Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1246727 original size:13 final size:13
Alignment explanation
Indices: 1246715--1246770 Score: 67
Period size: 13 Copynumber: 4.0 Consensus size: 13
1246705 AATAAGAAAT
1246715 AATAATAATAAATA
1 AATAATAAT-AATA
1246729 AATTACAATAATAATA
1 AA-T--AATAATAATA
*
1246745 AATGATAATAATA
1 AATAATAATAATA
1246758 AATAATAATAATA
1 AATAATAATAATA
1246771 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 21 0.57
14 2 0.05
15 2 0.05
16 6 0.16
17 6 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:1246728 original size:10 final size:10
Alignment explanation
Indices: 1246697--1246768 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 10
1246687 ACAAAAACAA
1246697 AATAATTAAAT
1 AATAA-TAAAT
*
1246708 AAGAA-ATAAT
1 AATAATA-AAT
1246718 AATAATAAAT
1 AATAATAAAT
*
1246728 AA-ATTACAAT
1 AATAATA-AAT
1246738 AATAATAAATGAT
1 AATAAT-AA--AT
1246751 AATAATAAAT
1 AATAATAAAT
1246761 AATAATAA
1 AATAATAA
1246769 TATATATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
9 4 0.08
10 27 0.54
11 8 0.16
12 3 0.06
13 8 0.16
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (10 bp):
AATAATAAAT
Found at i:1246742 original size:23 final size:21
Alignment explanation
Indices: 1246697--1246772 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 21
1246687 ACAAAAACAA
*
1246697 AATAAT-TAAATAAGAAATAAT
1 AATAATAT-AATAATAAATAAT
1246718 AATAATA-AATAAATTACAATAAT
1 AATAATATAAT-AA-TA-AATAAT
1246741 AATAAATGATAATAATAAATAAT
1 AAT-AAT-ATAATAATAAATAAT
1246764 AATAATATA
1 AATAATATA
1246773 TATATATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
20 3 0.06
21 11 0.23
22 4 0.09
23 18 0.38
24 5 0.11
25 3 0.06
26 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (21 bp):
AATAATATAATAATAAATAAT
Found at i:1246744 original size:16 final size:16
Alignment explanation
Indices: 1246718--1246758 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1246708 AAGAAATAAT
*
1246718 AATAATAAATAAATTAC
1 AATAAT-AATAAATGAC
*
1246735 AATAATAATAAATGAT
1 AATAATAATAAATGAC
1246751 AATAATAA
1 AATAATAA
1246759 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AATAATAATAAATGAC
Found at i:1246940 original size:11 final size:11
Alignment explanation
Indices: 1246924--1246948 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1246914 TATAATATAT
1246924 AAATGTTTTCA
1 AAATGTTTTCA
1246935 AAATGTTTTCA
1 AAATGTTTTCA
1246946 AAA
1 AAA
1246949 CTATATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1246949 original size:38 final size:37
Alignment explanation
Indices: 1246902--1247033 Score: 141
Period size: 36 Copynumber: 3.6 Consensus size: 37
1246892 AAAATATTTT
*
1246902 TTTTTAAAACTATATAATATATAAATGTTTTCAAAATG-
1 TTTTCAAAACTATAT-ATATATAAA-GTTTTCAAAATGC
* *
1246940 TTTTCAAAACTATAT-CATATAAA-TTTTCAAAAATGT
1 TTTTCAAAACTATATATATATAAAGTTTTC-AAAATGC
*
1246976 TTTTCAAAACTATATATAT-TATACGTTTTCAAAATGC
1 TTTTCAAAACTATATATATATA-AAGTTTTCAAAATGC
1247013 TTTT-AAATA-TATATATATATA
1 TTTTCAAA-ACTATATATATATA
1247034 TATATATATA
Statistics
Matches: 82, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
34 5 0.06
35 6 0.07
36 36 0.44
37 16 0.20
38 19 0.23
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTCAAAACTATATATATATAAAGTTTTCAAAATGC
Found at i:1247026 original size:2 final size:2
Alignment explanation
Indices: 1247019--1247092 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1247009 ATGCTTTTAA
1247019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1247061 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
1247093 TTTCAAAATG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1247165 original size:36 final size:36
Alignment explanation
Indices: 1247081--1247167 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 36
1247071 ATATATATAT
* ** *
1247081 ATATATATATATTTTCAAAATGTTTTCAAAGACTAT
1 ATATATATATATTTTCAAAATGTTTTCAAAAAAAAC
1247117 ATATTATATATATTTT-AAAATGTTTTCGAAAAAAAAAC
1 ATA-TATATATATTTTCAAAATGTTTTC--AAAAAAAAC
1247155 ATATATTATATAT
1 ATATA-TATATAT
1247168 ATATATATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
36 14 0.33
37 14 0.33
38 15 0.35
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (36 bp):
ATATATATATATTTTCAAAATGTTTTCAAAAAAAAC
Found at i:1247490 original size:20 final size:20
Alignment explanation
Indices: 1247442--1247500 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1247432 AATAGTTTCT
** *
1247442 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1247462 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1247482 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1247501 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1247788 original size:22 final size:22
Alignment explanation
Indices: 1247761--1247804 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1247751 GATGGAGATA
1247761 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1247783 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1247805 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1248078 original size:61 final size:61
Alignment explanation
Indices: 1247972--1248109 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
1247962 CGCTTTGAAA
* * * * *
1247972 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1248033 ATCTCGTTGCGATTTTGTATTATCACATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1248094 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1248110 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCACATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1248081 original size:20 final size:20
Alignment explanation
Indices: 1247972--1248106 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
1247962 CGCTTTGAAA
*
1247972 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1247993 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1248013 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1248033 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* *
1248054 ATCACATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1248074 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1248094 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1248107 TTTCCCAATT
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1248125 original size:61 final size:61
Alignment explanation
Indices: 1247972--1248127 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
1247962 CGCTTTGAAA
* ** * * * *
1247972 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * * *
1248033 ATCTCGTTGCGATTTTGTATTATCACATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1248094 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
1248128 TTACTTATTC
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
61 75 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1248217 original size:21 final size:21
Alignment explanation
Indices: 1248177--1248217 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1248167 ACTGTAGACC
**
1248177 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1248198 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1248218 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1248547 original size:60 final size:59
Alignment explanation
Indices: 1248482--1248613 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 59
1248472 TCATGTGATA
** * * * *
1248482 ATTTTGTAACTTTTAATGCTTGGGGGACTCAACAAAGCAACATCCTATAGTCGAAGGACC
1 ATTTTGTAACTTTTAATAATCGAGAGACTCAACAAAGCAACACCCTATAGTCG-AGGACC
* *
1248542 ATTTTGTAACTTTTAATAATCGAGAGACTCAACAAAGCATCACCCTATAGTCGGGGACC
1 ATTTTGTAACTTTTAATAATCGAGAGACTCAACAAAGCAACACCCTATAGTCGAGGACC
1248601 A-TTTGTATACTTT
1 ATTTTGTA-ACTTT
1248614 ACCCTTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 6 0.10
59 11 0.17
60 46 0.73
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAATCGAGAGACTCAACAAAGCAACACCCTATAGTCGAGGACC
Found at i:1249823 original size:20 final size:20
Alignment explanation
Indices: 1249800--1249851 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1249790 TCACAATTGG
1249800 ATAATTTTTAAAAAAATTAT
1 ATAATTTTTAAAAAAATTAT
*
1249820 ATAAAATTTT-AAAAAATTAT
1 AT-AATTTTTAAAAAAATTAT
*
1249840 ATATTTTTTAAA
1 ATAATTTTTAAA
1249852 CTAAAAACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 16 0.59
21 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTTTTAAAAAAATTAT
Found at i:1254155 original size:39 final size:39
Alignment explanation
Indices: 1254101--1254179 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 39
1254091 CTGCACGGAA
1254101 CACATGTTGCACTCGAA-CCTCCCAATACCGGTCAAGCAT
1 CACATGTTGCACTCGAATCC-CCCAATACCGGTCAAGCAT
1254140 CACATGTTGCACTCGAATCCCCCAATACCGGTCAAGCAT
1 CACATGTTGCACTCGAATCCCCCAATACCGGTCAAGCAT
1254179 C
1 C
1254180 TTCCAAATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 37 0.95
40 2 0.05
ACGTcount: A:0.28, C:0.37, G:0.15, T:0.20
Consensus pattern (39 bp):
CACATGTTGCACTCGAATCCCCCAATACCGGTCAAGCAT
Found at i:1254937 original size:16 final size:16
Alignment explanation
Indices: 1254916--1254950 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1254906 ATAATATTAA
1254916 AATTATAAGTGTTTAT
1 AATTATAAGTGTTTAT
1254932 AATTATAAGTGTTTAT
1 AATTATAAGTGTTTAT
1254948 AAT
1 AAT
1254951 GAAATTCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
AATTATAAGTGTTTAT
Found at i:1256162 original size:60 final size:60
Alignment explanation
Indices: 1256038--1256170 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
1256028 AAATTACAGT
* * **** * *
1256038 AAAG-TACACAAATAGTCTCTCGACTATAGGGTGTTGCTTTGTTGAGTCTTTTGATTATTG
1 AAAGTTACA-AAATAGTCTCTCGACTATAGGGCGTTGCTTTGCTGAGTCCACCGACTATTA
*
1256098 AAAGTTACAAAATCGTC-CTCTGACTATAGGGCGTTGCTTTGCTGAGTCCACCGACTATTA
1 AAAGTTACAAAATAGTCTCTC-GACTATAGGGCGTTGCTTTGCTGAGTCCACCGACTATTA
1256158 AAAGTTACAAAAT
1 AAAGTTACAAAAT
1256171 GATCACCTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 55 0.89
61 4 0.06
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (60 bp):
AAAGTTACAAAATAGTCTCTCGACTATAGGGCGTTGCTTTGCTGAGTCCACCGACTATTA
Found at i:1258796 original size:31 final size:30
Alignment explanation
Indices: 1258761--1258824 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1258751 GGTGATAGAG
*
1258761 TTTAGGAGGGTCAACTTAAAATTTTAAAAAA
1 TTTA-GAGGGTCAAATTAAAATTTTAAAAAA
* * * *
1258792 TTTAGAGGTTGAAATTAAATTTTTTAAAAA
1 TTTAGAGGGTCAAATTAAAATTTTAAAAAA
1258822 TTT
1 TTT
1258825 TGAAGGGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTAGAGGGTCAAATTAAAATTTTAAAAAA
Found at i:1258938 original size:30 final size:30
Alignment explanation
Indices: 1258876--1258947 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1258866 GTATAACTAA
* * *
1258876 AATTTTTAAAATTTTGAGAGGTTTAATGAG
1 AATTTTAAAAATTTGGAGAGGTTTAATAAG
*
1258906 AATTTTAAAAATTATGGAG-GGTTTATTAAG
1 AATTTTAAAAATT-TGGAGAGGTTTAATAAG
*
1258936 AATATTCAAAAA
1 AAT-TTTAAAAA
1258948 AAATTAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 24 0.69
31 11 0.31
ACGTcount: A:0.43, C:0.01, G:0.17, T:0.39
Consensus pattern (30 bp):
AATTTTAAAAATTTGGAGAGGTTTAATAAG
Found at i:1259764 original size:23 final size:24
Alignment explanation
Indices: 1259714--1259804 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 24
