Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 62 of 126
Found at i:18112082 original size:115 final size:115
Alignment explanation
Indices: 18111880--18112110 Score: 356
Period size: 115 Copynumber: 2.0 Consensus size: 115
18111870 TCGTCGTGAG
*
18111880 TATATGAATCATTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTT
1 TATATGAATCATTTACGGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCTTT
* * * *
18111945 TATGGACTATAAGGTCCGATGAC-TATGTGTCATCGTGAGTATATGAATCC
66 CACGGACTATAAGGTCCGATGACATAT-AGTCATCGTGAGCATATGAATCC
*
18111995 TATATGAATCCTTTACGGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCTTT
1 TATATGAATCATTTACGGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCTTT
* * * *
18112060 CACGGATTATGAGGTCTGATGACATATAGTCATCGTGAGCATATGGATCC
66 CACGGACTATAAGGTCCGATGACATATAGTCATCGTGAGCATATGAATCC
18112110 T
1 T
18112111 TTTTCGGATT
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
115 102 0.97
116 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (115 bp):
TATATGAATCATTTACGGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCTTT
CACGGACTATAAGGTCCGATGACATATAGTCATCGTGAGCATATGAATCC
Found at i:18112127 original size:167 final size:167
Alignment explanation
Indices: 18111828--18112153 Score: 498
Period size: 167 Copynumber: 2.0 Consensus size: 167
18111818 TCATTGTGAG
*
18111828 TATATGAATCCTTTACGGATTATGAGGTCCAATAACTATGTGTCGTCGTGAGTATATGAATCATT
1 TATATGAATCCTTTACGGATTATGAGGTCCAATAACTATGTGTCATCGTGAGTATATGAATCATT
* *
18111893 TACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTATGGACTATAAG
66 TACGGATTATGAGGTCCGATGACTATGAGTCATCGTGAGCATATGAATCTTTTATGGACTATAAG
* *
18111958 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCC
131 GTCCGATGAATATGTGTCATCGTAAGTATATGAATCC
*
18111995 TATATGAATCCTTTACGGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATC-TT
1 TATATGAATCCTTTACGGATTATGAGGTCCAATAACTATGTGTCATCGTGAGTATATGAATCATT
* * *
18112059 TCACGGATTATGAGGTCTGATGACATAT-AGTCATCGTGAGCATATGGATCCTTTT-TCGGA-TT
66 T-ACGGATTATGAGGTCCGATGAC-TATGAGTCATCGTGAGCATATGAAT-CTTTTAT-GGACTA
*
18112121 TAAGGTCCGATGAATTTGTGTCATCGTAAGTAT
127 TAAGGTCCGATGAATATGTGTCATCGTAAGTAT
18112154 TAAATAGGAA
Statistics
Matches: 145, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
166 3 0.02
167 131 0.90
168 11 0.08
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (167 bp):
TATATGAATCCTTTACGGATTATGAGGTCCAATAACTATGTGTCATCGTGAGTATATGAATCATT
TACGGATTATGAGGTCCGATGACTATGAGTCATCGTGAGCATATGAATCTTTTATGGACTATAAG
GTCCGATGAATATGTGTCATCGTAAGTATATGAATCC
Found at i:18113971 original size:59 final size:59
Alignment explanation
Indices: 18113857--18113971 Score: 135
Period size: 59 Copynumber: 1.9 Consensus size: 59
18113847 GCCAAGCACC
* * * *
18113857 AAAAAAACCATTTTTTAATTCATATTTTTATGGGTTTCGACCATTGGTTATCAAATACG
1 AAAAAAACCATTTTTTAATTCATATTTTTATGGGTGTCGACCATTAGATAGCAAATACG
** *
18113916 AAAAAAATTATTTTTT-ATTCGTATTATTTATGGGTGTC-AGCCATTAGATAGCAAAT
1 AAAAAAACCATTTTTTAATTCATATT-TTTATGGGTGTCGA-CCATTAGATAGCAAAT
18113972 GCCAAAATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 9 0.19
59 38 0.81
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (59 bp):
AAAAAAACCATTTTTTAATTCATATTTTTATGGGTGTCGACCATTAGATAGCAAATACG
Found at i:18114202 original size:56 final size:55
Alignment explanation
Indices: 18114141--18114264 Score: 126
Period size: 54 Copynumber: 2.2 Consensus size: 55
18114131 AAACACCTGG
* * * *
18114141 AAAAAATAATTTTGGTATCTGAAAAAGAGGGTG-CAGCCATGGGTTGGTAGACACCT
1 AAAAAATAATTTT-GTATCTGAAAAAG-GGGTGTCAGCCATGGCTTGGCAAACACCC
* * * *
18114197 AAAAAAT-GTTTTTTATTTGAAAAAGGGGTGTCGGCCATGGCTTGGCAAACACCC
1 AAAAAATAATTTTGTATCTGAAAAAGGGGTGTCAGCCATGGCTTGGCAAACACCC
*
18114251 AAGAAATTAATTTT
1 AA-AAAATAATTTT
18114265 TTATGCTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
53 5 0.09
54 31 0.56
55 8 0.15
56 11 0.20
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (55 bp):
AAAAAATAATTTTGTATCTGAAAAAGGGGTGTCAGCCATGGCTTGGCAAACACCC
Found at i:18114249 original size:54 final size:58
Alignment explanation
Indices: 18114110--18114249 Score: 137
Period size: 54 Copynumber: 2.5 Consensus size: 58
18114100 TTTTCATTTT
* * *
18114110 GGGTGTCGGTCATGTATTGACAAACACCTGGAAAAAATAATTTTGGTATCTGAAAAAGA
1 GGGTGTCGGCCATGGATTGGCAAACACCT-GAAAAAATAATTTTGGTATCTGAAAAAGA
* * * * * * *
18114169 GGGTG-CAGCCATGGGTTGGTAGACACCT-AAAAAAT-GTTTT-TTATTTGAAAAAG-
1 GGGTGTCGGCCATGGATTGGCAAACACCTGAAAAAATAATTTTGGTATCTGAAAAAGA
*
18114222 GGGTGTCGGCCATGGCTTGGCAAACACC
1 GGGTGTCGGCCATGGATTGGCAAACACC
18114250 CAAGAAATTA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
53 5 0.08
54 29 0.44
55 4 0.06
56 7 0.11
58 16 0.24
59 5 0.08
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (58 bp):
GGGTGTCGGCCATGGATTGGCAAACACCTGAAAAAATAATTTTGGTATCTGAAAAAGA
Found at i:18118131 original size:32 final size:33
Alignment explanation
Indices: 18118064--18118131 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
18118054 TCTTGTTGGG
* * *
18118064 TTTGATTTTCCTTTGTGGTAGGTCTATGTCGGA
1 TTTGATTTTCCTTTGTGGTAGATCTATGCCAGA
18118097 TTTGA-TTTCCTTTGTGGTAGCATCTAT-CCAGA
1 TTTGATTTTCCTTTGTGGTAG-ATCTATGCCAGA
18118129 TTT
1 TTT
18118132 CATCAGCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (33 bp):
TTTGATTTTCCTTTGTGGTAGATCTATGCCAGA
Found at i:18138935 original size:20 final size:19
Alignment explanation
Indices: 18138899--18138940 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
18138889 TAAAAAAATT
18138899 AACGGTCAAAGTCAAAGTC
1 AACGGTCAAAGTCAAAGTC
*
18138918 AACGGTCAATGATCAAAGTC
1 AACGGTCAAAG-TCAAAGTC
18138938 AAC
1 AAC
18138941 ATGTCTGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (19 bp):
AACGGTCAAAGTCAAAGTC
Found at i:18145029 original size:13 final size:13
Alignment explanation
Indices: 18145013--18145037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18145003 AACAGTCAAA
18145013 GTCAAAGTCAACG
1 GTCAAAGTCAACG
18145026 GTCAAAGTCAAC
1 GTCAAAGTCAAC
18145038 ATGTTTGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:18156690 original size:80 final size:80
Alignment explanation
Indices: 18156551--18156711 Score: 232
Period size: 80 Copynumber: 2.0 Consensus size: 80
18156541 GGTACAATCC
* * * * *
18156551 ATACTAAAGCTAAGAAATTGGACTAAAACTCACACATGACAACTACATATAATGGGACTCAGACA
1 ATACTAAAGCTAAGAAACTCGACTAAAACTCACACATGACAAATACACATAATGAGACTCAGACA
18156616 CCTACACATATAATT
66 CCTACACATATAATT
* * *
18156631 ATACTAAAGCTAAGAAACTCGACTAAAACTCACACATGACAAATGCACATGATGAGACTCGGACA
1 ATACTAAAGCTAAGAAACTCGACTAAAACTCACACATGACAAATACACATAATGAGACTCAGACA
**
18156696 CCTATGCATATAATT
66 CCTACACATATAATT
18156711 A
1 A
18156712 GATATAGTAG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (80 bp):
ATACTAAAGCTAAGAAACTCGACTAAAACTCACACATGACAAATACACATAATGAGACTCAGACA
CCTACACATATAATT
Found at i:18158741 original size:31 final size:31
Alignment explanation
Indices: 18158673--18158733 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
18158663 ATAACTGCCA
18158673 AATGACTTAAATAAAAACTTTTAAATAGTTC
1 AATGACTTAAATAAAAACTTTTAAATAGTTC
* *
18158704 AATGACTTAAATGAAAACTTTTGAATAGTT
1 AATGACTTAAATAAAAACTTTTAAATAGTT
18158734 TGGTGACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTTAAATAGTTC
Found at i:18173142 original size:22 final size:22
Alignment explanation
Indices: 18173114--18173160 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
18173104 CTGTACTCAT
18173114 AAACAAATTGCCAACAAAGATG
1 AAACAAATTGCCAACAAAGATG
18173136 AAACAAATTGCCAACAAAGATG
1 AAACAAATTGCCAACAAAGATG
18173158 AAA
1 AAA
18173161 GATCTTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (22 bp):
AAACAAATTGCCAACAAAGATG
Found at i:18176734 original size:15 final size:16
Alignment explanation
Indices: 18176714--18176743 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18176704 TTTTAATTTT
18176714 TTATTT-ACTTTTCAG
1 TTATTTCACTTTTCAG
18176729 TTATTTCACTTTTCA
1 TTATTTCACTTTTCA
18176744 TCATGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTTCACTTTTCAG
Found at i:18177164 original size:11 final size:11
Alignment explanation
Indices: 18177137--18177166 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
18177127 AACTTGTGCA
18177137 TCCAAAAACAC
1 TCCAAAAACAC
18177148 TCCCAAAAACAC
1 T-CCAAAAACAC
18177160 TCCAAAA
1 TCCAAAA
18177167 CCTTTATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:18178920 original size:18 final size:19
Alignment explanation
Indices: 18178894--18178931 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
18178884 TGATTGGTTC
18178894 GAGGGGCAA-GAAAAGAAA
1 GAGGGGCAAGGAAAAGAAA
* *
18178912 GAGGTGCAAGGGAAAGAAA
1 GAGGGGCAAGGAAAAGAAA
18178931 G
1 G
18178932 TGAAGAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.05, G:0.42, T:0.03
Consensus pattern (19 bp):
GAGGGGCAAGGAAAAGAAA
Found at i:18199024 original size:43 final size:43
Alignment explanation
Indices: 18198969--18199052 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
18198959 CAGTGCAACA
18198969 ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
1 ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
*
18199012 ATTAAAGGAATGATATTTTAGGATCTTTAGCTATATTAGTG
1 ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTG
18199053 GATGTAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (43 bp):
ATTAAAGGAATGATATTCTAGGATCTTTAGCTATATTAGTGCG
