Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 44 of 214
Found at i:12119725 original size:15 final size:13
Alignment explanation
Indices: 12119658--12119749 Score: 82
Period size: 13 Copynumber: 7.2 Consensus size: 13
12119648 AATTTAATGA
12119658 AATACATAAATAT
1 AATACATAAATAT
*
12119671 AATA-ATACATGAT
1 AATACATAAAT-AT
* * **
12119684 AATGCATGAATGC
1 AATACATAAATAT
12119697 AATACATAAATAT
1 AATACATAAATAT
12119710 AATACAT-AATA-
1 AATACATAAATAT
* *
12119721 ATATATATAAATGT
1 A-ATACATAAATAT
12119735 AATACATAAATAT
1 AATACATAAATAT
12119748 AA
1 AA
12119750 CAAGGATAAG
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
11 1 0.02
12 14 0.23
13 40 0.67
14 5 0.08
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (13 bp):
AATACATAAATAT
Found at i:12121023 original size:23 final size:24
Alignment explanation
Indices: 12120982--12121031 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
12120972 GGACTTTATT
12120982 TTTTTTTATTTTGGGTTTGTTTGA
1 TTTTTTTATTTTGGGTTTGTTTGA
* *
12121006 TTTTTTTATTTT-GTTTTGTTTTA
1 TTTTTTTATTTTGGGTTTGTTTGA
12121029 TTT
1 TTT
12121032 ATTTGGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78
Consensus pattern (24 bp):
TTTTTTTATTTTGGGTTTGTTTGA
Found at i:12121036 original size:18 final size:18
Alignment explanation
Indices: 12120997--12121035 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
12120987 TTATTTTGGG
12120997 TTTGTTTGATTTTTTTAT
1 TTTGTTTGATTTTTTTAT
12121015 TTTGTTTTG-TTTTATTTAT
1 TTTG-TTTGATTTT-TTTAT
12121034 TT
1 TT
12121036 GGGTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTGTTTGATTTTTTTAT
Found at i:12122608 original size:18 final size:17
Alignment explanation
Indices: 12122585--12122627 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
12122575 ATACAAGTAC
*
12122585 TTTGGTTGGTAATGTGAA
1 TTTGGTTGATAAT-TGAA
12122603 TTTGGTTTGATAATTGAA
1 TTTGG-TTGATAATTGAA
12122621 TTGTGGT
1 TT-TGGT
12122628 GCCAATGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (17 bp):
TTTGGTTGATAATTGAA
Found at i:12124968 original size:18 final size:17
Alignment explanation
Indices: 12124922--12124969 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
12124912 CAAAATTGTT
12124922 ATGTGAAGTGAATAAGC
1 ATGTGAAGTGAATAAGC
* *
12124939 -TCGTGAATTGAACTAGGC
1 AT-GTGAAGTGAA-TAAGC
12124957 ATGTGAAGTGAAT
1 ATGTGAAGTGAAT
12124970 TAAATATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 13 0.52
19 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.27
Consensus pattern (17 bp):
ATGTGAAGTGAATAAGC
Found at i:12125113 original size:41 final size:41
Alignment explanation
Indices: 12125056--12125141 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
12125046 TAGTGAAAAG
12125056 ATTATAATAAGACATAATGTGAATAAAAGTGTTAAAAATAA
1 ATTATAATAAGACATAATGTGAATAAAAGTGTTAAAAATAA
12125097 ATTATAATAAGACATAATGTGAATAAAAGTGTTAAAAATAA
1 ATTATAATAAGACATAATGTGAATAAAAGTGTTAAAAATAA
12125138 ATTA
1 ATTA
12125142 ATGTGATATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (41 bp):
ATTATAATAAGACATAATGTGAATAAAAGTGTTAAAAATAA
Found at i:12128177 original size:15 final size:15
Alignment explanation
Indices: 12128153--12128208 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
12128143 TTTAGAAAAC
*
12128153 ATATAAAAATTTATA
1 ATATATAAATTTATA
12128168 ATATATAAA--T-TA
1 ATATATAAATTTATA
12128180 ATA-A-AAATTTATA
1 ATATATAAATTTATA
* *
12128193 ATTTATAATTTTATA
1 ATATATAAATTTATA
12128208 A
1 A
12128209 AAATATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
10 3 0.09
11 1 0.03
12 6 0.18
13 5 0.15
14 1 0.03
15 17 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATAAATTTATA
Found at i:12128183 original size:25 final size:25
Alignment explanation
Indices: 12128155--12128227 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
12128145 TAGAAAACAT
12128155 ATAAAAATTTATAATATATAAATTA
1 ATAAAAATTTATAATATATAAATTA
* * *
12128180 ATAAAAATTTATAATTTATAATTTT
1 ATAAAAATTTATAATATATAAATTA
* *
12128205 ATAAAAATATATAAACATATAAA
1 ATAAAAATTTAT-AATATATAAA
12128228 AGAACTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 33 0.82
26 7 0.17
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAAATTTATAATATATAAATTA
Found at i:12131307 original size:44 final size:44
Alignment explanation
Indices: 12131170--12131507 Score: 134
Period size: 44 Copynumber: 7.8 Consensus size: 44
12131160 ACTTGATGCG
* * * * *
12131170 ATCTGCTCTATTGCAACCTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTCTTACTTCA
* ** * * * * *
12131214 ATCCGCTCCACCACAACCTCAGGGAAATAGGAT-TATCGACTTTA
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTCT-TACTTCA
*
12131258 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTT-CTTCA
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCT-CTTACTTCA
* * * ** * * * *
12131302 GTCTGCCCCATTGTGACTTTAGGGGGATAAGACCTGCTTAC-TCA
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCT-CTTACTTCA
* * * * * * *
12131346 GTCTGCTCTACTACAACCTCAGGAAGATAAGA-C-CTGA-TGCG
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTCTTACTTCA
** * * * * * *
12131387 ATCCACTCTACTGCAACTTTAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTCTTACTTCA
* * * * * * *
12131431 ATCCGCTCCACTACAACTTCAAGGAGATAGGATTATCGGT--TTCA
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGA-TCTC-TTACTTCA
* * * *
12131475 ATCTGCTCCGCTGTAACTTCAGCGAGATAAGAT
1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGAT
12131508 TTGTAGTTTC
Statistics
Matches: 213, Mismatches: 71, Indels: 21
0.70 0.23 0.07
Matches are distributed among these distances:
41 28 0.13
42 1 0.00
43 7 0.03
44 171 0.80
45 4 0.02
46 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTCTTACTTCA
Found at i:12132836 original size:15 final size:14
Alignment explanation
Indices: 12132809--12132860 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
12132799 TTAGCCTCTC
12132809 CATTTTTACTTTTT
1 CATTTTTACTTTTT
*
12132823 CATTTTTCATTTTTT
1 CATTTTT-ACTTTTT
12132838 CATTTTTTACTCTTTT
1 CA-TTTTTACT-TTTT
12132854 -ATTTTTA
1 CATTTTTA
12132861 GTTTGAGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 13 0.39
15 11 0.33
16 9 0.27
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (14 bp):
CATTTTTACTTTTT
Found at i:12150492 original size:3 final size:3
Alignment explanation
Indices: 12150484--12150525 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
12150474 TATATATAGG
* *
12150484 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12150526 GGAGCTGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12156068 original size:23 final size:24
Alignment explanation
Indices: 12156023--12156068 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12156013 GCGCATTATG
* *
12156023 TTGGCCTTTGTGGTGTACTTCTGT
1 TTGGCCTTTGTGGCGTACATCTGT
12156047 TTGGCCTTTGTGGCGTA-ATCTG
1 TTGGCCTTTGTGGCGTACATCTG
12156069 CTAAGCCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.07, C:0.17, G:0.30, T:0.46
Consensus pattern (24 bp):
TTGGCCTTTGTGGCGTACATCTGT
Found at i:12159185 original size:42 final size:42
Alignment explanation
Indices: 12159107--12159210 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
12159097 AACCCTACTG
*
12159107 GGTTTCCGTTCAGCTCTTTTGACCTTCAGCTTAACCCTTATA
1 GGTTTCCGTTCAGCTCTTATGACCTTCAGCTTAACCCTTATA
* * *
12159149 GGTTTTCGTTCAGCTCTTATGAGCTTTC-G-TTCAACCCTTATG
1 GGTTTCCGTTCAGCTCTTATGA-CCTTCAGCTT-AACCCTTATA
* * *
12159191 GGTTTCTGTTTAGCACTTAT
1 GGTTTCCGTTCAGCTCTTAT
12159211 ATGCTTCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
41 2 0.04
42 46 0.88
43 4 0.08
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (42 bp):
GGTTTCCGTTCAGCTCTTATGACCTTCAGCTTAACCCTTATA
Found at i:12159949 original size:13 final size:13
Alignment explanation
Indices: 12159931--12159955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12159921 TAAGTTATAT
12159931 GTGTGAAAATTTC
1 GTGTGAAAATTTC
12159944 GTGTGAAAATTT
1 GTGTGAAAATTT
12159956 GATAGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:12161655 original size:41 final size:41
Alignment explanation
Indices: 12161610--12161796 Score: 234
Period size: 41 Copynumber: 4.6 Consensus size: 41
12161600 CGTTTAAAAC
* * * *
12161610 CTAGCAGGCTTAAG-GCCGGTGAAGTTATTTGGACTTTATGT
1 CTAGCAGGCTT-TGTGCCGGTGAAATAATTCGGACTTTATGT
*
12161651 CTAGCAGGCTTTGTGCCAGTGAAATAATTCGGACTTTATGT
1 CTAGCAGGCTTTGTGCCGGTGAAATAATTCGGACTTTATGT
12161692 CTAGCAGGCTTTGTGCCGGTGAAATAATTCGGACTTTATGT
1 CTAGCAGGCTTTGTGCCGGTGAAATAATTCGGACTTTATGT
* * * ** *
12161733 CTAACAGGCTTTGTGCTGGTGAAATAATTTGGACGATAAGT
1 CTAGCAGGCTTTGTGCCGGTGAAATAATTCGGACTTTATGT
*
12161774 CTAGCAGGCTAAT-TGCCGGTGAA
1 CTAGCAGGCT-TTGTGCCGGTGAA
12161797 TTGAATCGGG
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 127 0.98
42 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (41 bp):
CTAGCAGGCTTTGTGCCGGTGAAATAATTCGGACTTTATGT
Found at i:12169134 original size:41 final size:41
Alignment explanation
Indices: 12169075--12169220 Score: 154
Period size: 41 Copynumber: 3.6 Consensus size: 41
12169065 TGTTTAAAAC
* * *
12169075 CTAGCAGGCTTAAG-GCCGGTGAAGTTATTCAGACTTTATGT
1 CTAGCAGGCTT-TGTGCCGGTGAAATAATTCAGACTTTATGT
* *
12169116 CTAGCAGGTTTTGTGCCGGTGAAATAATTCGGACTTTATGT
1 CTAGCAGGCTTTGTGCCGGTGAAATAATTCAGACTTTATGT
* * * *
12169157 CTAGCAGGCTTTGTGCTGGTGAAATAATTCGGACGATAAT-T
1 CTAGCAGGCTTTGTGCCGGTGAAATAATTCAGAC-TTTATGT
*
12169198 CTAGCAGGCTAAT-TGCCGGTGAA
1 CTAGCAGGCT-TTGTGCCGGTGAA
12169221 TTGAATCGGG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.01
41 86 0.95
42 4 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (41 bp):
CTAGCAGGCTTTGTGCCGGTGAAATAATTCAGACTTTATGT
Found at i:12171751 original size:15 final size:15
Alignment explanation
Indices: 12171731--12171759 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12171721 AGACCCCGAC
12171731 TAAGATAATATATTA
1 TAAGATAATATATTA
12171746 TAAGATAATATATT
1 TAAGATAATATATT
12171760 TTTTATGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TAAGATAATATATTA
Found at i:12173926 original size:21 final size:23
Alignment explanation
Indices: 12173900--12173950 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
12173890 AATCAAATTG
* *
12173900 ACACACATAAAACACTGAATATA