1259704 AAGTATTGTA
*
1259714 TTTTAATTAAATTAT-ATTAATAT
1 TTTTAATTAATTTATAATTAATAT
1259737 TTTTAATTAATTTATAATT-ATAT
1 TTTTAATTAATTTATAATTAATAT
* * *
1259760 ATTT-AGTACTTTATAATTTAATAT
1 TTTTAATTAATTTATAA-TTAATAT
1259784 TTTATAAATTAATTTAATAAT
1 TTT-T-AATTAATTT-ATAAT
1259805 ACTTATCGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
22 10 0.19
23 23 0.43
24 9 0.17
25 1 0.02
27 7 0.13
28 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (24 bp):
TTTTAATTAATTTATAATTAATAT
Found at i:1259787 original size:15 final size:15
Alignment explanation
Indices: 1259754--1259796 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1259744 TAATTTATAA
*
1259754 TTATATATTTAGTACT
1 TTATA-ATTTAATACT
*
1259770 TTATAATTTAATATT
1 TTATAATTTAATACT
*
1259785 TTATAAATTAAT
1 TTATAATTTAAT
1259797 TTAATAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATAATTTAATACT
Found at i:1262902 original size:21 final size:21
Alignment explanation
Indices: 1262871--1262950 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
1262861 GATTTTGATT
*
1262871 TTGATTTTTTGAAGCTATATAC
1 TTGA-TTTTTGGAGCTATATAC
* *
1262893 TTAAATTTTGGAGCTATATAC
1 TTGATTTTTGGAGCTATATAC
1262914 TTGATTTTTGGAGCTATATAC
1 TTGATTTTTGGAGCTATATAC
1262935 TTGATTTTTGGAGCTA
1 TTGATTTTTGGAGCTA
1262951 GTTCCTACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 50 0.94
22 3 0.06
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.47
Consensus pattern (21 bp):
TTGATTTTTGGAGCTATATAC
Found at i:1263321 original size:13 final size:13
Alignment explanation
Indices: 1263303--1263329 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1263293 TATTCGGCCA
1263303 TAGGGAAGAAAAT
1 TAGGGAAGAAAAT
1263316 TAGGGAAGAAAAT
1 TAGGGAAGAAAAT
1263329 T
1 T
1263330 GGGGGGAAAT
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:0.52, C:0.00, G:0.30, T:0.19
Consensus pattern (13 bp):
TAGGGAAGAAAAT
Found at i:1265142 original size:3 final size:3
Alignment explanation
Indices: 1265134--1265169 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1265124 TTGTCCCGTT
1265134 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1265170 AATAATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1265193 original size:13 final size:13
Alignment explanation
Indices: 1265177--1265209 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1265167 TTAAATAATA
*
1265177 ATTACTAATAAAT
1 ATTACAAATAAAT
1265190 ATTACAAATAAAT
1 ATTACAAATAAAT
1265203 ATTACAA
1 ATTACAA
1265210 GTGGCCCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTACAAATAAAT
Found at i:1272501 original size:19 final size:20
Alignment explanation
Indices: 1272462--1272513 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1272452 GAAACCCCTT
1272462 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
1272483 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1272502 TGAAGATACATG
1 TGAAAATACATG
1272514 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1274777 original size:53 final size:54
Alignment explanation
Indices: 1274613--1274914 Score: 367
Period size: 54 Copynumber: 5.6 Consensus size: 54
1274603 GAACACCAGC
* ** * *
1274613 GTGCAATTCACGGAATTCATCATATGTTGATGAACAACTTTTTCGACACTAATT
1 GTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGT
* * * *
1274667 GTGCAATTCACGGAATTCAACATATGCTGATGAACAACCATTTCGGAACTAAGT
1 GTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGT
* *
1274721 GTGCAATTCACATAATTCATCATATGTTGAT-AACAACCGTTTCGGCACTAAGT
1 GTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGT
** * *
1274774 GTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTCGGCACTAAGT
1 GTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGT
* * * *
1274828 GTGCAATTCACATAATTCATC-TATATTGATGAACAACCATTTTGGCACTAGGT
1 GTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGT
** * *
1274881 GTGCAACCCAC-GAAATTCATAATATGTTTATGAA
1 GTGCAATTCACAG-AATTCATCATATGTTGATGAA
1274915 TGACCGTATA
Statistics
Matches: 214, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
53 91 0.43
54 123 0.57
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
GTGCAATTCACAGAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGT
Found at i:1274805 original size:107 final size:108
Alignment explanation
Indices: 1274613--1274914 Score: 401
Period size: 107 Copynumber: 2.8 Consensus size: 108
1274603 GAACACCAGC
** ** * *
1274613 GTGCAATTCACGGAATTCATCATATGTTGATGAACAACTTTTTCGACACTAATTGTGCAATTCAC
1 GTGCAATTCACATAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGTGTGCAATTCAC
* *
1274678 GGAATTCAACATATGCTGATGAACAACCATTTCGGAACTAAGT
66 GGAATTCATCATATGTTGATGAACAACCATTTCGGAACTAAGT
* *
1274721 GTGCAATTCACATAATTCATCATATGTTGAT-AACAACCGTTTCGGCACTAAGTGTGCAATTCAT
1 GTGCAATTCACATAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGTGTGCAATTCAC
* * *
1274785 GGAATTCATCATATGTTGATGAACAATCGTTTCGGCACTAAGT
66 GGAATTCATCATATGTTGATGAACAACCATTTCGGAACTAAGT
* * * **
1274828 GTGCAATTCACATAATTCATC-TATATTGATGAACAACCATTTTGGCACTAGGTGTGCAACCCAC
1 GTGCAATTCACATAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGTGTGCAATTCAC
* * *
1274892 GAAATTCATAATATGTTTATGAA
66 GGAATTCATCATATGTTGATGAA
1274915 TGACCGTATA
Statistics
Matches: 171, Mismatches: 22, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
106 8 0.05
107 134 0.78
108 29 0.17
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (108 bp):
GTGCAATTCACATAATTCATCATATGTTGATGAACAACCATTTCGGCACTAAGTGTGCAATTCAC
GGAATTCATCATATGTTGATGAACAACCATTTCGGAACTAAGT
Found at i:1274931 original size:161 final size:160
Alignment explanation
Indices: 1274613--1274939 Score: 417
Period size: 161 Copynumber: 2.0 Consensus size: 160
1274603 GAACACCAGC
* *
1274613 GTGCAATTCACGGAATTCATCATATGTTGATGAACAACTTTTTCGACACTAATTGTGCAATTCAC
1 GTGCAATTCACGGAATTCATCATATGTTGATGAACAACTGTTTCGACACTAAGTGTGCAATTCAC
* ** *
1274678 GGAATTCAACATATGCTGATGAACAACCATTTCGGAACTAAGTGTGCAATTCACATAATTCATCA
66 AGAATTCAACATAT-CTGATGAACAACCATTTCGGAACTAAGTGTGCAACCCACATAATTCATAA
* *
1274743 TATGTTGATAACAACCGTTTCGGCACTAAGT
130 TATGTTGATAACAACCGTATAGGCACTAAGT
* *
1274774 GTGCAATTCATGGAATTCATCATATGTTGATGAACAA-TCGTTTCGGCACTAAGTGTGCAATTCA
1 GTGCAATTCACGGAATTCATCATATGTTGATGAACAACT-GTTTCGACACTAAGTGTGCAATTCA
* * * * *
1274838 CATAATTCATCTATAT-TGATGAACAACCATTTTGGCACTAGGTGTGCAACCCACGA-AATTCAT
65 CAGAATTCAAC-ATATCTGATGAACAACCATTTCGGAACTAAGTGTGCAACCCAC-ATAATTCAT
* ** *
1274901 AATATGTTTATGAATGACCGTATAGGCACTACGT
128 AATATGTTGAT-AACAACCGTATAGGCACTAAGT
1274935 GTGCA
1 GTGCA
1274940 TCGTAAAGAA
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
160 50 0.35
161 89 0.62
162 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (160 bp):
GTGCAATTCACGGAATTCATCATATGTTGATGAACAACTGTTTCGACACTAAGTGTGCAATTCAC
AGAATTCAACATATCTGATGAACAACCATTTCGGAACTAAGTGTGCAACCCACATAATTCATAAT
ATGTTGATAACAACCGTATAGGCACTAAGT
Found at i:1282310 original size:54 final size:54
Alignment explanation
Indices: 1282228--1282512 Score: 354
Period size: 54 Copynumber: 5.3 Consensus size: 54
1282218 TTACCAAATG
* * * *
1282228 GGCACCAAGTGTGCAATTCACGAAATTCATCATATGTTTATGAACAACCATTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
1282282 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
1282336 GGCACTAAGTGTACAATTAACGGAATTCATCATATGTTGATGAAAAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
** * * *
1282390 GTTACTAAGTGTGCAATTCACGGAATTCATTATATATTGATGAACAACTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
* ** ** * * ** * *
1282444 GGCACTAGGTGCACAACCCACGGAATTCATAATATGTTTATGAATGACCGTATA
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
*
1282498 GGCACTACGTGTGCA
1 GGCACTAAGTGTGCA
1282513 TCGCAACAAA
Statistics
Matches: 198, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 198 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:1284807 original size:39 final size:38
Alignment explanation
Indices: 1284724--1284808 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
1284714 ATGTTGAGAT
* *
1284724 ATTTTGAAGGCTCACATCAGCATGAAAACTTTTGGGGC
1 ATTTTGAAGGCTCACATCAGCAAGAAAACTGTTGGGGC
* *
1284762 ATTTTGAAGGCTCATATTAGCAAGAAGTAA-TGTTGGGGC
1 ATTTTGAAGGCTCACATCAGCAAGAA--AACTGTTGGGGC
1284801 ATTTTGAA
1 ATTTTGAA
1284809 CGTTCGTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 23 0.56
39 16 0.39
40 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.32
Consensus pattern (38 bp):
ATTTTGAAGGCTCACATCAGCAAGAAAACTGTTGGGGC
Found at i:1286491 original size:250 final size:250
Alignment explanation
Indices: 1286050--1287279 Score: 1973
Period size: 250 Copynumber: 4.9 Consensus size: 250
1286040 TAAGTTGTTT
1286050 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* *
1286115 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTTATAAATCCTTCA
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
*
1286180 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGT
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGC
* *
1286245 AAGATGATAGGTCTTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
196 AAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
*
1286300 TGAAAATGAGAAAGTGATTTTCAAATTTTCTCATTTAATCTTTTC-GAAAAATGAAATTGTTGAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTG-AAAATGAAATTGTTGAA
* * *
1286364 AAGTAAGAAAATGAATTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGAAAATCCTTC
65 AAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTC
* * *
1286429 AGGTCATCAGTATGTCTTTCGAGTATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG
130 AGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAG
* * ** *
1286494 CAAGATGATAAATACTTCGGGTCATCTATAAAACCTTCAGGTAGGACGTTCTCACA
195 CAAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
* * * *
1286550 TGAACATGAGAAAGTAATTTTCAAAGTTTTTCATTTAATCTTTTCTAAAAATGAAATTGTTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* *
1286615 AGTAAGAAAGTGATTTCCAAAGTTTCTTA-CTAGTAAATTATTTCCAAAATTTGTAAATCCTTCG
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
* * * * *
1286679 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCAGATCATATGTAATTCTTTCAAGC
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGC
*
1286744 AAGATGATAAGTCCTTCGGGTCATTCGTAAAACCTTCAGGTAGGATGTTCTCACA
196 AAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
* *
1286799 TGAAAATGAGAAAGTGGTTTTCAAAGTTTCTCATTTAATATTTTCTGAAAATGAAATTGTTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* *
1286864 AGTAAGAAAGCGATTTCCAAAGTTTTTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTC-
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
* *
1286928 GAGTCATTAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTC-GGTTCATCTGTAAGTCTTTCGA
131 G-GTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGG-TCATCTGTAAGTCTTTCGA
*
1286992 GCAAGATGATAAGTCCTTCTGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
194 GCAAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
* *
1287049 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAATATGAAATTATTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* **
1287114 AGTAAAAAAGAAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
* * * * *
1287179 GGTTATCAGTAAGTTTTTCGAGCATGATGCTTAAATCATTCATGTCAACTGTAAGTCTTTCGAGC
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGC
