Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 196 of 198
Found at i:61151931 original size:58 final size:58
Alignment explanation
Indices: 61151866--61151982 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
61151856 AAAGAAAAAC
61151866 GACTGTGAAAAATAAAGGTTTATATACAAAATTGGCCCCCGTAGTATATATATTTCAT
1 GACTGTGAAAAATAAAGGTTTATATACAAAATTGGCCCCCGTAGTATATATATTTCAT
61151924 GACTGTGAAAAATAAAGGTTTATATACAAAATTGGCCCCCGTAGTATATATATTTCAT
1 GACTGTGAAAAATAAAGGTTTATATACAAAATTGGCCCCCGTAGTATATATATTTCAT
61151982 G
1 G
61151983 TTTAGTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (58 bp):
GACTGTGAAAAATAAAGGTTTATATACAAAATTGGCCCCCGTAGTATATATATTTCAT
Found at i:61159715 original size:31 final size:31
Alignment explanation
Indices: 61159672--61159755 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
61159662 TTTGTGTGGT
*
61159672 TAATTAGAATTTTC-AAAAATTTGAGAGAGACC
1 TAATTA-AATTTTCTAAAAATTTCA-AGAGACC
* *
61159704 TAATTAAATTTTCTAAAAGTTTCAAGAGAGC
1 TAATTAAATTTTCTAAAAATTTCAAGAGACC
* *
61159735 -AATAAAATTATCTAAAAATTT
1 TAATTAAATTTTCTAAAAATTT
61159756 TAGGGGGCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.40
31 13 0.29
32 14 0.31
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (31 bp):
TAATTAAATTTTCTAAAAATTTCAAGAGACC
Found at i:61164630 original size:30 final size:30
Alignment explanation
Indices: 61164595--61164657 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
61164585 ATAAAACTTA
* *
61164595 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTCTGTTATTACTTTAAAGACAT
* *
61164625 TTGTTAATTCTGTTATTACTTTAGAGGCAT
1 TTGTTAATTCTGTTATTACTTTAAAGACAT
61164655 TTG
1 TTG
61164658 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.54
Consensus pattern (30 bp):
TTGTTAATTCTGTTATTACTTTAAAGACAT
Found at i:61164772 original size:63 final size:63
Alignment explanation
Indices: 61164703--61164829 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
61164693 TATGCATATT
*
61164703 TTTTAAAGCTTATTTTCAATTTGCTGAGAAATATGTATTTTGATGTTTTTAGTATTTTTGATA
1 TTTTAAAGCTTATTTTCAATTTGCTGAGAAATATGTATTTTGATGTTTTTAATATTTTTGATA
*
61164766 TTTTAAAGTTTATTTTCAATTTGCTGAGAAATATGTATTTTGATGTTTTTAATATTTTTGATA
1 TTTTAAAGCTTATTTTCAATTTGCTGAGAAATATGTATTTTGATGTTTTTAATATTTTTGATA
61164829 T
1 T
61164830 ATTATATATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (63 bp):
TTTTAAAGCTTATTTTCAATTTGCTGAGAAATATGTATTTTGATGTTTTTAATATTTTTGATA
Found at i:61164874 original size:12 final size:12
Alignment explanation
Indices: 61164844--61164876 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
61164834 TATATATTTT
61164844 AAAATT-ATATA
1 AAAATTAATATA
61164855 AAAA-TAATATA
1 AAAATTAATATA
61164866 AAAATTAATAT
1 AAAATTAATAT
61164877 GGTAGGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:61179018 original size:2 final size:2
Alignment explanation
Indices: 61179011--61179039 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61179001 TCTACAAATT
61179011 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 T
61179040 CTTATTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61193617 original size:118 final size:120
Alignment explanation
Indices: 61193338--61193662 Score: 381
Period size: 118 Copynumber: 2.7 Consensus size: 120
61193328 TCTAGTTAAT
* * * *
61193338 ATTGGATTCTCGGGTTCGGGTCAGTTTGGTCAATCCAAGTTCGAATCATTTCTGATTTGGATCAT
1 ATTGGATTCTTGGGTTCAGGTCAGTTTGGTCAATCCAAGTTCAAATCATTTCTGGTTTGGATCAT
* * * * *
61193403 TTTCGGGTTCGGGTTATTGGCTTTTTATTTTCAATCAGGTTTGAGTTCGGGTTAATCGG
66 TTTCAGGTTCGGGTTATTGACTTTCTA--TTC-A-CAGGATTGAGTTCAGGTTAATCGG
* *
61193462 ATTGGATCCTTGAGTTCAGGTCAGTTTGGTCAATCCAAGTTCAAATCATTTCTGGTTTGGATCAC
1 ATTGGATTCTTGGGTTCAGGTCAGTTTGGTCAATCCAAGTTCAAATCATTTCTGGTTTGGATCA-
* *
61193527 TTTTCAGGTTGGGGTTATTGACTTTCTA-TC-GA-GATTGAGTTCAGGTTAATTC-G
65 TTTTCAGGTTCGGGTTATTGACTTTCTATTCACAGGATTGAGTTCAGGTTAA-TCGG
* * * *
61193580 ATTGGATTCTTGGGTTCAGGTCA-TTTCGGTCAATCCAATTTCAAATCATTTTTAGTTTGGATTA
1 ATTGGATTCTTGGGTTCAGGTCAGTTT-GGTCAATCCAAGTTCAAATCATTTCTGGTTTGGATCA
* *
61193644 TTTTCAAGTTCGGGCTATT
65 TTTTCAGGTTCGGGTTATT
61193663 AATTTTTTAT
Statistics
Matches: 176, Mismatches: 22, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
117 19 0.11
118 70 0.40
119 3 0.02
122 2 0.01
124 58 0.33
125 24 0.14
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.42
Consensus pattern (120 bp):
ATTGGATTCTTGGGTTCAGGTCAGTTTGGTCAATCCAAGTTCAAATCATTTCTGGTTTGGATCAT
TTTCAGGTTCGGGTTATTGACTTTCTATTCACAGGATTGAGTTCAGGTTAATCGG
Found at i:61198343 original size:6 final size:6
Alignment explanation
Indices: 61198322--61198357 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
61198312 TCCTCCGCGC
* *
61198322 CCTCTA CCCCTA CCTCTC CCTCTA CCTCTA CCTCTA
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA
61198358 TTAGCTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.56, G:0.00, T:0.31
Consensus pattern (6 bp):
CCTCTA
Found at i:61198344 original size:18 final size:18
Alignment explanation
Indices: 61198321--61198356 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61198311 TTCCTCCGCG
61198321 CCCTCTACCCCTACCTCT
1 CCCTCTACCCCTACCTCT
*
61198339 CCCTCTACCTCTACCTCT
1 CCCTCTACCCCTACCTCT
61198357 ATTAGCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.58, G:0.00, T:0.31
Consensus pattern (18 bp):
CCCTCTACCCCTACCTCT
Found at i:61200537 original size:32 final size:32
Alignment explanation
Indices: 61200501--61200564 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
61200491 ATTACATGAT
61200501 AAGTATAAATATATGCCCG-ATCAAGGTAAAGG
1 AAGTATAAATATATGCCCGAAT-AAGGTAAAGG
**
61200533 AAGTATAAATATATGTTCGAATAAGGTAAAGG
1 AAGTATAAATATATGCCCGAATAAGGTAAAGG
61200565 TTTTGTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (32 bp):
AAGTATAAATATATGCCCGAATAAGGTAAAGG
Found at i:61204785 original size:31 final size:29
Alignment explanation
Indices: 61204720--61204782 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 29
61204710 GATTAATGAG
*
61204720 AATTTTCAAAAATTTGAGGGAGCCTAATTAA
1 AATTTTCAAAAATTTCAGGGAG-C-AATTAA
61204751 AATTTTCTAAAAATTTCAGGGAG-AATTCAA
1 AATTTTC-AAAAATTTCAGGGAGCAATT-AA
61204781 AA
1 AA
61204783 ATTCTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.14
30 4 0.14
31 7 0.24
32 14 0.48
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (29 bp):
AATTTTCAAAAATTTCAGGGAGCAATTAA
Found at i:61212313 original size:13 final size:13
Alignment explanation
Indices: 61212280--61212306 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61212270 ATTAAAGCTT
61212280 TTGAAATATATGG
1 TTGAAATATATGG
61212293 TTGAAATATATGG
1 TTGAAATATATGG
61212306 T
1 T
61212307 GCTAATAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TTGAAATATATGG
Found at i:61217796 original size:21 final size:22
Alignment explanation
Indices: 61217760--61217817 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
61217750 TGATGAAGGA
* *
61217760 TGAATTCATAAATTTTA-GAAAT
1 TGAATT-ATAATTTTTATAAAAT
61217782 TGAATTATAATTTTTATAAAAT
1 TGAATTATAATTTTTATAAAAT
* *
61217804 TAAAATATAATTTT
1 TGAATTATAATTTT
61217818 ATATTGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TGAATTATAATTTTTATAAAAT
Found at i:61217819 original size:21 final size:21
Alignment explanation
Indices: 61217770--61217842 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 21
61217760 TGAATTCATA
* * *
61217770 AATTTTA-GAAATTGAATTAT
1 AATTTTATAAAATTAAAATAT
61217790 AATTTTTATAAAATTAAAATAT
1 AA-TTTTATAAAATTAAAATAT
**
61217812 AATTTTATATTGTATTAAAATAT
1 AATTTTATA--AAATTAAAATAT
61217835 AATTTTAT
1 AATTTTAT
61217843 TATTTTAGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.05
21 12 0.27
22 12 0.27
23 18 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
AATTTTATAAAATTAAAATAT
Found at i:61218446 original size:31 final size:30
Alignment explanation
Indices: 61218343--61218447 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
61218333 ATTCTGTTTA
*
61218343 AGTACCAAATTAAATATTAAAATCAAATTT
1 AGTACCAAATTAAATATTAAAATTAAATTT
** * *
61218373 ATGTATTAAATTTAATATTATAATTAAACTTGT
1 A-GTACCAAATTAAATATTAAAATTAAA-TT-T
* *
61218406 -GTACAAAATTAAACATTAAAATTAAATTT
1 AGTACCAAATTAAATATTAAAATTAAATTT
61218435 AGATACCAAATTA
1 AG-TACCAAATTA
61218448 TATACTAAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
29 1 0.02
30 4 0.07
31 51 0.86
32 2 0.03
33 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (30 bp):
AGTACCAAATTAAATATTAAAATTAAATTT
Found at i:61218883 original size:112 final size:114
Alignment explanation
Indices: 61218677--61218899 Score: 290
Period size: 112 Copynumber: 2.0 Consensus size: 114