Found at i:18201580 original size:24 final size:24
Alignment explanation
Indices: 18201553--18201651 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
18201543 AGAGTTTGAC
18201553 TGAAACAAATAAACAAAGTTTAAT
1 TGAAACAAATAAACAAAGTTTAAT
* *
18201577 TGAAACAAATAAATAGAGTTTAAT
1 TGAAACAAATAAACAAAGTTTAAT
* *
18201601 TGAAACACATAAACAAAATTTAAT
1 TGAAACAAATAAACAAAGTTTAAT
* * *
18201625 TGAAACAAAATATATAGAGTTTAAT
1 TGAAAC-AAATAAACAAAGTTTAAT
18201650 TG
1 TG
18201652 GAAGATTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
24 48 0.76
25 15 0.24
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (24 bp):
TGAAACAAATAAACAAAGTTTAAT
Found at i:18201605 original size:48 final size:49
Alignment explanation
Indices: 18201543--18201651 Score: 166
Period size: 48 Copynumber: 2.2 Consensus size: 49
18201533 TAAACTAATA
* * *
18201543 AGAGTTTGACTGAAACAAATAAACAAAGTTTAATTGAAAC-AAATAAAT
1 AGAGTTTAATTGAAACAAATAAACAAAATTTAATTGAAACAAAATAAAT
* *
18201591 AGAGTTTAATTGAAACACATAAACAAAATTTAATTGAAACAAAATATAT
1 AGAGTTTAATTGAAACAAATAAACAAAATTTAATTGAAACAAAATAAAT
18201640 AGAGTTTAATTG
1 AGAGTTTAATTG
18201652 GAAGATTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 36 0.65
49 19 0.35
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.28
Consensus pattern (49 bp):
AGAGTTTAATTGAAACAAATAAACAAAATTTAATTGAAACAAAATAAAT
Found at i:18203378 original size:15 final size:15
Alignment explanation
Indices: 18203358--18203387 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18203348 GGAAATATGG
18203358 AATGTTAAATGAATA
1 AATGTTAAATGAATA
*
18203373 AATGTTGAATGAATA
1 AATGTTAAATGAATA
18203388 GTATTGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (15 bp):
AATGTTAAATGAATA
Found at i:18203495 original size:36 final size:36
Alignment explanation
Indices: 18203455--18203526 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
18203445 ATATGTAAAC
18203455 TCACTAACCTTGTGAGACTTGTGATGTATATAGGTA
1 TCACTAACCTTGTGAGACTTGTGATGTATATAGGTA
*
18203491 TCACTAACCTTGTGCGACTTGTGATGTATATAGGTA
1 TCACTAACCTTGTGAGACTTGTGATGTATATAGGTA
18203527 ATTAATGAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (36 bp):
TCACTAACCTTGTGAGACTTGTGATGTATATAGGTA
Found at i:18205120 original size:238 final size:238
Alignment explanation
Indices: 18204700--18205173 Score: 786
Period size: 238 Copynumber: 2.0 Consensus size: 238
18204690 CTGAGAGATT
* * * * **
18204700 TGTCTGACATTGTCCCATGTTCAGTTGAATTGCCAAATGGTGGAATAATTGTAGTACTAAAAGAA
1 TGTCTGACATTATCCCATGTTCAGCTGAATTGCCAAATGGTGAAACAATTGTAACACTAAAAGAA
* *
18204765 GGAATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACATATTCTTTTTGTTCCTAATTTAGAATA
66 GGAATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACAAATTCTTTTTGTGCCTAATTTAGAATA
*
18204830 CAATTTGATTTCTATTTCACAACTTCTTAATGACTTAAATATGGTATTGCAAATCACTAACAAAA
131 CAATTTGATTTCTATTTCACAACTTCTTAATGACTCAAATATGGTATTGCAAATCACTAACAAAA
18204895 TATGTGTTATACATGACCGAAATACGAGGAGGCTGATTGGATC
196 TATGTGTTATACATGACCGAAATACGAGGAGGCTGATTGGATC
* *
18204938 TGTCTGACATTATCCCATGTTTAGCTGAATTGCTAAATGGTGAAACAATTGTAACACTAAAAGAA
1 TGTCTGACATTATCCCATGTTCAGCTGAATTGCCAAATGGTGAAACAATTGTAACACTAAAAGAA
* *
18205003 GGAATGGGGCATCTTGGAGAAGGATTGGAGTTGCAACAAATTCTTTTTGTGCCTAATTTAGAATA
66 GGAATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACAAATTCTTTTTGTGCCTAATTTAGAATA
* * * *
18205068 TAATTTGATTTCTATTTCACAACTTCTTAATTACTCAAATATGGTGTTGCAAATCACTAATAAAA
131 CAATTTGATTTCTATTTCACAACTTCTTAATGACTCAAATATGGTATTGCAAATCACTAACAAAA
*
18205133 TATGTGTTATACATGATCGAAATACGAGGAGGCTGATTGGA
196 TATGTGTTATACATGACCGAAATACGAGGAGGCTGATTGGA
18205174 GCGGGTGAAC
Statistics
Matches: 218, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
238 218 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (238 bp):
TGTCTGACATTATCCCATGTTCAGCTGAATTGCCAAATGGTGAAACAATTGTAACACTAAAAGAA
GGAATGAGGCATCTTGGAGAAGGATTGAAGTTGCAACAAATTCTTTTTGTGCCTAATTTAGAATA
CAATTTGATTTCTATTTCACAACTTCTTAATGACTCAAATATGGTATTGCAAATCACTAACAAAA
TATGTGTTATACATGACCGAAATACGAGGAGGCTGATTGGATC
Found at i:18208148 original size:40 final size:40
Alignment explanation
Indices: 18207972--18208148 Score: 171
Period size: 40 Copynumber: 4.5 Consensus size: 40
18207962 AATGATCTAA
* * * * *
18207972 CAGTG-TTACAGTATCACTGCTAATTCAGTTGT-ATACCG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTTATAATATCG
* * * * *
18208010 CAGTGTTTATAGTGTCACCGCCAGTTTAGTTGTAATGTCG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTTATAATATCG
* * * *
18208050 TAGTGTTTACAGTGTCCCTGCCAGTTTAG-TAGTAATATTG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTTA-TAATATCG
* *
18208090 CAGTGTTTAAAATGTCACTGCCAGTTCAGTTATAATATCG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTTATAATATCG
*
18208130 CAGTGGTTACAGTGTCACT
1 CAGTGTTTACAGTGTCACT
18208149 ATCTGTTCAG
Statistics
Matches: 111, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
38 5 0.05
39 22 0.20
40 82 0.74
41 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (40 bp):
CAGTGTTTACAGTGTCACTGCCAGTTCAGTTATAATATCG
Found at i:18208161 original size:80 final size:80
Alignment explanation
Indices: 18208009--18208167 Score: 201
Period size: 80 Copynumber: 2.0 Consensus size: 80
18207999 GTTGTATACC
* * * * * * * * *
18208009 GCAGTGTTTATAGTGTCACCGCCAGTTTAGTTGTAATGTCGTAGTGTTTACAGTGTCCCTGCCAG
1 GCAGTGTTTAAAATGTCACCGCCAGTTCAGTTATAATATCGCAGTGGTTACAGTGTCACTACCAG
*
18208074 TTTAGTAGTAATATT
66 TTCAGTAGTAATATT
* * *
18208089 GCAGTGTTTAAAATGTCACTGCCAGTTCAGTTATAATATCGCAGTGGTTACAGTGTCACTATCTG
1 GCAGTGTTTAAAATGTCACCGCCAGTTCAGTTATAATATCGCAGTGGTTACAGTGTCACTACCAG
18208154 TTCAGTAGTAATAT
66 TTCAGTAGTAATAT
18208168 CCACGTGGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (80 bp):
GCAGTGTTTAAAATGTCACCGCCAGTTCAGTTATAATATCGCAGTGGTTACAGTGTCACTACCAG
TTCAGTAGTAATATT
Found at i:18213245 original size:12 final size:12
Alignment explanation
Indices: 18213224--18213258 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
18213214 CTGGATACAT
*
18213224 GCCCGTGTGCTA
1 GCCCGTGTGCCA
*
18213236 GCCTGTGTGCCA
1 GCCCGTGTGCCA
18213248 GCCCGTGTGCC
1 GCCCGTGTGCC
18213259 CTCAAACAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.37, G:0.34, T:0.23
Consensus pattern (12 bp):
GCCCGTGTGCCA
Found at i:18217512 original size:16 final size:16
Alignment explanation
Indices: 18217491--18217533 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
18217481 ATTACAATTT
*
18217491 ATATATTAATAAGTAA
1 ATATATTAATAAATAA
18217507 ATATATT-ATAAAATAA
1 ATATATTAAT-AAATAA
*
18217523 ATATATAAATA
1 ATATATTAATA
18217534 TTAATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATATTAATAAATAA
Found at i:18229547 original size:18 final size:18
Alignment explanation
Indices: 18229524--18229558 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18229514 CTTACTAATC
18229524 TATGTATA-AAAATATATA
1 TATGTATACAAAA-ATATA
18229542 TATGTATACAAAAATAT
1 TATGTATACAAAAATAT
18229559 GTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (18 bp):
TATGTATACAAAAATATA
Found at i:18229964 original size:20 final size:20
Alignment explanation
Indices: 18229916--18229958 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
18229906 ATGCCCGCAA
18229916 CTACCGATACTTGTACACTT
1 CTACCGATACTTGTACACTT
18229936 CTACCGATACTTGTACACTT
1 CTACCGATACTTGTACACTT
18229956 CTA
1 CTA
18229959 TTGATAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (20 bp):
CTACCGATACTTGTACACTT
Found at i:18233288 original size:29 final size:29
Alignment explanation
Indices: 18233246--18233333 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
18233236 TTTTCCTCCA
18233246 TACTTTGGTGTTAGTTCCATGAAATGACT
1 TACTTTGGTGTTAGTTCCATGAAATGACT
18233275 TACTTTGGTGTTAGTTCCATGAAATGACT
1 TACTTTGGTGTTAGTTCCATGAAATGACT
18233304 TACTTTGGTGTTAGTTCCATGAAATGACT
1 TACTTTGGTGTTAGTTCCATGAAATGACT
18233333 T
1 T
18233334 TTGTCACTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (29 bp):
TACTTTGGTGTTAGTTCCATGAAATGACT
Found at i:18238371 original size:20 final size:20
Alignment explanation
Indices: 18238346--18238385 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18238336 ATTCAAACAT
18238346 ATTTTTTAATCACTTATATC
1 ATTTTTTAATCACTTATATC
*
18238366 ATTTTTTAATCACTTGTATC
1 ATTTTTTAATCACTTATATC
18238386 GCATGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTTTAATCACTTATATC
Found at i:18247256 original size:58 final size:59
Alignment explanation
Indices: 18247190--18247310 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 59
18247180 ACCCATCAAC
* * *
18247190 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTCAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTAAAATAACACTAAT
*
18247248 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAAATAACACTAAT
1 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTAAAATAACACTAAT
18247307 AAAC
1 AAAC
18247311 AACTCCTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 46 0.79
59 12 0.21
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (59 bp):
AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTAAAATAACACTAAT
Found at i:18250544 original size:6 final size:6
Alignment explanation
Indices: 18250519--18250569 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
18250509 ATGATTTGAA
*
18250519 AATGA- AATGA- AATTGA- AATGAG AATGAA AATGAG AATGAG AATGAG
1 AATGAG AATGAG AA-TGAG AATGAG AATGAG AATGAG AATGAG AATGAG
18250565 AATGA
