Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 31
Found at i:4849244 original size:3 final size:3
Alignment explanation
Indices: 4849236--4849303 Score: 102
Period size: 3 Copynumber: 22.7 Consensus size: 3
4849226 GGCCCGTTTG
* *
4849236 TAA TAA TAA -AA TAA TAA TAA AAA TAA TAA TAA TAA TAA TCA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4849283 TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TA
4849304 GTAAATGGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:4852734 original size:26 final size:26
Alignment explanation
Indices: 4852705--4852761 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
4852695 ATTAAATATG
*
4852705 TTTTCAAAAACTA-TATTTTTATTTAC
1 TTTTCAAAAA-TATTATTATTATTTAC
* * *
4852731 TTTTTAAATATATTATTATTATTTTC
1 TTTTCAAAAATATTATTATTATTTAC
4852757 TTTTC
1 TTTTC
4852762 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTCAAAAATATTATTATTATTTAC
Found at i:4852736 original size:11 final size:11
Alignment explanation
Indices: 4852720--4852798 Score: 52
Period size: 11 Copynumber: 6.7 Consensus size: 11
4852710 AAAAACTATA
4852720 TTTTTATTTAC
1 TTTTTATTTAC
* *
4852731 TTTTTAAATATAT
1 TTTTT--ATTTAC
*
4852744 TATTATTATTTTC
1 T-TT-TTATTTAC
*
4852757 TTTTCTTTTTA-
1 TTTT-TATTTAC
4852768 TTTTTATTTAC
1 TTTTTATTTAC
*
4852779 TTTTTATTTAT
1 TTTTTATTTAC
4852790 TTATTTATT
1 TT-TTTATT
4852799 ATTTATTTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
10 5 0.10
11 22 0.42
12 12 0.23
13 9 0.17
14 2 0.04
15 2 0.04
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTATTTAC
Found at i:4852769 original size:22 final size:21
Alignment explanation
Indices: 4852743--4852806 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
4852733 TTTAAATATA
* *
4852743 TTATTATTATTTTCTTTTCTTT
1 TTATTATTATTTACTTTT-TAT
*
4852765 TTATTTTTATTTACTTTTTAT
1 TTATTATTATTTACTTTTTAT
4852786 TTA-T-TTATTTA-TTATTTAT
1 TTATTATTATTTACTT-TTTAT
4852805 TT
1 TT
4852807 CAGGTTAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 2 0.05
19 14 0.37
20 1 0.03
21 5 0.13
22 16 0.42
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTATTATTATTTACTTTTTAT
Found at i:4852788 original size:4 final size:4
Alignment explanation
Indices: 4852770--4852806 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
4852760 TCTTTTTATT
*
4852770 TTTA TTTA CTT- TTTA TTTA TTTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4852807 CAGGTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 5 0.17
4 24 0.83
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4852800 original size:11 final size:10
Alignment explanation
Indices: 4852764--4852806 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
4852754 TTCTTTTCTT
4852764 TTTATTTTTA
1 TTTATTTTTA
4852774 TTTACTTTTTA
1 TTTA-TTTTTA
4852785 TTTA--TTTA
1 TTTATTTTTA
4852793 TTTATTATTTA
1 TTTATT-TTTA
4852804 TTT
1 TTT
4852807 CAGGTTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.28
10 4 0.14
11 17 0.59
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:4855114 original size:13 final size:13
Alignment explanation
Indices: 4855096--4855127 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4855086 GTAGTAAGTT
4855096 GTTAATCTTCGGA
1 GTTAATCTTCGGA
4855109 GTTAATCTTCGGA
1 GTTAATCTTCGGA
*
4855122 GGTAAT
1 GTTAAT
4855128 TTCTGAAACA
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:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (13 bp):
GTTAATCTTCGGA
Found at i:4856684 original size:13 final size:13
Alignment explanation
Indices: 4856666--4856697 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4856656 GCAATAAGTT
4856666 GTTAATCTTCGGA
1 GTTAATCTTCGGA
4856679 GTTAATCTTCGGA
1 GTTAATCTTCGGA
*
4856692 GGTAAT
1 GTTAAT
4856698 TTCTGAAACA
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:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (13 bp):
GTTAATCTTCGGA
Found at i:4860517 original size:16 final size:15
Alignment explanation
Indices: 4860492--4860558 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 15
4860482 TTTTGGTATG
4860492 TATATATAGTATATA
1 TATATATAGTATATA
4860507 TATATTATAGTATATTCGAAAA
1 TATA-TATAGTATA-T-----A
4860529 TATATATAGTATATA
1 TATATATAGTATATA
*
4860544 TAT-TATAATATATA
1 TATATATAGTATATA
4860558 T
1 T
4860559 TTTTTGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
14 11 0.25
15 8 0.18
16 9 0.20
17 1 0.02
20 1 0.02
21 9 0.20
22 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (15 bp):
TATATATAGTATATA
Found at i:4860587 original size:26 final size:27
Alignment explanation
Indices: 4860543--4860598 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
4860533 TATAGTATAT
4860543 ATATTATAATATATATTTTTTGAAAAC
1 ATATTATAATATATATTTTTTGAAAAC
* * *
4860570 ATATT-TAATATTTTTTTTTTGAAATC
1 ATATTATAATATATATTTTTTGAAAAC
4860596 ATA
1 ATA
4860599 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (27 bp):
ATATTATAATATATATTTTTTGAAAAC
Found at i:4860639 original size:14 final size:15
Alignment explanation
Indices: 4860619--4860656 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
4860609 TATAATATAT
4860619 AATATATATTTTTTA
1 AATATATATTTTTTA
*
4860634 AA-ATATAGTTTTTA
1 AATATATATTTTTTA
4860648 AATATATAT
1 AATATATAT
4860657 ATATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
AATATATATTTTTTA
Found at i:4861917 original size:20 final size:19
Alignment explanation
Indices: 4861894--4861935 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
4861884 ACTTAATACT
4861894 ATTTATT-ATAAATATTAATA
1 ATTTATTCA-AAATATTAA-A
4861914 ATTTATTCAAAATATTAAA
1 ATTTATTCAAAATATTAAA
4861933 ATT
1 ATT
4861936 ACATAGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTATTCAAAATATTAAA
Found at i:4863182 original size:12 final size:11
Alignment explanation
Indices: 4863165--4863199 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
4863155 TTCGGATCTT
4863165 ATAATAATAATA
1 ATAAT-ATAATA
4863177 ATAATATATATA
1 ATAATATA-ATA
4863189 ATAATATAATA
1 ATAATATAATA
4863200 TATTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATATAATA
Found at i:4863200 original size:15 final size:15
Alignment explanation
Indices: 4863164--4863202 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4863154 CTTCGGATCT
4863164 TATAATA-ATAATAA
1 TATAATATATAATAA
4863178 TA-ATATATATAATAA
1 TATA-ATATATAATAA
4863193 TATAATATAT
1 TATAATATAT
4863203 TATTATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 5 0.23
15 15 0.68
16 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAATATATAATAA
Found at i:4863461 original size:35 final size:35
Alignment explanation
Indices: 4863422--4863555 Score: 218
Period size: 35 Copynumber: 3.9 Consensus size: 35
4863412 GAATCAAATT
*
4863422 ACTTCACTATTCTTAC-GTGAAGGTTGAAATGATGA
1 ACTTCACTACTCTT-CTGTGAAGGTTGAAATGATGA
4863457 ACTTCACTACTCTTCTGTGAAGGTTGAAATGATGA
1 ACTTCACTACTCTTCTGTGAAGGTTGAAATGATGA
* *
4863492 ACTTCACTACTCTTCCGTGAAGGCTGAAATGATGA
1 ACTTCACTACTCTTCTGTGAAGGTTGAAATGATGA
4863527 ACTTCACTACTCTTCTGTGAAGGTT-AAAT
1 ACTTCACTACTCTTCTGTGAAGGTTGAAAT
4863556 CGAATTACTT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
34 5 0.05
35 88 0.95
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (35 bp):
ACTTCACTACTCTTCTGTGAAGGTTGAAATGATGA
Found at i:4863675 original size:35 final size:34
Alignment explanation
Indices: 4863625--4863714 Score: 137
Period size: 35 Copynumber: 2.6 Consensus size: 34
4863615 GATTTGATTC
*
4863625 CACTACTCTTTCGTGAAGGCTGAAATGAT-AGACTT
1 CACTACTCTTCCGTGAAGG-TGAAATGATGA-ACTT
4863660 CACTACTCTTCCGTGAAGGTCGAAATGATGAACTT
1 CACTACTCTTCCGTGAAGGT-GAAATGATGAACTT
4863695 CACTACTCTTCCGTGAAGGT
1 CACTACTCTTCCGTGAAGGT
4863715 TGAATCGAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
34 1 0.02
35 50 0.96
36 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (34 bp):
CACTACTCTTCCGTGAAGGTGAAATGATGAACTT
Found at i:4863746 original size:164 final size:164
Alignment explanation
Indices: 4863461--4863803 Score: 512
Period size: 164 Copynumber: 2.1 Consensus size: 164
4863451 TGATGAACTT
*
4863461 CACTACTC-TTCTGTGAAGGTTGAAATGATGAACTTCACTACTCTTCCGTGAAGGCTGAAATGAT
1 CACTACTCTTTC-GTGAAGGCTGAAATGATGAACTTCACTACTCTTCCGTGAAGGCTGAAATGAT
* * *
4863525 GAACTTCACTACTCTTCTGTGAAGGTTAAATCGAATTACTTGAAAATAATATGTTTCACTACCCT
65 GAACTTCACTACTCTTCCGTGAAGGTTAAATCGAATTACTTGAAAAGAATATGTTTCACTACACT
*
4863590 TCCATAAAGATCATATTCGAGGTTTGATTTGATTC
130 TCCATAAAGATCAGATTCGAGGTTTGATTTGATTC
4863625 CACTACTCTTTCGTGAAGGCTGAAATGAT-AGACTTCACTACTCTTCCGTGAAGG-TCGAAATGA
1 CACTACTCTTTCGTGAAGGCTGAAATGATGA-ACTTCACTACTCTTCCGTGAAGGCT-GAAATGA
* * * * * *
4863688 TGAACTTCACTACTCTTCCGTGAAGGTTGAATCGAATTACTTTAAAAGAATTTGTTTCATTATAT
64 TGAACTTCACTACTCTTCCGTGAAGGTTAAATCGAATTACTTGAAAAGAATATGTTTCACTACAC
* *
4863753 TTCTATGAAGATCAGATTCGAGGTTTGATTTGATTC
129 TTCCATAAAGATCAGATTCGAGGTTTGATTTGATTC
*
4863789 CACTACTCTTCCGTG
1 CACTACTCTTTCGTG
4863804 GAGATCTTAC
Statistics
Matches: 162, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
163 2 0.01
164 157 0.97