61218667 TTATTTTTGA
* *
61218677 TGCTATGGCATTTTTAAGAAGACTACTTGTTTAAAATTGGAAATTAAGGAAGTTAATTTCTCTTT
1 TGCTATGGCATTTTCAAGAAGACTACTTGTTTAAAATTGGAAA-TAA-GAAGTTAATTGCTCTTT
* *
61218742 GCTTTGATTTCATGGAAAACCCAAATTGACTTCTTATATGAAAGCCGCAGT
64 GCTTTGATTCCATGGAAAACCCAAATTGACTTATTATATGAAAGCCGCAGT
* * * *
61218793 TGCTATGGCATTTTCAAG-AGATTTCTTGTTTAAAATTGGAAA-CA-AAGTTAATTGCTCTTTGT
1 TGCTATGGCATTTTCAAGAAGACTACTTGTTTAAAATTGGAAATAAGAAGTTAATTGCTCTTTGC
* ** *
61218855 TTTAGCTTCCATGGAAAATTCAAATTGACTTATTATTTGAAAGCC
66 TTT-GATTCCATGGAAAACCCAAATTGACTTATTATATGAAAGCC
61218900 TCGCTAACTC
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
111 19 0.20
112 35 0.37
113 1 0.01
115 22 0.23
116 17 0.18
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (114 bp):
TGCTATGGCATTTTCAAGAAGACTACTTGTTTAAAATTGGAAATAAGAAGTTAATTGCTCTTTGC
TTTGATTCCATGGAAAACCCAAATTGACTTATTATATGAAAGCCGCAGT
Found at i:61222669 original size:22 final size:22
Alignment explanation
Indices: 61222644--61222686 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61222634 TAAAAAAAAT
*
61222644 TATTT-TAAAAAATATATATATA
1 TATTTATAAAAAAAAT-TATATA
61222666 TATTTATAAAAAAAATTATAT
1 TATTTATAAAAAAAATTATAT
61222687 TTGATGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTTATAAAAAAAATTATATA
Found at i:61225936 original size:17 final size:17
Alignment explanation
Indices: 61225911--61225944 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61225901 TAATTTACTA
*
61225911 TTTTTTAAATAAAATAG
1 TTTTCTAAATAAAATAG
61225928 TTTTCTAAATAAAATAG
1 TTTTCTAAATAAAATAG
61225945 ACAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTTCTAAATAAAATAG
Found at i:61229247 original size:54 final size:54
Alignment explanation
Indices: 61229173--61229279 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
61229163 CCGCTATTAT
** ** *
61229173 CCACCAACCCTTCCTCTCCGCTTCCATTCACCACTTTTCCTCCACCATCATCCA
1 CCACCAACCCTTCCTCTCCGCCACCAGCCACCACTTTTCCTCCACCACCATCCA
*
61229227 CCACCAACCCTTCC-CTTCCGCCACCAGCCACCACTTTTCCTCCGCCACCATCC
1 CCACCAACCCTTCCTC-TCCGCCACCAGCCACCACTTTTCCTCCACCACCATCC
61229280 TCCAATATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.02
54 45 0.98
ACGTcount: A:0.18, C:0.55, G:0.04, T:0.23
Consensus pattern (54 bp):
CCACCAACCCTTCCTCTCCGCCACCAGCCACCACTTTTCCTCCACCACCATCCA
Found at i:61244415 original size:12 final size:12
Alignment explanation
Indices: 61244385--61244428 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
61244375 CGAGCAAATC
**
61244385 ATGATGATCATA
1 ATGATGATCACG
*
61244397 ATAATGATCACG
1 ATGATGATCACG
61244409 ATGATGATCACG
1 ATGATGATCACG
61244421 ATGATGAT
1 ATGATGAT
61244429 GATCATAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (12 bp):
ATGATGATCACG
Found at i:61248218 original size:21 final size:20
Alignment explanation
Indices: 61248185--61248223 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
61248175 TTTTATATTA
*
61248185 AGTTGAGTGAAATGAAATTCG
1 AGTTGAATGAAAT-AAATTCG
*
61248206 AGTTGAATTAAATAAATT
1 AGTTGAATGAAATAAATT
61248224 TGTTCAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTTGAATGAAATAAATTCG
Found at i:61249694 original size:21 final size:22
Alignment explanation
Indices: 61249661--61249707 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
61249651 TTTTAAATGG
* *
61249661 AAAATGATAGTGACATAACAAT
1 AAAAGGATAGTGAAATAACAAT
*
61249683 AAAAGGAT-GTGAAATAACATT
1 AAAAGGATAGTGAAATAACAAT
61249704 AAAA
1 AAAA
61249708 TGCGTGCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAAGGATAGTGAAATAACAAT
Found at i:61250078 original size:27 final size:27
Alignment explanation
Indices: 61250037--61250088 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
61250027 TAGTATTGGC
*
61250037 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCACCAATGGTGGT
* *
61250064 GCCTATTTGGGAGGCACCAATGGTG
1 GCCTATCTGGAAGGCACCAATGGTG
61250089 AACAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGAAGGCACCAATGGTGGT
Found at i:61250166 original size:21 final size:23
Alignment explanation
Indices: 61250122--61250173 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
61250112 CAAATTACTA
*
61250122 ACAA-ATTAATTATAAAATAATT
1 ACAATATTAATTACAAAATAATT
61250144 ACAATATTAA-TACAAAA-AATT
1 ACAATATTAATTACAAAATAATT
61250165 ACAATATTA
1 ACAATATTA
61250174 CAATATATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 13 0.46
22 10 0.36
23 5 0.18
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (23 bp):
ACAATATTAATTACAAAATAATT
Found at i:61250223 original size:27 final size:25
Alignment explanation
Indices: 61250188--61250257 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 25
61250178 ATATCCCCAC
*
61250188 ATTATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAA-TA-AAA
61250215 ATTACAATATTCATAC--AA-AAAA
1 ATTACAATATTCATACAAAATAAAA
*
61250237 ATTGCAATATTCATACAAAAT
1 ATTACAATATTCATACAAAAT
61250258 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 18 0.47
23 1 0.03
24 2 0.05
25 2 0.05
27 15 0.39
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (25 bp):
ATTACAATATTCATACAAAATAAAA
Found at i:61251725 original size:48 final size:48
Alignment explanation
Indices: 61251653--61251744 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
61251643 GGGAATTCTG
* *
61251653 TTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTGCTA
1 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAAGCGTTTTTGCTA
* *
61251701 TTGAATCATTTATCATTGCGAGTTAGGCTGACTTAAGCGTTTTT
1 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAAGCGTTTTT
61251745 AAGCAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (48 bp):
TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAAGCGTTTTTGCTA
Found at i:61252742 original size:31 final size:31
Alignment explanation
Indices: 61252697--61252766 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
61252687 AGAAAAATTT
*
61252697 AATAGTCTAGTGACTTAAATAAAAACTTTCA
1 AATAGTTTAGTGACTTAAATAAAAACTTTCA
* * *
61252728 AGTAGTTTAGTGACTTAAATGAGAACTTTCA
1 AATAGTTTAGTGACTTAAATAAAAACTTTCA
61252759 AATAGTTT
1 AATAGTTT
61252767 CATAATCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (31 bp):
AATAGTTTAGTGACTTAAATAAAAACTTTCA
Found at i:61253612 original size:30 final size:30
Alignment explanation
Indices: 61253555--61253612 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
61253545 AATGTTCTTT
* *
61253555 TAAAAATTTATTTTAATATAATTTTTAATG
1 TAAAAATATATTTTAATATAATATTTAATG
*
61253585 TAAAAATATATATTTAA-ATTATATTTAA
1 TAAAAATATAT-TTTAATATAATATTTAA
61253613 ATCCGTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TAAAAATATATTTTAATATAATATTTAATG
Found at i:61258326 original size:57 final size:57
Alignment explanation
Indices: 61258217--61258327 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 57
61258207 ATTGAATCTT
*
61258217 AAATTTGAGTGTAACACAGGGATGAAAATTGAAAATTGACCATTATTGTATAAATTA
1 AAATTTGAGTGTAACACAGGGATGAAAATTGAAAATTGACCATTATTCTATAAATTA
* * * *
61258274 AAATTTGAGTGTAGCA-TGAGGATTAAAATTGAAAATTTACCATT-TTACTATAAA
1 AAATTTGAGTGTAACACAG-GGATGAAAATTGAAAATTGACCATTATT-CTATAAA
61258328 ATGCAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 3 0.06
57 44 0.94
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.33
Consensus pattern (57 bp):
AAATTTGAGTGTAACACAGGGATGAAAATTGAAAATTGACCATTATTCTATAAATTA
Found at i:61260655 original size:6 final size:6
Alignment explanation
Indices: 61260644--61260678 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
61260634 CGAACATAAT
61260644 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
61260679 TATGATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:61272916 original size:218 final size:218
Alignment explanation
Indices: 61272535--61272972 Score: 831
Period size: 218 Copynumber: 2.0 Consensus size: 218
61272525 ATTCCAATAC
61272535 ATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTC
1 ATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTC
*
61272600 AGCACACCATATTTCAATGCATTGATCTAGTATGCTAAAATTATAACACATAATTTAATAAGTCG
66 AGCACACCATATTTCAATGCATTGATCTAGTATGCAAAAATTATAACACATAATTTAATAAGTCG
*
61272665 ATGAACAAAGACATTCAAGATGCTATAGTTCAATACATAGATGACAAACAAAGATGAATGCAGAT
131 ACGAACAAAGACATTCAAGATGCTATAGTTCAATACATAGATGACAAACAAAGATGAATGCAGAT
61272730 CAAAATCCAAGAGCAAAGACGTG
196 CAAAATCCAAGAGCAAAGACGTG
61272753 ATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTC
1 ATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTC
61272818 AGCACACCATATTTCAATGCATTGATCTAGTATGCAAAAATTATAACACATAATTTAATAAGTCG
66 AGCACACCATATTTCAATGCATTGATCTAGTATGCAAAAATTATAACACATAATTTAATAAGTCG
