA
3150189 -TTTT-T-TA
1 TTTTTATCTA
*
3150196 ATTTTATCTA
1 TTTTTATCTA
3150206 TTTTTATCTA
1 TTTTTATCTA
3150216 TTTTT
1 TTTTT
3150221 TTGCTGCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
7 2 0.07
8 5 0.18
9 5 0.18
10 16 0.57
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTATCTA
Found at i:3153098 original size:21 final size:21
Alignment explanation
Indices: 3153058--3153098 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3153048 ACTTGGAGGG
3153058 GGAAGGAAGAAAGAAAAGAAA
1 GGAAGGAAGAAAGAAAAGAAA
*
3153079 GGAA-GAAGAAATGAAGAGAA
1 GGAAGGAAGAAA-GAAAAGAA
3153099 TATATGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (21 bp):
GGAAGGAAGAAAGAAAAGAAA
Found at i:3155769 original size:30 final size:30
Alignment explanation
Indices: 3155735--3155792 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3155725 ATCAACCCCA
3155735 TAACTTTT-CAAAATTATCAAATAAGTCCCT
1 TAACTTTTACAAAATTA-CAAATAAGTCCCT
* *
3155765 TAACTTTTACTAAATTACAAATTAGTCC
1 TAACTTTTACAAAATTACAAATAAGTCC
3155793 AAATGATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (30 bp):
TAACTTTTACAAAATTACAAATAAGTCCCT
Found at i:3158854 original size:29 final size:29
Alignment explanation
Indices: 3158804--3158881 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
3158794 ATTAAATTAA
3158804 TATCTTAACATTGAAAATATATATATTACTCT
1 TATCTTAAC-TT-AAAA-ATATATATTACTCT
* * *
3158836 TGTCTTAACTTAAAAATATATTTTATTCT
1 TATCTTAACTTAAAAATATATATTACTCT
* *
3158865 TATTTTAAATTAAAAAT
1 TATCTTAACTTAAAAAT
3158882 TTATTTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.65
30 4 0.10
31 2 0.05
32 8 0.20
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (29 bp):
TATCTTAACTTAAAAATATATATTACTCT
Found at i:3159065 original size:30 final size:29
Alignment explanation
Indices: 3158957--3159271 Score: 177
Period size: 30 Copynumber: 10.9 Consensus size: 29
3158947 ATTCTTATAT
* * *
3158957 TATTTTAAAATTAAGATAAAAATAAAATA
1 TATTTTTAAGTTAAAATAAAAATAAAATA
* *
3158986 TATTTTAAAGTTAAAAGAAAAATAAAATA
1 TATTTTTAAGTTAAAATAAAAATAAAATA
* * *
3159015 GATGTTTTAAGTAAAAAATAAGAATAAAATA
1 TAT-TTTTAAGT-TAAAATAAAAATAAAATA
* ** *
3159046 TATATTTTATGTTAAAATAAGGATAAATTA
1 TAT-TTTTAAGTTAAAATAAAAATAAAATA
* * ** * * *
3159076 TATTTAATAATTTAAGGTAAGAATATAGTA
1 TATTT-TTAAGTTAAAATAAAAATAAAATA
* *
3159106 TATGTATTAAGTTAAAATCAAAAT--AATA
1 TAT-TTTTAAGTTAAAATAAAAATAAAATA
3159134 TATTTTTAAAAGTTAAAATAAAAATAAAATA
1 TATTTTT--AAGTTAAAATAAAAATAAAATA
* *
3159165 TA-TTTTAAGTT---AT---GATAAGAT-
1 TATTTTTAAGTTAAAATAAAAATAAAATA
* *
3159186 TA-TTTTAAGTTAAAATAATAATAAAATC
1 TATTTTTAAGTTAAAATAAAAATAAAATA
* **
3159214 TATTTTTAGGTTAAGAA-AGGGAATAAAATA
1 TATTTTTAAGTTAA-AATA-AAAATAAAATA
* * *
3159244 GATTTAATAATTTAAAATAAAAATAAAA
1 TATTT-TTAAGTTAAAATAAAAATAAAA
3159272 AAATTTAATG
Statistics
Matches: 220, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
21 11 0.05
22 6 0.03
24 2 0.01
25 2 0.01
27 9 0.04
28 13 0.06
29 56 0.25
30 83 0.38
31 38 0.17
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
TATTTTTAAGTTAAAATAAAAATAAAATA
Found at i:3159203 original size:21 final size:22
Alignment explanation
Indices: 3159154--3159208 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3159144 AGTTAAAATA
3159154 AAAATAAAATATATTTTAAGTT
1 AAAATAAAATATATTTTAAGTT
** *
3159176 ATGATAAGAT-TATTTTAAGTT
1 AAAATAAAATATATTTTAAGTT
3159197 AAAATAATAATA
1 AAAATAA-AATA
3159209 AAATCTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (22 bp):
AAAATAAAATATATTTTAAGTT
Found at i:3166992 original size:21 final size:21
Alignment explanation
Indices: 3166967--3167006 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3166957 CTTTTTCATT
* *
3166967 ATTCTTCTTCTTCTTATTCTC
