Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 427 of 444
Found at i:123514623 original size:29 final size:30
Alignment explanation
Indices: 123514575--123514642 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
123514565 TTTTAATAGT
*
123514575 TTAT-ATTTTTATAATTTTTAAAGGATTAAA
1 TTATAATTTTTATAATTTTTAAA-GAGTAAA
*
123514605 TTA-AATTTTTATCA-TTTTAAAGAGTAAA
1 TTATAATTTTTATAATTTTTAAAGAGTAAA
123514633 TTATAATTTT
1 TTATAATTTT
123514643 ACTATTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 9 0.26
29 13 0.38
30 12 0.35
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (30 bp):
TTATAATTTTTATAATTTTTAAAGAGTAAA
Found at i:123518898 original size:1 final size:1
Alignment explanation
Indices: 123518892--123518936 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
123518882 CCCTTGTTAC
* * * *
123518892 AAAAAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
123518937 GTAGGCTGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:123526330 original size:14 final size:14
Alignment explanation
Indices: 123526311--123526338 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
123526301 TTATTCTTCT
123526311 ATGATCCAACTATG
1 ATGATCCAACTATG
123526325 ATGATCCAACTATG
1 ATGATCCAACTATG
123526339 CTAGGCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
ATGATCCAACTATG
Found at i:123533955 original size:129 final size:129
Alignment explanation
Indices: 123533725--123534262 Score: 479
Period size: 129 Copynumber: 4.2 Consensus size: 129
123533715 TGATTTCCAG
* * ** * *
123533725 CCTGTTACCCTACTACTTA-GGGGTTAAGATCTGTAAATTCAGTCTAATACCCTATTGCTTAGGG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGGG
* * * ***
123533789 GGTTAAGGCCATTCGTCTTCGATCTGTTTTCCTACTGCTTAGGGCA-TTAAGATCTGCAATTTGG
66 GGTTAAGGCCCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGG-AGTTAAGATCTGCAATTCAA
* *
123533853 TCTGTTACCCTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGGG
1 CCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGGG
* * * *
123533918 GTTTAAGGCCCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAG
66 GGTTAAGGCCCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGTTAAGATCTG-CAATTCAA
* * * * *
123533983 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCTTCGT--CTTC-GATCTGCTCCACTACTGCTT
1 CCTGTTACCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTCAG-CCTGTTACACTACTGCTT
* * ** * * * * * *
123534045 AGGGAGATAA-GATC-T-GTAATTCAACCTG-TTACCCTACTGCTTAGGG-TTTAAGGTTCTTCG
62 AGGGGGTTAAGGCCCTTCGT-CTTCGATCTGCTT-CCCTACTGCTTAGGGAGTTAA-GATCTGC-
** *
123534105 TCTTCGA
123 AATTCAA
* * * *
123534112 TCTGCTT-CCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGG
1 CCTG-TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGG
** * * *
123534176 GGGTTAAGGTTCTTTGTCTTCGATCTGC-TCCACTACTGCTTAGGGAGATAAGATCTGTAATTCA
65 GGGTTAAGGCCCTTCGTCTTCGATCTGCTTCC-CTACTGCTTAGGGAGTTAAGATCTGCAATTCA
123534240 A
129 A
123534241 CCTGTTACCCTACTGCTTAGGG
1 CCTGTTACCCTACTGCTTAGGG
123534263 TTTAAGGTTC
Statistics
Matches: 326, Mismatches: 62, Indels: 43
0.76 0.14 0.10
Matches are distributed among these distances:
126 2 0.01
127 1 0.00
128 56 0.17
129 169 0.52
130 62 0.19
131 33 0.10
132 1 0.00
133 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (129 bp):
CCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGGG
GGTTAAGGCCCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGTTAAGATCTGCAATTCAA
Found at i:123533973 original size:87 final size:86
Alignment explanation
Indices: 123533860--123534287 Score: 675
Period size: 87 Copynumber: 5.0 Consensus size: 86
123533850 TGGTCTGTTA
* * * *
123533860 CCCTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
**
123533925 GCCCTTCGTCTTCGATCTGCTT
66 GTTCTTCGTCTTCGATCTGC-T
* *
123533947 CCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
123534012 GTTCTTCGTCTTCGATCTGCT
66 GTTCTTCGTCTTCGATCTGCT
*
123534033 CCACTACTGCTTAGGGAGATAAGATCTGT-AATTCAACCTGTTACCCTACTGCTTA-GGGTTTAA
1 CC-CTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
123534096 GGTTCTTCGTCTTCGATCTGCTT
65 GGTTCTTCGTCTTCGATCTGC-T
* *
123534119 CCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
*
123534184 GTTCTTTGTCTTCGATCTGCT
66 GTTCTTCGTCTTCGATCTGCT
*
123534205 CCACTACTGCTTAGGGAGATAAGATCTGT-AATTCAACCTGTTACCCTACTGCTTA-GGGTTTAA
1 CC-CTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAA
123534268 GGTTCTTCGTCTTCGATCTG
65 GGTTCTTCGTCTTCGATCTG
123534288 TTACACCATT
Statistics
Matches: 318, Mismatches: 18, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
85 79 0.25
86 84 0.26
87 155 0.49
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (86 bp):
CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
GTTCTTCGTCTTCGATCTGCT
Found at i:123534106 original size:172 final size:172
Alignment explanation
Indices: 123533862--123534287 Score: 762
Period size: 172 Copynumber: 2.5 Consensus size: 172
123533852 GTCTGTTACC
* * * * * *
123533862 CTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACACTACTGCTTAGGGGTTTAAGGC
1 CTACTGCTTAGGGAGATAAGATCTGT-AATTCAACCTGTTACCCTACTGCTTA-GGGTTTAAGGT
*
123533927 CCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACC
64 TCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACC
123533992 CTACTGCTTAGGGGGTTAAGGTTCTTCGTCTTCGATCTGCTCCA
129 CTACTGCTTAGGGGGTTAAGGTTCTTCGTCTTCGATCTGCTCCA
123534036 CTACTGCTTAGGGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGTTTAAGGTTC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGTTTAAGGTTC
123534101 TTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACCCT
66 TTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACCCT
*
123534166 ACTGCTTAGGGGGTTAAGGTTCTTTGTCTTCGATCTGCTCCA
131 ACTGCTTAGGGGGTTAAGGTTCTTCGTCTTCGATCTGCTCCA
123534208 CTACTGCTTAGGGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGTTTAAGGTTC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGTTTAAGGTTC
123534273 TTCGTCTTCGATCTG
66 TTCGTCTTCGATCTG
123534288 TTACACCATT
Statistics
Matches: 244, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
172 197 0.81
173 24 0.10
174 23 0.09
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (172 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGTTTAAGGTTC
TTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGAGCTAAGATCTGTAAATTCAGCCTGTTACCCT
ACTGCTTAGGGGGTTAAGGTTCTTCGTCTTCGATCTGCTCCA
Found at i:123542371 original size:19 final size:20
Alignment explanation
Indices: 123542335--123542376 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
123542325 GGGTCTTTTC
* *
123542335 GAAATTTAATACACATG-AT
1 GAAATGTAATACAAATGAAT
*
123542354 GAAATGTAATGCAAATGAAT
1 GAAATGTAATACAAATGAAT
123542374 GAA
1 GAA
123542377 TGCAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (20 bp):
GAAATGTAATACAAATGAAT
Found at i:123546157 original size:2 final size:2
Alignment explanation
Indices: 123546150--123546178 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123546140 ATTTTTAAAA
123546150 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
123546179 AAATTTATAA
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:123549253 original size:16 final size:16
Alignment explanation
Indices: 123549232--123549263 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
123549222 GATTGAAATT
123549232 TGAAATAACCCAAAAG
1 TGAAATAACCCAAAAG
123549248 TGAAATAACCCAAAAG
1 TGAAATAACCCAAAAG
123549264 CCCTTGTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
TGAAATAACCCAAAAG
Found at i:123549863 original size:44 final size:46
Alignment explanation
Indices: 123549815--123549910 Score: 160
Period size: 44 Copynumber: 2.1 Consensus size: 46
123549805 AATATAAATT
*
123549815 ATATGAAATTTGTGGTAAACTAATAAAATAAA-GTAGAA-AATTTG
1 ATATGAAATTTGTGGTAAACTAATAAAATAAAGGTAAAATAATTTG
123549859 ATATGAAATTTGTGGTAAACTAATAAAATAAAGTGTAAAATAATTTG
1 ATATGAAATTTGTGGTAAACTAATAAAATAAAG-GTAAAATAATTTG
123549906 ATATG
1 ATATG
123549911 TGAAATAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 32 0.67
46 5 0.10
47 11 0.23
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (46 bp):
ATATGAAATTTGTGGTAAACTAATAAAATAAAGGTAAAATAATTTG
Found at i:123550732 original size:16 final size:16
Alignment explanation
Indices: 123550687--123550723 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
123550677 GGAAGTGGAG
123550687 AAGCTGAGAAAGTTAT
1 AAGCTGAGAAAGTTAT
123550703 AAGCTGAGAAAGTTAT
1 AAGCTGAGAAAGTTAT
123550719 AAGCT
1 AAGCT
123550724 TTAAAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (16 bp):
AAGCTGAGAAAGTTAT
Found at i:123551042 original size:3 final size:3
Alignment explanation
Indices: 123551034--123551262 Score: 62
Period size: 3 Copynumber: 76.3 Consensus size: 3
123551024 TTAATATGTC
* * * * *
123551034 ATT ATT ATT ATT -TT GTT AAT ATT AAT ATT ATA ATT A-T ACT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
123551079 TTT ATTT ATTT ATG GTT -TT ATT ATT AATT CATT AAT -TT ACT ATT ATT
1 ATT A-TT A-TT ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT ATT ATT
** * * * *
123551126 AAC A-T ATT ATT ATT ATT AAGGT ATT AAT ACT ACT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -A-TT ATT ATT ATT ATT A-TT ATT ATT ATT
** * * * * *
123551173 ACC ATT -TT CATT ACT ATT ATT TTT ATT TTT ATT ACT ATT A-T CTT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
123551217 ACT ATT ATT TTT ATT TTT ATT AAT ATT ATCT -TT TTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
123551262 A
1 A
123551263 CCTTTTTGCT
Statistics
Matches: 161, Mismatches: 49, Indels: 32
0.67 0.20 0.13
Matches are distributed among these distances:
2 13 0.08
3 127 0.79
4 20 0.12
5 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:123551224 original size:32 final size:32
Alignment explanation
Indices: 123551161--123551248 Score: 131
Period size: 32 Copynumber: 2.7 Consensus size: 32
123551151 AATACTACTA
* * *
123551161 TTTATTATTATTACCATTTTCATTACTATTATT
1 TTTATTTTTATTACTATTATC-TTACTATTATT
123551194 TTTATTTTTATTACTATTATCTTACTATTATT
1 TTTATTTTTATTACTATTATCTTACTATTATT
*
123551226 TTTATTTTTATTAATATTATCTT
1 TTTATTTTTATTACTATTATCTT
123551249 TTTTATTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 33 0.65
33 18 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTATTTTTATTACTATTATCTTACTATTATT
Found at i:123551251 original size:18 final size:18
Alignment explanation
Indices: 123551230--123551269 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
123551220 ATTATTTTTA
*
123551230 TTTTTATTAATATTATCT
1 TTTTTATTAATATTACCT
*
123551248 TTTTTATTATTATTACCT
1 TTTTTATTAATATTACCT
123551266 TTTT
1 TTTT
123551270 GCTATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATTAATATTACCT
Found at i:123551531 original size:3 final size:3
Alignment explanation
Indices: 123551525--123551632 Score: 53
Period size: 3 Copynumber: 36.0 Consensus size: 3
123551515 TAATTTAATG
* * * * * *
123551525 TAT TAT TTT CTAT TAT TAT TAT TAA TAT CAC TAT TAT CAT CAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
123551571 TAT TA- TAT TA- TAA TACCT CT-T TAT TAT TAT TAC TAT T-G TAT TAT
1 TAT TAT TAT TAT TAT TA--T -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
123551615 TAC TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