1 ACACACACAAGACACTGAATATA
*
12173923 ACACACACAAGATACTGAATATA
1 ACACACACAAGACACTGAATATA
12173946 ACACA
1 ACACA
12173951 AATAGAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.24, G:0.06, T:0.16
Consensus pattern (23 bp):
ACACACACAAGACACTGAATATA
Found at i:12175128 original size:9 final size:9
Alignment explanation
Indices: 12175114--12175308 Score: 71
Period size: 10 Copynumber: 20.7 Consensus size: 9
12175104 ATATAAACTT
12175114 TAAAAATTA
1 TAAAAATTA
12175123 TAAAAATTTA
1 TAAAAA-TTA
*
12175133 TAAGAAATCA
1 TAA-AAATTA
*
12175143 TACAAACTTA
1 TA-AAAATTA
*
12175153 TAAATATTA
1 TAAAAATTA
12175162 TAAAAAATTA
1 T-AAAAATTA
12175172 T-AAAATCTA
1 TAAAAAT-TA
*
12175181 -ATAAATT-
1 TAAAAATTA
12175188 TAAAAAATTA
1 T-AAAAATTA
12175198 T-AAAATTGA
1 TAAAAATT-A
*
12175207 TAAAACATATT
1 TAAAA-AT-TA
* *
12175218 TAAAATTTTG
1 TAAAA-ATTA
*
12175228 TAAAAACTCA
1 TAAAAA-TTA
**
12175238 -AAAATAAAA
1 TAAAA-ATTA
*
12175247 TAATAAATTC
1 TAA-AAATTA
12175257 TAATAAATTA
1 TAA-AAATTA
12175267 TAAAAATATA
1 TAAAAAT-TA
*
12175277 TATAAA-TA
1 TAAAAATTA
*
12175285 CTAAAAAAT-
1 -TAAAAATTA
*
12175294 TAGAAATTA
1 TAAAAATTA
12175303 TAAAAA
1 TAAAAA
12175309 ATAAAGTCTT
Statistics
Matches: 139, Mismatches: 26, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
8 20 0.14
9 45 0.32
10 59 0.42
11 14 0.10
12 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:12175153 original size:20 final size:19
Alignment explanation
Indices: 12175108--12175202 Score: 72
Period size: 18 Copynumber: 5.1 Consensus size: 19
12175098 AAATTGATAT
*
12175108 AAACTT-TAAAAATTATAA
1 AAACTTATAAAAATCATAA
* *
12175126 AAATTTATAAGAAATCATAC
1 AAACTTATAA-AAATCATAA
* *
12175146 AAACTTATAAATATTATAA
1 AAACTTATAAAAATCATAA
*
12175165 AAAATTAT-AAAATC-TAA
1 AAACTTATAAAAATCATAA
* *
12175182 TAAATTTA-AAAAATTATAA
1 -AAACTTATAAAAATCATAA
12175201 AA
1 AA
12175203 TTGATAAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.05
18 22 0.37
19 19 0.32
20 16 0.27
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (19 bp):
AAACTTATAAAAATCATAA
Found at i:12175169 original size:29 final size:29
Alignment explanation
Indices: 12175120--12175203 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
12175110 ACTTTAAAAA
* *
12175120 TTATAAAAATTTATAAGAAATCATACAAA-C
1 TTATAAATA-TTATAAAAAATCATA-AAATC
*
12175150 TTATAAATATTATAAAAAATTATAAAATC
1 TTATAAATATTATAAAAAATCATAAAATC
* *
12175179 TAAT-AA-ATT-TAAAAAATTATAAAAT
1 TTATAAATATTATAAAAAATCATAAAAT
12175204 TGATAAAACA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.33
27 3 0.06
28 5 0.10
29 17 0.35
30 8 0.16
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.35
Consensus pattern (29 bp):
TTATAAATATTATAAAAAATCATAAAATC
Found at i:12175306 original size:17 final size:18
Alignment explanation
Indices: 12175261--12175311 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
12175251 AAATTCTAAT
*
12175261 AAATTATAAAAATATATAT
1 AAATTATAAAAA-ATATAG
12175280 AAA-TACTAAAAAAT-TAG
1 AAATTA-TAAAAAATATAG
12175297 AAATTATAAAAAATA
1 AAATTATAAAAAATA
12175312 AAGTCTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 13 0.46
18 6 0.21
19 9 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATTATAAAAAATATAG
Found at i:12175643 original size:19 final size:19
Alignment explanation
Indices: 12175619--12175691 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
12175609 AATCTTCAAG
12175619 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12175638 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
12175657 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12175676 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12175692 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12176020 original size:6 final size:7
Alignment explanation
Indices: 12175981--12176011 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12175971 GATTTAGTCC
12175981 TTTTTTA
1 TTTTTTA
12175988 TTTTTTA
1 TTTTTTA
12175995 TTTTTTA
1 TTTTTTA
*
12176002 GTTTTTA
1 TTTTTTA
12176009 TTT
1 TTT
12176012 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:12176035 original size:21 final size:22
Alignment explanation
Indices: 12176009--12176057 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
12175999 TTAGTTTTTA
*
12176009 TTTATTTTTATTAAAT-TTAAT
1 TTTATTGTTATTAAATATTAAT
* *
12176030 TTTATTGTTATTAAGTATTATT
1 TTTATTGTTATTAAATATTAAT
12176052 TTTATT
1 TTTATT
12176058 ATATATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATTGTTATTAAATATTAAT
Found at i:12176751 original size:13 final size:14
Alignment explanation
Indices: 12176717--12176753 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
12176707 TTTTTTTTCA
12176717 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
12176732 TAT-TTATTT-GTT
1 TATATTATTTCGTT
12176744 TATATTATTT
1 TATATTATTT
12176754 ATACGTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:12178338 original size:25 final size:25
Alignment explanation
Indices: 12178307--12178356 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12178297 ATGTATTTAC
* *
12178307 CATTCAATTTAACGTTTATCGATTA
1 CATTCAATTCAACGTTTATCAATTA
12178332 CATTCAATTCAACGTTTATCAATTA
1 CATTCAATTCAACGTTTATCAATTA
12178357 TATTTGGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (25 bp):
CATTCAATTCAACGTTTATCAATTA
Found at i:12179379 original size:20 final size:20
Alignment explanation
Indices: 12179356--12179394 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12179346 ATTTTTACAT
12179356 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
12179376 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
12179395 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:12181458 original size:19 final size:19
Alignment explanation
Indices: 12181430--12181493 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
12181420 AAATTTCGAG
* *
12181430 GATATACAATCTTAAATAT
1 GATATGCAATCTTAGATAT
12181449 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12181468 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
12181489 GATAT
1 GATAT
12181494 ATACAATCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 22 0.54
21 19 0.46
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12181512 original size:19 final size:21
Alignment explanation
Indices: 12181431--12181506 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
12181421 AATTTCGAGG
*
12181431 ATATACAATCTTAAATATG--
1 ATATACAATCTTAGATATGAT
*
12181450 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
12181471 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
12181492 ATATACAATCTTAGA
1 ATATACAATCTTAGA
12181507 AGATATGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 17 0.33
21 35 0.67
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:12181987 original size:12 final size:12
Alignment explanation
Indices: 12181955--12181988 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12181945 TTTTATTCTA
*
12181955 TTTTATTAATTT
1 TTTTATTATTTT
12181967 TTTTATTATTTT
1 TTTTATTATTTT
12181979 TTTTATTATT
1 TTTTATTATT
12181989 ATATTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:12182381 original size:51 final size:52
Alignment explanation
Indices: 12182271--12182382 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 52
12182261 TTCCACGTTT
**
12182271 TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATATTTTA
1 TATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTA
* * * * *
12182322 TATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTATTTTA
1 TATATATATACTTATATATTTCATT-TTTTCATAAATGCATGAATATATTTTA
12182373 TATATATATA
1 TATATATATA
12182383 AGTTTTATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 28 0.55
52 23 0.45
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (52 bp):
TATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATATTTTA
Found at i:12187285 original size:15 final size:15
Alignment explanation
Indices: 12187265--12187298 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12187255 TTCAAAAAAA
12187265 AAAAGAGAAA-GAAAG
1 AAAAGA-AAACGAAAG
12187280 AAAAGAAAACGAAAG
1 AAAAGAAAACGAAAG
12187295 AAAA
1 AAAA
12187299 AGGAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAAACGAAAG
Found at i:12187288 original size:22 final size:21
Alignment explanation
Indices: 12187270--12187315 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
12187260 AAAAAAAAAG
12187270 AGAAAGAAAGAAAAGAAAACGAA
1 AGAAA-AAAGAAAAGAAAAC-AA
*
12187293 AGAAAAAGGAAAAGAAAAGCAA
1 AGAAAAAAGAAAAGAAAA-CAA
12187315 A
1 A
12187316 AGGAGAGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAAAAAGAAAAGAAAACAA
Found at i:12188755 original size:44 final size:44
Alignment explanation
Indices: 12188575--12188979 Score: 152
Period size: 44 Copynumber: 9.2 Consensus size: 44
12188565 AAGATTGTAG
* * *
12188575 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATAGCAA
* * **
12188619 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCA-CACA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGATAGCA-A
* * * * * ** * * * * * *
12188663 GTCTTGTCTCTCTGAGCAGCAACGGAGAAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATAGCAA
**
12188707 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATAGCAA
* * ** *
12188751 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGATAGCAA
** * * * * * * * * *
12188795 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTAAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATAGCAA
* * * * *
12188839 ATCTTATCTCCGTAAGTAGTAGTGGAGCAGATCAAAGATGGAAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATAGCAA
* *
12188883 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-TCA-CAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGAT-AGCAA
* * * * *
12188926 ATCATTGTCTCTCTGAGCAGTAGTGGAGTAGATCAAAGATTA-CAA
1 ATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGA-TAGCAA
12188971 ATCTTATCT
1 ATCTTATCT
12188980 TTCCAAGATA
Statistics
Matches: 251, Mismatches: 86, Indels: 48
0.65 0.22 0.12
Matches are distributed among these distances:
42 12 0.05
43 24 0.10
44 182 0.73
45 25 0.10
46 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATAGCAA
Found at i:12188770 original size:132 final size:132