165 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (164 bp):
CACTACTCTTTCGTGAAGGCTGAAATGATGAACTTCACTACTCTTCCGTGAAGGCTGAAATGATG
AACTTCACTACTCTTCCGTGAAGGTTAAATCGAATTACTTGAAAAGAATATGTTTCACTACACTT
CCATAAAGATCAGATTCGAGGTTTGATTTGATTC
Found at i:4863894 original size:20 final size:20
Alignment explanation
Indices: 4863858--4863921 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
4863848 ATACTGACAG
4863858 ATGACCCGAAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
* * *
4863878 ATTACCTGAAGGCTTTACAA
1 ATGACCCGAAGGATTTACAA
* *
4863898 ATGACCCGAAGGTTTTATAA
1 ATGACCCGAAGGATTTACAA
4863918 ATGA
1 ATGA
4863922 GTGGGAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (20 bp):
ATGACCCGAAGGATTTACAA
Found at i:4867402 original size:166 final size:167
Alignment explanation
Indices: 4867128--4867460 Score: 643
Period size: 166 Copynumber: 2.0 Consensus size: 167
4867118 CATGTTCAAA
4867128 TAAGATGTTTTAAAATGAAATGTACAATAGTGGTAGATAACAGTTTCCCCTTATTTATCTAACTA
1 TAAGATGTTTTAAAATGAAATGTACAATAGTGGTAGATAACAGTTTCCCCTTATTTATCTAACTA
4867193 TCCCATTACTCTTTGAATGTTGGATGTGTAATTAGACCATGG-TTTTGTCTATATTTGCACCCCA
66 TCCCATTACTCTTTGAATGTTGGATGTGTAATTAGACCATGGTTTTTGTCTATATTTGCACCCCA
4867257 TTTTCTTGATCATTTC-TTGGTAGCTTCTTTGGATGAG
131 -TTTCTTGATCATTTCTTTGGTAGCTTCTTTGGATGAG
4867294 TAAGATGTTTTAAAATGAAATGTACAATAGTGGTAGATAACAGTTTCCCCTTATTTATCTAACTA
1 TAAGATGTTTTAAAATGAAATGTACAATAGTGGTAGATAACAGTTTCCCCTTATTTATCTAACTA
4867359 TCCCATTACTCTTTGAATGTTGGATGTGTAATTAGACCATGGTTTTTGTCTATATTTGCACCCCA
66 TCCCATTACTCTTTGAATGTTGGATGTGTAATTAGACCATGGTTTTTGTCTATATTTGCACCCCA
4867424 TTTCTTGATCATTTCTTTGGTAGCTTCTTTGGATGAG
131 TTTCTTGATCATTTCTTTGGTAGCTTCTTTGGATGAG
4867461 CCTTCAGATT
Statistics
Matches: 165, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
166 122 0.74
167 43 0.26
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (167 bp):
TAAGATGTTTTAAAATGAAATGTACAATAGTGGTAGATAACAGTTTCCCCTTATTTATCTAACTA
TCCCATTACTCTTTGAATGTTGGATGTGTAATTAGACCATGGTTTTTGTCTATATTTGCACCCCA
TTTCTTGATCATTTCTTTGGTAGCTTCTTTGGATGAG
Found at i:4870174 original size:41 final size:43
Alignment explanation
Indices: 4870117--4870199 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 43
4870107 TATATACATC
* * * *
4870117 CTAACCTCATGCTTTCTACTTC-CATGC-TTTGTTTGGAAAAA
1 CTAACCGCATGATTTCTACTTCACATGCATTTATTCGGAAAAA
*
4870158 CTAACCGCATGATTTCTAGTTCACATGCATTTATTCGGAAAA
1 CTAACCGCATGATTTCTACTTCACATGCATTTATTCGGAAAA
4870200 TAAAGTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 19 0.54
42 5 0.14
43 11 0.31
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (43 bp):
CTAACCGCATGATTTCTACTTCACATGCATTTATTCGGAAAAA
Found at i:4871182 original size:20 final size:20
Alignment explanation
Indices: 4871155--4871200 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
4871145 TACTACTTAA
4871155 TAAT-ATTTATT-ATAAATAT
1 TAATAATTTATTCA-AAATAT
4871174 TAATAATTTATTCAAAATAT
1 TAATAATTTATTCAAAATAT
4871194 TAA-AATT
1 TAATAATT
4871201 ACATAGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 16 0.64
21 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAATTTATTCAAAATAT
Found at i:4872417 original size:15 final size:15
Alignment explanation
Indices: 4872381--4872419 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4872371 CTTCGGGTCT
4872381 TATAAT-TATAATAA
1 TATAATATATAATAA
4872395 TA-ATATATATAATAA
1 TATA-ATATATAATAA
4872410 TATAATATAT
1 TATAATATAT
4872420 TATTATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 4 0.18
15 16 0.73
16 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATATATAATAA
Found at i:4873139 original size:24 final size:27
Alignment explanation
Indices: 4873107--4873165 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
4873097 TTATTTGAGT
4873107 TTATATAAAGTTAAT-TCAATT-AAAAA
1 TTAT-TAAAGTTAATCTCAATTGAAAAA
* *
4873133 -TATTAAATTTTATCTCAATTGAAAAA
1 TTATTAAAGTTAATCTCAATTGAAAAA
4873159 TTATTAA
1 TTATTAA
4873166 GATTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 8 0.29
25 9 0.32
26 5 0.18
27 6 0.21
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (27 bp):
TTATTAAAGTTAATCTCAATTGAAAAA
Found at i:4873282 original size:2 final size:2
Alignment explanation
Indices: 4873275--4873321 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4873265 TAGCCAACAT
4873275 TA TA TA TA 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 TA TA TA TA TA
4873316 TA TA TA
1 TA TA TA
4873322 GAGAGAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4873326 original size:2 final size:2
Alignment explanation
Indices: 4873321--4873355 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4873311 TATATTATAT
4873321 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4873356 TTATTACTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4884728 original size:3 final size:3
Alignment explanation
Indices: 4884720--4884756 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
4884710 CCAACAAAGG
*
4884720 CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
4884757 AATTACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:4900348 original size:39 final size:39
Alignment explanation
Indices: 4900292--4900404 Score: 172
Period size: 39 Copynumber: 2.9 Consensus size: 39
4900282 TATATGATTA
**
4900292 TATTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTTT
1 TATTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTCC
*
4900331 TGTTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTCC
1 TATTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTCC
* * *
4900370 TATTTTGTAAAAAGAAATAAATTGTTAGATTTATT
1 TATTTTGTAAAAGGAAATAAATCGTTGGATTTATT
4900405 GTTGAATTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (39 bp):
TATTTTGTAAAAGGAAATAAATCGTTGGATTTATTTTCC
Found at i:4900455 original size:51 final size:51
Alignment explanation
Indices: 4900354--4900455 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
4900344 GAAATAAATC
* * * *
4900354 GTTGGATTTATTTTCCTATTTTGTAAAAAGAAATAAATTGTTAGATTTATT
1 GTTGAATTTATTTTCCTATGTTGTAAAAAGAAATAAATTGTTAAAATTATT
*
4900405 GTTGAATTTATTTTCCTGTGTTGTAAAAAGAAATAAATCT-TTAAAATTATT
1 GTTGAATTTATTTTCCTATGTTGTAAAAAGAAATAAAT-TGTTAAAATTATT
4900456 TTCTTGGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (51 bp):
GTTGAATTTATTTTCCTATGTTGTAAAAAGAAATAAATTGTTAAAATTATT
Found at i:4910126 original size:21 final size:21
Alignment explanation
Indices: 4910102--4910141 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4910092 AGGGATTTTA
*
4910102 AAGGGGAGTATTGATACTTCC
1 AAGGGGAGTATCGATACTTCC
4910123 AAGGGGAGTATCGATACTT
1 AAGGGGAGTATCGATACTT
4910142 GGTAGCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (21 bp):
AAGGGGAGTATCGATACTTCC
Found at i:4913951 original size:24 final size:24
Alignment explanation
Indices: 4913922--4913995 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
4913912 TCGATTCGTT
* *
4913922 TATGTTCACGAACAAATTTGTTTA
1 TATGTTCATGAACAAATTTGTCTA
4913946 TATGTTCATGAACAAATTTGTCTA
1 TATGTTCATGAACAAATTTGTCTA
4913970 TATGTTCATGAACAAATTTGTCTA
1 TATGTTCATGAACAAATTTGTCTA
4913994 TA
1 TA
4913996 AGGTTATTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
TATGTTCATGAACAAATTTGTCTA
Found at i:4915788 original size:23 final size:23
Alignment explanation
Indices: 4915758--4915813 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
4915748 ACGTTAAACG
*
4915758 AACGTTAAACTAAACTATTCACA
1 AACGTTAAACTAAAATATTCACA
* *
4915781 AACGTTAAACTAAAATGTTCACG
1 AACGTTAAACTAAAATATTCACA
4915804 AACGTTAAAC
1 AACGTTAAAC
4915814 GTAAGCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (23 bp):
AACGTTAAACTAAAATATTCACA
Found at i:4915962 original size:3 final size:3
Alignment explanation
Indices: 4915954--4916028 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
4915944 CAGTTTACTT
** * * *
4915954 TTA TTA TTA TTA AAA TTC TTA TTA TTA TTAA ATA TTC TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* *
4916000 TTA ATA TCA -TA TATA TTA TATA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA T-TA TTA TTA T
4916029 CCCAACTTTT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
2 1 0.02
3 45 0.83
4 8 0.15
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:4915992 original size:19 final size:18
Alignment explanation
Indices: 4915954--4916003 Score: 91
Period size: 19 Copynumber: 2.7 Consensus size: 18
4915944 CAGTTTACTT
4915954 TTATTATTATTAAAATTC
1 TTATTATTATTAAAATTC
4915972 TTATTATTATTAAATATTC
1 TTATTATTATTAAA-ATTC
4915991 TTATTATTATTAA
1 TTATTATTATTAA
4916004 TATCATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTATTATTAAAATTC
Found at i:4916017 original size:34 final size:37
Alignment explanation
Indices: 4915954--4916028 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 37
4915944 CAGTTTACTT
* *
4915954 TTATTATTATTAAAATTCTTATTATTATTAAATATTC
1 TTATTATTATTAAAATTCATATTATTATTAAATATTA
* *
4915991 TTATTATTATTAATA-TCATA-TA-TATTATATATTA
1 TTATTATTATTAAAATTCATATTATTATTAAATATTA
4916025 TTAT
1 TTAT
4916029 CCCAACTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 14 0.41