123551633 ATTTTCCCTT
Statistics
Matches: 78, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
2 6 0.08
3 69 0.88
4 2 0.03
6 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:123551614 original size:14 final size:15
Alignment explanation
Indices: 123551595--123551635 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
123551585 ACCTCTTTAT
*
123551595 TATTATTACTATT-G
1 TATTATTACTATTAC
123551609 TATTATTACTATTAC
1 TATTATTACTATTAC
123551624 TATTATTA-TATT
1 TATTATTACTATT
123551636 TTCCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (15 bp):
TATTATTACTATTAC
Found at i:123558162 original size:34 final size:34
Alignment explanation
Indices: 123558103--123558176 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
123558093 AGTGCCACGA
*
123558103 TTCACAACTCAGTATGGAAACACCATACCTACGT
1 TTCACAACTCAGTATAGAAACACCATACCTACGT
* * *
123558137 TTCACAGCTCGGTATAGAAATACCATACCTACGT
1 TTCACAACTCAGTATAGAAACACCATACCTACGT
123558171 TTCACA
1 TTCACA
123558177 CTTTGCCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (34 bp):
TTCACAACTCAGTATAGAAACACCATACCTACGT
Found at i:123558274 original size:27 final size:27
Alignment explanation
Indices: 123558231--123558295 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
123558221 GATCATTGAA
* *
123558231 CACTTTGCTATGTTTGGCACACTATAT
1 CACTTTGCCATGATTGGCACACTATAT
*
123558258 CACTTTGCCATGATTGGCACACTTTAT
1 CACTTTGCCATGATTGGCACACTATAT
123558285 CACTTTGCCAT
1 CACTTTGCCAT
123558296 AGTTCAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (27 bp):
CACTTTGCCATGATTGGCACACTATAT
Found at i:123558438 original size:31 final size:31
Alignment explanation
Indices: 123558403--123558542 Score: 217
Period size: 31 Copynumber: 4.5 Consensus size: 31
123558393 AGCTACCTGG
123558403 AGCTACCACTTTTCACTAATCAGGTAGCCGA
1 AGCTACCACTTTTCACTAATCAGGTAGCCGA
* * *
123558434 AGCTACTACTTTTCACTCATCAAGTAGCCGA
1 AGCTACCACTTTTCACTAATCAGGTAGCCGA
* *
123558465 AGCTACCATTTTTCACTAATCAGGTAGCTGA
1 AGCTACCACTTTTCACTAATCAGGTAGCCGA
* *
123558496 AGCTACCATTTTTCACTGATCAGGTAGCCGA
1 AGCTACCACTTTTCACTAATCAGGTAGCCGA
123558527 AGCTACCACTTTTCAC
1 AGCTACCACTTTTCAC
123558543 ATTGTACACA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 98 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
AGCTACCACTTTTCACTAATCAGGTAGCCGA
Found at i:123558619 original size:33 final size:32
Alignment explanation
Indices: 123558535--123558647 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 32
123558525 GAAGCTACCA
* * * *
123558535 CTTTTCACATTGTACACACAAGGCGTACATTTC
1 CTTTTCA-AGTGTACATACAAAGTGTACATTTC
*
123558568 CTTTTCAAGTGTACATACAAAGTGTACTTTTC
1 CTTTTCAAGTGTACATACAAAGTGTACATTTC
* *
123558600 CTTTTTAAGTCGTACATACACAGTGTACATTTC
1 CTTTTCAAGT-GTACATACAAAGTGTACATTTC
*
123558633 CTTTTCTAGTTGTAC
1 CTTTTCAAG-TGTAC
123558648 CTTTTAGGTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 29 0.43
33 38 0.56
34 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (32 bp):
CTTTTCAAGTGTACATACAAAGTGTACATTTC
Found at i:123560373 original size:31 final size:32
Alignment explanation
Indices: 123560333--123560410 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
123560323 ATACTAAATA
*
123560333 AATAATATTAAAATAATAATAAATATCTCATT
1 AATAATATTAAAATAATAATAAATATCTAATT
**
123560365 AA-AATATTAATAA-AATAATATTTATCTAATT
1 AATAATATTAA-AATAATAATAAATATCTAATT
123560396 AATTAAT-TTAAAATA
1 AA-TAATATTAAAATA
123560411 TTATCAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 27 0.69
32 9 0.23
33 3 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAATATTAAAATAATAATAAATATCTAATT
Found at i:123570992 original size:39 final size:39
Alignment explanation
Indices: 123570926--123571488 Score: 285
Period size: 36 Copynumber: 15.3 Consensus size: 39
123570916 AATCTTATTG
* *
123570926 AGTA-TAATCAGTGGATAATGCTCGTTTGAGCACGCATTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCAC-CATTC
* *
123570965 AGT-GTAATCAGTGGATATTACTTGTTTGAGCAACTATTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGC-ACCATTC
*
123571004 AGTAG-AATCAGTGGACATTGCTTGTTTGAGCA-CATTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* *
123571041 AGTAG-GA-CGAGTAGATATTGCTTG-TTGAGCA-C-TTC
1 AGTAGTAATC-AGTGGATATTGCTTGTTTGAGCACCATTC
* * * *
123571076 TAGTAG-AATTAGTAGATATTACTCT-TTTGTGCA-C-TTC
1 -AGTAGTAATCAGTGGATATTGCT-TGTTTGAGCACCATTC
* * * *
123571113 AGTAG-AATCAGTAGACATTGCTCGTTTGAGCA-CATTT
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* * * *
123571150 AGTAG-GATCAGTAGATATTGCTCG-TTGAGCA-CTTTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* * * *
123571186 AGTAG-GACCAGTAGATATTG-TTCG-TTGAGCA-CTTTC
1 AGTAGTAATCAGTGGATATTGCTT-GTTTGAGCACCATTC
* *
123571222 AATAG-AATCAGTAGATATTGCTCT-TTTGAGCA-CATTC
1 AGTAGTAATCAGTGGATATTGCT-TGTTTGAGCACCATTC
* * * * *
123571259 AGTAG-AATAAGTAGACATTGCTCGTTTGAGCA-TATTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* * * * *
123571296 AATAG-GATCAGTAGATATTGCTCG-TTGAGCA-CTTTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* * *
123571332 AGTAGT-ATCAGTAGATATTGCTCGTTTGAGCA-CTTTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* * * *
123571369 AGTAG-AATCAATAGG-CATTGCTCGTTTGAGC-TCATTC
1 AGTAGTAATCAGT-GGATATTGCTTGTTTGAGCACCATTC
* * * * ***
123571406 AGTAG-GATCAATAGATATTGCTT-ATTGAGC-TTTTTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
* * *
123571442 AATAGT-ATCAGTAGATATTACTTG-TTGAGCA-C-TTC
1 AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
123571477 AGTAG-AATCAGT
1 AGTAGTAATCAGT
123571489 ATTTCATTTT
Statistics
Matches: 441, Mismatches: 58, Indels: 54
0.80 0.10 0.10
Matches are distributed among these distances:
35 17 0.04
36 181 0.41
37 179 0.41
38 3 0.01
39 58 0.13
40 3 0.01
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (39 bp):
AGTAGTAATCAGTGGATATTGCTTGTTTGAGCACCATTC
Found at i:123571061 original size:37 final size:37
Alignment explanation
Indices: 123570926--123571489 Score: 517
Period size: 37 Copynumber: 15.4 Consensus size: 37
123570916 AATCTTATTG
* * * *
123570926 AGTATAATCAGTGGATAATGCTCGTTTGAGCACGCATTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCA--CATTC
* *
123570965 AGT-GTAATCAGTGGATATTACTTGTTTGAGCAACTATTC
1 AGTAG-AATCAGTAGATATTGCTTGTTTGAGC-AC-ATTC
* *
123571004 AGTAGAATCAGTGGACATTGCTTGTTTGAGCACATTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
*
123571041 AGTAGGA-CGAGTAGATATTGCTTG-TTGAGCAC-TTC
1 AGTAGAATC-AGTAGATATTGCTTGTTTGAGCACATTC
* * *
123571076 TAGTAGAATTAGTAGATATTACTCT-TTTGTGCAC-TTC
1 -AGTAGAATCAGTAGATATTGCT-TGTTTGAGCACATTC
* * *
123571113 AGTAGAATCAGTAGACATTGCTCGTTTGAGCACATTT
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* * *
123571150 AGTAGGATCAGTAGATATTGCTCG-TTGAGCACTTTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* * *
123571186 AGTAGGACCAGTAGATATTG-TTCG-TTGAGCACTTTC
1 AGTAGAATCAGTAGATATTGCTT-GTTTGAGCACATTC
*
123571222 AATAGAATCAGTAGATATTGCTCT-TTTGAGCACATTC
1 AGTAGAATCAGTAGATATTGCT-TGTTTGAGCACATTC
* * * *
123571259 AGTAGAATAAGTAGACATTGCTCGTTTGAGCATATTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* * * *
123571296 AATAGGATCAGTAGATATTGCTCG-TTGAGCACTTTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* * *
123571332 AGTAGTATCAGTAGATATTGCTCGTTTGAGCACTTTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* ** * *
123571369 AGTAGAATCAATAGGCATTGCTCGTTTGAGCTCATTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* * * ***
123571406 AGTAGGATCAATAGATATTGCTT-ATTGAGCTTTTTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
* * *
123571442 AATAGTATCAGTAGATATTACTTG-TTGAGCAC-TTC
1 AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
123571477 AGTAGAATCAGTA
1 AGTAGAATCAGTA
123571490 TTTCATTTTT
Statistics
Matches: 444, Mismatches: 63, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
35 18 0.04
36 180 0.41
37 183 0.41
38 4 0.01
39 57 0.13
40 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (37 bp):
AGTAGAATCAGTAGATATTGCTTGTTTGAGCACATTC
Found at i:123571134 original size:109 final size:108
Alignment explanation
Indices: 123570971--123571481 Score: 503
Period size: 110 Copynumber: 4.7 Consensus size: 108
123570961 ATTCAGTGTA
* * * * *
123570971 ATCAGTGGATATTACTTGTTTGAGCAACTATTCAGTAGAATCAGTGGACATTGCTTGTTTGAGCA
1 ATCAGTAGATATTGCTCG-TTGAGC-ACT-TTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCA
* *
123571036 CATTCAGTAGGACGAGTAGATATTGCTTGTTGAGCACTTCTAGTAGA
63 CATTCAGTAGGAC-AGTAGATATTGCTCGTTGAGCACTTCTAGTAGG
* * * *
123571083 ATTAGTAGATATTACTCTTTTGTGCAC-TTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACA
1 ATCAGTAGATATTGCTC-GTTGAGCACTTTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACA
*
123571147 TTTAGTAGGATCAGTAGATATTGCTCGTTGAGCACTT-TCAGTAGG
65 TTCAGTAGGA-CAGTAGATATTGCTCGTTGAGCACTTCT-AGTAGG
* * * * *
123571192 ACCAGTAGATATTGTTCGTTGAGCACTTTCAATAGAATCAGTAGATATTGCTCTTTTGAGCACAT
1 ATCAGTAGATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACAT
* * * * *
123571257 TCAGTAGAATAAGTAGACATTGCTCGTTTGAGCATATTC-AATAGG
66 TCAGTAGGA-CAGTAGATATTGCTCG-TTGAGCA-CTTCTAGTAGG
* * *
123571302 ATCAGTAGATATTGCTCGTTGAGCACTTTCAGTAGTATCAGTAGATATTGCTCGTTTGAGCACTT
1 ATCAGTAGATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACAT
* * ** *
123571367 TCAGTAGAATCAATAGGCATTGCTCGTTTGAGCTCATTC-AGTAGG
66 TCAGTAGGA-CAGTAGATATTGCTCG-TTGAGCAC-TTCTAGTAGG
* ** ** * * * * *
123571412 ATCAATAGATATTGCTTATTGAGCTTTTTCAATAGTATCAGTAGATATTACTTG-TTGAGCAC-T
1 ATCAGTAGATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACAT
123571475 TCAGTAG
66 TCAGTAG
123571482 AATCAGTATT
Statistics
Matches: 346, Mismatches: 45, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
108 16 0.05
109 151 0.44
110 156 0.45
111 4 0.01
112 19 0.05
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (108 bp):
ATCAGTAGATATTGCTCGTTGAGCACTTTCAGTAGAATCAGTAGACATTGCTCGTTTGAGCACAT
TCAGTAGGACAGTAGATATTGCTCGTTGAGCACTTCTAGTAGG
Found at i:123571153 original size:73 final size:73
Alignment explanation
Indices: 123570926--123571489 Score: 515
Period size: 73 Copynumber: 7.7 Consensus size: 73
123570916 AATCTTATTG
* * * * * * *
123570926 AGTATAATCAGTGGATAATGCTCGTTTGAGCACGCATTCAGT-GTAATCAGTGGATATTACTTGT
1 AGTAGAATCAGTAGATATTGCTCTTTTGAGCA--CATTCAGTAG-AATCAGTAGATATTGCTCGT
123570990 TTGAGCAACTATT
63 TTGAGC-ACT-TT
* * * *
123571003 CAGTAGAATCAGTGGACATTGCT-TGTTTGAGCACATTCAGTAGGA-CGAGTAGATATTGCTTG-
1 -AGTAGAATCAGTAGATATTGCTCT-TTTGAGCACATTCAGTAGAATC-AGTAGATATTGCTCGT
123571065 TTGAGCACTTCT
63 TTGAGCACTT-T
* * * *
123571077 AGTAGAATTAGTAGATATTACTCTTTTGTGCAC-TTCAGTAGAATCAGTAGACATTGCTCGTTTG
1 AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTAGATATTGCTCGTTTG
123571141 AGCACATTT
66 AGCAC-TTT
* * * * * *
123571150 AGTAGGATCAGTAGATATTGCTC-GTTGAGCACTTTCAGTAGGACCAGTAGATATTGTTCG-TTG
1 AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTAGATATTGCTCGTTTG
123571213 AGCACTTT
66 AGCACTTT
* * *
123571221 CAATAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATAAGTAGACATTGCTCGTTT
1 -AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTAGATATTGCTCGTTT
123571286 GAGCA-TATT
65 GAGCACT-TT
* * * * *
123571295 CAATAGGATCAGTAGATATTGCTC-GTTGAGCACTTTCAGTAGTATCAGTAGATATTGCTCGTTT