Alignment explanation
Indices: 12188533--12188945 Score: 668
Period size: 132 Copynumber: 3.1 Consensus size: 132
12188523 AACACCAAGC
12188533 CTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 CTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
*
12188598 GGAGCAAATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACACA
66 GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACACA
12188663 GT
131 GT
* *
12188665 CTTGTCTCTCTGAGCAGCAACGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 CTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* *
12188730 GGAGCAGATCGAAGATAGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC-CA
66 GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAC-
*
12188794 AGC
130 AGT
* * * *
12188797 CTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTAAAGATTGTAGATCTTATCTCCGTAAGTAGTAGT
1 CTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
* *
12188862 GGAGCAGATCAAAGATGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACA-A
66 GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACACA
*
12188926 AT
131 GT
*
12188928 CATTGTCTCTCTGAGCAG
1 C-TTGTCTCCCTGAGCAG
12188946 TAGTGGAGTA
Statistics
Matches: 259, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
131 3 0.01
132 256 0.99
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
CTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACACA
GT
Found at i:12188996 original size:220 final size:220
Alignment explanation
Indices: 12188710--12189176 Score: 677
Period size: 220 Copynumber: 2.1 Consensus size: 220
12188700 ATTGTAGATC
* * * *
12188710 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGCAAATCTTATCTTTCCAAGATAGTGGG
1 TTATCTCACTGAGCAGTAGTGGAGTAGATCAAAGATAGCAAATCTTATCTTTCCAAGATAGTGGG
* * *
12188775 AAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTAAAGATTGTAGA
66 AAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTAAAGATTGTAGA
* * **
12188840 TCTTATCTCCGTAAGTAGTAGTGGAGCAGATCAAAGAT-GGAAAATCTTATCTTTCCAAGATAGT
131 TCTTATCTCCCTAAGCAGTAGTAAAGCAGATCAAAG-TCGGAAAATCTTATCTTTCCAAGATAGT
* * *
12188904 GGGAAGCAGATTTAAGTCACAAATCA
195 AGGAAGCAGATTTAAGCCACAAAGCA
* *
12188930 TTGTCTCTCTGAGCAGTAGTGGAGTAGATCAAAGATTA-CAAATCTTATCTTTCCAAGATAGTGG
1 TTATCTCACTGAGCAGTAGTGGAGTAGATCAAAGA-TAGCAAATCTTATCTTTCCAAGATAGTGG
* * *
12188994 GAAGTAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGAAGAAGGTTGAAGATTGTAG
65 GAAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTAAAGATTGTAG
* *
12189059 ATCTTATTTCCCTAAGCAGTAGTAAAGCAGATCAAAGTCGGCAAATCTTATCTTTCCAAGATAGT
130 ATCTTATCTCCCTAAGCAGTAGTAAAGCAGATCAAAGTCGGAAAATCTTATCTTTCCAAGATAGT
* *
12189124 AGGAAGCAGATTTAAGCCACCAAGCC
195 AGGAAGCAGATTTAAGCCACAAAGCA
* *
12189150 TTATCTCACTGAGCAGCAGCGGAGTAG
1 TTATCTCACTGAGCAGTAGTGGAGTAG
12189177 GTCGAAGTTG
Statistics
Matches: 219, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
219 1 0.00
220 216 0.99
221 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (220 bp):
TTATCTCACTGAGCAGTAGTGGAGTAGATCAAAGATAGCAAATCTTATCTTTCCAAGATAGTGGG
AAGCAGATTTAAGCCACAAAGCCTTGTCTCCCTGAGCAGCAGCGAAGAAGGTTAAAGATTGTAGA
TCTTATCTCCCTAAGCAGTAGTAAAGCAGATCAAAGTCGGAAAATCTTATCTTTCCAAGATAGTA
GGAAGCAGATTTAAGCCACAAAGCA
Found at i:12189002 original size:44 final size:44
Alignment explanation
Indices: 12188867--12189002 Score: 127
Period size: 44 Copynumber: 3.1 Consensus size: 44
12188857 GTAGTGGAGC
* *
12188867 AGATCAAAGATGGA-AAATCTTATCTTTCCAAGATAGTGGGAAGC
1 AGATCAAAGAT-CACAAATCTTATCTTTCCAAGATAGTGGGAAGT
** * * **
12188911 AGATTTAAG-TCACAAATCATTGTCTCTCTGAGCAGTAGT-GG-AGT
1 AGATCAAAGATCACAAATC-TTATCTTTCCAAG-A-TAGTGGGAAGT
*
12188955 AGATCAAAGATTACAAATCTTATCTTTCCAAGATAGTGGGAAGT
1 AGATCAAAGATCACAAATCTTATCTTTCCAAGATAGTGGGAAGT
12188999 AGAT
1 AGAT
12189003 TTAAGCCACA
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
42 5 0.07
43 9 0.13
44 41 0.59
45 11 0.16
46 4 0.06
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (44 bp):
AGATCAAAGATCACAAATCTTATCTTTCCAAGATAGTGGGAAGT
Found at i:12189005 original size:88 final size:88
Alignment explanation
Indices: 12188856--12189033 Score: 286
Period size: 88 Copynumber: 2.0 Consensus size: 88
12188846 CTCCGTAAGT
*
12188856 AGTAGTGGAGCAGATCAAAGATGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGT
1 AGTAGTGGAGCAGATCAAAGATGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
*
12188921 CACAAATCATTGTCTCTCTGAGC
66 CACAAAGCATTGTCTCTCTGAGC
* * *
12188944 AGTAGTGGAGTAGATCAAAGAT-TACAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAG
1 AGTAGTGGAGCAGATCAAAGATGGA-AAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAG
*
12189008 CCACAAAGCCTTGTCTCTCTGAGC
65 CCACAAAGCATTGTCTCTCTGAGC
12189032 AG
1 AG
12189034 CAGCGAAGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 1 0.01
88 82 0.99
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (88 bp):
AGTAGTGGAGCAGATCAAAGATGGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
CACAAAGCATTGTCTCTCTGAGC
Found at i:12189352 original size:44 final size:44
Alignment explanation
Indices: 12189255--12189415 Score: 129
Period size: 44 Copynumber: 3.8 Consensus size: 44
12189245 GAAGATGGCA
* * **
12189255 AATCTTATCTCCCCGAAGTTGCAGTGGAGCAGATTAGAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAGAAACGAT
* *
12189299 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCA-AAAC-ATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAGAAACGA-T
* * * *
12189342 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATC-G---CGTCT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAGAAACG-AT
* * *
12189383 AGTCTTATTTCCCTAAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
12189416 CTAAGTAAAC
Statistics
Matches: 93, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
40 20 0.22
41 8 0.09
42 1 0.01
43 11 0.12
44 53 0.57
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAGAAACGAT
Found at i:12189740 original size:19 final size:19
Alignment explanation
Indices: 12189712--12189775 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
12189702 AATTTTCGAG
*
12189712 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12189731 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12189750 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
12189771 GATAT
1 GATAT
12189776 ATACAATCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12189794 original size:19 final size:21
Alignment explanation
Indices: 12189713--12189788 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
12189703 ATTTTCGAGG
12189713 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
*
12189732 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
12189753 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
12189774 ATATACAATCTTAGA
1 ATATACAATCTTAGA
12189789 AGATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.34
21 35 0.66
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:12190256 original size:15 final size:15
Alignment explanation
Indices: 12190232--12190269 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12190222 GTTTTTATTC
12190232 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
12190246 TGTTATTATTATTTT
1 TATTATTATTAATTT
12190261 TATTATTAT
1 TATTATTAT
12190270 ATTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:12190279 original size:15 final size:13
Alignment explanation
Indices: 12190226--12190285 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 13
12190216 TTTTAGGTTT
*
12190226 TTATTCTATTTTA
1 TTATTATATTTTA
*
12190239 TTAATT-T-TGTTA
1 TT-ATTATATTTTA
12190251 TTATTAT-TTTTA
1 TTATTATATTTTA
12190263 TTATTATATTATATA
1 TTATTATATT-T-TA
12190278 TTATTATA
1 TTATTATA
12190286 CCTACATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 3 0.08
12 18 0.45
13 5 0.12
14 4 0.10
15 10 0.25
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATTATATTTTA
Found at i:12192274 original size:6 final size:6
Alignment explanation
Indices: 12192259--12192308 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
12192249 TTTGCAACCC
* * *
12192259 AAGGGA AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG GAGAGG AATGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AA-GGGG
12192308 A
1 A
12192309 GAAGAAGGCG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
6 34 0.89
7 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.62, T:0.02
Consensus pattern (6 bp):
AAGGGG
Found at i:12192309 original size:12 final size:12
Alignment explanation
Indices: 12192265--12192316 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12192255 ACCCAAGGGA
* *
12192265 AAGGGGAAGGGG
1 AAGGGGGAGAGG
* *
12192277 AAGGGGAAGGGG
1 AAGGGGGAGAGG
12192289 AAGGGGGAGAGG
1 AAGGGGGAGAGG
* *
12192301 AATGGGGAGAAG
1 AAGGGGGAGAGG
12192313 AAGG
1 AAGG
12192317 CGTCATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.62, T:0.02
Consensus pattern (12 bp):
AAGGGGGAGAGG
Found at i:12193947 original size:10 final size:10
Alignment explanation
Indices: 12193934--12194029 Score: 62
Period size: 10 Copynumber: 10.2 Consensus size: 10
12193924 AACTTATTAT
12193934 ATTTTTATAA
1 ATTTTTATAA
12193944 ATTTTTAT-A
1 ATTTTTATAA
*
12193953 ATATTTAT--
1 ATTTTTATAA
* *
12193961 GTTTTTATTA
1 ATTTTTATAA
* *
12193971 TTTTTTAT-G
1 ATTTTTATAA
12193980 ATTTTTATAA
1 ATTTTTATAA
12193990 ATTTTT-TATA
1 ATTTTTATA-A
* *
12194000 ATTTAT-TAG
1 ATTTTTATAA
12194009 ATTTTTATAA
1 ATTTTTATAA
*
12194019 A-GTTTATAA
1 ATTTTTATAA
12194028 AT
1 AT
12194030 CTTATGATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
8 6 0.09
9 30 0.44
10 32 0.47
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:12193952 original size:38 final size:37
Alignment explanation
Indices: 12193909--12194027 Score: 109
Period size: 38 Copynumber: 3.2 Consensus size: 37
12193899 ATTAAAAAAA
*
12193909 TTTATAATTTATTAGAACTTATTATATTTTTATAAATT
1 TTTATAATTT-TTAGAATTTATTATATTTTTATAAATT
* ** *
12193947 TTTATAATATTTATGTTTTTATTAT-TTTTTAT-GATT
1 TTTATAATTTTTA-GAATTTATTATATTTTTATAAATT
* * *
12193983 TTTATAAATTTTTTATAATTTATTAGATTTTTATAAA-G
1 TTTAT-AA-TTTTTAGAATTTATTATATTTTTATAAATT
12194021 TTTATAA
1 TTTATAA
12194028 ATCTTATGAT
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
36 8 0.12
37 21 0.33