1 AATGA
18250570 TATGAAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 10 0.24
6 32 0.76
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (6 bp):
AATGAG
Found at i:18250563 original size:35 final size:33
Alignment explanation
Indices: 18250518--18250590 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 33
18250508 GATGATTTGA
*
18250518 AAATGAAATGA-AATTGAAATGAGAATGAAAATG
1 AAATGAAATGAGAA-TGAAATGAAAATGAAAATG
* *
18250551 AGAATGAGAATGAGAATGATATGAAAATGGAAATG
1 A-AATGA-AATGAGAATGAAATGAAAATGAAAATG
18250586 AAATG
1 AAATG
18250591 GACTATAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.03
34 9 0.26
35 22 0.65
36 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.21
Consensus pattern (33 bp):
AAATGAAATGAGAATGAAATGAAAATGAAAATG
Found at i:18250592 original size:11 final size:10
Alignment explanation
Indices: 18250518--18250590 Score: 65
Period size: 12 Copynumber: 6.5 Consensus size: 10
18250508 GATGATTTGA
18250518 AAATGAAATG
1 AAATGAAATG
18250528 AAATTGAAATG
1 AAA-TGAAATG
18250539 AGAATGAAAATG
1 A-AATG-AAATG
18250551 AGAATGAGAATG
1 A-AATGA-AATG
*
18250563 AGAATGATATG
1 A-AATGAAATG
18250574 AAAATGGAAATG
1 -AAAT-GAAATG
18250586 AAATG
1 AAATG
18250591 GACTATAGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
10 4 0.07
11 21 0.38
12 30 0.55
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.21
Consensus pattern (10 bp):
AAATGAAATG
Found at i:18255055 original size:22 final size:22
Alignment explanation
Indices: 18255014--18255054 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
18255004 TTTGTGTTTA
18255014 AGTTTTGAGGGTTTTATTTTTG
1 AGTTTTGAGGGTTTTATTTTTG
18255036 AGTTTT-AGGG-TTTATTTTT
1 AGTTTTGAGGGTTTTATTTTT
18255055 TATCTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (22 bp):
AGTTTTGAGGGTTTTATTTTTG
Found at i:18258668 original size:27 final size:28
Alignment explanation
Indices: 18258638--18258691 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
18258628 TTAGAATAGG
*
18258638 AAAATGAGAAAA-AGAAAGAA-AAAAAAT
1 AAAAAGAGAAAAGA-AAAGAAGAAAAAAT
18258665 AAAAAGAGAAAAGAAAAGAAGAAAAAA
1 AAAAAGAGAAAAGAAAAGAAGAAAAAA
18258692 ATATTTGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (28 bp):
AAAAAGAGAAAAGAAAAGAAGAAAAAAT
Found at i:18258689 original size:21 final size:19
Alignment explanation
Indices: 18258644--18258690 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
18258634 TAGGAAAATG
18258644 AGAAAAAGAAAGAAAAAAA
1 AGAAAAAGAAAGAAAAAAA
*
18258663 ATAAAAAGAGAA-AAGAAAAGA
1 AGAAAAAGA-AAGAA-AAAA-A
18258684 AGAAAAA
1 AGAAAAA
18258691 AATATTTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.43
20 6 0.26
21 7 0.30
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AGAAAAAGAAAGAAAAAAA
Found at i:18264315 original size:109 final size:110
Alignment explanation
Indices: 18264123--18264320 Score: 256
Period size: 109 Copynumber: 1.8 Consensus size: 110
18264113 AACAGTTTTT
** * * * *
18264123 GATTTTAAAATAGGATGTTCAATTACTTAAGTTTAAAGAAAAACCATACTCAGCACGTTATGGCA
1 GATTTTAAAATAGGATACTCAATTACTTAAGTTCAAAGAAAAACCATACCCAACACGTTAGGGCA
***
18264188 CAATTTTTTGATTCCCCTAAAATAATAGAACATCGAGCATTTATC
66 CAATTTTCAAATTCCCCTAAAATAATAGAACATCGAGCATTTATC
* * * *
18264233 GATTTT-AAATAGGATACTCAATTATTTATGTTCAAAGAAAAACCATACCCAATATGTTAGGGCA
1 GATTTTAAAATAGGATACTCAATTACTTAAGTTCAAAGAAAAACCATACCCAACACGTTAGGGCA
18264297 CAATTTCTCAAATT-CCCTAAAATA
66 CAATTT-TCAAATTCCCCTAAAATA
18264321 GAAGAATATT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
109 64 0.86
110 10 0.14
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (110 bp):
GATTTTAAAATAGGATACTCAATTACTTAAGTTCAAAGAAAAACCATACCCAACACGTTAGGGCA
CAATTTTCAAATTCCCCTAAAATAATAGAACATCGAGCATTTATC
Found at i:18266966 original size:20 final size:19
Alignment explanation
Indices: 18266943--18267013 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
18266933 TCTCGACCTC
18266943 TATTTTTTCTTTTTCTTTCT
1 TATTTTTTCTTTTTCTTT-T
*
18266963 TATTTTTCCTTTTTCCTTTT
1 TATTTTTTCTTTTT-CTTTT
* *
18266983 TCTTTTTTCTTTTTTTTTT
1 TATTTTTTCTTTTTCTTTT
*
18267002 TCTTTTTT-TTTT
1 TATTTTTTCTTTT
18267014 GGTGAAATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.09
19 12 0.26
20 26 0.57
21 4 0.09
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (19 bp):
TATTTTTTCTTTTTCTTTT
Found at i:18266975 original size:7 final size:6
Alignment explanation
Indices: 18266946--18267013 Score: 75
Period size: 6 Copynumber: 10.8 Consensus size: 6
18266936 CGACCTCTAT
* *
18266946 TTTTTC TTTTTC TTTCTTA TTTTTCC TTTTTCC TTTTTC TTTTTTC TTTTTT
1 TTTTTC TTTTTC TTT-TTC TTTTT-C TTTTT-C TTTTTC -TTTTTC TTTTTC
18266998 TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTT
18267014 GGTGAAATAC
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.09
6 27 0.49
7 23 0.42
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:18266996 original size:13 final size:13
Alignment explanation
Indices: 18266945--18267013 Score: 88
Period size: 13 Copynumber: 5.4 Consensus size: 13
18266935 TCGACCTCTA
18266945 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
* *
18266958 TTTCTTATTTTTCC
1 TTTTTTCTTTTT-C
*
18266972 TTTTTCCTTTTTC
1 TTTTTTCTTTTTC
18266985 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
18266997 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
18267009 TTTTT
1 TTTTT
18267014 GGTGAAATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
12 17 0.35
13 22 0.45
14 10 0.20
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:18267923 original size:7 final size:7
Alignment explanation
Indices: 18267913--18267970 Score: 71
Period size: 7 Copynumber: 8.1 Consensus size: 7
18267903 GGTTTTCATC
*
18267913 TTTCCTT
1 TTTCTTT
18267920 TTTCTTT
1 TTTCTTT
18267927 TCTTCTTT
1 T-TTCTTT
*
18267935 TTTCTAT
1 TTTCTTT
*
18267942 TTTCTAT
1 TTTCTTT
*
18267949 TTTCTAT
1 TTTCTTT
18267956 TTTCTTT
1 TTTCTTT
18267963 TTTCTTT
1 TTTCTTT
18267970 T
1 T
18267971 CTTTTTGGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
7 40 0.85
8 7 0.15
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:18269572 original size:415 final size:415
Alignment explanation
Indices: 18268802--18269635 Score: 1391
Period size: 415 Copynumber: 2.0 Consensus size: 415
18268792 AAAATGCATG
*
18268802 CAAAAAGGCATTGATTCTAGTTCAATTCCATTAGAACAACTTTACTAGAAAACAAATTTCTTTAC
1 CAAAAAGACATTGATTCTAGTTCAATTCCATTAGAACAACTTTACTAGAAAACAAATTTCTTTAC
*
18268867 ATAAGGCAGATACATATATGGTCGTGCCTTAATGCTAAAAGCCTTAATCTTCCAAGCTAATTTTT
66 ATAAGGCAGATACATATATGGTCGTGCCTTAATGCTAAAAGCCTTAATCTTCCAAGCTAAATTTT
* * *
18268932 TCTCTGATTTAACTCCGATTTCAAGCTCAAAACATCGGTCTTGAATGGCTAACGTCTGCAAGTGG
131 GCTCCGATTTAACTCCGATTTCAAGCTCAAAACATCGGTCATGAATGGCTAACGTCTGCAAGTGG
* *
18268997 TTAGTCACTTCTCGTCTTTGGAACAAAGCTTCATTCGCAACATAGTCTCTATCTTTGACCTGCCT
196 TTAGTCACTTCTCCTCTATGGAACAAAGCTTCATTCGCAACATAGTCTCTATCTTTGACCTGCCT
*
18269062 GTGAAAGCGTTGAAGTTATTTTTCAATATTAATTGTTTGTTACTACAGTTTCCTGGAGAAGCTCA
261 GTGAAAGCGTTGAAGTTATTTTTCAATATTAACTGTTTGTTACTACAGTTTCCTGGAGAAGCTCA
* * *
18269127 ACTCGTAGTTCACAATTCCATAGTGAGACTT-AAAGTTCTTCTACCTTTTAACTCCTCATTATTG
326 ACTCGTAGTTCACAACTCCACAATGAGACTTGAAA-TTCTTCTACCTTTTAACTCCTCATTATTG
* *
18269191 GCTTAACTTGCCTTTCAGCTCAGTCA
390 GCCTAACTTGCCTTTCAACTCAGTCA
* *
18269217 CAAAAAGACATTGATTCTAGTTCAATTCCATTAGAACAACTTTATTAGAAAATAAATTTCTTTAC
1 CAAAAAGACATTGATTCTAGTTCAATTCCATTAGAACAACTTTACTAGAAAACAAATTTCTTTAC
* *
18269282 ATAAGGTAGATACATATATGGTCGTGCCTTAATGCTCAAAGCCTTAATCTTCCAAGCTAAATTTT
66 ATAAGGCAGATACATATATGGTCGTGCCTTAATGCTAAAAGCCTTAATCTTCCAAGCTAAATTTT
*
18269347 GCTCCGATTTAACTCCGATTTCAAGCTCAAAACATCGGTCATGAATGGCTAAGGTCTGCAAGTGG
131 GCTCCGATTTAACTCCGATTTCAAGCTCAAAACATCGGTCATGAATGGCTAACGTCTGCAAGTGG
* *
18269412 TTAGTCACTTCTCCTCTATGGAACAAAGCTTCGTTCGCAACATAGTCTCTATCTTTGACCTGCTT
196 TTAGTCACTTCTCCTCTATGGAACAAAGCTTCATTCGCAACATAGTCTCTATCTTTGACCTGCCT
* * * * *
18269477 GTGAAAGCGTTGAAGTTATTTTTTAATATTCACTGTTTGTTTCTATAGTTTCTTGGAGAAGCTCA
261 GTGAAAGCGTTGAAGTTATTTTTCAATATTAACTGTTTGTTACTACAGTTTCCTGGAGAAGCTCA
* * *
18269542 ACTTGTAGTTCACAACTCCACAATGAGACTTGAAATTCTTCTACCTTTTAACTCTTCATTCTTGG
326 ACTCGTAGTTCACAACTCCACAATGAGACTTGAAATTCTTCTACCTTTTAACTCCTCATTATTGG
*
18269607 CCTAACTTGCCTTTCAACTTAGTCA
391 CCTAACTTGCCTTTCAACTCAGTCA
18269632 CAAA
1 CAAA
18269636 TTCGAGACTA
Statistics
Matches: 389, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
415 386 0.99
416 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (415 bp):
CAAAAAGACATTGATTCTAGTTCAATTCCATTAGAACAACTTTACTAGAAAACAAATTTCTTTAC
ATAAGGCAGATACATATATGGTCGTGCCTTAATGCTAAAAGCCTTAATCTTCCAAGCTAAATTTT
GCTCCGATTTAACTCCGATTTCAAGCTCAAAACATCGGTCATGAATGGCTAACGTCTGCAAGTGG
TTAGTCACTTCTCCTCTATGGAACAAAGCTTCATTCGCAACATAGTCTCTATCTTTGACCTGCCT
GTGAAAGCGTTGAAGTTATTTTTCAATATTAACTGTTTGTTACTACAGTTTCCTGGAGAAGCTCA
ACTCGTAGTTCACAACTCCACAATGAGACTTGAAATTCTTCTACCTTTTAACTCCTCATTATTGG
CCTAACTTGCCTTTCAACTCAGTCA
Found at i:18273105 original size:109 final size:110
Alignment explanation
Indices: 18272951--18273154 Score: 268
Period size: 109 Copynumber: 1.9 Consensus size: 110
18272941 TAAATAACAC
*** * * * *
18272951 TTATCGATTTTAAAATAGGATGTTCAATTACTTAGGTTTAGAGAAAAA-TCATACTCAGCACGTT
1 TTATCGATTTTAAAATAGGACACTCAATTACTTAGGTTCAAAGAAAAACT-ATACCCAACACGTT
* *
18273015 AGGGCACAATTTTTCGATTCCCCTAAAATAATAGAACATCGAGCAT
65 AGGGCACAATTTCTCGAATCCCCTAAAATAATAGAACATCGAGCAT