35 2 0.06
36 4 0.12
37 14 0.41
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (37 bp):
TTATTATTATTAAAATTCATATTATTATTAAATATTA
Found at i:4916432 original size:12 final size:12
Alignment explanation
Indices: 4916402--4916447 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
4916392 AAAGAAAACA
4916402 GAGAGCAAGAACCC
1 GAGAGCAAGAA--C
4916416 GAGAGCAAGAAC
1 GAGAGCAAGAAC
*
4916428 GAGAGCAAGGAC
1 GAGAGCAAGAAC
4916440 AGAGAGCA
1 -GAGAGCA
4916448 GAAAATCGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 12 0.40
13 7 0.23
14 11 0.37
ACGTcount: A:0.46, C:0.20, G:0.35, T:0.00
Consensus pattern (12 bp):
GAGAGCAAGAAC
Found at i:4917720 original size:21 final size:21
Alignment explanation
Indices: 4917681--4917720 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4917671 ATATTCTTAA
*
4917681 ATAAATAAATATTCTATTTTT
1 ATAAATAAATATTCAATTTTT
4917702 ATAAATAATATATT-AATTT
1 ATAAATAA-ATATTCAATTT
4917721 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAATAAATATTCAATTTTT
Found at i:4918393 original size:24 final size:24
Alignment explanation
Indices: 4918366--4918432 Score: 57
Period size: 28 Copynumber: 2.7 Consensus size: 24
4918356 AATTTTTATA
4918366 TATACTTATTATTTTCA-TAATATT
1 TATA-TTATTATTTTCATTAATATT
*
4918390 TATATGTATATTATTTTTTATTAATATT
1 TATA--T-TATTA-TTTTCATTAATATT
*
4918418 TTTATT-TTATTTTCA
1 TATATTATTATTTTCA
4918433 AGTATTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
23 5 0.14
24 7 0.20
25 2 0.06
26 6 0.17
27 5 0.14
28 10 0.29
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (24 bp):
TATATTATTATTTTCATTAATATT
Found at i:4918408 original size:28 final size:30
Alignment explanation
Indices: 4918349--4918418 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 30
4918339 TAATTCTTGC
*
4918349 TTTTCA-AA-ATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATATACTTATTA
*
4918377 TTTTCATAATATTTATATGTATA-TTATT-
1 TTTTCATAATATTTATATATATACTTATTA
4918405 TTTT-ATTAATATTT
1 TTTTCA-TAATATTT
4918419 TTATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 1 0.03
28 18 0.49
29 7 0.19
30 11 0.30
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTCATAATATTTATATATATACTTATTA
Found at i:4925927 original size:75 final size:75
Alignment explanation
Indices: 4925840--4925980 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 75
4925830 ATCAACAAGA
* * *
4925840 AGCAAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAGT-TGGAATATTAATGCATTTTGA
1 AGCAAATATTGGGGCATGCTGAAAGCCCATTTCAATCAAAA-TCAGGAATATTAATGCATTTTGA
4925904 ACATTTGTATC
65 ACATTTGTATC
* * * *
4925915 AGCAAATATTGGGGCATGCTGAAAGTCCATTTTAATCAGAATCAGGAATGTTAATGCATTTTGAA
1 AGCAAATATTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTAATGCATTTTGAA
4925980 C
66 C
4925981 GCTGGGGCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 1 0.02
75 57 0.98
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (75 bp):
AGCAAATATTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTAATGCATTTTGAA
CATTTGTATC
Found at i:4926875 original size:76 final size:76
Alignment explanation
Indices: 4926749--4927071 Score: 515
Period size: 76 Copynumber: 4.3 Consensus size: 76
4926739 CCCATATCCA
* * **
4926749 TAAGACCTACAGTGCAGAATGTTTTCAAAAAGCATTCACGAGCTTTTTGATGTTTTTAAAGCCTC
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTC
* *
4926814 TGTGTCATCTG
66 CGGGTCATCTG
* *
4926825 TAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGGTTTTAAAGCCTC
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTC
4926890 CGGGTCATCTG
66 CGGGTCATCTG
* *
4926901 TAAGACCTACAGTGTAGGATGTTTTTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTC
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTC
4926966 CGGGTCATCTG
66 CGGGTCATCTG
* *
4926977 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA--TATTTAAAGCCTC
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTC
4927040 CGGGTCATCTG
66 CGGGTCATCTG
*
4927051 TAAGACCTACAGTGCAAGATG
1 TAAGACCTACAGTGCAGGATG
4927072 ATAAGACCTT
Statistics
Matches: 229, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
74 42 0.18
76 187 0.82
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (76 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTC
CGGGTCATCTG
Found at i:4927204 original size:118 final size:116
Alignment explanation
Indices: 4926977--4927239 Score: 429
Period size: 118 Copynumber: 2.2 Consensus size: 116
4926967 GGGTCATCTG
* * *
4926977 TAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTATAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATATTTAAAGCCTCCA
*
4927042 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
* *
4927093 TAAGACCTACAGTGCAGAATGTTTTCAAAAAGCCTTTGGGAGCTTTTTAATATTTTCAAAGCCTC
1 TAAGACCTATAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATA-TTT-AAAGCCTC
4927158 CAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
64 CAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
*
4927211 TAAGACCTATGGTGCA-AGATGTTTTCAAA
1 TAAGACCTATAGTGCAGA-ATGTTTTCAAA
4927240 TGAGATTTCA
Statistics
Matches: 136, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
116 48 0.35
117 4 0.03
118 84 0.62
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (116 bp):
TAAGACCTATAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTAATATTTAAAGCCTCCA
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
Found at i:4927503 original size:3 final size:3
Alignment explanation
Indices: 4927495--4927555 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
4927485 TAGTTTACTT
** * * *
4927495 TTA TTA TTA TTA AAA TTC TTA TTA TTA TTA ATA TCA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
4927540 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
4927556 AATAAAATAC
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 1 0.02
3 38 0.84
4 6 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:4930121 original size:9 final size:9
Alignment explanation
Indices: 4930107--4930135 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4930097 ATAATCAAAC
4930107 AAAATAATA
1 AAAATAATA
4930116 AAAATAAT-
1 AAAATAATA
4930124 AAAATAATA
1 AAAATAATA
4930133 AAA
1 AAA
4930136 TGGGTTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATAATA
Found at i:4930127 original size:8 final size:8
Alignment explanation
Indices: 4930107--4930136 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
4930097 ATAATCAAAC
4930107 AAAATAAT
1 AAAATAAT
4930115 AAAAATAAT
1 -AAAATAAT
4930124 AAAATAAT
1 AAAATAAT
4930132 AAAAT
1 AAAAT
4930137 GGGTTGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:4932316 original size:61 final size:64
Alignment explanation
Indices: 4932228--4932372 Score: 206
Period size: 61 Copynumber: 2.3 Consensus size: 64
4932218 CTGCACTAAG
* *
4932228 CTTACGCTCTAGTGCTAATCCGGATATGACACATAAGGTCGTGCCCACCACCTACAC-TAG-GT
1 CTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTCATGCCCACCACCTACACTTAGTGT
* * *
4932290 -TTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTATGCCCTCCACCTGCACTTAGTGT
1 CTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTCATGCCCACCACCTACACTTAGTGT
*
4932353 CCTTACACACTAGTGCTAAT
1 -CTTACACTCTAGTGCTAAT
4932373 ATAAACATGT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
61 51 0.70
62 3 0.04
63 2 0.03
65 17 0.23
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (64 bp):
CTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTCATGCCCACCACCTACACTTAGTGT
Found at i:4933893 original size:30 final size:30
Alignment explanation
Indices: 4933838--4933895 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
4933828 ATAATCCACA
*
4933838 ACTTTTCCAAAATTACTAATTTGGTCCCCTT
1 ACTTTTCAAAAATTACTAA-TTGGTCCCCTT
4933869 ACTTTTCAAAAATTACATAA-TGGTCCC
1 ACTTTTCAAAAATTAC-TAATTGGTCCC
4933896 AAATTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 7 0.28
31 15 0.60
32 3 0.12
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
ACTTTTCAAAAATTACTAATTGGTCCCCTT
Found at i:4938691 original size:7 final size:7
Alignment explanation
Indices: 4938679--4938719 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
4938669 TTCTTTGTTT
4938679 CTCTCCA
1 CTCTCCA
4938686 CTCTCCA
1 CTCTCCA
4938693 CTCTCCA
1 CTCTCCA
4938700 CTCTCCA
1 CTCTCCA
4938707 CTCTCCA
1 CTCTCCA
4938714 CTCTCC
1 CTCTCC
4938720 TTGGCCTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.12, C:0.59, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCTCCA
Found at i:4943992 original size:28 final size:29
Alignment explanation
Indices: 4943943--4943999 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
4943933 CTTTACTCTC
* **
4943943 TTTTATTTTATTCATTGTACTTTT-AATT
1 TTTTAATTTATTCATTAAACTTTTGAATT
*
4943971 TTTTAATTTATTTATTAAACTTTTGAATT
1 TTTTAATTTATTCATTAAACTTTTGAATT
4944000 GTTTCTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTAATTTATTCATTAAACTTTTGAATT
Found at i:4957419 original size:61 final size:61
Alignment explanation
Indices: 4957324--4957441 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
4957314 TGTTTTTTAG
* * *