* *
1287244 AAGATGATAAGTCCTTTGGGTCATCCGTAAGACCTT
196 AAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTT
1287280 TGGGAAAGAT
Statistics
Matches: 896, Mismatches: 77, Indels: 14
0.91 0.08 0.01
Matches are distributed among these distances:
249 227 0.25
250 667 0.74
251 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (250 bp):
TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGC
AAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
Found at i:1286518 original size:41 final size:42
Alignment explanation
Indices: 1286420--1286520 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
1286410 CAAAATTTGA
* * * * * *
1286420 AAATCCTTCAGGTCATCAGTATGTCTTTCGAGTATGATGCTT
1 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGCAT
1286462 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG-AT
1 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGCAT
*
1286503 AAATACTTCGGGTCATCT
1 AAATCCTTCGGGTCATCT
1286521 ATAAAACCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (42 bp):
AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGCAT
Found at i:1286715 original size:42 final size:41
Alignment explanation
Indices: 1286668--1286767 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
1286658 CCAAAATTTG
* * *
1286668 TAAATCCTTCGGGTCATCA-GTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCAT-ATGTAAGTCTTTCAAGCAAGATG-A
* * * *
1286710 TAAATCATTCAGATCATATGTAATTCTTTCAAGCAAGATGA
1 TAAATCCTTCGGGTCATATGTAAGTCTTTCAAGCAAGATGA
*
1286751 TAAGTCCTTCGGGTCAT
1 TAAATCCTTCGGGTCAT
1286768 TCGTAAAACC
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 14 0.30
42 32 0.70
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATATGTAAGTCTTTCAAGCAAGATGA
Found at i:1286965 original size:42 final size:42
Alignment explanation
Indices: 1286918--1286999 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1286908 CCAAAATTTG
* *
1286918 TAAATCCTTCGAG-TCAT-TAGTAAGTCTTTTGAGCATGATGCT
1 TAAATCCTTCG-GTTCATCT-GTAAGTCTTTCGAGCAAGATGCT
1286960 TAAATCCTTCGGTTCATCTGTAAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGGTTCATCTGTAAGTCTTTCGAGCAAGATG
1287000 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 1 0.03
42 34 0.94
43 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGGTTCATCTGTAAGTCTTTCGAGCAAGATGCT
Found at i:1286994 original size:499 final size:499
Alignment explanation
Indices: 1286050--1287279 Score: 1982
Period size: 499 Copynumber: 2.5 Consensus size: 499
1286040 TAAGTTGTTT
1286050 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* *
1286115 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCTAAAATTTATAAATCCTTCA
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
* * *
1286180 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGT
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCA-GTCATATGTAAGTCTTTCGAGC
* *
1286245 AAGATGATAGGTCTTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACATGAAAATGAG
195 AAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACATGAAAATGAG
* *
1286310 AAAGTGATTTTCAAATTTTCTCATTTAATCTTTTCGAAAAATGAAATTGTTGAAAAGTAAGAAAA
260 AAAGTGATTTTCAAAGTTTCTCATTTAATATTTTCGAAAAATGAAATTGTTGAAAAGTAAGAAAA
*
1286375 TGAATTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGAAAATCCTTCAGGTCATCAGT
325 CGAATTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGAAAATCCTTCAGGTCATCAGT
* *
1286440 ATGTCTTTCGAGTATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAA
390 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAA
*
1286505 ATACTTCGGGTCATCTATAAAACCTTCAGGTAGGACGTTCTCACA
455 ATACTTCGGGTCATCCATAAAACCTTCAGGTAGGACGTTCTCACA
* * * *
1286550 TGAACATGAGAAAGTAATTTTCAAAGTTTTTCATTTAATCTTTTCTAAAAATGAAATTGTTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* *
1286615 AGTAAGAAAGTGATTTCCAAAGTTTCTTA-CTAGTAAATTATTTCCAAAATTTGTAAATCCTTCG
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
* *
1286679 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCAGATCATATGTAATTCTTTCAAGC
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCAG-TCATATGTAAGTCTTTCGAGC
*
1286744 AAGATGATAAGTCCTTCGGGTCATTCGTAAAACCTTCAGGTAGGATGTTCTCACATGAAAATGAG
195 AAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACATGAAAATGAG
*
1286809 AAAGTGGTTTTCAAAGTTTCTCATTTAATATTTTCTG-AAAATGAAATTGTTGAAAAGTAAGAAA
260 AAAGTGATTTTCAAAGTTTCTCATTTAATATTTTC-GAAAAATGAAATTGTTGAAAAGTAAGAAA
* * * * *
1286873 GCGATTTCCAAAGTTTTTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTC-GAGTCATTA
324 ACGAATTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGAAAATCCTTCAG-GTCATCA
* *
1286937 GTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGTTCATCTGTAAGTCTTTCGAGCAAGATGAT
388 GTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGAT
* * * * *
1287002 AAGTCCTTCTGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACA
453 AAATACTTCGGGTCATCCATAAAACCTTCAGGTAGGACGTTCTCACA
* *
1287049 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAATATGAAATTATTGAAA
1 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
* **
1287114 AGTAAAAAAGAAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
66 AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
* *
1287179 GGTTATCAGTAAGTTTTTCGAGCATGATGCTTAAATCATTCATGTCA-ACTGTAAGTCTTTCGAG
131 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCA-GTCATA-TGTAAGTCTTTCGAG
* *
1287243 CAAGATGATAAGTCCTTTGGGTCATCCGTAAGACCTT
194 CAAGATGATAAGTCCTTCGGGTCATCCGTAAAACCTT
1287280 TGGGAAAGAT
Statistics
Matches: 671, Mismatches: 53, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
498 2 0.00
499 454 0.68
500 214 0.32
501 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (499 bp):
TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAA
AGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAATCCTTCA
GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCAGTCATATGTAAGTCTTTCGAGCA
AGATGATAAGTCCTTCGGGTCATCCGTAAAACCTTCAGGTAGGATGTTCTCACATGAAAATGAGA
AAGTGATTTTCAAAGTTTCTCATTTAATATTTTCGAAAAATGAAATTGTTGAAAAGTAAGAAAAC
GAATTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGAAAATCCTTCAGGTCATCAGTA
AGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAA
TACTTCGGGTCATCCATAAAACCTTCAGGTAGGACGTTCTCACA
Found at i:1287215 original size:42 final size:42
Alignment explanation
Indices: 1287168--1287249 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
1287158 CCAAAATTTG
* * * * *
1287168 TAAATCCTTCAGGTTATCAGTAAGTTTTTCGAGCATGATGCT
1 TAAATCATTCAGGTCAACAGTAAGTCTTTCGAGCAAGATGCT
* *
1287210 TAAATCATTCATGTCAACTGTAAGTCTTTCGAGCAAGATG
1 TAAATCATTCAGGTCAACAGTAAGTCTTTCGAGCAAGATG
1287250 ATAAGTCCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (42 bp):
TAAATCATTCAGGTCAACAGTAAGTCTTTCGAGCAAGATGCT
Found at i:1287436 original size:3 final size:3
Alignment explanation
Indices: 1287428--1287457 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1287418 TTGTCCCGTT
*
1287428 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1287458 ATAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1287694 original size:29 final size:29
Alignment explanation
Indices: 1287661--1287717 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1287651 CAAAATTTTT
**
1287661 TCTAGTGACTAAAATATAAGTTTTGAAAG
1 TCTAGTGACTAAAATATAAACTTTGAAAG
* *
1287690 TCTAGTGGCTAAAGTATAAACTTTGAAA
1 TCTAGTGACTAAAATATAAACTTTGAAA
1287718 AGTTTAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (29 bp):
TCTAGTGACTAAAATATAAACTTTGAAAG
Found at i:1295541 original size:27 final size:27
Alignment explanation
Indices: 1295511--1295563 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1295501 TTGAGTAAAT
1295511 TATTGAATGATGGAAAATTATTAGTAC
1 TATTGAATGATGGAAAATTATTAGTAC
*
1295538 TATTGAATGCTGGAAAATTATTAGTA
1 TATTGAATGATGGAAAATTATTAGTA
1295564 TTCTGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (27 bp):
TATTGAATGATGGAAAATTATTAGTAC
Found at i:1296435 original size:36 final size:36
Alignment explanation
Indices: 1296387--1296485 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
1296377 GAGTATTATT
* *
1296387 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTAACATATC
1296423 AGCTTTGGTACATTCGTGTATCAATGTTAACATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTAACATATC
* *
1296459 AGGTTTGGTACATTTGTGTATCAATGT
1 AGCTTTGGTACATTCGTGTATCAATGT
1296486 CCAGCACATT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (36 bp):
AGCTTTGGTACATTCGTGTATCAATGTTAACATATC
Found at i:1303036 original size:28 final size:28
Alignment explanation
Indices: 1302996--1303053 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1302986 ACCTAGGATG
1302996 CACATCTGATTTTGATAGGTGAGTTTTC
1 CACATCTGATTTTGATAGGTGAGTTTTC
1303024 CACATCTGATTTTGATAGGTGAGTTTTC
1 CACATCTGATTTTGATAGGTGAGTTTTC
1303052 CA
1 CA
1303054 TCAGAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (28 bp):
CACATCTGATTTTGATAGGTGAGTTTTC
Found at i:1303937 original size:56 final size:56
Alignment explanation
Indices: 1303871--1303982 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
1303861 ACACCTTACA
* *
1303871 GACTCAATTGTTTAAAATTAAATTCTCTAAAAATAATAATATTTTGTTTTACTATT
1 GACTCAATTGTTTAAAATTAAATTCTCTAAAAACAATAACATTTTGTTTTACTATT
* *
1303927 GACTCAATTGTTTAAACTTGAATTCTCTAAAAACAATAACATTTTGTTTTACTATT
1 GACTCAATTGTTTAAAATTAAATTCTCTAAAAACAATAACATTTTGTTTTACTATT
1303983 CGGATTGATG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (56 bp):
GACTCAATTGTTTAAAATTAAATTCTCTAAAAACAATAACATTTTGTTTTACTATT
Found at i:1305229 original size:89 final size:89
Alignment explanation
Indices: 1305078--1305256 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
1305068 ATTCGTAGTG
*
1305078 TTTCGTTGTGTTGCGATTATAATTTAATGCTATGATGTCGTATCAATCAAAGGTAATTATGGATC
1 TTTCGTTGTGTTGCGATCATAATTTAATGCTATGATGTCGTATCAATCAAAGGTAATTATGGATC
*
1305143 TCAATGAATGATAGACTTCATGAA
66 TCAAGGAATGATAGACTTCATGAA
* *
1305167 TTTCGTTGTGTTGCGATCATAATTTAATTCTATGATGTCGTATGAATCAAAGGTAATTATGGATC
1 TTTCGTTGTGTTGCGATCATAATTTAATGCTATGATGTCGTATCAATCAAAGGTAATTATGGATC
1305232 TCAAGGAATGATAGACTTCATGAA
66 TCAAGGAATGATAGACTTCATGAA
1305256 T
1 T
1305257 GAGAGCAAGT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (89 bp):
TTTCGTTGTGTTGCGATCATAATTTAATGCTATGATGTCGTATCAATCAAAGGTAATTATGGATC
TCAAGGAATGATAGACTTCATGAA
Found at i:1307187 original size:2 final size:2
Alignment explanation
Indices: 1307180--1307212 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1307170 TAAACAAATT
1307180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1307213 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1307986 original size:122 final size:122
Alignment explanation
Indices: 1307769--1308016 Score: 451
Period size: 122 Copynumber: 2.0 Consensus size: 122
1307759 AGACCATGTC
** *
1307769 GAGGACAATCTCTCAAGTTCGAAACATGCTTCATTTGCACGACTCGAAGGCTTGCAATCATAACA
1 GAGGACAATCTCTCAAGTTCGAAACATGCTTCATTTGCAAAACTCGAAAGCTTGCAATCATAACA
*
1307834 GCAACGGCGTCCCAAGTTTCTCACTACACCCATTATCCAATTAACAAAAGCAACCAA
66 GCAACGGCGTCCCAAGTTTCTCACTACACCCATTATCCAATGAACAAAAGCAACCAA
1307891 GAGGACAATCTCTCAAGTTCGAAACATGCTTCATTTGCAAAACTCGAAAGCTTGCAATCATAACA
1 GAGGACAATCTCTCAAGTTCGAAACATGCTTCATTTGCAAAACTCGAAAGCTTGCAATCATAACA
*
1307956 GCAACGGCGTCCCAAGTTTCTCACTACACCCATTATCCAATGAACAAAGGCAACCAA