1 -AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTAGATATTGCTCGTTT
123571359 GAGCACTTT
65 GAGCACTTT
* ** * * * *
123571368 CAGTAGAATCAATAGGCATTGCTCGTTTGAGCTCATTCAGTAGGATCAATAGATATTGCT--TAT
1 -AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTAGATATTGCTCGT-T
**
123571431 TGAGCTTTTT
64 TGAGCACTTT
* * * *
123571441 CAATAGTATCAGTAGATATTACT-TGTTGAGCAC-TTCAGTAGAATCAGTA
1 -AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTA
123571490 TTTCATTTTT
Statistics
Matches: 408, Mismatches: 62, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
71 17 0.04
72 66 0.16
73 198 0.49
74 70 0.17
75 7 0.02
76 22 0.05
77 1 0.00
78 27 0.07
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (73 bp):
AGTAGAATCAGTAGATATTGCTCTTTTGAGCACATTCAGTAGAATCAGTAGATATTGCTCGTTTG
AGCACTTT
Found at i:123574579 original size:13 final size:13
Alignment explanation
Indices: 123574563--123574587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123574553 TTTTATCTAC
123574563 CATTTTTCTTTTT
1 CATTTTTCTTTTT
123574576 CATTTTTCTTTT
1 CATTTTTCTTTT
123574588 GGATAGATTC
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
CATTTTTCTTTTT
Found at i:123580895 original size:254 final size:254
Alignment explanation
Indices: 123580424--123580899 Score: 686
Period size: 254 Copynumber: 1.9 Consensus size: 254
123580414 GTGAATATTG
*
123580424 AGATTCTCTTATTTCGAAGAAATAAAACATCACAACTAGCACGTAGGACACAACATTTCAAACCT
1 AGATTCTCTTATTTCGAAGAAATAAAACATCACAACCAGCACGTAGGACACAACATTTCAAACCT
* * *
123580489 TCGATATCAAAATCGTCTCATAATTCCCAAAATTTATGCATTGAAAATTTAAAAAGGATATTCGG
66 TCGATATCAAAATCATCTCATAATTCCCAAAACTTATGCATTGAAAATTTAAAAAGGATATTCAG
* * * * *
123580554 TCGTTCGGTCAAACGATAAATTGAAACCCAGCACGTAGGGCACAATTTCTCGAAATTTCCAAATA
131 TCGTTCGGCCAAACGATAAATCGAAACCCAACACGTAAGGCACAATTTCTCGAAATTTCCAAACA
*
123580619 CGAAATATTGCCTTGTTTTAAAAAGTCTTGAATAAAAATTCAATAGTATGAAACGATTA
196 CAAAATATTGCCTTGTTTTAAAAAGTCTTGAATAAAAATTCAATAGTATGAAACGATTA
* * * * *
123580678 AGATTCTCTTGTTTCGAAGAAATAAAATATCACATCCAGCACGTAGGACACGATATTTCAAACCT
1 AGATTCTCTTATTTCGAAGAAATAAAACATCACAACCAGCACGTAGGACACAACATTTCAAACCT
* * * * * *
123580743 TCGATA-CTAAAATTATCTCATGATTTCCAAAACTTATGCGTTGAAATTTTAAAAAATGATATTC
66 TCGATATC-AAAATCATCTCATAATTCCCAAAACTTATGCATTGAAAATTT-AAAAAGGATATTC
* * *
123580807 AGTTGTTCGGCCAAACGATAAATCGAAACCCAACACGTAAGGCACGATTTTCTCG-AATTTCTAA
129 AGTCGTTCGGCCAAACGATAAATCGAAACCCAACACGTAAGGCAC-AATTTCTCGAAATTTCCAA
*
123580871 ACACAAAATATTGCCTTGTTTAAAAAAGT
193 ACACAAAATATTGCCTTGTTTTAAAAAGT
123580900 TTCCTTTATT
Statistics
Matches: 194, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
253 1 0.01
254 100 0.52
255 85 0.44
256 8 0.04
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (254 bp):
AGATTCTCTTATTTCGAAGAAATAAAACATCACAACCAGCACGTAGGACACAACATTTCAAACCT
TCGATATCAAAATCATCTCATAATTCCCAAAACTTATGCATTGAAAATTTAAAAAGGATATTCAG
TCGTTCGGCCAAACGATAAATCGAAACCCAACACGTAAGGCACAATTTCTCGAAATTTCCAAACA
CAAAATATTGCCTTGTTTTAAAAAGTCTTGAATAAAAATTCAATAGTATGAAACGATTA
Found at i:123581702 original size:48 final size:47
Alignment explanation
Indices: 123581650--123581750 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 47
123581640 AAATAAAAAA
*
123581650 ATAAAAAAATGAAACTAAAAAGGTTAAGGATTGAATTGCAAATTGGG
1 ATAAAAAAATGAAACTAAAAAGGTTAAGGATTGAATTGAAAATTGGG
123581697 TATAAAAAAATGAAACTAAAAAGGTTAAGGATTGAATTGAAAATTGGG
1 -ATAAAAAAATGAAACTAAAAAGGTTAAGGATTGAATTGAAAATTGGG
123581745 ATAAAA
1 ATAAAA
123581751 TTAGGGGGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 6 0.12
48 46 0.88
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.24
Consensus pattern (47 bp):
ATAAAAAAATGAAACTAAAAAGGTTAAGGATTGAATTGAAAATTGGG
Found at i:123586761 original size:40 final size:40
Alignment explanation
Indices: 123586691--123586908 Score: 318
Period size: 40 Copynumber: 5.5 Consensus size: 40
123586681 AACCCAAGTA
* * *
123586691 CCTTCGGAATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
123586730 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
123586770 CCTTCGGGA-TGTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACT-TAGCCCGGATATAGTAACTCGCACAAATG
* *
123586810 CCTTCGGGACGTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
123586850 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
123586890 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
123586909 TTATCATCCG
Statistics
Matches: 165, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
39 15 0.09
40 150 0.91
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:123594901 original size:40 final size:40
Alignment explanation
Indices: 123594824--123595041 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
123594814 AACCCAAGTA
* *
123594824 CCTTCGGGATTTAG-CCGGATATAGCT-ACTC-AATCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCA-CAAATG
*
123594863 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
123594903 CCTTCGGGACGTAGCCCGGATATAGTATCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
123594943 CCTTCGGGACGTAGCTCGAATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
123594983 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
123595023 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
123595042 TTATCATCCG
Statistics
Matches: 159, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.09
40 143 0.90
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:123604244 original size:14 final size:14
Alignment explanation
Indices: 123604225--123604251 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
123604215 GTGAATATAT
123604225 GTGATCCAACTATG
1 GTGATCCAACTATG
123604239 GTGATCCAACTAT
1 GTGATCCAACTAT
123604252 ACTAAACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
GTGATCCAACTATG
Found at i:123608187 original size:48 final size:48
Alignment explanation
Indices: 123608155--123608267 Score: 172
Period size: 48 Copynumber: 2.3 Consensus size: 48
123608145 ATTAGTATCC
* *
123608155 ATTCAAGATAAAATAATATATAAAACTCTTTAAAAATAATATATAAACA
1 ATTCAAAAT-AAATAATATATAAAACTCTTTAAAAAAAATATATAAACA
* *
123608204 ATTCAAAATATATAATATATAAAACTCTTTAAAAATAATATATAAACA
1 ATTCAAAATAAATAATATATAAAACTCTTTAAAAAAAATATATAAACA
*
123608252 ATTCAAAATATATAAT
1 ATTCAAAATAAATAAT
123608268 GTGTAAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 54 0.87
49 8 0.13
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (48 bp):
ATTCAAAATAAATAATATATAAAACTCTTTAAAAAAAATATATAAACA
Found at i:123608191 original size:23 final size:23
Alignment explanation
Indices: 123608164--123608249 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
123608154 CATTCAAGAT
123608164 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTCTTTA
* **
123608187 AAAATAATATATAAACAAT-TCAA
1 AAAATAATATATAAA-ACTCTTTA
123608210 AATATATAATATATAAAACTCTTTA
1 AA-A-ATAATATATAAAACTCTTTA
123608235 AAAATAATATATAAA
1 AAAATAATATATAAA
123608250 CAATTCAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 31 0.58
24 6 0.11
25 16 0.30
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATATATAAAACTCTTTA
Found at i:123608274 original size:25 final size:25
Alignment explanation
Indices: 123608190--123608267 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
123608180 CTCTTTAAAA
123608190 ATAATATATAAACAATTCAAAATAT
1 ATAATATATAAACAATTCAAAATAT
* **
123608215 ATAATATATAAA-ACTCTTTAAA-A-
1 ATAATATATAAACAAT-TCAAAATAT
123608238 ATAATATATAAACAATTCAAAATAT
1 ATAATATATAAACAATTCAAAATAT
123608263 ATAAT
1 ATAAT
123608268 GTGTAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 16 0.37
24 6 0.14
25 21 0.49
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATATATAAACAATTCAAAATAT
Found at i:123608275 original size:48 final size:48
Alignment explanation
Indices: 123608167--123608267 Score: 202
Period size: 48 Copynumber: 2.1 Consensus size: 48
123608157 TCAAGATAAA
123608167 ATAATATATAAAACTCTTTAAAAATAATATATAAACAATTCAAAATAT
1 ATAATATATAAAACTCTTTAAAAATAATATATAAACAATTCAAAATAT
123608215 ATAATATATAAAACTCTTTAAAAATAATATATAAACAATTCAAAATAT
1 ATAATATATAAAACTCTTTAAAAATAATATATAAACAATTCAAAATAT
123608263 ATAAT
1 ATAAT
123608268 GTGTAAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (48 bp):
ATAATATATAAAACTCTTTAAAAATAATATATAAACAATTCAAAATAT
Found at i:123608543 original size:32 final size:31
Alignment explanation
Indices: 123608479--123608562 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 31
123608469 AATAGAAATA
123608479 AAATATAATAAATAAAAATAAATAATAGTAG
1 AAATATAATAAATAAAAATAAATAATAGTAG
* * *
123608510 AAATATAAATAGATAAATAAT-AATAGTATTAG
1 AAATAT-AATAAATAAA-AATAAATAATAGTAG
*
123608542 -AATA-AA-AAATAAATATAAATA
1 AAATATAATAAATAAAAATAAATA
123608563 GAAACATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
27 2 0.04
28 10 0.22
29 2 0.04
31 10 0.22
32 18 0.40
33 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (31 bp):
AAATATAATAAATAAAAATAAATAATAGTAG
Found at i:123615604 original size:12 final size:13
Alignment explanation
Indices: 123615587--123615616 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
123615577 AGGGCATCTT
123615587 AAAAAAAAGA-AA
1 AAAAAAAAGAGAA
123615599 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
123615612 AAAAA
1 AAAAA
123615617 GGGTGATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:123615604 original size:14 final size:14
Alignment explanation
Indices: 123615587--123615616 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
123615577 AGGGCATCTT
123615587 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
*
123615601 AAAAAAGAGAAAAA
1 AAAAAAAAGAAAAA
123615615 AA
1 AA
123615617 GGGTGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:123616801 original size:75 final size:73
Alignment explanation
Indices: 123616536--123616925 Score: 380
Period size: 75 Copynumber: 5.3 Consensus size: 73
123616526 CGATTTCTAT
* * * * * ** *
123616536 TTTTCAATTTATGTTTTC-AAAAATCAATTCATATTGCTATAGGTGAATTGAGCCTCGGGGCACG
1 TTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACG
*
123616600 CTGAGGTA
66 TTGAGGTA
* ***
123616608 TTTTCAATTAT-TGTTTGTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACA
1 TTTTCAATT-TCTGTTT-TCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACA
* *
123616672 CGCTGAGATAA
64 CGTTGAGGT-A
* * * *
123616683 TTTT-TATTTCTG-TTTC-AAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACG
123616745 TTGAGGTA
66 TTGAGGTA
** *
123616753 TTTTCAATTTCTGTCTTTCAAAAAATTCAACTCATACGGCAAGAAGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGT-TTTCAAAAAA-TCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACA
123616818 CGTTGAGGTA
64 CGTTGAGGTA
* * *
123616828 TTTTCAATTTCTATCTTTCAAAATAATCAACTCATATTGCGAGAGGTGAGTCGAG-CTC-AGATC
1 TTTTCAATTTCTGT-TTTCAAAA-AATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGA-C
*
123616891 ACATGTCGAGGTA
63 AC--GTTGAGGTA
* *
123616904 TTTTCAAATTCTGCGTTTCAAA
1 TTTTCAATTTCTG-TTTTCAAA
123616926 TTAAGTTTCA
Statistics
Matches: 273, Mismatches: 30, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
70 5 0.02
71 51 0.19
72 16 0.06
73 13 0.05
74 61 0.22
75 99 0.36
76 28 0.10
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (73 bp):
TTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACG
TTGAGGTA
Found at i:123616831 original size:145 final size:146