4957324 GGTTTGCTTGATTATTTTTTCCTGAAATTCATGTATTTTTTTCGTATTATTTCTTCTTTCA
1 GGTTTGCTTGATTAATTTTTCCTAAAATTCATGTATTTTTTGCGTATTATTTCTTCTTTCA
4957385 GGTTTGCTTGATTAATTTTTCCTAAAATTCATGTATTTTTTGCGTATTATTTCTTCT
1 GGTTTGCTTGATTAATTTTTCCTAAAATTCATGTATTTTTTGCGTATTATTTCTTCT
4957442 CTCACTCTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.18, C:0.13, G:0.12, T:0.58
Consensus pattern (61 bp):
GGTTTGCTTGATTAATTTTTCCTAAAATTCATGTATTTTTTGCGTATTATTTCTTCTTTCA
Found at i:4959358 original size:20 final size:20
Alignment explanation
Indices: 4959344--4959441 Score: 124
Period size: 20 Copynumber: 4.9 Consensus size: 20
4959334 AATCGCAATA
* *
4959344 CGATTATGACTATCGTAACG
1 CGATTCTGACTATCGCAACG
* * *
4959364 TGATTATGACTATCGCAATG
1 CGATTCTGACTATCGCAACG
*
4959384 AGATTCTGACTATCGCAACG
1 CGATTCTGACTATCGCAACG
*
4959404 CGATGCTGACTATCGCAACG
1 CGATTCTGACTATCGCAACG
*
4959424 CGATGCTGACTATCGCAA
1 CGATTCTGACTATCGCAA
4959442 TGTGATTTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (20 bp):
CGATTCTGACTATCGCAACG
Found at i:4959381 original size:40 final size:40
Alignment explanation
Indices: 4959335--4959448 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 40
4959325 GAATATGTAA
* *
4959335 ATCGCAATACGATTATGACTATCGTAACGTGATTATGACT
1 ATCGCAATACGATTCTGACTATCGCAACGTGATTATGACT
* **
4959375 ATCGCAATGA-GATTCTGACTATCGCAACGCGATGCTGACT
1 ATCGCAAT-ACGATTCTGACTATCGCAACGTGATTATGACT
** * *
4959415 ATCGCAACGCGATGCTGACTATCGCAATGTGATT
1 ATCGCAATACGATTCTGACTATCGCAACGTGATT
4959449 TTCAAAGCGC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
40 60 0.98
41 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (40 bp):
ATCGCAATACGATTCTGACTATCGCAACGTGATTATGACT
Found at i:4959399 original size:60 final size:60
Alignment explanation
Indices: 4959335--4959448 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
4959325 GAATATGTAA
* * * * *
4959335 ATCGCAATACGATTATGACTATCGTAACGTGATTATGACTATCGCAATGAGATTCTGACT
1 ATCGCAACACGATGATGACTATCGCAACGCGATGATGACTATCGCAATGAGATTCTGACT
* * * *
4959395 ATCGCAACGCGATGCTGACTATCGCAACGCGATGCTGACTATCGCAATGTGATT
1 ATCGCAACACGATGATGACTATCGCAACGCGATGATGACTATCGCAATGAGATT
4959449 TTCAAAGCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (60 bp):
ATCGCAACACGATGATGACTATCGCAACGCGATGATGACTATCGCAATGAGATTCTGACT
Found at i:4959652 original size:22 final size:22
Alignment explanation
Indices: 4959627--4959670 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4959617 ACATCCGTCC
4959627 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
* *
4959649 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCAGTCT
4959671 ATCTCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:4960140 original size:20 final size:20
Alignment explanation
Indices: 4960051--4960157 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
4960041 AGAATCGCAA
* *
4960051 TGCGATTTT-AGTTTCGCAT
1 TGCGATTTTCATTTTCGCGT
4960070 TGCGATTTTCATTTT-GCGT
1 TGCGATTTTCATTTTCGCGT
** **
4960089 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
4960109 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
4960129 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
4960149 TGCGATTTT
1 TGCGATTTT
4960158 AAGTTTCAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
19 23 0.31
20 52 0.69
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:4960164 original size:20 final size:20
Alignment explanation
Indices: 4960121--4960164 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4960111 CGATAGTCAT
* *
4960121 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
4960141 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
4960161 TTTC
1 TTTC
4960165 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:4962057 original size:20 final size:20
Alignment explanation
Indices: 4962032--4962099 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
4962022 TAGTTTACTT
**
4962032 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAATTTGACTA
*
4962052 TCGCAAAGCGAATTTGACTA
1 TCGCAACGCGAATTTGACTA
*
4962072 TCGCAACGCGAATTTTACTA
1 TCGCAACGCGAATTTGACTA
4962092 TCGCAACG
1 TCGCAACG
4962100 AAAGAATCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATTTGACTA
Found at i:4962186 original size:20 final size:20
Alignment explanation
Indices: 4962142--4962197 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
4962132 GCGATTCTCT
**
4962142 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
4962162 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
* *
4962182 TGTTGTGATAGTCATT
1 CGTTGCGATAGTCATT
4962198 CGTGTTGCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:4962789 original size:21 final size:21
Alignment explanation
Indices: 4962698--4962802 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
4962688 GACTCACCTG
*
4962698 TCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
4962719 TTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
4962740 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
4962761 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* * *
4962782 TAATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
4962803 CCAACATTCT
Statistics
Matches: 62, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:4964230 original size:14 final size:14
Alignment explanation
Indices: 4964193--4964254 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
4964183 TTGCTTGTTT
*
4964193 AATTGATTTATAAA
1 AATTGATTTGTAAA
4964207 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
4964221 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
4964236 TATTGATGTGTAAA
1 AATTGATTTGTAAA
4964250 TAATT
1 -AATT
4964255 CTTATTTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:4964391 original size:20 final size:20
Alignment explanation
Indices: 4964375--4964426 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4964365 ACTCAAAGTT
*
4964375 GCAATGCGAAAGACAAAATC
1 GCAACGCGAAAGACAAAATC
4964395 GCAACGCGAAAGACAAAATC
1 GCAACGCGAAAGACAAAATC
4964415 GCAACGCGAAAG
1 GCAACGCGAAAG
4964427 TCAATTCGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.06
Consensus pattern (20 bp):
GCAACGCGAAAGACAAAATC
Found at i:4964442 original size:19 final size:20
Alignment explanation
Indices: 4964420--4964462 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4964410 AAATCGCAAC
*
4964420 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
4964439 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
4964459 GCGA
1 GCGA
4964463 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:4964500 original size:20 final size:20
Alignment explanation
Indices: 4964474--4964714 Score: 160
Period size: 20 Copynumber: 12.9 Consensus size: 20
4964464 TTTCTCGTTG
4964474 CGCGTTGCGATAATCAAATT
1 CGCGTTGCGATAATCAAATT
*
4964494 TGCGTTGCGAT--T----TT
1 CGCGTTGCGATAATCAAATT
* * * *
4964508 CTCGTTGGGATAGTCAAATA
1 CGCGTTGCGATAATCAAATT
*
4964528 CCCGTTGCGATAATCAAATT
1 CGCGTTGCGATAATCAAATT
4964548 CGCGTTGCGATAATCAAATT
1 CGCGTTGCGATAATCAAATT
*
4964568 CGCGTTGCGATAGA-CATATT
1 CGCGTTGCGATA-ATCAAATT
*
4964588 CGTGTTGCGAT--T----TT
1 CGCGTTGCGATAATCAAATT
* * * *
4964602 TGCATTGCGATAGTCATATT
1 CGCGTTGCGATAATCAAATT
** *
4964622 CGTATTGCGATAGTCAAATT
1 CGCGTTGCGATAATCAAATT
*
4964642 CGCGTTGC---AAT---TTT
1 CGCGTTGCGATAATCAAATT
* *
4964656 TGAGTTGCGATAATCAAATT
1 CGCGTTGCGATAATCAAATT
*
4964676 CGCGTTGCGATAGTCAAATT
1 CGCGTTGCGATAATCAAATT
*
4964696 CGCGTTGCGATATTCAAAT
1 CGCGTTGCGATAATCAAAT
4964715 GAATGTGTAA
Statistics
Matches: 172, Mismatches: 29, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
14 28 0.16
16 2 0.01
17 5 0.03
18 1 0.01
20 135 0.78
21 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATAATCAAATT
Found at i:4964502 original size:41 final size:41
Alignment explanation
Indices: 4964433--4964578 Score: 119
Period size: 41 Copynumber: 3.8 Consensus size: 41
4964423 AAAGTCAATT
* * *
4964433 CGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTG
1 CGCGTTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTG
**
4964474 CGCGTTGCGATAATCAAATTTGCGTTGCGATTTTCTCGTT-
1 CGCGTTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTG
* * ** ***
4964514 ---G--G-GATAGTCAAATACCCGTTGCGATAATCAAATT-
1 CGCGTTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTG
*
4964548 CGCGTTGCGATAATCAAATTCGCGTTGCGAT
1 CGCGTTGCGATAATCAAATACGCGTTGCGAT
4964579 AGACATATTC
Statistics
Matches: 82, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
34 23 0.28
35 1 0.01
37 2 0.02
39 1 0.01
40 20 0.24
41 35 0.43
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (41 bp):
CGCGTTGCGATAATCAAATACGCGTTGCGATTTTCTCGTTG
Found at i:4964610 original size:54 final size:54
Alignment explanation
Indices: 4964551--4964706 Score: 224
Period size: 54 Copynumber: 2.9 Consensus size: 54
4964541 TCAAATTCGC
* * *
4964551 GTTGCGATAATCAAATTCGCGTTGCGATAGACATATTCGTGTTGCGATTTTTGCA
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG-A
* * ** *
4964606 -TTGCGATAGTCATATTCGTATTGCGATAGTCAAATTCGCGTTGCAATTTTTGA
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