66 GCAACGGCGTCCCAAGTTTCTCACTACACCCATTATCCAATGAACAAAAGCAACCAA
1308013 GAGG
1 GAGG
1308017 CACAGAAAAC
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 121 1.00
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (122 bp):
GAGGACAATCTCTCAAGTTCGAAACATGCTTCATTTGCAAAACTCGAAAGCTTGCAATCATAACA
GCAACGGCGTCCCAAGTTTCTCACTACACCCATTATCCAATGAACAAAAGCAACCAA
Found at i:1310176 original size:13 final size:12
Alignment explanation
Indices: 1310145--1310179 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1310135 TTATATCCCC
1310145 ATTTTAAAAATT
1 ATTTTAAAAATT
1310157 ATTTTAAAATATT
1 ATTTTAAAA-ATT
*
1310170 TTTTTAAAAA
1 ATTTTAAAAA
1310180 ATTAATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTTAAAAATT
Found at i:1310517 original size:23 final size:23
Alignment explanation
Indices: 1310473--1310518 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1310463 TATATATTTG
*
1310473 AAAATTATTTTATTAAAGTTTTT
1 AAAATTATTTTATCAAAGTTTTT
1310496 AAAATTATTTT-TACAAA-TTTTT
1 AAAATTATTTTAT-CAAAGTTTTT
1310518 A
1 A
1310519 TCAATGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
AAAATTATTTTATCAAAGTTTTT
Found at i:1319235 original size:35 final size:35
Alignment explanation
Indices: 1319191--1319260 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1319181 TAAAAAATTT
*
1319191 AAAATTTTAAGTTGGCCGT-AGACTATCACTAAGTA
1 AAAATTTTAAGTT-GCCCTAAGACTATCACTAAGTA
1319226 AAAATTTTAAGTTGCCCTAAGACTATCACTAAGTA
1 AAAATTTTAAGTTGCCCTAAGACTATCACTAAGTA
1319261 TAGCGGTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (35 bp):
AAAATTTTAAGTTGCCCTAAGACTATCACTAAGTA
Found at i:1325014 original size:31 final size:31
Alignment explanation
Indices: 1324941--1325027 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
1324931 GTTATATATG
* *
1324941 TCCAAAATGATGACGTGACAAATGTCATGTG
1 TCCAAAGTGATGACGTGACAAATGTCATGTA
* * *
1324972 TCCAAATTGATGACGTGGA-ACATGTTATGTA
1 TCCAAAGTGATGACGT-GACAAATGTCATGTA
* * *
1325003 TCTAAAGTGATGACATGACACATGT
1 TCCAAAGTGATGACGTGACAAATGT
1325028 AACAAATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.04
31 43 0.91
32 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (31 bp):
TCCAAAGTGATGACGTGACAAATGTCATGTA
Found at i:1333811 original size:80 final size:81
Alignment explanation
Indices: 1333661--1333853 Score: 194
Period size: 80 Copynumber: 2.4 Consensus size: 81
1333651 GGATTCATTT
* * * *
1333661 ATAGTGGCGTTTTTTCAACAAACGCCGCAATAGAATAGTACTTTAGCGGCGTTTTTATACAAACA
1 ATAGTGGCGTTTTCTCAACAAACGCCGCAATAGAATAGTACTTTAACGGCGTTTGTATAAAAACA
1333726 ACGCAATAGGTCATCC
66 ACGCAATAGGTCATCC
* * *
1333742 ATAGTGGCG-TTTCTCAATAAACGCCGTGAA-A-AAGTAGTACTTTAACTGCGTTTGTATAAAAA
1 ATAGTGGCGTTTTCTCAACAAACGCCG-CAATAGAA-TAGTACTTTAACGGCGTTTGTATAAAAA
*** * *
1333804 TGCCGCAATAGGGTTTATCT
64 CAACGCAATA-GG-TCATCC
* * *
1333824 ATAGTGGCATTTTTTTAACAAACGCCGCAA
1 ATAGTGGCGTTTTCTCAACAAACGCCGCAA
1333854 AAGGGTTGTA
Statistics
Matches: 90, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
79 2 0.02
80 47 0.52
81 13 0.14
82 14 0.16
83 14 0.16
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (81 bp):
ATAGTGGCGTTTTCTCAACAAACGCCGCAATAGAATAGTACTTTAACGGCGTTTGTATAAAAACA
ACGCAATAGGTCATCC
Found at i:1333927 original size:41 final size:40
Alignment explanation
Indices: 1333835--1333927 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
1333825 TAGTGGCATT
* *
1333835 TTTTTAACAAACGCCGCAAAAGGGTTGTACTTTAGCGGTG
1 TTTTTAACAAACGCCGCAAAAGAGTAGTACTTTAGCGGTG
*
1333875 TTTTTCAACAAACGCCGCAACAA-AGTAGTACTTTAGTGGTG
1 TTTTT-AACAAACGCCGCAA-AAGAGTAGTACTTTAGCGGTG
1333916 TTTTTATACAAA
1 TTTTTA-ACAAA
1333928 AGTCACAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
40 6 0.13
41 39 0.83
42 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (40 bp):
TTTTTAACAAACGCCGCAAAAGAGTAGTACTTTAGCGGTG
Found at i:1343198 original size:43 final size:43
Alignment explanation
Indices: 1343137--1343231 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
1343127 ATTGTATGCA
* * *
1343137 CTAGGTATTGATATTGGTCACCCAGGTACCAATACCTCTCTTG
1 CTAGGTATCGATACTGGTCACCCAAGTACCAATACCTCTCTTG
1343180 CTAGGTATCGATACTGGTCACCCAAGTACCAATACCTCTCTTG
1 CTAGGTATCGATACTGGTCACCCAAGTACCAATACCTCTCTTG
1343223 CTAGGTATC
1 CTAGGTATC
1343232 AATATCGTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (43 bp):
CTAGGTATCGATACTGGTCACCCAAGTACCAATACCTCTCTTG
Found at i:1343234 original size:22 final size:22
Alignment explanation
Indices: 1343160--1343235 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
1343150 TTGGTCACCC
1343160 AGGTACCAATACCTCTCTTGCT
1 AGGTACCAATACCTCTCTTGCT
* * * ** *
1343182 AGGTATCGATA-CTGGTC-ACCC
1 AGGTACCAATACCT-CTCTTGCT
*
1343203 AAGTACCAATACCTCTCTTGCT
1 AGGTACCAATACCTCTCTTGCT
*
1343225 AGGTATCAATA
1 AGGTACCAATA
1343236 TCGTTCTTAA
Statistics
Matches: 36, Mismatches: 15, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
21 13 0.36
22 23 0.64
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (22 bp):
AGGTACCAATACCTCTCTTGCT
Found at i:1357052 original size:2 final size:2
Alignment explanation
Indices: 1357045--1357096 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1357035 TCTTAACAGC
1357045 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
1357087 TA TA TA TA TA
1 TA TA TA TA TA
1357097 CACACACACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1357837 original size:22 final size:22
Alignment explanation
Indices: 1357809--1357865 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1357799 TTATACAGGT
1357809 AGTATCGATACCCCTATGAAGG
1 AGTATCGATACCCCTATGAAGG
1357831 AGTATCGATACCCCTATGAAGG
1 AGTATCGATACCCCTATGAAGG
*
1357853 AGTACCGATACCC
1 AGTATCGATACCC
1357866 ATACGTTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (22 bp):
AGTATCGATACCCCTATGAAGG
Found at i:1360533 original size:43 final size:43
Alignment explanation
Indices: 1360448--1360611 Score: 179
Period size: 42 Copynumber: 3.8 Consensus size: 43
1360438 TAATTAGCGA
* * * * * *
1360448 CGTTTGTATCTAAAAACGACGCTATAGATC-TAAACTTTTGCGG
1 CGTTTGT-TCCAAAAACGTCGCTATAAATCTTGACCTTCTGCGG
* * * *
1360491 CGTTTGTTCCAAAAACGCCCCTATATATCTCGACCTTCTGCGG
1 CGTTTGTTCCAAAAACGTCGCTATAAATCTTGACCTTCTGCGG
* *
1360534 CGTTTGTTCCAAAAACGTCGCTATAAAT-TTGACTTTTTGCGG
1 CGTTTGTTCCAAAAACGTCGCTATAAATCTTGACCTTCTGCGG
* *
1360576 CGTTTATTCCAAAAACGTCGCTATAGATCTTGACCT
1 CGTTTGTTCCAAAAACGTCGCTATAAATCTTGACCT
1360612 ATTGTGGCGT
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 55 0.54
43 47 0.46
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (43 bp):
CGTTTGTTCCAAAAACGTCGCTATAAATCTTGACCTTCTGCGG
Found at i:1360623 original size:43 final size:43
Alignment explanation
Indices: 1360448--1360623 Score: 203
Period size: 43 Copynumber: 4.1 Consensus size: 43
1360438 TAATTAGCGA
* * * *
1360448 CGTTTGTATCTAAAAACGACGCTATAGATC-TAAACTTTTGCGG
1 CGTTTGT-TCCAAAAACGTCGCTATAGATCTTGACCTTTTGCGG
* * * * *
1360491 CGTTTGTTCCAAAAACGCCCCTATATATCTCGACCTTCTGCGG
1 CGTTTGTTCCAAAAACGTCGCTATAGATCTTGACCTTTTGCGG
* *
1360534 CGTTTGTTCCAAAAACGTCGCTATAAAT-TTGACTTTTTGCGG
1 CGTTTGTTCCAAAAACGTCGCTATAGATCTTGACCTTTTGCGG
* * *
1360576 CGTTTATTCCAAAAACGTCGCTATAGATCTTGACCTATTGTGG
1 CGTTTGTTCCAAAAACGTCGCTATAGATCTTGACCTTTTGCGG
1360619 CGTTT
1 CGTTT
1360624 TTGGTTCTCA
Statistics
Matches: 112, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 55 0.49
43 57 0.51
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (43 bp):
CGTTTGTTCCAAAAACGTCGCTATAGATCTTGACCTTTTGCGG
Found at i:1360623 original size:85 final size:86
Alignment explanation
Indices: 1360448--1360611 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 86
1360438 TAATTAGCGA
* * *
1360448 CGTTTGTATCTAAAAACGACGCTATAGATCTAAACTTTTGCGGCGTTTGTTCCAAAAACGCCCCT
1 CGTTTGTATCCAAAAACGACGCTATAAATCTAAACTTTTGCGGCGTTTATTCCAAAAACGCCCCT
*
1360513 ATATATCTCGACCTTCTGCGG
66 ATAGATCTCGACCTTCTGCGG
* ** * *
1360534 CGTTTGT-TCCAAAAACGTCGCTATAAAT-TTGACTTTTTGCGGCGTTTATTCCAAAAACGTCGC
1 CGTTTGTATCCAAAAACGACGCTATAAATCTAAAC-TTTTGCGGCGTTTATTCCAAAAACGCCCC
*
1360597 TATAGATCTTGACCT
65 TATAGATCTCGACCT
1360612 ATTGTGGCGT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 3 0.04
85 57 0.85
86 7 0.10
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (86 bp):
CGTTTGTATCCAAAAACGACGCTATAAATCTAAACTTTTGCGGCGTTTATTCCAAAAACGCCCCT
ATAGATCTCGACCTTCTGCGG
Found at i:1361440 original size:21 final size:19
Alignment explanation
Indices: 1361411--1361459 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1361401 GTATACATTT
*
1361411 TTTTAAAATAAAATACATAAA
1 TTTTGAAATAAAAT-CA-AAA
* *
1361432 TTTTGAAATAAACTGAAAA
1 TTTTGAAATAAAATCAAAA
1361451 TTTTGAAAT
1 TTTTGAAAT
1361460 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.48
20 1 0.04
21 12 0.48
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (19 bp):
TTTTGAAATAAAATCAAAA
Found at i:1371918 original size:11 final size:9
Alignment explanation
Indices: 1371888--1371912 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1371878 TATAGTATGT
1371888 ATTTTTTTA
1 ATTTTTTTA
1371897 ATTTTTTTA
1 ATTTTTTTA
1371906 ATTTTTT
1 ATTTTTT
1371913 GATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:1374909 original size:16 final size:15
Alignment explanation
Indices: 1374890--1374925 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1374880 AATAGAAATA
1374890 AAGATCAAGAGAAGAG
1 AAGATCAAGAGAAG-G
*
1374906 AAGATCCAGAGAAGG
1 AAGATCAAGAGAAGG
1374921 AAGAT
1 AAGAT
1374926 AGATTTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.53, C:0.08, G:0.31, T:0.08
Consensus pattern (15 bp):
AAGATCAAGAGAAGG
Found at i:1375167 original size:19 final size:19
Alignment explanation
Indices: 1375143--1375180 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1375133 TTCTCACCAA
1375143 CATAATGTAATTTGCAAAC
1 CATAATGTAATTTGCAAAC
*
1375162 CATAATGTGATTTGCAAAC
1 CATAATGTAATTTGCAAAC
1375181 AAACAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (19 bp):
CATAATGTAATTTGCAAAC
Found at i:1379161 original size:30 final size:28
Alignment explanation
Indices: 1379127--1379192 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
1379117 TTTTGTGTTG
* *
1379127 TTAATATTAATATGATATT-TTAGTATCATT
1 TTAATATAAATATGA-ATTATTAATAT-A-T
*
1379157 TTAATAAAAATATGAATTATTAATATAT
1 TTAATATAAATATGAATTATTAATATAT
1379185 TTAATATA
1 TTAATATA
1379193 TATTTATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 8 0.26
29 4 0.13
30 19 0.61
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
TTAATATAAATATGAATTATTAATATAT
Found at i:1379200 original size:23 final size:24
Alignment explanation
Indices: 1379173--1379218 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1379163 AAAATATGAA
1379173 TTATTAATATATTTAAT-ATATAT
1 TTATTAATATATTTAATAATATAT
*
1379196 TTATTAATATTTTTAATAATATA
1 TTATTAATATATTTAATAATATA
1379219 ATATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTAATATATTTAATAATATAT
Found at i:1379210 original size:12 final size:12
Alignment explanation
Indices: 1379177--1379234 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
1379167 TATGAATTAT
1379177 TAATATATTTAA
1 TAATATATTTAA
*
1379189 T-ATATATTTAT
1 TAATATATTTAA
*
1379200 TAATATTTTTAA
1 TAATATATTTAA
*
1379212 TAATATAATATAA