*
61272883 ACGAACAAAGACATTCAAGATGCTATGGTTCAATACATAGATGACAAACAAAGATGAATGCAGAT
131 ACGAACAAAGACATTCAAGATGCTATAGTTCAATACATAGATGACAAACAAAGATGAATGCAGAT
* *
61272948 CTAAATCCAAGAGCAAAGATGTG
196 CAAAATCCAAGAGCAAAGACGTG
61272971 AT
1 AT
61272973 TTTAAACATT
Statistics
Matches: 215, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
218 215 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.24
Consensus pattern (218 bp):
ATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTC
AGCACACCATATTTCAATGCATTGATCTAGTATGCAAAAATTATAACACATAATTTAATAAGTCG
ACGAACAAAGACATTCAAGATGCTATAGTTCAATACATAGATGACAAACAAAGATGAATGCAGAT
CAAAATCCAAGAGCAAAGACGTG
Found at i:61273034 original size:166 final size:166
Alignment explanation
Indices: 61272753--61273059 Score: 427
Period size: 166 Copynumber: 1.8 Consensus size: 166
61272743 CAAAGACGTG
* * * *
61272753 ATAGATGACAATCAAAGATGGATATAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAGCATTC
1 ATAGATGACAAACAAAGATGAATACAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAACATTC
* * * * * *
61272818 AGCACACCATATTTCAATGCATTGATCTAGTATGCAAAAATTATAACACATAATTTAATAAGTCG
66 AACACACCATATTTCAATACATAGATCTAGTATGCAAAAATTAGAACACATAATTCAATAAGTCA
*
61272883 ACGAACAAAGACATTCAAGATGCTATGGTTCAATAC
131 ACAAACAAAGACATTCAAGATGCTATGGTTCAATAC
* ** ***
61272919 ATAGATGACAAACAAAGATGAATGCAGATCTAAATCCAAGAGC-AAAGATGTGATTTTAAACATT
1 ATAGATGACAAACAAAGATGAATACAGATAAAAATCCAAGAGCGAAA-ACAAGATTTTAAACATT
* *
61272983 CAACACACCATATTTCGATACATAGATCTAGTATGCAAAATTTAGAACACATAATTCAATAAGTC
65 CAACACACCATATTTCAATACATAGATCTAGTATGCAAAAATTAGAACACATAATTCAATAAGTC
61273048 AACAAACAAAGA
130 AACAAACAAAGA
61273060 TGAATATAAG
Statistics
Matches: 121, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
165 3 0.02
166 118 0.98
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (166 bp):
ATAGATGACAAACAAAGATGAATACAGATAAAAATCCAAGAGCGAAAACAAGATTTTAAACATTC
AACACACCATATTTCAATACATAGATCTAGTATGCAAAAATTAGAACACATAATTCAATAAGTCA
ACAAACAAAGACATTCAAGATGCTATGGTTCAATAC
Found at i:61273258 original size:61 final size:64
Alignment explanation
Indices: 61273184--61273310 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 64
61273174 ACAAGTTCTA
* *
61273184 AAACACTCAACAT-GCCATATTACAATACATT-CAAAAGCAATTCAGAAATAG-CTTGAAACCC
1 AAACACTCAACATGGCCATAGTACAATACATTAAAAAAGCAATTCAGAAATAGACTTGAAACCC
* * * *
61273245 AAACACTCAACATGGCTATAGTACAATACATTAAAAAAAGCAATTTAGAAATGGATTTGAAACCC
1 AAACACTCAACATGGCCATAGTACAATACATT-AAAAAAGCAATTCAGAAATAGACTTGAAACCC
61273310 A
1 A
61273311 CTTGTGGTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
61 13 0.23
62 16 0.29
64 17 0.30
65 10 0.18
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.22
Consensus pattern (64 bp):
AAACACTCAACATGGCCATAGTACAATACATTAAAAAAGCAATTCAGAAATAGACTTGAAACCC
Found at i:61274005 original size:31 final size:31
Alignment explanation
Indices: 61273965--61274023 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
61273955 AAATAGTCAC
*
61273965 TAAATTATTCAAAAGTTTTCATTTAAGCTAT
1 TAAACTATTCAAAAGTTTTCATTTAAGCTAT
*
61273996 TAAACTATTCAAAAGTTTTTATTTAAGC
1 TAAACTATTCAAAAGTTTTCATTTAAGC
61274024 CACTGGGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (31 bp):
TAAACTATTCAAAAGTTTTCATTTAAGCTAT
Found at i:61277708 original size:16 final size:17
Alignment explanation
Indices: 61277689--61277721 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61277679 ATGATGGTAC
61277689 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
61277705 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
61277722 TGTTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:61280945 original size:25 final size:25
Alignment explanation
Indices: 61280882--61280995 Score: 87
Period size: 25 Copynumber: 4.6 Consensus size: 25
61280872 GGATACACCA
*
61280882 CAGCTCGTATGAGCTTCTCGATT-T
1 CAGCTCGTATGAGCTTATCGATTCT
*
61280906 GCAGCTTGTGA-GAGCTTATCGATTCT
1 -CAGCTCGT-ATGAGCTTATCGATTCT
* *
61280932 CAGCTCGTATGAGCTGA-CTGATTCA
1 CAGCTCGTATGAGCTTATC-GATTCT
*
61280957 CAGCTCGTGA-GAG-TATACCGATTCAT
1 CAGCTCGT-ATGAGCT-TATCGATTC-T
61280983 -AGCTCGTATGAGC
1 CAGCTCGTATGAGC
61280996 ATATATGTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
24 4 0.06
25 64 0.89
26 4 0.06
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTATCGATTCT
Found at i:61280961 original size:50 final size:51
Alignment explanation
Indices: 61280882--61280995 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 51
61280872 GGATACACCA
* ** * *
61280882 CAGCTCGTATGAGCTTCTCGATTTGCAGCTTGTGAGAGCT-TATCGATTC-T
1 CAGCTCGTATGAGCTACTCGATTCACAGCTCGTGAGAG-TATACCGATTCAT
61280932 CAGCTCGTATGAGCTGACT-GATTCACAGCTCGTGAGAGTATACCGATTCAT
1 CAGCTCGTATGAGCT-ACTCGATTCACAGCTCGTGAGAGTATACCGATTCAT
61280983 -AGCTCGTATGAGC
1 CAGCTCGTATGAGC
61280996 ATATATGTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 1 0.02
50 52 0.93
51 3 0.05
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (51 bp):
CAGCTCGTATGAGCTACTCGATTCACAGCTCGTGAGAGTATACCGATTCAT
Found at i:61290755 original size:6 final size:6
Alignment explanation
Indices: 61290744--61290768 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61290734 AATTATATTG
61290744 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
61290769 TTGTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:61291409 original size:29 final size:32
Alignment explanation
Indices: 61291358--61291419 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
61291348 AGTCTATATC
61291358 TTTAAAATTTTAAAAGGATTAAA-T-CAATTT
1 TTTAAAATTTTAAAAGGATTAAAGTGCAATTT
* * *
61291388 TTTAAATTTTTGAAGGGA-TAAAGTGCAATTT
1 TTTAAAATTTTAAAAGGATTAAAGTGCAATTT
61291419 T
1 T
61291420 ACCATTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.15
30 16 0.59
31 7 0.26
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTAAAATTTTAAAAGGATTAAAGTGCAATTT
Found at i:61291900 original size:13 final size:12
Alignment explanation
Indices: 61291876--61291911 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
61291866 TTCAAGTTTA
61291876 AGGAATTAATAC
1 AGGAATTAATAC
61291888 AGGAATATAATAC
1 AGGAAT-TAATAC
*
61291901 GGGAATTAATA
1 AGGAATTAATA
61291912 GCCAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (12 bp):
AGGAATTAATAC
Found at i:61294771 original size:120 final size:120
Alignment explanation
Indices: 61294541--61294888 Score: 614
Period size: 120 Copynumber: 2.9 Consensus size: 120
61294531 TTTCCAACTT
* *
61294541 AAATTTAT--TTAAAAT-TTTAATATTTAAATCTTGACTCATGGAAAAGGAAATATTACATGATT
1 AAATTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAAATATTACATGATT
61294603 T-TTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATTATATAAAAATTAA
66 TGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATTATATAAAAATTAA
*
61294657 AAATTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAAATATTACATGGTT
1 AAATTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAAATATTACATGATT
*
61294722 TGTTTATTTTCAAGATTAAATAGTAATGCATTTTTTAAAATTATATAAAAATTAA
66 TGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATTATATAAAAATTAA
* *
61294777 AAATTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAAATATTACATTATG
1 AAATTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAAATATTACATGATT
61294842 TGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATTATATA
66 TGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATTATATA
61294889 TGTACAAGCC
Statistics
Matches: 220, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
116 8 0.04
118 7 0.03
119 45 0.20
120 160 0.73
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (120 bp):
AAATTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAAATATTACATGATT
TGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATTATATAAAAATTAA
Found at i:61295248 original size:3 final size:3
Alignment explanation
Indices: 61295234--61295327 Score: 104
Period size: 3 Copynumber: 31.7 Consensus size: 3
61295224 TAGCTTTTTC
* *
61295234 ATT ATT -TT ATT ATT ATC ATT ATT ATT ATT ATC ATT ATT ATT ATCT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * *
61295279 -TT ACT ATT ATT ATT ATT ATT A-T ATTT ATT AAT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
61295323 ATT AT
1 ATT AT
61295328 GTTTTTTATA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
2 5 0.07
3 68 0.89
4 3 0.04
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:61295661 original size:14 final size:14
Alignment explanation
Indices: 61295642--61295671 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61295632 ACCTTTGTAA
*
61295642 ATATATATACATAT