38 34 0.53
39 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (37 bp):
TTTATAATTTTTAGAATTTATTATATTTTTATAAATT
Found at i:12193965 original size:27 final size:27
Alignment explanation
Indices: 12193930--12193988 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
12193920 TTAGAACTTA
12193930 TTATATTTTTATAAATTTTTATAATAT
1 TTATATTTTTATAAATTTTTATAATAT
* * * * *
12193957 TTATGTTTTTATTATTTTTTATGATTT
1 TTATATTTTTATAAATTTTTATAATAT
12193984 TTATA
1 TTATA
12193989 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (27 bp):
TTATATTTTTATAAATTTTTATAATAT
Found at i:12193966 original size:18 final size:17
Alignment explanation
Indices: 12193945--12193993 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
12193935 TTTTTATAAA
12193945 TTTTTATAATATTTATG
1 TTTTTATAATATTTATG
* *
12193962 TTTTTATTATTTTTTATG
1 TTTTTA-TAATATTTATG
12193980 ATTTTTATAA-ATTT
1 -TTTTTATAATATTT
12193994 TTTATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTATAATATTTATG
Found at i:12193998 original size:27 final size:27
Alignment explanation
Indices: 12193963--12194042 Score: 72
Period size: 29 Copynumber: 2.9 Consensus size: 27
12193953 ATATTTATGT
12193963 TTTTATTATTTTTTATGATTTTTATAAA
1 TTTT-TTATTTTTTATGATTTTTATAAA
12193991 TTTTTTATAATTTATTA-GATTTTTATAAA
1 TTTTTTAT--TTT-TTATGATTTTTATAAA
* * ** *
12194020 GTTTATAAATCTTATGATTTTTA
1 TTTTTTATTTTTTATGATTTTTA
12194043 ACAAGAGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 3 0.07
27 13 0.30
28 4 0.09
29 20 0.47
30 3 0.07
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (27 bp):
TTTTTTATTTTTTATGATTTTTATAAA
Found at i:12194011 original size:29 final size:30
Alignment explanation
Indices: 12193962--12194019 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
12193952 AATATTTATG
* *
12193962 TTTTTATTATTTTTTATGATTTTTATAAAT
1 TTTTTATAATTTATTATGATTTTTATAAAT
12193992 TTTTTATAATTTATTA-GATTTTTATAAA
1 TTTTTATAATTTATTATGATTTTTATAAA
12194020 GTTTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (30 bp):
TTTTTATAATTTATTATGATTTTTATAAAT
Found at i:12194034 original size:29 final size:27
Alignment explanation
Indices: 12193974--12194042 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 27
12193964 TTTATTATTT
* *
12193974 TTTATGATTTTTATAAATTTTTTATAA
1 TTTATGATTTTTATAAAGTTTATATAA
12194001 TTTATTAGATTTTTATAAAGTTTATA-AA
1 TTTA-T-GATTTTTATAAAGTTTATATAA
12194029 TCTTATGATTTTTA
1 T-TTATGATTTTTA
12194043 ACAAGAGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 12 0.32
28 5 0.14
29 20 0.54
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.59
Consensus pattern (27 bp):
TTTATGATTTTTATAAAGTTTATATAA
Found at i:12198603 original size:10 final size:10
Alignment explanation
Indices: 12198588--12198712 Score: 100
Period size: 10 Copynumber: 12.3 Consensus size: 10
12198578 TTTTTACTTT
12198588 AAAAATTTTA
1 AAAAATTTTA
12198598 AAAAATTTTA
1 AAAAATTTTA
12198608 AAAATTATTTTA
1 AAAA--ATTTTA
12198620 AAAATATTTT-
1 AAAA-ATTTTA
12198630 -AAAATTTT-
1 AAAAATTTTA
12198638 AAAAATTTTA
1 AAAAATTTTA
12198648 AAAATATTTTA
1 AAAA-ATTTTA
12198659 AAAATATTTT-
1 AAAA-ATTTTA
* *
12198669 -TAAA-TTAA
1 AAAAATTTTA
*
12198677 AAAAATTTAAA
1 AAAAATTT-TA
12198688 AAAAGTATTTTA
1 AAAA--ATTTTA
*
12198700 AAATATTTTA
1 AAAAATTTTA
12198710 AAA
1 AAA
12198713 TTAAAAAAAT
Statistics
Matches: 99, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
7 2 0.02
8 6 0.06
9 16 0.16
10 29 0.29
11 28 0.28
12 14 0.14
13 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:12198676 original size:28 final size:28
Alignment explanation
Indices: 12198586--12198690 Score: 82
Period size: 28 Copynumber: 3.9 Consensus size: 28
12198576 CATTTTTACT
12198586 TTAAAAATTTTAAAAA-ATTTTAAAAA--
1 TTAAAAA-TTTAAAAATATTTTAAAAATT
*
12198612 TT---ATTTTAAAAATATTTT-AAAATT
1 TTAAAAATTTAAAAATATTTTAAAAATT
12198636 TTAAAAATTTTAAAAATATTTTAAAAATAT
1 TTAAAAA-TTTAAAAATATTTTAAAAAT-T
** * *
12198666 TTTTAAA-TTAAAAAAATTTAAAAAA
1 TTAAAAATTTAAAAATATTTTAAAAA
12198691 AGTATTTTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
22 12 0.19
23 6 0.09
24 2 0.03
26 2 0.03
27 1 0.02
28 30 0.47
29 5 0.08
30 6 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAAAAATTTAAAAATATTTTAAAAATT
Found at i:12198688 original size:9 final size:9
Alignment explanation
Indices: 12198585--12198690 Score: 70
Period size: 9 Copynumber: 11.0 Consensus size: 9
12198575 CCATTTTTAC
*
12198585 TTTAAAAAT
1 TTTAAAAAA
12198594 TTTAAAAAA
1 TTTAAAAAA
12198603 TTTTAAAAATTA
1 -TTTAAAAA--A
12198615 TTTTAAAAATA
1 -TTTAAAAA-A
* *
12198626 TTTTAAAAT
1 TTTAAAAAA
*
12198635 TTTAAAAAT
1 TTTAAAAAA
12198644 TTTAAAAATA
1 TTTAAAAA-A
12198654 TTTTAAAAATA
1 -TTTAAAAA-A
**
12198665 TTT-TTAAA
1 TTTAAAAAA
*
12198673 TTAAAAAAA
1 TTTAAAAAA
12198682 TTTAAAAAA
1 TTTAAAAAA
12198691 AGTATTTTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
8 3 0.04
9 37 0.46
10 18 0.22
11 12 0.15
12 10 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:12198713 original size:10 final size:10
Alignment explanation
Indices: 12198585--12198713 Score: 92
Period size: 11 Copynumber: 12.8 Consensus size: 10
12198575 CCATTTTTAC
12198585 TTTAAAA-AT
1 TTTAAAATAT
*
12198594 TTTAAAAAAT
1 TTTAAAATAT
12198604 TTTAAAAATTAT
1 TTT-AAAA-TAT
12198616 TTTAAAAATAT
1 TTT-AAAATAT
12198627 TTT-AAA-AT
1 TTTAAAATAT
12198635 TTTAAAA-AT
1 TTTAAAATAT
12198644 TTTAAAAATAT
1 TTT-AAAATAT
12198655 TTTAAAAATAT
1 TTT-AAAATAT
*
12198666 TTT-TAA-A-
1 TTTAAAATAT
* *
12198673 TTAAAAAAAT
1 TTTAAAATAT
*
12198683 TTAAAAAAAGTAT
1 TT--TAAAA-TAT
12198696 TTTAAAATAT
1 TTTAAAATAT
12198706 TTTAAAAT
1 TTTAAAAT
12198714 TAAAAAAATA
Statistics
Matches: 102, Mismatches: 6, Indels: 23
0.78 0.05 0.18
Matches are distributed among these distances:
7 2 0.02
8 8 0.08
9 21 0.21
10 22 0.22
11 30 0.29
12 15 0.15
13 4 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:12198715 original size:40 final size:39
Alignment explanation
Indices: 12198597--12198722 Score: 182
Period size: 40 Copynumber: 3.2 Consensus size: 39
12198587 TAAAAATTTT
*
12198597 AAAAAATTTTAAAAATTATTTTAAAAATATTTTAAAATTT
1 AAAAAATTTTAAAAA-TATTTTAAAAATATTTTAAAATTA
* *
12198637 TAAAAATTTTAAAAATATTTTAAAAATATTTTTAAATTA
1 AAAAAATTTTAAAAATATTTTAAAAATATTTTAAAATTA
*
12198676 AAAAAATTTAAAAAAAGTATTTT-AAAATATTTTAAAATTA
1 AAAAAATTT-TAAAAA-TATTTTAAAAATATTTTAAAATTA
12198716 AAAAAAT
1 AAAAAAT
12198723 AAATATATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
39 30 0.38
40 42 0.54
41 6 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (39 bp):
AAAAAATTTTAAAAATATTTTAAAAATATTTTAAAATTA
Found at i:12203659 original size:27 final size:26
Alignment explanation
Indices: 12203621--12203689 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
12203611 GTGGAGGGTA
*
12203621 TCCCATGGGCGGCACCAAAGGTGCCTT
1 TCCCAT-GGCGGCACCAAAGGTGCCAT
* *
12203648 TCCCATAGGCGGCACCGATGGTGCCAT
1 TCCCAT-GGCGGCACCAAAGGTGCCAT
12203675 TCCCATGAGCGGCAC
1 TCCCATG-GCGGCAC
12203690 TGCCCATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (26 bp):
TCCCATGGCGGCACCAAAGGTGCCAT
Found at i:12203780 original size:5 final size:5
Alignment explanation
Indices: 12203752--12203825 Score: 55
Period size: 5 Copynumber: 15.4 Consensus size: 5
12203742 GAAAGAAGAA
* * * * *
12203752 GAAA- GAAAG AAAAA GAAAG AAAAG GAAAG GAGAG GAGAG GAAA- GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
* * *
12203800 AAAAA G-AAG GAAAG AAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GA
12203826 GAAGAGGAGA
Statistics
Matches: 53, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
4 11 0.21
5 42 0.79
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:12203813 original size:43 final size:41
Alignment explanation
Indices: 12203748--12203857 Score: 161
Period size: 43 Copynumber: 2.6 Consensus size: 41
12203738 GAGGGAAAGA
12203748 AGAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAGGAGAGG
1 AGAAGAAAGAAA-AAAAAGAAAGAAAAGGAAAGGAGA--AGAGG
*
12203792 A-AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGG
1 AGAAGAAAGAAAAA-AAAGAAAGAAAAGGAAAGGAGAAGAGG
12203833 AGAAG-AAGAAAAAAAAGAAAGAAAA
1 AGAAGAAAGAAAAAAAAGAAAGAAAA
12203858 AGAAGGAAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
40 11 0.18
41 14 0.23
42 5 0.08
43 31 0.50
44 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (41 bp):
AGAAGAAAGAAAAAAAAGAAAGAAAAGGAAAGGAGAAGAGG
Found at i:12203852 original size:9 final size:10
Alignment explanation
Indices: 12203796--12203958 Score: 64
Period size: 10 Copynumber: 15.6 Consensus size: 10
12203786 GAGAGGAAAG
12203796 AAAGAAA-AA
1 AAAGAAAGAA
*
12203805 GAAGGAAAGAA
1 -AAAGAAAGAA
* *
12203816 AAGGAAAGGA
1 AAAGAAAGAA
* *
12203826 GAAGAGGAGAA
1 AAAGA-AAGAA
*
12203837 GAAGAAA-AA
1 AAAGAAAGAA
12203846 AAAGAAAGAA
1 AAAGAAAGAA
*
12203856 AAAGAAGGAA
1 AAAGAAAGAA
12203866 AGAA-AAAGGAA
1 A-AAGAAA-GAA
* *
12203877 AGGAGAAGAGGA
1 A-AAGAA-AGAA
* *
12203889 GAAGAAGAAAA
1 AAAGAA-AGAA
12203900 AAAGAAAGAA
1 AAAGAAAGAA
*
12203910 AAAGAAGGAA
1 AAAGAAAGAA
12203920 AGAA-AAAGGAA
1 A-AAGAAA-GAA
*
12203931 AGGAGAAGAGAA
1 A-AAGAA-AGAA
*
12203943 AAAAAAAGAA
1 AAAGAAAGAA
*
12203953 GAAGAA
1 AAAGAA
12203959 GAAGAGGGGA
Statistics
Matches: 117, Mismatches: 25, Indels: 22
0.71 0.15 0.13
Matches are distributed among these distances:
9 8 0.07
10 56 0.48
11 41 0.35
12 10 0.09
13 2 0.02
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:12203891 original size:22 final size:22
Alignment explanation
Indices: 12203825--12203891 Score: 53
Period size: 25 Copynumber: 2.9 Consensus size: 22
12203815 AAAGGAAAGG
* *
12203825 AGAAGAGGAGAAGAAGAAAAAAA
1 AGAA-AGGAGAAGAGGAGAAAAA
* *
12203848 AGAAAGAAAAAGAAGGAAAGAAAAA
1 AGAAAGGAGAAG-AGG--AGAAAAA
*
12203873 GGAAAGGAGAAGAGGAGAA
1 AGAAAGGAGAAGAGGAGAA
12203892 GAAGAAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
22 10 0.29
23 6 0.18
24 3 0.09
25 15 0.44
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
AGAAAGGAGAAGAGGAGAAAAA
Found at i:12203918 original size:43 final size:43
Alignment explanation
Indices: 12203745--12203962 Score: 140
Period size: 46 Copynumber: 4.7 Consensus size: 43
12203735 GGAGAGGGAA
*
12203745 AGAAGAAGAAAGAAAGAAA-AAGAAAGAAAAGGAAAGGAGAGGAGAGG