1 TAATAT-ATTTAA
1379225 TAATAATATT
1 TAAT-ATATT
1379235 ATTACAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 10 0.27
12 15 0.41
13 10 0.27
14 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATATATTTAA
Found at i:1379880 original size:26 final size:25
Alignment explanation
Indices: 1379835--1379884 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
1379825 TTATCCAAAA
1379835 AATAATAATATACTCAATTATATTAT
1 AATAATAATATACT-AATTATATTAT
1379861 AATAATATATGATACT-ATTATATT
1 AATAATA-AT-ATACTAATTATATT
1379885 CTTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.68
27 2 0.09
28 5 0.23
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (25 bp):
AATAATAATATACTAATTATATTAT
Found at i:1382226 original size:12 final size:12
Alignment explanation
Indices: 1382209--1382233 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1382199 AGAAAATTAA
1382209 AAAATTTAAATT
1 AAAATTTAAATT
1382221 AAAATTTAAATT
1 AAAATTTAAATT
1382233 A
1 A
1382234 CCCGATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:1383785 original size:36 final size:37
Alignment explanation
Indices: 1383610--1383922 Score: 259
Period size: 37 Copynumber: 8.8 Consensus size: 37
1383600 ATTTTTTCTT
*
1383610 AAACTATATA-T-TAT-A-TTTT-AAAAA-AGTTTTCA
1 AAACTATATATTATATAATTTTTCAAAAATA-TTTTAA
* * *
1383642 AAACTATATATTATAT-AGTTTTC-AAAATGTTTT-T
1 AAACTATATATTATATAATTTTTCAAAAATATTTTAA
* * *
1383676 AAA--A-ATATTATATAAGTTTTCAAAAAATGTTTTTTTA
1 AAACTATATATTATATAATTTTTC-AAAAA--TATTTTAA
* *
1383713 AAACTATATATTATATAATTTTTCAAAAATGTTTTTA
1 AAACTATATATTATATAATTTTTCAAAAATATTTTAA
1383750 AAACTATATATTATATAATTTTTCAAAAATATTTTAA
1 AAACTATATATTATATAATTTTTCAAAAATATTTTAA
* * *
1383787 AAACTATATACTATATAAGTTTTC-AAAATGTTTTAA
1 AAACTATATATTATATAATTTTTCAAAAATATTTTAA
* * *
1383823 AAACTATACACTATATAAATGTTTTC-AAAATGTTTTAA
1 AAACTATATATTATAT-AAT-TTTTCAAAAATATTTTAA
*
1383861 AAACTCTATA-T-TAT-A-TTTT-AAAAATATTTTCAA
1 AAACTATATATTATATAATTTTTCAAAAATATTTT-AA
* *
1383894 AAACTATATAATATATAAATTTTTGAAAA
1 AAACTATATATTATAT-AATTTTTCAAAA
1383923 TCGTTTTCTG
Statistics
Matches: 240, Mismatches: 17, Indels: 41
0.81 0.06 0.14
Matches are distributed among these distances:
31 9 0.04
32 31 0.13
33 12 0.05
34 13 0.05
35 15 0.06
36 34 0.14
37 71 0.30
38 29 0.12
39 10 0.04
40 16 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AAACTATATATTATATAATTTTTCAAAAATATTTTAA
Found at i:1383896 original size:33 final size:32
Alignment explanation
Indices: 1383832--1383909 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
1383822 AAAACTATAC
* * *
1383832 ACTATATAA-ATGTTTTCAAAATGTTTTAAAA
1 ACTATATAATATATTTTAAAAATATTTTAAAA
* *
1383863 ACTCTATATTATATTTTAAAAATATTTTCAAAA
1 ACTATATAATATATTTTAAAAATATTTT-AAAA
1383896 ACTATATAATATAT
1 ACTATATAATATAT
1383910 AAATTTTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 7 0.18
32 15 0.39
33 16 0.42
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (32 bp):
ACTATATAATATATTTTAAAAATATTTTAAAA
Found at i:1384690 original size:84 final size:84
Alignment explanation
Indices: 1384602--1385256 Score: 713
Period size: 84 Copynumber: 7.9 Consensus size: 84
1384592 GTTTGCCTCT
* * * * * *
1384602 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGACATATATCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
* *
1384667 CTACAAATGATGTGTCTTG
66 CTGCAAATGATGTGCCTTG
* * * *
1384686 GAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTCGGCATATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
* *
1384751 CTACAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
1384770 GAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-TCACATATAACCCTTCTAG-CATTGAGTTA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTCGAC-TTAAGTTA
* *
1384833 TGCTGTAAATGATGTGCCCTCG
64 TGCTGCAAATGATGTG-CCTTG
* ** * * * * *
1384855 AAGCTGAATGTAATCGAACTCGAGGGT-TTCTGG-T---AGATAGCCCTTCTTGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGTTGACAGATAACCCTTCTCGACTTAAGTTAT
* *
1384915 GCTGCAAATTATGTGTCTTG
65 GCTGCAAATGATGTGCCTTG
*
1384935 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
* *
1385000 CTGCAGATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * *
1385019 GAGCTGAGCGTAGTCAAACTCGAAGGTCTTATGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGTTGACAGATAACCCTTCTCGACTTAAGTTAT
** *
1385083 GCTATAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* * * * * * * * *
1385104 AAGCTGAGGGTAATCGAACTTGAGGGTC--T--TTGACATATAGCCCTTCTCGACTTAAGCTATT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
1385165 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
*
1385184 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
1385249 CTGCAAAT
66 CTGCAAAT
1385257 AGTTTCTTTT
Statistics
Matches: 470, Mismatches: 84, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
80 55 0.12
81 71 0.15
82 3 0.01
83 3 0.01
84 279 0.59
85 59 0.13
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:1384999 original size:249 final size:249
Alignment explanation
Indices: 1384603--1385256 Score: 1024
Period size: 249 Copynumber: 2.6 Consensus size: 249
1384593 TTTGCCTCTG
* * *
1384603 AGCTG-AGTGTAATCGAACTCGAAGGTCTTCGGTTGACATATATCCCTTCTCGACTTAAGCTATG
1 AGCTGAAG-GTAATCGAACTCGAGGGTC-T---TTGACAGATAGCCCTTCTCGACTTAAGCTATG
* * * *
1384667 CTACAAATGATGTGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTCGGCATATAACC
61 CTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
*
1384732 CTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGT
126 CTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGT
* * *
1384797 CTTTTGGTCACATATAACCCTTCTAGCATTGAGTTATGCTGTAAATGATGTGCCCTCGA
191 CTTATGGTCACAGATAACCCTTCTAGCATTGAGTTATGCTATAAATGATGTGCCCTCGA
* ** *
1384856 AGCTGAATGTAATCGAACTCGAGGGT-TTCTGGTAGATAGCCCTTCTTGACTTAAGCTATGCTGC
1 AGCTGAAGGTAATCGAACTCGAGGGTCTT-TGACAGATAGCCCTTCTCGACTTAAGCTATGCTGC
*
1384920 AAATTATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
65 AAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
*
1384985 TCGACTTAAGTTATGCTGCAGATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTA
130 TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTA
* *
1385050 TGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGA
195 TGGTCACAGATAACCCTTCTAGCATTGAGTTATGCTATAAATGATGTGCCCTCGA
* * * *
1385105 AGCTGAGGGTAATCGAACTTGAGGGTCTTTGACATATAGCCCTTCTCGACTTAAGCTATTCTGCA
1 AGCTGAAGGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
*
1385170 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
66 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1385235 CGACTTAAGTTATGCTGCAAAT
131 CGACTTAAGTTATGCTGCAAAT
1385257 AGTTTCTTTT
Statistics
Matches: 368, Mismatches: 30, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
248 1 0.00
249 341 0.93
250 2 0.01
251 1 0.00
253 22 0.06
254 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
AGCTGAAGGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
CGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTAT
GGTCACAGATAACCCTTCTAGCATTGAGTTATGCTATAAATGATGTGCCCTCGA
Found at i:1385155 original size:165 final size:165
Alignment explanation
Indices: 1384595--1385256 Score: 710
Period size: 165 Copynumber: 4.0 Consensus size: 165
1384585 AAATTTGGTT
* * *
1384595 TGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGACATATATCCCTTCTCGACTTA
1 TGCCTCGGAGCTGAGCGTAATCGAACTCGAAGGTCTT--GTTGACATATAACCCTTCTCGACTTA
* * * *
1384660 AGCTATGCTACAAATGATGTGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTCGGCA
64 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-GACA
* *
1384725 TATAACCCTTCTCGACTTAAGTTATGCTACAAATGATA
128 GATAACCCTTCTCGACTTAAGTTATGCTACAAATGATG
* * * *
1384763 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTT-TTGGTCACATATAACCCTTCTAG-CAT
1 TGCCTCGGAGCTGAGCGTAATCGAACTCGAAGGTCTTGTT-G--ACATATAACCCTTCTCGAC-T
* * * * * ** * *
1384826 TGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAATGTAATCGAACTCGAGGGT-TTCTGGT-
62 TAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGTG
* * * * *
1384889 --AGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATTATG
125 ACAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATG
* * * * *
1384928 TGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTCGGAGCTGAGCGTAATCGAACTCGAAGGTC-TT-GTTGACATATAACCCTTCTCGACTTA
* * * *
1384993 AGTTATGCTGCAGATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTATGGTGACA
64 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGTGACA
* * * *
1385058 GATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
128 GATAACCCTTCTCGACTTAAGTTATGCTACAAATGATG
* * * * *
1385096 TGCCCTCGAAGCTGAGGGTAATCGAACTTGAGGGTC-T-TTGACATATAGCCCTTCTCGACTTAA
1 TG-CCTCGGAGCTGAGCGTAATCGAACTCGAAGGTCTTGTTGACATATAACCCTTCTCGACTTAA
* *
1385159 GCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
65 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAG
*
1385224 ATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
129 ATAACCCTTCTCGACTTAAGTTATGCTACAAAT
1385257 AGTTTCTTTT
Statistics
Matches: 406, Mismatches: 72, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
164 28 0.07
165 213 0.52
166 4 0.01
167 3 0.01
168 104 0.26
169 54 0.13
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (165 bp):
TGCCTCGGAGCTGAGCGTAATCGAACTCGAAGGTCTTGTTGACATATAACCCTTCTCGACTTAAG
CTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
AACCCTTCTCGACTTAAGTTATGCTACAAATGATG
Found at i:1386574 original size:95 final size:94
Alignment explanation
Indices: 1386411--1386598 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 94
1386401 ATATGTAAAT
* * * *
1386411 ACCTTTATTAGGTTAGTTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTACCTTAGAAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTACCTTAGAAGG
*
1386476 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTATATA-TATAATC
** * *
1386506 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTTGGGGCGTTTAACCAATT-GCTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTACCT-TAGAAG
*
1386570 GACAACTCAAGTTTTATTATATATATAAT
65 GACAACTCAAGCTTTATTATATATATAAT
1386599 AGTATAATAT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 8 0.10
95 74 0.90
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (94 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTACCTTAGAAGG
ACAACTCAAGCTTTATTATATATATAATC
Found at i:1389975 original size:15 final size:14
Alignment explanation
Indices: 1389945--1389971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1389935 AAAAAACATA
1389945 AAAAAGAAAATAAT
1 AAAAAGAAAATAAT
1389959 AAAAAGAAAATAA
1 AAAAAGAAAATAA
1389972 ATAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (14 bp):
AAAAAGAAAATAAT
Found at i:1390128 original size:36 final size:35
Alignment explanation
Indices: 1390042--1390293 Score: 177
Period size: 36 Copynumber: 6.9 Consensus size: 35
1390032 ATATATTATA
1390042 TTTT-AAAAAA-GTTTTCAAAACTATATATTATAT-AG
1 TTTTCAAAAAATGTTTT-AAAA--ATATATTATATAAG
*
1390077 TTTTC--AAAATGTTTTTAAAA-ATATTATATAAG
1 TTTTCAAAAAATGTTTTAAAAATATATTATATAAG
1390109 TTTTCAAAAAAATGTTTTTTAAAAACTATATATTATATAA-
1 TTTTC-AAAAAATG--TTTT-AAAA--ATATATTATATAAG
** *
1390149 TTTTTTAAAAATGTTTTAAAACTATATATTATATAAT
1 TTTTCAAAAAATGTTTTAAAA--ATATATTATATAAG