Alignment explanation
Indices: 123616536--123616925 Score: 373
Period size: 145 Copynumber: 2.6 Consensus size: 146
123616526 CGATTTCTAT
* * * * * * * *
123616536 TTTTCAATTT-ATGTTTTCAAAAATCAATTCATATTGCTATAGGTGAATTGAGCCTCGGGGCACG
1 TTTTCAATTTCAT-CTTTCAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGACACG
* ** * *
123616600 CTGAGGTATTTTCAATTAT-TGT-TTGTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
64 TTGAGGTATTTTCAATT-TCTGTCTT-TCAAAAAATCAACTCATACGGCAAGAAGTGAGTTGAGC
***
123616663 CTTGGGACACGCTGAGATAA
127 CTCAAGACACGCTGAGATAA
* * * *
123616683 TTTT-TATTTC-TGTTTCAAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGT
1 TTTTCAATTTCATCTTTCAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGACACGT
123616746 TGAGGTATTTTCAATTTCTGTCTTTCAAAAAATTCAACTCATACGGCAAGAAGTGAGTTGAGCCT
65 TGAGGTATTTTCAATTTCTGTCTTTCAAAAAA-TCAACTCATACGGCAAGAAGTGAGTTGAGCCT
* *
123616811 CAAGACACGTTGAGGT-A
129 CAAGACACGCTGAGATAA
* *
123616828 TTTTCAATTTCTATCTTTCAAAATAATCAACTCATATTGCGAGAGGTGAGTCGAG-CTCAGATCA
1 TTTTCAATTTC-ATCTTTCAAAAT--TCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGA-CA
* *
123616892 CATGTCGAGGTATTTTCAAATTCTG-CGTTTCAAA
62 C--GTTGAGGTATTTTCAATTTCTGTC-TTTCAAA
123616926 TTAAGTTTCA
Statistics
Matches: 200, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
144 1 0.00
145 72 0.36
146 51 0.25
147 4 0.02
148 13 0.06
149 6 0.03
150 26 0.13
151 27 0.14
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (146 bp):
TTTTCAATTTCATCTTTCAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGACACGTT
GAGGTATTTTCAATTTCTGTCTTTCAAAAAATCAACTCATACGGCAAGAAGTGAGTTGAGCCTCA
AGACACGCTGAGATAA
Found at i:123618832 original size:3 final size:3
Alignment explanation
Indices: 123618826--123618989 Score: 74
Period size: 3 Copynumber: 54.7 Consensus size: 3
123618816 TTTTTTTACA
* * *
123618826 TAT TAT TAA TAT TAT TAC TAT TAC T-T TAT T-T CTAT TAT TAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT
* * * * * *
123618870 TAT TAT TAC TGT TAG TAT TAT T-T TCAT TAC TAT TAT TTT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* * * *
123618915 TA- TAT TAAT TAT T-T TCT AACG TAT TAT TAT TACT AAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT
*
123618961 T-T CTAGT T-T TAT TAT TAT TAT TAA TAT TA
1 TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TA
123618990 GTGTATGTAT
Statistics
Matches: 119, Mismatches: 26, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
2 12 0.10
3 95 0.80
4 11 0.09
5 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:123619013 original size:17 final size:16
Alignment explanation
Indices: 123618991--123619022 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
123618981 TTAATATTAG
123618991 TGTATGTATATTATATA
1 TGTATGTATA-TATATA
123619008 TGTATGTATATATAT
1 TGTATGTATATATAT
123619023 TTACATATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TGTATGTATATATATA
Found at i:123619015 original size:21 final size:20
Alignment explanation
Indices: 123618979--123619023 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
123618969 TTATTATTAT
*
123618979 TATTAATATTAGTGTATGTA
1 TATTAATATTAGTGTATATA
123618999 TATTATATATGTA-TGTATATA
1 TATTA-ATAT-TAGTGTATATA
123619020 TATT
1 TATT
123619024 TACATATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
TATTAATATTAGTGTATATA
Found at i:123619254 original size:23 final size:23
Alignment explanation
Indices: 123619227--123619345 Score: 90
Period size: 20 Copynumber: 5.2 Consensus size: 23
123619217 TTTTCAATAT
123619227 TATATTTTTTATATATTATTATA
1 TATATTTTTTATATATTATTATA
123619250 TATA--TTTTA-ATATTATTAGTTA
1 TATATTTTTTATATATTATTA--TA
*
123619272 TATATTTTTTATACTATTA-TATG
1 TATATTTTTTATA-TATTATTATA
* *
123619295 TATA-TTTCTA-ATATTA-TATTG
1 TATATTTTTTATATATTATTA-TA
* *
123619316 TATATTTCTAATACTATTATTTATA
1 TATATTTTTTATA-TATTA-TTATA
123619341 TATAT
1 TATAT
123619346 ATATATATAT
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
20 16 0.21
21 12 0.15
22 14 0.18
23 10 0.13
24 10 0.13
25 9 0.12
26 7 0.09
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (23 bp):
TATATTTTTTATATATTATTATA
Found at i:123619290 original size:43 final size:42
Alignment explanation
Indices: 123619223--123619363 Score: 135
Period size: 44 Copynumber: 3.3 Consensus size: 42
123619213 TATGTTTTCA
*
123619223 ATATTATAT-TTTTTATATATTATTATATATATTT-TAATATT
1 ATATTATATATTTTT-TATACTATTATATATATTTCTAATATT
123619264 ATTAGTTATATATTTTTTATACTATTATATGTATATTTCTAATATT
1 A-TA-TTATATATTTTTTATACTATTATA--TATATTTCTAATATT
* * * * * *
123619310 ATATTGTATATTTCTAATACTATTATTTATATATAT-ATATAT
1 ATATTATATATTTTTTATACTATTATATATATTTCTAATAT-T
123619352 ATATATATATAT
1 ATAT-TATATAT
123619364 GTGTGTGTGT
Statistics
Matches: 84, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
41 5 0.06
42 14 0.17
43 23 0.27
44 25 0.30
45 9 0.11
46 8 0.10
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (42 bp):
ATATTATATATTTTTTATACTATTATATATATTTCTAATATT
Found at i:123619344 original size:2 final size:2
Alignment explanation
Indices: 123619337--123619363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
123619327 TACTATTATT
123619337 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 T
123619364 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123621888 original size:88 final size:88
Alignment explanation
Indices: 123621737--123622298 Score: 840
Period size: 88 Copynumber: 6.4 Consensus size: 88
123621727 GCTTATGATT
* * * * *
123621737 TGTAATCTTCAGCCTGCTT-CCTTACTGCTTAGGGGGATAAGGCTCACAGTCTTCAATCCGCTCC
1 TGTAATCTTCAGCCTG-TTACCCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCC
*
123621801 ACTACTGCTTAGGGAGATAAGATT
65 ACTACTGCTTAGGGAGATAAGATC
* * * * *
123621825 TGTAATTTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAGGCTCA-TCGTCTTCGATCTGCTCC
1 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACT-GCCTTCGATCCGCTCC
* *
123621889 ATTACTGCTTATGGAGATAAGATC
65 ACTACTGCTTAGGGAGATAAGATC
* * *
123621913 TGTAATCTCCAGCCTGCTAACCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCCA
1 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCCA
123621978 CTACTGCTTAGGGAGATAAGATC
66 CTACTGCTTAGGGAGATAAGATC
*
123622001 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTAACTGCCTTCGATCCGCTCCA
1 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCCA
*
123622066 CTACTGCTTAGGAAGATAAGATC
66 CTACTGCTTAGGGAGATAAGATC
* *
123622089 TGTAATCTTCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACTGCCTTTGATCCGCTCCA
1 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCCA
123622154 CTACTGCTTAGGGAGATAAGATC
66 CTACTGCTTAGGGAGATAAGATC
* * **** *
123622177 TGTAATCTTCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGACTCACCATTTTCAATCCGCTCCA
1 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCCA
*
123622242 CTACTGCTTAGGGAGATAAGATA
66 CTACTGCTTAGGGAGATAAGATC
123622265 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGG
1 TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGG
123622299 AGATAAGATC
Statistics
Matches: 433, Mismatches: 38, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
87 2 0.00
88 430 0.99
89 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (88 bp):
TGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCCGCTCCA
CTACTGCTTAGGGAGATAAGATC
Found at i:123622320 original size:44 final size:44
Alignment explanation
Indices: 123621802--123622309 Score: 277
Period size: 44 Copynumber: 11.5 Consensus size: 44
123621792 ATCCGCTCCA
* * *
123621802 CTACTGCTTAGGGAGATAAGATTTGTAATTTTCAGCCTGTTTCC
1 CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
* * * * * ** * *
123621846 CTACTACTTAGGGGGTTAAG-GCTCATCGTCTTC-GATCTGCT-CC
1 CTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAG-CCTGTTACC
* * * * *
123621889 ATTACTGCTTATGGAGATAAGATCTGTAATCTCCAGCCTGCTAAC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
* * * * * * *
123621934 CTACTGCTTAGGGGGTTAAG-GCT-CACTGCCTTCGATCC-GCT-CC
1 CTACTGCTTAGGGAGATAAGATCTGTAAT--CTTC-AGCCTGTTACC
123621977 ACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
* * * * *
123622022 CTACTGCTTAGGGGGTTAAG-GC--TAACTGCCTTCGATCC-GCT-CC
1 CTACTGCTTAGGGAGATAAGATCTGTAA-T--CTTC-AGCCTGTTACC
*
123622065 ACTACTGCTTAGGAAGATAAGATCTGTAATCTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
* * * * * * *
123622110 CTACTGCTTAAGGG-GTTAAG-GCT-CACTGCCTTTGATCC-GCT-CC
1 CTACTGCTT-AGGGAGATAAGATCTGTAAT--C-TTCAGCCTGTTACC
123622153 ACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
* * * * *
123622198 CTACTGCTTAAGGG-GTTAAGA-CT-CACCATTTTCAATCC-GCT-CC
1 CTACTGCTT-AGGGAGATAAGATCTGTA--ATCTTC-AGCCTGTTACC
*
123622241 ACTACTGCTTAGGGAGATAAGATATGTAATCTTCAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
123622286 CTACTGCTTAGGGAGATAAGATCT
1 CTACTGCTTAGGGAGATAAGATCT
123622310 AAAATTTTCA
Statistics
Matches: 342, Mismatches: 78, Indels: 88
0.67 0.15 0.17
Matches are distributed among these distances:
41 3 0.01
42 6 0.02
43 40 0.12
44 245 0.72
45 39 0.11
46 6 0.02
47 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACC
Found at i:123622518 original size:178 final size:178
Alignment explanation
Indices: 123622297--123623572 Score: 1745
Period size: 178 Copynumber: 7.2 Consensus size: 178
123622287 TACTGCTTAG
** * *
123622297 GGAGATAAGATCTAAAATTTTCAGTCTGCTTCCTTGTTACCTCAGGAAGATAAGACTTGTATCTT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
* * ** *
123622362 CGACTTGCTCTCTTGCTACCTTAGAGAGATAAAACCGGTGGCTAAAATCTGCTCTATAGCTGATA
66 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCTGATA
* * * **
123622427 CATGGAGATAAGACTCACCATTTTTTATCTGCTCTATAGTCGATATGT
131 CATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
*
123622475 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCAT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
* * *
123622540 CAACCTGCTCTCTTACTACCTTAGAGAGATAAGGCCGATGGCTAAAATCTGCTCCATAGCCGATA
66 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCTGATA
* * *
123622605 CATGGAGATAAGACTCGCCATTTTTTATCTACTCTATAGCCGATATAT
131 CATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
* *
123622653 GGAGATAAAATCTGTAATTTTCAGTCTGCTTCTTTTCTACCTCAGGAAGATAAGACTTGTATCTT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
* *
123622718 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGATGGCTAAAATCTGCTCCATAGCCGATA
66 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCTGATA
* * * *
123622783 CATGGAGACAAGACTCGCCATTTCTGATATGCTCCATAGCCGATACAT
131 CATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
123622831 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
*
123622896 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGATGGCTAAAATCTGCTCCATAGAC-GAT
66 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAG-CTGAT
* * *
123622960 ACATGGAGACAAGACTCGCCATTTTTTATATGCTCCATAGCCTATACAT
130 ACATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
*
123623009 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
* * * * * * * *
123623074 CAACTTGCTCTTTTGCAACCTCAAAGAGATAAGGCTGGTGGCTAAAATATGCTCCATA-ATCGAT
66 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCT-GAT
* * * * *
123623138 ACATGGAGATAAGACTCGTCATTTCTGATCTGCTCTATAGCCGATACAC