1 AGAAGAAGAAAAAAAGAAAGAA-AAAG--AAGGAAAGGAGA--AGAGG
* *
12203792 A-AAGAA-AGAAAAAGAAGGAAAGAA-AAGGAAAGGAGAAGAGG
1 AGAAGAAGAAAAAAAGAAAGAAA-AAGAAGGAAAGGAGAAGAGG
12203833 AGAAGAAGAAAAAAAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGG
1 AGAAGAAG----AAAA-AAAG--AAAGAA--AAAG---AAGGAAAGGAGAAGAGG
* *
12203888 AGAAGAAGAAAAAAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGG
1 AGAAGAAGAAAAAAAGAAAGAAAAAGAAGGAAAGGAGAA-G--AGG
* *
12203934 AGAAG-AGAAAAAAAAAGAAGAAGAAGAAG
1 AGAAGAAGAAAAAAAGA-AAGAAAAAGAAG
12203963 AGGGGAGGAA
Statistics
Matches: 141, Mismatches: 9, Indels: 43
0.73 0.05 0.22
Matches are distributed among these distances:
41 6 0.04
42 5 0.04
43 23 0.16
44 1 0.01
45 19 0.13
46 32 0.23
47 4 0.03
48 10 0.07
50 9 0.06
51 6 0.04
52 1 0.01
55 25 0.18
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (43 bp):
AGAAGAAGAAAAAAAGAAAGAAAAAGAAGGAAAGGAGAAGAGG
Found at i:12203952 original size:55 final size:54
Alignment explanation
Indices: 12203792--12203940 Score: 282
Period size: 54 Copynumber: 2.8 Consensus size: 54
12203782 AGAGGAGAGG
12203792 AAAGAAAGAAAAAGAAGGAAAG-AAAAGGAAAGGAGAAGAGGAGAAGAAGAAAAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGGAGAAGAAG-AAAA
12203846 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGGAGAAGAAGAAAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGGAGAAGAAGAAAA
12203900 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAG
12203941 AAAAAAAAAG
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
54 67 0.71
55 27 0.29
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (54 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGGAGAAGAAGAAAA
Found at i:12204800 original size:284 final size:283
Alignment explanation
Indices: 12204351--12204924 Score: 1017
Period size: 284 Copynumber: 2.0 Consensus size: 283
12204341 TGAAACAAAG
* *
12204351 TAAAATTATAAAATTAGAAATTATGATATTTTTTAAAATAATAAAATGCGAGAAAAAATACGAAG
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAATAATAAAATACGAGAAAAAATACGAAG
* *
12204416 AAATGGCCGAAGTAAGAGTGTTTTACAATTTTTTTAAAAATTCAGAAATAATTAATACAAATATT
66 AAATGACCGAAGTAAGAGTGTTTTACAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATT
12204481 TCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAAAG
131 TCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAAAG
* *
12204546 TAATAAAATTTGGGAAAATAATACGAGCAAAGGGCAAGAATAAGGG-TTTTTT-ACACTAAATTA
196 TAACAAAATTCGGGAAAATAATACGAGCAAAGGGCAAGAATAAGGGTTTTTTTGACACTAAATTA
12204609 ATTTAAAAAACACACTAAATTAA
261 ATTTAAAAAACACACTAAATTAA
12204632 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAATAATAAAATACAGAGAAAAAATACGAA
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAATAATAAAATAC-GAGAAAAAATACGAA
* *
12204697 GAAATGACTGAAGTAAGATTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATA
65 GAAATGACCGAAGTAAGAGTGTTTTAC-AAATTTTTTAAAAATTCAGAAATAATTAATACAAATA
*
12204762 TTTTTAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
129 -TTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
*
12204827 AAGTAACAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTGACACTAAA
193 AAGTAACAAAATTCGGGAAAATAATACGAGCAAAGGGCAAGAATAAGGGTTTTTTTGACACTAAA
12204892 TTAATTTAAAAAACACACTAAATTAA
258 TTAATTTAAAAAACACACTAAATTAA
12204918 TAAATTT
1 TAAATTT
12204925 CAAACATAAT
Statistics
Matches: 278, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
281 47 0.17
282 39 0.14
283 36 0.13
284 109 0.39
285 6 0.02
286 41 0.15
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (283 bp):
TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAATAATAAAATACGAGAAAAAATACGAAG
AAATGACCGAAGTAAGAGTGTTTTACAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATT
TCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGAAAG
TAACAAAATTCGGGAAAATAATACGAGCAAAGGGCAAGAATAAGGGTTTTTTTGACACTAAATTA
ATTTAAAAAACACACTAAATTAA
Found at i:12208657 original size:27 final size:27
Alignment explanation
Indices: 12208617--12208682 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
12208607 TAACACGAGT
*
12208617 GGTGCCGCCCATGGGAATGGCACCATC
1 GGTGCCGCCTATGGGAATGGCACCATC
* *
12208644 GGTGCCGCCTATGGGAATGGCACCTTT
1 GGTGCCGCCTATGGGAATGGCACCATC
12208671 GGTGCCGCCTAT
1 GGTGCCGCCTAT
12208683 CAGTATCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTATGGGAATGGCACCATC
Found at i:12213829 original size:4 final size:4
Alignment explanation
Indices: 12213820--12213865 Score: 74
Period size: 4 Copynumber: 11.0 Consensus size: 4
12213810 AACTTAAGCC
12213820 TTTA TTTA TTTA TTTA TTTCA TTCTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTT-A TT-TA TTTA TTTA TTTA TTTA TTTA
12213866 CAAGCAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 33 0.82
5 6 0.15
6 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:12213877 original size:26 final size:26
Alignment explanation
Indices: 12213822--12213878 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
12213812 CTTAAGCCTT
** **
12213822 TATTTATTTATTTATTTCATTCTATT
1 TATTTATTTATTTATTTCAAGCTAAA
12213848 TATTTATTTATTTATTTACAAGC-AAA
1 TATTTATTTATTTATTT-CAAGCTAAA
12213874 TATTT
1 TATTT
12213879 TTTTCCAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (26 bp):
TATTTATTTATTTATTTCAAGCTAAA
Found at i:12224320 original size:14 final size:14
Alignment explanation
Indices: 12224303--12224329 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12224293 TGTAAAATAT
12224303 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
12224317 TTTCTGGAAAATG
1 TTTCTGGAAAATG
12224330 TTTTACTTCT
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:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (14 bp):
TTTCTGGAAAATGA
Found at i:12224347 original size:20 final size:20
Alignment explanation
Indices: 12224319--12224356 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12224309 GAAAATGATT
*
12224319 TCTGGAAAATGTTTTACTTC
1 TCTGGAAAATGATTTACTTC
*
12224339 TCTGTAAAATGATTTACT
1 TCTGGAAAATGATTTACT
12224357 GAAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (20 bp):
TCTGGAAAATGATTTACTTC
Found at i:12224471 original size:20 final size:20
Alignment explanation
Indices: 12224443--12224519 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
12224433 TCCGGAAAAG
12224443 TTATTTTTACATATATTAAA
1 TTATTTTTACATATATTAAA
* *
12224463 TTGTTTTTACATATATATTAA
1 TTATTTTTACATATAT-TAAA
* *
12224484 TAAATTTTT--ATATTTTAAA
1 T-TATTTTTACATATATTAAA
12224503 TTATTTTTACATATATT
1 TTATTTTTACATATATT
12224520 GCAATGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.13
19 4 0.09
20 26 0.58
21 4 0.09
22 5 0.11
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (20 bp):
TTATTTTTACATATATTAAA
Found at i:12224558 original size:18 final size:18
Alignment explanation
Indices: 12224535--12224570 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12224525 GATTTATTTA
12224535 TAAATAAATAAATCAAAT
1 TAAATAAATAAATCAAAT
* *
12224553 TAAATATATCAATCAAAT
1 TAAATAAATAAATCAAAT
12224571 GGTTTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATAAATAAATCAAAT
Found at i:12226843 original size:21 final size:22
Alignment explanation
Indices: 12226809--12226854 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
12226799 GAGGATGTGG
12226809 AAGAAGATTTGCTTAGAAGAGA
1 AAGAAGATTTGCTTAGAAGAGA
12226831 AAGAAGA-TTGCTTAGAAGAGA
1 AAGAAGATTTGCTTAGAAGAGA
12226852 AAG
1 AAG
12226855 GAGAAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.28, T:0.20
Consensus pattern (22 bp):
AAGAAGATTTGCTTAGAAGAGA
Found at i:12240249 original size:38 final size:38
Alignment explanation
Indices: 12240198--12240274 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
12240188 ATAGCAGCTC
12240198 AGTCTCAGAAATTTGGCCTCATACACGGCCACAGTTCT
1 AGTCTCAGAAATTTGGCCTCATACACGGCCACAGTTCT
12240236 AGTCTCAGAAATTTGGCCTCATACACGGCCACAGTTCT
1 AGTCTCAGAAATTTGGCCTCATACACGGCCACAGTTCT
12240274 A
1 A
12240275 TCCCCTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (38 bp):
AGTCTCAGAAATTTGGCCTCATACACGGCCACAGTTCT
Found at i:12246001 original size:63 final size:63
Alignment explanation
Indices: 12245902--12246038 Score: 256
Period size: 63 Copynumber: 2.2 Consensus size: 63
12245892 GACTTCAGGT
*
12245902 ATTATTTTGTAAAATATCTATGCCCTCATGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
1 ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
*
12245965 ATTATTTTGTAAAATATCTATGCCTTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
1 ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
12246028 ATTATTTTGTA
1 ATTATTTTGTA
12246039 GTTTTCTCCT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (63 bp):
ATTATTTTGTAAAATATCTATGCCCTCAAGCAAGCTTCCAATCATTCAAAAGTTAACAGAGGA
Found at i:12249049 original size:3 final size:3
Alignment explanation
Indices: 12249041--12249088 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
12249031 GAGAAGCTTA
12249041 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
12249089 CACCACCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:12252608 original size:26 final size:24
Alignment explanation
Indices: 12252532--12252610 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 24
12252522 CCTCTCAAAA
12252532 AATTCAAAATAATCTTAAAAAATATT
1 AATTCAAAA-AAT-TTAAAAAATATT
** * *
12252558 TTTTCAAAAAAAATTATAAATATATAT
1 AATTC-AAAAAATTTA-AAAAATAT-T
12252585 AATTCAAAAAATTTAAGAAAATATT
1 AATTCAAAAAATTTAA-AAAATATT
12252610 A
1 A
12252611 TTTGTGTAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
25 6 0.15
26 27 0.66
27 8 0.20
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.35
Consensus pattern (24 bp):
AATTCAAAAAATTTAAAAAATATT
Found at i:12256075 original size:18 final size:19
Alignment explanation
Indices: 12256048--12256084 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
12256038 GAGATAACAA
12256048 GGATGAGAAATGGA-TATG
1 GGATGAGAAATGGAGTATG
*
12256066 GGATGGGAAATGGAGTATG
1 GGATGAGAAATGGAGTATG
12256085 AAATGACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.43, T:0.22
Consensus pattern (19 bp):
GGATGAGAAATGGAGTATG
Found at i:12259239 original size:20 final size:20
Alignment explanation
Indices: 12259184--12259242 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