* * *
18273061 TTATCGATTTT-AAATAGGACACTCAATTATTTAGGTTCAAAGAAAAACTATACCCAATATGTTA
1 TTATCGATTTTAAAATAGGACACTCAATTACTTAGGTTCAAAGAAAAACTATACCCAACACGTTA
*
18273125 GGGCATAATTTCTCGAATCCCCTAAAATAA
66 GGGCACAATTTCTCGAATCCCCTAAAATAA
18273155 AAGCAAATTA
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
109 68 0.85
110 12 0.15
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (110 bp):
TTATCGATTTTAAAATAGGACACTCAATTACTTAGGTTCAAAGAAAAACTATACCCAACACGTTA
GGGCACAATTTCTCGAATCCCCTAAAATAATAGAACATCGAGCAT
Found at i:18273392 original size:26 final size:27
Alignment explanation
Indices: 18273351--18273404 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
18273341 AAATAGAACG
18273351 AAATGATTAAATTTTAAAAAAAAAATA
1 AAATGATTAAATTTTAAAAAAAAAATA
* * *
18273378 AAATGATTTAA-TTTAAAATAATAATA
1 AAATGATTAAATTTTAAAAAAAAAATA
18273404 A
1 A
18273405 TAAGGTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (27 bp):
AAATGATTAAATTTTAAAAAAAAAATA
Found at i:18276941 original size:20 final size:20
Alignment explanation
Indices: 18276918--18276957 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18276908 TTTTATCGAT
18276918 ACCTATAA-ACAGACTACCGA
1 ACCTATAATACAG-CTACCGA
18276938 ACCTATAATACAGCTACCGA
1 ACCTATAATACAGCTACCGA
18276958 TACTAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.30, G:0.10, T:0.17
Consensus pattern (20 bp):
ACCTATAATACAGCTACCGA
Found at i:18286691 original size:33 final size:33
Alignment explanation
Indices: 18286626--18286717 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
18286616 TTGACTGCTA
* * **
18286626 GGGAGGGTGATGTTGAAGAGGCAGAAGTTGATG
1 GGGAGGGTGATGTTGAAGGGGTAGAAACTGATG
18286659 GGGAGGGTGATGTTGAAGGGGTAGAAACTGATG
1 GGGAGGGTGATGTTGAAGGGGTAGAAACTGATG
* * * *
18286692 GTGAAGGTGTTCTTGAAGGGGTAGAA
1 GGGAGGGTGATGTTGAAGGGGTAGAA
18286718 GCTATTGGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.27, C:0.03, G:0.47, T:0.23
Consensus pattern (33 bp):
GGGAGGGTGATGTTGAAGGGGTAGAAACTGATG
Found at i:18288095 original size:30 final size:30
Alignment explanation
Indices: 18288059--18288115 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
18288049 AAATTATGAG
* *
18288059 ATTTCATGATTTGGGAATAAGGGATTAGGC
1 ATTTCATGATTTGAGAATAAAGGATTAGGC
18288089 ATTTCATGATTTGAGAATAAAGGATTA
1 ATTTCATGATTTGAGAATAAAGGATTA
18288116 AGTAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
ATTTCATGATTTGAGAATAAAGGATTAGGC
Found at i:18288223 original size:16 final size:17
Alignment explanation
Indices: 18288186--18288234 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
18288176 CATGATTTGG
*
18288186 GGATTTTAA-AAATTAA
1 GGATTTTAAGATATTAA
18288202 GG-TTTTAAGATATT-A
1 GGATTTTAAGATATTAA
*
18288217 GGATTTTTAGAT-TTAA
1 GGATTTTAAGATATTAA
18288233 GG
1 GG
18288235 TTTCACGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (17 bp):
GGATTTTAAGATATTAA
Found at i:18291063 original size:14 final size:14
Alignment explanation
Indices: 18291044--18291073 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18291034 ATTTTTTAAC
18291044 ATAATCATTAGATA
1 ATAATCATTAGATA
18291058 ATAATCATTAGATA
1 ATAATCATTAGATA
18291072 AT
1 AT
18291074 GATTATGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
ATAATCATTAGATA
Found at i:18291453 original size:19 final size:19
Alignment explanation
Indices: 18291429--18291541 Score: 96
Period size: 20 Copynumber: 6.1 Consensus size: 19
18291419 AACTTATTTC
*
18291429 TTGATTTTTAAATTTACTT
1 TTGATTTTTAAATTTAATT
18291448 TTGATTTTTTAAATTTAATT
1 TTGA-TTTTTAAATTTAATT
* *
18291468 TCGATTTTTTAA-TT--TT
1 TTGATTTTTAAATTTAATT
18291484 TT-A-TTTTAAATTGTAATT
1 TTGATTTTTAAATT-TAATT
18291502 AAATT-ATTTTTAAA-TTAATT
1 ---TTGATTTTTAAATTTAATT
*
18291522 TTGATTTTTAAAATTAATT
1 TTGATTTTTAAATTTAATT
18291541 T
1 T
18291542 CTTTTTAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
14 6 0.08
15 2 0.03
16 4 0.05
17 2 0.03
18 13 0.17
19 18 0.23
20 22 0.28
21 4 0.05
22 7 0.09
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTGATTTTTAAATTTAATT
Found at i:18291547 original size:18 final size:17
Alignment explanation
Indices: 18291432--18291561 Score: 74
Period size: 20 Copynumber: 7.3 Consensus size: 17
18291422 TTATTTCTTG
*
18291432 ATTTTTAAATTTACTTTT
1 ATTTTTAAA-TTAATTTT
*
18291450 GATTTTTTAAATTTAATTTCG
1 -A-TTTTTAAA-TTAATTT-T
*
18291471 ATTTTTTAATT--TTTT
1 ATTTTTAAATTAATTTT
18291486 A-TTTTAAATTGTAATTAAATT
1 ATTTTTAAA-T-TAATT---TT
18291507 ATTTTTAAATTAATTTT
1 ATTTTTAAATTAATTTT
18291524 GATTTTTAAAATTAA-TTT
1 -ATTTTT-AAATTAATTTT
*
18291542 CTTTTT-AATT-ATTTT
1 ATTTTTAAATTAATTTT
18291557 ATTTT
1 ATTTT
18291562 ACAACCATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 30
0.71 0.05 0.23
Matches are distributed among these distances:
14 7 0.08
15 13 0.14
16 4 0.04
17 7 0.08
18 13 0.14
19 15 0.16
20 21 0.23
21 4 0.04
22 7 0.08
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTTAAATTAATTTT
Found at i:18291561 original size:15 final size:16
Alignment explanation
Indices: 18291505--18291561 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 16
18291495 TGTAATTAAA
18291505 TTATTTTTAAATTAATT
1 TTATTTTTAAATT-ATT
*
18291522 TTGATTTTTAAAATTAAT
1 TT-ATTTTT-AAATTATT
*
18291540 TTCTTTTT-AATTATT
1 TTATTTTTAAATTATT
18291555 TTATTTT
1 TTATTTT
18291562 ACAACCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.35
17 7 0.21
18 10 0.29
19 5 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTTTTAAATTATT
Found at i:18291587 original size:73 final size:72
Alignment explanation
Indices: 18291435--18291589 Score: 161
Period size: 73 Copynumber: 2.1 Consensus size: 72
18291425 TTTCTTGATT
* * ***
18291435 TTTAAATTTACTTTTGATTTTTTAAATTTAATTTCGATTTTTTAATTTTTTATTTTAAATTGTAA
1 TTTAAA-TTAATTTTGATTTTTTAAAATTAATTTC-A-TTTTTAATTTTTTATTTTAAACCATAA
**
18291500 TTAAATTATT
63 TTAAATTAAA
*
18291510 TTTAAATTAATTTTGA-TTTTTAAAATTAATTTC-TTTTTAATTATTTTATTTTACAACCATATT
1 TTTAAATTAATTTTGATTTTTTAAAATTAATTTCATTTTTAATT-TTTTATTTTA-AACCATAAT
*
18291573 TAATTTTAAA
64 TAA-ATTAAA
18291583 TTTAAAT
1 TTTAAAT
18291590 CTGGTATTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
70 9 0.13
71 10 0.15
72 8 0.12
73 26 0.38
74 9 0.13
75 6 0.09
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (72 bp):
TTTAAATTAATTTTGATTTTTTAAAATTAATTTCATTTTTAATTTTTTATTTTAAACCATAATTA
AATTAAA
Found at i:18294839 original size:17 final size:16
Alignment explanation
Indices: 18294808--18294841 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18294798 ATATAAAAAT
18294808 TTAAATTTAAATTTTA
1 TTAAATTTAAATTTTA
*
18294824 TTAAATATTTAATTTTA
1 TTAAAT-TTAAATTTTA
18294841 T
1 T
18294842 CTCTATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTTAAATTTTA
Found at i:18302301 original size:14 final size:14
Alignment explanation
Indices: 18302255--18302295 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
18302245 AAAATTTTGA
*
18302255 GGTTTAAGGTTTAG
1 GGTTTTAGGTTTAG
*
18302269 GGTTTTAGTTTTAG
1 GGTTTTAGGTTTAG
18302283 GGTTTTAGGTTTA
1 GGTTTTAGGTTTA
18302296 AAGTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (14 bp):
GGTTTTAGGTTTAG
Found at i:18302871 original size:27 final size:27
Alignment explanation
Indices: 18302812--18302874 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
18302802 GATACTCTTG
* *
18302812 GCCTGACCAACCCGTACTATGGCCATG
1 GCCTGACCAACCCGTACTATAGCCATC
* **
18302839 GCCTGACCAACCCGTATTATAGTTATC
1 GCCTGACCAACCCGTACTATAGCCATC
*
18302866 GTCTGACCA
1 GCCTGACCA
18302875 CTCGAGAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (27 bp):
GCCTGACCAACCCGTACTATAGCCATC
Found at i:18303092 original size:22 final size:21
Alignment explanation
Indices: 18303062--18303102 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18303052 AACTAACATT
* *
18303062 GTTTGCCCATCATATAAATATG
1 GTTTCCCCATC-TAGAAATATG
18303084 GTTTCCCCATCTAGAAATA
1 GTTTCCCCATCTAGAAATA
18303103 CCATTGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
GTTTCCCCATCTAGAAATATG
Found at i:18305200 original size:21 final size:21
Alignment explanation
Indices: 18305154--18305204 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18305144 AGAAAATTTT
18305154 ATAAAATA-AATGAAAAACAA
1 ATAAAATATAATGAAAAACAA
* *
18305174 AAAAAATATAAT-AACATACAA
1 ATAAAATATAATGAA-AAACAA
18305195 ATAAAATATA
1 ATAAAATATA
18305205 TAAACACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.20
Consensus pattern (21 bp):
ATAAAATATAATGAAAAACAA
Found at i:18305210 original size:21 final size:21
Alignment explanation
Indices: 18305154--18305220 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
18305144 AGAAAATTTT
*
18305154 ATAAAATAAATGAAA-A-ACAA
1 ATAAAATATAT-AAACATACAA
*
18305174 AAAAAATATA-ATAACATACAA
1 ATAAAATATATA-AACATACAA
*
18305195 ATAAAATATATAAACACTATAA
1 ATAAAATATATAAACA-TACAA
18305217 ATAA
1 ATAA
18305221 GAAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 2 0.05
20 9 0.24
21 17 0.45
22 9 0.24
ACGTcount: A:0.70, C:0.07, G:0.01, T:0.21
Consensus pattern (21 bp):
ATAAAATATATAAACATACAA
Found at i:18305476 original size:26 final size:25
Alignment explanation
Indices: 18305447--18305521 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 25
18305437 CATTTAATCA
* *
18305447 AAAATTAAATTAACAAACAATTTTTT
1 AAAATTAAATTAAAAAACAA-ATTTT
*
18305473 AAAAATAAATTAAAATCAACAAATTTT
1 AAAATTAAATTAAAA--AACAAATTTT