130 ACATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
* * * *
123623187 GGAGATAAGGTCTGTAATTTTCAGTCTGCTT-TCTTGCCACCTCAAGAAGATAAGACTTGTGA-A
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCT-TTGCTACCTCAGGAAGATAAGACTTGT-ATC
* * ** * * *
123623250 TTCAACCTGCTCTCTTGCTTCCTCAGAGAGATAAGGTTGGTGGCTAAAATTTACTCTATAG-TCG
64 TTCAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCT-G
* *
123623314 ATACATGGAGATAAGACTCGCCATTTTTTATCTACTCCATAGTCGATACAT
128 ATACATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
* * *
123623365 GGAGATAAGATTTGTAATTTTCAGTCTGCTTCCTTACTACCTCAGGAAGATAAGACTTGTATCTT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
* * * * **
123623430 CAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCAGGTGCCTAAAATCTACTAGATAG-TCGAT
66 CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCT-GAT
* * * *
123623494 ACATGGAGATAAGACTCGCCATTTCTGATCTACTCCATAGTCGATACAT
130 ACATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
** * * * *
123623543 AAAGATAAAATCTATAATTTTTAGCCTGCT
1 GGAGATAAGATCTGTAATTTTCAGTCTGCT
123623573 ACCCTACTGC
Statistics
Matches: 995, Mismatches: 95, Indels: 16
0.90 0.09 0.01
Matches are distributed among these distances:
177 1 0.00
178 992 1.00
179 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (178 bp):
GGAGATAAGATCTGTAATTTTCAGTCTGCTTCTTTGCTACCTCAGGAAGATAAGACTTGTATCTT
CAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCCGGTGGCTAAAATCTGCTCCATAGCTGATA
CATGGAGATAAGACTCGCCATTTTTTATCTGCTCCATAGCCGATACAT
Found at i:123625350 original size:16 final size:16
Alignment explanation
Indices: 123625314--123625367 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
123625304 TTCCACAATC
* *
123625314 TTTTTTTGTTGTTTTTG
1 TTTTTTTGTT-TCTTTA
123625331 TTTTTATT-TTTCTTTA
1 TTTTT-TTGTTTCTTTA
*
123625347 TTTTTTTGTTTCTTTC
1 TTTTTTTGTTTCTTTA
123625363 TTTTT
1 TTTTT
123625368 GGCTGCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.06
16 21 0.66
17 7 0.22
18 2 0.06
ACGTcount: A:0.04, C:0.06, G:0.07, T:0.83
Consensus pattern (16 bp):
TTTTTTTGTTTCTTTA
Found at i:123630518 original size:29 final size:30
Alignment explanation
Indices: 123630485--123630566 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
123630475 AAATAATAAT
* *
123630485 GAAAATAATATTAGTATATAAATAGAAATA
1 GAAAATAATAATAGTATAGAAATAGAAATA
* *
123630515 -AAAAT-ATAATAATAGTAGAAATATAAATA
1 GAAAATAATAATAGTA-TAGAAATAGAAATA
123630544 GATAAATAATAATAGTATTAGAA
1 GA-AAATAATAATAGTA-TAGAA
123630567 TAACAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.17
29 17 0.40
30 1 0.02
31 4 0.10
32 13 0.31
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (30 bp):
GAAAATAATAATAGTATAGAAATAGAAATA
Found at i:123630540 original size:14 final size:15
Alignment explanation
Indices: 123630520--123630560 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
123630510 AAATAAAAAT
123630520 ATAATAATAGTAGAA
1 ATAATAATAGTAGAA
*
123630535 AT-ATAAATAG-ATAA
1 ATAAT-AATAGTAGAA
123630549 ATAATAATAGTA
1 ATAATAATAGTA
123630561 TTAGAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
ATAATAATAGTAGAA
Found at i:123631134 original size:5 final size:5
Alignment explanation
Indices: 123631126--123631169 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
123631116 ATAATTTAAT
*
123631126 AATAA AATAA AATAA AATAA AGTAA AATAA AA-ACA AA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATA-A AATAA AATAA
123631170 TATCTTCCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AATAA
Found at i:123631659 original size:47 final size:47
Alignment explanation
Indices: 123631596--123631694 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 47
123631586 AATATAAATT
*
123631596 ATATGAAATTTTTGGTAAACTAATAAAATAAAGTAG-AAAATAATTTG
1 ATATGAAATTTGTGGTAAACTAATAAAATAAAGT-GTAAAATAATTTG
123631643 ATATGAAATTTGTGGTAAACTAATAAAATAAAGTGTAAAATAATTTG
1 ATATGAAATTTGTGGTAAACTAATAAAATAAAGTGTAAAATAATTTG
123631690 ATATG
1 ATATG
123631695 TGAAATAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 1 0.02
47 49 0.98
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.34
Consensus pattern (47 bp):
ATATGAAATTTGTGGTAAACTAATAAAATAAAGTGTAAAATAATTTG
Found at i:123636175 original size:27 final size:26
Alignment explanation
Indices: 123636127--123636178 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
123636117 GCGAGGCTGC
*
123636127 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
123636153 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
123636179 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:123636860 original size:27 final size:27
Alignment explanation
Indices: 123636829--123636947 Score: 166
Period size: 27 Copynumber: 4.4 Consensus size: 27
123636819 ATGGCAAAAT
* * * *
123636829 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
123636856 TGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
123636883 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
123636910 GGTAATTTTACCCTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
123636937 GGTAATTCTAC
1 GGTAATTCTAC
123636948 AACTTATCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:123643551 original size:51 final size:48
Alignment explanation
Indices: 123643439--123643579 Score: 178
Period size: 51 Copynumber: 2.9 Consensus size: 48
123643429 GCTTAACATG
* *
123643439 TTATTCATTACTTTATTTTTTGA-ATTTTTTGTGAGTTTTATATTAAC
1 TTATTCATTACTTTATTTTTTGATTTTTTTTGTGAATTTTATATTAAC
*
123643486 TCATTCATTACTTTATTTTTTTGATTTTTTTTG-GAATAAATTTATATTAAC
1 TTATTCATTACTTTA-TTTTTTGATTTTTTTTGTGAAT---TTTATATTAAC
* *
123643537 TTATTCATTACTTTATTTTTTGATTCTTTTCTGTGAGTTTTAT
1 TTATTCATTACTTTATTTTTTGATT-TTTTTTGTGAATTTTAT
123643580 TTTTCTAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
47 14 0.17
48 11 0.14
49 12 0.15
50 10 0.12
51 31 0.38
52 3 0.04
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (48 bp):
TTATTCATTACTTTATTTTTTGATTTTTTTTGTGAATTTTATATTAAC
Found at i:123645454 original size:7 final size:7
Alignment explanation
Indices: 123645442--123645472 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
123645432 ACTAAGAAAT
123645442 AAAAAGG
1 AAAAAGG
123645449 AAAAAGG
1 AAAAAGG
123645456 AAAAAGG
1 AAAAAGG
123645463 AAAAAGG
1 AAAAAGG
123645470 AAA
1 AAA
123645473 TCCAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:123648574 original size:79 final size:79
Alignment explanation
Indices: 123648350--123648586 Score: 287
Period size: 79 Copynumber: 3.0 Consensus size: 79
123648340 CTCTCGAGTC
* * * * *
123648350 ATATCTCATGTAACTGTAGTGAATCAAGATTACCTTTTT-AGGTGAAATCCTACCCACCTTAAGT
1 ATATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTCAGGTCAAATCCTATCCACCTTAAGT
* * *
123648414 TATCATAAGGAATC
66 TACCATAATGAATT
* * * * * *
123648428 ATGTATCGTATAACTGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCATAGGT
1 ATATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTCAGGTCAAATCCTATCCACCTTAAGT
123648493 TACCATAATGAATT
66 TACCATAATGAATT
* ***
123648507 ATATATCATGTAACCGTAGCGAATCAGGATTACCTTTTTCAGGTCAAATCCTATTTGCCTTAAGT
1 ATATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTCAGGTCAAATCCTATCCACCTTAAGT
* *
123648572 TACCGTAGTGAATT
66 TACCATAATGAATT
123648586 A
1 A
123648587 AGAATAAATC
Statistics
Matches: 132, Mismatches: 26, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
78 32 0.24
79 100 0.76
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (79 bp):
ATATATCATGTAACTGTAGCGAATCAGGATTACCTTTTTCAGGTCAAATCCTATCCACCTTAAGT
TACCATAATGAATT
Found at i:123648615 original size:40 final size:40
Alignment explanation
Indices: 123648551--123648645 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
123648541 TTTTTCAGGT
** * * *
123648551 CAAATCCTATTTGCCTTAAGTTACCGTAGTGAATTAAGAA
1 CAAATCCTATTCACTTTAAATTACCATAGTGAATTAAGAA
* *
123648591 TAAATCCTATTCACTTTAAATTACCATAGTGAATTAGGAA
1 CAAATCCTATTCACTTTAAATTACCATAGTGAATTAAGAA
*
123648631 CAAATCCTATCCACT
1 CAAATCCTATTCACT
123648646 CTGAGGTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (40 bp):
CAAATCCTATTCACTTTAAATTACCATAGTGAATTAAGAA
Found at i:123650351 original size:7 final size:7
Alignment explanation
Indices: 123650328--123650361 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
123650318 TTATATATTA
123650328 AATAAATT
1 AATAAA-T
123650336 AAT-AAT
1 AATAAAT
123650342 AATAAAT
1 AATAAAT
123650349 AATAAAT
1 AATAAAT
123650356 AATAAA
1 AATAAA
123650362 ATATCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.16
7 18 0.72
8 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:123650656 original size:22 final size:22
Alignment explanation
Indices: 123650609--123650658 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
123650599 TCATTCCACC
* *
123650609 CTTTAAATTTTTACTATTGGCC
1 CTTTAAATTTTTACTATTGACA
*
123650631 CTTTAAATTTTT-CATATTTACA
1 CTTTAAATTTTTAC-TATTGACA
123650653 CTTTAA
1 CTTTAA
123650659 CCCTTCAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.28, C:0.16, G:0.04, T:0.52
Consensus pattern (22 bp):
CTTTAAATTTTTACTATTGACA
Found at i:123653607 original size:22 final size:22
Alignment explanation
Indices: 123653581--123653624 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
123653571 ATATTGAATA
123653581 ATTTATTAAAATAATAAATTAT
1 ATTTATTAAAATAATAAATTAT
* * *
123653603 ATTTATTATATTAATAATTTAT
1 ATTTATTAAAATAATAAATTAT
123653625 TATAAGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTAAAATAATAAATTAT
Found at i:123657656 original size:22 final size:22
Alignment explanation
Indices: 123657617--123657658 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
123657607 TACCAAATAG
* *
123657617 ATGTATCTTTCCATAAAATATA
1 ATGTATCTTTCAACAAAATATA
*
123657639 ATGTATCTTTTAACAAAATA
1 ATGTATCTTTCAACAAAATA
123657659 CCCATTCATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
ATGTATCTTTCAACAAAATATA
Found at i:123666313 original size:12 final size:12
Alignment explanation
Indices: 123666296--123666365 Score: 88
Period size: 13 Copynumber: 5.6 Consensus size: 12
123666286 TTCACTTTCA
123666296 AAAAAAAAAGAG
1 AAAAAAAAAGAG
123666308 AAAAAAGAAAGAG
1 AAAAAA-AAAGAG
123666321 AAAAAAGGAAA-AG
1 AAAAAA--AAAGAG
*
123666334 AAAAAAGAAGAG
1 AAAAAAAAAGAG
123666346 AAAAAAAAAGAG
1 AAAAAAAAAGAG
123666358 AAAGAAAA
1 AAA-AAAA
123666366 GAAAAGCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
11 2 0.04
12 22 0.42
13 24 0.46
14 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:123666345 original size:38 final size:38
Alignment explanation
Indices: 123666296--123666371 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
123666286 TTCACTTTCA
*
123666296 AAAAAAAAAGAGAAAAAAGAAAGAGAAA-AAAGGAAAAG
1 AAAAAAAAAGAGAAAAAA-AAAGAGAAAGAAAAGAAAAG
*
123666334 AAAAAAGAAGAGAAAAAAAAAGAGAAAGAAAAGAAAAG
1 AAAAAAAAAGAGAAAAAAAAAGAGAAAGAAAAGAAAAG
123666372 CAAATGAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 9 0.26
38 26 0.74
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (38 bp):
AAAAAAAAAGAGAAAAAAAAAGAGAAAGAAAAGAAAAG
Found at i:123666368 original size:26 final size:24
Alignment explanation
Indices: 123666296--123666360 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 24
123666286 TTCACTTTCA
123666296 AAAAAAAAAGAGAAAAAAGAAAGAG