1 ATATATATACACAT
61295656 ATATATATACACAT
1 ATATATATACACAT
61295670 AT
1 AT
61295672 TTTAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATATACACAT
Found at i:61296802 original size:120 final size:120
Alignment explanation
Indices: 61296589--61296987 Score: 753
Period size: 120 Copynumber: 3.3 Consensus size: 120
61296579 GGTGTCAACA
61296589 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAA
1 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAA
61296654 ATATTACATTATTTGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATT
66 ATATTACATTATTTGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATT
*
61296709 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGAAAAAAGAA
1 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAA
*
61296774 ATATTACATTATTTGTTTATTTTGAAGATTAAATAGAAATGCATTTTTTAAAATT
66 ATATTACATTATTTGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATT
61296829 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAA
1 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAA
* *
61296894 ATATTACATGATTTGTTTATTTTCAAGATTAAATATAAATGCATTTTTTAAAATT
66 ATATTACATTATTTGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATT
*
61296949 ATATAAAAATTAAAATTTTATAATTAAACTATTAAATAT
1 ATATAAAAATTAAAATTTTATAATTAAAATATTAAATAT
61296988 CTCAATGAAA
Statistics
Matches: 272, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 272 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (120 bp):
ATATAAAAATTAAAATTTTATAATTAAAATATTAAATATTTAAATCTTGACTCATGGAAAAAGAA
ATATTACATTATTTGTTTATTTTCAAGATTAAATAGAAATGCATTTTTTAAAATT
Found at i:61300254 original size:120 final size:119
Alignment explanation
Indices: 61300098--61300358 Score: 382
Period size: 120 Copynumber: 2.2 Consensus size: 119
61300088 CCAACTTAAA
* * *
61300098 TTTATTTAAAACT-TTAATATTTAAATCTTTACTCATGGAAAAGGAAATATTACATGATTTGTTT
1 TTTAATTAAAA-TATTAATATTTAAACCTTGACTCATGGAAAAGGAAATATTACATGATTTGTTT
* *
61300162 ATTTTCAAGGTTAAATAGGAATGCA-TTTTTTAAAATTATATAAAAAATAAAAAT
65 ATTTTCAAGATTAAATAGAAATGCATTTTTTTAAAATTATATAAAAAATAAAAAT
* *
61300216 TTATAATTAATATATTAAATATTTAAACCTTGACTCATGGAAAGGGAAATATTACATGATTTGTT
1 TT-TAATTAAAATATT-AATATTTAAACCTTGACTCATGGAAAAGGAAATATTACATGATTTGTT
* * *
61300281 TATTTTCAAGATTAAATAGAAATGCATTTTTTTTTAAATTATATAAAAAATTATAAT
64 TATTTTCAAGATTAAATAGAAATGCA-TTTTTTTAAAATTATATAAAAAATAAAAAT
61300338 TTTAATTAAAATATTAATATT
1 TTTAATTAAAATATTAATATT
61300359 ACATAATTTG
Statistics
Matches: 127, Mismatches: 11, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
118 3 0.02
119 9 0.07
120 75 0.59
121 12 0.09
122 28 0.22
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (119 bp):
TTTAATTAAAATATTAATATTTAAACCTTGACTCATGGAAAAGGAAATATTACATGATTTGTTTA
TTTTCAAGATTAAATAGAAATGCATTTTTTTAAAATTATATAAAAAATAAAAAT
Found at i:61309930 original size:12 final size:12
Alignment explanation
Indices: 61309913--61309937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61309903 CGACCTAACA
61309913 ATGCAGTGGTCG
1 ATGCAGTGGTCG
61309925 ATGCAGTGGTCG
1 ATGCAGTGGTCG
61309937 A
1 A
61309938 AGTAGACATG
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:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (12 bp):
ATGCAGTGGTCG
Found at i:61311749 original size:26 final size:27
Alignment explanation
Indices: 61311698--61311753 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
61311688 TGATTCAATT
61311698 ATTTATATTTAAATAAATAAACATATCA
1 ATTTATATTTAAATAAATAAACATAT-A
*
61311726 ATTTAT-TTTAATATTAA-AAA-ATATA
1 ATTTATATTTAA-ATAAATAAACATATA
61311751 ATT
1 ATT
61311754 AGTATGTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 8 0.31
28 10 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTTATATTTAAATAAATAAACATATA
Found at i:61312528 original size:19 final size:19
Alignment explanation
Indices: 61312491--61312528 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
61312481 TTTGTCACCA
61312491 TAAATTTGATAGATAAAAAT
1 TAAATTTGA-AGATAAAAAT
61312511 TAAATTTG-AGATTAAAAA
1 TAAATTTGAAGA-TAAAAA
61312529 ATTATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 6 0.35
20 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (19 bp):
TAAATTTGAAGATAAAAAT
Found at i:61315451 original size:22 final size:22
Alignment explanation
Indices: 61315402--61315441 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
61315392 TTGATTATAT
61315402 TTAAAATA--TTAAATATTTAA
1 TTAAAATAGTTTAAATATTTAA
61315422 TTAAAATAGTTTAAATATTT
1 TTAAAATAGTTTAAATATTT
61315442 TTTATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
TTAAAATAGTTTAAATATTTAA
Found at i:61317673 original size:23 final size:23
Alignment explanation
Indices: 61317636--61317694 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
61317626 TTTCCTTCCA
61317636 CTTTCCCTCTCTTTCC-TTTCTCT
1 CTTT-CCTCTCTTTCCTTTTCTCT
*
61317659 CTTTCCTCTCATTTCCTTTTTTCT
1 CTTTCCTCTC-TTTCCTTTTCTCT
*
61317683 TTTTCCTCTCTT
1 CTTTCCTCTCTT
61317695 AGAAAACCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 6 0.19
23 11 0.34
24 15 0.47
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (23 bp):
CTTTCCTCTCTTTCCTTTTCTCT
Found at i:61317683 original size:22 final size:23
Alignment explanation
Indices: 61317636--61317694 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
61317626 TTTCCTTCCA
61317636 CTTTCCCTCTCTTTCCTTTCTCT
1 CTTTCCCTCTCTTTCCTTTCTCT
*
61317659 CTTT-CCTCTCATTTCCTTT-TTT
1 CTTTCCCTCTC-TTTCCTTTCTCT
*
61317681 CTTTTTCCTCTCTT
1 C-TTTCCCTCTCTT
61317695 AGAAAACCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 9 0.28
23 17 0.53
24 6 0.19
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (23 bp):
CTTTCCCTCTCTTTCCTTTCTCT
Found at i:61322464 original size:2 final size:2
Alignment explanation
Indices: 61322457--61322496 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
61322447 ACTTTTATTT
61322457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61322497 ATTAAAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61329104 original size:13 final size:13
Alignment explanation
Indices: 61329074--61329112 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
61329064 TTGCATGTAT
61329074 TTTATTTGTTTAAA
1 TTTATTT-TTTAAA
*
61329088 TTTATTTTTTAAG
1 TTTATTTTTTAAA
61329101 TTTATATTTTTA
1 TTTAT-TTTTTA
61329113 TCTAAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (13 bp):
TTTATTTTTTAAA
Found at i:61334636 original size:21 final size:21
Alignment explanation
Indices: 61334610--61334652 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
61334600 GTACATCGTT
61334610 AACAGAAGCTCGTGAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
61334631 AACAGAAGCTCGTGAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
61334652 A
1 A
61334653 TCCACCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.33, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCGTGAGAGCTG
Found at i:61338835 original size:20 final size:20
Alignment explanation
Indices: 61338810--61338849 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61338800 AATATTTTCC
*
61338810 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
61338830 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
61338850 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:61338851 original size:34 final size:35
Alignment explanation
Indices: 61338798--61338864 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61338788 CAAACACCAG
*
61338798 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
61338833 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
61338865 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:61339430 original size:7 final size:7
Alignment explanation
Indices: 61339420--61339462 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
61339410 CCGTTTATTT
61339420 TTTAAAA
1 TTTAAAA
61339427 TTTAAAA
1 TTTAAAA
*
61339434 TTTAGATA
1 TTTA-AAA
*
61339442 TTAAAAA
1 TTTAAAA
61339449 TTTAAAA
1 TTTAAAA
*
61339456 TGTAAAA
1 TTTAAAA
61339463 AAATTAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (7 bp):
TTTAAAA
Found at i:61339461 original size:15 final size:14
Alignment explanation
Indices: 61339420--61339463 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
61339410 CCGTTTATTT
*
61339420 TTTAAAATTTAAAA
1 TTTAAAATTAAAAA
*
61339434 TTTAGATATTAAAAA
1 TTTA-AAATTAAAAA
61339449 TTTAAAATGTAAAAA
1 TTTAAAAT-TAAAAA
61339464 AATTAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (14 bp):
TTTAAAATTAAAAA
Found at i:61349490 original size:4 final size:4
Alignment explanation
Indices: 61349457--61349515 Score: 73