18305500 AAAATTTAAATTAAAAAACAAA
1 AAAA-TTAAATTAAAAAACAAA
18305522 CAAACCCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 19 0.45
27 8 0.19
28 15 0.36
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAATTAAATTAAAAAACAAATTTT
Found at i:18306322 original size:21 final size:22
Alignment explanation
Indices: 18306287--18306327 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18306277 CCATATTTCC
* *
18306287 GAAAATATATTACAA-ATAAGT
1 GAAAATAAATAACAACATAAGT
18306308 GAAAATAAATAACAACATAA
1 GAAAATAAATAACAACATAA
18306328 AGTTATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (22 bp):
GAAAATAAATAACAACATAAGT
Found at i:18313045 original size:31 final size:31
Alignment explanation
Indices: 18312972--18313048 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
18312962 TTGGTCTAAT
*
18312972 TTAAGTTTTGAATTTGACAATTGTTTTCACA
1 TTAAGATTTGAATTTGACAATTGTTTTCACA
* * *
18313003 TTGAGACTTGAATTTGGCAATTGTTTTCACA
1 TTAAGATTTGAATTTGACAATTGTTTTCACA
18313034 TTAATG-TTTGAATTT
1 TTAA-GATTTGAATTT
18313049 TAGGGTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (31 bp):
TTAAGATTTGAATTTGACAATTGTTTTCACA
Found at i:18313644 original size:21 final size:20
Alignment explanation
Indices: 18313620--18313659 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
18313610 ATGATTTAGT
18313620 TTTTGAAATATATATTTTTTA
1 TTTTGAAATATAT-TTTTTTA
*
18313641 TTTTGATATATATTTTTTT
1 TTTTGAAATATATTTTTTT
18313660 GTCTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTGAAATATATTTTTTTA
Found at i:18318980 original size:28 final size:27
Alignment explanation
Indices: 18318927--18318980 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
18318917 TTTAATTTCG
** *
18318927 AAATTGAGTAAATTAATTTTTCTCAAA
1 AAATTGAGTAAATTAATTCCTATCAAA
*
18318954 AAATTGGAGTAATTTAATTCCTATCAA
1 AAATT-GAGTAAATTAATTCCTATCAA
18318981 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (27 bp):
AAATTGAGTAAATTAATTCCTATCAAA
Found at i:18320320 original size:21 final size:21
Alignment explanation
Indices: 18320293--18320343 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
18320283 GGATTATGTA
18320293 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * *
18320314 GTTTGGATTTCTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
18320335 ATTTGGATT
1 ATTTGGATT
18320344 ATGCTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:18321225 original size:14 final size:15
Alignment explanation
Indices: 18321197--18321226 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18321187 AAGGGAGAGC
18321197 AATGGGAGAAGGAAA
1 AATGGGAGAAGGAAA
18321212 AATGGGAG-AGGAAA
1 AATGGGAGAAGGAAA
18321226 A
1 A
18321227 GTCAAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.40, T:0.07
Consensus pattern (15 bp):
AATGGGAGAAGGAAA
Found at i:18325974 original size:21 final size:22
Alignment explanation
Indices: 18325949--18325998 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
18325939 TTTTTAATTA
18325949 TTTTATTCA-AAATTA-ATAAAT
1 TTTTATT-ATAAATTAGATAAAT
*
18325970 TTTTATTATAAATTAGATCAAT
1 TTTTATTATAAATTAGATAAAT
*
18325992 TCTTATT
1 TTTTATT
18325999 TAATTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTATTATAAATTAGATAAAT
Found at i:18325997 original size:22 final size:21
Alignment explanation
Indices: 18325958--18325998 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18325948 ATTTTATTCA
*
18325958 AAATTAATAAATTTTTATTAT
1 AAATTAATAAATTCTTATTAT
*
18325979 AAATTAGATCAATTCTTATT
1 AAATTA-ATAAATTCTTATT
18325999 TAATTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATTAATAAATTCTTATTAT
Found at i:18326265 original size:18 final size:18
Alignment explanation
Indices: 18326233--18326284 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
18326223 TTGGGATGAG
18326233 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
18326249 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
18326267 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
18326285 CAATTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:18327293 original size:19 final size:19
Alignment explanation
Indices: 18327254--18327289 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18327244 AAAAAAGCAA
*
18327254 AAGTTCAAGTAAACAACAT
1 AAGTCCAAGTAAACAACAT
18327273 AAGTCCAAGT-AACAACA
1 AAGTCCAAGTAAACAACA
18327290 ATAACACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (19 bp):
AAGTCCAAGTAAACAACAT
Found at i:18327403 original size:13 final size:13
Alignment explanation
Indices: 18327366--18327408 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18327356 ACATCATTCC
18327366 AAACAACAACAAAA
1 AAACAAC-ACAAAA
* *
18327380 AAAAAAAACAAAA
1 AAACAACACAAAA
18327393 AAACAACACAACAA
1 AAACAACACAA-AA
18327407 AA
1 AA
18327409 GTCAAATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAACACAAAA
Found at i:18327723 original size:57 final size:58
Alignment explanation
Indices: 18327625--18327743 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 58
18327615 AAAAGGAGTT
* *
18327625 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGAGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
* *
18327683 GTTTATGAGTGTT-TTTAAGAATGAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
18327740 GTTT
1 GTTT
18327744 GTTGATGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 44 0.77
58 13 0.23
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
Found at i:18328631 original size:29 final size:29
Alignment explanation
Indices: 18328588--18328665 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
18328578 TGGTATCAGT
* *
18328588 AAAACACTTCTAACTGGAAGCGTTAAAGG
1 AAAACGCTTCCAACTGGAAGCGTTAAAGG
*
18328617 AAAACGCTTCCAACTGGAAGCTTTAAAGG
1 AAAACGCTTCCAACTGGAAGCGTTAAAGG
*
18328646 AAAACGCTTCCAGCTGGAAG
1 AAAACGCTTCCAACTGGAAG
18328666 TGCTTTCCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (29 bp):
AAAACGCTTCCAACTGGAAGCGTTAAAGG
Found at i:18329012 original size:19 final size:19
Alignment explanation
Indices: 18328983--18329031 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
18328973 AGTAAGAAGT
18328983 AAAAAAT-AAAAACCCTAA
1 AAAAAATCAAAAACCCTAA
*
18329001 AAAAAATC-AAAACCCTAC
1 AAAAAATCAAAAACCCTAA
**
18329019 AATTAATCAAAAA
1 AAAAAATCAAAAA
18329032 AATTAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAAATCAAAAACCCTAA
Found at i:18329030 original size:18 final size:18
Alignment explanation
Indices: 18328983--18329017 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18328973 AGTAAGAAGT
*
18328983 AAAAAATAAAAACCCTAA
1 AAAAAATCAAAACCCTAA
18329001 AAAAAATCAAAACCCTA
1 AAAAAATCAAAACCCTA
18329018 CAATTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAATCAAAACCCTAA
Found at i:18329037 original size:13 final size:13
Alignment explanation
Indices: 18329019--18329050 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18329009 AAAACCCTAC
18329019 AATTAATCAAAAA
1 AATTAATCAAAAA
*
18329032 AATTAATCTAAAA
1 AATTAATCAAAAA
18329045 AATTAA
1 AATTAA
18329051 AAAAATCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAATCAAAAA
Found at i:18329199 original size:41 final size:41
Alignment explanation
Indices: 18329149--18329250 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
18329139 GTACCATGCA
*
18329149 AAAAGCACTTTCA-CCAGGAAGCGTTTTTCTGCATTTCACCTG
1 AAAA-CACTTCCAGCCA-GAAGCGTTTTTCTGCATTTCACCTG
*
18329191 AAAACACTTCCAGCTAGAAGCGTTTTTCTGCATTTCACCTG
1 AAAACACTTCCAGCCAGAAGCGTTTTTCTGCATTTCACCTG
*
18329232 AAAA-ACTTCCAGCTAGAAG
1 AAAACACTTCCAGCCAGAAG
18329251 TGCTTTCAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
40 15 0.26
41 36 0.63
42 6 0.11
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (41 bp):
AAAACACTTCCAGCCAGAAGCGTTTTTCTGCATTTCACCTG
Found at i:18333194 original size:17 final size:18
Alignment explanation
Indices: 18333155--18333194 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
18333145 AGACTGTAGC
18333155 AATAATGATATAAAATAT
1 AATAATGATATAAAATAT
* *
18333173 CATAAT-ATATAAAATTT
1 AATAATGATATAAAATAT
18333190 AATAA
1 AATAA
18333195 ACATTAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
AATAATGATATAAAATAT
Found at i:18334916 original size:14 final size:15
Alignment explanation
Indices: 18334897--18334934 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
18334887 ATTAACTTTT
18334897 AATTCAATAATT-AA
1 AATTCAATAATTCAA
18334911 AATTC-ATCAATTCAA
1 AATTCAAT-AATTCAA
18334926 AATTCAATA
1 AATTCAATA
18334935 TAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.10
14 9 0.43
15 8 0.38
16 2 0.10
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:18340531 original size:38 final size:39
Alignment explanation
Indices: 18340469--18340542 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
18340459 CAATTTATAT
* *
18340469 ATTTAAAATTTTTAATAAATATTTTTTGAGTTTTTACAC
1 ATTTAAAATTTTTAATAAATATTTTTAGAATTTTTACAC
* * *
18340508 ATTTGAAA-TTTTCATATATATTTTTAGAATTTTTA
1 ATTTAAAATTTTTAATAAATATTTTTAGAATTTTTA
18340543 AAAATAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 23 0.77
39 7 0.23
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.55
Consensus pattern (39 bp):
ATTTAAAATTTTTAATAAATATTTTTAGAATTTTTACAC
Found at i:18348825 original size:23 final size:23
Alignment explanation
Indices: 18348795--18348841 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18348785 TGTTTACAGT
18348795 CTCACTACCAGTTCAGATATAGC