4964659 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
4964707 ATTCAAATGA
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.01
54 86 0.99
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
Found at i:4964940 original size:140 final size:140
Alignment explanation
Indices: 4964688--4964954 Score: 516
Period size: 140 Copynumber: 1.9 Consensus size: 140
4964678 CGTTGCGATA
* *
4964688 GTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAG
1 GTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAG
4964753 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
66 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
4964818 ACACATAATT
131 ACACATAATT
4964828 GTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAG
1 GTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAG
4964893 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
4964955 TACAACGTTT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
GTCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAG
CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
ACACATAATT
Found at i:4965035 original size:18 final size:18
Alignment explanation
Indices: 4965009--4965049 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
4964999 AGGTGAAGCC
*
4965009 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
4965027 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
4965045 GATTG
1 GATTG
4965050 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:4967175 original size:21 final size:21
Alignment explanation
Indices: 4967148--4967197 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
4967138 GTTAAGGGAG
*
4967148 TTACGTGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
* **
4967169 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAATACT
4967190 TTACGTGA
1 TTACGTGA
4967198 AGACAATGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:4967634 original size:21 final size:20
Alignment explanation
Indices: 4967606--4967722 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 20
4967596 AGTACCTGTC
4967606 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCC-CTCCT
* *
4967627 ATCATTCAAGAGACACCTCCT
1 ATCGTTCAAGAGGC-CCTCCT
* *
4967648 ACCGTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGG-CCCTCCT
* * *
4967669 ACCATTCAAGAGGCCC-CTGT
1 ATCGTTCAAGAGGCCCTC-CT
4967689 CATCGTTCAAGAGGTCCCTCCT
1 -ATCGTTCAAGAGG-CCCTCCT
*
4967711 ATCGTTCGAGAG
1 ATCGTTCAAGAG
4967723 CCCGATTCAC
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 66 0.86
22 6 0.08
23 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCTCCT
Found at i:4967696 original size:42 final size:42
Alignment explanation
Indices: 4967599--4967709 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
4967589 AGCCCGAAGT
* * *
4967599 ACCTGTCATCGTTCAAGAGGCCTCTCCTATCATTCAAGAGAC
1 ACCTGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGAC
* * *
4967641 ACCT-CCTACCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGC
1 ACCTGTC-ATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGAC
* *
4967683 CCCTGTCATCGTTCAAGAGGTCCCTCC
1 ACCTGTCATCGTTCAAGAGGCCCCTCC
4967710 TATCGTTCGA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.02
42 55 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
ACCTGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGAC
Found at i:4969108 original size:63 final size:64
Alignment explanation
Indices: 4969038--4969185 Score: 235
Period size: 63 Copynumber: 2.3 Consensus size: 64
4969028 AAATTGATGT
*
4969038 ATTTGTAAAAGTTTATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT-CTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * ***
4969101 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTTTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
4969165 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
4969186 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 45 0.58
64 33 0.42
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:4969276 original size:20 final size:20
Alignment explanation
Indices: 4969253--4969313 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
4969243 CTTTCGCAAC
4969253 GCGAAAGTCAAATTCGCGTT
1 GCGAAAGTCAAATTCGCGTT
* * ***
4969273 GCGATAGTTAAATTCGCAAC
1 GCGAAAGTCAAATTCGCGTT
*
4969293 GCGAAAGTCAAATTCGTGTT
1 GCGAAAGTCAAATTCGCGTT
4969313 G
1 G
4969314 TGATTTTTAC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCGTT
Found at i:4969373 original size:29 final size:29
Alignment explanation
Indices: 4969341--4969397 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
4969331 TTTCGCGTTT
*
4969341 CGAATTTGAATTTCGCAACAATCGCAACG
1 CGAATTTGAATTTCGCAACAATCACAACG
4969370 CGAATTTGAATTTCGCAACAATCACAAC
1 CGAATTTGAATTTCGCAACAATCACAAC
4969398 AAAAAATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (29 bp):
CGAATTTGAATTTCGCAACAATCACAACG
Found at i:4969591 original size:18 final size:18
Alignment explanation
Indices: 4969568--4969603 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4969558 AAGCCGGTTG
*
4969568 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
4969586 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
4969604 CCTTTTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:4970648 original size:18 final size:18
Alignment explanation
Indices: 4970625--4970661 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4970615 CAAAATTTAT
4970625 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
4970643 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
4970661 A
1 A
4970662 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:4971075 original size:25 final size:25
Alignment explanation
Indices: 4971047--4971096 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4971037 CATTATTTTC
* *
4971047 CAAATAATGTACCTATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
4971072 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
4971097 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:4971217 original size:29 final size:29
Alignment explanation
Indices: 4971175--4971235 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
4971165 CTTTCGCAAC
* *
4971175 GCGAAAGTCAAATTTGCGTTGCGATTGTT
1 GCGAAAGTCAAATTCGCATTGCGATTGTT
*
4971204 GCGAAAGTCAAATTCGCATTGCGATTTTT
1 GCGAAAGTCAAATTCGCATTGCGATTGTT
4971233 GCG
1 GCG
4971236 TTGCGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (29 bp):
GCGAAAGTCAAATTCGCATTGCGATTGTT
Found at i:4971503 original size:18 final size:18
Alignment explanation
Indices: 4971480--4971515 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4971470 AAGCTGGTTG
4971480 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
4971498 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
4971516 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:4973619 original size:24 final size:24
Alignment explanation
Indices: 4973592--4973659 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
4973582 TTGAAACATC
4973592 ATCAAAATCCGAATATTGACCAAG
1 ATCAAAATCCGAATATTGACCAAG
* ***
4973616 ATCAAAGTCCGGGCATTGACCAAG
1 ATCAAAATCCGAATATTGACCAAG
* * *
4973640 ATCAAATTTCGAATACTGAC
1 ATCAAAATCCGAATATTGAC
4973660 TAGTACTCAT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAATATTGACCAAG
Found at i:4974424 original size:16 final size:17
Alignment explanation
Indices: 4974388--4974427 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
4974378 GAAATCATTG
4974388 AAAAATTATATAGAAAT
1 AAAAATTATATAGAAAT
*
4974405 -AAAATTATGTA-AAAT
1 AAAAATTATATAGAAAT
4974420 AAAAATTA
1 AAAAATTA
4974428 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAAATTATATAGAAAT
Found at i:4974608 original size:20 final size:20
Alignment explanation
Indices: 4974565--4974672 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 20
4974555 AAAACATTTG
* *
4974565 TGTTGCGAAAATAAAA--CC
1 TGTTGCGAAATTAAAATTCA
4974583 TGTTGCGAAATTAAAATTCA
1 TGTTGCGAAATTAAAATTCA
4974603 TGTTGCG-AATTCGAAAA-TCGA
1 TGTTGCGAAATT--AAAATTC-A
* * *
4974624 -GTTGCGAACTCAGAAATTGA
1 TGTTGCGAAATTA-AAATTCA
* *
4974644 -GTTGCGAATTTGAAATTCA
1 TGTTGCGAAATTAAAATTCA
4974663 GTGTTGCGAA
1 -TGTTGCGAA
4974673 TTTGTAAATC
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
18 15 0.21
19 11 0.15
20 29 0.41
21 16 0.23
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCA
Found at i:4974722 original size:40 final size:41
Alignment explanation
Indices: 4974647--4974724 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
4974637 AAATTGAGTT
* * *
4974647 GCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATCGCAAC
1 GCGAATTTGAAATTCAGCGTTACGAATTTGGAAATCGCAAC
4974688 GCGAATTTGTAAA-TCA-CGTTACGAATTTGGAAATCGC
1 GCGAATTTG-AAATTCAGCGTTACGAATTTGGAAATCGC
4974725 GTTGTGAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 18 0.55
41 12 0.36
42 3 0.09
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (41 bp):
GCGAATTTGAAATTCAGCGTTACGAATTTGGAAATCGCAAC
Found at i:4974736 original size:20 final size:20
Alignment explanation