1 ATTCTTCTTCATATTATTCTC
3166988 ATTCTTCTTCATATTATTC
1 ATTCTTCTTCATATTATTC
3167007 GTCTCCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTCTTCTTCATATTATTCTC
Found at i:3168432 original size:23 final size:23
Alignment explanation
Indices: 3168397--3168444 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3168387 ATCAAATACA
* *
3168397 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGCAGCGCTTAT
*
3168420 ATAATGTAATAGGCAGCGCTTAT
1 ATAATATAATAGGCAGCGCTTAT
3168443 AT
1 AT
3168445 TAACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGCAGCGCTTAT
Found at i:3169185 original size:182 final size:182
Alignment explanation
Indices: 3168875--3169329 Score: 707
Period size: 182 Copynumber: 2.5 Consensus size: 182
3168865 ACTTTTTTAC
* *
3168875 TACCGGTTTTGTCATTTCGATACCGATTTTGTCATATTTTTACCTGTTATATTATTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
* * *
3168940 TACATTTTTATAAAGTAT-AAACACTTTATTGGCGCCATAACTTCTTTTCTTTTAAATTCCAAAA
66 TACATTTTTATAAAGTATCGAA-ACTTTATTAGCGCCATAACTTCTTCTCTTTTAAATTCCAAAA
* * *
3169004 TTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTT
130 GTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
* * * * *
3169057 TATCGGTTTTATCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATTGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
*
3169122 TACATTTTTATAAAGTATCGAAACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGAAACTTTATTAGCGCCATAACTTCTTCTCTTTTAAATTCCAAAAG
3169187 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
* ** * *
3169239 TACCTGTTTTGTCATTTATAGATCGGTTTTGTCAT-TTTTTACCTGTTATATTGTTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
*
3169303 TACATTTTTATAAAGTATCGACACTTT
66 TACATTTTTATAAAGTATCGAAACTTT
3169330 CAATATATCC
Statistics
Matches: 247, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 52 0.21
182 193 0.78
183 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
TACATTTTTATAAAGTATCGAAACTTTATTAGCGCCATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
Found at i:3169438 original size:112 final size:111
Alignment explanation
Indices: 3169201--3169661 Score: 753
Period size: 112 Copynumber: 4.1 Consensus size: 111
3169191 GATACTTATA
* * *
3169201 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
3169266 TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
3169312 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTACAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
3169377 TTTGTCATTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
3169424 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
3169489 CTTT-TCATTTTTTTAGCTGTTATATTGTTATGGATCGATACATTTTT
66 -TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
3169536 ATAAAATATCGACACTTTCAATATATCCGATAGCGCTTTACCTGCTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
3169601 TTTGTTATTTTTTACCTGTTATATTGTTATGGATTAATATATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
3169647 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
3169662 AAACCGACAA
Statistics
Matches: 328, Mismatches: 19, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
111 119 0.36
112 206 0.63
113 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:3169614 original size:223 final size:223
Alignment explanation
Indices: 3169201--3169661 Score: 755
Period size: 223 Copynumber: 2.1 Consensus size: 223
3169191 GATACTTATA
*
3169201 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
3169266 TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTC
66 TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAATATCGACACTTTC
* * *
3169331 AATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTACAGACCGATTTTGTCATTTTTTTATCTG