Period size: 4 Copynumber: 13.8 Consensus size: 4
61349447 TTCCATTCTT
*
61349457 TTTC TCTTC TTTTC TTTT TTTCC TTTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC T-TTC -TTTC TTTC TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC
61349505 TTTC TTTC TTT
1 TTTC TTTC TTT
61349516 ACCTTTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
4 38 0.78
5 7 0.14
6 4 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:61356515 original size:22 final size:23
Alignment explanation
Indices: 61356490--61356542 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
61356480 AAAGGAATTT
*
61356490 GAAAAAACAAA-TGACATTTTTA
1 GAAAAAAAAAAGTGACATTTTTA
*
61356512 GAAAAAAAAAAGTGATATTTTTA
1 GAAAAAAAAAAGTGACATTTTTA
61356535 -AAAAAAAA
1 GAAAAAAAA
61356543 TATTTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.25
Consensus pattern (23 bp):
GAAAAAAAAAAGTGACATTTTTA
Found at i:61356516 original size:21 final size:20
Alignment explanation
Indices: 61356491--61356542 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
61356481 AAGGAATTTG
*
61356491 AAAAAACAAATGACATTTTT
1 AAAAAAAAAATGACATTTTT
*
61356511 AGAAAAAAAAAAGTGATATTTTT
1 --AAAAAAAAAA-TGACATTTTT
61356534 AAAAAAAAA
1 AAAAAAAAA
61356543 TATTTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 9 0.33
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (20 bp):
AAAAAAAAAATGACATTTTT
Found at i:61360567 original size:35 final size:35
Alignment explanation
Indices: 61360521--61360590 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
61360511 AAGGAAAAAG
61360521 TTAAAATATATTGACAATCCCTTCATTTTGGCAAA
1 TTAAAATATATTGACAATCCCTTCATTTTGGCAAA
61360556 TTAAAATATATTGACAATCCCTTCATTTTGGCAAA
1 TTAAAATATATTGACAATCCCTTCATTTTGGCAAA
61360591 ATTTGAGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (35 bp):
TTAAAATATATTGACAATCCCTTCATTTTGGCAAA
Found at i:61366451 original size:17 final size:17
Alignment explanation
Indices: 61366429--61366462 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61366419 GCCCGTTTTT
*
61366429 AATAAACACAAAAAAAA
1 AATAAAAACAAAAAAAA
*
61366446 AATAAAAATAAAAAAAA
1 AATAAAAACAAAAAAAA
61366463 TATTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (17 bp):
AATAAAAACAAAAAAAA
Found at i:61367135 original size:19 final size:19
Alignment explanation
Indices: 61367079--61367137 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 19
61367069 AAGGAAACAC
61367079 GTCTAAAGGTACGTGTCAA
1 GTCTAAAGGTACGTGTCAA
* *
61367098 GCCTGAAAGGGGAACGTGTCAA
1 GTCT-AAA--GGTACGTGTCAA
61367120 GTCTAAAGGTACGTGTCA
1 GTCTAAAGGTACGTGTCA
61367138 CTTTCTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 13 0.39
20 3 0.09
21 3 0.09
22 14 0.42
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (19 bp):
GTCTAAAGGTACGTGTCAA
Found at i:61369371 original size:2 final size:2
Alignment explanation
Indices: 61369364--61369408 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
61369354 CCATTACTTT
61369364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61369406 TA T
1 TA T
61369409 CCAAAGTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61372268 original size:58 final size:58
Alignment explanation
Indices: 61372193--61372302 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
61372183 ACTTTTTCCT
* *
61372193 AATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGATACTTAACTTTTTTGGGTCC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGATACCTAACTTTTTTGGGTCC
* * * * * *
61372251 AATTTGGTATCTGAACTTGACTCTTTTTCCTAATTTGGTACCTAATTTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGATACCTAACTTTTTT
61372303 TTCTTCGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (58 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGATACCTAACTTTTTTGGGTCC
Found at i:61377278 original size:20 final size:20
Alignment explanation
Indices: 61377255--61377296 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
61377245 GGAGAACAAA
61377255 AGAAAAAAAAAGAGAAGAAG
1 AGAAAAAAAAAGAGAAGAAG
* *
61377275 AGAAGAAAAAGGAGAAGAAG
1 AGAAAAAAAAAGAGAAGAAG
61377295 AG
1 AG
61377297 GGCGGGAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAAAAAAAGAGAAGAAG
Found at i:61380943 original size:29 final size:29
Alignment explanation
Indices: 61380909--61380968 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
61380899 ATTTAACTTA
61380909 ATTTTAAAATTTAAAAAATAGAAAATTTC
1 ATTTTAAAATTTAAAAAATAGAAAATTTC
61380938 ATTTTAAAATTTAAAAAATAGAAAATTTC
1 ATTTTAAAATTTAAAAAATAGAAAATTTC
61380967 AT
1 AT
61380969 GTAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTTTAAAATTTAAAAAATAGAAAATTTC
Found at i:61381826 original size:13 final size:13
Alignment explanation
Indices: 61381796--61381881 Score: 50
Period size: 13 Copynumber: 6.7 Consensus size: 13
61381786 AAAATAAACA
*
61381796 TTAAA-ATCAAAC
1 TTAAATATCAAAT
*
61381808 TCAAATATCAAAT
1 TTAAATATCAAAT
** *
61381821 TTAAATAAAAAAA
1 TTAAATATCAAAT
*
61381834 TTAAATATTAAA-
1 TTAAATATCAAAT
* *
61381846 ATAAATATTAAAT
1 TTAAATATCAAAT
* *
61381859 TCAAATACCAAAT
1 TTAAATATCAAAT
*
61381872 ATTATATATC
1 -TTAAATATC
61381882 CCAAATAATA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
12 15 0.27
13 34 0.62
14 6 0.11
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAATATCAAAT
Found at i:61381855 original size:19 final size:19
Alignment explanation
Indices: 61381776--61381858 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
61381766 TTTTAAAAAA
* *
61381776 ATTAAATACTAAAATAAAC
1 ATTAAATATTAAAATAAAT
* *
61381795 ATTAAA-ATCAAACTCAAAT
1 ATTAAATATTAAAAT-AAAT
* * *
61381814 ATCAAAT-TTAAATAAAAAA
1 ATTAAATATTAAA-ATAAAT
61381833 ATTAAATATTAAAATAAAT
1 ATTAAATATTAAAATAAAT
61381852 ATTAAAT
1 ATTAAAT
61381859 TCAAATACCA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
18 5 0.10
19 38 0.79
20 5 0.10
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTAAATATTAAAATAAAT
Found at i:61392368 original size:12 final size:13
Alignment explanation
Indices: 61392353--61392399 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
61392343 TCTTTTGATG
61392353 AGTAT-TTTTCAA
1 AGTATCTTTTCAA
* *
61392365 AGTATGTTCTCAA
1 AGTATCTTTTCAA
*
61392378 AATAT-TTTTCAA
1 AGTATCTTTTCAA
61392390 AGTATCTTTT
1 AGTATCTTTT
61392400 AAATCCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (13 bp):
AGTATCTTTTCAA
Found at i:61395055 original size:8 final size:8
Alignment explanation
Indices: 61395042--61395070 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
61395032 TTAAGGATTG
61395042 AAATTTGA
1 AAATTTGA
61395050 AAATTTGA
1 AAATTTGA
61395058 AAATTTGA
1 AAATTTGA
61395066 AAATT
1 AAATT
61395071 ATAATGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (8 bp):
AAATTTGA
Found at i:61398657 original size:82 final size:81
Alignment explanation
Indices: 61398557--61398717 Score: 250
Period size: 82 Copynumber: 2.0 Consensus size: 81
61398547 AAAACTACCA
** * ** * *
61398557 TTATCTGTTTGTTGATTCAAGTTTGTTGTTCGGAATTTGGTTCCGGGACAAATCTTGCATGCCGA
1 TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGAC-AATCTTGCATACCAA
61398622 GAAACTAATTCTTTTCG
65 GAAACTAATTCTTTTCG
61398639 TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGACAATCTTGCATACCAAG
1 TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGACAATCTTGCATACCAAG
61398704 AAACTAATTCTTTT
66 AAACTAATTCTTTT
61398718 TATTATATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 28 0.39
82 44 0.61
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (81 bp):
TTATCTGTTTGTTGATTCAAGTTTGTCATTCAGAATCCGGTTCCGGGACAATCTTGCATACCAAG
AAACTAATTCTTTTCG
Found at i:61402400 original size:24 final size:24
Alignment explanation
Indices: 61402350--61402398 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
61402340 CCAAAATATT
*
61402350 TTCAAAATTAATTTCTTTTTTGAAA
1 TTCAAAATTAATTTATTTTTT-AAA
*
61402375 TTCAAATTTAATTTATTTGTTTAA
1 TTCAAAATTAATTTATTT-TTTAA
61402399 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (24 bp):
TTCAAAATTAATTTATTTTTTAAA
Found at i:61402462 original size:19 final size:19
Alignment explanation
Indices: 61402438--61402493 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 19
61402428 TAAGAGTGAG
*
61402438 TTTTATTAATATTTTTAGT
1 TTTTATTAATATTTTTAAT
*
61402457 TTTTA-TATTA-TTTTAAT
1 TTTTATTAATATTTTTAAT
*
61402474 TTTT-TTAA-ATTTTAAAT
1 TTTTATTAATATTTTTAAT
61402491 TTT
1 TTT
61402494 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 21 0.68
18 4 0.13
19 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTATTAATATTTTTAAT
Found at i:61402477 original size:7 final size:7
Alignment explanation