Indices: 4974689--4974727 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4974679 AATCGCAACG
*
4974689 CGAATTTGTAAATCACGTTA
1 CGAATTTGGAAATCACGTTA
*
4974709 CGAATTTGGAAATCGCGTT
1 CGAATTTGGAAATCACGTT
4974728 GTGAATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
CGAATTTGGAAATCACGTTA
Found at i:4974788 original size:20 final size:21
Alignment explanation
Indices: 4974765--4974803 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4974755 ACATATTCGC
4974765 GTTGCGAATTT-GAAAATCTT
1 GTTGCGAATTTGGAAAATCTT
4974785 GTTGCGAATTTGGAAAATC
1 GTTGCGAATTTGGAAAATC
4974804 GCAACTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (21 bp):
GTTGCGAATTTGGAAAATCTT
Found at i:4975003 original size:2 final size:2
Alignment explanation
Indices: 4974984--4975072 Score: 114
Period size: 2 Copynumber: 45.0 Consensus size: 2
4974974 TTCTCTTTTA
*
4974984 AT AT AGT AT AT AT GT AT AT A- ACT A- AT AT A- AGT A- AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT
4975023 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
4975065 AT AT AT AT
1 AT AT AT AT
4975073 TAAAGAACAC
Statistics
Matches: 78, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.05
2 70 0.90
3 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4975162 original size:14 final size:15
Alignment explanation
Indices: 4975124--4975163 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
4975114 ATAGTTTATA
4975124 AAAATCCTAAACCCT
1 AAAATCCTAAACCCT
*
4975139 AAAAT-ATAAACCCT
1 AAAATCCTAAACCCT
4975153 -AAATCCTAAAC
1 AAAATCCTAAAC
4975164 TTTATAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 13 0.59
15 5 0.23
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATCCTAAACCCT
Found at i:4975348 original size:35 final size:36
Alignment explanation
Indices: 4975278--4975351 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
4975268 ACAATAGTTA
* *
4975278 ATATATGTAACTTATAGTATATGTATACATGTAAACT
1 ATATATGTAACTTATAGTACATGTATA-ATATAAACT
*
4975315 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACTTATAGTACATGTATAATATAAACT
4975350 AT
1 AT
4975352 GTATAGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 9 0.26
37 25 0.74
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (36 bp):
ATATATGTAACTTATAGTACATGTATAATATAAACT
Found at i:4975365 original size:2 final size:2
Alignment explanation
Indices: 4975353--4975384 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
4975343 ATAAACTATG
4975353 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
4975385 TCATATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4975491 original size:13 final size:13
Alignment explanation
Indices: 4975473--4975516 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
4975463 AAAAAAATCC
4975473 TAAACCCTAAACA
1 TAAACCCTAAACA
4975486 TAAA-CCTAAACCA
1 TAAACCCTAAA-CA
4975499 TAAACCCTAAACA
1 TAAACCCTAAACA
4975512 TAAAC
1 TAAAC
4975517 AATAGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
13 17 0.59
14 6 0.21
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAACCCTAAACA
Found at i:4975624 original size:20 final size:19
Alignment explanation
Indices: 4975596--4975687 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 19
4975586 CATGTATCAT
*
4975596 GTATGTATAAACTATGTATA
1 GTATATATAAACTATGT-TA
4975616 GTATATATAAACTATG-TA
1 GTATATATAAACTATGTTA
*
4975634 -TATATATAACCTATAGTATA
1 GTATATATAAACTAT-GT-TA
4975654 TGTATATATACAATCTAT-TTA
1 -GTATATATA-AA-CTATGTTA
4975675 -TAT-TATAAACTAT
1 GTATATATAAACTAT
4975688 ATGTAACCTA
Statistics
Matches: 62, Mismatches: 3, Indels: 18
0.75 0.04 0.22
Matches are distributed among these distances:
16 4 0.06
17 15 0.24
18 7 0.11
19 3 0.05
20 17 0.27
21 2 0.03
22 9 0.15
23 1 0.02
24 4 0.06
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (19 bp):
GTATATATAAACTATGTTA
Found at i:4975636 original size:15 final size:18
Alignment explanation
Indices: 4975612--4975659 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
4975602 ATAAACTATG
4975612 TATAGTATATATA-AA-C
1 TATAGTATATATATAACC
4975628 TAT-GTATATATATAACC
1 TATAGTATATATATAACC
*
4975645 TATAGTATATGTATA
1 TATAGTATATATATA
4975660 TATACAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 4 0.14
18 10 0.36
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (18 bp):
TATAGTATATATATAACC
Found at i:4975648 original size:24 final size:21
Alignment explanation
Indices: 4975587--4975641 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
4975577 CTTATAGTGC
* *
4975587 ATGTATCATGTATGTATAAACT
1 ATGTAT-ATATATATATAAACT
*
4975609 ATGTATA-GTATATATAAACT
1 ATGTATATATATATATAAACT
4975629 ATGTATATATATA
1 ATGTATATATATA
4975642 ACCTATAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 19 0.63
21 5 0.17
22 6 0.20
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (21 bp):
ATGTATATATATATATAAACT
Found at i:4975677 original size:37 final size:36
Alignment explanation
Indices: 4975601--4975687 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 36
4975591 ATCATGTATG
* *
4975601 TATAAACTATGTATAGTATATATAAACTATGTATATA
1 TATAAACTATGTATAGTATATAT-AACAATCTATATA
*
4975638 TATAACCTATAGTATATGTATATAT-ACAATCTATTTATA
1 TATAAACTAT-GTATA-GTATATATAACAATCTA--TATA
4975677 TTATAAACTAT
1 -TATAAACTAT
4975688 ATGTAACCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
37 15 0.37
38 5 0.12
39 12 0.29
40 9 0.22
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (36 bp):
TATAAACTATGTATAGTATATATAACAATCTATATA
Found at i:4975782 original size:21 final size:21
Alignment explanation
Indices: 4975728--4975782 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4975718 ATATTAGTGT
*
4975728 ACTATAGTTTATACTTTATAA
1 ACTATAGTTTATAATTTATAA
* * *
4975749 CCTATGGTATATAATTTATAA
1 ACTATAGTTTATAATTTATAA
4975770 ACTATAGTTTATA
1 ACTATAGTTTATA
4975783 TTAATGTACT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ACTATAGTTTATAATTTATAA
Found at i:4975835 original size:31 final size:30
Alignment explanation
Indices: 4975794--4975945 Score: 121
Period size: 31 Copynumber: 4.8 Consensus size: 30
4975784 TAATGTACTA
* *
4975794 TATAGTTTATATTAATGTTAATTATCTTAAC
1 TATAATTTATATTAATATTAATTAT-TTAAC
4975825 TATAATTTATATTAATA-TAGTATATAGTTTATA-
1 TATAATTTATATTAATATTA--AT-TA-TTTA-AC
* **
4975858 AATTTTATTATATTAATATTAATTATATTAAC
1 TATAAT-TTATATTAATATTAATTAT-TTAAC
* *
4975890 TATAGTTTATATTAATATTAATGT-TATAGAC
1 TATAATTTATATTAATATTAAT-TATTTA-AC
*
4975921 TATATTTTATATTAATATTAATTAT
1 TATAATTTATATTAATATTAATTAT
4975946 AAATTATAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
30 5 0.05
31 58 0.59
32 11 0.11
33 10 0.10
34 13 0.13
35 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (30 bp):
TATAATTTATATTAATATTAATTATTTAAC
Found at i:4975928 original size:65 final size:61
Alignment explanation
Indices: 4975790--4976015 Score: 175
Period size: 65 Copynumber: 3.7 Consensus size: 61
4975780 ATATTAATGT
* * *
4975790 ACTATATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTATATAG
1 ACTATA-ATTTTATATTAATATTAATTATATTAACTATAATTTATATTAATATAGTATATAG
** *
4975852 TTTATAAATTTTATTATATTAATATTAATTATATTAACTATAGTTTATATTAATATTAATGT-TA
1 ACTAT-AA--TT-TTATATTAATATTAATTATATTAACTATAATTTATATTAATA-T-A-GTATA
4975916 TAG
59 TAG
* * *
4975919 ACTAT-ATTTTATATTAATATTAATTATA--AATTATAAATTATA--AACTATATTATATTA-
1 ACTATAATTTTATATTAATATTAATTATATTAACTATAATTTATATTAA-TATAGTATA-TAG
* *
4975976 A-TATAAGTTAATATTAAT-TATAATTATATTAA-TATTAATT
1 ACTATAATTTTATATTAATAT-TAATTATATTAACTA-TAATT
4976016 ATAATATATA
Statistics
Matches: 134, Mismatches: 15, Indels: 33
0.74 0.08 0.18
Matches are distributed among these distances:
56 5 0.04
57 23 0.17
58 7 0.05
59 8 0.06
60 11 0.08
62 24 0.18
63 3 0.02
64 1 0.01
65 40 0.30
66 1 0.01
67 9 0.07
68 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (61 bp):
ACTATAATTTTATATTAATATTAATTATATTAACTATAATTTATATTAATATAGTATATAG
Found at i:4975953 original size:96 final size:99
Alignment explanation
Indices: 4975794--4976049 Score: 255
Period size: 96 Copynumber: 2.6 Consensus size: 99
4975784 TAATGTACTA
* * * * **
4975794 TATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTAATA-TAGTATATAGTTTATA
1 TATAGTTTATATTAATATTAATT-T-ATAACTATATTTTATATTAATATTAAT-TATAAATTATA
4975858 AA-T-T-T-TATTATATTAATATTAA-TT-ATATTAAC
63 AATTATATATATTATATTAATA-TAAGTTAATATTAAC
4975890 TATAGTTTATATTAATATTAATGTTATAGACTATATTTTATATTAATATTAATTATAAATTATAA
1 TATAGTTTATATTAATATTAAT-TTATA-ACTATATTTTATATTAATATTAATTATAAATTATAA
*
4975955 ATTATAAACTATATTATATTAATATAAGTTAATATTAAT
64 ATTAT--A-TATATTATATTAATATAAGTTAATATTAAC
* *
4975994 TATA-ATTATATTAATATTAA-TTATAA-TATATAATTAT-TATAATATTAATTATAAAT
1 TATAGTTTATATTAATATTAATTTATAACTATAT-TTTATAT-TAATATTAATTATAAAT
4976050 AGTTAATTAA
Statistics
Matches: 137, Mismatches: 9, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
95 2 0.01
96 51 0.37
97 5 0.04
98 1 0.01
99 6 0.04
100 22 0.16
101 5 0.04
102 4 0.03
103 30 0.22
104 11 0.08
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (99 bp):
TATAGTTTATATTAATATTAATTTATAACTATATTTTATATTAATATTAATTATAAATTATAAAT