131 AATATATCCGATAGCGCTTTACCTGCTTTGTCATTTACAGACCGATTTTGTCATTTTTTTACCTG
*
3169396 TTATATTGTTATGGATCGATACATTTTT
196 TTATATTGTTATGGATCAATACATTTTT
* *
3169424 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
3169489 CTTT-TCATTTTTTTAGCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTT
66 -TTTGTCA-TTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAATATCGACACTT
* * *
3169553 TCAATATATCCGATAGCGCTTTACCTGCTTTGTCATTTATAGACCGGTTTTGTTA-TTTTTTACC
129 TCAATATATCCGATAGCGCTTTACCTGCTTTGTCATTTACAGACCGATTTTGTCATTTTTTTACC
* *
3169617 TGTTATATTGTTATGGATTAATATATTTTT
194 TGTTATATTGTTATGGATCAATACATTTTT
3169647 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
3169662 AAACCGACAA
Statistics
Matches: 221, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
223 115 0.52
224 106 0.48
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (223 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAATATCGACACTTTC
AATATATCCGATAGCGCTTTACCTGCTTTGTCATTTACAGACCGATTTTGTCATTTTTTTACCTG
TTATATTGTTATGGATCAATACATTTTT
Found at i:3178659 original size:80 final size:80
Alignment explanation
Indices: 3178471--3179531 Score: 1296
Period size: 80 Copynumber: 13.1 Consensus size: 80
3178461 TCTTACTTTC
* * * * *
3178471 AGCTATGCTGTAAATTTGATTTGCCTCTGAGATGAGTGTAATCGAACTCGAAGGTATTCTGGTGA
1 AGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT-T-G-G-
* * *
3178536 CAAATAGCCCTTCTCGCCTTG
60 CAGATAACCCTTCTAGCCTTG
* *
3178557 AGCTATGCTGTAAATGATGTGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
3178622 ACCCTTCTAGCCTTG
66 ACCCTTCTAGCCTTG
* * * *
3178637 AGTTATGCTACAAATGATGTGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
* *
3178702 GCCCTTCTTGCCTTG
66 ACCCTTCTAGCCTTG
* * * * * * * *
3178717 AACTATACTGCAAATGATGTGACATGGAGCTGAGCGGAATCGAACTCGAAGATCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
* * *
3178782 GCCCTTATTGCCTTG
66 ACCCTTCTAGCCTTG
* * * *
3178797 AGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGGAATCAAACTCAAAGGTCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
3178862 ACCCTTCTAGCCTTG
66 ACCCTTCTAGCCTTG
* * * *
3178877 AGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAAATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
*
3178942 GCCCTTCTAGCCTTG
66 ACCCTTCTAGCCTTG
* * * * *
3178957 AGCTATGCTGCAAATGATGTGTCTTTGAGTTGAGTGGAATCGAACTCGAAGATCTTTGGAAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
*
3179022 ACCCTTCTACCCTTG
66 ACCCTTCTAGCCTTG
* * * * * *
3179037 AGTTATGCTGAAAATGATGTGCCTTGGATCTGAGTGTAGTCGAACTCGAAGGTCTTTGGAAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
* *
3179102 ACCCTTCTTGTCTTG
66 ACCCTTCTAGCCTTG
* * * *
3179117 AGCTATGTTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
*
3179182 GCCCTTCTAGCCTTG
66 ACCCTTCTAGCCTTG
* * * *
3179197 AGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGGAATCGAACTCAAATGTCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
*
3179262 ACCCTTCTAGCATTG
66 ACCCTTCTAGCCTTG
* * * * * *
3179277 AGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
* *
3179342 GCCCTTCTTGCCTTG
66 ACCCTTCTAGCCTTG
* * * *
3179357 AGCTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
* *
3179422 TCCCTTCTTA-CCTTA
66 ACCCTTC-TAGCCTTG
* * * *
3179437 AGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
1 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGCA
*
3179502 GATAATCCTTCTAGCCTTG
62 GATAACCCTTCTAGCCTTG
*
3179521 AGTTATGCTGC
1 AGCTATGCTGC
3179532 CAATAGTTTC
Statistics
Matches: 848, Mismatches: 121, Indels: 14
0.86 0.12 0.01
Matches are distributed among these distances:
80 759 0.90
81 2 0.00
82 2 0.00
83 3 0.00
84 68 0.08
86 14 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (80 bp):
AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATA
ACCCTTCTAGCCTTG
Found at i:3180899 original size:99 final size:98
Alignment explanation
Indices: 3180718--3180925 Score: 255
Period size: 99 Copynumber: 2.1 Consensus size: 98
3180708 GGGACATCTC
* * * *
3180718 AATA-TATAAACACCTTTATCTGGTTAGCTGAATTTCCATAAAGCCGGGGCGTTTAACCAATTGC
1 AATATTATAATCACCTTTATCAGGCTAGCTGAATTTCCATAAAGCCGGGGCATTTAACCAATTGC
3180782 CTTAGAGGAACAACTCAAGCTTTATTGTAT-AT
66 CTTAGAGGAACAACTCAAGCTTTATTGTATAAT
* *
3180814 -ATATTATAATCACCTTTATCAGGCTAGTTGAATCTTATCCATAAAGCCGGGGCATTTAACTAAT
1 AATATTATAATCACCTTTATCAGGCTAGCTGAA--TT-TCCATAAAGCCGGGGCATTTAACCAAT
* *
3180878 TG-CTCTAGA-GAGACAATTCAAGTTTTATTGTATACAT
63 TGCCT-TAGAGGA-ACAACTCAAGCTTTATTGTATA-AT
3180915 AATATTATAAT
1 AATATTATAAT
3180926 TTGGGTATAC
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
95 3 0.03
96 24 0.25
98 6 0.06
99 50 0.53
101 2 0.02
102 10 0.11
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (98 bp):
AATATTATAATCACCTTTATCAGGCTAGCTGAATTTCCATAAAGCCGGGGCATTTAACCAATTGC
CTTAGAGGAACAACTCAAGCTTTATTGTATAAT
Found at i:3185124 original size:23 final size:23
Alignment explanation
Indices: 3185094--3185177 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
3185084 CTCATATAAA
3185094 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3185117 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
3185140 TGCACCGTAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3185163 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3185178 TATAATATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3186819 original size:22 final size:23
Alignment explanation
Indices: 3186781--3186825 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3186771 TTTACAATTT
3186781 TCCTTTAGGGGGAATCGGTTCCC
1 TCCTTTAGGGGGAATCGGTTCCC
*
3186804 TCCTTT-GGGGGTATCGGTTCCC
1 TCCTTTAGGGGGAATCGGTTCCC
3186826 CCATGACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.09, C:0.27, G:0.31, T:0.33
Consensus pattern (23 bp):
TCCTTTAGGGGGAATCGGTTCCC
Found at i:3186879 original size:21 final size:21
Alignment explanation
Indices: 3186853--3186896 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3186843 TTTTTATTCG
* *
3186853 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
3186874 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
3186895 CT
1 CT
3186897 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:3190282 original size:23 final size:23
Alignment explanation
Indices: 3190248--3190308 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3190238 CTCATATAAA
*
3190248 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
3190271 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
3190294 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
3190309 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:3191911 original size:22 final size:22
Alignment explanation
Indices: 3191886--3191928 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3191876 TTTTCCTTTA
*
3191886 GGGGGAATCGGTTCCCTCATGT
1 GGGGGAATCGGTTCCCCCATGT
*
3191908 GGGGGTATCGGTTCCCCCATG
1 GGGGGAATCGGTTCCCCCATG
3191929 ATATTCTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.37, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCCATGT
Found at i:3192882 original size:14 final size:14
Alignment explanation
Indices: 3192839--3192894 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
3192829 AAAACAAATA
* *
3192839 AATAAAATAATAAT
1 AATAATATAATATT
*
3192853 AATAATATACTAATT
1 AATAATATAAT-ATT
3192868 AATAATATAATATT
1 AATAATATAATATT
3192882 AACT-ATATAATAT
1 AA-TAATATAATAT
3192895 ATACTTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATATAATATT
Found at i:3193034 original size:36 final size:35