1 AAAAAAAAAGAGAAAAAAG-AAGAG
123666321 AAAAAAGGAAA-AGAAAAAAGAAGAG
1 AAAAAA--AAAGAGAAAAAAGAAGAG
123666346 AAAAAAAAAGAGAAA
1 AAAAAAAAAGAGAAA
123666361 GAAAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.08
24 5 0.14
25 17 0.46
26 9 0.24
27 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAGAGAAAAAAGAAGAG
Found at i:123667959 original size:133 final size:133
Alignment explanation
Indices: 123667717--123668671 Score: 908
Period size: 133 Copynumber: 7.3 Consensus size: 133
123667707 AAATTTCGAC
* ** *
123667717 AGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAATTTTGACGAATCTTATCTCCATATAT
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAACAGATCAAATTTTGGTGAATCTTATCTCCATGTAT
*
123667782 CAGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAT
66 CGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAT
123667847 ACT
131 ACT
* * *
123667850 AGATCTTATCTTCGCTGAGTAAGAGCGGAACAGATCAAATTTTAGTGAATCTTATCTCCATGTAT
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAACAGATCAAATTTTGGTGAATCTTATCTCCATGTAT
* *
123667915 CGACAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCATTGAGCAGGAGTGGAGCAGGCTAAAT
66 CGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAT
123667980 ACT
131 ACT
* * *
123667983 AGATCTTATCTTCGCTGAGCAAGAGCGGAGCAGATCAAATTTTGGTGAATTTTATCTCCATGTAT
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAACAGATCAAATTTTGGTGAATCTTATCTCCATGTAT
* **
123668048 CGGCAATGGAGTAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAAACTAAAT
66 CGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAT
123668113 ACT
131 ACT
* * ** * * * * ** * * *
123668116 AG-----ATCTTCG--GAGCA-GATC-AAATTTTGGT-GAATCTT-ATCCCAT-GTATCGGCAAT
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAA--CAGATCAAATTTTGGT-GAATCTTATC-TCCAT
* * * * ** * * ** * * * * * * *
123668169 GGAGCAG-ATTTCAGC-CA--CCAGCC-TTATCTTTA-C-TGAGTAGGAG-TGGAGCAGGCTA-A
62 GTATCGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACT--GAGCAGGAG-TGG--AGC
** *
123668225 ATACTAGAT-CT
122 AGGCTAAATACT
* ** ** *
123668236 -TATCTTCGCTGAGCAGGAGC-GGAGC-----AGATCAAATTTTGGTGAATCTTATCTCCATGTA
1 AGATCTTATCTTCGC-TGAGCAGGAGCGGAACAGATCAAATTTTGGTGAATCTTATCTCCATGTA
123668294 TCGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
65 TCGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
123668359 TACT
130 TACT
** *
123668363 AGATCTTATCTTCGCTGAGCAGGAGCGGGGCAGATCAAATTTTGGTGAATCTTATCTCCATGTAC
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAACAGATCAAATTTTGGTGAATCTTATCTCCATGTAT
*
123668428 CGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAAT
66 CGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAT
123668493 ACT
131 ACT
* *
123668496 AGATCTTATCTTCGCTGAGCAGGAGC-AAAGCAGATCAAATTTTGATGAATCTTATCTCCATGTA
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAA-CAGATCAAATTTTGGTGAATCTTATCTCCATGTA
* * ** * * *
123668560 TCGGGAATGGAGCAGATTCCAATCATCAGCCTTGTCTTCACTGAGCAGGAATGGAGCAGGCTAAA
65 TCGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA
*
123668625 CATACC
129 -ATACT
** * ***
123668631 AGATCTTATCTTTACTGAGTAGGAGTAAAACAGATCAAATT
1 AGATCTTATCTTCGCTGAGCAGGAGCGGAACAGATCAAATT
123668672 ACAGCAGATC
Statistics
Matches: 665, Mismatches: 115, Indels: 82
0.77 0.13 0.10
Matches are distributed among these distances:
118 3 0.00
119 5 0.01
120 12 0.02
121 14 0.02
122 15 0.02
123 11 0.02
124 14 0.02
125 18 0.03
126 18 0.03
127 23 0.03
128 26 0.04
129 3 0.00
133 461 0.69
134 2 0.00
135 37 0.06
136 3 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (133 bp):
AGATCTTATCTTCGCTGAGCAGGAGCGGAACAGATCAAATTTTGGTGAATCTTATCTCCATGTAT
CGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAT
ACT
Found at i:123668374 original size:43 final size:44
Alignment explanation
Indices: 123668191--123668656 Score: 143
Period size: 43 Copynumber: 10.5 Consensus size: 44
123668181 AGCCACCAGC
* *
123668191 CTTATCTTTACTGAGTAGGAGTGGAGCAGGCT-AAATACTAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACTAGAT
* * * ** *
123668234 CTTATCTTCGCTGAGCAGGAGCGGAGCA-GATCAAATTTTGGTGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACT--AG-AT
* * * ** *** * *
123668280 CTTATCTCCA-TGTATC-GGCAATGGAGCAGATTTCAGCCACCAG-C
1 CTTATCTTCACTG-AGCAGG-AGTGGAGCAG-GCTCAAATACTAGAT
123668324 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAATACTAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACTAGAT
* * * * ** *
123668367 CTTATCTTCGCTGAGCAGGAGCGGGGCA-GATCAAATTTTGGTGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACT--AG-AT
* * * ** *** * *
123668413 CTTATCTCCA-TGTA-CCGGCAATGGAGCAGATTTCAGCCACCAG-C
1 CTTATCTTCACTG-AGCAGG-AGTGGAGCAG-GCTCAAATACTAGAT
*
123668457 CTTATCTTCACTGAGCAGGAGTGGAGTAGGCT-AAATACTAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACTAGAT
* *** * **
123668500 CTTATCTTCGCTGAGCAGGAGCAAAGCA-GATCAAATTTTGATGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACT-A-G-AT
* * * * ** * *
123668546 CTTATCTCCA-TGTATCGGGAATGGAGCAGATTCCAAT-CATCAG-C
1 CTTATCTTCACTG-AGCAGGAGTGGAGCAGGCTCAAATAC-T-AGAT
* * * *
123668590 CTTGTCTTCACTGAGCAGGAATGGAGCAGGCTAAACATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAA-ATACTAGAT
* *
123668635 CTTATCTTTACTGAGTAGGAGT
1 CTTATCTTCACTGAGCAGGAGT
123668657 AAAACAGATC
Statistics
Matches: 287, Mismatches: 103, Indels: 64
0.63 0.23 0.14
Matches are distributed among these distances:
42 16 0.06
43 89 0.31
44 65 0.23
45 45 0.16
46 59 0.21
47 7 0.02
48 6 0.02
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTCAAATACTAGAT
Found at i:123668493 original size:380 final size:381
Alignment explanation
Indices: 123667742--123668642 Score: 1336
Period size: 380 Copynumber: 2.3 Consensus size: 381
123667732 TGAGCAGGAG
123667742 CGGAGCAGATCAAATTTTGACGAATCTTATCTCCATATATCAGCAATGGAGCAGATTTCAGCCAC
1 CGGAGCAGATCAAATTTTGACGAATCTTATCTCCATATATCAGCAATGGAGCAGATTTCAGCCAC
*
123667807 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAGTAA
66 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAGCAA
123667872 GAGCGGAACAGATCAAATTTTAGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTCAGC
131 GAGCGGAACAGATCAAATTTTAGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTCAGC
*
123667937 CACCAGCCTTATCTTCATTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAG
196 CACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAG
* * *
123668002 CAAGAGCGGAGCAGATCAAATTTTGGTGAATTTTATCTCCATGTATCGGCAATGGAGTAGATTTC
261 CAAGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTC
123668067 AGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAAACTAAATACTAGATCTT
326 AGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAAACTAAATACTAGATCTT
** * *
123668123 CGGAGCAGATCAAATTTTGGTGAATCTTATC-CCATGTATCGGCAATGGAGCAGATTTCAGCCAC
1 CGGAGCAGATCAAATTTTGACGAATCTTATCTCCATATATCAGCAATGGAGCAGATTTCAGCCAC
* * *
123668187 CAGCCTTATCTTTACTGAGTAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAGCAG
66 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAGCAA
* * *
123668252 GAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGC
131 GAGCGGAACAGATCAAATTTTAGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTCAGC
123668317 CACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAG
196 CACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAG
* *
123668382 CAGGAGCGGGGCAGATCAAATTTTGGTGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTC
261 CAAGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTC
* **
123668447 AGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAATACTAGATCTTATCTTCGCT
326 AGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAAACTAAATACTAG-----ATC-T---T
* * * *
123668512 GAGCAGGAGCAAAGCAGATCAAATTTTGATGAATCTTATCTCCATGTATCGGGAATGGAGCAGAT
1 ---C--G-G---AGCAGATCAAATTTTGACGAATCTTATCTCCATATATCAGCAATGGAGCAGAT
* ** * * * *
123668577 TCCAATCATCAGCCTTGTCTTCACTGAGCAGGAATGGAGCAGGCTAAACATACCAGATCTTATCT
57 TTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-ATACTAGATCTTATCT
123668642 T
120 T
123668643 TACTGAGTAG
Statistics
Matches: 468, Mismatches: 31, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
380 326 0.70
381 29 0.06
385 3 0.01
386 1 0.00
389 1 0.00
392 1 0.00
394 1 0.00
395 1 0.00
398 27 0.06
399 60 0.13
400 2 0.00
401 16 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (381 bp):
CGGAGCAGATCAAATTTTGACGAATCTTATCTCCATATATCAGCAATGGAGCAGATTTCAGCCAC
CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAGCAA
GAGCGGAACAGATCAAATTTTAGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTCAGC
CACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACTAGATCTTATCTTCGCTGAG
CAAGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTC
AGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAAACTAAATACTAGATCTT
Found at i:123668917 original size:29 final size:29
Alignment explanation
Indices: 123668884--123668947 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
123668874 CCAAATTAAA
123668884 CACCCCACTAAACCGA-CCACTAACTCCAT
1 CACCCCACTAAACC-ATCCACTAACTCCAT
* *
123668913 CACCCTACTAAACCATCCACTACCTCCAT
1 CACCCCACTAAACCATCCACTAACTCCAT
123668942 CACCCC
1 CACCCC
123668948 CACACCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.31, C:0.52, G:0.02, T:0.16
Consensus pattern (29 bp):
CACCCCACTAAACCATCCACTAACTCCAT
Found at i:123668960 original size:37 final size:37
Alignment explanation
Indices: 123668913--123668987 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
123668903 CTAACTCCAT
123668913 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
*
123668950 CACCCTACTAAACCGTCCACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
123668987 C
1 C
123668988 TACCTCCATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.55, G:0.01, T:0.16
Consensus pattern (37 bp):
CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
Found at i:123668989 original size:18 final size:18
Alignment explanation
Indices: 123668929--123669001 Score: 78
Period size: 18 Copynumber: 4.0 Consensus size: 18
123668919 ACTAAACCAT
123668929 CCACTACCTCCATCACCC
1 CCACTACCTCCATCACCC
* * *
123668947 CCAC-ACC-CTACTAAACCGT
1 CCACTACCTCCA-T-CACC-C
123668966 CCACTACCTCCATCACCC
1 CCACTACCTCCATCACCC
123668984 CCACTACCTCCATCACCC
1 CCACTACCTCCATCACCC
123669002 TACTTGTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 25 0.57
19 7 0.16
20 4 0.09
21 2 0.05
ACGTcount: A:0.25, C:0.58, G:0.01, T:0.16
Consensus pattern (18 bp):
CCACTACCTCCATCACCC
Found at i:123669445 original size:19 final size:18
Alignment explanation
Indices: 123669421--123669488 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
123669411 TTATGTTTCA
123669421 TATTATTATATTATTTATT
1 TATTATTATA-TATTTATT
123669440 TATTATTATATATTTA-T
1 TATTATTATATATTTATT
* * *
123669457 TATGTAATATATATATATA
1 TAT-TATTATATATTTATT
123669476 TA-TA-TATATATTT
1 TATTATTATATATTT
123669489 TTAAGCGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.19
17 6 0.14
18 17 0.40
19 12 0.28
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TATTATTATATATTTATT
Found at i:123669448 original size:14 final size:14
Alignment explanation
Indices: 123669429--123669484 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