1 CTCACTACCAGTTCAGATATAGC
18348818 CTCACTACCAGTTCAGATATAGC
1 CTCACTACCAGTTCAGATATAGC
18348841 C
1 C
18348842 AAGGGTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.26
Consensus pattern (23 bp):
CTCACTACCAGTTCAGATATAGC
Found at i:18354409 original size:160 final size:159
Alignment explanation
Indices: 18354130--18354451 Score: 527
Period size: 160 Copynumber: 2.0 Consensus size: 159
18354120 TAACAACTTT
*
18354130 TTCAACTGGTTAAAACTTTGTTGACACTTTTCAGACCACACGAACTGAATGTTTTTCTGTAGCAA
1 TTCAACTGGTTAAAACTTTGCTGACACTTTTCAGACCACACGAACTGAATGTTTTTCTGTAGCAA
* * * *
18354195 CCTCATCATCGGTAAGACTATTATGGAAAAGCCTTTCACGAACCGACGGTAATATCCTGCTAATC
66 CCTCATCATCGATAAGACTATGATGGAAAAGCCTTTCACGAACCGACAGTAATATCCTGCCAATC
* * *
18354260 CTAGGAAACTAAGTACCTTAGAGACATTC
131 CTAGGAAACTAAGTACCTCAAAAACATTC
*
18354289 TTCAACTGGTTAAAACTTTGCTGACACTTTTCAGACCATACGAACTGAATGTTTTTTCTGTAGCA
1 TTCAACTGGTTAAAACTTTGCTGACACTTTTCAGACCACACGAACTGAATG-TTTTTCTGTAGCA
* *
18354354 ACCTCATCATCGATAAGGCTATGATGGAAAAGCCTTTCACGAACCGACAGTAATATCTTGCCAAT
65 ACCTCATCATCGATAAGACTATGATGGAAAAGCCTTTCACGAACCGACAGTAATATCCTGCCAAT
*
18354419 CCTAGGAAACTACGTACCTCAAAAACATTC
130 CCTAGGAAACTAAGTACCTCAAAAACATTC
18354449 TTC
1 TTC
18354452 GGTATCTTCC
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
159 49 0.33
160 101 0.67
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (159 bp):
TTCAACTGGTTAAAACTTTGCTGACACTTTTCAGACCACACGAACTGAATGTTTTTCTGTAGCAA
CCTCATCATCGATAAGACTATGATGGAAAAGCCTTTCACGAACCGACAGTAATATCCTGCCAATC
CTAGGAAACTAAGTACCTCAAAAACATTC
Found at i:18361821 original size:24 final size:26
Alignment explanation
Indices: 18361770--18361826 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
18361760 AAATTATAAG
* *
18361770 TAAAATAAAATAGAAATTTTTTTGAC
1 TAAAATAAAATAGAAATTTTATTAAC
*
18361796 TAAAA-AAAATATAAA-TTTATTAAC
1 TAAAATAAAATAGAAATTTTATTAAC
18361820 TAAAATA
1 TAAAATA
18361827 TAAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.44
25 10 0.37
26 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (26 bp):
TAAAATAAAATAGAAATTTTATTAAC
Found at i:18361844 original size:21 final size:20
Alignment explanation
Indices: 18361796--18361845 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
18361786 TTTTTTTGAC
*
18361796 TAAAA-AAAATATAAATTTA
1 TAAAATAAAATATAAATATA
* *
18361815 TTAACTAAAATATAAAATATA
1 TAAAATAAAATAT-AAATATA
18361836 TAAAATAAAA
1 TAAAATAAAA
18361846 GAACCAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 7 0.29
21 14 0.58
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATAAAATATAAATATA
Found at i:18363224 original size:20 final size:21
Alignment explanation
Indices: 18363182--18363227 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
18363172 CACAGGGGAT
*
18363182 ATGTTGCAACATAAGCCTCCA
1 ATGTTGCAACATAAGCATCCA
*
18363203 ATGTTGCAACAT-AGGATCCA
1 ATGTTGCAACATAAGCATCCA
18363223 ATGTT
1 ATGTT
18363228 CTGACACCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (21 bp):
ATGTTGCAACATAAGCATCCA
Found at i:18370095 original size:16 final size:17
Alignment explanation
Indices: 18370074--18370108 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18370064 GGATGTTACA
*
18370074 ATCTATAT-TTTATATG
1 ATCTATATATGTATATG
18370090 ATCTATATATGTATATG
1 ATCTATATATGTATATG
18370107 AT
1 AT
18370109 ATATCCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (17 bp):
ATCTATATATGTATATG
Found at i:18370801 original size:26 final size:25
Alignment explanation
Indices: 18370758--18370810 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
18370748 GCTTTAGTTA
** *
18370758 AAGACTGTGATATGAACTATGAACT
1 AAGACTGTGATAAAAACTATAAACT
*
18370783 AAGACATGTGATAAAAACTCTAAACT
1 AAGAC-TGTGATAAAAACTATAAACT
18370809 AA
1 AA
18370811 TCTGTACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (25 bp):
AAGACTGTGATAAAAACTATAAACT
Found at i:18373551 original size:16 final size:16
Alignment explanation
Indices: 18373526--18373561 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18373516 TGGTTCATTG
18373526 TAATGGAATAGAGCTA
1 TAATGGAATAGAGCTA
* *
18373542 TAATGTAATAGAGCTG
1 TAATGGAATAGAGCTA
18373558 TAAT
1 TAAT
18373562 AGGGCTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGCTA
Found at i:18373641 original size:44 final size:46
Alignment explanation
Indices: 18373559--18373647 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
18373549 ATAGAGCTGT
*
18373559 AATAGGGCTGTAATCAGTATTTCAGTTGTTTGGTTGAATGGAATGG
1 AATAGAGCTGTAATCAGTATTTCAGTTGTTTGGTTGAATGGAATGG
*
18373605 AATAGAGCTGTAAT-AGTA-TTC-TTGTGTTTGGTTGAATGGAATG
1 AATAGAGCTGTAATCAGTATTTCAGT-TGTTTGGTTGAATGGAATG
18373648 ATGCTGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 22 0.55
45 4 0.10
46 13 0.32
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.38
Consensus pattern (46 bp):
AATAGAGCTGTAATCAGTATTTCAGTTGTTTGGTTGAATGGAATGG
Found at i:18375284 original size:2 final size:2
Alignment explanation
Indices: 18375277--18375313 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18375267 ATTCTAAATC
18375277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18375314 CTAGTTACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18387690 original size:195 final size:195
Alignment explanation
Indices: 18387284--18387730 Score: 476
Period size: 195 Copynumber: 2.3 Consensus size: 195
18387274 AAAATCGACA
* *
18387284 CGATGGCTGAGGTACCACATATGTTGCT-AGTCCTCAACAGCTCGTGTGAGCAGCATCGTGAGTC
1 CGATGGCTGAGGTACCGCATATGTTG-TGAGTCCTCAACAGCTCGTGTGAGCAGCATCGTGACTC
* * * *
18387348 AAGAAATGAGAAAAGAATCGAATAATGGATTACATGCCCTACGATGTTTGAGATTTATGCATAAG
65 AAGAAATGAGAAAAGAATCCAATAATGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAG
* * * * * * *
18387413 TGCATATTCTCGATAGCTCGTGTGAGCAGCATTGTTAGGGAACAGTTATATGCACAAATATCGTA
130 TCCATACTCTCGACAGATCGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAAACACCGTA
*
18387478 T
195 C
* * *
18387479 CGATGGCTGAGGTACCGCATATGTTGTGAATCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
1 CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAGCATCGTGACTCA
* * * * * * * * * * *
18387544 GGAAA-GAGATATGGATCCTA-AATGGATTATAGGCTCTACGGTGGTTGGGA-CTATGCTTTA-T
66 AGAAATGAGAAAAGAATCCAATAATGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGT
* *
18387605 CCATACTCTCGACAGATCGTGTGAGCAGCATCGTTAGGGAACAGTT-TATAGTACTGATAGGCAC
131 CCATACTCTCGACAGATCGTGTGAGCAGCATCGTTAGGGAACAGTTATAT-GCAC--A-A-ACAC
18387669 CGTAC
191 CGTAC
* * ** *
18387674 CGATGGTTGGGGTACCGCATAT-TTACGAGTCCTCAATAGCTCGTGTGAGCAGCATCG
1 CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAGCATCG
18387731 AGTACTGGTA
Statistics
Matches: 209, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
190 3 0.01
191 45 0.22
192 7 0.03
193 25 0.12
194 42 0.20
195 87 0.42
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAGCATCGTGACTCA
AGAAATGAGAAAAGAATCCAATAATGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGT
CCATACTCTCGACAGATCGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAAACACCGTAC
Found at i:18397465 original size:7 final size:7
Alignment explanation
Indices: 18397436--18397501 Score: 57
Period size: 7 Copynumber: 9.9 Consensus size: 7
18397426 AGCGTTGATT
18397436 GTTGACC
1 GTTGACC
*
18397443 ATTGACC
1 GTTGACC
18397450 GTTGA--
1 GTTGACC
*
18397455 -TTGAGC
1 GTTGACC
*
18397461 GTTGACT
1 GTTGACC
18397468 GTTGACC
1 GTTGACC
*
18397475 ATTGACC
1 GTTGACC
*
18397482 GTTGATC
1 GTTGACC
*
18397489 GTTGATC
1 GTTGACC
18397496 GTTGAC
1 GTTGAC
18397502 TTTTTCCGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
4 4 0.09
7 43 0.91
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (7 bp):
GTTGACC
Found at i:18397471 original size:32 final size:32
Alignment explanation
Indices: 18397425--18397487 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
18397415 ACCTTTGGCC
*
18397425 GAGCGTTGATTGTTGACCATTGACCGTTGATT
1 GAGCGTTGACTGTTGACCATTGACCGTTGATT
18397457 GAGCGTTGACTGTTGACCATTGACCGTTGAT
1 GAGCGTTGACTGTTGACCATTGACCGTTGAT
18397488 CGTTGATCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (32 bp):
GAGCGTTGACTGTTGACCATTGACCGTTGATT
Found at i:18398686 original size:6 final size:6
Alignment explanation
Indices: 18398656--18398699 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
18398646 AATTATAGAC
* *
18398656 TTATAT TATATAC TTATAT TT-TAT TTATAT TTACAT TTATAT TT
1 TTATAT T-TATAT TTATAT TTATAT TTATAT TTATAT TTATAT TT
18398700 GTGAATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 22 0.69
7 5 0.16
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:18400876 original size:21 final size:21
Alignment explanation
Indices: 18400839--18400889 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
18400829 TCATTAAGCT
*
18400839 TTAA-TAAATCATTTTTAAATC
1 TTAATTAAATCATATTTAAA-C
*
18400860 TTAATTAAATC-TATTTATAC
1 TTAATTAAATCATATTTAAAC
18400880 TTAATATAAA
1 TTAAT-TAAA
18400890 CCATGTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTAAATCATATTTAAAC
Found at i:18406896 original size:67 final size:65
Alignment explanation
Indices: 18406781--18406968 Score: 252
Period size: 67 Copynumber: 2.9 Consensus size: 65
18406771 AACGCTAGGA
* * * * *
18406781 AGCAATCAAATTAAAGCAGAAGGTAA-TTAAGGGGACCAAAGATGAAGTTAAACCAACACTGGAG
1 AGCAATTAAATTAAAGCAAAAAGCAATTTAAAGGGACCAAAGATGAAGTTAAACCAACACTGGAG
* *
18406845 AGCAATTAAATTAAAGCAAAAAAGCAATTTAAAGGGACCAAAAGATGAAGTTAAATCAACGCTGG