12259174 ATGTGTAATT
* * *
12259184 AGGAGCACCGTAATGCAAAC
1 AGGAGCACCATAGTGCTAAC
* *
12259204 AGGAGCA-CAAATGTGCTATC
1 AGGAGCACCATA-GTGCTAAC
12259224 AGGAGCACCATAGTGCTAA
1 AGGAGCACCATAGTGCTAA
12259243 TAGAGGTATT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (20 bp):
AGGAGCACCATAGTGCTAAC
Found at i:12260223 original size:324 final size:323
Alignment explanation
Indices: 12259634--12260580 Score: 1617
Period size: 324 Copynumber: 2.9 Consensus size: 323
12259624 GAACTAGAAT
* * ** *
12259634 GTAGGGATTATTCTGTAGTTTTTTATTTCCTCGATTATCAACAACTTGATCTATATAATAGTTAA
1 GTAGGGACTATTCTGCAGTTTTTCCTTTCCCCGATTATCAACAACTTGATCTATATAATAGTTAA
*
12259699 AATTCAAATTATCAATTCAAAAATCATTATATCACTCAAATACATGCATATGACCTTTTAATTTC
66 AATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTC
12259764 ATTTTACATAATTTCCCTAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTA
131 ATTTTACATAATTTCCC-AAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTA
* *
12259829 TAACTTACACAATTAAAC-TCAATTTTTCATTCCAATTTCATTTACATCCTTCTACAGCCCTCTA
195 TAACTTTCACAATTAAACTTC-ATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTA
* *
12259893 AACTCTAAATTTATATAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAGCTGAAAC
259 AACTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAAC
12259958 GTAGGGACTATTCTGCAGTTTTTCCTTTCCCCCGATTATCAACAACTTGATCTATATAATAGTTA
1 GTAGGGACTATTCTGCAGTTTTTCCTTT-CCCCGATTATCAACAACTTGATCTATATAATAGTTA
*
12260023 AAATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGATCTTTTAATTT
65 AAATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTT
12260088 CATTTTACATAATTTCCCAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTA
130 CATTTTACATAATTTCCCAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTA
12260153 TAACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAA
195 TAACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAA
*
12260218 ACTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAAT
260 ACTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAAC
12260282 GTAGGGACTATTCTGCAGTTTTTCCTTTCCCCGATTATCAACAACTTGATCTATATAATAGTTAA
1 GTAGGGACTATTCTGCAGTTTTTCCTTTCCCCGATTATCAACAACTTGATCTATATAATAGTTAA
*
12260347 AATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGTATATGACCTTTTAATTTC
66 AATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTC
* ** * * * *
12260412 ATTTTACACAATTTCCTTGAACTTTTATATTTTATTCAAGTTAATCTCTAAAACAAAAACTATTA
131 ATTTTACATAATTTCC-CAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTA
* * * * *
12260477 TAAATTTCAAAATTAAACTTTATTTTTCATTCCAATTTCAATTATATCCTTCTACATCCCTCTAA
195 TAACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAA
*
12260542 ACTCTAAATTTATAGAATTTTCATGTCACTTTTTTCATA
260 ACTCTAAATTTATAGAATTTTCATGTCACTTTTATCATA
12260581 TTCACAATTT
Statistics
Matches: 593, Mismatches: 27, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
323 115 0.19
324 360 0.61
325 118 0.20
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (323 bp):
GTAGGGACTATTCTGCAGTTTTTCCTTTCCCCGATTATCAACAACTTGATCTATATAATAGTTAA
AATTCAAATTATCAATTCAAAAAGCATTATATCACTCAAATACATGCATATGACCTTTTAATTTC
ATTTTACATAATTTCCCAAACTTTTATATTTTATTCAATTTAATCCCTAAAACCAAGACTATTAT
AACTTTCACAATTAAACTTCATTTTTCATTCCAATTTCAATTACATCCTTCTACAGCCCTCTAAA
CTCTAAATTTATAGAATTTTCATGTCACTTTTATCATAACACAACCAACTAACGAACTGAAAC
Found at i:12265193 original size:16 final size:16
Alignment explanation
Indices: 12265169--12265202 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12265159 TGAATTTTTC
*
12265169 TTATTTTTTCAAATTT
1 TTATATTTTCAAATTT
*
12265185 TTATATTTTTAAATTT
1 TTATATTTTCAAATTT
12265201 TT
1 TT
12265203 CTTCAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTTTCAAATTT
Found at i:12266192 original size:19 final size:20
Alignment explanation
Indices: 12266168--12266205 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12266158 AGAGAGTTCA
12266168 ACTTTAAT-TAAAATTAATC
1 ACTTTAATATAAAATTAATC
*
12266187 ACTTTAATATTAAATTAAT
1 ACTTTAATATAAAATTAAT
12266206 ATAAACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
ACTTTAATATAAAATTAATC
Found at i:12266245 original size:17 final size:18
Alignment explanation
Indices: 12266223--12266266 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
12266213 TATCAAGATA
12266223 AATATTAGAT-TAAATTT
1 AATATTAGATATAAATTT
*
12266240 AATATTAAGATAATCAATTT
1 AATATT-AGAT-ATAAATTT
12266260 AATATTA
1 AATATTA
12266267 AATTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 4 0.17
19 1 0.04
20 12 0.52
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
AATATTAGATATAAATTT
Found at i:12266261 original size:68 final size:68
Alignment explanation
Indices: 12266182--12266312 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
12266172 TAATTAAAAT
* * * * *
12266182 TAATCACTTTAATATTAAATTAATATAAA-CTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCAATTTAATATTAAATTAATA-AAATATTATCAAAATAAATATTAAATTAAATTAAATATT
12266246 AAGA
65 AAGA
* *
12266250 TAATCAATTTAATATTAAATTTATAAAATATTATCAAAATAATTATTAAATTAAATTAAATAT
1 TAATCAATTTAATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAATTAAATAT
12266313 GAAATTTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 3 0.05
68 52 0.95
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (68 bp):
TAATCAATTTAATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAATTAAATATTA
AGA
Found at i:12267459 original size:16 final size:16
Alignment explanation
Indices: 12267431--12267473 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
12267421 TCTTCAGGTG
*
12267431 AAGAAAGAATATGCTC
1 AAGAAAGAGTATGCTC
*
12267447 AATAAAGAGTATGCTC
1 AAGAAAGAGTATGCTC
12267463 AAGAAAGAGTA
1 AAGAAAGAGTA
12267474 CGCCTAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (16 bp):
AAGAAAGAGTATGCTC
Found at i:12269106 original size:18 final size:18
Alignment explanation
Indices: 12269083--12269118 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12269073 GTGTGGGCTT
*
12269083 CACGGGCGTGTGAGCCCA
1 CACGGGCATGTGAGCCCA
*
12269101 CACGGGCATGTGGGCCCA
1 CACGGGCATGTGAGCCCA
12269119 AAATTCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.33, G:0.39, T:0.11
Consensus pattern (18 bp):
CACGGGCATGTGAGCCCA
Found at i:12275528 original size:51 final size:50
Alignment explanation
Indices: 12275411--12275590 Score: 170
Period size: 51 Copynumber: 3.6 Consensus size: 50
12275401 GATGGTCATG
** * * * *
12275411 TGTGTAGTACTATGTGCAGGCTACTATTTGTACCAGA-A-TGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-AT-GATCACA
* *
12275461 TGTGTAGTACTATGTGCAAGCTACTATGCGT-TCCGGATAGCT-TCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTAT-CGGATAG-TAT-GATCACA
* * * *
12275512 TGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATAGTGATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-ATGATCACA
12275563 TGTGTAGTACTATGTGCAGGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
12275591 TGAATCGATA
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
50 32 0.30
51 72 0.67
52 2 0.02
53 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTATGATCACA
Found at i:12275592 original size:26 final size:26
Alignment explanation
Indices: 12275512--12275592 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
12275502 TTCGATCACG
12275512 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
12275538 CGTGTATTGGA-TA-GTG-ATGG-TCAC-A
1 TGTGTA--GTACTATGTGCA-GGCT-ACTA
12275563 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
12275589 TGTG
1 TGTG
12275593 AATCGATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 15 0.36
26 19 0.45
27 2 0.05
28 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:12275675 original size:46 final size:44
Alignment explanation
Indices: 12275597--12275686 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 44
12275587 TATGTGAATC
* *
12275597 GATATCATTAATTATAAGGTGGTTGTTATGTGCTG-ATCCCACCG
1 GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CCACCG
* *
12275641 GATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCCACCG
1 GATATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCCACCG
12275687 TGTATCTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 13 0.33
45 2 0.05
46 22 0.56
47 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (44 bp):
GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCACCG
Found at i:12275837 original size:16 final size:16
Alignment explanation
Indices: 12275816--12275847 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12275806 TGATTGAAAG
*
12275816 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
12275832 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
12275848 GGAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:12280721 original size:25 final size:24
Alignment explanation
Indices: 12280693--12280777 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
12280683 TATTTGAATG
*
12280693 GCCTATGTGGCATATAATCTGGAAA
1 GCCTATGTGGCATATTATCT-GAAA
*
12280718 GCCTTTGTGG--TGAGTTATCTGAAA
1 GCCTATGTGGCAT-A-TTATCTGAAA
*
12280742 GGCTTATGTGGCATATTATCTAGAAA
1 -GCCTATGTGGCATATTATCT-GAAA
12280768 GCCT-TGTGGC
1 GCCTATGTGGC
12280778 GAGTTATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
23 1 0.02
24 11 0.22
25 31 0.63
26 5 0.10
27 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (24 bp):
GCCTATGTGGCATATTATCTGAAA
Found at i:12280734 original size:50 final size:50
Alignment explanation
Indices: 12280665--12280795 Score: 174
Period size: 50 Copynumber: 2.6 Consensus size: 50
12280655 CAAACCACAC
* * * *
12280665 AAAGCCTTTTTGGCAAGTTATTTGAATGGCCTATGTGGCATATAATCTGG
1 AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATAATCTAG
* * * *
12280715 AAAGCCTTTGTGGTGAGTTATCTGAAAGGCTTATGTGGCATATTATCTAG
1 AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATAATCTAG
*
12280765 AAAGCC-TTGTGGCGAGTTATTTAAAAGGCCT
1 AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCT
12280796 TTATGACATA
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 21 0.30
50 48 0.70
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (50 bp):
AAAGCCTTTGTGGCGAGTTATTTGAAAGGCCTATGTGGCATATAATCTAG
Found at i:12289174 original size:147 final size:149
Alignment explanation