TATATATATTATATTAATATAAGTTAATATTAAC
Found at i:4976005 original size:31 final size:33
Alignment explanation
Indices: 4975825--4976047 Score: 110
Period size: 34 Copynumber: 6.6 Consensus size: 33
4975815 TTATCTTAAC
*
4975825 TATAATTTATATTAATAT-AGTATATAGTTTATAAAT
1 TATAA-TTATATTAATATAAGTATA-A-TATAT-AAT
* *
4975861 T-TTATTATATTAATATTAA-T-T-ATAT-TAAC
1 TATAATTATATTAATA-TAAGTATAATATATAAT
* *
4975890 TATAGTTTATATTAATATTAATGTTATAGACTATAT-TT
1 TATA-ATTATATTAATA-TAA-G-TATA-A-TATATAAT
* *
4975928 TAT-ATTAATATTAATTATAAATTATAA-ATTATAAAC
1 TATAATT-ATATTAA-TAT-AAGTATAATA-TAT-AAT
4975964 TAT-ATTATATTAATATAAGT-TAATAT-TAAT
1 TATAATTATATTAATATAAGTATAATATATAAT
*
4975994 TATAATTATATTAATATTAATTATAATATATAAT
1 TATAATTATATTAATA-TAAGTATAATATATAAT
* *
4976028 TATTATAATATTAATTATAA
1 TATAATTATATTAA-TATAA
4976048 ATAGTTAATT
Statistics
Matches: 147, Mismatches: 16, Indels: 50
0.69 0.08 0.23
Matches are distributed among these distances:
29 3 0.02
30 7 0.05
31 30 0.20
32 9 0.06
33 11 0.07
34 38 0.26
35 15 0.10
36 14 0.10
37 9 0.06
38 10 0.07
39 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (33 bp):
TATAATTATATTAATATAAGTATAATATATAAT
Found at i:4976034 original size:16 final size:15
Alignment explanation
Indices: 4975984--4976058 Score: 73
Period size: 15 Copynumber: 4.8 Consensus size: 15
4975974 TAATATAAGT
*
4975984 TAATATTAATTATAA
1 TAATATTAATTATTA
*
4975999 TTATATTAATATTAATTA
1 TAATATT-A-ATT-ATTA
4976017 TAATATATAATTATTA
1 TAATAT-TAATTATTA
4976033 TAATATTAATTA-TA
1 TAATATTAATTATTA
4976047 -AATAGTTAATTA
1 TAATA-TTAATTA
4976059 ATAAAAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
13 4 0.08
14 9 0.17
15 12 0.23
16 11 0.21
17 6 0.12
18 9 0.17
19 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
TAATATTAATTATTA
Found at i:4976036 original size:28 final size:27
Alignment explanation
Indices: 4975990--4976047 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
4975980 AAGTTAATAT
4975990 TAATTATAATTATATTAATATTAATTA
1 TAATTATAATTATATTAATATTAATTA
4976017 TAATATATAATTAT-TATAATATTAATTA
1 TAAT-TATAATTATAT-TAATATTAATTA
4976045 TAA
1 TAA
4976048 ATAGTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAATTATAATTATATTAATATTAATTA
Found at i:4976062 original size:15 final size:14
Alignment explanation
Indices: 4975934--4976068 Score: 63
Period size: 14 Copynumber: 9.5 Consensus size: 14
4975924 ATTTTATATT
4975934 AATATTAATT-ATA
1 AATATTAATTAATA
*
4975947 AATTATAAATT-ATA
1 AA-TATTAATTAATA
*
4975961 AACTA-T-ATTATATT
1 AA-TATTAATTA-ATA
4975975 AATA-TAAGTTAATA
1 AATATTAA-TTAATA
*
4975989 TTAAT-TATAATTATATT
1 --AATAT-TAATTA-ATA
4976006 AATATTAATT-AT-
1 AATATTAATTAATA
*
4976018 AATATATAATTATTA
1 AATAT-TAATTAATA
4976033 TAATATTAATT-ATA
1 -AATATTAATTAATA
4976047 AATAGTTAATTAATA
1 AATA-TTAATTAATA
*
4976062 AAAATTA
1 AATATTA
4976069 TATAGTGATG
Statistics
Matches: 96, Mismatches: 9, Indels: 33
0.70 0.07 0.24
Matches are distributed among these distances:
12 8 0.08
13 16 0.17
14 33 0.34
15 22 0.23
16 12 0.12
17 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (14 bp):
AATATTAATTAATA
Found at i:4976068 original size:28 final size:28
Alignment explanation
Indices: 4975954--4976068 Score: 80
Period size: 28 Copynumber: 4.0 Consensus size: 28
4975944 ATAAATTATA
*
4975954 AATTATAAACTATATTATATTAATAT-AAGTT
1 AATTAT-AA-TATA-TA-ATTAATATAAAATT
*
4975985 AA-TATTAAT-TATAATT-ATATTAATATT
1 AATTA-TAATATATAATTAATA-TAAAATT
* *
4976012 AATTATAATATATAATTATTATAATATT
1 AATTATAATATATAATTAATATAAAATT
4976040 AATTATAA-ATAGTTAATTAATA-AAAATT
1 AATTATAATATA--TAATTAATATAAAATT
4976068 A
1 A
4976069 TATAGTGATG
Statistics
Matches: 71, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
25 3 0.04
26 4 0.06
27 14 0.20
28 32 0.45
29 11 0.15
30 4 0.06
31 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTATAATATATAATTAATATAAAATT
Found at i:4976071 original size:103 final size:102
Alignment explanation
Indices: 4975853--4976049 Score: 262
Period size: 103 Copynumber: 1.9 Consensus size: 102
4975843 AGTATATAGT
* *
4975853 TTATAAATTTTATTATATTAATATTAATTATATTAACTATAGTTTATATTAATATTAATGTTATA
1 TTATAAATTATATTATATTAATATTAATTATATTAACTATAGATTATATTAATATTAA-GTTATA
*
4975918 GACTATATTTTATATTAATATTAATTATAAATTATAAA
65 GACTATATATTATATTAATATTAATTATAAATTATAAA
* *
4975956 TTATAAACTATATTATATTAATA-TAAGTTAATATTAATTATA-ATTATATTAATATTAA-TTAT
1 TTATAAATTATATTATATTAATATTAA-TT-ATATTAACTATAGATTATATTAATATTAAGTTAT
4976018 A-A-TATATAATTAT-TATAATATTAATTATAAAT
64 AGACTATAT-ATTATAT-TAATATTAATTATAAAT
4976050 AGTTAATTAA
Statistics
Matches: 85, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
99 6 0.07
100 22 0.26
101 5 0.06
102 3 0.04
103 38 0.45
104 11 0.13
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (102 bp):
TTATAAATTATATTATATTAATATTAATTATATTAACTATAGATTATATTAATATTAAGTTATAG
ACTATATATTATATTAATATTAATTATAAATTATAAA
Found at i:4976857 original size:30 final size:29
Alignment explanation
Indices: 4976787--4976914 Score: 87
Period size: 30 Copynumber: 4.2 Consensus size: 29
4976777 CGACCCAAAC
** * *
4976787 CCAAACCCAAACTTGAACCTAACCCCTAA
1 CCAAACCCAAACTAAAACCCAAACCCTAA
** *
4976816 CTGAACTCAAACCTAAAACCCAAACCCTAA
1 CCAAACCCAAA-CTAAAACCCAAACCCTAA
4976846 CCAAACCCAAACTGAACCAAGCCCAAA-CCTGAA
1 CCAAACCCAAACT-AA--AA-CCCAAACCCT-AA
** *
4976879 CCCAAATTCAAACTCAAACCCAAACCCTAA
1 -CCAAACCCAAACTAAAACCCAAACCCTAA
4976909 CTCAAA
1 C-CAAA
4976915 TTCAAAAAAC
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
29 11 0.14
30 36 0.47
31 5 0.06
32 5 0.06
33 9 0.12
34 11 0.14
ACGTcount: A:0.45, C:0.39, G:0.04, T:0.12
Consensus pattern (29 bp):
CCAAACCCAAACTAAAACCCAAACCCTAA
Found at i:4976879 original size:17 final size:17
Alignment explanation
Indices: 4976831--4976880 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
4976821 CTCAAACCTA
4976831 AAACCCAAACCCT-AACC
1 AAACCCAAA-CCTGAACC
4976848 AAACCCAAA-CTGAACC
1 AAACCCAAACCTGAACC
*
4976864 AAGCCCAAACCTGAACC
1 AAACCCAAACCTGAACC
4976881 CAAATTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
17 16 0.53
ACGTcount: A:0.46, C:0.42, G:0.06, T:0.06
Consensus pattern (17 bp):
AAACCCAAACCTGAACC
Found at i:4977316 original size:102 final size:102
Alignment explanation
Indices: 4977140--4977477 Score: 525
Period size: 102 Copynumber: 3.3 Consensus size: 102
4977130 TTGAAAGAGG
* *
4977140 TAAATAAACTGTTTAATTTCTAGCCACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGG-T
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTC-GGAT
* *
4977204 TGCTTTTATAAGGTTGTTAGCTACCTTTATTTATAGTT
65 TGCTTTTATAAGGTTGTTAGCTACATTTATTTACAGTT
* *
4977242 TAAATAGACTGTTTAATTTGTAGCTACTGTTGTTTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
4977307 GCTTTTATAAGGTTGTTAGCTACATTTATTTACAGTT
66 GCTTTTATAAGGTTGTTAGCTACATTTATTTACAGTT
* * ** * *
4977344 TAAATAAGCTATTTAATTCATATCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGATT
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
*
4977409 GCTTTTATAAGGTTGTTAGCTGCATTTATTTACAGTT
66 GCTTTTATAAGGTTGTTAGCTACATTTATTTACAGTT
* *
4977446 TATATAAACTGTTTAATTTGTAGCTATTGTTG
1 TAAATAAACTGTTTAATTTGTAGCTACTGTTG
4977478 GTTGTTCATT
Statistics
Matches: 213, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 2 0.01
102 211 0.99
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.50
Consensus pattern (102 bp):
TAAATAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
GCTTTTATAAGGTTGTTAGCTACATTTATTTACAGTT
Found at i:4980155 original size:12 final size:11
Alignment explanation
Indices: 4980129--4980167 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
4980119 GAATTGACTC
*
4980129 AAATGTTATTT
1 AAATTTTATTT
4980140 AAATTTTATATT
1 AAATTTTAT-TT
4980152 AAATTTTATTT
1 AAATTTTATTT
4980163 AAATT
1 AAATT
4980168 ATCATTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (11 bp):
AAATTTTATTT
Found at i:4980430 original size:14 final size:14
Alignment explanation
Indices: 4980411--4980457 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
4980401 ATTTTTTCTT
4980411 TATATAAATTAAAC
1 TATATAAATTAAAC
4980425 TATAT-AATT----
1 TATATAAATTAAAC
4980434 TATATAAATTAAAC
1 TATATAAATTAAAC
*
4980448 TATATTAATT
1 TATATAAATT
4980458 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:4980436 original size:23 final size:24
Alignment explanation
Indices: 4980409--4980458 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
4980399 TTATTTTTTC
4980409 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
4980432 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
4980456 TTT
1 TTT
4980459 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:4983251 original size:20 final size:20
Alignment explanation
Indices: 4983214--4983267 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
4983204 CGATTCAAGT
* *
4983214 GGTATCGATACAAAGAGG-G
1 GGTATCGATACCATGAGGAG
*
4983233 GAGTATCGATACCATGAGGAT
1 G-GTATCGATACCATGAGGAG
4983254 GGTATCGATACCAT
1 GGTATCGATACCAT
4983268 TGAGCACAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCATGAGGAG
Found at i:4983779 original size:55 final size:55