1 AGCAATTAAATTAAAGC-AAAAAGCAATTTAAAGGGACC-AAAGATGAAGTTAAACCAACACTGG
18406910 AG
64 AG
* * * *
18406912 AGTAATTAAATTAAAGCAAAAAGCAATTTGAAGGGACCAAAGATGAAATTAATCCAA
1 AGCAATTAAATTAAAGCAAAAAGCAATTTAAAGGGACCAAAGATGAAGTTAAACCAA
18406969 AAGTAAAACG
Statistics
Matches: 109, Mismatches: 12, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
64 16 0.15
65 22 0.20
66 30 0.28
67 41 0.38
ACGTcount: A:0.50, C:0.12, G:0.20, T:0.18
Consensus pattern (65 bp):
AGCAATTAAATTAAAGCAAAAAGCAATTTAAAGGGACCAAAGATGAAGTTAAACCAACACTGGAG
Found at i:18409708 original size:50 final size:50
Alignment explanation
Indices: 18409648--18409749 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
18409638 AGTATGGTAA
18409648 GTTCCAGTTAATGGTTGTTTATTGTCTCAAGTGTGATCTGAGTTTGAGTC
1 GTTCCAGTTAATGGTTGTTTATTGTCTCAAGTGTGATCTGAGTTTGAGTC
18409698 GTTCCAGTTAATGGTTGTTTATTGTCTCAAGTGTGATCTGAGTTTGAGTC
1 GTTCCAGTTAATGGTTGTTTATTGTCTCAAGTGTGATCTGAGTTTGAGTC
18409748 GT
1 GT
18409750 GTCAGTCGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (50 bp):
GTTCCAGTTAATGGTTGTTTATTGTCTCAAGTGTGATCTGAGTTTGAGTC
Found at i:18412132 original size:64 final size:65
Alignment explanation
Indices: 18412005--18412375 Score: 424
Period size: 64 Copynumber: 5.9 Consensus size: 65
18411995 ACGCTAGGAA
* * * * *
18412005 GCAATCAAATTAAAGCAGAAGGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGAGG
1 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTGGAGG
* * *
18412070 GCAATTAAATTAAAGCAAAAAGCAATTTAAAGGG-CCAAAGATGAAGTTAAACCAACGTTGGAGA
1 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTGGAGG
* **
18412134 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAATTAATTCAA------A-G
1 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTGGAGG
* * * *** * *
18412192 GTAA--AACGTTAGAAG-GAGGGGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGA
1 GCAATTAA-ATTA-AAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTGGA
18412254 GG
64 GG
* * *
18412256 GCAATTAAATTAAAGCAAAAAGCAATTTAAAGGG-CCAAAGATGAAGTTAAACCAACGTTGGAGA
1 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTGGAGG
* *
18412320 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAATTAATCCAA
1 GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAA
18412376 AAGTAAAACG
Statistics
Matches: 254, Mismatches: 38, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
56 2 0.01
57 34 0.13
58 6 0.02
59 1 0.00
63 1 0.00
64 127 0.50
65 81 0.32
66 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (65 bp):
GCAATTAAATTAAAGCAAAAAGTAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTGGAGG
Found at i:18412339 original size:186 final size:186
Alignment explanation
Indices: 18412025--18412397 Score: 728
Period size: 186 Copynumber: 2.0 Consensus size: 186
18412015 TAAAGCAGAA
18412025 GGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGAGGGCAATTAAATTAAAGCAAAA
1 GGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGAGGGCAATTAAATTAAAGCAAAA
18412090 AGCAATTTAAAGGGCCAAAGATGAAGTTAAACCAACGTTGGAGAGCAATTAAATTAAAGCAAAAA
66 AGCAATTTAAAGGGCCAAAGATGAAGTTAAACCAACGTTGGAGAGCAATTAAATTAAAGCAAAAA
* *
18412155 GTAATTTAAAGGGACCAAAGATGAAATTAATTCAAAGGTAAAACGTTAGAAGGAGG
131 GTAATTTAAAGGGACCAAAGATGAAATTAATCCAAAAGTAAAACGTTAGAAGGAGG
18412211 GGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGAGGGCAATTAAATTAAAGCAAAA
1 GGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGAGGGCAATTAAATTAAAGCAAAA
18412276 AGCAATTTAAAGGGCCAAAGATGAAGTTAAACCAACGTTGGAGAGCAATTAAATTAAAGCAAAAA
66 AGCAATTTAAAGGGCCAAAGATGAAGTTAAACCAACGTTGGAGAGCAATTAAATTAAAGCAAAAA
18412341 GTAATTTAAAGGGACCAAAGATGAAATTAATCCAAAAGTAAAACGTTAGAAGGAGG
131 GTAATTTAAAGGGACCAAAGATGAAATTAATCCAAAAGTAAAACGTTAGAAGGAGG
18412397 G
1 G
18412398 CTTCAACCTC
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (186 bp):
GGTAATTTAAGGGGACCAAAGATGAAGTTAGACCAACGCTGGAGGGCAATTAAATTAAAGCAAAA
AGCAATTTAAAGGGCCAAAGATGAAGTTAAACCAACGTTGGAGAGCAATTAAATTAAAGCAAAAA
GTAATTTAAAGGGACCAAAGATGAAATTAATCCAAAAGTAAAACGTTAGAAGGAGG
Found at i:18415145 original size:2 final size:2
Alignment explanation
Indices: 18415138--18415166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18415128 ACTTACATAC
18415138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18415167 ACATTTATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18415774 original size:90 final size:87
Alignment explanation
Indices: 18415584--18415809 Score: 244
Period size: 90 Copynumber: 2.5 Consensus size: 87
18415574 TTAAGGGTGT
* *
18415584 AAAAAGCCCTCAAA-CTTTCTCAAAAAAGCAATTAAGTCCCTCTTTTTTATTGCACCATTTGGAT
1 AAAAAGCCCTCAAACCTTT-TAAAAAAAGCAATTAAGTCCCTCTTTTTTATTGCACCAATTGGAT
*
18415648 ACTTAAACTTTCAAAATGTATCA
65 ACTTAAACTTTCAAAATGCATCA
* * *
18415671 AAAAAGCCGTCAAACCTTTTAAAAAAAGCAATTAAG-CCCTTACTTTTTTTTTTGCACTTAATTG
1 AAAAAGCCCTCAAACCTTTTAAAAAAAGCAATTAAGTCCC-T-C-TTTTTTATTGCAC-CAATTG
* *
18415735 CG-TACTTAAACTTTTAAAATGCATTA
62 -GATACTTAAACTTTCAAAATGCATCA
* *
18415761 AAAATA-CCCTCAAACTTTTTCAAAAAAAAGCAATTAAGTCTCTACTTTT
1 AAAA-AGCCCTCAAACCTTTT--AAAAAAAGCAATTAAGTCCCT-CTTTT
18415810 ATTAAAAAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
86 3 0.03
87 30 0.25
88 5 0.04
89 12 0.10
90 41 0.35
91 6 0.05
92 19 0.16
93 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.35
Consensus pattern (87 bp):
AAAAAGCCCTCAAACCTTTTAAAAAAAGCAATTAAGTCCCTCTTTTTTATTGCACCAATTGGATA
CTTAAACTTTCAAAATGCATCA
Found at i:18415900 original size:21 final size:20
Alignment explanation
Indices: 18415876--18415930 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
18415866 TTAAATTTTT
18415876 AAAAAATATTAAAAATTAGAA
1 AAAAAATATTAAAAA-TAGAA
* *
18415897 AAAAAAT-TATAAAAATCGTA
1 AAAAAATAT-TAAAAATAGAA
18415917 AAAAAATA-TAAAAA
1 AAAAAATATTAAAAA
18415931 GTAAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 6 0.20
20 11 0.37
21 13 0.43
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATATTAAAAATAGAA
Found at i:18415910 original size:9 final size:9
Alignment explanation
Indices: 18415898--18416065 Score: 73
Period size: 9 Copynumber: 17.8 Consensus size: 9
18415888 AAATTAGAAA
18415898 AAAAATTAT
1 AAAAATTAT
18415907 AAAAATCGTA-
1 AAAAAT--TAT
*
18415917 AAAAAATAT
1 AAAAATTAT
*
18415926 AAAAAGTA-
1 AAAAATTAT
**
18415934 AAATTTTAT
1 AAAAATTAT
18415943 AAAAATCGTA-
1 AAAAAT--TAT
18415953 AAAAATTAT
1 AAAAATTAT
18415962 -AAAATATAT
1 AAAAAT-TAT
*
18415971 AAAAATATAAA
1 AAAAAT-T-AT
18415982 AAAAATTAT
1 AAAAATTAT
*
18415991 -AAAATTTT
1 AAAAATTAT
18415999 ATAAAATCGTA-
1 A-AAAAT--TAT
18416010 AGAAAATTAT
1 A-AAAATTAT
18416020 ACAAAA-TAT
1 A-AAAATTAT
*
18416029 AAAGAAATAT
1 AAA-AATTAT
18416039 -AAAATTCAT
1 AAAAATT-AT
18416048 AAAAAAATTAT
1 --AAAAATTAT
18416059 AAAAATT
1 AAAAATT
18416066 TTCGTACTAA
Statistics
Matches: 124, Mismatches: 14, Indels: 42
0.69 0.08 0.23
Matches are distributed among these distances:
8 26 0.21
9 40 0.32
10 32 0.26
11 19 0.15
12 7 0.06
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:18415919 original size:19 final size:18
Alignment explanation
Indices: 18415897--18416064 Score: 117
Period size: 19 Copynumber: 8.9 Consensus size: 18
18415887 AAAATTAGAA
18415897 AAAAAATTATAAAAATCGT
1 AAAAAATTATAAAAAT-GT
*
18415916 AAAAAAATATAAAAA-GT
1 AAAAAATTATAAAAATGT
**
18415933 AAAATTTTATAAAAATCGT
1 AAAAAATTATAAAAAT-GT
*
18415952 AAAAAATTATAAAATATAT
1 AAAAAATTATAAAA-ATGT
* *
18415971 AAAAATATAAAAAAAAT-T
1 AAAAA-ATTATAAAAATGT
* *
18415989 ATAAAATTTTATAAAATCGT
1 AAAAAATTATA-AAAAT-GT
*
18416009 AAGAAAATTATACAAAATAT
1 AA-AAAATTATA-AAAATGT
* *
18416029 AAAGAAA-TATAAAATTCAT
1 AAA-AAATTATAAAAAT-GT
18416048 AAAAAAATTATAAAAAT
1 -AAAAAATTATAAAAAT
18416065 TTTCGTACTA
Statistics
Matches: 118, Mismatches: 19, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
17 17 0.14
18 14 0.12
19 46 0.39
20 28 0.24
21 13 0.11
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (18 bp):
AAAAAATTATAAAAATGT
Found at i:18415929 original size:29 final size:29
Alignment explanation
Indices: 18415897--18416031 Score: 89
Period size: 36 Copynumber: 4.4 Consensus size: 29
18415887 AAAATTAGAA
18415897 AAAAAATTATAAAAATCGTAAAAAAATAT
1 AAAAAATTATAAAAATCGTAAAAAAATAT
*
18415926 AAAAAGTAAAATTTTATAAAAATCGTAAAAAATTAT
1 ---AA--AAAA--TTATAAAAATCGTAAAAAAATAT
* *
18415962 AAAATA-TATAAAAAT-ATAAAAAAA-ATT
1 AAAAAATTATAAAAATCGTAAAAAAATA-T
* * *
18415989 ATAAAATTTTATAAAATCGTAAGAAAATTAT
1 AAAAAATTATA-AAAATCGTAA-AAAAATAT
*
18416020 ACAAAA-TATAAA
1 AAAAAATTATAAA
18416032 GAAATATAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
26 1 0.01
27 12 0.15
28 12 0.15
29 7 0.09
30 6 0.07
31 13 0.16
32 3 0.04
33 2 0.02
34 4 0.05
36 22 0.27
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (29 bp):
AAAAAATTATAAAAATCGTAAAAAAATAT
Found at i:18415964 original size:10 final size:10
Alignment explanation
Indices: 18415875--18416063 Score: 64
Period size: 10 Copynumber: 19.6 Consensus size: 10
18415865 ATTAAATTTT
18415875 TAAAAAA-TA
1 TAAAAAATTA
*
18415884 TTAAAAATTAGA
1 TAAAAAATT--A
*
18415896 AAAAAAATTA
1 TAAAAAATTA
**
18415906 T-AAAAATCG
1 TAAAAAATTA
*
18415915 TAAAAAAATA
1 TAAAAAATTA
*
18415925 T-AAAAA--G
1 TAAAAAATTA
**
18415932 TAAAATTTTA
1 TAAAAAATTA
**
18415942 T-AAAAATCG
1 TAAAAAATTA
18415951 TAAAAAATTA
1 TAAAAAATTA
*
18415961 TAAAATA-TA
1 TAAAAAATTA
18415970 T-AAAAATATA
1 TAAAAAAT-TA