Alignment explanation
Indices: 3192985--3193098 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 35
3192975 TTTTTTTTAA
3192985 AAACTATATATTATATATATTTTCAAAATTATTTC
1 AAACTATATATTATATATATTTTCAAAATTATTTC
* * *
3193020 ATAACTATACATTATATA-AGTTTTCAAAATTTTTTAA
1 A-AACTATATATTATATATA-TTTTCAAAATTATTT-C
** *
3193057 AAACCCTATA-T-TATATATTTTCAAAAATGATTTC
1 AAACTATATATTATATATATTTTC-AAAATTATTTC
3193091 AAACTATA
1 AAACTATA
3193099 ATATATTTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
34 15 0.24
35 12 0.19
36 35 0.56
37 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (35 bp):
AAACTATATATTATATATATTTTCAAAATTATTTC
Found at i:3193668 original size:27 final size:25
Alignment explanation
Indices: 3193633--3193743 Score: 80
Period size: 27 Copynumber: 4.0 Consensus size: 25
3193623 GTTAGATCGT
*
3193633 AAAATAAAATAAATAAATGTTAAATAA
1 AAAAGAAAA-AAATAAA-GTTAAATAA
*
3193660 AAAAGAAAAAAAACAAAGGTTAAATTAAGA
1 AAAAG-AAAAAAATAAA-GTTAAA-T-A-A
3193690 AATAAGAATAAAAATAAAGTTAAGAT-A
1 AA-AAGAA-AAAAATAAAGTTAA-ATAA
*
3193717 AAAAGAAATAATAATAAAGTGAAATAA
1 AAAAGAAA-AA-AATAAAGTTAAATAA
3193744 TATTAAAAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
25 1 0.01
26 9 0.13
27 30 0.43
28 5 0.07
29 1 0.01
30 11 0.16
31 12 0.17
ACGTcount: A:0.69, C:0.01, G:0.10, T:0.20
Consensus pattern (25 bp):
AAAAGAAAAAAATAAAGTTAAATAA
Found at i:3193733 original size:16 final size:16
Alignment explanation
Indices: 3193686--3193758 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
3193676 AGGTTAAATT
*
3193686 AAGAAATAAGAATAAA
1 AAGAAATAATAATAAA
* *
3193702 AATAAAGTTAA-GATAAA
1 AAGAAA--TAATAATAAA
3193719 AAGAAATAATAATAAA
1 AAGAAATAATAATAAA
** *
3193735 GTGAAATAATATTAAA
1 AAGAAATAATAATAAA
3193751 AGAGAAAT
1 A-AGAAAT
3193759 GAAGAAAATG
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.07
16 23 0.52
17 15 0.34
18 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AAGAAATAATAATAAA
Found at i:3193797 original size:36 final size:36
Alignment explanation
Indices: 3193755--3193823 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
3193745 ATTAAAAGAG
*
3193755 AAATGAAGAAAATGTTAAATTTTAAAAGAAATAAAA
1 AAATGAAGAAAATATTAAATTTTAAAAGAAATAAAA
* *
3193791 AAATGAAGAGAATATTAATTTTTAAAAGAAATA
1 AAATGAAGAAAATATTAAATTTTAAAAGAAATA
3193824 TTAAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.28
Consensus pattern (36 bp):
AAATGAAGAAAATATTAAATTTTAAAAGAAATAAAA
Found at i:3193825 original size:19 final size:19
Alignment explanation
Indices: 3193764--3193842 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 19
3193754 GAAATGAAGA
*
3193764 AAATGTTAAATTTTAAAAG
1 AAATATTAAATTTTAAAAG
* ** * *
3193783 AAATA-AAAAAATGAAGAG
1 AAATATTAAATTTTAAAAG
*
3193801 -AATATTAATTTTTAAAAG
1 AAATATTAAATTTTAAAAG
*
3193819 AAATATTAAATTTTAGAAG
1 AAATATTAAATTTTAAAAG
3193838 AAATA
1 AAATA
3193843 AAAAATAATA
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
17 4 0.09
18 15 0.34
19 25 0.57
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (19 bp):
AAATATTAAATTTTAAAAG
Found at i:3195068 original size:16 final size:15
Alignment explanation
Indices: 3195028--3195073 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3195018 AATAAAATGA
3195028 ACTAAATA-AATAAT
1 ACTAAATATAATAAT
3195042 A-TAAATAATAATATAT
1 ACTAAAT-ATAATA-AT
3195058 ACTAAATATAATAAT
1 ACTAAATATAATAAT
3195073 A
1 A
3195074 AAAACTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.18
14 2 0.07
15 7 0.25
16 9 0.32
17 5 0.18
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
ACTAAATATAATAAT
Found at i:3195071 original size:26 final size:26
Alignment explanation
Indices: 3195034--3195084 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3195024 ATGAACTAAA