Indices: 61402476--61402500 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61402466 ATTTTAATTT
61402476 TTTTAAA
1 TTTTAAA
61402483 TTTTAAA
1 TTTTAAA
61402490 TTTTAAA
1 TTTTAAA
61402497 TTTT
1 TTTT
61402501 TTACTTTGAC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:61407370 original size:23 final size:23
Alignment explanation
Indices: 61407354--61407399 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
61407344 AACAAATTAG
61407354 ACTAATTGAACTAAACACACACA
1 ACTAATTGAACTAAACACACACA
61407377 ACTAATTGAACTAAACACACACA
1 ACTAATTGAACTAAACACACACA
61407400 TGGCAGCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.17
Consensus pattern (23 bp):
ACTAATTGAACTAAACACACACA
Found at i:61418187 original size:142 final size:140
Alignment explanation
Indices: 61417856--61418207 Score: 372
Period size: 140 Copynumber: 2.5 Consensus size: 140
61417846 AGTGAGCTCA
* * * * * * *
61417856 ACCTGTCAAATGTTACCACTTTGAGCCAACTTAGCTAAT-TTCTGGTTTCGCTGCTACCTATATA
1 ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
* *
61417920 TAGATATGGATATCTTAGACATGATATTACCTGTGCATCATCACCACTGCCCTTTTTGTTTTCAG
66 TAGATATGGATATCTTACACATGATATTACCTGTGCATCATCACCACTG-CATTTTTGTTTTCAG
**
61417985 GCTCTGGACTC
130 GCTCCAGACTC
* * * *** *
61417996 ATCTGTTAAATGTCACCTCTTTGAACCAACTTAGCTAA-GTTCCACGTTCACTGCTTCCCATATA
1 ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
* * * *
61418060 TAGATGA-GGATATCTTACTCATGACTCTTATCTGTGCATCATCACGACTG-ATTGTATTGTTTT
66 TAGAT-ATGGATATCTTACACATGA-TATTACCTGTGCATCATCACCACTGCATT-T-TTGTTTT
* *
61418123 CCGGCTCCAGACTTG
127 CAGGCTCCAGAC-TC
* **
61418138 ACCTGTTACACGTCACCACTTTGAACCAACTTAGC-AATGTTCTGGGTTCACTGCTACCGGTATA
1 ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
61418202 TAGATA
66 TAGATA
61418208 CAGATAAATA
Statistics
Matches: 173, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
139 2 0.01
140 72 0.42
141 42 0.24
142 57 0.33
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (140 bp):
ACCTGTTAAACGTCACCACTTTGAACCAACTTAGCTAATGTTCTGGGTTCACTGCTACCCATATA
TAGATATGGATATCTTACACATGATATTACCTGTGCATCATCACCACTGCATTTTTGTTTTCAGG
CTCCAGACTC
Found at i:61420354 original size:20 final size:20
Alignment explanation
Indices: 61420302--61420361 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
61420292 ACTATAACCT
61420302 TTTATTCGAATTTTTG-AAA
1 TTTATTCGAATTTTTGAAAA
**
61420321 TACAATT--AAGTTTTTGAAAA
1 T-TTATTCGAA-TTTTTGAAAA
61420341 TTTATTCGAATTTTT-AAAA
1 TTTATTCGAATTTTTGAAAA
61420360 TT
1 TT
61420362 AATTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
18 2 0.06
19 16 0.50
20 12 0.38
21 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTATTCGAATTTTTGAAAA
Found at i:61420714 original size:116 final size:114
Alignment explanation
Indices: 61420594--61420825 Score: 353
Period size: 116 Copynumber: 2.0 Consensus size: 114
61420584 AAAAAAATAA
* *
61420594 AAAAAATAAACCAATTTAAATTGAATTATCATAAATAATTC-AAAAAATCCAATCT-AACTAACC
1 AAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAAATCCAAT-TGAACTAACC
61420657 AAAG-TTAACCCAAACATATACATTAATATTGGTGAACATTCATTATTTAAAAT
65 -AAGTTTAACCCAAACATAT--ATT-ATATTGGTGAACATTCATTATTTAAAAT
* *
61420710 AAAAAATAAACCAATCTAAATCGAATTGTCATAAATAATTCAAAAAAATTCAATTGAACTAACCA
1 AAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAAATCCAATTGAACTAACCA
*
61420775 AGTTTATCCCAAACATATATTATATTGGTGAACATTCATTATTTAAAAT
66 AGTTTAACCCAAACATATATTATATTGGTGAACATTCATTATTTAAAAT
61420824 AA
1 AA
61420826 GGAAAGTTTT
Statistics
Matches: 108, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
114 30 0.28
115 3 0.03
116 42 0.39
117 33 0.31
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (114 bp):
AAAAAATAAACCAATCTAAATCGAATTATCATAAATAATTCAAAAAAATCCAATTGAACTAACCA
AGTTTAACCCAAACATATATTATATTGGTGAACATTCATTATTTAAAAT
Found at i:61434454 original size:9 final size:9
Alignment explanation
Indices: 61434440--61434476 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
61434430 TATAGTTTGA
61434440 TATTCGAAT
1 TATTCGAAT
61434449 TATTCGAAT
1 TATTCGAAT
*
61434458 TATTCGAGT
1 TATTCGAAT
61434467 TATTCGAAT
1 TATTCGAAT
61434476 T
1 T
61434477 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:61438315 original size:16 final size:16
Alignment explanation
Indices: 61438291--61438321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61438281 AAAATTATTA
61438291 AATTAAATTTAATTTT
1 AATTAAATTTAATTTT
*
61438307 AATTTAATTTAATTT
1 AATTAAATTTAATTT
61438322 AAAATTATTA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTAAATTTAATTTT
Found at i:61439695 original size:16 final size:16
Alignment explanation
Indices: 61439653--61439696 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
61439643 TGTTTAATTG
61439653 AAAATTTTAAAAATAA
1 AAAATTTTAAAAATAA
*
61439669 AAAAATTTAAAAAT-A
1 AAAATTTTAAAAATAA
*
61439684 GAAATTTATAAAA
1 AAAATTT-TAAAA
61439697 TATGGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AAAATTTTAAAAATAA
Found at i:61440500 original size:14 final size:14
Alignment explanation
Indices: 61440481--61440520 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
61440471 TTGATTGCCA
61440481 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
61440495 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
61440509 GGAAAATGTTTT
1 GTAAAATGTTTT
61440521 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:61440529 original size:20 final size:20
Alignment explanation
Indices: 61440504--61440543 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61440494 CGTAAAATGA
*
61440504 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
61440524 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
61440544 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:61440533 original size:34 final size:35
Alignment explanation
Indices: 61440489--61440555 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61440479 CAGTAAAATG
* *
61440489 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
61440523 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
61440556 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:61441893 original size:24 final size:26
Alignment explanation
Indices: 61441839--61441893 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
61441829 CTAATTAATG
61441839 TAAATTAAAATAAGTATCAGATATAA
1 TAAATTAAAATAAGTATCAGATATAA
* *
61441865 AAAATTAGAAT-A-TATCA-ATATCAA
1 TAAATTAAAATAAGTATCAGATAT-AA
61441889 TAAAT
1 TAAAT
61441894 CTGGACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 4 0.16
24 11 0.44
25 1 0.04
26 9 0.36
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (26 bp):
TAAATTAAAATAAGTATCAGATATAA
Found at i:61442068 original size:21 final size:22
Alignment explanation
Indices: 61442042--61442082 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
61442032 ATTTAAACTT
61442042 AATTTTTAAT-ATATATTTATA
1 AATTTTTAATGATATATTTATA
*
61442063 AATTTTTAATGATTTATTTA
1 AATTTTTAATGATATATTTA
61442083 ATTGAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AATTTTTAATGATATATTTATA
Found at i:61442383 original size:15 final size:16
Alignment explanation
Indices: 61442363--61442397 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
61442353 AGAAGTGACA
61442363 TAATAAAATTAA-ATT
1 TAATAAAATTAACATT
61442378 TAATAAAATTAACATT
1 TAATAAAATTAACATT
61442394 TAAT
1 TAAT
61442398 CTAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAAAATTAACATT
Found at i:61446997 original size:13 final size:13
Alignment explanation
Indices: 61446964--61447003 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
61446954 CCGAAACTTT
*
61446964 AAAAAATTA-TGA
1 AAAAAATTATTCA
*
61446976 AACAAATTATTCA
1 AAAAAATTATTCA
61446989 AAAAAATTATTCA
1 AAAAAATTATTCA
61447002 AA
1 AA
61447004 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAAAATTATTCA
Found at i:61453278 original size:26 final size:27
Alignment explanation
Indices: 61453244--61453295 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
61453234 CGTGTTTATG
*
61453244 TTTCATTATT-TAATTAAATAATTTTA
1 TTTCATTATTATAATAAAATAATTTTA
* *
61453270 TTTCGTTATTATTATAAAATAATTTT
1 TTTCATTATTATAATAAAATAATTTT
61453296 TATATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTCATTATTATAATAAAATAATTTTA
Found at i:61458000 original size:2 final size:2
Alignment explanation
Indices: 61457993--61458087 Score: 160
Period size: 2 Copynumber: 48.5 Consensus size: 2
61457983 NNNNNNNNNN
61457993 TA TA TA TA TA TA T- 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
61458034 TA TA TA T- TA TA -A 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