1390186 TTTTCAAAAAA-GTTTTAAAAACTATATACTATATAAG
1 TTTTCAAAAAATGTTTTAAAAA-TATAT--TATATAAG
*
1390223 TTTTC--AAAATGTTTTAAAAACTATACAATATATAAATG
1 TTTTCAAAAAATGTTTTAAAAA-TAT--ATTATAT-AA-G
1390261 TTTTC--AAAATGTTTTCAAAACTATATATTATAT
1 TTTTCAAAAAATGTTTT-AAAA--ATATATTATAT
1390294 TTTAAAAATA
Statistics
Matches: 184, Mismatches: 9, Indels: 45
0.77 0.04 0.19
Matches are distributed among these distances:
31 9 0.05
32 8 0.04
34 8 0.04
35 24 0.13
36 47 0.26
37 31 0.17
38 26 0.14
39 11 0.06
40 8 0.04
41 12 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTTCAAAAAATGTTTTAAAAATATATTATATAAG
Found at i:1390158 original size:109 final size:108
Alignment explanation
Indices: 1390032--1390293 Score: 327
Period size: 109 Copynumber: 2.4 Consensus size: 108
1390022 TTCTTAAACT
* * * *
1390032 ATATATTATATTTTAAAAAAGTTTTCAAAACTATATATTATAT-AGTTTTC-AAAATGTTTTTAA
1 ATATATAATATTTTAAAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAAAAGTTTTAAA
*
1390095 AA-ATAT-TATATAAGTTTTCAAAAAAATGTTTTTTAAAAACTATATA
66 AACATATATATATAAGTTTTC---AAAATG--TTTTAAAAACTATACA
* * *
1390141 TTATATAATTTTTTAAAAATGTTTT-AAAACTATATATTATATAATTTTTCAAAAAAGTTTTAAA
1 ATATATAATATTTTAAAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAAAAGTTTTAAA
1390205 AACTATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATACA
66 AAC-ATATA-TATATAAGTTTTCAAAATGTTTTAAAAACTATACA
* *
1390250 ATATATAAATGTTTTCAAAATGTTTTCAAAACTATATATTATAT
1 ATATAT-AATATTTTAAAAATGTTTTCAAAACTATATATTATAT
1390294 TTTAAAAATA
Statistics
Matches: 134, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
108 17 0.13
109 47 0.35
110 30 0.22
111 23 0.17
112 4 0.03
114 13 0.10
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (108 bp):
ATATATAATATTTTAAAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAAAAGTTTTAAA
AACATATATATATAAGTTTTCAAAATGTTTTAAAAACTATACA
Found at i:1390272 original size:11 final size:11
Alignment explanation
Indices: 1390256--1390280 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1390246 TACAATATAT
1390256 AAATGTTTTCA
1 AAATGTTTTCA
1390267 AAATGTTTTCA
1 AAATGTTTTCA
1390278 AAA
1 AAA
1390281 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1390318 original size:33 final size:32
Alignment explanation
Indices: 1390251--1390326 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
1390241 AACTATACAA
* * *
1390251 TATATAA-ATGTTTTCAAAATGTTTTCAAAAC
1 TATATAATATATTTTAAAAATATTTTCAAAAC
*
1390282 TATATATTATATTTTAAAAATATTTTCAAAAGC
1 TATATAATATATTTTAAAAATATTTTCAAAA-C
1390315 TATATAATATAT
1 TATATAATATAT
1390327 AAATTTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 6 0.16
32 20 0.53
33 12 0.32
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATAATATATTTTAAAAATATTTTCAAAAC
Found at i:1390387 original size:2 final size:2
Alignment explanation
Indices: 1390382--1390423 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1390372 CAAAAAACAC
* * *
1390382 TA TA TA TA TA TA TA TA CA CA TA TA TA TA TA TA TG 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
1390424 ATAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1390736 original size:28 final size:29
Alignment explanation
Indices: 1390696--1390755 Score: 70
Period size: 32 Copynumber: 2.0 Consensus size: 29
1390686 TCAATTAAAT
*
1390696 TATATAGGGAAAA-TA-AAAAATAAGAAA
1 TATATAGGAAAAATTATAAAAATAAGAAA
1390723 TATATTAGGAAAAATCTTATAAAAATAAGAAA
1 TATA-TAGGAAAAA--TTATAAAAATAAGAAA
1390755 T
1 T
1390756 TTTTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.15
28 8 0.30
31 2 0.07
32 13 0.48
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.25
Consensus pattern (29 bp):
TATATAGGAAAAATTATAAAAATAAGAAA
Found at i:1390981 original size:4 final size:4
Alignment explanation
Indices: 1390972--1391000 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1390962 CGAAAACATA
1390972 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1391001 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1391004 original size:3 final size:3
Alignment explanation
Indices: 1390996--1391044 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1390986 ATTTATTTAT
1390996 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1391044 T
1 T
1391045 ATTGTTTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1398237 original size:65 final size:65
Alignment explanation
Indices: 1398116--1398293 Score: 205
Period size: 65 Copynumber: 2.7 Consensus size: 65
1398106 TTTGAAATTG
* * * ** *
1398116 TTTCCCTTGAAACACAAATCTTTGAGTCTTTTTCTCTTAAAACAAAATTTTATCTCTCTTGAGAC
1 TTTCTCTTGAAACAC-CATCTGTGAGTCAGTTTCCCTTAAAAC-AAATTTTATCTCTCTTGAGAC
1398181 AA
64 AA
* *
1398183 TTTCTCTTGAAACACCATCTGTGAGAT-AGTTTCCCTTAAAACAAATTTTGTCTCTCTTGATACA
1 TTTCTCTTGAAACACCATCTGTGAG-TCAGTTTCCCTTAAAACAAATTTTATCTCTCTTGAGACA
*
1398247 G
65 A
* * * *
1398248 TTTCTCTTGAAACATCATCTTTGAGTCTGTTTCCCTTGAAACAAAT
1 TTTCTCTTGAAACACCATCTGTGAGTCAGTTTCCCTTAAAACAAAT
1398294 CCCTAAAGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
64 1 0.01
65 60 0.62
66 20 0.21
67 15 0.16
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (65 bp):
TTTCTCTTGAAACACCATCTGTGAGTCAGTTTCCCTTAAAACAAATTTTATCTCTCTTGAGACAA
Found at i:1398543 original size:134 final size:131
Alignment explanation
Indices: 1398292--1398590 Score: 355
Period size: 134 Copynumber: 2.3 Consensus size: 131
1398282 CTTGAAACAA
* * * * * *
1398292 ATCCCTAAAGATGGCCTGTCATCCTCATCGCGTAGGAACCGTGCCATCCATCGCCCAGACCTCCT
1 ATCCCTAAATATGGCATGTCATCCTCATCGCGTAAGAACCATGCCATCCACCGACCAGACCTCCT
* * *
1398357 CATCACGTAGGAGCCGCGTCAACCTCAGATAACCAGTCATCCTCACCGCGTAGGAACAATGTCAT
66 CATCACATAGGAGCCGCGTCAACCTCAGATAACCAGCCATCCTCACCACGTAGGAAC--TGT-AT
1398422 CATC
128 CATC
* * * *
1398426 ATTCCTAAATATGGCATGTAATCCTCATCGCGTAAGAATCATGCCATCCACCGACCAGATCTCCT
1 ATCCCTAAATATGGCATGTCATCCTCATCGCGTAAGAACCATGCCATCCACCGACCAGACCTCCT
* * * * * * * *
1398491 CATCACATAGGTGTCGTGTCAACCTCAGATAACCAGCCGTTCTCATCACGTAGGAACTGTGTTAT
66 CATCACATAGGAGCCGCGTCAACCTCAGATAACCAGCCATCCTCACCACGTAGGAACTGTATCAT
1398556 C
131 C
* * *
1398557 ATCCCTAAATATGGCTTATCATCCTCATCACGTA
1 ATCCCTAAATATGGCATGTCATCCTCATCGCGTA
1398591 GGAGCCGTGT
Statistics
Matches: 139, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
131 33 0.24
132 3 0.02
134 103 0.74
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAATATGGCATGTCATCCTCATCGCGTAAGAACCATGCCATCCACCGACCAGACCTCCT
CATCACATAGGAGCCGCGTCAACCTCAGATAACCAGCCATCCTCACCACGTAGGAACTGTATCAT
C
Found at i:1398965 original size:20 final size:23
Alignment explanation
Indices: 1398921--1398971 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 23
1398911 GTCGAAAAAA
1398921 TATTATTTATTATTAATAATAAT
1 TATTATTTATTATTAATAATAAT
*
1398944 TATTA-TTATT-TTAATTAT-AT
1 TATTATTTATTATTAATAATAAT
1398964 TATT-TTTA
1 TATTATTTA
1398972 CAGCCCAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.35
21 7 0.27
22 5 0.19
23 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTTATTATTAATAATAAT
Found at i:1398971 original size:15 final size:15
Alignment explanation
Indices: 1398940--1398969 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1398930 TTATTAATAA
1398940 TAATTATTATTATTT
1 TAATTATTATTATTT
1398955 TAATTA-TATTATTT
1 TAATTATTATTATTT
1398969 T
1 T
1398970 TACAGCCCAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTATTATTATTT
Found at i:1400207 original size:20 final size:21
Alignment explanation
Indices: 1400184--1400223 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1400174 ATGTCTTTGT
1400184 ATTTAATAGTA-ATTTTCAAC
1 ATTTAATAGTATATTTTCAAC
* *
1400204 ATTTACTCGTATATTTTCAA
1 ATTTAATAGTATATTTTCAA
1400224 GTTTCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTAATAGTATATTTTCAAC
Found at i:1403119 original size:14 final size:15
Alignment explanation
Indices: 1403100--1403128 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1403090 AATATTTTAA
1403100 ATATTTTA-AATAAT
1 ATATTTTATAATAAT
1403114 ATATTTTATAATAAT
1 ATATTTTATAATAAT
1403129 TTACTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTTTATAATAAT
Found at i:1403158 original size:22 final size:22
Alignment explanation
Indices: 1403091--1403162 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 22
1403081 AAATATATCA
* *
1403091 ATATTTTAAATATTTTAAATAAT
1 ATATTTTTAATA-ATTAAATAAT
*
1403114 ATATTTTATAATAATT---TACT
1 ATATTTT-TAATAATTAAATAAT
1403134 ATATTTTTAATAATTAAATAAT
1 ATATTTTTAATAATTAAATAAT
1403156 ATATTTT
1 ATATTTT
1403163 AACATTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
19 8 0.20
20 10 0.24
22 10 0.24
23 9 0.22
24 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTTTTAATAATTAAATAAT
Found at i:1403169 original size:20 final size:19
Alignment explanation
Indices: 1403105--1403169 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 19
1403095 TTTAAATATT
1403105 TTAAATAATATATTTTATAA
1 TTAAATAATATATTTTA-AA
* *
1403125 -TAATTTACTATATTTTTAATAA
1 TTAA-ATAATATA-TTTT-A-AA
1403147 TTAAATAATATATTTTAACA
1 TTAAATAATATATTTTAA-A
1403167 TTA
1 TTA
1403170 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 8 0.22
22 10 0.28
23 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATAATATATTTTAAA
Found at i:1404900 original size:20 final size:21
Alignment explanation
Indices: 1404854--1404903 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1404844 TAAAAAATCA
* *
1404854 TAAAATAATACATAATTATTC
1 TAAAATATTAAATAATTATTC
1404875 TAAAATATTAAATAATTATT-
1 TAAAATATTAAATAATTATTC
1404895 TAAAATATT
1 TAAAATATT
1404904 TAGAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAATATTAAATAATTATTC
Found at i:1404938 original size:17 final size:17
Alignment explanation
Indices: 1404918--1404951 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1404908 AAAAAATATG
1404918 AAATATAAAATGTTAAA
1 AAATATAAAATGTTAAA
* *
1404935 AAATATTAAATTTTAAA
1 AAATATAAAATGTTAAA
1404952 GATTCGTTTG
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:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATAAAATGTTAAA
Found at i:1405715 original size:3 final size:3
Alignment explanation
Indices: 1405707--1405748 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1405697 GAGGTAAAGA
1405707 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1405749 TATGAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1407565 original size:29 final size:28
Alignment explanation
Indices: 1407478--1407569 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
1407468 GACCTTTTCA
* *
1407478 TGTAATTTATAAAAATTATAGGTA-TTAT
1 TGTAATTTATAAAAGTT-TTGGTATTTAT
* * *
1407506 TGTAATTTATGAGAAGTTTT-TTCTTTGAT
1 TGTAATTTAT-AAAAGTTTTGGTATTT-AT
1407535 TGTAATTTATAAATAGTTTTGGTATTTAT
1 TGTAATTTATAAA-AGTTTTGGTATTTAT
1407564 TGTAAT
1 TGTAAT
1407570 ATTAAAATGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.02
28 15 0.29
29 31 0.61
30 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.52
Consensus pattern (28 bp):
TGTAATTTATAAAAGTTTTGGTATTTAT
Found at i:1408297 original size:3 final size:3
Alignment explanation
Indices: 1408289--1408315 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1408279 ATCTAATGCA
1408289 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1408316 TTCATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1410010 original size:20 final size:19