123669419 CATATTATTA
*
123669429 TATTATTTATTTAT
1 TATTATATATTTAT
123669443 TATTATATATTTAT
1 TATTATATATTTAT
*
123669457 TATGTAATATATATAT
1 TAT-T-ATATATTTAT
123669473 ATATATATATAT
1 -TAT-TATATAT
123669485 ATTTTTAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 16 0.44
15 1 0.03
16 15 0.42
17 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TATTATATATTTAT
Found at i:123669456 original size:22 final size:22
Alignment explanation
Indices: 123669420--123669476 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
123669410 GTTATGTTTC
*
123669420 ATATTAT-TATATTATTTATTTA
1 ATATTATATATATTA-TTATGTA
*
123669442 TTATTATATAT-TTATTATGTA
1 ATATTATATATATTATTATGTA
123669463 ATATATATATATAT
1 ATAT-TATATATAT
123669477 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 9 0.31
22 16 0.55
23 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATTATATATATTATTATGTA
Found at i:123669468 original size:2 final size:2
Alignment explanation
Indices: 123669446--123669486 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
123669436 TATTTATTAT
* *
123669446 TA TA TA TT TA T- TA TG TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123669486 T
1 T
123669487 TTTTAAGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:123670166 original size:127 final size:126
Alignment explanation
Indices: 123669930--123670174 Score: 418
Period size: 127 Copynumber: 1.9 Consensus size: 126
123669920 CATTGATCTT
* **
123669930 CTCTCAAAATTTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTTTCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
123669995 ACGTACTGGGTTTCGCTTTCTTTCTTTGTCTTGAAGATTCGAATATCCTCTTACCAGTTCA
66 ACGTACTGGGTTTCGCTTTCTTTCTTTGTCTTGAAGATTCGAATATCCTCTTACCAGTTCA
*
123670056 CTCTCAAAAAATTTTCAAAATAAGGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCT
1 CTCTC-AAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCT
* * *
123670121 AATGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
65 AACGTACTGGGTTTCGCTTTCTTTCTTTGTCTTGAAGATTCGAATATCCTCTTA
123670175 AGGCTAAAAC
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
126 5 0.05
127 106 0.95
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (126 bp):
CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
ACGTACTGGGTTTCGCTTTCTTTCTTTGTCTTGAAGATTCGAATATCCTCTTACCAGTTCA
Found at i:123674457 original size:2 final size:2
Alignment explanation
Indices: 123674450--123674475 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
123674440 CGTGGAAATC
123674450 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
123674476 TTGTCGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123675553 original size:26 final size:24
Alignment explanation
Indices: 123675511--123675558 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
123675501 TCAATTATAA
*
123675511 AAAAAAAATTTATTTTAAGCACCC
1 AAAAAAAATTTAATTTAAGCACCC
123675535 AAAAAAAATTTACAATTTAAGCAC
1 AAAAAAAATTT--AATTTAAGCAC
123675559 TCACATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.27
Consensus pattern (24 bp):
AAAAAAAATTTAATTTAAGCACCC
Found at i:123675804 original size:6 final size:6
Alignment explanation
Indices: 123675795--123675819 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
123675785 ATTTTATATC
123675795 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
123675820 ATAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:123676018 original size:51 final size:51
Alignment explanation
Indices: 123675922--123676024 Score: 116
Period size: 51 Copynumber: 2.0 Consensus size: 51
123675912 TTATTTTTAT
** * **
123675922 ATTTTTTAAAATTATGATTAAATTGAAAAAATTTATAAATTTTGAGAGTTA
1 ATTTTTTAAAATTATGACAAAATTGAAAAAATATATAAAAGTTGAGAGTTA
* ** * *
123675973 ATTTTTTAAAATTATGACAAAATTGATATGATATGTAAAAGTTGAGGGTTA
1 ATTTTTTAAAATTATGACAAAATTGAAAAAATATATAAAAGTTGAGAGTTA
123676024 A
1 A
123676025 ATTTATTATT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.44, C:0.01, G:0.14, T:0.42
Consensus pattern (51 bp):
ATTTTTTAAAATTATGACAAAATTGAAAAAATATATAAAAGTTGAGAGTTA
Found at i:123681245 original size:18 final size:17
Alignment explanation
Indices: 123681222--123681268 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 17
123681212 TAGTAAATAA
123681222 TAATAATAAATATAATGC
1 TAATAATAAA-ATAATGC
123681240 TAATAA-AAAAT-A-GC
1 TAATAATAAAATAATGC
123681254 -AATAATAAAATAATG
1 TAATAATAAAATAATG
123681269 ATATTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 2 0.08
16 3 0.12
17 3 0.12
18 6 0.23
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (17 bp):
TAATAATAAAATAATGC
Found at i:123681347 original size:14 final size:15
Alignment explanation
Indices: 123681324--123681358 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
123681314 ACAATAACAG
*
123681324 AAATATAAA-TAGAT
1 AAATAAAAATTAGAT
123681338 AAATAAAAATTAGAT
1 AAATAAAAATTAGAT
123681353 AAATAA
1 AAATAA
123681359 TAAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AAATAAAAATTAGAT
Found at i:123681389 original size:3 final size:3
Alignment explanation
Indices: 123681381--123681566 Score: 119
Period size: 3 Copynumber: 63.0 Consensus size: 3
123681371 AGATGAAAAT
* * * * * *
123681381 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ATA GT- ATG TTAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * * * *
123681425 ATA ATA GTA ATA ATA ATT ACA AGA ATG ATA ATG ATA ATA A-A ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * *
123681471 ATA AAA ATA ATA ATA CTA ATG TTA ATG TTA ATA AAA ATA AAA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
123681519 ATA ATA GTA ATA ATA ATA ACA ATA ATA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
123681567 GTGTTAGACA
Statistics
Matches: 132, Mismatches: 46, Indels: 10
0.70 0.24 0.05
Matches are distributed among these distances:
2 6 0.05
3 125 0.95
4 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:123681403 original size:14 final size:14
Alignment explanation
Indices: 123681386--123681412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
123681376 AAAATATAAT
123681386 AATAGTAATAATAC
1 AATAGTAATAATAC
123681400 AATAGTAATAATA
1 AATAGTAATAATA
123681413 GTATGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGTAATAATAC
Found at i:123687193 original size:40 final size:40
Alignment explanation
Indices: 123687138--123687213 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
123687128 CATGTCAATC
*
123687138 TTGATGTAAATTTAAATTTTTTAACTATTTATTTTAAATT
1 TTGATGTAAATTTAAAGTTTTTAACTATTTATTTTAAATT
123687178 TTGATGTAAATTTAAAGTTTTTAACTATTTATTTTA
1 TTGATGTAAATTTAAAGTTTTTAACTATTTATTTTA
123687214 TGTAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.57
Consensus pattern (40 bp):
TTGATGTAAATTTAAAGTTTTTAACTATTTATTTTAAATT
Found at i:123687863 original size:4 final size:4
Alignment explanation
Indices: 123687854--123687880 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
123687844 TTCGTTAACT
123687854 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
123687881 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:123688821 original size:14 final size:15
Alignment explanation
Indices: 123688802--123688831 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
123688792 AGATATAATC
123688802 AAAAAATTTATTCAA
1 AAAAAATTTATTCAA
*
123688817 AAAAAATTTCTTCAA
1 AAAAAATTTATTCAA
123688832 CTTAACATTA
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATTTATTCAA
Found at i:123690441 original size:2 final size:2
Alignment explanation
Indices: 123690436--123690462 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
123690426 CATAGTTTAC
123690436 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 T
123690463 TTCACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123691772 original size:14 final size:14
Alignment explanation
Indices: 123691753--123691779 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
123691743 TTGTTTGCCA
123691753 GGAAAATATTTTCT
1 GGAAAATATTTTCT
123691767 GGAAAATATTTTC
1 GGAAAATATTTTC
123691780 CTGGTTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
GGAAAATATTTTCT
Found at i:123692202 original size:28 final size:29
Alignment explanation
Indices: 123692162--123692227 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
123692152 TTATTTAATC
123692162 TGTTTGTTTCTGGATTTTG-TAAAGTTTA
1 TGTTTGTTTCTGGATTTTGATAAAGTTTA
*
123692190 TGTTTGTTTCTGGGTTTTGCATAAAGTTTA
1 TGTTTGTTTCTGGATTTTG-ATAAAGTTTA
*
123692220 TGCTTGTT
1 TGTTTGTT
123692228 GTTCGTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 18 0.53
30 16 0.47
ACGTcount: A:0.15, C:0.06, G:0.23, T:0.56
Consensus pattern (29 bp):
TGTTTGTTTCTGGATTTTGATAAAGTTTA
Found at i:123695057 original size:4 final size:4
Alignment explanation
Indices: 123695048--123695083 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
123695038 GAGCAAACGT
*
123695048 GAAA GAAA G-AA GAAA GAAA GAAA GAAA GAAA AAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
123695084 GAAATTTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:123697612 original size:32 final size:31
Alignment explanation
Indices: 123697557--123697638 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
123697547 TTGAAATTTT
*
123697557 AGTTTGTTGGATTTTGGAATTATTATGTCTTGA
1 AGTTTGTTGGATATT-GAATTATTATGT-TTGA
* *
123697590 A-TTTGTTAGATATTGAATTTATTATGTTTTA
1 AGTTTGTTGGATATTGAA-TTATTATGTTTGA
*
123697621 AGCTTGTTGGATATTGAA
1 AGTTTGTTGGATATTGAA
123697639 GTGATTGACA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
31 7 0.17
32 34 0.81
33 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (31 bp):
AGTTTGTTGGATATTGAATTATTATGTTTGA
Found at i:123699164 original size:3 final size:3
Alignment explanation
Indices: 123699156--123699204 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
123699146 ATTTAATTGC
123699156 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
123699204 A
1 A
123699205 AAAACTAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:123699326 original size:18 final size:18
Alignment explanation
Indices: 123699303--123699337 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
123699293 ATTAAATATA
*
123699303 ATAATTGTAATTATAAGC
1 ATAATTCTAATTATAAGC
*
123699321 ATAATTCTAATTTTAAG
1 ATAATTCTAATTATAAG
123699338 AAAATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (18 bp):
ATAATTCTAATTATAAGC
Found at i:123700161 original size:12 final size:11
Alignment explanation
Indices: 123700139--123700164 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
123700129 TGATTATAAG
123700139 AGTTTTTAAAA
1 AGTTTTTAAAA
123700150 AGTTTTTAAAA
1 AGTTTTTAAAA
123700161 AGTT
1 AGTT
123700165 GGCCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (11 bp):
AGTTTTTAAAA
Found at i:123700986 original size:21 final size:20
Alignment explanation
Indices: 123700962--123701006 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
123700952 ACTTCGTAAC
123700962 AAAACAATAACAT-AAGTGACT
1 AAAAC-ATAACATGAA-TGACT
*
123700983 AAAACGTAACATGAATGACT
1 AAAACATAACATGAATGACT
123701003 AAAA
1 AAAA
123701007 TGTAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAACATAACATGAATGACT
Found at i:123700994 original size:20 final size:20
Alignment explanation