61458074 TA TA TA TA TCA TA T
1 TA TA TA TA T-A TA T
61458088 TTACTCCTTT
Statistics
Matches: 89, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.03
2 84 0.94
3 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61463443 original size:16 final size:16
Alignment explanation
Indices: 61463422--61463462 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
61463412 TTGACCATTT
61463422 TAAAATATACAT-AAAC
1 TAAAATATA-ATCAAAC
*
61463438 TAAAAT-TAATCAAAT
1 TAAAATATAATCAAAC
61463453 TAAAATATAA
1 TAAAATATAA
61463463 AGATTAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 11 0.50
16 9 0.41
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATATAATCAAAC
Found at i:61465854 original size:33 final size:33
Alignment explanation
Indices: 61465817--61465880 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
61465807 ATTTGTTGTG
*
61465817 TATTAGCTGTAT-ATCACAGCCACGTTGCAAGCC
1 TATTAGCTGTATGAT-ACAGCCACGTCGCAAGCC
*
61465850 TATTAGCTGTGTGATACAGCCACGTCGCAAG
1 TATTAGCTGTATGATACAGCCACGTCGCAAG
61465881 TTTGCTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (33 bp):
TATTAGCTGTATGATACAGCCACGTCGCAAGCC
Found at i:61470901 original size:2 final size:2
Alignment explanation
Indices: 61470894--61470937 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
61470884 TCATTTCTTT
61470894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61470936 TA
1 TA
61470938 CTAATTAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61470952 original size:6 final size:6
Alignment explanation
Indices: 61470943--61470972 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
61470933 ATATACTAAT
61470943 TAACAA TAACAA TAACAA TAACAA TAACAA
1 TAACAA TAACAA TAACAA TAACAA TAACAA
61470973 ATATCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
TAACAA
Found at i:61471130 original size:18 final size:19
Alignment explanation
Indices: 61471109--61471144 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
61471099 ATTATTTATC
61471109 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
61471127 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
61471145 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:61471153 original size:19 final size:18
Alignment explanation
Indices: 61471113--61471155 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
61471103 TTTATCTAAT
*
61471113 AAATATCTTTTAAATAAT
1 AAATATCTTTTAAATAAC
61471131 AAATATCTATTT-AATATAC
1 AAATATCT-TTTAAATA-AC
61471150 AAATAT
1 AAATAT
61471156 AAATATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATCTTTTAAATAAC
Found at i:61471284 original size:22 final size:22
Alignment explanation
Indices: 61471239--61471286 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
61471229 ATATAATAAT
*
61471239 AATAATATTATTATTATTATTA
1 AATAATATTATTAATATTATTA
*
61471261 AATAATATTAATTAATGTTA-TA
1 AATAATATT-ATTAATATTATTA
61471283 AATA
1 AATA
61471287 TCTTTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATAATATTATTAATATTATTA
Found at i:61473437 original size:139 final size:138
Alignment explanation
Indices: 61473264--61473523 Score: 400
Period size: 139 Copynumber: 1.9 Consensus size: 138
61473254 ACCCGGACCC
* * *
61473264 GGGATTTATTTCGATTGATTCATTCAGTTACCTTTAAAAGATGGCA-TCAGATATATATGGGGTT
1 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTC-GACATATATGGGGTT
61473328 CGGAA-ACCAATATCTATACCAA-AAGGGAAACTTTTAATCATTTGGGGCGTATTGAAAAGTGTC
65 -GGAATACCAATATCTATA-CAATAAGGGAAACTTTTAATCATTT-GGGCGTATTGAAAAGTGTC
61473391 GTGTGCTCAGAT
127 GTGTGCTCAGAT
*
61473403 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTT
1 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTG
* * *
61473468 GAATCCCAATATCTATACAATAAGGGAAAGTTTTAATCATTTGGGTGTATTGAAAA
66 GAATACCAATATCTATACAATAAGGGAAACTTTTAATCATTTGGGCGTATTGAAAA
61473524 CTCAGAGAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
138 19 0.17
139 90 0.81
140 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (138 bp):
GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTG
GAATACCAATATCTATACAATAAGGGAAACTTTTAATCATTTGGGCGTATTGAAAAGTGTCGTGT
GCTCAGAT
Found at i:61473690 original size:159 final size:158
Alignment explanation
Indices: 61473395--61473870 Score: 612
Period size: 160 Copynumber: 3.0 Consensus size: 158
61473385 AGTGTCGTGT
* * * * * *
61473395 GCTCAGATGGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATA
1 GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
* *
61473460 TGGGGTTTGAATCCCAATATCTATA-CAATAAGGGAAAGTTTTAATCATTTGGGTGTATTGAAAA
66 TGGGG-TCGAATCCCAATATCTATACCAA-AAGGGAAACTTTTAATCATTTGGGTGTATTGAAAA
* *
61473524 CTCAGAGAATGTGTCGTGGTGCTAAAAATGG
129 -TTAGAGAATGTGTCATGGTGCTAAAAATGG
* ** * * *
61473555 GCTCGGATGGGACTTATTTCGAGTGATTCATTTAGCCACCTTTAAAAGATGACACCCAACAGATT
1 GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
* * *
61473620 TGGGGTCGAATCCCAATATCTGTACCAAAAGGGAAACTTTTAATCATTTGAGTGTACTGAAAATT
66 TGGGGTCGAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAAATT
** * *
61473685 GAGAGAATGTGTCACAGCGCTAAAAATGT
131 -AGAGAATGTGTCATGGTGCTAAAAATGG
* * * * *
61473714 GCTCGAATGGGACTTCTTTCGATTGATTCATCCAACTATCTTTAAAAGATGGCATCCAACATATT
1 GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
* *
61473779 TGGGGTACGAATCCCAATATCTATACCAAAAGGGAAACTTCTAATCATTTGGGTGTATTGAAAGT
66 TGGGGT-CGAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAAAT
*
61473844 CTAGAGACTGTGTCATGGTGCTAAAAA
130 -TAGAGAATGTGTCATGGTGCTAAAAA
61473871 AGTGCTTGGA
Statistics
Matches: 269, Mismatches: 43, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
158 1 0.00
159 132 0.49
160 135 0.50
161 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (158 bp):
GCTCGGATGGGACTTATTTCGATTGATTCATCCAGCCACCTTTAAAAGATGGCATCCAACATATT
TGGGGTCGAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAAATT
AGAGAATGTGTCATGGTGCTAAAAATGG
Found at i:61483024 original size:101 final size:101
Alignment explanation
Indices: 61482906--61483171 Score: 360
Period size: 101 Copynumber: 2.6 Consensus size: 101
61482896 AAAACTTTTT
* *
61482906 TTTTTTTAATTTGATGGTATAATTTTTCCCCAAGTCCCTGTACTC-TTGAAAATTTGAAATTAAT
1 TTTTTTTAATTTGATGGTCTAATTTTTCCCCAAGTCCCTATACTCTTTGAAAATTTGAAATT--T
61482970 T-TTTTTTAAAAGAGAACTTGAAGCCAGTTGCAAAAAC
64 TATTTTTTAAAAGAGAACTTGAAGCCAGTTGCAAAAAC
* *
61483007 TTTTTTTAATTTGATGGTCTAA-TTTTCACCCAAGTCTCTATACTCTTTGAAATTTTGAAATTTT
1 TTTTTTTAATTTGATGGTCTAATTTTTC-CCCAAGTCCCTATACTCTTTGAAAATTTGAAATTTT
* * * *
61483071 ATTTTTTATATGATAACTTGAAGTCAGTTGCAAAAAC
65 ATTTTTTAAAAGAGAACTTGAAGCCAGTTGCAAAAAC
* * *
61483108 TTTTTTTAAATTTAATGATCTAATTTTGT-CCCAAATCCCTATACTCTTTGAAAATTTGAAATTT
1 TTTTTTT-AATTTGATGGTCTAATTTT-TCCCCAAGTCCCTATACTCTTTGAAAATTTGAAATTT
61483172 AATCCTTCTT
Statistics
Matches: 146, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
100 7 0.05
101 75 0.51
102 60 0.41
103 3 0.02
104 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (101 bp):
TTTTTTTAATTTGATGGTCTAATTTTTCCCCAAGTCCCTATACTCTTTGAAAATTTGAAATTTTA
TTTTTTAAAAGAGAACTTGAAGCCAGTTGCAAAAAC
Found at i:61486159 original size:12 final size:12
Alignment explanation
Indices: 61486142--61486166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61486132 AAGACACACA
61486142 TAATCAATAAAT
1 TAATCAATAAAT
61486154 TAATCAATAAAT
1 TAATCAATAAAT
61486166 T
1 T
61486167 TCATCCAAAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATCAATAAAT
Found at i:61500061 original size:29 final size:29
Alignment explanation
Indices: 61500019--61500078 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
61500009 TAAAAGGGAA
61500019 AAAATAATGAAAAATAAAATACCTTAGTT
1 AAAATAATGAAAAATAAAATACCTTAGTT
61500048 AAAATAATGAAAAATAAAATACCTTAGTT
1 AAAATAATGAAAAATAAAATACCTTAGTT
61500077 AA
1 AA
61500079 CTCAAAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAATAATGAAAAATAAAATACCTTAGTT
Found at i:61502632 original size:6 final size:6
Alignment explanation
Indices: 61502621--61502682 Score: 70
Period size: 6 Copynumber: 9.7 Consensus size: 6
61502611 AATAAATCCA
* *
61502621 AAAAAT AAAAAT AAAAAT AAAAAAT AAAAAT AAAAAAT TAATAT GAAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT -AAAAAT AAAAAT -AAAAAT
61502672 AAAAAAT AAAA
1 -AAAAAT AAAA
61502683 TCTAGTTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
6 26 0.54
7 22 0.46
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:61502633 original size:19 final size:19
Alignment explanation
Indices: 61502609--61502656 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
61502599 AAAGCTTGCC
**
61502609 AAAATAAATCCAAAAAATA
1 AAAATAAAAACAAAAAATA
*