Alignment explanation
Indices: 1409971--1410012 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1409961 TTTCTTCGAT
1409971 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1409990 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1410010 ATT
1 ATT
1410013 TATAAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1410085 original size:120 final size:121
Alignment explanation
Indices: 1409880--1410116 Score: 279
Period size: 120 Copynumber: 2.0 Consensus size: 121
1409870 AATTTAAAAA
* * *
1409880 AATATATTAATATATATAAATAAGATATTTACTTATTTAGAAATATCAGAAAAGGACTTCTAGGT
1 AATATATTAATATATATAAATAAGATATTTACTTATTTAAAAATATCAGAAAAGGACATCCAGGT
*
1409945 GTCTTAAGACAGCTCTTTTCTTCGATA-TTAAAAAATAAATAAATAATTAAAACAATT
66 GTCTTAAGACAGCTCTTTTCTT-AATATTTAAAAAATAAATAAAT-ATTAAAACAATT
* *
1410002 AATATA-TAAT-T-TATAAAGTATGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAG
1 AATATATTAATATATATAAA-TAAGATATTTACTTATTTAAAAATATCAGAAAA-GGACATCCAG
* * * * *
1410064 TTGTTTTAAGACTGGC-C-TTTCTTAATATTTTGAAAAATAAATATATATTAAAA
64 GTGTCTTAAGAC-AGCTCTTTTCTTAATA-TTTAAAAAATAAATAAATATTAAAA
1410117 TATGATAAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
119 9 0.09
120 44 0.44
121 38 0.38
122 8 0.08
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (121 bp):
AATATATTAATATATATAAATAAGATATTTACTTATTTAAAAATATCAGAAAAGGACATCCAGGT
GTCTTAAGACAGCTCTTTTCTTAATATTTAAAAAATAAATAAATATTAAAACAATT
Found at i:1411641 original size:3 final size:3
Alignment explanation
Indices: 1411633--1411700 Score: 100
Period size: 3 Copynumber: 22.0 Consensus size: 3
1411623 TTATTTATTA
* *
1411633 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
1411680 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
1411701 CAAATAAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1412069 original size:84 final size:83
Alignment explanation
Indices: 1411949--1412141 Score: 278
Period size: 84 Copynumber: 2.3 Consensus size: 83
1411939 CTTTCAGATG
* * *
1411949 AGTTCTTCTCATTATGAACATTTCTGGAAATGTTGATGTTGATCCATCTACTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAGT
*
1412014 TAAACAAAAGGTTAAACA
66 CAAACAAAAGGTTAAACA
*
1412032 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTAATTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTT-TCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAG
** *
1412097 TCATGCAAAAGGTTGAACA
65 TCAAACAAAAGGTTAAACA
**
1412116 AACTCTTCTCATTATGAACTTCTTCT
1 AGTTCTTCTCATTATGAACTT-TTCT
1412142 TCCTTCTTCA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
83 21 0.21
84 76 0.78
85 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (83 bp):
AGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAGT
CAAACAAAAGGTTAAACA
Found at i:1412471 original size:113 final size:113
Alignment explanation
Indices: 1412206--1412942 Score: 918
Period size: 113 Copynumber: 6.6 Consensus size: 113
1412196 TGATTAAACT
* * * *
1412206 AAAGTCGAACAAATTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
1412271 TGAACTTTTTCTGGAAAAGCTGATCCATC-AAGTAATGGATT--TGC-A
66 TGAACTCTATCTGGAAAAGCTGATCCATCGAA-TGATGAATTCAAGCGA
* *
1412316 AAAGGTTGAACAAATTCTTCTCATTATGAATTTC-TCATTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1412380 TATGAACTCTACCTGGTAATA-CTGAAT-CATCGAATGATGAATTCAAGCGA
64 TATGAACTCTATCTGG-AAAAGCTG-ATCCATCGAATGATGAATTCAAGCGA
1412430 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * **
1412495 TGAACTTTTTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGC-A
66 TGAACTCTATCTGGAAAAGCTGATCCATCGAA-TGATGAATTCAAGCGA
* * * *
1412542 AAAGGTTGAACAAATTCTTCTTATTATGAA----------CTTCTTCAGATAAATTCTTCTCATT
1 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * * *
1412597 ATGAACTTTCTATGGAAAAGTTGATCCATCTAGTGATGAATTCAAACGA
65 ATGAACTCTATCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGA
1412646 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
1412711 TGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGA
66 TGAACTCTATCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGA
* *
1412759 AAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
1412824 TGAACTTTTTCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGA
66 TGAACTCTATCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGA
*
1412872 AAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1412937 TGAACT
66 TGAACT
1412943 TCTTCAGATA
Statistics
Matches: 548, Mismatches: 54, Indels: 47
0.84 0.08 0.07
Matches are distributed among these distances:
103 84 0.15
104 5 0.01
110 5 0.01
111 80 0.15
112 18 0.03
113 350 0.64
114 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTATCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGA
Found at i:1412742 original size:329 final size:327
Alignment explanation
Indices: 1412246--1412907 Score: 1028
Period size: 329 Copynumber: 2.0 Consensus size: 327
1412236 TTCTTCTTCT
* * * * *
1412246 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTAATGGAT
1 TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGCTGATCCATCAAGTAATGAAT
** *
1412311 TTGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTCATTCCTTCTTCAGATGAGTTCTTC
66 TAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCATTCCTTCTTCAGATGAGTTCTTC
*
1412376 TCATTATGAACTCTACCTGGTAATACTGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
131 TCATTATGAACTCGACCTGGTAATACTGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
1412441 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
196 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
* **
1412506 TGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGC-AAAAGGTTGAACAAATTCTTCTTATTAT
261 TGGAAAAGCTGATCCATCGAA-TGATGAATTCAAGCGAAAA-GTTGAACAAATTCTTCTTATTAT
1412569 GAAC
324 GAAC
* * *
1412573 TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGATCCATCTAGTGATGAAT
1 TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGCTGATCCATCAAGTAATGAAT
*
1412638 TCAAACGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTT
66 T--AAC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTC-TCATTCCTTCTTCAGATGAGTT
*
1412701 CTTCTCATTATGAACTCGACCTGGTAATGCTG-ATCCATCGAATGATGAATTCAAGCGAAAAGTT
127 CTTCTCATTATGAACTCGACCTGGTAATACTGAAT-CATCGAATGATGAATTCAAGCGAAAAGTT
* *
1412765 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
191 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * *
1412830 TTTTCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTTAT
256 TTTTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTTAT
1412895 TATGAAC
321 TATGAAC
1412902 TTCTTC
1 TTCTTC
1412908 TTCCTTCTTC
Statistics
Matches: 306, Mismatches: 22, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
327 58 0.19
328 2 0.01
329 234 0.76
330 12 0.04
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (327 bp):
TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGCTGATCCATCAAGTAATGAAT
TAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCATTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTCGACCTGGTAATACTGAATCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
TGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTTCTTATTATGA
AC
Found at i:1412878 original size:226 final size:223
Alignment explanation
Indices: 1412206--1412942 Score: 962
Period size: 216 Copynumber: 3.3 Consensus size: 223
1412196 TGATTAAACT
* * * *
1412206 AAAGTCGAACAAATTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * *
1412271 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTAATGGATT--TGC-AAAAGGTTGAACAAATTC
66 TGAACTCTTTCTGGTAATGCTGATCCATCAA-TGATGAATTCAAGCGAAAA-GTTGAACAAATTC
* * *
1412333 TTCTCATTATGAATTTCTCATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGT
129 TTCTTATTATGAACTTCTC-TT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGT
*
1412397 AATACTGAAT-CATCGAATGATGAATTCAAGCGA
191 AATGCTG-ATCCATCGAATGATGAATTCAAGCGA
1412430 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * **
1412495 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC-AAAAGGTTGAACAAATTC
66 TGAACTCTTTCTGGTAATGCTGATCCATCAA-TGATGAATTCAAGCGAAAA-GTTGAACAAATTC
* * * * *
1412559 TTCTTATTATGAA--------CTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAA
129 TTCTTATTATGAACTTCTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAAT
* * * *
1412616 GTTGATCCATCTAGTGATGAATTCAAACGA
194 GCTGATCCATCGAATGATGAATTCAAGCGA
1412646 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*** *
1412711 TGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCT
66 TGAACTCTTTCTGGTAATGCTGATCCATC-AATGATGAATTCAAGCGAAAAGTTGAACAAATTCT
*
1412776 TCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGTAA
130 TCTTATTATGAACTTC-TCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAA
1412841 TGCTGATCCATCGAATGATGAATTCAAGCGA
193 TGCTGATCCATCGAATGATGAATTCAAGCGA
*
1412872 AAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1412937 TGAACT
66 TGAACT
1412943 TCTTCAGATA
Statistics
Matches: 458, Mismatches: 39, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
215 4 0.01
216 181 0.40
217 6 0.01
224 101 0.22
225 1 0.00
226 165 0.36
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (223 bp):
AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTTCTGGTAATGCTGATCCATCAATGATGAATTCAAGCGAAAAGTTGAACAAATTCTT
CTTATTATGAACTTCTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAATGC
TGATCCATCGAATGATGAATTCAAGCGA
Found at i:1412947 original size:30 final size:30
Alignment explanation
Indices: 1412911--1412973 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1412901 CTTCTTCTTC
* *
1412911 CTTCTTCAGATGAGTTCTTCTCATTATGAA
1 CTTCTTCAGATAAATTCTTCTCATTATGAA
1412941 CTTCTTCAGATAAATTCTTCTCATTATGAA
1 CTTCTTCAGATAAATTCTTCTCATTATGAA
1412971 CTT
1 CTT
1412974 TCTATGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (30 bp):
CTTCTTCAGATAAATTCTTCTCATTATGAA
Found at i:1412947 original size:256 final size:255
Alignment explanation
Indices: 1412685--1413198 Score: 850
Period size: 256 Copynumber: 2.0 Consensus size: 255
1412675 CTTCTTCTTC
* * * *
1412685 CTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGACCTGGTAATGCTGATCCATCGAATGATGA
1 CTTCTTCAGATAAATTCTTCTCATTATGAACTTCGA--TGGAAAAGCTGATCCATCGAATGATGA
* * *
1412749 ATTCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTT
64 ATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT
****
1412814 CTTCTCATTATGAACTTTTTCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
129 CTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
*
1412879 AACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
194 AACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1412941 CTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGATCCATCTAGTGATGAA
1 CTTCTTCAGATAAATTCTTCTCATTATGAAC-TTCGATGGAAAAGCTGATCCATCGAATGATGAA
1413006 TTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
65 TTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1413071 TTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGA
130 TTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGA
1413136 ACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
195 ACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1413197 CT