Indices: 12288789--12289186 Score: 520
Period size: 147 Copynumber: 2.7 Consensus size: 149
12288779 AGTTTTGATT
* *
12288789 TTTTAAAAAAAGAGATTTTAGATTTT-AACAAATAAAAATATGA-TTTTTTAGTTATTTTAAAGG
1 TTTTAAAAAAA-AGA--TTAGATTTTGAA-AAATAAAAATCTGATTTTTTTAGTCATTTTAAAGG
* * * * * *
12288852 AAAGATAAAAATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTATTTCAAAGTAAAAGTTTTA
62 AAAGTTTAAAATTTTAAAACAAAGTTTTGA---TTTTTTTCAACTACTTAAAAATAAAAGCTTTA
12288917 ATCTTTAAGAAAAAATAGTGTTTTTC
124 ATCTTTAAGAAAAAATAGTGTTTTTC
** * * *
12288943 TTTTAAAAAAAATTTTAGATTTTGGAAAATAAAAATCTGCTTTTTTTAGTCATTTTAAAGAAAAG
1 TTTTAAAAAAAAGATTAGATTTTGAAAAATAAAAATCTGATTTTTTTAGTCATTTTAAAGGAAAG
* *
12289008 TTTAAAATTTTAAAGCAAAGTTTTGATTTTTTTCAATTACTTAAAAATAAAAGCTTTAATCTTTA
66 TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTTAAAAATAAAAGCTTTAATCTTTA
12289073 AG-AAAAATAGTG-TTTT-
131 AGAAAAAATAGTGTTTTTC
*
12289089 TTTTAAAGGAGAAAGATTAGATTTTGAAAAATAAAAATCT-ATTTTTTTAGTCATTTTAAAGGAA
1 TTTTAAA--AAAAAGATTAGATTTTGAAAAATAAAAATCTGATTTTTTTAGTCATTTTAAAGGAA
*
12289153 AGTTTAAAGTTTTAAAACAAAGTTTTGATTTTTT
64 AGTTTAAAATTTTAAAACAAAGTTTTGATTTTTT
12289187 AACTATTTTG
Statistics
Matches: 217, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
146 7 0.03
147 58 0.27
148 37 0.17
149 36 0.17
151 21 0.10
152 46 0.21
153 1 0.00
154 11 0.05
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.43
Consensus pattern (149 bp):
TTTTAAAAAAAAGATTAGATTTTGAAAAATAAAAATCTGATTTTTTTAGTCATTTTAAAGGAAAG
TTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTACTTAAAAATAAAAGCTTTAATCTTTA
AGAAAAAATAGTGTTTTTC
Found at i:12289236 original size:147 final size:147
Alignment explanation
Indices: 12288787--12289270 Score: 504
Period size: 147 Copynumber: 3.3 Consensus size: 147
12288777 AAAGTTTTGA
* *
12288787 TTTTTTAAAAAAAGAGATTTTAGATTTT-AACAAATAAAAATATGA-TTTTTTAGTTATTTTAAA
1 TTTTTTAAAAAAA-AGA--TTAGATTTTGAA-AAATAAAAATCTGATTTTTTTAGTCATTTTAAA
* * *
12288850 GGAAAGATAAAAATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTATTTCAAAGTAAAAGTTT
62 GGAAAGTTTAAAATTTTAAAACAAAGTTTTGA---TTTTTTTCAACTATTT-AAAATAAAAGTTT
*
12288915 TAATCTTTAAGAAAAAATAGTGTTTT
123 TAATCTTTAAG-AAAAATAATGTTTT
* ** * * *
12288941 TCTTTTAAAAAAAATTTTAGATTTTGGAAAATAAAAATCTGCTTTTTTTAGTCATTTTAAAGAAA
1 TTTTTTAAAAAAAAGATTAGATTTTGAAAAATAAAAATCTGATTTTTTTAGTCATTTTAAAGGAA
* * * *
12289006 AGTTTAAAATTTTAAAGCAAAGTTTTGATTTTTTTCAATTACTTAAAAATAAAAGCTTTAATCTT
66 AGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTA-TTTAAAATAAAAGTTTTAATCTT
*
12289071 TAAGAAAAAT-A-GTGTT
130 TAAGAAAAATAATGTTTT
*
12289087 TTTTTTAAAGGAGAAAGATTAGATTTTGAAAAATAAAAATCT-ATTTTTTTAGTCATTTTAAAGG
1 TTTTTTAAA--AAAAAGATTAGATTTTGAAAAATAAAAATCTGATTTTTTTAGTCATTTTAAAGG
* * * *
12289151 AAAGTTTAAAGTTTTAAAACAAAGTTTTGA-TTTTTT-AACTATTTTGAAAT-AAGGTTTTGAT-
64 AAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTA-TTTAAAATAAAAGTTTTAATC
* *
12289212 TTTAAAGAAAATTAATGATTT
128 TTT-AAGAAAAATAATGTTTT
* * * *
12289233 TTTTCTAAAGAAAA-CTTTGATTTTGTAAAAA-AAAAATC
1 TTTTTTAAAAAAAAGATTAGATTTTG-AAAAATAAAAATC
12289271 CAGCAACCAT
Statistics
Matches: 280, Mismatches: 41, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
143 19 0.07
144 24 0.09
145 11 0.04
146 29 0.10
147 48 0.17
148 33 0.12
149 34 0.12
150 2 0.01
151 21 0.08
152 46 0.16
153 1 0.00
154 12 0.04
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.43
Consensus pattern (147 bp):
TTTTTTAAAAAAAAGATTAGATTTTGAAAAATAAAAATCTGATTTTTTTAGTCATTTTAAAGGAA
AGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTAAAATAAAAGTTTTAATCTTT
AAGAAAAATAATGTTTT
Found at i:12291688 original size:25 final size:25
Alignment explanation
Indices: 12291654--12291703 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12291644 CTTTTACTAA
12291654 AGCTACCTTTTTATTTCTCAATCCT
1 AGCTACCTTTTTATTTCTCAATCCT
12291679 AGCTACCTTTTTATTTCTCAATCCT
1 AGCTACCTTTTTATTTCTCAATCCT
12291704 TGCGTCTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.28, G:0.04, T:0.48
Consensus pattern (25 bp):
AGCTACCTTTTTATTTCTCAATCCT
Found at i:12301059 original size:4 final size:4
Alignment explanation
Indices: 12301050--12301094 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
12301040 TGACCCAATA
* * * *
12301050 TCAT TCAT TCAT TCAT TCAT CCAT TCCT TCAC TCAT TCGT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
12301095 TGTTTATTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.20, C:0.31, G:0.02, T:0.47
Consensus pattern (4 bp):
TCAT
Found at i:12306334 original size:42 final size:41
Alignment explanation
Indices: 12306265--12306393 Score: 143
Period size: 42 Copynumber: 3.1 Consensus size: 41
12306255 AAGGAAAACA
* *
12306265 TTCATTGAATTTAGAGGCTCATGTGTGGAGGTCCGTTTACTT
1 TTCATTGAATTTAGAGACCCA-GTGTGGAGGTCCGTTTACTT
* * * *
12306307 TTCATTGTATTTAGAGACCCAGATGTGGAGGTTCATTCACTT
1 TTCATTGAATTTAGAGACCCAG-TGTGGAGGTCCGTTTACTT
* *
12306349 TTCATTGCATCTAGAGACCCAG-GTGCGAAGGTCCGTTTACTT
1 TTCATTGAATTTAGAGACCCAGTGTG-G-AGGTCCGTTTACTT
12306391 TTC
1 TTC
12306394 TAGTTTACTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.04
41 2 0.03
42 68 0.93
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
TTCATTGAATTTAGAGACCCAGTGTGGAGGTCCGTTTACTT
Found at i:12306421 original size:16 final size:16
Alignment explanation
Indices: 12306400--12306430 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12306390 TTTCTAGTTT
*
12306400 ACTTTTCATTGCATTG
1 ACTTTTCATTACATTG
12306416 ACTTTTCATTACATT
1 ACTTTTCATTACATT
12306431 TAGAGACCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (16 bp):
ACTTTTCATTACATTG
Found at i:12307281 original size:150 final size:148
Alignment explanation
Indices: 12307170--12307777 Score: 795
Period size: 147 Copynumber: 4.1 Consensus size: 148
12307160 TTTTTTTAAC
* *
12307170 AAATAAAAATCTGTTTTTGTTTTAGTTATTTTAAAGGAAAGTTTAAATTTTTAAAACAAAATTTT
1 AAATAAAAATCT-TTTTT-TTTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTT
* * *
12307235 GA-TTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATCTTTAA-AAAAATAGTATTTTTTTTCTA
64 GATTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAAATAGT-GTTTTTTT-T-
12307298 AAAAAAGGAGAAAGTTTAGATTTTGAA
126 ---AAA-GAGAAAGTTTAGATTTTGAA
* *
12307325 AAATAAAAATC-TATTTTTTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGA
1 AAATAAAAATCTTTTTTTTTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGA
12307389 TTTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAAATAGTGTTTTTTTTAAAA
66 -TTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAAATAGTGTTTTTTTT-AAA
12307454 GAGAAAGTTTAGATTTTGAA
129 GAGAAAGTTTAGATTTTGAA
12307474 AAATAAAAAT-TTATTTTTTCTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTT
1 AAATAAAAATCTT-TTTTTT-TTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTT
*
12307538 GATTTTTTTTCAACTACTTCAAAATAAAAACTTTAATCTTTAAGAAAAATA--GTTTTTTTTAAA
64 GATTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAAATAGTGTTTTTTTTAAA
*
12307601 GGAGAAAGTTTAGATTTTTAA
129 -GAGAAAGTTTAGATTTTGAA
* * * *
12307622 AAATAAAAATCTATTTTTTTAAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTAA
1 AAATAAAAATCTTTTTTTTTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTT-G
* * * * * * *
12307687 ATTTTTTTT-AACTATTTCGAAAT-AAGGTTTTAATTTTTAAGAAAAATAATGATTTTTTCTAAA
65 ATTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAAATAGTG-TTTTTTTTAAA
*
12307750 GA-AAACTTT-GATTTTGCAA
129 GAGAAAGTTTAGATTTTG-AA
*
12307769 AAAAAAAAA
1 AAATAAAAA
12307778 AAATTGACCA
Statistics
Matches: 415, Mismatches: 25, Indels: 34
0.88 0.05 0.07
Matches are distributed among these distances:
146 27 0.07
147 73 0.18
148 56 0.13
149 42 0.10
150 57 0.14
151 45 0.11
152 45 0.11
153 5 0.01
154 45 0.11
155 20 0.05
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (148 bp):
AAATAAAAATCTTTTTTTTTTAGTCATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGA
TTTTTTTTCAACTACTTCAAAATAAAAGCTTTAATCTTTAAGAAAAATAGTGTTTTTTTTAAAGA
GAAAGTTTAGATTTTGAA
Found at i:12307692 original size:21 final size:20
Alignment explanation
Indices: 12307647--12307691 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
12307637 TTTTTAAGTC
**
12307647 ATTTTAAAGGAAAGTTTAAA
1 ATTTTAAAACAAAGTTTAAA
*
12307667 ATTTTAAAACAAAGTTTTAA
1 ATTTTAAAACAAAGTTTAAA
12307687 ATTTT
1 ATTTT
12307692 TTTTAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (20 bp):
ATTTTAAAACAAAGTTTAAA
Found at i:12308215 original size:7 final size:6
Alignment explanation
Indices: 12308195--12308235 Score: 55
Period size: 6 Copynumber: 6.3 Consensus size: 6
12308185 AATATACTAG
12308195 TTAGTT TTAGTT TTAAGTT TTAAGTTT TTAGTT TTAGTT TT
1 TTAGTT TTAGTT TT-AGTT TT-AG-TT TTAGTT TTAGTT TT
12308236 CAATTCCCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.55
7 11 0.33
8 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (6 bp):
TTAGTT
Found at i:12308222 original size:14 final size:13
Alignment explanation
Indices: 12308197--12308235 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
12308187 TATACTAGTT
12308197 AGTTTTAGTTTTA
1 AGTTTTAGTTTTA
*
12308210 AGTTTTAAGTTTTT
1 AGTTTT-AGTTTTA
12308224 AGTTTTAGTTTT
1 AGTTTTAGTTTT
12308236 CAATTCCCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (13 bp):
AGTTTTAGTTTTA
Found at i:12310183 original size:19 final size:19
Alignment explanation
Indices: 12310135--12310185 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
12310125 TAATAATTTG
12310135 ATAATTTTACTAACAATTA
1 ATAATTTTACTAACAATTA
*
12310154 ATACA----ATTAACAATTA
1 ATA-ATTTTACTAACAATTA
12310170 ATAATTTTACTAACAA
1 ATAATTTTACTAACAA
12310186 AATGTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
19 10 0.40
20 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATTTTACTAACAATTA
Found at i:12310273 original size:112 final size:112
Alignment explanation
Indices: 12310127--12310691 Score: 1008
Period size: 112 Copynumber: 5.1 Consensus size: 112
12310117 CTAACAATTA
*
12310127 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTC
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
*
12310192 AAATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
66 AGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
*
12310239 ATAATTTGATAATTTTACTAACAATTAGTACAATTAACAATTAATAATTTTACTAACAAAATGTT