61502628 AAAATAAAAATAAAAAATA
1 AAAATAAAAACAAAAAATA
61502647 AAAATAAAAA
1 AAAATAAAAA
61502657 ATTAATATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAATAAAAACAAAAAATA
Found at i:61502637 original size:7 final size:7
Alignment explanation
Indices: 61502620--61502682 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
61502610 AAATAAATCC
61502620 AAAAAAT
1 AAAAAAT
61502627 -AAAAAT
1 AAAAAAT
61502633 -AAAAAT
1 AAAAAAT
61502639 AAAAAAT
1 AAAAAAT
61502646 -AAAAAT
1 AAAAAAT
61502652 AAAAAAT
1 AAAAAAT
* *
61502659 -TAATAT
1 AAAAAAT
*
61502665 GAAAAAT
1 AAAAAAT
61502672 AAAAAAT
1 AAAAAAT
61502679 AAAA
1 AAAA
61502683 TCTAGTTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
6 22 0.46
7 26 0.54
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:61502669 original size:14 final size:13
Alignment explanation
Indices: 61502621--61502682 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
61502611 AATAAATCCA
61502621 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
61502633 AAAAATAAAAAAT
1 AAAAATAAAAAAT
61502646 AAAAATAAAAAAT
1 AAAAATAAAAAAT
* * *
61502659 TAATATGAAAAAT
1 AAAAATAAAAAAT
61502672 AAAAAATAAAA
1 -AAAAATAAAA
61502683 TCTAGTTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
12 6 0.14
13 29 0.69
14 7 0.17
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.18
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:61504865 original size:15 final size:16
Alignment explanation
Indices: 61504827--61504863 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
61504817 GGATATGAAT
*
61504827 ATTTTTAAATAATGTA
1 ATTTTTATATAATGTA
61504843 ATTTTTATATAATGTA
1 ATTTTTATATAATGTA
61504859 ATTTT
1 ATTTT
61504864 ATTTGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
ATTTTTATATAATGTA
Found at i:61505871 original size:17 final size:18
Alignment explanation
Indices: 61505846--61505881 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
61505836 TTCTCTCATG
*
61505846 TTTATTATTTATT-ATTT
1 TTTAATATTTATTAATTT
61505863 TTTAATATTTATTAATTT
1 TTTAATATTTATTAATTT
61505881 T
1 T
61505882 ATATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTAATATTTATTAATTT
Found at i:61509688 original size:240 final size:227
Alignment explanation
Indices: 61509231--61509760 Score: 503
Period size: 240 Copynumber: 2.3 Consensus size: 227
61509221 TTCAAAATCT
* * * * * *
61509231 TATATCTATGAACTAGAAGATC----AAACATCACCAGAACTCCTTCACTATGTATGCACTATGA
1 TATATATATGAACTAGAAGATCAATAAAACATCACTAGCACTTC-TCACTATGTATGAATTATGA
* * *
61509292 ACTTACGATTGTTATATTTTGCTACTAAAATCTACACCTGAAATAAATTACAGTTTCATTTCAAA
65 ACTTACCATTGTTATATTTTACTACTAAAATCTACACCTGAAATAAATTACAGTTTCATTCCAAA
** * *
61509357 TTTTAAACTTTCTCAAATTTCCGTTCAAACTTTCATATGATACTAATCAAGTTAAAAAATTAGCC
130 TTCAAAACTTTCTCAAATTTCCATTCAAACTCTCATATGATACTAATCAAGTT-AAAAATTAGCC
* * *
61509422 AAAAAACTTCAAAATATTATATATTATGTGTGTGTGTGTATATA
194 AAAAAAC-ACAAAATA-TATATATTA--------TATATATATA
*
61509466 TATATATATGAACTAGAAGATCAATAAAACATCACTAGCACTTCATCACTATGCATGAATTATGA
1 TATATATATGAACTAGAAGATCAATAAAACATCACTAGCACTTC-TCACTATGTATGAATTATGA
*
61509531 ACTTAACCATTGTTATATTTTACTACTAAAATCTACACCTGAACCTCATATAAATTACAGTTTTA
65 ACTT-ACCATTGTTATATTTTACTACTAAAATCTACACCTG-A----A-ATAAATTACAGTTTCA
*
61509596 TTCCAAGTTCAAAAC-TTCTCAAATAGGTTCCATTCAAACTCTCATATGATA-TCAATCAAGTT-
123 TTCCAAATTCAAAACTTTCTCAAAT---TTCCATTCAAACTCTCATATGATACT-AATCAAGTTA
* **
61509658 AAATTTAG-CAAAAGAA-ACAGCA-A-A-ATATTATATATATATA
184 AAAATTAGCCAAAA-AACACAAAATATATATATTATATATATATA
* * *
61509698 TATATATATGAACTAGTAGATCAATAAAAACATCACTATCAC-TC-CACTAAGTATGAATTATGA
1 TATATATATGAACTAGAAGATCAAT-AAAACATCACTAGCACTTCTCACTATGTATGAATTATGA
61509761 CTGCTAAAAT
Statistics
Matches: 251, Mismatches: 27, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
230 17 0.07
232 34 0.14
233 15 0.06
235 21 0.08
239 36 0.14
240 40 0.16
241 2 0.01
243 1 0.00
244 3 0.01
245 15 0.06
246 35 0.14
247 1 0.00
248 31 0.12
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (227 bp):
TATATATATGAACTAGAAGATCAATAAAACATCACTAGCACTTCTCACTATGTATGAATTATGAA
CTTACCATTGTTATATTTTACTACTAAAATCTACACCTGAAATAAATTACAGTTTCATTCCAAAT
TCAAAACTTTCTCAAATTTCCATTCAAACTCTCATATGATACTAATCAAGTTAAAAATTAGCCAA
AAAACACAAAATATATATATTATATATATATA
Found at i:61511239 original size:18 final size:18
Alignment explanation
Indices: 61511216--61511250 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61511206 TCTTTTATTG
*
61511216 TTTTTTTAAGAATGGTTT
1 TTTTTTTAAAAATGGTTT
61511234 TTTTTTTAAAAATGGTT
1 TTTTTTTAAAAATGGTT
61511251 CAATCGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TTTTTTTAAAAATGGTTT
Found at i:61511363 original size:9 final size:9
Alignment explanation
Indices: 61511351--61511423 Score: 65
Period size: 10 Copynumber: 7.7 Consensus size: 9
61511341 TTTATGATTT
61511351 TTTTTATAA
1 TTTTTATAA
61511360 TTTTTATAA
1 TTTTTATAA
*
61511369 GTTTATATCAA
1 -TTTTTAT-AA
* *
61511380 TTTTAATAT
1 TTTTTATAA
61511389 TTTTTCATAA
1 TTTTT-ATAA
*
61511399 TTTTTACAA
1 TTTTTATAA
*
61511408 TTTTTTATTA
1 -TTTTTATAA
61511418 TTTTTA
1 TTTTTA
61511424 AAGTATTATG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 23 0.45
10 26 0.51
11 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:61511492 original size:18 final size:18
Alignment explanation
Indices: 61511461--61511507 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
61511451 TGTAAATACC
*
61511461 TTTTATTAATTTTATAATTT
1 TTTTA-TAA-TTTATAATAT
*
61511481 TTTTATAATTTATTATAT
1 TTTTATAATTTATAATAT
61511499 TTTTATAAT
1 TTTTATAAT
61511508 ATTTGTATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 3 0.12
20 5 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTATAATAT
Found at i:61511606 original size:20 final size:20
Alignment explanation
Indices: 61511581--61511623 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
61511571 TTTTTTATAA
61511581 TTTATTT-TGAATTATTTTAT
1 TTTATTTAT-AATTATTTTAT
61511601 TTTATTTATAATTATTTTAT
1 TTTATTTATAATTATTTTAT
61511621 TTT
1 TTT
61511624 TAATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTTATAATTATTTTAT
Found at i:61511633 original size:15 final size:15
Alignment explanation
Indices: 61511574--61511632 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
61511564 TTTAATATTT
61511574 TTTATAATTTATTTTGA
1 TTTATAA-TTATTTT-A
* *
61511591 ATTAT-TTTATTTTA
1 TTTATAATTATTTTA
61511605 TTTATAATTATTTTA
1 TTTATAATTATTTTA
*
61511620 TTTTTAA-TATTTT
1 TTTATAATTATTTT
61511633 TTATGAGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.31
15 21 0.58
17 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATAATTATTTTA
Found at i:61511870 original size:5 final size:5
Alignment explanation
Indices: 61511853--61511888 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
61511843 CATACAAACC
61511853 TATTA TA-TA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
61511889 ACTTGTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:61513581 original size:26 final size:26
Alignment explanation
Indices: 61513487--61513581 Score: 84
Period size: 26 Copynumber: 3.5 Consensus size: 26
61513477 TTGTTATTAA
*
61513487 AATTTAATAAGATTATTATTAAAAAT
1 AATTTAATAAAATTATTATTAAAAAT
**
61513513 AATTTAATAAAAATAAATATT-TTAACCAT
1 AATTTAAT-AAAAT---TATTATTAAAAAT
* * * *
61513542 ATTTTAACATAATTATTATTAAATAT
1 AATTTAATAAAATTATTATTAAAAAT
61513568 AATTTAATAAAATT
1 AATTTAATAAAATT
61513582 CTTAATATAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
25 4 0.08
26 25 0.47
27 4 0.08
28 4 0.08
29 12 0.23
30 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (26 bp):
AATTTAATAAAATTATTATTAAAAAT
Found at i:61515912 original size:37 final size:38
Alignment explanation
Indices: 61515859--61515934 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
61515849 AAAACTACAA
*
61515859 GAGATTCTCAACTGTCAG-TTTTTAATAAATGCCAAAT
1 GAGATTCTCAAATGTCAGTTTTTTAATAAATGCCAAAT
61515896 GAGATTCTCAAATGTCAGTTTTTTAATAAATGCCAAAT
1 GAGATTCTCAAATGTCAGTTTTTTAATAAATGCCAAAT
61515934 G
1 G
61515935 CTAATGACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 17 0.46
38 20 0.54
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (38 bp):
GAGATTCTCAAATGTCAGTTTTTTAATAAATGCCAAAT
Found at i:61524899 original size:21 final size:20
Alignment explanation
Indices: 61524867--61524906 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
61524857 GTAAAATGTG
61524867 TTAAATATTAAATAATATAT
1 TTAAATATTAAATAATATAT
*
61524887 TTAATTATGTAAATAATATA
1 TTAAATAT-TAAATAATATA
61524907 ATGAAATCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TTAAATATTAAATAATATAT
Done.