*
18415980 AAAAAAATTA
1 TAAAAAATTA
*
18415990 T--AAAATTT
1 TAAAAAATTA
* **
18415998 TATAAAATCG
1 TAAAAAATTA
18416008 TAAGAAAATTA
1 TAA-AAAATTA
*
18416019 TACAAAA-TA
1 TAAAAAATTA
18416028 TAAAGAAA-TA
1 TAAA-AAATTA
18416038 T--AAAATTCA
1 TAAAAAATT-A
18416047 TAAAAAAATTA
1 T-AAAAAATTA
18416058 TAAAAA
1 TAAAAA
18416064 TTTTCGTACT
Statistics
Matches: 129, Mismatches: 31, Indels: 39
0.65 0.16 0.20
Matches are distributed among these distances:
7 4 0.03
8 16 0.12
9 33 0.26
10 47 0.36
11 15 0.12
12 14 0.11
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:18416059 original size:58 final size:56
Alignment explanation
Indices: 18415897--18416062 Score: 137
Period size: 58 Copynumber: 2.9 Consensus size: 56
18415887 AAAATTAGAA
* * * * **
18415897 AAAAAATTATAAAA-ATCGTAAAAAAATATAAAAA--GTAAAATTTTATAAAAATCGT
1 AAAAAATTATAAAATAT-ATAAAAATATAAAAAAATTATAAAAAATTAT-AAAATCGT
**
18415952 AAAAAATTATAAAATATATAAAAATATAAAAAAAATTATAAAATTTTATAAAATCGT
1 AAAAAATTATAAAATATATAAAAATAT-AAAAAAATTATAAAAAATTATAAAATCGT
*
18416009 AAGAAAATTATACAAA-ATATAAAGAA-AT-ATAAAATTCATAAAAAAATTATAAAA
1 AA-AAAATTATA-AAATATATAAA-AATATAAAAAAATT-AT-AAAAAATTATAAAA
18416063 ATTTTCGTAC
Statistics
Matches: 95, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
55 22 0.23
56 15 0.16
57 12 0.13
58 41 0.43
59 5 0.05
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (56 bp):
AAAAAATTATAAAATATATAAAAATATAAAAAAATTATAAAAAATTATAAAATCGT
Found at i:18416339 original size:10 final size:9
Alignment explanation
Indices: 18416324--18416385 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 9
18416314 AAAAAGTTTG
18416324 AATTTTTAA
1 AATTTTTAA
18416333 TAATTTTTAA
1 -AATTTTTAA
*
18416343 AGTTTTT-A
1 AATTTTTAA
18416351 AATTTTTATTA
1 AATTTTTA--A
18416362 AA-TTTTAA
1 AATTTTTAA
18416370 TAATTTTCTAA
1 -AATTTT-TAA
18416381 AATTT
1 AATTT
18416386 ATTTTTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 8 0.18
9 8 0.18
10 22 0.50
11 6 0.14
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (9 bp):
AATTTTTAA
Found at i:18423727 original size:22 final size:21
Alignment explanation
Indices: 18423675--18423737 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
18423665 TTGAATTGGG
* *
18423675 TTTAGGGTTTGGGTGATTTGGT
1 TTTAAGGTTTGGGT-ATTAGGT
18423697 TTTAAGGTTTGGGTATTAGGT
1 TTTAAGGTTTGGGTATTAGGT
*
18423718 TTTCATGGTTTTGGGT-TTAG
1 TTT-AAGG-TTTGGGTATTAG
18423738 ACATACACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 9 0.25
22 20 0.56
23 7 0.19
ACGTcount: A:0.13, C:0.02, G:0.35, T:0.51
Consensus pattern (21 bp):
TTTAAGGTTTGGGTATTAGGT
Found at i:18428267 original size:7 final size:7
Alignment explanation
Indices: 18428257--18428323 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
18428247 TTGTTGATCG
18428257 TTGACCA
1 TTGACCA
*
18428264 TTGACCG
1 TTGACCA
* *
18428271 GTGACCG
1 TTGACCA
18428278 TTGACCA
1 TTGACCA
18428285 TTGACCA
1 TTGACCA
*
18428292 TTG-CTCG
1 TTGAC-CA
*
18428299 TTGA-CT
1 TTGACCA
18428305 TTGACCA
1 TTGACCA
*
18428312 TTGACCG
1 TTGACCA
18428319 TTGAC
1 TTGAC
18428324 TTTTTCCAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
6 6 0.12
7 43 0.88
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.31
Consensus pattern (7 bp):
TTGACCA
Found at i:18428300 original size:21 final size:21
Alignment explanation
Indices: 18428250--18428323 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
18428240 CTATTAATTG
* *
18428250 TTGATCGTTGACCATTGACCG
1 TTGACCGTTGACCATTGACCA
*
18428271 GTGACCGTTGACCATTGACCA
1 TTGACCGTTGACCATTGACCA
*
18428292 TTG-CTCGTTGA-CTTTGACCA
1 TTGAC-CGTTGACCATTGACCA
18428312 TTGACCGTTGAC
1 TTGACCGTTGAC
18428324 TTTTTCCAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (21 bp):
TTGACCGTTGACCATTGACCA
Found at i:18428310 original size:20 final size:20
Alignment explanation
Indices: 18428272--18428326 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
18428262 CATTGACCGG
*
18428272 TGACCGTTGACCATTGACCAT
1 TGACCGTTGA-CTTTGACCAT
18428293 TG-CTCGTTGACTTTGACCAT
1 TGAC-CGTTGACTTTGACCAT
18428313 TGACCGTTGACTTT
1 TGACCGTTGACTTT
18428327 TTCCAAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
TGACCGTTGACTTTGACCAT
Found at i:18429527 original size:6 final size:6
Alignment explanation
Indices: 18429482--18429540 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
18429472 AGAGATTAAT
*
18429482 TATTTA T-TTTA T-TTTA -ATTATA GACTTTA TATTATA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATT-TA TA-TTTA TATT-TA TATTTA TATTTA
*
18429530 TATATA TATTT
1 TATTTA TATTT
18429541 GTGAATGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 11 0.24
6 22 0.49
7 10 0.22
8 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:18429530 original size:14 final size:13
Alignment explanation
Indices: 18429482--18429539 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
18429472 AGAGATTAAT
18429482 TATTTAT-TT-TA
1 TATTTATATTATA
18429493 T-TTTA-ATTATA
1 TATTTATATTATA
*
18429504 GACTTTATATTATA
1 TA-TTTATATTATA
18429518 TATTTATATT-TA
1 TATTTATATTATA
*
18429530 TATATATATT
1 TATTTATATT
18429540 TGTGAATGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.15
11 3 0.08
12 11 0.28
13 12 0.31
14 7 0.18
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TATTTATATTATA
Found at i:18432254 original size:68 final size:69
Alignment explanation
Indices: 18432124--18432255 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 69
18432114 TGATTAAACT
* * * *
18432124 TAATCACTTTAATATTAAATTAACATAATATTTATCAAGATAACTATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAACAAAATATCTATCAAAATAACTATTAAATTAAATTTAATATT
18432189 AAGA
66 AAGA
* * * *
18432193 TAATCACTTTAATATTAATTTAATAAAATA-CTATTAAAATAATTATTAAATTAAATTTAATAT
1 TAATCACTTTAATATTAAATTAACAAAATATCTATCAAAATAACTATTAAATTAAATTTAATAT
18432256 CAAACTATTA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
68 28 0.51
69 27 0.49
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAACAAAATATCTATCAAAATAACTATTAAATTAAATTTAATATT
AAGA
Found at i:18432263 original size:37 final size:36
Alignment explanation
Indices: 18432201--18432276 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
18432191 GATAATCACT
18432201 TTAATATTAATTTAATAAAATACTATTAAAATAATTA
1 TTAATATTAATTTAATAAAATACTATTAAAATAA-TA
*
18432238 TTAA-ATTAAATTTAATATCAA-ACTATTAAAATAATA
1 TTAATATT-AATTTAATA-AAATACTATTAAAATAATA
18432274 TTA
1 TTA
18432277 TTTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 8 0.22
37 26 0.72
38 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (36 bp):
TTAATATTAATTTAATAAAATACTATTAAAATAATA
Found at i:18439203 original size:18 final size:19
Alignment explanation
Indices: 18439180--18439215 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
18439170 CCATTTAGTC
18439180 AAATTAAGTC-TCAAATAA
1 AAATTAAGTCTTCAAATAA
18439198 AAATTAAGTCTTCAAATA
1 AAATTAAGTCTTCAAATA
18439216 CTTGAGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (19 bp):
AAATTAAGTCTTCAAATAA
Found at i:18439560 original size:42 final size:42
Alignment explanation
Indices: 18439509--18439733 Score: 315
Period size: 43 Copynumber: 5.3 Consensus size: 42
18439499 TTATGCGGAA
18439509 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCCCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCCCAC
* * *
18439551 ATGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCGC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTCCCAC
* *
18439594 AAGCGTCGCTAAAGGCCATGTTTTTTAGCGGCGCTTTTCCCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTCCCAC
* * **
18439637 AAGCGCCACTAAAGGCCATGTTCTTTAGCGGCACTTTATCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCCCAC
** *
18439679 AAATGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCTCCAA
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTC-CCAC
18439722 AAGCGCCGCTAA
1 AAGCGCCGCTAA
18439734 TATAACAGAT
Statistics
Matches: 158, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 71 0.45
43 87 0.55
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTCCCAC
Found at i:18439822 original size:15 final size:15
Alignment explanation
Indices: 18439802--18439830 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18439792 CCTGTAAATT
18439802 CAAATCCAACCAATG
1 CAAATCCAACCAATG
18439817 CAAATCCAACCAAT
1 CAAATCCAACCAAT
18439831 AACTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:18440061 original size:11 final size:11
Alignment explanation
Indices: 18440045--18440082 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
18440035 TTCCTTCGCT
18440045 TGCCTCGCTGC
1 TGCCTCGCTGC
18440056 TGCCTC-C-GC
1 TGCCTCGCTGC
18440065 TTGCCTCGCTGC
1 -TGCCTCGCTGC
18440077 TGCCTC
1 TGCCTC
18440083 CACTTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 2 0.08
10 7 0.29
11 13 0.54
12 2 0.08
ACGTcount: A:0.00, C:0.47, G:0.24, T:0.29
Consensus pattern (11 bp):
TGCCTCGCTGC
Found at i:18440078 original size:24 final size:21
Alignment explanation
Indices: 18440031--18440083 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
18440021 CTTGTAGCCT
* *
18440031 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
18440052 CTGCTGCCTCCGCTTGCCTCG
1 CTGCTGCCTCCGCTTGCCTCG
18440073 CTGCTGCCTCC
1 CTGCTGCCTCC
18440084 ACTTTAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.21, T:0.32
Consensus pattern (21 bp):
CTGCTGCCTCCGCTTGCCTCG
Done.