1 CT
1413199 CAAACTGGTA
Statistics
Matches: 240, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
256 237 0.99
258 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (255 bp):
CTTCTTCAGATAAATTCTTCTCATTATGAACTTCGATGGAAAAGCTGATCCATCGAATGATGAAT
TCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAA
CAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
Found at i:1413012 original size:369 final size:369
Alignment explanation
Indices: 1412556--1413311 Score: 1449
Period size: 369 Copynumber: 2.0 Consensus size: 369
1412546 GTTGAACAAA
*
1412556 TTCTTCTTATTATGAACTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGA
1 TTCTTCTCATTATGAACTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGA
1412621 TCCATCTAGTGATGAATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
66 TCCATCTAGTGATGAATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
1412686 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAAT
131 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAAT
* *
1412751 TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCT
196 TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCT
****
1412816 TCTCATTATGAACTTTTTCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAA
261 TCTCATTATGAACTCAAACTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAA
1412881 CAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
326 CAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1412925 TTCTTCTCATTATGAACTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGA
1 TTCTTCTCATTATGAACTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGA
1412990 TCCATCTAGTGATGAATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
66 TCCATCTAGTGATGAATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
1413055 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAAT
131 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAAT
1413120 TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCT
196 TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCT
1413185 TCTCATTATGAACTCAAACTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAA
261 TCTCATTATGAACTCAAACTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAA
1413250 CAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
326 CAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1413294 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
1413312 CTCTCTGGAA
Statistics
Matches: 380, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
369 380 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (369 bp):
TTCTTCTCATTATGAACTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGA
TCCATCTAGTGATGAATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
TTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAAT
TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCAAACTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAA
CAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:1413057 original size:143 final size:143
Alignment explanation
Indices: 1412799--1413085 Score: 475
Period size: 143 Copynumber: 2.0 Consensus size: 143
1412789 TTCTTCTTCT
* * * * * *
1412799 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGTAATGCTGATCCATCGAATGATGAAT
1 TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGCTGATCCATCGAATGATGAAT
* *
1412864 TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
66 TCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1412929 TCTCATTATGAAC
131 TCTCATTATGAAC
* * *
1412942 TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGTTGATCCATCTAGTGATGAAT
1 TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGCTGATCCATCGAATGATGAAT
1413007 TCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
66 TCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1413072 TCTCATTATGAAC
131 TCTCATTATGAAC
1413085 T
1 T
1413086 CGACCTGGTA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
143 133 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (143 bp):
TTCTTCAGATAAATTCTTCTCATTATGAACTTTCTATGGAAAAGCTGATCCATCGAATGATGAAT
TCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAAC
Found at i:1413080 original size:113 final size:112
Alignment explanation
Indices: 1412941--1413342 Score: 599
Period size: 113 Copynumber: 3.6 Consensus size: 112
1412931 TCATTATGAA
* * * * *
1412941 CTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTA-TGGAAAAGTTGATCCATCTAGTGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAAC--TCTACTGGAAAAGCTGATCCATCGAATGATGA
* *
1413005 ATTCAAACGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
64 ATTCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTC
* * *
1413054 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTA-CTGGAAAAGCTGATCCATCGAATGATGAA
*
1413119 TTCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTC
65 TTCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTC
* * *
1413167 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCAAACTGGTAATGCTGATCCATCGAATGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TACTGGAAAAGCTGATCCATCGAATGATGAA
1413232 TTCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTC
65 TTCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTC
* * *
1413280 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAATGATG
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-ACTGGAAAAGCTGATCCATCGAATGATG
1413343 GATTTGAATC
Statistics
Matches: 266, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
111 3 0.01
113 262 0.98
114 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAAAGCTGATCCATCGAATGATGAAT
TCAAGCGAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTC
Found at i:1413775 original size:22 final size:22
Alignment explanation
Indices: 1413750--1413826 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
1413740 GATAAAGCTT
* *
1413750 TCATCTTTGAAAAGAGAAACTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1413772 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1413794 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1413816 TCATCTTTGAA
1 TCATCTTTGAA
1413827 GAGTGTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1416561 original size:114 final size:114
Alignment explanation
Indices: 1416361--1416583 Score: 383
Period size: 114 Copynumber: 2.0 Consensus size: 114
1416351 GATCATGCAG
* * *
1416361 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1416426 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
1416475 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
1416540 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
1416584 TCACCTGGCA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1418854 original size:26 final size:26
Alignment explanation
Indices: 1418820--1418870 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1418810 CTTGATTCAA
*
1418820 TTTTCCTTTTTCTTT-TTTTTTCTTTT
1 TTTTCCTTTTT-TTTCTTCTTTCTTTT
*
1418846 TTTTTCTTTTTTTTCTTCTTTCTTT
1 TTTTCCTTTTTTTTCTTCTTTCTTT
1418871 GCTGGATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTTCCTTTTTTTTCTTCTTTCTTTT
Found at i:1418862 original size:9 final size:10
Alignment explanation
Indices: 1418826--1418859 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
1418816 TCAATTTTCC
1418826 TTTTTCTTTT
1 TTTTTCTTTT
1418836 TTTTTCTTTT
1 TTTTTCTTTT
1418846 TTTTTCTTTT
1 TTTTTCTTTT
1418856 TTTT
1 TTTT
1418860 CTTCTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1422103 original size:14 final size:14
Alignment explanation
Indices: 1422070--1422121 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1422060 ATGACATAAA
* *
1422070 AAATGCAAAGATGCC
1 AAATGTAAAAATG-C
*
1422085 AAATGTAAACATGC
1 AAATGTAAAAATGC
*
1422099 AAATGTAAAAATGT
1 AAATGTAAAAATGC
1422113 AAATGTAAA
1 AAATGTAAA
1422122 TACAAACGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (14 bp):
AAATGTAAAAATGC
Found at i:1424250 original size:20 final size:19
Alignment explanation
Indices: 1424211--1424252 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1424201 TTTCTTCGAT
1424211 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1424230 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1424250 ATT
1 ATT
1424253 TATAAAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1424325 original size:120 final size:121
Alignment explanation
Indices: 1424120--1424356 Score: 261
Period size: 120 Copynumber: 2.0 Consensus size: 121
1424110 AATTTAAAAA
* * * * *
1424120 AATATATTAATATATATAAATAAGATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGT
1 AATATATTAATATATATAAATAAGATATTTACTTATTTAAAAATATCAGAAAAGGACATCCAAGT
*
1424185 GTCTTAAGACAGCTCTTTTCTTCGATA-TTAAAAAATAAATAAATAATTAAAACAATT
66 GTCTTAAGACAGCTCTTTTCTT-AATATTTAAAAAATAAATAAAT-ATTAAAACAATT
* *
1424242 AATATA-TAAT-T-TATAAAGTATGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAA
1 AATATATTAATATATATAAA-TAAGATATTTACTTATTTAAAAATATCAGAAAA-GGACATCCAA
* * * * *
1424304 TTGTTTTAAGACTGAC-C-TTTCTTAATATTTTGAAAAATAAATATATATTAAAA
64 GTGTCTTAAGACAG-CTCTTTTCTTAATA-TTTAAAAAATAAATAAATATTAAAA
1424357 TATGATAAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
119 9 0.09
120 44 0.45
121 37 0.38
122 7 0.07
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (121 bp):
AATATATTAATATATATAAATAAGATATTTACTTATTTAAAAATATCAGAAAAGGACATCCAAGT
GTCTTAAGACAGCTCTTTTCTTAATATTTAAAAAATAAATAAATATTAAAACAATT
Found at i:1425133 original size:88 final size:88
Alignment explanation
Indices: 1424984--1425161 Score: 311
Period size: 88 Copynumber: 2.0 Consensus size: 88
1424974 TTAAGCCGGC
* *
1424984 CCCAAGGATCACCTTTCTCATTTCTTCCTTTATTCTTTTCTCTCTAACAGAGAGAAAAAAATTTC
1 CCCAAGGATCACCCTTCTCATTTCTTCCTTTATTCTTTTATCTCTAACAGAGAGAAAAAAATTTC
* *
1425049 TCTCTGTCTTCTCTCTAAACTCT
66 TCTATGTCTTCTCTCTAAACCCT
*
1425072 CCCAAGGATCACCCTTCTCATTTCTTCCTTTCTTCTTTTATCTCTAACAGAGAGAAAAAAATTTC
1 CCCAAGGATCACCCTTCTCATTTCTTCCTTTATTCTTTTATCTCTAACAGAGAGAAAAAAATTTC
1425137 TCTATGTCTTCTCTCTAAACCCT
66 TCTATGTCTTCTCTCTAAACCCT
1425160 CC
1 CC
1425162 ACCGGAGGGA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.24, C:0.30, G:0.07, T:0.39
Consensus pattern (88 bp):
CCCAAGGATCACCCTTCTCATTTCTTCCTTTATTCTTTTATCTCTAACAGAGAGAAAAAAATTTC
TCTATGTCTTCTCTCTAAACCCT
Found at i:1425971 original size:3 final size:3
Alignment explanation
Indices: 1425963--1426024 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
1425953 TTATTTATTA
* * *
1425963 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT ATT AAT AAT AAT AAAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
1426010 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
1426025 CAAATGAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:1426003 original size:31 final size:30
Alignment explanation
Indices: 1425958--1426024 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
1425948 TGTAATTATT
* *
1425958 TATTAA-ATAATAATAATATATAATATTAA
1 TATTAATATAATAATAATAAATAATAATAA
1425987 TATTAATATTAATAATAATAAATAATAATAA
1 TATTAATA-TAATAATAATAAATAATAATAA
*
1426018 TAATAAT
1 TATTAAT
1426025 CAAATGAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 6 0.18
30 1 0.03
31 26 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TATTAATATAATAATAATAAATAATAATAA
Done.