Alignment explanation
Indices: 4983683--4983851 Score: 266
Period size: 55 Copynumber: 3.0 Consensus size: 55
4983673 ATTACCAAAT
* * * *
4983683 GGCACTAAGTGTGCAAAAAGTTAAGAAATTCATAATGAGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
*
4983740 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
*
4983795 GGCACTATGTGTTCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
4983850 GG
1 GG
4983852 AAATATATGT
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 88 0.84
56 4 0.04
57 13 0.12
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:4983873 original size:55 final size:55
Alignment explanation
Indices: 4983704--4983903 Score: 253
Period size: 55 Copynumber: 3.6 Consensus size: 55
4983694 TGCAAAAAGT
* *
4983704 TAAGAAATTCATAATGAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAAC
1 TAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGCACTATGTGTACAAAAC
* * *
4983759 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCACTATGTGTTCAAAAC
1 TAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGCACTATGTGTACAAAAC
* * * * *
4983814 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGAAATATATGTACAACTA-
1 TAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGCACTATGTGTACAA-AAC
*
4983869 TAAGAAGTTCATAATAA-T-TAGGTGAATTTCCGTAT
1 TAAGAAATTCATAATAAGTGTA--TGAATTTCCGTAT
4983904 TAGTAGTGGG
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.02
54 1 0.01
55 126 0.97
56 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (55 bp):
TAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGCACTATGTGTACAAAAC
Found at i:4993938 original size:24 final size:24
Alignment explanation
Indices: 4993906--4993954 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4993896 CAAGATTATG
4993906 GCCTAACTGTGCATTTGACAGAAA
1 GCCTAACTGTGCATTTGACAGAAA
4993930 GCCTAACTGTGCATTTGACAGAAA
1 GCCTAACTGTGCATTTGACAGAAA
4993954 G
1 G
4993955 GTTTCAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
GCCTAACTGTGCATTTGACAGAAA
Found at i:4994175 original size:45 final size:45
Alignment explanation
Indices: 4994108--4994565 Score: 736
Period size: 45 Copynumber: 10.2 Consensus size: 45
4994098 CGTATAAAAA
*
4994108 TGGCATGAAAGGATGCCCAAATAATAATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* * * *
4994153 TGGCATGAAATGATGCCAAAATAATGATACATATGGGTGCATTAA
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* *
4994198 TGGCGTGAAAGGATGCCAAAATAATGATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
*
4994243 TGGCATGAAAGGATGCCAAAATAATAATGCATATAGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* *
4994288 TGGCATAAAAGGATGCCAAAATAATGATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* *
4994333 TGGCATGAAAGGATTCCAAAATAATTATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* * *
4994378 TGGCATGAAATGATACCAAAATAATAATGCTTATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
4994423 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* * *
4994468 TGCCATGAAATGATGCCAAAATGATAATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
* *
4994513 TGGCCTGAAAGGATGCTAAAATAATAATGCATATGGGTGCATTAT
1 TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
4994558 TGGCATGA
1 TGGCATGA
4994566 TAGAATTTCA
Statistics
Matches: 379, Mismatches: 34, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 379 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (45 bp):
TGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTAT
Found at i:5005471 original size:15 final size:15
Alignment explanation
Indices: 5005448--5005496 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
5005438 CGCCCCGCAT
*
5005448 CCGCACCGCATCCAC
1 CCGCACCGCATCCGC
*
5005463 CCGCCCCGCATCCGC
1 CCGCACCGCATCCGC
5005478 CCGCACCGCATCCGC
1 CCGCACCGCATCCGC
5005493 CCGC
1 CCGC
5005497 CCAACTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.12, C:0.63, G:0.18, T:0.06
Consensus pattern (15 bp):
CCGCACCGCATCCGC
Found at i:5005492 original size:26 final size:26
Alignment explanation
Indices: 5005435--5005494 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
5005425 TTGAGACCTT
*
5005435 ACCCGCCCCGCATCCGCACCGCATCC
1 ACCCGCCCCGCATCCGCACCGCACCC
5005461 ACCCGCCCCGCATCCGC-CCGCACCGC
1 ACCCGCCCCGCATCCGCACCGCACC-C
*
5005487 ATCCGCCC
1 ACCCGCCC
5005495 GCCCAACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.13, C:0.63, G:0.17, T:0.07
Consensus pattern (26 bp):
ACCCGCCCCGCATCCGCACCGCACCC
Found at i:5006788 original size:43 final size:42
Alignment explanation
Indices: 5006666--5006969 Score: 149
Period size: 43 Copynumber: 7.1 Consensus size: 42
5006656 AGTCACCATT
* *
5006666 TTTTTCAT-TTTATAATTAG-GTC-CTTAATTTTTTAAATCTTA-
1 TTTTT-ATCTTTATAATT-GTGTCTC-TAATTTTTTCAATCTCAC
* * *
5006707 TTTTTTTACATTTATAATTGATGTC-CTAATGATATTCAATCTCAC
1 TTTTTAT-C-TTTATAATTG-TGTCTCTAAT-TTTTTCAATCTCAC
*
5006752 TTTTTATCTTTATAATTGTGATCTCTAATTTTTTCAATC-CCC
1 TTTTTATCTTTATAATTGTG-TCTCTAATTTTTTCAATCTCAC
* * *
5006794 TTTTTTTATCTTTATAATTGAGGCTCTTAATTTTGT-AATCTCAC
1 --TTTTTATCTTTATAATTGTGTCTC-TAATTTTTTCAATCTCAC
* * * *
5006838 -TTTTAACTTTATAATTGAGGCTTTTAAGTTTTTTTCAATCTCAC
1 TTTTTATCTTTATAATTGTGTC-TCTAA--TTTTTTCAATCTCAC
* * ** * * * * *
5006882 TTTCTACCTTTCCAATTGACGGCCCTAAATTTTTCAATCTCAA
1 TTTTTATCTTTATAATTG-TGTCTCTAATTTTTTCAATCTCAC
* * * * * *
5006925 TTTCTACCTTTATAATCGATGCCTCTAATGTTTT-AATCCCAC
1 TTTTTATCTTTATAATTG-TGTCTCTAATTTTTTCAATCTCAC
5006967 TTT
1 TTT
5006970 CTAATTATAT
Statistics
Matches: 209, Mismatches: 35, Indels: 37
0.74 0.12 0.13
Matches are distributed among these distances:
40 1 0.00
41 28 0.13
42 15 0.07
43 84 0.40
44 56 0.27
45 22 0.11
46 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (42 bp):
TTTTTATCTTTATAATTGTGTCTCTAATTTTTTCAATCTCAC
Found at i:5006825 original size:44 final size:44
Alignment explanation
Indices: 5006664--5006884 Score: 176
Period size: 43 Copynumber: 5.1 Consensus size: 44
5006654 GGAGTCACCA
* *
5006664 TTTTTTTCAT-TTTATAATT-AGGTCCTTAATTTTTTAAATCTTA-
1 TTTTTTT-ATCTTTATAATTGAGGT-CTTAATTTTTTCAATCTCAC
* * * *
5006707 TTTTTTTA-CATTTATAATTGATGTCCTAATGATATTCAATCTCAC
1 TTTTTTTATC-TTTATAATTGAGGTCTTAAT-TTTTTCAATCTCAC
* * *
5006752 --TTTTTATCTTTATAATTGTGATCTCTAATTTTTTCAATC-CCC
1 TTTTTTTATCTTTATAATTGAGGTCT-TAATTTTTTCAATCTCAC
*
5006794 TTTTTTTATCTTTATAATTGAGGCTCTTAATTTTGT-AATCTCAC
1 TTTTTTTATCTTTATAATTGAGG-TCTTAATTTTTTCAATCTCAC
* *
5006838 ---TTTTAACTTTATAATTGAGGCTTTTAAGTTTTTTTCAATCTCAC
1 TTTTTTTATCTTTATAATTGAGG-TCTTAA--TTTTTTCAATCTCAC
5006882 TTT
1 TTT
5006885 CTACCTTTCC
Statistics
Matches: 141, Mismatches: 20, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
41 25 0.18
42 3 0.02
43 56 0.40
44 54 0.38
45 3 0.02
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (44 bp):
TTTTTTTATCTTTATAATTGAGGTCTTAATTTTTTCAATCTCAC
Found at i:5006854 original size:41 final size:42
Alignment explanation
Indices: 5006741--5006972 Score: 170
Period size: 43 Copynumber: 5.4 Consensus size: 42
5006731 CCTAATGATA
* * * *
5006741 TTCAATCTCACTTTTTATCTTTATAATTG-TGATCTCTAATTTT
1 TTCAATCTCACTTTCTACCTTTATAATTGAGGCTCT-TAA-TTT
* * *
5006784 TTCAATC-CCCTTTTTTTATCTTTATAATTGAGGCTCTTAATTT
1 TTCAATCTCAC--TTTCTACCTTTATAATTGAGGCTCTTAATTT
* *
5006827 TGT-AATCTCACTTT-TAACTTTATAATTGAGGCTTTTAAGTTTTT
1 T-TCAATCTCACTTTCTACCTTTATAATTGAGGCTCTTAA---TTT
** * *
5006871 TTCAATCTCACTTTCTACCTTTCCAATTGACGGCCCTAAATTT
1 TTCAATCTCACTTTCTACCTTTATAATTGA-GGCTCTTAATTT
* * *
5006914 TTCAATCTCAATTTCTACCTTTATAATCGATGC-CTCTAATGTT
1 TTCAATCTCACTTTCTACCTTTATAATTGAGGCTCT-TAAT-TT
*
5006957 TT-AATCCCACTTTCTA
1 TTCAATCTCACTTTCTA
5006973 ATTATATTTG
Statistics
Matches: 156, Mismatches: 20, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
41 24 0.15
42 22 0.14
43 49 0.31
44 39 0.25
45 16 0.10
46 6 0.04
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.49
Consensus pattern (42 bp):
TTCAATCTCACTTTCTACCTTTATAATTGAGGCTCTTAATTT
Found at i:5006863 original size:21 final size:21
Alignment explanation
Indices: 5006797--5006864 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
5006787 AATCCCCTTT
*
5006797 TTTTATCTTTATAATTGAGGC
1 TTTTAACTTTATAATTGAGGC
* * * *
5006818 TCTTAATTTTGTAATCTCA--C
1 TTTTAACTTTATAAT-TGAGGC
5006838 TTTTAACTTTATAATTGAGGC
1 TTTTAACTTTATAATTGAGGC
5006859 TTTTAA
1 TTTTAA
5006865 GTTTTTTTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 18 0.51
22 2 0.06
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTTAACTTTATAATTGAGGC
Found at i:5009247 original size:29 final size:31
Alignment explanation
Indices: 5009202--5009277 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
5009192 TTAATCAAAA
*
5009202 TATTAAT-TATTAAAATAT-TAA-AATATATT
1 TATTAATAT-TTATAATATATAATAATATATT
*
5009231 TATTAATATTTATAATAATATAATATTATATT
1 TATTAATATTTATAAT-ATATAATAATATATT
5009263 T-TTAATA-TTATAATA
1 TATTAATATTTATAATA
5009278 AAATATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 14 0.34
30 10 0.24
31 9 0.22
32 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TATTAATATTTATAATATATAATAATATATT
Done.