Indices: 123700969--123701017 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
123700959 AACAAAACAA
123700969 TAACATAAGTGACTAAAACG
1 TAACATAAGTGACTAAAACG
*
123700989 TAACATGAA-TGACTAAAATG
1 TAACAT-AAGTGACTAAAACG
*
123701009 TAATATAAG
1 TAACATAAG
123701018 ATCAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.24
Consensus pattern (20 bp):
TAACATAAGTGACTAAAACG
Found at i:123702092 original size:2 final size:2
Alignment explanation
Indices: 123702085--123702115 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
123702075 ACATTGTTTA
*
123702085 AT AT AT AT AA 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 AT A
123702116 CGCGCGAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:123702371 original size:2 final size:2
Alignment explanation
Indices: 123702354--123702392 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
123702344 ATTTTAAAGA
*
123702354 AT AT GAT AT TT 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
123702393 TTTTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:123703144 original size:31 final size:29
Alignment explanation
Indices: 123703101--123703172 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
123703091 TACAAAAATT
* *
123703101 GTCACTTTTGTTTGCATCAGGTTACATTTTA
1 GTCACTTATGTTTG-A-AAGGTTACATTTTA
* *
123703132 GTCACTTATGTTTGAAATGTTACGTTTTA
1 GTCACTTATGTTTGAAAGGTTACATTTTA
123703161 GTCACTTATGTT
1 GTCACTTATGTT
123703173 ATTATTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 23 0.62
30 1 0.03
31 13 0.35
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (29 bp):
GTCACTTATGTTTGAAAGGTTACATTTTA
Found at i:123704206 original size:31 final size:29
Alignment explanation
Indices: 123704141--123704214 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
123704131 ACAAAATAGT
**
123704141 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGGCA
* *
123704170 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAACGTAACAT--GGCA
123704201 AACATAAGTGACTA
1 AACATAAGTGACTA
123704215 TTTTGGTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGGCA
Found at i:123704556 original size:2 final size:2
Alignment explanation
Indices: 123704551--123704581 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
123704541 TTCTCTTTTT
123704551 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 T
123704582 TTTCTTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123704632 original size:28 final size:27
Alignment explanation
Indices: 123704595--123704651 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
123704585 CTTATCCAAA
**
123704595 TTTTTTATGATGGAATAGTATCAATAC
1 TTTTTTATGAACGAATAGTATCAATAC
*
123704622 TTTTTTGATGAACGAATATTATCAATAC
1 TTTTTT-ATGAACGAATAGTATCAATAC
123704650 TT
1 TT
123704652 AATCATTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (27 bp):
TTTTTTATGAACGAATAGTATCAATAC
Found at i:123705090 original size:28 final size:29
Alignment explanation
Indices: 123705059--123705124 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
123705049 ATTTTTAAAC
*
123705059 AAGCCCTTAACCTAT-TTTTTAGT-AAAA
1 AAGCCCTTAACCTATATTTTTACTCAAAA
*
123705086 TAAGCCCTTAACTTATAGTTTTTACTCAAAA
1 -AAGCCCTTAACCTATA-TTTTTACTCAAAA
123705117 AAGCCCTT
1 AAGCCCTT
123705125 TATTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 14 0.42
30 15 0.45
31 4 0.12
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (29 bp):
AAGCCCTTAACCTATATTTTTACTCAAAA
Found at i:123705333 original size:28 final size:27
Alignment explanation
Indices: 123705279--123705330 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
123705269 AAACTATAAA
123705279 TTAAGGGCTTATTTAACTAAAAAATAGG
1 TTAAGGGCTTATTTAAC-AAAAAATAGG
* *
123705307 TTAAGGGCTTGTTTAA-AAATAATA
1 TTAAGGGCTTATTTAACAAAAAATA
123705331 TAGTGAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
28 15 0.68
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (27 bp):
TTAAGGGCTTATTTAACAAAAAATAGG
Found at i:123709456 original size:7 final size:7
Alignment explanation
Indices: 123709444--123709480 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
123709434 CTGAGTAATC
123709444 TTTTGTT
1 TTTTGTT
123709451 TTTTGTT
1 TTTTGTT
123709458 TTTTGTT
1 TTTTGTT
123709465 TTTTGTT
1 TTTTGTT
123709472 TTTT-TT
1 TTTTGTT
123709478 TTT
1 TTT
123709481 ATCAATATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTGTT
Found at i:123712215 original size:17 final size:17
Alignment explanation
Indices: 123712193--123712229 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
123712183 ACCCTACTTG
*
123712193 CCACTAACTCCATCACC
1 CCACTAACCCCATCACC
*
123712210 CCACTAACCCCATTACC
1 CCACTAACCCCATCACC
123712227 CCA
1 CCA
123712230 TTTGCCACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.54, G:0.00, T:0.16
Consensus pattern (17 bp):
CCACTAACCCCATCACC
Found at i:123712588 original size:3 final size:3
Alignment explanation
Indices: 123712575--123712720 Score: 72
Period size: 3 Copynumber: 49.0 Consensus size: 3
123712565 TATTTTTAAA
*
123712575 TAT TGT TAT TAT TAT TA- TATT TAT TA- TAT TA- TATT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
123712618 TAC TGT TAC TAT TAT T-T TAT ATATT TAT TAT CAT TATT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT TAT TA-T TA-T TAT TAT
** * * ** * *
123712666 TAT TAT TGG TAA CA- TAT TGC TAT TTT TAT TAT T-T TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
123712712 TAT TAT TAT
1 TAT TAT TAT
123712721 CATGGTACTA
Statistics
Matches: 107, Mismatches: 24, Indels: 24
0.69 0.15 0.15
Matches are distributed among these distances:
2 13 0.12
3 78 0.73
4 15 0.14
5 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:123712604 original size:17 final size:17
Alignment explanation
Indices: 123712584--123712672 Score: 66
Period size: 17 Copynumber: 5.4 Consensus size: 17
123712574 ATATTGTTAT
123712584 TATTATTATATTTA-T-
1 TATTATTATATTTATTA
*
123712599 TA-TATTATATTTATTT
1 TATTATTATATTTATTA
*
123712615 TATTACTGT-TA-CTATTA
1 TATTA-T-TATATTTATTA
*
123712632 TTTTA-TATATTTATTA
1 TATTATTATATTTATTA
123712648 TCATTATT-TATTTATTA
1 T-ATTATTATATTTATTA
123712665 TTATTATT
1 -TATTATT
123712673 GGTAACATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
14 12 0.20
15 5 0.08
16 8 0.14
17 28 0.47
18 5 0.08
19 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (17 bp):
TATTATTATATTTATTA
Found at i:123712655 original size:13 final size:12
Alignment explanation
Indices: 123712581--123712671 Score: 62
Period size: 14 Copynumber: 7.1 Consensus size: 12
123712571 TAAATATTGT
123712581 TATTA-TTATTA
1 TATTATTTATTA
123712592 TATTTATTATATTA
1 TA-TTATT-TATTA
123712606 TATTTATTTTATTA
1 TA-TTA-TTTATTA
* *
123712620 CTGTTACTATTATTT
1 -TATTA-T-TTATTA
123712635 TATATATTTATTA
1 TAT-TATTTATTA
123712648 TCATTATTTATT-
1 T-ATTATTTATTA
123712660 TATTA-TTATTA
1 TATTATTTATTA
123712671 T
1 T
123712672 TGGTAACATA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
10 5 0.08
11 7 0.11
12 4 0.06
13 15 0.23
14 25 0.38
15 10 0.15
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:123712703 original size:20 final size:20
Alignment explanation
Indices: 123712680--123712718 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
123712670 ATTGGTAACA
* *
123712680 TATTGCTATTTTTATTATTT
1 TATTACTATTGTTATTATTT
*
123712700 TATTATTATTGTTATTATT
1 TATTACTATTGTTATTATT
123712719 ATCATGGTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TATTACTATTGTTATTATTT
Found at i:123713189 original size:15 final size:16
Alignment explanation
Indices: 123713169--123713201 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
123713159 ATATATTTTT
123713169 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
123713184 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
123713201 T
1 T
123713202 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:123713287 original size:22 final size:22
Alignment explanation
Indices: 123713248--123713306 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
123713238 GTTTTAAGAA
*
123713248 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
123713269 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
123713291 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
123713307 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:123713326 original size:26 final size:24
Alignment explanation
Indices: 123713277--123713336 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
123713267 ATTTGTTTTA
* *
123713277 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTAAAAT
123713301 ATATTTGATTTATTATATTTTAAAAT
1 ATATTT-ATTT-TTATATTTTAAAAT
* *
123713327 TTTTTTATTT
1 ATATTTATTT
123713337 AATGAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.20
25 8 0.27
26 16 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTAAAAT
Found at i:123713336 original size:25 final size:26
Alignment explanation
Indices: 123713280--123713337 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
123713270 TGTTTTAATA
* *
123713280 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTAAAATATAT
* *
123713305 TTGATTTATTATATTTTAAAAT-TTT
1 TTTATTTATTATATTTTAAAATATAT
123713330 TTTATTTA
1 TTTATTTA
123713338 ATGAAATAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTATTTATTATATTTTAAAATATAT
Found at i:123714381 original size:125 final size:125
Alignment explanation
Indices: 123714157--123714387 Score: 288
Period size: 125 Copynumber: 1.8 Consensus size: 125
123714147 GGATTTCTAA
* *
123714157 AAAATAAGGAAATATTTCGTGTTTGGAAATTCGAGAAATCGTGCCCTACTGTGCTGGGTTTCGAT
1 AAAATAAGGAAATATTTCGTGTTTGGAAATTCGAGAAATCGTGCCCAACTGTGCTGGGTTTCGAC
*** * **
123714222 TTTTTGTTCAACTGAATAACTGAATATCCTTTTGAAATTTCGTCCATGTTTTCTTAAATT
66 TTACCGTTCAACAGAATAACCAAATATCCTTTTGAAATTTCGTCCATGTTTTCTTAAATT
* * * *
123714282 AAAATGAGGCAATATTTTGTGTTTGGAATTTCGAGAAATCGTGCCCAA-TCGTGCTGGGTTTCGA
1 AAAATAAGGAAATATTTCGTGTTTGGAAATTCGAGAAATCGTGCCCAACT-GTGCTGGGTTTCGA
* *
123714346 CTTACCGTTTAACCAG-ATAGCCAAATATTCC-TTTGAAATTTC
65 CTTACCGTTCAA-CAGAATAACCAAATA-TCCTTTTGAAATTTC
123714388 AAATGCATGA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
124 1 0.01
125 83 0.93
126 5 0.06
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (125 bp):
AAAATAAGGAAATATTTCGTGTTTGGAAATTCGAGAAATCGTGCCCAACTGTGCTGGGTTTCGAC
TTACCGTTCAACAGAATAACCAAATATCCTTTTGAAATTTCGTCCATGTTTTCTTAAATT
Found at i:123716653 original size:2 final size:2
Alignment explanation
Indices: 123716646--123716679 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
123716636 TAATTTACAA
123716646 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
123716680 TAGGAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123717909 original size:30 final size:28
Alignment explanation
Indices: 123717837--123717909 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 28
123717827 CGGGTTAGTG
123717837 ATTTAATATAAATATAAATATATAATTATT
1 ATTTAA-AT-AATATAAATATATAATTATT
*
123717867 ATTTAAAT-ATATAATTAATATAA-TATT
1 ATTTAAATAATATAAAT-ATATAATTATT
*
123717894 TTTATAACATAATATA
1 ATT-TAA-ATAATATA
123717910 TTTGGGCCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 13 0.35
28 9 0.24
29 4 0.11
30 11 0.30
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTAAATAATATAAATATATAATTATT
Done.