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
*
12310304 AGATTTTACAAAATGTTTTGAGTGGTAGTAACAATTAATAATTTGAT
66 AGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
*
12310351 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAAGTAATAATTTTACTAACAAAATGTT
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
12310416 AGATTTTACAAAATGTTTTGACTGGT-GTAACAATTAATAATTTGAT
66 AGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
12310462 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
*
12310527 AGATTTTACAAAATATTTTGACTGGTAGTAACAATTAATAATTTGAT
66 AGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
*
12310574 ATAATTTGATAATTTTATTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
* ** * *
12310639 AAATTTTACAAAATGTTTTGACTGGTACAAAAAAAT-ATAATTTGAT
66 AGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
12310685 ATAATTT
1 ATAATTT
12310692 TAATAACAAT
Statistics
Matches: 436, Mismatches: 16, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
111 126 0.29
112 310 0.71
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (112 bp):
ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
AGATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGAT
Found at i:12310529 original size:223 final size:223
Alignment explanation
Indices: 12310127--12310691 Score: 1006
Period size: 223 Copynumber: 2.5 Consensus size: 223
12310117 CTAACAATTA
*
12310127 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTC
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
12310192 AAATTTTACAAAATGTTTTGACTGGTAGTAACAATTAATAATTTGATATAATTTGATAATTTTAC
66 AAATTTTACAAAATGTTTTGACTGGT-GTAACAATTAATAATTTGATATAATTTGATAATTTTAC
* *
12310257 TAACAATTAGTACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTT
130 TAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTT
*
12310322 TGAGTGGTAGTAACAATTAATAATTTGAT
195 TGACTGGTAGTAACAATTAATAATTTGAT
*
12310351 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAAGTAATAATTTTACTAACAAAATGTT
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
*
12310416 AGATTTTACAAAATGTTTTGACTGGTGTAACAATTAATAATTTGATATAATTTGATAATTTTACT
66 AAATTTTACAAAATGTTTTGACTGGTGTAACAATTAATAATTTGATATAATTTGATAATTTTACT
12310481 AACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTTT
131 AACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTTT
12310546 GACTGGTAGTAACAATTAATAATTTGAT
196 GACTGGTAGTAACAATTAATAATTTGAT
*
12310574 ATAATTTGATAATTTTATTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
1 ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
** **
12310639 AAATTTTACAAAATGTTTTGACTGGTACAA-AAAAATATAATTTGATATAATTT
66 AAATTTTACAAAATGTTTTGACTGGTGTAACAATTA-ATAATTTGATATAATTT
12310692 TAATAACAAT
Statistics
Matches: 327, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
222 3 0.01
223 236 0.72
224 88 0.27
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (223 bp):
ATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTT
AAATTTTACAAAATGTTTTGACTGGTGTAACAATTAATAATTTGATATAATTTGATAATTTTACT
AACAATTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATATTTT
GACTGGTAGTAACAATTAATAATTTGAT
Found at i:12310711 original size:22 final size:23
Alignment explanation
Indices: 12310701--12310762 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
12310691 TTAATAACAA
* **
12310701 TTAATTTTAATAACAAT-TTTTT
1 TTAATTTTAATAAAAATATAATT
12310723 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
12310746 TTAATTTTAATCAAAAA
1 TTAATTTTAAT-AAAAA
12310763 ACGGGTCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 14 0.40
24 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:12310727 original size:16 final size:16
Alignment explanation
Indices: 12310686--12310718 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12310676 TAATTTGATA
12310686 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
12310702 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
12310718 T
1 T
12310719 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:12311137 original size:25 final size:24
Alignment explanation
Indices: 12311109--12311155 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
12311099 TCACTTGCAT
12311109 TTATACA-TTATATATTTAATGTTAA
1 TTATACACTT-TAT-TTTAATGTTAA
*
12311134 TTATGCACTTTATTTTAATGTT
1 TTATACACTTTATTTTAATGTT
12311156 TTATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTATACACTTTATTTTAATGTTAA
Found at i:12311198 original size:10 final size:10
Alignment explanation
Indices: 12311179--12311235 Score: 69
Period size: 10 Copynumber: 5.4 Consensus size: 10
12311169 CACTTGTATA
12311179 ATTTTTATTT
1 ATTTTTATTT
*
12311189 ATTCTTATTT
1 ATTTTTATTT
12311199 CATTTTTATTT
1 -ATTTTTATTT
*
12311210 ATTTTCATGTCT
1 ATTTTTAT-T-T
12311222 ATTTTTATTT
1 ATTTTTATTT
12311232 ATTT
1 ATTT
12311236 ATTTTTACGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 21 0.52
11 11 0.28
12 8 0.20
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:12311203 original size:21 final size:22
Alignment explanation
Indices: 12311179--12311235 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
12311169 CACTTGTATA
*
12311179 ATTTTTATTTATTCTT-ATTTC-
1 ATTTTTATTTATT-TTCATGTCT
12311200 ATTTTTATTTATTTTCATGTCT
1 ATTTTTATTTATTTTCATGTCT
12311222 ATTTTTATTTATTT
1 ATTTTTATTTATTT
12311236 ATTTTTACGC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 17 0.52
22 14 0.42
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (22 bp):
ATTTTTATTTATTTTCATGTCT
Found at i:12316121 original size:79 final size:78
Alignment explanation
Indices: 12316019--12316242 Score: 281
Period size: 79 Copynumber: 2.8 Consensus size: 78
12316009 GCTACTAGTT
* *
12316019 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
12316084 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
12316099 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
12316163 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
12316177 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
12316241 GA
63 GA
12316243 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
78 36 0.29
79 56 0.44
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:12316136 original size:39 final size:40
Alignment explanation
Indices: 12316019--12316242 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
12316009 GCTACTAGTT
* *
12316019 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
12316059 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
12316099 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
12316138 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
12316177 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
12316218 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12316243 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:12318144 original size:17 final size:17
Alignment explanation
Indices: 12318109--12318141 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12318099 TCAAGATAAG
*
12318109 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
12318126 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
12318142 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:12318453 original size:19 final size:20
Alignment explanation
Indices: 12318429--12318471 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12318419 TTCGACCAGT
12318429 TTTTGG-GTCTC-AGCCTCAA
1 TTTTGGAGTCTCGAGCC-CAA
*
12318448 TTTTGGATTCTCGAGCCCAA
1 TTTTGGAGTCTCGAGCCCAA
12318468 TTTT
1 TTTT
12318472 CAAATTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (20 bp):
TTTTGGAGTCTCGAGCCCAA
Found at i:12319358 original size:28 final size:26
Alignment explanation
Indices: 12319292--12319369 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 26
12319282 ATATTTTAGT
12319292 TAATATATATTATATTTATT-TACTTAA
1 TAATA-ATATTATA-TTATTATACTTAA
12319319 TAAATAAGTATTATATTAATTATA-TAATAA
1 T-AATAA-TATTATATT-ATTATACT--TAA
12319349 TAATAATATTATTATTATTAT
1 TAATAATATTA-TATTATTAT
12319370 TGTTGTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
27 4 0.09
28 25 0.57
29 11 0.25
30 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TAATAATATTATATTATTATACTTAA
Found at i:12320374 original size:22 final size:21
Alignment explanation
Indices: 12320346--12320413 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
12320336 CTCTCTGATA
12320346 TTTAGCACGTTAGTGCTCTCTG
1 TTTAGCAC-TTAGTGCTCTCTG
*
12320368 TTTAGCACATCT-GTGCTCTCTA
1 TTTAGCAC-T-TAGTGCTCTCTG
**
12320390 CATAGCACTTCAGTGCTCTCTG
1 TTTAGCACTT-AGTGCTCTCTG
12320412 TT
1 TT
12320414 CATTAGTGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 33 0.92
23 1 0.03
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
TTTAGCACTTAGTGCTCTCTG
Found at i:12320561 original size:31 final size:31
Alignment explanation
Indices: 12320503--12320561 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
12320493 AAGAATATGA
* *
12320503 GATAGTGAATTGAAAATAGAATGTGAAAAAC
1 GATAGTGAATTGAAAACAGAATATGAAAAAC
*
12320534 GATAGTGAATTGAAAACATAATATGAAA
1 GATAGTGAATTGAAAACAGAATATGAAA
12320562 TATGTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.24
Consensus pattern (31 bp):
GATAGTGAATTGAAAACAGAATATGAAAAAC
Found at i:12323307 original size:20 final size:20
Alignment explanation
Indices: 12323282--12323347 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
12323272 ATTACAATCT
12323282 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTTTAAA
* *
12323302 AATTCAAAAT-CTTTATAAA
1 AATTCAAAATAATTTTTAAA
*
12323321 AATTTTAAAATTTATATTTTTAAA
1 AA-TTCAAAA--TA-ATTTTTAAA
12323345 AAT
1 AAT
12323348 ATAAAAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 9 0.25
20 16 0.44
22 1 0.03
23 1 0.03
24 9 0.25
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTCAAAATAATTTTTAAA
Found at i:12323322 original size:19 final size:20
Alignment explanation
Indices: 12323282--12323324 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
12323272 ATTACAATCT
*
12323282 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTATAAA
*
12323302 AATTCAAAAT-CTTTATAAA
1 AATTCAAAATAATTTATAAA
12323321 AATT
1 AATT
12323325 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTCAAAATAATTTATAAA
Done.