*
3195034 TAAATAATATAAATAATAA-TATATAC
1 TAAATAATAT-AATAAAAACTATATAC
3195060 TAAAT-ATAATAATAAAAACTATATA
1 TAAATAAT-ATAATAAAAACTATATA
3195085 ATACTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAATAATATAATAAAAACTATATAC
Found at i:3195113 original size:14 final size:15
Alignment explanation
Indices: 3195094--3195123 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3195084 AATACTGTAA
3195094 TTTCAAAAA-TATAT
1 TTTCAAAAATTATAT
3195108 TTTCAAAAATTATAT
1 TTTCAAAAATTATAT
3195123 T
1 T
3195124 ATATGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTCAAAAATTATAT
Found at i:3195181 original size:36 final size:36
Alignment explanation
Indices: 3195118--3195352 Score: 226
Period size: 36 Copynumber: 6.3 Consensus size: 36
3195108 TTTCAAAAAT
* * *
3195118 TATATTATATGTTTTTAAAAATCGTTTTAAAAAACCA
1 TATATTATATG-TTTTCAAAATAGTTTTAAAAAACTA
*
3195155 TATACTATATGTTTTCAAAATAGTTTTTTTTTAAAAAACTA
1 TATATTATATGTTTTCAAAATAG-----TTTTAAAAAACTA
*
3195196 TATATTATACGTTTTCAAAACTA-TTTT-AAAAACTA
1 TATATTATATGTTTTCAAAA-TAGTTTTAAAAAACTA
** *
3195231 TATATTATATGTTTTCAAAACCGTTTTTAAAAACTA
1 TATATTATATGTTTTCAAAATAGTTTTAAAAAACTA
*
3195267 TATATTATATGTTTTCAAAACTA-TTTTTAAAAACTA
1 TATATTATATGTTTTCAAAA-TAGTTTTAAAAAACTA
* *
3195303 TAT-TATATATGTTTTTAAAAAATATGTTTTCAAAAACTA
1 TATAT-TATATG-TTTT-CAAAATA-GTTTTAAAAAACTA
3195342 TATATATATAT
1 TATAT-TATAT
3195353 ATATATATAT
Statistics
Matches: 170, Mismatches: 13, Indels: 27
0.81 0.06 0.13
Matches are distributed among these distances:
35 32 0.19
36 64 0.38
37 16 0.09
38 4 0.02
39 15 0.09
40 7 0.04
41 30 0.18
42 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATTATATGTTTTCAAAATAGTTTTAAAAAACTA
Found at i:3195329 original size:15 final size:15
Alignment explanation
Indices: 3195309--3195338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3195299 ACTATATTAT
*
3195309 ATATGTTTTTAAAAA
1 ATATGTTTTCAAAAA
3195324 ATATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
3195339 CTATATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
ATATGTTTTCAAAAA
Found at i:3195347 original size:2 final size:2
Alignment explanation
Indices: 3195340--3195369 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3195330 TTTCAAAAAC
3195340 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3195370 TTTCAGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3195352 original size:112 final size:110
Alignment explanation
Indices: 3195072--3195352 Score: 308
Period size: 112 Copynumber: 2.5 Consensus size: 110
3195062 AATATAATAA
*
3195072 TAAAAACTATATA-ATACTGTAATTTCAAAAATATATTTTCAAAAA-T-TATATTATATGTTTTT
1 TAAAAACTATATATATA-TGT-TTTTCAAAAATAT-TTTTCAAAAACTATATATTATATGTTTTT
*
3195134 AAAAATCGTTTTAAAAAACCATATACTATATGTTTTCAAAATAGTTTTTTTT
63 AAAAACCGTTTTAAAAAACCATATACTATATGTTTTCAAAATA----TTTTT
* * *
3195186 TAAAAAACTATATATTATACG-TTTTCAAAACTA-TTTT-AAAAACTATATATTATATG-TTTTC
1 T-AAAAACTATATA-TATATGTTTTTCAAAAATATTTTTCAAAAACTATATATTATATGTTTTTA
* * *
3195247 AAAACCGTTTTTAAAAACTATATATTATATGTTTTCAAAACTA-TTTT
64 AAAACCGTTTTAAAAAACCATATACTATATGTTTTCAAAA-TATTTTT
*
3195294 TAAAAACTATATTATATATGTTTTTAAAAAATATGTTTTCAAAAACTATATATATATAT
1 TAAAAACTATA-TATATATGTTTTTCAAAAATAT-TTTTCAAAAACTATATAT-TATAT
3195353 ATATATATAT
Statistics
Matches: 144, Mismatches: 11, Indels: 26
0.80 0.06 0.14
Matches are distributed among these distances:
107 15 0.10
108 17 0.12
110 4 0.03
111 18 0.12
112 50 0.35
113 13 0.09
114 11 0.08
115 12 0.08
116 1 0.01
117 3 0.02
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (110 bp):
TAAAAACTATATATATATGTTTTTCAAAAATATTTTTCAAAAACTATATATTATATGTTTTTAAA
AACCGTTTTAAAAAACCATATACTATATGTTTTCAAAATATTTTT
Done.